bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fiber enhancement and 3D orientation analysis in label-free two-photon fluorescence microscopy
Authors: Sorelli Michele , Costantini Irene , Bocchi Leonardo , Axer Markus , Pavone Francesco Saverio , Mazzamuto Giacomo 
Published: October 2022

Abstract3D fluorescence microscopy can be profitably used in combination with tissue clearing and myelin labeling techniques for investigating the human brain myeloarchitectonics with sub-micrometric resolution, and for providing detailed histological reference data for the validation of diffusion magnetic resonance imaging (dMRI) tractography. Differently from state-of-the-art polarimetry-based neuroimaging modalities such as 3D polarized light imaging and 3D polarized-sensitive optical coherence tomography, the quantitative histological analysis of cortical and white matter fiber architectures from fluorescence microscopy images requires the estimation of fiber orientations via image processing techniques, as Fourier or structure tensor analysis. However, these can be error-prone as they are not able to detect myelinated fibers in surrounding brain tissue. Here we present a novel image processing pipeline built around a 3D Frangi filter able to enhance fiber structures of varying diameters in tiled brain section reconstructions of arbitrary size, and to produce accurate 3D fiber orientation maps in both grey and white matter regions, while preserving the native resolution of the employed microscopy system. The developed software tool also features the estimation of fiber orientation distribution functions which, in view of their widespread use in the neuroimaging community, may favor a multimodal comparison with brain connectivity data obtained from the aforementioned label-free optical modalities, and the validation of modern dMRI-based tractography. The proposed image processing pipeline was applied to brain samples treated according to a novel label-free preparation technique capable of enhancing the autofluorescence of myelinated fiber axons, thus demonstrating the feasibility of single fiber orientation analyses in fluorescence microscopy without the need for exogenous staining.
Genetic mapping revealsPou2af2-dependent tuning of tuft cell differentiation and intestinal type 2 immunity
Authors: Nadjsombati Marija S. , Niepoth Natalie , Webeck Lily M. , Kennedy Elizabeth A. , Jones Danielle L. , Baldridge Megan T. , Bendesky Andres , von Moltke Jakob 
Published: October 2022

AbstractChemosensory epithelial tuft cells contribute to innate immunity at barrier surfaces, but their differentiation from epithelial progenitors is not well understood. Here we exploited differences between inbred mouse strains to identify an epithelium-intrinsic mechanism that regulates tuft cell differentiation and tunes innate type 2 immunity in the small intestine. Balb/cJ (Balb) mice had fewer intestinal tuft cells than C57BL/6J (B6) mice and failed to respond to the tuft cell ligand succinate. A majority of this differential succinate response was determined by a single genetic locus from 50-67Mb on chromosome 9 (Chr9). Congenic Balb mice carrying the B6 Chr9 locus had elevated baseline numbers of tuft cells and responded to succinate. The Chr9 locus includesPou2af2, a transcriptional cofactor essential for tuft cell development. Epithelial crypts expressed a previously unannotated short isoform ofPou2af2that uses a novel transcriptional start site and encodes a non-functional protein. Low tuft cell numbers and the resulting lack of succinate response in Balb mice was explained by a preferential expression of the short isoform. Physiologically, differentialPou2af2isoform usage tuned innate type 2 immunity in the small intestine. Balb mice maintained responsiveness to helminth pathogens while ignoring commensalTritrichomonasprotists and reducing norovirus burdens.One Sentence SummaryGenetic mapping identifiesPou2af2isoform usage as a novel regulator of tuft cell differentiation that tunes intestinal innate type 2 immunity.
The genetic basis of variation immune defense againstLysinibacillus fusiformisinfection inDrosophila melanogaster
Authors: Smith Brittny R. , Patch Kistie B. , Unckless Robert L. 
Published: October 2022

AbstractThe genetic causes of phenotypic variation often differ depending on the population examined, particularly if the populations were founded by relatively small numbers of genotypes. Similarly, the genetic causes of phenotypic variation among similar traits (resistance to different xenobiotic compounds or pathogens) may also be completely different or only partially overlapping. Differences in genetic causes for variation in the same trait among populations suggests considerable context dependence for how selection might act on those traits. Similarities in the genetic causes of variation for different traits, on the other hand, suggests pleiotropy which also would influence how natural selection would shape variation in a trait. We characterized immune defense against a naturalDrosophilapathogen, the Gram-positiveLysinibacillus fusiformis, in three different populations and found almost no overlap in the genetic architecture of variation in survival post infection. However, when comparing our results to a similar experiment with the fungal pathogen,B. bassiana, we found a convincing shared QTL peak for both pathogens. This peak contains theBomanincluster ofDrosophilaimmune effectors. RNAi knockdown experiments confirms a role of some of these genes in immune defense against both pathogens. This suggests that natural selection may act on the entire cluster ofBomaningenes (and the linked region under the QTL) or specific peptides for specific pathogens.Author SummaryLike most traits, the way individuals respond to infection vary among individuals within a population. Some of this variation is caused by genetic differences in the host organism. Over the past decade, two prominent resources were developed to assess genetic variation for complex traits of the fruit fly,Drosophila melanogasterand map the genetic variants responsible. We recently described a strain ofLysinibacillus fusiformisbacteria, which was isolated from fruit flies and is moderately virulent when flies are infected. We mapped genetic variation in resistanceL. fusiformisusing these mapping resources. We find that among the resources, different changes were associated with immune defense. However, we also found that within a resource, the same region of the genome was associated with resistance to bothL. fusiformisand a fungal pathogen. These results suggest that different populations adapt differently to the same pathogens, but two distinct pathogens share similar causes of genetic variation within a single population.
Hidden endosymbionts: A male-killer concealed by another endosymbiont and a nuclear suppressor
Authors: Richardson Kelly M. , Ross Perran A. , Cooper Brandon S. , Conner William R. , Schmidt Tom , Hoffmann Ary A. 
Published: October 2022

AbstractMaternally transmitted endosymbiotic bacteria that cause male killing (MK) have only been described from a few insects, but this may reflect challenges in their detection rather than a rarity of MK. Here we identify MKWolbachiain populations ofDrosophila pseudotakahashii, present at a low frequency (around 4%) in natural populations and previously undetected due to a different fixedWolbachiastrain in this species expressing a different reproductive manipulation, cytoplasmic incompatibility (CI). The MK phenotype was eliminated after tetracycline treatment that removedWolbachia. Molecular analyses indicated the MK phenotype to be expressed when a secondWolbachiastrain was present alongside the CIWolbachia. A genomic analysis highlightedWolbachiaregions diverged between the strains involving 17 genes and also identified theWolbachiaas representing an outgroup to a clade ofWolbachiainfectingmelanogaster-group species, includingwRi-like andwMel-like strains. Doubly infected males induced CI with uninfected females but not females singly infected with CI-causingWolbachia. The MK phenotype manifested at the larval stage and was transmitted maternally at a high fidelity but with occasional loss of the MKWolbachiastrain. A rapidly spreading dominant nuclear suppressor genetic element affecting MK was identified through backcrossing and subsequent analysis with ddRAD SNPs of theD. pseudotakahashiigenome. These findings highlight the complexity of nuclear and microbial components affecting MK endosymbiont detection and dynamics in populations, and the challenges of making connections between endosymbionts and the host phenotypes affected by them.
Multimodal mapping of cell types and projections in the central nucleus of the amygdala
Authors: Wang Yuhan , Krabbe Sabine , Eddison Mark , Henry Fredrick E. , Fleishman Greg , Lemire Andrew L. , Wang Lihua , Korff Wyatt , Tillberg Paul W. , Lüthi Andreas , Sternson Scott M. 
Published: October 2022

AbstractThe central nucleus of the amygdala (CEA) is a brain region that integrates external and internal sensory information and executes innate and adaptive behaviors through distinct output pathways. Despite its complex functions, the diversity of molecularly defined neuronal types in the CEA and their contributions to major axonal projection targets have not been examined systematically. Here, we performed single-cell RNA-sequencing (scRNA-Seq) to classify molecularly defined cell types in the CEA and identified marker-genes to map the location of these neuronal types usingexpansionassisted iterative fluorescence insituhybridization (EASI-FISH). We developed new methods to integrate EASI-FISH with 5-plex retrograde axonal labeling to determine the spatial, morphological, and connectivity properties of ∼30,000 molecularly defined CEA neurons. Our study revealed spatio-molecular organization of the CEA, with medial and lateral CEA associated with distinct cell families. We also found a long-range axon projection network from the CEA, where target regions receive inputs from multiple molecularly defined cell types. Axon collateralization was found primarily among projections to hindbrain targets, which are distinct from forebrain projections. This resource reports marker-gene combinations for molecularly defined cell types and axon-projection types, which will be useful for selective interrogation of these neuronal populations to study their contributions to the diverse functions of the CEA.
Development of an IntelliCage based Cognitive Bias Test for Mice
Authors: Kahnau Pia , Jaap Anne , Urmersbach Birk , Diederich Kai , Lewejohann Lars 
Published: October 2022

AbstractThe cognitive bias test is used to measure the emotional state of animals with regard to future expectations. Thus, the test offers a unique possibility to assess animal welfare with regard to housing and testing conditions of laboratory animals. So far, however, the performance of such a test is time consuming and requires the presence of an experimenter. Therefore, we developed an automated and home-cage based cognitive bias test based on the IntelliCage system. We present several developmental steps to improve the experimental design leading to a successful measurement of cognitive bias in group-housed female C57BL/6J mice. The automated and home-cage based test design allows to obtain individual data from group-housed mice, to test the mice in their familiar environment, and during their active phase. By connecting the test-cage to the home-cage via a gating system, the mice participated in the test on a self-chosen schedule, indicating high motivation to actively participate in the experiment. We propose that this should have a positive effect on the animals themselves as well as on the data. Unexpectedly, the mice showed an optimistic cognitive bias after enrichment was removed and additional restraining. An optimistic expectation of the future as a consequence of worsening environmental conditions, however, can also be interpreted as an active coping strategy in which a potential profit is sought to be maximized through a higher willingness to take risks.
Novel husbandry practices result in rapid rates of growth and sexual maturation without impacting adult behavior in the blind Mexican cavefish
Authors: Kozol Robert A. , Yuiska Anders , Han Ji Heon , Tolentino Bernadeth , Lopatto Arthur , Lewis Peter , Paz Alexandra , Keene Alex C. , Kowalko Johanna E. , Duboué Erik R 
Published: October 2022

AbstractThe development of animal model systems is dependent on the standardization of husbandry protocols that increase fecundity and reduce generation time. The blind Mexican tetra,Astyanax mexicanus, is an emerging genetic vertebrate model for evolution and biomedical research. Surface and cave populations ofA. mexicanushave independently evolved, providing a model system for studying the genetic basis of divergent biological traits. While a rapid increase in the use ofA. mexicanushas led to the generation of genetic tools including gene-editing and transgenesis, a slow and inconsistent growth rate remains a major limitation to the expanded application ofA. mexicanus. The optimization of husbandry protocols that maximizes high-nutrient feed, smaller tank densities and larger tank sizes across development, would facilitate faster growth and expand the use of this model. Here, we describe standardized husbandry practices that optimize growth through a high protein diet, increased feeding, growth sorting of larvae and juveniles, and tank size transitions based on standard length. These changes to husbandry had a significant effect on growth rates and decreased the age of sexual maturity in comparison to our previous protocols. To determine whether our nutritional change and increased feeding impacted behavior, we tested fish in exploration and schooling assays. We found that a change in diet had no effect on the behaviors we tested, suggesting that increased feeding and rapid growth will not impact the natural variation in behavioral traits. Taken together, this standardized husbandry protocol will accelerate the development ofA. mexicanusas a genetic model.
MSBooster: Improving Peptide Identification Rates using Deep Learning-Based Features
Authors: Yang Kevin L , Yu Fengchao , Teo Guo Ci , Demichev Vadim , Ralser Markus , Nesvizhskii Alexey I 
Published: October 2022

AbstractPeptide identification in liquid chromatography-tandem mass spectrometry (LC-MS/MS) experiments relies on computational algorithms for matching acquired MS/MS spectra against sequences of candidate peptides using database search tools, such as MSFragger. Here, we present a new tool, MSBooster, for rescoring peptide-to-spectrum matches using additional features incorporating deep learning-based predictions of peptide properties, such as LC retention time, ion mobility, and MS/MS spectra. We demonstrate the utility of MSBooster, in tandem with MSFragger and Percolator, in several different workflows, including nonspecific searches (immunopeptidomics), direct identification of peptides from data independent acquisition data, single-cell proteomics, and data generated on an ion mobility separation-enabled timsTOF MS platform. MSBooster is fast, robust, and fully integrated into the widely used FragPipe computational platform.
Retention time prediction to facilitate molecular structure identification with tandem mass spectrometry
Authors: Friedlos Patrik , Gasser Lilian , Harris Eliza 
Published: October 2022

AbstractComparing measured and predicted chromatographic retention time can improve molecular structure assignment in applications such as coupled liquid chromatography-tandem mass spectrometry. We assess a range of different machine learning methods to predict hydrophobicity, a molecular property that can be used as a proxy for retention time. The performance of the models is evaluated on the benchmark Martel and SAMPL7 datasets. We find that more powerful models perform better when predicting in-sample but not necessarily when generalizing to out-of-sample molecular families. We also find that ensemble methods can outperform individual models. Additionally, a multitask learning model shows promise for improving the generalization ability of graph neural networks for hydrophobicity prediction. Finally, we discuss how the ability of graph neural networks to generalize for molecular property prediction could be improved further.
mRNA therapy restores ureagenesis and corrects glutathione metabolism in argininosuccinic aciduria
Authors: Gurung Sonam , Timmermand Oskar V. , Perocheau Dany , Gil-Martinez Ana Luisa , Minnion Magdalena , Touramanidou Loukia , Fang Sherry , Messina Martina , Khalil Youssef , Barber Abigail R. , Edwards Richard S. , Finn Patrick F. , Cavedon Alex , Siddiqui Summar , Rice Lisa , Martini Paolo G.V. , Mills Philippa B. , Waddington Simon N. , Gissen Paul , Eaton Simon , Ryten Mina , Feelisch Martin , Frassetto Andrea , Witney Timothy H. , Baruteau Julien 
Published: October 2022

AbstractArgininosuccinate lyase (ASL) is a key enzyme integral to the hepatic urea cycle which is required for ammonia detoxification, and the citrulline-nitric oxide (NO) cycle for NO production. ASL deficient patients present with argininosuccinic aciduria (ASA), an inherited metabolic disease with hyperammonaemia and a chronic systemic phenotype with neurocognitive impairment and chronic liver disease. ASL deficiency as an inherited model of systemic NO deficiency, shows enhanced nitrosative and oxidative stress. Here, we describe the dysregulation of glutathione biosynthesis and upstream cysteine utilization in ASL-deficient patients and mice using targeted metabolomics andin vivopositron emission tomography (PET) imaging using (S)-4-(3-18F-fluoropropyl)-L-glutamate ([18F]FSPG). Upregulation of cysteine metabolism contrasted with glutathione depletion and down-regulated antioxidant pathways.hASLmRNA encapsulated in lipid nanoparticles corrected and rescued the neonatal and adult Asl-deficient mouse phenotypes, respectively, enhancing ureagenesis and glutathione metabolism and ameliorating chronic liver disease. We further present [18F]FSPG PET as a novel non-invasive diagnostic tool to assess liver disease and therapeutic efficacy in ASA. These findings support clinical translation of mRNA therapy for ASA.
The IRE1α-XBP1 signaling axis promotes glycolytic reprogramming in response to inflammatory stimuli
Authors: English Bevin C. , Savage Hannah P. , Mahan Scott P. , Diaz-Ochoa Vladimir E. , Young Briana M. , Abuaita Basel H. , Sule Gautam , Knight Jason S. , O’Riordan Mary X. , Bäumler Andreas J. , Tsolis Renée M. 
Published: October 2022

ABSTRACTImmune cells must be able to adjust their metabolic programs to effectively carry out their effector functions. Here, we show that the ER stress sensor IRE1α and its downstream transcription factor XBP1 enhance the upregulation of glycolysis in classically activated macrophages (CAM). The IRE1α-XBP1 signaling axis supports this glycolytic switch in macrophages when activated by LPS stimulation or infection with the intracellular bacterial pathogenBrucella abortus. Importantly, these different inflammatory stimuli have distinct mechanisms of IRE1α activation; while TLR4 supports glycolysis under both conditions, TLR4 is required for activation of IRE1α in response to LPS treatment but notB. abortusinfection. Though IRE1α and XBP1 are necessary for maximal induction of glycolysis in CAM, activation of this pathway is not sufficient to increase the glycolytic rate of macrophages, indicating that the cellular context in which this pathway is activated ultimately dictates the cell’s metabolic response and that IRE1α activation may be a way to fine-tune metabolic reprogramming.IMPORTANCEThe immune system must be able to tailor its response to different types of pathogens in order to eliminate them and protect the host. When confronted with bacterial pathogens, macrophages, frontline defenders in the immune system, switch to a glycolysis-driven metabolism to carry out their antibacterial functions. Here, we show that IRE1α, a sensor of ER stress, and its downstream transcription factor XBP1 support glycolysis in macrophages during infection withBrucella abortusor challenge withSalmonellaLPS. Interestingly, these stimuli activate IRE1α by independent mechanisms. While the IRE1α-XBP1 signaling axis promotes the glycolytic switch, activation of this pathway is not sufficient to increase glycolysis in macrophages. This study furthers our understanding of the pathways that drive macrophage immunometabolism and highlights a new role for IRE1α and XBP1 in innate immunity.
Dual receptive fields underlying target and wide-field motion sensitivity in looming sensitive descending neurons
Authors: Nicholas Sarah , Ogawa Yuri , Nordström Karin 
Published: October 2022

AbstractResponding rapidly to visual stimuli is fundamental for many animals. For example, predatory birds and insects alike have amazing target detection abilities, with incredibly short neural and behavioral delays, enabling efficient prey capture. Similarly, looming objects need to be rapidly avoided to ensure immediate survival, as these could represent approaching predators. MaleEristalis tenaxhoverflies are non-predatory, highly territorial insects, that perform high-speed pursuits of conspecifics and other territorial intruders. During the initial stages of the pursuit the retinal projection of the target is very small, but grows to a larger object before physical interaction. Supporting such behaviors,E. tenaxand other insects have both target-tuned and loom-sensitive neurons in the optic lobes and the descending pathways. We here show that these visual stimuli are not necessarily encoded in parallel. Indeed, we describe a class of descending neurons that respond to small targets, to looming and to widefield stimuli. We show that these neurons have two distinct receptive fields where the dorsal receptive field is sensitive to the motion of small targets and the ventral receptive field responds to larger objects or widefield stimuli. Our data suggest that the two receptive fields have different pre-synaptic input, where the inputs are not linearly summed. This novel and unique arrangement could support different behaviors, including obstacle avoidance, flower landing, target pursuit or capture.Significance StatementIf you are playing baseball, when the ball is far away, it appears as a very small object on your retina. However, as the ball gets closer, its image becomes a rapidly expanding object. Here, we show that within the hoverfly visual system, a single neuron could respond to both of these images. Indeed, we found a class of descending neurons with dual sensitivity, separated into two distinct parts of the visual field. The neurons have a more dorsal receptive field that is sensitive to small targets and a more ventral receptive field that is sensitive to larger objects.