bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bacterial Form I’ rubisco has smaller carbon isotope fractionation than its Form I counterpart
Authors: Wang Renée Z. , Liu Albert K. , Banda Douglas M. , Fischer Woodward W. , Shih Patrick M. 
Published: March 2023

AbstractForm I rubiscos evolved in Cyanobacteria ≥2.5 billion years ago and are enzymatically unique due to the presence of small subunits (RbcS) that cap both ends of an octameric large subunit (RbcL) rubisco assembly to form a hexadecameric (L8S8) holoenzyme. Although RbcS was previously thought to be integral to Form I rubisco stability, the recent discovery of a closely related sister clade of octameric rubiscos (Form I’; L8) demonstrates that the enzyme complex assembles without small subunits (Banda et al. 2020). Rubisco also displays a kinetic isotope effect (KIE) where the 3PG product is depleted in13C relative to12C. In Cyanobacteria only two Form I KIE measurements exist, making interpretation of bacterial carbon isotope data difficult. To aid comparison, we measuredin vitrothe KIEs of Form I’ (CandidatusPromineofilum breve) and Form I (Synechococcus elongatusPCC 6301) rubiscos and found the KIE to be smaller in the L8rubisco (16.25 ± 1.36‰ vs. 22.42 ± 2.37‰ respectively). Therefore, while small subunits may not be necessary for protein stability, they may affect the KIE. Our findings may provide insight into the function of RbcS and allow more refined interpretation of environmental carbon isotope data.
Cholangiocyte primary cilia transduce a fluid shear signal to increase KLF2 via the actin cytoskeleton
Authors: Wehrkamp Cody J. , Oleksijew Andrew M. , Mansini Adrian P. , Gradilone Sergio A. , Mohr Ashley M. , Mott Justin L. 
Published: March 2023

AbstractCholangiocarcinoma is an aggressive solid tumor formed in the bile duct epithelium. Often this tumor obstructs bile flow, known as cholestasis. Normal cholangiocytes detect bile flow in the ductal lumen with an extension of the apical membrane called the primary cilium. However, these sensory organelles are often lost in malignant cells. Krüppel-like factor 2 (KLF2) is an important flow-sensitive transcription factor involved in shear stress response in endothelial cells, and has anti-proliferative, anti-inflammatory, and anti-angiogenic effects. The potential role of KLF2 in cholangiocyte flow detection and in cholangiocarcinoma is unknown. We hypothesized that reduced bile flow contributes to malignant features in cholangiocarcinoma through regulation of KLF2 signaling. We observed that primary cilia were expressed in normal cholangiocytes but were absent in malignant cells. KLF2 expression was higher in normal cells compared to malignant. Depletion of cilia in normal cells led to a decrease in KLF2 expression and increased cilia number was associated with increased KLF2. Enforced KLF2 expression inhibited cell proliferation, migration, and also decreased cell death induction in malignant cells. Applied media flow over cholangiocytes increased KLF2 and cilia depletion completely blocked flow-induced KLF2 expression. Disruption of filamentous actin decreased KLF2 expression, suggesting the cilium may communicate through a cytoskeletal mechanotransduction pathway. Our studies demonstrate that cilia positively regulated KLF2 protein levels and increased fluid flow induced KLF2 expression for the first time in cholangiocytes, emphasizing the importance of reestablishing bile flow in cholestatic cholangiocarcinoma.
Farnesoid X receptor agonism prevents neutrophil extracellular traps via reduced sphingosine-1-phosphate in chronic kidney disease
Authors: Jones Bryce A. , Myakala Komuraiah , Guha Mahilan , Davidson Shania , Adapa Sharmila , Santiago Isabel Lopez , Schaffer Isabel , Yue Yang , Allegood Jeremy , Cowart Lauren A. , Wang Xiaoxin X. , Rosenberg Avi Z. , Levi Moshe 
Published: March 2023

AbstractBackgroundActivation of the farnesoid X receptor (FXR) reduces renal inflammation, but the underlying mechanisms remain elusive. Neutrophil extracellular traps (NETs) are webs of DNA formed when neutrophils undergo specialized programmed cell death (NETosis). Sphingosine-1-phosphate (S1P) is a signaling lipid that stimulates NETosis via its receptor on neutrophils. Here, we identify FXR as a negative regulator of kidney NETosis via repressing S1P signaling in male but not female mice.MethodsWe determined the effects of the FXR agonist obeticholic acid (OCA) in mouse models of adenosine phosphoribosyltransferase deficiency and Alport syndrome. We assessed renal NETosis by immunofluorescence in these models and in biopsies from patients with Alport syndrome (6 male, 9 female). We also inhibited de novo sphingosine production in Alport mice to show a causal relationship between S1P signaling and renal NETosis.ResultsRenal FXR activity is greatly reduced in both models, and OCA prevents kidney fibrosis, inflammation, and lipotoxicity. OCA reduces renal neutrophilic inflammation and NETosis in male adenine and Alport mice, but not in female adenine mice. Extensive NETosis was also identified in human Alport kidney biopsies. Kidney sphingosine kinase 1 (Sphk1) expression is increased in mice with kidney disease and reduced by OCA in male but not female mice. Also, Sphk1 expression correlates with NETosis in male but not female mice. Short-term inhibition of sphingosine synthesis reduces neutrophilic inflammation and NETosis.ConclusionFXR agonism represses kidney Sphk1 expression in male but not female mice. This inhibits renal S1P signaling, thereby reducing neutrophilic inflammation and NETosis in a sex-dependent manner.
Biophysical Characterization and Interaction study of WhiB6 Protein ofMycobacterium tuberculosiswith Nucleic Acid
Authors: Kumari Sonam , Singh Ruchi , Teena  , Siddhanta Soumik , Deep Shashank 
Published: March 2023

ABSTRACTTuberculosis is an intractable disease because of the peculiar nature of the virulent properties ofMycobacterium tuberculosis. The WhiB6 protein, a transcriptional regulator, plays a crucial role in the virulence systems ofMtb. It regulates the expression of genes essential for the virulence pathways by binding to their promoter region;espAis one such gene. Herein, we have used biophysical methods, including steady-state intrinsic fluorescence spectroscopy, circular dichroism spectroscopy, Isothermal titration calorimetry (ITC), and Surface-Enhanced Raman Spectroscopy (SERS) to understand the interaction of WhiB6 protein withespApromoter DNA. For the first time, we report the conformational details and biophysical parameters related to the WhiB6-espApromoter DNA interaction. WhiB6 binds the DNA with moderate affinity, as revealed by ITC. CD and SERS studies suggest subtle perturbation in the secondary conformation of the protein on binding to the DNA. SERS provided detailed structural insights into the WhiB6 protein and the amino acids involved in the interaction, which could be harnessed to find suitable inhibitors of the protein-DNA interaction. Preventing the binding of WhiB6 with promoter DNA of the virulence genes can hinder the functioning ofMtband hence can act as an effective therapeutic intervention for tuberculosis.
Decision-making dynamics are predicted by arousal and uninstructed movements
Authors: Hulsey Daniel , Zumwalt Kevin , Mazzucato Luca , McCormick David A. , Jaramillo Santiago 
Published: March 2023

AbstractDuring sensory-guided behavior, an animal’s decision-making dynamics unfold through sequences of distinct performance states, even while stimulus-reward contingencies remain static. Little is known about the factors that underlie these changes in task performance. We hypothesize that these decision-making dynamics can be predicted by externally observable measures, such as uninstructed movements and changes in arousal. Here, combining behavioral experiments in mice with computational modeling, we uncovered lawful relationships between transitions in strategic task performance states and an animal’s arousal and uninstructed movements. Using hidden Markov models applied to behavioral choices during sensory discrimination tasks, we found that animals fluctuate between minutes-long optimal, sub-optimal and disengaged performance states. Optimal state epochs were predicted by intermediate levels, and reduced variability, of pupil diameter, along with reduced variability in face movements and locomotion. Our results demonstrate that externally observable uninstructed behaviors can predict optimal performance states, and suggest mice regulate their arousal during optimal performance.
Isolation of ACE2-dependent and -independent sarbecoviruses from Chinese horseshoe bats
Authors: Guo Hua , Li Ang , Dong Tian-Yi , Si Hao-Rui , Hu Ben , Li Bei , Zhu Yan , Shi Zheng-Li , Letko Michael 
Published: March 2023

ABSTRACTWhile the spike proteins from SARS-CoV and SARS-CoV-2 bind to host ACE2 to infect cells, the majority of bat sarbecoviruses cannot use ACE2 from any species. Despite their discovery almost 20 years ago, ACE2-independent sarbecoviruses have never been isolated from field samples, leading to the assumption these viruses pose little risk to humans. We have previously shown how spike proteins from a small group of ACE2-independent bat sarbecoviruses may possess the ability to infect human cells in the presence of exogenous trypsin. Here, we adapted our earlier findings into a virus isolation protocol, and recovered two new ACE2-dependent viruses, RsYN2012 and RsYN2016, as well as an ACE2-independent virus, RsHuB2019. Although our stocks of RsHuB2019 rapidly acquired a tissue-culture adaption that rendered the spike protein resistant to trypsin, trypsin was still required for viral entry, suggesting limitations on the exogenous entry factors that support bat sarbecoviruses. Electron microscopy revealed ACE2-independent sarbecoviruses have a prominent spike corona and share similar morphology to other coronaviruses. Our findings demonstrate a broader zoonotic threat posed by sarbecoviruses and shed light onto the intricacies of coronavirus isolation and propagationin vitro.SIGNIFICANCESeveral coronaviruses have transmitted from animals to people and 20 years of virus discovery studies have uncovered thousands of new coronavirus sequences in nature. Most of the animal-derived sarbecoviruses have never been isolated in culture due to cell incompatibilities and a poor understanding of thein vitrorequirements for their propagation. Here, we built on our growing body of work characterizing viral entry mechanisms of bat sarbecoviruses in human cells and have developed a virus isolation protocol that allows for exploration of these understudied viruses. Our protocol is robust and practical, leading to successful isolation of more sarbecoviruses than previous approaches and from field samples that had been collected over a 10-year longitudinal study.
Hogs sleep like logs: wild boars reduce the risk of anthropic disturbance by adjusting where they rest
Authors: Fradin Gustave , Chamaillé-Jammes Simon 
Published: March 2023

AbstractMany animals living in anthropized landscapes try to avoid encountering people by being active at night. By doing so, however, they risk being disturbed while at rest during the day. To mitigate this risk, diurnally resting species may be highly selective about where they rest. Here, we used GPS and activity sensors to study how wild boars (Sus scrofa) adjust their resting site selection and visitation patterns to the risk of disturbance by people. The data was complemented with audio recordings from animal-borne loggers to evaluate the efficacy of wild boars’ resting strategy in reducing the probability of encountering people while at rest. Generally, we found that wild boars did not specifically avoid resting near villages or roads, i.e. where the risk of encountering people is higher, if they could find sites with suitable vegetation cover. Wild boars could actually rest close to villages with very little risk of being disturbed. Resting sites located close to villages were visited more repeatedly that those located further away, suggesting that focusing on a few familiar and quiet resting sites was a successful strategy for resting undisturbed in an anthropized landscape.
White matter properties in fronto-parietal tracts predict maladaptive functional activation and deficient response inhibition in ADHD
Authors: Smullen Daniel , Bagshaw Andrew P. , Shalev Lilach , Tsafrir Shlomit , Kolodny Tamar , Mevorach Carmel 
Published: March 2023

AbstractResponse inhibition, defined as the ability to suppress inappropriate responses, is a key characteristic of adaptive human behaviour. However, in individuals with attention deficit hyperactivity disorder (ADHD) it is often impaired and is linked to broad life outcomes. Previous neuroimaging investigations have indicated a myriad of brain networks in response inhibition, which limit its utility in understanding and overcoming response inhibition difficulties. More recently, it has been suggested that a specific fronto-parietal functional circuitry between the inferior frontal gyrus (IFG) and the intraparietal sulcus (IPS), dictates the recruitment of the IPS in response inhibition in ADHD. To ascertain the critical role of the IFG-IPS functional circuit and its relevance to response inhibition in ADHD, it is crucial to understand the underlying structural architecture of this circuit so that the functional relevance could be interpreted correctly. Here we investigated the white matter pathways connecting the IFG and IPS using seed-based probabilistic tractography on diffusion data in 42 ADHD and 24 neurotypicals and assessed their impact on both the recruitment of IPS in response inhibition scenarios and on response inhibition performance in a Go/No-go task. Our results showed that individual differences in the structural properties of the IPS-IFG circuit, including tract volume and diffusivity, were linked to IPS activation and even predicted response inhibition performance outside the scanner. These findings highlight the structural-functional coupling of the IFG-IPS circuit in response inhibition in ADHD and confirm a structural basis for maladaptive functional top-down control in deficient inhibition in ADHD. Our results also support the notion of ADHD as a continuum and suggest that individual differences in tract-specific functional and structural connectivity could serve as neuromarkers of ADHD.
Patient and cell-type specific hiPSC-modeling of a truncating titin variant associated with atrial fibrillation
Authors: Huang Kate , Ashraf Mishal , Rohani Leili , Luo Yinhan , Sacayanan Ardin , Huang Haojun , Haegert Anne , Volik Stanislav , Sar Funda , LeBihan Stéphane , Liew Janet , Roberts Jason D. , Tibbits Glen F. , Churko Jared M. , Sanatani Shubhayan , Collins Colin , Brunham Liam R. , Laksman Zachary W. 
Published: March 2023

AbstractBackgroundProtein truncating mutations in the titin gene are associated with increased risk of atrial fibrillation (AF). However, little is known regarding the underlying pathophysiology.MethodsWe identified a heterozygous titin truncating variant in a patient with unexplained early-onset AF using whole exome sequencing. We used atrial and ventricular patient induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs), CRISPR/Cas9 genetic correction, and engineered heart tissue (EHT) constructs to evaluate the impact of the titin truncating variant on electrophysiology, sarcomere structure, contractility, and gene expression.ResultsWe generated atrial and ventricular iPSC-CMs from the AF patient with the titin truncating variant and a CRISPR/Cas9 genome corrected isogenic control. We demonstrate that the titin truncating variant increases susceptibility to pacing-induced arrhythmia (prevalence of arrhythmogenic phenotypes, 85.7% versus 14.2%;P= 0.03), promotes sarcomere disorganization (mean ± SEM, 66.3 ± 6.8% versus 88.0 ± 2.9%;P= 0.04) in atrial iPSC-CMs, and reduces contractile force (0.013 ± 0.003 mN versus 0.027 ± 0.004 mN;P< 0.01) in atrial EHTs compared to isogenic controls. In ventricular iPSC-CMs, this variant led to altered electrophysiology (90.0% versus 33.3%;P= 0.02) and sarcomere organization (62.0 ± 3.9% versus 82.9 ± 2.9%;P< 0.01) with no change in EHT contractility compared to isogenic controls. RNA-sequencing revealed an upregulation of cell adhesion and extracellular matrix genes in the presence of the titin truncating variant for both atrial and ventricular EHTs.ConclusionsIn a patient with early-onset unexplained AF and normal ventricular function, iPSC-CMs with a titin truncating variant showed structural and electrophysiological abnormalities in both atrial and ventricular preparations, while only atrial EHTs demonstrated reduced contractility. Whole transcriptome sequencing showed upregulation of genes involved in cell-cell and cell-matrix interactions in both atrial and ventricular EHTs. Together, these findings suggest titin truncating variants promote the development of AF through remodeling of atrial cardiac tissue and provide insight into the chamber-specific effects of titin truncating variants.
In VitroEvolution to Increase the Titers of Difficult Bacteriophages: Rapid Appelmans Protocol
Authors: Kok Danielle N. , Turnbull Joanne , Takeuchi Nobuto , Tsourkas Philippos K. , Hendrickson Heather L. 
Published: March 2023

AbstractBacteriophages are becoming increasingly important in the race to find alternatives to antibiotics. Unfortunately, bacteriophages that might otherwise be useful are sometimes discarded due to low titers making them unsuitable for downstream applications. Here, we present two distinct approaches to experimentally evolve novel New ZealandPaenibacillus larvaebacteriophages. The first approach uses the traditional agar-overlay method, whereas the other was a Rapid Appelmans Protocol (RAP) modelled after the established Appelmans Method. Both approaches resulted in an increase in plaque-forming units (PFU/mL). The RAP approach was significantly faster and simpler, and allowed us to evolve a set of bacteriophages in as little as four days, increasing titers 100-1000-fold relative to their ancestors. The resultant titers were sufficient to extract and sequence DNA from these bacteriophages. An analysis of these phage genomes is provided. We also propose a model that describes the parameters that allow the RAP approach to select improvement of bacteriophage titer. The RAP approach is an effective method for experimentally evolving previously intractable bacteriophages in a high-throughput and expeditious manner.
Differential allelic representation (DAR) identifies candidate eQTLs and improves transcriptome analysis
Authors: Baer Lachlan , Barthelson Karissa , Postlethwait John , Adelson David , Pederson Stephen , Lardelli Michael 
Published: March 2023

ABSTRACTIn comparisons between mutant and wild-type genotypes, transcriptome analysis can reveal the direct impacts of a mutation, together with the homeostatic responses of the biological system. Recent studies have highlighted that, when homozygous mutations are studied in non-isogenic backgrounds, genes from the same chromosome as a mutation often appear over-represented among differentially expressed (DE) genes. One hypothesis suggests that DE genes chromosomally linked to a mutation may not reflect true biological responses to the mutation but, instead, result from differences in representation of expression quantitative trait loci (eQTLs) between sample groups selected on the basis of mutant or wild-type genotype. This is problematic when inclusion of spurious DE genes in a functional enrichment study results in incorrect inferences of mutation effect. Here we show thatchromosomally co-located differentially expressed genes(CC-DEGs) can also be observed in analyses of dominant mutations in heterozygotes. We define a method and a metric to quantify, in RNA-sequencing data, localised differential allelic representation (DAR) between groups of samples subject to differential expression analysis. We show how the DAR metric can predict regions prone to eQTL-driven differential expression, and how it can improve functional enrichment analyses through gene exclusion or weighting of gene-level rankings. Advantageously, this improved ability to identify probable eQTLs also reveals examples of CC-DEGs thatarelikely to be functionally related to a mutant phenotype. This supports a long-standing prediction that selection for advantageous linkage disequilibrium influences chromosome evolution. By comparing the genomes of zebrafish (Danio rerio) and medaka (Oryzias latipes), a teleost with a conserved ancestral karyotype, we find possible examples of chromosomal aggregation of CC-DEGs during evolution of the zebrafish lineage. The DAR metric provides a solid foundation for addressing the eQTL issue in new and existing datasets because it relies solely on RNA-sequencing data.
Combined analysis of transposable elements and structural variation in maize genomes reveals genome contraction outpaces expansion
Authors: Munasinghe Manisha , Read Andrew , Stitzer Michelle C. , Song Baoxing , Menard Claire , Ma Kristy Yubo , Brandvain Yaniv , Hirsch Candice N. , Springer Nathan 
Published: March 2023

AbstractBackgroundStructural differences between genomes are a major source of genetic variation that contributes to phenotypic differences. Transposable elements, mobile genetic sequences capable of increasing their copy number and propagating themselves within genomes, can generate structural variation. However, their repetitive nature makes it difficult to characterize fine-scale differences in their presence at specific positions, limiting our understanding of their impact on genome variation. Domesticated maize is a particularly good system for exploring the impact of transposable element proliferation as over 70% of the genome is annotated as transposable elements. High-quality transposable element annotations were recently generated forde-novogenome assemblies of 26 diverse inbred maize lines.ResultsWe generated base-pair resolved pairwise alignments between the B73 maize reference genome and the remaining 25 inbred maize line assemblies. From this data, we classified transposable elements as either shared or polymorphic in a given pairwise comparison. Our analysis uncovered substantial structural variation between lines, representing both putative insertion and deletion events. Putative insertions in SNP depleted regions, which represent recently diverged identity by state blocks, suggest some TE families may still be active. However, our analysis reveals that, genome-wide, deletions of transposable elements account for more structural variation than insertions. These deletions are often large structural variants containing multiple transposable elements.ConclusionsCombined, our results highlight how transposable elements contribute to structural variation and demonstrate that deletion events are a major contributor to genomic differences.