bluuebunny/crossref_metadata_2025 huggingface dataset:
Astrocytic TDP-43 dysregulation impairs memory by modulating antiviral pathways and interferon-inducible chemokines
Authors: Licht-Murava Avital , Meadows Samantha M. , Palaguachi Fernando , Song Soomin C. , Bram Yaron , Zhou Constance , Jackvony Stephanie , Schwartz Robert E. , Froemke Robert C. , Orr Adam L. , Orr Anna G.
Published: September 2022

TDP-43 pathology is prevalent in dementia but the cell type-specific effects of TDP-43 are not clear and therapeutic strategies to alleviate TDP-43-linked cognitive decline are lacking. We found that patients with Alzheimer’s disease (AD) or frontotemporal dementia (FTD) have aberrant TDP-43 accumulation in hippocampal astrocytes. In mouse models, induction of widespread or hippocampus-targeted accumulation in astrocytic TDP-43 caused progressive memory loss and localized changes in antiviral gene expression. These changes were cell-autonomous and correlated with impaired astrocytic defense against infectious viruses. Among the changes, astrocytes had elevated levels of interferon-inducible chemokines and neurons had elevated levels of the corresponding chemokine receptor CXCR3 in presynaptic terminals. CXCR3 stimulation altered presynaptic function and promoted neuronal hyperexcitability, akin to the effects of astrocytic TDP-43, and blockade of CXCR3 reduced this activity. Ablation of CXCR3 also prevented TDP-43-linked memory loss. Thus, astrocytic TDP-43 dysfunction contributes to cognitive impairment through aberrant chemokine-mediated astrocytic-neuronal interactions.

In dementia, protein buildup in glia enhances chemokine signaling to synapses and impairs specific aspects of neurocognitive function.
Assessing the utility of death assemblages as reference conditions in a common benthic index (M-AMBI) with simulations
Authors: Smith Jansen A. , Pruden Matthew J. , Handley John C. , Durham Stephen R. , Dietl Gregory P.
Published: September 2022

Incorporating paleontological data into the methods and formats already familiar to conservation practitioners may facilitate greater use of paleontological data in conservation practice. Benthic indices (e.g., Multivariate - AZTI Marine Biotic Index; M-AMBI) already incorporate reference conditions and are a good candidate for integration. In simulations of living communities under constant and changing environmental conditions, we evaluate the capacity of death assemblage reference conditions to replicate M-AMBI values when used in place of reference conditions from the final ten generations of the simulation or all five hundred simulated generations.

Reference conditions from all death assemblage scenarios successfully replicated correct remediation decisions in the majority of simulation runs with environmental change and stability. Variations in M-AMBI values were due to overestimated richness and diversity in the death assemblages but effects of changes to these parameters varied across scenarios, emphasizing the importance of evaluating multiple metrics. Time averaging was largely beneficial, particularly when environmental change occurred and short-term ecological observations (ten generations) produced incorrect remediation decisions. When the duration of time averaging is known, death assemblages can provide valuable long-term perspectives with the potential to outperform temporally constrained baseline information from monitoring the living community.

Supplementary material

All R code used to produce the simulation, analyze outputs, and create figures is available at: https://doi.org/10.5281/zenodo.6355921. The simulated data is also available at this location. Supplementary figures and analyses referred to in the text are available at the end of this document.
Targeted multi-omic analysis of human skin tissue identifies alterations of conventional and unconventional T cells associated with burn injury
Authors: Labuz Daniel , Lewis Giavonni , Fleming Irma D. , Thompson Callie M. , Zhai Yan , Firpo Matthew A. , Leung Daniel T.
Published: September 2022

Burn injuries are a leading cause of unintentional injury, associated with a dysfunctional immune response and an increased risk of infections. Despite this, little is known about the role of T cells in human burn injury. In this study, we compared the activation and function of conventional T cells and unconventional T cell subsets in skin tissue from acute burn (within 7 days from initial injury) burn, late phase burn (beyond 7 days from initial injury), and non-burn patients. We compared T cell functionality by a combination of flow cytometry and a multi-omic single-cell approach with targeted transcriptomics and protein expression. We found a significantly lower proportion of CD8+ T cells in burn skin compared to non-burn skin, with CD4+ T cells making up the bulk of the T cell population. Both conventional and unconventional burn tissue T cells show significantly higher IFN-γ and TNF-α levels after stimulation than non-burn skin T cells. In sorted T cells, clustering showed that burn tissue had significantly higher expression of homing receptors CCR7, S1PR1, and SELL compared to non-burn skin. In unconventional T cells, including mucosal-associated invariant T (MAIT) and γδ T cells, we see significantly higher expression of cytotoxic molecules GZMB, PRF1, and GZMK. Multi-omics analysis of conventional T cells suggests a shift from tissue-resident T cells in non-burn tissue to a circulating T cell phenotype in burn tissue. In conclusion, by examining skin tissue from burn patients, our results suggest that T cells in burn tissue have a pro-inflammatory rather than a homeostatic tissue-resident phenotype, and that unconventional T cells have a higher cytotoxic capacity. Our findings have the potential to inform the development of novel treatment strategies for burns.
The role of myosin contractility as a molecular determinant of traction force regulation
Authors: Ghosh Debsuvra , Ghosh Subhadip , Chaudhuri Abhishek
Published: September 2022

Cells generate traction forces on the extracellular matrix to crawl forward. A complex molecular machinery is involved in the generation, transmission, and transduction of cellular forces inside and outside of cells. The molecular clutch hypothesis, with motors as rudimentary force generators, has been beneficial in modelling the distinctive biomechanical roles played by the components of this machinery. In this paper, we propose an analytical model that incorporates the active dynamics of myosin motors and establishes their roles in regulating the traction force in an experimentally accessible parameter space. As the parameters pertaining to molecular determinants are varied, we show that the system traverses between diverse states of stabilities - from decaying oscillations to self-sustaining limit cycles. The hallmarks of motor-clutch models like load-and-fail dynamics and shift in traction optima are successfully encapsulated. Modulating myosin activity in our model via different pathways exhibits striking shifts in optimal stiffness, providing excellent agreement with experiments and additional testable predictions.
An oligogenic architecture underlying ecological and reproductive divergence in sympatric populations
Authors: Briševac Dušica , Peralta Carolina M. , Kaiser Tobias S.
Published: September 2022

The evolutionary trajectories and genetic architectures underlying ecological divergence with gene flow are poorly understood. Sympatric timing types of the intertidal insect Clunio marinus (Diptera) from Roscoff (France) differ in lunar reproductive timing. One type reproduces at full moon, the other at new moon, controlled by a circalunar clock of yet unknown molecular nature. Lunar reproductive timing is a magic trait for a sympatric speciation process, as it is both ecologically relevant and entails assortative mating. Here we show that the difference in reproductive timing is controlled by at least four quantitative trait loci (QTL) on three different chromosomes. They are partly associated with complex inversions, but differentiation of the inversion haplotypes cannot explain the different phenotypes. The most differentiated locus in the entire genome, with QTL support, is the period locus, implying that this gene could not only be involved in circadian timing but also in lunar timing. Our data indicate that magic traits can be based on an oligogenic architecture and can be maintained by selection on several unlinked loci.
Spatial Transcriptomics Using Multiplexed Deterministic Barcoding in Tissue
Authors: Wirth Johannes , Compera Nina , Yin Kelvin , Brood Sophie , Chang Simon , Martinez-Jimenez Celia P. , Meier Matthias
Published: September 2022

In this study, we present a multiplexed version of deterministic barcoding in tissue (xDbit) to acquire spatially resolved transcriptomes of nine tissue sections in parallel. New microfluidic chips were developed to spatially encode mRNAs over a total tissue area of 1.17 cm2 with spots of 50 μm×50 μm. Optimization of the biochemical protocol increased read and gene counts per spot by one order of magnitude compared with previous reports. Furthermore, the introduction of alignment markers allows seamless registration of images and spatial transcriptomic spot coordinates. Together with technological advances, we provide an open-source computational pipeline to transform raw sequencing data from xDbit experiments into the AnnData format. The functionality of xDbit was demonstrated by the acquisition of 18 spatially resolved transcriptomic datasets from five different murine organs, including cerebellum, liver, kidney, spleen, and heart. Factor analysis and deconvolution of xDbit spatial transcriptomes allowed for in-depth characterization of the murine kidney.
Label-free imaging of 3D pluripotent stem cell differentiation dynamics on chip
Authors: Atwell Scott , Waibel Dominik J. E. , Boushehri Sayedali Shetab , Marr Carsten , Meier Matthias
Published: September 2022

The dynamic chemical and architectural microenvironments of 3D stem cell cultures can be controlled by integration into a microfluidic chip. Massive parallelized 3D stem cell cultures for engineering in vitro human cell types require new imaging methods with high time and spatial resolution to fully exploit technological advances in cell culture. Here, we introduce a label-free deep learning method called Bright2Nuc to predict in silico nuclear staining in 3D from bright-field images obtained using traditional confocal microscopy. Bright2Nuc was trained and applied to several hundred 3D human induced pluripotent stem cell cultures differentiating towards definitive endoderm on a microfluidic platform. Combined with existing image analysis tools, Bright2Nuc segmented individual nuclei from bright-field images, quantified their morphological properties, predicted stem cell differentiation state, and tracked the cells over time. Our methods are available in an open-source pipeline that enables researchers to upscale 3D cell phenotyping in stem cell culture.
Incidental Temporal Binding in Rats: A Novel Behavioral Task Relevant to Episodic Memory
Authors: Radostova Dominika , Kuncicka Daniela , Krajcovic Branislav , Hejtmanek Lukas , Petrasek Tomas , Svoboda Jan , Stuchlik Ales , Brozka Hana
Published: September 2022

We designed a behavioral task called One-Trial Trace Escape Reaction (OTTER), in which rats incidentally associate two temporally discontinuous stimuli: a neutral acoustic cue (CS) with an aversive stimulus (US) which occurs two seconds later (CS-2s-US sequence). Rats are first habituated to two similar environmental contexts (A and B), each consisting of an interconnected dark and light chamber. Next, rats experience the CS-2s-US sequence in the dark chamber of one of the contexts (either A or B); the US is terminated immediately after a rat escapes into the light chamber. The CS-2s-US sequence is presented only once to ensure the incidental acquisition of the association. The recall is tested 24 h later when rats are presented with only the CS in the alternate context (B or A), and their behavioral response is observed. Our results show that 59 % of the rats responded to the CS by escaping to the light chamber, although they experienced only one CS-2s-US pairing. The OTTER task offers a flexible high throughput tool to study memory acquired incidentally after a single experience. Incidental acquisition of association between temporally discontinuous events is highly relevant to episodic memory formation.
Characterizing the targets of transcription regulators by aggregating ChIP-seq and perturbation expression data sets
Authors: Morin Alexander , Chu Eric Ching-Pan , Sharma Aman , Adrian-Hamazaki Alex , Pavlidis Paul
Published: September 2022

Mapping the gene targets of chromatin-associated transcription regulators (TRs) is a major goal of genomics research. ChIP-seq of TRs and experiments that perturb a TR and measure the differential abundance of gene transcripts are a primary means by which direct relationships are tested on a genomic scale. It has been reported that there is poor overlap in the evidence across gene regulation strategies, emphasizing the need for integrating results from multiple experiments. While research consortia interested in gene regulation have produced a valuable trove of high-quality data, there is an even greater volume of TR-specific data throughout the literature. In this study, we demonstrate a workflow for the identification, uniform processing, and aggregation of ChIP-seq and TR perturbation experiments for the ultimate purpose of ranking human and mouse TR-target interactions. Focusing on an initial set of eight regulators (ASCL1, HES1, MECP2, MEF2C, NEUROD1, PAX6, RUNX1, and TCF4), we identified 497 experiments suitable for analysis. We used this corpus to examine data concordance, to identify systematic patterns of the two data types, and to identify putative orthologous interactions between human and mouse. We build upon commonly used strategies to forward a procedure for aggregating and combining these two genomic methodologies, assessing these rankings against independent literature-curated evidence. Beyond a framework extensible to other TRs, our work also provides empirically ranked TR-target listings, as well as transparent experiment-level gene summaries for community use.
A cross-species study of sex chromosome dosage effects on mammalian brain anatomy
Authors: Guma Elisa , Beauchamp Antoine , Liu Siyuan , Levitis Elizabeth , Clasen Liv S. , Torres Erin , Blumenthal Jonathan , Lalonde Francois , Qiu Lily R. , Hrncir Haley , MacKenzie-Graham Allan , Yang Xia , Arnold Arthur P. , Lerch Jason P , Raznahan Armin
Published: September 2022

All eutherian mammals show chromosomal sex determination with contrasting sex chromosome dosages (SCDs) between males (XY) and females (XX). Studies in transgenic mice and humans with sex chromosome trisomy (SCT) have revealed direct SCD effects on regional mammalian brain anatomy, but we lack a formal test for cross-species conservation of these effects. Here, we develop a harmonized framework for comparative structural neuroimaging and apply this to systematically profile SCD effects on regional brain anatomy in both humans and mice by contrasting groups with SCT (XXY and XYY) vs. XY controls. We show that total brain size is substantially altered by SCT in humans (significantly decreased by XXY and increased by XYY), but not in mice. Controlling for global effects reveals robust and spatially convergent effects of XXY and XYY on regional brain volume in humans, but not mice. However, mice do show subtle effects of XXY and XYY on regional volume, although there is not a general spatial convergence in these effects within mice or between species. Notwithstanding this general lack of conservation in SCT effects, we detect several brain regions that show overlapping effects of XXY and XYY both within and between species (cerebellum, parietal, and orbitofrontal cortex) - thereby nominating high priority targets for future translational dissection of SCD effects on the mammalian brain. Our study introduces a generalizable framework for comparative neuroimaging in humans and mice and applies this to achieve a cross-species comparison of SCD effects on the mammalian brain through the lens of SCT.

Highlights

Parallel structural neuroimaging in humans and mice with sex chromosome trisomies

Divergent X- and Y-chromosome effects on human brain size, but convergent effects on regional anatomy

Muted impact of additional X or Y on mouse brain, but subtle regional effects evident

Evidence for conserved cross-species impact of X and Y on fronto-parietal cortices and cerebellum
Hemisynthetic derivatives of the natural alkaloid trilobine are fast-acting antimalarial compounds with sustained activity in multi-drug resistant P. falciparum isolates
Authors: Nardella Flore , Dobrescu Irina , Hassan Haitham , Rodrigues Fabien , Thiberge Sabine , Silva Liliana Mancio , Tafit Ambre , Jallet Corinne , Cadet-Daniel Véronique , Goussin Stéphane , Lorthiois Audrey , Menon Yoann , Molinier Nicolas , Pechalrieu Dany , Long Christophe , Sautel François , Matondo Mariette , Duchateau Magalie , Medard Guillaume , Witkowski Benoit , Scherf Artur , Halby Ludovic , Arimondo Paola B.
Published: September 2022

Malaria eradication requires the development of new drugs to combat drug-resistant parasites. The search for new chemical scaffolds that target novel pathways of the human malaria parasite Plasmodium falciparum is of highest priority. We identified bisbenzylisoquinoline alkaloids isolated from Cocculus hirsutus. (trilobine derivatives) as active in the nanomolar range against P. falciparum blood stages. Synthesis of a library of 94 hemi-synthetic derivatives allowed us to identify compound 84 that kills multi-drug resistant clinical isolates in the nanomolar range (median IC50 ranging from 35-88nM). Efforts were made to obtain compounds with significantly improved preclinical properties. Out of those, compound 125 delays the onset of parasitemia in P. berghei infected mice and inhibits P. falciparum transmission stages in vitro (culture assays) and in vivo using membrane feeding assay in the Anopheles stephensi vector. Compound 125 also impairs P. falciparum development in sporozoite-infected hepatocytes, in the low micromolar range. Finally, we used a chemical pull-down strategy to identify potential protein targets of this chemical family. Mass spectrometry analysis identified the parasite interactome with trilobine derivatives, identifying protein partners belonging to metabolic pathways that have not been previously targeted by antimalarial drugs or implicated in drug-resistance mechanisms.
Extending Conway’s Game of Life
Authors: Getz Wayne M , Salter Richard
Published: September 2022

We introduce an extension to Conway’s Game of Life (GoL) that allows more than 2 states (dead/alive; 0/1) to be specified. State 0 is reserved for dead or lifeless cells, and states 1 to n − 1 for cells that are “alive.” Associated with state σ is the value vσ of cells such that v0 = 0, v1 = 1, and for σ = 2, …, n − 1 the cell value vσ is free to be assigned any positive integer value. The value Vij of the Moore neighborhood surrounding cells at array locations (i, j) (i = 1, …, r rows, j = 1, …, c) is the sum of state values of the 8 cells that touch the cell at location (i, j) (4 north, south, east and west side cells and 4 NE, NW, SE, and SW corner cells; except for boundary cells, which have 5 neighbors on an edge or 3 neighbors on a corner, and noting that torroidal arrays have no boundaries). The game is based on a set of rules involving the values Vij that determine whether cells at locations (i, j) in state σ, stay in this state or progress to state σ + 1, σ = 0, …, n − 2, or die (remain dead in the case of dead cells). Specifically, for two non-negative constants 0 ≤ pσL ≤ pσU, if Vij< pσL, Vij ∈ [pσL, pσU] or Vij> pσU then a cell in state σ at location (i, j) respectively stays in state σ, progresses to state σ + 1, or dies. In this paper, we illustrate some of the properties of such games of life with three, four and six states, identifying still-life, oscillator, glider and replicator pattern sequences. We also examine the long term behavior of patterns arising from random and regular (stripped diagonals) starting configurations, as well as set-piece motifs. Most importantly, we introduce two freely downloadable, Numerus runtime alterable model platforms (Numerus RAMPs) that can be used to simulate the three and four state GoLs discussed in this paper, and provide a guide on how these RAMPs can be used to explore the behavior of our GoLs.
General cognitive performance declines with female age and is negatively related to fledging success in a wild bird
Authors: Soravia Camilla , Ashton Benjamin J. , Thornton Alex , Ridley Amanda R.
Published: September 2022

Identifying the causes and fitness consequences of intraspecific variation in cognitive performance is fundamental to understand how cognition evolves. Selection may act on different cognitive traits separately or jointly as part of the general cognitive performance of the individual. To date, few studies have examined simultaneously whether individual cognitive performance covaries across different cognitive tasks, the relative importance of individual and social attributes in determining cognitive variation, and its fitness consequences in the wild. Here, we tested 38 wild southern pied babblers (Turdoides bicolor) on a cognitive test battery targeting associative learning, reversal learning and inhibitory control. We found that a single factor explained 59.5% of the variation in individual cognitive performance across tasks, suggestive of a general cognitive factor. General cognitive performance varied by age and sex; declining with age in females but not males. Older females also tended to produce a higher average number of fledglings per year compared to younger females. Analysing over 10 years of breeding data, we found that individuals with lower general cognitive performance produced more fledglings per year. Collectively, our findings support the existence of a trade-off between cognitive performance and reproductive success in a wild bird.
Multiset partial least squares with rank order of groups for integrating multi-omics data
Authors: Yamamoto Hiroyuki
Published: September 2022

As more multi-omics data such as metabolome, proteome and transcriptome data are acquired, statistical analyses to integrate multi-omics data has been required. Multivariate analysis for integration of multi-omics data has been proposed such as multiset partial least squares (PLS). However, when we want to extract scores about the rank order of groups such as severity of disease as well as difference of groups, we could not always extract scores with rank order of groups by using multiset PLS. Therefore, we proposed multiset PLS with rank order of groups (multiset PLS-ROG) to integrate multiple omics dataset. We visualized multiple omics data by using multiset PLS-ROG in two studies of multi-omics and multi-organ derived metabolome data. After we visualize data and focus on a specific score with phenotype of interest, it is important to select compounds to identify biomarker candidates or make biological inferences. In ordinary principal component analysis (PCA) or PLS, we could select statistical significantly compounds correlated with PC or PLS score by using PC or PLS loadings. However, multiset PLS loading has not been used because its statistical property has not been clarified. Then, we clarified statistical property of multiset PLS and multiset PLS-ROG loading, and we could identify statistically significant compounds by using statistical hypothesis testing. We implemented multiset PLS-ROG to R loadings package, freely available in CRAN.
ROBUST AND EFFICIENT ACTIVE GENETICS GENE CONVERSION IN THE RAT AND MOUSE
Authors: Lai Chenyen , Alvarez Oscar , Read Kristen , van Fossan Don , Conner Christopher M. , Xu Shannon (Xaing-Ru) , Cowley Dale O. , Gantz Valentino , Webb David R. , Jarnagin Kurt
Published: September 2022

The utility of Active Genetic (AG) gene conversion systems in rats and mice holds great promise for facilitating the production of complex strains harboring multiple humanizing genes. The practical application of such systems requires the identification of a robust, reusable, and highly efficient system. By characterizing twenty-eight different promoter and target site pairs we aimed to define the parameters needed to establish an efficient conversion system in male and female rats and mice. Using three specific meiosis prophase I active promoters to drive Cas9 expression. We studied several variables, including the number of Cas9 target sites, the distance between target sites, the cis versus trans configuration in linked pairs, and the effect of Cas9 copy number.

In the rat, three of twelve tested configurations provided efficient AG gene conversion in the 22% - 67% range, and four others catalyzed AG in the 0.7-1% range. The ratDdx4(Vasa) promoter provides higher AG efficiency than theSycp1promoter. In mice, ten of sixteen tested configurations, using theSycp1andpSycp1promoters, provided efficiency in the 0.3% - 3.2% range. In rats, Cas9 expression levels are remarkably well correlated with AG gene conversion efficiency. The rat cis rCyp3A1/rCyp3A2locus was the most successful configuration, with gene conversion efficiencies of 0.7%-67%. This target site has a special property; the two Cas9 target sites are nearly perfectly homologous in the 100 bases around the gRNA target site.

Our findings identify key parameters that improve AG efficiency, including the use of two Cas9 target sites, and efficient promoters that drive high levels of Cas9 expression that are correctly timed during gamete development. These findings also uncover the unexpected benefit of high homology at paired gRNA target sites to promote efficiency. We provide new data to guide future efforts to develop yet further improved AG systems.
Cinemeducation improves early clinical exposure to Inborn Errors of Metabolism
Authors: Dutta Atanu Kumar , Oberoi Aroma , Goswami Kalyan , Modi Jyoti Nath , Goyal Parmod Kumar , Samuel Sangeetha , Mondal Tanushree , Sahoo Sibasish , Pal Amit
Published: September 2022

Background

Cinemeducation has been shown to be an effective tool to help the students develop humanistic skills. However, there is a dearth of studies to find out if this can also be utilized to improve the interest and satisfaction of students learning about rare diseases such as the Inborn Errors of Metabolism. The aim was to introduce cinemeducation as part of early clinical exposure in teaching the inborn errors of metabolism for first-year MBBS students in the Department of Biochemistry. The Objectives were 1) to develop, validate and assess the feasibility of structured modules on Cinemeducation in teaching the Inborn Errors of Metabolism, 2) to study the impact of Cinemeducation on the satisfaction, interest, and academic performance of first-year MBBS students and 3) to study the perception of students and faculty towards Cinemeducation

Methods

This was a quasi-experimental, cross-over study involving 100 MBBS students in the Department of Biochemistry, AIIMS Kalyani. Movie clips prepared from Lorenzo’s Oil (for Lipid metabolism) and Extraordinary Measures (for Lysosomal Storage Disease) and corresponding paper-based cases; questionnaires and feedback forms were validated by expert group review. Analysis of quantitative data was performed in GraphPad, MS Excel and MAXQDA2022 software.

Findings, Discussions and Conclusions

Students’ academic performance was found to be improved in the groups where the Extraordinary Measures movie was used for Cinemeducation. Both learners and facilitators were satisfied with Cinemeducation. Cinemeducation was effectively introduced for teaching Inborn Errors of Metabolism in the Department of Biochemistry.
Effects of inbound attendees of a mass gathering event on the COVID-19 epidemic using individual-based simulations
Authors: Saito Masaya M. , Katayama Kotoe , Naruse Akira , Ruan Peiying , Murakami Michio , Okuda Tomoaki , Ysutaka Tetsuo , Naito Wataru , Tsubokura Masaharu , Imoto Seiya
Published: September 2022

Given that mass gathering events involve heterogeneous and time-varying contact between residents and visitors, we sought to identify possible measures to prevent the potential acceleration of the outbreak of an emerging infectious disease induced by such events. An individual-based simulator was built based on a description of the reproduction rate among people infected with the infectious disease in a hypothetical city. Three different scenarios were assessed using our simulator, in which controls aimed at reduced contact were assumed to be carried out only in the main event venue or at subsequent additional events, or in which behavior restrictions were carried out among the visitors to the main event. The simulation results indicated that the increase in the number of patients with COVID-19 could possibly be suppressed to a level equivalent to that if the event were not being held so long as the prevalence among visitors was only slightly higher than that among domestic residents and strict requirements were applied to the activities of visitors.
Assessment of Knowledge on Human Mpox Virus among General Population in Bangladesh
Authors: Nath Sudipta Deb , Islam A.M. Khairul , Majumder Koushik , Rimti Fahmida Hoque , Das Jyoti , Tabassum Mustari Nailah , Oishee Arefin Naher , Mahmood Tarannum , Paul Monisha , Akhter Muntasrina , Bhadra Alok Bijoy , Rimu Fariha Hoque , Chakraborty Snahasish , Shom Preetom , Nosaibah Sirajum Monira , Rahman Md Ashikur , Khan Ahmed Safwan , Anjum Anika , Khan Sushmita , Hossain M. Mahbub , Hawlader Mohammad Delwer Hossain
Published: September 2022

Introduction

Mpox (Monkeypox) is a zoonotic Orthopox virus of the Poxviridae family. The general public in Bangladesh should be informed about Mpox to reduce the burden of a possible epidemic in the community.

Objective

The study aimed to determine the level of public awareness and knowledge about Mpox among the general community to provide information regarding future preventive measures.

Materials and Method

From May to June 2022, this nationwide cross-sectional study was conducted in eight administrative divisions in Bangladesh. We determined the sample size using Cochran’s formula. Through a semi-structured questionnaire, data regarding sociodemographic characteristics and knowledge about Mpox were collected via face-to-face interviews. IBM SPSS v.25 was used to analyze the data.

Result

Among the total of 1,711 respondents to the questionnaire, almost two-thirds (N=1139) of the respondents had heard about Mpox prior to the study. We observed poor knowledge scores (mean ± sd) about the transmission pathways (0.71 ± 0.73), vaccination (0.09 ± 0.27), and the signs and symptoms of Mpox (1.91 ± 1.50). Most participants were also unaware of the treatment options of Mpox (0.22 ± 0.59). Educational status and occupation were found to affect the knowledge significantly (p value<0.001). This study showed that the higher the education level, the higher the knowledge level.

Conclusion

The general community has a minimal understanding of the spread of Mpox and its prevention. This virus requires additional research on its epidemiology, ecology, and biology in endemic regions to be comprehended and prevented.
Risk averse reproduction numbers improve resurgence detection
Authors: Parag Kris V , Obolski Uri
Published: September 2022

Theeffective reproduction number Ris a prominent statistic for inferring the transmissibility of infectious diseases and effectiveness of interventions.Rpurportedly provides an easy-to-interpret threshold for deducing whether an epidemic will grow (R>1) or decline (R<1). We posit that this interpretation can be misleading and statistically overconfident when applied to infections accumulated from groups featuring heterogeneous dynamics. These groups may be delineated by geography, infectiousness or sociodemographic factors. In these settings,Rimplicitly weights the dynamics of the groups by their number of circulating infections. We find that this weighting can cause delayed detection of outbreak resurgence and premature signalling of epidemic control because it underrepresents the risks from highly transmissible groups. ApplyingE-optimalexperimental design theory, we develop a weighting algorithm to minimise these issues, yielding therisk averse reproduction number E. Using simulations, analytic approaches and real-world COVID-19 data stratified at the city and district level, we show thatEmeaningfully summarises transmission dynamics across groups, balancing bias from the averaging underlyingRwith variance from directly using local group estimates. AnE>1 generates timely resurgence signals (upweighting risky groups), while anE<1 ensures local outbreaks are under control. We proposeEas an alternative toRfor informing policy and assessing transmissibility at large scales (e.g., state-wide or nationally), whereRis commonly computed but well-mixed or homogeneity assumptions break down.

Author Summary

How can we meaningfully summarise the transmission dynamics of an infectious disease? This question, although fundamental to epidemiology and crucial for informing the design and implementation of interventions (e.g., quarantines), is still not resolved. Current practice is to estimate theeffective reproduction number R, which counts the average number of new infections generated per past infection, at large scales (e.g., nationally). An estimatedR>1 signals epidemic growth. WhileRis easily interpreted and computed in real time, it averages infections across diverse locations or socio-demographic groups that likely possess different transmission dynamics. We prove that this averaging inRreduces sensitivity to resurgence, makingR>1 slow to reflect realistic epidemic growth. This delay can substantially misinform policymakers and impede interventions. We apply optimal design theory to derive therisk averse reproduction number Eas an alternative summary of diverse transmission dynamics. Using mathematical arguments, simulations and empirical COVID-19 datasets, we show thatE>1 is an improved threshold for resurgence, providing timelier signals for informing policy or interventions and better uncertainty quantification. Further,Emaintains the computability and interpretability ofR. We proposeEas meaningful statistic at large scales, where the averaging withinRlikely misrepresents the diversity of transmission dynamics.
Integrating phylogenetics with intron positions illuminates the origin of the complex spliceosome
Authors: Vosseberg Julian , Stolker Daan , von der Dunk Samuel H. A. , Snel Berend
Published: September 2022

Eukaryotic genes are characterised by the presence of introns that are removed from the pre-mRNA by the spliceosome. This ribonucleoprotein complex is comprised of multiple RNA molecules and over a hundred proteins, which makes it one of the most complex molecular machines that originated during the prokaryote-to-eukaryote transition. Previous work has established that these introns and the spliceosomal core originated from self-splicing introns in prokaryotes. Yet it remains largely elusive how the spliceosomal core expanded by recruiting many additional proteins. In this study we use phylogenetic analyses to infer the evolutionary history of the 145 proteins that we could trace back to the spliceosome in the last eukaryotic common ancestor (LECA). We found that an overabundance of proteins derived from ribosome-related processes were added to the prokaryote-derived core. Extensive duplications of these proteins substantially increased the complexity of the emerging spliceosome. By comparing the intron positions between spliceosomal paralogs, we infer that most spliceosomal complexity postdates the spread of introns through the proto-eukaryotic genome. The reconstruction of early spliceosomal evolution provides insight into the driving forces behind the emergence of complexes with many proteins during eukaryogenesis.
Asymmetric Reconstruction of the Aquareovirus Core at Near-Atomic Resolution and Mechanism of Transcription Initiation
Authors: Stevens Alexander , Cui Yanxiang , Shivakoti Sakar , Zhou Z. Hong
Published: September 2022

The Reoviridae family of dsRNA viruses is characterized by its members’ capacity for endogenous transcription of their multipartite genomes within proteinaceous capsids of 1 to 3 layers. These viruses share inner core particles (ICPs) that conform to icosahedral, T=2*, symmetry, but differ in two major respects: first, the presence or absence of RNA-capping turrets at each icosahedral vertex; second, the number of additional host-specific capsid layers that are often lost upon cell entry. While the role of these additional layers in host infection is generally understood, the absence of asymmetric ICP structures from turreted, multilayered reoviruses has obfuscated our understanding of how successive removal of these external layers impact the structural organization of the ICP and transcription initiation. Here, we present the 3.3 Å resolution structure of the aquareovirus (ARV) ICP, and atomic models of the capsid proteins VP3 and VP6, transcriptional enzymatic complex (TEC) subunits VP2 and VP4, and RNA-capping turret protein VP1. These structures reveal significant differences when compared to those of the coated ARV, as well as their counterparts in single-layered cytoplasmic polyhedrosis virus (CPV). Compared to the double-layered ARV virion and infectious subvirion particle structures, the ARV ICP undergoes significant capsid expansion and widening of the nucleotide processing channels in its TEC and turret. Thus, the loss of outer capsid layers may regulate transcription initiation in ARV, unlike CPV which relies solely on allosteric regulation by binding transcriptional cofactors. These results shed new light on the mechanism of transcription initiation amongst turreted, multilayered members of Reoviridae.
CRISPR Mediated Transactivation in the Human Disease Vector Aedes aegypti
Authors: Bui Michelle , Benetta Elena Dalla , Dong Yuemei , Zhao Yunchong , Yang Ting , Li Ming , Antoshechkin Igor A , Buchman Anna , Bottino-Rojas Vanessa , James Anthony A. , Perry Michael W. , Dimopoulos George , Akbari Omar S
Published: September 2022

As a major insect vector of multiple arboviruses, Aedes aegypti poses a significant global health and economic burden. A number of genetic engineering tools have been exploited to understand its biology with the goal of reducing its impact. For example, current tools have focused on knocking-down RNA transcripts, inducing loss-of-function mutations or expressing exogenous DNA. However, methods for transactivating endogenous genes have not been developed. To fill this void, here we developed a CRISPR activation (CRISPRa) system in Ae. aegypti to transactivate target gene expression. Gene expression is activated through pairing a catalytically-inactive (‘dead’) Cas9 (dCas9) with a highly-active tripartite activator, VP64-p65-Rta (VPR) and synthetic guide RNA (sgRNA) complementary to a user defined target-gene promoter region. As a proof of concept, we demonstrate that engineered Ae. aegypti mosquitoes harboring a binary CRISPRa system can be used to effectively overexpress two developmental genes, even-skipped (eve) and hedgehog (hh), resulting in observable morphological phenotypes. We also used this system to overexpress the positive transcriptional regulator of the Toll immune pathway known as AaRel1, which resulted in a significant suppression of dengue virus serotype 2 (DENV2). This system provides a versatile tool for research pathways not previously possible in Ae. aegypti, such as programmed overexpression of endogenous genes, and may lead to the development of innovative vector control tools.
Lateral line hair cells integrate mechanical and chemical cues to orient navigation
Authors: Desban Laura , Roussel Julian , Mirat Olivier , Lejeune François-Xavier , Keiser Ludovic , Michalski Nicolas , Wyart Claire
Published: September 2022

The lateral line is a superficial sensory system responding to environmental hydrodynamic changes to orient locomotion of aquatic vertebrate species. Whether this system also detects chemical cues is unknown. We find that zebrafish lateral line hair cells express numerous chemoreceptors, including ionotropic receptors for serotonin. We show that the serotonin enriched in skin neuroepithelial cells is released upon injury and that environmental serotonin activates lateral line hair cells. We show that larval zebrafish exposed to serotonin in their environment rely on the lateral line to swim fast and away. These results uncover the sensory versatility of lateral line hair cells and how these properties modulate navigation in response to environmental stimuli.
Protein composition of axonal dopamine release sites in the striatum
Authors: Kershberg Lauren , Banerjee Aditi , Kaeser Pascal S.
Published: September 2022

Mechanisms of neuromodulatory transmission in the brain remain ambiguous. Dopamine is a prototypical neuromodulator, and it was recently found that its secretion relies on active zone-like release site assemblies. Here, we use in vivo biotin-identification (iBioID) proximity proteomics in mouse striatum to isolate dopamine release site proteins enriched over the general dopamine axonal protein content. Using three bait proteins, we identified 527 proteins that fall into several synaptic protein classes, including active zone, Ca2+ regulatory and synaptic vesicle proteins. We also detected many proteins not previously associated with synaptic exocytosis. Knockout of the presynaptic organizer protein RIM profoundly disrupted dopamine release site composition assessed by iBioID, while Synaptotagmin-1 knockout did not. α-Synuclein, a protein linked to Parkinson’s disease, was enriched at release sites, and this enrichment was lost in both tested mutants. We conclude that RIM organizes scaffolded dopamine release sites and we define the protein composition of these sites.
Quantification of Monosynaptic Rabies Tracing Efficiency
Authors: Patiño Maribel , Lagos Willian N. , Patne Neelakshi S. , Miyazaki Paula A. , Callaway Edward M.
Published: September 2022

Retrograde monosynaptic tracing using glycoprotein-deleted rabies virus is an important component of the toolkit for investigation of neural circuit structure and connectivity. It allows for the identification of first-order presynaptic connections to cell populations of interest across both the central and peripheral nervous system, helping to decipher the complex connectivity patterns of neural networks that give rise to brain function. Despite its utility, the efficiency with which genetically modified rabies virus spreads retrogradely across synapses remains uncertain. While past studies have revealed conditions that can increase or decrease the numbers of presynaptic cells labeled, it is unknown what proportion of total inputs to a starter cell of interest are labeled. It is also unknown whether synapses that are more proximal or distal to the cell body are labeled with different efficiencies. Here we use a new rabies virus construct that allows for the simultaneous labeling of pre and postsynaptic specializations to quantify efficiency of spread at the synaptic level in mouse primary visual cortex. We demonstrate that with typical conditions about 40% of first-order presynaptic excitatory inputs are labeled. We show that using matched tracing conditions there is similar efficiency of spread from excitatory or inhibitory starter cell types. Furthermore, we find no difference in the efficiency of labeling of excitatory inputs to postsynaptic sites at different subcellular locations.
The core effector RipE1 ofRalstonia solanacearuminteracts with and cleaves Exo70B1 and is recognized by the Ptr1 immune receptor
Authors: Tsakiri Dimitra , Kotsaridis Konstantinos , Marinos Sotiris , Michalopoulou Vassiliki A. , Kokkinidis Michael , Sarris Panagiotis F.
Published: September 2022

Ralstonia solanacearumdepends on numerous virulence factors, also known as effectors, to promote disease in a wide range of economically important host plants. Although some of these effectors have been characterized, none have yet been shown to target the host’s secretion machinery. Here, we used an extended library of NLR plant immune receptor integrated domains (IDs), to identify new effector targets. The screen uncovered that the core effector RipE1, of theR. solanacearumspecies complex, among other targets, associates with Arabidopsis exocyst component Exo70B1. RipE1, in accordance with its predicted cysteine protease activity, cleaves Exo70B1in vitroand also promotes Exo70B1 degradationin planta. RipE1 enzymatic activity additionally results in the activation of TN2-dependent ectopic cell death. TN2 is an atypical NLR that has been proposed to guard Exo70B1. Despite the fact that RipE1 has been previously reported to activate defense responses in model plant species, we present here aNicotianaspecies, in which RipE1 expression does not activate cell death. In addition, we discovered that RipE1 is recognized by Ptr1, aNicotiana benthamianaCC-NLR, via its cysteine protease activity. Overall, this study uncovers a new RipE1 host target and a new RipE1-activated NLR while providing evidence and novel tools to advance in-depth studies of RipE1 and homologous effectors.

Author Summary

Bacterial wilt disease caused byRalstonia solanacearum, poses a serious global threat for a wide range of agriculturally important plant species. This Gram-negative bacterium utilizes a collection of Type III Secretion System (T3SS) effectors to manipulate host cell defense and physiology. In this study, we searched for new subcellular plant targets of the coreR. solanacearumeffector RipE1, a cysteine protease. We discovered that RipE1 has multiple potential eukaryotic targets and further elucidated its association with the host exocyst complex. Using Artificial Intelligence (AI)-based predictions and performing bothin vitroandin plantaassays, we found that RipE1 promotes the degradation of plant exocyst component Exo70B1 through its enzymatic activity. Apart from being the first report of aR. solanacearumeffector targeting a component of the host secretion machinery, our findings also identify an NLR from a model plant species that is able to recognize RipE1 protease activity and provide evidence that can lead to the discovery of additional RipE1 targets inside the host cell.
A neuroepithelial wave of BMP signalling drives anteroposterior specification of the tuberal hypothalamus
Authors: Chinnaiya Kavitha , Burbridge Sarah , Jones Aragorn , Kim Dong Won , Place Elsie , Manning Elizabeth , Groves Ian , Sun Changyu , Towers Matthew , Blackshaw Seth , Placzek Marysia
Published: September 2022

The tuberal hypothalamus houses several major hypothalamic nuclei, dozens of transcriptionally distinct cell types, and clinically relevant cell populations implicated in obesity and related metabolic disorders. Building on recent advances in the field, here we draw upon transcriptional, signalling, and fate mapping analyses of chicken embryos and neuroepithelial explants to analyze tuberal hypothalamic development. We show that a wave of BMP signalling sweeps through early floor plate-like progenitors overlying prospective Rathke’s pouch as they track anteriorly. The timing of BMP signalling correlates with cell fate, with anterior tuberal specification complete by Hamilton-Hamburger (HH) stage 10 but posterior tuberal progenitors requiring BMPs after this point. scRNA-Seq profiling of FGF10-expressing cells, a proxy for cells with active BMP signalling, through HH8-21 reveals transcriptional differences that may underlie their differing response to BMPs, and the switch from neuroepithelial progenitors to stem-like radial glial cells. This study provides an integrated account of the development of the tuberal hypothalamus.