bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deficiency of thyroid hormone receptor protects retinal pigment epithelium and photoreceptors from cell death in a mouse model of age-related macular degeneration
Authors: Ma Hongwei , Yang Fan , Ding Xi-Qin 
Published: March 2022

AbstractAge-related macular degeneration (AMD) is the leading cause of vision loss in the elderly. Progressive dystrophy of the retinal pigment epithelium (RPE) and photoreceptors is the characteristic of dry AMD, and oxidative stress/damage plays a central role in the pathogenic lesion of the disease. Thyroid hormone (TH) regulates cell growth, differentiation, and metabolism, and regulates development/function of photoreceptors and RPE in the retina. Population-/patient-based studies suggest an association of high free-serum TH levels with increased risk of AMD. We recently showed that suppressing TH signaling by antithyroid treatment reduces cell damage/death of the RPE and photoreceptors in an oxidative-stress/sodium iodate (NaIO3)-induced mouse model of AMD. This work investigated the effects of TH receptor (THR) deficiency on cell damage/death of the RPE and photoreceptors and the contribution of the receptor subtypes. Treatment with NaIO3 induced RPE and photoreceptor cell death/necroptosis, destruction, and oxidative damage. The phenotypes were significantly diminished in Thrα1−/−, Thrb−/−, and Thrb2−/− mice, compared with that in the wild-type (C57BL/6 J) mice. The involvement of the receptor subtypes varies in the RPE and retina. Deletion of Thrα1 or Thrb protected RPE, rods, and cones, whereas deletion of Thrb2 protected RPE and cones but not rods. Gene-expression analysis showed that deletion of Thrα1 or Thrb abolished/suppressed the NaIO3-induced upregulation of the genes involved in cellular oxidative-stress responses, necroptosis/apoptosis signaling, and inflammatory responses. In addition, THR antagonist effectively protected ARPE-19 cells and hRPE cells from NaIO3-induced cell death. This work demonstrates the involvement of THR signaling in cell damage/death of the RPE and photoreceptors after oxidative-stress challenge and the receptor-subtype contribution. Findings from this work support a role of THR signaling in the pathogenesis of AMD and the strategy of suppressing THR signaling locally in the retina for protection of the RPE/retina in dry AMD.
Massively parallel reporter perturbation assays uncover temporal regulatory architecture during neural differentiation
Authors: Kreimer Anat , Ashuach Tal , Inoue Fumitaka , Khodaverdian Alex , Deng Chengyu , Yosef Nir , Ahituv Nadav 
Published: March 2022

AbstractGene regulatory elements play a key role in orchestrating gene expression during cellular differentiation, but what determines their function over time remains largely unknown. Here, we perform perturbation-based massively parallel reporter assays at seven early time points of neural differentiation to systematically characterize how regulatory elements and motifs within them guide cellular differentiation. By perturbing over 2,000 putative DNA binding motifs in active regulatory regions, we delineate four categories of functional elements, and observe that activity direction is mostly determined by the sequence itself, while the magnitude of effect depends on the cellular environment. We also find that fine-tuning transcription rates is often achieved by a combined activity of adjacent activating and repressing elements. Our work provides a blueprint for the sequence components needed to induce different transcriptional patterns in general and specifically during neural differentiation.
Atomic resolution dynamics of cohesive interactions in phase-separated Nup98 FG domains
Authors: Najbauer Eszter E. , Ng Sheung Chun , Griesinger Christian , Görlich Dirk , Andreas Loren B. 
Published: March 2022

AbstractCohesive FG domains assemble into a condensed phase forming the selective permeability barrier of nuclear pore complexes. Nanoscopic insight into fundamental cohesive interactions has long been hampered by the sequence heterogeneity of native FG domains. We overcome this challenge by utilizing an engineered perfectly repetitive sequence and a combination of solution and magic angle spinning NMR spectroscopy. We map the dynamics of cohesive interactions in both phase-separated and soluble states at atomic resolution using TROSY for rotational correlation time (TRACT) measurements. We find that FG repeats exhibit nanosecond-range rotational correlation times and remain disordered in both states, although FRAP measurements show slow translation of phase-separated FG domains. NOESY measurements enable the direct detection of contacts involved in cohesive interactions. Finally, increasing salt concentration and temperature enhance phase separation and decrease local mobility of FG repeats. This lower critical solution temperature (LCST) behaviour indicates that cohesive interactions are driven by entropy.
Progression of type 1 diabetes from latency to symptomatic disease is predicted by distinct autoimmune trajectories
Authors: Kwon Bum Chul , Anand Vibha , Achenbach Peter , Dunne Jessica L. , Hagopian William , Hu Jianying , Koski Eileen , Lernmark Åke , Lundgren Markus , Ng Kenney , Toppari Jorma , Veijola Riitta , Frohnert Brigitte I. ,   the T1DI Study Group
Published: March 2022

AbstractDevelopment of islet autoimmunity precedes the onset of type 1 diabetes in children, however, the presence of autoantibodies does not necessarily lead to manifest disease and the onset of clinical symptoms is hard to predict. Here we show, by longitudinal sampling of islet autoantibodies (IAb) to insulin, glutamic acid decarboxylase and islet antigen-2 that disease progression follows distinct trajectories. Of the combined Type 1 Data Intelligence cohort of 24662 participants, 2172 individuals fulfill the criteria of two or more follow-up visits and IAb positivity at least once, with 652 progressing to type 1 diabetes during the 15 years course of the study. Our Continuous-Time Hidden Markov Models, that are developed to discover and visualize latent states based on the collected data and clinical characteristics of the patients, show that the health state of participants progresses from 11 distinct latent states as per three trajectories (TR1, TR2 and TR3), with associated 5-year cumulative diabetes-free survival of 40% (95% confidence interval [CI], 35% to 47%), 62% (95% CI, 57% to 67%), and 88% (95% CI, 85% to 91%), respectively (p < 0.0001). Age, sex, and HLA-DR status further refine the progression rates within trajectories, enabling clinically useful prediction of disease onset.
Single amino acid bionanozyme for environmental remediation
Authors: Makam Pandeeswar , Yamijala Sharma S. R. K. C. , Bhadram Venkata S. , Shimon Linda J. W. , Wong Bryan M. , Gazit Ehud 
Published: March 2022

AbstractEnzymes are extremely complex catalytic structures with immense biological and technological importance. Nevertheless, their widespread environmental implementation faces several challenges, including high production costs, low operational stability, and intricate recovery and reusability. Therefore, the de novo design of minimalistic biomolecular nanomaterials that can efficiently mimic the biocatalytic function (bionanozymes) and overcome the limitations of natural enzymes is a critical goal in biomolecular engineering. Here, we report an exceptionally simple yet highly active and robust single amino acid bionanozyme that can catalyze the rapid oxidation of environmentally toxic phenolic contaminates and serves as an ultrasensitive tool to detect biologically important neurotransmitters similar to the laccase enzyme. While inspired by the laccase catalytic site, the substantially simpler copper-coordinated bionanozyme is ∼5400 times more cost-effective, four orders more efficient, and 36 times more sensitive compared to the natural protein. Furthermore, the designed mimic is stable under extreme conditions (pH, ionic strength, temperature, storage time), markedly reusable for several cycles, and displays broad substrate specificity. These findings hold great promise in developing efficient bionanozymes for analytical chemistry, environmental protection, and biotechnology.
RUFY3 links Arl8b and JIP4-Dynein complex to regulate lysosome size and positioning
Authors: Kumar Gaurav , Chawla Prateek , Dhiman Neha , Chadha Sanya , Sharma Sheetal , Sethi Kanupriya , Sharma Mahak , Tuli Amit 
Published: March 2022

AbstractThe bidirectional movement of lysosomes on microtubule tracks regulates their whole-cell spatial arrangement. Arl8b, a small GTP-binding (G) protein, promotes lysosome anterograde trafficking mediated by kinesin-1. Herein, we report an Arl8b effector, RUFY3, which regulates the retrograde transport of lysosomes. We show that RUFY3 interacts with the JIP4-dynein-dynactin complex and facilitates Arl8b association with the retrograde motor complex. Accordingly, RUFY3 knockdown disrupts the positioning of Arl8b-positive endosomes and reduces Arl8b colocalization with Rab7-marked late endosomal compartments. Moreover, we find that RUFY3 regulates nutrient-dependent lysosome distribution, although autophagosome-lysosome fusion and autophagic cargo degradation are not impaired upon RUFY3 depletion. Interestingly, lysosome size is significantly reduced in RUFY3 depleted cells, which could be rescued by inhibition of the lysosome reformation regulatory factor PIKFYVE. These findings suggest a model in which the perinuclear cloud arrangement of lysosomes regulates both the positioning and size of these proteolytic compartments.
Inorganic phosphate in growing calcium carbonate abalone shell suggests a shared mineral ancestral precursor
Authors: Ajili Widad , Tovani Camila B. , Fouassier Justine , de Frutos Marta , Laurent Guillaume Pierre , Bertani Philippe , Djediat Chakib , Marin Frédéric , Auzoux-Bordenave Stéphanie , Azaïs Thierry , Nassif Nadine 
Published: March 2022

AbstractThe presence of phosphate from different origins (inorganic, bioorganic) is found more and more in calcium carbonate-based biominerals. Phosphate is often described as being responsible for the stabilization of the transient amorphous calcium carbonate phase. In order to specify the composition of the mineral phase deposited at the onset of carbonated shell formation, the present study investigates, down to the nanoscale, the growing shell from the European abalone Haliotis tuberculata, using a combination of solid state nuclear magnetic resonance, scanning transmission electron microscope and spatially-resolved electron energy loss spectroscopy techniques. We show the co-occurrence of inorganic phosphate with calcium and carbonate throughout the early stages of abalone shell formation. One possible hypothesis is that this first-formed mixed mineral phase represents the vestige of a shared ancestral mineral precursor that appeared early during Evolution. In addition, our findings strengthen the idea that the final crystalline phase (calcium carbonate or phosphate) depends strongly on the nature of the mineral-associated proteins in vivo.
Rational design of hairpin RNA excited states reveals multi-step transitions
Authors: Han Ge , Xue Yi 
Published: March 2022

AbstractRNA excited states represent a class of high-energy-level and thus low-populated conformational states of RNAs that are sequestered within the free energy landscape until being activated by cellular cues. In recent years, there has been growing interest in structural and functional studies of these transient states, but the rational design of excited states remains unexplored. Here we developed a method to design small hairpin RNAs with predefined excited states that exchange with ground states through base pair reshuffling, and verified these transient states by combining NMR relaxation dispersion technique and imino chemical shift prediction. Using van’t Hoff analysis and accelerated molecular dynamics simulations, a mechanism of multi-step sequential transition has been revealed. The efforts made in this study will expand the scope of RNA rational design, and also contribute towards improved predictions of RNA secondary structure.
New recognition specificity in a plant immune receptor by molecular engineering of its integrated domain
Authors: Cesari Stella , Xi Yuxuan , Declerck Nathalie , Chalvon Véronique , Mammri Léa , Pugnière Martine , Henriquet Corinne , de Guillen Karine , Chochois Vincent , Padilla André , Kroj Thomas 
Published: March 2022

AbstractPlant nucleotide-binding and leucine-rich repeat domain proteins (NLRs) are immune sensors that recognize pathogen effectors. Here, we show that molecular engineering of the integrated decoy domain (ID) of an NLR can extend its recognition spectrum to a new effector. We relied for this on detailed knowledge on the recognition of the Magnaporthe oryzae effectors AVR-PikD, AVR-Pia, and AVR1-CO39 by, respectively, the rice NLRs Pikp-1 and RGA5. Both receptors detect their effectors through physical binding to their HMA (Heavy Metal-Associated) IDs. By introducing into RGA5_HMA the AVR-PikD binding residues of Pikp-1_HMA, we create a high-affinity binding surface for this effector. RGA5 variants carrying this engineered binding surface perceive the new ligand, AVR-PikD, and still recognize AVR-Pia and AVR1-CO39 in the model plant N. benthamiana. However, they do not confer extended disease resistance specificity against M. oryzae in transgenic rice plants. Altogether, our study provides a proof of concept for the design of new effector recognition specificities in NLRs through molecular engineering of IDs.
Breakdown of semiclassical description of thermoelectricity in near-magic angle twisted bilayer graphene
Authors: Ghawri Bhaskar , Mahapatra Phanibhusan S. , Garg Manjari , Mandal Shinjan , Bhowmik Saisab , Jayaraman Aditya , Soni Radhika , Watanabe Kenji , Taniguchi Takashi , Krishnamurthy H. R. , Jain Manish , Banerjee Sumilan , Chandni U. , Ghosh Arindam 
Published: March 2022

AbstractThe planar assembly of twisted bilayer graphene (tBLG) hosts multitude of interaction-driven phases when the relative rotation is close to the magic angle (θm = 1.1∘). This includes correlation-induced ground states that reveal spontaneous symmetry breaking at low temperature, as well as possibility of non-Fermi liquid (NFL) excitations. However, experimentally, manifestation of NFL effects in transport properties of twisted bilayer graphene remains ambiguous. Here we report simultaneous measurements of electrical resistivity (ρ) and thermoelectric power (S) in tBLG for several twist angles between θ ~ 1.0 − 1.7∘. We observe an emergent violation of the semiclassical Mott relation in the form of excess S close to half-filling for θ ~ 1.6∘ that vanishes for θ ≳ 2∘. The excess S (≈2 μV/K at low temperatures T ~ 10 K at θ ≈ 1.6∘) persists upto ≈40 K, and is accompanied by metallic T-linear ρ with transport scattering rate (τ−1) of near-Planckian magnitude τ−1 ~ kBT/ℏ. Closer to θm, the excess S was also observed for fractional band filling (ν ≈ 0.5). The combination of non-trivial electrical transport and violation of Mott relation provides compelling evidence of NFL physics intrinsic to tBLG.
Transposon insertional mutagenesis of diverse yeast strains suggests coordinated gene essentiality polymorphisms
Authors: Chen Piaopiao , Michel Agnès H. , Zhang Jianzhi 
Published: March 2022

AbstractDue to epistasis, the same mutation can have drastically different phenotypic consequences in different individuals. This phenomenon is pertinent to precision medicine as well as antimicrobial drug development, but its general characteristics are largely unknown. We approach this question by genome-wide assessment of gene essentiality polymorphism in 16 Saccharomyces cerevisiaestrains using transposon insertional mutagenesis. Essentiality polymorphism is observed for 9.8% of genes, most of which have had repeated essentiality switches in evolution. Genes exhibiting essentiality polymorphism lean toward having intermediate numbers of genetic and protein interactions. Gene essentiality changes tend to occur concordantly among components of the same protein complex or metabolic pathway and among a group of over 100 mitochondrial proteins, revealing molecular machines or functional modules as units of gene essentiality variation. Most essential genes tolerate transposon insertions consistently among strains in one or more coding segments, delineating nonessential regions within essential genes.
Endothelial pannexin-1 channels modulate macrophage and smooth muscle cell activation in abdominal aortic aneurysm formation
Authors: Filiberto Amanda C. , Spinosa Michael D. , Elder Craig T. , Su Gang , Leroy Victoria , Ladd Zachary , Lu Guanyi , Mehaffey J. Hunter , Salmon Morgan D. , Hawkins Robert B. , Ravichandran Kodi S. , Isakson Brant E. , Upchurch Gilbert R. , Sharma Ashish K. 
Published: March 2022

AbstractPannexin-1 (Panx1) channels have been shown to regulate leukocyte trafficking and tissue inflammation but the mechanism of Panx1 in chronic vascular diseases like abdominal aortic aneurysms (AAA) is unknown. Here we demonstrate that Panx1 on endothelial cells, but not smooth muscle cells, orchestrate a cascade of signaling events to mediate vascular inflammation and remodeling. Mechanistically, Panx1 on endothelial cells acts as a conduit for ATP release that stimulates macrophage activation via P2X7 receptors and mitochondrial DNA release to increase IL-1β and HMGB1 secretion. Secondly, Panx1 signaling regulates smooth muscle cell-dependent intracellular Ca2+ release and vascular remodeling via P2Y2 receptors. Panx1 blockade using probenecid markedly inhibits leukocyte transmigration, aortic inflammation and remodeling to mitigate AAA formation. Panx1 expression is upregulated in human AAAs and retrospective clinical data demonstrated reduced mortality in aortic aneurysm patients treated with Panx1 inhibitors. Collectively, these data identify Panx1 signaling as a contributory mechanism of AAA formation.
cAMP and c-di-GMP synergistically support biofilm maintenance through the direct interaction of their effectors
Authors: Liu Cong , Sun Di , Liu Jiawen , Chen Ying , Zhou Xuge , Ru Yunrui , Zhu Jingrong , Liu Weijie 
Published: March 2022

AbstractNucleotide second messengers, such as cAMP and c-di-GMP, regulate many physiological processes in bacteria, including biofilm formation. There is evidence of cross-talk between pathways mediated by c-di-GMP and those mediated by the cAMP receptor protein (CRP), but the mechanisms are often unclear. Here, we show that cAMP-CRP modulates biofilm maintenance in Shewanella putrefaciens not only via its known effects on gene transcription, but also through direct interaction with a putative c-di-GMP effector on the inner membrane, BpfD. Binding of cAMP-CRP to BpfD enhances the known interaction of BpfD with protease BpfG, which prevents proteolytic processing and release of a cell surface-associated adhesin, BpfA, thus contributing to biofilm maintenance. Our results provide evidence of cross-talk between cAMP and c-di-GMP pathways through direct interaction of their effectors, and indicate that cAMP-CRP can play regulatory roles at the post-translational level.
Sociality predicts orangutan vocal phenotype
Authors: Lameira Adriano R. , Santamaría-Bonfil Guillermo , Galeone Deborah , Gamba Marco , Hardus Madeleine E. , Knott Cheryl D. , Morrogh-Bernard Helen , Nowak Matthew G. , Campbell-Smith Gail , Wich Serge A. 
Published: March 2022

AbstractIn humans, individuals’ social setting determines which and how language is acquired. Social seclusion experiments show that sociality also guides vocal development in songbirds and marmoset monkeys, but absence of similar great ape data has been interpreted as support to saltational notions for language origin, even if such laboratorial protocols are unethical with great apes. Here we characterize the repertoire entropy of orangutan individuals and show that in the wild, different degrees of sociality across populations are associated with different ‘vocal personalities’ in the form of distinct regimes of alarm call variants. In high-density populations, individuals are vocally more original and acoustically unpredictable but new call variants are short lived, whereas individuals in low-density populations are more conformative and acoustically consistent but also exhibit more complex call repertoires. Findings provide non-invasive evidence that sociality predicts vocal phenotype in a wild great ape. They prove false hypotheses that discredit great apes as having hardwired vocal development programmes and non-plastic vocal behaviour. Social settings mould vocal output in hominids besides humans.
DNA is loaded through the 9-1-1 DNA checkpoint clamp in the opposite direction of the PCNA clamp
Authors: Zheng Fengwei , Georgescu Roxana E. , Yao Nina Y. , O’Donnell Michael E. , Li Huilin 
Published: March 2022

AbstractThe 9-1-1 DNA checkpoint clamp is loaded onto 5′-recessed DNA to activate the DNA damage checkpoint that arrests the cell cycle. The 9-1-1 clamp is a heterotrimeric ring that is loaded in Saccharomyces cerevisiae by Rad24-RFC (hRAD17-RFC), an alternate clamp loader in which Rad24 replaces Rfc1 in the RFC1-5 clamp loader of proliferating cell nuclear antigen (PCNA). The 9-1-1 clamp loading mechanism has been a mystery, because, unlike RFC, which loads PCNA onto a 3′-recessed junction, Rad24-RFC loads the 9-1-1 ring onto a 5′-recessed DNA junction. Here we report two cryo-EM structures of Rad24-RFC–DNA with a closed or 27-Å open 9-1-1 clamp. The structures reveal a completely unexpected mechanism by which a clamp can be loaded onto DNA. Unlike RFC, which encircles DNA, Rad24 binds 5′-DNA on its surface, not inside the loader, and threads the 3′ ssDNA overhang into the 9-1-1 clamp from above the ring.