bluuebunny/crossref_metadata_2025 huggingface dataset:
Phylogenetic diversity of 200+ isolates of the ectomycorrhizal fungusCenococcum geophilumassociated withPopulus trichocarpasoils in the Pacific Northwest, USA and comparison to globally distributed representatives
Authors: Vélez Jessica M. , Morris Reese M. , Vilgalys Rytas , Labbé Jessy , Schadt Christopher W.
Published: March 2020

The ectomycorrhizal fungal symbiontCenococcum geophilumis of great interest as it is globally distributed, associates with many plant species, and has resistance to multiple environmental stressors.C. geophilumis only known from asexual states but is often considered a cryptic species complex, since extreme phylogenetic divergence is often observed within morphologically identical strains. Alternatively,C. geophilummay represent a highly diverse single species, which would suggest cryptic but frequent recombination. Here we describe a new isolate collection of 229C. geophilumisolates from soils underPopulus trichocarpaat 123 collection sites spanning a ~283 mile north-south transect in Washington and Oregon, USA (PNW). To further understanding of the phylogenetic relationships withinC. geophilum, we performed maximum likelihood phylogenetic analyses to assess divergence within the PNW isolate collection, as well as a globalGAPDHphylogenetic analysis of 789 isolates with publicly available data from the United States, Europe, Japan, and other countries. Phylogenetic analyses of the PNW isolates revealed three distinct phylogenetic groups, with 15 clades that strongly resolved at >80% bootstrap support based on aGAPDHphylogeny and one clade segregating strongly in two principle component analyses. The abundance and representation of PNW isolate clades varied greatly across the North-South range, including a monophyletic group of isolates that spanned nearly the entire gradient at ~250 miles. A direct comparison between theGAPDHand ITS phylogenies combined with additional analyses revealed stark incongruence between the ITS andGAPDHgene regions, implicating probable intra-species recombination between PNW isolates. In the global isolate collection phylogeny, 34 clades were strongly resolved at >80% bootstrap support, with some clades having intra- and intercontinental distributions. These data are highly suggestive of divergence within multiple cryptic species, however additional analyses such as higher resolution genotype-by-sequencing approaches are needed to distinguish potential species boundaries and recombination patterns.
Supertertiary protein structure affects an allosteric network
Authors: Laursen Louise , Kliche Johanna , Gianni Stefano , Jemth Per
Published: March 2020

The notion that protein function is allosterically regulated by structural or dynamic changes in proteins has been extensively investigated in several protein domains in isolation. In particular, PDZ domains have represented a paradigm for these studies, despite providing conflicting results. Furthermore, it is still unknown how the association between protein domains in supramodules, consitituting so-called supertertiary structure, affects allosteric networks. Here, we experimentally mapped the allosteric network in a PDZ:ligand complex, both in isolation and in the context of a supramodular structure, and show that allosteric networks in a PDZ domain are highly dependent on the supertertiary structure in which they are present. This striking sensitivity of allosteric networks to presence of adjacent protein domains is likely a common property of supertertiary structures in proteins. Our findings have general implications for prediction of allosteric networks from primary and tertiary structure and for quantitative descriptions of allostery.
Myoelectric digit action decoding with multi-label, multi-class classification: an offline analysis
Authors: Krasoulis Agamemnon , Nazarpour Kianoush
Published: March 2020

The ultimate goal of machine learning-based myoelectric control is simultaneous and independent control of multiple degrees of freedom (DOFs), including wrist and digit artificial joints. For prosthetic finger control, regression-based methods are typically used to reconstruct position/velocity trajectories from surface electromyogram (EMG) signals. Although such methods have produced highly-accurate results in offline analyses, their success in real-time prosthesis control settings has been rather limited. In this work, we propose action decoding, a paradigm-shifting approach for independent, multi-digit movement intent decoding based on multi-label, multi-class classification. At each moment in time, our algorithm classifies movement action for each available DOF into one of three categories: open, close, or stall (i.e., no movement). Despite using a classifier as the decoder, arbitrary hand postures are possible with our approach. We analyse a public dataset previously recorded and published by us, comprising measurements from 10 able-bodied and two transradial amputee participants. We demonstrate the feasibility of using our proposed action decoding paradigm to predict movement action for all five digits as well as rotation of the thumb. We perform a systematic offline analysis by investigating the effect of various algorithmic parameters on decoding performance, such as feature selection and choice of classification algorithm and multi-output strategy. The outcomes of the offline analysis presented in this study will be used to inform the real-time implementation of our algorithm. In the future, we will further evaluate its efficacy with real-time control experiments involving upper-limb amputees.
Loss of Hem1 disrupts macrophage function and impacts on migration, phagocytosis and integrin-mediated adhesion
Authors: Stahnke Stephanie , Döring Hermann , Kusch Charly , de Gorter David J.J. , Dütting Sebastian , Guledani Aleks , Pleines Irina , Schnoor Michael , Sixt Michael , Geffers Robert , Rohde Manfred , Müsken Mathias , Kage Frieda , Steffen Anika , Faix Jan , Nieswandt Bernhard , Rottner Klemens , Stradal T.E.B.
Published: March 2020

The hematopoietic-specific protein 1 (Hem1) comprises an essential subunit of the WAVE Regulatory Complex (WRC) in immune cells. WRC has a fundamental role in Arp2/3 complex activation and the protrusion of branched actin networks in motile cells.

Hem1 deficiency leads to suppression of the entire WRC in immune cells. Defective WRC function in macrophages results in loss of lamellipodia and migration defects. Moreover, phagocytosis, commonly accompanied by lamellipodium protrusion during cup formation, is altered in Hem1 null cells concerning frequency and efficacy. When analyzing cell spreading, adhesion and podosome formation, we found that Hem1 null cells are capable, in principle, of podosome formation and consequently, do not show any quantitative differences in extracellular matrix degradation. Their adhesive behavior, however, was significantly altered. Specifically, adhesion as well as de-adhesion of Hem1 null cells was strongly compromised, likely contributing to the observed reduced efficiency of phagocytosis. In line with this, phosphorylation of the prominent adhesion component paxillin was diminished. Non-hematopoietic somatic cells disrupted in expression for both Hem1 and its ubiquitous orthologue Nck-associated protein 1 (Nap1) or the essential WRC components Sra-1/PIR121 did not only confirm defective paxillin phosphorylation, but also revealed that paxillin turnover in focal adhesions is accelerated in the absence of WRC. Finally, adhesion assays using platelets lacking functional WRC as model system unmasked radically decreased αIIbβ3 integrin activation.

Our results thus demonstrate that WRC-driven actin networks impact on integrin-dependent processes controlling formation and dismantling of different types of cell-substratum adhesion.

One sentence summary

Interference of Hem1 function in mice and cells uncovers a hitherto unrecognized role in integrin-mediated cell adhesion that is crucial for macrophage function and connects to recently discovered immunodeficiencies in patients carrying Hem1 mutations.
Activation of p21 limits acute lung injury and induces early senescence after acid aspiration and mechanical ventilation
Authors: Blázquez-Prieto Jorge , Huidobro Covadonga , López-Alonso Inés , Amado-Rodriguez Laura , Martín-Vicente Paula , López-Martínez Cecilia , Crespo Irene , Pantoja Cristina , Fernandez-Marcos Pablo J , Serrano Manuel , Sznajder Jacob I , Albaiceta Guillermo M
Published: March 2020

The p53/p21 pathway is activated in response to cell stress. However, its role in acute lung injury has not been elucidated. Acute lung injury is associated with disruption of the alveolo-capillary barrier leading to acute respiratory distress syndrome (ARDS). Mechanical ventilation may be necessary to support gas exchange in patients with ARDS, however, high positive airway pressures can cause regional overdistension of alveolar units and aggravate lung injury. Here, we report that acute lung injury and alveolar overstretching activate the p53/p21 pathway to maintain homeostasis and avoid massive cell apoptosis. A systematic pooling of transcriptomic data from animal models of lung injury demonstrates the enrichment of specific p53- and p21-dependent gene signatures and a validated senescence profile. In a clinically relevant, murine model of acid aspiration and mechanical ventilation, we observed changes in the nuclear envelope and the underlying chromatin, DNA damage and activation of theTp53/p21 pathway. Absence ofCdkn1adecreased the senescent response, but worsened lung injury due to increased cell apoptosis. Conversely, treatment with lopinavir/ritonavir led toCdkn1aoverexpression and ameliorated cell apoptosis and lung injury. The activation of these mechanisms was associated with early markers of senescence, including expression of senescence-related genes and increases in senescence-associated heterochromatin foci in alveolar cells. Autopsy samples from lungs of patients with ARDS revealed increased senescence-associated heterochromatin foci. Collectively, these results suggest that acute lung injury activates p53/p21 as an anti-apoptotic mechanism to ameliorate damage, but with the side effect of induction of senescence.
Fibrinolytic niche is requested for alveolar type 2 cell-mediated alveologenesis and injury repair
Authors: Gibran Ali , Zhao Runzhen , Zhang Mo , Jain Krishan G. , Chang Jianjun , Komatsu Satoshi , Fang Xiaohui , Zhou Beiyun , Liang Jiurong , Jiang Dianhua , Ikebe Mistuo , Matthay Michael A , Ji Hong-Long
Published: March 2020

COVID-19, SARS, and MERS are featured by fibrinolytic dysfunction. To test the role of the fibrinolytic niche in the regeneration of alveolar epithelium, we compared the self-renewing capacity of alveolar epithelial type 2 (AT2) cells and its differentiation to AT1 cells between wild type (wt) and fibrinolytic niche deficient mice (Plau−/−andSerpine1Tg). A significant reduction in both proliferation and differentiation of deficient AT2 cells was observedin vivoand in 3D organoid cultures. This decrease was mainly restored by uPA derived A6 peptide, a binding fragment to CD44 receptors. The proliferative and differential rate of CD44+AT2 cells was greater than that of CD44−controls. There was a reduction in transepithelial ion transport in deficient monolayers compared to wt cells. Moreover, we found a marked suppression in total AT2 cells and CD44+subpopulation in lungs from brain dead patients with acute respiratory distress syndrome (ARDS) and a mouse model infected by influenza viruses. Thus, we demonstrate that the fibrinolytic niche can regulate AT2-mediated homeostasis and regeneration via a novel uPA-A6-CD44+-ENaC cascade.
Differential alphavirus defective RNA diversity between intracellular and encapsidated compartments is driven by subgenomic recombination events
Authors: Langsjoen RM , Muruato AE , Kunkel SR , Jaworski E , Routh A
Published: March 2020

Alphaviruses are positive-sense RNA arboviruses that can cause either a chronic arthritis or a potentially lethal encephalitis. Like other RNA viruses, alphaviruses produce truncated, defective genomes featuring large deletions during replication. Defective RNAs (D-RNAs) have primarily been isolated from virions after high-multiplicity of infection passaging. Here, we aimed to characterize both intracellular and packaged viral D-RNA populations during early passage infections under the hypothesis that D-RNAs arisede novointracellularly that may not be packaged and thus have remained undetected. To this end, we generated NGS libraries using RNA derived from passage 1 (P1) stock chikungunya virus (CHIKV) 181/clone 25, intracellular virus, and encapsidated P2 virus and analyzed samples for D-RNA expression, followed by diversity and differential expression analyses. We found that the diversity of D-RNA species is significantly higher for intracellular D-RNA populations than encapsidated and specific populations of D-RNAs are differentially expressed between intracellular and encapsidated compartments. Importantly, these trends were likewise observed in a murine model of CHIKV 15561 infection, as well asin vitrostudies using related Mayaro, Sindbis, and Aura viruses. Additionally, we identified a novel subtype of subgenomic D-RNA that are conserved across arthritogenic alphaviruses. D-RNAs specific to intracellular populations were defined by recombination events specifically in the subgenomic region, which was confirmed by direct RNA nanopore sequencing of intracellular CHIKV RNAs. Together, these studies show that only a portion of D-RNAs generated intracellularly are packaged and D-RNAs readily arisede novoin the absence of transmitted template.

IMPORTANCE

Our understanding of viral defective RNAs (D-RNAs), or truncated viral genomes, comes largely from passaging studies in tissue culture under artificial conditions and/or packaged viral RNAs. Here, we show that specific populations of alphavirus D-RNAs arisede novoand that they are not packaged into virions, thus imposing a transmission bottleneck and impeding their prior detection. This raises important questions about the roles of D-RNAs, both in nature and in tissue culture, during viral infection and whether their influence is constrained by packaging requirements. Further, during the course of these studies, we found a novel type of alphavirus D-RNA that is enriched intracellularly; dubbed subgenomic D-RNAs (sgD-RNAs), they are defined by deletion boundaries between capsid/E3 and E1/3’UTR regions and are common to chikungunya, Mayaro, Sindbis, and Aura viruses. These sgD-RNAs are enriched intracellularly and do not appear to be selectively packaged, and additionally may exist as subgenome-derived transcripts.
Epigenetic downregulation of HER2 during EMT leads to tumor resistance to HER2-targeted therapies in breast cancer
Authors: Nami Babak , Ghanaeian Avrin , Wang Zhixiang
Published: March 2020

HER2 receptor tyrosine kinase (encoded byERBB2gene) is overexpressed in approximately 25% of all breast cancer tumors (known as HER2-positive breast cancers). Overexpression of HER2 causes overactivation of downstream receptor tyrosine kinase pathways including PI3K/Akt and MAPK pathways and is a poor prognosis factor in breast cancer. Tyrosine kinase inhibitor lapatinib and anti-HER2 monoclonal antibodies trastuzumab and pertuzumab are FDA-approved HER2-targeted drugs for treatment of HER2-positive breast cancers. However, development of de novo resistance to HER2 blockade occurs in majority of patients after treatment started. Resistance to HER2 targeting therapies partially due to the loss of HER2 expression on their tumor cells during the treatment. But little is known about the exact mechanism of loss of HER2 on originally HER2-positive tumor cells. Downregulation of extracellular HER2 by metalloproteinases during epithelial-mesenchymal transition (EMT) in trastuzumab-resistant/lapatinib-sensitive cells has been shown by limited studies, however, the mechanism of ERBB2 gene silencing during EMT and in the mesenchymal-like cells derived from trastuzumab-resistant/lapatinib-resistant HER2-positive breast tumors was entirely unknown. In this study, hypothesized that EMT abrogates HER2 expression by chromatin-based epigenetic silencing ofERBB2gene as a mechanism of acquired resistance to HER2-targeted therapies. we found that HER2 expression is positively and negatively correlated with the expression of epithelial and mesenchymal phenotype marker genes respectively in breast cancer tumors. We also found that chromatin ofERBB2gene in HER2-high epithelial-like breast cancer cells is active, while, the chromatin is inactive in HER2-low mesenchymal-like cells. HER2-low breast cancer cell line also revealed less promoter-enhancer interaction and small chromatin loops compared to the HER2-high cell lines. The lower HER2 expression, the higher EMT phenotype, and inactivated chromatin all were found correlated with a lower response to lapatinib. The higher EMT phenotype was found correlated with a lower response to lapatinib. We also found that induction of EMT of HER2-positive breast cancer BT474 cells results in downregulated HER2 expression and lower binding rate of trastuzumab to the cells. These results show that the downregulation of HER2 in mesenchymal-like cells in the culture of HER2-positive breast cancer cell lines was due toERBB2gene silencing by epigenetic reprogramming of the cells during EMT. These results indicate thatERBB2gene silencing by epigenetic regulation during EMT is the main mechanism of resistance of HER2-positive breast cancer cells to trastuzumab and lapatinib.
Chromosome-scale genome assemblies of aphids reveal extensively rearranged autosomes and long-term conservation of the X chromosome
Authors: Mathers Thomas C. , Wouters Roland H. M. , Mugford Sam T. , Swarbreck David , Van Oosterhout Cock , Hogenhout Saskia A.
Published: March 2020

Large-scale chromosome rearrangements are arguably the most dramatic type of mutations, often leading to rapid evolution and speciation. However, chromosome dynamics have only been studied at the sequence level in a small number of model systems. In insects, Diptera (flies and mosquitoes) and Lepidoptera (butterflies and moths) have high levels of chromosome conservation. Whether this truly reflects the diversity of insect genome evolution is questionable given that many species exhibit rapid karyotype evolution. Here, we investigate chromosome evolution in aphids – an important group of hemipteran plant pests – using newly generated chromosome-scale genome assemblies of the green peach aphid (Myzus persicae) and the pea aphid (Acyrthosiphon pisum), and a previously published chromosome-scale assembly of the corn-leaf aphid (Rhopalosiphum maidis). We find that aphid autosomes have undergone dramatic reorganisation over the last 30 million years, to the extent that chromosome homology cannot be determined between aphids from the tribes Macrosiphini (M. persicaeandA. pisum) and Aphidini (R. maidis). In contrast, gene content of the aphid sex (X) chromosome remained unchanged despite rapid sequence evolution, low gene expression and high transposable element load. To test whether rapid evolution of genome structure is a hallmark of Hemiptera, we compared our aphid assemblies to chromosome-level assemblies of two blood-feeding Hemiptera (Rhodnius prolixusandTriatoma rubrofasciata). Despite being more diverged, the blood-feeding hemipterans have conserved synteny and we detect only two chromosome fusion or fission events. The exceptional rate of structural evolution of aphid autosomes renders them an important emerging model system for studying the role of large-scale genome rearrangements in evolution.
A model to estimate bed demand for COVID-19 related hospitalization
Authors: Zhang Teng , McFarlane Kelly , Vallon Jacqueline , Yang Linying , Xie Jin , Blanchet Jose , Glynn Peter , Staudenmayer Kristan , Schulman Kevin , Scheinker David
Published: March 2020

As of March 23, 2020 there have been over 354,000 confirmed cases of coronavirus disease 2019 (COVID-19) in over 180 countries, the World Health Organization characterized COVID-19 as a pandemic, and the United States (US) announced a national state of emergency.1, 2, 3 In parts of China and Italy the demand for intensive care (IC) beds was higher than the number of available beds.4, 5 We sought to build an accessible interactive model that could facilitate hospital capacity planning in the presence of significant uncertainty about the proportion of the population that is COVID-19+ and the rate at which COVID-19 is spreading in the population. Our approach was to design a tool with parameters that hospital leaders could adjust to reflect their local data and easily modify to conduct sensitivity analyses.

We developed a model to facilitate hospital planning with estimates of the number of Intensive Care (IC) beds, Acute Care (AC) beds, and ventilators necessary to accommodate patients who require hospitalization for COVID-19 and how these compare to the available resources. Inputs to the model include estimates of the characteristics of the patient population and hospital capacity. We deployed this model as an interactive online tool.6 The model is implemented in R 3.5, RStudio, RShiny 1.4.0 and Python 3.7. The parameters used may be modified as data become available, for use at other institutions, and to generate sensitivity analyses.

We illustrate the use of the model by estimating the demand generated by COVID-19+ arrivals for a hypothetical acute care medical center. The model calculated that the number of patients requiring an IC bed would equal the number of IC beds on Day 23, the number of patients requiring a ventilator would equal the number of ventilators available on Day 27, and the number of patients requiring an AC bed and coverage by the Medicine Service would equal the capacity of the Medicine service on Day 21.

In response to the COVID-19 epidemic, hospitals must understand their current and future capacity to care for patients with severe illness. While there is significant uncertainty around the parameters used to develop this model, the analysis is based on transparent logic and starts from observed data to provide a robust basis of projections for hospital managers. The model demonstrates the need and provides an approach to address critical questions about staffing patterns for IC and AC, and equipment capacity such as ventilators.
Prediction of coronary disease incidence in the general population by circulating RNY(YRNA)-derived small RNA
Authors: Costa Vera L. , Ruidavet Jean-Bernard , Bongard Vanina , Perret Bertrand , Repetto Emanuela , Stathopoulou Maria G. , Serra Fabrizio , Benahmed Mohamed , Claire Mauduit , Grandjean Valerie , Ferrières Jean , Martinez Laurent O. , Trabucchi Michele
Published: March 2020

During the development of atherosclerotic lesion, s-RNYs (small RNAs of about 24/34 nucleotides) are derived by the processing of long Ro-associated non-coding RNAs (RNYs) in macrophages. The levels of serum s-RNYs have been found significantly upregulated in patients with coronary heart disease (CHD) compared to age-matched healthy individuals. The present study aimed to examine the predictive value of serum s-RNYs for CHD events in the general population.

Within the frame of nested-case-control study, the GENES study, we measured the absolute expression of a RNY-derived small RNA, the s-RNY1-5p, in the serum of healthy individuals who encountered a CHD event within 12 years of follow-up (n = 31) (Cases) and compared them to individuals who remained event-free (Controls) (n = 30).

The expression of s-RNY1-5p in serum was significantly upregulated in Cases compared to Controls (p = 0.027). The proportion of CHD event-free was significantly higher among individuals with serum s-RNY1-5p below the median value (631 molecule / mL). In a multivariate model adjusted for age, smoking and treatment for hypertension, diabetes and dyslipidemia, the risk of CHD events increased more than 4-fold in individuals with serum s-RNY1-5p above the median value (HR, 4.36; 95%CI, 1.22-15.60). Significant association with CHD events was also observed when considering s-RNY1-5p as a continuous variable (p = 0.022). Serum s-RNY1-5p is an independent predictor of CHD in healthy individuals and could be considered as a biomarker in primary prevention of cardiovascular diseases.

TRANSLATIONAL PERSPECTIVES

Here, we reported that s-RNY1-5p was significantly upregulated in the serum of individuals who underwent CHD and was positively associated with CHD events. Those results argue in favor of s-RNY1-5p being a novel predictive molecular biomarker for cardiovascular events. In the future, measurement of s-RNY1-5p expression levels and other 5’ s-RNYs, such as s-RNY4-5p, could be used in clinical practice in addition to classical risk factors to identify those high-risk individuals who might benefit from prevention medicine.
Whole GenomeDe NovoVariant Identification with FreeBayes and Neural Network Approaches
Authors: Richter Felix , Morton Sarah U. , Qi Hongjian , Kitaygorodsky Alexander , Wang Jiayao , Homsy Jason , DePalma Steven , Patel Nihir , Gelb Bruce D. , Seidman Jonathan G. , Seidman Christine E. , Shen Yufeng
Published: March 2020

Motivation

De novovariant (DNV) calling typically relies on heuristic filters intrinsic to specific platforms and variant calling algorithms. FreeBayes and neural network approaches have overcome this limitation for variant calling, and we implemented a similar approach for DNV identification.

Results

We developed a DNV calling framework that uses Genome Analysis Toolkit (GATK), FreeBayes and a neural network trained on Integrative Genomics Viewer pile-up plots (IGV-bot). We identified DNVs in 2,390 WGS trios and benchmarked results against heuristics based on GATK parameters. Results were validatedin silicoand with Sanger sequencing, with the latter showing true positive rates of 98.4% and 97.3% for SNVs and indels, respectively. Taken together we describe a scalable framework for DNV identification based on both FreeBayes and neural network methods.

Availability

Source code and documentation are available athttps://github.com/ShenLab/igv-classifierandhttps://github.com/frichter/dnv_pipelineunder the MIT license.

Contact

ys2411@cumc.columbia.edu
SINGLe: Accurate detection of single nucleotide polymorphisms using nanopore sequencing in gene libraries
Authors: Rocío Espada , Nikola Zarevski , Adèle Dramé-Maigné , Yannick Rondelez
Published: March 2020

Nanopore sequencing is a powerful single molecule DNA sequencing technology which offers high throughput and long sequence reads. Nevertheless, its high native error rate limits the direct detection of point mutations in individual reads of amplicon libraries, as these mutations are difficult to distinguish from the sequencing noise.

In this work, we developed SINGLe (SNPs In Nanopore reads of Gene Libraries), a computational method to reduce the noise in nanopore reads of amplicons containing point variations. Our approach uses the fact that all reads are very similar to a wild type sequence, for which we experimentally characterize the position-specific systematic sequencing error pattern. We then use this information to reweight the confidence given to nucleotides that do not match the wild type in individual variant reads. We tested this method in a set of variants of KlenTaq, where the true mutation rate was well below the sequencing noise. SINGLe improves between 4 and 9 fold the signal to noise ratio, in comparison to the data returned by the basecaller guppy. Downstream, this approach improves variants clustering and consensus calling.

SINGLe is simple to implement and requires only a few thousands reads of the wild type sequence of interest, which can be easily obtained by multiplexing in a single minION run. It does not require any modification in the experimental protocol, it does not imply a large loss of sequencing throughput, and it can be incorporated downstream of standard basecalling.
Mechanisms of Action of Autophagy Modulators Dissected by Quantitative Systems Pharmacology Analysis
Authors: Shi Qingya , Pei Fen , Perlmutter David H. , Liu Bing , Bahar Ivet
Published: March 2020

Autophagy plays an essential role in cell survival/death and functioning. Modulation of autophagy has been recognized as a promising therapeutic strategy against diseases/disorders associated with uncontrolled growth or accumulation of biomolecular aggregates, organelles or cells including those caused by cancer, aging, neurodegeneration, and liver diseases such as α1-antitrypsin deficiency. Numerous pharmacological agents that enhance or suppress autophagy have been discovered. However, their molecular mechanisms of action are far from clear. Here we collected a set of 225 autophagy modulators and carried out a comprehensive quantitative systems pharmacology (QSP) analysis of their targets using both existing databases and predictions made by our machine learning algorithm. Autophagy modulators include several highly promiscuous drugs (e.g. artenimol and olanzapine acting as activator, fostamatinib as inhibitor, or melatonin as dual-modulator), as well as selected drugs uniquely targeting specific proteins (∼30% of modulators). They are mediated by three layers of regulation: (i) pathways involving core autophagy-related (ATG) proteins such as mTOR, AKT, and AMPK; (ii) upstream signaling events that regulates the activity of ATG pathways such as calcium-, cAMP-, and MAPK-signaling pathways; and (iii) transcription factors regulating the expression ATG proteins such as TFEB, TFE3, HIF-1, FoxO, and NF-κB. Our results suggest that PKA serves as a linker bridging between various signal transduction events and autophagy. These new insights contribute to a better assessment of the mechanism of action of autophagy modulators as well as their side effects, development of novel polypharmacological strategies, and identification of drug repurposing opportunities.
miRSwitch: Detecting microRNA arm shift and switch events
Authors: Kern Fabian , Amand Jeremy , Senatorov Ilya , Isakova Alina , Backes Christina , Meese Eckart , Keller Andreas , Fehlmann Tobias
Published: March 2020

Arm selection, the preferential expression of a 3′ or 5′ mature microRNA (miRNA), is a highly dynamic and tissue-specific process. Time-dependent expression shifts or switches between the arms are also relevant for human diseases. We present miRSwitch, a web server to facilitate the analysis and interpretation of arm selection events. Our species-independent tool evaluates pre-processed small non-coding RNA sequencing (sncRNA-seq) data, i.e. expression matrices or output files from miRNA quantification tools (miRDeep2, miRMaster, sRNAbench). miRSwitch highlights potential changes in the distribution of mature miRNAs from the same precursor. Group comparisons from one or several user-provided annotations (e.g. disease states) are possible. Results can be dynamically adjusted by choosing from a continuous range of highly specific to very sensitive parameters. Users can compare potential arm shifts in the provided data to a human reference map of pre-computed arm shift frequencies. We created this map from 46 tissues and 30,521 samples. As case studies we present novel arm shift information in a Alzheimer’s disease biomarker data set and from a comparison of tissues inHomo sapiensandMus musculus. In summary, miRSwitch offers a broad range of customised arm switch analyses along with comprehensive visualisations, and is freely available at:https://www.ccb.uni-saarland.de/mirswitch/.
Estimating the maximum daily number of incident COVID-19 cases manageable by a healthcare system
Authors: Giannakeas Vasily , Bhatia Deepit , Warkentin Matthew T. , Bogoch Isaac I. , Stall Nathan M.
Published: March 2020

The COVID-19 Acute and Intense Resource Tool (CAIC-RT) is an interactive online tool capable of estimating the maximum daily number of incident COVID- 19 cases that a healthcare system could manage given age-based case distribution and severity.
Developmental regulation of cell type-specific transcription by novel promoter-proximal sequence elements
Authors: Lu Dan , Sin Ho-Su , Lu Chenggang , Fuller Margaret T.
Published: March 2020

Cell type-specific transcriptional programs that drive differentiation of specialized cell types are key players in development and tissue regeneration. One of the most dramatic changes in the transcription program in Drosophila occurs with the transition from proliferating spermatogonia to differentiating spermatocytes, with >3000 genes either newly expressed or expressed from new alternative promoters in spermatocytes. Here we show that opening of these promoters from their closed state in precursor cells requires function of the spermatocyte-specific tMAC complex, localized at the promoters. The spermatocyte-specific promoters lack the previously identified canonical core promoter elements except for the Inr. Instead, these promoters are enriched for the binding site for the TALE-class homeodomain transcription factors Achi/Vis and for a motif originally identified under tMAC ChIP-seq peaks. The tMAC motif resembles part of the previously identified 14-bp β2UE1 element critical for spermatocyte-specific expression. Analysis of downstream sequences relative to transcription start site usage suggested that ACA and CNAAATT motifs at specific positions can help promote efficient transcription initiation. Our results reveal how promoter-proximal sequence elements that recruit and are acted upon by cell type-specific chromatin binding complexes help establish a robust, cell type-specific transcription program for terminal differentiation.
Embryo integrity regulates maternal proteostasis and stress resilience
Authors: Sala Ambre J. , Bott Laura C. , Brielmann Renee M. , Morimoto Richard I.
Published: March 2020

The proteostasis network is regulated by transcellular communication to promote health and fitness in metazoans. In Caenorhabditis elegans, signals from the germline initiate the decline of proteostasis and repression of cell stress responses at reproductive maturity, indicating that commitment to reproduction is detrimental to somatic health. Here we show that proteostasis and stress resilience are also regulated by embryo-to-mother communication in reproductive adults. To identify genes that act directly in the reproductive system to regulate somatic proteostasis, we performed a tissue targeted genetic screen for germline modifiers of polyglutamine aggregation in muscle cells. We found that inhibiting the formation of the extracellular vitelline layer of the fertilized embryo inside the uterus suppresses aggregation, improves stress resilience in an HSF-1-dependent manner, and restores the heat-shock response in the somatic tissues of the parent. This pathway relies on DAF-16/FOXO activation in vulval tissues to maintain stress resilience in the mother, suggesting that the integrity of the embryo is monitored by the vulva to detect damage and initiate an organismal protective response. Our findings reveal a previously undescribed transcellular pathway that links the integrity of the developing progeny to proteostasis regulation in the parent.
Manual measurement of angles in backscattered and transmission Kikuchi diffraction patterns
Authors: Nolze Gert , Tokarski Tomasz , Cios Grzegorz , Winkelmann Aimo
Published: March 2020

A historical tool for crystallographic analysis is provided by the Hilton net, which can be used for manually surveying the crystal lattice as it is manifested by the Kikuchi bands in a gnomonic projection. For a quantitative analysis using the Hilton net, the projection centre as the relative position of the signal source with respect to the detector plane needs to be known. Interplanar angles are accessible with a precision and accuracy which is estimated to be ≤0.3°. Angles between any directions,e.g.zone axes, are directly readable. Finally, for the rare case of an unknown projection-centre position, its determination is demonstrated by adapting an old approach developed for photogrammetric applications. It requires the indexing of four zone axes [uvw]iin a backscattered Kikuchi diffraction pattern of a known phase collected under comparable geometric conditions.
In-house texture measurement using a compact neutron source
Authors: Xu Pingguang , Ikeda Yoshimasa , Hakoyama Tomoyuki , Takamura Masato , Otake Yoshie , Suzuki Hiroshi
Published: March 2020

In order to improve the instrumental accessibility of neutron diffraction techniques, many emerging compact neutron sources and in-house neutron diffractometers are being developed, even though the precision level of neutron diffraction experiments performed on such instruments was thought to be incomparable with that of large-scale neutron facilities. As a challenging project, the RIKEN accelerator-driven compact neutron source (RANS) was employed here to establish the technical environment for texture measurements, and the recalculated pole figures and orientation distribution functions of an interstitial-free steel sheet obtained from RANS were compared with the results from another two neutron diffractometers well established for texture measurement. These quantitative comparisons revealed that the precise neutron diffraction texture measurement at RANS has been realized successfully, and the fine region division of the neutron detector panel is invaluable for improving the stereographic resolution of texture measurements. Moreover, through selectively using the parts of the obtained neutron diffraction patterns that exhibit good statistics, the Rietveld texture analysis improves the reliability of the texture measurement to a certain extent. These technical research results may accelerate the development of other easily accessible techniques for evaluation of engineering materials using compact neutron sources, and also help to improve the data-collection efficiency for various time-resolved scattering experiments at large-scale neutron facilities.
Comparison of azimuthal plots for reflection high-energy positron diffraction (RHEPD) and reflection high-energy electron diffraction (RHEED) for Si(111) surface
Authors: Mitura Zbigniew
Published: March 2020

Azimuthal plots for RHEPD (reflection high-energy positron diffraction) and RHEED (reflection high-energy electron diffraction) were calculated using dynamical diffraction theory and then compared. It was assumed that RHEPD and RHEED azimuthal plots can be collected practically by recording the intensity while rotating the sample around the axis perpendicular to the surface (for the case of X-ray diffraction, such forms of data are called Renninger scans). It was found that RHEPD plots were similar to RHEED plots if they were compared at Bragg reflections of the same order. RHEPD plots can also be determined in the region of total external reflection and for such conditions multiple scattering effects turned out to be very weak. The findings for azimuthal plots are also discussed in the context of the formation mechanisms of Kikuchi patterns.
Sample deposition onto cryo-EM grids: from sprays to jets and back
Authors: Klebl David P. , Monteiro Diana C. F. , Kontziampasis Dimitrios , Kopf Florian , Sobott Frank , White Howard D. , Trebbin Martin , Muench Stephen P.
Published: March 2020

Despite the great strides made in the field of single-particle cryogenic electron microscopy (cryo-EM) in microscope design, direct electron detectors and new processing suites, the area of sample preparation is still far from ideal. Traditionally, sample preparation involves blotting, which has been used to achieve high resolution, particularly for well behaved samples such as apoferritin. However, this approach is flawed since the blotting process can have adverse effects on some proteins and protein complexes, and the long blot time increases exposure to the damaging air–water interface. To overcome these problems, new blotless approaches have been designed for the direct deposition of the sample on the grid. Here, different methods of producing droplets for sample deposition are compared. Using gas dynamic virtual nozzles, small and high-velocity droplets were deposited on cryo-EM grids, which spread sufficiently for high-resolution cryo-EM imaging. For those wishing to pursue a similar approach, an overview is given of the current use of spray technology for cryo-EM grid preparation and areas for enhancement are pointed out. It is further shown how the broad aspects of sprayer design and operation conditions can be utilized to improve grid quality reproducibly.
The crystal structure of the heme d
1 biosynthesis-associated small c-type cytochrome NirC reveals mixed oligomeric states in crystallo
Authors: Klünemann Thomas , Henke Steffi , Blankenfeldt Wulf
Published: March 2020

Monoheme c-type cytochromes are important electron transporters in all domains of life. They possess a common fold hallmarked by three α-helices that surround a covalently attached heme. An intriguing feature of many monoheme c-type cytochromes is their capacity to form oligomers by exchanging at least one of their α-helices, which is often referred to as 3D domain swapping. Here, the crystal structure of NirC, a c-type cytochrome co-encoded with other proteins involved in nitrite reduction by the opportunistic pathogen Pseudomonas aeruginosa, has been determined. The crystals diffracted anisotropically to a maximum resolution of 2.12 Å (spherical resolution of 2.83 Å) and initial phases were obtained by Fe-SAD phasing, revealing the presence of 11 NirC chains in the asymmetric unit. Surprisingly, these protomers arrange into one monomer and two different types of 3D domain-swapped dimers, one of which shows pronounced asymmetry. While the simultaneous observation of monomers and dimers probably reflects the interplay between the high protein concentration required for crystallization and the structural plasticity of monoheme c-type cytochromes, the identification of conserved structural motifs in the monomer together with a comparison with similar proteins may offer new leads to unravel the unknown function of NirC.
Task design and assignment of full-text generation on mass Chinese historical archives in digital humanities
Authors: Liang Jihong , Wang Hao , Li Xiaojing
Published: March 2020

Purpose

The purpose of this paper is to explore the task design and assignment of full-text generation on mass Chinese historical archives (CHAs) by crowdsourcing, with special attention paid to how to best divide full-text generation tasks into smaller ones assigned to crowdsourced volunteers and to improve the digitization of mass CHAs and the data-oriented processing of the digital humanities.

Design/methodology/approach

This paper starts from the complexities of character recognition of mass CHAs, takes Sheng Xuanhuai archives crowdsourcing project of Shanghai Library as a case study, and makes use of the theories of archival science, including diplomatics of Chinese archival documents, and the historical approach of Chinese archival traditions as the theoretical basis and analysis methods. The results are generated through the comprehensive research.

Findings

This paper points out that volunteer tasks of full-text generation include transcription, punctuation, proofreading, metadata description, segmentation, and attribute annotation in digital humanities and provides a metadata element set for volunteers to use in creating or revising metadata descriptions and also provides an attribute tag set. The two sets can be used across the humanities to construct overall observations about texts and the archives of which they are a part. Along these lines, this paper presents significant insights for application in outlining the principles, methods, activities, and procedures of crowdsourced full-text generation for mass CHAs.

Originality/value

This study is the first to explore and identify the effective design and allocation of tasks for crowdsourced volunteers completing full-text generation on CHAs in digital humanities.
The impact of urban façade quality on affective feelings
Authors: Hollander Justin B. , Anderson Eric C.
Published: March 2020

Purpose

Much of the current literature on streetscape design emphasizes a need for well-articulated edge conditions to enhance pedestrian-orientation and the reason appears to lie in evolutionary biology: humans have a psychological preference for wall-hugging due to a well-established trait in other species: thigmotaxis.

Design/methodology/approach

This study seeks to explore the relationship between urban facades and affective feelings through an empirical study, which asks: how do people perceive edge conditions in urban environments? Through a study of affect relative to edge conditions, greater insight can be generated as to the human experience in the built environment. We conducted a laboratory experiment with 76 subjects who each viewed 40 images of urban facades and rated each based on their emotional reaction.

Findings

Each subject also completed two validated individual trait difference measures. We found that those images depicting thigmotaxic facades were more highly rated than other facades.

Originality/value

High quality edge environment resulted in people feeling more pleasant than low quality edges.
Dynamic capabilities for SME participation in public procurement
Authors: Akenroye Temidayo O. , Owens Jonathan D. , Elbaz Jamal , Durowoju Olatunde A.
Published: March 2020

Purpose

Although small- and medium-sized enterprises (SMEs) play major roles in most economies in terms of job creation, innovation and contribution to national income, they are often underrepresented in public procurement markets. This paper aims to explore how the dynamic capabilities theory can improve SME participation in public procurement.

Design/methodology/approach

Through a systematic literature review, the paper identifies common barriers to the effective participation of SMEs in public procurement and explores the applicability of the dynamic capabilities theory in addressing these barriers.

Findings

A theoretical analysis was conducted to identify possible relationships between the factors reported in the literature as barriers to SME participation in public procurement and different components of the dynamic capabilities of firms (i.e. sensing, seizing, reconfiguring and learning). Seven key propositions were generated to guide future research.

Research limitations/implications

Despite its contributions, this paper is based solely on a systematic literature review and theoretical analysis. Future studies could use meta-analysis to review multiple studies relating to the nexus between SMEs and public procurement, hence improving methodological rigour.

Practical implications

The paper contributes to the ongoing debate about whether and how SMEs can leverage their resources and capabilities to develop self-help strategies to improve participation in public procurement, an area yet underexplored in the literature.

Originality/value

This is one of the few studies examining the implications of firm-level capabilities of SME activity in public procurement markets. The findings may be beneficial to SME managers/owners, particularly regarding firms' ability to leverage resources and capabilities to participate effectively in public procurement.