bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of meiotic recombination inDrosophila simulansshows heterozygous inversions do not cause an interchromosomal effect
Authors: Man Bowen , Kim Elizabeth , Vadlakonda Alekhya , Stern David L. , Crown K. Nicole 
Published: March 2024

AbstractChromosome inversions are of unique importance in the evolution of genomes and species because when heterozygous with a standard arrangement chromosome, they suppress meiotic crossovers within the inversion. In Drosophila species, heterozygous inversions also cause the interchromosomal effect, whereby the presence of a heterozygous inversion induces a dramatic increase in crossover frequencies in the remainder of the genome within a single meiosis. To date, the interchromosomal effect has been studied exclusively in species that also have high frequencies of inversions in wild populations. We took advantage of a recently developed approach for generating inversions inDrosophila simulans, a species that does not have inversions in wild populations, to ask if there is an interchromosomal effect. We used the existing chromosome 3R balancer and generated a new chromosome 2L balancer to assay for the interchromosomal effect genetically and cytologically. We found no evidence of an interchromosomal effect inD. simulans. To gain insight into the underlying mechanistic reasons, we qualitatively analyzed the relationship between meiotic double-strand break formation and synaptonemal complex assembly. We find that the synaptonemal complex is assembled prior to double-strand break formation as inD. melanogaster; however, we show that the synaptonemal complex is assembled prior to localization of the oocyte determination factor Orb, whereas inD. melanogaster, synaptonemal complex formation does not begin until Orb is localized. Together, our data show heterozygous inversions inD. simulansdo not induce an interchromosomal effect and that there are differences in the developmental programming of the early stages of meiosis.
RESTandRCORgenes display distinct expression profiles in neurons and astrocytes using 2D and 3D human pluripotent stem cell models
Authors: Maksour Simon , Ng Neville , Hulme Amy J. , Miellet Sara , Engel Martin , Muñoz Sonia Sanz , Balez Rachelle , Rollo Ben , Finol-Urdaneta Rocio K. , Ooi Lezanne , Dottori Mirella 
Published: March 2024

AbstractRepressor element-1 silencing transcription factor (REST) is a transcriptional repressor involved in neurodevelopment and neuroprotection. REST forms a complex with the REST corepressors, CoREST1, CoREST2, or CoREST3 (encoded byRCOR1,RCOR2, andRCOR3, respectively). Emerging evidence suggests that the CoREST family can target unique genes independently of REST, in various neural and glial cell types during different developmental stages. However, there is limited knowledge regarding the expression and function of the CoREST family in human neurodevelopment. To address this gap, we employed 2D and 3D human pluripotent stem cell (hPSC) models to investigateRESTandRCORgene expression levels. Our study revealed a significant increase inRCOR3expression in glutamatergic cortical and GABAergic ventral forebrain neurons, as well as mature functional NGN2-induced neurons. Additionally, a simplified astrocyte transdifferentiation protocol resulted in a significant decrease inRCOR2expression following differentiation.RESTexpression was notably reduced in mature neurons and cerebral organoids, along withRCOR2in the latter. In summary, our findings provide the first insights into the cell-type-specific expression patterns ofRCORgenes in human neuronal and glial differentiation. Specifically,RCOR3expression increases in neurons, whileRCOR2levels decrease in astrocytes. The dynamic expression patterns ofRESTandRCORgenes during hPSC neuronal and glial differentiation underscore the potential distinct roles played by REST and CoREST proteins in regulating the development of these cell types in humans.Graphical abstractHighlightsRESTandRCORgenes display cell-type specific expression patterns in neural cellsRCOR3(encodes CoREST3) is upregulated during neuronal and astrocyte differentiationRCOR2(encodes CoREST2) is downregulated during differentiation of astrocytesEvidence of potential cell-type specific functions of the CoREST family
A genome-wide association study implicates the olfactory system inDrosophila melanogasterdiapause-associated lifespan extension and fecundity
Authors: Easwaran Sreesankar , Montell Denise J. 
Published: March 2024

ABSTRACTThe effects of environmental stress on animal life are gaining importance with climate change. Diapause is a dormancy program that occurs in response to an adverse environment, followed by resumption of development and reproduction upon the return of favorable conditions. Diapause is a complex trait, so we leveraged theDrosophilagenetic reference panel (DGRP) lines and conducted a Genome-Wide Association Study (GWAS) to characterize the genetic basis of diapause. We assessed post-diapause and non-diapause fecundity across 193 DGRP lines. GWAS revealed 546 genetic variants, encompassing single nucleotide polymorphisms, insertions and deletions associated with post-diapause fecundity. We identified 291 candidate diapause-associated genes, 40 of which had previously been associated with diapause, and 89 of which were associated with more than one SNP. Gene network analysis indicated that the diapause-associated genes were primarily linked to neuronal and reproductive system development. Similarly, comparison with results from other fly GWAS revealed the greatest overlap with olfactory-behavior-associated and fecundity-and-lifespan-associated genes. An RNAi screen of selected candidates identified two neuronal genes, Dip-𝛾 and Scribbler, to be required during recovery for post-diapause fecundity. We complemented the genetic analysis with a test of which neurons are required for successful diapause. We found that although amputation of the antenna had little to no effect on non-diapause lifespan, it reduced diapause lifespan and postdiapause fecundity. We further show that olfactory receptor neurons and temperature-sensing neurons are required for successful recovery from diapause. Our results provide insights into the molecular, cellular, and genetic basis of adult reproductive diapause inDrosophila.
A cross sectional survey of Australian and New Zealand specialist trainees’ research experiences and outputs
Authors: Stehlik Paulina , Withers Caitlyn , Bourke Rachel , Barnett Adrian , Brandenburg Caitlin , Noble Christy , Bannach-Brown Alexandra , Keijzers Gerben , Scott Ian , Glasziou Paul , Veysey Emma , Mickan Sharon , Morgan Mark , Joshi Hitesh , Forrest Kirsty , Campbell Thomas , Henry David 
Published: March 2024

AbstractObjectiveTo explore medical trainees’ experiences and views concerning college-mandated research projects.SettingOnline survey (Apr-Dec 2021) of current and recent past trainees of Australian and New Zealand colleges recruited through 11 principal colleges and snowballing.ParticipantsCurrent trainee or completed training in the past 5 years.Main outcome measuresWe asked participants: whether they were required to conduct research as part of their college training, how they conducted their research, and their research activity after training. Respondents were invited to submit project reports for reporting and methodological quality evaluation. Data were analysed descriptively.ResultsOf the 372 respondents, 313 (86%) were required to complete one or more projects. Of the 177 who had completed their project (representing 267 projects), 76 provided information on 92 studies, with 34 reports submitted for evaluation. Most respondents developed their own research questions, study design and protocol, and conducted research in their own time, with 56% (38/68) stating they had the skills to complete their project. Most project teams consisted of their own medical specialty followed by statisticians, but seldom others.44% (30/68) were satisfied with their research experience, and 53% (36/67) supported mandatory projects. Half (87/174) felt research was important for career development, 72% (44/61) considered initiating research post-training, and 54% (33/61) participated in it.Commonly expressed themes were time-burden of conducting projects, production of research waste, and the importance of research for skills development. Of the 34 submitted reports, 75% were published and 82% had a clear research question. Only three had a low risk of bias.ConclusionMajority of respondents conducted projects, but few shared details or reports. Despite valuing their research experiences and seeing clinical relevance, time conflicts and research waste were common concerns. Colleges should focus on enhanced research methods training and creating trainee research collaboratives.Protocol registrationhttps://doi.org/10.17605/OSF.IO/BNGZKSummary boxMajority of medical specialty trainees are required to conduct a research project to develop their research skills.We found the learning experiences are inconsistent, and the quality of research produced even more so.A new approach is required that is tailored to the research skills required by most practicing clinicians, namely being expert in applying research to practice and in participating in collaborative research. Those wishing to become leaders in research should be supported to do so via a specialised well-supported pathway.
Personalized phosphoproteomics of skeletal muscle insulin resistance and exercise links MINDY1 to insulin action
Authors: Needham Elise J. , Hingst Janne R. , Onslev Johan D. , Diaz-Vegas Alexis , Leandersson Magnus R. , Kristensen Jonas Møller , Kido Kohei , Richter Erik A. , Højlund Kurt , Parker Benjamin L. , Cooke Kristen , Yang Guang , Pehmøller Christian , Humphrey Sean J. , James David E. , Wojtaszewski Jørgen F.P. 
Published: March 2024

SummaryType 2 diabetes is preceded by a defective insulin response, yet our knowledge of the precise mechanisms is incomplete. Here, we investigate how insulin resistance alters signalling responses in skeletal muscle and how this is modified by exercise. We measured parallel phenotypes and phosphoproteomes of insulin resistant and insulin sensitive individuals as they responded to exercise and insulin (n=19, 114 biopsies), quantifying over 12,000 phosphopeptides in each biopsy. Our personalized phosphoproteomics approach revealed that insulin resistant individuals have selective and time-dependent signalling alterations. Insulin resistant subjects have reduced insulin-stimulated mTORC1 responses and alterations to non-canonical rather than canonical insulin signalling. Prior exercise promotes insulin sensitivity even in insulin resistant individuals by ‘priming’ a portion of insulin signalling prior to insulin infusion. This includes MINDY1 S441, which is elevated in insulin-sensitive subjects and primed by prior exercise. MINDY1 contains a missense variant that is protective for type 2 diabetes but its role in disease risk is unknown. We show that MINDY1 S441 phosphorylation is downstream of AKT, and MINDY1 knockdown enhances insulin-stimulated glucose uptake in rat myotubes. This work delineates the signalling alterations in insulin resistant skeletal muscle and how exercise partially counteracts these and identifies MINDY1 as a regulator of insulin action.HighlightsInsulin resistance primarily alters non-canonical insulin signalling.mTORC1 substrates were most defective in insulin resistance.Exercise counteracts insulin signalling defects including MINDY1 S441.MINDY1 is a negative regulator of insulin sensitivity in rat myotubes and S441 is downstream of AKT.
Prevalence of differences of sex development in children and adolescents in Switzerland from 2000-2019
Authors: Metzger Sara , Sommer Grit , Flück Christa E. 
Published: March 2024

AbstractObjectiveReliable data on prevalence of differences of sex development (DSD) are lacking. We aimed to estimate population-based prevalence of DSD in Switzerland.DesignRetrospective population-based study including children and adolescents with DSD according to Chicago Consensus, born in Switzerland from 2000-2019.MethodsEndocrine care centers in ten Swiss Children’s Hospitals and eight private endocrine practices collected DSD data through the I-DSD registry or case report forms. We calculated prevalence for DSD diagnostic groups and analyzed trends in prevalence.ResultsOver the 20-year study period, we identified 561 individuals with DSD. Almost half (n=266, 47%) had sex chromosome DSD, 177 (32%) had 46,XY DSD and 118 (21%) had 46, XX DSD. Causes for 46,XY DSD were disturbed androgen synthesis or action (37/177, 21%), atypical gonadal development (28/177, 16%), or other causes (112/177, 63%). Causes for 46,XX DSD were androgen excess (99/118, 84%), atypical gonadal development (8/118, 7%), or other causes (11/118, 9%). On average, 28 new cases were born with DSD annually. Prevalence was 17 for sex chromosome DSD, 12 for 46,XY DSD and 8 for 46,XX DSD per 100’000 live births and year. One per 7’500 newborn girls had 46,XX congenital adrenal hyperplasia (CAH).ConclusionPrevalence of sex chromosome DSD was lower than expected because of underreporting due to late diagnosis. Prevalence of 46,XX CAH is similar to newborn screening data, suggesting good completeness of cases. For complex DSD cases, we expect complete coverage. This study provides a valuable resource for policymaking and (inter)national research on DSD.
Uncovering disease-related multicellular pathway modules on large-scale single-cell transcriptomes with scPAFA
Authors: Huang Zhuoli , Zheng Yuhui , Wang Weikai , Zhou Wenwen , Wei Chen , Zhang Xiuqing , Jin Xin , Yin Jianhua 
Published: March 2024

AbstractPathway analysis is a crucial analytical phase in disease research on single-cell RNA sequencing (scRNA-seq) data, offering biological interpretations based on prior knowledge. However, currently available tools for generating cell-level pathway activity scores (PAS) exhibit computational inefficacy in large-scale scRNA-seq datasets. Besides, disease-related pathways are commonly identified by cross-condition comparisons in each cell type, neglecting the potential multicellular patterns. Here, we present single-cell pathway activity factor analysis (scPAFA), a Python library designed for large-scale single-cell dataset allowing rapid PAS computation and uncovering biologically interpretable disease-related multicellular pathway modules, which are low-dimensional representations of disease-related PAS variance in multiple cell types. Application on colorectal cancer (CRC) dataset with 371,223 cells and large-scale lupus atlas over 1.2 million cells demonstrated that scPAFA can achieve > 33-fold decreases in runtime of PAS computation and further identified reliable and interpretable multicellular pathway modules that capture the transcriptomic features of CRC tumor status and transcriptional abnormalities in lupus patients, respectively.
An Lgr5-independent developmental lineage is involved in mouse intestinal regeneration
Authors: Marefati Maryam , Fernandez-Vallone Valeria , Leprovots Morgane , Vasile Gabriella , Libert Frédérick , Lefort Anne , Dinsart Gilles , Weber Achim , Jetzer Jasna , Garcia Marie-Isabelle , Vassart Gilbert 
Published: March 2024

AbstractCollagenase/dispase treatment of intestinal tissue from adult mice generates cells growing in matrigel as stably replatable cystic spheroids in addition to differentiated organoids. Contrary to classical EDTA-derived organoids, these spheroids display poor intestinal differentiation and are independent of Rspondin/Noggin/EGF for growth. Their transcriptome resembles strikingly that of fetal intestinal spheroids, with downregulation of crypt base columnar cell (CBC) markers (Lgr5, Ascl2, Smoc2, Olfm4). In addition, they display upregulation of inflammatory and mesenchymal genetic programs, together with robust expression of YAP target genes. Lineage tracing, cell-sorting and single cell RNA sequencing experiments demonstrate that adult spheroid-generating cells belong to a hitherto undescribed developmental lineage, independent of Lgr5+ve CBCs, and are involved in regeneration of the epithelium following CBC ablation.
Cellular and circuit mechanisms underlying binocular vision
Authors: Honnuraiah Suraj , Huang Helena , Ryan William J. , Broersen Robin , Connelly William M. , Stuart Greg J. 
Published: March 2024

SummaryHow binocular visual information is combined at the level of single neurons in the brain is not fully understood. Here, we show in mice that callosal input from the opposite visual cortex (V1) plays a critical role in this process.In vivowe find this callosal projection carries ipsilateral eye information and synapses exclusively onto binocular neurons. Using the presence of callosal input to identify binocular neuronsin vitro,at the cellular level we show that binocular neurons are less excitable than monocular neurons due to high expression of Kv1 potassium channels. At the circuit level we find that only monocular neurons send callosal projections to the opposite V1, whereas binocular neurons do not. Finally, using dual-colour optogenetics we show that most binocular and monocular neurons receive direct input from the thalamus. In summary, we describe distinct cellular and circuit mechanisms underlying processing of binocular visual information in mouse V1.
Presynaptic occlusion of NMDA receptor-dependent potentiation in Synaptophysin family knockouts
Authors: del Olmo-Cabrera Sergio , Gotor Juan José Rodríguez , Verhaeghe Rémy , Wesseling John F. 
Published: March 2024

AbstractBaseline synaptic strength is elevated in knockouts missing the synaptophysin family of synaptic vesicle proteins because of increased probability of release of release-ready vesicles. Here we show that the longest lasting component of long-term potentiation (LTP) is: (a) eliminated at Schaffer collateral synapses under standard conditions; (b) rescued by reducing extracellular Ca2+enough to lower baseline synaptic strength to wildtype levels; and, (c) eliminated at wildtype synapses by increasing Ca2+enough to elevate baseline to knockout levels. Next, an earlier component of LTP, lasting less than 1 hr, was eliminated first at knockouts and then wildtype by elevating baseline further. And, the LTP that was eliminated could be recovered by subsequently reducing extracellular Ca2+back to the permissive level. In sum, NMDA receptor-dependent LTP maintenance and expression are separable mechanisms at extensively studied Schaffer collateral synapses, and expression of multiple components can be occluded by enhancing the mechanism that catalyzes synaptic vesicle exocytosis from presynaptic terminals.
CB1Cannabinoid Receptor Agonists Induce Acute Respiratory Depression in Awake Mice
Authors: Watkins Joshua , Aradi Petra , Hahn Rachel , Katona Istvan , Mackie Ken , Makriyannis Alexandros , Hohmann Andrea G. 
Published: March 2024

AbstractRecreational use of synthetic cannabinoid agonists (i.e., “Spice” compounds) that target the Cannabinoid Type 1 receptor (CB1) can cause respiratory depression in humans. However, Δ9-tetrahydrocannabinol (THC), the major psychoactive phytocannabinoid in cannabis, is not traditionally thought to interact with CNS control of respiration, based largely upon sparse labeling of CB1 receptors in the medulla and few reports of clinically significant respiratory depression following cannabis overdose. The respiratory effects of CB1agonists have rarely been studiedin vivo, suggesting that additional inquiry is required to reconcile the conflict between conventional wisdom and human data. Here we used whole body plethysmography to examine the respiratory effects of the synthetic high efficacy CB1agonist CP55,940, and the low efficacy CB1agonist Δ9-tetrahydrocannabinol in male and female mice. CP55,940 and THC, administered systemically, both robustly suppressed minute ventilation. Both cannabinoids also produced sizable reductions in tidal volume, decreasing both peak inspiratory and expiratory flow - measures of respiratory effort. Similarly, both drugs reduced respiratory frequency, decreasing both inspiratory and expiratory time while markedly increasing expiratory pause, and to a lesser extent, inspiratory pause. Respiratory suppressive effects occurred at lower doses in females than in males, and at many of the same doses shown to produce cardinal behavioral signs of CB1activation. We next used RNAscopein situhybridization to localize CB1mRNA to glutamatergic neurons in the medullary pre-Bötzinger Complex, a critical nucleus in controlling respiration. Our results show that, contrary to previous conventional wisdom, CB1mRNA is expressed in glutamatergic neurons in a brain region essential for breathing and CB1agonists can cause significant respiratory depression.
Redirecting DNA repair for efficient CRISPR-Cas-based gene targeting in tomato
Authors: Van Vu Tien , Nguyen Ngan Thi , Kim Jihae , Vu Minh Huy , Song Young Jong , Tran Mil Thi , Sung Yeon Woo , Kim Jae-Yean 
Published: March 2024

ABSTRACTThe CRISPR-Cas-based gene targeting (GT) method has enabled precise modifications of genomic DNA ranging from single base to several kilobase scales through homologous recombination (HR). In plant somatic cells, canonical nonhomologous end-joining (cNHEJ) is the predominant mechanism for repairing double-stranded breaks (DSBs), thus limiting the HR-mediated GT. In this study, we implemented various approaches to shift the repair pathway preference toward HR by using a dominant-negative KU80 mutant protein (KUDN) to disrupt the initiation of cNHEJ and enhance DSB end resection through nucleases. Our results show from 1.71- to 3.55-fold improvement of the GT efficiency at the callus stage and a more remarkable, up to 9.84-fold, increase in GT efficiency at two specific tomato loci,SlHKT1;2andSlEPSPS1, when we screened transformants obtained from the KUDN-mediated cNHEJ suppression approach. With practical levels of efficiency, this enhanced KUDN-based GT tool successfully facilitated GT at an additional locus,SlCAB13. These findings provide a promising method for more efficient and precise plant breeding in the future.
Her9 controls the stemness properties of the hindbrain boundary cells
Authors: Engel-Pizcueta Carolyn , Hevia Covadonga F , Voltes Adrià , Livet Jean , Pujades Cristina 
Published: March 2024

ABSTRACTDifferent spatiotemporal distribution of progenitor/neurogenic capacities permits that brain regions engage asynchronously in neurogenesis. In the hindbrain, rhombomere progenitor cells are the main contributors to neurons during the first neurogenic phase, whereas boundary cells participate later, relying on Notch3-activity. To analyze the mechanism(s) that maintain boundary cells as proliferative progenitors not engaging in neurogenesis, we addressed the role of the zebrafish Hes1 ortholog, Her9, in this cell population.her9expression is temporarily sustained in boundary cells in a Notch-independent manner while they behave as non-neurogenic progenitors. Functional manipulations demonstrate that Her9 inhibits the onset of Notch-signaling and the neurogenic program, thus keeping boundary cells in the progenitor state. Combining multicolor clonal analysis with functional approaches, we reveal a role of Her9 in the expansion of boundary progenitors by promoting symmetric proliferative divisions and preventing neurogenic cell divisions. Moreover, Her9 regulates the proliferation of boundary cells by inhibiting the cell cycle genecdkn1caand potentially interplaying with CyclinD1. Altogether, Her9 maintains the stemness and proliferation of hindbrain boundary progenitors at early embryonic stages.