bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractThe 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

AbstractBackgroundCinemeducation 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 CinemeducationMethodsThis 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 ConclusionsStudents’ 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

AbstractGiven 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

AbstractIntroductionMpox (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.ObjectiveThe 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 MethodFrom 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.ResultAmong 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.ConclusionThe 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

AbstractTheeffective 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 SummaryHow 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

AbstractEukaryotic 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

AbstractThe 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

AbstractAs 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

AbstractThe 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

AbstractMechanisms 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

ABSTRACTRetrograde 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

AbstractRalstonia 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 SummaryBacterial 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.