bluuebunny/crossref_metadata_2025 huggingface dataset:
Development of web-based quality-assurance tool for radiotherapy target delineation for head and neck cancer: quality evaluation of nasopharyngeal carcinoma
Authors: Kim Jun Won , Marsilla Joseph , Kazmierski Michal , Tkachuk Denis , Huang Shao Hui , Xu Wei , Cho John , Ringash Jolie , Bratman Scott , Haibe-Kains Benjamin , Hope Andrew
Published: February 2021

Purpose

We developed QUANNOTATE, a new web-application for rapid review of radiotherapy (RT) target volumes, and used it to evaluate the relationship between target delineation compliance with the international guidelines and treatment outcomes in nasopharyngeal carcinoma (NPC) patients undergoing definitive RT.

Methods and Materials

The dataset used for this study consists of anonymized CT simulation scans, RT structures, and clinical data of 332 pathologically confirmed NPC patients treated with intensity-modulated RT between July 2005 and August 2017. We imported the contours of intermediate risk clinical target volumes of the primary tumor (IR-CTVp) receiving 56 Gy into QUANNOTATE. We determined inclusion of anatomic sites within IR-CTVp in accordance with 2018 International guideline for CTV delineation for NPC and correlated the results with time to local failure (TTLF) using Cox-regression.

Results

At a median follow-up of 5.6 years, 5-year TTLF and overall survival rates were 93.1% and 85.9% respectively. The most frequently non-guideline compliant anatomic sites were sphenoid sinus (n = 69, 20.8%), followed by cavernous sinus (n = 38, 19.3%), left and right petrous apices (n = 37 and 32, 11.1% and 9.6%), clivus (n = 14, 4.2%), and right and left foramen rotundum (n = 14 and 12, 4.2% and 3.6%). Among 23 patients with a local failure (6.9%), the number of non-compliant cases were 8 for sphenoid sinus, 7 cavernous sinus, 4 left and 3 right petrous apices, and 2 clivus. Compared to conforming cases, cases which did not contour the cavernous sinus had a higher local failure (LF) rate (89.1% vs 93.6%, p= 0.013). Multivariable analysis confirmed that lack of cavernous sinus contouring was prognostic for LF.

Conclusions

QUANNOTATE allowed rapid review of target volumes in a large patient cohort. Despite an overall high compliance with the international guidelines, undercoverage of the cavernous sinus was correlated with LF.
Genetic Variations in Evolutionary Accelerated Regions Disrupt Cognition in Schizophrenia
Authors: Bhattacharyya Upasana , Kukshal Prachi , Bhatia Triptish , Deshpande Smita N , Thelma B.K
Published: February 2021

Cognition is believed to be a product of human evolution, while schizophrenia is ascribed as the by-product with cognitive impairment as it’s genetically mediated endophenotype. Genomic loci associated with these traits are enriched with recent evolutionary markers such as Human accelerated regions (HARs). HARs are markedly different in humans since their divergence with chimpanzees and mostly regulate gene expression by binding to transcription factors and/or modulating chromatin interactions. We hypothesize that variants within HARs may alter such functions and thus contribute to disease pathogenesis. 49 systematically prioritized variants from 2737 genome-wide HARs were genotyped in a north-Indian schizophrenia cohort (331 cases, 235 controls). Six variants were significantly associated with cognitive impairment in schizophrenia, thirteen with general cognition in healthy individuals. These variants were mapped to 122 genes; predicted to alter 70 transcription factors binding sites and overlapped with promoters, enhancers and/or repressors. These genes and TFs are implicated in neurocognitive phenotypes, autism, schizophrenia and bipolar disorders; a few are targets of common or repurposable antipsychotics suggesting their draggability; and enriched for immune response and brain developmental pathways. Immune response has been more strongly targeted by natural selection during human evolution and has a prominent role in neurodevelopment. Thus, its disruption may have deleterious consequences for neuronal and cognitive functions. Importantly, among the 15 associated SNPs, 12 showed association in several independent GWASs of different neurocognitive functions. Further analysis of HARs may be valuable to understand their role in cognition biology and identify improved therapeutics for schizophrenia.
Knowledge, Attitude, and Practices towards SARS-COV-2 Infection in the United Arab Emirates Population: a Cross-sectional Survey-based Study
Authors: Alremeithi Hamda Musabbah , Alghefli Aljazia Khalfan , Almadhani Rouqyah , AlKetbi Latifa Baynouna
Published: February 2021

In the current situation involving the novel coronavirus disease (COVID-19), the disease containment depends mainly on the population’s preventive practices and self-isolation. In this study, we explored the adult population’s approach towards COVID-19 in UAE between the 4th and 14th of April 2020. We used a community-based, cross-sectional study using a self-administered electronic questionnaire covering five different aspects: demographics, knowledge, practice, attitude, source and trust of information, and a patient health questionnaire (PHQ-2) for depression screening. A total of 1,867 people responded to the survey. Knowledge results were better in people with higher education levels, non-UAE nationals, those with a higher PHQ-2 score, or with a positive contact history with a SARS-COV-2 infected patient. The best practice scores were shown by participants with high knowledge scores and education levels. Depression risk was significantly higher in men, non-UAE nationals, in those with lower knowledge scores, and younger ages. The most followed practices were staying home, handwashing, avoiding social gatherings, limiting three people per vehicle, and avoiding public transportation. The least practiced measures were covering the face while sneezing or coughing and wearing masks. Although staying home was reported by 92.5% of participants, 22.6% mentioned that they were visited by more than 2 people and visited others in 18.4% during the last week. Social media was the source of information for 82.1% of the participants, and most trusted doctors and healthcare providers. A depression risk was present in 18.9% of the participants and the majority of respondents agreed that SARS-COV-2 infection will finally be successfully controlled. The obtained results on knowledge and practices, although satisfactory, could be insufficient to prevent this pandemic from being contained. We recommend the intensification of awareness programs and good practices. Mental health is an area worth further studies.
Music therapy as a migraine treatment: protocol for a systematic review and meta-analysis
Authors: Sanchez Alessio Alberto Gilardi , Guevara Bartolini Milena Ana Micaela , Acosta Maria Luz Pantoja , Lazo-Porras Maria
Published: February 2021

Introduction

Headache disorders are one of the most common health problems worldwide, they can be classified into primary and secondary disorders. In the primary group, migraine - the second most common type of headache - is the most disabling one and one of the most important reasons why its treatment is mandatory. Migraine treatment involves different steps and kinds of medical therapy and patient education, and in these past years studies have been exploring the effect music therapy can have in reducing the severity and duration of an acute migraine attack. It has been reported that adding music to the pharmacological treatment can help decrease the pain severity, thus, reducing the disability migraine can cause.

Objective

Evaluate the effectiveness of music therapy as a treatment or coadjuvant of migraine attacks in people who suffer this condition.

Methods and analysis

This protocol is consistent with the methodology recommended by the PRISMA-P and the Cochrane handbook for systematic reviews of interventions. This study will be carried out as a systematic review and meta-analysis. In order to do so, electronic searches will be performed in PubMed, Medline and Cochrane (through Ovid) and Embase. The data range parameters used in searching all databases are from the last 20 years. Randomized controlled trials (RCTs) published in English, Spanish, French and Portuguese; with the primary outcomes being reduction of headache intensity, resolution of the migraine and decreased frequency of migraine attacks. Three investigators will screen all retrieved studies titles and abstracts, making a first preliminary list. A second screen will be done by the same three investigators similarly to the first one, but reviewing the full texts and building the final list. Then, the evaluation of the risk of bias and extraction of all data will be performed. The risk of bias of the included RCTs will be evaluated by the Cochrane Collaboration’s tool. A qualitative synthesis will be provided in text and tables, to summarize the main results of the selected publications. The heterogeneity between studies will be assessed through the I2 statistic. If there is sufficient homogeneity across outcomes, a meta-analysis will be conducted.

Conclusions

This systematic review will provide evidence regarding the effectiveness of music therapy as a single or coadjuvant treatment in patients with migraine attacks. Based on this analysis, it will be feasible to know whether this intervention is effective in the reduction of the intensity of the migraine attack, if it can help resolve the migraine attack, or reduce the frequency of migraine attacks.
A meta-analysis of 20 years of data on people who inject drugs in metropolitan Chicago to inform computational modeling
Authors: Boodram Basmattee , Mackesy-Amiti Mary Ellen , Khanna Aditya , Brickman Bryan , Dahari Harel , Ozik Jonathan
Published: February 2021

Progress toward hepatitis C virus (HCV) elimination in the United States is not on track to meet targets, as injection drug use continues to drive increasing HCV incidence. Computational models are useful in understanding the complex interplay of individual, social, and structural level factors that might alter HCV incidence, prevalence, transmission, and disease progression. However, these models need to be informed with real socio-behavioral data. We conducted a meta-analysis of research studies spanning 20 years of research and interventions with people who inject drugs in metropolitan Chicago to produce parameters for a synthetic population for a computational model. We then fit an exponential random graph model (ERGM) using the network estimates from the meta-analysis in order to develop the dynamic component of a realistic agent-based model.
Apical contacts stemming from incomplete delamination guide progenitor cell allocation through a dragging mechanism
Authors: Pulgar Eduardo , Schwayer Cornelia , Guerrero Néstor , López Loreto , Márquez Susana , Härtel Steffen , Soto Rodrigo , Heisenberg Carl-Philipp , Concha Miguel L.
Published: February 2021

The developmental strategies used by progenitor cells to endure a safe journey from their induction place towards the site of terminal differentiation are still poorly understood. Here we uncovered a progenitor cell allocation mechanism that stems from an incomplete process of epithelial delamination that allows progenitors to coordinate their movement with adjacent extra-embryonic tissues. Progenitors of the zebrafish laterality organ originate from the surface epithelial enveloping layer by an apical constriction process of cell delamination. During this process, progenitors retain long-term apical contacts that enable the epithelial layer to pull a subset of progenitors along their way towards the vegetal pole. The remaining delaminated progenitors follow apically-attached progenitors’ movement by a co-attraction mechanism, avoiding sequestration by the adjacent endoderm, ensuring their fate and collective allocation at the differentiation site. Thus, we reveal that incomplete delamination serves as a cellular platform for coordinated tissue movements during development.

Impact Statement

Incomplete delamination serves as a cellular platform for coordinated tissue movements during development, guiding newly formed progenitor cell groups to the differentiation site.
Brain Morphometry and Diminished Physical Growth in Bangladeshi Children Growing up in Extreme Poverty: a Longitudinal Study
Authors: Turesky Ted K. , Shama Talat , Kakon Shahria Hafiz , Haque Rashidul , Islam Nazrul , Someshwar Amala , Petri William A. , Nelson Charles A. , Gaab Nadine
Published: February 2021

Diminished physical growth is a common marker of malnutrition and it affects approximately 200 million children worldwide. Despite its importance and prevalence, it is not clear whether diminished growth affects brain development and neurocognitive outcomes. Further, diminished growth is more common in areas of extreme poverty, raising the possibility that it may serve as a mechanism for previously shown links between poverty and brain development. To address these questions, 79 children growing up in an extremely poor, urban area of Bangladesh underwent MRI at 6 years. Structural brain images were submitted to Mindboggle software, a Docker-compliant and highly reproducible tool for tissue segmentation and regional estimations of volume, surface area, cortical thickness, travel depth, and mean curvature. Diminished growth predicted brain morphometry and mediated the link between poverty and brain morphometry most consistently for white matter and subcortical volumes. Meanwhile, brain volume in left pallidum and right ventral diencephalon mediated the relationship between diminished growth and full-scale IQ. These findings offer malnutrition as one possible mechanism by which poverty affects brain development and neurocognitive outcomes in areas of extreme poverty.
Natural selections on both amino acid sequences and expression levels are determinants of ohnolog retention
Authors: Miao Lin , Li Miaoxin
Published: February 2021

The mechanism of ohnolog retention is a subject of concern in evolutionary biology. Natural selections on coding sequences and gene dosages have been proposed to be determinants of ohnolog retention. However, the relationship between the two models is not widely accepted, and the role of regulatory sequences on ohnolog retention has long been neglected. In this study, based on a model of complex traits’ genetic architecture, we compared the natural selection’s strength on corresponding sequences between ohnologs and non-ohnologs by comparing complex traits’ heritability enrichments. We showed that complex traits’ regulatory sequences’ heritability enrichments (p= 1.1 × 10−5in 5 kb flanking regions) and expression-mediated heritability enrichments (p= 2.1 × 10−5) of ohnologs were significantly higher than non-ohnologs. Then, we deduced that regulatory sequences of ohnologs were under substantial natural selection, which was also a determent of ohnolog retention. Meanwhile, we showed that in coding sequences, the complex traits’ heritability enrichments of ohnologs were significantly higher than of non-ohnologs (p= 9.9 × 10−5), supporting the ohnolog retention model of natural selection on coding sequences. We also showed that complex traits’ causal gene expression effect sizes of ohnologs were significantly larger than of non-ohnologs (p= 8.8 × 10−6), supporting the ohnolog retention model of natural selection on gene dosages. In conclusion, we provide the first unified framework to show that both amino acid sequences and expression levels of ohnologs are under substantial selection, which may end the long-standing debate on ohnolog retention models.
Agency rescues competition for credit assignment among predictive cues from adverse learning conditions
Authors: Kang Mihwa , Reverte Ingrid , Volz Stephen , Kaufman Keith , Fevola Salvatore , Matarazzo Anna , Alhazmi Fahd H. , Marquez Inmaculada , Iordanova Mihaela D. , Esber Guillem R.
Published: February 2021

A fundamental assumption of learning theories is that the credit assigned to predictive cues is not simply determined by their probability of reinforcement, but by their ability to compete with other cues present during learning. This assumption has guided behavioral and neural science research for decades, and tremendous empirical and theoretical advances have been made identifying the mechanisms of cue competition. However, when learning conditions are not optimal (e.g., when training is massed), credit assignment is no longer competitive. This is a catastrophic failure of the learning system that exposes the individual’s vulnerability to form spurious associations in the real world. Here, we uncover that cue competition can be rescued when conditions are suboptimal provided that the individual has agency over the learning experience. Our findings reveal a new connection between agency over learning and credit assignment to cues, and open new avenues of investigation into the underlying mechanisms.
Dual mechanisms of opioid-induced respiratory depression in the inspiratory rhythm-generating network
Authors: Baertsch Nathan A , Bush Nicholas E , Burgraff Nicholas J , Ramirez Jan-Marino
Published: February 2021

The analgesic utility of opioid-based drugs is limited by the life-threatening risk of respiratory depression. Opioid-induced respiratory depression (OIRD), mediated by the μ-opioid receptor (MOR), is characterized by a pronounced decrease in the frequency and regularity of the inspiratory rhythm, which originates from the medullary preBötzinger Complex (preBӧtC). To unravel the cellular- and network-level consequences of MOR activation in the preBötC, MOR-expressing neurons were optogenetically identified and manipulated in transgenic micein vitroandin vivo. Based on these results, a model of OIRD was developedin silico. We conclude that hyperpolarization of MOR-expressing preBötC neurons alone does not phenocopy OIRD. Instead, the effects of MOR activation are twofold: 1) pre-inspiratory spiking is reduced and 2) excitatory synaptic transmission is suppressed, thereby disrupting network-driven rhythmogenesis. These dual mechanisms of opioid action act together to make the normally robust inspiratory-rhythm-generating network particularly prone to collapse when challenged with exogenous opioids.
A novel morphometric signature of brain alterations in type 2 diabetes: patterns of changed cortical gyrification
Authors: Crisóstomo Joana , Duarte João V. , Moreno Carolina , Gomes Leonor , Castelo-Branco Miguel
Published: February 2021

Type 2 diabetes is a chronic disease that creates atrophic signatures in the brain, including decreases of total and regional volume of grey matter, white matter, and cortical thickness. However, there is a lack of studies assessing cortical gyrification in type 2 diabetes. Changes in this emerging feature has been associated mainly with genetic legacy, but environmental factors may also play a role. Here, we investigated alterations of the gyrification index and classical morphometric measures in type 2 diabetes, a disease with complex etiology with both underlying genetic and more preponderant environmental factors.

In this cross-sectional study we analyzed brain anatomical magnetic resonance images of 86 participants with type 2 diabetes and 40 healthy control participants, to investigate structural alterations in type 2 diabetes, including whole-brain volumetric measures, local alterations of grey matter volume, cortical thickness and the gyrification index.

We found concordant significant decrements in total and regional grey matter volume, and cortical thickness. Surprisingly, the cortical gyrification index was found to be mainly increased in cortical sensory areas in type 2 diabetes. Moreover, it correlated with features of metabolic control. Our findings challenge the classical neurodevelopmental association of gyrification mostly with genetic determinants. While we found mainly increased gyrification in more genetically constrained sensory areas in type 2 diabetes, our correlation results concurrently suggest an influence of metabolic control in alterations of gyrification in type 2 diabetes. Further studies should address causal influences of genetic and/or environmental factors in patterns of cortical gyrification in type 2 diabetes.
MtrA regulation of essential peptidoglycan cleavage inMycobacterium tuberculosisduring infection
Authors: Peterson Eliza J. R. , Brooks Aaron N , Reiss David J. , Kaur Amardeep , Wu Wei-Ju , Morrison Robert , Srinivas Vivek , Turkarslan Serdar , Pan Min , Carter Warren , Arrieta-Ortiz Mario L. , Ruiz Rene A. , Bhatt Apoorva , Baliga Nitin S.
Published: February 2021

The success ofMycobacterium tuberculosis(Mtb) is largely due to its ability to withstand multiple stresses encountered in the host. Here, we present a data-driven model that captures the dynamic interplay of environmental cues and genome-encoded regulatory programs in Mtb. The model captures the genome-wide distribution ofcis-acting gene regulatory elements and the conditional influences of transcription factors at those elements to elicit environment-specific responses. Analysis of transcriptional responses that may be essential for Mtb to survive acidic stress within the maturing macrophage, identified regulatory control by the MtrAB two-component signal system. Using genome-wide transcriptomics as well as imaging studies, we have characterized the MtrAB circuit by tunable CRISPRi knockdown in both Mtb and the non-pathogenic organism,M. smegmatis(Msm). These experiments validated the essentiality of MtrA in Mtb, but not Msm. We identified that MtrA regulates multiple enzymes that cleave cell wall peptidoglycan and is required for efficient cell division. Moreover, our results suggest that peptidoglycan cleavage, regulated by MtrA, is necessary for Mtb to survive intracellular stress. Further, we present MtrA as an attractive drug target, as even weak repression ofmtrAresults in loss of Mtb viability and completely clears the bacteria with low-dose isoniazid or rifampicin treatment.
Visual object categorization in infancy
Authors: Spriet Céline , Abassi Etienne , Hochmann Jean-Rémy , Papeo Liuba
Published: February 2021

Humans make sense of the world by organizing things into categories. When and how does this process begin? We investigated whether real-world object categories that spontaneously emerge in the first months of life match categorical representations of objects in the human visual cortex. Taking infants’ looking times as a measure of similarity, we defined a representational space where each object was defined in relation to others of the same or different categories. This space was compared with hypothesis-based and fMRI-based models of visual-object categorization in the adults’ visual cortex. Analyses across different age groups revealed an incremental process with two milestones. Between 4 and 10 months, visual exploration guided by saliency gives way to an organization according to the animate-inanimate distinction. Between 10 and 19 months, a category spurt leads towards a mature organization. We propose that these changes underlie the coupling betweenseeingandthinkingin the developing mind.
A crosswalk to align the GSS and NIH grants databases based on university names
Authors: Pickett Christopher L.
Published: February 2021

Notable reports over the past dozen years have recommended the federal government and others improve data collection on the research workforce in the United States. The federal government already collects a wealth of data, but important datapoints, like the number of biomedical postdocs working in the U.S., for example, are still not well defined. Furthermore, of the data that are collected, differences in collection method and data naming conventions, like inconsistent naming of universities, hinders our ability to merge information across different datasets. Here I describe the creation of three macros meant to align the National Center for Science and Engineering Statistics’ Survey of Graduate Students and Postdoctorates in Science and Engineering (GSS) with NIH grants databases based on consolidating university names under a single name common to both databases. Aligning these databases will allow for a deeper understanding of how various federal and university policies affect the number trainees, grants, and funding at individual institutions.
Pathogenic tau accelerates aging-associated activation of transposable elements in the mouse central nervous system
Authors: Ramirez Paulino , Sun Wenyan , Zuniga Gabrielle , Thomas Elizabeth Ochoa , DeVos Sarah L. , Hyman Bradley , Chiu Gabriel , Roy Ethan R. , Cao Wei , Orr Miranda , Buggia-Prevot Virginie , Ray William J. , Frost Bess
Published: February 2021

Transposable elements comprise almost half of the mammalian genome. A growing body of evidence suggests that transposable element dysregulation accompanies brain aging and neurodegenerative disorders, and that transposable element activation is neurotoxic. Recent studies have identified links between pathogenic forms of tau, a protein that accumulates in Alzheimer disease and related tauopathies, and transposable element-induced neurotoxicity. Starting with transcriptomic analyses, we find that age- and tau-induced transposable element activation occurs in the mouse brain. Among transposable elements that are activated at the RNA level in the context of brain aging and tauopathy, we find that the endogenous retrovirus (ERV) class of retrotransposons is particularly enriched. We show that protein encoded byIntracisternal A-particle, a highly active mouse ERV, is elevated in brains of tau transgenic mice. We further demonstrate that brains of tau transgenic mice contain increased DNA copy number of transposable elements, raising the possibility that these elements actively retrotranspose in the context of tauopathy. Taken together, our study lays the groundwork for future mechanistic studies focused on transposable element regulation in the aging mouse brain and in mouse models of tauopathy, while providing support for therapeutic approaches targeting transposable element activation for Alzheimer disease and related tauopathies.
Self-contained and modular structured illumination microscope
Authors: Van den Eynde Robin , Vandenberg Wim , Hugelier Siewert , Bouwens Arno , Hofkens Johan , Müller Marcel , Dedecker Peter
Published: February 2021

We present a modular implementation of structured illumination microscopy (SIM) that is fast, largely self-contained and that can be added onto existing fluorescence microscopes. Our instrument, which we call HIT-SIM, can theoretically deliver well over 50 super-resolved images per second and is readily compatible with existing acquisition software packages. We provide a full technical package consisting of schematics, a list of components and an alignment scheme that provides detailed specifications and assembly instructions. We illustrate the performance of the instrument by imaging optically large samples containing sequence-specifically stained DNA fragments.
The type 2 asthma mediator IL-13 inhibits SARS-CoV-2 infection of bronchial epithelium
Authors: Bonser Luke R. , Eckalbar Walter L. , Rodriguez Lauren , Shen Jiangshan , Koh Kyung Duk , Zlock Lorna T. , Christenson Stephanie , Woodruff Prescott G. , Finkbeiner Walter E. , Erle David J.
Published: February 2021

Rationale

Asthma is associated with chronic changes in the airway epithelium, a key target of SARS-CoV-2. Many epithelial changes are driven by the type 2 cytokine IL-13, but the effects of IL-13 on SARS-CoV-2 infection are unknown.

Objectives

We sought to discover how IL-13 and other cytokines affect expression of genes encoding SARS-CoV-2-associated host proteins in human bronchial epithelial cells (HBECs) and determine whether IL-13 stimulation alters susceptibility to SARS-CoV-2 infection.

Methods

We used bulk and single cell RNA-seq to identify cytokine-induced changes in SARS-CoV-2-associated gene expression in HBECs. We related these to gene expression changes in airway epithelium from individuals with mild-moderate asthma and chronic obstructive pulmonary disease (COPD). We analyzed effects of IL-13 on SARS-CoV-2 infection of HBECs.

Measurements and Main Results

Transcripts encoding 332 of 342 (97%) SARS-CoV-2-associated proteins were detected in HBECs (≥1 RPM in 50% samples). 41 (12%) of these mRNAs were regulated by IL-13 (>1.5-fold change, FDR < 0.05). Many IL-13-regulated SARS-CoV-2-associated genes were also altered in type 2 high asthma and COPD. IL-13 pretreatment reduced viral RNA recovered from SARS-CoV-2 infected cells and decreased dsRNA, a marker of viral replication, to below the limit of detection in our assay. Mucus also inhibited viral infection.

Conclusions

IL-13 markedly reduces susceptibility of HBECs to SARS-CoV-2 infection through mechanisms that likely differ from those activated by type I interferons. Our findings may help explain reports of relatively low prevalence of asthma in patients diagnosed with COVID-19 and could lead to new strategies for reducing SARS-CoV-2 infection.
Capturing single-copy nuclear genes, organellar genomes, and nuclear ribosomal DNA from deep genome skimming data for plant phylogenetics: A case study in Vitaceae
Authors: Liu Bin-Bin , Ma Zhi-Yao , Ren Chen , Hodel Richard G.J. , Sun Miao , Liu Xiu-Qun , Liu Guang-Ning , Hong De-Yuan , Zimmer Elizabeth A. , Wen Jun
Published: February 2021

With the decreasing cost and availability of many newly developed bioinformatics pipelines, next-generation sequencing (NGS) has revolutionized plant systematics in recent years. Genome skimming has been widely used to obtain high-copy fractions of the genomes, including plastomes, mitochondrial DNA (mtDNA), and nuclear ribosomal DNA (nrDNA). In this study, through simulations, we evaluated optimal (minimum) sequencing depth and performance for recovering single-copy nuclear genes (SCNs) from genome skimming data, by subsampling genome resequencing data and generating 10 datasets with different sequencing coveragein silico. We tested the performance of the four datasets (plastome, nrDNA, mtDNA, and SCNs) obtained from genome skimming based on phylogenetic analyses of theVitisclade at the genus-level and Vitaceae at the family-level, respectively. Our results showed that optimal minimum sequencing depth for high-quality SCNs assembly via genome skimming was about 10× coverage. Without the steps of synthesizing baits and enrichment experiments, we showcase that deep genome skimming (DGS) is effective for capturing large datasets of SCNs, in addition to plastomes, mtDNA, and entire nrDNA repeats, and may serve as an economical alternative to the widely used target enrichment Hyb-Seq approach.
Efficient in vivo genome editing mediated by stem cells-derived extracellular vesicles carrying designer nucleases
Authors: Bobis-Wozowicz Sylwia , Kania Karolina , Nit Kinga , Blazowska Natalia , Kmiotek-Wasylewska Katarzyna , Paw Milena , Karnas Elzbieta , Szyposzynska Agnieszka , Tyszka-Czochara Malgorzata , Woznicka Olga , Boruczkowski Dariusz , Mussolino Claudio , Łabaj Paweł P. , Schambach Axel , Madeja Zbigniew , Cathomen Toni , Zuba-Surma Ewa K.
Published: February 2021

Precise genome editing using designer nucleases (DNs), such as zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) and the clustered regularly interspaced short palindromic repeat/Cas9 (CRISPR/Cas9) system, has become a method of choice in a variety of biological and biomedical applications in recent years. Notably, efficacy of these systems is currently under scrutiny in about 50 clinical trials. Although high DNs activity in various cell typesin vitrohas already been achieved, efficientin vivogenome editing remains a challenge. To solve this problem, we employed stem cells-derived extracellular vesicles (EVs) as carriers of DNs. We used umbilical cord-derived mesenchymal stem cells (UC-MSCs) and induced pluripotent stem cells (iPSCs) as EV-producer cells, since they are both applied in regenerative medicine. In our proof-of-concept studies, we achieved up to 50% of EGFP marker gene knockoutin vivousing EVs carrying either ZFN, TALEN or the CRISPR/Cas9 system, particularly in the liver. Importantly, we obtained almost 50% of modified alleles in the liver of the experimental animals, when targeting thePcsk9gene, whose overexpression is implicated in hypercholesterolemia. Taken together, our data provide strong evidence that stem cells-derived EVs constitute a robust tool in delivering DNsin vivo, which may be harnessed to clinical practice in the future.
The CCL2 Chemokine Promotes Early Seeding of the Latent HIV Reservoir
Authors: Packard Thomas A. , Schwarzer Roland , Herzig Eytan , Rao Deepashri , Luo Xiaoyu , Egedal Johanne H. , Hsiao Feng , Widera Marek , Hultquist Judd F. , Grimmett Zachary W. , Messer Ronald J. , Krogan Nevan J. , Deeks Steven G. , Roan Nadia R. , Dittmer Ulf , Hasenkrug Kim J. , Greene Warner C.
Published: February 2021

HIV infects long-lived CD4 memory T cells establishing a latent viral reservoir that necessitates lifelong anti-retroviral therapy (ART). How this reservoir is formed so swiftly remains unknown. We now show the innate inflammatory response to HIV infection results in CCL2 chemokine release, which can drive recruitment of cells expressing the CCR2 receptor including a subset of central memory CD4 T cells. Supporting a role for the CCL2/CCR2 axis in rapid reservoir formation, we find 1) treatment of humanized mice with anti-CCL2 antibodies during HIV infection decreases reservoir seeding and 2) CCR2/5+ cells from the blood of HIV-infected individuals on long term ART contain significantly more provirus than CCR2/5-negative memory or naïve cells. Together, these studies support a model where the host’s innate inflammatory CCL2 response to HIV infection recruits CCR2/5+ central memory CD4 T cells to zones of virus-associated inflammation likely contributing to rapid formation of the latent HIV reservoir.

GRAPHICAL ABSTRACT

Why is the latent HIV reservoir established so early following infection? An innate immune response occurs during acute infection that establishes a “zone of inflammation” (step 1). The CCL2 chemokine is produced in part through IFI16 sensing of HIV DNA in abortively infected cells. CCL2 promotes rapid recruitment of CCR2/5+ memory CD4 T cells (step 2). Many of these cells become productively infected (step 3) and a fraction become latently infected (step 4). Thus, HIV hijacks the host inflammatory response to rapidly establish the latent reservoir. In support of this model, we find HIV reservoir reduction in humanized mice treated with anti-CCL2 antibodies during early infection. Further, we find that CCR2/5+ CD4 T cells harbor a substantial fraction of detectable proviruses in the blood of HIV-infected individuals on long-term suppressive ART.

Abstract Figure
Ear wound healing in MRL/MpJ mice is associated with gut microbiome composition and is transferable to non-healer mice via microbiome transplantation
Authors: Velasco Cassandra , Dunn Christopher , Sturdy Cassandra , Izda Vladislav , Martin Jake , Rivas Alexander , McNaughton Jeffrey , Jeffries Matlock A.
Published: February 2021

Objective

Adult cartilage has limited repair capacity. MRL/MpJ mice, by contrast, are capable of spontaneously healing ear punctures. This study was undertaken to characterize microbiome differences between healer and nonhealer mice and to evaluate microbiome transplantation as a novel regenerative therapy.

Methods

We transplanted C57BL/6J mice with MRL/MpJ cecal contents in mice at weaning and as adults (n=57) and measured earhole closure 4 weeks after a 2.0mm punch and compared to vehicle-transplanted MRL and B6 (n=25) and B6-transplanted MRL (n=20) mice. Sex effects, timing of transplant relative to earpunch, and transgenerational heritability were evaluated. In a subset (n=58), cecal microbiomes were profiled by 16S sequencing and compared to earhole closure rates. Microbial metagenomes were imputed using PICRUSt.

Results

Transplantation of B6 mice with MRL microbiota, either in weanlings or adults, improved earhole closure rates. Transplantation prior to ear punch was associated with the greatest earhole closure. Offspring of transplanted mice healed better than controls. Several microbiome clades were correlated with healing, including Firmicutes, Lactobacillales, and Verrucomicrobia. Gram-negative organisms were reduced. Females of all groups tended to heal better than males, female microbiota resembled MRL mice.

Conclusion

In this study, we found an association between the microbiome and tissue regeneration in MRL mice and demonstrate that this trait can be transferred to nonhealer mice via microbiome transplantation. We identified several microbiome clades associated with healing. Future studies should evaluate the mechanisms underlying these findings and confirm our results in murine OA.
Misinformation, Perceptions Towards COVID-19 and Willingness to be Vaccinated: A Population-Based Survey in Yemen
Authors: Bitar Ahmad Naoras , Zawiah Mohammed , Al-Ashwal Fahmi Y. , Kubas Mohammed , Saeed Ramzi Mukred , Abduljabbar Rami , Jaber Ammar Ali Saleh , Sulaiman Syed Azhar Syed , Khan Amer Hayat
Published: February 2021

Background

Since the beginning of the COVID-19 outbreak, many pharmaceutical companies were racing to develop a safe and effective COVID-19 vaccine. Simultaneously, rumors and misinformation about COVID-19 were and still widely spreading. Therefore, this study aimed to investigate the prevalence of COVID-19 misinformation among the Yemeni population and its association with vaccine acceptance and perceptions.

Methods

A cross-sectional online survey was conducted in four major cities in Yemen. The constructed questionnaire consisted of four main sections (sociodemographic data, misinformation, perceptions (perceived susceptibility, severity and worry), and vaccination acceptance evaluation). Subject recruitment and data collection were conducted online utilizing social websites and using the snowball sampling technique. Descriptive and inferential analyses were performed using SPSS version 27.

Results

The total number of respondents was 484. Over 60% of them were male and had a university education, more than half had less than 100$ monthly income and were Khat chewers, while only 18% were smokers. Misinformation prevalence ranged from 8.9% to 38.9%, depending on the statement being asked. Men, university education, higher income, employment, and living in urban areas were associated with a lower misinformation level (p<0.05). Statistically significant association (p<0.05) between university education, living in urban areas, and being employed with perceived susceptibility were observed. The acceptance rate was 61.2% for free vaccines, but it decreased to 43% if they had to purchase it. Females, respondents with lower monthly income, and those who believed that pharmaceutical companies made the virus for financial gains were more likely to reject the vaccination (p<0.05).

Conclusion

The study revealed that the acceptance rate to take a vaccine was suboptimal and significantly affected by gender, misinformation, cost, and income. Furthermore, being female, Nonuniversity educated, low-income, and living in rural areas were associated with higher susceptibility to misinformation about COVID-19. These findings show a clear link between misinformation susceptibility and willingness to vaccinate. Focused awareness campaigns to decrease misinformation and emphasize the vaccination’s safety and efficacy might be fundamental before initiating any mass vaccination in Yemen.
A systematic analysis of metabolic pathways in the human gut microbiota
Authors: Andreu Victòria Pascal , Augustijn Hannah E. , Chen Lianmin , Zhernakova Alexandra , Fu Jingyuan , Fischbach Michael A. , Dodd Dylan , Medema Marnix H.
Published: February 2021

The gut microbiota produce hundreds of small molecules, many of which modulate host physiology. Although efforts have been made to identify biosynthetic genes for secondary metabolites, the chemical output of the gut microbiome consists predominantly of primary metabolites. Here, we systematically profile primary metabolic genes from the gut microbiome, identifying 19,885 gene clusters in 4,240 high-quality microbial genomes. We find marked differences in pathway distribution among phyla, reflecting distinct strategies for energy capture. These data explain taxonomic differences in short-chain fatty acid production and suggest a characteristic metabolic niche for each taxon. Analysis of 1,135 subjects from a Dutch population-based cohort shows that the level of 14 microbiome-derived metabolites in plasma is almost completely uncorrelated with the metagenomic abundance of the corresponding biosynthetic genes, revealing a crucial role for pathway-specific gene regulation and metabolite flux. This work is a starting point for understanding differences in how bacterial taxa contribute to the chemistry of the microbiome.
Decoupling the bridge helix of Cas12a results in a reduced trimming activity and impaired conformational transitions
Authors: Wörle Elisabeth , Jakob Leonhard , Schmidbauer Andreas , Zinner Gabriel , Grohmann Dina
Published: February 2021

The widespread and versatile prokaryotic CRISPR-Cas systems (clustered regularly interspaced short palindromic repeats and associated Cas proteins) constitute powerful weapons against foreign nucleic acids. Recently, the single-effector nuclease Cas12a that belongs to the type V CRISPR-Cas system was added to the Cas enzymes repertoire employed for gene editing purposes. Cas12a is a bilobal enzyme composed of the REC and Nuc lobe connected by a central structural element, the so-called bridge helix (BH). We generated BH mutants and integrated biochemical and single-molecule FRET (smFRET) studies to elucidate the role of the BH for the enzymatic activity and conformational flexibility ofFrancisella novicidaCas12a. We demonstrate that the BH impacts the trimming activity of Cas12a resulting in Cas12a variants with improved cleavage accuracy. Single-molecule FRET measurements reveal the hitherto unknown open and closed state of apo Cas12a. BH mutants preferentially adopt the open state. Transition to the closed state of the Cas12a-crRNA complex is inefficient in BH mutants but the semi-closed state of the ternary complex can be adopted even if the BH is deleted in its entirety. Taken together, these insights reveal that the BH is a structural element that influences the catalytic activity and impacts conformational transitions of FnCas12a.
Screening of different cytotoxicity methods for the assessment of ENDS toxicity relative tobacco cigarettes
Authors: Caruso Massimo , Emma Rosalia , Rust Sonja , Distefano Alfio , Carota Giuseppe , Pulvirenti Roberta , Polosa Riccardo , Volti Giovanni Li
Published: February 2021

Electronic Nicotine Delivery Systems (ENDS), i.e., electronic cigarettes (e-cigs) and Tobacco Heating Products (THPs), are rapidly growing in popularity. The marketing of these products is regulated by specific rules in the European Union and in the US, which permit their legal sales. Nonetheless, comprehensive quality and safety requirements for regulatory purposes are still under development. Cytotoxicity studies are an important initial step in appraising the potential toxicity of ENDS. The aim of the present study was to screen a battery of different in vitro cytotoxicity methods for the assessment of toxicity induced by ENDS. We evaluated different cytotoxicity assays, including neutral red uptake (NRU), 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT), Annexin V apoptosis, High Content Screening (HCS) assays and Real Time Cell Analysis (RTCA), to compare two e-cigs (Vype ePen 3 and Vype eStick Maxx) and two THPs (IQOS and GLO™) with the 1R6F reference tobacco cigarette. Human bronchial epithelial cells (H292) were exposed to 1R6F smoke (5 puffs by HCI regime), ePen vapor (10 puffs by modified HCI regime), eStick vapor (25 puffs by CRM81 regime), IQOS vapor (7 puffs by HCI regime) and GLO vapor (8 puffs by HCI regime) at air-liquid interface. All tests showed reduced cell viability following 1R6F smoke exposure and slight or no reduction with ENDS at 24 hours compared to controls. In addition, Annexin V and RTCA exhibited a further significant reduction in cell viability following 1R6F exposure compared with other assays. Furthermore, Annexin V allowed to discriminate viable cells from those in early/late apoptosis. Finally, RTCA and HCS being time-resolved analyses allowed also to determine the kinetic dependency parameter for toxicity of smoke/vapor chemicals on cell viability. In conclusion, NRU assay may be considered a suitable test, especially when combined with a time-resolved test, for assessing the kinetic of cytotoxicity induced by these products.
Pyroptosis of syncytia formed by fusion of SARS-CoV-2 Spike and ACE2 expressing cells
Authors: Ma Huabin , Zhu Zhoujie , Lin Huaipeng , Wang Shanshan , Zhang Peipei , Li Yanguo , Li Long , Wang Jinling , Zhao Yufen , Han Jiahuai
Published: February 2021

SARS-Cov-2 infected cells fused with the ACE2-positive neighboring cells forming syncytia. However, the effect of syncytia in disease development is largely unknown. We established anin vitrocell-cell fusion system and used it to mimic the fusion of SARS-CoV-2 infected cells with ACE2-expressing cells to form syncytia. We found that Caspase-9 was activated after syncytia formation, and Caspase-3/7 was activated downstream of Caspase-9, but it triggered GSDME-dependent pyroptosis rather than apoptosis. What is more, single cell RNA-sequencing data showed that both ACE2 and GSDME were expression in alveolar type 2 cells in human lung. We propose that pyroptosis is the fate of syncytia formed by SARS-CoV-2 infected host cells and ACE2-positive cells, which indicated that lytic death of syncytia may contribute to the excessive inflammatory responses in severe COVID-19 patients.
Endoribonuclease activity of XRN-2 is critical for RNA metabolism and survival ofCaenorhabditis elegans
Authors: Sardar Moumita , Samajdar Aniruddha , Wani Adil R , Chatterjee Saibal
Published: February 2021

microRNAs (miRNAs) are known to regulate a vast majority of the eukaryotic genes by post-transcriptional means, and multiple nucleases play critical roles in the biogenesis and turnover of these regulators. A number of studies have indicated that turnover is important for determining the abundance of miRNAs, and thus, in turn govern their functionality. Recent research inCaenorhabditis eleganshas revealed an ATP-independent endoribonuclease activity of the ‘miRNase’-XRN-2. Here, we report the characterization of this new enzymatic activity of the fundamentally important XRN-2, and show that it is critical for miRNA turnover and survival of quiescent dauer worms. The dual enzymatic activity of XRN-2 capacitates the mechanism of miRNA turnover to be dynamic, which might confer adaptive advantage to the organism. In continuously growing worms, this new enzymatic activity does not act on miRNAs, but it is important for the generation of mature ribosomal RNAs, which in turn is critical for translation, and thus indispensable for the survival of worms.