bluuebunny/crossref_metadata_2025 huggingface dataset:
Trends in the Geospatial Distribution of Inpatient Adult Surgical Services across the United States
Authors: Diaz Adrian , Schoenbrunner Anna , Pawlik Timothy M.
Published: May 2019

Objective:

The aim of this study was to define trends in the geographic distribution of surgical services in the United States to assess possible geographic barriers and disparities in access to surgical care.

Summary Background Data:

Despite the increased need and utilization of surgical procedures, Americans often face challenges in gaining access to health care that may be exacerbated by the closure and consolidation of hospitals. Although access to surgical care has been evaluated relative to the role of insurance, race, and health literacy/education, the relationship of geography and travel distance to access has not been well studied.

Methods:

The 2005 and 2015 American Hospital Association annual survey was used to identify hospitals with surgical capacity; the data were merged with 2010 Census Bureau data to identify the distribution of the US population relative to hospital location, and geospatial analysis tools were used to examine a service area of real driving time surrounding each hospital.

Results:

Although the number of hospitals that provided surgical services slightly decreased over the time periods examined (2005, n = 3791; 2015, n = 3391; P<0.001), the number of major surgery hospitals increased from 2005 (n = 539) to 2015 (n = 749) (P<0.001). The geographic location of hospitals that provided surgical services changed over time. Specifically, although in 2005 852 hospitals were located in a rural area, that number had decreased to 679 by 2015 (P<0.001). Of particular note, from 2005 to 2015 there was an 82% increase in the number of people who lived further than 60 minutes from any hospital (P<0.001). However, the number of people who lived further than 60 minutes from a major surgery hospital decreased (P<0.001).

Conclusions:

Although the number of rural hospitals decreased over the last decade, the number of large, academic medical centers has increased; in turn, there has been an almost doubling in the number of people who live outside a 60-minute driving range to a hospital capable of performing surgery.
Loss of premature stop codon in theWall-Associated Kinase 91(OsWAK91) gene confers sheath blight disease resistance in rice
Authors: Al-Bader Noor , Meier Austin , Geniza Matthew , Gongora Yamid Sanabria , Oard James , Jaiswal Pankaj
Published: May 2019

The genetic arms race between pathogen and host plant is a tug of war that has been ongoing for millennia. The “battles” are those of disruption, restoration of signaling and information transmission on a subcellular level. One such battle occurs between rice an important crop that feeds 50% of the world population and the sheath blight disease (SB) caused by the fungusRhizoctonia solani. It results in 10□30% global yield loss annually and can reach 50% under severe outbreak. Many Receptor□like kinases (RLKs) are recruited as soldiers in these battles. Wall Associated Receptor Kinases (WAKs) a subfamily of receptor-like kinases have been shown to play a role in fungal defense. Here we show that rice geneOsWAK91, present in the major SB resistance QTL region on Chromosome□9 is a key component in defense against rice sheath blight. An SNP mutation C/T separates susceptible variety, Cocodrie (CCDR) from the resistant line MCR010277 (MCR). The resistant allele C results in the stop codon loss that results in 68 amino acids longer C□terminus carrying longer protein kinase domain and phosphorylation sites. Our genotype and phenotype analysis of the top 20 individuals of the double haploid SB population shows a strong correlation with the SNP. The susceptible allele appears as a recent introduction found in the japonica subspecies reference genome and a majority of the tropical and temperate japonica lines sequenced by the 3000 rice genome project. Multiple US commercial varieties with japonica background carry the susceptible allele and are known for SB susceptibility. This discovery opens the possibility of introducing resistance alleles into high yielding commercial varieties to reduce yield losses incurred by the disease.
Benchmarking Single-Cell RNA Sequencing Protocols for Cell Atlas Projects
Authors: Mereu Elisabetta , Lafzi Atefeh , Moutinho Catia , Ziegenhain Christoph , MacCarthy Davis J. , Alvarez Adrian , Batlle Eduard , Sagar  , Grün Dominic , Lau Julia K. , Boutet Stéphane C. , Sanada Chad , Ooi Aik , Jones Robert C. , Kaihara Kelly , Brampton Chris , Talaga Yasha , Sasagawa Yohei , Tanaka Kaori , Hayashi Tetsutaro , Nikaido Itoshi , Fischer Cornelius , Sauer Sascha , Trefzer Timo , Conrad Christian , Adiconis Xian , Nguyen Lan T. , Regev Aviv , Levin Joshua Z. , Parekh Swati , Janjic Aleksandar , Wange Lucas E. , Bagnoli Johannes W. , Enard Wolfgang , Gut Marta , Sandberg Rickard , Gut Ivo , Stegle Oliver , Heyn Holger
Published: May 2019

Single-cell RNA sequencing (scRNA-seq) is the leading technique for charting the molecular properties of individual cells. The latest methods are scalable to thousands of cells, enabling in-depth characterization of sample composition without prior knowledge. However, there are important differences between scRNA-seq techniques, and it remains unclear which are the most suitable protocols for drawing cell atlases of tissues, organs and organisms. We have generated benchmark datasets to systematically evaluate techniques in terms of their power to comprehensively describe cell types and states. We performed a multi-center study comparing 13 commonly used single-cell and single-nucleus RNA-seq protocols using a highly heterogeneous reference sample resource. Comparative and integrative analysis at cell type and state level revealed marked differences in protocol performance, highlighting a series of key features for cell atlas projects. These should be considered when defining guidelines and standards for international consortia, such as the Human Cell Atlas project.
Seasonal and depth variations in diet composition and dietary overlap between three native killifish of an emblematic tropical-mountain lake: Lake Titicaca (Bolivia)
Authors: Loayza Erick
Published: May 2019

Lake Titicaca (∼3800 m a.s.l.), an emblematic tropical-mountain ecosystem is the major source of fish for people on the Altiplano. The Andean killifish genus Orestias, represent an important resource for local fisheries in Lake Titicaca. It has been suggested that exist an effect of segregation in the Lake Titicaca in order to avoid competition for food resource between native fish species, due most of Orestias species share the littoral habitat, which is now also share with introduced species. Such scenario increases the pressure for food resource. Here I examined the gut content of O. luteus, O. agassizii and O. mulleri (Cuvier & Valenciennes, 1846) from a bay of Lake Titicaca during rainy (April) and dry season (July) with the predominance method, frequency of occurrence and numerical percentage to describe the diet and dietary overlap between these native fish. I also applied a PERMANOVA test in order to determine diet variations related to depth and seasonally, as well as the Levins and Pianka’s index to test diet breadth and dietary overlap respectively. 396 gut contents were evaluated, identifying a high frequency of amphipods and molluscs in the three Orestias native species. Diet breadth revelled a selectivity for a few preys and the composition of the diets was influenced mainly by depth, followed by seasonality (PERMANOVA, P = <0.05). Dietary overlapping between O. luteus and O. agassizii was evidenced in the rainy season. During the dry season, the three species undergone dietary overlapping. This study provided a detail knowledge on the diet variations of native species in Lake Titicaca, especially for Orestias mulleri, a little-known species. Here I also discussed the importance of the amphipods as a food resource in Lake Titicaca not only for fish community, but for the food web in general. The seasonal and depth diet variations here discussed are relevant for fisheries management and conservation and could be used to guide aquaculture development in Lake Titicaca.
Application of TurboID-mediated proximity labeling for mapping a GSK3 kinase signaling network in Arabidopsis
Authors: Kim Tae-Wuk , Park Chan Ho , Hsu Chuan-Chih , Zhu Jia-Ying , Hsiao Yuchun , Branon Tess , Xu Shou-Ling , Ting Alice Y , Wang Zhi-Yong
Published: May 2019

Transient protein-protein interactions (PPIs), such as those between posttranslational modifying enzymes and their substrates, play key roles in cellular regulation, but are difficult to identify. Here we demonstrate the application of enzyme-catalyzed proximity labeling (PL), using the engineered promiscuous biotin ligase TurboID, as a sensitive method for characterizing PPIs in signaling networks. We show that TurboID fused with the GSK3-like kinase BIN2 or a PP2A phosphatase biotinylates their known substrate, the BZR1 transcription factor, with high specificity and efficiency. We optimized the protocol of biotin labeling and affinity purification in transgenic Arabidopsis expressing a BIN2-TurboID fusion protein. Subsequent quantitative mass spectrometry (MS) analysis identified about three hundred proteins biotinylated by BIN2-TurboID more efficiently than the YFP-TurboID control. These include a significant subset of previously proven BIN2 interactors and a large number of new BIN2-proximal proteins that uncover a broad BIN2 signaling network. Our study illustrates that PL-MS using TurboID is a powerful tool for mapping signaling networks, and reveals broad roles of BIN2 kinase in cellular signaling and regulation in plants.

Impact Statement

TurboID-mediated proximity labeling is a powerful tool for protein interactomics in plants.
Quantitative proteomics indicate a strong correlation of mitotic phospho-/dephosphorylation with non-structured regions of substrates
Authors: Yamazaki Hiroya , Kosako Hidetaka , Yoshimura Shige H.
Published: May 2019

Protein phosphorylation plays a critical role in the regulation and progression of mitosis. More than 10,000 phosphorylated residues and the associated kinases have been identified to date via proteomic analyses. Although some of these phosphosites are associated with regulation of either protein-protein interactions or the catalytic activity of the substrate protein, the roles of most mitotic phosphosites remain unclear. In this study, we examined structural properties of mitotic phosphosites and neighboring residues to understand the role of heavy phosphorylation in non-structured domains. Quantitative mass spectrometry analysis of mitosis-arrested and non-arrested HeLa cells revealed >4,100 and >2,200 residues either significantly phosphorylated or dephosphorylated, respectively, at mitotic entry. The calculated disorder scores of amino acid sequences of neighboring individual phosphosites revealed that >70% of dephosphorylated phosphosites exist in disordered regions, whereas 50% of phosphorylated sites exist in non-structured domains. A clear inverse correlation was observed between probability of phosphorylation in non-structured domain and increment of phosphorylation in mitosis. These results indicate that at entry to mitosis, a significant number of phosphate groups are removed from non-structured domains and transferred to more-structured domains. Gene ontology term analysis revealed that mitosis-related proteins are heavily phosphorylated, whereas RNA-related proteins are both dephosphorylated and phosphorylated, suggesting that heavy phosphorylation/dephosphorylation in non-structured domains of RNA-binding proteins plays a role in dynamic rearrangement of RNA-containing organelles, as well as other intracellular environments.

Significance Statement

Progression of mitosis is tightly regulated by protein phosphorylation/dephosphorylation. Although proteomic studies have identified tens of thousands of phosphosites in mitotic cells, the roles of them remain to be answered. We approached this question from the viewpoint of the higher-order structure of phosphosites. Quantitative proteomics and bioinformatic analyses revealed that more than 70% of mitotic dephosphorylation events occurred in non-structured regions. Non-structured regions of cellular proteins are attracting considerable attention in terms of their involvement in dynamic rearrangements of intracellular membrane-less organelles and protein assembly/disassembly processes. Our results suggest the possibility that a vast amount of mitosis-associated dephosphorylation/phosphorylation at non-structured regions plays a role in regulating the dynamic assembly/disassembly of intracellular architectures and organelles such as chromosomes and nucleolus.
The Glycolytic Protein Phosphofructokinase Dynamically Relocalizes into Subcellular Compartments with Liquid-like Properties in vivo
Authors: Jang SoRi , Xuan Zhao , Lagoy Ross C. , Jawerth Louise M. , Gonzalez Ian , Singh Milind , Prashad Shavanie , Kim Hee Soo , Patel Avinash , Albrecht Dirk R. , Hyman Anthony A. , Colón-Ramos Daniel A.
Published: May 2019

While much is known about the biochemical regulation of glycolytic enzymes, less is understood about how they are organized inside cells. Here we built a hybrid microfluidic-hydrogel device for use in Caenorhabditis elegans to systematically examine and quantify the dynamic subcellular localization of the rate-limiting enzyme of glycolysis, phosphofructokinase-1/PFK-1.1. We determine that endogenous PFK-1.1 localizes to distinct, tissue-specific subcellular compartments in vivo. In neurons, PFK-1.1 is diffusely localized in the cytosol, but capable of dynamically forming phase-separated condensates near synapses in response to energy stress from transient hypoxia. Restoring animals to normoxic conditions results in the dispersion of PFK-1.1 in the cytosol, indicating that PFK-1.1 reversibly organizes into biomolecular condensates in response to cues within the cellular environment. PFK-1.1 condensates exhibit liquid-like properties, including spheroid shapes due to surface tension, fluidity due to deformations, and fast internal molecular rearrangements. Prolonged conditions of energy stress during sustained hypoxia alter the biophysical properties of PFK-1.1 in vivo, affecting its viscosity and mobility within phase-separated condensates. PFK-1.1’s ability to form tetramers is critical for its capacity to form condensates in vivo, and heterologous self-association domain such as cryptochrome 2 (CRY2) is sufficient to constitutively induce the formation of PFK-1.1 condensates. PFK-1.1 condensates do not correspond to stress granules and might represent novel metabolic subcompartments. Our studies indicate that glycolytic protein PFK-1.1 can dynamically compartmentalize in vivo to specific subcellular compartments in response to acute energy stress via multivalency as phase-separated condensates.
Defining the root endosphere and rhizosphere microbiomes from the World Olive Germplasm Collection
Authors: Fernández-González Antonio J. , Villadas Pablo J. , Cabanás Carmen Gómez-Lama , Valverde-Corredor Antonio , Belaj Angjelina , Mercado-Blanco Jesús , Fernández-López Manuel
Published: May 2019

Up to date, the bacterial and fungal microbial communities from the olive (Olea europaeaL.) root systems have not been simultaneously studied. In this work, we show that microbial communities from the olive root endosphere are less diverse than those from the rhizosphere. But more relevant was to unveil that olive belowground communities are mainly shaped by the genotype of the cultivar when growing under the same environmental, pedological and agronomic conditions. Furthermore,Actinophytocola,StreptomycesandPseudonocardiaare the most abundant bacterial genera in the olive root endosphere,Actinophytocolabeing the most prevalent genus by far. In contrast,Gp6,Gp4,RhizobiumandSphingomonasare the main genera in the olive rhizosphere.Canalisporium,Aspergillus,MinimelanolocusandMacrophominaare the main fungal genera present in the olive root system. Interestingly enough, a high proportion of so far unclassified fungal sequences at class level were detected in the rhizosphere. From the belowground microbial profiles here reported, it can be concluded that the genusActinophytocolamay play an important role in olive adaptation to environmental stresses. Moreover, the huge unknown fungal diversity suggests that there are still some fungi with important ecological and biotechnological implications that have yet to be discovered.
Evolution-driven attenuation of alphaviruses highlights key glycoprotein determinants regulating viral infectivity and dissemination
Authors: Noval Maria G. , Rodriguez-Rodriguez Bruno A. , Rangel Margarita , Stapleford Kenneth A.
Published: May 2019

Understanding the fundamental mechanisms of arbovirus transmission and pathogenesis is essential to develop new strategies for treatment and prevention. We previously took anin vivoevolution-based approach and identified the chikungunya virus E1 glycoprotein residue 80 to play a critical role in viral transmission and pathogenesis. In this study, we address the genetic robustness and function of position 80 and demonstrate that this highly conserved residue is a key determinant in alphavirus infectivity and dissemination through modulation of viral fusion and cholesterol dependence. In addition, in studying the evolution of position 80, we identified a network of glycoprotein residues, including epidemic determinants, that regulate virus dissemination and infectivity. These studies underscore the importance of taking evolution-based approaches to not only identify key viral determinants driving arbovirus transmission and pathogenesis but also to uncover fundamental aspects of arbovirus biology.
Hypermutation inCryptococcusreveals a novel pathway to 5-fluorocytosine (5FC) resistance
Authors: Billmyre R. Blake , Clancey Shelly Applen , Li Lucy X. , Doering Tamara L. , Heitman Joseph
Published: May 2019

Drug resistance is a critical challenge in treating infectious disease. For fungal infections, this issue is exacerbated by the limited number of available and effective antifungal agents. Patients infected with the fungal pathogenCryptococcusare most effectively treated with a combination of amphotericin B and 5-fluorocytosine (5FC). Isolates causing infections frequently develop resistance to 5FC although the mechanism of this resistance is poorly understood. Here we show that resistance is acquired more frequently in isolates with defects in DNA mismatch repair that confer an elevated mutation rate. Natural isolates ofCryptococcuswith mismatch repair defects have recently been described and defective mismatch repair has been reported in other pathogenic fungi. In addition, whole genome sequencing was utilized to identify mutations associated with 5FC resistancein vitro. Using a combination of candidate-based Sanger and whole genome Illumina sequencing, the presumptive genetic basis of resistance in 16 independent isolates was identified, including mutations in the known resistance genesFUR1andFCY2, as well as a novel gene,UXS1. Mutations inUXS1lead to accumulation of a metabolic intermediate that appears to suppress toxicity of both 5FC and its toxic derivative 5FU. Interestingly, while aUXS1ortholog has not been identified in other fungi likeSaccharomyces cerevisiae, where the mechanisms underlying 5FC and 5FU resistance were elucidated, aUXS1ortholog is found in humans, suggesting that mutations inUXS1in cancer cells may also play a role in resistance to 5FU when used during cancer chemotherapy in humans.
Aβ42 oligomers trigger synaptic loss through CAMKK2-AMPK-dependent effectors coordinating mitochondrial fission and mitophagy
Authors: Lee Annie , Kondapalli Chandana , Virga Daniel M. , Lewis Tommy L. , Koo So Yeon , Ashok Archana , Mairet-Coello Georges , Herzig Sebastien , Shaw Reuben , Sproul Andrew , Polleux Franck
Published: May 2019

During the early stages of Alzheimer’s disease (AD) in both mouse models and human patients, soluble forms of Amyloid-β1-42 oligomers (Aβ42o) trigger loss of excitatory synapses (synaptotoxicity) in cortical and hippocampal pyramidal neurons (PNs) prior to the formation of insoluble Aβ plaques. We observed a spatially restricted structural remodeling of mitochondria in the apical tufts of CA1 PNs dendrites in the hAPPSWE,IND transgenic AD mouse model (J20), corresponding to the dendritic domain receiving presynaptic inputs from the entorhinal cortex and where the earliest synaptic loss is detected in vivo. We also observed significant loss of mitochondrial biomass in human neurons derived from a new model of human ES cells where CRISPR-Cas9-mediated genome engineering was used to introduce the ‘Swedish’ mutation bi-allelically (APPSWE/SWE). Recent work uncovered that Aβ42o mediates synaptic loss by over-activating the CAMKK2-AMPK kinase dyad, and that AMPK is a central regulator of mitochondria homeostasis in non-neuronal cells. Here, we demonstrate that Aβ42o-dependent over-activation of CAMKK2-AMPK mediates synaptic loss through coordinated MFF-dependent mitochondrial fission and ULK2-dependent mitophagy in dendrites of PNs. We also found that the ability of Aβ42o-dependent mitochondrial remodeling to trigger synaptic loss requires the ability of AMPK to phosphorylate Tau on Serine 262. Our results uncover a unifying stress-response pathway triggered by Aβo and causally linking structural remodeling of dendritic mitochondria to synaptic loss.
Proxies of CRISPR-Cas9 activity to aid in the identification of mutagenized Arabidopsis plants
Authors: Li Renyu , Vavrik Charles , Danna Cristian H.
Published: May 2019

CRISPR-Cas9 has become the preferred gene editing technology to obtain loss-of-function mutants in plants, and hence a valuable tool to study gene function. This is mainly due to the easy reprograming of Cas9 specificity using customizable small non-coding RNAs, and to the ability to target several independent genes simultaneously. Despite these advances, the identification of CRISPR-edited plants remains time and resource consuming. Here, based on the premise that one editing event in one locus is a good predictor of editing event/s in other locus/loci, we developed a CRISPR co-editing selection strategy that greatly facilitates the identification of CRISPR-mutagenized Arabidopsis plants. This strategy is based on targeting the gene/s of interest simultaneously with a proxy of CRISPR-Cas9-directed mutagenesis. The proxy is an endogenous gene whose loss-of-function mutation produces an easy-to-detect visible phenotype that is unrelated to the expected phenotype of the gene/s under study. We tested this strategy via assessing the frequency of co-editing of three functionally unrelated proxies. We found all three proxies predicted the occurrence of mutations in either or both of the other two proxies with efficiencies ranging from 40% to 100%, dramatically reducing the number of plants that need to be screened to identify CRISPR mutants. This selection strategy provides a framework to facilitate gene function studies of gene families as well as the function of single copy genes in polyploid plant species where the identification of multiplex mutants remains challenging.
Low additive genetic variation in a trait under selection in domesticated rice
Authors: Karavolias Nicholas G. , Greenberg Anthony J. , Barrero Luz S. , Maron Lyza G. , Shi Yuxin , Monteverde Eliana , Piñeros Miguel A. , McCouch Susan R.
Published: May 2019

Quantitative traits are important targets of both natural and artificial selection. The genetic architecture of these traits and its change during the adaptive process is thus of fundamental interest. The fate of the additive effects of variants underlying a trait receives particular attention because they constitute the genetic variation component that is transferred from parents to offspring and thus governs the response to selection. While estimation of this component of phenotypic variation is challenging, the increasing availability of dense molecular markers puts it within reach. Inbred plant species offer an additional advantage because phenotypes of genetically identical individuals can be measured in replicate. This makes it possible to estimate marker effects separately from the contribution of the genetic background. We focused on root growth in domesticated rice,Oryza sativa, under normal and aluminum (Al) stress conditions, a trait under recent selection because it correlates with survival under drought. A dense single nucleotide polymorphism (SNP) map is available for all accessions studied. Taking advantage of this map and a set of Bayesian models, we assessed additive marker effects. While total genetic variation accounted for a large proportion of phenotypic variance, marker effects contributed little information, particularly in the Al-toleranttropical japonicapopulation of rice. We were unable to identify any loci associated with root growth in this population. Models estimating the aggregate effects of all measured genotypes like-wise produced low estimates of marker heritability and were unable to predict total genetic values accurately. Our results support the long-standing conjecture that additive genetic variation is depleted in traits under selection. We further provide evidence that this depletion is due to the prevalence of low-frequency alleles that underlie the trait.
Reduced Cognitive Performance in Aged Rats Correlates with Increased Excitation/Inhibition Ratio in the Dentate Gyrus in Response to Lateral Entorhinal Input
Authors: Tran Trinh , Bridi Michelle , Koh Ming Teng , Gallagher Michela , Kirkwood Alfredo
Published: May 2019

Aging often impairs cognitive functions associated with the medial temporal lobe (MTL). Anatomical studies identified the layer II pyramidal cells of the lateral entorhinal cortex (LEC) as one of the most vulnerable elements within the MTL. These cells provide a major excitatory input to the dentate gyrus hippocampal subfield by synapsing onto granule cells and onto local inhibitory interneurons, and a fraction of these contacts are lost in aged individuals with impaired learning. Using optogenetics we evaluated the functional status of the remaining inputs in an outbred rat model of aging that distinguishes between learning impaired and learning unimpaired individuals. We found that aging affects the pre- and postsynaptic strength of the LEC inputs onto granule cells. However, the magnitude these changes was similar in impaired and un-impaired rats. In contrast, the recruitment of inhibition by LEC activation was selectively reduced in the aged impaired subjects. These findings are consistent with the notion that the preservation of an adequate balance of excitation and inhibition is crucial for maintain proficient memory performance during aging.
A zero-inflated gamma model for post-deconvolved calcium imaging traces
Authors: Wei Xue-Xin , Zhou Ding , Grosmark Andres , Ajabi Zaki , Sparks Fraser , Zhou Pengcheng , Brandon Mark , Losonczy Attila , Paninski Liam
Published: May 2019

Calcium imaging is a critical tool for measuring the activity of large neural populations. Much effort has been devoted to developing “pre-processing” tools applied to calcium video data, addressing the important issues of e.g., motion correction, denoising, compression, demixing, and deconvolution. However, computational modeling of deconvolved calcium signals (i.e., the estimated activity extracted by a pre-processing pipeline) is just as critical for interpreting calcium measurements. Surprisingly, these issues have to date received significantly less attention. To fill this gap, we examine the statistical properties of the deconvolved activity estimates, and propose several density models for these random signals. These models include a zero-inflated gamma (ZIG) model, which characterizes the calcium responses as a mixture of a gamma distribution and a point mass which serves to model zero responses. We apply the resulting models to neural encoding and decoding problems. We find that the ZIG model out-performs simpler models (e.g., Poisson or Bernoulli models) in the context of both simulated and real neural data, and can therefore play a useful role in bridging calcium imaging analysis methods with tools for analyzing activity in large neural populations.
Machine learning to detect Alzheimer’s disease from circulating non-coding RNAs
Authors: Ludwig Nicole , Fehlmann Tobias , Gogol Manfred , Maetzler Walter , Deutscher Stephanie , Gurlit Simone , Schulte Claudia , von Thaler Anna-Katharina , Deuschle Christian , Metzger Florian , Berg Daniela , Suenkel Ulrike , Keller Verena , Backes Christina , Lenhof Hans-Peter , Meese Eckart , Keller Andreas
Published: May 2019

Background

To develop therapeutics for Alzheimer’s disease, early detection of patients awakes new hope. Circulating small non-coding RNAs are among the prominent candidates for a blood-based diagnosis, requiring however growing cohort sizes.

Methods

We determined abundance levels of 21 known circulating microRNAs in 465 individuals encompassing Alzheimer’s patients and controls recruited in US and Germany. We computed models to assess the relation between microRNA-expression and phenotypes, gender, age and disease severity (Mini-Mental State Examination MMSE).

Results

20 of 21 miRNAs were consistently dys-regulated in the US and Germany. 18 were significantly correlated to neurodegeneration (adjusted p<0.05) with highest significance for miR-532-5p (adjusted p=4.8×10−30). Ten miRNAs were significantly correlated with MMSE, in particular miR-26a/26b-5p (adjusted p=0.0002). Machine learning models reached an AUC value of 87.6% in differentiating AD patients from controls.

Conclusions

Our data provide strong evidence for the relevance of circulating non-coding RNAs to detect Alzheimer’s from a blood sample.
Quantification of DNA damage induced γH2AX focus formation via super-resolution dSTORM localization microscopy
Authors: Varga Dániel , Majoros Hajnalka , Újfaludi Zsuzsanna , Erdélyi Miklós , Pankotai Tibor
Published: May 2019

In eukaryotic cells, each process, in which DNA is involved, should take place in the context of chromatin structure. DNA double-strand breaks (DSBs) are one of the most deleterious damages often leading to chromosomal rearrangement. In response to environmental stresses, cells have developed repair mechanisms to eliminate the DSBs. Upon DSB induction, several factors play roles in chromatin relaxation by catalysing the appropriate histone posttranslational modification (PTM) steps, therefore promoting the access of the repair factors to the DSBs. Among these PTMs, the phosphorylation of the histone variant H2AX at its Ser139 residue (also known as γH2AX) could be observed at the break sites. The structure of γH2AX focus has to be organized during the repair as it contributes to accessibility of specific repair proteins to the damaged site. Our aim was to develop a quantitative approach to analyse the morphology of individual repair foci by super-resolution dSTORM microscopy to gain insight into genome organization in DNA repair. We have established a specific dSTORM measurement process by developing a new analytical algorithm for gaining quantitative information about chromatin morphology and repair foci topology at individual γH2AX enriched repair focus. By this method we quantified unique repair foci to show the average distribution of γH2AX clusters. By monitoring γH2AX signal, we could reach 20 nm spatial resolution and resolve a single DNA damage spot, which allow us to identify different chromatin sub-clusters around the break site. Additionally, based on our new analysis method, we were able to show the number of nucleosomes in each sub-cluster that could allow us to define the possible chromatin structure and the nucleosome density around the break sites. This method is the first demonstration of a single-cell based quantitative measurement of a discrete repair focus, which could provide new opportunities to categorize spatial organization of dot patterns by parametric determination of topological similarity.
Discovery, Expression, Cellular Localization, and Molecular Properties of a Novel, Alternative Spliced HP1γ Isoform, Lacking the Chromoshadow Domain
Authors: Mathison Angela , De Assuncao Thiago Milech , Dsouza Nikita R. , Williams Monique , Zimmermann Michael T. , Lomberk Gwen , Urrutia Raul
Published: May 2019

By reading the H3K9Me3 mark through their N-terminal chromodomain (CD), HP1 proteins play a significant role in cancer-associated processes, including cell proliferation, differentiation, chromosomal stability, and DNA repair. Here, we used a combination of bioinformatics-based methodologies, as well as experimentally-derived datasets, that reveal the existence of a novel short HP1γ (CBX3) isoform, named here sHP1γ, generated by alternative splicing of the CBX3 locus. The sHP1γ mRNA encodes a protein composed of 101 residues and lacks the C-terminal chromoshadow domain (CSD) that is required for dimerization and heterodimerization in the previously described 183 a. a HP1γ protein. Fold recognition, order-to-disorder calculations, threading, homology-based molecular modeling, docking, and molecular dynamic simulations show that the sHP1γ is comprised of a CD flanked by intrinsically disordered regions (IDRs) with an IDR-CD-IDR domain organization and likely retains the ability to bind to the H3K9Me3. Both qPCR analyses and mRNA-seq data derived from large-scale studies confirmed that sHP1γ mRNA is expressed in the majority of human tissues at approximately constant ratios with the chromoshadow domain containing isoform. However, sHP1γ mRNA levels appear to be dysregulated in different cancer types. Thus, our data supports the notion that, due to the existence of functionally different isoforms, the regulation of HP1γ-mediated functions is more complex than previously anticipated.
Staphylococcus aureus infects osteoclasts and replicates intracellularly
Authors: Krauss Jennifer L , Roper Philip M , Ballard Anna , Shih Chien-Cheng , Fitzpatrick James AJ , Cassat James E , Ng Pei Ying , Pavlos Nathan J , Veis Deborah J
Published: May 2019

Osteomyelitis (OM), or inflammation of bone tissue, occurs most frequently as a result of bacterial infection and severely perturbs bone structure. The majority of OM is caused by Staphylococcus aureus, and even with proper treatment, OM has a high rate of recurrence and chronicity. While S. aureus has been shown to infect osteoblasts, persist intracellularly, and promote the release of pro-osteoclastogenic cytokines, it remains unclear whether osteoclasts (OCs) are also a target of intracellular infection. In this study, we examined the interaction between S. aureus and OCs, demonstrating internalization of GFP-labeled bacteria by confocal microscopy, both in vitro and in vivo. Utilizing an intracellular survival assay and flow cytometry during OC differentiation from bone marrow macrophages (BMMs), we found that the intracellular burden of S. aureus increases after initial infection in cells with at least 2 days of exposure to the osteoclastogenic cytokine receptor activator of nuclear factor kappa-B ligand (RANKL). Presence of dividing bacteria was confirmed via visualization by transmission electron microscopy. In contrast, undifferentiated BMMs, or those treated with interferon-γ or IL-4, had fewer internal bacteria, or no change, respectively, at 18 hours post infection, compared to 1.5 hours post infection. To further explore the signals downstream of RANKL, we manipulated NFATc1 and alternative NF-κB, which controls NFATc1 and other factors affecting OC function, finding that intracellular bacterial growth correlates with NFATc1 levels in RANKL-treated cells. Confocal microscopy in mature OCs showed a range of intracellular infection that correlated inversely with S. aureus and phagolysosome colocalization. The ability of OCs to become infected, paired with their diminished bactericidal capacity compared to BMMs, could promote OM progression by allowing S. aureus to evade initial immune regulation and proliferate at the periphery of lesions where OCs and bone remodeling are most abundant.

Author Summary

The inflammation of bone tissue is called osteomyelitis, and most cases are caused by an infection with the bacterium Staphylococcus aureus. To date, the bone building cells, osteoblasts, have been implicated in the progression of these infections, but not much is known about how the bone resorbing cells, osteoclasts, participate. In this study, we show that S. aureus can infect osteoclasts and proliferate inside these cells, whereas macrophages, immune cells related to osteoclasts, destroy the bacteria. These findings elucidate a unique role for osteoclasts to harbor bacteria during infection, providing a possible mechanism by which bacteria could evade destruction by the immune system. Therapeutic interventions that target osteoclasts specifically might reduce the severity of OM or improve antibiotic responses.
Characterization of ammonium dihydrogen phosphate crystals for soft X-ray optics of the Beam Expander Testing X-ray facility (BEaTriX)
Authors: Ferrari Claudio , Beretta Sara , Salmaso Bianca , Pareschi Giovanni , Tagliaferri Gianpiero , Basso Stefano , Spiga Daniele , Pelliciari Carlo , Giro Enrico
Published: May 2019

A new type of X-ray facility, the Beam Expander Testing X-ray facility (BEaTriX), has been designed and is now under construction at INAF–Osservatorio Astronomico di Brera (Merate, Italy) to perform the acceptance tests of the silicon pore optics modules of the ATHENA X-ray telescope. Crystals of high perfection and large dimensions are needed in order to obtain a wide beam (20 × 6 cm) with an X-ray divergence of <0.5′′ and an X-ray energy purity ΔE/E < 10−5. To generate X-ray diffracted beams at an X-ray energy of 1.49 keV, ammonium dihydrogen phosphate (ADP) crystals have been considered among other possible choices, because of their reported crystal quality and because they can be grown at sufficiently large size at a reasonable price. In the present paper, the results of the characterization of crystalline quality and lattice planarity of a 20 × 20 × 2 mm ADP sample are reported.
Varieties of 12-fold rosettes and their applications in Moroccan geometric ornament
Authors: Aboufadil Youssef , Thalal Abdelmalek , El Idrissi Raghni My Ahmed , Jali Abdelaziz , Oueriagli Amane
Published: May 2019

This work is devoted to the study of the 12-fold rosettes frequently encountered in Islamic art, especially in Moroccan ornamentation. Several types of 12-fold rosettes are described according to the geometric shape of their petals. They have a large number of variants and offer the possibility of building new, previously unknown rosettes, while respecting the construction methodHasbaused by master craftsmen. Artisans developed a technique for combining different types of 12-fold rosettes to construct infinite periodic tiling belonging to the 17 crystallographic groups. This technique enabled them to diversify the repeated patterns based on 12-fold rosettes. An analysis of their tiling suggests a method based on elementary geometry to build new patterns with different types of 12-fold overlapped rosettes and their variants. A procedure based on combination of the distances between two overlapped rosettes is then proposed, which enables generation of new periodic and quasiperiodic patterns.
PDB2INS: bridging the gap between small-molecule and macromolecular refinement
Authors: Lübben Anna V. , Sheldrick George M.
Published: May 2019

The open-source Python program PDB2INS is designed to prepare a .ins file for refinement with SHELXL [Sheldrick (2015). Acta Cryst. C71, 3–8], taking atom coordinates and other information from a Protein Data Bank (PDB)-format file. If PDB2INS is provided with a four-character PDB code, both the PDB file and the accompanying mmCIF-format reflection data file (if available) are accessed via the internet from the PDB public archive [Read et al. (2011). Structure, 19, 1395–1412] or optionally from the PDB_REDO server [Joosten, Long, Murshudov & Perrakis (2014). IUCrJ, 1, 213–220]. The SHELX-format .ins (refinement instructions and atomic coordinates) and .hkl (reflection data) files can then be generated without further user intervention, appropriate restraints etc. being added automatically. PDB2INS was tested on the 23 974 X-ray structures deposited in the PDB between 2008 and 2018 that included reflection data to 1.7 Å or better resolution in a recognizable format. After creating the two input files for SHELXL without user intervention, ten cycles of conjugate-gradient least-squares refinement were performed. For 96% of these structures PDB2INS and SHELXL completed successfully without error messages.
Direct measurement of X-ray-induced heating of microcrystals
Authors: Warren Anna J. , Axford Danny , Owen Robin L.
Published: May 2019

Temperature control is a key aspect of macromolecular crystallography, with the technique of cryocooling routinely being used to mitigate X-ray-induced damage. Beam-induced heating could cause the temperature of crystals to rise above the glass transition temperature, greatly increasing the rate of damage. X-ray-induced heating of ruby crystals of 20–40 µm in size has been quantified non-invasively by monitoring the emission wavelengths of X-ray-induced fluorescence during exposure to the X-ray beam. For the beam sizes and dose rates typically used in macromolecular crystallography, the temperature rises are of the order of 20 K. The temperature changes observed are compared with models in the literature and can be used as a validation tool for future models.
CSR communication in stakeholder networks: a semiotic perspective
Authors: Lång Stefan , Ivanova-Gongne Maria
Published: May 2019

Purpose

This paper is explorative in its nature and aims to create a deeper understanding of corporate social responsibility (CSR) communication within stakeholder networks. In particular, the purpose of this paper is to focus on how CSR communication is organised and communicated within stakeholder networks from a semiotic perspective. More specifically, the paper looks at the CSR communication of Nordic-based multinational companies.

Design/methodology/approach

The research design of this study is twofold. First, eight in-depth interviews were conducted with senior managers in five Nordic-based global industrial companies in order to understand how their CSR communication is organised. Second, CSR messages from the interviewed companies’ websites and annual sustainability reports were semiotically analysed in order to understand the codes used in the CSR message in the communication to the stakeholder network.

Findings

The result of the research consists of a communication platform for CSR communication in stakeholder networks and a list of specific semiotic codes applied to CSR messages targeting various actors in a company’s stakeholder network. The developed CSR communication platform together with the specific CSR codes have practical value for managers aiming to develop the company’s CSR communication in a stakeholder network context.

Originality/value

The study contributes to the scarce literature on CSR communication in business management. It particularly highlights the need to consider a more in-depth, semiotic approach, when developing and studying CSR communication in a stakeholder network context.
Local rooting and creativity within the fashion industry in Beirut
Authors: Ben Hassen Tarek , Tremblay Diane-Gabrielle
Published: May 2019

Purpose

The purpose of this paper is to analyze the factors that make Beirut a fashion hub by studying the characteristics of creativity and the role of the different stakeholders in setting an environment that encourages creativity in Beirut.

Design/methodology/approach

The methodology of this research is based on a literature review and information collected through semi-structured interviews with the different stakeholders of the sector.

Findings

The research reveals three results. First, this dynamic fashion design in Beirut is explained by the international success of some Lebanese fashion designers. Second, as there is an absence of any form of governmental intervention, the development of the sector is totally based on private business initiatives. Third, the research demonstrates the importance of the local culture, knowledge exchanges and lifestyle in shaping creativity and designers’ careers in Beirut.

Originality/value

These findings contribute to the clarification and critical analysis of the current state of fashion design in Beirut, which would have several policy implications.
Achieving continued usage in online banking: a post-adoption study
Authors: Oertzen Anna-Sophie , Odekerken-Schröder Gaby
Published: May 2019

Purpose

Despite ample research on the adoption of online banking, the post-adoption phase remains largely neglected. The purpose of this paper is to develop a new conceptual model to investigate drivers, attitudes and behaviours in the post-adoption phase of the e-postbox, a co-creative online banking feature.

Design/methodology/approach

Research from bank marketing, services marketing, information systems and relationship management informs the proposed post-adoption model. Empirical tests rely on structural equation modelling and a sample of 750 current customers of the e-postbox of a large German bank.

Findings

The proposed model provides a multifaceted view of the post-adoption phase, including task-related, organisation-related and interpersonal communication-related drivers. This study reveals the importance of integrating dual interpersonal communication as a post-adoption driver and a post-adoption behaviour. It also extends the technology acceptance model by applying it to the post-adoption phase. Significant effects of age further suggest that younger customers express the most favourable attitudes towards and highest intentions to continue using the e-postbox; interestingly, older customers use it more and share more word-of-mouth.

Research limitations/implications

This paper develops a post-adoption model that highlights the importance of continued usage for successful co-creation between the bank and its customers.

Practical implications

Managers can encourage continued usage during the post-adoption phase of a co-creative, digitalised service, which determines the retention of current customers and opportunities to attain new customers.

Originality/value

This study defines and establishes constructs for the post-adoption phase and categorises them according to post-adoption drivers, attitudes and behaviours.
Religiously permissible consumption
Authors: Maison Dominika , Marchlewska Marta , Zein Rizqy Amelia , Syarifah Dewi , Purba Herison
Published: May 2019

Purpose

The purpose of this paper is to investigate the influence of the halal label on product perceptions among Muslims high (vs low) in the centrality of their religion.

Design/methodology/approach

It was hypothesized that a halal label would predict positive product perceptions, especially among those Muslims who scored high in the Centrality of Religiosity Scale (CRS). The study was conducted among 187 Muslims in Indonesia, a country in which Islam is the dominant religion. We used an experimental design where two products (cake and energy drink), with (n = 85) or without (n = 102) the halal label (depending on the experimental condition), were displayed. The participants were randomly assigned to the research conditions. Following product exposure, the participants evaluated products on perception scales (e.g. tasty, healthy). Finally, the centrality of religiosity (moderator variable) was measured.

Findings

The results of the analysis showed that the halal label increased positive product perceptions among those Muslims who scored high in the CRS. A similar pattern of results was obtained for both products (cake and energy drink), though the described effect was even more pronounced in the case of the energy drink.

Originality/value

Results shed light on the role of religiosity in consumption, especially in consumers’ responses to the halal label.