bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structures of the Cmr-β Complex Reveal the Regulation of the Immunity Mechanism of Type III-B CRISPR-Cas
Authors: Sofos Nicholas , Feng Mingxia , Stella Stefano , Pape Tillmann , Fuglsang Anders , Lin Jinzhong , Huang Qihong , Li Yingjun , She Qunxin , Montoya Guillermo 
Published: June 2020

AbstractCmr-β is a Type III-B CRISPR-Cas complex that upon target RNA recognition unleashes a multifaceted immune response against invading genetic elements, including ssDNA cleavage, cyclic oligoadenylate synthesis, and also a unique UA-specific ssRNA hydrolysis by the Cmr2 subunit. Here, we present the structure-function relationship of Cmr-β unveiling how binding of the target RNA regulates the Cmr2 activities. CryoEM analysis revealed the unique subunit architecture of Cmr-β and captured the complex in different conformational stages of the immune response, including the non-cognate and cognate target-RNA bound complexes. The binding of the target RNA induces a conformational change of Cmr2, which together with the complementation between the 5’-handle in the crRNA and the 3’-antitag of the target RNA, activate different configurations in a unique loop of the Cmr3 subunit, which acts as an allosteric sensor signaling the self vs. non-self recognition. These findings highlight the diverse defense strategies of Type III complexes.
Epithelial Morphogenesis Driven by Cell-Matrix vs. Cell-Cell Adhesion
Authors: Wang Shaohe , Matsumoto Kazue , Yamada Kenneth M. 
Published: June 2020

SUMMARYMany embryonic organs undergo epithelial morphogenesis to form tree-like hierarchical structures. However, it remains unclear what drives the budding and branching of stratified epithelia, such as in embryonic salivary gland and pancreas. Here, we performed live-organ imaging of mouse embryonic salivary glands at single-cell resolution to reveal that budding morphogenesis is driven by expansion and folding of a distinct epithelial surface cell sheet characterized by strong cell-matrix adhesions and weak cell-cell adhesions. Profiling of single-cell transcriptomes of this epithelium revealed spatial patterns of transcription underlying these cell adhesion differences. We then synthetically reconstituted budding morphogenesis by experimentally suppressing E-cadherin expression and inducing basement membrane formation in 3D spheroid cultures of engineered cells, which required β1 integrin-mediated cell-matrix adhesion for successful budding. Thus, stratified epithelial budding, the key first step of branching morphogenesis, is driven by an overall combination of strong cell-matrix adhesion and weak cell-cell adhesion by peripheral epithelial cells.
DNA origami demonstrate the unique stimulatory power of single pMHCs as T-cell antigens
Authors: Hellmeier Joschka , Platzer Rene , Eklund Alexandra S. , Schlichthärle Thomas , Karner Andreas , Motsch Viktoria , Kurz Elke , Bamieh Victor , Brameshuber Mario , Preiner Johannes , Jungmann Ralf , Stockinger Hannes , Schütz Gerhard J. , Huppa Johannes B. , Sevcsik Eva 
Published: June 2020

ABSTRACTT-cells detect with their T-cell antigen receptors (TCRs) the presence of rare peptide/MHC complexes (pMHCs) on the surface of antigen presenting cells (APCs). How they convert a biochemical interaction into a signaling response is poorly understood, yet indirect evidence pointed to the spatial antigen arrangement on the APC surface as a critical factor. To examine this, we engineered a biomimetic interface based on laterally mobile functionalized DNA origami platforms, which allow for nanoscale control over ligand distances without interfering with the cell-intrinsic dynamics of receptor clustering. We found that the minimum signaling unit required for efficient T-cell activation consisted of two ligated TCRs within a distance of 20 nanometers, if TCRs were stably engaged by monovalent antibody fragments. In contrast, antigenic pMHCs stimulated T-cells robustly as well-isolated entities. These results identify the minimal requirements for effective TCR-triggering and validate the exceptional stimulatory potency of transiently engaging pMHCs.
In situclassification of cell types in human kidney tissue using 3D nuclear staining
Authors: Woloshuk Andre , Khochare Suraj , Almulhim Aljohara Fahad , McNutt Andrew , Dean Dawson , Barwinska Daria , Ferkowicz Michael , Eadon Michael T. , Kelly Katherine J. , Dunn Kenneth W. , Hasan Mohammad A. , El-Achkar Tarek M. , Winfree Seth 
Published: June 2020

AbstractTo understand the physiology and pathology of disease, capturing the heterogeneity of cell types within their tissue environment is fundamental. In such an endeavor, the human kidney presents a formidable challenge because its complex organizational structure is tightly linked to key physiological functions. Advances in imaging-based cell classification may be limited by the need to incorporate specific markers that can link classification to function. Multiplex imaging can mitigate these limitations, but requires cumulative incorporation of markers, which may lead to tissue exhaustion. Furthermore, the application of such strategies in large scale 3-dimensional (3D) imaging is challenging. Here, we propose that 3D nuclear signatures from a DNA stain, DAPI, which could be incorporated in most experimental imaging, can be used for classifying cells in intact human kidney tissue. We developed an unsupervised approach that uses 3D tissue cytometry to generate a large training dataset of nuclei images (NephNuc), where each nucleus is associated with a cell type label. We then devised various supervised machine learning approaches for kidney cell classification and demonstrated that a deep learning approach outperforms classical machine learning or shape-based classifiers. Specifically, a custom 3D convolutional neural network (NephNet3D) trained on nuclei image volumes achieved a balanced accuracy of 80.26%. Importantly, integrating NephNet3D classification with tissue cytometry allowedin situvisualization of cell type classifications in kidney tissue. In conclusion, we present a tissue cytometry and deep learning approach forin situclassification of cell types in human kidney tissue using only a DNA stain. This methodology is generalizable to other tissues and has potential advantages on tissue economy and non-exhaustive classification of different cell types.
Modulation of A2aR Oligomerisation by Conformational State and PIP2Interactions Revealed by MD Simulations and Markov Models
Authors: Song Wanling , Duncan Anna L. , Sansom Mark S.P. 
Published: June 2020

AbstractG protein-coupled receptors (GPCRs) play key roles in cellular signalling. GPCRs are suggested to form dimers and higher order oligomers in response to activation. However, we do not fully understand GPCR activation at larger scales and in anin vivocontext. We have characterised oligomeric configurations of the adenosine 2a receptor (A2aR) by combining large-scale molecular dynamics simulations with Markov state models. Receptor activation results in enhanced oligomerisation, more diverse oligomer populations, and a more connected oligomerisation network. The active state conformation of the A2aR shifts protein-protein association interfaces to those involving intracellular loop ICL3 and transmembrane helix TM6. Binding of PIP2to A2aR stabilises protein-protein interactions via PIP2-mediated association interfaces. These results indicate that A2aR oligomerisation is responsive to the local membrane lipid environment. This in turn suggests a modulatory effect on A2aR whereby a given oligomerisation profile favours the dynamic formation of specific supra-molecular signalling complexes.
Noise-induced scaling in skull suture interdigitation
Authors: Naroda Yutoh , Endo Yoshie , Yoshimura Kenji , Ishii Hiroshi , Ei Shin-Ichiro , Miura Takashi 
Published: June 2020

AbstractSutures, the thin, soft tissue between skull bones, serve as the major craniofacial growth centers during postnatal development. In a newborn skull, the sutures are straight; however, as the skull develops, the sutures wind dynamically to form an interdigitation pattern. Moreover, the final winding pattern had been shown to have fractal characteristics. Although various molecules involved in suture development have been identified, the mechanism underlying the pattern formation remains unknown. In a previous study, we reproduced the formation of the interdigitation pattern in a mathematical model combining an interface equation and a convolution kernel. However, the generated pattern had a specific characteristic length, and the model was unable to produce a fractal structure with the model.In the present study, we focused on the anterior part of the sagittal suture and formulated a new mathematical model with time–space-dependent noise that was able to generate the fractal structure. We reduced our previous model to represent the linear dynamics of the centerline of the suture tissue and included a time–space-dependent noise term. We showed theoretically that the final pattern from the model follows a scaling law due to the scaling of the dispersion relation in the full model, which we confirmed numerically. Furthermore, we observed experimentally that stochastic fluctuation of the osteogenic signal exists in the developing skull, and found that actual suture patterns followed a scaling law similar to that of the theoretical prediction.Author summarySkull sutures (thin, undifferentiated tissue between bones) act as the growth centers for the skull. Sutures are straight at birth but later develop an interdigitated pattern that ultimately becomes a fractal structure. While our previous mathematical model of sutures generated a periodic pattern, the mechanism underlying the fractal structure formation remained to be elucidated. Here, we focused only on the anterior part of the sagittal suture and formulated a reduced model representing the initial linear phase of pattern formation with the addition of a time–space-dependent noise term. We showed analytically that the model generates patterns with a scaling law. This result was confirmed numerically and experimentally.
Adult survival is reduced when endogenous period deviates from 24h in a non-human primate (Microcebus murinus), depending on sex and season
Authors: Hozer Clara , Perret Martine , Pavard Samuel , Pifferi Fabien 
Published: June 2020

SummaryCircadian rhythms are ubiquitous attributes across living organisms and allow the coordination of internal biological functions with optimal phases of the environment, suggesting a significant adaptive advantage. The endogenous period calledtaulies close to 24h and is thought to be implicated in individuals’ fitness: according to the circadian resonance theory, fitness is reduced whentaugets far to 24h. In this study, we measured the endogenous period of 142 mouse lemurs (Microcebus. murinus), and analyzed how it affects their survival. We found different effects according to sex and season. No impact oftauon mortality was found in females. However, in males, the deviation oftaufrom 24h substantially increased mortality, particularly during the inactive season (winter). These results, comparable to other observations in mice or drosophila, show that captive gray mouse lemurs enjoy better fitness when their circadian period closely matches the environmental periodicity. In addition to their deep implications in health and aging research, these results raise further ecological and evolutionary issues regarding the relationships between fitness and circadian clock.
Genomes of Thaumarchaeota from deep sea sediments reveal specific adaptations of three independently evolved lineages
Authors: Kerou Melina , Ponce-Toledo Rafael I. , Zhao Rui , Abby Sophie S. , Hirai Miho , Nomaki Hidetaka , Takaki Yoshihiro , Nunoura Takuro , Jørgensen Steffen L. , Schleper Christa 
Published: June 2020

AbstractMarine sediments represent a vast habitat for complex microbiomes. Among these, ammonia oxidizing archaea (AOA) of the phylum Thaumarchaeota are one of the most common, yet little explored inhabitants, that seem extraordinarily well adapted to the harsh conditions of the subsurface biosphere. We present 11 metagenome-assembled genomes of the most abundant AOA clades from sediment cores obtained from the Atlantic Mid-Ocean ridge flanks and Pacific abyssal plains. Their phylogenomic placement reveals three independently evolved clades within the orderCa.Nitrosopumilales, of which no cultured representative is known yet. In addition to the gene sets for ammonia oxidation and carbon fixation known from other AOA, all genomes encode an extended capacity for the conversion of fermentation products that can be channeled into the central carbon metabolism, as well as uptake of amino acids probably for protein maintenance or as an ammonia source. Two lineages encode an additional (V-type) ATPase and a large repertoire of gene repair systems that may allow to overcome challenges of high hydrostatic pressure. We suggest that the adaptive radiation of AOA into marine sediments occurred more than once in evolution and resulted in three distinct lineages with particular adaptations to this extremely energy limiting and high-pressure environment.
Systems genetic analysis of binge-like eating in a C57BL/6J x DBA/2J-F2 cross
Authors: Yao Emily J. , Babbs Richard K. , Kelliher Julia C. , Luttik Kimberly P. , Damaj M. Imad , Mulligan Megan K. , Bryant Camron D. 
Published: June 2020

ABSTRACTObjectiveBinge eating is a heritable quantitative trait associated with eating disorders (ED) and refers to the rapid consumption of a large quantity of energy-dense food that is associated with loss of control, anxiety, and depression. Binge Eating Disorder is the most common ED in adults in the US; however, the genetic basis is unknown. We previously identified robust mouse inbred strain differences between C57BL/6J and DBA/2J in binge-like eating (BLE) of sweetened palatable food(PF) in an intermittent access, conditioned place preference paradigm.MethodsTo map the genetic basis of BLE, we phenotyped and genotyped 128 C57BL/6J x DBA/2J-F2 mice.ResultsWe identified a quantitative trait locus (QTL) on chromosome 13 influencing progressive changes in body weight across training days (LOD = 5.5; 26-39 cM). We also identified two sex-combined QTLs influencing PF intake on chromosome 5 (LOD = 5.6; 1.5-LOD interval = 21-28 cM) and 6 (LOD = 5.3; 1.5-LOD interval = 50-59 cM). Furthermore, sex-specific analyses revealed that the chromosome 6 locus was driven by males (1.5-LOD interval: 52-59 cM) and identified a female-selective QTL for BLE on chromosome 18 (LOD = 4.1; 1.5-LOD interval: 23-35 cM). Systems genetic analysis of the chromosome 6 locus for BLE using GeneNetwork legacy trait datasets from BXD recombinant inbred strains identifiedAdipor2andPlxnd1as two positional, functional, biological candidate genes.DiscussionWe identified genetic loci influencing BLE. Future studies will phenotype BXD recombinant inbred strains to fine map loci and support candidate gene nomination and validation.
Cell cycle checkpoints cooperate to suppress DNA and RNA associated molecular pattern recognition and anti-tumor immune responses
Authors: Chen Jie , Harding Shane M , Natesan Ramakrishnan , Tian Lei , Benci Joseph L , Li Weihua , Minn Andy J , Asangani Irfan A , Greenberg Roger A 
Published: June 2020

SummaryThe DNA dependent pattern recognition receptor, cGAS mediates communication between genotoxic stress and the immune system. Mitotic chromosome missegregation is an established stimulator of cGAS activity, however, it is unclear if progression through mitosis is required for cancer cell intrinsic activation of immune mediated anti-tumor responses. Moreover, it is unknown if disruption of cell cycle checkpoints can restore responses in cancer cells that are recalcitrant to DNA damage induced inflammation. Here we demonstrate that prolonged cell cycle arrest at the G2-mitosis boundary from either CDK1 inhibition or excessive DNA damage prevents inflammatory stimulated gene expression and immune mediated destruction of distal tumors. Remarkably, DNA damage induced inflammatory signaling is restored in a cGAS-and RIG-I-dependent manner upon concomitant disruption of p53 and the G2 checkpoint. These findings link aberrant cell progression and p53 loss to an expanded spectrum of damage associated molecular pattern recognition and have implications for the design of rational approaches to augment antitumor immune responses.
Infrared Nanospectroscopy Reveals the Molecular Interaction Fingerprint of an Aggregation Inhibitor with Single Aβ42 Oligomers
Authors: Ruggeri Francesco Simone , Habchi Johnny , Chia Sean , Vendruscolo Michele , Knowles Tuomas P. J. 
Published: June 2020

ABSTRACTVery significant efforts have been devoted in the last twenty years to developing compounds that can interfere with the aggregation pathways of proteins related to misfolding disorders, including Alzheimer’s and Parkinson’s diseases. However, no disease-modifying drug has become available for clinical use to date for these conditions. One of the main reasons for this failure is the incomplete knowledge of the molecular mechanisms underlying the process by which small molecules interact with protein aggregates and interfere with their aggregation pathways. Here, we leverage the single molecule level morphological and chemical sensitivity of infrared nanospectroscopy to provide the first direct measurement of the interaction between single Aβ42 oligomeric and fibrillar species and an aggregation inhibitor, bexarotene, originally an anticancer drug capable recently shown to be able to inhibit Aβ42 aggregation in animal models of Alzheimer’s disease. Our results demonstrate that the carbonyl group of this compound interacts with Aβ42 aggregates through a single hydrogen bond. These results establish infrared nanospectroscopy as powerful tool in structure-based drug discovery for protein misfolding diseases.
Membrane interactions accelerate the self-aggregation of huntingtin exon 1 fragments in a polyglutamine length-dependent manner
Authors: Marquette A. , Bechinger B. 
Published: June 2020

ABSTRACTThe accumulation of aggregated protein is a typical hallmark of many human neurodegenerative disorders including Huntington’s disease. Misfolding of the amyloidogenic proteins gives rise to self-assembled complexes and fibers. The huntingtin protein is characterized by a segment of consecutive glutamines, which when exceeding a certain number of residues results in the occurrence of the disease. Furthermore, it has also been demonstrated that the 17-residue amino-terminal domain of the protein (htt17), located upstream of this polyglutamine tract, strongly correlates with aggregate formation and pathology. Here we demonstrate that membrane interactions strongly accelerate the oligomerization and β-amyloid fibril formation of htt17-polyglutamine segments. By using a combination of biophysical approaches the kinetics of fibre formation has been quantitatively investigated and found to be strongly dependent to the presence of lipids, the length of the polyQ expansion and the polypeptide-to-lipid ratio. Finally, the implications for therapeutic approaches are discussed.Statement of significanceThe quantitative analysis of the aggregation kinetics of amino-terminal fragments of huntingtin demonstrate the importance of the 17-residue amino-terminal membrane anchor and a resulting dominant effect of membranes in promoting the aggregation of polyglutamines. Other parameters further modulating the association kinetics are the length of the polyglutamine stretch and the peptide concentration. The findings can have important impact on finding new therapies to treat Huntington’s and other polyglutamine related diseases.
Integration of viral transcriptome sequencing with structure and sequence motifs predicts novel regulatory elements in SARS-CoV-2
Authors: Cox Brian J. 
Published: June 2020

SummaryIn the last twenty years, three separate coronaviruses have left their typical animal hosts and became human pathogens. An area of research interest is coronavirus transcription regulation that uses an RNA-RNA mediated template-switching mechanism. It is not known how different transcriptional stoichiometries of each viral gene are generated. Analysis of SARS-CoV-2 RNA sequencing data from whole RNA transcriptomes identified TRS dependent and independent transcripts. Integration of transcripts and 5’-UTR sequence motifs identified that the pentaloop and the stem-loop 3 were also located upstream of spliced genes. TRS independent transcripts were detected as likely non-polyadenylated. Additionally, a novel conserved sequence motif was discovered at either end of the TRS independent splice junctions. While similar both SARS viruses generated similar TRS independent transcripts they were more abundant in SARS-CoV-2. TRS independent gene regulation requires investigation to determine its relationship to viral pathogenicity.
How does the strength of selection influence genetic correlations ?
Authors: Chantepie Stéphane , Chevin Luis-Miguel 
Published: June 2020

AbstractGenetic correlations between traits can strongly impact evolutionary responses to selection, and may thus impose constraints on adaptation. Theoretical and empirical work has made it clear that, without strong linkage, genetic correlations at evolutionary equilibrium result from an interplay of correlated pleiotropic effects of mutations, and correlational selection favoring combinations of trait values. However, it is not entirely clear how the strength of stabilizing selection influences this compromise between mutation and selection effects on genetic correlations. Here, we show that the answer to this question crucially depends on the intensity of genetic drift. In large, effectively infinite populations, genetic correlations are unaffected by the strength of selection, regardless of whether the genetic architecture involves common small-effect mutations (Gaussian regime), or rare large-effect mutations (House-of-Cards regime). In contrast in finite populations, the strength of selection does affect genetic correlations, by shifting the balance from drift-dominated to selection-dominated evolutionary dynamics. The transition between these domains depends on mutation parameters to some extent, but with a similar dependence of genetic correlation on the strength of selection. Our results are particularly relevant for understanding how senescence shapes patterns of genetic correlations across ages, and genetic constraints on adaptation during colonization of novel habitats.
Single-axon level automatic segmentation and feature extraction from immuhistochemical images of peripheral nerves
Authors: Tóth Viktor , Jayaprakash Naveen , Abbas Adam , Khan Ariba , Zanos Stavros , Zanos Theodoros P. 
Published: June 2020

AbstractQuantitative descriptions of the morphology and structure of peripheral nerves is central in the development of bioelectronic devices interfacing the nerves. While histological procedures and microscopy techniques yield high-resolution detailed images of individual axons, automated methods to extract relevant information at the single-axon level are not widely available. We implemented a segmentation algorithm that allows for subsequent feature extraction in immunohistochemistry (IHC) images of peripheral nerves at the single fiber scale. These features include short and long cross-sectional diameters, area, perimeter, thickness of surrounding myelin and polar coordinates of single axons within a nerve or nerve fascicle. We evaluated the performance of our algorithm using manually annotated IHC images of 27 fascicles of the swine cervical vagus; the accuracy of single-axon detection was 82%, and of the classification of fiber myelination was 89%.