bluuebunny/crossref_metadata_2025_split huggingface dataset:
Compartment-Specific Activation of the Proton-Sensor GPR65 is Uncoupled from Receptor Trafficking
Authors: Morales Rodríguez Loyda M. , Crilly Stephanie E. , Rowe Jacob B. , Isom Daniel G. , Puthenveedu Manojkumar A. 
Published: March 2023

ABSTRACTThe canonical view of G protein-coupled receptor (GPCR) function is that receptor trafficking is tightly coupled to signaling. GPCRs remain on the plasma membrane (PM) at the cell surface until they are activated, after which they are desensitized and internalized into endosomal compartments. This canonical view presents an interesting context for proton-sensing GPCRs because they are more likely to be activated in acidic endosomal compartments than at the PM. Here we show that the trafficking of the prototypical proton-sensor GPR65 is fully uncoupled from signaling, unlike that of other known mammalian GPCRs. GPR65 internalized and localized to early and late endosomes, from where they signal at steady state, irrespective of extracellular pH. Acidic extracellular environments stimulated receptor signaling at the PM in a dose-dependent manner, although endosomal GPR65 was still required for a full signaling response. Receptor mutants that were incapable of activating cAMP trafficked normally, internalized, and localized to endosomal compartments. Our results show that GPR65 is constitutively active in endosomes, and suggest a model where changes in extracellular pH reprograms the spatial pattern of receptor signaling and biases the location of signaling to the cell surface.
Clonal associations of lymphocyte subsets and functional states revealed by single cell antigen receptor profiling of T and B cells in rheumatoid arthritis synovium
Authors: Dunlap Garrett , Wagner Aaron , Meednu Nida , Zhang Fan , Jonsson A. Helena , Wei Kevin , Sakaue Saori , Nathan Aparna ,   Accelerating Medicines Partnership Program: Rheumatoid Arthritis and Systemic Lupus Erythematosus (AMP RA/SLE) Network, Bykerk Vivian P. , Donlin Laura T. , Goodman Susan M. , Firestein Gary S. , Boyle David L. , Holers V. Michael , Moreland Larry W. , Tabechian Darren , Pitzalis Costantino , Filer Andrew , Raychaudhuri Soumya , Brenner Michael B. , McDavid Andrew , Rao Deepak A. , Anolik Jennifer H. 
Published: March 2023

AbstractRheumatoid arthritis (RA) is an autoimmune disease initiated by antigen-specific T cells and B cells, which promote synovial inflammation through a complex set of interactions with innate immune and stromal cells. To better understand the phenotypes and clonal relationships of synovial T and B cells, we performed single-cell RNA and repertoire sequencing on paired synovial tissue and peripheral blood samples from 12 donors with seropositive RA ranging from early to chronic disease. Paired transcriptomic-repertoire analyses highlighted 3 clonally distinct CD4 T cells populations that were enriched in RA synovium: T peripheral helper (Tph) and T follicular helper (Tfh) cells, CCL5+ T cells, and T regulatory cells (Tregs). Among these cells, Tph cells showed a unique transcriptomic signature of recent T cell receptor (TCR) activation, and clonally expanded Tph cells expressed an elevated transcriptomic effector signature compared to non-expanded Tph cells. CD8 T cells showed higher oligoclonality than CD4 T cells, and the largest CD8 T cell clones in synovium were highly enriched inGZMK+ cells. TCR analyses revealed CD8 T cells with likely viral-reactive TCRs distributed across transcriptomic clusters and definitively identified MAIT cells in synovium, which showed transcriptomic features of TCR activation. Among B cells, non-naive B cells including age-associated B cells (ABC),NR4A1+activated B cells, and plasma cells, were enriched in synovium and had higher somatic hypermutation rates compared to blood B cells. Synovial B cells demonstrated substantial clonal expansion, with ABC, memory, and activated B cells clonally linked to synovial plasma cells. Together, these results reveal clonal relationships between functionally distinct lymphocyte populations that infiltrate RA synovium.
Reconstruction of segmental duplication rates and associated genomic features by network analysis
Authors: Abdullaev Eldar T , Haridoss Dinesh A , Arndt Peter F 
Published: March 2023

AbstractSegmental duplications (SDs) are long genomic duplications fixed in a genome. SDs play an important evolutionary role: entire genes together with regulatory sequences can be duplicated. Ancestral segmental duplications gave rise to genes involved in human brain development, as well as provided sites for further genomic rearrangements. Some duplicated loci were extensively studied, however, universal principles or biological factors of SDs propagation are not fully described yet. Segmental duplications can be arranged into a network where edges correspond to real duplication events, while nodes to affected genomic sites. This gave us an opportunity to estimate how many duplications happened in each locus. We studied genomic features associated with increased duplication rates with especial interest in high-copy repeats distribution relative to duplicated regions breakpoints. Our comprehensive study of genomic features associated with duplications and those associated with increased duplication rates allowed us to identify several biological factors affecting a segmental duplication process. We found genomic features associated with increased duplication rates, three signatures of duplication process and associations of SDs with different classes of high-copy repeats.
Contribution of default mode network to game and delayed-response task performance: power and connectivity analyses of theta oscillation in the monkey
Authors: Kodama Tohru , Kojima Takashi , Honda Yoshiko , Hosokawa Takayuki , Karashima Akihiro , Watanabe Masataka 
Published: March 2023

AbstractNeuroimaging studies have demonstrated the presence of a default mode network (DMN) which shows greater activity during rest, and an executive network (EN) which is activated during cognitive tasks. DMN and EN are thought to have competing functions.However, recent studies reported that the two networks show coactivation during some cognitive tasks. To clarify how DMN works and how DMN interacts with EN for cognitive control, we recorded EEG activities in the medial prefrontal (anterior DMN: aDMN), posterior cingulate/precuneus (posterior DMN: pDMN), and lateral prefrontal (EN) areas in the monkey. As cognitive tasks, we employed a monkey-monkey competitive video game (GAME) and a delayed-response (DR) task. We focused on theta oscillation because of its importance in cognitive control. We also examined theta band connectivity among the three network areas using the Granger causality analysis.DMN and EN were found to work cooperatively in both tasks. In all the three network areas, we found GAME-task-related, but no DR-task-related, increase in theta power from the resting level, maybe because of the higher cognitive demand associated with the GAME task performance. The information flow conveyed by the theta oscillation was directed more to aDMN than from aDMN for both tasks. The GAME-task-related increase in theta power in aDMN is supposed to be supported by more information flow conveyed by the theta oscillation from EN and pDMN.
FIREBALL: A tool to fit protein phase diagrams based on mean-field theories for polymer solutions
Authors: Farag Mina , Holehouse Alex S. , Zeng Xiangze , Pappu Rohit V. 
Published: March 2023

AbstractBiomolecular condensates form via phase transitions of condensate-specific biomacromolecules. Intrinsically disordered regions (IDRs) featuring the appropriate sequence grammar can contribute homotypic and heterotypic interactions to the driving forces for phase separation of multivalent proteins. At this juncture, experiments and computations have matured to the point where the concentrations of coexisting dense and dilute phases can be quantified for individual IDRs in complex milieus bothin vitroandin vivo. For a macromolecule such as a disordered protein in a solvent, the locus of points that connects concentrations of the two coexisting phases defines a phase boundary or binodal. Often, only a few points along the binodal, especially in the dense phase, are accessible for measurement. In such cases and for quantitative and comparative analysis of parameters that describe the driving forces for phase separation, it is useful to fit measured or computed binodals to well-known mean-field free energies for polymer solutions. Unfortunately, the non-linearity of the underlying free energy functions makes it challenging to put mean-field theories into practice. Here, we present FIREBALL, a suite of computational tools designed to enable efficient construction, analysis, and fitting to experimental or computed data of binodals. We show that depending on the theory being used, one can also extract information regarding coil-to-globule transitions of individual macromolecules. Here, we emphasize the ease-of-use and utility of FIREBALL using examples based on data for two different IDRs.Statement of SignificanceMacromolecular phase separation drives the assembly of membraneless bodies known as biomolecular condensates. Measurements and computer simulations can now be brought to bear to quantify how the concentrations of macromolecules in coexisting dilute and dense phases vary with changes to solution conditions. These mappings can be fit to analytical expressions for free energies of solution to extract information regarding parameters that enable comparative assessments of the balance of macromolecule-solvent interactions across different systems. However, the underlying free energies are non-linear and fitting them to actual data is non-trivial. To enable comparative numerical analyses, we introduce FIREBALL, a user-friendly suite of computational tools that allows one to generate, analyze, and fit phase diagrams and coil-to-globule transitions using well-known theories.
The Effect of Intradialytic Exercise on Calcium, Phosphorus and Parathyroid Hormone: A Randomized Controlled Trial
Authors: Tabibi Mohammadali , Wilund Kenneth R , Salimian Nasrin , Nikbakht Saghar , Soleymany Mahsa , Roshanaeian Zahra , Ahmadi Saghar 
Published: March 2023

AbstractIntroductionPatients with kidney failure experience derangements of circulating markers of mineral metabolism and dysregulation of skeletal and cardiovascular physiology which results in high mortality rate in these patients. This study aimed to evaluate the effect of intradialytic concurrent exercise on regulation of theses abnormalities related parameters in patients receiving hemodialysis (HD).MethodsIn this randomized controlled trial conducted in a HD center in Iran, adult patients receiving chronic HD were randomized to intradialytic exercise (60 minutes) in the second hour of thrice weekly dialysis for 6 months (intervention) or no intradialytic exercise (control). The primary outcomes were serum calcium, serum phosphorous and parathyroid hormone levels. Secondary outcomes were serum alkaline phosphatase and calcium-phosphorous productResultsThe study included 44 participants randomized to intervention (n=22) or control (n=22). During the 6-month intervention period, significant between-group changes were observed in all primary and secondary outcomes between the intervention and control groups. The analysis showed a significant decrease in serum levels of phosphorous and parathyroid hormone (P < 0.05). Statistical analyses reveal a significant increase in serum calcium (P < 0.05) as well as a significant decrease in serum phosphorous, parathyroid hormone, alkaline phosphatase and calcium-phosphorous product (P < 0.05).ConclusionIntradialytic exercise performed for at least 60 minutes during thrice weekly dialysis sessions improves bone mineral metabolism in adult patients receiving HD. Further studies should focus on observing the effect of different types of exercise on bone mineral disorders and all-cause mortality in HD patients.Trial registrationClinicalTrials.govIdentifier:NCT04916743, Registered on June 8th,2021. Registered trial name: The Effect of Intradialytic Exercise on Calcium, Phosphorous and Parathyroid Hormone: A Randomized Controlled Trial
The Unique Neural Signature of Your Trip: Functional Connectome Fingerprints of Subjective Psilocybin Experience
Authors: Tolle Hanna M. , Farah Juan Carlos , Mallaroni Pablo , Mason Natasha L. , Ramaekers Johannes G. , Amico Enrico 
Published: March 2023

AbstractThe emerging neuroscientific frontier of brain fingerprinting has recently established that human functional connectomes (FCs) exhibitfingerprint-likeidiosyncratic features, which map onto heterogeneously distributed behavioural traits. Here, we harness brain-fingerprinting tools to extract FC features that predict subjective drug experience induced by the psychedelic psilocybin. Specifically, in neuroimaging data of healthy volunteers under the acute influence of psilocybin or a placebo, we show that, post psilocybin administration, FCs become more idiosyncratic due to greater inter-subject dissimilarity. Moreover, whereas in placebo subjects idiosyncratic features are primarily found in the frontoparietal network, in psilocybin subjects they concentrate in the default-mode network (DMN). Crucially, isolating the latter revealed an FC pattern that predicts subjective psilocybin experience and is characterised by reduced within-DMN and DMN-limbic connectivity, as well as increased connectivity between the DMN and attentional systems. Overall, these results contribute to bridging the gap between psilocybin-mediated effects on brain and behaviour, while demonstrating the value of a brain-fingerprinting approach to pharmacological neuroimaging.Author summaryThe trending field of brain fingerprinting focuses on characterising fingerprint-like idiosyncratic features of human functional connectomes (FCs), which have been shown to predict heterogeneously distributed behavioural traits. Here, we apply brain-fingerprinting methods to fMRI data from subjects who were administered the psychedelic psilocybin or a placebo. We find that, compared to the placebo condition, subjects under acute psilocybin effects exhibited more idiosyncratic FCs, with idiosyncratic features being largely concentrated in the default-mode network (DMN). Furthermore, we isolated an idiosyncratic FC pattern that predicted reports of subjective psilocybin experiences. This pattern was characterised by altered DMN connectivity, specifically by reduced within-DMN and DMN-limbic connectivity, and increased connectivity between the DMN and attentional systems. This work paves the way for exciting new research harnessing pharmacological brain fingerprinting.
Characterisation of the bovine C-type lectin receptor Mincle and potential evidence for an endogenous ligand1
Authors: Holder Angela , Kolakowski Jeannine , Rosentreter Chloe , Knuepfer Ellen , Jégouzo Sabine A. F. , Rosenwasser Oliver , Harris Heather , Baumgaertel Lotta , Gibson Amanda , Werling Dirk 
Published: March 2023

AbstractInnate immune receptors that form complexes with secondary receptors, activating multiple signalling pathways, modulate cellular activation and play essential roles in regulating homeostasis and immunity. We have previously identified a variety of bovine C-type lectin-like receptors that possess similar functionality than their human orthologues. Mincle (CLEC4E), a heavily glycosylated monomer, is involved in the recognition of the mycobacterial component Cord factor (trehalose 6,6′-dimycolate). Here we characterise the bovine homologue of Mincle (boMincle), and demonstrate that the receptor is structurally and functionally similar to the human orthologue (huMincle), although there are some notable differences. In the absence of cross-reacting antibodies, boMincle-specific antibodies were created and used to demonstrate that, like the human receptor, boMincle is predominantly expressed by myeloid cells. BoMincle surface expression increases during the maturation of monocytes to macrophages. However, boMincle mRNA transcripts were also detected in granulocytes, B cells, and T cells. Finally, we show that boMincle binds to isolated bovine CD4+T cells in a specific manner, indicating the potential to recognize endogenous ligands. This suggests that the receptor might also play a role in homeostasis in cattle.
Early life stress in male mice blunts responsiveness in a translationally-relevant reward task
Authors: Hisey Erin E. , Fritsch Emma L. , Ressler Kerry J. , Kangas Brian D. , Carlezon William A. 
Published: March 2023

ABSTRACTEarly-life stress (ELS) leaves signatures upon the brain that persist throughout the lifespan and increase the risk of psychiatric illnesses including mood and anxiety disorders. In humans, myriad forms of ELS—including childhood abuse, bullying, poverty, and trauma—are increasingly prevalent. Understanding the signs of ELS, including those associated with psychiatric illness, will enable improved treatment and prevention. Here we developed a novel procedure to model human ELS in mice and identify translationally-relevant biomarkers of mood and anxiety disorders. We exposed male mice (C57BL/6J) to an early-life (juvenile) chronic social defeat stress (jCSDS) and examined social interaction and responsivity to reward during adulthood. As expected, jCSDS-exposed mice showed a socially avoidant phenotype in open-field social interaction tests. However, sucrose preference tests failed to demonstrate ELS-induced reductions in choice for the sweetened solution, suggesting no effect on reward function. To explore whether other tasks might be more sensitive to changes in motivation, we tested the mice in the Probabilistic Reward Task (PRT), a procedure often used in humans to study reward learning deficits associated with depressive illness. In a touchscreen PRT variant that was reverse-translated to maximize alignment with the version used in human subjects, mice exposed to jCSDS displayed significant reductions in the tendency to develop response biases for more richly-rewarded stimuli, a hallmark sign of depression (anhedonia) when seen in humans. Our findings suggest that translationally-relevant procedures that utilize the same endpoints across species may enable the development of improved model systems that more accurately predict outcomes in humans.
A generalizable protocol for expression and purification of membrane-bound bacterial phosphoglycosyl transferases in liponanoparticles
Authors: Dodge Greg J. , Bernstein Hannah M. , Imperiali Barbara 
Published: March 2023

AbstractPhosphoglycosyl transferases (PGTs) are among the first membrane-bound enzymes involved in the biosynthesis of bacterial glycoconjugates. Robust expression and purification protocols for an abundant subfamily of PGTs remains lacking. Recent advancements in detergent-free methods for membrane protein solubilization open the door for purification of difficult membrane proteins directly from cell membranes into native-like liponanoparticles. By leveraging autoinduction,in vivoSUMO tag cleavage, styrene maleic acid co-polymer liponanoparticles (SMALPs), and Strep-Tag purification, we have established a robust workflow for expression and purification of previously unobtainable PGTs. The material generated from this workflow is extremely pure and can be directly visualized by Cryogenic Electron Microscopy (CryoEM). The methods presented here promise to be generalizable to additional membrane proteins recombinantly expressed inE. coliand should be of interest to the greater membrane proteomics community.HighlightsExpression and purification of full-length Lg-PGTs has proven challenging.Autoinduction andin vivoUlp1 cleavage produces active full-length Lg-PGTs.SMA and DIBMA are vastly superior to DDM for Lg-PGT solubilization.Strep-tag purification yields SMALPs suitable for CryoEM characterization.
Single-cell analysis of shared signatures and transcriptional diversity during zebrafish development
Authors: Sur Abhinav , Wang Yiqun , Capar Paulina , Margolin Gennady , Farrell Jeffrey A. 
Published: March 2023

AbstractDuring development, animals generate distinct cell populations with specific identities, functions, and morphologies. We mapped transcriptionally distinct populations across 489,686 cells from 62 stages during wild-type zebrafish embryogenesis and early larval development (3–120 hours post-fertilization). Using these data, we identified the limited catalog of gene expression programs reused across multiple tissues and their cell-type-specific adaptations. We also determined the duration each transcriptional state is present during development and suggest new long-term cycling populations. Focused analyses of non-skeletal muscle and the endoderm identified transcriptional profiles of understudied cell types and subpopulations, including the pneumatic duct, individual intestinal smooth muscle layers, spatially distinct pericyte subpopulations, and homologs of recently discovered humanbest4+ enterocytes. The transcriptional regulators of these populations remain unknown, so we reconstructed gene expression trajectories to suggest candidates. To enable additional discoveries, we make this comprehensive transcriptional atlas of early zebrafish development available through our website, Daniocell.
Uncovering plant microbiomes using long-read metagenomic sequencing
Authors: Masuda Sachiko , Gan Pamela , Kiguchi Yuya , Anda Mizue , Sasaki Kazuhiro , Shibata Arisa , Iwasaki Wataru , Suda Wataru , Shirasu Ken 
Published: March 2023

AbstractThe microbiome of plants plays a pivotal role in their growth and health. Despite its importance, many fundamental questions about the microbiome remain largely unanswered, such as the identification of colonizing bacterial species, the genes they carry, and the location of these genes on chromosomes or plasmids. To gain insights into the genetic makeup of the rice leaf microbiome, we performed a metagenomic analysis using long-read sequences, and developed a genomic DNA extraction method that provides relatively intact DNA for long-read sequencing. 1.8 Gb reads were assembled into 26,067 contigs, including 136 circular sequences of less than 1 Mbp, as well as 172 large (≥ 1 Mbp) sequences, six of which were circularized. Within these contigs, 669 complete 16S rRNA genes were clustered into 166 bacterial species, 130 of which showed low identity to previously defined sequences, suggesting that they represent novel species. The large circular contigs contain novel chromosomes and a megaplasmid, and most of the smaller circular contigs (<1 Mbp) were defined as novel plasmids or bacteriophages. One circular contig represents the complete chromosome of an uncultivated bacterium in the candidate phylumCandidatus Saccharibacteria. Our findings demonstrate the efficacy of long-read-based metagenomics for profiling microbial communities and discovering novel sequences in plant-microbiome studies.