bluuebunny/crossref_metadata_2025_split huggingface dataset:
The evolution of red blood cell shape in a continental radiation of fishes
Authors: Martins Brenda Oliveira , Franco-Belussi Lilian , Siqueira Mayara Schueroff , Fernandes Carlos E. , Provete Diogo B. 
Published: April 2020

AbstractThe size and shape of Red Blood Cells (RBC) can provide key information on life history strategies in vertebrates. However, little is known about how RBC shape evolved in response to environmental factors and the role of phylogenetic relationship. Here, we analyzed RBC morphometrics in a continental radiation of fishes testing the hypothesis that phylogenetic relationship determines species occupation of morphospace. We collected blood samples of five specimens of 15 freshwater fish species from six orders and used basic stereological methods to measure cell and nucleus area, perimeter, and diameter, cell and nucleus volume, nucleus:cytoplasm ratio, and shape factor of 50 cells per specimen. Then, we conducted a phylogenetic Principal Components Analysis using a dated phylogeny and built a phylomorphospace. To test if the phylogenetic relationship predicted the phenotypic similarity of species, we calculated multivariate phylogenetic signal. We also estimated the evolution rate of RBC shape for each node and tip using ridge regression. Finally, we tested if the position in the water column influenced RBC shape using a phylogenetic GLS. RBC shape seems to have evolved in a non-stationary way because the distribution pattern of species in the phylomorphospace is independent of the phylogeny. Accordingly, the rate of evolution for shape was highly heterogeneous, with an increase in the genusPygocentrus. Water column position does not influence RBC shape. In conclusion, RBC shape seem to have evolved in response to multiple selective pressures independent of life history characters.
High-affinity agonist binding to C5aR results from a cooperative two-site binding mechanism
Authors: Dumitru Andra C. , Krishna Deepak R. N. V. , Liu Heng , Koehler Melanie , Zhang Cheng , Fan Hao , Alsteens David 
Published: April 2020

AbstractA current challenge in the field of life sciences is to decipher, in their native environment, the functional activation of cell surface receptors upon binding of complex ligands. Lack of suitable nanoscopic methods has hampered our ability to meet this challenge in an experimental manner. Here, we use for the first time the interplay between atomic force microscopy, steered molecular dynamics and functional assays to elucidate the complex ligand-binding mechanism of C5a with the human G protein-coupled C5a receptor (C5aR). We have identified two independent binding sites acting in concert where the N-terminal C5aR serves as kinetic trap and the transmembrane domain as functional site. Our results corroborate the two-site binding model and clearly identify a cooperative effect between two binding sites within the C5aR. We anticipate that our methodology could be used for development and design of new therapeutic agents to negatively modulate C5aR activity.
Cells and gene expression programs in the adult human heart
Authors: Litviňuková Monika , Talavera-López Carlos , Maatz Henrike , Reichart Daniel , Worth Catherine L. , Lindberg Eric L. , Kanda Masatoshi , Polanski Krzysztof , Fasouli Eirini S. , Samari Sara , Roberts Kenny , Tuck Liz , Heinig Matthias , DeLaughter Daniel M. , McDonough Barbara , Wakimoto Hiroko , Gorham Joshua M. , Nadelmann Emily R. , Mahbubani Krishnaa T. , Saeb-Parsy Kourosh , Patone Giannino , Boyle Joseph J. , Zhang Hongbo , Zhang Hao , Viveiros Anissa , Oudit Gavin Y. , Bayraktar Omer , Seidman J. G. , Seidman Christine , Noseda Michela , Hübner Norbert , Teichmann Sarah A. 
Published: April 2020

SummaryCardiovascular disease is the leading cause of death worldwide. Advanced insights into disease mechanisms and strategies to improve therapeutic opportunities require deeper understanding of the molecular processes of the normal heart. Knowledge of the full repertoire of cardiac cells and their gene expression profiles is a fundamental first step in this endeavor. Here, using large-scale single cell and nuclei transcriptomic profiling together with state-of-the-art analytical techniques, we characterise the adult human heart cellular landscape covering six anatomical cardiac regions (left and right atria and ventricles, apex and interventricular septum). Our results highlight the cellular heterogeneity of cardiomyocytes, pericytes and fibroblasts, revealing distinct subsets in the atria and ventricles indicative of diverse developmental origins and specialized properties. Further we define the complexity of the cardiac vascular network which includes clusters of arterial, capillary, venous, lymphatic endothelial cells and an atrial-enriched population. By comparing cardiac cells to skeletal muscle and kidney, we identify cardiac tissue resident macrophage subsets with transcriptional signatures indicative of both inflammatory and reparative phenotypes. Further, inference of cell-cell interactions highlight a macrophage-fibroblast-cardiomyocyte network that differs between atria and ventricles, and compared to skeletal muscle. We expect this reference human cardiac cell atlas to advance mechanistic studies of heart homeostasis and disease.
α-Synuclein-112 impairs synaptic vesicle recycling consistent with its enhanced membrane binding properties
Authors: Soll Lindsey G. , Eisen Julia N. , Vargas Karina J. , Medeiros Audrey T. , Hammar Katherine M. , Morgan Jennifer R. 
Published: April 2020

ABSTRACTSynucleinopathies are neurological disorders associated with α-synuclein overexpression and aggregation. While it is well established that overexpression of wild type α-synuclein (α-syn-140) leads to cellular toxicity and neurodegeneration, much less is known about other naturally occurring α-synuclein splice isoforms. In this study we provide the first detailed examination of the synaptic effects caused by one of these splice isoforms, α-synuclein-112 (α-syn-112). α-Syn-112 is produced by an in-frame excision of exon 5, resulting in deletion of amino acids 103-130 in the C-terminal region. α-Syn-112 is upregulated in the substantia nigra, frontal cortex, and cerebellum of parkinsonian brains and is correlated with susceptibility to sporadic Parkinson’s disease (PD), dementia with Lewy bodies (DLB) and multiple systems atrophy (MSA). We report here that α-syn-112 binds strongly to anionic phospholipids when presented in highly-curved liposomes, similar to α-syn-140. However, α-syn-112 bound significantly stronger to all phospholipids tested, including the phosphoinositides. α-Syn-112 also dimerized and trimerized on isolated synaptic membranes, while α-syn-140 remained largely monomeric. When introduced acutely to lamprey synapses, α-syn-112 robustly inhibited synaptic vesicle recycling. Interestingly, α-syn-112 produced effects on the plasma membrane and clathrin-mediated synaptic vesicle endocytosis that were phenotypically intermediate between those caused by monomeric and dimeric α-syn-140. These findings indicate that α-syn-112 exhibits enhanced phospholipid binding and oligomerizationin vitroand consequently interferes with synaptic vesicle recyclingin vivoin ways that are consistent with its biochemical properties. This study provides additional evidence suggesting that impaired vesicle endocytosis is a cellular target of excess α-synuclein and advances our understanding of potential mechanisms underlying disease pathogenesis in the synucleinopathies.
Accumulation of dead cells from contact killing facilitates coexistence in bacterial biofilms
Authors: Steinbach Gabi , Crisan Cristian , Ng Siu Lung , Hammer Brian , Yunker Peter 
Published: April 2020

AbstractBacterial communities govern their composition using a wide variety of social interactions, some of which are antagonistic. Many antagonistic mechanisms, such as the Type VI Secretion System (T6SS), require killer cells to directly contact target cells. The T6SS is hypothesized to be a highly potent weapon, capable of facilitating the invasion and defense of bacterial populations. However, we find that the efficacy of the T6SS is severely limited by the material consequences of cell death. Through experiments withVibrio choleraestrains that kill via the T6SS, we show that dead cell debris quickly accumulates at the interface that forms between competing strains, preventing contact and thus preventing killing. While previous experiments have shown that T6SS killing can reduce a population of target cells by as much as one-million-fold, we find that as a result of the formation of dead cell debris barriers, the impact of T6SS killing depends sensitively on the initial concentrations of killer and target cells. Therefore, while the T6SS provides defense against contacting competitors on a single cell level, it is incapable of facilitating invasion or the elimination of competitors on a community level.
Size-Based Characterization of Freshwater Dissolved Organic Matter finds Similarities within a Water Body Type across Different Canadian Ecozones
Authors: Aukes Pieter J. K. , Schiff Sherry L. , Venkiteswaran Jason J. , Elgood Richard J. , Spoelstra John 
Published: April 2020

ABSTRACTDissolved Organic Matter (DOM) represents a mixture of organic molecules that vary due to different source materials and degree of processing. Characterizing how DOM composition evolves along the aquatic continuum can be difficult. Using a size-exclusion chromatography technique (LC-OCD), we assessed the variability in DOM composition from both surface and groundwaters across a number of Canadian ecozones (mean annual temperature spanning −10 to +6 C). A wide range in DOM concentration was found from 0.2 to 120 mg C/L. Proportions of different size-based groupings across ecozones were variable, yet similarities between specific water-body types, regardless of location, suggest commonality in the processes dictating DOM composition. A PCA identified 70% of the variation in LC-OCD derived DOM compositions could be explained by the water-body type. We find that DOM composition within a specific water-body type is similar regardless of the differences in climate or surrounding vegetation where the sample originated from.HighlightsSize-exclusion chromatography (using LC-OCD) is a fast and effective tool to quantify differences in DOM composition across different environmentsProportions of biopolymers and low molecular weight fractions can distinguish between surface and groundwater DOMSimilar water-body types have comparable DOM size compositions across ecozones that range in annual air temperatures from –10 to 6ºC
A novelAxin2knock-in mouse model for visualization and lineage tracing of WNT/CTNNB1 responsive cells
Authors: van de Moosdijk Anoeska Agatha Alida , van de Grift Yorick Bernardus Cornelis , de Man Saskia Madelon Ada , Zeeman Amber Lisanne , van Amerongen Renée 
Published: April 2020

AbstractWnt signal transduction controls tissue morphogenesis, maintenance and regeneration in all multicellular animals. In mammals, the WNT/CTNNB1 (Wnt/β-catenin) pathway controls cell proliferation and cell fate decisions before and after birth. It plays a critical role at multiple stages of embryonic development, but also governs stem cell maintenance and homeostasis in adult tissues. However, it remains challenging to monitor endogenous WNT/CTNNB1 signaling dynamicsin vivo. Here we report the generation and characterization of a new knock-in mouse strain that doubles as a fluorescent reporter and lineage tracing driver for WNT/CTNNB1 responsive cells. We introduced a multi-cistronic targeting cassette at the 3’ end of the universal WNT/CTNNB1 target geneAxin2. The resulting knock-in allele expresses a bright fluorescent reporter (3xNLS-SGFP2) and a doxycycline-inducible driver for lineage tracing (rtTA3). We show that theAxin2P2A-rtTA3-T2A-3xNLS-SGFP2strain labels WNT/CTNNB1 cells at multiple anatomical sites during different stages of embryonic and postnatal development. It faithfully reports the subtle and dynamic changes in physiological WNT/CTNNB1 signaling activity that occurin vivo. We expect this mouse strain to be a useful resource for biologists who want to track and trace the location and developmental fate of WNT/CTNNB1 responsive stem cells in different contexts.Abstract Figure
Modular genetic control of social status in a cichlid fish
Authors: Alward Beau A. , Laud Vibhav , Skalnik Christopher J. , York Ryan A. , Juntti Scott , Fernald Russell D. 
Published: April 2020

AbstractSocial hierarchies are ubiquitous in social species and profoundly influence physiology and behavior. Androgens like testosterone have been strongly linked to social status, yet the molecular mechanisms regulating social status are not known. The African cichlid fishAstatotilapia burtoniis a powerful model species for elucidating the role of androgens in social status given their rich social hierarchy and genetic tractability. DominantA. burtonimales possess large testes, bright coloration, and perform aggressive and reproductive behaviors while non-dominant males do not. Social status inA. burtoniis in flux, however, as males alter their status depending on the social environment. Due to a teleost-specific whole-genome duplication,A. burtonipossess two androgen receptor (AR) paralogs,ARαandARβ, providing a unique opportunity to disentangle the role of gene duplication in the evolution of social systems. Here, we used CRISPR/Cas9 gene editing to generate AR mutantA. burtoniand performed a suite of experiments to interrogate the mechanistic basis of social dominance. We find thatARβ, but notARα, is required for testes growth and bright coloration, whileARα, but notARβ, is required for the performance of reproductive behavior and aggressive displays. Both receptors are required to reduce flees from females and either AR is sufficient for attacking males. Thus, social status inA. burtoniis inordinately dissociable and under the modular control of two AR paralogs. This type of non-redundancy may be important in facilitating social plasticity inA. burtoniand other species whose social status relies on social experience.Significance StatementSocial rank along a hierarchy determines physiological state and behavioral performance. A ubiquitous feature of social hierarchies is the communication of rank through non-physical signaling systems (e.g., coloration) and aggression, traits that correlate with the reproductive status of an individual. Despite the links identified between social status, physiology, and behavior, the molecular basis of social status is not known. Here, we genetically dissect social status in the African cichlid fishAstatotilapia burtoniusing CRISPR/Cas9 gene editing. We show that two distinct androgen receptor (AR) genes control social status in a highly modular manner. This type of coordination of social status may be fundamental across species that rely on social information to optimally guide physiology and behavior.
Expansion of the circadian transcriptome inBrassica rapaand genome-wide diversification of paralog expression patterns
Authors: Greenham Kathleen , Sartor Ryan C. , Zorich Stevan , Lou Ping , Mockler Todd C. , McClung C. Robertson 
Published: April 2020

AbstractAn important challenge of crop improvement strategies is assigning function to paralogs in polyploid crops. Gene expression is one method for determining the activity of paralogs; however, the majority of transcript abundance data represents a static point that does not consider the spatial and temporal dynamics of the transcriptome. Studies in Arabidopsis have estimated up to 90% of the transcriptome to be under diel or circadian control depending on the condition. As a result, time of day effects on the transcriptome have major implications on how we characterize gene activity. In this study, we aimed to resolve the circadian transcriptome in the polyploid cropBrassica rapaand explore the fate of multicopy orthologs of Arabidopsis circadian regulated genes. We performed a high-resolution time course study with 2 h sampling density to capture the genes under circadian control. Strikingly, more than two-thirds of expressed genes exhibited rhythmicity indicative of circadian regulation. To compare the expression patterns of paralogous genes, we developed a program in R called DiPALM (Differential Pattern Analysis by Linear Models) that analyzes time course data to identify transcripts with significant pattern differences. Using DiPALM, we identified genome-wide divergence of expression patterns among retained paralogs. Cross-comparison with a previously generated diel drought experiment inB. raparevealed evidence for differential drought response for these diverging paralog pairs. Using gene regulatory network models we compared transcription factor targets betweenB. rapaand Arabidopsis circadian networks to reveal additional evidence for divergence in expression betweenB. rapaparalogs that may be driven in part by variation in conserved non coding sequences. These findings provide new insight into the rapid expansion and divergence of the transcriptional network in a polyploid crop and offer a new method for assessing paralog activity at the transcript level.SignificanceThe circadian regulation of the transcriptome leads to time of day changes in gene expression that coordinates environmental conditions with physiological responses.Brassica rapa, a morphologically diverse crop species, has undergone whole genome triplication since diverging from Arabidopsis resulting in an expansion of gene copy number. To examine how this expansion has influenced the circadian transcriptome we developed a new method for comparing gene expression patterns. This method facilitated the discovery of genome-wide expansion of expression patterns for genes present in multiple copies and divergence in temporal abiotic stress response. We find support for conserved sequences outside the gene body contributing to these expression pattern differences and ultimately generating new connections in the gene regulatory network.
Temporal Analysis of T-Cell Receptor-Imposed Forces via Quantitative Single Molecule FRET Measurements
Authors: Göhring Janett , Kellner Florian , Schrangl Lukas , Platzer René , Klotzsch Enrico , Stockinger Hannes , Huppa Johannes B. , Schütz Gerhard J. 
Published: April 2020

ABSTRACTMechanical forces acting on ligand-engaged T-cell receptors (TCRs) have previously been implicated in T-cell antigen recognition, yet their magnitude, spread, and temporal behavior are still poorly defined. We here report a FRET-based sensor equipped with a TCR-reactive single chain antibody fragment, which was tethered to planar supported lipid bilayers (SLBs) and informs most directly on the magnitude and kinetics of TCR-imposed forces at the single molecule level. When confronting T-cells with gel-phase SLBs we observed both prior and upon T-cell activation a single, well-resolvable force-peak of approximately 5 pN and force loading rates on the TCR of 1.5 pN per second. When facing fluid SLBs instead, T-cells still exerted tensile forces yet with threefold reduced magnitude and only prior to but not upon activation. Our findings do not only provide first truly molecular information on TCR-imposed forces within the immunological synapse, they also recalibrate their significance in antigen recognition.
A Molecular Mechanism for Turning off IRE1α Signaling During Endoplasmic Reticulum Stress
Authors: Li Xia , Sun Sha , Appathurai Suhila , Sundaram Arunkumar , Plumb Rachel , Mariappan Malaiyalam 
Published: April 2020

SummaryMisfolded proteins in the endoplasmic reticulum (ER) activate IRE1α endoribonuclease in mammalian cells, which mediates XBP1 mRNA splicing to produce an active transcription factor. This promotes the expression of specific genes to alleviate ER stress and thereby attenuating IRE1α. Although sustained activation of IRE1α is linked to human diseases, it is not clear how IRE1α is attenuated during ER stress. Here, we identify that Sec63 is a subunit of the previously identified IRE1α/Sec61 translocon complex. We find that Sec63 recruits and activates BiP ATPase through its luminal J-domain to bind onto IRE1α. This leads to inhibition of higher-order oligomerization and attenuation of IRE1α RNase activity during prolonged ER stress. In Sec63 deficient cells, IRE1α remains activated for a long time despite the presence of excess BiP in the ER. Thus, our data suggest that the Sec61 translocon bridges IRE1α with Sec63/BiP to regulate the dynamics of IRE1α signaling in cells.
Focused ultrasound stimulates ER localized mechanosensitive PANNEXIN-1 to mediate intracellular calcium release in invasive cancer cells
Authors: Lee Nan Sook , Yoon Chi Woo , Wang Qing , Moon Sunho , Koo Kweon Mo , Jung Hayong , Chen Ruimin , Jiang Laiming , Lu Gengxi , Fernandez Antony , Chow Robert H. , Weitz Andrew C. , Salvaterra Paul M. , Pinaud Fabien , Shung K. Kirk 
Published: April 2020

ABSTRACTFocused ultrasound (FUS) is a rapidly developing stimulus technology with the potential to uncover novel mechanosensory dependent cellular processes. Since it is noninvasive, it holds great promise for future therapeutic applications in patients used either alone or as a complement to boost existing treatments. For example, FUS stimulation causes invasive but not noninvasive cancer cell lines to exhibit marked activation of calcium signaling pathways. Here, we identify the membrane channel PANNEXIN1 (PANX1) as a mediator for activation of calcium signaling in invasive cancer cells. Knockdown of PANX1 decreases calcium signaling in invasive cells, while PANX1 overexpression enhances calcium elevations in non-invasive cancer cells. We demonstrate that FUS may directly stimulate mechanosensory PANX1 localized in endoplasmic reticulum to evoke calcium release from internal stores. This process does not depend on mechanosensory stimulus transduction through an intact cytoskeleton and does not depend on plasma membrane localized PANX1. Plasma membrane localized PANX1 however plays a different role in mediating the spread of intercellular calcium waves via ATP release. Additionally, we show that FUS stimulation evokes cytokine/chemokine release from invasive cancer cells, suggesting that FUS could be an important new adjuvant treatment to improve cancer immunotherapy.