bluuebunny/crossref_metadata_2025 huggingface dataset:
Tumour neoantigen heterogeneity thresholds provide a time window for combination immunotherapy
Authors: Aguadé-Gorgorió Guim , Solé Ricard
Published: October 2020

Following the advent of cancer immunotherapy, increasing insight has been gained on the role of mutational load and neoantigens as key ingredients in T cell recognition of malignancies. However, not all highly mutational tumours react to immune therapies, and initial success is often followed by eventual relapse. Heterogeneity in the neoantigen landscape of a tumour might be key in the failure of immune surveillance. In this work, we present a mathematical framework to describe how neoantigen distributions shape the immune response. The model predicts the existence of an antigen diversity threshold level beyond which T cells fail at controlling heterogeneous tumours. Incorporating this diversity marker adds predictive value to antigen load for two cohorts of anti-CTLA-4 treated melanoma patients. Furthermore, our analytical approach indicates rapid increases in epitope heterogeneity in early malignancy growth following immune escape. We propose a combination therapy scheme that takes advantage of preexisting resistance to a targeted agent. The model indicates that the selective sweep for a resistant subclone reduces neoantigen heterogeneity, and we postulate the existence of a time window before tumour relapse where checkpoint blockade immunotherapy can become more effective.
Credibility of preprints: an interdisciplinary survey of researchers
Authors: Soderberg Courtney K. , Errington Timothy M. , Nosek Brian A.
Published: October 2020

Preprints increase accessibility and can speed scholarly communication if researchers view them as credible enough to read and use. Preprint services do not provide the heuristic cues of a journal's reputation, selection, and peer-review processes that, regardless of their flaws, are often used as a guide for deciding what to read. We conducted a survey of 3759 researchers across a wide range of disciplines to determine the importance of different cues for assessing the credibility of individual preprints and preprint services. We found that cues related to information about open science content and independent verification of author claims were rated as highly important for judging preprint credibility, and peer views and author information were rated as less important. As of early 2020, very few preprint services display any of the most important cues. By adding such cues, services may be able to help researchers better assess the credibility of preprints, enabling scholars to more confidently use preprints, thereby accelerating scientific communication and discovery.
Analysis of complete Campylobacter concisus genomes identifies genomospecies features, secretion systems and novel plasmids and their association with severe ulcerative colitis
Authors: Liu Fang , Chen Siying , Luu Laurence Don Wai , Lee Seul A. , Tay Alfred Chin Yen , Wu Ruochen , Riordan Stephen M. , Lan Ruiting , Liu Lu , Zhang Li
Published: October 2020

Campylobacter concisus

is an emerging enteric pathogen that is associated with several gastrointestinal diseases, such as inflammatory bowel disease (IBD), which includes Crohn’s disease (CD) and ulcerative colitis (UC). Currently, only three complete

C. concisus

genomes are available and more complete

C. concisus

genomes are needed in order to better understand the genomic features and pathogenicity of this emerging pathogen. DNA extracted from 22

C

.

concisus

strains were subjected to Oxford Nanopore genome sequencing. Complete genome assembly was performed using Nanopore genome data in combination with previously reported short-read Illumina data. Genome features of complete

C. concisus

genomes were analysed using bioinformatic tools. The enteric disease associations of

C. concisus

plasmids were examined using 239

C

.

concisus

strains and confirmed using PCRs. Proteomic analysis was used to examine T6SS secreted proteins. We successfully obtained 13 complete

C. concisus

genomes in this study. Analysis of 16 complete

C. concisus

genomes (3 from public databases) identified multiple novel plasmids. pSma1 plasmid was found to be associated with severe UC. Sec-SRP, Tat and T6SS were found to be the main secretion systems in

C. concisus

and proteomic data showed a functional T6SS despite the lack of ClpV. T4SS was found in 25% of complete

C. concisus

genomes. This study also found that GS2 strains had larger genomes and higher GC content than GS1 strains and more often had plasmids. In conclusion, this study provides fundamental genomic data for understanding

C. concisus

plasmids, genomospecies features, evolution, secretion systems and pathogenicity.
Quantifying SARS-CoV-2 spread in Switzerland based on genomic sequencing data
Authors: Nadeau Sarah , Beckmann Christiane , Topolsky Ivan , Vaughan Timothy , Hodcroft Emma , Schär Tobias , Nissen Ina , Santacroce Natascha , Burcklen Elodie , Ferreira Pedro , Jablonski Kim Philipp , Posada-Céspedes Susana , Capece Vincenzo , Seidel Sophie , de Souza Noemi Santamaria , Martinez-Gomez Julia M. , Cheng Phil , Bosshard Philipp P. , Levesque Mitchell P. , Kufner Verena , Schmutz Stefan , Zaheri Maryam , Huber Michael , Trkola Alexandra , Cordey Samuel , Laubscher Florian , Gonçalves Ana Rita , Leuzinger Karoline , Stange Madlen , Mari Alfredo , Roloff Tim , Seth-Smith Helena , Hirsch Hans H. , Egli Adrian , Redondo Maurice , Kobel Olivier , Noppen Christoph , Beerenwinkel Niko , Neher Richard A. , Beisel Christian , Stadler Tanja
Published: October 2020

Pathogen genomes provide insights into their evolution and epidemic spread. We sequenced 1,439 SARS-CoV-2 genomes from Switzerland, representing 3-7% of all confirmed cases per week. Using these data, we demonstrate that no one lineage became dominant, pointing against evolution towards general lower virulence. On an epidemiological level, we report no evidence of cryptic transmission before the first confirmed case. We find many early viral introductions from Germany, France, and Italy and many recent introductions from Germany and France. Over the summer, we quantify the number of non-traceable infections stemming from introductions, quantify the effective reproductive number, and estimate the degree of undersampling. Our framework can be applied to quantify evolution and epidemiology in other locations or for other pathogens based on genomic data.

One Sentence Summary

We quantify SARS-CoV-2 spread in Switzerland based on genome sequences from our nation-wide sequencing effort.
A universal framework for detecting cis-regulatory diversity in DNA regulatory regions
Authors: Biswas Anushua , Narlikar Leelavati
Published: October 2020

High-throughput sequencing-based assays measure different biochemical activities pertaining to gene regulation, genome-wide. These activities include protein-DNA binding, enhancer-activity, open chromatin, and more. A major goal is to understand underlying sequence components, or motifs, that can explain the measured activity. It is usually not one motif, but a combination of motifs bound by cooperatively acting proteins that confers activity to such regions. Furthermore, although having a single type of activity, the regions can still be diverse, governed by different combinations of proteins/motifs. Current approaches do not take into account this issue of combinatorial diversity. We present a new statistical frameworkcisDiversity, which models regions as diverse modules characterized by combinations of motifs, while simultaneously learning the motifs themselves. We show that ChIP-seq data for the CTCF protein in fly contains diverse sequence structures, with most direct CTCF-binding sites situated far from promoters, giving insights into its co-factors and potential role in looping. Human CTCF-bound regions, on the other hand, have a different architecture. BecausecisDiversitydoes not rely on knowledge of motifs, modules, cell-type, or organism, it is general enough to be applied to regions reported by most high-throughput assays. Indeed, enhancer predictions resulting from different assays—GRO-cap, STARR-seq, and those measuring chromatin structure—show distinct modules and combinations of TF binding sites, some specific to the assay. No module occurs universally in all enhancer-assays. Finally, analysis of accessible chromatin suggests that regions open in one cell-state encode information about future states, with certain modules staying open and others closing down later. The code is freely available athttps://github.com/NarlikarLab/cisDIVERSITY.
Harnessing multivariate, penalized regression methods for genomic prediction and QTL detection to cope with climate change affecting grapevine
Authors: Brault Charlotte , Doligez Agnès , le Cunff Loïc , Coupel-Ledru Aude , Simonneau Thierry , Chiquet Julien , This Patrice , Flutre Timothée
Published: October 2020

Viticulture has to cope with climate change and decrease pesticide inputs, while maintaining yield and wine quality. Breeding is a potential key to meet this challenge, and genomic prediction is a promising tool to accelerate breeding programs, multivariate methods being potentially more accurate than univariate ones. Moreover, some prediction methods also provide marker selection, thus allowing quantitative trait loci (QTLs) detection and allowing the identification of positional candidate genes. We applied several methods, interval mapping as well as univariate and multivariate penalized regression, in a bi-parental grapevine progeny, in order to compare their ability to predict genotypic values and detect QTLs. We used a new denser genetic map, simulated two traits under four QTL configurations, and re-analyzed 14 traits measured in semi-controlled conditions under different watering conditions. Using simulations, we recommend the penalized regression method Elastic Net (EN) as a default for genomic prediction, and controlling the marginal False Discovery Rate on EN selected markers to prioritize the QTLs. Indeed, penalized methods were more powerful than interval mapping for QTL detection across various genetic architectures. Multivariate prediction did not perform better than its univariate counterpart, despite strong genetic correlation between traits. Using experimental data, penalized regression methods proved as very efficient for intra-population prediction whatever the genetic architecture of the trait, with accuracies reaching 0.68. These methods applied on the denser map found new QTLs controlling traits linked to drought tolerance and provided relevant candidate genes. These methods can be applied to other traits and species.
Tumorigenic epithelial clusters are less sensitive to moderate osmotic stresses due to low amounts of junctional E-cadherin
Authors: Mohammed Danahe , Chan Park Young , Fredberg Jeffrey J. , Weitz David A.
Published: October 2020

The migration of tumorigenic epithelial cells is a critical step for metastatic breast cancer progression. Although the role of the extracellular matrix in breast cancer cell migration has been extensively described, the effect of osmotic stress on the migration of tumor breast epithelial cohorts remains unclear. Most of our understanding on the effect of osmotic stresses on cell migration comes from studies at the level of the single cell in isolation and does not take into account cell-cell interactions. Here, we study the impact of moderate osmotic stress on the migration of epithelial clusters composed of either non-tumorigenic or tumorigenic epithelial cells. We observe a decrease in migration distance and speed for non-tumorigenic epithelial cells but not for tumorigenic ones. To explain these differences, we investigate how osmotic stress impacts the mechanical properties of cell clusters and affects cell volumes. After application of osmotic stress renal epithelial cells become stiffer whereas non-tumorigenic and tumorigenic breast epithelial cells do not. In addition, tumorigenic cells are shown to be less sensitive to osmotic stress than non-tumorigenic cells, and this difference is associated with lower levels of E-cadherin expression. Using EGTA treatments, we confirm that the establishment of cell-cell adhesive interactions is a key component of the behavior of epithelial clusters in response to osmotic stress. This study provides evidence on the low sensitivity of tumorigenic epithelial clusters to moderate osmotic stress and highlights the importance of cadherin-based junctions in response to osmotic stress.
Poxviruses capture host genes by LINE-1 retrotransposition
Authors: Fixsen Sarah M. , Cone Kelsey R. , Goldstein Stephen A. , Sasani Thomas A. , Quinlan Aaron R. , Rothenburg Stefan , Elde Nels C.
Published: October 2020

Horizontal gene transfer (HGT) provides a major source of genetic variation. Many viruses, including poxviruses, encode genes with crucial functions directly gained by gene transfer from hosts. The mechanism of transfer to poxvirus genomes is unknown. Using genome analysis and experimental screens of infected cells, we discovered a central role for Long Interspersed Nuclear Element-1 (LINE-1) retrotransposition in HGT to virus genomes. The process recapitulates processed pseudogene generation, but with host messenger RNA directed into virus genomes. Intriguingly, hallmark features of retrotransposition appear to favor virus adaption through rapid duplication of captured host genes on arrival. Our study reveals a previously unrecognized conduit of genetic traffic with fundamental implications for the evolution of many virus classes and their hosts.

Active selfish genetic elements in infected cells aid virus adaptation by catalyzing transfer of host genes to virus genomes.
Optimal COVID-19 quarantine and testing strategies
Authors: Wells Chad R. , Townsend Jeffrey P. , Pandey Abhishek , Moghadas Seyed M. , Krieger Gary , Singer Burton , McDonald Robert H. , Fitzpatrick Meagan C. , Galvani Alison P.
Published: October 2020

As economic woes of the COVID-19 pandemic deepen, strategies are being formulated to avoid the need for prolonged stay-at-home orders, while implementing risk-based quarantine, testing, contact tracing and surveillance protocols. Given limited resources and the significant economic, public health, and operational challenges of the current 14-day quarantine recommendation, it is vital to understand if shorter but equally effective quarantine and testing strategies can be deployed. To quantify the probability of post-quarantine transmission upon isolation of a positive test, we developed a mathematical model in which we varied quarantine duration and the timing of molecular tests for three scenarios of entry into quarantine. Specifically, we consider travel quarantine, quarantine of traced contacts with an unknown time if infection, and quarantine of cases with a known time of exposure. With a one-day delay between test and result, we found that testing on exit (or entry and exit) can reduce the duration of a 14-day quarantine by 50%, while testing on entry shortened quarantine by at most one day. Testing on exit more effectively reduces post-quarantine transmission than testing upon entry. Furthermore, we identified the optimal testing date within quarantines of varying duration, finding that testing on exit was most effective for quarantines lasting up to seven days. As a real-world validation of these principles, we analyzed the results of 4,040 SARS CoV-2 RT-PCR tests administered to offshore oil rig employees. Among the 47 positives obtained with a testing on entry and exit strategy, 16 cases that previously tested negative at entry were identified, with no further cases detected among employees following quarantine exit. Moreover, this strategy successfully prevented an expected nine offshore transmission events stemming from cases who had tested negative on the entry test, each one a serious concern for initiating rapid spread and a disabling outbreak in the close quarters of an offshore rig. This successful outcome highlights that appropriately timed testing can make shorter quarantines more effective, thereby minimizing economic impacts, disruptions to operational integrity, and COVID-related public health risks.
Modelling trachoma post 2020: Opportunities for mitigating the impact of COVID-19 and accelerating progress towards elimination
Authors: Borlase Anna , Blumberg Seth , Callahan E Kelly , Deiner Michael S , Nash Scott D , Porco Travis C , Solomon Anthony W , Lietman Thomas M , Prada Joaquin M , Hollingsworth T. Dèirdre
Published: October 2020

Background

The COVID-19 pandemic has disrupted planned annual antibiotic mass drug administration (MDA) activities which have formed the cornerstone of the largely successful global efforts to eliminate trachoma as a public health problem.

Methods

Using a mathematical model we investigate the impact of interruption to MDA in trachoma-endemic settings. We evaluate potential measures to mitigate this impact and consider alternative strategies for accelerating progress in those areas where the trachoma elimination targets may not be achievable otherwise.

Results

We demonstrate that for districts which were hyperendemic at baseline, or where the trachoma elimination thresholds have not already been achieved after 3 rounds of MDA, the interruption to planned MDA could lead to a delay greater than the duration of interruption. We also show that an additional round of MDA in the year following MDA resumption could effectively mitigate this delay. For districts where probability of elimination under annual MDA was already very low, we demonstrate that more intensive MDA schedules are needed to achieve agreed targets.

Conclusion

Through appropriate use of additional MDA, the impact of COVID-19 in terms of delay to reaching trachoma elimination targets can be effectively mitigated. Additionally, more frequent MDA may accelerate progress towards 2030 goals.
Evaluation of the Abbott Architect, Roche Elecsys and Virtus S1 SARS-CoV-2 antibody tests in community-managed COVID-19 cases
Authors: Johnston Sebastian L. , McKay Paul F , Kebadze Tatiana , Hu Kai , Samnuan Karnyart , Aniscenko Juliya , Cameron Aoife , Patel Neeta , Randell Paul , Shattock Robin J , Edwards Michael R
Published: October 2020

Background

Antibody testing can help define how protective immunity to SARS-CoV-2 is and how long this immunity lasts. Many antibody tests have been evaluated in hospitalised rather than community based COVID-19 cases. Virtus Respiratory Research Ltd (Virtus) has developed its own quantitative IgM and IgG SARS CoV-2 antibody assay. We report its validation and performance characteristics and compare its performance with the Abbott Architect and Roche Elecsys assays in community COVID cases.

Methods

We developed a quantitative antibody test to detect IgM and IgG to the SARS-CoV-2 S1 spike protein (the Virtus test) and validated this test in 107 “true positive” sera from 106 community-managed and 1 hospitalised COVID-19 cases and 208 “true negative” serum samples. We validated the Virtus test against a neutralising antibody test. We determined sensitivities of the Abbott test in the 107 true positive samples and the Roche test in a subset of 75 true positive samples.

Results

The Virtus quantitative test was positive in 93 of 107 (87%) community cases of COVID-19 and both IgM and IgG levels correlated strongly with neutralising antibody titres (r=0.75 for IgM, r=0.71 for IgG, P<0.0001 for both antibodies). The specificity of the Virtus test was 98.6% for low level antibody positives, 99.5% for moderate positives and 100% for high or very high positives. The Abbott test had a sensitivity of 68%. In the 75 sample subset, the Virtus test was positive in 91%, the Roche test in 69%.

Conclusions

The Abbott and Roche tests had sensitives of 68% and 69% respectively in this community set of COVID-19 sera, while the Virtus test had sensitivities of 87% and 91% in the same sample sets. The strong positive correlation with virus neutralization suggests a positive Virtus quantitative antibody test is likely predictive of protective against recurrent COVID-19.

Funding

The development of the Virtus test and sample testing with all antibody tests was funded by Virtus Respiratory Research Ltd. The research studies providing 111 of the 208 of the “true negative” samples was supported by MRC Grant numbers MR/M025330/1 and G1100238 and by the National Institute of Health Research (NIHR) Imperial Biomedical Research Centre (BRC), SLJ is a NIHR Emeritus Senior Investigator and is funded in part by European Research Council Advanced Grant 788575 and the Asthma UK Clinical Chair (grant CH11SJ). The views expressed are those of the author(s) and not necessarily those of the NIHR or the Department of Health and Social Care.
The neural circuitry underlying the “rhythm effect” in stuttering
Authors: Frankford Saul A. , Heller Murray Elizabeth S. , Masapollo Matthew , Cai Shanqing , Tourville Jason A. , Nieto-Castañón Alfonso , Guenther Frank H.
Published: October 2020

Purpose

Stuttering is characterized by intermittent speech disfluencies which are dramatically reduced when speakers synchronize their speech with a steady beat. The goal of this study was to characterize the neural underpinnings of this phenomenon using functional magnetic resonance imaging.

Method

Data were collected from 17 adults who stutter and 17 adults who do not stutter while they read sentences aloud either in a normal, self-paced fashion or paced by the beat of a series of isochronous tones (“rhythmic”). Task activation and task-based functional connectivity analyses were carried out to compare neural responses between speaking conditions and groups.

Results

Adults who stutter produced fewer disfluent trials in the rhythmic condition than in the normal condition. While adults who do not stutter had greater activation in the rhythmic condition compared to the normal condition in regions associated with speech planning, auditory feedback control, and timing perception, adults who stutter did not have any significant changes. However, adults who stutter demonstrated increased functional connectivity between bilateral inferior cerebellum and bilateral orbitofrontal cortex as well as increased connectivity among cerebellar regions during rhythmic speech as compared to normal speech.

Conclusion

Modulation of connectivity in the cerebellum and prefrontal cortex during rhythmic speech suggests that this fluency-inducing technique activates a compensatory timing system in the cerebellum and potentially modulates top-down motor control and attentional systems. These findings corroborate previous work associating the cerebellum with fluency in adults who stutter and indicate that the cerebellum may be targeted to enhance future therapeutic interventions.
Epitranscriptomic editing of the RNA N6-methyladenosine modification by dCasRx conjugated methyltransferase and demethylase
Authors: Xia Zhen , Tang Min , Zhang Hongyan , Gimple Ryan C. , Prager Briana C. , Tang Hongzhen , Sun Chongran , Liu Fuyi , Lin Peng , Mei Yutang , Du Ruoxin , Rich Jeremy N. , Xie Qi
Published: October 2020

N6-methyladenosine (m6A) is the most common modification on endogenous RNA transcripts in mammalian cells. Currently, the lack of precise single-nucleotide RNA modification tools makes it challenging to understand the relationship between site-specific RNA methylation and the corresponding phenotypic outcomes. Here, we developed a bidirectional dCasRx epitranscriptome editing platform composed of a nucleus-localized dCasRx conjugated with either a methyltransferase, METTL3, or a demethylase, ALKBH5, to manipulate methylation events at targeted m6A sites in HEK293T and glioma stem cells. This platform specifically and efficiently edited m6A modifications at targeted sites, modulating both gene expression and cell proliferation. We then employed the dCasRx epitranscriptomic editor to further elucidate the molecular function of m6A-binding proteins YTH (DF1, DF2, DF3) family and found that the YTH paralogs act together to mediate RNA degradation. These findings collectively demonstrate that the dCasRx epitranscriptome perturbation platform reported in this study can be employed as site-specific m6A editors for delineating the functional roles of individual m6A modifications in the mammalian epitranscriptome.
BrainGENIE: The Brain Gene Expression and Network Imputation Engine
Authors: Hess Jonathan L. , Quinn Thomas P. , Zhang Chunling , Hearn Gentry C. , Chen Samuel ,   Neuropsychiatric Consortium for Analysis and Sharing of Transcriptomes, Kong Sek Won , Cairns Murray J. , Tsuang Ming T. , Faraone Stephen V. , Glatt Stephen J.
Published: October 2020

In vivoexperimental analysis of human brain tissue poses substantial challenges and ethical concerns. We developed a novel method called the Brain Gene Expression and Network Imputation Engine (BrainGENIE) that uses peripheral-blood transcriptomes to predict brain-tissue-specific gene-expression levels.BrainGENIEreliably predicted brain-tissue-specific expression levels for 1,733 – 11,569 genes (false-discovery rate-adjustedp<0.05), including many transcripts that cannot be predicted reliably by a transcriptome imputation method such asPrediXcan. We tested the generalizability ofBrainGENIEin external within-individual data fromex vivoperipheral blood andpostmortembrain samples from the Religious Orders Study and Memory and Aging Project, wherein we validated 39% of predicted gene expression levels as concordant with observed expression levels in dorsolateral prefrontal cortex and 23% in caudate.BrainGENIErecapitulated diagnosis-related gene expression changes in brain better than direct correlations from blood and predictions fromPrediXcan. BrainGENIEcomplements and, in some ways, outperforms existing transcriptome-imputation tools, providing biologically meaningful predictions and opening new research avenues.
Negative durotaxis: cell movement toward softer environments
Authors: Isomursu Aleksi , Park Keun-Young , Hou Jay , Cheng Bo , Shamsan Ghaidan , Fuller Benjamin , Kasim Jesse , Mahmoodi M. Mohsen , Lu Tian Jian , Genin Guy M. , Xu Feng , Lin Min , Distefano Mark , Ivaska Johanna , Odde David J.
Published: October 2020

Durotaxis – the ability of cells to sense and migrate along stiffness gradients – is important for embryonic development and has been implicated in pathologies including fibrosis and cancer. Although cellular processes can sometimes turn toward softer environments, durotaxis at the level of cells has thus far been observed exclusively as migration from soft to stiff regions. The molecular basis of durotaxis, especially the factors that contribute to different durotactic behaviors in various cell types, are still inadequately understood. With the recent discovery of ‘optimal stiffness’, where cells generate maximal traction forces on substrates in an intermediate stiffness range, we hypothesized that some migratory cells may be capable of moving away from stiff environments and toward matrix on which they can generate more traction. Combining hydrogel-based stiffness gradients, live-cell imaging, genetic manipulations, and computational modeling, we found that cells move preferentially toward their stiffness optimum for maximal force transmission. Importantly, we directly observed biased migration toward softer environments, i.e. ‘negative durotaxis’, in human glioblastoma cells. This directional migration did not coincide with changes in FAK, ERK or YAP signaling, or with altered actomyosin contractility. Instead, integrin-mediated adhesion and motor-clutch dynamics alone are sufficient to generate asymmetric traction to drive both positive and negative durotaxis. We verified this mechanistically by applying a motor-clutch-based model to explain negative durotaxis in the glioblastoma cells and in neurites, and experimentally by switching breast cancer cells from positive to negative durotaxis via talin downregulation. Our results identify the likely molecular mechanisms of durotaxis, with a cell’s contractile and adhesive machinery dictating its capacity to exert traction on mechanically distinct substrates, directing cell migration.
Phytochemical screening ofColocasia giganteaandColocasia affinis(Family: Araceae) using1H-NMR and13C-NMR techniques
Authors: Alam Safaet , Haque Mohammad Rashedul
Published: October 2020

Colocasia affinisandColocasia giganteaare two of commonly found species underColocasiagenus. Folkloric use of these plants ascertains their ethnopharmacological importance and these plants are eaten as vegetables in several regions all around the world whileColocasia giganteahas planted as an ornamental plant too. Phytochemical screening of dichloromethane fractions of these plants using several separation techniques along followed by1H-NMR and13C-NMR techniques provide flavonoids and some other phyto compounds. However, in total 7 compounds were isolated from these plants i.e. penduletin (1), 7,8 -(3”,3”-dimethyl-pyrano)-4’-hydroxy flavonol (2), mixture of 7,8 -(3’’,3’’-dimethyl-pyrano)-4’-hydroxy flavonol fromC. affinisand mixture of α-amyrin and β-amyrin (3), penduletin (5), monoglyceride of stearic acid (6) fromC. gigantea.
Differentiation of Human induced Pluripotent Stem Cells to Authentic Macrophages using Fully Defined, Serum Free, Open Source Media
Authors: Vaughan-Jackson Alun , Stodolak Szymon , Ebrahimi Kourosh H. , Browne Cathy , Reardon Paul K. , Pires Elisabete , Gilbert-Jaramillo Javier , Cowley Sally A. , James William S.
Published: October 2020

Human iPSC and macrophages derived from them are increasingly popular tools for research into both infectious and degenerative diseases. However, as the field strives for greater modelling accuracy, it is becoming ever more challenging to justify the use of undefined and proprietary media for the culture of these cells. We describe here two fully defined, serum-free, open-source media for the culture of iPSC and differentiation of iPSC-derived macrophages. These media are equally capable of maintaining these cells compared to commercial alternatives. The macrophages differentiated in these defined media display improved terminally differentiated cell characteristics, reduced basal expression of induced anti-viral response genes, and improved polarisation capacity. We conclude that cells cultured in these media are an appropriate and malleable model for tissue resident macrophages, on which future differentiation techniques can be built.
SplineDist: Automated Cell Segmentation With Spline Curves
Authors: Mandal Soham , Uhlmann Virginie
Published: October 2020

We present SplineDist, an instance segmentation convolutional neural network for bioimages extending the popular StarDist method. While StarDist describes objects as star-convex polygons, SplineDist uses a more flexible and general representation by modelling objects as planar parametric spline curves. Based on a new loss formulation that exploits the properties of spline constructions, we can incorporate our new object model in StarDist’s architecture with minimal changes. We demonstrate in synthetic and real images that SplineDist produces segmentation outlines of equal quality than StarDist with smaller network size and accurately captures non-star-convex objects that cannot be segmented with StarDist.
Single-cell RNA-seq analysis of human coronary arteries using an enhanced workflow reveals SMC transitions and candidate drug targets
Authors: Ma Wei Feng , Hodonsky Chani J. , Turner Adam W. , Wong Doris , Song Yipei , Barrientos Nelson B. , Mosquera Jose Verdezoto , Miller Clint L.
Published: October 2020

Background and Aims

The atherosclerotic plaque microenvironment is highly complex, and selective agents that modulate plaque stability or other plaque phenotypes are not yet available. We sought to investigate the human atherosclerotic cellular environment using scRNA-seq to uncover potential therapeutic approaches. We aimed to make our workflow user-friendly, reproducible, and applicable to other disease-specific scRNA-seq datasets.

Methods

Here we incorporate automated cell labeling, pseudotemporal ordering, ligand-receptor evaluation, and drug-gene interaction analysis into an enhanced and reproducible scRNA-seq analysis workflow. Notably, we also developed an R Shiny based interactive web application to enable further exploration and analysis of the scRNA dataset.

Results

We applied this analysis workflow to a human coronary artery scRNA dataset and revealed distinct derivations of chondrocyte-like and fibroblast-like cells from smooth muscle cells (SMCs), and show the key changes in gene expression along their de-differentiation path. We highlighted several key ligand-receptor interactions within the atherosclerotic environment through functional expression profiling and revealed several attractive avenues for future pharmacological repurposing in precision medicine. Further, our interactive web application,PlaqView(www.plaqview.com), allows other researchers to easily explore this dataset and benchmark applicable scRNA-seq analysis tools without prior coding knowledge.

Conclusions

These results suggest novel effects of chemotherapeutics on the atherosclerotic cellular environment and provide future avenues of studies in precision medicine. This publicly available workflow will also allow for more systematic and user-friendly analysis of scRNA datasets in other disease and developmental systems.PlaqViewallows for rapid visualization and analysis of atherosclerosis scRNA-seq datasets without the need of prior coding experience. Future releases ofPlaqViewwill feature additional larger scRNA-seq and scATAC-seq atherosclerosis-related datasets, thus providing a critical resource for the field by promoting data harmonization and biological interpretation.
Learning and motor inhibitory control in crows and domestic chickens
Authors: Wascher Claudia A.F. , Allen Katie , Szipl Georgine
Published: October 2020

Cognitive abilities allow animals to navigate through complex, fluctuating environments. In the present study, we tested the performance of a captive group of eight crows,Corvus corone, and ten domestic chickens,Gallus gallus domesticus, in the cylinder task, as a test of motor inhibitory control, and reversal learning as a measure of learning ability and behavioural flexibility. Four crows and nine chickens completed the cylinder task, eight crows and six chickens completed the reversal learning experiment. Crows performed better in the cylinder task compared to chickens. In the reversal learning experiment, species did not significantly differ in the number of trials until learning criterion was reached. Performance in the reversal learning experiment did not correlate with performance in the cylinder task in chickens. Our results suggest crows to possess better motor inhibitory control compared to chickens. In contrast, learning performance in a reversal learning task did not differ between the species, indicating similar levels of behavioural flexibility. Interestingly, we describe notable individual differences in performance. We stress the importance not only to compare cognitive performance between species but also between individuals of the same species when investigating the evolution of cognitive skills.
Genomic Analyses of New Genes and Their Phenotypic Effects Reveal Rapid Evolution of Essential Functions in Drosophila Development
Authors: Xia Shengqian , VanKuren Nicholas W. , Chen Chunyan , Zhang Li , Kemkemer Clause , Shao Yi , Jia Hangxing , Lee UnJin , Advani Alexander S. , Gschwend Andrea , Vibranovski Maria , Chen Sidi , Zhang Yong E. , Long Manyuan
Published: October 2020

It is a conventionally held dogma that the genetic basis underlying development is conserved in a long evolutionary time scale. Ample experiments based on mutational, biochemical, functional, and complementary knockdown/knockout approaches have revealed the unexpectedly important role of recently evolved new genes in the development ofDrosophila. The recent progress in the analyses of gene effects and improvements in the computational identification of new genes, which has led to large sample sizes of new genes, open the door to investigate the evolution of gene essentiality with a phylogenetically high resolution. These advancements also raised interesting issues related to phenotypic effect analyses of genes, particularly of those that recently originated. Here we reported our analyses of these issues, including the dating of gene ages, the interpretation of RNAi data that may confuse false positive/false negative rates, and the potential confounding impact of compensation and developmental effects that were not considered during previous CRISPR knockout experiments. We further analyzed new data from knockdowns of 702 new genes (~66% of total 1,070Drosophila melanogasternew genes), revealing a similarly high proportion of essential genes from recent evolution, compared to those found in distant ancestors ofD. melanogaster. Knockout of a few young genes detected analogous essentiality. Furthermore, our experimentally determined distribution and comparison of knockdown efficiency in different RNAi libraries provided valuable data for general functional analyses of genes. Taken together, these data, along with an improved understanding of the phenotypic effect analyses of new genes, provide further evidence to the conclusion that new genes inDrosophilaquickly evolved essential functions in viability during development.
DNA damage-signaling, homologous recombination and genetic mutation induced by 5-azacytidine and DNA-protein crosslinks inEscherichia coli
Authors: Klaric Julie A. , Glass David J. , Perr Eli L. , Reuven Arianna D. , Towne Mason J. , Lovett Susan T.
Published: October 2020

Covalent linkage between DNA and proteins produces highly toxic lesions and can be caused by commonly used chemotherapeutic agents, by internal and external chemicals and by radiation. In this study, usingEscherichia coli, we investigate the consequences of 5-azacytidine (5-azaC), which traps covalent complexes between itself and the Dcm cytosine methyltransferase protein. DNA protein crosslink-dependent effects can be ascertained by effects that arise in wild-type but not indcmΔ strains. We find that 5-azaC induces the bacterial DNA damage response and stimulates homologous recombination, a component of which is Dcm-dependent. Template-switching at an imperfect inverted repeat (“quasipalindrome”, QP) is strongly enhanced by 5-azaC and this enhancement was entirely Dcm-dependent. The SOS response helps ameliorate the mutagenic effect of 5-azaC but unbalanced expression of the SOS-induced DNA polymerases, especially PolIV, stimulates QP-associated mutagenesis. In the absence of Lon protease, Dcm-dependent QP-mutagenesis is elevated, suggesting it may play a role in 5-azaC tolerance. Deletions at short tandem repeats, which occur likewise by a replication template-switch, are elevated, but only modestly, by 5-azaC. We see evidence for Dcm-dependent and-independent killing by 5-azaC in sensitive mutants, such asrecA,recB, andlon; homologous recombination and deletion mutations are also stimulated in part by a Dcm-independent effect of 5-azaC. Whether this occurs by a different protein/DNA crosslink or by an alternative form of DNA damage is unknown.

Highlights

5-azacytidine is broadly mutagenic and recombinogenic

In E. coli, 5-azaC promotes genetic instability through Dcm methyltransferase.

There are other, unknown lesions induced by 5-azaC besides Dcm/DNA crosslinks

5-azaC induces the SOS response, protecting cells from killing and genetic instability
Tuning intrinsic disorder predictors for virus proteins
Authors: Almog Gal , Olabode Abayomi S , Poon Art FY
Published: October 2020

Many virus-encoded proteins have intrinsically disordered regions that lack a stable folded threedimensional structure. These disordered proteins often play important functional roles in virus replication, such as down-regulating host defense mechanisms. With the widespread availability of next-generation sequencing, the number of new virus genomes with predicted open reading frames is rapidly outpacing our capacity for directly characterizing protein structures through crystallography. Hence, computational methods for structural prediction play an important role. A large number of predictors focus on the problem of classifying residues into ordered and disordered regions, and these methods tend to be validated on a diverse training set of proteins from eukaryotes, prokaryotes and viruses. In this study, we investigate whether some predictors outperform others in the context of virus proteins. We evaluate the prediction accuracy of 21 methods, many of which are only available as web applications, on a curated set of 126 proteins encoded by viruses. Furthermore, we apply a random forest classifier to these predictor outputs. Based on cross-validation experiments, this ensemble approach confers a substantial improvement in accuracy,e.g., a mean 36% gain in Matthews correlation coefficient. Lastly, we apply the random forest predictor to SARS-CoV-2 ORF6, an accessory gene that encodes a short (61 AA) and moderately disordered protein that inhibits the host innate immune response.
Development and validation of an open-source, disposable, 3D-printed in vitro environmental exposure system for Transwell® culture inserts
Authors: Chandiramohan Abiram , Dabaghi Mohammedhossein , Aguiar Jennifer A. , Tiessen Nicholas , Stewart Mary , Cao Quynh T. , Nguyen Jenny P. , Makhdami Nima , Cox Gerard , Doxey Andrew C. , Hirota Jeremy A.
Published: October 2020

Accessible in vitro models recapitulating the human airway that are amenable to study whole cannabis smoke exposure are needed for immunological and toxicological studies that inform public health policy and recreational cannabis use. In the present study, we developed and validated a novel 3D printed In Vitro Exposure System (IVES) that can be directly applied to study the effect of cannabis smoke exposure on primary human bronchial epithelial cells.

Using commercially available design software and a 3D printer, we designed a four-chamber Transwell® insert holder for exposures to whole smoke. Software was used to model gas distribution, concentration gradients, velocity profile and shear stress within IVES. Following simulations, primary human bronchial epithelial cells cultured at air-liquid interface on Transwell® inserts were exposed to whole cannabis smoke. Following 24 hours, outcome measurements included cell morphology, epithelial barrier function, lactate dehydrogenase (LDH) levels, cytokine and gene expression.

Whole smoke delivered through IVES possesses velocity profiles consistent with uniform gas distribution across the four chambers and complete mixing. Airflow velocity ranged between 1.0-1.5 μm s−1 and generated low shear stresses (<< 1 Pa). Human airway epithelial cells exposed to cannabis smoke using IVES showed changes in cell morphology and disruption of barrier function without significant cytotoxicity. Cannabis smoke elevated IL-1 family cytokines and elevated CYP1A1 and CYP1B1 expression relative to control.

IVES represents an accessible, open-source, exposure system that can be used to model varying types of cannabis smoke exposures with human airway epithelial cells grown under air-liquid interface culture conditions.
Benchmarking common preprocessing strategies in early childhood functional connectivity MRI
Authors: Graff Kirk , Tansey Ryann , Ip Amanda , Rohr Christiane , Dimond Dennis , Dewey Deborah , Bray Signe
Published: October 2020

Functional connectivity magnetic resonance imaging (FC-MRI) has been widely used to investigate neurodevelopment. However, FC-MRI is vulnerable to head motion, which is associated with age and distorts FC estimates. Numerous preprocessing strategies have been developed to mitigate confounds, each with advantages and drawbacks. Preprocessing strategies for FC-MRI have typically been validated and compared using resting state data from adults. However, FC-MRI in young children presents a unique challenge due to relatively high head motion and a growing use of passive viewing paradigms to mitigate motion. This highlights a need to compare processing choices in pediatric samples. To this end, we leveraged longitudinal, passive viewing fMRI data collected from 4 to 8-year-old children. We systematically investigated combinations of widely used and debated preprocessing strategies, namely global signal regression, volume censoring, ICA-AROMA, and bandpass filtering. We implemented commonly used metrics of noise removal (i.e. quality control-functional connectivity), metrics sensitive to individual differences (i.e. connectome fingerprinting), and, because data was collected during a passive viewing task, we also assessed the impact on stimulus-evoked responses (i.e. intersubject correlations; ISC). We found that the most efficacious pipeline included censoring, global signal regression, bandpass filtering, and head motion parameter regression. Despite the drawbacks of noise-mitigation steps, our findings show benefits for both noise removal and information retention in a high-motion early childhood sample.

Highlights

- We evaluated 27 preprocessing pipelines in passive viewing data from young children

- Pipelines were evaluated on noise-removed and information retained

- Pipelines that included censoring and GSR outperformed alternatives across benchmarks

- For high-motion scans, preprocessing choices substantially alter connectomes
Robust Encoding of Abstract Rules by Distinct Neuronal Populations in Primate Visual Cortex
Authors: Jonikaitis Donatas , Nissim Nir , Xia Ruobing , Moore Tirin
Published: October 2020

It is widely known that neural activity in sensory representations is modulated by cognitive factors such as attention, reward value and working memory. In such cases, sensory responses are found to reflect a selection of the specific sensory information needed to achieve behavioral goals. In contrast, more abstract behavioral constraints that do not involve stimulus selection, such as task rules, are thought to be encoded by neurons at later stages. We show that information about abstract rules is encoded by neurons in primate visual cortex in the absence of sensory stimulation. Furthermore, we show that rule information is greatest among neurons with the least visual activity and the weakest coupling to local neuronal networks. Our results identify rule-specific signals within a sensory representation and suggest that distinct mechanisms exist there for mapping rule information onto sensory guided decisions.