bluuebunny/crossref_metadata_2025 huggingface dataset:
LncRNA H19X is required for placenta development and angiogenesis through regulating a noncoding RNA regulatory network
Authors: Tongtong Li , Cao Yacong , Zou Yanting , Yang Ye , Ke Wang , Gelin Huang , Xiaoliang Li , Rui Zheng , Li Tang , Jiao Lv , Ming Yang , Jiabei He , Xiaohu Zhang , Shujun Bai , Qintong Li , Lang Qin , Miao Zhao Xiao , Wenming Xu
Published: November 2020

H19X is a lncRNA specifically expressed in the placenta, whose expression is induced by hypoxia. H19X overexpression promoted trophoblast proliferation and invasion, while its knockdown or knockout inhibited trophoblast proliferation and invasion. Mechanistically, we demonstrated that reciprocal regulation exists with miR-424/miR-503 in the control of genes related to placental development and angiogenesis, including VEGF and VEGFR2. H19X inhibited ubiquitination of PIWIL1, thereby maintaining its stability and homeostatic expression of piRNAs. PIWIL1 overexpression rescued the defects of cell behavior caused by H19X KO. H19X deletion led to compromised HIF-1A/HIF-2A expression, which was correlated with the dysregulation of downstream genes under hypoxic conditions. CRISPR/Cas-9 knockout of H19X in animals led to defective placenta differentiation and compromised embryo development under hypoxic conditions. Western blotting showed reduced expression levels of PIWIL1 as well as angiogenesis marker genes, including VEGF and VEGFR2, in H19X KO mice. Thus, this study provides evidence of an unexpected link among lncRNA, miRNA, PIWIL1-related piRNA, and angiogenesis in placentation, the dysregulation of which leads to poor placental development and embryo loss under hypoxic conditions.
TRPV channel OCR-2 is distributed alongC. eleganschemosensory cilia by diffusion in a local interplay with intraflagellar transport
Authors: van Krugten Jaap , Danné Noémie , Peterman Erwin J.G.
Published: November 2020

Sensing and reacting to the environment is essential for survival and procreation of most organisms.Caenorhabditis eleganssenses soluble chemicals with transmembrane proteins (TPs) in the cilia of its chemosensory neurons. Development, maintenance and function of these cilia relies on intraflagellar transport (IFT), in which motor proteins transport cargo, including sensory TPs, back and forth along the ciliary axoneme. Here we use live fluorescence imaging to show that IFT machinery and the sensory TP OCR-2 reversibly redistribute along the cilium after exposure to repellant chemicals. To elucidate the underlying mechanisms, we performed single-molecule tracking experiments and found that OCR-2 distribution depends on an intricate interplay between IFT-driven transport, normal diffusion and subdiffusion that depends on the specific location in the cilium. These insights in the role of IFT on the dynamics of cellular signal transduction contribute to a deeper understanding of the regulation of sensory TPs and chemosensing.
Unscheduled origin building in S-phase upon tight CDK1 inhibition suppresses CFS instability
Authors: Brison Olivier , Gnan Stefano , Azar Dana , Schmidt Mélanie , Koundrioukoff Stéphane , El-Hilali Sami , Jaszczyszyn Yan , Lachages Anne-Marie , Thermes Claude , Chen Chun-Long , Debatisse Michelle
Published: November 2020

Genome integrity requires replication to be completed before chromosome segregation. This coordination essentially relies on replication-dependent activation of a dedicated checkpoint that inhibits CDK1, delaying mitotic onset. Under-replication of Common Fragile Sites (CFSs) however escapes surveillance, which triggers chromosome breakage. Using human cells, we asked here whether such leakage results from insufficient CDK1 inhibition under modest stresses used to destabilize CFSs. We found that tight CDK1 inhibition suppresses CFS instability. Repli-Seq and molecular combing analyses consistently showed a burst of replication initiations in mid S phase across large origin-poor domains shaped by transcription, including CFSs. Strikingly, CDC6 or CDT1 depletion or CDC7-DBF4 inhibition during the S phase prevented both extra-initiations and CFS rescue, showing that CDK1 inhibition promotes targeted and mistimed building of functional extra-origins. In addition to delay mitotic onset, checkpoint activation therefore advances replication completion of chromosome domains at risk of under-replication, two complementary roles preserving genome stability.
Mechanistic modeling suggests that low-intensity focused ultrasound can selectively recruit myelinated or unmyelinated nerve fibers
Authors: Lemaire Théo , Vicari Elena , Neufeld Esra , Kuster Niels , Micera Silvestro
Published: November 2020

Low-Intensity Focused Ultrasound Stimulation (LIFUS) holds promise for the remote modulation of neuronal activity, but an incomplete mechanistic characterization hinders its clinical maturation. Here, we developed a computational framework to model intramembrane cavitation in multi-compartmental, morphologically-realistic neuronal representations, and used it to investigate ultrasound neuromodulation of peripheral nerves by spatially-varying pressure fields. Our findings show that LIFUS offers distinct parametric sub-spaces to selectively recruit myelinated or unmyelinated axons and modulate their spiking activity over physiologically relevant regimes and within safe exposure limits. This singular feature, explained by fiber-specific differences in membrane electromechanical coupling, consistently explains recent empirical findings and suggests that LIFUS can preferentially target nociceptive and sensory fibers to enable peripheral therapeutic applications not addressable by electric stimulation. These results open up new opportunities for the development of more selective and effective peripheral neuroprostheses. Our framework can be readily applied to other neural targets to establish application-specific LIFUS protocols.
Adipose Triglyceride Lipase protects the endocytosis of renal cells on a high fat diet inDrosophila
Authors: Lubojemska Aleksandra , Stefana M. Irina , Lampe Lena , Yoshimura Azumi , Burrell Alana , Collinson Lucy , Gould Alex P.
Published: November 2020

Obesity-related renal lipotoxicity and chronic kidney disease (CKD) are prevalent pathologies with complex aetiologies. One hallmark of renal lipotoxicity is the ectopic accumulation of lipid droplets in kidney podocytes and in proximal tubule cells. Renal lipid droplets are observed in human CKD patients and in high-fat diet rodent models but their precise role remains unclear. Here, we establish a high-fat diet model inDrosophilathat recapitulates renal lipid droplets and several other aspects of mammalian CKD. Cell-type specific genetic manipulations show that lipid can overflow from adipose tissue and is taken up by renal cells called nephrocytes. A high-fat diet drives nephrocyte lipid uptake via the multiligand receptor Cubilin, leading to the ectopic accumulation of lipid droplets. These nephrocyte lipid droplets correlate with ER and mitochondrial deficits, as well as with impaired macromolecular endocytosis, a key conserved function of renal cells. Nephrocyte knockdown of diglyceride acyltransferase 1 (DGAT1), overexpression of adipose triglyceride lipase (ATGL) and epistasis tests together reveal that fatty acid flux through the lipid droplet triglyceride compartment protects the ER, mitochondria and endocytosis of renal cells. Strikingly, boosting nephrocyte expression of the lipid droplet resident enzyme ATGL is sufficient to rescue high-fat diet induced defects in renal endocytosis. Moreover, endocytic rescue requires a conserved mitochondrial regulator, peroxisome proliferator-activated receptor-gamma coactivator 1α (PGC1α). This study demonstrates that lipid droplet lipolysis counteracts the harmful effects of a high-fat diet via a mitochondrial pathway that protects renal endocytosis. It also provides a genetic strategy for determining whether lipid droplets in different biological contexts function primarily to release beneficial or to sequester toxic lipids.
EcDNA hubs drive cooperative intermolecular oncogene expression
Authors: Hung King L. , Yost Kathryn E. , Xie Liangqi , Wu Sihan , Lange Joshua T. , Duffy Connor V. , Kraft Katerina , Tang Jun , Shi Quanming , Rose John C. , Corces M. Ryan , Granja Jeffrey M. , Li Rui , Rajkumar Utkrisht , Tjian Robert , Bafna Vineet , Mischel Paul S. , Liu Zhe , Chang Howard Y.
Published: November 2020

Extrachromosomal DNAs (ecDNAs) are prevalent in human cancers and mediate high oncogene expression through elevated copy number and altered gene regulation1. Gene expression typically involves distal enhancer DNA elements that contact and activate genes on the same chromosome2,3. Here we show that ecDNA hubs, comprised of ~10-100 ecDNAs clustered in the nucleus of interphase cells, drive intermolecular enhancer input for amplified oncogene expression. Single-molecule sequencing, single-cell multiome, and 3D enhancer connectome reveal subspecies ofMYC-PVT1ecDNAs lacking enhancers that access intermolecular and ectopic enhancer-promoter interactions in ecDNA hubs. ecDNA hubs persist without transcription and are tethered by BET protein BRD4. BET inhibitor JQ1 disperses ecDNA hubs, preferentially inhibits ecDNA oncogene transcription, and kills ecDNA+ cancer cells. Two amplified oncogenesMYCandFGFR2intermix in ecDNA hubs, engage in intermolecular enhancer-promoter interactions, and transcription is uniformly sensitive to JQ1. Thus, ecDNA hubs are nuclear bodies of many ecDNAs tethered by proteins and platforms for cooperative transcription, leveraging the power of oncogene diversification and combinatorial DNA interactions. We suggest ecDNA hubs, rather than individual ecDNAs, as units of oncogene function, cooperative evolution, and new targets for cancer therapy.
piNET: An Automated Proliferation Index Calculator Framework for Ki67 Breast Cancer Images
Authors: Geread Rokshana Stephny , Sivanandarajah Abishika , Brouwer Emily , Wood Geoffrey A. , Androutsos Dimitrios , Faragalla Hala , Khademi April
Published: November 2020

In this work, a novel proliferation index (PI) calculator for Ki67 images called piNET is proposed. It is successfully tested on four datasets, from three scanners comprised of patches, tissue microarrays (TMAs) and wholeslide images (WSI), representing a diverse multicentre dataset for evaluating Ki67 quantification. Compared to state-of-the-art methods, piNET consistently performs the best over all datasets with an average PI difference of 5.603%, PI accuracy rate of 86% and correlation coefficient R = 0.927. The success of the system can be attributed to a number of innovations. Firstly, this tool is built based on deep learning, which can adapt to wide variability of medical images – and it was posed as a detection problem to mimic pathologists’ workflow which improves accuracy and efficiency. Secondly, the system is trained purely on tumour cells, which reduces false positives from non-tumour cells without needing the usual pre-requisite tumour segmentation step for Ki67 quantification. Thirdly, the concept of learning background regions through weak supervision is introduced, by providing the system with ideal and non-ideal (artifact) patches that further reduces false positives. Lastly, a novel hotspot analysis is proposed to allow automated methods to score patches from WSI that contain “significant” activity.
Intra-individual variability in task performance after cognitive training is associated with long-term outcomes in children
Authors: Cubillo A , Hermes H , Berger E , Winkel K , Schunk D , Fehr E , Hare T. A.
Published: November 2020

The benefits and mechanistic effects of working memory training in children are the subject of much research and debate. The cumulative evidence indicates that training can alter brain structure and function in the short term and have lasting effects on behaviour. We show that five weeks of working memory training led to greater activity in prefrontal and striatal brain regions, better accuracy, and reduced intra-individual variability in response times. The reduction in intra-individual variability can be explained by changes to the evidence accumulation rates and thresholds in a sequential sampling decision model. Critically, intra-individual variability was more closely associated with academic skills and mental health 6-12 months after the end of training than task accuracy. These results indicate that intra-individual variability may be a useful way to quantify the immediate impact of cognitive training interventions and predict the future emergence of academic and socioemotional skills.
CD28 costimulatory domain protects against tonic signaling-induced functional impairment in CAR-Tregs
Authors: Lamarthée Baptiste , Marchal Armance , Charbonnier Soëli , Blein Tifanie , Martin Emmanuel , Vogt Katrin , Titeux Matthias , Delville Marianne , Vinçon Hélène , Six Emmanuelle , Pallet Nicolas , Anglicheau Dany , Legendre Christophe , Taupin Jean-Luc , Sawitzki Birgit , Latour Sylvain , Cavazzana Marina , André Isabelle , Zuber Julien
Published: November 2020

The use of chimeric antigen receptor (CAR)-engineered regulatory T cells (Tregs) has emerged as a promising strategy to promote immune tolerance in transplantation. However, in conventional T cells (Tconvs), CAR expression is often associated with tonic signaling resulting from ligand-independent baseline activation. Tonic signaling may cause CAR-T cell dysfunction, especially when the CAR structure incorporates the CD28 costimulatory domain (CSD) rather than the 4-1BB CSD.

Here, we explored the impact of tonic signaling on human CAR-Tregs according to the type of CSD. Compared to CD28-CAR-Tregs, 4-1BB-CAR-Tregs showed enhanced proliferation and greater activation of MAP kinase and mTOR pathways but exhibited decreased lineage stability and reduced abilities to produce IL-10 and be restimulated through the CAR. Although both CAR-Treg populations were suppressivein vivo,cell tracking with bioluminescence imaging found longer persistence for CD28-CAR-Tregs than for 4-1BB-CAR-Tregs. This study demonstrates that CD28-CAR best preserves Treg function and survival in the context of tonic signaling, in contrast with previous findings for Tconvs.

Lamarthée et al investigated the impact of chimeric antigen receptor (CAR) tonic signaling on CAR-engineered Tregs according to the incorporated costimulatory domain (either CD28 or 4-1BB). CD28 ameliorated Treg stability, long-term survival and function compared to 4-1BB.
Frontoparietal pattern similarity analyses of cognitive control in monozygotic twins
Authors: Tang Rongxiang , Etzel Joset A. , Kizhner Alexander , Braver Todd S.
Published: November 2020

The ability to flexibly adapt thoughts and actions in a goal-directed manner appears to rely on cognitive control mechanisms that are strongly impacted by individual differences. A powerful research strategy for investigating the nature of individual variation is to study monozygotic (identical) twins. Evidence of twin effects have been observed in prior behavioral and neuroimaging studies, yet within the domain of cognitive control, it remains to be demonstrated that the neural underpinnings of such effects are specific and reliable. Here, we utilize a multi-task, within-subjects event-related neuroimaging design with functional magnetic resonance imaging to investigate twin effects through multivariate pattern similarity analyses. We focus on fronto-parietal brain regions exhibiting consistently increased activation associated with cognitive control demands across four task domains: selective attention, context processing, multi-tasking, and working memory. Healthy young adult monozygotic twin pairs exhibited increased similarity of within- and cross-task activation patterns in these fronto-parietal regions, relative to unrelated pairs. Twin activation pattern similarity effects were clearest under high control demands, were not present in a set of task-unrelated parcels or due to anatomic similarity, and were primarily observed during the within-trial timepoints in which the control demands peaked. Together, these results indicate that twin similarity in the neural representation of cognitive control may be domain-general but also functionally and temporally specific in relation to the level of control demand. The findings suggest a genetic and/or environmental basis for individual variation in cognitive control function, and highlight the potential of twin-based neuroimaging designs for exploring heritability questions within this domain.
Peroxisome import stress impairs ribosome biogenesis and induces integrative stress response through eIF2α phosphorylation
Authors: Huang Kerui , Kim Jinoh , Vo Pham , Miao Ting , Bai Hua
Published: November 2020

Peroxisome biogenesis diseases (PBDs) are characterized by global defects in peroxisomal function and can result in severe brain, liver, kidney, and bone malfunctions. PBDs are due to mutations in peroxisome biogenesis factors (PEX genes) that are responsible for peroxisome assembly and function. Increasing evidence suggests that peroxisome import functions decline during aging. However, the transcriptome profiling of peroxisome import defects and how they affect disease development are still lacking.PEX5encodes the cytoplasmic receptors for peroxisome-targeting signal types 1. We generate knock-in human HEK293 cells mutant using CRISPR to transiently expressPEX5cysteine 11 to alanine mutant (PEX5C11A), which blocks PEX5 recycling and exerts dominant negative effect onPEX5mediated peroxisome import. To identify conserved responses, we perform transcriptomic analysis onDrosophilaoenocyte-specific Pex1, Pex12 and Pex5 knockdowns and on human cells with impaired peroxisome import (PEX5C11Aand PEX5 siRNA respectively). PEX5C11Ainduction triggers vast transcriptomic changes, including decreased oxidative phosphorylation, increased MAPK signaling and HIPPO signaling. PEX5 siRNA specifically decreases spliceosome activity and increases cholesterol metabolism. Using gene set enrichment analysis (GSEA), we identify protein processing in endoplasmic reticulum pathway, specifically ER-associated protein degradation (ERAD) pathway is induced in all PEX knockdowns inDrosophila. Peroxisome dysfunction elevates eIF2α phosphorylation in bothDrosophilaand human cell culture independent ofXBP1activation, suggesting increased integrative stress response (ISR). Moreover, peroxisome stress decreases ribosome biogenesis genes and impairs ribosome biogenesis in flies and human cells. Specifically, peroxisome stress impairs the 5’-ETS cleavage activity during the ribosome biogenesis and dampens 40S small ribosomal export in both flies and human. Our results suggest that reduced ribosome biogenesis and elevated ISR could be conserved cellular response to peroxisome import stress.
Disentangling genetic feature selection and aggregation in transcriptome-wide association studies
Authors: Cao Chen , Kwok Devin , Li Qing , He Jingni , Guo Xingyi , Zhang Qingrun , Long Quan
Published: November 2020

The success of transcriptome-wide association studies (TWAS) has led to substantial research towards improving its core component of genetically regulated expression (GReX). GReX links expression information with phenotype by serving as both the outcome of genotype-based expression models and the predictor for downstream association testing. In this work, we demonstrate that current linear models of GReX inadvertently combine two separable steps of machine learning - feature selection and aggregation - which can be independently replaced to improve overall power. We show that the monolithic approach of GReX limits the adaptability of TWAS methodology and practice, especially given low expression heritability.
Supporting Student Learning and Experiences in the Lab: (How) Should We Design Their Groups?
Authors: Tan Tanya Y. , Barker Megan K.
Published: November 2020

Undergraduate science students spend a substantial amount of time working in their laboratory groups, and instructors want to make evidence-based decisions on how to best set up these groups. Despite several studies on group composition, the evidence appears to be quite context-specific, and very little has been published about lab groups. Further, many studies focus solely on conceptual learning; however, the lab is an important venue for also supporting non-content outcomes such as confidence, process skills, team skills, and attitudes. Thus, in our introductory course on molecules, cells, and physiology we were interested in the impact of group composition, on a spread of student outcomes. Students were either placed into groups by the instructor, or self-selected into groups. To assess the impact of group composition on student outcome, we collected pre/post data from >500 students over 2 semesters. Our measures assess conceptual knowledge, confidence in lab skills, attitudes toward group learning, lab grades, gender, year of study, and (via open-ended questions) student perspectives. Using a multiple regression approach, we established models that predict student outcomes based on their individual attributes and on their lab group attributes. Surprisingly, the hetero/homogeneity of the initial group, and whether the groups were student- or instructor-selected, did not affect student outcomes in these models. Further MANCOVA analysis demonstrated that student interaction outside of the lab time was the strongest predictor of positive student attitudes toward group learning. Student perspectives on group formation are mixed, and suggest that a simple and flexible choice approach may best support our students. Overall, these findings have clear implications for our course design and instructional choices: we should focus our efforts to promote positive student interactions, rather than worrying about initial composition.
An Adhesive-Based Fabrication Technique for Culture of Lung Airway Epithelial Cells with Applications in Microfluidics and Lung-on-a-Chip
Authors: Tiessen Nicholas , Dabaghi Mohammadhossein , Cao Quynh , Chandiramohan Abiram , Selvaganapathy P. Ravi , Hirota Jeremy A.
Published: November 2020

1

This work describes a versatile and cost-effective cell culture method for growing adherent cells on a porous membrane using pressure-sensitive double-sided adhesives. This technique allows cell culture using conventional methods and easy transfer to microfluidic chip devices. To support the viability of our system, we evaluate the toxicity effect of four different adhesives on two distinct airway epithelial cell lines and show functional applications for microfluidic cell culture chip fabrication. We showed that cells could be grown and expanded on a “floating” membrane, which can be transferred upon cell confluency to a microfluidic chip for further analysis. The viability of cells and their inflammatory responses to IL-1β stimulation was investigated. Such a technique would be useful to culture cells in a conventional fashion, which is more convenient and faster, and stimulate cells in an advanced model with perfusion when needed.
Impact of Chrysin on Vitamin D and Bone Health - Preclinical Studies
Authors: Kasarla Siva Swapna , Dodoala Sujatha , Sampathi Sunitha , Talluri Narendra Kumar
Published: November 2020

Vitamin D deficiency is an endemic problem existing worldwide. Although several strategies were established to enhance vitamin D3levels, studies specifically focussing inhibition of vitamin D metabolism which may prolong the availability of active vitamin D in pathological conditions are less explored. Studies also suggest that higher doses of vitamin D3fail to achieve optimum vitamin D levels. In this context, we focussed on the enzyme CYP3A4 which promotes inactivation of active vitamin D. The current study was aimed to decipher the impact of chrysin, a proven CYP3A4 inhibitor as an intervention and its effects in combination with low dose vitamin D3(40 IU) and bone health in vitamin D deficiency condition. Thein-vivoactivity of chrysin was evaluated on female Wistar albino rats fed with a vitamin D deficient diet to attain vitamin D deficiency for 28 days. Chrysin was given alone and in combination with calcium carbonate (CaCO3) and/or vitamin D3. All the therapeutic interventions were assessed for serum 25-OH-D3 by LC-MS, biochemical, urinary, and bone parameters. Animals treated with chrysin alone and in combination with low dose vitamin D3and/or CaCO3showed an eminent rise in serum 25-OH-D3 levels along with increased serum biochemical parameters. On contrary, a significant decrease in the urinary parameters followed by beneficial effects on bone parameters was noticed in contrast with the vitamin D deficient diet group. Our findings revealed that although chrysin alone showed a notable effect on 25-OH-D3 and osseous tissue, comparatively it showed intensified therapeutic effect in combination with vitamin D3and CaCO3which can be employed as a cost-effective option to improve bone health.

Graphical Abstract
Helicobacter pyloriand Epstein-Barr virus coinfection stimulates the aggressiveness in gastric cancer through the regulation of gankyrin
Authors: Kashyap Dharmendra , Baral Budhadev , Varshney Nidhi , Singh Anil Kumar , Jha Hem Chandra
Published: November 2020

Persistent coinfection ofHelicobacter pylori (H. pylori)and Epstein-Barr virus (EBV) promotes aggressive gastric carcinoma. The molecular mechanisms underlying the aggressiveness inH. pyloriand EBV coinfected gastric cancer is not well characterized. In the current study, we investigated the molecular mechanism involved in the cooperation ofH. pyloriand EBV-driven proliferation of gastric epithelial cells. Results showed that the coinfections are significantly more advantageous to the pathogens to create a microenvironment that favors the higher pathogen-associated gene expression. The EBV latent genes EBNA1 and EBNA3C are highly overexpressed in the coinfections compared to individual EBV infection at different time points (12 and 24 hrs). TheH. pylori-associated genes 16s rRNA, CagA, and BabA has also been highly overexpressed in coinfections compared toH. pylorialone. Gankyrin is a small protein of 25 KDa involved in multiple biological and physiological processes. The upregulation of gankyrin modulates the various cell signaling pathways, leading to oncogenesis. The gankyrin shows a similar expression pattern as EBNA3C at both transcript and protein levels, suggesting a possible correlation. Further EBV andH. pyloricreate microenvironments that induce cell transformation and oncogenesis by dysregulation of the cell-cycle regulator, GC marker, cell migration, DNA response, and antiapoptotic genes in infected gastric epithelial cells by enhancing the expression of gankyrin. Our study provides new insights into the molecular mechanism where the interplay between two oncogenic agents (H. pyloriand EBV) leads to the enhanced carcinogenic activity of gastric epithelial cells through overexpression of oncoprotein gankyrin.

Importance

In the present study, we have evaluated the synergistic effect of EBV andH. pyloriinfection on gastric epithelial cells in various coinfection models. These coinfection models depict the first exposures of gastric epithelial cells with EBV and then theH. pylori.While other coinfection models narrated the first exposures ofH. pylorifollowed by the infection of EBV. This led to an enhanced oncogenic phenotype in gastric epithelial cells. We determined the coinfection of EBV andH. pylorienhanced the expression of oncogenic protein gankyrin. The interplay between EBV andH. pyloripromotes the oncogenic properties of AGS cells through the newly discovered oncoprotein gankyrin. EBV andH. pylorimediated upregulation of gankyrin further dysregulates various cancer-associated hallmarks of genes such as cell-migratory, gastric cancer marker, tumor suppressor, DNA damage response, and proapoptotic genes.
Bacterial inhibition of CD8+T-cells mediated cell death promotes neuroinvasion and within-host persistence
Authors: Maudet Claire , Kheloufi Marouane , Levallois Sylvain , Gaillard Julien , Huang Lei , Gaultier Charlotte , Tsai Yu-Huan , Disson Olivier , Lecuit Marc
Published: November 2020

Central nervous system infections are amongst the most severe1,2, yet the mechanisms by which pathogens access the brain remain poorly understood. The model microorganismListeria monocytogenes (Lm)is a major foodborne pathogen that causes neurolisteriosis, one of the deadliest central nervous system infections3,4. While immunosuppression is a well-established host risk factor for neurolisteriosis3,5, little is known regarding the bacterial factors underlyingLmneuroinvasion. We have developed a clinically-relevant experimental model of neurolisteriosis, using hypervirulent neuroinvasive strains6inoculated in a humanized mouse model of infection7, and we show that the bacterial protein InlB protects infected monocytes from CD8+T-cells Fas-mediated cell death, in a c-Met/PI3-kinase/FLIP-dependent manner. This blockade of anti-Lmspecific cellular immune response lengthens infected monocytes lifespan, favoringLmtransfer from infected monocytes to the brain. The intracellular niche created by InlB-mediated cell-autonomous immunosuppression also promotesLmfecal shedding, accounting for its selection as aLmcore virulence gene. Here, we have uncovered an unanticipated specific mechanism by which a bacterial pathogen confers to the cells it infects an increased lifespan by rendering them resistant to cell-mediated immunity. This promotesLmwithin-host persistence and dissemination to the central nervous system, and transmission.
Protein Cargo Assessment through Residue Alterations
Authors: Arslan Ahmed
Published: November 2020

Motivation

The transport of proteins plays a crucial role in the cellular phenotype. Changes in the protein targeting sequence can result in missing protein delivery to the right destination and at the right time, and can disrupt various cellular pathways. Given the importance of single residue change(s) in the protein targeting sequence we developed a missing computational method.

Results

By taking into account various protein features like conservation, protein modifications, charge, isoelectric effect and biochemical properties of peptides, the method,TransSite, assess the impact of mutations on the protein transportation. We applied this method to big human (cancer proteins) and nonhuman data, and discovered, in both cases, several phenotype related proteins harbour recurring mutations in their targeting sequences.

Availability

https://github.com/AhmedArslan/TransSite

Contact

aarslan@staford.edu

Supplementary information

Supplementary data are available at#online.
Intranasal oxytocin drives coordinated social approach
Authors: Monari Patrick K. , Rieger Nathaniel S. , Schefelker Juliette , Marler Catherine A.
Published: November 2020

Coordinated responses to challenge are essential to survival for bonded monogamous animals and may depend on behavioral compatibility. Oxytocin (OT) context-dependently regulates social affiliation and vocal communication, but its role in pair members’ decision to jointly respond to challenge is unclear. To test for OT effects, California mouse females received an intranasal dose of OT (IN-OT) or saline after bonding with males either matched or in their approach response to an aggressive vocal challenge. Pair mates were re-tested jointly for approach response, time spent together, and vocalizations. Females and males converged in their approach after pairing, but mismatched pairs with females given a single dose of IN-OT displayed a greater convergence that resulted from behavioral changes by both pair members. Unpaired females given IN-OT did not change their approach, indicating a social partner was necessary for effects to emerge. Moreover, IN-OT increased time spent approaching together, suggesting behavioral coordination beyond a further increase in bonding. This OT-induced increase in joint approach was associated with a decrease in the proportion of sustained vocalizations, a type of vocalization that can be associated with intra-pair conflict. Our results expand OT’s effects on behavioral coordination and underscore the importance of emergent social context.
Temporal dynamics of animacy categorization in the brain of patients with mild cognitive impairment
Authors: Karimi Hamed , Marefat Haniye , Khanbagi Mahdiyeh , Kalafatis Chris , Modarres Hadi , Vahabi Zahra , Khaligh-Razavi Seyed-Mahdi
Published: November 2020

Electroencephalography (EEG) has been commonly used to measure brain alterations in Alzheimer’s Disease (AD). However, reported changes are limited to those obtained from using univariate measures, including activation level and frequency bands. To look beyond the activation level, we used multivariate pattern analysis (MVPA) to extract patterns of information from EEG responses to images in an animacy categorization task. Comparing healthy controls (HC) with patients with mild cognitive impairment (MCI), we found that the neural speed of animacy information processing is decreased in MCI patients. Moreover, we found critical time-points during which the representational pattern of animacy for MCI patients was significantly discriminable from that of HC, while the activation level remained unchanged. Together, these results suggest that the speed and pattern of animacy information processing provide clinically useful information as a potential biomarker for detecting early changes in MCI and AD patients.
Type I interferons promote germinal centers through B cell intrinsic signaling and dendritic cell dependent Th1 and Tfh cell lineages
Authors: Dahlgren Madelene W. , Plumb Adam W. , Niss Kristoffer , Lahl Katharina , Brunak Søren , Johansson-Lindbom Bengt
Published: November 2020

Type I interferons (IFNs) play an essential role in antiviral immunity, correlate with severity of systemic autoimmune disease, and are likely to represent a key component of mRNA vaccine-adjuvanticity. Relevant to all, type I IFNs can enhance germinal center (GC) B cell responses but underlying signaling pathways are incompletely understood due to pleiotropic effects in multiple cell types. Here, we demonstrate that a succinct type I IFN response promotes GC formation and associated IgG subclass distribution primarily through signaling in cDCs and B cells. Type I IFN signaling in cDCs, distinct from cDC1, stimulates development of separable Tfh and Th1 cell subsets. However, Th cell-derived IFN-γ induces T-bet expression and IgG2c isotype switching prior to this bifurcation and has no evident effects once GCs andbona fideTfh cells developed. This pathway acts in synergy with early B cell-intrinsic type I IFN signaling, which reinforces T-bet expression in B cells and leads to a selective amplification of the IgG2c+GC B cell response. Despite the strong Th1 polarizing effect of type I IFNs, the Tfh cell subset develops into IL-4 producing cells that control the overall magnitude of the GCs and promote generation of IgG1+GC B cells. Thus, type I IFNs act on B cells and cDCs to drive GC formation and to coordinate IgG subclass distribution through parallel Th1 and Tfh cell-dependent pathways.
Cellulosic wall thickenings restrict cell expansion to shape the 3D puzzle sclereids of the walnut shell
Authors: Antreich Sebastian J. , Xiao Nannan , Huss Jessica C. , Gierlinger Notburga
Published: November 2020

Walnut (Juglans regia) kernels are protected by a tough shell consisting of polylobate sclereids that interlock into a 3D puzzle. The shape transformations from isodiametric to lobed cells is well documented for 2D pavement cells, but not for 3D puzzle sclereids. Here, we tackle the morphogenesis of these cells by using a combination of different imaging techniques. Serial face-microtomy enabled us to reconstruct tissue growth of whole walnut fruits in 3D and serial block face-scanning electron microscopy exposed cell shapes and their transformation in 3D during shell tissue development. In combination with Raman and fluorescence microscopy we revealed multiple loops of cellulosic thickenings in cell walls, acting as stiff restrictions during cell expansion and leading to the lobed cell shape. Our findings contribute to a better understanding of the 3D shape transformation of polylobate sclereids and the role of pectin and cellulose within this process.
Scalable pooled CRISPR screens with single-cell chromatin accessibility profiling
Authors: Liscovitch-Brauer Noa , Montalbano Antonino , Deng Jiale , Méndez-Mancilla Alejandro , Wessels Hans-Hermann , Moss Nicholas G. , Kung Chia-Yu , Sookdeo Akash , Guo Xinyi , Geller Evan , Jaini Suma , Smibert Peter , Sanjana Neville E.
Published: November 2020

Pooled CRISPR screens have been used to identify genes responsible for specific phenotypes and diseases, and, more recently, to connect genetic perturbations with multi-dimensional gene expression profiles. Here, we describe a method to link genome-wide chromatin accessibility to genetic perturbations in single cells. This scalable, cost-effective method combines pooled CRISPR perturbations with a single-cell combinatorial indexing assay for transposase-accessible chromatin (CRISPR-sciATAC). Using a human and mouse species-mixing experiment, we show that CRISPR-sciATAC separates single cells with a low doublet rate. Then, in human myelogenous leukemia cells, we apply CRISPR-sciATAC to target 21 chromatin-related genes that are frequently mutated in cancer and 84 subunits and cofactors of chromatin remodeling complexes, generating chromatin accessibility data for ~30,000 single cells. Using this large-scale atlas, we correlate loss of specific chromatin remodelers with changes in accessibility — globally and at the binding sites of individual transcription factors. For example, we show that loss of the H3K27 methyltransferase EZH2 leads to increased accessibility at heterochromatic regions involved in embryonic development and triggers expression of multiple genes in theHOXAandHOXDclusters. At a subset of regulatory sites, we also analyze dynamic changes in nucleosome spacing upon loss of chromatin remodelers. CRISPR-sciATAC is a high-throughput, low-cost single-cell method that can be applied broadly to study the role of genetic perturbations on chromatin in normal and disease states.
STATegra: Multi-omics data integration - A conceptual scheme and a bioinformatics pipeline
Authors: Planell Nuria , Lagani Vincenzo , Sebastian-Leon Patricia , van der Kloet Frans , Ewing Ewoud , Karathanasis Nestoras , Urdangarin Arantxa , Arozarena Imanol , Jagodic Maja , Tsamardinos Ioannis , Tarazona Sonia , Conesa Ana , Tegner Jesper , Gomez-Cabrero David
Published: November 2020

Technologies for profiling samples using different omics platforms have been at the forefront since the human genome project. Large-scale multi-omics data hold the promise of deciphering different regulatory layers. Yet, while there is a myriad of bioinformatics tools, each multi-omics analysis appears to start from scratch with an arbitrary decision over which tools to use and how to combine them. It is therefore an unmet need to conceptualize how to integrate such data and to implement and validate pipelines in different cases. We have designed a conceptual framework (STATegra), aiming it to be as generic as possible for multi-omics analysis, combining machine learning component analysis, non-parametric data combination and a multi-omics exploratory analysis in a step-wise manner. While in several studies we have previously combined those integrative tools, here we provide a systematic description of the STATegra framework and its validation using two TCGA case studies. For both, the Glioblastoma and the Skin Cutaneous Melanoma cases, we demonstrate an enhanced capacity to identify features in comparison to single-omics analysis. Such an integrative multi-omics analysis framework for the identification of features and components facilitates the discovery of new biology. Finally, we provide several options for applying the STATegra framework when parametric assumptions are fulfilled, and for the case when not all the samples are profiled for all omics. The STATegra framework is built using several tools, which are being integrated step-by-step as OpenSource in the STATegRa Bioconductor packagehttps://bioconductor.org/packages/release/bioc/html/STATegra.html.
Environmental DNA sampling provides new management strategies for vernal pool branchiopods in California
Authors: Kieran Shannon Rose , Hull Joshua , Finger Amanda
Published: November 2020

California’s vernal pools are declining ecosystems that support valuable native plant and animal diversity. Vernal pool branchiopods are particularly at risk from vernal pool habitat loss and conservation efforts have targeted their long-term protection through the establishment of preserves and conservation banks. These conservation strategies require repeated, perpetual monitoring of preserved habitat, which is currently carried out through dip-net surveys and visual identification of specimens. Dip-netting may be destructive and frequently requires some sacrifice of protected species. Environmental DNA offers a new, modern method to monitor many protected freshwater organisms. We designed qPCR-based species-specific assays for four of California’s vernal pool branchiopods: The Vernal Pool Fairy ShrimpBranchinecta lynchi(BRLY), the Midvalley Fairy ShrimpBranchinecta mesovallensis(BRME), and the Conservancy Fairy ShrimpBranchinecta conservatio(BRCO), and the Vernal Pool Tadpole ShrimpLepidurus packardi(LEPA). We tested these assays using eDNA sampling protocols alongside traditional dip-net surveys to assess their viability as an alternative method to monitor vernal pool branchiopods. Based on occupancy modeling, each of our assays achieved a 95% or higher detection rate when using optimized sampling protocols.
A putativeermgene is present inΔermB Clostridioides difficileisolates showing high levels of resistance to clindamycin
Authors: Ramírez-Hernández Viviana , Ramírez-Vargas Gabriel
Published: November 2020

Clostridioidesdifficile has become the leading cause of hospital-acquired diarrhea. Clindamycin is a member of the macrolide-lincosamide-streptogramin B family of protein synthesis inhibitors. Been the ribosomal methylation the most widespread mechanism of resistance to these antibiotics inC difficile ermgenes usually produce high levels of resistance to these drugs. In this short report we present evidence about the presence of an unreported putativeermgene inC difficileisolates that despite of presenting a ΔermBgenotype maintain high levels of clindamycin resistance.
Co-existence of prediction and error signals in electrophysiological responses to natural speech
Authors: Broderick Michael P. , Lalor Edmund C.
Published: November 2020

Prior knowledge facilitates perception and allows us to interpret our sensory environment. However, the neural mechanisms underlying this process remain unclear. Theories of predictive coding propose that feedback connections between cortical levels carry predictions about upcoming sensory events whereas feedforward connections carry the error between the prediction and the sensory input. Although predictive coding has gained much ground as a viable mechanism for perception, in the context spoken language comprehension it lacks empirical support using more naturalistic stimuli. In this study, we investigated theories of predictive coding using continuous, everyday speech. EEG recordings from human participants listening to an audiobook were analysed using a 2-stage regression framework. This tested the effect of top-down linguistic information, estimated using computational language models, on the bottom-up encoding of acoustic and phonetic speech features. Our results show enhanced encoding of both semantic predictions and surprising words, based on preceding context. This suggests that signals pertaining to prediction and error units can be observed in the same electrophysiological responses to natural speech. In addition, temporal analysis of these signals reveals support for theories of predictive coding that propose that perception is first biased towards what is expected followed by what is informative.

Significance Statement

Over the past two decades, predictive coding has grown in popularity as an explanatory mechanism for perception. However, there has been lack of empirical support for this theory in research studying natural speech comprehension. We address this issue by developing an analysis framework that tests the effects of top-down linguistic information on the auditory encoding of continuous speech. Our results provide evidence for the co-existence of prediction and error signals and support theories of predictive coding using more naturalistic stimuli.
Whole genome sequence analysis of Shigella from Malawi identifies fluoroquinolone resistance
Authors: Stenhouse George E. , Jere Khuzwayo C. , Peno Chikondi , Bengtsson Rebecca J. , Chinyama End , Mandolo Jonathan , Cain Amy K. , Iturriza-Gómara Miren , Bar-Zeev Naor , Cunliffe Nigel A. , Cornick Jennifer , Baker Kate S.
Published: November 2020

Increasing antimicrobial resistance and limited alternative treatments led to fluoroquinolone resistant Shigella strain inclusion on the WHO global priority pathogens list. In this study we characterised multiple Shigella isolates from Malawi with whole genome sequence analysis, identifying the acquirable fluoroquinolone resistance determinant qnrS1.
Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion
Authors: Slováková Jana , Sikora Mateusz , Caballero-Mancebo Silvia , Krens S.F. Gabriel , Kaufmann Walter A. , Huljev Karla , Heisenberg Carl-Philipp
Published: November 2020

Tension of the actomyosin cell cortex plays a key role in determining cell-cell contact growth and size. The level of cortical tension outside of the cell-cell contact, when pulling at the contact edge, scales with the total size to which a cell-cell contact can grow1,2. Here we show in zebrafish primary germ layer progenitor cells that this monotonic relationship only applies to a narrow range of cortical tension increase, and that above a critical threshold, contact size inversely scales with cortical tension. This switch from cortical tension increasing to decreasing progenitor cell-cell contact size is caused by cortical tension promoting E-cadherin anchoring to the actomyosin cytoskeleton, thereby increasing clustering and stability of E-cadherin at the contact. Once tension-mediated E-cadherin stabilization at the contact exceeds a critical threshold level, the rate by which the contact expands in response to pulling forces from the cortex sharply drops, leading to smaller contacts at physiologically relevant timescales of contact formation. Thus, the activity of cortical tension in expanding cell-cell contact size is limited by tension stabilizing E-cadherin-actin complexes at the contact.
2019 Association of Biomolecular Resource Facilities Multi-Laboratory Data-Independent Acquisition Study
Authors: Neely Benjamin A. , Stemmer Paul M. , Searle Brian C. , Herring Laura E. , Martin LeRoy , Midha Mukul K. , Phinney Brett S. , Shan Baozhen , Palmblad Magnus , Wang Yan , Jagtap Pratik D. , Kirkpatrick Joanna
Published: November 2020

Despite the advantages of fewer missing values by collecting fragment ion data on all analytes in the sample, as well as the potential for deeper coverage, the adoption of data-independent acquisition (DIA) in core facility settings has been slow. The Association of Biomolecular Resource Facilities conducted a large interlaboratory study to evaluate DIA performance in laboratories with various instrumentation. Participants were supplied with generic methods and a uniform set of test samples. The resulting 49 DIA datasets act as benchmarks and have utility in education and tool development. The sample set consisted of a tryptic HeLa digest spiked with high or low levels of four exogenous proteins. Data are available in MassIVE MSV000086479. Additionally, we demonstrate how the data can be analysed by focusing on two datasets using different library approaches and show the utility of select summary statistics. These data can be used by DIA newcomers, software developers, or DIA experts evaluating performance with different platforms, acquisition settings and skill levels.