bluuebunny/crossref_metadata_2025_split huggingface dataset:
Native extracellular matrix probes to target patient- and tissue- specific cell-microenvironment interactions by force spectroscopy
Authors: Holuigue H. , Nacci L. , Di Chiaro P. , Chighizola M. , Locatelli I. , Schulte C. , Alfano M. , Diaferia G.R. , Podestà A. 
Published: December 2022

AbstractAtomic Force Microscopy (AFM) is successfully used for the quantitative investigation of the cellular mechanosensing of the microenvironment. To this purpose, several force spectroscopy approaches aim at measuring the adhesive forces between two living cells and also between a cell and a suitable reproduction of the extracellular matrix (ECM), typically exploiting tips suitably functionalised with single components (e.g. collagen, fibronectin) of the ECM. However, these probes only poorly reproduce the complexity of the native cellular microenvironment and consequently of the biological interactions.We developed a novel approach to produce AFM probes that faithfully retain the structural and biochemical complexity of the ECM; this was achieved by attaching to an AFM cantilever a micrometric slice of native decellularised ECM, which was cut by laser microdissection. We demonstrate that these probes preserve the morphological, mechanical, and chemical heterogeneity of the ECM.Native ECM probes can be used in force spectroscopy experiments aimed at targeting cell-microenvironment interactions. Here, we demonstrate the feasibility of dissecting mechanotransductive cell-ECM interactions in the 10 pN range. As proof-of-principle, we tested a rat bladder ECM probe against the AY-27 rat bladder cancer cell line. On the one hand, we obtained reproducible results using different probes derived from the same ECM regions; on the other hand, we detected differences in the adhesion patterns of distinct bladder ECM regions, such as submucosa and detrusor, in line with the disparities in composition and biophysical properties of these ECM regions.Our results demonstrate that native ECM probes, produced from patient-specific regions of organs and tissues, can be used to investigate cell-microenvironment interactions and early mechanotransductive processes by force spectroscopy. This opens new possibilities in the field of personalised medicine.
Growth/differentiation factor 15 controls number of ependymal and neural stem cells in the ventricular-subventricular zone
Authors: Baur Katja , Carrillo-García Carmen , Şan Şeydanur , von Hahn Manja , Strelau Jens , Hölzl-Wenig Gabriele , Mandl Claudia , Ciccolini Francesca 
Published: December 2022

AbstractLate in neural development, the expression of growth/differentiation factor (GDF) 15 increases in the germinal epithelium of the murine ganglionic eminence (GE), especially in progenitors with characteristics of neural stem cells (NSCs). However, the function of GDF15 in this region is still unknown. We here show that apical progenitors in the E18 GE also express the GDF15 receptor and that ablation of GDF15 promotes proliferation and cell cycle progression of apically and subapically dividing progenitors. A similar phenotype was also observed in the adult ventricular subventricular zone (V-SVZ). At both ages, increased proliferation leads to the transient generation of more neuronal progenitors, which is compensated by cell death, and to a permanent increase in the number of ependymal cells and apical NSCs. We also found that GDF15 receptor-expressing cells display immunoreactivity for the epidermal growth factor receptor (EGFR), which is also involved in progenitor proliferation, and that manipulation of GDF15 affects the expression of EGFR in mutant progenitors. Moreover, our data indicate that EGFR signalling in WT and mutant progenitors relies on distinct transduction modes. However, only exposure to exogenous GDF15, but not to EGF, normalized proliferation and the number of apical progenitors, indicating that alteration in EGFR signalling is not the main mechanism by which GDF15 affects proliferation in the embryonic GE.Taken together, GDF15 directly regulates proliferation of apical progenitors in the developing GE, thereby affecting the number of total ependymal cells and NSCs in this region.
An Autoimmune Transcriptional Circuit Driving Foxp3+Regulatory T cell Dysfunction
Authors: Sumida Tomokazu S. , Lincoln Matthew R. , He Liang , Park Yongjin , Ota Mineto , Stillwell Helen A. , Leissa Greta A. , Fujio Keishi , Kulminski Alexander M. , Epstein Charles B. , Bernstein Bradley E. , Kellis Manolis , Hafler David A. 
Published: December 2022

AbstractAutoimmune diseases, among the most common disorders of young adults, are mediated by genetic and environmental factors. While CD4+Foxp3+regulatory T cells (Tregs) play a central role in preventing autoimmunity, the molecular mechanism underlying their dysfunction is unknown. Here, we performed comprehensive transcriptomic and epigenomic profiling of Tregs in the autoimmune disease multiple sclerosis (MS) to identify central transcriptional programs regulating human autoimmunity. We discovered that upregulation of a primate-specific shortPRDM1isoform (PRDM1-S) inducesSGK1independent from evolutionally conserved longPRDM1, leading to destabilization of Foxp3 and Treg dysfunction. This aberrantPRDM1-S/SGK1axis is shared among other autoimmune diseases. Furthermore, by chromatin landscape profiling in MS Tregs we identified aPRDM1-Sspecificcis-regulatory element associated with enriched binding of AP-1/IRF transcription factors. Our study identifies evolutionally emergedPRDM1-Sand epigenetic priming of AP-1/IRF as key drivers of pathogenic Treg programs leading to human autoimmune disease.
Structural insights into HIV-1 polyanion-dependent capsid lattice formation revealed by single particle cryo-EM
Authors: Highland Carolyn M. , Tan Aaron , Ricaña Clifton L. , Briggs John A.G. , Dick Robert A. 
Published: December 2022

AbstractThe HIV-1 capsid houses the viral genome and interacts extensively with host cell proteins throughout the viral life cycle. It is composed of capsid protein (CA), which assembles into a conical fullerene lattice composed of roughly 200 CA hexamers and 12 CA pentamers. Previous structural analyses of individual CA hexamers and pentamers have provided valuable insight into capsid structure and function, but high-resolution information about these assemblies in the broader context of the capsid lattice is lacking. In this study, we combined cryo-electron tomography and single particle analysis cryo-electron microscopy to determine high-resolution structures of continuous regions of the capsid lattice containing both hexamers and pentamers. We also developed a new method ofin vitrolattice assembly that enabled us to directly study the lattice under a wider range of conditions than has previously been possible. Using this approach, we identified a critical role for inositol hexakisphosphate (IP6) in pentamer formation and determined the structure of the CA lattice bound to the capsid-targeting antiretroviral drug GS-6207 (Lenacapvir). Our work reveals new structural details of the mature HIV-1 CA lattice and establishes the combination of lattice templating and single particle analysis as a robust strategy for studying retroviral capsid structure and capsid interactions with host proteins and antiviral compounds.Significance statementThe mature HIV-1 capsid is composed of the capsid (CA) protein arranged in a conical lattice of hexamers and pentamers. Numerous structures of individual CA hexamers and pentamers alone have been published, but the molecular details of these assemblies in a more global, lattice-wide context are lacking. Here, we present high-resolution cryo-electron microscopy structures of continuous regions of the capsid lattice containing both hexamers and pentamers. We also describe key differences in the assembly and structures of these oligomers that have important implications for understanding retroviral maturation and for ongoing efforts to pharmacologically target the HIV-1 capsid.
Rhythmic temporal coordination of neural activity prevents representational conflict during working memory
Authors: Abdalaziz Miral , Redding Zach V. , Fiebelkorn Ian C. 
Published: December 2022

SUMMARYSelective attention1is characterized by alternating states associated with either attentional sampling or attentional shifting, helping to avoid functional conflicts by isolating function-specific neural activity in time2–5. We hypothesized that such rhythmic temporal coordination might also help to avoid representational conflicts during working memory6. Multiple items can be simultaneously held in working memory, and these items can be represented by overlapping neural populations7–9. Traditional theories propose that short-term storage of to-be-remembered items occurs through persistent neural activity10–12, but when neurons are simultaneously representing multiple items, persistent activity creates a potential for representational conflicts. In comparison, more recent, ‘activity-silent’ theories of working memory propose that synaptic changes also contribute to the short-term storage of to-be-remembered items13–16. Transient bursts in neural activity17, rather than persistent activity, could serve to occasionally refresh these synaptic changes. Here, we used EEG and response times (RTs) to test whether rhythmic temporal coordination helps to isolate neural activity associated with different to-be-remembered items, which would help to avoid representational conflicts. Consistent with this hypothesis, we report that the relative strength of different item representations alternates over time as a function of frequency-specific phase. Although RTs were linked to theta (~6Hz) and beta (~25 Hz) phase during a memory delay, the relative strength of item representations only alternated as a function of beta phase. The present findings (i) are consistent with rhythmic temporal coordination being a general mechanism for avoiding either functional or representational conflicts during cognitive processes, and (ii) inform models describing the role of oscillatory dynamics in organizing working memory13,18–21.
Two structural switches in HIV-1 capsid regulate capsid curvature and host factor binding
Authors: Stacey James C.V. , Tan Aaron , Lu John M. , James Leo C. , Dick Robert A. , Briggs John A.G. 
Published: December 2022

AbstractThe mature HIV-1 capsid protects the viral genome and interacts with host proteins to travel from the cell periphery into the nucleus. To achieve this, the capsid protein, CA, constructs conical capsids from a lattice of hexamers and pentamers, and engages in and then relinquishes multiple interactions with cellular proteins in an orchestrated fashion. Cellular host factors including Nup153, CPSF6 and Sec24C engage the same pocket within CA hexamers. How CA assembles pentamers and hexamers of different curvatures, how CA oligomerization states or curvature might modulate host-protein interactions, and how binding of multiple co-factors to a single site is coordinated, all remain to be elucidated. Here, we have resolved the structure of the mature HIV-1 CA pentamer and hexamer from conical CA-IP6polyhedra to high resolution. We have determined structures of hexamers in the context of multiple lattice curvatures and number of pentamer contacts. Comparison of these structures, bound or not to host protein peptides, revealed two structural switches within HIV-1 CA that modulate peptide binding according to CA lattice curvature and whether CA is hexameric or pentameric. These observations suggest that the conical HIV-1 capsid has different host-protein binding properties at different positions on its surface, which may facilitate cell entry and represent an evolutionary advantage of conical morphology.Significance statementHIV-1 particles contain a characteristic, conical capsid that shields the genome from the cellular immune system and recruits cellular proteins to direct the capsid to the nucleus. The cone forms from hexamers of CA protein, and twelve pentamers that accommodate curvature. We obtained detailed 3D models of pentamers and hexamers at positions on capsid surfaces with different curvatures. We find two places in CA that switch conformation according to the local capsid curvature and whether CA is in a pentamer or hexamer. We also obtained models of CA bound to peptides from cellular proteins. The data show how switches in CA help it form a cone shape, and interact differently with cellular proteins at different positions on the cone surface.
Purifying and balancing selection on embryonic semi-lethal haplotypes in a wild mammal
Authors: Stoffel M.A. , Johnston S.E. , Pilkington J.G. , Pemberton J.M 
Published: December 2022

AbstractEmbryonic lethal mutations are arguably the earliest and most severe manifestation of inbreeding depression, but their impact on wild populations is not well understood. Here, we combined genomic, fitness and life-history data from 5,925 wild Soay sheep sampled over nearly three decades to explore the impact of embryonic lethal mutations and their evolutionary dynamics. We searched for haplotypes which in their homozygous state are unusually rare in the offspring of known carrier parents and found three putatively semi-lethal haplotypes with 27-46% fewer homozygous offspring than expected. Two of these haplotypes are decreasing in frequency, and gene-dropping simulations through the pedigree suggest that this is partially due to purifying selection. In contrast, the frequency of the third semi-lethal haplotype remains relatively stable over time. We show that the haplotype could be maintained by balancing selection because it is also associated with increased postnatal survival and body weight and because its cumulative frequency change is lower than in most drift-only simulations. Our study highlights embryonic mutations as a largely neglected contributor to inbreeding depression and provides a rare example of how harmful genetic variation can be maintained through balancing selection in a wild mammal population.
SLC26A3 (DRA) is stimulated in a synergistic, intracellular Ca2+dependent manner by cAMP AND ATP in intestinal epithelial cells
Authors: Sarker Rafiquel , Lin Ruxian , Singh Varsha , Donowitz Mark , Tse Chung Ming 
Published: December 2022

ABSTRACTIn polarized intestinal epithelial cells, DRA is a brush border (BB) Cl-/HCO3-exchanger that is part of neutral NaCl absorption under baseline conditions but in cAMP driven diarrheas it is stimulated and contributes to increased anion secretion. To further understand regulation of DRA in conditions mimicking some diarrheal diseases, differentiated Caco-2/BBE cells were exposed to forskolin and ATP. Forskolin and ATP both acutely stimulated DRA in a concentration dependent manner. Forskolin at 1µM and ATP at 0.25 µM had minimal to no effect on DRA activity given individually; however, together, they stimulated DRA activity to levels seen with maximum concentrations of forskolin and ATP alone. In Caco-2/BBE cells expressing the Ca2+indicator GCaMP6s, ATP alone increased Ca2+in a concentration dependent manner, while forskolin (1 µM), that by itself did not significantly alter Ca2+, followed by 0.25 µM ATP produced a large increase in Ca2+that was ∼equal to the elevation caused by 1 µM ATP. BAPTA-AM pretreatment prevented the ATP and forskolin/ATP synergistic increased DRA activity and the increase in intracellular Ca2+caused by ATP/forskolin. Conclusion: In Caco-2/BBE cells subthreshold concentrations of forskolin (cAMP) and ATP (Ca2+) synergistically increased intracellular Ca2+and stimulated DRA activity with both being blocked by BAPTA-AM pretreatment. Diarrheal diseases such as bile acid diarrhea, in which both cAMP and Ca2+are elevated, are likely to be associated with stimulated DRA activity contributing to increased anion secretion, while separation of DRA from NHE3 contributes to reduced NaCl absorption.
Dynamic DNA methylation turnover in gene bodies is associated with enhanced gene expression plasticity in plants
Authors: Williams Clara J. , Dai Dawei , Tran Kevin A. , Monroe J. Grey , Williams Ben P 
Published: December 2022

ABSTRACTBackgroundIn several eukaryotes, DNA methylation occurs within the coding regions of many genes, termed gene body methylation (GbM). Whereas the role of DNA methylation on the silencing of transposons and repetitive DNA is well understood, gene body methylation is not associated with transcriptional repression, and its biological importance has remained unclear.ResultsWe report a newly discovered type of GbM in plants, which is under constitutive addition and removal by dynamic methylation modifiers in all cells, including the germline. Methylation at Dynamic GbM genes is removed by the DRDD demethylation pathway and added by an unknown source of de novo methylation, most likely the maintenance methyltransferase MET1. We show that the Dynamic GbM state is present at homologous genes across divergent lineages spanning over 100 million years, indicating evolutionary conservation. We demonstrate that Dynamic GbM is tightly associated with the presence of a promoter or regulatory chromatin state within the gene body, in contrast to other gene body methylated genes. We find Dynamic GbM is associated with enhanced gene expression plasticity across development and diverse physiological conditions, whereas stably methylated GbM genes exhibit reduced plasticity. Dynamic GbM genes exhibit reduced dynamic range indrddmutants, indicating a causal link between DNA demethylation and enhanced gene expression plasticity.ConclusionsThis study proposes a new model for GbM in regulating gene expression plasticity, including a newly discovered type of GbM in which increased gene expression plasticity is associated with the activity of DNA methylation writers and erasers and the enrichment of a regulatory chromatin state.
Evolutionary shortcuts via multi-nucleotide substitutions and their impact on natural selection analyses
Authors: Lucaci Alexander G , Zehr Jordan D , Enard David , Thornton Joseph W. , Kosakovsky Pond Sergei L. 
Published: December 2022

AbstractInference and interpretation of evolutionary processes, in particular of the types and targets of natural selection affecting coding sequences, are critically influenced by the assumptions built into statistical models and tests. If certain aspects of the substitution process (even when they are not of direct interest) are presumed absent or are modeled with too crude of a simplification, estimates of key model parameters can become biased, often systematically, and lead to poor statistical performance. Previous work established that failing to accommodate multi-nucleotide (or multi-hit, MH) substitutions strongly biases dN/dS-based inference towards false positive inferences of diversifying episodic selection, as does failing to model variation in the rate of synonymous substitution (SRV) among sites. Here we develop an integrated analytical framework and software tools to simultaneously incorporate these sources of evolutionary complexity into selection analyses. We found that both MH and SRV are ubiquitous in empirical alignments, and incorporating them has a strong effect on whether or not positive selection is detected, (1.4-fold reduction) and on the distributions of inferred evolutionary rates. With simulation studies, we show that this effect is not attributable to reduced statistical power caused by using a more complex model. After a detailed examination of 21 benchmark alignments and a new high-resolution analysis showing which parts of the alignment provide support for positive selection, we show that MH substitutions occurring along shorter branches in the tree explain a significant fraction of discrepant results in selection detection. Our results add to the growing body of literature which examines decadesold modeling assumptions (including MH) and finds them to be problematic for comparative genomic data analysis. Because multi-nucleotide substitutions have a significant impact on natural selection detection even at the level of an entire gene, we recommend that selection analyses of this type consider their inclusion as a matter of routine. To facilitate this procedure, we developed, implemented, and benchmarked a simple and well-performing model testing selection detection framework able to screen an alignment for positive selection with two biologically important confounding processes: site-to-site synonymous rate variation, and multi-nucleotide instantaneous substitutions.
Transposons contribute to the functional diversification of the head, gut, and ovary transcriptomes acrossDrosophilanatural strains
Authors: Coronado-Zamora Marta , González Josefa 
Published: December 2022

ABSTRACTTranscriptomes are dynamic, with cells, tissues, and body parts expressing particular sets of transcripts. Transposons are a known source of transcriptome diversity, however studies often focus on a particular type of chimeric transcript, analyze single body parts or cell types, or are based on incomplete transposon annotations from a single reference genome. In this work, we have implemented a method based onde novotranscriptome assembly that minimizes the potential sources of errors while identifying a comprehensive set of gene-TE chimeras. We applied this method to head, gut and ovary dissected from fiveDrosophila melanogasternatural strains, with individual reference genomes available. We found that ∼19% of body part- specific transcripts are gene-TE chimeras. Overall, chimeric transcripts contribute a mean of 43% to the total gene expression, and they provide DNA binding, catalytic activity, and DNA polymerase activity protein domains. Our comprehensive dataset is a rich resource for follow- up analysis. Moreover, because transposable elements are present in virtually all species sequenced to date, their relevant role in spatially restricted transcript expression is likely not exclusive to the species analyzed in this work.
Genetic fine-mapping from summary data using a non-local prior improves detection of multiple causal variants
Authors: Karhunen Ville , Launonen Ilkka , Järvelin Marjo-Riitta , Sebert Sylvain , Sillanpää Mikko J. 
Published: December 2022

AbstractGenome-wide association studies (GWAS) have been successful in identifying genomic loci associated with complex traits. Genetic fine-mapping aims to detect independent causal variants from the GWAS-identified loci, adjusting for linkage disequilibrium (LD) patterns. The use of GWAS summary statistics and an adequate LD reference enable large sample sizes for fine-mapping, without direct access to individual-level data. We presentFiniMOM(fine-mapping using a product inverse-moment priors), a novel Bayesian fine-mapping method for summarized genetic associations. For causal effects, the method uses a non-local inverse-moment prior, which is a natural prior distribution to model non-null effects in finite samples. A beta-binomial prior is set for the number of causal variants, with a parameterization that can be used to control for potential misspecifications in the LD reference. We test the performance of our method against a current state-of-the-art fine-mapping method SuSiE (sum-of-single-effects) across a range of simulated scenarios aimed to mimic a typical GWAS on circulating protein levels, and an applied example. The results show improved credible set coverage and power of the proposed method, especially in the case of multiple causal variants within a locus. The superior performance and the flexible parameterization to control for misspecified LD reference makeFiniMOMa competitive alternative to other fine-mapping methods for summarized genetic data.