bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrated transcriptome, DNA methylome and chromatin state accessibility landscapes reveal regulators of Atlantic salmon maturation
Authors: Mohamed Amin R. , Naval-Sanchez Marina , Menzies Moira , Evans Bradley , King Harry , Reverter Antonio , Kijas James W. 
Published: August 2020

AbstractDespite sexual development being ubiquitous to vertebrates, the epigenetic mechanisms controlling this fundamental transition remain largely undocumented in many organisms. Through whole-methylome, whole-transcriptome and chromatin landscape sequencing, we discovered global control mechanisms as well as specific regulators of sexual maturation in Atlantic salmon. This large integrated study was based on an experimental time course that successfully sampled the period when Atlantic salmon commence their trajectory towards sexual maturation. Co-analysis of DNA methylome and gene expression changes revealed chromatin remodelling genesarid1bandsmarca2were both significantly hypermethylated and upregulated in the ovary during the onset of maturation. We also observed changes in chromatin state landscape occurred early in the transition and were strongly correlated with fundamental remodelling of gene expression. Finally, we integrated our multiomics datasets to identifytrim25andznf423as key regulators in the pituitary that underwent 60 fold change in connectivity during the transition to sexual maturation. The study provides a comprehensive view of the spatiotemporal changes involved in a complex trait and opens the door to future efforts aiming to manipulate puberty in an economically important aquaculture species.
Targeting uncoupling of copy number and gene expression in cancers
Authors: Mohanty Vakul , Wang Fang , Mills Gordon , Chen Ken 
Published: August 2020

AbstractThe high degree of aneuploidy in cancer is likely tolerated via extensive uncoupling of copy number (CN) and mRNA expression (UCNE) of deleterious genes located in copy number aberrations (CNAs). To test the extent and role of UCNE in cancer, we performed integrative analysis of multiomics data across The Cancer Genome Atlas (TCGA), encompassing ∼ 5000 individual tumors. We found many genes having UCNE, the degree of which are associated with increased oncogenic signaling, proliferation and immune-suppression. The occurrence of UCNE appears to be orchestrated by complex epigenetic and regulatory changes, with transcription factors (TFs) playing a prominent role. To further dissect the regulatory mechanisms, we developed a systems-biological approach to identify candidate TFs, which upon perturbation can offset UCNE and reduce tumor fitness. Applying our approach on TCGA data, we identified 20 putative targets, 45% of which were validated by independent sources. Among them areIRF1, which plays a prominent role in anti-tumor immunity and response to immune checkpoint therapy,ETS1, TRIM21andGATA3, which are associated with anti-tumor immunity, tumor proliferation and metastasis. Together, our study indicates that UCNE is likely an important mechanism in cancer development that can be exploited therapeutically.
Optimized Vivid-derived Magnets photodimerizers for subcellular optogenetics
Authors: Benedetti Lorena , Marvin Jonathan S. , Falahati Hanieh , Guillén-Samander Andres , Looger Loren L. , De Camilli Pietro 
Published: August 2020

ABSTRACTLight-inducible dimerization protein modules enable precise temporal and spatial control of biological processes in non-invasive fashion. Among them, Magnets are small modules engineered from theNeurospora crassaphotoreceptor Vivid by orthogonalizing the homodimerization interface into complementary heterodimers. Both Magnets components, which are well-tolerated as protein fusion partners, are photoreceptors requiring simultaneous photoactivation to interact, enabling high spatiotemporal confinement of dimerization with a single-excitation wavelength. However, Magnets require concatemerization for efficient responses and cell preincubation at 28°C to be functional. Here we overcome these limitations by engineering an optimized Magnets pair requiring neither concatemerization nor low temperature preincubation. We validated these “enhanced” Magnets (eMags) by using them to rapidly and reversibly recruit proteins to subcellular organelles, to induce organelle contacts, and to reconstitute OSBP-VAP ER-Golgi tethering implicated in phosphatidylinositol-4-phosphate transport and metabolism. eMags represent a very effective tool to optogenetically manipulate physiological processes over whole cells or in small subcellular volumes.
Celsr1 and CAMSAP3 differently regulate intercellular and intracellular cilia orientation in oviduct multiciliated cells
Authors: Usami Fumiko Matsukawa , Arata Masaki , Shi Dongbo , Oka Sanae , Higuchi Yoko , Tissir Fadel , Takeichi Masatoshi , Fujimori Toshihiko 
Published: August 2020

SummaryThe molecular mechanisms by which cilia orientation is coordinated within and between multiciliated cells (MCCs) is not fully understood. By observing the orientation of basal bodies (BB) in MCCs of mouse oviducts, here, we show that Celsr1, a planar cell polarity (PCP) factor involved in tissue polarity regulation, is dispensable for determining BB orientation in individual cells, whereas CAMSAP3, a microtubule minus-end regulator, is critical for this process but not for PCP. MCCs exhibit a characteristic BB orientation and microtubule gradient along the tissue axis, and these intracellular polarities were maintained in the cells lacking Celsr1, although the intercellular coordination of the polarities was partly disrupted. On the other hand, CAMSAP3 regulated the assembly of microtubules interconnecting BBs by localizing at the BBs, and its mutation led to disruption of intracellular coordination of BB orientation, but not affecting PCP factor localization. Thus, both Celsr1 and CAMSAP3 are responsible for BB orientation but in distinct ways; and therefore, their cooperation should be critical for generating functional multiciliated tissues.
Fine-tuning Nanog expression heterogeneity by altering MicroRNA regulation
Authors: Samanta Tagari , Kar Sandip 
Published: August 2020

AbstractNanog exhibits a robust heterogeneous expression pattern within a population of embryonic stem cells (ESCs) under varied culture conditions. However, an efficient way to fine-tune the Nanog expression heterogeneity remains elusive. Herein, by employing a stochastic modeling approach, we demonstrate that Nanog expression heterogeneity can be controlled by modulating the regulatory features of a Nanog transcript specific microRNA. We demonstrate how and why the extent of origin dependent fluctuations in Nanog expression level can be altered by varying either the binding efficiency of the microRNA-mRNA complex or the expression level of the respective microRNA. Moreover, our model makes experimentally feasible and insightful predictions to maneuver the Nanog expression heterogeneity explicitly to achieve cell-type specific differentiation of ESCs.
Micro-topographical guidance of macropinocytic signaling patches
Authors: Honda Gen , Saito Nen , Fujimori Taihei , Hashimura Hidenori , Nakamura Mitsuru J. , Nakajima Akihiko , Sawai Satoshi 
Published: August 2020

AbstractIn fast moving cells such as amoeba and immune cells, spatio-temporal regulation of dendritic actin filaments shapes large-scale plasma membrane protrusions. Despite the importance in migration as well as in particle and liquid ingestion, how these processes are affected by the micrometer-scale surface features is poorly understood. Here, through quantitative imaging analysis ofDictyosteliumon micro-fabricated surfaces, we show that there is a distinct mode of topographically guided cell migration ‘phagotaxis’ directed by the macropinocytic Ras/PI3K signaling patches. The topography guidance was PI3K-dependent and involved nucleation of a patch at the convex curved surface and confinement at the concave surface. Due to the topography-dependence, constitutive cup formation for liquid uptake in the axenic strain is also destined to trace large surface features. Given the fact that PI3K-dependency of phagocytosis are restricted to large particles in bothDictyosteliumand immune cells, topography-dependency and the dual-use of membrane cups may be wide-spread.
MyoD is a structure organizer of 3D genome architecture in muscle cells
Authors: Chen Qian , Chen Fengling , Wang Ruiting , Shi Minglei , Chen Antony K. , Ma Zhao , Li Guohong , Wang Min , Li Hu , Zhang Xu , Ma Jinbiao , Zhong Jiayun , Chen Meihong , Zhang Michael Q. , Zhang Yong , Chen Yang , Zhu Dahai 
Published: August 2020

AbstractThe genome is not a linear molecule of DNA randomly folded in the nucleus, but exists as an organized, three-dimensional (3D) dynamic architecture. Intriguingly, it is now clear that each cell type has a unique and characteristic 3D genome organization that functions in determining cell identity during development. A currently challenging basic question is how cell-type specific 3D genome structures are established during development. Herein, we analyzed 3D genome structures in primary myoblasts and myocytes from MyoD knockout (MKO) and wild type (WT) mice and discovered that MyoD, a pioneer transcription factor (TF), can function as a “genome organizer” that specifies the proper 3D genome architecture unique to muscle cell development. Importantly, we genetically demonstrate that H3K27ac is insufficient for establishing MyoD-induced chromatin loops in muscle cells. The establishment of MyoD’s “architectural role” should have profound impacts on advancing understanding of other pioneer transcription factors in orchestrating lineage specific 3D genome organization during development in a potentially very large number of cell types in diverse organisms.
TLR4 signaling and macrophage inflammatory responses are dampened by GIV/Girdin
Authors: Swanson Lee , Katkar Gajanan D. , Tam Julian , Pranadinata Rama F. , Chareddy Yogitha , Coates Jane , Amandachar Mahitha Shree , Castillo Vanessa , Olson Joshua , Nizet Victor , Kufareva Irina , Das Soumita , Ghosh Pradipta 
Published: August 2020

AbstractSensing of pathogens by Toll-like receptor 4 (TLR4) induces an inflammatory response; controlled responses confer immunity but uncontrolled responses cause harm. Here we define how a multi-modular scaffold, GIV (a.k.a Girdin) titrates such inflammatory response in macrophages. Upon challenge with either live microbes or microbe-derived lipopolysaccharides (LPS, a ligand for TLR4), macrophages with GIV mount a more tolerant (hypo-reactive) transcriptional response and suppress pro-inflammatory cytokines and signaling pathways (i.e., NFkB and CREB) downstream of TLR4 compared to their GIV-depleted counterparts. Myeloid-specific gene depletion studies confirmed that the presence of GIV ameliorates DSS-induced colitis and sepsis-induced death. The anti-inflammatory actions of GIV are mediatedviaits C-terminally located TIR-like BB-loop (TILL)-motif which binds the cytoplasmic TIR-modules of TLR4 in a manner that precludes receptor dimerization; the latter is a pre-requisite for pro-inflammatory signaling. Binding of GIV’s TILL motif to other TIR modules inhibits pro-inflammatory signalingviaother TLRs, suggesting a convergent paradigm for fine-tuning macrophage inflammatory responses.SignificanceTo ensure immunity, and yet limit pathology, inflammatory responses must be confined within the proverbial ‘Goldilockszone’. TLR4 is the prototypical sensor that orchestrates inflammatory responses through a series of well characterized downstream cascades. How TLR4 signals are confined remain incompletely understood. Using trans-scale approaches ranging from disease modeling in live animals, through cell-based interventional studies, to structure-guided biochemical studies that offer an atomic-level resolution, this study unravels the existence of a ‘brake’ within the TLR4 signaling cascade, i.e., GIV; the latter is a prototypical member of an emerging class of scaffold proteins. By showing that GIV uses conserved mechanisms to impact multi-TLR signaling, this work unravels a multi-scale point of convergence of immune signaling of broader impact beyond TLR4.
Size Effect on Structure and Stiffness of Viral DNA during Temperature Variation
Authors: Zhang Cheng-Yin , Zhang Neng-Hui 
Published: August 2020

AbstractStructure and stiffness of nucleic acids are closely related to viral infectivity. The article is aimed to clarify a recent controversy on structure variation of viral DNA in temperature-dependent experiments. A multi-scale correlation between microscopic structure of viral DNA and its bulk stiffness is formulated by presenting a two-zone mesoscopic free energy model. Results reveal that the increasing temperature promotes DNA structure transformation from order to disorder, and leads to size effect on temperature-dependency of stiffness and structure of viral DNA.
Live imaging and biophysical modeling support a button-based mechanism of somatic homolog pairing inDrosophila
Authors: Child Myron , Bateman Jack R. , Jahangiri Amir , Reimer Armando , Lammers Nicholas C. , Sabouni Nica , Villamarin Diego , McKenzie-Smith Grace C. , Johnson Justine E. , Jost Daniel , Garcia Hernan G. 
Published: August 2020

AbstractThe spatial configuration of the eukaryotic genome is organized and dynamic, providing the structural basis for regulated gene expression in living cells. InDrosophila melanogaster, 3D genome organization is characterized by somatic homolog pairing, where homologous chromosomes are intimately paired from end to end; however, the process by which homologs identify one another and pair has remained mysterious. A recent model proposed that specifically interacting “buttons” encoded along the lengths of homologous chromosomes drive somatic homolog pairing. Here, we turned this hypothesis into a precise biophysical model to demonstrate that a button-based mechanism can lead to chromosome-wide pairing. We tested our model and constrained its free parameters using live-imaging measurements of chromosomal loci tagged with the MS2 and PP7 nascent RNA labeling systems. Our analysis showed strong agreement between model predictions and experiments in the separation dynamics of tagged homologous loci as they transition from unpaired to paired states, and in the percentage of nuclei that become paired as embryonic development proceeds. In sum, as a result of this dialogue between theory and experiment, our data strongly support a button-based mechanism of somatic homolog pairing inDrosophilaand provide a theoretical framework for revealing the molecular identity and regulation of buttons.
The Impact of Pf Bacteriophages on the Fitness ofPseudomonas aeruginosa; A Mathematical Modeling Approach
Authors: Pourtois Julie D. , Kratochvil Michael J. , Chen Qingquan , Haddock Naomi L. , Burgener Elizabeth B. , De Leo Giulio A. , Bollyky Paul L. 
Published: August 2020

AbstractPseudomonas aeruginosa(Pa) is a major bacterial pathogen responsible for chronic lung infections in cystic fibrosis patients. Recent work by ourselves and others has implicated Pf bacteriophages, non-lytic filamentous viruses produced byPa, in the chronicity and severity ofPainfections. Pf phages act as structural elements inPabiofilms and sequester aerosolized antibiotics, thereby contributing to antibiotic tolerance. Consistent with a selective advantage in this setting, the prevalence of Pf+ bacteria increases over time in these patients. However, the production of Pf phages comes at a metabolic cost to bacteria, such that Pf+ strains grow more slowly than Pf- strains in vitro. Here, we use a mathematical model to investigate how these competing pressures might influence the relative abundance of Pf+ versus Pf- strains in different settings. Our model predicts that Pf+ strains ofPacan only outcompete Pf- strains if the benefits of phage production falls solely onto Pf+ strains and not onto the overall bacterial community in the lung. Further, phage production only leads to a net positive gain in fitness at antibiotic concentrations slightly above the minimum inhibitory concentration (i.e., concentrations for which the benefits of antibiotic sequestration outweigh the metabolic cost of phage production), but which are not lethal for Pf+ strains. As a result, our model predicts that frequent administration of intermediate doses of antibiotics with low decay rates favors Pf+ over Pf- strains. These models inform our understanding of the ecology of Pf phages and suggest potential treatment strategies for Pf+Painfections.ImportanceFilamentous phages are a frontier in bacterial pathogenesis, but the impact of these phages on bacterial fitness is unclear. In particular, Pf phages produced byPapromote antibiotic tolerance but are metabolically expensive to produce, suggesting that competing pressures may influence the prevalence of Pf+ versus Pf- strains ofPain different settings. Our results identify conditions likely to favor Pf+ strains and thus antibiotic tolerance. This study contributes to a better understanding of the unique ecology of filamentous phages and may facilitate improved treatment strategies for combating antibiotic tolerance.
Sequence-encoded and Composition-dependent Protein-RNA Interactions Control Multiphasic Condensate Morphologies
Authors: Kaur Taranpreet , Raju Muralikrishna , Alshareedah Ibraheem , Davis Richoo B. , Potoyan Davit A. , Banerjee Priya R. 
Published: August 2020

ABSTRACTMultivalent protein-protein and protein-RNA interactions are the drivers of biological phase separation. Biomolecular condensates typically contain a dense network of multiple proteins and RNAs, and their competing molecular interactions play key roles in regulating the condensate composition and structure. Employing a ternary system comprising of a prion-like polypeptide (PLP), arginine-rich polypeptide (RRP), and RNA, we show that competition between the PLP and RNA for a single shared partner, the RRP, leads to RNA-induced demixing of PLP-RRP condensates into stable coexisting phases−homotypic PLP condensates and heterotypic RRP-RNA condensates. The morphology of these biphasic condensates (non-engulfing/ partial engulfing/ complete engulfing) is determined by the RNA-to-RRP stoichiometry and the hierarchy of intermolecular interactions, providing a glimpse of the broad range of multiphasic patterns that are accessible to these condensates. Our findings provide a minimal set of physical rules that govern the composition and spatial organization of multicomponent and multiphasic biomolecular condensates.
Structural classification of neutralizing antibodies against the SARS-CoV-2 spike receptor-binding domain suggests vaccine and therapeutic strategies
Authors: Barnes Christopher O. , Jette Claudia A. , Abernathy Morgan E. , Dam Kim-Marie A. , Esswein Shannon R. , Gristick Harry B. , Malyutin Andrey G. , Sharaf Naima G. , Huey-Tubman Kathryn E. , Lee Yu E. , Robbiani Davide F. , Nussenzweig Michel C. , West Anthony P. , Bjorkman Pamela J. 
Published: August 2020

AbstractThe COVID-19 pandemic presents an urgent health crisis. Human neutralizing antibodies (hNAbs) that target the host ACE2 receptor-binding domain (RBD) of the SARS-CoV-2 spike1–5 show therapeutic promise and are being evaluated clincally6–8. To determine structural correlates of SARS-CoV-2 neutralization, we solved 8 new structures of distinct COVID-19 hNAbs5 in complex with SARS-CoV-2 spike trimer or RBD. Structural comparisons allowed classification into categories: (1) VH3-53 hNAbs with short CDRH3s that block ACE2 and bind only to “up” RBDs, (2) ACE2-blocking hNAbs that bind both “up” and “down” RBDs and can contact adjacent RBDs, (3) hNAbs that bind outside the ACE2 site and recognize “up” and “down” RBDs, and (4) Previously-described antibodies that do not block ACE2 and bind only “up” RBDs9. Class 2 comprised four hNAbs whose epitopes bridged RBDs, including a VH3-53 hNAb that used a long CDRH3 with a hydrophobic tip to bridge between adjacent “down” RBDs, thereby locking spike into a closed conformation. Epitope/paratope mapping revealed few interactions with host-derived N-glycans and minor contributions of antibody somatic hypermutations to epitope contacts. Affinity measurements and mapping of naturally-occurring and in vitro-selected spike mutants in 3D provided insight into the potential for SARS-CoV-2 escape from antibodies elicited during infection or delivered therapeutically. These classifications and structural analyses provide rules for assigning current and future human RBD-targeting antibodies into classes, evaluating avidity effects, suggesting combinations for clinical use, and providing insight into immune responses against SARS-CoV-2.
Protein Phosphatase 1 in association with Bud14 inhibits mitotic exit inSaccharomyces cerevisiae
Authors: Kocakaplan Dilara , Karabürk Hüseyin , Dilege Cansu , Kirdok Idil , Bektaş Şeyma Nur , Caydasi Ayse Koca 
Published: August 2020

AbstractMitotic exit in budding yeast is dependent on correct orientation of the mitotic spindle along the cell polarity axis. When accurate positioning of the spindle fails, a surveillance mechanism named the Spindle Position Checkpoint (SPOC) prevents cells from exiting mitosis. Mutants with a defective SPOC become multinucleated and lose their genomic integrity. Yet, a comprehensive understanding of the SPOC mechanism is missing. In this study, we identified the type 1 protein phosphatase, Glc7, in association with its regulatory protein Bud14 as a novel checkpoint component. We further showed that Glc7-Bud14 promotes dephosphorylation of the SPOC effector protein Bfa1. Our results suggest a model in which two mechanisms act in parallel for a robust checkpoint response: first, the SPOC kinase Kin4 isolates Bfa1 away from the inhibitory kinase Cdc5 and second, Glc7-Bud14 dephosphorylates Bfa1 to fully activate the checkpoint effector.
FlyWire: Online community for whole-brain connectomics
Authors: Dorkenwald Sven , McKellar Claire , Macrina Thomas , Kemnitz Nico , Lee Kisuk , Lu Ran , Wu Jingpeng , Popovych Sergiy , Mitchell Eric , Nehoran Barak , Jia Zhen , Bae J. Alexander , Mu Shang , Ih Dodam , Castro Manuel , Ogedengbe Oluwaseun , Halageri Akhilesh , Ashwood Zoe , Zung Jonathan , Brittain Derrick , Collman Forrest , Schneider-Mizell Casey , Jordan Chris , Silversmith William , Baker Christa , Deutsch David , Encarnacion-Rivera Lucas , Kumar Sandeep , Burke Austin , Gager Jay , Hebditch James , Koolman Selden , Moore Merlin , Morejohn Sarah , Silverman Ben , Willie Kyle , Willie Ryan , Yu Szi-chieh , Murthy Mala , Seung H. Sebastian 
Published: August 2020

ABSTRACTDue to advances in automated image acquisition and analysis, new whole-brain connectomes beyondC. elegansare finally on the horizon. Proofreading of whole-brain automated reconstructions will require many person-years of effort, due to the huge volumes of data involved. Here we present FlyWire, an online community for proofreading neural circuits in a fly brain, and explain how its computational and social structures are organized to scale up to whole-brain connectomics. Browser-based 3D interactive segmentation by collaborative editing of a spatially chunked supervoxel graph makes it possible to distribute proofreading to individuals located virtually anywhere in the world. Information in the edit history is programmatically accessible for a variety of uses such as estimating proofreading accuracy or building incentive systems. An open community accelerates proofreading by recruiting more participants, and accelerates scientific discovery by requiring information sharing. We demonstrate how FlyWire enables circuit analysis by reconstructing and analysing the connectome of mechanosensory neurons.