bluuebunny/crossref_metadata_2025 huggingface dataset:
Automated Feature Extraction from Large Cardiac Electrophysiological Data Sets
Authors: Jurkiewicz John , Kroboth Stacie , Zlochiver Viviana , Hinow Peter
Published: October 2020

Rationale

A new multi-electrode array-based application for the long-term recording of action potentials from electrogenic cells makes possible exciting cardiac electrophysiology studies in health and disease. With hundreds of simultaneous electrode recordings being acquired over a period of days, the main challenge becomes achieving reliable signal identification and quantification.

Objective

We set out to develop an algorithm capable of automatically extracting regions of high-quality action potentials from terabyte size experimental results and to map the trains of action potentials into a low-dimensional feature space for analysis.

Methods and Results

Our automatic segmentation algorithm finds regions of acceptable action potentials in large data sets of electrophysiological readings. We use spectral methods and support vector machines to classify our readings and to extract relevant features. We are able to show that action potentials from the same cell site can be recorded over days without detrimental effects to the cell membrane. The variability between measurements 24 h apart is comparable to the natural variability of the features at a single time point.

Conclusions

Our work contributes towards a non-invasive approach for cardiomyocyte functional maturation, as well as developmental, pathological and pharmacological studies. As the human-derived cardiac model tissue has the genetic makeup of its donor, a powerful tool for individual drug toxicity screening emerges.
Rice Calcium/Calmodulin-Dependent Protein Kinase Directly Phosphorylates a Mitogen-Activated Protein Kinase Kinase to Regulate Abscisic Acid Responses
Authors: Chen Min , Ni Lan , Chen Jing , Sun Manman , Qin Caihua , Zhang Gang , Zhang Aying , Jiang Mingyi
Published: October 2020

Ca2+/calmodulin (CaM)-dependent protein kinase (CCaMK) is an important positive regulator of abscisic acid (ABA) and abiotic stress signaling in plants and is believed to act upstream of mitogen-activated protein kinase (MAPK) in ABA signaling. However, it is unclear how CCaMK activates MAPK in ABA signaling. Here, we show that OsDMI3, a rice (Oryza sativa) CCaMK, directly interacts with and phosphorylates OsMKK1, a MAPK kinase (MKK) in rice, in vitro and in vivo. OsDMI3 was found to directly phosphorylate Thr-25 in the N-terminus of OsMKK1, and this Thr-25 phosphorylation is OsDMI3-specific in ABA signaling. The activation of OsMKK1 and its downstream kinase OsMPK1 is dependent on Thr-25 phosphorylation of OsMKK1 in ABA signaling. Moreover, ABA treatment also induces the phosphorylation in the activation loop of OsMKK1, and the two phosphorylations in the N-terminus and in the activation loop are independent. Further analyses revealed that OsDMI3-mediated phosphorylation of OsMKK1 positively regulates ABA responses in seed germination, root growth, and tolerance to both water stress and oxidative stress. Our results indicate that OsMKK1 is a direct target of OsDMI3, and OsDMI3-mediated phosphorylation of OsMKK1 plays an important role in the activation of MAPK cascade and ABA signaling.

One-sentence summary

OsMKK1 is a direct target of OsDMI3, and OsDMI3-mediated phosphorylation of OsMKK1 plays an important role in the activation of MAPK cascade and ABA signaling.

The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantcell.org) is: Mingyi Jiang (myjiang@njau.edu.cn)
Cancer immunotherapy by NC410, a LAIR-2 Fc protein blocking LAIR-collagen interaction
Authors: Ramos M. Inês Pascoal , Tian Linjie , de Ruiter Emma J. , Song Chang , Paucarmayta Ana , Singh Akashdip , Elshof Eline , Vijver Saskia V. , Shaik Jahangheer , Bosiacki Jason , Cusumano Zachary , Liu Linda , Langermann Sol , Willems Stefan , Flies Dallas , Meyaard Linde
Published: October 2020

Collagens are a primary component of the extracellular matrix and are functional ligands for the inhibitory immune receptor leukocyte associated immunoglobulin-like receptor-1 (LAIR-1). Leukocyte associated immunoglobulin-like receptor-2 (LAIR-2) is a secreted protein that can act as a decoy receptor by binding collagen with higher affinity than LAIR-1. We propose that collagens promote immune evasion by interacting with LAIR-1 and that LAIR-2 could release LAIR-1 mediated immune suppression. Analysis of public datasets shows high LAIR-2 expression being associated with a favorable outcome in certain tumors. We designed a dimeric LAIR-2 with a functional IgG1 Fc tail, NC410, and showed that NC410 reduces tumor growth and increases T cell expansion and effector function in humanized tumor models. Immunohistochemical analysis of human tumors shows that NC410 binds to collagen-rich areas where LAIR-1+immune cells are localized. Our findings show that NC410 might be a powerful new strategy for cancer immunotherapy for immune-excluded tumors.
Variations of intracellular density during the cell cycle arise from tip-growth regulation in fission yeast
Authors: Odermatt Pascal D. , Miettinen Teemu P. , Kang Joon Ho , Bostan Emrah , Manalis Scott , Huang Kerwyn Casey , Chang Fred
Published: October 2020

Intracellular density impacts the physical nature of the cytoplasm and can globally affect cellular processes, yet density regulation remains poorly understood. Here, using a new quantitative phase imaging method, we determined that dry-mass density varies during the cell cycle in fission yeast. Density decreased during G2, increased in mitosis and cytokinesis, and rapidly dropped at cell birth. These density variations were explained by a constant rate of biomass synthesis, coupled to slowdown of volume growth during cell division and rapid expansion post-cytokinesis. Arrest at specific cell-cycle stages led to continued increases or decreases in density. Spatially heterogeneous patterns of density suggested links between density regulation and tip growth, and septum bending away from higher-density daughters linked density to intracellular osmotic pressure. Our results demonstrate that systematic density variations during the cell cycle are predominantly due to modulation of volume expansion, and reveal functional consequences of density gradients and cell-cycle arrests.
Databiology Lab CORONAHACK: Collection of Public COVID-19 Data
Authors: Pérez Juan Caballero , Contreras José Manuel Caballero , de Blas Pérez Carlos , Alvarez Felipe Leza
Published: October 2020

COVID-19 has had an unprecedented global impact in health and economy affecting millions of persons world-wide. To support and enable a collaborative response from the global research communities, we created a data collection for different public sources for anonymized patient clinical data, imaging datasets, molecular data as nucleotide and protein sequences for the SARS-CoV-2 virus, reports of count of cases and deaths per city/country, and other economic indicators in Databiology Lab (https://www.lab.databiology.net/) where researchers could access these data assets and use the hundreds of available open source bioinformatic applications to analyze them. These data assets are regularly updated and was used in a successful virtual 3-day hackathon organized by Databiology Ltd and Mindstream-AI where hundreds of attendees to work collaboratively to analyze these data collections.
Identification of specific biomarkers and pathways in the synovial tissues of patients with osteoarthritis in comparison to rheumatoid arthritis
Authors: Gu Hanming , Yuan Gongsheng
Published: October 2020

Osteoarthritis and rheumatoid arthritis are two common arthritis with different pathogenesis. Here, we explore the difference of genes and biological pathways in human synovial fibroblasts by using a bioinformatics method to clarify their potential pathogenesis. The GSE7669 dataset was originally produced by using an Affymetrix Human Genome U95 platform. We used the KEGG and GO analysis to identify the functional categories and pathways. Our results suggested that biological adhesion and cell adhesion are the main signaling pathways in osteoarthritis in comparison to rheumatoid arthritis. Furthermore, Albumin, MAPK3, PTPRC, COL1A1, and CXCL12 may be key genes in osteoarthritis. Therefore, our study provides potential targets for the specific and accurate therapy of osteoarthritis.
Histone H2A ubiquitination resulting from Brap loss of function connects multiple aging hallmarks and accelerates neurodegeneration
Authors: Guo Y. , Chomiak A. A. , Hong Y. , Lowe C. C. , Chan W-C. , Andrade J. , Pan H. , Zhou X. , Berezovski E. , Monuki E. S. , Feng Y.
Published: October 2020

Aging is an intricate process that is characterized by multiple hallmarks including stem cell exhaustion, genome instability, epigenome alteration, impaired proteostasis, and cellular senescence. While each of these traits is detrimental at the cellular level, it remains unclear how they are interconnected to cause systemic organ deterioration. Here we show that abrogating Brap, a BRCA1 associated protein important for neurogenesis, results in cellular senescence with persistent DNA double-strand breaks and elevation of histone H2A mono- and poly-ubiquitination (H2Aub). The high H2Aub initiates histone proteolysis, leading to both epigenetic alteration and proteasome overflow. These defects induce neuroinflammation, impair proteostasis, accelerate neurodegeneration, and substantially shorten lifespan in mice carrying Brap deletions in the brain. We further show H2Aub is also increased in human brain tissues of Alzheimer’s disease. These data together suggest that chromatin aberrations mediated by H2Aub act as a nexus of multiple aging hallmarks and promote tissue-wide degeneration.
NG2+/Nestin+mesenchymal stem cells dictate DTC dormancy in the bone marrow through TGFβ2
Authors: Nobre Ana Rita , Risson Emma , Singh Deepak K. , Di Martino Julie , Cheung Julie F. , Wang Jiapeng , Johnson John , Russnes Hege G. , Bravo-Cordero Jose Javier , Birbrair Alexander , Naume Bjorn , Azhar Mohamad , Frenette Paul S. , Aguirre-Ghiso Julio A.
Published: October 2020

In the bone marrow (BM) microenvironment, NG2+/Nestin+mesenchymal stem cells (MSCs) promote hematopoietic stem cell (HSC) quiescence1,2. Importantly, the BM can also harbour disseminated tumour cells (DTCs) from multiple cancers, which, like HSCs, can remain dormant3. The BM signals are so growth-restrictive that dormant BM DTCs can persist for years to decades only to awaken and fuel lethal metastasis3–10. The mechanisms and niche components regulating DTC dormancy remain largely unknown. Here, we reveal that periarteriolar BM-resident NG2+/Nestin+MSCs can instruct breast cancer (BC) DTCs to enter dormancy. NG2+/Nestin+MSCs produce TGFβ2 and BMP7 and activate a quiescence pathway dependent on TGFBRIII and BMPRII, whichviap38-kinase result in p27-CDK inhibitor induction. Importantly, genetic depletion of the NG2+/Nestin+MSCs or conditional knock-out of TGFβ2 in the NG2+/Nestin+MSCs led to awakening and bone metastatic expansion of otherwise dormant p27+/Ki67−DTCs. Our results provide a direct proof that HSC dormancy niches control BC DTC dormancy. Given that aged NG2+/Nestin+MSCs can lose homeostatic control of HSC dormancy, our results suggest that aging or extrinsic factors that affect the NG2+/Nestin+MSC niche may result in a break from dormancy and BC bone relapse.
Theta-gamma coupling depends on breathing rate
Authors: Hammer Maximilian , Schwale Chrysovalandis , Brankačk Jurij , Draguhn Andreas , Tort Adriano BL
Published: October 2020

Temporal coupling between theta and gamma oscillations is a hallmark activity pattern of several cortical networks and becomes especially prominent during REM sleep. In a parallel approach, nasal breathing has been recently shown to generate phase-entrained network oscillations which also modulate gamma. Both slow rhythms (theta and respiration-entrained oscillations) have been suggested to aid large-scale integration but they differ in frequency, display low coherence, and modulate different gamma sub-bands. Respiration and theta are therefore believed to be largely independent. In the present work, however, we report an unexpected but robust relation between theta-gamma coupling and respiration in mice. Interestingly, this relation takes place not through the phase of individual respiration cycles, but through respiration rate: the strength of theta-gamma coupling exhibits an inverted V-shaped dependence on breathing rate, leading to maximal coupling at breathing frequencies of 4-6 Hz. Noteworthy, when subdividing sleep epochs into phasic and tonic REM patterns, we find that breathing differentially relates to theta-gamma coupling in each state, providing new evidence for their physiological distinctiveness. Altogether, our results reveal that breathing correlates with brain activity not only through phase-entrainment but also through rate-dependent relations with theta-gamma coupling. Thus, the link between respiration and other patterns of cortical network activity is more complex than previously assumed.
OmicLoupe: Facilitating biological discovery by interactive exploration of multiple omic datasets and statistical comparisons
Authors: Willforss Jakob , Siino Valentina , Levander Fredrik
Published: October 2020

Visual exploration of gene product behavior across multiple omic datasets can pinpoint technical limitations in data and reveal biological trends. The OmicLoupe software was developed to facilitate such exploration and provides more than 15 interactive cross-dataset visualizations for omic data. It expands visualizations to multiple datasets for quality control, statistical comparisons and overlap and correlation analyses, while allowing for rapid inspection and downloading of selected features. The usage of OmicLoupe is demonstrated in three diverse studies, including an analysis of SARS-CoV-2 infection across omic layers, based on previously published proteomics and transcriptomics studies. OmicLoupe is available at quantitativeproteomics.org/omicloupe
Quantifying growth perturbations over the fattening period in swine via mathematical modelling
Authors: Manuel Revilla , Guillaume Lenoir , Loïc Flatres-Grall , Rafael Muñoz-Tamayo , Friggens Nicolas C
Published: October 2020

Abstract

Background

Resilience can be defined as the capacity of animals to cope with short-term perturbations in their environment and return rapidly to their pre-challenge status. In a perspective of precision livestock farming, it is key to create informative indicators for general resilience and therefore incorporate this concept in breeding goals. In the modern swine breeding industry, new technologies such as automatic feeding system are increasingly common and can be used to capture useful data to monitor animal phenotypes such as feed efficiency. This automatic and longitudinal data collection integrated with mathematical modelling has a great potential to determine accurate resilience indicators, for example by measuring the deviation from expected production levels over a period of time.

Results

This work aimed at developing a modelling approach for facilitating the quantification of pig resilience during the fattening period, from approximately 34 kg to 105 kg of body weight. A total of 13 093 pigs, belonging to three different genetic lines were monitored (Pietrain, Pietrain NN and Duroc) since 2015, and body weight measures registered (approximately 11.1 million of weightings) with automatic feeding systems. We used the Gompertz model and linear interpolation on body weight data to quantify individual deviations from expected production, thereby creating a resilience index (ABC). The estimated heritabilities ofABCare low but not zero from 0.03 to 0.04 (± 0.01) depending on the breed.

Conclusions

Our model-based approach can be useful to quantify pig responses to perturbations using exclusively the growth curves and should contribute to the genetic improvement of resilience of fattening pigs by providing a resilience index.
Selection of internal references for transcriptomics and RT-qPCR assays in Neurofibromatosis type 1 (NF1) related Schwann cell lines
Authors: Gu Yi-Hui , Cui Xi-Wei , Ren Jie-Yi , Long Man-Mei , Wang Wei , Wei Cheng-Jiang , Aimaier Rehanguli , Li Yue-Hua , Chung Man-Hon , Gu Bin , Li Qing-Feng , Wang Zhi-Chao
Published: October 2020

Transcriptomics has been widely applied in uncovering disease mechanisms and screening potential biomarkers. Internal reference selection determines the accuracy and reproducibility of data analyses. The aim of this study was to identify the most qualified reference genes for the relative quantitation analysis of transcriptomics and real-time quantitative reverse-transcription PCR in fourteen NF1 related cell lines, including non-tumor, benign and malignant Schwann cell lines. The expression characteristics of eleven candidate reference genes (RPS18, ACTB, B2M, GAPDH, PPIA, HPRT1, TBP, UBC, RPLP0, TFRC and RPL32) were screened and analyzed by four software programs: geNorm, NormFinder, BestKeeper and RefFinder. Results showed that GAPDH, the most used internal reference gene, was significantly unstable. The combinational use of two reference genes (PPIA and TBP) was optimal in malignant Schwann cell lines and the use of single reference genes (PPIA or PRLP0) alone or in combination was optimal in benign Schwann cell lines. Our recommended internal reference genes may improve the accuracy and reproducibility of the results of transcriptomics and real-time quantitative reverse-transcription PCR in further gene expression analyses of NF1 related tumors.
Atlas of tissue-specific and tissue-preferential gene expression in ecologically and economically significant coniferPinus sylvestris
Authors: Cervantes Sandra , Vuosku Jaana , Paczesniak Dorota , Pyhäjärvi Tanja
Published: October 2020

Despite their ecological and economical importance, conifers genomic resources are limited, mainly due to the large size and complexity of their genomes. Additionally, the available genomic resources lack complete structural and functional annotation. Transcriptomic resources have been commonly used to compensate for these deficiencies, though for most conifer species they are limited to a small number of tissues, or capture only a fraction of the genes present in the genome.

Here we provide an atlas of gene expression patterns for coniferPinus sylvestrisacross five tissues: embryo, megagametophyte, needle, phloem, and vegetative bud. We used a wide range of tissues and focused our analyses on the expression profiles of genes at tissue level. We provide comprehensive information of the per-tissue normalized expression level, indication of tissue preferential upregulation and tissue-specificity of expression. We identified a total of 48,001 tissue preferentially upregulated and tissue specifically expressed genes, of which 28% have annotation in the Swiss-Prot database. Even though most of the putative genes identified do not have functional information in current biological databases, the tissue-specific patterns discovered provide valuable information about their potential functions for further studies, as for example in the areas of plant physiology, population genetics, and genomics in general. As we provide information on tissue specificity at both diploid and haploid life stages, our data will also contribute to the understanding of evolutionary rates of different tissue types and ploidy levels.
Discovering the drivers of clonal hematopoiesis
Authors: Pich Oriol , Reyes-Salazar Iker , Gonzalez-Perez Abel , Lopez-Bigas Nuria
Published: October 2020

Mutations in genes that confer a selective advantage to hematopoietic stem cells (HSCs) in certain conditions drive clonal hematopoiesis (CH). While some CH drivers have been identified experimentally or through epidemiological studies, the compendium of all genes able to drive CH upon mutations in HSCs is far from complete. We propose that identifying signals of positive selection in blood somatic mutations may be an effective way to identify CH driver genes, similarly as done to identify cancer genes. Using a reverse somatic variant calling approach, we repurposed whole-genome and whole-exome blood/tumor paired samples of more than 12,000 donors from two large cancer genomics cohorts to identify blood somatic mutations. The application of IntOGen, a robust driver discovery pipeline, to blood somatic mutations across both cohorts, and more than 24,000 targeted sequenced samples yielded a list of close to 70 genes with signals of positive selection in CH, available athttp://www.intogen.org/ch. This approach recovers all known CH genes, and discovers novel candidates. Generating this compendium is an essential step to understand the molecular mechanisms of CH and to accurately detect individuals with CH to ascertain their risk to develop related diseases.
SARS-CoV-2 Variants Reveal Features Critical for Replication in Primary Human Cells
Authors: Pohl Marie O. , Busnadiego Idoia , Kufner Verena , Glas Irina , Karakus Umut , Schmutz Stefan , Zaheri Maryam , Abela Irene , Trkola Alexandra , Huber Michael , Stertz Silke , Hale Benjamin G.
Published: October 2020

Since entering the human population, SARS-CoV-2 (the causative agent of COVID-19) has spread worldwide, causing >100 million infections and >2 million deaths. While large-scale sequencing efforts have identified numerous genetic variants in SARS-CoV-2 during its circulation, it remains largely unclear whether many of these changes impact adaptation, replication or transmission of the virus. Here, we characterized 14 different low-passage replication-competent human SARS-CoV-2 isolates representing all major European clades observed during the first pandemic wave in early 2020. By integrating viral sequencing data from patient material, virus stocks, and passaging experiments, together with kinetic virus replication data from non-human Vero-CCL81 cells and primary differentiated human bronchial epithelial cells (BEpCs), we observed several SARS-CoV-2 features that associate with distinct phenotypes. Notably, naturally-occurring variants in Orf3a (Q57H) and nsp2 (T85I) were associated with poor replication in Vero-CCL81 cells but not in BEpCs, while SARS-CoV-2 isolates expressing the Spike D614G variant generally exhibited enhanced replication abilities in BEpCs. Strikingly, low-passage Vero-derived stock preparation of 3 SARS-CoV-2 isolates selected for substitutions at positions 5/6 of E, and were highly attenuated in BEpCs, revealing a key cell-specific function to this region. Rare isolate-specific deletions were also observed in the Spike furin-cleavage site during Vero-CCL81 passage, but these were rapidly selected against in BEpCs, underscoring the importance of this site for SARS-CoV-2 replication in primary human cells. Overall, our study uncovers sequence features in SARS-CoV-2 variants that determine cell-specific virus replication, and highlights the need to monitor SARS-CoV-2 stocks carefully when phenotyping newly emerging variants or potential variants-of-concern.
Dynamic targeting enables domain-general inhibitory control over action and thought by the prefrontal cortex
Authors: Apšvalka Dace , Ferreira Catarina S. , Schmitz Taylor W. , Rowe James B. , Anderson Michael C.
Published: October 2020

Successful self-control requires the ability to stop unwanted actions or thoughts. Stopping is regarded as a central function of inhibitory control, a mechanism enabling the suppression of diverse mental content, and strongly associated with the prefrontal cortex. A domain-general inhibitory control capacity, however, would require the region or regions implementing it to dynamically shift top-down inhibitory connectivity to diverse target regions in the brain. Here we show that stopping unwanted thoughts and stopping unwanted actions engage common regions in the right anterior dorsolateral and right ventrolateral prefrontal cortex, and that both areas exhibit this dynamic targeting capacity. Within each region, pattern classifiers trained to distinguish stopping actions from making actions also could identify when people were suppressing their thoughts (and vice versa) and could predict which people successfully forgot thoughts after inhibition. Effective connectivity analysis revealed that both regions contributed to action and thought stopping, by dynamically shifting inhibitory connectivity to motor area M1 or to the hippocampus, depending on the goal, suppressing task-specific activity in those regions. These findings support the existence of a domain-general inhibitory control mechanism that contributes to self-control and establish dynamic inhibitory targeting as a key mechanism enabling these abilities.
Configurable Digital Virus Counter on Robust Universal DNA Chips
Authors: Seymour Elif , Ünlü Nese Lortlar , Carter Eric P. , Connor John H. , Ünlü M. Selim
Published: October 2020

Here, we demonstrate real-time multiplexed virus detection by applying DNA-directed antibody immobilization technique to a single-particle interferometric reflectance imaging sensor (SP-IRIS). In this technique, the biosensor chip surface spotted with different DNA sequences is converted to a multiplexed antibody array by flowing antibody-DNA conjugates and allowing specific DNA-DNA hybridization. The resulting antibody array is shown to detect three different recombinant Vesicular Stomatitis Viruses (rVSVs) genetically engineered to express surface glycoproteins of Ebola, Marburg, and Lassa viruses in real-time in a disposable microfluidic cartridge. We also show that this method can be modified to produce a single-step, homogeneous assay format by mixing the antibody-DNA conjugates with the virus sample in solution phase prior to flowing in the microfluidic cartridge, eliminating the antibody immobilization step. This homogenous approach achieved detection of the model Ebola virus, rVSV-EBOV, at a concentration of 100 PFU/ml in 1 hour. Finally, we demonstrate the feasibility of this homogeneous technique as a rapid test using a passive microfluidic cartridge. A concentration of 104PFU/ml was detectable under 10 minutes for the rVSV-Ebola virus. Utilizing DNA microarrays for antibody-based diagnostics is an alternative approach to antibody microarrays and offers advantages such as configurable sensor surface, long-term storage ability, and decreased antibody use. We believe these properties will make SP-IRIS a versatile and robust platform for point-of-care diagnostics applications.
Loss of coordinated expression between ribosomal and mitochondrial genes revealed by comprehensive characterization of a large family with a rare mendelian disorder
Authors: Panici Brendan , Nakajima Hosei , Carlston Colleen M. , Ozadam Hakan , Cenik Can , Cenik Elif Sarinay
Published: October 2020

Non-canonical intronic variants are a poorly characterized yet highly prevalent class of alterations associated with Mendelian disorders. Here, we report the first RNA expression and splicing analysis from a family whose members carry a non-canonical splice variant in an intron of RPL11 (c.396+3A>G). This mutation is causative for Diamond Blackfan Anemia (DBA) in this family despite incomplete penetrance and variable expressivity. Our analyses revealed a complex pattern of disruptions with many novel junctions of RPL11. These include an RPL11 transcript that is translated with a late stop codon in the 3’ untranslated region (3’UTR) of the main isoform. We observed that RPL11 transcript abundance is comparable among carriers regardless of symptom severity. Interestingly, both the small and large ribosomal subunit transcripts were significantly overexpressed in individuals with a history of anemia in addition to congenital abnormalities. Finally, we discovered that coordinated expression between mitochondrial components and RPL11 was lost in all carriers, which may lead to variable expressivity. Overall, this study highlights the importance of RNA splicing and expression analyses in families for molecular characterization of Mendelian diseases.
Asymmetric directed functional connectivity within the frontoparietal motor network during motor imagery and execution
Authors: Ogawa Takeshi , Shimobayashi Hideki , Hirayama Jun-ichiro , Kawanabe Motoaki
Published: October 2020

Both imagery and execution of motor controls consist of interactions within a neuronal network, including frontal motor-related regions and posterior parietal regions. To reveal neural representation in the frontoparietal motor network, two approaches have been proposed thus far: one is decoding of actions/modes related to motor control from the spatial pattern of brain activity; another is to estimate directed functional connectivity, which means a directed association between two brain regions within motor regions. However, directed connectivity among multiple regions of the motor network during motor imagery (MI) or motor execution (ME) has not been investigated. Here, we attempted to characterize the directed functional connectivity within the frontoparietal motor-related networks between the MI and ME conditions. We developed a delayed sequential movement and imagery task to evoke brain activity associated with data under ME and MI via functional magnetic resonance imaging scanning. We applied a causal discovery approach, linear non-Gaussian acyclic causal model, to identify directed functional connectivity among the frontoparietal motor-related brain regions for each condition. We demonstrated higher directed functional connectivity from the contralateral dorsal premotor cortex (dPMC) to the primary motor cortex (M1) in ME than in MI. We mainly identified significant direct effects of the dPMC and ventral premotor cortex (vPMC) to the parietal regions. In particular, connectivity from the dPMC to the superior parietal lobule in the same hemisphere showed significant positive effects across all conditions. Contrastingly, interlateral connectivities from the vPMC to the superior parietal lobule showed significantly negative effects across all conditions. Finally, we found positive effects from A1 to M1 in the same hemisphere, such as the audio-motor pathway. These results indicated that the sources of motor command originated in d/vPMC influenced M1 and parietal regions as achieving ME and MI. Additionally, sequential sounds may functionally facilitate temporal motor processes.
Membrane Shape Remodeling by Protein Crowding
Authors: Liese Susanne , Carlson Andreas
Published: October 2020

The steric repulsion between proteins on biological membranes is one of the most generic mechanisms that cause membrane shape changes. We present a minimal model where a spontaneous curvature is induced by steric repulsion between membrane-associated proteins. Our results show that the interplay between the induced spontaneous curvature and the membrane tension determine the energy minimizing shapes, which describe the wide range of experimentally observed membrane shapes,i.e. flat membranes, spherical vesicles, elongated tubular protrusions, and pearling structures.
Cell group analysis reveals changes in upper-layer neurons associated with schizophrenia
Authors: Dai Rujia , Chen Lulu , Liu Sihan , Wu Chiung-Ting , Chen Yu , Jiang Yi , Dai Jiacheng , Wang Qihang , Kopp Richard , Yu Guoqiang , Wang Yue , Chen Chao , Liu Chunyu
Published: October 2020

Genome-wide association studies (GWAS) of schizophrenia (SCZ) have revealed over 100 risk loci. We investigated whether these SCZ-associated variants regulate gene expression by cell type. Using a fully unsupervised deconvolution method, we calculated gene expression by clusters of estimated cell types (cell-groups, CGs). Five CGs emerged in the dorsolateral prefrontal cortices (DLPFC) of 341 donors with and without SCZ. By mapping expression quantitative trait loci (eQTL) per CG, we partitioned the heritability of SCZ risk in GWAS by CGs. CG-specific expressions and eQTLs were replicated in both a deconvoluted bulk tissue data set with a different method and also in sorted-cell expression data. Further, we characterized CG-specific gene differential expression and cell proportion changes in SCZ brains. We found upper-layer neurons in the DLPFC to be associated with SCZ based on enrichment of SCZ heritability in eQTLs, disease-related transcriptional signatures, and decreased cell proportion. Our study suggests that neurons and related anomalous circuits in the upper layers of the DLPFC may have a major contribution to SCZ risk.
Single cell transcriptional profiling reveals helper, effector, and regulatory MAIT cell populations enriched during homeostasis and activation
Authors: Vorkas Charles Kyriakos , Krishna Chirag , Li Kelin , Aubé Jeffrey , Fitzgerald Daniel W. , Mazutis Linas , Leslie Christina S. , Glickman Michael S.
Published: October 2020

Mucosal-associated invariant T (MAIT) cells are innate-like lymphocytes that recognize microbial vitamin B metabolites and have emerging roles in infectious disease, autoimmunity, and cancer. Although MAIT cells are identified by a semi-invariant T cell receptor, their phenotypic and functional heterogeneity is not well understood. Here we present an integrated single cell transcriptomic analysis of over 76,000 human MAIT cells during acute and chronic antigen-specific activation with the MR1 ligand 5-OP-RU and non-specific TCR stimulation. We show that MAIT cells span a broad range of homeostatic, effector, helper, tissue-infiltrating, regulatory, and exhausted phenotypes, with distinct gene expression programs associated with CD4+or CD8+co-expression. During acute activation, MAIT cells rapidly adopt a cytotoxic phenotype characterized by high expression ofGZMB,IFNGandTNF. In contrast, chronic stimulation induces heterogeneous states defined by proliferation, cytotoxicity, immune modulation, and exhaustion. These scRNAseq-defined MAIT cell subtypes were also detected in individuals recently exposed toMycobacterium tuberculosisinfection, confirming their presence during human infection. Our study provides the first comprehensive atlas of human MAIT cells in activation conditions and defines substantial functional heterogeneity, suggesting complex roles in health and disease.
Mammalian Cell Proliferation Requires Noncatalytic Functions of O-GlcNAc Transferase
Authors: Levine Zebulon G. , Potter Sarah C. , Joiner Cassandra M. , Fei George Q. , Nabet Behnam , Sonnett Matthew , Zachara Natasha E. , Gray Nathanael S. , Paulo Joao A. , Walker Suzanne
Published: October 2020

O-GlcNAc transferase (OGT), found in the nucleus and cytoplasm of all mammalian cell types, is essential for cell proliferation. Why OGT is required for cell growth is not known. OGT performs two enzymatic reactions in the same active site. In one, it glycosylates thousands of different proteins, and in the other, it proteolytically cleaves another essential protein involved in gene expression. Deconvoluting OGT’s myriad cellular roles has been challenging because genetic deletion is lethal; complementation methods have not been established. Here, we developed approaches to replace endogenous OGT with separation-of-function variants to investigate the importance of OGT’s enzymatic activities for cell viability. Using genetic complementation, we found that OGT’s glycosyltransferase function is required for cell growth but its protease function is dispensable. We next used complementation to construct a cell line with degron-tagged wild-type OGT. When OGT was degraded to very low levels, cells stopped proliferating but remained viable. Adding back catalytically-inactive OGT rescued growth. Therefore, OGT has an essential noncatalytic role that is necessary for cell proliferation. By developing a method to quantify how OGT’s catalytic and noncatalytic activities affect protein abundance, we found that OGT’s noncatalytic functions often affect different proteins from its catalytic functions. Proteins involved in oxidative phosphorylation and the actin cytoskeleton were especially impacted by the noncatalytic functions. We conclude that OGT integrates both catalytic and noncatalytic functions to control cell physiology.

Significance

Mammalian cells contain only one glycosyltransferase, OGT, that operates in the nucleus and cytoplasm rather than the secretory pathway. OGT is required for cell proliferation, but a basic unanswered question is what OGT functions are essential. This question is challenging to address because OGT has thousands of glycosylation substrates, two different enzymatic activities, and a large number of binding partners. Here, by establishing genetic tools to replace endogenous OGT with variants that preserve only a subset of its activities, we show that only a low level of glycosylation activity is required to maintain cell viability; however, cell proliferation requires noncatalytic OGT function(s). The ability to replace OGT with variants provides a path to identifying its essential substrates and binding partners.
Genome-wide CRISPR screens reveal multitiered mechanisms through which mTORC1 senses mitochondrial dysfunction
Authors: Condon Kendall J. , Orozco Jose M. , Adelmann Charles H. , Spinelli Jessica B. , van der Helm Pim W. , Roberts Justin M. , Kunchok Tenzin , Sabatini David M.
Published: October 2020

In mammalian cells, nutrients and growth factors signal through an array of upstream proteins to regulate the mTORC1 growth control pathway. Because the full complement of these proteins has not been systematically identified, we developed a FACS-based CRISPR-Cas9 genetic screening strategy to pinpoint genes that regulate mTORC1 activity. Along with almost all known positive components of the mTORC1 pathway, we identified many new genes that impact mTORC1 activity, includingDCAF7, CSNK2B, SRSF2, IRS4, CCDC43, andHSD17B10. Using the genome-wide screening data, we generated a focused sublibrary containing single guide RNAs (sgRNAs) targeting hundreds of genes and carried out epistasis screens in cells lacking nutrient- and stress-responsive mTORC1 modulators, including GATOR1, AMPK, GCN2, and ATF4. From these data, we pinpointed mitochondrial function as a particularly important input into mTORC1 signaling. While it is well appreciated that mitochondria signal to mTORC1, the mechanisms are not completely clear. We find that the kinases AMPK and HRI signal, with varying kinetics, mitochondrial distress to mTORC1, and that HRI acts through the ATF4-dependent upregulation of both Sestrin2 and Redd1. Loss of both AMPK and HRI is sufficient to make mTORC1 largely resistant to mitochondrial dysfunction. Taken together, our data reveal a catalog of genes that impact the mTORC1 pathway and clarify the multifaceted ways in which mTORC1 senses mitochondrial dysfunction.
Enhancing the signal-to-noise ratio and generating contrast for cryo-EM images with convolutional neural networks
Authors: Palovcak Eugene , Asarnow Daniel , Campbell Melody G. , Yu Zanlin , Cheng Yifan
Published: October 2020

In cryogenic electron microscopy (cryo-EM) of radiation-sensitive biological samples, both the signal-to-noise ratio (SNR) and the contrast of images are critically important in the image-processing pipeline. Classic methods improve low-frequency image contrast experimentally, by imaging with high defocus, or computationally, by applying various types of low-pass filter. These contrast improvements typically come at the expense of the high-frequency SNR, which is suppressed by high-defocus imaging and removed by low-pass filtration. Recently, convolutional neural networks (CNNs) trained to denoise cryo-EM images have produced impressive gains in image contrast, but it is not clear how these algorithms affect the information content of the image. Here, a denoising CNN for cryo-EM images was implemented and a quantitative evaluation of SNR enhancement, induced bias and the effects of denoising on image processing and three-dimensional reconstructions was performed. The study suggests that besides improving the visual contrast of cryo-EM images, the enhanced SNR of denoised images may be used in other parts of the image-processing pipeline, such as classification and 3D alignment. These results lay the groundwork for the use of denoising CNNs in the cryo-EM image-processing pipeline beyond particle picking.
Electron image contrast analysis of mosaicity in rutile nanocrystals using direct electron detection
Authors: Yoon Aram , Shao Yu-Tsun , Howe Jane , Zuo Jian-Min
Published: October 2020

Direct electron detection provides high detective quantum efficiency, significantly improved point spread function and fast read-out which have revolutionized the field of cryogenic electron microscopy. However, these benefits for high-resolution electron microscopy (HREM) are much less exploited, especially for in situ study where major impacts on crystallographic structural studies could be made. By using direct detection in electron counting mode, rutile nanocrystals have been imaged at high temperature inside an environmental transmission electron microscope. The improvements in image contrast are quantified by comparison with a charge-coupled device (CCD) camera and by image matching with simulations using an automated approach based on template matching. Together, these approaches enable a direct measurement of 3D shape and mosaicity (∼1°) of a vacuum-reduced TiO2 nanocrystal about 50 nm in size. Thus, this work demonstrates the possibility of quantitative HREM image analysis based on direct electron detection.
Robot compliant catching by Maxwell model based Cartesian admittance control
Authors: Fu Le , Zhao Jie
Published: October 2020

Purpose

Admittance control is a typical complaint control methodology. Traditionally, admittance control systems are based on a dynamical relationship described by Voigt model. By contrast, after changing connection of spring and damper, Maxwell model produces different dynamics and has shown better impact absorption performance. This paper aims to design a novel compliant control method based on Maxwell model and implement it in a robot catching scenario.

Design/methodology/approach

To achieve this goal, this paper proposed a Maxwell model based admittance control scheme. Considering several motion stages involved in one catching attempt, the following approaches are adopted. First, Kalman filter is used to process the position data stream acquired from motion capture system and predict the subsequent object flying trajectory. Then, a linear segments with parabolic blends reaching motion is generated to achieve time-optimal movement under kinematic and joint inherent constraints. After robot reached the desired catching point, the proposed Maxwell model based admittance controller performs such as a cushion to moderate the impact between robot end-effector and flying object.

Findings

This paper has experimentally demonstrated the feasibility and effectiveness of the proposed method. Compared with typical Voigt model based compliant catching, less object bounding away from end-effector happens and the success rate of catching has been improved.

Originality/value

The authors proposed a novel Maxwell model based admittance control method and demonstrated its effectiveness in a robot catching scenario. The author’s approach may inspire other related researchers and has great potential of practical usage in a widespread of robot applications.
Back and forth to the campus: Tackling invasions through service-learning activities in higher education
Authors: Servia María J. , Cao Anxo , Lueje Yaiza R.
Published: October 2020

Purpose

Invasive species are under the spotlight because of their detrimental effects on biodiversity. However, management of invasions presents multiple dimensions frequently difficult to disentangle. This complex topic has been tackled through a service-learning project on an invasive insect (Vespa velutina), a bee-eating species invading Europe. Specifically, this paper aims to assess the educational needs and motivations detected in a local population for the control ofV. velutina, and evaluate the educational achievements of students participating in the project.

Design/methodology/approach

The paper illustrates how students prepared the service activity, which consisted in a quiz and interviews to public in a honey festival located in an area that has invested heavily in the control of the hornet. They informed visitors on its biology and impacts, and collected information on visitors’ knowledge and attitudes towards the hornet. This information was taken back to the class and discussed in an open debate.

Findings

The service activity uncovered important knowledge gaps of the local population and revealed the attachment to controversial control methods. Students acknowledged that the project met a real community need and valued the contact with the public, and the presentation of the project in the Faculty favored a debate on invasions management and biodiversity protection under the framework of campus sustainability.

Originality/value

While students are familiar with actions on campus sustainability, they are seldom confronted with the evaluation of management decisions on complex topics involving multiple dimensions. This service-learning project showed a good potential for fostering in-depth debates and promoting student engagement in campus sustainable initiatives.
Examining the factors influencing smartphone apps use at tourism destinations: a UTAUT model perspective
Authors: Kamboj Shampy , Joshi Richa
Published: October 2020

Purpose

Tourists regularly make use of their smartphones while staying at tourist destinations. Several studies have studied the outcomes of smartphone use at travel destinations. The current paper believes tourists’ use of their smartphone or its apps because of their contact with tour friends, social loneliness-related concerns or its aesthetic scope. The purpose of this paper is to identify the factors of continued use of smartphone apps via travelers during their stay at a tourism destination, framed within the UTAUT2 model (unified theory of acceptance and use of technology), given intrinsic user attributes (innovativeness), tourism destination aspect (aesthetic scope and social loneliness) and one of the key characteristics of mobile devices (portability).

Design/methodology/approach

The sample consists of 357 smartphone users who travelled to some tourist destinations and used some mobile apps during their stay. Data was analyzed using the structural equation modeling approach.

Findings

The findings of the study show that the UTAUT2 model can effectively explain the use of smartphone apps at tourism destinations and characteristics of the user and mobile device, does affect behaviour outcomes (smartphone, intention to reuse app, satisfaction towards trip and loyalty towards app).

Originality/value

This paper is mainly important due to its emphasis on smartphone apps’ use during the travel stay, as the majority of the existing literature focusses on prior steps ( service booking).