bluuebunny/crossref_metadata_2025_split huggingface dataset:
SiglecFhigh neutrophils in lung tumor tissues suppress local CD8 T cell responses and limit the efficacy of anti PD-L1 antibodies
Authors: Simoncello Francesca , Piperno Giulia Maria , Caronni Nicoletta , Battini Tiziana , Cappelletto Ambra , Bicciato Silvio , Benvenuti Federica 
Published: October 2021

AbstractBackgroundTumor infiltrating neutrophils generally correlates to worst prognosis and refractoriness to immunotherapy yet the complexity and significance of diverse subsets resident in tumor tissues has just begun to emerge. In lung tumors, a network of neutrophils states with graded protumorigenic properties is conserved between mouse and humans and include a subset of mature, long lived cells expressing the sialic-acid-binding protein SiglecF (SiglecFhigh neu). The mechanism of recruitment of SiglecFhigh neu into tumor tissues and the impact on local anti-tumor T cell responses and interference with immunotherapy is still elusive.MethodsWe used an immunogenic model of KrasG12D Tp53 null adenocarcinoma of the lung to screen for factors inducing the recruitment of SiglecFhigh neu, followed by gene editing to delete selected candidates. We analyzed frequencies and effector functions of endogenous CD8 T cell responses in controls and SiglecFhigh neu depleted tumors by flow cytometry and functional assays. Tissues fluorescence and confocal imaging of lung sections was used to explore the relative distribution of neu and CD8 T cells. To establish the impact of SiglecFhigh neu on anti-tumoral immune responses we treated cohort of animals with anti-PD-L1 antibodies to evaluate tumor growth in control conditions and under therapy.ResultsWe found that tumor tissues express high levels of CXCL5, mapping to cancer cells. Upon deletion of chemokine expression by gene editing, the recruitment of SiglecFhigh neu was almost entirely abrogated. In tumors depleted of SiglecFhigh neu, the density of tumor specific endogenous CD8 T cells was 3-fold higher than in controls and showed significantly enhanced activation and effector functions. Importantly, checkpoint blockade with anti PD-L1 antibodies was ineffective in control tumors but showed a significant benefit in SiglecFhigh neu depleted tumors.ConclusionThis study demonstrates that SiglecFhigh neu differentiating in lung tumor tissues inhibit local CD8 T cell responses and interfere with the success of checkpoint blockade. These data suggest that blocking selectively tissue resident neu may promote better responses to immunotherapy.
Cytometric Analysis of Diverse Glaucophyte Species Reveals Distinctive Signals Useful for Fluorescence-Based Detection and Sorting
Authors: Calvaruso Rossella , Lawrence Janice , Reyes-Prieto Adrian 
Published: October 2021

AbstractGlaucophytes, red algae and viridiplants (green algae and land plants) are formally united in the supergroup Archaeplastida. Although diverse molecular and genomic evidence suggest the common origin of the three Archaeplastida lineages, the lack of a robust glaucophyte knowledgebase has limited comprehensive evaluations of competing hypotheses. Glaucophytes are rare and apparently confined to freshwater habitats. However, the distribution and diversity of these algae have not been thoroughly explored owing to challenges with detecting and isolating novel specimens. Here we examined the cytometric signatures of representative species of the genera Cyanophora, Cyanoptyche, Glaucocystis and Gloeochaete for a distinctive signal that would aid identification. Most glaucophytes analyzed presented a relatively high red fluorescence signal due to the presence of the blue phycobiliproteins C-phycocyanin and allophycocyanin. Cell-size differences and the concurrent presence of the red phycobiliprotein phycoerythrin in other algal lineages, such as red algae and cryptophytes, allowed us to distinguish glaucophytes from other photosynthetic cells containing blue phycobiliproteins. Our results indicate that the peculiar autofluorescence signal of glaucophytes will facilitate further identification and isolation on novel specimens of this scarce but important algal group.
De novo motor learning of a bimanual control task over multiple days of practice
Authors: Haith Adrian M. , Yang Christopher , Pakpoor Jina , Kita Kahori 
Published: October 2021

AbstractAlthough much research on motor learning has focused on how we adapt our movements to maintain performance in the face of imposed perturbations, in many cases we must learn new skills from scratch, or de novo. In comparison to adaptation, relatively little is known about de novo learning. In part, this is because learning a new skill can involve many challenges, including learning to recognize new patterns of sensory input and generate new patterns of motor output. However, even with familiar sensory cues and well-practiced movements, the problem of quickly selecting the appropriate actions in response to the current state is challenging. Here, we devised a bimanual hand-to-cursor mapping which isolates this control problem. We find that participants initially struggled to control the cursor under this bimanual mapping, despite explicit knowledge of the mapping. Performance improved steadily over multiple days of practice, however. Participants exhibited no aftereffects when reverting to a veridical cursor, confirming that participants learned the new task de novo, rather than through adaptation. Corrective responses to mid-movement perturbations of the target were initially weak, but with practice, participants gradually became able to respond rapidly and robustly to these perturbations. After four days of practice, participants’ behavior under the bimanual mapping almost matched performance with a veridically mapped cursor. However, there remained a small but persistent difference in performance level. Our findings illustrate the dynamics and limitations of learning a novel controller and introduce a promising paradigm for tractably investigating this aspect of motor skill learning.
Structural anther mimics improve reproductive success through dishonest signalling that enhances both attraction and the morphological fit of pollinators with flowers
Authors: Newman Ethan L , Khoury Katharine L , van Niekerk Sandy E , Peter Craig I 
Published: October 2021

SummaryNumerous studies have identified traits associated with pollen mimicry, however, the processes underlying floral deception remains poorly documented for these structures. We studied the importance of attraction and mechanical fit of anther mimics inTritonia laxifolia(Iridaceae) and their relative contributions to reproductive success.To determine anther mimics role in pollinator attraction, we offered bees’ binary preferences to flowers painted with UV absorbent and reflecting paint. We also conducted preference experiments between flowers with excised anther mimics and unmanipulated controls, from which mechanical fit was assessed using single visits. Anther mimics effects on female reproductive success was determined using similar treatments, but on rooted plants.Bees preferred UV absorbent over UV reflecting anther mimics. Preference for flowers with and without the three-dimensional structures was equal. Single visits resulted in more pollen deposition on unmanipulated controls over flowers with their anther mimics excised, which was directly linked to pollen-collecting behaviour. Controls with unmanipulated anther mimics experienced more seed set than those with their anther mimics excised.This study provides insights into pollinator-mediated selection on deceptive floral signals and shows that three-dimensional anther mimics increases reproductive success through both attraction and pollen collecting behaviours that improves the fit between flowers and pollinators.
DNA-PK Promotes DNA End Resection at DNA Double Strand Breaks in G0 cells
Authors: Fowler Faith C. , Chen Bo-Ruei , Zolnerowich Nicholas , Wu Wei , Pavani Raphael , Paiano Jacob , Peart Chelsea , Nussenzweig André , Sleckman Barry P. , Tyler Jessica K. 
Published: October 2021

AbstractDNA double-strand break (DSB) repair by homologous recombination is confined to the S and G2 phases of the cell cycle partly due to 53BP1 antagonizing DNA end resection in G1 phase and non-cycling quiescent (G0) cells where DSBs are predominately repaired by non-homologous end joining (NHEJ). Unexpectedly, we uncovered extensive MRE11- and CtIP-dependent DNA end resection at DSBs in G0 mammalian cells. A whole genome CRISPR/Cas9 screen revealed the DNA-dependent kinase (DNA-PK) complex as a key factor in promoting DNA end resection in G0 cells. In agreement, depletion of FBXL12, which promotes ubiquitylation and removal of the KU70/KU80 subunits of DNA-PK from DSBs, promotes even more extensive resection in G0 cells. In contrast, a requirement for DNA-PK in promoting DNA end resection in proliferating cells at the G1 or G2 phase of the cell cycle was not observed. Our findings establish that DNA-PK uniquely promotes DNA end resection in G0, but not in G1 or G2 phase cells, and has important implications for DNA DSB repair in quiescent cells.
Cytotoxic CD4+ T cells driven by T-cell intrinsic IL-18R/MyD88 signaling predominantly infiltrate Trypanosoma cruzi-infected hearts
Authors: Barbosa Carlos-Henrique. D. , Canto Fábio B. , Gomes Ariel , Brandão Layza M. , Lima Jéssica R. , Melo Guilherme A. , Granato Alessandra , Neves Eula G.A. , Dutra Walderez O. , Oliveira Ana C. , Nóbrega Alberto , Bellio Maria 
Published: October 2021

AbstractIncreasing attention has been directed to cytotoxic CD4+ T cells (CD4CTLs) in different pathologies, both in humans and mice. The impact of CD4CTLs in immunity and the mechanisms controlling their generation, however, remain poorly understood. Here, we show that CD4CTLs abundantly differentiate during mouse infection with the intracellular parasite Trypanosoma cruzi. CD4CTLs display parallel kinetics to Th1 cells in the spleen, mediate specific cytotoxicity against cells presenting pathogen-derived antigens and express immunoregulatory and/or exhaustion markers. We demonstrate that CD4CTL absolute numbers and activity are severely reduced in both Myd88-/- and Il18ra-/- mice. Of note, the infection of mixed-bone marrow chimeras revealed that WT but not Myd88-/- cells transcribe the CD4CTL gene signature and that Il18ra-/- and Myd88-/- CD4+ T cells phenocopy each other. Moreover, adoptive transfer of WT CD4+GzB+ T cells to infected Il18ra-/- mice extended their survival. Importantly, cells expressing the CD4CTL phenotype predominate among CD4+ T cells infiltrating the infected mouse cardiac tissue and are increased in the blood of Chagas patients, in which the frequency of CD4CTLs correlates with the severity of cardiomyopathy. Our findings describe CD4CTLs as a major player in immunity to a relevant human pathogen and disclose T-cell intrinsic IL-18R/MyD88 signaling as a key pathway controlling the magnitude of the CD4CTL response.
Defining Cardiac Cell Populations and Relative Cellular Composition of the Early Fetal Human Heart
Authors: Dewing Jennifer M. , Saunders Vinay , O’Kelly Ita , Wilson David I. 
Published: October 2021

ABSTRACTThe human heart is primarily composed of cardiomyocytes, fibroblasts, endothelial and smooth muscle cells. Reliable identification of fetal cardiac cell types using protein markers is important for understanding cardiac development and delineating the cellular composition of the human heart during early development, which remains largely unknown. The aim of this study was to use immunohistochemistry (IHC), flow cytometry and RT-PCR analyses to investigate the expression and specificity of commonly used cardiac cell markers in the early human fetal heart (8-12 post-conception weeks). The expression of previously reported protein markers for the detection of cardiomyocytes (Myosin Heavy Chain (MHC) and Troponin I (cTnI)), fibroblasts (DDR2, Thy1, Vimentin), endothelial cells (CD31) and smooth muscle cells (α-SMA) were assessed. Flow cytometry revealed two distinct populations of cTnI expressing cells based on fluorescence intensity: cTnIHigh and cTnILow. MHC positive cardiomyocytes were cTnIHigh, whereas MHC negative non-myocyte cells were cTnILow. cTnI expression in non-myocytes was further confirmed by IHC and RT-PCR analyses, suggesting troponins are not cardiomyocyte-specific and may play distinct roles in non-muscle cells during early development. Vimentin was confirmed to be enriched in cultured fibroblast populations and flow cytometry revealed VimHigh and VimLow cell populations in the fetal heart. MHC positive cardiomyocytes were VimLow whilst CD31 positive endothelial cells were VimHigh. Based on the markers investigated, we estimate fetal human cardiomyocyte populations comprise 75-80% of total cardiac cells and exhibit the following marker profile: α-MHC+/cTnIHigh/VimLow. For the non-cardiomyocyte population, we estimate they comprise 20-25% of total cardiac cells and exhibit the following marker profile: α-MHC-/cTnILow/VimHigh. Our study suggests the marker profiles and proportions of fetal cardiac populations are distinct from that of the adult heart.
Probing behavior of the corn leafhopperDalbulus maidison susceptible and resistant maize hybrids
Authors: Carpane Pablo Daniel , Catalano María Inés 
Published: October 2021

AbstractThe corn leafhopperDalbulus maidisis the main vector of the pathogens that cause corn stunt, a major disease of maize in the Americas. As host resistance is an efficient tool to control diseases, the findings of a previous report showed that some corn hybrids are resistant toD. maidis. In this work, we assessed the probing behavior ofD. maidison susceptible and resistant corn hybrids using EPG (Electrical Penetration Graph) technology. Fifteen-day-old females were monitored for 20 hours, with access to hybrids DK390, DK670, DK79-10, and DK72-10. Hybrids DK390 and DK72-10 showed resistance toD. maidisin phloem, since insects feeding on these hybrids presented more salivation events in phloem without subsequent ingestion, which are seen as failed attempts to ingest. A reduction of the total duration of phloem ingestion was observed, and accordingly of the time spent by insects with access to these hybrids on xylem ingestion. The hybrid DK390 also had mesophyll resistance, seen as less probing time and a higher number of probes of short duration. These findings support and are consistent with previous research, providing useful information to characterize maize hybrids resistant toD. maidis, and so to corn stunt.
Spatiotemporal mapping of gene expression landscapes and developmental trajectories during zebrafish embryogenesis
Authors: Liu Chang , Li Rui , Li Young , Lin Xiumei , Wang Shuowen , Liu Qun , Zhao Kaichen , Yang Xueqian , Shi Xuyang , Ma Yuting , Pei Chenyu , Wang Hui , Bao Wendai , Hui Junhou , Berberoglu Michael Arman , Sahu Sunil Kumar , Esteban Miguel A. , Ma Kailong , Fan Guangyi , Li Yuxiang , Liu Shiping , Chen Ao , Xu Xun , Dong Zhiqiang , Liu Longqi 
Published: October 2021

SUMMARYVertebrate embryogenesis is a remarkably dynamic process during which numerous cell types of different lineages generate, change, or disappear within a short period of time. A major challenge in understanding this process is the lack of topographical transcriptomic information that can help correlate microenvironmental cues within the hierarchy of cell fate decisions. Here, we employed Stereo-seq, a high-definition spatially resolved transcriptomic technology, to dissect the spatiotemporal dynamics of gene expression and regulatory networks in the developing zebrafish embryos. We profiled 91 embryo sections covering six critical time points during the first 24 hours of development, obtaining a total of 139,391 spots at cellular size (∼100 μm2) with spatial coordinates. Meanwhile, we identified spatial modules and co-varying genes for specific tissue organizations. By performing the integrative analysis of the Stereo-seq and scRNA-seq data from each time point, we reconstructed the spatially resolved developmental trajectories of cell fate transitions and molecular changes during zebrafish embryogenesis. We further investigated the spatial distribution of ligand-receptor pairs for major signaling pathways and identified novel interactions that potentially crosstalk with the Notch signaling pathway during zebrafish development. Our study constitutes a fundamental reference for further studies aiming to understand vertebrate development.
ChemChaste: Simulating spatially inhomogenous biochemical reaction-diffusion systems for modelling cell-environment feedbacks
Authors: Johnson Connah G. M. , Fletcher Alexander G. , Soyer Orkun S. 
Published: October 2021

AbstractMotivationSpatial organisation plays an important role in the function of many biological systems, from cell fate specification in animal development to multi-step metabolic conversions in microbial communities. The study of such systems benefits from the use of spatially explicit computational models that combine a discrete description of cells with a continuum description of one or more chemicals diffusing within a surrounding bulk medium. These models allow thein silicotesting and refinement of mechanistic hypotheses. However, most existing models of this type do not account for concurrent bulk and intracellular biochemical reactions and their possible coupling.ResultsHere, we describe ChemChaste, an extension for the open-source C++ computational biology library Chaste. ChemChaste enables the spatial simulation of both multicellular and bulk biochemistry by expanding on Chaste’s existing capabilities. In particular, ChemChaste enables: (i) simulation of an arbitrary number of spatially diffusing chemicals; (ii) spatially heterogeneous chemical diffusion coefficients; and (iii) inclusion of both bulk and intracellular biochemical reactions and their coupling. ChemChaste also introduces a file-based interface that allows users to define the parameters relating to these functional features without the need to interact directly with Chaste’s core C++ code. We describe ChemChaste and demonstrate its functionality using a selection of chemical and biochemical exemplars, with a focus on demonstrating increased ability in modelling bulk chemical reactions and their coupling with intracellular reactions.Availability and implementationChemChaste is a free, open-source C++ library, available via GitHub athttps://github.com/OSS-Lab/ChemChasteunder the BSD license.ContactO.Soyer@warwick.ac.ukora.g.fletcher@sheffield.ac.uk
The natural history of the black soldier fly,Hermetia illucens: insights from complete mitochondrial genome sequences
Authors: Guilliet J , Baudouin G , Pollet N , Filée J 
Published: October 2021

AbstractThe Black Soldier Fly (BSF)Hermetia illucensis a cosmopolitan fly heavily used by industrial companies to reduce biowaste and produce protein and fat for poultry and aquaculture feed. However, the natural history and the genetic diversity of the BSF is poorly known. In this study, we analysed 677 CO1 sequences derived from samples found all over the five continents leading us to the discovery of 52 haplotypes including 10 major haplotypes. We refined the definition of these haplotypes by sequencing 59 mitochondrial genomes. We could derive an estimate of the separation events of the different haplotypes at more than two million years for the oldest branches. This worldwide cryptic genetic and genomic diversity is mirrored at local scale in France in which we found five major haplotypes sometimes in sympatry. Our data resolve the phylogenetic relationships between the major lineages and give insights into the dispersal and the numbers of BSF neo-introduction at global and local scales. Our results indicate that the genetic and genomic diversity of commercial BSF stock is very low and these brood stock participated in the dissemination of the BSF in the wild. Taken together these results call for a better understanding of the genomic diversity of the BSF to unravel possible specific adaptations of the different lineages for industrial needs and to initiate the selection process.
Structural basis for long-chain isoprenoids synthesis by cis-prenyltransferases
Authors: Giladi Moshe , Bar-El Michal Lisnyansky , Vaňková Pavla , Ferofontov Alisa , Melvin Emelia , Kavan Daniel , Redko Boris , Haimov Elvira , Wiener Reuven , Man Petr , Haitin Yoni 
Published: October 2021

AbstractIsoprenoids are the largest group of natural products, found in all living organisms and play an essential role in numerous cellular processes. These compounds are synthesized by prenyltransferases, catalyzing the condensation reaction between an allylic diphosphate primer and a variable number of isopentenyl diphosphate (C5) units. This superfamily of enzymes can be subdivided into trans- or cis-prenyltransferases according to the stereoisomerism of the product. The cis branch can be further classified according to product length. While the active site volume was suggested to determine the final length in enzymes synthesizing short- and medium-chain products (up to C60), long-chain enzymes (up to C120) and rubber synthases (>C10,000) fail to conform to this paradigm. Here, to resolve the structural basis for long-chain isoprenoid synthesis, we focused on the human cis-prenyltransferase complex (hcis-PT). This enzyme, peripheral to the endoplasmic reticulum membrane, produces the precursor for dolichol phosphate, a membrane residing glycosyl carrier. In line with its crucial role in the cellular protein glycosylation machinery, disease-causing mutations in hcis-PT were shown to result in a wide spectrum of clinical phenotypes. The crystallographic structures of hcis-PT in four different substrate/product-bound conformations revealed an outlet enabling product elongation into the bulk solvent. Moreover, hydrogen-deuterium exchange mass spectrometry analysis in solution showed that the hydrophobic active site core is flanked by dynamic regions consistent with separate inlet and outlet orifices. Finally, using a fluorescent substrate analog and a fluorescently-labeled lipid nanodiscs, we show that product elongation and membrane association are closely correlated. Together, our results support directional product synthesis in long-chain enzymes and rubber synthases, with a distinct substrate inlet and product outlet, allowing direct membrane insertion of the elongating isoprenoid during catalysis. This mechanism uncouples active site volume from product length and circumvents the need to expulse hydrophobic product into a polar environment prior to membrane insertion.
Systematic reduction of the dimensionality of natural scenes allows accurate predictions of retinal ganglion cell spike outputs
Authors: Freedland Julian , Rieke Fred 
Published: October 2021

AbstractThe mammalian retina engages a broad array of linear and nonlinear circuit mechanisms to convert natural scenes into retinal ganglion cell (RGC) spike outputs. Although many individual integration mechanisms are well understood, predictive models of natural scene encoding perform poorly, likely due to interactions among the active mechanisms. Here, we identified spatial integration mechanisms relevant for natural scene encoding and used computational modeling to predict spike outputs in primate parasol RGCs. Our approach was to simplify the structure of natural scenes and empirically ask whether these changes were reflected in RGC spike responses. We observed that reducing natural movies to 16 linearly integrated regions described ∼80% of the structure of parasol RGC spike responses. We then used simplified stimuli to create high-dimensional metamers that recapitulated the spike response of full-field naturalistic movies. Finally, we identified the retinal computations that convert natural images in 16-dimensional space into 1-dimensional spike outputs.