bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exploring cell surface-nanopillar interactions with 3D super-resolution microscopy
Authors: Roy Anish R. , Zhang Wei , Jahed Zeinab , Tsai Ching-Ting , Cui Bianxiao , Moerner W.E. 
Published: June 2021

AbstractPlasma membrane topography has been shown to strongly influence the behavior of many cellular processes such as clathrin-mediated endocytosis, actin rearrangements, and others. Recent studies have used 3D nanostructures such as nanopillars to imprint well-defined membrane curvatures (the “nano-bio interface”). In these studies, proteins and their interactions were probed by 2D fluorescence microscopy. However, the low resolution and limited axial detail of such methods are not optimal to determine the relative spatial position and distribution of proteins along a 100 nm-diameter object, which is below the optical diffraction limit. Here, we introduce a general method to explore the nanoscale distribution of proteins at the nano-bio interface with 10-20 nm precision using 3D single-molecule super-resolution (SR) localization microscopy. This is achieved by combining a silicone oil immersion objective and 3D double-helix point-spread function microscopy. We carefully optimize the objective to minimize spherical aberrations between quartz nanopillars and the cell. To validate the 3D SR method, we imaged the 3D shape of surface-labeled nanopillars and compared the results with electron microscopy measurements. Turning to transmembrane-anchored labels in cells, the high quality 3D SR reconstructions reveal the membrane tightly wrapping around the nanopillars. Interestingly, the cytoplasmic protein AP-2 involved in clathrin-mediated endocytosis accumulates along the nanopillar above a specific threshold of 1/R membrane curvature. Finally, we observe that AP-2 and actin preferentially accumulate at positive Gaussian curvature near the pillar caps. Our results establish a general method to investigate the nanoscale distribution of proteins at the nano-bio interface using 3D SR microscopy.
A novel Toxoplasma IMC sutures-associated protein regulates suture protein targeting and colocalizes with membrane trafficking machinery
Authors: Chern Jessica H. , Moon Andy S. , Chen Allan L. , Sha Jihui , Wohlschlegel James A. , Bradley Peter J. 
Published: June 2021

AbstractThe cytoskeleton ofToxoplasma gondiiis composed of the inner membrane complex (IMC) and an array of underlying microtubules that provide support at the periphery of the parasite. Specific subregions of the IMC carry out distinct roles in replication, motility, and host cell invasion. Building on our previousin vivobiotinylation (BioID) experiments of the IMC, we identify here a novel protein that localizes to discrete punctae that are embedded in the parasite’s cytoskeleton along the IMC sutures. Gene knockout analysis shows that loss of the protein results in defects in cytoskeletal suture protein targeting, cytoskeletal integrity, parasite morphology, and host cell invasion. We then use deletion analyses to identify a domain in the N-terminus of the protein that is critical for both localization and function. Finally, we use the protein as bait forin vivobiotinylation which identifies several other proteins that colocalize in similar spot-like patterns. These putative interactors include several proteins that are implicated in membrane trafficking and are also associated with the cytoskeleton. Together, this data reveals an unexpected link between the IMC sutures and membrane trafficking elements of the parasite and suggests that the sutures punctae are likely a portal for trafficking cargo across the IMC.
A Multiparametric Activity Profiling Platform for Neuron Disease Phenotyping and Drug Screening
Authors: Boivin Bruno , Roet Kasper C.D. , Huang Xuan , Karhohs Kyle W. , Rohban Mohammad H. , Sandoe Jack , Wiskow Ole , Maeda Rie , Grantham Alyssa , Dornon Mary K. , Shao Jenny , Frost Devlin , Baker Dylan , Eggan Kevin , Carpenter Anne E. , Woolf Clifford J. 
Published: June 2021

ABSTRACTPatient stem cell-derived models enable imaging of complex disease phenotypes and the development of scalable drug discovery platforms. Current preclinical methods for assessing cellular activity do not, however, capture the full intricacies of disease-induced disturbances, and instead typically focus on a single parameter, which impairs both the understanding of disease and the discovery of effective therapeutics. Here, we describe a cloud-based image processing and analysis platform that captures the intricate activity profile revealed by GCaMP fluorescent recordings of intracellular calcium changes and enables discovery of molecules that correct 153 parameters that define the amyotrophic lateral sclerosis motor neuron disease phenotype. In a high-throughput screen we identified compounds that revert the multiparametric disease profile to that found in healthy cells, a novel and robust measure of therapeutic potential quite distinct from unidimensional screening. This platform can guide the development of therapeutics that counteract the multifaceted pathological features of diseased cellular activity.
Multiple modes of regulation control dynamic transcription patterns during the mitosis-G1 transition
Authors: Wojenski Luke A. , Wainman Lauren M. , Villafano Geno , Kuhlberg Chris , Nanda Pariksheet , Core Leighton 
Published: June 2021

AbstractFollowing cell division, genomes must reactivate gene expression patterns that reflect the identity of the cell. Here, we use PRO-seq to examine the mechanisms that reestablish transcription patterns after mitosis. We uncover regulation of the transcription cycle at multiple steps including initiation, promoter-proximal pause positioning and escape, poly-A site cleavage and termination during the mitotic-G1 transition. During mitosis, RNA polymerase activity is retained at initiation sites, albeit shifted in position relative to non-mitotic cells. This activity is strongly linked to maintenance of local chromatin architecture during mitosis and is more predictive of rapid gene reactivation than histone modifications previously associated with bookmarking. These molecular bookmarks, combined with sequence-specific transcription factors, direct expression of select cell growth and cell specific genes during mitosis followed by reactivation of functional gene groups with distinct kinetics after mitosis. This study details how dynamic regulation of transcription at multiple steps contributes to gene expression during the cell cycle.
The noncoding RNA PRANCR regulates splicing of Fibronectin-1 to control keratinocyte proliferation and migration
Authors: Otten Auke B.C. , Amarbayar Oyumergen , Cai Pengfei , Cheng Binbin , Qu Kun , Sun Bryan K. 
Published: June 2021

AbstractMost human genes undergo alternative splicing (AS), but the regulation and functional consequences of most splicing events remain unknown. Long noncoding RNAs (lncRNAs) have recently been discovered to have novel roles in the regulation of AS. Here we investigate whether PRANCR, a lncRNA recently identified to be essential for epidermis formation, functions by controlling AS of cell fate genes. Using transcriptome-wide analysis, we identified 238 exonic splicing events regulated by PRANCR. Among these is alternative splicing of an exon containing the extra domain A (EDA) in the gene fibronectin-1 (FN1). Expression of the FN1-EDA+ isoform is enriched in proliferating keratinocytes. We find that PRANCR regulates EDA inclusion by controlling expression of the serine/arginine-rich splicing factors (SRSFs) 1 and 7. Depletion of PRANCR or FN1-EDA resulted in decreased proliferation, increased CDKN1A/p21, and inhibition of keratinocyte migration. We find that these cellular phenotypes can be explained by reduced phosphorylation of focal adhesion kinase (FAK). Collectively, these results identify a lncRNA regulating skin function through alternative splicing of a cell fate gene.
Molecular evidence for sweeping discontinuity between peracarid (Crustacea) fauna of Macaronesian islands and nearby continental coasts: over fifty candidate endemic species
Authors: Vieira Pedro E , Desiderato Andrea , Azevedo Sofia L , Esquete Patricia , Costa Filipe O , Queiroga Henrique 
Published: June 2021

AbstractOceanic islands are recognized evolutionary hotspots for terrestrial organisms, but little is known about their impact on marine organisms’ evolution and biogeography. The volcanic archipelagos of Macaronesia occupy a vast and complex region which is particularly suitable to investigate marine island biogeography.In this study, we used mitochondrial DNA sequences to investigate the genetic diferentiation between the populations from Webbnesia (i.e. Madeira, Selvagens and Canaries) and adjacent coasts, of 23 intertidal peracarid species. All species had unexpectedly high intraspecific genetic distances, reaching more than 20% in some cases. Between 79 and 95 Molecular Operational Taxonomic Units (MOTUs) were found in these species. Webbnesia populations displayed an impressive genetic diversity and high endemicity, with 83% of the MOTUs being private to these islands, particularly La Palma and Madeira. Network analyses suggested higher similarity between Webbnesia and Azores than with adjacent continental coasts.These results reveal an unanticipated and sweeping biogeographic discontinuity of peracaridean fauna between Webbnesia and the Iberian Peninsula, raising suspicion about the possible occurrence of identical patterns in other groups of marine invertebrates in the region. We emphasize the unique genetic heritage hosted by these islands, underlining the need to consider the fine scale endemicity in marine conservation efforts.
Structurally conserved domains between flavivirus and alphavirus fusion glycoproteins contribute to replication in mammals and infectious virion production
Authors: Rangel Margarita V. , Catanzaro Nicholas , Thannickal Sara A. , Crotty Kelly A. , Noval Maria G. , Johnson Katherine E.E. , Ghedin Elodie , Lazear Helen M. , Stapleford Kenneth A. 
Published: June 2021

AbstractAlphaviruses and flaviviruses have class II fusion glycoproteins that are essential for virion assembly and infectivity. Importantly, the tip of domain II is structurally conserved between the alphavirus and flavivirus fusion proteins, yet whether these structural similarities between virus families translate to functional similarities is unclear. Using in vivo evolution of Zika virus (ZIKV), we identified several novel emerging variants including an envelope glycoprotein variant in β-strand c (V114M) of domain II. We have previously shown that the analogous β-strand c and the ij loop, located in the tip of domain II of the alphavirus E1 glycoprotein, are important for infectivity. This led us to hypothesize that flavivirus E β-strand c also contributes to flavivirus infection. We generated this ZIKV glycoprotein variant and found that while it had little impact on infection in mosquitoes, it reduced replication in human cells and mice, and increased virus sensitivity to ammonium chloride, as seen for alphaviruses. In light of these results and given our alphavirus ij loop studies, we mutated a conserved alanine at the tip of the flavivirus ij loop to valine to test its effect on ZIKV infectivity. Interestingly, this mutation inhibited infectious virion production of ZIKV and yellow fever virus, but not West Nile virus. Together, these studies show that structurally analogous residues in the alphavirus and flavivirus class II fusion proteins contribute to virus infection in vivo and highlight these shared domains as targets for broad-spectrum arbovirus therapies.Author SummaryArboviruses are a significant global public health threat, yet there are no antivirals targeting these viruses. This problem is in part due to our lack of knowledge on the molecular mechanisms involved in the arbovirus life cycle. In particular, virus entry and assembly are essential processes in the virus life cycle and steps that can be targeted for the development of antiviral therapies. Therefore, understanding common, fundamental mechanisms used by different arboviruses for entry and assembly is essential. In this study, we show that flavivirus and alphavirus residues located in structurally conserved and analogous regions of the class II fusion proteins contribute to common mechanisms of entry, dissemination, and infectious virion production. These studies highlight how class II fusion proteins function and provide novel targets for development of antivirals.
High CXCL6 drives matrix expression and correlate with markers of poor outcome in IPF
Authors: Bahudhanapati Harinath , Tan Jiangning , Apel Rosa Marie , Seeliger Benjamin , Li Xiaoyun , Chen Ting-Yun , Sullivan Daniel , Sembrat John , Rojas Mauricio , Tabib Tracy , Valenzi Eleanor , Lafyatis Robert , Jawale Chetan , Biswas Partha , Tedrow John , Adams Taylor , Kaminski Naftali , Wuyts Wim A , McDyer John F , Alder Jonathan K , Zhang Yingze , Nouraie Mehdi , Prasse Antje , Kass Daniel J 
Published: June 2021

AbstractSignaling via G protein-coupled receptors (GPCRs) can modulate levels of cyclic adenosine monophosphate (cAMP) and shape the functions of fibroblasts in idiopathic pulmonary fibrosis (IPF). We have identified Chemokine (C-X-C) Motif Ligand 6 (CXCL6) as a potential pro-fibrotic GPCR ligand. We tested the function of CXCL6 inex vivohuman donor and fibrotic lung fibroblasts and in an animal model of pulmonary fibrosis. We also measured levels of CXCL6 in the blood and bronchoalveolar lavage (BAL) of patients with IPF. CXCL6 decreased cAMP levels in a dose-dependent manner in Donor and IPF Fibroblasts. CXCL6 mRNA and protein were localized to epithelial cells. Administration of mCXCL5 (LIX, murine CXCL6 homologue) to mice increased collagen synthesis with and without bleomycin. CXCL6 increased Collagen I and α-SMA levels in Donor and IPF Fibroblasts. Silencing of CXCR1/2 as well as Reparixin, a CXCR1/2 inhibitor, blocked effects of CXCL6. Treprostinil blocked effects of CXCL6 only on levels of α-SMA but not on Collagen I. CXCL6 levels in the BAL of two separate cohorts of patients with IPF was associated with poor survival. We conclude that high CXCL6 drives fibroblast function and correlates with poor outcomes in IPF.
Norepinephrine Potentiates and Serotonin Depresses Visual Cortical Responses by Transforming Eligibility Traces
Authors: Hong Su Z. , Mesik Lukas , Grossman Cooper D. , Cohen Jeremiah Y. , Lee Boram , Lee Hey-Kyoung , Hell Johannes W. , Kirkwood Alfredo 
Published: June 2021

AbstractReinforcement allows organisms to learn which stimuli predict subsequent biological relevance. Hebbian mechanisms of synaptic plasticity are insufficient to account for reinforced learning because neuromodulators signaling biological relevance are delayed with respect to the neural activity associated with the stimulus. A theoretical solution is the concept of eligibility traces (eTraces), silent synaptic processes elicited by activity which upon arrival of a neuromodulator are converted into a lasting change in synaptic strength. Previously we demonstrated in visual cortical slices the Hebbian induction of eTraces and their conversion into LTP and LTD by the retroactive action of norepinephrine and serotonin Here we show in vivo in V1 that the induction of eTraces and their conversion to LTP/D by norepinephrine and serotonin respectively potentiates and depresses visual responses. We also show that the integrity of this process is crucial for ocular dominance plasticity, a canonical model of experience-dependent plasticity.
Engineering 3D Vascularized Adipose Tissue Construct using a Decellularized Lung Matrix
Authors: DeBari Megan K. , Ng Wai Hoe , Griffin Mallory D. , Kokai Lauren E. , Marra Kacey G. , Rubin J. Peter , Ren Xi , Abbott Rosalyn D. 
Published: June 2021

AbstractCritically sized defects in subcutaneous white adipose tissue result in extensive disfigurement and dysfunction and remain a reconstructive challenge for surgeons; as larger defect sizes are correlated with higher rates of complications and failure due to insufficient vascularization following implantation. Our study demonstrates for the first-time a method to engineer perfusable, pre-vascularized, high-density adipose grafts that combine patient-derived adipose cells with a decellularized lung matrix (DLM). The lung is one of the most vascularized organs with high flow, low resistance, and a large blood-alveolar interface separated by a thin basement membrane. For our work, the large volume capacity within the alveolar compartment was repurposed for high-density adipose cell filling, while the acellular vascular bed provided efficient graft perfusion throughout. Both adipocytes and hASCs were successfully delivered and remained in the alveolar space even after weeks of culture. While adipose derived cells maintained their morphology and functionality in both static and perfusion DLM cultures, perfusion culture offered enhanced outcomes over static culture. Furthermore, we demonstrate that endothelial cells seamlessly integrate into the acellular vascular tree of the DLM with adipocytes. These results support that the DLM is a unique platform for creating vascularized adipose tissue grafts for large defect filling.
Trash-basket epiphytes as secondary foundation species: a review of their distribution and effects on biodiversity and ecosystem functions
Authors: Ortega-Solis Gabriel , Díaz Iván A. , Mellado-Mansilla Daniela , Tejo Camila , Tello Francisco , Craven Dylan , Kreft Holger , Armesto Juan J. 
Published: June 2021

ABSTRACTBackgroundSecondary foundation species (FS) are organisms that inhabit ecosystems structurally defined by a primary foundation species, providing additional structure to habitats and communities. Trash-basket epiphytes (TBE) are secondary FS that enhance arboreal soil accumulation, providing shelter to animals, and rooting sites for plants. While their importance may vary across biomes, TBE have been overlooked as drivers of biodiversity and ecosystem functions. Here, we discuss the prevalence of TBE across biomes, their effects on biodiversity and ecosystem functions, and future research directions.MethodsWe performed a systematic literature review of articles, books and theses and collated and synthesised information about the taxonomic distribution of TBE, their effects on ecosystem functions, and reports of plant-animal and plant-plant interactions. Then, we analysed the global distribution of TBE using a generalized linear model and summarised two studies to assess their effects on soil invertebrates.ResultsWe identified 120 publications describing 209 species of TBE. Most TBE belong to Araceae (43%), Polypodiaceae (23%), and Orchidaceae (14%) and occur in all tropical and southern temperate forests. TBE richness peaks in the South-American Pacific mangroves, Eastern Cordillera Real, and the Napo moist forests. TBE effects on ecosystem functions include arboreal soil accumulation, water retention and temperature regulation in the canopy, and nutrient leaching through stem-flow. TBE provide shelter to species in more than 97 animal families, including from invertebrates to mammals, while 72 vascular plants have been reported to root in arboreal soil of TBE.ConclusionsTBE are a compelling group of model organisms that can be used to study ecological processes such as facilitation cascades, niche construction, extended phenotypes, or the effects of secondary FS on biodiversity and ecosystem functioning. TBE should also be included in forest management plans to enhance the availability of microhabitats in the canopy supporting its associated flora and fauna.
Dopamine release in nucleus accumbens core during social behaviors in mice
Authors: Dai Bing , Sun Fangmiao , Kuang Amy , Li Yulong , Lin Dayu 
Published: June 2021

AbstractSocial behaviors are among the most important and rewarding motivational behaviors. How dopamine, a “reward” signal, releases in the nucleus accumbens (NAc) during social behaviors has become a topic of interest for decades. However, limitations in early recording methods, such as microdialysis, prevented a complete understanding of moment-to-moment dopamine responses during social behaviors. Here, we employ a genetically encoded dopamine sensor, GRABDA2h, to record dopamine activity in the NAc core in mice and find acute changes in extracellular dopamine levels during all three phases of social behaviors: approach, investigation and consummation. Dopamine release during approach phase correlates with animal’s motivation towards the conspecific whereas its release during consummatory phase signals the valence of the experience. Furthermore, dopamine release during sexual and aggressive behaviors shows sex differences that correlate with the potential value of those experiences. Overall, our results reveal rich and temporally precise motivation and value information encoded by NAc dopamine during social behaviors and beyond.
Parameter identifiability and model selection for sigmoid population growth models
Authors: Simpson Matthew J , Browning Alexander P , Warne David J , Maclaren Oliver J , Baker Ruth E 
Published: June 2021

AbstractSigmoid growth models, such as the logistic, Gompertz and Richards’ models, are widely used to study population dynamics ranging from microscopic populations of cancer cells, to continental-scale human populations. Fundamental questions about model selection and parameter estimation are critical if these models are to be used to make practical inferences. However, the question of parameter identifiability – whether a data set contains sufficient information to give unique or sufficiently precise parameter estimates – is often overlooked. We use a profile-likelihood approach to explore practical parameter identifiability using data describing the re-growth of hard coral. With this approach, we explore the relationship between parameter identifiability and model misspecification, finding that the logistic growth model does not suffer identifiability issues for the type of data we consider whereas the Gompertz and Richards’ models encounter practical non-identifiability issues. This analysis of parameter identifiability and model selection is important because different growth models are used within areas of the biological modelling literature without necessarily considering whether parameters are identifiable, or checking statistical assumptions underlying model adequacy. Standard practices that do not consider parameter identifiability can lead to unreliable or imprecise parameter estimates and potentially misleading mechanistic interpretations. While tools developed here focus on three standard sigmoid growth models only, our theoretical developments are applicable to any sigmoid growth model and any relevant data set. MATLAB implementations of all software are available onGitHub.