bluuebunny/crossref_metadata_2025_split huggingface dataset:
Enhanced hexamerization of insulin via assembly pathway rerouting revealed by single particle studies
Authors: Bohr Freja , Bohr Søren S.-R. , Mishra Narendra Kumar , Foutel Nicolás Sebastian González , Pinholt Henrik Dahl , Wu Shunliang , Nielsen Emilie Milan , Zhang Min , Kjaergaard Magnus , Jensen Knud J. , Hatzakis Nikos S. 
Published: April 2022

AbstractInsulin formulations are the hallmark of interventions for treatment of diabetes. Understanding the mechanism that governs insulin self assembly or disassembly —and the role of stabilizing additives—are essential for improving insulin formulations. We report here the real-time direct observation of single insulin self-assembly and disassembly events using single molecule fluorescence microscopy. Our direct observations revealed previously unaccounted monomeric additions to occur to all types of assemblies and allowed us to quantify the existence, abundance and kinetic characterization of diverse assembly pathways involving monomeric dimers or tetrameric insulin species. We proposed and experimentally validated a model where the insulin self-assembly pathway is rerouted favoring monomeric or oligomeric assembly events by solution concentration, additives and formulations. Our rate simulation predicted the abundance of each oligomeric species across a concentration range of 6 orders of magnitude. Besides providing fundamental new insights, the results and toolbox here can be universally applied contributing to the development of optimal insulin formulations and the deciphering of oligomerization mechanisms for other proteins.
Salicin modifies osteoarthritis progression by binding on IRE1α and inhibiting IRE1α mediated endoplasmic reticulum stress
Authors: Zhu Zhenglin , Gao Shengqiang , Chen Cheng , Xu Wei , Xiao Pengcheng , Chen Zhiyu , Du Chengcheng , Chen Bowen , Gao Yan , Wang Chunli , Liao Junyi , Huang Wei 
Published: April 2022

AbstractObjectivesTo investigate the effect and mechanisms of salicin (SA) on osteoarthritis (OA) progression.MethodsPrimary rat chondrocytes were stimulated with TNF-α and treated with or without SA. CCK-8 was utilized to determine the cytotoxicity of SA. RT-qPCR, Western Blotting and immunofluorescence staining were used to detect inflammatory factors, cartilage matrix degeneration markers, cell proliferation and apoptosis markers expression at mRNA and protein levels respectively. EdU assay and flow cytometer analysis were utilized for evaluating cell proliferation and apoptosis. RNA-sequencing, molecular docking, drug affinity responsive target stability and WB were applied to clarify mechanisms. Rat OA model was used to evaluate the effect of intra-articular injection of SA on OA progression.ResultsNo obvious cytotoxicity was found with the treatment of 10 μM SA. SA rescued TNF-α induced degeneration of cartilage matrix, inhibition of chondrocytes proliferation, and promotion of chondrocytes apoptosis. In mechanism, we clarified SA could directly bind on IRE1α and occupy IRE1α phosphorylation site, followed with inhibiting IRE1α phosphorylation and regulating IRE1α mediated endoplasmic reticulum (ER) stress by IRE1α-IκBα-p65 signaling. Finally, intra-articular injection of SA loaded PLGA could ameliorate OA progression by inhibiting IRE1α mediated ER stress in OA model.ConclusionsSA alleviates OA by directly binding on ER stress regulator IRE1α and inhibits IRE1α mediated ER stress by IRE1α-IκBα-p65 signaling. Topical use of small molecular drug SA holds the potential of modifying OA progression.
A Lysozyme Murein Hydrolase with Broad-spectrum Antibacterial Activity from Enterobacter Phage myPSH1140
Authors: Ramesh Nachimuthu , Manohar Prasanth , Eniyan Kandasamy , Archana Loganathan , Athira Sudarsanan , Loh Belinda , Ma Long , Leptihn Sebastian 
Published: April 2022

AbstractBacteriophages and bacteriophage-derived peptidoglycan hydrolases (endolysins) present promising alternatives for the treatment of infections caused by multi-drug resistant Gram-negative and Gram-positive pathogens. In this study, Gp105, a putative lysozyme murein hydrolase from Enterobacter phage myPSH1140 was characterized in silico, in vitro as well as in vivo using the purified protein. Gp105 contains a T4-type lysozyme-like domain (IPR001165) and belongs to Glycoside hydrolase family 24 (IPR002196). The putative endolysin indeed had strong antibacterial activity against Gram-negative pathogens including E. cloacae, K. pneumoniae, P. aeruginosa, S. marcescens, Citrobacter sp. and A. baumannii. Also, an in vitro peptidoglycan hydrolysis assay showed strong activity against purified peptidoglycans. This study demonstrates the potential of Gp105 to be used as an antibacterial protein to combat Gram-negative pathogens.
Fixed-Target Serial Crystallography at Structural Biology Center
Authors: Sherrell Darren A. , Lavens Alex , Wilamowski Mateusz , Kim Youngchang , Chard Ryan , Lazarski Krzysztof , Rosenbaum Gerold , Vescovi Rafael , Johnson Jessica L. , Akins Chase , Chang Changsoo , Michalska Karolina , Babnigg Gyorgy , Foster Ian , Joachimiak Andrzej 
Published: April 2022

ABSTRACTSerial synchrotron crystallography enables studies of protein structures under physiological temperature and reduced radiation damage by collection of data from thousands of crystals. The Structural Biology Center at Sector 19 of the Advanced Photon Source has implemented a fixed-target approach with a new 3D printed mesh-holder optimized for sample handling. The holder immobilizes a crystal suspension or droplet emulsion on a nylon mesh, trapping and sealing a near-monolayer of crystals in its mother liquor between two thin mylar films. Data can be rapidly collected in scan mode and analyzed in near real-time using piezoelectric linear stages assembled in an XYZ arrangement, controlled with a graphical user interface and analyzed by using a high-performance computing pipeline. Here, the system was applied to two β-lactamases: a class D serine β-lactamase from Chitinophaga pinensis DSM 2588 and L1 metallo-β -lactamase from Stenotrophomonas maltophilia K279a.
Transformation of the symbiotic alga Oophila amblystomatis : a new toolbox for animal-algae symbiosis studies
Authors: Genot Baptiste , Burns John A 
Published: April 2022

AbstractThe ability to conduct reverse genetic studies in symbiotic systems is enabled by transgene expression and transformation of at least one partner. The symbiotic relationship between the yellow spotted salamander, Ambystoma maculatum, and the green alga, Oophila amblystomatis, is a unique model of vertebrate-algae symbiosis. Despite over 130 years of scientific study, there are still many open questions in this symbiosis. Transgene expression in one partner will accelerate research into the symbiotic relationship. In this paper we describe a tool and method for expression of foreign DNA in, and presumed transformation of, the alga O. amblystomatis. We successfully introduced heritable antibiotic resistance to algal cultures, and observed expression of a green fluorescent reporter protein in all transfected and presumably transformed algal populations. The outcomes of this work enable genetic manipulation of the symbiotic alga Oophila amblystomatis, allowing direct testing of hypotheses derived from gene expression or genomic studies that will usher in a deeper understanding of the A. maculatum-O. amblystomatis symbiotic system.Summary statementGenetic tools stimulate new possibilities for research in living systems. This work describes a new tool for transformation of a symbiotic alga that enters vertebrate tissues and cells.
Rapid Rerouting of Myosin Traffic at the T Cell Immunological Synapse
Authors: Mąka Robert , Plewa Natalia , Cichoń Urszula , Krysztofiak Katarzyna , Rokicka Jagoda J. , Rock Ronald S. 
Published: April 2022

AbstractCytoskeletal motors travel in patterns set by the architecture of their tracks. Nevertheless, we have a limited understanding of how cells dynamically reorganize their traffic patterns in response to signaling events. To investigate cytoskeletal motor rerouting, we used T cells as a model system. Upon an encounter between a T cell and an antigen presenting cell, the T cell builds a specialized interface with spatially organized immunoreceptors and adhesion molecules called the immunological synapse (IS). The IS also constructs new actin networks within minutes that define the synaptic structure. Here we track the movements of single myosin motors along presynaptic and synaptic actin networks of the T cell. We find that both myosin-5 and myosin-6 reroute after IS construction. For example, most myosin-5 traffic moves inward at the IS, although most of the IS actin filaments have a barbed end out orientation. This anomalous myosin-5 traffic pattern indicates that the IS makes two types of actin networks: a structural network that controls IS shape, and a distinct trafficking network that supports myosin motility. We disrupt these trafficking networks with chemical probes against actin, which inhibits the appearance of cell surface markers of T cell activation. Our results highlight the importance of the sparse actin networks at the center of the IS in T cell function.
A salt bridge-mediated resistance mechanism to FtsZ inhibitor PC190723 revealed by a cell-based screen
Authors: Sharma Ajay Kumar , Poddar Sakshi Mahesh , Chakraborty Joyeeta , Nayak Bhagyashri Soumya , Kalathil Srilakshmi , Mitra Nivedita , Gayathri Pananghat , Srinivasan Ramanujam 
Published: April 2022

AbstractBacterial cell division proteins, especially the tubulin homolog FtsZ, have emerged as strong targets for developing new antibiotics. Here, we have utilized the fission yeast heterologous expression system to develop a cell-based assay to screen for small molecules that directly and specifically target the bacterial cell division protein FtsZ. The strategy also allows for simultaneous assessment of the toxicity of the drugs to eukaryotic yeast cells. As a proof-of-concept of the utility of this assay, we demonstrate the effect of the inhibitors sanguinarine, berberine and PC190723 on FtsZ. Though sanguinarine and berberine affect FtsZ polymerization, they exert a toxic effect on the cells. Further, using this assay system, we show that PC190723 affectsHelicobacter pyloriFtsZ function and gain new insights into the molecular determinants of resistance to PC190723. Based on sequence and structural analysis and site-specific mutations, we demonstrate that the presence of salt-bridge interactions between the central H7 helix and beta-strands S9 and S10 mediate resistance to PC190723 in FtsZ. The single-stepin vivocell-based assay using fission yeast enabled us to dissect the contribution of sequence-specific features of FtsZ and cell permeability effects associated with bacterial cell envelopes. Thus, our assay serves as a potent tool to rapidly identify novel compounds targeting polymeric bacterial cytoskeletal proteins like FtsZ to understand how they alter polymerization dynamics and address resistance determinants in targets.
Circadian clock control of MRTF-SRF pathway suppresses beige adipocyte thermogenic recruitment
Authors: Xiong Xuekai , Li Weini , Liu Ruya , Saha Pradip , Yechoor Vijay , Ma Ke 
Published: April 2022

ABSTRACTThe morphological transformation of adipogenic progenitors into mature adipocytes requires dissolution of cytoskeleton driven by progressive loss of MRTF-SRF activity. Circadian clock confers temporal control in adipogenic differentiation, and MRTF-SRF inhibits beige adipocyte development. Here we identify that key components of the actin cytoskeleton-MRTF/SRF signaling cascade are direct transcriptional targets of circadian clock, and a clock-MRTF/SRF regulatory axis suppresses beige adipocyte thermogenic recruitment. Genetic loss- or gain-of-functions of the core clock regulator, Brain and Muscle Arnt-like 1 (Bmal1), altered actin cytoskeleton organization, cell shape and SRF activity. Genes involved in actin dynamic-MRTF-SRF pathway display diurnal expression profiles in beige adipose tissue, with identification of Bmal1 direct transcriptional regulation. Using beige adipocyte-selective genetic models together with pharmacological approaches, we demonstrate that Bmal1 inhibits beige adipogenesis and thermogenic capacity via the MRTF-SRF pathway. Selective ablation of Bmal1 induced beigeing, whereas its targeted overexpression attenuated the beige thermogenic program resulting in obesity. Collectively, our findings define a novel circadian clock control in actin cytoskeleton-MRTF-SRF signaling that suppresses beige adipogenesis to maintain metabolic homeostasis.
The intergenerational transmission of educational attainment: A closer look at the (interrelated) roles of paternal involvement and genetic inheritance
Authors: Verweij Renske , Keizer Renske 
Published: April 2022

AbstractNumerous studies have documented a strong intergenerational transmission of educational attainment. In explaining this transmission, separate fields of research have studied separate mechanisms. To obtain a more complete understanding, the current study integrates insights from the fields of behavioural sciences and genetics and examines the extent to which factors from each field are unique underlying mechanisms, correlate with each other, and/or act as important confounders in the intergenerational transmission of educational attainment. Specifically, we focus on paternal involvement as our behavioural indicator and children’s polygenic score (PGS) for education as our genetic indicator and assess the role that fathers play in the intergenerational transmission of educational attainment. To answer our research questions, we use rich data from The National Longitudinal Study of Adolescent to Adult Health (n=4,579). Firstly, results from our mediation analyses showed that about 4 per cent of the effect of fathers’ educational attainment on children’s educational attainment is explained by paternal involvement, whereas a much larger share, 21 per cent, is explained by children’s education PGS. Secondly, our results showed that these genetic and behavioural influences are significantly correlated to each other. Thirdly, we found support for genetic confounding, as adding children’s education PGS to the model reduced the effect of paternal involvement by 11 per cent. Fourthly, evidence for social confounding was almost negligible (a reduction of half a per cent of the genetic effect). Our findings highlight the importance of integrating insights and data from multiple disciplines in understanding the mechanisms underlying the intergenerational transmission of inequality, as our study reveals that behavioural and genetic influences overlap, correlate, and confound each other as mechanisms underlying this transmission.
Deposit-feeding worms control subsurface ecosystem functioning in intertidal sediment with strong physical forcing
Authors: Deng Longhui , Meile Christof , Fiskal Annika , Bölsterli Damian , Han Xingguo , Gajendra Niroshan , Dubois Nathalie , Bernasconi Stefano M. , Lever Mark A. 
Published: April 2022

AbstractIntertidal sands are global hotspots of terrestrial and marine carbon cycling with strong hydrodynamic forcing by waves and tides and high macrofaunal activity. Yet, the relative importance of hydrodynamics and macrofauna in controlling these ecosystems remains unclear. Here we compare bacterial, archaeal, and eukaryotic communities in upper intertidal sands dominated by subsurface deposit-feeding worms (Abarenicola pacifica) to adjacent worm-free areas. We show that hydrodynamic forcing controls organismal assemblages in surface sediments, while in deeper layers selective feeding by worms on fine, algae-rich particles strongly decreases the abundance and richness of all three domains. In these deeper layers, bacterial and eukaryotic network connectivity decreases, while percentages of taxa involved in degradation of refractory organic macrostructures, oxidative nitrogen and sulfur cycling, and macrofaunal symbioses, increase. Our findings reveal macrofaunal activity as the key driver of ecosystem functioning and carbon cycling in intertidal sands below the mainly physically controlled surface layer.Significance StatementHydrodynamics and bioturbation are the main forces controlling chemical exchanges between sediment and seawater in coastal environments. However, little is known about the relative impact of both processes on sediment biological communities. We show that intertidal sand ecosystems dominated by lugworms can be divided into vertically distinct hydrodynamically and biologically controlled layers. Hydrodynamic forcing controls biological communities in surface layers by regulating organic carbon and electron acceptor inputs. By contrast, lugworms structure subsurface ecosystems through the selective consumption of fine particles, which diminishes microbial and eukaryotic populations and weakens ecological networks, while promoting the burial of, mostly terrestrial, macrodetritus. Our study demonstrates that globally distributed marine invertebrates control intertidal sand ecosystems below the physically controlled surface layer.
Stabilizing brain-computer interfaces through alignment of latent dynamics
Authors: Karpowicz Brianna M. , Ali Yahia H. , Wimalasena Lahiru N. , Sedler Andrew R. , Keshtkaran Mohammad Reza , Bodkin Kevin , Ma Xuan , Miller Lee E. , Pandarinath Chethan 
Published: April 2022

AbstractIntracortical brain-computer interfaces (iBCIs) restore motor function to people with paralysis by translating brain activity into control signals for external devices. In current iBCIs, instabilities at the neural interface result in a degradation of decoding performance, which necessitates frequent supervised recalibration using new labeled data. One potential solution is to use the latent manifold structure that underlies neural population activity to facilitate a stable mapping between brain activity and behavior. Recent efforts using unsupervised approaches have improved iBCI stability using this principle; however, existing methods treat each time step as an independent sample and do not account for latent dynamics. Dynamics have been used to enable high performance prediction of movement intention, and may also help improve stabilization. Here, we present a platform for Nonlinear Manifold Alignment with Dynamics (NoMAD), which stabilizes iBCI decoding using recurrent neural network models of dynamics. NoMAD uses unsupervised distribution alignment to update the mapping of nonstationary neural data to a consistent set of neural dynamics, thereby providing stable input to the iBCI decoder. In applications to data from monkey motor cortex collected during motor tasks, NoMAD enables accurate behavioral decoding with unparalleled stability over weeks-to months-long timescales without any supervised recalibration.
A transcriptional network required for Toxoplasma gondii tissue cyst formation is dispensable for long-term persistence
Authors: Borrelli Sarah Sokol , Reilly Sarah M. , Sharp Katherine G. , Cabo Leah F. , Alrubaye Hisham S. , Di Genova Bruno Martorelli , Boyle Jon P. 
Published: April 2022

AbstractCyst formation is a key feature of the T. gondii life cycle but the genetic networks that drive this process are not yet fully characterized. To identify new components of this network, we compared T. gondii to its nearest extant relative Hammondia hammondi given the critical differences between these species in the timing and efficiency of cyst formation. Using transcriptional data from critical developmental and pH exposure time points from both species, we identified the gene TGVEG_311100, which we named Regulator of Cystogenesis 1 (ROCY1), as being both necessary and sufficient for cyst formation in T. gondii. Compared to WT parasites, TGVEGΔROCY1 parasites formed significantly fewer tissue cysts in response to alkaline pH stress in vitro and cysts were nearly undetectable in mouse brains for up to 9 weeks post-infection. Overexpression of tagged ROCY1 in WT parasites was sufficient to induce cyst formation in vitro in both WT and ROCY1-deficient parasites, demonstrating that ROCY1 is both necessary and sufficient for cyst formation. Moreover this induction of cyst formation required at least 1 of 3 predicted CCCH Zinc finger domains. Mice chronically infected with ΔROCY1 parasites had detectable tachyzoites in the brain for up to 37 days post-infection (while mice infected with WT parasites did not), and CNS transcriptional analyses at day 30 post-infection throughout the chronic phase of infection revealed inflammatory signatures consistent with acute infection in ΔROCY1 parasites compared to WT. Despite our inability to detect brain cysts in infected mice, both WT and ΔROCY1 knockout parasites reactivated after dexamethasone treatment with similar timing and magnitude for up to 5 months post infection, challenging the paradigm that long term parasite persistence in the CNS requires cyst formation. These data identify a new regulator of cyst formation in T. gondii that is both necessary and sufficient for cyst formation, and whose function relies on its conserved nucleic acid binding motif.
Structures and comparison of endogenous 2-oxoglutarate and pyruvate dehydrogenase complexes from bovine kidney
Authors: Liu Shiheng , Xia Xian , Zhen James , Li Zihang , Zhou Z. Hong 
Published: April 2022

AbstractThe α-keto acid dehydrogenase complex family catalyzes the essential oxidative decarboxylation of α-keto acids to yield acyl-CoA and NADH. Despite performing the same overarching reaction, members of the family have different component structures and structural organization between each other and across phylogenetic species. While native structures of α-keto acid dehydrogenase complexes from bacteria and fungi became available recently, the atomic structure and organization of their mammalian counterparts in their native states remain unknown. Here, we report the cryo electron microscopy (cryoEM) structures of the endogenous cubic 2-oxoglutarate dehydrogenase complex (OGDC) and icosahedral pyruvate dehydrogenase complex (PDC) cores from bovine kidney determined at 3.5 Å and 3.8 Å resolution, respectively. The structures of multiple protein were reconstructed from a single lysate sample, allowing direct structural comparison without the concerns of differences arising from sample preparation and structure determination. Although native and recombinant E2 core scaffold structures are similar, native structures are decorated with their peripheral E1 and E3 subunits. Asymmetric sub-particle reconstructions support heterogeneity in the arrangements of these peripheral subunits. Additionally, despite sharing a similar monomeric fold, OGDC and PDC E2 cores have distinct interdomain and intertrimer interactions, which suggests a means of modulating self-assembly to mitigate heterologous binding between mismatched E2 species. The lipoyl moiety lies near a mobile gatekeeper within the interdomain active site of OGDC E2 and PDC E2. Analysis of the two-fold related intertrimer interface identified secondary structural differences and chemical interactions between icosahedral and cubic geometries of the core. Taken together, our study provides direct structural comparison of OGDC and PDC from the same source and offers new insights into determinants of interdomain interactions and of architecture diversity among α-keto acid dehydrogenase complexes.