bluuebunny/crossref_metadata_2025_split huggingface dataset:
Asymmetrical gene flow between coastal and inland dunes in a threatened digger wasp
Authors: Batsleer Femke , Gallin Matthieu , Delafonteyne Moyra , Dekeukeleire Daan , T’Jollyn Filiep , Vantieghem Pieter , Broeck An Vanden , Mergeay Joachim , Maes Dirk , Bonte Dries 
Published: September 2022

1.AbstractConnectivity is a species- and landscape-specific measure that is key to species conservation in fragmented landscapes. However, information on connectivity is often lacking, especially for insects which are known to be severely declining. Patterns of gene flow constitute an indirect measure of functional landscape connectivity. We studied the population genetic structure of the rare digger wasp Bembix rostrata in coastal and inland regions in and near Belgium. The species is restricted to sandy pioneer vegetations for nesting and is well known for its philopatry as it does not easily colonize vacant habitat. It has markedly declined in the last century, especially in the inland region where open sand habitat has decreased in area and became highly fragmented. To assess within and between region connectivity, we used mating system independent population genetic methods suitable for haplodiploid species. We found more pronounced genetic structure in the small and isolated inland populations as compared to the well-connected coastal region. We also found a pattern of asymmetrical gene flow from coast to inland, including a few rare dispersal distances up to 200 to 300 km based on assignment tests. We point to demography, wind and difference in dispersal capacities as possible underlying factors that can explain the discrepancy in connectivity and asymmetrical gene flow between the different regions. Despite B. rostrata being a poor colonizer, gene flow between existing populations appeared not highly restricted, especially at the coast. Therefore, to improve the conservation status of B. rostrata, the primary focus should be to preserve and create sufficient habitat for this species to increase the number and quality of (meta)populations, rather than focusing on landscape connectivity itself.
A bipartite function of ESRRB can integrate signaling over time to balance self-renewal and differentiation
Authors: Knudsen Teresa E. , Hamilton William , Proks Martin , Lykkegaard Maria , Nielsen Alexander V. , Trusina Ala , Brickman Joshua M. 
Published: September 2022

SummaryCooperative DNA binding of transcription factors (TFs) integrates external stimuli and context across tissues and time. Naïve mouse embryonic stem cells are derived from early development and can sustain the pluripotent identity indefinitely. Here we ask whether TFs associated with pluripotency evolved to directly support this state, or if the state emerges from their combinatorial action. NANOG and ESRRB are key pluripotency factors that co-bind DNA. We find that when both factors are expressed, ESRRB supports pluripotency. However, when NANOG is not present, ESRRB supports a bistable culture of cells with an embryo-like primitive endoderm identity ancillary to pluripotency. The stoichiometry between NANOG and ESRRB quantitatively influences differentiation, and in silico modeling of bipartite TF activity suggests ESRRB safeguards plasticity in differentiation. Thus, the concerted activity of cooperative TFs can transform their effect to sustain intermediate cell identities and allow ex vivo expansion of highly stable stem cell models.
Neuraminidase activity modulates cellular co-infection during influenza A virus multicycle growth
Authors: Guo Zijian , He Yuanyuan , Benegal Ananya N. , Vahey Michael D. 
Published: September 2022

AbstractInfection of individual cells by multiple virions plays critical roles in the replication and spread of many viruses, but mechanisms that control cellular co-infection during multi-cycle viral growth remain unclear. Here, we investigate virus-intrinsic factors that control cellular co-infection by influenza A virus (IAV). Using quantitative fluorescence to track the spread of virions from single infected cells, we identify the IAV surface protein neuraminidase (NA) as a key determinant of cellular co-infection. We map this effect to NA’s ability to deplete viral receptors from both infected and neighboring uninfected cells. In cases where viral infectious potential is low, genetic or pharmacological inhibition of NA increases the local spread of infection by increasing the viral load received by neighboring cells. These results identify virus-intrinsic factors that contribute to cellular multiplicity of infection, and suggest that optimal levels of NA activity depend on the infectious potential of the virus in question.
Using Packing Defects in Heterogeneous Biological Membrane as a Lens to Explore Protein Localization Propensity and Small Molecule Permeability
Authors: Tripathy Madhusmita , Srivastava Anand 
Published: September 2022

AbstractPlasma membrane (PM) heterogeneity has long been implicated in various cellular functions. However, mechanistic principles governing functional regulations of lipid environment is not well understood due to the inherent complexities associated with the relevant length and time scales that limit both direct experimental measurements and their interpretation. In this context, computer simulation holds immense potential to investigate molecular-level interactions that lead to PM heterogeneity and the related functions. Herein, we investigate spatial and dynamic heterogeneity in model membranes with coexisting liquid ordered and liquid disordered phases and characterize the membrane order in terms of the topological changes in lipid local environment using the non-affine parameter (NAP) frame-work. Furthermore, we probe the packing defects in membrane with coexisting fluid phases, which can be considered as the conjugate of membrane order assessed in terms of the NAP. In doing so, we formalize the connection between membrane packing and local membrane order and use that to explore the mechanistic principles behind preferential localization of proteins in mixed phase membranes and membrane permeability of small molecules. Our observations suggest that heterogeneity in mixed phase membranes follow some generic features, where functions may arise based on packing-related basic design principles.SignificanceFunctionally important complex lateral and transverse structures in biological membrane result from the differential molecular interactions among a rich variety of lipids and other building blocks. The nature of molecular packing in membrane is a manifestation of these interactions. In this work, using some of the ideas from the Physics of amorphous materials and glasses, we quantify the correlation between heterogeneous membrane organization and the three dimensional packing defects. Subsequently, we investigate the packing-based molecular design-level features that drive preferential localization of peptides in heterogeneous membrane and membrane permeation of small molecules.
The Arabidopsis MCTP member QUIRKY regulates the formation of the STRUBBELIG receptor kinase complex
Authors: Chen Xia , Leśniewska Barbara , Vaddepalli Prasad , Schneitz Kay 
Published: September 2022

AbstractIntercellular communication plays a central role in organogenesis. Tissue morphogenesis inArabidopsis thalianarequires signaling mediated by a cell surface complex containing the atypical receptor kinase STRUBBELIG (SUB) and the multiple C2 domains and transmembrane region protein QUIRKY (QKY). QKY is required to stabilize SUB at the plasma membrane. However, it is unclear what the in vivo architecture of the QKY/SUB signaling complex is, how it is controlled, and how it relates to the maintenance of SUB at the cell surface. Using a combination of yeast two-hybrid assays and Förster resonance energy transfer (FRET)/fluorescence lifetime imaging microscopy (FLIM) in epidermal cells of seedling roots we find that QKY promotes the formation of SUB homo-oligomers in vivo, a process that appears to involve an interaction between the extracellular domains of SUB. We also show that QKY and SUB physically interact and form a complex at the cell surface in vivo. In addition, the data show that the N-terminal C2A-B region of QKY interacts with the intracellular domain of SUB. They further reveal that this interaction is essential to maintain SUB levels at the cell surface. Finally, we provide evidence that QKY forms homo-multimers in vivo in a SUB-independent manner. We suggest a model in which the physical interaction of QKY with SUB mediates the oligomerization of SUB and attenuates its internalization, thereby maintaining sufficiently high levels of SUB at the cell surface required for the control of tissue morphogenesis.
An endosymbiont harvest: Phylogenomic analysis of Wolbachia genomes from the Darwin Tree of Life biodiversity genomics project
Authors: Vancaester Emmelien , Blaxter Mark 
Published: September 2022

AbstractThe Darwin Tree of Life project aims to sequence all described terrestrial and aquatic eukaryotic species found in Britain and Ireland. Reference genome sequences are generated from single individuals for each target species. In addition to the target genome, sequenced samples often contain genetic material from microbiomes, endosymbionts, parasites and other cobionts. Wolbachia endosymbiotic bacteria are found in a diversity of terrestrial arthropods and nematodes, with supergroups A and B the most common in insects. We identified and assembled 110 complete Wolbachia genomes from 93 host species spanning 92 families by filtering data from 368 insect species generated by the Darwin Tree of Life project. From 15 infected species we assembled more than one Wolbachia genome, including cases where individuals carried simultaneous supergroup A and B infections. Different insect orders had distinct patterns of infection, with Lepidopteran hosts mostly infected with supergroup B, while infections in Diptera and Hymenoptera were dominated by A-type Wolbachia. Other than these large-scale order-level associations, host and Wolbachia phylogenies revealed no (or very limited) cophylogeny. This points to the occurrence of frequent host switching events, including between insect orders, in the evolutionary history of the Wolbachia pandemic. While supergroup A and B genomes had distinct GC% and GC skew, and B genomes had a larger core gene set and tended to be longer, it was the abundance of active and pseudogenised copies of bacteriophage WO who was a strong determinant of Wolbachia genome size. Mining raw genome data generated for reference genome assemblies is a robust way of identifying and analysing cobiont genomes and giving greater ecological context for their hosts.
Down-regulated GAS6 impairs synovial macrophage efferocytosis and promotes obesity-associated osteoarthritis
Authors: Zihao Yao , Weizhong Qi , Liangliang Liu , Yan Shao , Hongbo Zhang , Jianbin Yin , Haoyan Pan , Xiongtian Guo , Anling Liu , Daozhang Cai , Xiaochun Bai , Haiyan Zhang 
Published: September 2022

AbstractObesity has always been considered a significant risk factor in OA progression, but the underlying mechanism of obesity-related inflammation in OA synovitis remains unclear. The present study found that synovial macrophages infiltrated and polarized in the obesity microenvironment and identified the essential role of M1 macrophages in impaired macrophage efferocytosis using pathology analysis of obesity-associated OA. The present study revealed that obese OA patients and ApoE−/− mice showed a more pronounced synovitis and enhanced macrophage infiltration in synovial tissue, accompanied by dominant M1 macrophage polarization. Obese OA mice had a more severe cartilage destruction and increased levels of synovial apoptotic cells than OA mice in the control group. Enhanced M1-polarized macrophages in obese synovium decreased growth arrest-specific 6 (GAS6) secretion, resulting in impaired macrophage efferocytosis in synovial apoptotic cells. Intracellular contents released by accumulated apoptotic cells further triggered an immune response and lead to a release of inflammatory factors, such as TNF-α, IL-1β, and IL-6, which induce chondrocyte homeostasis dysfunction in obese OA patients. Intra-articular injection of GAS6 restored the phagocytic capacity of macrophages, reduced the accumulation of local apoptotic cells, and decreased the levels of TUNEL- and caspase-3-positive cells, preserving cartilage thickness and preventing the progression of obesity-associated OA. Therefore, blocking M1 macrophage polarization or intra-articular injection of GAS6 is a potential therapeutic strategy for obesity-associated OA.
DAXX adds a de novo H3.3K9me3 deposition pathway to the histone chaperone network
Authors: Carraro Massimo , Hendriks Ivo A. , Hammond Colin M. , Solis Victor , Völker-Albert Moritz , Elsborg Jonas D. , Weisser Melanie B. , Spanos Christos , Montoya Guillermo , Rappsilber Juri , Imhof Axel , Nielsen Michael L. , Groth Anja 
Published: September 2022

SUMMARYA multitude of histone chaperones are required to protect histones after their biosynthesis until DNA deposition. They cooperate through the formation of co-chaperone complexes, but the crosstalk between nucleosome assembly pathways remains enigmatic. Using explorative interactomics approaches, we characterize the organization of the histone H3–H4 chaperones network and define the interplay between histone chaperone systems. We identify and validate several novel histone dependent complexes and predict the structure of the ASF1 and SPT2 co-chaperone complex, expanding the role of ASF1 in histone dynamics. We show that DAXX acts separately from the rest of the network, recruiting heterochromatin factors and promoting lysine 9 tri-methylation of new histone H3.3 prior to deposition onto DNA. With its functionality, DAXX provides a molecular mechanism for de novo heterochromatin assembly. Collectively, our findings provide a new framework for understanding how cells orchestrate histone supply and comply with chromatin dynamics throughout the cell cycle.
VLA-4 suppression by senescence signals regulates meningeal immunity and leptomeningeal metastasis
Authors: Li Jiaqian , Huang Di , Lei Bingxi , Huang Jingying , Zhao Qiyi , Su Shicheng , Wang Ying 
Published: September 2022

AbstractLeptomeningeal metastasis is associated with dismal prognosis and has few treatment options. However, very little is known about the immune response to leptomeningeal metastasis. Here, by establishing an immunocompetent mouse model of breast cancer leptomeningeal metastasis, we found that tumor-specific CD8+T cells were generated in deep cervical lymph nodes (dCLNs) and played an important role in controlling leptomeningeal metastasis. Mechanistically, T cells in dCLNs displayed a senescence phenotype and their recruitment was impaired in mice bearing cancer cells that preferentially colonized in leptomeningeal space. Upregulation of p53 suppressed the transcription of VLA-4 in senescent dCLN T cells and consequently inhibited their migration to the leptomeningeal compartment. Clinically, CD8+T cells from cerebrospinal fluid of patients with leptomeningeal metastasis exhibited senescence and VLA-4 downregulation. Collectively, our findings demonstrated that CD8+T cell immunosenescence drives leptomeningeal metastasis.
Comprehensive identification, isolation, and culture of human breast cell types
Authors: Thi Kate , Del Toro Katelyn , Licon-Munoz Yamhilette , Sayaman Rosalyn W. , Hines William C. 
Published: September 2022

AbstractTissues are formed and shaped by cells of many different types and are orchestrated through countless interactions among the cells—and the myriad of molecules they synthesize. Deciphering a tissue’s biological complexity thus requires studying it at cell-level resolution, where molecular and biochemical features of different cell types can be explored and thoroughly dissected. Unfortunately, the lack of comprehensive methods to identify, isolate, and culture each cell type from many tissues has impeded progress. Here, we present a method for the breadth of cell types composing the human breast. Our goal has long been to understand the essence of each of these different breast cell types, that is, to reveal the underlying biology explaining their intrinsic features, the consequences of interactions, and their contributions to the tissue as a whole. This biological exploration has required cell purification, deep-RNA sequencing—and a thorough dissection of the genes and pathways defining each cell type, which we present in an adjoining article. Here, we present an exhaustive cellular dissection of the human breast, where we explore its cellular composition and histological organization. Moreover, we introduce a novel fluorescence-activated cell sorting (FACS) antibody panel and rigorous gating strategy capable of isolating each of the twelve major breast cell types to purity. Finally, we describe the creation of primary cell models from nearly every one of these breast cell types—some being the first of their kind— and submit these as critical tools for studying the dynamic cellular interactions within breast tissues and tumors. Together, this body of work and derived resources deliver a unique perspective of the breast, revealing insights into its cellular, molecular, and biochemical composition.
Proteome-Wide Photo-Crosslinking Enables Residue-Level Visualization of Protein Interaction Networks in vivo
Authors: Faustino Anneliese M. , Sharma Piyoosh , Yadav Divya , Fried Stephen D. 
Published: September 2022

ABSTRACTCrosslinking mass spectrometry (XL-MS) is emerging as a unique method at the crossroads of structural and cellular biology, uniquely capable of identifying protein-protein interactions with residue-level resolution and on the proteome-wide scale. With the development of crosslinkers that can form linkages inside cells and easily cleave during fragmentation on the mass spectrometer (MS-cleavable crosslinks), it has become increasingly facile to identify contacts between any two proteins in complex samples, including in live cells or tissues. Photo-crosslinkers possess the advantages of high temporal resolution and high reactivity, thereby engaging all residue-types (rather than just lysine); nevertheless, photo-crosslinkers have not enjoyed widespread use, and have yet to be employed for proteome-wide studies, because their products are challenging to identify, and an MS-cleavable photo-crosslinker has not yet been reported. Here, we demonstrate the synthesis and application of two heterobifunctional photo-crosslinkers that feature diazirines and N-hydroxy-succinimidyl carbamate groups, the latter of which unveil MS-cleavable linkage upon acyl transfer to protein targets. Moreover, these crosslinkers demonstrate high water-solubility and cell-permeability. Using these compounds, we demonstrate the feasibility of proteome-wide photo-crosslinking mass spectrometry (photo-XL-MS), both in extracts and in cellulo. These studies provide a partial interaction map of the E. coli cytosol with residue-level resolution. We find that photo-XL-MS has a propensity to capture protein-protein interactions, particularly involving low-abundance uncharacterized proteins, suggesting it could be a powerful tool to shed light on the “darker” corners of the proteome. Overall, we describe methods that enable the detection of protein quinary interaction networks in their native environment at residue-level resolution proteome-wide, and we expect they will prove useful toward the effort to explore the molecular sociology of the cell.TOC graphic
Structural characterization of human tryptophan hydroxylase 2 reveals L-Phe as the superior regulatory domain ligand relevant for serotonin biosynthesis
Authors: Vedel Ida M. , Prestel Andreas , Zhang Zhenwei , Skawinska Natalia T. , Stark Holger , Harris Pernille , Kragelund Birthe B. , Peters Günther H. J. 
Published: September 2022

AbstractTryptophan hydroxylase 2 (TPH2) catalyzes the rate-limiting step in the biosynthesis of serotonin in the brain. Consequently, regulation of TPH2 is relevant for serotonin related diseases, yet, the regulatory mechanism of TPH2 is poorly understood and structural as well as dynamical insights are missing. Here, we use NMR spectroscopy to determine the structure of a 47 N-terminally truncated variant of the regulatory domain (RD) dimer of human TPH2 in complex with L-Phe, and show that L-Phe is the superior RD ligand compared to the natural substrate, L-Trp. Using cryo-EM we obtain a low-resolution structure of a similarly truncated variant of the complete tetrameric enzyme with dimerized RDs. The cryo-EM 2D class averages additionally indicate that the RDs are dynamic in the tetramer and likely exist in a monomer-dimer equilibrium. Our results provide structural information on the RD both as an isolated domain and in the TPH2 tetramer, which will facilitate future elucidation of TPH2’s regulatory mechanism affecting serotonin regulation.
A small molecule RIG-I agonist serves to adjuvant broad multifaceted influenza virus vaccine immunity
Authors: Hemann Emily A. , Knoll Megan L. , Wilkins Courtney R. , Subra Caroline , Green Richard , García-Sastre Adolfo , Thomas Paul G. , Trautmann Lydie , Ireton Renee , Loo Yueh-Ming , Gale Michael 
Published: September 2022

AbstractRetinoic acid-inducible gene I (RIG-I) is essential for activating host cell innate immunity to regulates the immune response against many RNA viruses. We identified a small molecule compound, KIN1148, that directly binds RIG-I to drive IRF3activation to impart the expression of IRF3-target genes, including specific immunomodulatory cytokines and chemokines. KIN1148 does not lead to ATPase activity or compete with ATP for binding but activates RIG-I to induce antiviral gene expression programs distinct from type I interferon (IFN) treatment. When administered in combination with a vaccine against influenza A virus (IAV), KIN1148 induces both neutralizing antibody and broadly cross-protective IAV-specific T cell responses compared to vaccination alone, which induces comparatively poor responses. This robust KIN1148-adjuvanted immune response protects mice from lethal H1N1 and H5N1 IAV challenge. Importantly, KIN1148 also augments human CD8+ T cell activation. Thus, we have identified a small molecule RIG-I agonist that serves as an effective adjuvant in inducing non-canonical RIG-I activation for induction of innate immune programs that enhance adaptive immune protection of antiviral vaccination.SummaryHemann, et. al. identify a small-molecule RIG-I agonist (KIN1148) that directly binds RIG-I for non-canonical activation and adjuvants pandemic and avian influenza virus vaccination. KIN1148 augments broadly neutralizing antibody and T cell responses in mice and enhances human DC maturation and CD8+ T cell activation.