bluuebunny/crossref_metadata_2025 huggingface dataset:
LRRC15 is an inhibitory receptor blocking SARS-CoV-2 spike-mediated entry in trans
Authors: Song Jaewon , Chow Ryan D. , Pena-Hernandez Mario , Zhang Li , Loeb Skylar A. , So Eui-Young , Liang Olin D. , Wilen Craig B. , Lee Sanghyun
Published: November 2021

SARS-CoV-2 infection is mediated by the entry receptor ACE2. Although attachment factors and co-receptors facilitating entry are extensively studied, cellular entry factors inhibiting viral entry are largely unknown. Using a surfaceome CRISPR activation screen, we identified human LRRC15 as an inhibitory receptor for SARS-CoV-2 entry. LRRC15 directly binds to the receptor-binding domain (RBD) of spike protein with a moderate affinity and inhibits spike-mediated entry. Analysis of human lung single cell RNA sequencing dataset reveals that expression of LRRC15 is primarily detected in fibroblasts and particularly enriched in pathological fibroblasts in COVID-19 patients. ACE2 and LRRC15 are not co-expressed in the same cell types in the lung. Strikingly, expression of LRRC15 in ACE2-negative cells blocks spike-mediated viral entry in ACE2+ cell in trans, suggesting a protective role of LRRC15 in a physiological context. Therefore, LRRC15 represents an inhibitory receptor for SARS-CoV-2 regulating viral entry in trans.
The PAIR-R24M Dataset for Multi-animal 3D Pose Estimation
Authors: Marshall Jesse D. , Klibaite Ugne , Gellis Amanda , Aldarondo Diego E. , Ölveczky Bence P. , Dunn Timothy W.
Published: November 2021

Understanding the biological basis of social and collective behaviors in animals is a key goal of the life sciences, and may yield important insights for engineering intelligent multi-agent systems. A critical step in interrogating the mechanisms underlying social behaviors is a precise readout of the 3D pose of interacting animals. While approaches for multi-animal pose estimation are beginning to emerge, they remain challenging to compare due to the lack of standardized training and benchmark datasets. Here we introduce the PAIR-R24M (Paired Acquisition of Interacting oRganisms - Rat) dataset for multi-animal 3D pose estimation, which contains 24.3 million frames of RGB video and 3D ground-truth motion capture of dyadic interactions in laboratory rats. PAIR-R24M contains data from 18 distinct pairs of rats and 24 different viewpoints. We annotated the data with 11 behavioral labels and 3 interaction categories to facilitate benchmarking in rare but challenging behaviors. To establish a baseline for markerless multi-animal 3D pose estimation, we developed a multi-animal extension of DANNCE, a recently published network for 3D pose estimation in freely behaving laboratory animals. As the first large multi-animal 3D pose estimation dataset, PAIR-R24M will help advance 3D animal tracking approaches and aid in elucidating the neural basis of social behaviors.
Genome-wide characterization of SARS-CoV-2 cytopathogenic proteins in the search of antiviral targets
Authors: Zhang Jiantao , Li Qi , Cruz Cosme Ruth S. , Gerzanich Volodymyr , Tang Qiyi , Simard J. Marc , Zhao Richard Y.
Published: November 2021

Therapeutic inhibition of critical viral functions is important for curtailing coronavirus disease-2019 (COVID-19). We sought to identify antiviral targets through genome-wide characterization of SARS-CoV-2 proteins that are crucial for viral pathogenesis and that cause harmful cytopathic effects. All twenty-nine viral proteins were tested in a fission yeast cell-based system using inducible gene expression. Twelve proteins including eight non-structural proteins (NSP1, NSP3, NSP4, NSP5, NSP6, NSP13, NSP14 and NSP15) and four accessory proteins (ORF3a, ORF6, ORF7a and ORF7b) were identified that altered cellular proliferation and integrity, and induced cell death. Cell death correlated with the activation of cellular oxidative stress. Of the twelve proteins, ORF3a was chosen for further study in mammalian cells. In human pulmonary and kidney epithelial cells, ORF3a induced cellular oxidative stress associated with apoptosis and necrosis, and caused activation of pro-inflammatory response with production of the cytokines TNF-α, IL-6, and IFN-β1, possibly through the activation of NF-κB. To further characterize the mechanism, we tested a natural ORF3a Beta variant, Q57H, and a mutant with deletion of the highly conserved residue, ΔG188. Compared to wild type ORF3a, the ΔG188 variant yielded more robust activation of cellular oxidative stress, cell death, and innate immune response. Since cellular oxidative stress and inflammation contribute to cell death and tissue damage linked to the severity of COVID-19, our findings suggest that ORF3a is a promising, novel therapeutic target against COVID-19.

Significance

The ongoing SARS-CoV-2 pandemic has claimed over 5 million lives with more than 250 million people infected world-wide. While vaccines are effective, the emergence of new viral variants could jeopardize vaccine protection. Antiviral drugs provide an alternative to battle against COVID-19. Our goal was to identify viral therapeutic targets that can be used in antiviral drug discovery. Utilizing a genome-wide functional analysis in a fission yeast cell-based system, we identified twelve viral candidates, including ORF3a, which cause cellular oxidative stress, inflammation and apoptosis and necrosis that contribute to COVID-19. Our findings indicate that antiviral agents targeting ORF3a could greatly impact COVID-19.
Measure by Measure: Resting Heart Rate Across the 24 Hour Cycle.
Authors: Speed Cathy A , Arneil Tom , Harle Robert K , Wilson Alex , Karthikesalingam Alan , McConnell Michael V , Phillips Justin P
Published: November 2021

Background: Photoplethysmography (PPG) sensors, typically found in wrist-worn devices, can continuously monitor heart rate (HR) in large populations in real-world settings. Resting heart rate (RHR) is an important biomarker of morbidities and mortality, but no universally accepted definition nor measurement criteria exist. In this study, we provide a working definition of RHR and describe a method for measurement of RHR recorded using PPG derived from wristband measurement across a 24-hour cycle.
Methods: 433 healthy subjects wore a wrist device that measured activity and HR for up to 3 months. HR during inactivity was recorded and the duration of inactivity needed for HR to stabilise was ascertained. We identified the lowest HR during each 24-hour cycle (true RHR) and examined the time of day or night this occurred. The variation of HR during inactivity through the 24-hour cycle was also assessed. The sample was also subdivided according to daily activity levels for subset analysis.
Findings: Adequate data was obtained for 19,242 days and 18,520 nights. HR stabilised in most subjects after 4 minutes of inactivity. Mean (SD) RHR for the sample was 54.5 (8.0) bpm (day) and 50.5 (7.6) bpm (night). RHR values were highest in the least active group (lowest MET quartile) . A circadian variation of HR during inactivity was confirmed, with the lowest values being between 0300 and 0700 hours for most subjects.
Interpretation: RHR measured using a PPG-based wrist-worn device is significantly lower at night than in the day, and a circadian rhythm of HR during inactivity was confirmed. Since RHR is such an important health metric, clarity on the definition and measurement methodology used is important. A minimum rest time of 4 minutes provides a reliable measurement of HR during inactivity and true RHR in a 24-hour cycle is best measured between 0300 and 0700 hours.
Funding: This study was funded by Google.
Increased risk of infection with SARS-CoV-2 Beta, Gamma, and Delta variant compared to Alpha variant in vaccinated individuals
Authors: Andeweg Stijn P. , Vennema Harry , Veldhuijzen Irene , Smorenburg Naomi , Schmitz Dennis , Zwagemaker Florian ,   SeqNeth Molecular surveillance group,   RIVM COVID-19 Molecular epidemiology group, van Gageldonk-Lafeber Arianne B. , Hahné Susan J.M. , Reusken Chantal , Knol Mirjam J. , Eggink Dirk
Published: November 2021

The extent to which severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOC) break through infection- or vaccine-induced immunity is not well understood. Here, we analyze 28,578 sequenced SARS-CoV-2 samples from individuals with known immune status obtained through national community testing in the Netherlands from March to August 2021. We find evidence for an increased risk of infection by the Beta (B.1.351), Gamma (P.1), or Delta (B.1.617.2) variants compared to the Alpha (B.1.1.7) variant after vaccination. No clear differences were found between vaccines. However, the effect was larger in the first 14-59 days after complete vaccination compared to 60 days and longer. In contrast to vaccine-induced immunity, no increased risk for reinfection with Beta, Gamma or Delta variants relative to Alpha variant was found in individuals with infection-induced immunity.
Microbial community analysis of biofilters reveals a dominance of either comammox Nitrospira or archaea as ammonia oxidizers in freshwater aquaria
Authors: McKnight Michelle M. , Neufeld Josh D.
Published: November 2021

Nitrification by aquarium biofilters transforms toxic ammonia waste (NH3/NH4+) to less toxic nitrate (NO3-) via nitrite (NO2-). Ammonia oxidation is mediated by ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), and the recently discovered complete ammonia oxidizing (comammox) Nitrospira. Prior to the discovery of comammox Nitrospira, previous research revealed that AOA dominate among ammonia oxidizers in freshwater biofilters. Here, we characterized the composition of aquarium filter microbial communities and quantified the abundance of all three known groups of ammonia oxidizers. Aquarium biofilter and water samples were collected from representative freshwater and saltwater systems in Southwestern Ontario, Canada. Using extracted DNA, we performed 16S rRNA gene sequencing and quantitative PCR (qPCR) to assess community composition and quantify the abundance of amoA genes, respectively. Our results show that aquarium biofilter microbial communities were consistently represented by putative heterotrophs of the Proteobacteria and Bacteroides phyla, with distinct profiles associated with fresh versus saltwater biofilters. Among nitrifiers, comammox Nitrospira amoA genes were detected in all 38 freshwater aquarium biofilter samples and were the most abundant ammonia oxidizer in 30 of these samples, with the remaining biofilters dominated by AOA, based on amoA gene abundances. In saltwater biofilters, AOA or AOB were differentially abundant, with no comammox Nitrospira detected. These results demonstrate that comammox Nitrospira play an important role in biofilter nitrification that has been previously overlooked and such microcosms are useful for exploring the ecology of nitrification for future research.
Structural biases in disordered proteins are prevalent in the cell
Authors: Moses David , Guadalupe Karina , Yu Feng , Flores Eduardo , Perez Anthony , McAnelly Ralph , Shamoon Nora M. , Cuevas-Zepeda Estefania , Merg Andrea D. , Martin Erik W. , Holehouse Alex S. , Sukenik Shahar
Published: November 2021

Intrinsically disordered proteins and protein regions (IDPs) are essential to cellular function in all proteomes. Unlike folded proteins, IDPs exist in an ensemble of rapidly interchanging conformations. IDP sequences encode interactions that create structural biases within the ensemble. Such structural biases determine the three-dimensional shape of IDP ensembles and can affect their activity. However, the plasticity and sensitivity of IDP ensembles means structural biases, often measured in vitro, may differ in the dynamic and heterogeneous intracellular environment. Here we reveal that structural biases found in vitro in well-studied IDPs persist inside human-derived cells. We further show that a subset of IDPs are able to sense changes in cellular physical-chemical composition and modulate their ensemble in response. We propose that IDP ensembles can evolve to sense and respond to intracellular physicochemical changes, or to resist them. This property can be leveraged for biological function, be the underlying cause of IDP-driven pathology, or be leveraged for the design of disorder-based biosensors and actuators.
Engineered ACE2-Fc counters murine lethal SARS-CoV-2 infection through direct neutralization and Fc-effector activities
Authors: Chen Yaozong , Sun Lulu , Ullah Irfan , Beaudoin-Bussières Guillaume , Anand Sai Priya , Hederman Andrew P. , Tolbert William D. , Sherburn Rebekah , Nguyen Dung N. , Marchitto Lorie , Ding Shilei , Wu Di , Luo Yuhong , Gottumukkala Suneetha , Moran Sean , Kumar Priti , Piszczek Grzegorz , Mothes Walther , Ackerman Margaret E. , Finzi Andrés , Uchil Pradeep D. , Gonzalez Frank J. , Pazgier Marzena
Published: November 2021

Soluble Angiotensin-Converting Enzyme 2 (ACE2) constitutes an attractive antiviral capable of targeting a wide range of coronaviruses utilizing ACE2 as their receptor. Here, using structure-guided approaches, we developed divalent ACE2 molecules by grafting the extracellular ACE2-domain onto a human IgG1 or IgG3 (ACE2-Fc). These ACE2-Fcs harbor structurally validated mutations that enhance spike (S) binding and remove angiotensin enzymatic activity. The lead variant bound tightly to S, mediated in vitro neutralization of SARS-CoV-2 variants of concern (VOCs) with sub-nanomolar IC50 and was capable of robust Fc-effector functions, including antibody-dependent-cellular cytotoxicity, phagocytosis and complement deposition. When tested in a stringent K18-hACE2 mouse model, it delayed death or effectively resolved lethal SARS-CoV-2 infection in a prophylactic or therapeutic setting utilizing the combined effect of neutralization and Fc-effector functions. These data confirm the utility of ACE2-Fcs as valuable agents in preventing and eliminating SARS-CoV-2 infection and demonstrate that ACE2-Fc therapeutic activity require Fc-effector functions.
Altered neurogenic pathways in experimental rat models of ischemic cerebral stroke: A transcriptome based meta-analysis
Authors: Roshan Syed Aasish , Elangovan Gayathri , Gunaseelan Dharani , K. Jayachandran Swaminathan , Kandasamy Mahesh , Anusuyadevi Muthuswamy
Published: November 2021

1)

Objectives

Promoting neurogenesis mediated recovery is one of the most sought after strategies in recovery after cerebral stroke. In this paper we elucidate how neurogenesis related genes are altered in the early stroke environment, to hint at potential pathways for therapeutic recovery.

Materials and Methods

Around 97 microarray datasets derived from stroke affected rat brains were collected from NCBI-GEO. Datasets were normalized and subjected to meta-analysis in Network Analyst to identify differentially expressed genes. Gene enrichment analyses were carried out using GSEA, and WebGestalt, and results were visualized using Cytoscape Enrichment mapping.

Results

Nearly 939 differentially expressing genes were identified in the cerebral stroke group. Among them 30 neurogenesis related genes were identified through enrichment mapping analysis, and 35 genes through Protein- Protein Interaction analysis. Highest upregulated neurogenesis genes were found to be TSPO, GFAP, VIM, and TGFB1. Highest Downregulated neurogenesis genes were found to be THY1, NR1D1, CDK5, STX1B, and NOG.

Conclusions

Through this study, we have identified that during the acute time frame after stroke, majority of the neurogenesis genes related to neural proliferation and neural differentiation are downregulated, while the majority of the genes related to neuronal migration were upregulated. Single or combined therapeutic approach against the identified dysregulated genes could greatly aid neural restoration and functional recovery during the postischemic stage.
Unravelling consensus genomic regions associated with quality traits in wheat (Triticum aestivum L.) using meta-analysis of quantitative trait loci
Authors: Gudi Santosh , Saini Dinesh K , Singh Gurjeet , Halladakeri Priyanka , Shamshad Mohammad , Tanin Mohammad Jafar , Kumar Pradeep , Sharma Achla
Published: November 2021

A meta-analysis of quantitative trait loci (QTLs) associated with following six major quality traits (i) arabinoxylan, (ii) dough rheology properties, (iii) nutritional traits, (iv) polyphenol content, (v) processing quality traits, and (vi) sedimentation volume was conducted in wheat. For this purpose, as many as 2458 QTLs were collected from the 50 mapping studies published during 2013-20. Of the total QTLs, 1126 QTLs were projected on to the consensus map saturated with 2,50,077 markers resulting into the identification of 110 meta-QTLs (MQTLs) with average confidence interval (CI) of 5.6 cM. These MQTLs had 18.84 times reduced CI compared to CI of initial QTLs. Fifty-one (51) MQTLs were also verified with the marker-trait associations (MTAs) detected in earlier genome-wide association studies (GWAS). Physical region occupied by a single MQTL ranged from 0.12 to 749.71 Mb with an average of 130.25 Mb. Candidate gene mining allowed the identification of 2533 unique gene models from the MQTL regions. In-silico expression analysis discovered 439 differentially expressed gene models with >2 transcripts per million (TPM) expression in grains and related tissues which also included 44 high-confidence candidate genes known to be involved in the various cellular and biochemical processes related to quality traits. Further, nine functionally characterized wheat genes associated with grain protein content, high molecular weight glutenin and starch synthase enzymes were also found to be co-localized with some of the MQTLs. In addition, synteny analysis between wheat and rice MQTL regions identified 23 wheat MQTLs syntenic to 16 rice MQTLs. Furthermore, 64 wheat orthologues of 30 known rice genes were detected in 44 MQTL regions. These genes encoded proteins mainly belonging to the following families: starch synthase, glycosyl transferase, aldehyde dehydrogenase, SWEET sugar transporter, alpha amylase, glycoside hydrolase, glycogen debranching enzyme, protein kinase, peptidase, legumain and seed storage protein enzyme.

Main Conclusion

Meta-QTL analysis in wheat for major quality traits identified 110 MQTLs with reduced confidence interval. Candidate gene mining and expression analysis discovered differentially expressed genes involve in quality traits.
Pulse-Width Modulation-based TMS mimics effects of conventional TMS on human primary motor cortex
Authors: Memarian Sorkhabi Majid , Wendt Karen , O’Shea Jacinta , Denison Timothy
Published: November 2021

Abstract

Objective

We developed a novel transcranial magnetic stimulation (TMS) device to generate flexible stimuli and patterns. The system synthesizes digital equivalents of analog waveforms, relying on the filtering properties of the nervous system. Here, we test the hypothesis that the novel pulses can mimic the effect of conventional pulses on the cortex.

Approach

A second-generation programmable TMS (pTMS2) stimulator with magnetic pulse shaping capabilities using pulse-width modulation (PWM) was tested. A computational and an in-human study on twelve healthy participants compared the neuronal effects of conventional and modulation-based stimuli.

Main results

Both the computational modeling and the in-human stimulation showed that the PWM-based system can synthesize pulses to effectively stimulate the human brain, equivalent to conventional stimulators. The comparison includes motor threshold, MEP latency and input-output curve measurements.

Significance

PWM stimuli can fundamentally imitate the effect of conventional magnetic stimuli while adding considerable flexibility to TMS systems, enabling the generation of highly configurable TMS protocols.

Highlights

The PWM method promises the implementation of flexible neurostimulation

PWM magnetic pulses were well tolerated by the participants without adverse events

RMTs and MEPs were compared for PWM and conventional stimuli

PWM-equivalent of conventional pulses has relatively similar effects on the cortex

The use of digital synthesis techniques to create novel patterns is a promising method for future neuromodulation
Non-invasive real-time access to spatial attention information from 3T fMRI BOLD signals
Authors: Loriette C. , De Sousa C. , Clavagnier S. , Lamberton F. , Ibarolla D. , Ben Hamed S.
Published: November 2021

Access to higher cognitive functions in real-time remains very challenging, because these functions are internally driven and their assessment is based onto indirect measures. In addition, recent finding show that these functions are highly dynamic. Previous studies using intra-cortical recordings in monkeys, succeed to access the (x,y) position of covert spatial attention, in real-time, using classification methods applied to monkey prefrontal multi-unit activity and local field potentials. In contrast, the direct access to attention with non-invasive methods is limited to predicting the attention localisation based on a quadrant classification. Here, we demonstrate the feasibility to track covert spatial attention localization using non-invasive fMRI BOLD signals, with an unprecedented spatial resolution. We further show that the errors produced by the decoder are not randomly distributed but concentrate on the locations neighbouring the cued location and that behavioral errors correlate with weaker decoding performance. Last, we also show that the voxels contributing to the decoder precisely match the visual retinotopic organization of the occipital cortex and that single trial access to attention is limited by the intrinsic dynamics of spatial attention. Taken together, these results open the way to the development of remediation and enhancement neurofeedback protocols targeting the attentional function.
Milk Exosomes Cross the Blood-Brain Barrier in Murine Cerebral Cortex Endothelial Cells and Promote Dendritic Complexity in the Hippocampus and Brain Function in C57BL/6J Mice
Authors: Zhou Fang , Ebea Pearl , Mutai Ezra , Sukreet Sonal , Navazesh Shya , Dogan Haluk , Li Wenhao , Cui Juan , Ji Peng , Ramirez Denise M. O. , Zempleni Janos
Published: November 2021

Background

Human milk contains large amounts of exosomes (MEs) and their regulatory microRNA cargos, whereas infant formulas contain only trace amounts of MEs and microRNAs. Breastfeeding has been implicated in optimal brain development but experimental evidence linking ME intake with brain development is limited.

Objectives

We assessed the transport of MEs across the blood-brain barrier (BBB) and ME accumulation in distinct regions of the brain in brain endothelial cells and suckling mice. We further assessed BME-dependent gene expression profiles and effects on the dendritic complexity of hippocampal granule cells and phenotypes of BME depletion in neonate, juvenile and adult mice.

Methods

The transfer of MEs across the BBB was assessed by using bovine MEs labeled with FM4-64 or loaded with IRDye-labeled miR-34a in murine brain endothelial bEnd.3 cell monolayers and dual chamber systems, and in wild-type newborn pups fostered to exosome and cargo tracking (ECT) dams that express MEs endogenously labeled with a CD63-eGFP fusion protein for subsequent analysis by serial two-photon tomography and staining with anti-eGFP antibodies. Effects of MEs on gene expression and dendritic architecture of granule cells was analyzed in hippocampi from juvenile mice fed exosome and RNA-depleted (ERD) and exosome and RNA-sufficient (ERS) diets by using RNA-sequencing analysis and Golgi-Cox staining followed by integrated neuronal tracing and morphological analysis of neuronal dendrites, respectively. Spatial learning and severity of kainic acid-induced seizures were assessed in mice fed ERD and ERS diets.

Results

bEnd.3 cells internalized MEs by using a saturable transport mechanism and secreted miR-34a across the basal membrane. MEs penetrated the entire brain in fostering experiments; major regions of accumulation included the hippocampus, cortex and cerebellum. Two hundred ninety-five genes were differentially expressed in hippocampi from male mice fed ERD and ERS diets; high-confidence gene networks included pathways implicated in axon guidance and calcium signaling. Only one gene was differentially expressed in females fed the experimental diets. Juvenile pups fed the ERD diet had reduced dendritic complexity of dentate granule cells in the hippocampus, scored nine-fold lower in the Barnes maze test of spatial learning and memory (P< 0.01), and the severity of seizures was 5-fold higher following kainic acid administration in adult mice fed the ERD diet compared to mice fed the ERS diet (P< 0.01).

Conclusions

MEs cross the BBB and contribute toward optimal neuronal development, spatial learning and memory, and resistance to kainic acid-induced seizures in mice.
RyR2/IRBIT regulates insulin gene transcription, insulin content, and secretion in the insulinoma cell line INS-1
Authors: Harvey Kyle E. , LaVigne Emily K. , Dar Mohd Saleem , Salyer Amy E. , Pratt Evan P.S. , Sample Paxton A. , Aryal Uma , Gowher Humaira , Hockerman Gregory H.
Published: November 2021

The role of ER Ca2+ release via ryanodine receptors (RyR) in pancreatic β-cell function is not well defined. Deletion of RyR2 from the rat insulinoma INS-1 (RyR2KO) enhanced the Ca2+ integral (AUC) stimulated by 7.5 mM glucose, and rendered it sensitive to block by the IP3 receptor inhibitor xestospongin C, coincident with reduced levels of the protein IP3Receptor Binding protein released with Inositol 1,4,5 Trisphosphate (IRBIT; aka AHCYL1). Deletion of IRBIT from INS-1 cells (IRBITKO) increased the Ca2+ AUC in response to 7.5 mM glucose and induced xestospongin sensitivity. Insulin content and basal (2.5 mM glucose) and 7.5 mM glucose-stimulated insulin secretion were reduced in RyR2KO cells and more modestly reduced in IRBITKO cells compared to controls. INS2 mRNA levels were reduced in both RyR2KO and IRBITKO cells, but INS1 mRNA levels were specifically decreased in RyR2KO cells. Nuclear localization of S-adenosylhomocysteinase (AHCY) was increased in RyR2KO and IRBITKO cells. DNA methylation of the INS1 and INS2 gene promotor regions was very low, and not different among RyR2KO, IRBITKO, and controls. In contrast, exon 2 of the INS1 and INS2 genes was more extensively methylated in RyR2KO and IRBITKO cells than in controls. Proteomics analysis using LC-MS/MS revealed that deletion of RyR2 or IRBIT resulted in differential regulation of 314 and 137 proteins, respectively, with 41 in common. These results suggest that RyR2 regulates IRBIT levels and activity in INS-1 cells, and together maintain insulin content and secretion, and regulate the proteome, perhaps via DNA methylation.

One sentence Summary

Deletion of RyR2 from INS-1 cells had the unanticipated effect of reducing IRBIT proteins levels, and both RyR2 and IRBIT contribute to maintenance of glucose- stimulated insulin secretion.
A Complete Pedigree-Based Graph Workflow for Rare Candidate Variant Analysis
Authors: Markello Charles , Huang Charles , Rodriguez Alex , Carroll Andrew , Chang Pi-Chuan , Eizenga Jordan , Markello Thomas , Haussler David , Paten Benedict
Published: November 2021

Methods that use a linear genome reference for genome sequencing data analysis are reference biased. In the field of clinical genetics for rare diseases, a resulting reduction in genotyping accuracy in some regions has likely prevented the resolution of some cases. Pangenome graphs embed population variation into a reference structure. While pangenome graphs have helped to reduce reference mapping bias, further performance improvements are possible. We introduce VG-Pedigree, a pedigree-aware workflow based on the pangenome-mapping tool of Giraffe (Sirén et al. 2021) and the variant-calling toolDeepTrio(Kolesnikov et al. 2021) using a specially-trained model for Giraffe-based alignments. We demonstrate mapping and variant calling improvements in both single-nucleotide variants (SNVs) and insertion and deletion (INDEL) variants over those produced by alignments created using BWA-MEM to a linear-reference and Giraffe mapping to a pangenome graph containing data from the 1000 Genomes Project. We have also adapted and upgraded the deleterious-variant (DV) detecting methods and programs of Gu et al. into a streamlined workflow (Gu et al. 2019). We used these workflows in combination to detect small lists of candidate DVs among 15 family quartets and quintets of the Undiagnosed Diseases Program (UDP). All candidate DVs that were previously diagnosed using the mendelian models covered by the previously published Gu et al. methods were recapitulated by these workflows. The results of these experiments indicate a slightly greater absolute count of DVs are detected in the proband population than in their matched unaffected siblings.
Automated methodology for optimal selection of minimum electrode subsets for accurate EEG source estimation based on Genetic Algorithm optimization
Authors: Soler A. , Moctezuma L. , Giraldo E. , Molinas M.
Published: November 2021

High-density Electroencephalography (HD-EEG) has been proven to be the most accurate option to estimate the neural activity inside the brain. Multiple studies report the effect of electrode number on source localization for specific sources and specific electrode configurations. The electrodes for these configurations have been manually selected to uniformly cover the entire head, going from 32 to 128 electrodes, but electrodes were not selected according to their contribution to accuracy. In this work, an optimization-based study is proposed to determine the minimum number of electrodes and identify optimal combinations of electrodes that can retain the localization accuracy of HD-EEG reconstructions. This optimization approach incorporates scalp landmark positions of widely used EEG montages. In this way, a systematic search for the minimum electrode subset is performed for single and multiple source localization problems. The Non-dominated Sorting Genetic Algorithm II (NSGA-II) combined with source reconstruction methods is used to formulate a multi-objective optimization problem that concurrently minimizes 1) the localization error for each source and 2) the number of required EEG electrodes. The method can be used for evaluating the source localization quality of low-density EEG systems (e.g. consumer-grade wearable EEG). We performed an evaluation over synthetic and real EEG dataset with known ground-truth. The experimental results show that optimal subsets with 6 electrodes can obtain an equal or better accuracy than HD-EEG (with more than 200 channels) for a single source case. This happened when reconstructing a particular brain activity in more than 88% of the cases (in synthetic signals) and 63% (in real signals), and in more than 88% and 73% of the cases when considering optimal combinations with 8 channels. For a multiple-source case of three sources (only with synthetic signals), it was found that optimized combinations of 8, 12 and 16 electrodes attained an equal or better accuracy than HD-EEG with 231 electrodes in at least 58%, 76%, and 82% of the cases respectively. Additionally, for such electrode numbers, a lower mean error and standard deviation than with 231 electrodes were obtained.

Highlights

The number of EEG electrodes and their locations can be optimized for reconstructing the brain source activity.

Optimally selected EEG electrodes can retain the accuracy of high density montages (256, 128 chs) for brain source estimation, when electrodes are selected according to their contribution to accuracy.

With optimization, selected combinations of EEG electrodes will flexibilize the estimation of the source activity.
A structural dynamics model for how CPEB3 binding to SUMO2 can regulate translational control in dendritic spines
Authors: Gu Xinyu , Schafer Nicholas P. , Bueno Carlos , Lu Wei , Wolynes Peter G.
Published: November 2021

A prion-like RNA-binding protein, CPEB3, can regulate local translation in dendritic spines. CPEB3 monomers repress translation, whereas CPEB3 aggregates activate translation of its target mRNAs. However, the CPEB3 aggregates, as long-lasting prions, may raise the problem of unregulated translational activation. Here, we propose a computational model of the complex structure between CPEB3 RNA-binding domain (CPEB3-RBD) and small ubiquitin-like modifier protein 2 (SUMO2). Free energy calculations suggest that the allosteric effect of CPEB3-RBD/SUMO2 interaction can amplify the RNA-binding affinity of CPEB3. Combining with previous experimental observations on the SUMOylation mode of CPEB3, this model suggests an equilibrium shift of mRNA from binding to deSUMOylated CPEB3 aggregates to binding to SUMOylated CPEB3 monomers in basal synapses. This work shows how a burst of local translation in synapses can be silenced following a stimulation pulse, and explores the CPEB3/SUMO2 interplay underlying the structural change of synapses and the formation of long-term memories.
Lateralization of autonomic activity in response to limb-specific threat
Authors: Kryklywy James H. , Lu Amy , Roberts Kevin H. , Rowan Matt , Todd Rebecca M.
Published: November 2021

In times of stress or danger, the autonomic nervous system (ANS) signals the fight or flight response. A canonical function of ANS activity is to globally mobilize metabolic resources, preparing the organism to respond to threat. Yet a body of research has demonstrated that, rather than displaying a homogenous pattern across the body, autonomic responses to arousing events — as measured through changes in electrodermal activity (EDA) — can differ between right and left body locations. Surprisingly, the metabolic function of such ANS asymmetry has not been investigated. In the current study, we investigated whether asymmetric autonomic responses could be induced through limb-specific aversive stimulation. Participants were given mild electric stimulation to either the left or right arm while EDA was monitored bilaterally. Across participants, a strong ipsilateral EDA response bias was observed, with increased EDA response in the hand adjacent to the stimulation. This effect was observable in over 50% of individual subjects. These results demonstrate that autonomic output is more complex than canonical interpretations suggest. We suggest that, in stressful situations, autonomic outputs can prepare either the whole-body fight or flight response, or a simply a limb-localized flick, which can effectively neutralize the threat while minimizing global resource consumption. These findings provide insight into the evolutionary pathway of neural systems processing general arousal by linking observed asymmetry in the peripheral arousal response to a historical leveraging of neural structures organized to mediate responses to localized threat.
The dynamics of HD-ZIP III - ZPR protein interactions play essential roles in embryogenesis, meristem function and organ development
Authors: Gruber Anna Vitlin , Kosty Melissa , Jami-Alahmadi Yasaman , Wohlschlegel James A. , Long Jeff A.
Published: November 2021

Maintaining a stem cell population while developing lateral organs is a crucial aspect of plant development. Studies have shown that a family of micro proteins, the LITTLE ZIPPERS (ZPR), are involved in this process by repressing the activity of HD-ZIP III transcription factors. However, the unique role of each ZPR has not been thoroughly characterized. In this work, we use genetics, imaging, and biochemistry to create a detailed picture of ZPR family expression and their specific interactions with HD-ZIP IIIs. CRISPR/Cas9 was implemented to isolate single loss-of-function ZPR alleles as well as higher-order mutant combinations. A single mutation in ZPR1, ZPR3, and ZPR4 affects the development of the cotyledons during embryogenesis. Additionally, double mutant analyses indicates both unique roles for each ZPR protein as well as redundancy. Using ZPR tagged lines we show that while ZPR3 and ZPR4 have a similar pattern of accumulation as the HD-ZIP IIIs, ZPR1 and ZPR2 accumulation is more limited. Immuno-precipitations (IP) with tagged ZPR proteins are mainly enriched with the anticipated HD-ZIP III partners. Although ZPRs interact with all HD-ZIP IIIs, an apparent preference of heterodimer formation with REVOLUTA is observed. Our work highlights that the dynamics of ZPR protein accumulation together with the strength of ZPR-HD-ZIP III interactions provide an added layer of complexity to the regulation of HD-ZIP IIIs during plant development.
A glycosylphosphatidylinositol-anchored α-amylase encoded by amyD contributes to a decrease in the molecular mass of cell wall α-1,3-glucan in Aspergillus nidulans
Authors: Miyazawa Ken , Yamashita Takaaki , Takeuchi Ayumu , Kamachi Yuka , Yoshimi Akira , Tashiro Yuto , Koizumi Ami , Yano Shigekazu , Kasahara Shin , Sano Motoaki , Yamagata Youhei , Nakajima Tasuku , Abe Keietsu
Published: November 2021

α-1,3-Glucan is one of the main polysaccharides in the cell wall of Aspergillus nidulans. We previously revealed that it plays a role in hyphal aggregation in liquid culture, and that its molecular mass (MM) in an agsA-overexpressing (agsAOE) strain was larger than that in an agsB-overexpressing (agsBOE) strain. The mechanism that regulates the MM of α-1,3-glucan is poorly understood. Although the gene amyD, which encodes glycosyl-phosphatidylinositol (GPI)-anchored α-amylase (AmyD), is involved in the biosynthesis of α-1,3-glucan in A. nidulans, how it regulates this biosynthesis remains unclear. Here we constructed strains with disrupted amyD (ΔamyD) or overexpressed amyD (amyDOE) in the genetic background of the ABPU1 (wild-type), agsAOE, or agsBOE strain, and characterized the chemical structure of α-1,3-glucans in the cell wall of each strain, focusing on their MM. The MM of α-1,3-glucan from the agsBOE amyDOE strain was smaller than that in the parental agsBOE strain. In addition, the MM of α-1,3-glucan from the agsAOE ΔamyD strain was greater than that in the agsAOE strain. These results suggest that AmyD is involved in decreasing the MM of α-1,3-glucan. We also found that the C-terminal GPI-anchoring region is important for these functions.
Precise identification of cancer cells from allelic imbalances in single cell transcriptomes
Authors: Trinh Mi K. , Pacyna Clarissa N. , Kildisiute Gerda , Anderson Nathaniel D. , Khabirova Eleonora , Behjati Sam , Young Matthew D.
Published: November 2021

A fundamental step of tumour single cell mRNA analysis is separating cancer and non-cancer cells. We show that the common approach to separation, using shifts in average expression, can lead to erroneous biological conclusions. By contrast, allelic imbalances representing copy number changes directly detect the cancer genotype and accurately separate cancer from non-cancer cells. Our findings provide a definitive approach to identifying cancer cells from single cell mRNA sequencing data.
Seasonal and spatial variability of antibiotic resistance genes and Class I integrons in rivers of the Mekong Delta, Vietnam
Authors: Pham Thi Thu Hang , Dang Khoa Dinh Hoang , Rohrbach Emmanuelle , Breider Florian , Rossi Pierre
Published: November 2021

Aquaculture activities continue to expand in Vietnam, covering an estimated 700,000 ha, with 89% of these culture ponds located in the Mekong Delta. Since 2009, large-scale bacterial outbreaks have spread in response to this intensive farming. Antibiotics, even those considered a last resort, have only partially mitigated this problem. A side effect of the massive use of these chemicals is the appearance of mobile genetic elements associated with antibiotic resistance genes (ARGs). The large-scale emergence of a diverse bacterial resistome, accompanied by severe economic losses, has posed significant health risks to local residents. In this study, the seasonal and spatial distributions of the class I integrase (CL1) intl1 and the ARGs sul2 (sulfonamide), BLA-oxa1 (ß-lactams), and ermB (erythromycin) were quantified from water and sediment samples collected during two consecutive seasons along the Vam Co River and its tributary (Long An province, Vietnam). Results showed that CL1 was present in all river compartments, reaching 2.98×104 copies/mL and 1.07×106 copies/g of sediment, respectively. The highest relative copy abundances to the 16S rDNA gene were measured in water samples, with up to 3.02% for BLA-oxa1, followed by sul2 (1.16%) and ermB (0.46%). Strong seasonal (dry season vs. rainy season) and spatial trends were recorded for all resistance genes. Higher amounts of ARGs in river water could be associated with higher antibiotic use during the rainy season. In contrast, higher amounts of ARGs were recorded in river sediments during the dry season, making this habitat a potential reservoir of transient genes. Finally, the observations made in this study allowed us to clarify the environmental and anthropogenic influences that may promote the dispersal and persistence of ARGS in this riverine ecosystem.

ABSTRACT ART

HIGHLIGHTS

In Vietnam, inland aquaculture massively relies on antibiotics to prevent epidemics

Resistance genes were quantified along two rivers of the Mekong delta

Seasonal (dry and rainy seasons) and spatial distributions were registered by qPCR

BLA-oxa1and sul2 reached highest abundances among bacterial communities

Strong seasonal patterns and local variabilities were measured for CL1s and ARGs
Small-angle scattering for beginners
Authors: Gommes Cedric J. , Jaksch Sebastian , Frielinghaus Henrich
Published: November 2021

Many experimental methods are available for the characterization of nanostructures, but most of them are limited by stringent experimental conditions. When it comes to analysing nanostructures in the bulk or in their natural environment – even as ordinary as water at room temperature – small-angle scattering (SAS) of X-rays or neutrons is often the only option. The rapid worldwide development of synchrotron and neutron facilities over recent decades has opened unprecedented possibilities for using SAS in situ and in a time-resolved way. But, in spite of its huge potential in the field of nanomaterials in general, SAS is covered far less than other characterization methods in non-specialized curricula. Presented here is a rigorous discussion of small-angle scattering, at a technical level comparable to the classical undergraduate coverage of X-ray diffraction by crystals and which contains diffraction as a particular case.
pyRS: a user-friendly package for the reduction and analysis of neutron diffraction data measured at the High Intensity Diffractometer for Residual Stress Analysis
Authors: Fancher Chris M. , Bunn Jeff R. , Bilheux Jean , Zhou Wenduo , Whitfield Ross E. , Borreguero Jose , Peterson Peter F.
Published: November 2021

The pyRS (Python residual stress) analysis software was designed to address the data reduction and analysis needs of the High Intensity Diffractometer for Residual Stress Analysis (HIDRA) user community. pyRS implements frameworks for the calibration and reduction of measured 2D data into intensity versus scattering vector magnitude and subsequent single-peak-fitting analysis to facilitate texture and residual strain/stress analysis. pyRS components are accessible as standalone user interfaces for peak-fitting and stress/strain analysis or as Python scripts. The scripting interface facilitates automated data reduction and peak-fitting analysis using an autoreduction protocol. Details of the implemented functionality are discussed.
Insights into the mechanism of high lipid–detergent crystallization of membrane proteins
Authors: Trampari Sofia , Neumann Caroline , Hjorth-Jensen Samuel J. , Shahsavar Azadeh , Quistgaard Esben M. , Nissen Poul
Published: November 2021

Obtaining well diffracting crystals of membrane proteins is often challenging, but chances can be improved by crystallizing them in lipidic conditions that mimic their natural membrane environments. One approach is the high lipid–detergent (HiLiDe) method, which works by mixing the target protein with high concentrations of lipid and detergent prior to crystallization. Although this approach is convenient and flexible, understanding the effects of systematically varying lipid/detergent ratios and a characterization of the lipid phases that form during crystallization would be useful. Here, a HiLiDe phase diagram is reported for the model membrane protein MhsT, which tracks the precipitation and crystallization zones as a function of lipid and detergent concentrations, and is augmented with data on crystal sizes and diffraction properties. Additionally, the crystallization of SERCA1a solubilized directly with native lipids is characterized as a function of detergent concentration. Finally, HiLiDe crystallization drops are analysed with transmission electron microscopy, which among other features reveals liposomes, stacked lamellae that may represent crystal precursors, and mature crystals with clearly discernible packing arrangements. The results emphasize the significance of optimizing lipid/detergent ratios over broad ranges and provide insights into the mechanism of HiLiDe crystallization.
Cryptocurrency as a safe haven for investment portfolios amid COVID-19 panic cases of Bitcoin, Ethereum and Litecoin
Authors: Marobhe Mutaju Isaack
Published: November 2021

Purpose

This article examines the susceptibility of cryptocurrencies to coronavirus disease 2019 (COVID-19) induced panic in comparison with major stock indices.

Design/methodology/approach

The author employs the Bayesian structural vector autoregression to examine the phenomenon in Bitcoin, Ethereum and Litecoin from 2nd January 2020 to 30th June 2021. A similar analysis is conducted for major stock indices, namely S&P 500, FTSE 100 and SSE Composite for comparison purposes.

Findings

The results suggest that cryptocurrencies returns suffered immensely in the early days of the COVID-19 outbreak following declarations of the disease as a global health emergency and eventually a pandemic in March 2020. However, the returns for all three cryptocurrencies recovered by April 2020 and remained resistant to further COVID-19 panic shocks. The results are dissimilar to those of S&P 500, FTSE 100 and SSE Composite values which were vulnerable to COVID-19 panic throughout the timeframe to June 2021. The results further reveal strong predictive power of Bitcoin on prices of other cryptocurrencies.

Research limitations/implications

The article provides evidence to support the cryptocurrency as a safe haven during COVID-19 school of thought given their resistance to subsequent shocks during COVID-19. Thus, the author stresses the need for diversification of investment portfolios by including cryptocurrencies given their uniqueness and resistance to shocks during crises.

Originality/value

The author makes use of the novel corona virus panic index to examine the magnitude of shocks in prices of cryptocurrencies during COVID-19.