bluuebunny/crossref_metadata_2025_split huggingface dataset:
Actomyosin contractility in olfactory placode neurons opens the skin epithelium to form the nostril
Authors: Baraban Marion , Pi Clara Gordillo , Bonnet Isabelle , Gilles Jean-François , Lejeune Camille , Cabrera Mélody , Tep Florian , Breau Marie Anne 
Published: July 2022

SummaryDespite their barrier function, epithelial layers can locally lose their integrity to create physiological openings during morphogenesis. The cellular and molecular mechanisms driving the formation of these epithelial breaks are only starting to be investigated. Here, we studied the formation of the zebrafish nostril (the olfactory orifice), which opens in the skin epithelium to expose the olfactory neurons to external odorant cues. Combining live imaging, drug treatments, laser ablation and tissue-specific functional perturbations, we demonstrate that the formation of the orifice is driven by a mechanical interplay between the olfactory placode neurons and the skin: the neurons pull on the overlying skin cells in an actomyosin-dependent manner, thus triggering the opening of the orifice. This work unravels an original mechanism to break an epithelial sheet, in which an adjacent group of cells instructs and mechanically assists the epithelium to induce its local rupture.
Mouse and cellular models of KPTN-related disorder implicate mTOR signalling in cognitive and progressive overgrowth phenotypes
Authors: Levitin Maria O. , Rawlins Lettie E , Sanchez-Andrade Gabriela , Arshad Osama A. , Collins Stephan C. , Sawiak Stephen J. , Iffland Phillip H. , Andersson Malin H.L. , Bupp Caleb , Cambridge Emma L. , Coomber Eve L. , Ellis Ian , Herkert Johanna C. , Ironfield Holly , Jory Logan , Kretz Perrine F. , Kant Sarina G. , Neaverson Alexandra , Nibbeling Esther , Rowley Christine , Relton Emily , Sanderson Mark , Scott Ethan M. , Stewart Helen , Shuen Andrew Y. , Schreiber John , Tuck Liz , Tonks James , Terkelsen Thorkild , van Ravenswaaij-Arts Conny , Vasudevan Pradeep , Wenger Olivia , Wright Michael , Day Andrew , Hunter Adam , Patel Minal , Lelliott Christopher J. , Crino Peter B. , Yalcin Binnaz , Crosby Andrew , Baple Emma L. , Logan Darren W. , Hurles Matthew E. , Gerety Sebastian S. 
Published: July 2022

AbstractKPTN-related disorder (KRD) is an autosomal recessive disorder associated with germline variants in KPTN (kaptin), a component of the mTOR regulatory complex KICSTOR. To gain further insights into the pathogenesis of KRD, we analysed mouse knockout and human stem cell KPTN loss-of-function models. Kptn−/− mice display many of the key KRD phenotypes, including brain overgrowth, behavioural abnormalities, and cognitive deficits. Assessment of affected individuals has identified concordant selectivity of cognitive deficits, postnatal onset of brain overgrowth, and a previously unrecognised KPTN dosage-sensitivity, resulting in increased head circumference in their heterozygous parents. Molecular and structural analysis of Kptn−/− mice revealed pathological changes, including differences in brain size, shape, and cell numbers primarily due to abnormal postnatal brain development. Both the mouse and differentiated iPSC models of the disorder display transcriptional and biochemical evidence for altered mTOR pathway signalling, supporting the role of KPTN in regulating mTORC1. Increased mTOR signalling downstream of KPTN is rapamycin sensitive, highlighting possible therapeutic avenues with currently available mTOR inhibitors. These findings place KRD in the broader group of mTORC1 related disorders affecting brain structure, cognitive function, and network integrity.
Variation in microbial feature perception in the Rutaceae family with immune receptor conservation in citrus
Authors: Trinh Jessica , Li Tianrun , Franco Jessica Y. , Toruño Tania Y. , Stevens Danielle M. , Thapa Shree P. , Wong Justin , Pineda Rebeca , Ávila de Dios Emmanuel , Kahn Tracy L. , Seymour Danelle K. , Ramadugu Chandrika , Coaker Gitta L. 
Published: July 2022

AbstractAlthough much is known about the responses of model plants to microbial features, we still lack an understanding of the extent of variation in immune perception across members of a plant family. In this work, we analyzed immune responses inCitrusand wild relatives, surveying 86 Rutaceae genotypes with differing leaf morphologies and disease resistances. We found that responses to microbial features vary both within and between members. Species in two subtribes, the Balsamocitrinae and Clauseninae, can recognize all tested microbial features (flg22, csp22, chitin), including one fromCandidatusLiberibacter species (csp22CLas), the bacterium associated with citrus greening disease aka Huanglongbing. We investigated differences at the receptor level for flagellin perception (FLS2 receptor) and chitin perception (LYK5 receptor) in citrus genotypes. We were able to characterize two genetically linkedFLS2homologs from ‘Frost Lisbon’ lemon (responsive) and ‘Washington navel’ orange (non-responsive). Surprisingly,FLS2homologs from responding and non-responding genotypes were expressed in citrus and functional when transferred to a heterologous system. ‘Washington navel’ orange weakly responds to chitin, but ‘Tango’ mandarin exhibits a robust response. LYK5 alleles were identical or nearly-identical between the two genotypes and able to complement theArabidopsis lyk4/lyk5-2mutant with respect to chitin perception. Collectively, our data indicates that differences in chitin and flg22 perception in these citrus genotypes are not the result of sequence polymorphisms at the receptor level. These findings shed light onto the diversity of perception of microbial features and highlight genotypes capable of recognizing polymorphic pathogen features.
A comprehensive update to theMycobacterium tuberculosisH37Rv reference genome
Authors: Chitale Poonam , Lemenze Alexander D. , Fogarty Emily C. , Shah Avi , Grady Courtney , Odom-Mabey Aubrey R. , Johnson W. Evan , Yang Jason H. , Eren A. Murat , Brosch Roland , Kumar Pradeep , Alland David 
Published: July 2022

AbstractH37Rv is the most widely usedM. tuberculosisstrain. Its genome is globally used as theM. tuberculosisreference sequence. We developed Bact-Builder, a pipeline that leverages consensus building to generate complete and highly accurate gap-closed bacterial genomes and applied it to three independently sequenced cultures of a parental H37Rv laboratory stock. Two of the 4,417,942 base-pair long H37Rv assemblies were 100% identical, with the third differing by a single nucleotide. Compared to the existing H37Rv reference, the new sequence contained approximately 6.4 kb additional base pairs encoding ten new regions. These regions included insertions in PE/PPE genes and new paralogs ofesxNandesxJ, which were differentially expressed compared to the reference genes. Additional sequencing and assembly with Bact-Builder confirmed that all 10 regions were also present in widely accepted strains of H37Rv: NR123 and TMC102. Bact-builder shows promise as an improved method to perform extremely accurate and reproduciblede novoassemblies of bacterial genomes. Furthermore, our findings provide important updates to the primary tuberculosis reference genome.
An oblique plane microscope for mesoscopic imaging of freely moving organisms with cellular resolution
Authors: Singh Rajwinder , Subramanian Kaushikaram , Power Rory M. , Paix Alexandre , Ikmi Aissam , Prevedel Robert 
Published: July 2022

AbstractSeveral important questions in biology require non-invasive and three-dimensional imaging techniques with appropriate spatiotemporal resolution that permit live organisms to move in an unconstrained fashion over an extended field-of-view. While selective-plane illumination microscopy (SPIM) has emerged as a powerful method to observe live biological specimens at high spatio-temporal resolution, typical implementations often necessitate constraining sample mounting or lack the required volumetric speed. Here, we report on an open-top, dual-objective oblique plane microscope (OPM) capable of observing millimeter sized, freely moving animals at cellular resolution. We demonstrate the capabilities of our mesoscopic OPM (MesOPM) by imaging the behavioural dynamics of the sea anemone Nematostella vectensis over 1.56 × 1.56 × 0.25 mm at 1.5 × 2.8 × 5.3µm resolution and 0.5Hz volume rate.
Probing the KRas Switch II Groove by Fluorine NMR Spectroscopy
Authors: Peacock D. Matthew , Kelly Mark J. S. , Shokat Kevan M. 
Published: July 2022

ABSTRACTWhile there has been recent success in the development of KRasG12C inhibitors, unmet needs for selective inhibitors and tool compounds targeting the remaining oncogenic KRas proteins remain. Here, we applied trifluoromethyl-containing ligands of KRas proteins as competitive probe ligands to assay the occupancy of the switch II pocket by 19F NMR spectroscopy. Structure-activity-relationship studies of probe ligands increased the sensitivity of the assay and identified structures that differentially detected each nucleotide state of KRasG12D. These differences in selectivity, combined with the high resolution of 19F NMR spectroscopy, enabled this method to be expanded to assay both nucleotide states of the protein simultaneously.Abstract Figure
Directional invariance in the Drosophila giant fiber escape circuit
Authors: Jang HyoJong , Goodman David P , von Reyn Catherine R 
Published: July 2022

AbstractAn animal’s nervous system recognizes visual features regardless of where the visual feature is located. However, the underlying mechanisms that enable location invariant feature detection are not fully understood, particularly when visual feature information contributed by each eye needs to be resolved. Here we investigate directional invariance of looming responses in descending neurons (DN) of Drosophila melanogaster. We find multiple looming responsive DN integrate looming information across both eyes, even though their dendrites are unilateral. One DN in particular, the giant fibers (GF), generates invariant looming responses across approach directions. We confirm visual information propagates to the GF from the contralateral eye through an as of yet unidentified pathway and demonstrate the absence of this pathway alters GF responses to looming stimuli from the ipsilateral eye. Our data highlight a role for bilateral visual integration in generating consistent escape responses that are robust across a wide range of stimulus locations and parameters.
Efficient knock-in method enabling lineage tracing in zebrafish
Authors: Mi Jiarui , Andersson Olov 
Published: July 2022

AbstractThe CRISPR-Cas9 system aids generation of knock-in zebrafish lines, but it has been hard to integrate large constructs and avoid disrupting the targeted genes. Here we devised a 3’ knock-in strategy of PCR-amplified dsDNA, which coded for fluorescence proteins and Cre recombinase in frame with the endogenous gene but separated from each other by self-cleavable peptides. Primers with 5’ AmC6 end-protections generated improved PCR amplicons harboring either short or long homologous arms, which were co-injected with pre-assembled Cas9/gRNA ribonucleoprotein complexes for early integration. We targeted four genetic loci (krt92,nkx6.1, krt4,andid2a) and generated ten knock-in lines, which function as reporters for the endogenous gene expression. The knocked-in iCre or CreERT2 were used for lineage tracing, which suggestednkx6.1+cells are multipotent pancreatic progenitors that gradually restrict to bipotent duct; whileid2a+cells are multipotent in both liver and pancreas and gradually restrict to ductal cells. Additionally, hepaticid2a+duct show progenitor properties upon extreme hepatocyte loss. Thus, we present an efficient knock-in technique with widespread use for both cellular labelling and lineage tracing.
Correlates of protection for booster doses of the BNT162b2 vaccine
Authors: Hertz Tomer , Levy Shlomia , Ostrovsky Daniel , Oppenheimer Hannah , Zismanov Shosh , Kuzmina Alona , Friedman Lilach M , Trifkovic Sanja , Brice David , Chun-Yang Lin , Shemer-Avni Yonat , Cohen-Lahav Merav , Amichay Doron , Keren-Naus Ayelet , Voloshin Olga , Weber Gabriel , Najjar-Debbiny Ronza , Chazan Bibiana , McGargill Maureen A. , Webby Richard , Chowers Michal , Novack Lena , Novack Victor , Taube Ran , Nesher Lior , Weinstein Orly 
Published: July 2022

AbstractVariants of concern (VOC) of SARS-CoV2 and waning immunity pose a serious global problem. Overall, vaccination and prior infection appear to provide significant protection to the majority of individuals, but some remain susceptible to infection and severe disease. Rigorously identifying a broad spectrum of correlates of protection (COP) is necessary to identify these susceptible populations. The extent to which additional booster doses provide protection is also poorly understood. To address this need, we conducted a multicenter prospective study assessing the association between serological profiles and the risk for SARS-CoV-2 infection, comparing those vaccinated with three to four doses of Pfizer BNT162b2 vaccine. Of 608 healthy adults, 365 received three doses and 243 received four doses. During the first 90 days of followup, 239 (39%) were infected, of whom 165/365 (45%) received 3 doses and 74/243 (30%) four doses. We found that the fourth dose elicited a significant rise in antibody binding and neutralizing titers against multiple variants, and reduced the risk of symptomatic infection by 37% [95% I, 15% - 54%]. We identified several parameters based on IgG and IgA binding that were COPs. The strongest association with infection risk was reduced IgG levels to RBD mutants and IgA levels to VOCs, which was a COP in the three-dose group (HR=6.34, p=0.008) and in the four-dose group (HR=8.14, p=0.018). A combination of two commercially available ELISA assays were also associated with protection in both groups (HR = 1.84, p = 0.002; HR = 2.01, p = 0.025, respectively). Most importantly, we identified a subset of individuals with low antibody levels after three doses of vaccine that responded with a significant boost in neutralizing antibody titers after a fourth dose, but were still at significantly increased susceptibility to infection when compared to those who had pre-existing high levels of neutralizing antibodies. Thus, we identify a highly susceptible population that remains susceptible despite apparent responsiveness to vaccines. Further, we develop several specific and sensitive COPs that show dramatic effect sizes and may be utilized to identify individuals most at risk from future exposures.
Attitudes toward COVID-19 pandemic among fully vaccinated individuals: evidence from Greece two years after the pandemic
Authors: Galanis Petros , Vraka Irene , Katsiroumpa Aglaia , Siskou Olga , Konstantakopoulou Olympia , Katsoulas Theodoros , Mariolis-Sapsakos Theodoros , Kaitelidou Daphne 
Published: July 2022

AbstractBackgroundConsidering the major effects of COVID-19 pandemic on health, social, economic, and political dimensions of all countries, positive attitudes toward COVID-19 pandemic are essential to control the pandemic. In our study, we investigated attitudes toward COVID-19 pandemic among fully COVID-19 vaccinated individuals two years after the pandemic and we identified predictors of attitudes.Materials and MethodsWe conducted an on-line cross-sectional study with 815 fully COVID-19 vaccinated individuals in Greece during May 2022. A self-administered and valid questionnaire was disseminated through social media platforms. We measured socio-demographic variables and COVID-19-related variables as potential predictors of attitudes toward COVID-19 pandemic. The outcome variable was attitudes toward COVID-19 pandemic (compliance with hygiene measures, trust in COVID-19 vaccination, fear of COVID-19, and information regarding the COVID-19 pandemic and vaccination).ResultsWe found a very high level of compliance with hygiene measures, a high level of trust and information about the COVID-19 pandemic and vaccination, and a moderate level of fear of COVID-19. Also, we identified that females, participants with a higher educational level, those with a chronic disease, those with a better self-perceived physical health, and those without a previous COVID-19 diagnosis adhered more in hygiene measures. Trust in COVID-19 vaccination was higher among females, older participants, those with a higher educational level, those with a better self-perceived physical health, and those without a previous COVID-19 diagnosis. Moreover, females, older participants, those with a higher educational level, those with a chronic disease, those with a better self-perceived physical health, those that received a flu vaccine in previous season, and those without a previous COVID-19 diagnosis experienced more fear of the COVID-19. Finally, level of information regarding COVID-19 pandemic and vaccination was higher for participants with a higher educational level, those without a chronic disease, those with a better self-perceived physical health, and those that received a flu vaccine in previous season.ConclusionsUnderstanding predictors of attitudes toward COVID-19 pandemic among fully vaccinated individuals is crucial for developing appropriate public health campaigns in the future. Vaccination should be accompanied by positive attitudes in order to decrease the frequency of negative outcomes of COVID-19, such as hospitalization, complications and mortality.
An Analysis of Oxycodone and Hydrocodone Distribution Trends in Delaware, Maryland, & Virginia Between 2006-2014
Authors: Eufemio Conor M. , Hagedorn Joseph D. , McCall Kenneth L. , Piper Brian J. 
Published: July 2022

AbstractObjectiveUnderstanding opioid use and distribution trends by geographic area is critical in addressing the ongoing opioid epidemic in the United States. This study is a county level analysis of oxycodone and hydrocodone use in Delaware, Maryland, and Virginia between 2006-2014.Materials and MethodsA retrospective analysis of oxycodone and hydrocodone distributed as collected by the Drug Enforcement Administration’s (DEA) Washington Post Automation of Reports and Consolidated Orders System (ARCOS) in Delaware, Maryland, and Virginia. Raw drug weights in each county were adjusted to “daily average dose” (grams/county population/365). Purchasing data collected from ARCOS was used to compare distribution trends during this period.ResultsThere was a 57.59% in the weight of oxycodone and hydrocodone between 2006-2014. Oxycodone prescriptions increased by 75.50% and hydrocodone by 11.05%. Oxycodone increased across all three states between 2006-2010 and declined until 2014. Hydrocodone also increased but to a lesser extent than oxycodone. There was substantial variability in daily average dose of both opioids at the county level in all states. Pharmacies accounted for largest portion of oxycodone (69.17%) and hydrocodone (75.27%) purchased in the region. Hospitals accounted for 26.67% of oxycodone and 22.76% hydrocodone purchased. Practitioners and mid-level providers did not significantly contribute to this increase.ConclusionIn the states of Maryland, Delaware, and Virginia, the distribution of the prescription opioids oxycodone and hydrocodone increased by 57.59%. Daily average dose increased between 2006-2010 in all three states followed by a decline until 2014. Variability in daily average dose by county highlights the relationship between geography and likelihood of receiving high dose opioids. It may further allude to effects of targeted distribution by pharmaceutical manufacturers and prescribing habits of geographically distinct healthcare entities. Relationships between location and opioid usage should continue to be investigated to promote rational use of controlled substances.
Influence of insertion sequences on population structure of phytopathogenic bacteria in the Ralstonia solanacearum species complex
Authors: Greenrod Samuel TE , Stoycheva Martina , Elphinstone John , Friman Ville-Petri 
Published: July 2022

AbstractRalstonia solanacearum species complex (RSSC) is a destructive group of plant pathogenic bacteria and the causative agent of bacterial wilt disease. Experimental studies have attributed RSSC virulence to insertion sequences (IS), transposable genetic elements which can both disrupt and activate host genes. Yet, the global diversity and distribution of RSSC IS are unknown. In this study, IS were bioinformatically identified in a diverse collection of 356 RSSC strains representing four phylogenetic lineages, and their diversity investigated based on genetic distance measures and comparisons with the ISFinder database. IS distributions were characterised using metadata on RSSC lineage classification and potential gene disruptions by IS were determined based on their proximity to coding sequences. In total, we found 24,732 IS belonging to eleven IS families and 26 IS subgroups, with over half of the IS found in the megaplasmid. While IS families were generally widespread across the RSSC phylogeny, IS subgroups showed strong lineage-specific distributions and genetically similar bacterial strains had similar IS contents. Further, IS present in multiple lineages were generally found in different genomic regions suggesting potential recent horizontal transfer. Finally, IS were found to disrupt many genes with predicted functions in virulence, stress tolerance, and metabolism, suggesting that they might be adaptive. This study highlights that RSSC insertion sequences track the evolution of their bacterial hosts, potentially contributing to both intra- and inter-lineage genetic diversity.