bluuebunny/crossref_metadata_2025_split huggingface dataset:
Local brainstem circuits contribute to reticulospinal output in the mouse
Authors: Chopek Jeremy W. , Zhang Ying , Brownstone Robert M 
Published: January 2021

ABSTRACTGlutamatergic reticulospinal neurons in the gigantocellular reticular nucleus (GRN) of the medullary reticular formation can function as command neurons, transmitting motor commands to spinal cord circuits. Recent advances in our understanding of this neuron-dense region have been facilitated by the discovery of expression of the transcriptional regulator, Chx10, in excitatory reticulospinal neurons. Here, we address the capacity of local circuitry in the GRN to contribute to reticulospinal output. We define two sub-populations of Chx10-expressing neurons in this region, based on distinct electrophysiological properties and somata size (small and large), and show that these correspond to local interneurons and reticulospinal neurons, respectively. Using focal release of caged-glutamate combined with patch clamp recordings, we demonstrated that Chx10 neurons form microcircuits in which the Chx10 interneurons project to and facilitate the firing of Chx10 reticulospinal neurons. We discuss the implications of these microcircuits in terms of movement selection.SIGNIFICANCE STATEMENTReticulospinal neurons in the medullary reticular formation play a key role in movement. The transcriptional regulator Chx10 defines a population of glutamatergic neurons in this region, a proportion of which have been shown to be involved in stopping, steering, and modulating locomotion. While it has been shown that these neurons integrate descending inputs, we asked whether local processing also ultimately contributes to reticulospinal outputs. Here, we define Chx10-expressing medullary reticular formation interneurons and reticulospinal neurons, and demonstrate how the former modulate the output of the latter. The results shed light on the internal organization and microcircuit formation of reticular formation neurons.
Neuroepithelial organoid patterning is mediated by Wnt-driven Turing mechanism
Authors: Fattah Abdel Rahman Abdel , Grebenyuk Sergei , Salmon Idris , Ranga Adrian 
Published: January 2021

AbstractCell patterning in epithelia is critical for the establishment of tissue function during development. The organization of patterns in these tissues is mediated by the interpretation of signals operating across multiple length scales. How epithelial tissues coordinate changes in cell identity across these length scales to orchestrate cellular rearrangements and fate specification remains poorly understood. Here, we use human neural tube organoids as model systems to interrogate epithelial patterning principles that guide domain specification.In silicomodeling of the patterning process by cellular automata, validated byin vitroexperiments, reveal that the initial positions of floor plate cells, coupled with activator-inhibitor signaling interactions, deterministically dictate the patterning outcome according to a discretized Turing reaction-diffusion mechanism. This model predicts an enhancement of organoid patterning by modulating inhibitor levels. Receptor-ligand interaction analysis of scRNAseq data from multiple organoid domains reveals WNT-pathway ligands as the specific inhibitory agents, thereby allowing for the experimental validation of model predictions. These results demonstrate that neuroepithelia employ reaction-diffusion-based mechanisms during early embryonic human development to organize cellular identities and morphogen sources to achieve patterning. The wider implementation of suchin vitroorganoid models in combination within-silicoagent-based modeling coupled to receptor-ligand analysis of scRNAseq data opens avenues for a broader understanding of dynamic tissue patterning processes.
The Th1 cell regulatory circuitry is largely conserved between human and mouse
Authors: Henderson Stephen , Pullabhatla Venu , Hertweck Arnulf , de Rinaldis Emanuele , Herrero Javier , Lord Graham M. , Jenner Richard G. 
Published: January 2021

ABSTRACTGene expression programmes controlled by lineage-determining transcription factors are often conserved between species. However, infectious diseases have exerted profound evolutionary pressure, and therefore the genes regulated by immune-specific transcription factors might be expected to exhibit greater divergence due to exposure to species-specific pathogens. T-bet (Tbx21) is the immune-specific lineage-defining transcription factor for T helper type I (Th1) immunity, which is fundamental for the immune response to intracellular pathogens but also underlies inflammatory diseases. We therefore compared T-bet genomic targets between mouse and human CD4+T cells and correlated T-bet binding patterns with species-specific gene expression. Remarkably, we show that the vast majority of T-bet regulated genes are conserved between mouse and human, either via preservation of a binding site or via an alternative binding site associated with transposon-linked insertion. We also identified genes that are specifically targeted by T-bet in humans or mice and which exhibited species-specific expression. These results provide a genome-wide cross-species comparison of T-bet target gene regulation that will enable more accurate translation of genetic targets and therapeutics from pre-clinical models of inflammatory disease into human clinical trials.
Characterization of a novel variant in the HR1 domain ofMFN2in a patient with ataxia, optic atrophy and sensorineural hearing loss
Authors: Sharma Govinda , Saubouny Rasha , Joel Matthew M , Martens Kristina , Martino Davide , de Koning A.P. Jason , Pfeffer Gerald , Shutt Timothy E. 
Published: January 2021

AbstractPathogenic variants inMFN2cause Charcot-Marie-Tooth disease (CMT) type 2A (CMT2A) and are the leading cause of the axonal subtypes of CMT. CMT2A is characterized by predominantly distal motor weakness and muscle atrophy, with highly variable severity and onset age. Notably, someMFN2variants can also lead to other phenotypes such as optic atrophy, hearing loss and lipodystrophy. Despite the clear link betweenMFN2and CMT2A, our mechanistic understanding of how dysfunction of the MFN2 protein causes human disease pathologies remains incomplete. This lack of understanding is due in part to the multiple cellular roles of MFN2. Though initially characterized for its role in mediating mitochondrial fusion, MFN2 also plays important roles in mediating interactions between mitochondria and other organelles, such as the endoplasmic reticulum and lipid droplets. Additionally, MFN2 is also important for mitochondrial transport, mitochondrial autophagy, and has even been implicated in lipid transfer. Though over 100 pathogenicMFN2variants have been described to date, only a few have been characterized functionally, and even then, often only for one or two functions. Here, we describe a novel homozygous MFN2 variant, D414V, in a patient presenting with cerebellar ataxia, deafness, blindness, and diffuse cerebral and cerebellar atrophy. Characterization of patient fibroblasts reveals phenotypes consistent with impaired MFN2 functions and expands the phenotypic presentation ofMFN2variants to include cerebellar ataxia.
The biogeographic history of eelpouts and related fishes: linking phylogeny, environmental change, and patterns of dispersal in a globally distributed fish group
Authors: Hotaling Scott , Borowiec Marek L. , Lins Luana S.F. , Desvignes Thomas , Kelley Joanna L. 
Published: January 2021

AbstractModern genetic data sets present unprecedented opportunities to understand the evolutionary origins of taxonomic groups comprising hundreds to thousands of species. When the timing of key events are known, it is also possible to investigate biogeographic history in the context of major phenomena (e.g., continental drift). In this study, we investigated the biogeographic history of the suborder Zoarcoidei, a globally distributed fish group that includes species inhabiting both poles and multiple taxa that produce antifreeze proteins to survive chronic subfreezing temperatures. We first generated a multi-locus, time-calibrated phylogeny for the group. We then used biogeographic modeling to reconstruct ancestral ranges across the tree and quantify the type and frequency of biogeographic events (e.g., founder, dispersal). With these results, we considered how the cooling of the Southern and Arctic Oceans, which reached their present-day subfreezing temperatures 10-15 million years ago (Mya) and 2-3 Mya, respectively, may have shaped the evolutionary history of Zoarcoidei, with an emphasis on the most speciose and widely distributed family, eelpouts (family Zoarcidae). Our phylogenetic results clarified standing issues in the Zoarcoidei taxonomy and showed that the group began to diversify in the Oligocene ∼31-32 Mya, with the center of origin for all families in north temperate waters. Within-area speciation was the most common biogeographic event in the group’s history (80% of all events) followed by dispersal (20%). Finally, we found mixed evidence for polar ocean cooling underpinning Zoarcoidei diversification, with support limited to eelpout speciation in the Southern Ocean over the last 10 million years.
Increased cortical volume without increased neuron number in heterozygousChd8mutant mouse cortex
Authors: Canales Cesar P. , Frank Samuel , Bennett Jeffrey , Beauregard Paris , Lavenex Pierre , Amaral David G. , Nord Alex. S. 
Published: January 2021

AbstractDe novo mutations in the chromatin-remodeling factorCHD8(Chromodomain-Helicase DNA-binding protein 8) have emerged as a key genetic risk factor for Autism Spectrum Disorder (ASD) and, more generally, neurodevelopmental disorders. Individuals with heterozygous mutations inCHD8typically present hallmarks of ASD with comorbid cognitive disability and macrocephaly. Knockdown or haploinsufficiency ofChd8in animal models has recapitulated phenotypes observed in patients, including increased head circumference and brain size. Here, we aimed to determine whether increased neuron numbers or soma size drives increased cortical volume. We performed design-based stereological analyses of cortical structure in adult male and female heterozygousChd8mice and wild-type littermate controls.Chd8haploinsufficient male mice displayed a ~8-12% increase in cortical volume, no differences in cortical neuron number and comparable neuronal soma size. Our study reproduced previous reports of increased brain size associated withCHD8mutation in humans and mice and are consistent with reported sex-specific impacts ofChd8mutations in mice and increased burden ofCHD8mutations in human males with ASD. These findings suggest that the nature of the cortical enlargement due toChd8haploinsufficiency is complex and appears to be due to a factor other than an increased neuron number or soma size.Lay SummaryWe measured the size and neuron number in the neocortex in mice with heterozygousChd8mutation, a model relevant to Autism Spectrum Disorder. We found an increased cortical volume in male mutants, which was not accompanied by increased neuron number or soma size. Our results indicate that the enlarged brain inChd8mutant mice is complex, more evident here in males, and is due to factors other than increased neuron number.
Human leukocyte antigen class II gene diversity tunes antibody repertoires to common pathogens
Authors: Khan Taushif , Rahman Mahbuba , Ahmed Ikhlak , Ali Fatima Al , Jithesh Puthen , Marr Nico 
Published: January 2021

AbstractAllelic diversity of HLA class II genes may help maintain humoral immunity against infectious diseases. We investigated the relative contribution of specific HLA class II alleles, haplotypes and genotypes on the variation of antibody responses to a variety of common pathogens in a cohort of 800 adults representing the general Arab population. We found that classical HLA class II gene heterozygosity confers a selective advantage. Moreover, we demonstrated that multiple HLA class II alleles play a synergistic role in shaping the antibody repertoire. Interestingly, associations of HLA-DRB1 genotypes with specific antigens were identified. Our findings suggest that HLA class II gene polymorphisms confer specific humoral immunity against common pathogens, which may have contributed to the genetic diversity of HLA class II loci during hominine evolution.
Saccharomyces cerevisiaegene expression during fermentation of Pinot noir wines at industrially relevant scale
Authors: Reiter Taylor , Montpetit Rachel , Byer Shelby , Frias Isadora , Leon Esmeralda , Viano Robert , Mcloughlin Michael , Halligan Thomas , Hernandez Desmon , Runnebaum Ron , Montpetit Ben 
Published: January 2021

AbstractDuring a wine fermentation,Saccharomyces cerevisiaetransforms grape must through metabolic activities that generate ethanol and other compounds. Thousands of genes change expression over the course of a wine fermentation to allowS. cerevisiaeto adapt to and dominate the fermentation environment. Investigations into these gene expression patterns have previously revealed genes that underlie cellular adaptation to the grape must and wine environment involving metabolic specialization and ethanol tolerance. However, the vast majority of studies detailing gene expression patterns have occurred in controlled environments that do not recapitulate the biological and chemical complexity of fermentations performed at production scale. Here, we present an analysis of theS. cerevisiaeRC212 gene expression program across 40 pilot-scale fermentations (150 liters) using Pinot noir grapes from 10 California vineyards across two vintages. We observe a core gene expression program across all fermentations irrespective of vintage similar to that of laboratory fermentations, in addition to novel gene expression patterns likely related to the presence of non-Saccharomycesmicroorganisms and oxygen availability during fermentation. These gene expression patterns, both common and diverse, provide insight intoSaccharomyces cerevisiaebiology critical to fermentation outcomes at industry-relevant scales.ImportanceThis study characterizedSaccharomyces cerevisiaeRC212 gene expression during Pinot noir fermentation at pilot scale (150 liters) using production-relevant conditions. The reported gene expression patterns of RC212 is generally similar to that observed in laboratory fermentation conditions, but also contains gene expression signatures related to yeast-environment interactions found in a production setting (e.g., presence of non-Saccharomycesmicroorganisms). Key genes and pathways highlighted by this work remain under-characterized, raising the need for further research to understand the roles of these genes and their impact on industrial wine fermentation outcomes.
Identification ofNocardiaspecies using Autof MS 1000 and Bruker MALDI-TOF MS systems: A comparison
Authors: Ma Bing , Tian Yunqi , Han Yungang , Ban Lifang , Yang Junwen , Qi Xinkun , Guo Changcheng , Wang Baoya , Yan Wenjuan , Ma Qiong , Wang Shanmei , Yuan Youhua , Li Yi 
Published: January 2021

ABSTRACTNocardiais an important cause of clinically invasive disease, but for most clinical laboratories, identification of these isolates to the species level is challenging. Recently, matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been widely used for identification of most bacterial and fungal isolates. In this multicenter study, we evaluated the identification ofNocardiaisolates using Autof MS1000 and Bruker Biotyper. A total of 86 non-duplicateNocardiaisolates from 7 hospital laboratories were evaluated. Further, we carried out sequence analysis of 16S rRNA,gyrB, secA1, hsp65, andrpoBgenes as a reference method forNocardiaspecies identification. The 86 isolates were directly spotted on the target plate and plate protein extraction was performed. Data were analyzed by SPSS 19.0. In total, 72 (83.7%) strains (score ≥ 9.0) and 70 (81.4%) strains (score ≥ 2.0) were correctly identified by the Autof MS1000 and Bruker Biotyper systems, respectively, at the species level. There was no significant difference (P > 0.05) between the two systems using the same protein extraction method. In conclusion, the Autof MS 1000 and Bruker MALDI-TOF systems showed no difference in identification ofNocardia spp. to the species level and could meet the most important clinical requirement for species identification.
The duration of antibiotic treatment is associated with carriage of toxigenic and atoxigenic strains ofClostridioides difficilein dogs
Authors: Albuquerque C. , Pagnossin D. , Landsgaard K , Simpson J. , Brown D. , Irvine J.J. , Candlish D. , Ridyard. A.E. , Douce G , Millins C 
Published: January 2021

AbstractClostridioides difficileis a leading cause of human antibiotic-associated diarrhoeal disease globally. Zoonotic reservoirs of infection are increasingly suspected to play a role in the emergence of this disease in the community and dogs are considered as one potential source. Here we use a canine case-control study at a referral veterinary hospital in Scotland to assess: i) the risk factors associated with carriage ofC. difficileby dogs, ii) whether carriage ofC. difficileis associated with clinical disease in dogs and iii) the similarity of strains isolated from dogs with local human clinical surveillance. The overall prevalence ofC. difficilecarriage in dogs was 18.7% (95% CI 14.8-23.2%, n=61/327) of which 36% (n=22/61) were toxigenic strains. We found risk factors related to prior antibiotic treatment were significantly associated withC. difficilecarriage by dogs. However, the presence of toxigenic strains ofC. difficilein a canine faecal sample was not associated with diarrhoeal disease in dogs. Active toxin was infrequently detected in canine faecal samples carrying toxigenic strains (2/11 samples). Both dogs in which active toxin was detected had no clinical evidence of gastrointestinal disease. Among the ten toxigenic ribotypes ofC. difficiledetected in dogs in this study, six of these (012, 014, 020, 026, 078, 106) were ribotypes commonly associated with human clinical disease in Scotland, while atoxigenic isolates largely belonged to 010 and 039 ribotypes. WhilstC. difficiledoes not appear commonly associated with diarrhoeal disease in dogs, antibiotic treatment increases carriage of this bacteria including toxigenic strains commonly found in human clinical disease.
Modifying TIMER, a slow-folding DsRed derivative, for optimal use in quickly-dividing bacteria
Authors: Patel Pavan , O’Hara Brendan J. , Aunins Emily , Davis Kimberly M. 
Published: January 2021

AbstractIt is now well appreciated that members of pathogenic bacterial populations exhibit heterogeneity in growth rates and metabolic activity, and it is known this can impact the ability to eliminate all members of the bacterial population during antibiotic treatment. It remains unclear which pathways promote slowed bacterial growth within host tissues, primarily because it has been difficult to identify and isolate slow growing bacteria from host tissues for downstream analyses. To overcome this limitation, we have developed a novel variant of TIMER, a slow-folding fluorescent protein, to identify subsets of slowly dividing bacteria within host tissues. The original TIMER folds too slowly for fluorescence accumulation in quickly replicating bacterial species (Escherichia coli, Yersinia pseudotuberculosis), however this TIMER42variant accumulates signal in late stationary phase cultures ofE. coliandY. pseudotuberculosis. We show TIMER42signal also accumulates during exposure to sources of nitric oxide (NO), suggesting TIMER42signal detects growth-arrested bacterial cells. In a mouse model ofY. pseudotuberculosisdeep tissue infection, TIMER42signal is clearly detected, and primarily accumulates in bacteria expressing markers of stationary phase growth. There was not significant overlap between TIMER42signal and NO-exposed subpopulations of bacteria within host tissues, suggesting NO stress was transient, allowing bacteria to recover from this stress and resume replication. This novel TIMER42variant represents a new faster folding TIMER that will enable additional studies of slow-growing subpopulations of bacteria, specifically within bacterial species that quickly divide.Author SummaryWe have generated a variant of TIMER that can be used to mark slow-growing subsets ofYersinia pseudotuberculosis, which has a relatively short division time, similar toE. coli. We used a combination of site-directed and random mutagenesis to generate the TIMER42variant, which has red fluorescent signal accumulation in post-exponential or stationary phase cells. We found that nitric oxide (NO) stress is sufficient to promote TIMER42signal accumulation in culture, however within host tissues, TIMER42signal correlates with a stationary phase reporter (dps). These results suggest NO may cause an immediate arrest in bacterial cell division, but during growth in host tissues exposure to NO is transient, allowing bacteria to recover from this stress and resume cell division. Thus instead of indicating a response to host stressors, TIMER42signal accumulation within host tissues appears to identify slow-growing cells that are experiencing nutrient limitation.
Cell cycle exit and stem cell differentiation are coupled through regulation of mitochondrial activity in the Drosophila testis
Authors: de la Maza Diego Sainz , Hof-Michel Silvana , Phillimore Lee , Bökel Christian , Amoyel Marc 
Published: January 2021

AbstractStem cells maintain tissue homeostasis by proliferating to replace cells lost to damage or natural turnover. Whereas stem and progenitor cells proliferate, fully differentiated cells exit the cell cycle. How cell identity and cell cycle state are coordinated during this process is still poorly understood. The Drosophila testis niche supports germline stem cells and somatic cyst stem cells (CySCs), which are the only proliferating somatic cells in the testis. CySCs give rise to post-mitotic cyst cells and therefore provide a tractable model to ask how stem cell identity is linked to proliferation. We show that the G1/S cyclin, Cyclin E, is required for CySC self-renewal; however, its canonical transcriptional regulator, a complex of the E2f1 and Dp transcription factors is dispensable for self-renewal and cell cycle progression. Nevertheless, we demonstrate that E2f1/Dp activity must be silenced to allow CySCs to differentiate. We show that E2f1/Dp activity inhibits the expression of genes important for mitochondrial activity. Furthermore, promoting mitochondrial activity or biogenesis is sufficient to rescue the differentiation of CySCs with ectopic E2f1/Dp activity but not their exit from the cell cycle. Our findings together indicate that E2f1/Dp coordinates cell cycle progression with stem cell identity by regulating the metabolic state of CySCs.