bluuebunny/crossref_metadata_2025 huggingface dataset:
On the complexity of resting state spiking activity in monkey motor cortex
Authors: Dąbrowska Paulina Anna , Voges Nicole , von Papen Michael , Ito Junji , Dahmen David , Riehle Alexa , Brochier Thomas , Grün Sonja
Published: May 2020

Resting state has been established as a classical paradigm of brain activity studies, mostly based on large scale measurements such as fMRI or M/EEG. This term typically refers to a behavioral state characterized by the absence of any task or stimuli. The corresponding neuronal activity is often called idle or ongoing. Numerous modeling studies on spiking neural networks claim to mimic such idle states, but compare their results to task- or stimulus-driven experiments, which might lead to misleading conclusions. To provide a proper basis for comparing physiological and simulated network dynamics, we characterize simultaneously recorded single neurons’ spiking activity in monkey motor cortex and show the differences from spontaneous and task-induced movement conditions. The resting state shows a higher dimensionality, reduced firing rates and less balance between population level excitation and inhibition than behavior-related states. Additionally, our results stress the importance of distinguishing between rest with eyes open and closed.
Serial cryoFIB/SEM reveals profound cytoarchitectural disruptions caused by a pathogenic mutation in Leigh syndrome patient cells
Authors: Zhu Yanan , Sun Dapeng , Schertel Andreas , Ning Jiying , Fu Xiaofeng , Gwo Pam Pam , Watson Alan M. , Freyberg Zachary , Zhang Peijun
Published: May 2020

The advancement of serial cryo-FIB/SEM offers a new opportunity to study large volumes of near-native, fully hydrated frozen cells and tissues at voxel sizes of 10 nm and below. We explored this capability for pathologic characterization of vitrified human patient cells. We demonstrate profound disruption of subcellular architecture in primary fibroblasts from a Leigh syndrome patient harboring a disease-causing mutation in USMG5 protein responsible for impaired mitochondrial energy production.
Posttranslational modification of the RHO of plants protein RACB by phosphorylation and cross-kingdom conserved ubiquitination
Authors: Weiß Lukas , Gaelings Lana , Reiner Tina , Mergner Julia , Kuster Bernhard , Fehér Attila , Hensel Götz , Gahrtz Manfred , Kumlehn Jochen , Engelhardt Stefan , Hückelhoven Ralph
Published: May 2020

Small RHO-type G-proteins act as signaling hubs and master regulators of polarity in eukaryotic cells. Their activity is tightly controlled, as defective RHO signaling leads to aberrant growth and developmental defects. Two major processes regulate G-protein activity: canonical shuttling between different nucleotide bound states and posttranslational modification (PTM), of which the latter can support or suppress RHO signaling, depending on the individual PTM. In plants, regulation of Rho of plants (ROPs) signaling activity has been shown to act through nucleotide exchange and GTP hydrolysis, as well as through lipid modification, but there is little data available on phosphorylation or ubiquitination of ROPs. Hence, we applied proteomic analyses to identify PTMs of the barley ROP RACB. We observedin vitrophosphorylation by barley ROP binding kinase 1 andin vivoubiquitination of RACB. Comparative analyses of the newly identified RACB phosphosites and human RHO protein phosphosites revealed conservation of modified amino acid residues, but no overlap of actual phosphorylation patterns. However, the identified RACB ubiquitination site is conserved in all ROPs fromHordeum vulgare,Arabidopsis thalianaandOryza sativaand in mammalian Rac1 and Rac3. Point mutation of this ubiquitination site leads to stabilization of RACB. Hence, this highly conserved lysine residue may regulate protein stability across different kingdoms.
Integrative Molecular Characterization of Sarcomatoid and Rhabdoid Renal Cell Carcinoma Reveals Determinants of Poor Prognosis and Response to Immune Checkpoint Inhibitors
Authors: Bakouny Ziad , Braun David A. , Shukla Sachet A. , Pan Wenting , Gao Xin , Hou Yue , Flaifel Abdallah , Tang Stephen , Bosma-Moody Alice , He Meng Xiao , Vokes Natalie , Nyman Jackson , Xie Wanling , Nassar Amin H. , Alaiwi Sarah Abou , Flippot Ronan , Bouchard Gabrielle , Steinharter John A. , Nuzzo Pier Vitale , Ficial Miriam , Sant’Angelo Miriam , Forman Juliet , Berchuck Jacob E. , Dudani Shaan , Bi Kevin , Park Jihye , Camp Sabrina , Sticco-Ivins Maura , Hirsch Laure , Wind-Rotolo Megan , Ross-Macdonald Petra , Sun Maxine , Lee Gwo-Shu Mary , Chang Steven L. , Wei Xiao X. , McGregor Bradley A. , Harshman Lauren C. , Genovese Giannicola , Ellis Leigh , Pomerantz Mark , Hirsch Michelle S. , Freedman Matthew L. , Atkins Michael B. , Wu Catherine J. , Ho Thai H. , Linehan W. Marston , McDermott David F. , Heng Daniel Y.C. , Viswanathan Srinivas R. , Signoretti Sabina , Van Allen Eliezer M. , Choueiri Toni K.
Published: May 2020

Sarcomatoid and rhabdoid (S/R) renal cell carcinoma (RCC) are highly aggressive tumors with limited molecular and clinical characterization. Emerging evidence suggests immune checkpoint inhibitors (ICI) are particularly effective for these tumors1–3, although the biological basis for this property is largely unknown. Here, we evaluate multiple clinical trial and real-world cohorts of S/R RCC to characterize their molecular features, clinical outcomes, and immunologic characteristics. We find that S/R RCC tumors harbor distinctive molecular features that may account for their aggressive behavior, includingBAP1mutations,CDKN2Adeletions, and increased expression ofMYCtranscriptional programs. We show that these tumors are highly responsive to ICI and that they exhibit an immune-inflamed phenotype characterized by immune activation, increased cytotoxic immune infiltration, upregulation of antigen presentation machinery genes, and PD-L1 expression. Our findings shed light on the molecular drivers of aggressivity and responsiveness to immune checkpoint inhibitors of S/R RCC tumors.
The apple palmitoyltransferase MdPAT16 regulates sugar content via an MdCBL1-MdCIPK13-MdSUT2.2 pathway
Authors: Jiang Han , Ma Qi-Jun , Zhong Ming-Shuang , Gao Huai-Na , Li Yuan-Yuan , Hao Yu-Jin
Published: May 2020

Protein palmitoylation, a post-translational protein modification, plays an important role in the regulation of substrate protein stability, protein interactions, and protein localization. It is generally believed that there are two mechanisms of palmitoylation: one by acyl-CoA and the other by protein acyltransferase (PAT). In this study, an MdPAT family member, MdPAT16, was identified and shown to have palmitoyltransferase activity. We found that this gene responded to salt stress and that its expression improved plant salt resistance. MdPAT16 was shown to interact with MdCBL1 and stabilize MdCBL1 protein levels through palmitoylation. MdPAT16 further regulated apple sugar content by stabilizing the MdCIPK13-MdSUT2.2 protein complex. We found that the N-terminal sequence of MdCBL1 contains a palmitoylation site and that the N-terminal deletion of MdCBL1 leads to changes in protein stability and subcellular localization. Finally, exogenous salt stress increased the interaction of MdPAT16 with MdCBL1 and the sugar content in apple. These findings suggest that MdPAT16 functions as a stable means for the palmitoylation of downstream protein. It may be a missing link in the plant salt stress response pathway and have an important impact on fruit quality.
2’-O-methylation alters the RNA secondary structural ensemble
Authors: Assi Hala Abou , Shi Honglue , Liu Bei , Clay Mary C. , Erharter Kevin , Kreutz Christopher , Holley Christopher L. , Al-Hashimi Hashim M.
Published: May 2020

2’-O-methyl (Nm) is a highly abundant post-transcriptional RNA modification that plays important biological roles through mechanisms that are not entirely understood. There is evidence that Nm can alter the biological activities of RNAs by biasing the ribose sugar pucker equilibrium toward the C3’-endoconformation formed in canonical duplexes. However, little is known about how Nm might more broadly alter the dynamic ensembles of non-canonical RNA motifs. Here, using NMR and the HIV-1 transactivation response (TAR) element as a model system, we show that Nm preferentially stabilizes alternative secondary structures in which the Nm-modified nucleotides are paired, increasing both the abundance and lifetime of a low-populated short-lived excited state by up to 10-fold. The extent of stabilization increased with number of Nm modifications and was also dependent on Mg2+. Through phi (Φ) value analysis, the Nm modification also provided rare insights into the structure of the transition state for conformational exchange. Our results suggest that Nm could alter the biological activities of Nm-modified RNAs by modulating their secondary structural ensembles as well as establish the utility of Nm as a tool for the discovery and characterization of RNA excited state conformations.
ACE2 expression in human dorsal root ganglion sensory neurons: implications for SARS-CoV-2 virus-induced neurological effects
Authors: Shiers Stephanie , Ray Pradipta R. , Wangzhou Andi , Tatsui Claudio Esteves , Rhines Larry , Li Yan , Uhelski Megan L , Dougherty Patrick M. , Price Theodore J
Published: May 2020

SARS-CoV-2 has created a global crisis. COVID-19, the disease caused by the virus, is characterized by pneumonia, respiratory distress and hypercoagulation and is often fatal1. An early sign of infection is loss of smell, taste and chemesthesis - loss of chemical sensation2. Other neurological effects of the disease have been described, but not explained3,4. We show that human dorsal root ganglion (DRG) neurons express the SARS-CoV-2 receptor5,6, ACE2. ACE2 mRNA is expressed by a subset of nociceptors that express MRGPRD mRNA suggesting that SARS-CoV-2 may gain access to the nervous system through entry into neurons that form free-nerve endings at the outer-most layers of skin and luminal organs. Therefore, sensory neurons are a potential target for SARS-CoV-2 invasion of the nervous system.
SPIAT: An R package for the Spatial Image Analysis of Cells in Tissues
Authors: Yang Tianpei , Ozcoban Volkan , Pasam Anu , Kocovski Nikolce , Pizzolla Angela , Huang Yu-Kuan , Bass Greg , Keam Simon P. , Neeson Paul J. , Sandhu Shahneen K. , Goode David L. , Trigos Anna S.
Published: May 2020

Spatial technologies that query the location of cells in tissues at single-cell resolution are gaining popularity and are likely to become commonplace. The resulting data includes the X, Y coordinates of millions of cells, cell phenotypes and marker or gene expression levels. However, to date, the tools for the analysis of this data are largely underdeveloped, making us severely underpowered in our ability to extract quantifiable information. We have developed SPIAT (SpatialImageAnalysis ofTissues), an R package with a suite of data processing, quality control, visualization, data handling and data analysis tools. SPIAT includes our novel algorithms for the identification of cell clusters, cell margins and cell gradients, the calculation of neighbourhood proportions, and algorithms for the prediction of cell phenotypes. SPIAT also includes speedy implementations of the calculation of cell distances and detection of cell communities. This version of SPIAT is directly compatible with Opal multiplex immunohistochemistry images analysed through the HALO and InForm analysis software, but its intuitive implementation allows use with a diversity of platforms. We expect SPIAT to become a user-friendly and speedy go-to package for the spatial analysis of cells in tissues.

SPIAT is available on Github:https://github.com/cancer-evolution/SPIAT
Duration of Viral Clearance in IDF Soldiers with Mild COVID-19
Authors: Talmy Tomer , Tsur Adili , Shabtay Or
Published: May 2020

Policies determining the duration of quarantine and return to work for confirmed COVID-19 patients still lack evidence. We report our findings regarding the duration of viral RNA positivity among a cohort of young patients with mild disease. Between March 20th, 2020, and May 10th, 2020, 219 soldiers were admitted to the Israel Defense Forces Medical Corps (IDF-MC) COVID-19 rehabilitation center following a positive RT-PCR test for SARS-CoV-2. 119 of these patients, 84 (70.6%) males, 35 (29.4%) females with a median age of 21 (IQR 19-25) were classified as having mild disease and had two consecutive negative RT-PCR tests by May 10th, 2020. The median time for SARS-CoV-2 positivity in nasopharyngeal or oropharyngeal swabs in the study population was 21 days (IQR 15-27) from symptom onset, with a range of 4 to 45 days. The results of this study suggest that in young and healthy adult patients with COVID-19, the median duration of viral positivity is around three weeks. This duration is higher than previously reported in other populations. Young and healthy adults comprise much of the population workforce, and the results of this study may assist in determining the isolation period for symptomatic adults and confirmed COVID-19 patients with mild symptoms. Further studies on this topic should look to expand and determine the intervals of serial testing for confirmed patients and determine the duration of SARS-CoV-2 positivity in other populations.
Transfer of orientation memories in untethered wood ants (Formica rufa) from walking in an arena to walking on a motion compensation treadmill
Authors: Goulard Roman , Buehlmann Cornelia , Niven Jeremy E. , Graham Paul , Webb Barbara
Published: May 2020

The scale of natural insect navigation during foraging makes it challenging to study, in a controlled way, the navigation processes that an insect brain can support. Virtual Reality and trackball setups have offered experimental control over visual environments while studying tethered insects, but potential limitations and confounds introduced by tethering motivates the development of alternative untethered solutions. In this paper we validate the use of a motion compensator (or ‘treadmill’) to study visually-driven behaviour of freely moving wood ants (Formica rufa). We show how this setup allows naturalistic walking behaviour and motivation over long timeframes. Furthermore, we show that ants are able to transfer associative and navigational memories from classical maze and arena contexts to our treadmill. Thus, we demonstrate the possibility to study navigational behaviour over ecologically relevant durations (and virtual distances) in precisely controlled environments, bridging the gap between natural and highly controlled laboratory experiments.

1

Summary statement

We have developed and validated a motion compensating treadmill for wood ants which opens new perspectives to study insect navigation behaviour in a fully controlled manner over ecologically relevant durations.
A chromosome-level genome assembly of the woolly apple aphid,Eriosoma lanigerum(Hausmann) (Hemiptera: Aphididae)
Authors: Biello Roberto , Singh Archana , Godfrey Cindayniah J. , Fernández Fernández Felicidad , Mugford Sam T. , Powell Glen , Hogenhout Saskia A. , Mathers Thomas C.
Published: May 2020

Woolly apple aphid (WAA,Eriosoma lanigerumHausmann) (Hemiptera: Aphididae), is a major pest of apple trees (Malus domestica, order Rosales) and is critical to the economics of the apple industry in most parts of the world. Here, we generated a chromosome-level genome assembly of WAA – representing the first genome sequence from the aphid subfamily Eriosomatinae – using a combination of 10X Genomics linked-reads andin vivoHi-C data. The final genome assembly is 327 Mb, with 91% of the assembled sequences anchored into six chromosomes. The contig and scaffold N50 values are 158 kb and 71 Mb, respectively, and we predicted a total of 28,186 protein-coding genes. The assembly is highly complete, including 97% of conserved arthropod single-copy orthologues based on BUSCO analysis. Phylogenomic analysis of WAA and nine previously published aphid genomes, spanning four aphid tribes and three subfamilies, reveals that the tribe Eriosomatini (represented by WAA) is recovered as a sister group to Aphidini + Macrosiphini (subfamily Aphidinae). We identified syntenic blocks of genes between our WAA assembly and the genomes of other aphid species and find that two WAA chromosomes (El5 and El6) map to the conserved Macrosiphini and Aphidini X chromosome. Our high-quality WAA genome assembly and annotation provides a valuable resource for research in a broad range of areas such as comparative and population genomics, insect-plant interactions and pest resistance management.
A peptide-level multiple imputation strategy accounting for the different natures of missing values in proteomics data
Authors: Gianetto Q. Giai , Wieczorek S. , Couté Y. , Burger T.
Published: May 2020

Motivation

Quantitative mass spectrometry-based proteomics data are characterized by high rates of missing values, which may be of two kinds: missing completely-at-random (MCAR) and missing not-at-random (MNAR). Despite numerous imputation methods available in the literature, none account for this duality, for it would require to diagnose the missingness mechanism behind each missing value.

Results

A multiple imputation strategy is proposed by combining MCAR-devoted and MNAR-devoted imputation algorithms. First, we propose an estimator for the proportion of MCAR values and show it is asymptotically unbiased under assumptions adapted to label-free proteomics data. This allows us to estimate the number of MCAR values in each sample and to take into account the nature of missing values through an original multiple imputation method. We evaluate this approach on simulated data and shows it outperforms traditionally used imputation algorithms.

Availability

The proposed methods are implemented in the R package imp4p (available on the CRAN Giai Gianetto (2020)), which is itself accessible through Prostar software.

Contact

quentin.giaigianetto@pasteur.fr;thomas.burger@cea.fr
Natural variation in insect egg-induced cell death uncovers a role for L-type LECTIN RECEPTOR KINASE-I.1 in Arabidopsis
Authors: Groux Raphaël , Gouhier-Darimont Caroline , Kerdaffrec Envel , Reymond Philippe
Published: May 2020

InArabidopsis thaliana, a hypersensitive-like response (HR-like) is triggered underneath the eggs of the large white butterflyPieris brassicae, and this response is dependent on salicylic acid (SA) accumulation and signaling. Previous reports indicate that the clade I L-type lectin receptor kinase LecRK-I.8 is involved in early steps of egg recognition. A genome-wide association study (GWAS) was used to better characterize the genetic structure of HR-like and discover loci that contribute to this response. We report here the identification of LecRK-I.1, a close homolog of LecRK-I.8, and show that two main haplotypes that explain part of the variation in HR-like segregate amongst natural Arabidopsis accessions. In addition, signatures of balancing selection at this locus suggest that it may be ecologically important. Disruption of LecRK-I.1 resulted in decreased HR-like and SA signaling, indicating that this protein is important for the observed responses. Furthermore, we provide evidence that LecRK-I.1 functions in the same signaling pathway as LecRK-I.8. Altogether, our results show that the response to eggs ofP. brassicaeis controlled by LecRKs that operate at various steps of the signaling pathway.
Development and on-site evaluation of an easy-to-perform and low-cost food pathogen diagnostic workflow for low-resource communities
Authors: Mason Michael Glenn , Botella José Ramón
Published: May 2020

Food-borne diseases are a leading cause of illness and death in many developing countries and thus, there is a real need to develop affordable and practical technologies that can help improve food safety in these countries. The ability to efficiently identify food pathogens is essential to allow national regulatory authorities to monitor food quality and implement safety protocols. In this study, we have developed a simple, low-cost ($0.76 (USD)) complete food pathogen diagnostic workflow ideally suited for deployment in low-resource environments that uses a simple four step process (sample enrichment, cell lysis, DNA amplification, and naked-eye readout). The minimal number of steps and equipment involved in our diagnostic workflow, as well as the simplicity of the yes/no flocculation readout, allows non-technical personnel to perform and interpret the assay. To evaluate the system’s performance, we tested the entire system on fresh produce samples collected from local farms and markets in Cambodia for the presence of theE. coli O157O-antigen polymerase,wzy. Although this was a proof-of-concept study, our system successfully revealed a clear correlation between the origin and condition of the produce collected and their likelihood of contamination. In conclusion, we believe that our easy-to-perform diagnostic system can have a significant impact on improving food quality and human health if adopted by regulatory authorities in developing countries due to the assay’s simplicity, affordability, and adaptability.
AutoNeuriteJ: An ImageJ plugin for measurement and classification of neuritic extensions
Authors: Boulan Benoit , Beghin Anne , Ravanello Charlotte , Deloulme Jean-Christophe , Gory-Fauré Sylvie , Andrieux Annie , Brocard Jacques , Denarier Eric
Published: May 2020

Morphometry characterization is an important procedure in describing neuronal cultures and identifying phenotypic differences. This task usually requires labor-intensive measurements and the classification of numerous neurites from large numbers of neurons in culture. To automate these measurements, we wrote AutoNeuriteJ, an imageJ/Fiji plugin that measures and classifies neurites from a very large number of neurons. We showed that AutoNeuriteJ is able to detect variations of neuritic growth induced by several compounds known to affect the neuronal growth. In these experiments measurement of more than 5000 mouse neurons per conditions was obtained within a few hours. Moreover, by analyzing mouse neurons deficient for the microtubule associated protein 6 (MAP6) and wild type neurons we illustrate that AutoNeuriteJ is capable to detect subtle phenotypic difference in axonal length. Overall the use of AutoNeuriteJ will provide rapid, unbiased and accurate measurement of neuron morphologies.
The postsynaptic MAGUK scaffold protein MPP2 organises a distinct interactome that incorporates GABAAreceptors at the periphery of excitatory synapses
Authors: Schmerl Bettina , Gimber Niclas , Kuropka Benno , Rentsch Jakob , Kunde Stella-Amrei , Ewers Helge , Freund Christian , Schmoranzer Jan , Rademacher Nils , Shoichet Sarah A.
Published: May 2020

Recent advances in imaging technology have highlighted that scaffold proteins and receptors are arranged in sub-synaptic nanodomains. The synaptic MAGUK scaffold protein MPP2 is a component of AMPA receptor-associated protein complexes and also binds to the synaptic cell adhesion molecule SynCAM1. Using super-resolution imaging, we now show that MPP2 and SynCAM1 are situated at the periphery of the postsynaptic density. In order to explore MPP2-associated protein complexes, we used a quantitative comparative mass spectrometry approach and identified multiple GABAAreceptor subunits among the novel synaptic MPP2 interactors. We further show that GABAAreceptors are found together with MPP2 in a subset of dendritic spines and thus highlight MPP2 as a scaffold molecule capable of acting as an adaptor molecule that links peripheral synaptic elements critical for inhibitory regulation to central structures at the PSD of glutamatergic synapses.
TSPAN1 promotes human pancreatic cancer cells proliferation by modulating CDK1 via Akt
Authors: Wang Xin , Gao Xiaozhuo , Tian Jiaxun , Zhang Rui , Qiao Yun , Hua Xiangdong , Shi Gang
Published: May 2020

Background

To explore the potential therapeutic target to treat pancreatic cancers, Tspan1 was detected in human pancreatic cancer tissue and human pancreatic ductal adenocarcinoma cells and functional role of Tspan1 on proliferation was explored and the mechanism was investigated.

Materials and Methods

Tspan1 in PCC tissue and PDAC cell lines was measured by qRT-PCR and Western blot. Tspan1 was knock-downed and over-expressed in cells via transfection with Tspan1-siRNA and pLNCX-TSPAN1-cDNA, cell survival, proliferation and cell cycle were measured with MTT, Alamar blue and Flow Cytometry assay. The mRNA and protein expression were assessed by qRT-PCR and Western blotting. The expression of PI3K, Akt and p-Akt were detected, and CDK1 siRNA and specific inhibitor of Akt were used to explore the mechanism of TSPAN1 promoting PDAC cells proliferation.

Results

Tspan1 expression in PCC tissue and PDAC cells was increased. Transfection of siRNA targeting Tspan1 in BxPC3 and PNAC-1 cells obviously decreased cell proliferation and down-regulated CDK1 expression. Consistently, both cell proliferation and CDK1 expression in BxPC3 and PNAC-1 cells were up-regulated with pLNCX-TSPAN1-cDNA transfection. Cell cycle analysis showed that after knockdown of Tspan1 the G2/M phase ratio was increased to cause mitosis arrest, and TSPAN1 overexpression caused cell cycle transition from G2 to M phase to promote cell proliferation. And these were dependent on the modulation of CDK1 expression via Akt.

Conclusion

Tspan1 up-regulates CDK1 expression via activating Akt to promote human PCC cell proliferation and silencing of Tspan1 may be a potential therapeutic target to treat pancreatic cancers.
CD147 (BSG) but notACE2expression is detectable in vascular endothelial cells within single cell RNA sequencing datasets derived from multiple tissues in healthy individuals
Authors: Ganier C , Du-Harpur X , Harun N , Wan B , Arthurs C , Luscombe NM , Watt FM , Lynch MD
Published: May 2020

Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and is associated with a wide range of systemic manifestations. Several observations support a role for vascular endothelial dysfunction in the pathogenesis including an increased incidence of thrombotic events and coagulopathy and the presence of vascular risk factors as an independent predictor of poor prognosis. It has recently been reported that endothelitis is associated with viral inclusion bodies suggesting a direct role for SARS-CoV-2 in the pathogenesis. The ACE2 receptor has been shown to mediate SARS-CoV-2 uptake and it has been proposed that CD147 (BSG) can function as an alternative cell surface receptor. To define the endothelial cell populations that are susceptible to infection with SARS-CoV-2, we investigated the expression of ACE2 as well as other genes implicated in the cellular entry of SARS-Cov-2 in the vascular endothelium through the analysis of single cell sequencing data derived from multiple human tissues (skin, liver, kidney, lung and intestine). We found that CD147 (BSG) but notACE2is detectable in vascular endothelial cells within single cell sequencing datasets derived from multiple tissues in healthy individuals. This implies that eitherACE2is not expressed in healthy tissue but is instead induced in response to SARS-Cov2 or that SARS-Cov2 enters endothelial cells via an alternative receptor such as CD147.
A Heat-Shock Inducible System for Flexible Gene Expression in Cereals
Authors: Harrington Sophie A. , Backhaus Anna E. , Fox Samantha , Rogers Christian , Borrill Philippa , Uauy Cristobal , Richardson Annis
Published: May 2020

Background

Functional characterisation of genes using transgenic methods is increasingly common in cereal crops. Yet standard methods of gene over-expression can lead to undesirable developmental phenotypes, or even embryo lethality, due to ectopic gene expression. Inducible expression systems allow the study of such genes by preventing their expression until treatment with the specific inducer. When combined with the Cre-Lox recombination system, inducible promoters can be used to initiate constitutive expression of a gene of interest. Yet while these systems are well established in dicot model plants, likeArabidopsis thaliana, they have not yet been implemented in grasses.

Results

Here we present an irreversible heat-shock inducible system developed using Golden Gate-compatible components which utilises Cre recombinase to drive constitutive gene expression in barley and wheat. We show that a heat shock treatment of 38 °C is sufficient to activate the construct and drive expression of the gene of interest. Modulating the duration of heat shock controls the density of induced cells. Short durations of heat shock cause activation of the construct in isolated single cells, while longer durations lead to global construct activation. The system can be successfully activated in multiple tissues and at multiple developmental stages and shows no activation at standard growth temperatures (~ 20 °C).

Conclusions

This system provides an adaptable framework for use in gene functional characterisation in cereal crops. The developed vectors can be easily adapted for specific genes of interest within the Golden Gate cloning system. By using an environmental signal to induce activation of the construct, the system avoids pitfalls associated with consistent and complete application of chemical inducers. As with any inducible system, care must be taken to ensure that the expected construct activation has indeed taken place.
SCAN-ATAC-Sim: a scalable and efficient method for simulating single-cell ATAC-seq data from bulk-tissue experiments
Authors: Chen Zhanlin , Zhang Jing , Liu Jason , Zhang Zixuan , Zhu Jiangqi , Lee Donghoon , Xu Min , Gerstein Mark
Published: May 2020

scATAC-seq is a powerful approach for characterizing cell-type-specific regulatory landscapes. However, it is difficult to benchmark the performance of various scATAC-seq analysis techniques (such as clustering and deconvolution) without havinga prioria known set of gold-standard cell types. To simulate scATAC-seq experiments with known cell-type labels, we introduce an efficient and scalable scATAC-seq simulation method (SCAN-ATAC-Sim) that down-samples bulk ATAC-seq data (e.g., from representative cell lines or tissues). Our protocol uses a consistent but tunable signal-to-noise ratio across cell types in a scATAC-seq simulation for integrating bulk experiments with different levels of background noise, and it independently samples twice without replacement to account for the diploid genome. Because it uses an efficient weighted reservoir sampling algorithm and is highly parallelizable with OpenMP, our implementation in C++ allows millions of cells to be simulated in less than an hour on a laptop computer.

Availability

SCAN-ATAC-Sim is available atscan-atac-sim.gersteinlab.org.

Contact

pi@gersteinlab.org

Supplementary information

Supplementary data are available atBioinformaticsonline.
Identification and analysis of splicing quantitative trait loci across multiple tissues in the human genome
Authors: Garrido-Martín Diego , Borsari Beatrice , Calvo Miquel , Reverter Ferran , Guigó Roderic
Published: May 2020

We have developed an efficient and reproducible pipeline for the discovery of genetic variants affecting splicing (sQTLs), based on an approach that captures the intrinsically multivariate nature of this phenomenon. We employed it to analyze the multi-tissue transcriptome GTEx dataset, generating a comprehensive catalogue of sQTLs in the human genome. A core set of these sQTLs is shared across multiple tissues. Downstream analyses of this catalogue contribute to the understanding of the mechanisms underlying splicing regulation. We found that sQTLs often target the global splicing pattern of genes, rather than individual splicing events. Many of them also affect gene expression, but not always of the same gene, potentially uncovering regulatory loci that act on different genes through different mechanisms. sQTLs tend to be preferentially located in introns that are post-transcriptionally spliced, which would act as hotspots for splicing regulation. While many variants affect splicing patterns by directly altering the sequence of splice sites, many more modify the binding of RNA-binding proteins (RBPs) to target sequences within the transcripts. Genetic variants affecting splicing can have a phenotypic impact comparable or even stronger than variants affecting expression, with those that alter RBP binding playing a prominent role in disease.
Effects of Post-Myocardial Infarction Heart Failure on the Bone Vascular Niche
Authors: Hoffmann Jedrzej , Luxán Guillermo , Abplanalp Wesley Tyler , Glaser Simone-Franziska , Rasper Tina , Fischer Ariane , Muhly-Reinholz Marion , John David , Assmus Birgit , Zeiher Andreas Michael , Dimmeler Stefanie
Published: May 2020

Bone vasculature provides protection and signals necessary to control stem cell quiescence and renewal1. Specifically, type H capillaries, which highly express Endomucin, constitute the endothelial niche supporting a microenvironment of osteoprogenitors and long-term hematopoietic stem cells2–4. The age-dependent decline in type H endothelial cells was shown to be associated with bone dysregulation and accumulation of hematopoietic stem cells, which display cell-intrinsic alterations and reduced functionality3. The regulation of bone vasculature by chronic diseases, such as heart failure is unknown. Here, we describe the effects of myocardial infarction and post-infarction heart failure on the vascular bone cell composition. We demonstrate an age-independent loss of type H bone endothelium in heart failure after myocardial infarction in both mice and in humans. Using single-cell RNA sequencing, we delineate the transcriptional heterogeneity of human bone marrow endothelium showing increased expression of inflammatory genes, includingIL1BandMYC, in ischemic heart failure. Inhibition of NLRP3-dependent IL-1β production partially prevents the post-myocardial infarction loss of type H vasculature in mice. These results provide a rationale for using anti-inflammatory therapies to prevent or reverse the deterioration of vascular bone function in ischemic heart disease.
ATM Inhibition Synergizes with Fenofibrate in High Grade Serous Ovarian Cancer Cells
Authors: Chen Chi-Wei , Buj Raquel , Dahl Erika S. , Leon Kelly E. , Aird Katherine M.
Published: May 2020

Background

Epithelial ovarian cancer (EOC) is the deadliest gynecological malignancy in the United States with high grade serous ovarian cancer (HGSOC) as the most commonly diagnosed subtype. While therapies targeting deficiencies in the homologous recombination (HR) pathway are emerging as the standard treatment for HGSOC patients, this strategy is limited to the 50% of patients with a deficiency in this pathway. Therefore, patients with HR-proficient tumors are likely to be resistant to these therapies and require alternative strategies.

Methods

Data from HGSOC patients in The Cancer Genome Atlas (TCGA) were analyzed for ATM status, ATM and PPARα expression, and used to perform Gene Set Enrichment Analysis (GSEA). Screening data from the Dependency Map were analyzed to identify FDA-approved drugs that preferentially inhibit ATM-low cancer cells.In vitrostudies were performed to determine whether ATM inhibitors synergize with the PPARα agonist fenofibrate in HGSOC cell lines.

Results

The HR gene Ataxia Telangiectasia Mutated (ATM) is wildtype in the majority of HGSOC patients and its kinase activity is upregulated compared to normal fallopian tube tissue. As high ATM has been associated with poor overall and progression-free survival, targeting ATM may be beneficial for a subset of HGSOC patients. Clinical trials of ATM inhibitors are commencing; however, ATM inhibitors are not effective as single agents. We aimed to explore novel therapeutic vulnerabilities of ATM deficient cells to develop a combinatorial therapy. Using data from TCGA, we found that multiple pathways related to metabolism are inversely correlated with ATM expression, suggesting that combining ATM inhibition and metabolic inhibition would be effective. Indeed, analysis of FDA-approved drugs from the Dependency Map demonstrated that ATM low cell lines are more sensitive to fenofibrate, a PPARα agonist that has been previously shown to affect multiple cellular metabolic pathways. Consistently, PPARα signaling is associated with ATM expression. We validated that combined inhibition of ATM and treatment with fenofibrate is synergistic in multiple HGSOC cell lines by inducing senescence.

Conclusions

Our results suggest that metabolic changes induced by ATM inhibitors are a potential target for the treatment for HGSOC.
Maternal blood metal concentrations and whole blood DNA methylation during pregnancy in the Early Autism Risk Longitudinal Investigation (EARLI)
Authors: Aung Max T. , Bakulski Kelly M. , Feinberg Jason I. , Dou John F. , Meeker John D. , Mukherjee Bhramar , Loch-Caruso Rita , Ladd-Acosta Christine , Volk Heather E. , Croen Lisa A. , Hertz-Picciotto Irva , Newschaffer Craig J. , Fallin M. Daniele
Published: May 2020

Background

Metals exposures have important health effects in pregnancy. The maternal epigenome may be responsive to these exposures. We tested whether metals are associated with concurrent differential maternal whole blood DNA methylation.

Methods

In the Early Autism Risk Longitudinal Investigation (EARLI) cohort, we measured first or second trimester maternal blood metals concentrations (cadmium, lead, mercury, manganese, and selenium) in 215 participants using inductively coupled plasma mass spectrometry. DNA methylation in maternal whole blood was measured in the same specimens on the Illumina 450K array (201 participants). A subset sample of 97 women had both measures available for analysis, all of whom did not report smoking during pregnancy. Linear regression was used to test for site-specific associations between individual metals and DNA methylation, adjusting for cell type composition and confounding variables. Discovery gene ontology analysis was conducted on the top 1,000 sites associated with each metal to elucidate downstream pathways.

Results

In multiple linear regression, we observed hypermethylation at 11 DNA methylation sites associated with lead (FDR q-value <0.1), near the genes CYP24A1, ASCL2, FAT1, SNX31, NKX6-2, LRC4C, BMP7, HOXC11, PCDH7, ZSCAN18, and VIPR2. Lead associated sites were enriched (FDR q-value <0.1) for the pathways cell adhesion, nervous system development, and calcium ion binding. Manganese was associated with hypermethylation at four DNA methylation sites (FDR q-value <0.1), one of which was near the gene ARID2. Manganese associated sites were enriched for cellular metabolism pathways (FDR q-value<0.1). Effect estimates for DNA methylation sites associated (p<0.05) with cadmium, lead, and manganese were highly correlated (Pearson ρ >0.86).

Discussion

Single DNA methylation sites associated with lead and manganese may be potential biomarkers of exposure or implicate downstream gene pathways. Future studies should replicate our findings to characterize potential toxicological mechanisms of trace metals through the maternal epigenome.
Non-pharmaceutical behavioural measures for droplet-borne biological hazards prevention: Health-EDRM for COVID-19 (SARS-CoV-2) Pandemic
Authors: Chan Emily Ying Yang , Shahzada Tayyab Salim , Sham Tiffany Sze Tung , Dubois Caroline , Huang Zhe , Liu Sida , Ying-en Ho Janice , KC Hung Kevin , On Kwok Kin , Kayano Ryoma , Shaw Rajib
Published: May 2020

Introduction

Non-pharmaceutical interventions to facilitate response to the COVID-19 pandemic, a disease caused by novel coronavirus SARS-CoV-2, are urgently needed. Using the WHO health emergency and disaster risk management (health-EDRM) framework, behavioural measures for droplet-borne communicable disease, with their enabling and limiting factors at various implementation levels were evaluated.

Sources of data

Keyword search was conducted in PubMed, Google Scholar, Embase, Medline, Science Direct, WHO and CDC online publication database. Using OCEBM as review criteria, 105 English-language articles, with ten bottom-up, non-pharmaceutical prevention measures, published between January 2000 and May 2020 were identified and examined.

Areas of Agreement

Evidence-guided behavioural measures against COVID-19 transmission for global at-risk communities are identified.

Area of Concern

Strong evidence-based systematic behavioural studies for COVID-19 prevention are lacking.

Growing points

Very limited research publications are available for non-pharmaceutical interventions to facilitate pandemic response.

Areas timely for research

Research with strong implementation feasibility that targets resource-poor settings with low baseline Health-EDRM capacity is urgently need.
COVID 19: An SEIR model predicting disease progression and healthcare outcomes for Pakistan
Authors: Ahmad Khan Ejaz , Umar Maida , Khalid Maryam
Published: May 2020

Background

Recent pandemic of the Noval Coronal Virus (COVID 19) has claimed more than 200,000 lives and about 3.8 million infected worldwide. Countries are being gradually exposed to its devastating threat without being properly prepared and with inadequate response. COVID 19’s first two cases were reported in Pakistan on February 26, 2020. We present a model depicting progression of epidemiology curve for Pakistan with and without interventions in view of its health system’ response capacity in near future.

Methodology

We used a modified compartmental epidemiological SEIR model to describe the outbreak of COVID-19 in Pakistan including the possibility of asymptomatic infection and presymptomatic transmission. The behavior of the dynamic model is determined by a set of clinical parameters and transmission rate.

Results

We estimated that in the absence of a set of proven interventions, the total susceptible population would be 43.24 million, exposed individuals would be almost 32 million, asymptomatic cases would be 13.13 million, mildly infected 30.64 million, severely infected slightly more than 6 million and critical cases would be around 967,000 in number. By that time, almost 760,000 fatalities of infected critical would have taken place. Comparing with the healthcare capacity of Pakistan, if we could “flatten the curve” to a level below the dashed grey line, the healthcare system will be capable of managing the cases with ideal healthcare facilities, where the grey line representing the healthcare capacity of Pakistan. With the intervention in place, the number of symptomatic infected individuals is expected to be almost 20 million.

Conclusion

We consider the impact of intervention and control measures on the spread of COVID-19 with 30% reduction in transmission from mild cases in case a set of interventions are judiciously in place to mitigate its impact.
Uncoupling of DNA replication and centrosome duplication cycles is a primary cause of haploid instability in mammalian somatic cells
Authors: Yoshizawa Koya , Yaguchi Kan , Uehara Ryota
Published: May 2020

Mammalian haploid somatic cells are unstable and prone to diploidize, but the cause of haploid instability remains largely unknown. Previously, we found that mammalian haploid somatic cells suffer chronic centrosome loss stemming from the uncoupling of DNA replication and centrosome duplication cycles. However, the lack of methodology to restore the coupling between DNA replication and centrosome duplication has precluded us from investigating the potential contribution of the haploidy-linked centrosome loss to haploid instability. In this study, we developed an experimental method that allows the re-coupling of DNA and centrosome cycles through the chronic extension of the G1/S phase without compromising cell proliferation using thymidine treatment/release cycles. Chronic extension of G1/S restored normal mitotic centrosome number and mitotic control, substantially improving the stability of the haploid state in HAP1 cells. Stabilization of the haploid state was compromised when cdk2 was inhibited during the extended G1/S, or when early G1 was chronically extended instead of G1/S, showing that the coupling of DNA and centrosome cycles rather than a general extension of the cell cycle is required for haploid stability. Our data indicate the chronic centriole loss arising from the uncoupling of centrosome and DNA cycles as a direct cause of genome instability in haploid somatic cells, and also demonstrate the feasibility of modulation of haploid stability through artificial coordination between DNA and centrosome cycles in mammalian somatic cells.
Genome-Wide Characterization of DNase I-Hypersensitive Sites and Cold Response Regulatory Landscapes in Grasses
Authors: Han Jinlei , Wang Pengxi , Wang Qiongli , Lin Qingfang , Chen Zhiyong , Yu Guangrun , Miao Chenyong , Dao Yihang , Wu Ruoxi , Schnable James C. , Tang Haibao , Wang Kai
Published: May 2020

Deep sequencing of DNase-I treated chromatin (DNase-seq) can be used to identify DNase I-hypersensitive sites (DHSs) and facilitates genome-scale mining of de novo cis-regulatory DNA elements. Here, we adapted DNase-seq to generate genome-wide maps of DHSs using control and cold-treated leaf, stem, and root tissues of three widely studied grass species: Brachypodium distachyon, foxtail millet (Setaria italica), and sorghum (Sorghum bicolor). Functional validation demonstrated that 12 of 15 DHSs drove reporter gene expression in transiently transgenic B. distachyon protoplasts. DHSs under both normal and cold treatment substantially differed among tissues and species. Intriguingly, the putative DHS-derived transcription factors (TFs) are largely colocated among tissues and species and include 17 ubiquitous motifs covering all grass taxa and all tissues examined in this study. This feature allowed us to reconstruct a regulatory network that responds to cold stress. Ethylene-responsive TFs SHINE3, ERF2, and ERF9 occurred frequently in cold feedback loops in the tissues examined, pointing to their possible roles in the regulatory network. Overall, we provide experimental annotation of 322,713 DHSs and 93 derived cold-response TF binding motifs in multiple grasses, which could serve as a valuable resource for elucidating the transcriptional networks that function in the cold-stress response and other physiological processes.
Moderation effect of competence of knowledge and innovation: case of Bali
Authors: Usman Irwan , Maupa Haris , Idrus Muhammad , Haerani Siti , Nurjanna Nurjanna
Published: May 2020

Purpose

This paper examines how market orientation and competence of knowledge reinforce the innovation and in turn improve the business performance.

Design/methodology/approach

This research applied research design with quantitative approach based on positivism philosophy, that is, research aimed to test the theory and data which is general to produce findings that are special through hypothesis test. This study was supplemented by field studies as a necessary source of data in the form of trends, attitudes, opinions, perceptions of owners, managers or senior employees of SMEs in the textile industry in Bali, related to the variables used in this study.

Findings

(1) Market orientation influences business performance, (2) competence of knowledge moderates the influence of market orientation on business performance, (3) innovation moderates the influence of market orientation on business performance.

Originality/value

(1) Novelty of this research is developing the concept of competence of knowledge associated with business performance in which this relationship has not yet been expressed. (2) Building the concept of innovation development of small-scale industry based on the market orientation. (3) Developing the concept of innovative development of small and medium enterprises of textile industry based on competence of knowledge. (4) Investigating the concept of market orientation and competence of knowledge in an integrated and holistic way to strengthen the innovation and business performance of SMEs of the textile industry in Bali.