bluuebunny/crossref_metadata_2025 huggingface dataset:
Shear Stress Initiates Endothelial to Mesenchymal Transition in Endocardial Endothelial Cells
Authors: Brown Kathleen N. , Phan Hong Kim T. , Mustafa Tasneem , Jui Elysa , Ahmad Fariha N. , Birla Ravi P. , Sucosky Philippe , Connell Jennifer P. , Keswani Sundeep G. , Grande-Allen K. Jane
Published: December 2022

Discrete subaortic stenosis (DSS) is a congenital heart disease characterized by the formation of a fibrotic membrane below the aortic valve. The underlying cellular mechanisms of this disease are currently unknown. As one of the distinguishing features of DSS is the elevated pressure gradient in the left ventricular outflow tract, it is hypothesized that membrane formation is caused by elevated wall shear stress applied to the endocardial endothelial cells (EECs), triggering fibrosis. To correlate shear stress to an EEC fibrotic phenotype, we applied fluid shear stress to EECs at physiological and pathological shear rates using a cone-and-plate device, designed to recapitulate physiological wall shear stress in a controlled in vitro environment. Controlled shear stress regimes were applied to EECs to replicate the conditions observed in DSS patients. We found that elevated shear stress triggered EEC alignment as well as endothelial-to-mesenchymal transformation (EndMT) signaling pathways driven by upregulation ofSNAI1gene expression. The EECs were then treated with a small molecule inhibitor of Snail1 protein, CYD19, to attempt to attenuate EndMT signaling, and subsequently subjected to pathological shear stress. The Snail1 inhibitor did downregulate selected markers of EndMT signaling, although only transiently. Interestingly, the application of shear stress had a greater effect on the EEC gene and protein expression than did the Snail1 inhibition. This investigation of EEC response to shear stress reveals the pronounced and complex effect of this mechanical stimulation on the EEC phenotype. Further study should reveal the mechanisms that drive fibrosis and the formation of the DSS membrane.
Predicting the Influence of Fat Food Intake on the Absorption and Systemic Exposure of Small Drugs using ANDROMEDA by Prosilico Software
Authors: Fagerholm Urban , Hellberg Sven , Alvarsson Jonathan , Spjuth Ola
Published: December 2022

Abstract

Introduction

The ANDROMEDA software by Prosilico has previously been successfully applied and validated for predictions of absorption characteristics of small drugs in man. The influence of fat food on the gastrointestinal uptake and systemic exposure of drugs have, however, not yet been evaluated with the software.

Objective and Methodology

The main objective was to use ANDROMEDA to predict area under the plasma concentration-time curve ratios in the fed (fat food) and fasted states (AUCfed/AUCfast) for small drugs (including those marketed in 2021) and compare results with corresponding measured clinical estimates. Actual dose sizes were considered. Another objective was to compare the performance of ANDROMEDAvsphysiologically based pharmacokinetic (PBPK) modelling and simulations by The Food Effect PBPK IQ Working Group. PBPK results generated using Simcyp and GastroPlus software were based on various physicochemical,in vitroandin vivodata and a decision tree for model verification and optimization.

Results and Discussion

63 drugs, including 17 new drugs, with observed AUCfed/AUCfastbetween 0.2 and 5.5 were found and used for this evaluation. Predicted AUCfed/AUCfasthad mean and maximum errors of 1.5- and 4.1-fold, respectively, and the predictive accuracy (correlation between predicted and observed AUCfed/AUCfast; Q2) was 0.3. 14 % of predictions had >2-fold error. For 72 % of drugs, food interaction class was correctly predicted. The level of predictive accuracy was overall similar to results obtained with PBPK modelling and simulations, however, with lower maximum error and higher compound coverage. With PBPK models, maximum simulation error was 7.7-fold and 3 highly lipophilic compounds were not possible to simulate.

Conclusion

The results validate ANDROMEDA for prediction of fat food-drug interaction size for small drugs in man. Major advantages with the methodology include that prediction results are produced directly from molecular structure and oral dose and are similar to PBPK-simulation results obtained usingin vitroand clinical data. Furthermore, ANDROMEDA showed lower maximum errors and wider compound range.
M-Band Wavelet-Based Imputation of scRNA-seq Matrix and Multi-view Clustering of Cell
Authors: Liu Zihuan , Liu Tong , Sun Wenke , Zhao Yongzhong , Wang Xiaodi
Published: December 2022

Wavelet analysis has been recognized as a cutting-edge and promising tool in the fields of signal processing and data analysis. However, application of wavelet-based method in single-cell RNA sequencing (scRNA-seq) data is little known. Here, we present M-band wavelet-based imputation of scRNA-seq matrix and multi-view clustering of cells (WIMC). We applied integration of M-band wavelet analysis and uniform manifold approximation and projection (UMAP) to a panel of single cell sequencing datasets by breaking up the data matrix into a trend (low frequency or low resolution) component and (M-1) fluctuation (high frequency or high resolution) components. We leverage a non-parametric wavelet-based imputation algorithm of sparse data that integrates M-band wavelet transform for recovering dropout events of scRNA-seq datasets. Our method is armed with multi-view clustering of cell types, identity, and functional states, enabling missing cell types visualization and new cell types discovery. Distinct to standard scRNA-seq workflow, our wavelet-based approach is a new addition to resolve the notorious chaotic sparsity of scRNA-seq matrix and to uncover rare cell types with a fine-resolution.

Author summary

We develop M-band wavelet-based imputation of scRNA-seq matrix and multi-view clustering of cells. Our new approach integrates M-band wavelet analysis and UMAP to a panel of single cell sequencing datasets via breaking up the data matrix into a trend (low frequency or low resolution) component and (M– 1) fluctuation (high frequency or high resolution) components. Our method enables us to efficiently impute sparse scRNA-seq data matrix and to examine multi-view clustering of cell types, identity, and functional states, potentializing missing cell types recovery, fine rare cell types discovery, as well as functional cell states exploration.
Design principles for perfect adaptation in biological networks with nonlinear dynamics
Authors: Bhattacharya Priyan , Raman Karthik , Tangirala Arun K.
Published: December 2022

Establishing a mapping between the emergent biological properties and the repository of network structures has been of great relevance in systems and synthetic biology. Adaptation is one such biological property of paramount importance that promotes regulation in the presence of environmental disturbances. This paper presents a nonlinear systems theory-driven framework to identify the design principles for perfect adaptation. Based on the prior information about the network, we frame precise mathematical conditions for adaptation using nonlinear systems theory. We first deduce the mathematical conditions for perfect adaptation for constant input disturbances. Subsequently, we first translate these conditions to specific necessary structural requirements for adaptation in networks of small size and then extend to argue that there exist only two classes of architectures for a network of any size that can provide local adaptation in the entire state space, namely, incoherent feed-forward structure and negative feedback loop with buffer node. The additional positiveness constraints further narrow the admissible set of network structures. This also aids in establishing the global asymptotic stability for the steady state given a constant input disturbance. The entire method does not assume any explicit knowledge of the underlying rate kinetics, barring some minimal assumptions. Finally, we also discuss the infeasibility of the incoherent feed-forward networks (IFFLP) to provide adaptation in the presence of downstream connections. Detailed and extensive simulation studies corroborate the theoretical findings. Moreover, we propose a generic and novel algorithm based on a nonlinear systems theory to unravel the design principles for global adaptation.
Optimising a coordinate ascent algorithm for the meta-analysis of test accuracy studies
Authors: Baragilly Mohammed , Willis Brian H
Published: December 2022

Meta-analysis may be used to summarise a test’s accuracy. Often the sensitivity and specificity are the measures of interest and as these are correlated a bivariate random effects model is commonly used to fit the data. This model has five parameters and it may be optimised using a Newton-Raphson based algorithm providing adequate initial values of the parameters are identified. Numerical methods may be used to estimate robust initial values but estimating these is computationally expensive and it is not clear whether they provide a significant advantage over closed form methods in terms of reducing bias, mean square error, average relative error, and coverage probability. Here we consider six closed form methods for estimating the initial values of the parameters for a co-ordinate ascent algorithm used to fit the bivariate model and compare them with numerically derived robust initial values. Using simulation studies we demonstrate that all the closed form methods lead to a reduction in computation time of around 80% and rank higher overall across the metrics when compared with the robust initial values method. Although no initial values estimator dominated the others across all parameters and metrics, the two-step Hedges-Olkin estimator ranked highest overall across the different scenarios.
A Meta-analysis of 2D vs. 3D Ovarian Cancer Cellular Models
Authors: Kerslake Rachel , Belay Birhanu , Panfilov Suzana , Hall Marcia , Kyrou Ioannis , Randeva Harpal S. , Hyttinen Jari , Karteris Emmanouil , Sisu Cristina
Published: December 2022

Three-dimensional (3D) cancer models are revolutionizing research, allowing for the recapitulation ofin vivolike response through the use of anin vitrosystem, more complex and physiologically relevant than traditional mono-layer culture. Cancers such as ovarian (OvCa), are prone to developing resistance and are often lethal, and stand to benefit greatly from the enhanced modelling emulated by 3D culture. However current models often fall short of predicted response where reproducibility is limited owing to the lack of standardized methodology and established protocols. This meta-analysis aims to assess the current scope of 3D OvCa models and the differences in genetic profile presented by a vast array of 3D cultures. A meta-analysis of the literature (Pubmed.gov) spanning 2012 – 2022, was used to identify studies with comparable monolayer (2D) counterparts in addition to RNA sequencing and microarray data. From the data 19 cell lines were found to show differential regulation in their gene expression profiles depending on the bio-scaffold (i.e. agarose, collagen or Matrigel) compared to 2D cell cultures. Top genes differentially expressed 2D vs. 3D include C3, CXCL1, 2 and 8, IL1B, SLP1, FN1, IL6, DDIT4, PI3, LAMC2, CCL20, MMP1, IFI27, CFB, and ANGPTL4. Top Enriched Gene sets for 2D vs. 3D include IFN-α and IFN-γ Response, TNF-α signalling, IL-6-JAK-STAT3 signalling, angiogenesis, hedgehog signalling, apoptosis, epithelial mesenchymal transition, hypoxia, and inflammatory response. Our transversal comparison of numerous scaffolds allowed us to highlight the variability that can be induced by these scaffolds in the transcriptional landscape as well as identifying key genes and biological processes that are hallmarks of cancer cells grown in 3D cultures. Future studies are needed to identify which is the most appropriate in vitro/preclinical model to study tumour microenvironment.

Ovarian cancer is one of the most lethal forms of female cancers. Cell culture is often the go to model to study the molecular processes of cancer. However, this is an oversimplification of the reality. 3D tissue culture has been developed to address the cell culture limitations and to provide a more realistic model of the system studied. Cells grown in 3D represent better the human tumour microenvironment. This meta-analysis is exploring the use of 3D tissue culture as a model of ovarian cancer. Our analysis shows that ovarian cancer cells grown in 3D exhibit enhanced regulation in processes pertinent to tumour development and progression. We identify a panel of genes associated with specific 3D growth conditions that could be used as conditional markers. Finally, we present an overview of the state-of-art of 3D culture with an extensive profile of the genes and pathways enhanced in ovarian cancer models.
3D-Mass Spectrometry Imaging of Micro-scale 3D Cell Culture Models in Cancer Research
Authors: Iakab Stefania-Alexandra , Keller Florian , Schmidt Stefan , Cordes Jonas , Zhou Qiuqin , Cairns James L. , Fischer Frank , Schneider Richard , Wolf Ivo , Rudolf Rüdiger , Hopf Carsten
Published: December 2022

Three-dimensional (3D) human cell culture models have emerged as a key technology for personalized medicine and for phenotypic compound screening in more disease-likein-vitrosystems. Mass spectrometry imaging (MSI) is one of the most versatile label-free techniques that enables simultaneous generation of spatial maps for multiple relevant molecules in these 3D-models. Here, we present an integrated platform for 3D-MSI of 3D-cell cultures comprising 3D-printed metal casting molds for freezing and embedding, MS imaging of 100 serial cryosections and their computational elastic 3D-reconstruction. With this platform, we monitored multiple lipids that were selectively associated with different cell-types or cell-cell interactions within 300 μm-scale fibroblast and colon cancer biculture spheroids. Our findings suggest that 3D-printing-aided precise preparation of serial sections from small spheroids and visualization of marker molecules in 3D can provide a detailed overview of the cellular metabolic interplay in 3D cell culture models in cancer research and drug discovery.
From Multi-Allele Fish to Non-Standard Environments, How ZFIN Assigns Phenotypes, Human Disease Models, and Gene Expression Annotations to Genes
Authors: Bradford Yvonne M. , Van Slyke Ceri E. , Howe Douglas G. , Fashena David , Frazer Ken , Martin Ryan , Paddock Holly , Pich Christian , Ramachandran Sridhar , Ruzicka Leyla , Singer Amy , Taylor Ryan , Tseng Wei-Chia , Westerfield Monte
Published: December 2022

Danio reriois a model organism used to investigate vertebrate development. Manipulation of the zebrafish genome and resultant gene products by mutation or targeted knockdown has made the zebrafish a good system for investigating gene function, providing a resource to investigate genetic contributors to phenotype and human disease. Phenotypic outcomes can be the result of gene mutation, targeted knockdown of gene products, manipulation of experimental conditions, or any combination thereof. Zebrafish have been used in various genetic and chemical screens to identify genetic and environmental contributors to phenotype and disease outcomes. The Zebrafish Information Network (ZFIN) is the central repository for genetic, genomic, and phenotypic data that result from research usingDanio rerio. Here we describe how ZFIN annotates phenotype, expression, and disease model data across various experimental designs, how we computationally determine wild-type gene expression, the phenotypic gene, and how these results allow us to propagate gene expression, phenotype, and disease model data to the correct gene, or gene related entity.
Persistence of cultivar alleles in wild carrot (Daucus carotaL.) populations in the United States
Authors: Hernández Fernando , Palmieri Luciano , Brunet Johanne
Published: December 2022

Cultivated species and their wild relatives often hybridize in the wild and crop-wild hybrids can survive and reproduce in some environments. However, it is unclear whether crop alleles are permanently incorporated into the wild genomes in the long run or whether they are purged by natural selection. This question is key to accurately assessing the risk of escape and spread of cultivar genes into wild populations. Here, we use genomic data and population genomic methods to study hybridization and introgression between cultivated and wild carrots (Daucus carotaL.) in the United States. We used single nucleotide polymorphisms (SNPs) obtained via genotyping by sequencing for 450 wild individuals from 29 wild georeferenced populations in seven states and 144 cultivars from the United States, Europe, and Asia. Cultivated and wild carrots formed two well differentiated groups, and evidence of crop-wild admixture was detected in several but not all the wild populations in the United States. Two regions were identified where cultivar alleles were introgressed into wild carrots: California and the Nantucket Island, in Massachusetts. In these areas, we found no support for adaptive (or maladaptive) introgression, instead, most crop alleles seemed to be neutral. Surprisingly, there was no evidence of introgression in some populations with a long-known history of sympatry with the crop, suggesting that post-hybridization barriers might prevent introgression in some areas. Further studies are needed to better delineate the geographic patterns of introgression, but our results support the introgression and persistence of cultivar genes in wild carrot populations.
RNA conformational propensities determine cellular activity
Authors: Kelly Megan L. , Roy Rohit , Geng Ainan , Ganser Laura R. , Manghrani Akanksha , Cullen Bryan R. , Schulze-Gahmen Ursula , Herschlag Daniel , Al-Hashimi Hashim M.
Published: December 2022

Cellular processes are the product of interactions between biomolecules, which associate to form biologically active complexes1. These interactions are mediated by intermolecular contacts, which if disrupted, lead to alterations in cell physiology. Nevertheless, the formation of intermolecular contacts nearly universally requires changes in the conformations of the interacting biomolecules. As a result, binding affinity and cellular activity crucially depend not only on the strength of the contacts, but also on the inherent propensities to form binding-competent conformational states2,3. Thus, conformational penalties are ubiquitous in biology and must be known in order to quantitatively model binding energetics for protein and nucleic acid interactions4,5. However, conceptual and technological limitations have hindered our ability to dissect and quantitatively measure how conformational propensities impact cellular activity. Here, we systematically altered and determined the propensities for forming the protein-bound conformation of HIV-1 TAR RNA. These propensities quantitatively predicted the binding affinities of TAR to the RNA-binding region of the Tat protein and predicted the extent of HIV-1 Tat-dependent transactivation in cells. Our results establish the role of ensemble-based conformational propensities in cellular activity and reveal an example of a cellular process driven by an exceptionally rare and short-lived RNA conformational state.
Inducible CRISPRi-based operon silencing and selectivein transgene complementation inBorrelia burgdorferi
Authors: Murphy Bryan T. , Wiepen Jacob J. , He Huan , Pramanik Ankita S. , Peters Jason M. , Stevenson Brian , Zückert Wolfram R.
Published: December 2022

To accelerate genetic studies on the Lyme disease pathogenBorrelia burgdorferi, we developed an enhanced CRISPR interference (CRISPRi) approach for IPTG-inducible repression of specificB. burgdorferigenes. The entire system is encoded on a compact 11-kb shuttle vector plasmid that allows for inducible expression of both the sgRNA module and a non-toxic codon-optimized dCas9 protein. We validated this CRISPRi system by targeting the genes encoding for OspA and OspB, abundant surface lipoproteins co-expressed by a single operon, and FlaB, the major subunit forming the periplasmic flagella. As in other systems, sgRNAs complementary to the non-template strand were consistently effective in gene repression, with 4- to 994-fold reductions in targeted transcript levels and concomitant reductions of in proteins levels. Furthermore, we showed thatospABknockdowns could be selectively complementedin transfor OspA expression via the insertion of synonymous or non-synonymous CRISPRi-resistant PAM mutant (PAM*)ospAalleles into a unique site within the plasmid. Together, this establishes CRISPRi PAM* as a robust new genetic tool to simplify the study ofB. burgdorferigenes, bypassing the need for gene disruptions by allelic exchange and avoiding rare-codon toxicity from heterologous expression of dCas9.

SIGNIFICANCE

Borrelia burgdorferi, the causative agent of Lyme disease, is a tick-borne pathogen of global importance. Here, we expand the genetic toolbox for studyingB. burgdorferiphysiology and pathogenesis by establishing a single-plasmid-based CRISPRi system with optionalin transcomplementation for the functional study of essential and non-essential proteins.
The two-component system CroRS regulates isoprenoid flux to mediate antimicrobial tolerance in the bacterial pathogenEnterococcus faecalis
Authors: Todd Rose Francesca O , Darnell Rachel L , Morris Sali , Paxie Olivia , Campbell Georgia , Cook Gregory M , Gebhard Susanne
Published: December 2022

Antimicrobial tolerance is the ability of a microbial population to survive, but not proliferate, during antimicrobial exposure. Significantly, it has been shown to precede the development of bona fide antimicrobial resistance. We have previously identified the two-component system CroRS as a critical regulator of tolerance to antimicrobials like teixobactin in the bacterial pathogenEnterococcus faecalis. To understand the molecular mechanism of this tolerance, we carried out RNA-seq analyses in theE. faecaliswild-type and isogenic ΔcroRSmutant to determine the teixobactin-induced CroRS regulon. We identified a 132 gene CroRS regulon and show CroRS upregulates expression of all major components of the enterococcal cell envelope in response to teixobactin challenge. To gain further insight into the function of this regulon we isolated and characterized ΔcroRSmutants recovered for wild-type growth and tolerance. We show introduction of a single stop codon in a heptaprenyl diphosphate synthase (hppS), a key enzyme in the synthesis of the quinone electron carrier demethylmenaquinone (DMK), is sufficient to rescue loss of cell envelope integrity in thecroRSdeletion strain. Based on these findings, we propose a model where CroRS acts as a gate-keeper of isoprenoid biosynthesis, mediating flux of isoprenoids needed for cell wall synthesis (undecaprenyl pyrophosphate; UPP) and respiration (DMK) to maintain cell wall homeostasis upon antimicrobial challenge. Dysregulation of this flux in the absence ofcroRSleads to a loss of tolerance, which is rescued by loss of function mutations in HppS, allowing an increase in isoprenoid flow to UPP and subsequently cell wall synthesis.

Importance

Antimicrobial tolerance is the ability of a microorganism to survive, but not grow upon antimicrobial challenge, and is an important precursor to the development of antimicrobial resistance (the ability to profilerate). Understanding the molecular mechanisms that underpin tolerance will therefore aid in hampering the development of resistance to novel antimicrobials such as teixobactin. CroRS is an essential two-component regulator of antimicrobial tolerance in the bacterial pathogenEnterococcus faecalis. We have determined the antimicrobial-induced CroRS regulon and identified key mutations in a heptaprenyl diphosphate synthase to uncover a novel mechanism of antimicrobial tolerance.
External validation and updating of clinical severity scores to guide referral of young children with acute respiratory infections in resource-limited primary care settings
Authors: Chandna Arjun , Mwandigha Lazaro , Koshiaris Constantinos , Limmathurotsakul Direk , Nosten Francois , Lubell Yoel , Perera-Salazar Rafael , Turner Claudia , Turner Paul
Published: December 2022

Background

Accurate and reliable guidelines for referral of children from resource-limited primary care settings are lacking. We identified three practicable paediatric severity scores (Liverpool quick Sequential Organ Failure Assessment [LqSOFA], quick Pediatric Logistic Organ Dysfunction-2 [qPELOD-2], and the modified Systemic Inflammatory Response Syndrome [mSIRS]) and externally validated their performance in young children presenting with acute respiratory infections to a primary care clinic located within a refugee camp on the Thailand-Myanmar border.

Methods

This secondary analysis of data from a longitudinal birth cohort study consisted of 3,010 acute respiratory infections in children aged ≤ 24 months. The primary outcome was receipt of supplemental oxygen. We externally validated the discrimination, calibration, and net-benefit of the scores, and quantified gains in performance that might be expected if they were deployed as simple clinical prediction models, and updated to include nutritional status and respiratory distress.

Results

104/3,010 (3.5%) presentations met the primary outcome. The LqSOFA score demonstrated the best discrimination (AUC 0.84; 95% CI 0.79-0.89) and achieved a sensitivity and specificity > 0.80. Converting the scores into clinical prediction models improved performance, resulting in ∼20% fewer unnecessary referrals and ∼30-60% fewer children incorrectly managed in the community.

Conclusions

The LqSOFA score is a promising triage tool for young children presenting with acute respiratory infections in resource-limited primary care settings. Where feasible, deploying the score as a simple clinical prediction model might enable more accurate and nuanced risk stratification, increasing applicability across a wider range of contexts.
A Randomized Placebo Controlled Clinical Trial of a Metabolic Shifting Probiotic, Sugar Shift, for the Treatment of T2DM
Authors: García Gissel , Soto Josanne , Rodríguez Lays , Nuez Maricela , Domínguez Noraika , Buchaca Emilio F. , Martínez Duniesky , Gómez Rolando J. , Ávila Yohanka , Carlin Martha R. , Cano Raúl J.
Published: December 2022

Type 2 diabetes mellitus (T2DM) is a chronic metabolic disorder characterized by hyperglycemia, insulin resistance and chronic inflammation. Probiotics have been claimed effective in the management of obesity and type 2 diabetes mellitus. BiotiQuest™ Sugar Shift is a symbiotic formulation rationally designed for the endogenous conversion of glucose and fructose to support restoration of the human gut microbiota, modulation of intestinal glucose, and the production of anti-inflammatory metabolites.

We report the results of a 12-week, double blind, placebo-controlled study designed to evaluate Sugar Shift in Cuban T2DM patients. Clinical parameters, including fasting and 2h post-prandial glucose, hemoglobin A1c, a lipid panel, insulin, creatinine, and serum lipopolysaccharide levels were assessed. Microbiome composition was assessed by 16S amplicon sequencing of the variable region V3-V4 of the 16S rRNA gene. Metabolic biomarkers were inferred from microbiome data by Kruskal-Wallis H test and LEfSe.

Fasting glucose, Insulin, and serum LPS levels decreased significantly at day 84 as compared to day 1 in the treated group and to control group. Hb A1c remained stable in the treatment group as compared to the controls but not show significant improvement in the study period.

Microbiome analysis showed significant increase in Chao1 alpha diversity in the treated group between day 1 and day 84. Taxonomic and functional biomarkers revealed significant differences between the Day 1 and Day 84 microbiome profiles in the treatment group, primarily associated with acetate, propionate, and butyrate production.

Our results indicate that Sugar Shift can be a suitable adjunct therapy to standard of care therapy in the management of T2DM based upon the improvement in key inflammatory and insulin resistance markers. These results were interpreted as an indication of favorable microbiome changes during the course of the treatment for 12 weeks.
A Binary RNA and DNA Self-Amplifying Platform for Next Generation Vaccines and Therapeutics
Authors: Jefferies Wilfred A. , Choi Kyung Bok , Ribeca Paolo , Kari Suresh , Young Jay , Hui Elizabeth , Qi Simon Yong , Garrosvillas Emmanuel , Lincez Pamela , Welch Tracy , Saranchova Iryna , Pfeifer Cheryl G.
Published: December 2022

Conventional mRNA-based vaccines were instrumental in lowering the burden of the pandemic on healthcare systems and in reducing mortality. However, such first-generation vaccines have significant weaknesses. Here, we describe a high-performance binary recombinant vectoral platform offering the flexibility to be used as a self-amplifying mRNA or a self-amplifying DNA. Both formats drive long-lasting expression and actuate robust antibody responses against SAR-CoV-2 spike, and neither format require encapsulation with lipid nanoparticles (LNP) in the generation immune responses. The platform combines the power of conventional mRNA with the low-dosage of self-amplifying vectors together with the simplicity, rapid creation, ease of storage, and convenience of distribution of plasmid DNA vectors. This platform promises to pave the way for more effective, less expensive, and truly democratized vaccines and therapeutics.

One-Sentence Summary

Gemini: a versatile platform that improves on existing vaccine formats in terms of effectiveness, manufacturing, distribution, and cost.
The interaction between random and systematic visual stimulation and infraslow quasiperiodic spatiotemporal patterns of whole brain activity
Authors: Xu Nan , Smith Derek M. , Jeno George , Seeburger Dolly T. , Schumacher Eric H. , Keilholz Shella D.
Published: December 2022

One prominent feature of the infraslow BOLD signal during rest or task is quasi-periodic spatiotemporal pattern (QPP) of signal changes that involves an alternation of activity in key functional networks and propagation of activity across brain areas, and that is known to tie to the infraslow neural activity involved in attention and arousal fluctuations. This ongoing whole-brain pattern of activity might potentially modify the response to incoming stimuli or be modified itself by the induced neural activity. To investigate this, we presented checkerboard sequences flashing at 6Hz to subjects. This is a salient visual stimulus that is known to produce a strong response in visual processing regions. Two different visual stimulation sequences were employed, a systematic stimulation sequence in which the visual stimulus appeared every 20.3 secs and a random stimulation sequence in which the visual stimulus occurred randomly every 14~62.3 secs. Three central observations emerged. First, the two different stimulation conditions affect the QPP waveform in different aspects, i.e., systematic stimulation has greater effects on its phase and random stimulation has greater effects on its magnitude. Second, the QPP was more frequent in the systematic condition with significantly shorter intervals between consecutive QPPs compared to the random condition. Third, the BOLD signal response to the visual stimulus across both conditions was swamped by the QPP at the stimulus onset. These results provide novel insights into the relationship between intrinsic patterns and stimulated brain activity.
Quantitative mapping of autophagic cargo during nutrient stress reveals YIPF3-YIPF4 as membrane receptors for Golgiphagy
Authors: Hickey Kelsey L. , Swarup Sharan , Smith Ian R. , Paoli Julia C. , Paulo Joao A. , Harper J. Wade
Published: December 2022

During nutrient stress, macroautophagy is employed to degrade cellular macromolecules, thereby providing biosynthetic building blocks while simultaneously remodeling the proteome. While the machinery responsible for initiation of macroautophagy is well characterized, our understanding of the extent to which individual proteins, protein complexes and organelles are selected for autophagic degradation, and the underlying targeting mechanisms is limited. Here, we use orthogonal proteomic strategies to provide a global molecular inventory of autophagic cargo during nutrient stress in mammalian cell lines. Through prioritization of autophagic cargo, we identify a heterodimeric pair of membrane-embedded proteins, YIPF3 and YIPF4, as receptors for Golgiphagy. During nutrient stress, YIPF4 is mobilized into ATG8-positive vesicles that traffic to lysosomes as measured via Golgiphagy flux reporters in a process that requires the VPS34 and ULK1-FIP200 arms of the autophagy system. Cells lacking YIPF3 or YIPF4 are selectively defective in elimination of Golgi membrane proteins during nutrient stress. By merging absolute protein abundance with autophagic turnover, we create a global protein census describing how autophagic degradation maps onto protein abundance and subcellular localization. Our results, available via an interactive web tool, reveal that autophagic turnover prioritizes membrane-bound organelles (principally Golgi and ER) for proteome remodeling during nutrient stress.

One-Sentence Summary

During nutrient stress, macroautophagy uses organelle-phagy receptors to prioritize recycling of Golgi and ER membrane proteins.
Molecular mechanisms regulating the pH-dependent pr/E interaction in yellow fever virus
Authors: Crampon E. , Covernton E. , Vaney M.C. , Dellarole M. , Sharma A. , Haouz A. , England P. , Lepault J. , Duquerroy S. , Rey F.A. , Barba-Spaeth G.
Published: December 2022

Flavivirus particles bud in the ER of infected cells as immature virions composed of 180 heterodimers of glycoproteins prM and E, associated as 60 (prM/E)3trimeric spikes. Exposure to the mildly acidic pH of the TGN results in dissociation of the trimeric spikes followed by reassociation of the prM/E protomers into 90 dimers organized in a characteristic herringbone pattern. The furin site in prM is exposed in the dimers for maturation of prM into M and pr. For flaviviruses such as the tick-borne encephalitis virus (TBEV) as well as for dengue virus, it was shown that at neutral pH pr loses affinity for E, such that it dissociates from the mature particle as soon as it reaches the external milieu, which is at neutral pH. Using a soluble recombinant form of E (sE) and pr from yellow fever virus (YFV), we show here that the affinity of pr for recombinant E protein remains high even at neutral pH. The X-ray structure of YFV pr/sE shows more extensive inter-chain hydrogen bonding than does the dengue or TBEV, and also that it retains the charge complementarity between the interacting surfaces of the two proteins even at neutral pH. We further show that pr blocks sE flotation with liposomes when exposed at low pH at a 1:1 stoichiometry, yet in the context of the virus particle, an excess of 10:1 pr:E ratio is required to block virus/liposome fusion. In aggregate, our results show that the paradigm obtained from earlier studies of other flaviviruses does not apply to yellow fever virus, the flavivirus type species. A mechanism that does not rely solely in a change in the environmental pH is thus required for the release of pr from the mature particles upon release from infected cells. These results open up new avenues to understand the activation mechanism that yields mature, infectious YFV particles.
Burst firing is required for induction of Hebbian LTP at lateral perforant path to hippocampal granule cell synapses
Authors: Kim Yoonsub , Kim Sooyun , Ho Won-Kyung , Lee Suk-Ho
Published: December 2022

High frequency burst firing is critical in summation of back-propagating action potentials (APs) in dendrites, which may greatly depolarize dendritic membrane potential. The physiological significance of burst firings of hippocampal dentate GCs in synaptic plasticity remains unknown. We found that GCs with low input resistance could be categorized into regular-spiking (RS) and burst-spiking (BS) cells based on their initial firing frequency (Finit) upon somatic rheobase current injection, and investigated how two types of GCs differ in long-term potentiation (LTP) induced by high-frequency lateral perforant pathway (LPP) inputs. Induction of Hebbian LTP at LPP synapses required at least three postsynaptic APs at Finithigher than 100 Hz, which was met in BS but not in RS cells. The synaptically evoked burst firing was critically dependent on persistent Na+current, which was larger in BS than RS cells. The Ca2+source for Hebbian LTP at LPP synapses was primarily provided by L-type calcium channels. In contrast, Hebbian LTP at medial PP synapses was mediated by T-type calcium channels, and could be induced regardless of cell types or Finitof postsynaptic APs. These results suggest that intrinsic firing properties affect synaptically driven firing patterns, and that bursting behavior differentially affects Hebbian LTP mechanisms depending on the synaptic input pathway.
Single-cell transcriptome analysis illuminating the characteristics of species-specific innate immune responses against viral infections
Authors: Aso Hirofumi , Ito Jumpei , Ozaki Haruka , Kashima Yukie , Suzuki Yutaka , Koyanagi Yoshio , Sato Kei
Published: December 2022

Bats harbor various viruses without severe symptoms and act as their natural reservoirs. The tolerance of bats against viral infections is assumed to originate from the uniqueness of their immune system. However, how immune responses vary between primates and bats remains unclear. Here, we characterized differences in the immune responses by peripheral blood mononuclear cells to various pathogenic stimuli between primates (humans, chimpanzees, and macaques) and bats (Egyptian fruit bats) using single-cell RNA sequencing. We show that the induction patterns of key cytosolic DNA/RNA sensors and antiviral genes differed between primates and bats. A novel subset of monocytes induced by pathogenic stimuli specifically in bats was identified. Furthermore, bats robustly respond to DNA virus infection even though major DNA sensors are dampened in bats. Overall, our data suggest that immune responses are substantially different between primates and bats, presumably underlying the difference in viral pathogenicity among the mammalian species tested.
EEG error-related potentials encode magnitude of errors and individual perceptual thresholds
Authors: Iwane Fumiaki , Iturrate Iñaki , Chavarriaga Ricardo , Millán José del R.
Published: December 2022

Error-related potentials (ErrP) are a prominent electroencephalogram (EEG) correlate of performance monitoring, and so crucial for learning and adapting our behavior. Although there exists an agreement that ErrP signal awareness to errors, it remains poorly understood whether they encode further information. Here we report an experiment with sixteen participants during three recording sessions in which occasional visuomotor rotations of varying magnitude occurred during a cursor reaching task. We designed a brain-computer interface (BCI) to detect ErrP in single trials that provided real-time feedback to participants by changing the color of the cursor upon ErrP detection. The individual ErrP-BCI decoders exhibited good transfer across recording sessions and scalability over the varying magnitude of errors. Our results indicate that ErrPs encode not only the conscious perception of errors, but also their magnitude, in their amplitude and latency. Furthermore, a non-linear relationship between the ErrP-BCI output and the magnitude of errors predicts individual perceptual thresholds to detect rotations. The uncovered relationship is consistent with non-human primate studies, which found a similar relationship between the size of errors and simple spike activity of Purkinje cells, and we conjecture a cerebellar contribution to ErrP. Our experimental setup and findings open new avenues to probe and extend current theories of performance monitoring, which are based on response conflict tasks, by incorporating continuous human-interaction tasks as well as analysis of the ErrP complex as a whole rather than individual peaks.
Regional genetic correlations highlight relationships between neurodegenerative diseases and the immune system
Authors: Lona-Durazo Frida , Reynolds Regina H. , Scholz Sonja W. , Ryten Mina , Taliun Sarah A. Gagliano
Published: December 2022

Neurodegenerative diseases, including Alzheimer’s disease (AD), Parkinson’s disease (PD), Lewy body dementia (LBD) and amyotrophic lateral sclerosis (ALS), are devastating complex diseases that result in a physical and psychological burden to patients and their families. There have been significant efforts to understand the genetic basis of neurodegenerative diseases resulting in the identification of disease risk-associated variants involved in several molecular mechanisms, including those that influence immune-related pathways. Regional genetic correlations, in contrast to genome-wide correlations, between pairs of immune and neurodegenerative traits have not been comprehensively explored, but such a regional assessment could shed light on additional immune-mediated risk-associated loci. Here, we systematically assessed the potential role of the immune system in five neurodegenerative diseases, by estimating regional genetic correlations between neurodegenerative diseases and immune-cell-derived single-cell expression quantitative trait loci (sc-eQTLs), using the recently developed method of Local Analysis of [co]Variant Association (LAVA). We used the most recently published genome-wide association studies (GWASes) for five neurodegenerative diseases and publicly available sc-eQTLs derived from 982 individuals from the OneK1K Consortium, capturing aspects of the innate and adaptive immune systems. Additionally, we tested GWASes from well-established immune-mediated diseases, Crohn’s disease (CD) and ulcerative colitis (UC), the immune-mediated neurodegenerative disease, multiple sclerosis (MS) and a well-powered GWAS with strong signal in the HLA region, schizophrenia (SCZ), as positive controls. Finally, we also performed regional genetic correlations between diseases and protein levels. We observed significant (FDR < 0.01) regional genetic correlations between sc-eQTLs and neurodegenerative diseases across 151 unique genes, spanning both the innate and adaptive immune systems, across most diseases tested (except for frontotemporal dementia (FTD) and LBD). Colocalization analyses on followed-up regional correlations highlighted immune-related candidate causal risk genes associated with neurodegenerative diseases. We also observed significant regional correlations with protein levels across 156 unique proteins, across all diseases tested, except for FTD. The outcomes of this study will improve our understanding of the immune component of neurodegeneration, which can be potentially used to repurpose existing immunotherapies used in clinical care for other immune-mediated diseases, to slow the progression of neurodegenerative diseases.
The relationship between maternal psychopathology and offspring incontinence and constipation at school age: a prospective cohort study
Authors: Sawyer Gemma , Heron Jon , Joinson Carol
Published: December 2022

Background

Maternal depression and anxiety may increase the risk of offspring incontinence; however, current evidence is unable to draw causal inferences. This study aimed to examine prospective associations between maternal psychopathology and offspring incontinence/constipation and examine evidence for causal intra-uterine effects.

Methods

The study used data from 6,489 children from the Avon Longitudinal Study of Parents and Children. Mothers provided data on depression and anxiety (antenatal and postnatal) and their child’s incontinence (daytime wetting, bedwetting, soiling) and constipation at age 7. We used multivariable logistic regression to examine evidence for independent effects of maternal depression/anxiety on offspring incontinence/constipation and explore a critical/sensitive period of exposure. A negative control design was utilised to examine evidence causal intra-uterine effects.

Results

Postnatal maternal psychopathology was associated with an increased risk of offspring incontinence and constipation (e.g. postnatal anxiety and daytime wetting OR: 1.53; 95% CI: 1.21-1.94), and data were consistent with a critical period model. There was evidence for an independent effect of maternal anxiety. Antenatal maternal psychopathology was associated with constipation (e.g. antenatal anxiety OR: 1.57; 95% CI: 1.25-1.98), but there was no evidence for a causal intra-uterine effect.

Limitations

Attrition and maternal reports without use of established diagnostic criteria for incontinence/constipation are potential limitations.

Conclusions

Children exposed to maternal postnatal psychopathology had a greater risk of incontinence/constipation, and maternal anxiety had stronger associations than depression.
Species and condition shape the mutational spectrum in experimentally evolved biofilms
Authors: Hu Guohai , Wang Yue , Liu Xin , Strube Mikael Lenz , Wang Bo , Kovács Ákos T.
Published: December 2022

Laboratory experimental evolution provides a powerful tool for studying microbial adaptation to different environments. To understand the differences and similarities of the dynamic evolutionary landscapes of two model species from theBacillusgenus as they adapt to abiotic and biotic surfaces, we revived the archived population samples from our four previous experimental evolution studies and performed longitudinal whole-population genome sequencing. Surprisingly, higher number of mutations, higher genotypic diversity, and higher evolvability were detected in the biotic conditions with smaller population size. Different adaptation strategies were observed in different environments within each species, with more diversified mutational spectrum detected in biotic conditions. The insertion sequences ofBacillus thuringiensisare critical for its adaptation to the plastic bead-attached biofilm environment, but insertion sequence mobility was a general phenomenon in this species independent of the selection condition. Additionally, certain parallel evolution has been observed across species and environments, particularly when two species adapt to the same environment at the same time. Further, our results suggest that the population size might be an important driver of evolution. Together, these results provide the first comprehensive mutational landscape of two bacterial species’ biofilms that is adapted to an abiotic and biotic surface.

Importance

Biofilm formation is a vital factor for the survival and adaptation of bacteria in diverse environmental niches. Experimental evolution combined with the advancement of whole-population genome sequencing provides us a powerful tool to understand the genomic dynamic of evolutionary adaptation to different environments, such as during biofilm development. Previous studies described the genetic and phenotypic changes of selected clones from experimentally evolvedBacillus thuringiensisandBacillus subtilisthat were adapted under abiotic and biotic biofilm conditions. However, the full understanding of the dynamic evolutionary landscapes was lacking. Further, the differences and similarities of adaptive mechanisms inB. thuringiensisandB. subtiliswere not identified. To overcome these limitations, we performed longitudinal whole-population genome sequencing to study the underlying genetic dynamics at high resolution. Our study provides the first comprehensive mutational landscape of two bacterial species’ biofilms that is adapted to an abiotic and biotic surface.