bluuebunny/crossref_metadata_2025 huggingface dataset:
Airway recommendations for perioperative patients during the COVID-19 pandemic: a scoping review
Authors: Grudzinski Alexa , Sun Billy , Zhang MengQi , Crnic Agnes , Djokhdem Abdul H , Hanna Mary , Montroy Joshua , Duggan Laura V , Hamilton Gavin M. , Fergusson Dean A , Boet Sylvain , McIsaac Daniel I , Lalu Manoj M
Published: August 2021

Purpose

Numerous guideline recommendations for airway and perioperative management during the COVID-19 pandemic have been published. We identified, synthesized, and compared guidelines intended for anesthesiologists.

Source

Member society websites of the World Federation of Societies of Anesthesiologists and the European Society of Anesthesiologists were searched. Recommendations focused on perioperative airway management of patients with proven or potential COVID-19 disease were included. Accelerated screening was used; data extraction was performed by one reviewer and verified by a second. Data was organized into themes based on perioperative phase of care.

Principal Findings

Thirty unique sets of recommendations were identified. None reported methods for systematically searching or selecting evidence to be included. Four were updated following initial publication. For induction and airway management, most recommended minimizing personnel and having the most experienced anesthesiologist perform tracheal intubation. Significant congruence was observed amongst recommendations that discussed personal protective equipment. Of those that discussed tracheal intubation methods, most (96%) recommended video laryngoscopy, while discordance existed regarding use of flexible bronchoscopy. Intraoperatively, 23% suggested specific anesthesia techniques and most (63%) recommended a specific operating room for patients with COVID-19. Postoperatively, a minority discussed extubation procedures (33%), or care in the recovery room (40%). Non-technical considerations were discussed in 27% and psychological support for healthcare providers in 10%.

Conclusion

Recommendations for perioperative airway management of patients with COVID-19 overlap to a large extent. However, we also identified significant differences. This may reflect the absence of a coordinated response towards studying and establishing best-practices in perioperative patients with COVID-19.

Registration

Open Science Framework (https://osf.io/a2k4u/)
A Master Autoantigen-ome Links Alternative Splicing, Female Predilection, and COVID-19 to Autoimmune Diseases
Authors: Wang Julia Y. , Roehrl Michael W. , Roehrl Victor B. , Roehrl Michael H.
Published: August 2021

Chronic and debilitating autoimmune sequelae pose a grave concern for the post-COVID-19 pandemic era. Based on our discovery that the glycosaminoglycan dermatan sulfate (DS) displays peculiar affinity to apoptotic cells and autoantigens (autoAgs) and that DS-autoAg complexes cooperatively stimulate autoreactive B1 cell responses, we compiled a database of 751 candidate autoAgs from six human cell types. At least 657 of these have been found to be affected by SARS-CoV-2 infection based on currently available multi-omic COVID data, and at least 400 are confirmed targets of autoantibodies in a wide array of autoimmune diseases and cancer. The autoantigen-ome is significantly associated with various processes in viral infections, such as translation, protein processing, and vesicle transport. Interestingly, the coding genes of autoAgs predominantly contain multiple exons with many possible alternative splicing variants, short transcripts, and short UTR lengths. These observations and the finding that numerous autoAgs involved in RNA-splicing showed altered expression in viral infections suggest that viruses exploit alternative splicing to reprogram host cell machinery to ensure viral replication and survival. While each cell type gives rise to a unique pool of autoAgs, 39 common autoAgs associated with cell stress and apoptosis were identified from all six cell types, with several being known markers of systemic autoimmune diseases. In particular, the common autoAg UBA1 that catalyzes the first step in ubiquitination is encoded by an X-chromosome escape gene. Given its essential function in apoptotic cell clearance and that X-inactivation escape tends to increase with aging, UBA1 dysfunction can therefore predispose aging women to autoimmune disorders. In summary, we propose a model of how viral infections lead to extensive molecular alterations and host cell death, autoimmune responses facilitated by autoAg-DS complexes, and ultimately autoimmune diseases. Overall, this master autoantigen-ome provides a molecular guide for investigating the myriad of autoimmune sequalae to COVID-19 and clues to the rare but reported adverse effects of the currently available COVID vaccines.
Epigenome-wide Association Study of Alcohol Use Disorder in Five Brain Regions
Authors: Zillich Lea , Frank Josef , Streit Fabian , Friske Marion M , Foo Jerome C , Sirignano Lea , Heilmann-Heimbach Stefanie , Dukal Helene , Degenhardt Franziska , Hoffmann Per , Hansson Anita C , Nöthen Markus M , Rietschel Marcella , Spanagel Rainer , Witt Stephanie H
Published: August 2021

Alcohol Use Disorder (AUD) is closely linked to the brain regions forming the neurocircuitry of addiction. Postmortem human brain tissue enables the direct study of the molecular pathomechanisms of AUD. This study aims to identify these mechanisms by examining differential DNA-methylation between cases with severe AUD (n=53) and controls (n=58) using a brain region-specific approach, in which sample sizes ranged between 46 and 94. Samples of the anterior cingulate cortex (ACC), Brodmann Area 9 (BA9), caudate nucleus (CN), ventral striatum (VS), and putamen (PUT) were investigated. DNA-methylation levels were determined using the Illumina HumanMethylationEPIC Beadchip. Epigenome-wide association analyses were carried out to identify differentially methylated CpG-sites and regions between cases and controls in each brain region. Weighted Correlation Network Analysis (WGCNA), gene-set and GWAS-enrichment analyses were performed. Two differentially methylated CpG-sites were associated with AUD in the CN, and 18 in VS (q<.05). No epigenome-wide significant CpG-sites were found in BA9, ACC, or PUT. Differentially methylated regions associated with AUD case-/control status (q< .05) were found in the CN (n=6), VS (n=18) and ACC (n=1). In the VS, the WGCNA-module showing the strongest association with AUD was enriched for immune-related pathways. This study is the first to analyze methylation differences between AUD cases and controls in multiple brain regions and consists of the largest sample to date. Several novel CpG-sites and regions implicated in AUD were identified, providing a first basis to explore epigenetic correlates of AUD.
Neural representations of others’ traits predict social decisions
Authors: Kobayashi Kenji , Kable Joseph W. , Hsu Ming , Jenkins Adrianna C.
Published: August 2021

To guide social interaction, people often rely on expectations about the traits of other people based on markers of social group membership, i.e., stereotypes. Although the influence of stereotypes on social behavior is widespread, key questions remain about how traits inferred from social group membership are instantiated in the brain and incorporated into neural computations that guide social behavior. Here, we show that the human lateral orbitofrontal cortex (OFC) represents the content of stereotypes about members of different social groups in the service of social decision-making. During fMRI scanning, participants decided how to distribute resources across themselves and members of a variety of social groups in a modified Dictator Game. Behaviorally, we replicated our recent finding that perceptions of others’ traits, captured by a two-dimensional framework of stereotype content (warmth and competence), biased participants’ monetary allocation choices in a context-dependent manner: recipients’ warmth increased advantageous inequity aversion and their competence increased disadvantageous inequity aversion. Neurally, representational similarity analysis (RSA) revealed that perceptions of others’ traits in the two-dimensional space were represented in the temporoparietal junction and superior temporal sulcus, two regions associated with mentalizing, and in the lateral OFC, known to represent latent environmental features during goal-directed outcome inference outside the social domain. Critically, only the latter predicted individual choices, suggesting that the effect of stereotypes on behavior is mediated by inference-based, domain-general decision-making processes in the OFC.
Severity, criticality, and fatality of the SARS-CoV-2 Beta variant
Authors: Abu-Raddad Laith J. , Chemaitelly Hiam , Ayoub Houssein H. , Yassine Hadi M. , Benslimane Fatiha M. , Al Khatib Hebah A. , Tang Patrick , Hasan Mohammad R. , Coyle Peter , AlMukdad Sawsan , Al Kanaani Zaina , Al Kuwari Einas , Jeremijenko Andrew , Kaleeckal Anvar Hassan , Latif Ali Nizar , Shaik Riyazuddin Mohammad , Abdul Rahim Hanan F. , Nasrallah Gheyath K. , Al Kuwari Mohamed Ghaith , Butt Adeel A. , Al Romaihi Hamad Eid , Al-Thani Mohamed H. , Al Khal Abdullatif , Bertollini Roberto
Published: August 2021

Severity (acute-care hospitalization), criticality (ICU hospitalization), and fatality of SARS-CoV-2 Beta (B.1.351) variant was investigated through case-control studies applied to complete national cohorts of infection, disease, and death cases in Qatar. Compared to Alpha (B.1.1.7) variant, odds of progressing to severe disease were 1.24-fold (95% CI: 1.11-1.39) higher for Beta. Odds of progressing to critical disease were 1.49-fold (95% CI: 1.13-1.97) higher. Odds of COVID-19 death were 1.57-fold (95% CI: 1.03-2.43) higher. Findings highlight risks to healthcare systems, particularly to intensive care facilities and resources, with increased circulation of Beta.
Estimating infection-related human mobility networks based on time series data of COVID-19 infection in Japan
Authors: Yamada Tetsuya , Shi Shoi
Published: August 2021

Comprehensive and evidence-based countermeasures against emerging infectious diseases have become increas-ingly important in recent years. COVID-19 and many other infectious diseases are spread by human movement and contact, but complex transportation networks in 21 century make it difficult to predict disease spread in rapidly changing situations. It is especially challenging to estimate the network of infection transmission in the countries that the traffic and human movement data infrastructure is not yet developed. In this study, we devised a method to estimate the network of transmission of COVID-19 from the time series data of its infection and applied it to determine its spread across areas in Japan. We incorporated the effects of soft lockdowns, such as the declaration of a state of emergency, and changes in the infection network due to government-sponsored travel promotion, and predicted the spread of infection using the Tokyo Olympics as a model. The models used in this study are available online, and our data-driven infection network models are scalable, whether it be at the level of a city, town, country, or continent, and applicable anywhere in the world, as long as the time-series data of infections per region is available. These estimations of effective distance and the depiction of infectious disease networks based on actual infection data are expected to be useful in devising data-driven countermeasures against emerging infectious diseases worldwide.
Lymphocyte count is a universal predictor to the health status and outcomes of patients with coronavirus disease 2019 (COVID-19): A systematic review and meta-regression analysis
Authors: Lai Kuan-Lang , Hu Fu-Chang , Wen Fang-Yu , Chen Ju-Ju
Published: August 2021

Background

This study aimed to evaluate the prediction capabilities of clinical laboratory biomarkers to the prognosis of COVID-19 patients.

Methods

Observational studies reporting at least 30 cases of COVID-19 describing disease severity or mortality were included. Meta-data of demographics, clinical symptoms, vital signs, comorbidities, and 14 clinical laboratory biomarkers on initial hospital presentation were extracted. Taking the outcome group as the analysis unit, meta-regression analysis with the generalized estimating equations (GEE) method for clustered data was performed sequentially. The unadjusted effect of each potential predictor of the three binary outcome variables (i.e., severe vs. non-severe, critically severe vs. non-critically severe, and dead vs. alive) was examined one by one by fitting three series of simple GEE logistic regression models due to missing data. The worst one was dropped one at a time. Then, a final multiple GEE logistic regression model for each of the three outcome variables was obtained.

Findings

Meta-data was extracted from 76 articles, reporting a total of 26,627 cases of COVID-19. Patients were recruited across 16 countries. The number of studies (patients) included in the final models of the analysis for severity, critical severity, and mortality was 38 studies (9,764 patients), 21 studies (4,792 patients), and 24 studies (14,825 patients), respectively. After adjusting for the effect of age, lymphocyte count mean or median ≤ 1.03 (estimated hazard ratio [HR] = 46.2594, p < 0.0001), smaller lymphocyte count mean or median (HR < 0.0001, p = 0.0028), and lymphocyte count mean or median ≤ 0.8714 (HR = 17.3756, p = 0.0079) were the strongest predictor of severity, critical severity, and mortality, respectively.

Interpretation

Lymphocyte count should be closely watched for COVID-19 patients in clinical practice.
COVID19 vaccine type and humoral immune response in patients receiving dialysis
Authors: Garcia Pablo , Anand Shuchi , Han Jialin , Montez-Rath Maria , Sun Sumi , Shang Tiffany , Parsonnet Julie , Chertow Glenn M , Schiller Brigitte , Abra Graham
Published: August 2021

Background

Patients on dialysis vaccinated with the attenuated adenovirus SARS-CoV-2 vaccine might mount an impaired response to vaccination.

Methods

We evaluated the humoral vaccination response among 2,099 fully vaccinated patients receiving dialysis. We used commercially available assays (Siemens) to assess prevalence of no response or diminished response to COVID-19 vaccination by vaccine type. We defined “no seroconversion” as lack of change from negative to positive in total RBD Ig antibody, no detectable response on semiquantitative RBD IgG antibody (index value <1) as “no RBD IgG response”, and a semiquantitative RBD IgG index value <10 as “diminished RBD IgG response”

Results

Of the 2,099 fully vaccinated patients on dialysis, the proportion receiving the mRNA1273, BNT162b2, and Ad26.COV2.S were 62% (n=1316), 20% (n=416) and 18% (n=367), respectively. A third (33.3%) of patients receiving the attenuated adenovirus Ad26.COV2.S vaccine failed to seroconvert and an additional 36% had no detectable or diminished IgG response even 28-60 days post vaccination.

Conclusion

One in three fully vaccinated patients receiving dialysis had evidence of an impaired immune response to the attenuated adenovirus Ad26.COV2.S vaccine.
BWA-mem is not the best aligner for ancient DNA short reads
Authors: Oliva Adrien , Tobler Raymond , Llamas Bastien , Souilmi Yassine
Published: August 2021

Xu and colleagues (Xu et al., 2021) recently suggested a new parameterisation of BWA-mem (Li, 2013) as an alternative to the current standard BWA-aln (Li and Durbin, 2009) to process ancient DNA sequencing data. The authors tested several combinations of the -k and -r parameters to optimise BWA-mem’s performance with degraded and contaminated ancient DNA samples. They report that using BWA-mem with −k 19 −r 2.5 parameters results in a mapping efficiency comparable to BWA-aln with −I 1024 −n 0.03 (i.e. a derivation of the standard parameters used in ancient DNA studies; (Schubert et al., 2012)), while achieving significantly faster run times.

We recently performed a systematic benchmark of four mapping software (i.e. BWA-aln, BWA-mem, NovoAlign (http://www.novocraft.com/products/novoalign), and Bowtie2 (Langmead and Salzberg, 2012) for ancient DNA sequencing data and quantified their precision, accuracy, specificity, and impact on reference bias (Oliva et al., 2021). Notably, while multiple parameterisations were tested for BWA-aln, NovoAlign, and Bowtie2, we only tested BWA-mem with default parameters.

Here, we use the alignment performance metrics from Oliva et al. to directly compare the recommended BWA-mem parameterisation reported in Xu et al. with the best performing alignment methods determined in the Oliva et al. benchmarks, and we make recommendations based on the results.
SigTools: Exploratory Visualization for Genomic Signals
Authors: Masoumi Shohre , Libbrecht Maxwell W. , Wiese Kay C.
Published: August 2021

Motivation

With the advancement of sequencing technologies, genomic data sets are constantly being expanded by high volumes of different data types. One recently introduced data type in genomic science is genomic signals, which are usually short-read coverage measurements over the genome. An example of genomic signals is Epigenomic marks which are utilized to locate functional and nonfunctional elements in genome annotation studies. To understand and evaluate the results of such studies, one needs to understand and analyze the characteristics of the input data.

Results

SigTools is an R-based genomic signals visualization package developed with two objectives: 1) to facilitate genomic signals exploration in order to uncover insights for later model training, refinement, and development by including distribution and autocorrelation plots. 2) to enable genomic signals interpretation by including correlation, and aggregation plots. Moreover, Sigtools also provides text-based descriptive statistics of the given signals which can be practical when developing and evaluating learning models. We also include results from 2 case studies. The first examines several previously studied genomic signals called histone modifications. This use case demonstrates how SigTools can be beneficial for satisfying scientists’ curiosity in exploring and establishing recognized datasets. The second use case examines a dataset of novel chromatin state features which are novel genomic signals generated by a learning model. This use case demonstrates how SigTools can assist in exploring the characteristics and behavior of novel signals towards their interpretation. In addition, our corresponding web application, SigTools-Shiny, extends the accessibility scope of these modules to people who are more comfortable working with graphical user interfaces instead of command-line tools.

Availability

SigTools source code, installation guide, and manual is available on http://github.com/shohre73.

Contact

shohre_masoumi@sfu.ca
Black Dots: Microcontact-Printed, Reference-Free Traction Force Microscopy
Authors: Beussman Kevin M. , Mollica Molly Y. , Leonard Andrea , Miles Jeffrey , Hocter John , Song Zizhen , Stolla Moritz , Han Sangyoon J. , Emery Ashley , Thomas Wendy E. , Sniadecki Nathan J.
Published: August 2021

Measuring the traction forces produced by cells provides insight into their behavior and physiological function. Here, we developed a technique (dubbed ‘black dots’) that microcontact prints a fluorescent micropattern onto a flexible substrate to measure cellular traction forces without constraining cell shape or needing to detach the cells. To demonstrate our technique, we assessed human platelets, which can generate a large range of forces within a population. We find platelets that exert more force have more spread area, are more circular, and have more uniformly distributed F-actin filaments. As a result of the high yield of data obtainable by this technique, we were able to evaluate multivariate mixed effects models with interaction terms and conduct a clustering analysis to identify clusters within our data. These statistical techniques demonstrated a complex relationship between spread area, circularity, F-actin dispersion, and platelet force, including cooperative effects that significantly associate with platelet traction forces.

GRAPHICAL ABSTRACT
Diverse but unique astrocytic phenotypes during embryonic stem cell differentiation, culturing and aging
Authors: Freitag Kiara , Eede Pascale , Ivanov Andranik , Schneeberger Shirin , Borodina Tatiana , Sauer Sascha , Beule Dieter , Heppner Frank L.
Published: August 2021

Astrocytes are resident glia cells of the central nervous system (CNS) that play complex and heterogeneous roles in brain development, homeostasis and disease. Since their vast involvement in health and disease is becoming increasingly recognized, suitable and reliable tools for studying these cells in vivo and in vitro are of utmost importance. One of the key challenges hereby is to adequately mimic their context-dependent in vivo phenotypes and functions in vitro. To better understand the spectrum of astrocytic variations in defined settings we performed a side-by-side-comparison of embryonic stem cell (ESC)-derived astrocytes as well as primary neonatal and adult astrocytes, revealing major differences on a functional and transcriptomic level, specifically on proliferation, migration, calcium signaling and cilium activity. Our results highlight the need to carefully consider the choice of astrocyte origin and phenotype with respect to age, isolation and culture protocols based on the respective biological question.
A Chromosome-level Genome Assembly of the Reed Warbler (Acrocephalus scirpaceus)
Authors: Sætre Camilla Lo Cascio , Eroukhmanoff Fabrice , Rönkä Katja , Kluen Edward , Thorogood Rose , Torrance James , Tracey Alan , Chow William , Pelan Sarah , Howe Kerstin , Jakobsen Kjetill S. , Tørresen Ole K.
Published: August 2021

The reed warbler (Acrocephalus scirpaceus) is a long-distance migrant passerine with a wide distribution across Eurasia. This species has fascinated researchers for decades, especially its role as host of a brood parasite, and its capacity for rapid phenotypic change in the face of climate change. Currently, it is expanding its range northwards in Europe, and is altering its migratory behaviour in certain areas. Thus, there is great potential to discover signs of recent evolution and its impact on the genomic composition of the reed warbler. Here we present a high-quality reference genome for the reed warbler, based on PacBio, 10X and Hi-C sequencing. The genome has an assembly size of 1,075,083,815 bp with a scaffold N50 of 74,438,198 bp and a contig N50 of 12,742,779 bp. BUSCO analysis using aves_odb10 as a model showed that 95.7% of genes in the assembly were complete. We found unequivocal evidence of two separate macrochromosomal fusions in the reed warbler genome, in addition to the previously identified fusion between chromosome Z and a part of chromosome 4A in the Sylvioidea superfamily. We annotated 14,645 protein-coding genes, of which 97.5% were complete BUSCO orthologs. This reference genome will serve as an important resource, and will provide new insights into the genomic effects of evolutionary drivers such as coevolution, range expansion, and adaptations to climate change, as well as chromosomal rearrangements in birds.

Significance statement

The reed warbler (Acrocephalus scirpaceus) has been lacking a genomic resource, despite having been broadly researched in studies of coevolution, ecology and adaptations to climate change. Here, we generated a chromosome-length genome assembly of the reed warbler, and found evidence of macrochromosomal fusions in its genome, which are likely of recent origin. This genome will provide the opportunity for a deeper understanding of the evolution of genomes in birds, as well as the evolutionary path and possible future of the reed warbler.
A vibrissa pathway that activates the limbic system
Authors: Elbaz Michaël , Callado-Pérez Amalia , Demers Maxime , Zhao Shengli , Foo Conrad , Kleinfeld David , Deschênes Martin
Published: August 2021

Vibrissa sensory inputs play a central role in driving rodent behavior. These inputs transit through the sensory trigeminal nuclei, which give rise to the ascending lemniscal and paralemniscal pathways. While lemniscal projections are somatotopically mapped from brain stem to cortex, those of the paralemniscal pathway are more widely distributed. Yet the extent and topography of paralemniscal projections are unknown, along with the potential role of these projections in controlling behavior. Here we used viral tracers to map paralemniscal projections. We find that this pathway broadcasts vibrissa-based sensory signals to brain stem regions that are involved in the regulation of autonomic functions and to forebrain regions that are involved in the expression of emotional reactions. We further provide evidence that GABAergic cells of the Kölliker-Fuse nucleus gate trigeminal sensory input in the paralemniscal pathway via a mechanism of presynaptic or extrasynaptic inhibition.
Integrative Gene Expression and Metabolic Analysis tool IgemRNA
Authors: Grausa Kristina , Mozga Ivars , Pleiko Karlis , Pentjuss Agris
Published: August 2021

Genome scale metabolic modelling is widely used technique to research metabolism impacts on organism’s properties. Additional omics data integration enables a more precise genotype-phenotype analysis for biotechnology, medicine and life sciences. Transcriptome data amounts rapidly increase each year. Many transcriptome analysis tools with integrated genome scale metabolic modelling are proposed. But these tools have own restrictions, compatibility issues and the necessity of previous experience and advanced user skills. We have analysed and classified published tools, summarized possible transcriptome pre-processing, and analysis methods and implemented them in the new transcriptome analysis tool IgemRNA. Tool novelty is the possibility of transcriptomics data pre-processing approach, analysis of transcriptome with or without genome scale metabolic models and different thresholding and gene mapping approach availability. In comparison with usual Gene set enrichment analysis methods, IgemRNA options provide additional transcriptome data validation, where minimal metabolic network connectivity and flux requirements are met. IgemRNA allows to process transcriptome datasets, compare data between different phenotypes, execute multiple analysis and data filtering functions. All this is done via graphical user interface. IgemRNA is compatible with Cobra Toolbox 3.0 and uses some of its functions for genome scale metabolic model optimization tasks. IgemRNA is open access software available at https://github.com/BigDataInSilicoBiologyGroup/IgemRNA.
Reduced expression of the psychiatric risk gene DLG2 (PSD93) impairs hippocampal synaptic integration and plasticity
Authors: Griesius Simonas , O’Donnell Cian , Waldron Sophie , Thomas Kerrie L. , Dwyer Dominic M. , Wilkinson Lawrence S. , Hall Jeremy , Robinson Emma S. J. , Mellor Jack R.
Published: August 2021

Background:Genetic variations indicating loss of function in theDLG2gene have been associated with markedly increased risk for schizophrenia, autism spectrum disorder, and intellectual disability.DLG2encodes the postsynaptic scaffolding protein DLG2 (PSD93) that interacts with NMDA receptors, potassium channels, and cytoskeletal regulators but the net impact of these interactions on synaptic plasticity, likely underpinning cognitive impairments associated with these conditions, remains unclear.Methods:Hippocampal CA1 neuronal excitability and synaptic function were investigated in a novel clinically relevant heterozygousDlg2+/−rat model usingex vivopatch-clamp electrophysiology, pharmacology, and computational modelling.Results:Dlg2+/−rats had increased NMDA receptor-mediated synaptic currents and, conversely, impaired associative long-term potentiation. This impairment resulted from an increase in potassium channel function leading to a decrease in input resistance and reduced supra-linear dendritic integration during induction of associative long-term potentiation. Enhancement of dendritic excitability by blockade of potassium channels or activation of muscarinic M1 receptors with selective allosteric agonist 77-LH-28-1 reduced the threshold for dendritic integration and 77-LH-28-1 rescued the associative long-term potentiation impairment in theDlg2+/−rats.Conclusions:Despite increasing synaptic NMDA receptor currents, the combined impact of reduced DLG2 impairs synaptic integration in dendrites resulting in disrupted associative synaptic plasticity. This biological phenotype can be reversed by compound classes used clinically such as muscarinic M1 receptor agonists and is therefore a potential target for therapeutic intervention.
Genome sequencing and assembly ofTinospora cordifolia(Giloy) plant
Authors: Mahajan Shruti , Chakraborty Abhisek , Sil Titas , Sharma Vineet K
Published: August 2021

During the ongoing COVID-19 pandemicTinospora cordifoliaalso known as Giloy gained immense popularity and use due to its immunity-boosting function and anti-viral properties.T. cordifoliais among the most important medicinal plants that has numerous therapeutic applications in health due to the production of a diverse array of secondary metabolites. Therefore, to gain genomic insights into the medicinal properties ofT. cordifolia, the first genome sequencing was carried out using 10x Genomics linked read technology and the draft genome assembly comprised of 1.01 Gbp. This is also the first genome sequenced from the plant family Menispermaceae. We also performed the first genome size estimation forT. cordifoliaand was found to be 1.13 Gbp. The deep sequencing of transcriptome from the leaf tissue was also performed followed by transcriptomic analysis to gain insights into the gene expression and functions. The genome and transcriptome assemblies were used to construct the gene set inT. cordifoliathat resulted in 19,474 coding gene sequences. Further, the phylogenetic position ofT. cordifoliawas also determined through the construction of a genome-wide phylogenetic tree using 35 other dicot species and one monocot species as an outgroup species.
IntroSpect: motif-guided immunopeptidome database building tool to improve the sensitivity of HLA binding peptide identification
Authors: Zhang Le , Liu Geng , Hou Guixue , Xiang Haitao , Zhang Xi , Huang Ying , Zhang Xiuqing , Li Bo , Lee Leo J
Published: August 2021

Although database search tools originally developed for shotgun proteome have been widely used in immunopeptidomic mass spectrometry identifications, they have been reported to achieve undesirably low sensitivities and/or high false positive rates as a result of the hugely inflated search space caused by the lack of specific enzymic digestions in immunopeptidome. To overcome such a problem, we have developed a motif-guided immunopeptidome database building tool named IntroSpect, which is designed to first learn the peptide motifs from high confidence hits in the initial search and then build a targeted database for refined search. Evaluated on three representative HLA class I datasets, IntroSpect can improve the sensitivity by an average of 80% comparing to conventional searches with unspecific digestions while maintaining a very high accuracy (∼96%) as confirmed by synthetic validation experiments. A distinct advantage of IntroSpect is that it does not depend on any external HLA data so that it performs equally well on both well-studied and poorly-studied HLA types, unlike a previously developed method SpectMHC. We have also designed IntroSpect to keep a global FDR that can be conveniently controlled, similar to conventional database search engines. Finally, we demonstrate the practical value of IntroSpect by discovering neoantigens from MS data directly. IntroSpect is freely available at https://github.com/BGI2016/IntroSpect.
Capillary-associated microglia regulate vascular structure and function through PANX1-P2RY12 coupling
Authors: Bisht Kanchan , Okojie Kenneth A. , Sharma Kaushik , Lentferink Dennis H. , Sun Yu-Yo , Chen Hong-Ru , Uweru Joseph O. , Amancherla Saipranusha , Calcuttawala Zainab , Campos-Salazar Antony Brayan , Corliss Bruce , Jabbour Lara , Benderoth Jordan , Friestad Bria , Mills William A. , Isakson Brant E. , Tremblay Marie-Ève , Kuan Chia-Yi , Eyo Ukpong B.
Published: August 2021

Microglia are brain-resident immune cells with a repertoire of functions in the developing, mature and pathological brain. Their wide-ranging roles in physiology include the clearance of cellular debris, elimination of excess synapses, regulation of neuronal activity and contributions to blood vessel development. Despite these known roles for microglia, the extent of their interactions with the vasculature and potential regulation of vascular physiology has been insufficiently explored. Here, using in vivo acute and longitudinal two-photon imaging in transgenic mice combined with electron microscopy, fixed tissue immunohistochemistry, pharmacological treatments and laser speckle imaging, we document the steady-state interactions between ramified CX3CR1+ myeloid cell somata and capillaries in the brain. We first confirm that these myeloid cells are bona fide microglia by molecular, morphological and ultrastructural approaches. Then we give a detailed spatio-temporal characterization of these capillary-associated microglia (CAMs) comparing and contrasting them with parenchymal microglia (PCMs) in their static, dynamic and chronic morphological activities including during microglial depletion and repopulation. Molecularly, we identify microglial-specific purinergic P2RY12 receptors as a receptor regulating CAM interactions under the control of released purines from pannexin 1 (PANX1) channels. Furthermore, to elucidate roles for microglia in vascular structure and function, we eliminated microglia and showed that this triggered capillary dilation, blood flow increase, and impaired vasodilative responses. We find that P2RY12−/− and PANX1−/− mice recapitulate these vascular impairments suggesting purines released through PANX1 channels play important roles in activating microglial P2RY12 receptors to regulate neurovascular structure and function.
ZeBox: A novel non-intrusive continuous-use technology to trap and kill airborne microbes
Authors: Phadke Kruttika S. , Madival Deepak G. , Venkataraman Janani , Kundu Debosmita , Ramanujan K. S. , Holla Nisha , Arakeri Jaywant , Tomar Gaurav , Datta Santanu , Ghatak Arindam
Published: August 2021

Preventing nosocomial infection is a major unmet need of our times. Existing air decontamination technologies suffer from demerits such as toxicity of exposure, species specificity, noxious gas emission, environment-dependent performance and high power consumption. Here, we present a novel technology called “ZeBox” that transcends the conventional limitations and achieves high microbicidal efficiency. In ZeBox, a non-ionizing electric field extracts naturally charged microbes from flowing air and deposits them on engineered microbicidal surfaces. The surface’s three dimensional topography traps the microbes long enough for them to be inactivated. The electric field and chemical surfaces synergistically achieve rapid inactivation of a broad spectrum of microbes. ZeBox achieved near complete kill of airborne microbes in challenge tests (5-9 log reduction) and >90% efficiency in a fully functional stem cell research facility in the presence of humans. Thus, ZeBox fulfills the dire need for a real-time, continuous, safe, trap-and-kill air decontamination technology.
Shisa7 phosphorylation regulates GABAergic transmission and neurodevelopmental behaviors
Authors: Wu Kunwei , Shepard Ryan David , Castellano David , Tian Qingjun , Dong Lijin , Lu Wei
Published: August 2021

GABA-A receptors (GABAARs) are crucial for development and regulation of the central nervous system. Altered GABAergic signaling is hypothesized to be involved in the pathophysiology of neurodevelopmental disorders. Nevertheless, how aberrant cellular and molecular mechanisms affect GABAARs in these diseases remain elusive. Recently, we identified Shisa7 as a GABAAR auxiliary subunit that modulates GABAAR trafficking, kinetics, and pharmacology, and discovered a phosphorylation site in Shisa7 (S405) critical for extrasynaptic α5-GABAAR trafficking and tonic inhibition. However, the role of S405 phosphorylation in the regulation of synaptic inhibition, plasticity, and behavior remains unknown. Here, we found that expression of a phospho-null mutant (Shisa7 S405A) in heterologous cells and neurons diminishes α2-GABAAR trafficking. Subsequently, we generate a Shisa7 S405A knock-in (KI) mouse line that displays reduced surface expression of GABAARs in hippocampal neurons. Importantly, both synaptic and tonic inhibition are decreased in KI mice. Moreover, chemically induced inhibitory long-term potentiation is impaired, highlighting a critical role of Shisa7 S405 in GABAergic plasticity. Lastly, KI mice exhibit enhanced locomotor activity and grooming associated with neurodevelopmental disorders. Collectively, our study reveals a phosphorylation site critical for Shisa7-dependent trafficking of synaptic and extrasynaptic GABAARs which contributes to behavioral endophenotypes displayed in neurodevelopmental disorders.
Burning for grassland pollination: recently burned patches promote plant flowering and insect pollinators
Authors: da Silva Goldas Camila , Podgaiski Luciana Regina , da Silva Carolina Veronese Corrêa , de Souza Mendonça Milton
Published: August 2021

Grasslands are historically and evolutionarily associated with disturbances, such as fire, that drive biodiversity assembly patterns and biotic interactions. Disturbance suppression in fire- prone ecosystems usually leads to a decline in forb diversity and flowering due to biomass accumulation, which could jeopardize pollinator diversity. In this study, we investigated patterns and drivers of plant flowering and flower insect visitor communities in a chronosequence of patches from different time-since-fire categories in Southern Brazilian grasslands. Old-burnt patches (more than 2 years since fire) had taller vegetation, more biomass and grass cover than intermediate (about 1 year after fire) and freshly-burnt patches (less than 6 months since fire), which had increased bare soil cover. Forb flower abundance was much higher in freshly-burnt patches, directly predicted by the degree of habitat openness. Pollinator insects were then benefited by floral resource aggregation in freshly-burnt patches, increasing in abundance (bees and butterflies) and species richness (bees). Beetle communities were positively influenced by vegetation height. Furthermore, plant species flowering and bee species composition varied between freshly and old-burnt grasslands, with indicator species found for all recovery stages but mainly freshly-burnt patches. Altogether, these results indicate the importance of maintaining freshly-burnt patches in the grassland landscape: it helps to sustain flower diversity, pollination services, and flowering plant reproduction. Our findings support the idea that a mosaic of grasslands from different times-since- fire should be considered for grassland conservation.
Uncertainty quantification in subject-specific estimation of local vessel mechanical properties
Authors: Rego Bruno V. , Weiss Dar , Bersi Matthew R. , Humphrey Jay D.
Published: August 2021

Quantitative estimation of local mechanical properties remains critically important in the ongoing effort to elucidate how blood vessels establish, maintain, or lose mechanical homeostasis. Recent advances based on panoramic digital image correlation (pDIC) have made high-fidelity 3D reconstructions of small-animal (e.g., murine) vessels possible when imaged in a variety of quasi-statically loaded configurations. While we have previously developed and validated inverse modeling approaches to translate pDIC-measured surface deformations into biomechanical metrics of interest, our workflow did not heretofore include a methodology to quantify uncertainties associated with local point estimates of mechanical properties. This limitation has compromised our ability to infer biomechanical properties on a subject-specific basis, such as whether stiffness differs significantly between multiple material locations on the same vessel or whether stiffness differs significantly between multiple vessels at a corresponding material location. In the present study, we have integrated a novel uncertainty quantification and propagation pipeline within our inverse modeling approach, relying on empirical and analytic Bayesian techniques. To demonstrate the approach, we present illustrative results for the ascending thoracic aorta from three mouse models, quantifying uncertainties in constitutive model parameters as well as circumferential and axial tangent stiffness. Our extended workflow not only allows parameter uncertainties to be systematically reported, but also facilitates both subject-specific and group-level statistical analyses of the mechanics of the vessel wall.
Myofiber injury induces capillary disruption and regeneration of disorganized microvascular networks
Authors: Jacobsen Nicole L. , Norton Charles E. , Shaw Rebecca L. , Cornelison DDW , Segal Steven S.
Published: August 2021

Myofibers regenerate following injury, however the microvasculature must also recover to restore skeletal muscle function. We aimed to define the nature of microvascular damage and repair during skeletal muscle injury and regeneration induced by BaCl2. To test the hypothesis that microvascular disruption occurred secondary to myofiber injury in mice, isolated microvessels were exposed to BaCl2 or the myotoxin was injected into the gluteus maximus (GM) muscle. In isolated microvessels, BaCl2 depolarized smooth muscle cells and endothelial cells while increasing [Ca2+]i, but did not elicit cell death. At 1 day post injury (dpi) of the GM, capillary fragmentation coincided with myofiber degeneration while arteriolar and venular networks remained intact; neutrophil depletion before injury did not prevent capillary damage. Perfused capillary networks reformed by 5 dpi in association with more terminal arterioles and were dilated through 10 dpi; with no change in microvascular area or branch point number in regenerating networks, fewer capillaries aligned with myofibers and capillary networks were no longer organized into microvascular units. By 21 dpi, capillary orientation and organization had nearly recovered to that in uninjured GM. We conclude that following their disruption secondary to myofiber damage, capillaries regenerate as disorganized networks that remodel while regenerated myofibers mature.
Microbial byproducts determine reproductive fitness of free-living and parasitic nematodes
Authors: Venzon Mericien , Das Ritika , Luciano Daniel J. , Burnett Julia , Park Hyun Shin , Devlin Joseph Cooper , Kool Eric T. , Belasco Joel G. , Hubbard E. Jane Albert , Cadwell Ken
Published: August 2021

A distinguishing feature of Trichuris nematodes is that these parasitic worms reproduce within the digestive tracts of humans and other mammalian hosts shedding thousands of eggs daily, facilitating their sustained presence in the environment and hampering eradication efforts. Although this aspect of the lifecycle places Trichuris in a microbiota-rich environment, metabolic byproducts of bacteria that facilitate the reproductive development of parasites are unknown. Here, we employ a pipeline using the well-characterized free-living nematode C. elegans to identify microbial factors with conserved roles in the reproduction of nematodes. A screen for E. coli mutants that impair C. elegans fertility identified genes in fatty acid biosynthesis and ethanolamine utilization pathways, including fabH and eutN. Trichuris muris eggs displayed defective hatching in the presence of E. coli deficient in fabH or eutN due to reduction in arginine or elevated levels of aldehydes, respectively. Remarkably, T. muris reared in gnotobiotic mice colonized with these E. coli mutants displayed profound abnormalities including morphological defects and a failure to lay viable eggs. These findings indicate that microbial byproducts mediate evolutionarily conserved transkingdom interactions that impact the reproductive fitness of distantly-related nematodes.
Effects of Cholesterol on the mechanism of fengycin, a biofungicide
Authors: Sur Sreyoshi , Grossfield Alan
Published: August 2021

Fengycins are a class of antifungal lipopeptides synthesized by the bacteria Bacillus subtilis, commercially available as the primary component of the agricultural fungicide Serenade®. They are toxic to fungi, but far less to mammalian cells. One key difference between mammalian and fungal cell membranes is the presence of cholesterol only in the former; recent experimental work showed that the presence of cholesterol reduces fengycin-induced membrane leakage. (1) Since our previous all-atom and coarse-grained simulations (2, 3) suggested that aggregation of membrane-bound fengycin is central to its ability to disrupt membranes, we hypothesized that cholesterol might reduce fengycin aggregation. Here, we test this hypothesis using coarse-grained molecular dynamics simulations, with sampling enhanced via the weighted ensemble method. The results indicate that cholesterol subtly alters the size distribution for fengycin aggregates, limits the lateral range of their membrane disordering, and reduces the ability of aggregates to bend the membrane. Taken together, these phenomena may account for cholesterol’s affects on fengycin activity.
NT-CRISPR: Combining natural transformation and CRISPR/Cas9 counterselection for markerless and scarless genome editing in Vibrio natriegens
Authors: Stukenberg Daniel , Hoff Josef , Faber Anna , Becker Anke
Published: August 2021

The fast-growing bacterium Vibrio natriegens has recently gained increasing attention as a novel chassis organism for a wide range of projects. To fully harness the potential of this fascinating bacterium, convenient and highly efficient genome editing methods are indispensable to create novel strains, tailored for specific applications. V. natriegens is able to take up free DNA and incorporate it into its genome by homologous recombination. This process, called natural transformation, was tamed for genome editing. It displays a high efficiency and is able to mediate uptake of multiple DNA fragments, thereby allowing multiple simultaneous edits. Here, we describe NT-CRISPR, a combination of natural transformation with CRISPR/Cas9 counterselection. In two temporally distinct steps, we first performed a genome edit by natural transformation and second, induced CRISPR/Cas9, targeting the wild type sequence, leading to death of non-edited cells. Through highly efficient cell killing with efficiencies of up to 99.999 %, integration of antibiotic resistance markers became dispensable and thus enabled scarless and markerless edits with single-base precision. We used NT-CRISPR for deletions, integrations and single-base modifications with editing efficiencies of up to 100 % and further demonstrated its applicability for the simultaneous deletion of multiple chromosomal regions. Lastly, we demonstrated that the near PAM-less Cas9 variant SpG Cas9 is compatible with NT-CRISPR and thereby massively broadens the target spectrum.