bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ym1 protein crystals promote type 2 immunity
Authors: Heyndrickx Ines , Deswarte Kim , Verstraete Kenneth , Verschueren Koen H. G. , Smole Ursula , Aegerter Helena , Dansercoer Ann , Hammad Hamida , Savvides Savvas N. , Lambrecht Bart N. 
Published: July 2023

AbstractSpontaneous protein crystallization is a rare event, yet protein crystals are frequently found in eosinophil-rich inflammation. In humans, Charcot-Leyden crystals (CLCs) are made from galectin-10 (Gal10) protein, an abundant protein in eosinophils. Whereas mice do not encode Gal10 in their genome, they do form pseudo-CLCs, made from the chitinase-like proteins Ym1 and/or Ym2, encoded byChil3andChil4and made by myeloid and epithelial cells respectively. Here, we investigated the biological effects of pseudo-CLCs since their function is currently unknown. We produced recombinant Ym1 crystals which were shown to have identical crystal packing and structure by X-ray crystallography asin vivonative crystals derived from murine lung. When administered to the airways of mice, crystalline but not soluble Ym1 stimulated innate and adaptive immunity and acted as a type 2 immune adjuvant for eosinophilic inflammation via triggering of dendritic cells (DCs). Murine Ym1 protein crystals found at sites of eosinophilic inflammation reinforce type 2 immunity and could serve as a surrogate model for studying the biology of human CLCs.
Interrogation of RNA-protein interaction dynamics in bacterial growth
Authors: Monti Mie , Herman Reyme , Davey Karen , Dawson Charlotte S. , Ule Jernej , Thomas Gavin H. , Willis Anne E. , Lilley Kathryn S. , Villanueva Eneko 
Published: July 2023

AbstractCharacterising RNA-protein interaction dynamics is fundamental to understand how bacteria respond to their environment. In this study, we have analysed the dynamics of 91% of theEscherichia coliexpressed proteome and the RNA-interaction properties of 271 RNA-binding proteins (RBPs) at different growth phases. We find that 68% of RBPs differentially bind RNA across growth phases and characterise 17 previously unannotated proteins as bacterial RBPs including YfiF, a ncRNA-binding protein. While these new RBPs are mostly present in Proteobacteria, two of them have human orthologs in the form of mitochondrial proteins associated with rare metabolic disorders. Moreover, we reveal novel RBP functions for proteins such as the chaperone HtpG, a new stationary phase tRNA-binding protein. Altogether, we provide the first dynamic RBPome of a bacterium, showcasing how this approach can reveal the function of uncharacterised proteins, and identify critical RNA-protein interactions for cell growth which could inform new antimicrobial therapies.
Multimodal optical mesoscopy reveals the quantity and spatial distribution of gram-positive biofilms inex vivotonsils
Authors: Clapperton Megan , Kunanandam Tash , Florea Catalina D. , Douglas Catriona M. , McConnell Gail 
Published: July 2023

AbstractBiofilms are known to be present in tonsils, but little is known about their spatial location and size distribution throughout the tonsil. Studies of the location and distribution of biofilms in tonsil specimens have thus far been limited to either high-magnification methods such as electron microscopy, which enables high resolution imaging but only from a tiny tissue volume, or lower magnification techniques such as light microscopy, which allow imaging of larger specimens but with poor spatial resolution. To overcome these limitations, we report the use of multimodal optical mesoscopy to visualize and quantify the number and spatial distribution of gram-positive biofilms in fresh, excised paediatric tonsils. This methodology supports simultaneous imaging of both the tonsil host and biofilms in whole mounts of tissue up to 5 mm × 5 mm × 3 mm with subcellular resolution throughout. A quantitative assessment of thirty-six tonsil specimens revealed no statistically significant difference between biofilm presence on the tonsil surface and the interior of the tonsil. This new quantitative mesoscale imaging approach may prove useful in understanding the role of biofilms in tonsillar diseases and other infections.
Direct recruitment of Mis18 to interphase spindle poles promotes CENP-A chromatin assembly
Authors: London Nitobe , Medina-Pritchard Bethan , Spanos Christos , Rappsilber Juri , Arulanandam Jeyaprakash , Allshire Robin C. 
Published: July 2023

SummaryCENP-A chromatin specifies mammalian centromere identity, and its chaperone HJURP replenishes CENP-A when recruited by the Mis18 complex (Mis18C) via M18BP/KNL2 to CENP-C at kinetochores during interphase. However, the Mis18C recruitment mechanism remains unresolved in species lacking M18BP1, such as fission yeast. Fission yeast centromeres cluster at G2 spindle pole bodies (SPBs) when CENP-ACnp1is replenished and where Mis18C also localizes. We show that SPBs play an unexpected role in concentrating Mis18C near centromeres through the recruitment of Mis18 by direct binding to the major SPBLInker ofNucleoskeleton andCytoskeleton (LINC) complex component Sad1. Mis18 recruitment by Sad1 is important for CENP-ACnp1chromatin establishment and acts in parallel with a CENP-C-mediated Mis18C recruitment pathway to maintain centromeric CENP-ACnp1, but is independent of Sad1-mediated centromere clustering. SPBs therefore provide a non-chromosomal scaffold for both Mis18C recruitment and centromere clustering during G2. This centromere-independent Mis18-SPB recruitment provides a mechanism that governsde novoCENP-ACnp1chromatin assembly by the proximity of appropriate sequences to SPBs and highlights how nuclear spatial organization influences centromere identity.
Phylogenomic analysis reveals the evolutionary origins of five independent clades of forage grasses within the African genusUrochloa
Authors: Masters Lizo E. , Tomaszewska Paulina , Schwarzacher Trude , Zuntini Alexandre R. , Heslop-Harrison Pat , Vorontsova Maria S. 
Published: July 2023

AbstractBackground and AimsThe grass genusUrochloa(Brachiaria) includes forage crops that are important for beef and dairy industries in tropical and sub-tropical Africa, South America, and Oceania/Australia. Economically important species includeU. brizantha,U. decumbens,U. humidicola,U. mutica,U. arrecta,U. trichopus,U. mosambicensis, andM. maximus, all native to the African continent. Perennial growth habits, large, fast growing palatable leaves, intra- and interspecific morphological variability, apomictic reproductive systems, and frequent polyploidy are widely shared within the genus. The combination of these traits likely favoured the selection for forage domestication and weediness, but trait emergence acrossUrochloacannot be modelled, as a robust phylogenetic assessment of the genus has not been conducted.MethodsUsing a target enrichment sequencing approach (Angiosperms353 baits), we inferred a species level phylogeny forUrochloa sensu lato, encompassing 57 species (∼50% of the genus) and outgroups. We determined the phylogenetic placement of agriculturally important species and identify their closest wild relatives. Further, we mapped key traits associated with forage crop potential to the species tree, exploring trait distribution across the genus.Key ResultsAgricultural species belong to five independent clades, includingU. brizanthaandU. decumbenslying in a previously defined species complex. Crop wild relatives were identified for these clades supporting previous sub-generic groupings inUrochloabased on morphology. Using ancestral trait estimation models, we find that five morphological traits that correlate with forage potential (perennial growth habits, culm height, leaf size, a winged rachis, and large seeds) independently evolved in forage clades.ConclusionsUrochloa s.l.is a highly diverse genus that contains numerous species with agricultural potential, including crop wild relatives that are currently underexploited. The African continent is the centre of origin for these clades and their conservation across their native distributions is essential. Genomic and phenotypic diversity in forage clade species and their wild relatives needs to be better assessed to improve sustainability inUrochloacultivar production.
Evolutionary origin, population diversity, and diagnostics for a cryptic hybrid pathogen
Authors: Steenwyk Jacob L. , Knowles Sonja , Bastos Rafael W. , Balamurugan Charu , Rinker David , Mead Matthew E. , Roberts Christopher D. , Raja Huzefa A. , Li Yuanning , Colabardini Ana Cristina , de Castro Patrícia Alves , dos Reis Thaila Fernanda , Canóvas David , Sanchez Rafael Luperini , Lagrou Katrien , Torrado Egídio , Rodrigues Fernando , Oberlies Nicholas H. , Zhou Xiaofan , Goldman Gustavo H. , Rokas Antonis 
Published: July 2023

AbstractCryptic fungal pathogens pose significant identification and disease management challenges due to their morphological resemblance to known pathogenic species while harboring genetic and (often) infection-relevant trait differences. The cryptic fungal pathogenAspergillus latus, an allodiploid hybrid originating fromAspergillus spinulosporusand an unknown close relative ofAspergillus quadrilineatuswithin sectionNidulantes, remains poorly understood. The absence of accurate diagnostics forA. latushas led to misidentifications, hindering epidemiological studies and the design of effective treatment plans. We conducted an in-depth investigation of the genomes and phenotypes of 44 globally distributed isolates (41 clinical isolates and three type strains) fromAspergillussectionNidulantes. We found that 21 clinical isolates wereA. latus; notably, standard methods of pathogen identification misidentified allA. latusisolates. The remaining isolates were identified asA. spinulosporus(8),A. quadrilineatus(1), orA. nidulans(11). Phylogenomic analyses shed light on the origin ofA. latus, indicating one or two hybridization events gave rise to the species during the Miocene, approximately 15.4 to 8.8 million years ago. Characterizing theA. latuspangenome uncovered substantial genetic diversity within gene families and biosynthetic gene clusters. Transcriptomic analysis revealed that both parental genomes are actively expressed in nearly equal proportions and respond to environmental stimuli. Further investigation into infection-relevant chemical and physiological traits, including drug resistance profiles, growth under oxidative stress conditions, and secondary metabolite biosynthesis, highlight distinct phenotypic profiles of the hybridA. latuscompared to its parental and closely related species. Leveraging our comprehensive genomic and phenotypic analyses, we propose five genomic and phenotypic markers as diagnostics forA. latusspecies identification. These findings provide valuable insights into the evolutionary origin, genomic outcome, and phenotypic implications of hybridization in a cryptic fungal pathogen, thus enhancing our understanding of the underlying processes contributing to fungal pathogenesis. Furthermore, our study underscores the effectiveness of extensive genomic and phenotypic analyses as a promising approach for developing diagnostics applicable to future investigations of cryptic and emerging pathogens.
Novel phosphatidylinositol flippases contribute to phosphoinositide homeostasis in the plasma membrane
Authors: Muranaka Yumeka , Shigetomi Ryo , Iwasaki Yugo , Hamamoto Asuka , Nakayama Kazuhisa , Takatsu Hiroyuki , Shin Hye-Won 
Published: July 2023

AbstractPhosphatidylinositol is a precursor of various phosphoinositides, which play crucial roles in intracellular signaling and membrane dynamics and have impact on diverse aspects of cell physiology. Phosphoinositide synthesis and turnover occur in the cytoplasmic leaflet of the organellar and plasma membranes. P4-ATPases (lipid flippases) are responsible for translocating membrane lipids from the exoplasmic (luminal) to the cytoplasmic leaflet, thereby regulating membrane asymmetry. However, the mechanism underlying phosphatidylinositol translocation across cellular membranes remains elusive. Here, we discovered that the phosphatidylcholine flippases ATP8B1, ATP8B2, and ATP10A can also translocate phosphatidylinositol at the plasma membrane. To explore the function of these phosphatidylinositol flippases, we used cells depleted of CDC50A, a protein necessary for P4-ATPase function. Upon activation of the Gq-coupled receptor, depletion of phosphatidylinositol 4,5-bisphosphate [PtdIns(4,5)P2] was accelerated inCDC50Aknockout cells compared with control cells, suggesting a decrease in PtdIns4,5P2levels within the plasma membrane of the knockout cells. These findings highlight the pivotal role of P4-ATPases in maintaining phosphoinositide homeostasis and suggest a mechanism for enrichment of phosphatidylinositol in the cytoplasmic leaflet of the plasma membrane.
A YTHDF-PABP axis is required for m6A-mediated organogenesis in plants
Authors: Tankmar Mathias Due , Reichel Marlene , Arribas-Hernández Laura , Brodersen Peter 
Published: July 2023

ABSTRACTN6-methyladenosine (m6A) in mRNA is key to eukaryotic gene regulation. Many m6A functions involve specialized RNA-binding proteins that recognize m6A via a YT521-B Homology (YTH) domain. YTH domain proteins contain long intrinsically disordered regions (IDRs) that may mediate phase separation and interaction with protein partners, but whose precise biochemical functions remain largely unknown. TheArabidopsis thalianaYTH domain proteins ECT2, ECT3 and ECT4 accelerate organogenesis through stimulation of cell division in organ primordia. Here, we focus on ECT2 to reveal molecular underpinnings of this function of ECT2/3/4. We show that stimulation of leaf formation requires the long N-terminal IDR, and we identify two short IDR-elements required for ECT2-mediated organogenesis. Of these two, a tyrosine-rich 19-amino acid region is necessary for binding to a small subset of proteins that includes the major cytoplasmic poly(A)-binding proteins PAB2, PAB4 and PAB8. Remarkably, overexpression of PAB4 in leaf primordia partially rescues the delayed leaf formation inect2 ect3 ect4mutants, suggesting that the ECT2-PAB2/4/8 interaction on target mRNAs of organogenesis-related genes may overcome limiting PAB concentrations in primordial cells.
Bestrophin-4 relays Hes4 and interacts with Twist1 to suppress epithelial-to-mesenchymal transition in colorectal cancer cells
Authors: Wang Zijing , Xia Bihan , Qi Shaochong , Zhang Xian , Zhang Xiaoshuang , Li Yan , Wang Huimin , Zhang Miao , Zhao Ziyi , Kerr David , Yang Li , Cai Shijie , Yang Jinlin 
Published: July 2023

AbstractBestrophin isoform 4 (BEST4) is a newly identified subtype of the calcium-activated chloride channel family. Analysis of colonic epithelial cell diversity by single cell RNA-sequencing has revealed the existence of a cluster ofBEST4+ mature colonocytes in humans. However, if the role ofBEST4is involved in regulating tumour progression remains largely unknown. In this study, we demonstrate thatBEST4overexpression attenuates cell proliferation, colony formation, and mobility in colorectal cancer (CRC)in vitro, and impedes the tumor growth and the liver metastasisin vivo.BEST4is coexpressed with hairy/enhancer of split 4 (Hes4) in the nucleus of cells, andHes4signalsBEST4by interacting with the upstream region of theBEST4promoter.BEST4is epistatic toHes4and downregulates Twist1, thereby inhibiting epithelial-to-mesenchymal transition (EMT) in CRC. Conversely, knockout of BEST4 using CRISPR/Cas9 in CRC cells revitalises tumor growth and induces EMT. Furthermore, the low level of theBEST4mRNA is correlated with advanced and the worse prognosis, suggesting its potential role in regulating CRC progression.
Histone deacetylation and cytosine methylation compartmentalize heterochromatic regions in the genome organization ofNeurospora crassa
Authors: Scadden Ashley W. , Graybill Alayne S. , Hull-Crew Clayton , Lundberg Tiffany J. , Lande Nickolas M. , Klocko Andrew D. 
Published: July 2023

AbstractChromosomes must correctly fold in eukaryotic nuclei for proper genome function. Eukaryotic organisms hierarchically organize their genomes, including in the fungusNeurospora crassa, where chromatin fiber loops compact into Topologically Associated Domain (TAD)-like structures formed by heterochromatic region aggregation. However, insufficient data exists on how histone post-translational modifications, including acetylation, affect genome organization. In Neurospora, the HCHC complex (comprised of the proteins HDA-1, CDP-2, HP1, and CHAP) deacetylates heterochromatic nucleosomes, as loss of individual HCHC members increases centromeric acetylation and alters the methylation of cytosines in DNA. Here, we assess if the HCHC complex affects genome organization by performing Hi-C in strains deleted of thecdp-2orchapgenes. CDP-2 loss increases intra– and inter-chromosomal heterochromatic region interactions, while loss of CHAP decreases heterochromatic region compaction. Individual HCHC mutants exhibit different patterns of histone post-translational modifications genome-wide: without CDP-2, heterochromatic H4K16 acetylation is increased, yet smaller heterochromatic regions lose H3K9 trimethylation and gain inter-heterochromatic region interactions; CHAP loss produces minimal acetylation changes but increases heterochromatic H3K9me3 enrichment. Loss of both CDP-2 and the DIM-2 DNA methyltransferase causes extensive genome disorder, as heterochromatic-euchromatic contacts increase despite additional H3K9me3 enrichment. Our results highlight how the increased cytosine methylation in HCHC mutants ensures genome compartmentalization when heterochromatic regions become hyperacetylated without HDAC activity.Significance StatementThe mechanisms driving chromosome organization in eukaryotic nuclei, including in the filamentous fungusNeurospora crassa, are currently unknown, but histone post-translational modifications may be involved. Histone proteins can be acetylated to form active euchromatin while histone deacetylases (HDACs) remove acetyl marks to form silent heterochromatin; these heterochromatic regions cluster, forming strong interactions, in Neurospora genome organization. Here, we show that mutants of a heterochromatin-specific HDAC, HCHC, increase heterochromatic histone acetylation genome-wide and contact probability between distant heterochromatic loci. HCHC loss also impacts cytosine methylation, and in strains lacking both the HCHC and cytosine methylation, heterochromatic regions interact more with euchromatin. Our results suggest cytosine methylation normally functions to segregate silent and active loci when heterochromatic acetylation increases.
Identifying novel age-modulating compounds and quantifying cellular aging using novel computational framework for evaluating transcriptional age
Authors: Zhang Chao , Saurat Nathalie , Cornacchia Daniela , Chung Sun Young , Sikder Trisha , Minotti Andrew , Studer Lorenz , Betel Doron 
Published: July 2023

AbstractThe differentiation of human pluripotent stem cells (hPSCs) provides access to most cell types and tissues. However, hPSC-derived lineages capture a fetal-stage of development and methods to accelerate progression to an aged identity are limited. Understanding the factors driving cellular age and rejuvenation is also essential for efforts aimed at extending human life and health span. A prerequisite for such studies is the development of methods to score cellular age and simple readouts to assess the relative impact of various age modifying strategies.Here we established a transcriptional score (RNAge) in young versus old primary fibroblasts, frontal cortex and substantia nigra tissue. We validated the score in independent RNA-seq datasets and demonstrated a strong cell and tissue specificity. In fibroblasts we observed a reset of RNAge during iPSC reprogramming while direct reprogramming of aged fibroblasts to induced neurons (iN) resulted in the maintenance of both a neuronal and a fibroblast aging signature. Increased RNAge in hPSC-derived neurons was confirmed for several age-inducing strategies such as SATB1 loss, progerin expression or chemical induction of senescence (SLO). Using RNAge as a probe set, we next performed an in-silico screen using the LINCS L1000 dataset. We identified and validated several novel age-inducing and rejuvenating compounds, and we observed that RNAage captures age-related changes associated with distinct cellular hallmarks of age. Our study presents a simple tool to score age manipulations and identifies compounds that greatly expand the toolset of age-modifying strategies in hPSC derived lineages.
SGLT2 transcriptomic expression atlas supports a kidney-centric role for empagliflozin’s benefits in heart failure
Authors: Mourad Omar , Vohra Shabana , Nunes Sara S 
Published: July 2023

AbstractSodium-glucose cotransporter 2 inhibitors (SGLT2i), such as empagliflozin, have shown remarkable benefits in reducing cardiovascular events and mortality in patients with heart failure (HF) irrespective of diabetic status. Because of the magnitude of the benefits and broad application in both HF with reduced and preserved ejection fraction (EF), there have been concerted efforts to identify a mechanism for the observed benefits. One hypothesis is that SGLT2i act directly on the heart. Given empagliflozin’s high specificity to SGLT2, we reasoned that SGLT2 expression would be a requirement for cells to respond to treatment. Here, we present a comprehensive transcriptomic analysis ofSLC5A2, which encodes SGLT2, at the single cell level in multiple datasets, confirmingSLC5A2expression in a subset of kidney epithelial cells but no meaningful expression in other cell types. This was true irrespective of developmental stage, disease state, sequencing method or depth, and species. Our findings support a kidney-centric role for the cardiovascular improvements reported in patients treated with SGLT2i.
Subcellular pathways through VG3 amacrine cells provide regionally tuned object-motion-selective signals in mouse retina
Authors: Friedrichsen Karl , Hsiang Jen-Chun , McCoy Liam , Valkova Katia , Kerschensteiner Daniel , Morgan Josh L. 
Published: July 2023

ABSTRACTWe combined subcellular calcium imaging and connectomic reconstruction to understand the flow of information through a plexus of excitatory VGluT3-expressing mouse retinal amacrine cells (VG3s). We found that VG3s received inputs from all nearby bipolar cell types but exhibited a strong preference for the fast type 3a bipolar cells. We used our connectivity map and physiological recordings to predict the influence of these bipolar cells on different types of RGCs innervated by VG3s and found that the depth of retinal ganglion cell (RGC) dendritic arbor stratification determined the RGC’s view of bipolar cells through the VG3 plexus. We also found that both VG3s and their RGC targets were often innervated by the same bipolar cells. RGCs that extend processes into the middle layers of the inner plexiform layer, therefore, encounter a plexus of small object motion selective glutamatergic excitation that is complementary to the local bipolar cell input.