bluuebunny/crossref_metadata_2025_split huggingface dataset:
HfaE is a component of the holdfast anchor complex that tethers the holdfast adhesin to the cell envelope
Authors: Chepkwony Nelson K. , Hardy Gail G. , Brun Yves V. 
Published: July 2022

ABSTRACTBacteria use adhesins to colonize different surfaces and form biofilms. The species of the Caulobacterales order use a polar adhesin called holdfast, composed of polysaccharides, proteins, and DNA to irreversibly adhere to surfaces. InC. crescentus,a freshwater Caulobacterales, the holdfast is anchored at the cell pole via theholdfastanchor (Hfa) proteins HfaA, HfaB, and HfaD. HfaA and HfaD co-localize with holdfast and are thought to form amyloid-like fibers that anchor holdfast to the cell envelope. HfaB, a lipoprotein, is required for translocation of HfaA and HfaD to the cell surface. Deletion of the anchor proteins leads to a severe defect in adherence resulting from holdfast not properly attached to the cell and shed into the medium. This phenotype is greater in a ΔhfaBthan a double ΔhfaA hfaDmutant, suggesting that HfaB has other functions besides the translocation of HfaA and HfaD. Here, we identify an additional HfaB-dependent holdfast anchoring protein, HfaE, which is predicted to be a secreted protein. HfaE is highly conserved among Caulobacterales species with no predicted function. In planktonic culture,hfaEmutants produce holdfasts and rosettes similar to wild type. However, holdfasts fromhfaEmutants bind to the surface but are unable to anchor cells, similar to other anchor mutants. We showed that fluorescently-tagged HfaE co-localizes with holdfast, and HfaE forms an SDS-resistant high molecular weight species consistent with amyloid fiber formation. We propose that HfaE is a novel holdfast anchor protein, and that HfaE functions to link holdfast material to the cell envelope.IMPORTANCEFor surface attachment and biofilm formation, bacteria produce adhesins that are composed of polysaccharides, proteins and DNA. Species in the Caulobacterales produce a specialized polar adhesin, holdfast, which is required for permanent attachment to surfaces. In this study, we evaluate the role of a newly identified holdfast anchor protein HfaE in holdfast anchoring to the cell surface in two different Caulobacterales with drastically different environments. We show that HfaE plays an important role in adhesion and biofilm formation in Caulobacterales. Our results provide insights into bacterial adhesins and how they interact with the cell envelope and surfaces.
A distinct symptom pattern emerges for COVID-19 Long-Haul: A nationwide study
Authors: Downs Charles A , Pinto Melissa D. , Huang Yong ,   Survivor Corps, El-Azab Sarah A. , Ramrakhiani Nathan S. , Barisano Anthony , Yu Lu , Taylor Kaitlyn , Esperanca Alvaro , Abrahim Heather L. , Hughes Thomas , Herrera Maria Giraldo , Rahmani Amir M. , Dutt Nikil , Chakraborty Rana , Mendiola Christian , Lambert Natalie 
Published: July 2022

ABSTRACTLong-haul COVID-19, also called Post-Acute Sequelae of SARS-CoV-2 (PASC), is a new illness caused by SARS-CoV-2 infection and characterized by the persistence of symptoms. The purpose of this cross-sectional study was to identify a distinct and significant temporal pattern of PASC symptoms (symptom type and onset) among a nationwide sample of PASC survivors (n= 5,652). The sample was randomly sorted into two independent samples for exploratory (EFA) and confirmatory factor analyses (CFA). Five factors emerged from the EFA: (1) cold & flu-like symptoms, (2) change in smell and/or taste, (3) dyspnea and chest pain, (4) cognitive & visual problems, and (5) cardiac symptoms. The CFA had excellent model fit (x2 = 513.721, df= 207, p<0.01, TLI= 0.952, CFI= 0.964, RMSEA= 0.024). These findings demonstrate a novel symptom pattern for PASC. These findings can enable nurses in the identification of at-risk patients and facilitate early, systematic symptom management strategies for PASC.
Sodium-glucose cotransporter 2 inhibitors versus dipeptidyl peptidase 4 inhibitors on new-onset overall cancer in type 2 diabetes mellitus: a population-based study
Authors: Chung Cheuk To , Lakhani Ishan , Chou Oscar Hou-In , Loy Lee Teddy Tai , Dee Christopher , Ng Kendrick , Wong Wing Tak , Liu Tong , Lee Sharen , Zhang Qingpeng , Yung Cheung Bernard Man , Tse Gary , Zhou Jiandong 
Published: July 2022

AbstractBackgroundThere is much uncertainty regarding the comparative risks of cancer for T2DM patients on SGLT2I versus DPP4I.MethodsThis population-based cohort study patients included T2DM patients who were administered with either SGLT2I or DPP4I between January 1st, 2015, to December 31st, 2020 in Hong Kong.ResultsAmongst 60112 T2DM patients (mean baseline age: 62.1±12.4 years, male: 56.36%), 18167 patients were SGLT2I users and 41945 patients were DPP4I users. Multivariate cox regression analysis revealed that SGLT2I usage was associated with a decreased risk of all-cause mortality (HR:0.92; 95%CI:0.84-0.99; P=0.04), cancer-related mortality (HR:0.58; 95%CI:0.42-0.80; P≤0.001) and a 30% risk reduction of new-onset overall cancer (HR:0.70; 95%CI:0.59-0.84; P≤0.001). Dapagliflozin and ertugliflozin both demonstrated superiority in relation to new-onset cancer development, with the former demonstrating a lowered risk of breast cancer (HR:0.48; 95%CI:0.27-0.83; P=0.001).ConclusionSGLT2I was associated with lower risk of all-cause mortality, cancer-related mortality and new-onset overall cancer compared to DPP4I.
Structures of the interleukin 11 signalling complex reveal dynamics of gp130 extracellular domains and the inhibitory mechanism of a cytokine variant
Authors: Metcalfe Riley D. , Hanssen Eric , Fung Ka Yee , Aizel Kaheina , Kosasih Clara C. , Zlatic Courtney O. , Doughty Larissa , Morton Craig J. , Leis Andrew P. , Parker Michael W. , Gooley Paul R. , Putoczki Tracy L. , Griffin Michael D.W. 
Published: July 2022

SummaryInterleukin (IL-)11, an IL-6 family cytokine, has pivotal roles in numerous autoimmune diseases, fibrotic complications, and solid cancers. Despite intense therapeutic targeting efforts, structural understanding of IL-11 signalling and mechanistic insights into current inhibitors is lacking. Here we present cryo-EM and crystal structures of the IL-11 signalling complex, including the complex containing the complete extracellular domains of the shared IL-6 family β-receptor, gp130. We show that the membrane-proximal domains of gp130 are dynamic and do not participate in complex assembly. We demonstrate that the cytokine mutant ‘IL-11 Mutein’ competitively inhibits signalling in human cell lines. Structural shifts in IL-11 Mutein underlie inhibitory activity by altering cytokine binding interactions at all three receptor-engaging sites and abrogating the final gp130 binding step. Our results reveal the structural basis of IL-11 signalling, define the molecular mechanisms of an inhibitor, and advance understanding of gp130-containing receptor complexes, with potential applications in therapeutic development.
Current state, existing challenges, and promising progress for de novo sequencing and assembly of monoclonal antibodies
Authors: Beslic Denis , Tscheuschner Georg , Renard Bernhard Y. , Weller Michael G. , Muth Thilo 
Published: July 2022

AbstractMonoclonal antibodies (mAbs) are biotechnologically produced proteins with various applications in research, therapeutics, and diagnostics. Their ability to recognize and bind to specific molecule structures makes them essential research tools and therapeutic agents. Sequence information of antibodies is helpful for understanding antibody-antigen interactions and ensuring their affinity and specificity. De novo protein sequencing based on mass spectrometry is a useful method to obtain the amino acid sequence of peptides and proteins without a priori knowledge. Deep learning-based approaches have been developed and applied more frequently to increase the accuracy of de novo sequencing. In this study, we evaluated five recently developed de novo sequencing algorithms (Novor, pNovo 3, DeepNovo, SMSNet, and PointNovo) in their ability to identify and assemble antibody sequences. The deep learning-based tools PointNovo and SMSNet showed an increased peptide recall across different enzymes and datasets compared to spectrum-graph-based approaches. We evaluated different error types of de novo peptide sequencing tools and their performance for different numbers of missing cleavage sites, noisy spectra, and peptides of various lengths. We achieved a sequence coverage of 93.15% to 99.07% on the light chains of three different antibody datasets using the de Bruijn assembler ALPS and the predictions from PointNovo. However, low sequence coverage and accuracy on the heavy chains demonstrate that complete de novo protein sequencing remains a challenging issue in proteomics that requires improved de novo error correction, alternative digestion strategies, and hybrid approaches such as homology search to achieve high accuracy on long protein sequences.
Trends in forest carbon offset markets in United States
Authors: Kaarakka Lilli , Rothey Julia , Dee Laura E. 
Published: July 2022

AbstractNatural climate solutions are gaining international policy attention – with forests highlighted as a primary pathway for storing carbon. However, evaluations of additional carbon benefits and the permanence of forest carbon offsets projects remain scarce. In response, we compiled a novel database to analyze trends in existing forest management projects from the two largest offset project registries in the only carbon market in United States. We find that improved forest management projects represent 96% of all credits from forestry projects and 58% of all credits and span diverse practices with different potential for carbon storage. Our results also show that 26% of existing forest C offsets in the US are at risk from wildfire. From a policy perspective, our results underscore the need for more sophisticated insurance mechanisms for forest carbon offset reversals, and for a framework to monitor and evaluate cumulative and future carbon benefits of forest-based offset projects.SignificanceWe assess trends in ownership, forest management practices and disturbance risks in existing forest carbon offset projects in the US.
The fitness landscape of the mobilized colistin resistance gene mcr-1
Authors: Guo Ziyan , Feng Siyuan , Liang Lujie , Li Jiachen , Zhong Lan-Lan , Zhao Hui , Tian Guo-bao , Yang Jian-Rong 
Published: July 2022

AbstractThe emergence and global discovery of the mobilized colistin resistance gene, mcr-1, limits the clinical effectiveness of colistin as last-resort antibiotic against multiple-drug resistant bacteria. Although MCR-1 exhibits low levels of colistin resistance in E. coli, it is currently unknown whether mcr-1 may potentially evolve a high level of colistin resistance in the future. Here, we generated mcr-1 mutant library that included 27,965 variants, covering 94.44% of the single-nucleotide mutations. We quantified the relative growth of these variant strains under colistin exposure. Notably, most mutations in the catalytic domain, but not in the transmembrane domain, reduce colistin resistance. The structural basis for the mutational effects revealed that the transmembrane domain may contribute to MCR-1 evolution. Altogether, our data shed light on the prediction of MCR-1 evolution, which could be useful for designing novel treatment strategies.
Computational design of peptides to target NaV1.7 channel with high potency and selectivity for the treatment of pain
Authors: Nguyen Phuong T. , Nguyen Hai M. , Wagner Karen M. , Stewart Robert G. , Singh Vikrant , Thapa Parashar , Chen Yi-Je , Lillya Mark W. , Ton Anh Tuan , Kondo Richard , Ghetti Andre , Pennington Michael W. , Hammock Bruce , Griffith Theanne N. , Sack Jon T. , Wulff Heike , Yarov-Yarovoy Vladimir 
Published: July 2022

AbstractThe voltage-gated sodium NaV1.7 channel plays a key role as a mediator of action potential propagation in C-fiber nociceptors and is an established molecular target for pain therapy. ProTx-II is a potent and moderately selective peptide toxin from tarantula venom that inhibits human NaV1.7 activation. Here we used available structural and experimental data to guide Rosetta design of potent and selective ProTx-II-based peptide inhibitors of human NaV1.7 channels. Functional testing of designed peptides using electrophysiology identified the PTx2-3127 and PTx2-3258 peptides with IC50s of 7 nM and 4 nM for hNaV1.7 and more than 1,000-fold selectivity over human NaV1.1, NaV1.3, NaV1.4, NaV1.5, NaV1.8, and NaV1.9 channels. PTx2-3127 inhibits NaV1.7 currents in mouse and human sensory neurons and shows efficacy in rat models of chronic and thermal pain when administered intrathecally. Rationally-designed peptide inhibitors of human NaV1.7 channels have transformative potential to define a new class of biologics to treat pain.
Structural and functional analysis of the cerato-platanin-like effector protein Cpl1 suggests diverging functions in smut fungi
Authors: Weiland Paul , Dempwolff Felix , Steinchen Wieland , Freibert Sven-Andreas , Glatter Timo , Martin Roman , Bange Gert , Altegoer Florian 
Published: July 2022

AbstractPlant pathogenic fungi are causative agents of the majority of plant diseases and can lead to severe crop loss in infected populations. Fungal colonization is achieved by combining different strategies, such as avoiding and counteracting the plant immune system and manipulating the host metabolome. Of major importance are effector proteins secreted by the fungi that fulfill diverse functions to support the infection process. Most of these proteins are highly specialized and structural and biochemical information is often absent. Here, we present the atomic structures of the cerato-platanin-like protein Cpl1 from Ustilago maydis and its homolog Uvi2 from Ustilago hordei. Both proteins adopt a double-Ψ-β-barrel architecture reminiscent of cerato-platanin proteins, a class so far not described in smut fungi. Our structure-function analysis shows that Cpl1 binds to soluble chitin fragments via two extended grooves at the dimer interface of the two monomer molecules. This carbohydrate-binding mode has not been observed previously and expands the repertoire of chitin-binding proteins. Cpl1 localizes to the cell wall of U. maydis and specifically enriches cell-wall degrading and -decorating proteins during maize infection. The architecture of Cpl1 harboring four surface exposed loop regions supports the idea that it might play a role in spatial coordination of these proteins. While deletion of cpl1 has only mild effects on the virulence of U. maydis, a recent study showed that deletion of uvi2 strongly impairs U. hordei virulence. Our structural comparison between Cpl1 and Uvi2 reveals sequence variations in the loop regions which might explain a diverging function.
Characterization of hepatitis B viral forms from patient plasma using velocity gradient: evidence for an excess of capsids in Dane particles enriched fractions
Authors: Pronier Charlotte , Bomo Jérémy , Besombes Juliette , Genet Valentine , Laperche Syria , Gripon Philippe , Thibault Vincent 
Published: July 2022

AbstractHepatitis B virus (HBV) morphogenesis is characterized by a large over-production of subviral particles and recently described new forms in parallel of complete viral particles (VP). This study was designed to depict circulating viral forms in HBV infected patient plasmas, using velocity gradients and most sensitive viral markers.Plasmas from chronic hepatitis B (CHB) patients, HBeAg positive or negative, genotype D or E, were fractionated on velocity and equilibrium gradients with or without detergent treatment. Antigenic and molecular markers were measured in plasma and in each collected fraction.Fast Nycodenz velocity gradients revealed good reproducibility and provided additional information to standard equilibrium sucrose gradients. HBV-RNAs circulated as enveloped particles in all plasmas, except one, and at lesser concentrations than VP. Calculations based on standardized measurements and relative virion and subviral particle molecular stoichiometry allowed to refine the experimental approach. For the HBeAg-positive plasma, VP were accompanied by an overproduction of enveloped capsids, either containing HBs, likely corresponding to empty virions, or for the main part, devoid of this viral envelope protein. Similarly, in the HBeAg-negative sample, HBs enveloped capsids, likely corresponding to empty virions, were detected and the presence of enveloped capsids devoid of HBs protein was suspected but not clearly evidenced due to the presence of contaminating high-density subviral particles. While HBeAg largely influences HBcrAg measurement and accounts for two-thirds of HBcrAg reactivity in HBeAg-positive patients, it remains a 10 times more sensitive marker than HBsAg to characterize VP containing fractions.Using Nycodenz velocity gradients and standardized biomarkers, our study proposes a detailed characterization of circulating viral forms in chronically HBV infected patients. We provide evidence for an excess of capsids in DNA enriched fractions, likely due to the presence of empty virions but also by capsids enveloped by an HBs free lipid layer. Identification of this new circulating viral particle sets the basis for studies around the potential role of these entities in hepatitis B pathogeny and their physiological regulation.
Plant genotype influence the structure of cereal seed fungal microbiome
Authors: Malacrinò Antonino , Abdelfattah Ahmed , Belgacem Imen , Schena Leonardo 
Published: July 2022

AbstractPlant genotype is a crucial factor for the assembly of the plant-associated microbial communities. However, we still know little about the variation of diversity and structure of plant microbiomes across host species and genotypes. Here, we used six species of cereals (Avena sativa, Hordeum vulgare, Secale cereale, Triticum aestivum, Triticum polonicum, and Triticum turgidum) to test whether the plant fungal microbiome varies across species, whether plant species use different mechanisms for microbiome assembly focusing on the plant ears. Using ITS2 amplicon sequencing, we found that host species influences the diversity and structure of the seed-associated fungal communities. Then, we tested whether plant genotype influences the structure of seed fungal communities across different cultivars of T. aestivum (Aristato, Bologna, Rosia, and Vernia) and T. turgidum (Capeiti, Cappelli, Mazzancoio, Trinakria, and Timilia). We found that cultivar influences the seed fungal microbiome in both species. We found that in T. aestivum the seed fungal microbiota is more influenced by stochastic processes, while in T. turgidum selection plays a major role. Collectively, our results contribute in filling the knowledge gap on the wheat seed microbiome assembly and might help in understanding how we can manipulate this process to improve agriculture sustainability.
Dissecting the roles of Expansion/Rebuf and the chitin synthase Krotzkopf Verkehrt in chitin deposition inDrosophila
Authors: De Giorgio Ettore , Giannios Panagiotis , Espinàs M. Lluisa , Llimargas Marta 
Published: July 2022

ABSTRACTChitin is a highly abundant polymer in nature and a principal component of apical extracellular matrices in insects. In addition, chitin has proved to be an excellent biomaterial with multiple applications. In spite of its importance, the molecular mechanisms of chitin biosynthesis and chitin structural diversity are not fully elucidated yet. To investigate these issues, we useDrosophilaas a model. We previously showed that chitin deposition in ectodermal tissues requires the concomitant activities of the chitin synthase enzyme Kkv and the functionally interchangeable proteins Exp and Reb. Here we carry out a cellular and molecular analysis of chitin deposition and we show that chitin polymerisation and chitin translocation to the extracellular space are uncoupled. We find that Kkv activity in chitin translocation, but not in polymerisation, requires the activity of Exp/Reb, and in particular of its conserved Nα-MH2 domain. The activity of Kkv in chitin polymerisation and translocation correlate with Kkv subcellular localisation, and in absence of Kkv-mediated extracellular chitin deposition, chitin accumulates intracellularly as membrane-less punctae. Furthermore, we find that Kkv and Exp/Reb display a largely complementary pattern at the apical domain, and that Exp/Reb activity regulates the topological distribution of Kkv at the apical membrane. We propose a model in which Exp/Reb regulates the organisation of Kkv complexes at the apical membrane which, in turn, regulates the function of Kkv in extracellular chitin translocation.
Distinct mechanisms of CB1 and GABABreceptor presynaptic modulation of striatal indirect pathway projections to mouse Globus Pallidus
Authors: Sitzia Giacomo , Abrahao Karina Possa , Liput Daniel , Calandra Gian Marco , Lovinger David M. 
Published: July 2022

AbstractPresynaptic modulation is a fundamental process regulating synaptic transmission. Striatal indirect pathway projections originate from A2A- expressing spiny projection neurons (iSPNs), targeting the globus pallidus external segment (GPe) and control the firing of the tonically active GPe neurons via GABA release. It is unclear if and how the presynaptic GPCRs, GABABand CB1 receptors, modulate iSPN-GPe projections. Here we used an optogenetic platform to study presynaptic Ca2+and GABAergic transmission at iSPN projections, using a genetic strategy to express the calcium sensor GCaMP6f or the excitatory channelrhodopsin (hChR2) on iSPNs. We found that P/Q-type calcium channels are the primary VGCC-subtype controlling presynaptic calcium and GABA release at iSPN-GPe projections. N-type and L-type VGCCs contribute to GABA release at iSPN-GPe synapses. GABABreceptor activation resulted in a reversible inhibition of presynaptic Ca2+transients (PreCaTs) and an inhibition of GABAergic transmission at iSPN-GPe synapses. CB1 receptor activation did not inhibit PreCaTs while inhibiting GABAergic transmission at iSPN-GPe projections. CB1 effects on GABAergic transmission persisted in experiments where NaVand KV1 were blocked, indicating a VGCC- and KV1 independent presynaptic mechanism of action of CB1 receptors. Taken together, presynaptic modulation of iSPN-GPe projections by CB1 and GABABreceptors is mediated by distinct mechanisms.Key PointsP/Q-type are the predominant VGCC controlling presynaptic Ca2+and GABA release on the striatal indirect pathway projectionsGABABreceptor modulate of iSPN-GPe projections via a VGCC- dependent mechanismCB1 receptors modulate iSPN-GPe projections via a VGCC- independent mechanism
3D Centroidnet: Nuclei Centroid Detection with Vector Flow Voting
Authors: Wu Liming , Chen Alain , Salama Paul , Dunn Kenneth W. , Delp Edward J. 
Published: July 2022

ABSTRACTAutomated microscope systems are increasingly used to collect large-scale 3D image volumes of biological tissues. Since cell boundaries are seldom delineated in these images, detection of nuclei is a critical step for identifying and analyzing individual cells. Due to the large intra-class variability in nuclei morphology and the difficulty of generating ground truth annotations, accurate nuclei detection remains a challenging task. We propose a 3D nuclei centroid detection method by estimating the “vector flow” volume where each voxel represents a 3D vector pointing to its nearest nuclei centroid in the corresponding microscopy volume. We then use a voting mechanism to estimate the 3D nuclei centroids from the “vector flow” volume. Our system is trained on synthetic microscopy volumes and tested on real microscopy volumes. The evaluation results indicate our method outperforms other methods both visually and quantitatively.