bluuebunny/crossref_metadata_2025_split huggingface dataset:
Physiological and metabolic insights into the first cultured anaerobic representative of deep-seaPlanctomycetesbacteria
Authors: Zheng Rikuan , Wang Chong , Liu Rui , Cai Ruining , Sun Chaomin 
Published: July 2023

AbstractPlanctomycetesbacteria are ubiquitously distributed across various biospheres and play key roles in global element cycles. However, few deep-seaPlanctomycetesmembers have been cultivated, limiting our understanding ofPlanctomycetesin the deep biosphere. Here, we have successfully cultured a novel strain ofPlanctomycetes(strain ZRK32) from a cold seep sediment, by using an enriched medium supplemented with rifampicin and different nitrogen sources. Our genomic, physiological and phylogenetic analyses indicate that strain ZRK32 is a novel species, which we propose be named:Poriferisphaera heterotrophicis. We show that strain ZRK32 replicates using a budding mode of division. Based on the combined results from growth assays and transcriptomic analyses, we found that rich nutrients, or supplementation with NO3-or NH4+promoted the growth of strain ZRK32 by facilitating energy production through the tricarboxylic acid (TCA) cycle and the Embden–Meyerhof–Parnas (EMP) glycolysis pathway. Moreover, supplementation with NO3-or NH4+induced strain ZRK32 to release a bacteriophage in a chronic manner, without host cell lysis. This bacteriophage then enabled strain ZRK32, and another marine bacterium that we studied, to metabolize nitrogen through the function of auxiliary metabolic genes (AMGs). Overall, these findings expand our understanding of deep-seaPlanctomycetesbacteria, while highlighting their ability to metabolize nitrogen when reprogrammed by chronic viruses.
Spinal neural tube formation and tail development in human embryos
Authors: Santos Chloe , Marshall Abigail R. , Murray Ailish , Metcalfe Kate , Narayan Priyanka , de Castro Sandra C. P. , Maniou Eirini , Greene Nicholas D. E. , Galea Gabriel L. , Copp Andrew J. 
Published: July 2023

ABSTRACTFormation of the nervous system in the spinal region of higher vertebrates involves primary and secondary neurulation, in which the neural tube forms by closure and canalisation respectively. These processes are incompletely understood in humans, in part due to the challenge of accessing neurulation-stage embryos (3-7 weeks post-conception). Here we present findings on completion of primary neurulation and formation of the ‘secondary body’ (including secondary neurulation) in 108 human embryos that span Carnegie Stages (CS) 10 to 18. Several outstanding questions on low spinal development in humans are addressed: we show that primary neurulation is completed at the human posterior neuropore with a pattern of neural plate bending similar to that in the mouse. There is no evidence of a ‘transition zone’ to secondary neurulation, which proceeds from CS13 with formation of a single lumen as in mouse, not coalescence of multiple lumens as has been claimed based on chick neurulation. Secondary neural tube ‘splitting’ is seen in the more proximal tail regions of 60% of human embryos. A somite is formed every 7 h in human, compared with 2 h in mice and a 5 h ‘segmentation clock’ in human organoids. Termination of axial elongation occurs after downregulation ofWNT3AandFGF8in the CS15 embryonic tailbud, with a ‘burst’ of apoptosis that may remove the neuro-mesodermal progenitors. We conclude that low spinal neurulation and secondary body formation follow a similar pattern in humans as in mammalian model systems such as mouse and rat. Investigators are now attempting to recapitulate events of neurulation in organoids derived from human stem cells, and our findings provide ‘normative data’ for interpretation of such in vitro results.
Heme oxygenase-1 expressing omental macrophages as a therapeutic target in ovarian high grade serous carcinoma
Authors: Spear Sarah , Le Saux Olivia , Mirza Hasan B. , Tyson Katie , Bickel Jasmine , Freile Fabio Grundland , Siskos Alexandros P. , Balcells Cristina , Walton Josephine B. , Woodman Chloé , Ennis Darren P. , Iyer Nayana , Hernandez Carmen Aguirre , Xu Yuewei , Spiliopoulou Pavlina , Brenton James D. , Costa-Pereira Ana P. , Keun Hector C. , Triantafyllou Evangelos , Arnold James N. , McNeish Iain A. 
Published: July 2023

AbstractOvarian high grade serous carcinoma (HGSC) remains a disease of poor prognosis that is unresponsive to current immune checkpoint inhibitors. Although PI3K pathway alterations are common in HGSC, attempts to target this pathway have been unsuccessful. We hypothesised aberrant PI3K pathway activation may alter the HGSC immune microenvironment and present a novel targeting strategy. We used both murine models and HGSC patient samples to study the impact of loss ofPten, a negative regulator of PI3K pathway signalling. We identified populations of resident macrophages specifically inPtennull omental tumours. These macrophages derive from peritoneal fluid macrophages and have a unique gene expression programme, marked by high levels ofHMOX1expression, the gene for the enzyme heme oxygenase-1. Targeting resident peritoneal macrophages prevents appearance of HMOX1himacrophages and in doing so reduces tumour growth. Furthermore, direct inhibition of HMOX1 extends survivalin vivo. HMOX1himacrophages with corresponding gene expression programmes are also identified in human HGSC tumours and their presence correlates with activated tumoural PI3K pathway/mTOR signalling and poor overall survival in HGSC patients. In contrast, tumours with low number of HMOX1himacrophages are marked by increased adaptive immune response gene expression. Our data suggest that HMOX1himacrophages represent a potential therapeutic target and biomarker for poor prognosis HGSC.
Identification of full-sibling families from natural single-tree ash progenies based on SSR markers and genome-wide SNPs
Authors: Krautwurst Melina , Past Franziska , Kersten Birgit , Bubner Ben , Müller Niels A. 
Published: July 2023

AbstractCommon ash,Fraxinus excelsior, is threatened by the invasive pathogenHymenoscyphus fraxineus, which causes ash dieback. The pathogen is rapidly spreading throughout Europe with severe ecological and economic consequences. Multiple studies have presented evidence for the existence of a small fraction of genotypes with low susceptibility. Such genotypes can be targets for natural and artificial selection to conserveF. excelsiorand associated ecosystems. To resolve the genetic architecture of variation in susceptibility it is necessary to analyze segregating populations. Here we employed about 1,000 individuals of each of four single-tree progenies from potentially tolerant mother trees to identify full-sibling (full-sib) families. To this end, we first genotyped all 4,000 individuals and the four mothers with eight SSR markers. We then used the program Colony to predict full-sibs without knowledge of the paternal genotypes. For each single-tree progeny, Colony predicted dozens of full-sib families, ranging from 3-165 individuals. In a next step, 910 individuals assigned to full-sib families with more than 30 individuals were subjected to high-resolution genotyping using over one million genome-wide SNPs which were identified with Illumina low-coverage resequencing. Using these SNP genotyping data in principal component analyses we were able to assign individuals to full-sib families with high confidence. Together the analyses revealed five large families with 80-212 individuals. These can be used to generate genetic linkage maps and to perform quantitative trait locus analyses for ash dieback susceptibility or other traits toH. fraxineusor other traits. The elucidation of the genetic basis of natural variation in ash may support breeding and conservation efforts and may contribute to more robust forest ecosystems.
Drosophilaaxis extension is robust to an orthogonal pull by invaginating mesoderm
Authors: Lye Claire M , Blanchard Guy B. , Evans Jenny , Nestor-Bergmann Alexander , Sanson Bénédicte 
Published: July 2023

AbstractAs tissues grow and change shape during animal development, they physically pull and push on each other and these mechanical interactions can be important for morphogenesis. DuringDrosophilagastrulation, mesoderm invagination temporally overlaps with the extension of the ectodermal germband; the latter is caused primarily by Myosin II-driven polarised cell intercalation. Here we investigate the impact of mesoderm invagination on ectoderm extension, examining possible mechanical and mechanotransductive effects on Myosin II recruitment and polarised cell intercalation. We find that the germband ectoderm is deformed by the mesoderm pulling in the orthogonal direction, showing mechanical coupling between these tissues. However, we do not find a significant change in Myosin II planar polarisation in response to mesoderm invagination, nor an effect on the rate of junction shrinkage leading to cell intercalation events. We find some impact on the orientation of neighbour exchange events, and an increased rate of growth of new cell junctions, but this makes little difference to the rate of cell intercalation. We conclude that the cellular mechanisms of axis extension are robust to the mechanical pull of mesoderm invagination.
Transcription regulates the spatio-temporal dynamics of genes through micro-compartmentalization
Authors: Salari Hossein , Fourel Geneviève , Jost Daniel 
Published: July 2023

AbstractAlthough our understanding of the involvement of heterochromatin architectural factors in shaping nuclear organization is improving, there is still ongoing debate regarding the role of active genes in this process. In this study, we utilize publicly-available Micro-C data from mouse embryonic stem cells to investigate the relationship between gene transcription and 3D gene folding. Our analysis uncovers a nonmonotonic - globally positive - correlation between intragenic contact density and Pol II occupancy, independent of cohesin-based loop extrusion. Through the development of a biophysical model integrating the role of transcription dynamics within a polymer model of chromosome organization, we demonstrate that Pol II-mediated attractive interactions with limited valency between transcribed regions yield quantitative predictions consistent with chromosome-conformation-capture and live-imaging experiments. Our work provides compelling evidence that transcriptional activity shapes the 4D genome through Pol II-mediated micro-compartmentalization.
R-loop landscapes in the developing human brain are linked to neural differentiation and cell-type specific transcription
Authors: LaMarca Elizabeth A. , Saito Atsushi , Plaza-Jennings Amara , Espeso-Gil Sergio , Hellmich Allyse , Fernando Michael B. , Javidfar Behnam , Liao Will , Estill Molly , Townsley Kayla , Florio Anna , Ethridge James E. , Do Catherine , Tycko Benjamin , Shen Li , Kamiya Atsushi , Tsankova Nadejda M. , Brennand Kristen J. , Akbarian Schahram 
Published: July 2023

ABSTRACTHere, we construct genome-scale maps for R-loops, three-stranded nucleic acid structures comprised of a DNA/RNA hybrid and a displaced single strand of DNA, in the proliferative and differentiated zones of the human prenatal brain. We show that R-loops are abundant in the progenitor-rich germinal matrix, with preferential formation at promoters slated for upregulated expression at later stages of differentiation, including numerous neurodevelopmental risk genes. RNase H1-mediated contraction of the genomic R-loop space in neural progenitors shifted differentiation toward the neuronal lineage and was associated with transcriptomic alterations and defective functional and structural neuronal connectivityin vivoandin vitro. Therefore, R- loops are important for fine-tuning differentiation-sensitive gene expression programs of neural progenitor cells.
Gene regulatory network analysis predicts cooperating transcription factor regulons required for FLT3-ITD+ AML growth
Authors: Coleman Daniel J.L. , Keane Peter , Luque-Martin Rosario , Chin Paulynn S , Blair Helen , Ames Luke , Kellaway Sophie G. , Griffin James , Holmes Elizabeth , Potluri Sandeep , Assi Salam A. , Bushweller John , Heidenreich Olaf , Cockerill Peter N. , Bonifer Constanze 
Published: July 2023

AbstractAML is a heterogenous disease caused by different mutations. We have previously shown that each mutational sub-type develops its specific gene regulatory network (GRN) with transcription factors interacting with multiple gene modules, many of which are transcription factor genes themselves. Here we hypothesized that highly connected nodes within such networks comprise crucial regulators of AML maintenance. We tested this hypothesis using FLT3-ITD mutated AML as a model and conducted an shRNA drop-out screen informed by this analysis. We show that AML-specific GRNs predict identifying crucial regulatory modules required for AML but not normal cellular growth. Furthermore, our work shows that all modules are highly connected and regulate each other. The careful multi-omic analysis of the role of one (RUNX1) module by shRNA and chemical inhibition shows that this transcription factor and its target genes stabilize the GRN of FLT3-ITD AML and that its removal leads to GRN collapse and cell death.
Into the deep: The subthalamic and para-subthalamic nuclei in behavioral avoidance
Authors: Serra Gian Pietro , Guillaumin Adriane , Vlcek Bianca , Delgado-Zabalza Lorena , Ricci Alessia , Rubino Eleonora , Dumas Sylvie , Baufreton Jérôme , Georges François , Wallén-Mackenzie Åsa 
Published: July 2023

AbstractThe subthalamic nucleus (STN) is a key component of the brain network for movement control. However, the STN is strikingly heterogeneous and also intricately engaged in limbic and cognitive functions. The STN shows aberrant firing activity in several neurological and neuropsychiatric disorders, including Parkinsońs disease (PD). Deep brain stimulation (DBS) in the STN alleviates motor impairment in PD, but patients have reported altered mood as adverse side-effect. Recent observations suggest that optogenetic STN activation in mice induces flight behavior. We hypothesized that STN activation stand at risk of causing an aversive response with behavioral avoidance as consequence. The STN is directly adjoined with the para-STN (pSTN), a hypothalamic area correlated with appetitive and aversive behavior. STN-DBS aiming to correct STN might thereby also modulate pSTN. To dissociate the impact of STN and pSTN, we took advantage of selective promoters in mice, identified in our recent RNA- sequencing of the subthalamic area, to selectively direct optogenetic excitation. Acute photostimulation resulted in aversion via both the STN and pSTN, but only STN- stimulation-paired cues resulted in conditioned avoidance. Viral-genetic tracing coupled with electrophysiological recordings identified a polysynaptic pathway from the STN to the lateral habenula, a critical hub for aversion and associated with clinical depression. This study demonstrates that STN activation is directly correlated with aversion, and thereby contributes neurobiological underpinnings to emotional affect upon STN manipulation with implications for STN-targeted treatment outcome.
Tailoring TfhProfiles Enhances Antibody Persistence to a Clade C HIV-1 Vaccine in Rhesus Macaques
Authors: Verma Anil , Hawes Chase E , Elizaldi Sonny R , Smith Justin C. , Rajasundaram Dhivyaa , Pedersen Gabriel Kristian , Shen Xiaoying , Williams LaTonya D , Tomaras Georgia D. , Kozlowski Pamela A. , Amara Rama R. , Iyer Smita S. 
Published: July 2023

ABSTRACTCD4 T follicular helper cells (Tfh) are essential for establishing serological memory and have distinct helper attributes that impact both the quantity and quality of the antibody response. Insights into Tfhsubsets that promote antibody persistence and functional capacity can critically inform vaccine design. Based on the Tfhprofiles evoked by the live attenuated measles virus vaccine, renowned for its ability to establish durable humoral immunity, we investigated the potential of a Tfh1/17 recall response during the boost phase to enhance persistence of HIV-1 Envelope (Env) antibodies in rhesus macaques. Using a DNA-prime encoding gp160 antigen and Tfhpolarizing cytokines (interferon protein-10 (IP-10) and interleukin-6 (IL-6)), followed by a gp140 protein boost formulated in a cationic liposome-based adjuvant (CAF01), we successfully generated germinal center (GC) Tfh1/17 cells. In contrast, a similar DNA-prime (including IP-10) followed by gp140 formulated with monophosphoryl lipid A (MPLA)+QS-21 adjuvant predominantly induced GC Tfh1 cells. While the generation of GC Tfh1/17 cells with CAF01 and GC Tfh1 cells with MPLA+QS-21 induced comparable peak Env antibodies, the latter group demonstrated significantly greater antibody concentrations at week 8 after final immunization which persisted up to 30 weeks (gp140 IgG ng/ml-MPLA; 5500; CAF01, 2155; p <0.05). Notably, interferon γ+ Env-specific Tfhresponses were consistently higher with gp140 in MPLA+QS-21 and positively correlated with Env antibody persistence. These findings suggest that vaccine platforms maximizing GC Tfh1 induction promote persistent Env antibodies, important for protective immunity against HIV.
Discovery of post-translationally modified self-peptides that promote hypertension
Authors: Bloodworth Nathaniel , Chen Wei , Patrick David , Palubinsky Amy , Phillips Elizabeth , Roeth Daniel , Kalkum Markus , Mallal Simon , Davies Sean , Ao Mingfang , Moretti Rocco , Meiler Jens , Harrison David G 
Published: July 2023

AbstractPost translational modifications can enhance immunogenicity of self-proteins. In several conditions including hypertension, systemic lupus, and heart failure, isolevuglandins (IsoLGs) are formed by lipid peroxidation and covalently bond with protein lysine residues. Here we show that the murine class-I major histocompatibility complex (MHC-I) variant H-2Dbuniquely presents isoLG modified peptides and developed a computational pipeline that identifies structural features for MHC-I accommodation of such peptides. We identified isoLG-adducted peptides from renal proteins including the sodium glucose transporter 2, Cadherin 16, Kelch Domain containing protein 7A and solute carrier family 23, that are recognized by CD8+T cells in tissues of hypertensive mice, induce T cell proliferationin vitro, and prime hypertension after adoptive transfer. Finally, we find similar patterns of isoLG-adducted antigen restriction in class-I human leukocyte antigens as in murine analogues. Thus, we have used a combined computational and experimental approach to define likely antigenic peptides in hypertension.
scRNA-seq reveals novel genetic pathways and sex chromosome regulation inTriboliumspermatogenesis
Authors: Robben Michael , Ramesh Balan , Pau Shana , Meletis Demetra , Luber Jacob , Demuth Jeffery 
Published: July 2023

AbstractInsights into single cell expression data are generally collected through well conserved biological markers that separate cells into known and unknown populations. Unfortunately for non-model organisms that lack known markers, it is often impossible to partition cells into biologically relevant clusters which hinders analysis into the species.Tribolium castaneum, the red flour beetle, lacks known markers for spermatogenesis found in insect species likeDrosophila melanogaster. Using single cell sequencing data collected from adult beetle testes, we implement a strategy for elucidating biologically meaningful cell populations by using transient expression stage identification markers, weighted principal component leiden clustering. We identify populations that correspond to observable points in sperm differentiation and find species specific markers for each stage. We also develop an innovative method to differentiate diploid from haploid cells based on scRNA-Seq reads and use it to corroborate our predicted demarcation of meiotic cell stages. Our results demonstrate that molecular pathways underlying spermatogenesis in Coleoptera are highly diverged from those in Diptera, relying on several genes with female meiotic pathway annotations. We find that the X chromosome is almost completely silenced throughout pre-meiotic and meiotic cells. Further evidence suggests that machinery homologous to the Drosophila dosage compensation complex (DCC) may mediate escape from meiotic sex chromosome inactivation and postmeiotic reactivation of the X chromosome.
Solution-state NMR Assignment and Secondary Structure Analysis of the MonomericPseudomonasBiofilm-Forming Functional Amyloid Accessory Protein FapA
Authors: Byeon Chang-Hyeock , Akbey Ümit 
Published: July 2023

AbstractFapA is an accessory protein within the biofilm forming functional bacterial amyloid related fap-operon inPseudomonas. We present a complete sequential assignment of1Hamide,13Cα,13Cβ, and15N NMR resonances for the functional form of the monomeric soluble FapA protein, comprising amino acids between 29-152. From these observed chemical shifts, the secondary structure propensities (SSPs) were determined. FapA predominantly adopts a random coil conformation, however, we also identified small propensities for α-helical and β-sheet conformations. Notably, these observed SSPs are smaller compared to the ones we recently observed for the monomeric soluble FapC protein. These NMR results will provide valuable insights into the activity of FapA in functional amyloid formation and regulation, that will also aid developing strategies targeting amyloid formation within biofilms and addressing chronic infections.
Single cell RNA analysis uncovers the cell differentiation trajectories and functionalization for air breathing of frog lung
Authors: Chang Liming , Chen Qiheng , Wang Bin , Liu Jiongyu , Zhang Meihua , Zhu Wei , Jiang Jianping 
Published: July 2023

AbstractThe evolution and development of vertebrate lungs have received extensive concerns for the significance in terrestrial adaptation. Amphibians possess the most primitive lungs among tetrapods, underscoring the evolutionary importance of lungs in bridging the transition from aquatic to terrestrial life. However, the intricate process of cell differentiation during amphibian lung development is still lacking. Using single cell RNA-seq, we identified 21 cell types in the developing lung of a land-dwelling frog (Microhyla fissipes). We elucidated that single type of alveolar epithelial cells (AECs) existed in amphibian and the diversity of AECs may correspond to the capacity for terrestrial adaptation in tetrapods. Based on pseudotime trajectories analysis, we revealed previously unrecognized developmental-specific transition cell states of epithelial and endothelial cells supporting the rapid morphogenesis of lung during metamorphic climax. We illustrated the cellular and molecular processes during lung functionalization. These findings uncover the cell differentiation trajectories and functionalization for air breathing of frog lungs and highlight the evolutionary peculiarity of the primitive lungs.Graphical abstract