bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Arabidopsis NRT1/PTR FAMILY Protein NPF7.3/NRT1.5 is an Indole-3-butyric Acid Transporter Involved in Root Gravitropism
Authors: Watanabe Shunsuke , Takahashi Naoki , Kanno Yuri , Suzuki Hiromi , Aoi Yuki , Takeda-Kamiya Noriko , Toyooka Kiminori , Kasahara Hiroyuki , Hayashi Ken-Ichiro , Umeda Masaaki , Seo Mitsunori 
Published: June 2020

AbstractActive membrane transport of plant hormones and their related compounds is an essential process that determines the distribution of the compounds within plant tissues and, hence, regulates various physiological events. Here, we report that the Arabidopsis NITRATE TRANSPORTER 1/PEPTIDE TRANSPORTER FAMILY 7.3 (NPF7.3) protein functions as a transporter of indole-3-butyric acid (IBA), a precursor of the major endogenous auxin indole-3-acetic acid (IAA). When expressed in yeast, NPF7.3 mediated cellular IBA uptake. Loss-of-functionnpf7.3mutants showed defective root gravitropism with reduced IBA levels and auxin responses. Nevertheless, the phenotype was restored by exogenous application of IAA but not by IBA treatment.NPF7.3was expressed in pericycle cells and the root tip region including root cap cells of primary roots where the IBA-to-IAA conversion occurs. Our findings indicate that NPF7.3-mediated IBA uptake into specific cells is required for the generation of appropriate auxin gradients within root tissues.
Aster repulsion drives local ordering in an active system
Authors: de-Carvalho Jorge , Tlili Sham , Hufnagel Lars , Saunders Timothy E. , Telley Ivo A. 
Published: June 2020

AbstractBiological systems are a form of active matter, which often undergo rapid changes in their material state,e.g. liquid to solid transitions. Yet, such systems often also display remarkably ordered structures. It remains an open question as to how local ordering occurs within active systems. Here, we utilise the rapid early development ofDrosophila melanogasterembryos to uncover the mechanisms driving short-ranged order. During syncytial stage, nuclei synchronously divide (within a single cell defined by the ellipsoidal eggshell) for nine cycles after which most of the nuclei reach the cell cortex. Despite the rapid nuclear division and repositioning, the spatial pattern of nuclei at the cortex is highly regular. Such precision is important for subsequent cellularisation and morphological transformations. We utiliseex vivoexplants and mutant embryos to reveal that microtubule asters ensure the regular distribution and maintenance of nuclear positions in the embryo. For large networks of nuclei, such as in the embryo, we predict – and experimentally verify – the formation of force chains. Theex vivoextracts enabled us to deduce the force potential between single asters. We use this to predict how the nuclear division axis orientation in smallex vivosystems depend on aster number. Finally, we demonstrate that, upon nucleus removal from the cortex, microtubule force potentials can reorient subsequent nuclear divisions to minimise the size of pattern defects. Overall, we show that short-ranged microtubule-mediated repulsive interactions between asters can drive ordering within an active system.
Structural basis of GIRK2 channel modulation by cholesterol and PIP2
Authors: Mathiharan Yamuna Kalyani , Glaaser Ian W. , Zhao Yulin , Robertson Michael J. , Skiniotis Georgios , Slesinger Paul A. 
Published: June 2020

ABSTRACTG protein-gated inwardly rectifying potassium (GIRK) channels play important roles in controlling cellular excitability in the heart and brain. While structural data begin to unravel the molecular basis for G protein and alcohol dependent activation of GIRK channels, little is known about the modulation by cholesterol. Here, we present cryo-electron microscopy (cryoEM) structures of GIRK2 in the presence and absence of the cholesterol analog cholesteryl hemisuccinate (CHS), and PIP2. The structures and their comparison reveal that CHS binds near PIP2in lipid-facing hydrophobic pockets of the transmembrane domain (TMD). CHS potentiates the effects of PIP2, which stabilizes the inter-domain region and promotes the engagement of the cytoplasmic domain (CTD) onto the transmembrane region. The results suggest that CHS acts as a positive allosteric modulator and identify novel therapeutic sites for modulating GIRK channels in the brain.
Adipose Tissue is a Critical Regulator of Osteoarthritis
Authors: Collins Kelsey H. , Lenz Kristin L. , Pollitt Eleanor N. , Ferguson Daniel , Hutson Irina , Springer Luke E. , Oestreich Arin K. , Tang Ruhang , Choi Yun-Rak , Meyer Gretchen A. , Teitelbaum Steven L. , Pham Christine T.N. , Harris Charles A. , Guilak Farshid 
Published: June 2020

AbstractOsteoarthritis (OA), the leading cause of pain and disability worldwide, disproportionally affects obese individuals. The mechanisms by which adipose tissue leads to the onset and progression of OA are unclear due to the complex interactions between the metabolic, biomechanical, and inflammatory factors that accompany obesity. We used a murine model of lipodystrophy (LD) to examine the direct contribution of adipose tissue to OA. Knee joints of LD mice were protected from spontaneous or post-traumatic OA, on either a chow and high fat diet, despite similar body weight and the presence of systemic inflammation. These findings indicate that adipose tissue itself plays a critical role in the pathophysiology of OA. Susceptibility to post-traumatic OA was reintroduced into LD mice using implantation of adipose tissue derived from wildtype animals or mouse embryonic fibroblasts that undergo spontaneous adipogenesis, implicating paracrine signaling from fat, rather than body weight, as a critical mediator of joint degeneration.
Akt is required for artery formation during embryonic vascular development
Authors: Zhou Wenping , Ristori Emma , He Liqun , Ghersi Joey J , Mehta Sameet , Zhang Rong , Betsholtz Christer , Nicoli Stefania , Sessa William C. 
Published: June 2020

SUMMARYOne of the first events in the development of the cardiovascular system is morphogenesis of the main embryonic artery, the dorsal aorta (DA). The DA forms via a conserved genetic process mediated by the migration, specification, and organization of endothelial progenitor cells into a distinct arterial lineage and vessel type. Several angiogenic factors activate different signaling pathways to control DA formation, however the physiological relevance of distinct kinases in this complex process remains unclear. Here, we identify the role of Akt during early vascular development by generating mutant zebrafish lines that lack expression ofaktisoforms. Live cell imaging coupled with single cell RNA sequencing ofaktmutants reveal that Akt is required for proper development of the DA by sustaining arterial cell progenitor specification and segregation. Mechanistically, inhibition of active FOXO inaktmutants rescues impaired arterial development but not the expression of arterial markers, whereas Notch activation rescues arterial marker expression. Our work suggests that Akt activity is critical for early artery development, in part via FOXO and Notch-mediated regulation.
Multiple competing RNA structures dynamically control alternative splicing in human ATE1 gene
Authors: Kalinina Marina , Skvortsov Dmitry , Kalmykova Svetlana , Ivanov Timofei , Dontsova Olga , Pervouchine Dmitri D. 
Published: June 2020

AbstractThe mammalianAte1gene encodes an arginyl transferase enzyme, which is essential for embryogenesis, male meiosis, and regulation of the cytoskeleton. Reduced levels ofAte1are associated with malignant transformations and serve as a prognostic indicator of prostate cancer metastasis. The tumor suppressor function ofAte1depends on the inclusion of one of the two mutually exclusive exons (MXE), exons 7a and 7b. Here, we report that the molecular mechanism underlying MXE splicing in Ate1 involves five conserved regulatory intronic elements R1–R5, of which R1 and R4 compete for base pairing with R3, while R2 and R5 form an ultra-long-range RNA structure spanning 30 Kb. In minigenes, single and double mutations that disrupt base pairings in R1R3 and R3R4 lead to the loss of MXE splicing, while compensatory triple mutations that restore the RNA structure also revert splicing to that of the wild type. Blocking the competing base pairings by locked nucleic acid (LNA)/DNA mixmers complementary to R3 leads to the loss of MXE splicing, while the disruption of the ultra-long-range R2R5 interaction changes the ratio of mutually exclusive isoforms in the endogenousAte1pre-mRNA. The upstream exon 7a becomes more included than the downstream exon 7b in response to RNA Pol II slowdown, however it fails to do so when the ultra-long-range R2R5 interaction is disrupted. In sum, we demonstrated that mutually exclusive splicing inAte1is controlled by two independent, dynamically interacting and functionally distinct RNA structure modules. The molecular mechanism proposed here opens new horizons for the development of therapeutic solutions, including antisense correction of splicing.
Per-sample standardization and asymmetric winsorization lead to accurate clustering of RNA-seq expression profiles
Authors: Risso Davide , Pagnotta Stefano M. 
Published: June 2020

AbstractMotivationData transformations are an important step in the analysis of RNA-seq data. Nonetheless, the impact of transformations on the outcome of unsupervised clustering procedures is still unclear.ResultsHere, we present an Asymmetric Winsorization per Sample Transformation (AWST), which is robust to data perturbations and removes the need for selecting the most informative genes prior to sample clustering. Our procedure leads to robust and biologically meaningful clusters both in bulk and in single-cell applications.AvailabilityThe AWST method is available athttps://github.com/drisso/awst. The code to reproduce the analyses is available athttps://github.com/drisso/awst_analysis.
Drebrin mediates scar formation and astrocyte reactivity during brain injury by inducing RAB8 tubular endosomes
Authors: Schiweck Juliane , Murk Kai , Ledderose Julia , Münster-Wandowski Agnieszka , Vida Imre , Eickholt Britta J. 
Published: June 2020

AbstractThe brain of mammals lacks a significant ability to regenerate neurons and is thus particularly vulnerable. To protect the brain from injury and disease, damage control by astrocytes through astrogliosis and scar formation is vital. Here, we show that brain injury triggers anad hocupregulation of the actin-binding protein Drebrin (DBN) in astrocytes, which is essential for the formation and maintenance of glial scarsin vivo. In turn, DBN loss leads to defective glial scar formation and excessive neurodegeneration following mild brain injuries. At the cellular level, DBN switches actin homeostasis from ARP2/3-dependent arrays to microtubule-compatible scaffolds and facilitates the formation of RAB8-positive membrane tubules. This injury-specific RAB8 membrane compartment serves as hub for the trafficking of surface proteins involved in astrogliosis and adhesive responses, such as β1-integrin. Our work identifies DBN as pathology-specific actin regulator, and establishes DBN-dependent membrane trafficking as crucial mechanism in protecting the brain from escalating damage following traumatic injuries.
Synchronization, stochasticity and phase waves in neuronal networks with spatially-structured connectivity
Authors: Kulkarni Anirudh , Ranft Jonas , Hakim Vincent 
Published: June 2020

AbstractOscillations in the beta/low gamma range (10-45 Hz) are recorded in diverse neural structures. They have successfully been modeled as sparsely synchronized oscillations arising from reciprocal interactions between randomly connected excitatory (E) pyramidal cells and local interneurons (I). The synchronization of spatially distant oscillatory spiking E-I modules has been well studied in the rate model framework but less so for modules of spiking neurons. Here, we first show that previously proposed modifications of rate models provide a quantitative description of spiking E-I modules of Exponential Integrate-and-Fire (EIF) neurons. This allows us to analyze the dynamical regimes of sparsely synchronized oscillatory E-I modules connected by long-range excitatory interactions, for two modules, as well as for a chain of such modules. For modules with a large number of neurons (> 105), we obtain results similar to previously obtained ones based on the classic deterministic Wilson-Cowan rate model, with the added bonus that the results quantitatively describe simulations of spiking EIF neurons. However, for modules with a moderate (~ 104) number of neurons, stochastic variations in the spike emission of neurons are important and need to be taken into account. On the one hand, they modify the oscillations in a way that tends to promote synchronization between different modules. On the other hand, independent fluctuations on different modules tend to disrupt synchronization. The correlations between distant oscillatory modules can be described by stochastic equations for the oscillator phases that have been intensely studied in other contexts. On shorter distances, we develop a description that also takes into account amplitude modes and that quantitatively accounts for our simulation data. Stochastic dephasing of neighboring modules produces transient phase gradients and the transient appearance of phase waves. We propose that these stochastically-induced phase waves provide an explanative framework for the observations of traveling waves in the cortex during beta oscillations.
A Deep Dive into DNA Base Pairing Interactions Under Water
Authors: Li Rongpeng , Mak Chi H. 
Published: June 2020

AbstractBase pairing plays a pivotal role in DNA functions and replication fidelity. But while the complementarity between Watson-Crick matched bases is generally believed to arise from the different number of hydrogen bonds in G|C pairs versus A|T, the energetics of these interactions are heavily renormalized by the aqueous solvent. Employing large-scale Monte Carlo simulations, we have extracted the solvent contribution to the free energy for canonical and some noncanonical and stacked base pairs. For all of them, the solvent’s contribution to the base pairing free energy is exclusively destabilizing. While the direct hydrogen bonding interactions in the G|C pair is much stronger than A|T, the thermodynamic resistance produced by the solvent also pushes back much stronger against G|C compared to A|T, generating an only ~1 kcal/mol free energy difference between them. We have profiled the density of water molecules in the solvent adjacent to the bases and observed a “freezing” behavior where waters are recruited into the gap between the bases to compensate for the unsatisfied hydrogen bonds between them. A very small number of water molecules that are associated with the Watson-Crick donor/acceptor atoms turn out to be responsible for the majority of solvent’s thermodynamic resistance to base pairing. The absence or presence of these near-field waters can be used to enhance fidelity during DNA replication.TOC Graphic
An OpenData portal to share COVID-19 drug repurposing data in real time
Authors: Brimacombe Kyle R. , Zhao Tongan , Eastman Richard T. , Hu Xin , Wang Ke , Backus Mark , Baljinnyam Bolormaa , Chen Catherine Z. , Chen Lu , Eicher Tara , Ferrer Marc , Fu Ying , Gorshkov Kirill , Guo Hui , Hanson Quinlin M. , Itkin Zina , Kales Stephen C. , Klumpp-Thomas Carleen , Lee Emily M. , Michael Sam , Mierzwa Tim , Patt Andrew , Pradhan Manisha , Renn Alex , Shinn Paul , Shrimp Jonathan H. , Viraktamath Amit , Wilson Kelli M. , Xu Miao , Zakharov Alexey V. , Zhu Wei , Zheng Wei , Simeonov Anton , Mathé Ewy A. , Lo Donald C. , Hall Matthew D. , Shen Min 
Published: June 2020

AbstractThe National Center for Advancing Translational Sciences (NCATS) has developed an online open science data portal for its COVID-19 drug repurposing campaign – named OpenData – with the goal of making data across a range of SARS-CoV-2 related assays available in real-time. The assays developed cover a wide spectrum of the SARS-CoV-2 life cycle, including both viral and human (host) targets. In total, over 10,000 compounds are being tested in full concentration-response ranges from across multiple annotated small molecule libraries, including approved drug, repurposing candidates and experimental therapeutics designed to modulate a wide range of cellular targets. The goal is to support research scientists, clinical investigators and public health officials through open data sharing and analysis tools to expedite the development of SARS-CoV-2 interventions, and to prioritize promising compounds and repurposed drugs for further development in treating COVID-19.
PIVOTAL: Prioritizing variants of uncertain significance with spatial genomic patterns in the 3D proteome
Authors: Liang Siqi , Mort Matthew , Stenson Peter D. , Cooper David N. , Yu Haiyuan 
Published: June 2020

ABSTRACTVariants of uncertain significance (VUS) have posed an increasingly prominent challenge to clinicians due to their growing numbers and difficulties in making clinical responses to them. Currently there are no existing methods that leverage the spatial relationship of known disease mutations and genomic properties for prioritizing variants of uncertain significance. More importantly, disease genes often associate with multiple clinically distinct diseases, but none of the existing variant prioritization methods provide clues as to the specific type of disease potentially associated with a given variant. We present PIVOTAL, a spatial neighborhood-based method using three-dimensional structural models of proteins, that significantly improves current variant prioritization tools and identifies potential disease etiology of candidate variants on a proteome scale. Using PIVOTAL, we made pathogenicity predictions for over 140,000 VUS and deployed a web application (http://pivotal.yulab.org) that enables users both to explore these data and to perform custom calculations.
Distinct Roles of Tumor-Associated Mutations in Collective Cell Migration
Authors: Lee Rachel M. , Vitolo Michele I. , Losert Wolfgang , Martin Stuart S. 
Published: June 2020

ABSTRACTRecent evidence suggests that groups of cells are more likely to form clinically dangerous metastatic tumors, emphasizing the importance of understanding mechanisms underlying collective behavior. The emergent collective behavior of migrating cell sheetsin vitrohas been shown to be disrupted in tumorigenic cells but the connection between this behavior andin vivotumorigenicity is unclear. Here we use particle image velocimetry to measure a multi-dimensional collective migration phenotype for genetically defined cell lines that range in theirin vivobehavior from non-tumorigenic to aggressively metastatic. By using cells with controlled mutations, we show that PTEN deletion enhances collective migration, while Ras activation suppresses it, even when combined with PTEN deletion. These opposing effects on collective migration phenotype of two mutations that are frequently found in patient tumors could be exploited in clinical assessments of metastatic potential or in the development of novel treatments for metastatic disease.
In vivofluorescence imaging with a flat, lensless microscope
Authors: Adams Jesse K. , Boominathan Vivek , Gao Sibo , Rodriguez Alex V. , Yan Dong , Kemere Caleb , Veeraraghavan Ashok , Robinson Jacob T. 
Published: June 2020

AbstractFluorescence imaging over large areas of the brain in freely behaving animals would allow researchers to better understand the relationship between brain activity and behavior; however, traditional microscopes capable of high spatial resolution and large fields of view (FOVs) require large and heavy lenses that restrict animal movement. While lensless imaging has the potential to achieve both high spatial resolution and large FOV with a thin lightweight device, lensless imaging has yet to be achievedin vivodue to two principal challenges: (a) biological tissue typically has lower contrast than resolution targets, and (b) illumination and filtering must be integrated into this non-traditional device architecture. Here, we show thatin vivofluorescence imaging is possible with a thin lensless microscope by optimizing the phase mask and computational reconstruction algorithms, and integrating fiber optic illumination and thin-film color filters. The result is a flat, lensless imager that achieves better than 10 μm spatial resolution and a FOV that is 30× larger than other cellular resolution miniature microscopes.
Mucosal vaccine adjuvant cyclic di-GMP differentiates lung moDCs into Bcl6+and Bcl6−mature moDCs to induce lung memory CD4+THcells and lung TFHcells respectively
Authors: Mansouri Samira , Katikaneni Divya S , Gogoi Himanshu , Jin Lei 
Published: June 2020

AbstractInduction of lung T-cell responses, including memory CD4+THand TFHcells, are highly desirable for vaccines against respiratory infections. We recently showed that the non-migratory monocytes-derived DCs (moDCs) induced lung TFHcells. However, the DCs subset inducing lung CD4+memory THcells is unknown. Here, using conditional knockout mice and adoptive cell transfer, we first established that moDCs are essential for lung mucosal, but are dispensable for systemic, vaccine responses. Next, we showed that intranasal administration of adjuvant cyclic di-GMP differentiated lung moDCs into Bcl6+and Bcl6-moDCs promoting lung memory THcells and lung TFHcells, respectively. Mechanistically, soluble TNF from lung TNFR2+cDC2 subpopulation mediates the induction of lung Bcl6+moDCs. Last, we designed fusion proteins targeting soluble or transmembrane TNF to lung moDCs and generated Bcl6+, Bcl6-lung moDCs respectively. Together, our study revealed lung mature moDCs heterogeneity and showed a moDCs-targeting strategy to enhance lung mucosal vaccine responses.
Single-cell analysis reveals diverse stromal subsets associated with immune evasion in triple-negative breast cancer
Authors: Wu Sunny Z. , Roden Daniel L. , Wang Chenfei , Holliday Holly , Harvey Kate , Cazet Aurélie S. , Murphy Kendelle J. , Pereira Brooke , Al-Eryani Ghamdan , Bartonicek Nenad , Hou Rui , Torpy James R. , Junankar Simon , Chan Chia-Ling , Lam Eric , Hui Mun N. , Gluch Laurence , Beith Jane , Parker Andrew , Robbins Elizabeth , Segara Davendra , Mak Cindy , Cooper Caroline , Warrier Sanjay , Forrest Alistair , Powell Joseph , O’Toole Sandra , Cox Thomas R. , Timpson Paul , Lim Elgene , Liu X. Shirley , Swarbrick Alexander 
Published: June 2020

AbstractThe tumour stroma regulates nearly all stages of carcinogenesis. Stromal heterogeneity in human triple-negative breast cancers (TNBCs) remains poorly understood, limiting the development of stromal-targeted therapies. Single cell RNA-sequencing of five TNBCs revealed two cancer-associated fibroblast (CAF) and two perivascular-like (PVL) subpopulations. CAFs clustered into two states, the first with features of myofibroblasts and the second characterised by high expression of growth factors and immunomodulatory molecules. PVL cells clustered into two states consistent with a differentiated and immature phenotype. We showed that these stromal states have distinct morphologies, spatial relationships and functional properties in regulating the extracellular matrix. Using cell-signalling predictions, we provide evidence that stromal-immune crosstalk actsviaa diverse array of immunoregulatory molecules. Importantly, the investigation of gene signatures from inflammatory-CAFs and differentiated-PVL cells in independent TNBC patient cohorts revealed strong associations with cytotoxic T-cell dysfunction and exclusion, respectively. Such insights present promising candidates to further investigate for new therapeutic strategies in the treatment of TNBCs.