bluuebunny/crossref_metadata_2025_split huggingface dataset:
Addressing Erroneous Scale Assumptions in Microbe and Gene Set Enrichment Analysis
Authors: McGovern Kyle C. , Nixon Michelle Pistner , Silverman Justin D. 
Published: March 2023

AbstractBy applying Differential Set Analysis (DSA) to sequence count data, researchers can determine whether groups of microbes or genes are differentially enriched. Yet these data lack information about the scale (i.e., size) of the biological system under study, leading some authors to call these data compositional (i.e., proportional). In this article we show that commonly used DSA methods make strong, implicit assumptions about the unmeasured system scale. We show that even small errors in these assumptions can lead to false positive rates as high as 70%. To mitigate this problem, we introduce a sensitivity analysis framework to identify when modeling results are robust to such errors and when they are suspect. Unlike standard benchmarking studies, our methods do not require ground-truth knowledge and can therefore be applied to both simulated and real data.
Patterns of Neural Activation During an Initial Social Stress Encounter are Predictive of Future Susceptibility or Resilience: A FosTRAP2 Study
Authors: Murra Dalia , Hilde Kathryn L. , Khalil Huzefa , Watson Stanley J. , Akil Huda 
Published: March 2023

ABSTRACTRepeated social stress is a significant factor in triggering depression in vulnerable individuals, and genetic and environmental factors interact to contribute to this vulnerability. Interestingly, the role of experience in shaping vulnerability is not well studied. To what extent does an individual’s initial reaction to a given stressor influence their response to similar stressors in the future? And how is this initial response encoded at the neural level to bias towards future susceptibility or resilience?The Chronic Social Defeat Stress (CSDS) mouse model offers an ideal opportunity to address these questions. Following 10 days of repeated social defeat, mice diverge into two distinct populations of social reactivity: resilient (interactive) and susceptible (avoidant). It is notable that the CSDS paradigm traditionally uses genetically inbred mice, indicating that this divergence is not genetically determined. Furthermore, the emergence of the two phenotypes only occurs following several days of exposure to stress, suggesting that the repeated experience of social defeat influences future susceptibility or resilience.In this study, we asked whether specific patterns of neural activation during the initial exposure to the social defeat stress can predict whether an individual will eventually emerge as resilient or susceptible. To address this question, we used Fos-TRAP2 mouse technology to capture brain-wide neural activation patterns elicited during the initial stress exposure, while allowing the mice to go on to experience the full course of CSDS and diverge into resilient and susceptible populations. Using a high-throughput brain-wide cell counting approach, we identified the bed nucleus of the stria terminalis and lateral septal nucleus as key hubs for encoding social defeat. We also identified the basomedial amygdala as a hub for encoding future susceptibility, and the hippocampal CA1 area and medial habenula for encoding future resilience.Our findings demonstrate that the initial experience with social stress induces a distinct brain-wide pattern of neural activation associated with defeat, as well as unique activation patterns that appear to set the stage for future resilience or susceptibility. This highly orchestrated response to defeat is seen especially in animals that emerge as resilient compared to susceptible. Overall, our work represents a critical starting place for elucidating mechanisms whereby early experiences can shape vulnerability to affective disorders.
Distinct Th17 effector cytokines differentially promote microglial and blood-brain barrier inflammatory responses during post-infectious encephalitis
Authors: Wayne Charlotte R. , Bremner Luca , Faust Travis E. , Durán-Laforet Violeta , Ampatey Nicole , Ho Sarah J. , Feinberg Philip A. , Arvanitis Panos , Ciric Bogoljub , Ruan Chunsheng , Elyaman Wassim , Delaney Shannon L. , Vargas Wendy S. , Swedo Susan , Menon Vilas , Schafer Dorothy P. , Cutforth Tyler , Agalliu Dritan 
Published: March 2023

SUMMARYGroup AStreptococcus(GAS) infections can cause neuropsychiatric sequelae in children due to post-infectious encephalitis. Multiple GAS infections induce migration of Th17 lymphocytes from the nose into the brain, which are critical for microglial activation, blood-brain barrier (BBB) and neural circuit impairment in a mouse disease model. How endothelial cells (ECs) and microglia respond to GAS infections, and which Th17-derived cytokines are essential for these responses are unknown. Using single-cell RNA sequencing and spatial transcriptomics, we found that ECs downregulate BBB genes and microglia upregulate interferon-response, chemokine and antigen-presentation genes after GAS infections. Several microglial-derived chemokines were elevated in patient sera. Administration of a neutralizing antibody against interleukin-17A (IL-17A), but not ablation of granulocyte-macrophage colony-stimulating factor (GM-CSF) in T cells, partially rescued BBB dysfunction and microglial expression of chemokine genes. Thus, IL-17A is critical for neuropsychiatric sequelae of GAS infections and may be targeted to treat these disorders.
CRISPR based programmable RNA editing in primary neurons
Authors: Ravichandran Karthick , Khargonkar Tulika , Samaddar Sarbani , Banerjee Sourav 
Published: March 2023

AbstractInvestigating the RNA regulation landscape primarily relies on our understanding of how RNA-protein interactions are governed in various cell types, including neurons. Analysis of RNA-protein interactions in physiological environments warrants the development of new tools that rely on RNA manipulation. Recently, A CRISPR-based RNA-editing tool (dCas13b-ADAR2DD) was developed to mitigate disease associated point mutations in cell lines. Here, we have explored the targeted sequence editing potential of the tool (dCas13b-ADAR2DDsystem) by adapting it to manipulate RNA function with an aim to visualize RNA editing in primary hippocampal neurons. This is a two-component system that includes a programmable guide RNA (gRNA) complementary to the target RNA, and a catalytically dead version of the Cas13b enzyme fused to ADAR. The RNA editing protocol outlined in this manuscript relies on using the gRNA-dependent targeting of dCas13b-ADAR fusion protein to the mutant form of mDendra transcript. We first abrogated the fluorescence of Dendra2 by introducing a nonsense mutation that precludes the formation of the functional protein. To visualize the efficacy of the RNA editing in neurons, we used the dCas13b-ADAR2DDsystem to edit specific nucleotides within the Dendra2 mRNA to restore the amino acid codes critical for Dendra2 fluorescence. This method therefore lays the foundation to future studies on the dynamicity of activity-induced RNA-protein interactions in neurons and can be extended to manipulate the endogenous RNome in diverse neuronal subtypes. Furthermore, this methodology will enable investigators to visualize the spatial and temporal resolution of RNA-protein interactions without altering the genomesviaconventional methods.HighlightsCRISPR-Cas13 based application that enables site specific A-to-I in target RNAs directed by gRNA; optimized in neurons.Enables the temporal mapping of developmentally relevant RNAs and their cis-interacting RNA binding proteins.
Parallel and divergent morphological adaptations underlying the evolution of jumping ability in ants
Authors: Aibekova Lazzat , Keller Roberto A. , Katzke Julian , Allman Daniel M , Garcia Francisco Hita , Labonte David , Narendra Ajay , Economo Evan P. 
Published: March 2023

ABSTRACTJumping is a rapid locomotory mode widespread in terrestrial organisms. However, it is a rare specialization in ants. Forward jumping has been reported within four distantly related ant genera:Gigantiops,Harpegnathos,Myrmecia, andOdontomachus. The temporal engagement of legs/body parts during jump, however, varies across these genera. It is unknown what morphological adaptations underlie such behaviors, and whether jumping in ants is solely driven directly by muscle contraction or additionally relies on elastic recoil mechanism. We investigate the morphological adaptations for jumping behavior by comparing differences in the locomotory musculature between jumping and non-jumping relatives using x-ray micro- CT and 3D morphometrics. We found that the size-specific volumes of the trochanter depressor muscle (scm6) of the middle and hind legs are 3-5 times larger in jumping ants, and that one coxal remotor muscle (scm2) is reduced in volume in the middle and/or hind legs. Notably, the enlargement in the volume of other muscle groups is directly linked to the legs or body parts engaged during the jump. Furthermore, a direct comparison of the muscle architecture revealed two significant differences between in jumping versus non-jumping ants: First, the relative Physiological Cross-Sectional Area (PCSA) of the trochanter depressor muscles of all three legs were larger in jumping ants, except in the front legs ofO. rixosusandM. nigrocincta; second, the relative muscle fiber length was shorter in jumping ants compared to non-jumping counterparts, except in the front legs ofO. rixosusandM. nigrocincta. This suggests that the difference in relative muscle volume in jumping ants is largely invested in the area (PCSA), and not in fiber length. There was no clear difference in the pennation angle between jumping and non-jumping ants. However, the length of hind legs relative to body length was longer in jumping ants. Based on direct comparison of the observed vs. possible work and power output during jumps, we surmise that direct muscle contractions suffice to explain jumping performance, in two species, but elastic recoil is likely important in one. We suggest that increased investment in jumping-relevant musculature is a primary morphological adaptation that separates jumping from non-jumping ants. These results elucidate the common and idiosyncratic morphological changes underlying this rare adaptation in ants.
Machine Learning to Identify Molecular Markers for Metabolic Disease Development Using Mouse Models
Authors: Yang Guiyan , Liu Rex , Rezaei Shahbaz , Liu Xin , Wan Yu-Jui Yvonne 
Published: March 2023

AbstractBackgroundAging, Western diet (WD) intake, and bile acid (BA) receptor farnesoid X receptor (FXR) inactivation are risk factors for metabolic disease development including nonalcoholic fatty liver disease (NAFLD) and chronic inflammation-related health issues such as dementia. The progression of the metabolic disease can be escalated when those risks are combined. Inactivation of FXR is cancer prone in both humans and mice. The current study used omics data generated within the gut-liver axis to classify those risks using bioinformatics and machine learning approaches.MethodsDifferent ages (5, 10, and 15 months) of wild-type (WT) and FXR knockout (KO) male mice were fed with either a healthy control diet (CD) or a WD since weaning. Hepatic transcripts, liver, serum, and urine metabolites, hepatic bile acids (BAs), as well as gut microbiota were used for risk prediction. A linear support vector machine withK-fold cross-validation was used for classification and feature selection.ResultsIncreased urine sucrose alone achieved 91% accuracy in predicting WD intake. Hepatic lithocholic acid (LCA) and serum pyruvate had 100% and 95% accuracy, respectively to classify age. Association analyses showed hepatic LCA was positively associated with serum concentrations of acetone, a ketone body, and 1,3-dihydroxyacetone (DHA), but negatively correlated with serum pyruvate. Urine metabolites (decreased creatinine and taurine as well as increased succinate) or gut microbiota (increasedDorea, Dehalobacterium, andOscillospira) could predict FXR functional status with greater than 90% accuracy. Integrated pathway analyses revealed that the predictors for diet and FXR expression were implicated in the central carbon metabolism in cancer. To assess the translational relevance, mouse hepatic transcripts were crosschecked with human NAFLD and hepatocellular carcinoma (HCC) datasets. WD-affected hepaticCyp39a1andGramd1bexpression were associated with human HCC and NAFLD, respectively. The metabolites and diseases interaction analyses uncovered that the identified features are implicated in human metabolic diseases, mental disorders, and cancer.ConclusionThe risk prediction using mouse models contributes to the identification of noninvasive biomarkers for early diagnosis of metabolic disease development.
Whitefly effector G4 interacts with tomato proteins of which MIPDB141 affects whitefly performance
Authors: Naalden Diana , Dermauw Wannes , Ilias Aris , Baggerman Geert , Mastop Marieke , Dangol Sarmina , Gaertner Nicolas , Roseboom Winfried , Kwaaitaal Mark , Kramer Gertjan , van den Burg Harrold A. , Vontas John , Van Leeuwen Thomas , Kant Merijn R. , Schuurink Robert C. 
Published: March 2023

AbstractThe phloem-feeding insectBemisia tabaciis an important pest, responsible for the transmission of several crop-threatening virus species. While feeding, the insect secretes a cocktail of effectors to modulate defense responses. Here, we present a set of proteins that was identified in artificial diet on whichB. tabaciwas salivating. We studied whether these candidate effectors can play a role in plant immune suppression. Effector G4 was the most robust suppressor of the flg22-induced ROS response when transiently expressed inNicotiana benthamiana. In addition, G4 was able to supress ROS inSolanum lycopersicum(tomato) andCapsicum annuum(pepper). Fused to a fluorescence tag, G4 localized in the cytoplasm inN. benthamiana. A yeast two-hybrid screen combined with a luciferase bimolecular complementation and co-localization assays resulted in the identification of two target proteins in tomato: REF-like stress related protein 1 (RSP1) and meloidogyne-induced giant cell protein DB141 (MIPDB141). Silencing ofMIPDB141in tomato, using virus-induced gene silencing, reduced whitefly fecundity up to 40% demonstrating that the protein is involved in susceptibility toB. tabaci. Together our data demonstrate that effector G4 impairs tomato immunity to whiteflies by interfering with the ROS production and via a direct interaction with tomato susceptibility protein MIPDB141.
Unraveling dynamically-encoded latent transcriptomic patterns in pancreatic cancer cells by topic modelling
Authors: Zhang Yichen , Khalilitousi Mohammadali (Sam) , Park Yongjin P 
Published: March 2023

AbstractBuilding a comprehensive topic model has become an important research tool in single-cell genomics. With a topic model, we can decompose and ascertain distinctive cell topics shared across multiple cells, and the gene programs implicated by each topic can later serve as a predictive model in translational studies. Here, we present a Bayesian topic model that can uncover short-term RNA velocity patterns from a plethora of spliced and unspliced single-cell RNA-seq counts. We showed that modelling both types of RNA counts can improve robustness in statistical estimation and reveal new aspects of dynamic changes that can be missed in static analysis. We showcase that our modelling framework can be used to identify statistically-significant dynamic gene programs in pancreatic cancer data. Our results discovered that seven dynamic gene programs (topics) are highly correlated with cancer prognosis and generally enrich immune cell types and pathways.
PHR1 and PHL1 mediate rapid high-light responses and acclimation to triose phosphate oversupply
Authors: Ackermann Lukas , Müller Monika , Hieber Alina Johanna , Klecker Maria 
Published: March 2023

ABSTRACTFluctuations in light intensity require immediate metabolic adjustment which includes reprogramming of both plastidial and nuclear gene expression, but the signaling pathways behind such responses are not fully understood. Here we report the identification of an early high-light responsive pathway inArabidopsis thalianathat depends on PHOSPHATE STARVATION RESPONSE 1 (PHR1) and PHR1-LIKE 1 (PHL1) transcription factors involved in low phosphate (Pi) signaling. High-light treatment rapidly induced the accumulation of PHR1-responsive transcripts in wildtype plants grown under nutrient-sufficient conditions, but not inphr1 phl1double knockout plants. Differences in starch accumulation and ATP levels were detected between wildtype andphr1 phl1mutants subjected to high light, suggesting a link between Pisignaling, carbohydrate partitioning, and energy status during stress. In line with a function of PHR1/PHL1 upon triose phosphate accumulation, we observed that blocking starch biosynthesis in thephr1 phl1double mutant, by introducing theagd1-1allele, causes a severe growth defect. Phenotypes of theadg1 phr1 phl1triple mutant such as high-light sensitivity and growth restriction in the absence of exogenously supplied sucrose resemble the previously described double mutantadg1 tpt-2, lacking a functional copy of the TRIOSE PHOSPHATE/PHOSPHATE TRANSLOCATOR (TPT), and we show that Piresponses are disturbed inadg1 tpt-2. We propose that Pisequestration by photosynthesis and import of Piinto the chloroplast transiently depletes cytosolic Pireserves upon sudden increases in light intensity. The low-Pisensing machinery in the nucleus consequently implements early high-light transcriptional responses, qualifying Pias a new operational retrograde signal.
Development of monoclonal antibody-based blocking ELISA for detecting SARS-CoV-2 exposure in animals
Authors: Yuan Fangfeng , Chen Chi , Covaleda Lina M. , Martins Mathias , Reinhart Jennifer M. , Sullivan Drew R. , Diel Diego G. , Fang Ying 
Published: March 2023

ABSTRACTThe global pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) poses a significant threat to public health. Besides humans, SARS-CoV-2 can infect several animal species. Highly sensitive and specific diagnostic reagents and assays are urgently needed for rapid detection and implementation of strategies for prevention and control of the infection in animals. In this study, we initially developed a panel of monoclonal antibodies (mAbs) against SARS-CoV-2 nucleocapsid (N) protein. To detect SARS-CoV-2 antibodies in a broad spectrum of animal species, a mAb-based bELISA was developed. Test validation using a set of animal serum samples with known infection status obtained an optimal percentage of inhibition (PI) cut-off value of 17.6% with diagnostic sensitivity of 97.8% and diagnostic specificity of 98.9%. The assay demonstrates high repeatability as determined by a low coefficient of variation (7.23%, 6.95%, and 5.15%) between-runs, within-run, and within-plate, respectively. Testing of samples collected over time from experimentally infected cats showed that the bELISA was able to detect seroconversion as early as 7 days post-infection. Subsequently, the bELISA was applied for testing pet animals with COVID-19-like symptoms and specific antibody responses were detected in two dogs. The panel of mAbs generated in this study provides a valuable tool for SARS-CoV-2 diagnostics and research. The mAb-based bELISA provides a serological test in aid of COVID-19 surveillance in animals.IMPORTANCEAntibody tests are commonly used as a diagnostic tool for detecting host immune response following infection. Serology (antibody) tests complement nucleic acid assays by providing a history of virus exposure, no matter symptoms developed from infection or the infection was asymptomatic. Serology tests for COVID-19 are in high demand, especially when the vaccines become available. They are important to determine the prevalence of the viral infection in a population and identify individuals who have been infected or vaccinated. ELISA is a simple and practically reliable serological test, which allows high-throughput implementation in surveillance studies. Several COVID-19 ELISA kits are available. However, they are mostly designed for human samples and species-specific secondary antibody is required for indirect ELISA format. This paper describes the development of an all species applicable monoclonal antibody (mAb)-based blocking ELISA to facilitate the detection and surveillance of COVID-19 in animals.
Connectome-constrained deep mechanistic networks predict neural responses across the fly visual system at single-neuron resolution
Authors: Lappalainen Janne K. , Tschopp Fabian D. , Prakhya Sridhama , McGill Mason , Nern Aljoscha , Shinomiya Kazunori , Takemura Shin-ya , Gruntman Eyal , Macke Jakob H. , Turaga Srinivas C. 
Published: March 2023

AbstractWe can now measure the connectivity of every neuron in a neural circuit, but we are still blind to other biological details, including the dynamical characteristics of each neuron. The degree to which connectivity measurements alone can inform understanding of neural computation is an open question. Here we show that with only measurements of the connectivity of a biological neural network, we can predict the neural activity underlying neural computation. We constructed a model neural network with the experimentally determined connectivity for 64 cell types in the motion pathways of the fruit fly optic lobe but with unknown parameters for the single neuron and single synapse properties. We then optimized the values of these unknown parameters using techniques from deep learning, to allow the model network to detect visual motion. Our mechanistic model makes detailed experimentally testable predictions for each neuron in the connectome. We found that model predictions agreed with experimental measurements of neural activity across 24 studies. Our work demonstrates a strategy for generating detailed hypotheses about the mechanisms of neural circuit function from connectivity measurements. We show that this strategy is more likely to be successful when neurons are sparsely connected—a universally observed feature of biological neural networks across species and brain regions.
Design of a holder for the improved maneuvering of the concurrent TMS-MRI setup
Authors: Lee Hsin-Ju , Woudsma KJ , Ishraq Moh , Lin Fa-Hsuan 
Published: March 2023

AbstractBackgroundConcurrent transcranial magnetic stimulation (TMS) and magnetic resonance imaging (MRI) is time-consuming because of the limited space in the MRI bore and the sophisticated placement and orientation of the TMS coil to elicit the desired brain activities and behaviors.ObjectiveWe developed a TMS coil holder capable of quick adjustment of the TMS coil position and orientation. The holder can also hold an MRI receiver coil array.MethodsA holder with one controlling knob, two omni-direction rotation joints, and two in-plane rotation joints was developed.ResultsDifferent TMS coil positions and orientations can be arranged and fixed in seconds. The holder can also accommodate two TMS coils to allow for multi-coil TMS-MRI.ConclusionOur development significantly improves the workflow of the concurrent TMS-MRI in new neuroscience studies and clinical applications.