bluuebunny/crossref_metadata_2025 huggingface dataset:
The Universal Endurance Microbiome?
Authors: Olbricht Hope , Twadell Kaitlyn , Sandel Brody , Stephens Craig , Whittall Justen
Published: July 2022

Billions of microbial cells sculpt the gut ecosystem, playing essential roles in human physiology. Since endurance athletes’ performance is often physiology-limited, understanding the composition and interactions within these athletes’ gut microbiomes could lead to improved performance. Previous studies describe differences in the relative abundance of bacterial taxa when comparing athletes versus controls or athletes before and after an endurance event, suggesting the existence of an “endurance microbiome”. However, there are inconsistencies among studies in which taxa correlate with extended physical exertion. Although these studies employed similar barcoding methods, variation in downstream bioinformatic analyses makes it difficult to determine whether inconsistencies are due to methodological differences or biological factors. Herein, we created a metagenomic bioinformatics workflow reanalyzing four 16S rDNA sequence datasets reflecting endurance athletes’ gut microbiomes, looking at alpha diversity, changes in relative abundance of gut microbiome genera, changes in pairwise correlations between bacterial genera and compared bacterial association networks. There were no significant differences in alpha diversity between any of the four treatment group comparisons. For relative abundance, there were no consistent differences in all four datasets, and only two genera were significantly different in 50% of the datasets. Although many genera showed changes in pairwise correlations in endurance microbiome samples from individual datasets, none were consistent across datasets. Collectively, these results suggest that either there is no universal endurance microbiome, or that it remains elusive even after controlling for the bioinformatic workflow and statistical analyses. Using this data, a power analysis indicates that sample sizes 150- to 800-fold larger than these published studies would be necessary to detect a 10% difference in relative abundance. Furthermore, 10- to 20-fold more samples will be needed to control for the multitude of covariates (genetic, metabolic, dietary, environmental, and pharmacological factors) that mold the gut microbiome of athletes and non-athletes alike.

I’m going to work so that it’s a pure guts race at the end, and if it is, I am the only one who can win it. - Steve Prefontaine
Hydrothermal Vent Species Assemblage Networks Identify Regional Connectivity Patterns in the Northwest Pacific
Authors: Brunner Otis , Chen Chong , Giguere Thomas , Kawagucci Shinsuke , Tunnicliffe Verena , Watanabe Hiromi , Mitarai Satoshi
Published: July 2022

The distribution of species among spatially isolated habitat patches supports regional biodiversity and stability, so understanding the underlying processes and structure is a key target of conservation. Although multivariate statistics can infer the connectivity processes driving species distribution, such as dispersal and habitat suitability, they rarely explore structure. Methods from graph theory, applied to distribution data, give insights into both connectivity pathways and processes by intuitively formatting the data as a network of habitat patches. We apply these methods to empirical data from the hydrothermal vent habitats of the Northwest Pacific. Hydrothermal vents are ‘oases’ of biological productivity and endemicity on the seafloor that are imminently threatened by anthropogenic disturbances with unknown consequences to biodiversity. Here, we describe the structure of hydrothermal vent species assemblage networks, how local and regional parameters affect their structure, and the implications this has for conservation. Two complementary networks were formed from an extensive species assemblage dataset: a bipartite network of species nodes linked to vent site nodes at which they are present, and a similarity network of vent site nodes linked by weighted edges based on their pairwise assemblage similarity. Using these networks, we assessed the role of individual vent sites in linking their network and identified biogeographic sub-regions. The three sub-regions and two outlying sites are separated by their spatial arrangement and local environmental filters. Both networks detected vent sites that play a disproportionately important role in regional pathways, while the bipartite network also identified key vent sites maintaining the distinct species assemblages of their sub-regions. These regional connectivity pathways provide insights into historical colonisation routes, while sub-regional connectivity pathways are of value when selecting sites for conservation and/or estimating the multi-vent impacts from proposed deep-sea mining.
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

Bacteria 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.

IMPORTANCE

For 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

Long-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

Background

There is much uncertainty regarding the comparative risks of cancer for T2DM patients on SGLT2I versus DPP4I.

Methods

This 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.

Results

Amongst 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).

Conclusion

SGLT2I 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

Interleukin (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

Monoclonal 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

Natural 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.

Significance

We 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

The 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.
Mechanistic multiscale modelling of energy metabolism in human astrocytes indicates morphological effects in Alzheimer’s Disease
Authors: Farina Sofia , Voorsluijs Valérie , Fixemer Sonja , Bouvier David , Claus Susanne , Bordas Stéphane P.A. , Skupin Alexander
Published: July 2022

Astrocytes with their specialized morphology are essential for brain homeostasis as metabolic mediators between blood vessels and neurons. In neurodegenerative diseases such as Alzheimer’s disease (AD), astrocytes adopt reactive profiles with molecular and morphological changes that could lead to the impairment of their metabolic support and impact disease progres-sion. However, the underlying mechanisms how metabolic function of human astrocytes is impaired by their morphological changes in AD is still elusive. To address this challenge, we developed and applied a metabolic multiscale modelling approach integrating the dynamics of metabolic energy pathways and physiological astrocyte morphologies acquired in human AD and age-matched control brain samples. The results demonstrate that the complex cell shape and intracellular organization of energetic pathways determine the metabolic profile and support capacity of astrocytes in health and AD conditions. Thus, our mechanistic approach indicates the importance of spatial orchestration in metabolism and allows for the identification of protective mechanisms against disease-associated metabolic impairments.
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

The 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

Plant 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

Hepatitis 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

Plant 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

Chitin 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

Presynaptic 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 Points

P/Q-type are the predominant VGCC controlling presynaptic Ca2+and GABA release on the striatal indirect pathway projections

GABABreceptor modulate of iSPN-GPe projections via a VGCC- dependent mechanism

CB1 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

Automated 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.
Dynamic regulation of inter-organelle communication by ubiquitylation controls skeletal muscle development and disease onset
Authors: Mansur Arian , Joseph Remi , Jean-Beltran Pierre Michael , Udeshi Namrata D. , Pearce Cadence , Jiang Hanjie , Iwase Reina , McNamara Elyshia , Widrick Jeff , Perez Claudio , Ravenscroft Gianina , Cole Philip A , Carr Steven A , Gupta Vandana A
Published: July 2022

Ubiquitin-proteasome system (UPS) dysfunction is associated with the pathology of a wide range of human diseases including myopathies and muscular atrophy. However, the mechanistic understanding of specific components on the regulation of protein turnover during development and disease progression in skeletal muscle is unclear. Mutations in KLHL40, an E3 ubiquitin ligase cullin3 (CUL3) substrate-specific adapter protein result in a severe form of congenital nemaline myopathy, but the events that initiate the pathology and the mechanism through which it becomes pervasive, remains poorly understood. To characterize the KLHL40-regulated ubiquitin modified proteome during skeletal muscle development and disease onset, we used global, quantitative mass spectrometry-based ubiquitylome and global proteome analyses of klhl40 mutant zebrafish during disease progression. Global proteomics during skeletal muscle development revealed extensive remodeling of functional modules linked with sarcomere formation, energy and biosynthetic metabolic processes and vesicle trafficking. Combined analysis of klh40 mutant muscle proteome and ubiquitylome identified thin filament proteins, metabolic enzymes and ER-Golgi vesicle trafficking pathway proteins regulated by ubiquitylation during muscle development. Our studies identified a role for KLHL40 as a negative regulator of ER-Golgi anterograde trafficking through ubiquitin-mediated protein degradation of secretion associated Ras related GTPase1a (Sar1a). In KLHL40 deficient muscle, defects in ER exit site vesicle formation alter Golgi compartment and downstream transport of extracellular cargo proteins, resulting in structural and functional abnormalities. Our work reveals that the muscle proteome is dynamically fine-tuned by ubiquitylation to regulate skeletal muscle development and uncovers new disease mechanisms for therapeutic development in patients.

Graphical Abstract
Global change drivers and the risk of infectious disease
Authors: Mahon Michael B. , Sack Alexandra , Aleuy O. Alejandro , Barbera Carly , Brown Ethan , Buelow Heather , Civitello David J. , Cohen Jeremy M. , de Wit Luz , Forstchen Meghan , Halliday Fletcher W. , Heffernan Patrick , Knutie Sarah A. , Korotasz Alexis , Larson Joanna G. , Rumschlag Samantha L. , Selland Emily , Shepack Alexander , Vincent Nitin , Rohr Jason R.
Published: July 2022

Anthropogenic change is contributing to the rise in emerging infectious diseases, but it remains unclear which global change drivers most increase disease and under what contexts. We amassed a dataset from the literature that includes 1,832 observations of infectious disease responses to global change drivers across 1,202 host-parasite combinations. We found that biodiversity loss, climate change, and introduced species were associated with increases in disease-related endpoints or harm (i.e., enemy release for introduced species), whereas urbanization was associated with decreases in disease endpoints. Natural biodiversity gradients, deforestation, forest fragmentation, and most classes of chemical contaminants had non-significant effects on these endpoints. Overall, these results were consistent across human and non-human diseases. Context-dependent effects of the global change drivers on disease were common and are discussed. These findings will help better target disease management and surveillance efforts towards global change drivers that increase disease.

One-Sentence Summary

Here we quantify which global change drivers increase infectious diseases the most to better target global disease management and surveillance efforts.
A versatile, high-efficiency platform for CRISPR-based gene activation
Authors: Heidersbach Amy J. , Dorighi Kristel M. , Gomez Javier A. , Jacobi Ashley M. , Haley Benjamin
Published: July 2022

CRISPR-mediated transcriptional activation (CRISPRa) is a powerful technology for inducing gene expression from endogenous loci with exciting applications in high throughput gain-of-function genomic screens and the engineering of cell-based models. However, current strategies for generating potent, stable, CRISPRa-competent cell-lines present limitations for the broad utility of this approach. Here, we provide a high-efficiency, self-selecting CRISPRa enrichment strategy, which combined with piggyBac transposon technology enables rapid production of CRISPRa-ready cell populations compatible with a variety of downstream assays. We complement this with a new, optimized guide RNA scaffold that significantly enhances CRISPRa functionality. Finally, we describe a novel, synthetic guide RNA tool set that enables transient, population-wide gene activation when used with the self-selecting CRISPRa system. Taken together, this versatile platform greatly enhances the potential for CRISPRa across a wide variety of cellular contexts.
Old Age Drives Fusion and Expansion of Vitellogenin Vesicles in the Intestine of Caenorhabditis elegans
Authors: Zhai Chao , Zhang Nan , Li Xi-Xia , Chen Xi , Sun Fei , Dong Meng-Qiu
Published: July 2022

Some of the most conspicuous aging phenotypes of C. elegans are related to post-reproductive production of vitellogenins (Vtg), which form yolk protein (YP) complexes after processing and lipid loading. Vtg/YP levels show huge increases with age, and inhibition of this extends lifespan, but how subcellular and organism-wide distribution of these proteins changes with age has not been systematically explored. Here this has been done to understand how vitellogenesis promotes aging. The age-associated changes of intestinal vitellogenin vesicles (VVs), pseudocoelomic yolk patches (PYPs), and gonadal yolk organelles (YOs) have been characterized by immuno-electron microscopy. We find that from reproductive adult day 2 (AD 2) to post-reproductive AD 6 and AD 9, intestinal VVs expand from 0.2 μm to 3-4 μm in diameter or by > 3,000 times in volume, PYPs increase by > 3 times in YP concentration and volume, while YOs in oocytes shrink slightly from 0.5 μm to 0.4 μm in diameter or by 60% in volume. In AD 6 and AD 9 worms, mis-localized YOs found in the hypodermis, uterine cells, and the somatic gonadal sheath can reach a size of 10 μm across in the former two tissues. This remarkable size increase of VVs and that of mis-localized YOs in post-reproductive worms are accompanied by extensive fusion between these Vtg/YP-containing vesicular structures in somatic cells. In contrast, no fusion is seen between YOs in oocytes. We propose that in addition to the continued production of Vtg, excessive fusion between VVs and mislocalized YOs in the soma worsen the aging pathologies seen in C. elegans.
Evaluating the Adoption of Voice Recognition Technology for Real-Time Dictation in a Rural Healthcare System: A Retrospective Analysis of Dragon Medical One
Authors: Onitilo Adedayo A. , Shour Abdul R. , Puthoff David S. , Tanimu Yusuf , Joseph Adedayo , Sheehan Michael T
Published: July 2022

Background

In 2013, Marshfield Clinic Health System (MCHS) implemented the Dragon Medical One (DMO) system provided by Nuance Management Center (NMC) for Real-Time Dictation (RTD), embracing the idea of streamlined clinic workflow, reduced dictation hours, and improved documentation legibility. Since then, MCHS has observed a trend of reduced time in documentation, however, the target goal of 100% adoption of voice recognition (VR)-based RTD has not been met.

Objective

To evaluate the uptake/adoption of VR technology for RTD in MCHS, between 2018-2020.

Methods

DMO data for 1,373 MCHS providers from 2018-2020 were analyzed. The study outcome was VR uptake, defined as the number of hours each provider used VR technology to dictate patient information, used as continuous, and classified as no/yes. Covariates included sex, age, US-trained/international medical graduates, trend, specialty, and facility. Descriptive statistics and unadjusted and adjusted logistic regression analyses were performed. Stata/SE.version.17 was used for analyses. P-values less than/equal to 0.05 were considered statistically significant.

Results

Of the 1,373 MCHS providers, the mean (SD) age was 48.3 (12.4) years. VR uptake was higher than no uptake (72.0% vs. 28.0%). In both unadjusted and adjusted analyses, VR uptake was 4.3 times and 7.7 times higher in 2019-2020 compared to 2018, respectively (OR:4.30,95%CI:2.44-7.46 and AOR:7.74,95%CI:2.51-23.86). VR uptake was 0.5 and 0.6 times lower among US-trained physicians compared to internationally-trained physicians (OR:0.53,95%CI:0.37-0.76 and AOR:0.58,95%CI:0.35-0.97). Uptake was 0.2 times lower among physicians aged 60/above than physicians aged 29/less (OR:0.20,95%CI:0.10-0.59, and AOR:0.17,95%CI:0.27-1.06).

Conclusion

Since 2018, VR adoption has increased significantly across MCHS. However, it was lower among US-trained physicians than among internationally-trained physicians (although internationally physicians were in minority) and lower among more senior physicians than among younger physicians. These findings provide critical information about VR trends, physician factors, and which providers could benefit from additional training to increase VR adoption in healthcare systems.
A single measurement of fecal hemoglobin concentration outperforms polygenic risk score in colorectal cancer risk assessment
Authors: Niedermaier Tobias , Alwers Elizabeth , Chen Xuechen , Heisser Thomas , Hoffmeister Michael , Brenner Hermann
Published: July 2022

PURPOSE

Polygenic risk scores (PRS) have been proposed and are increasingly used for risk assessment in colorectal cancer (CRC) screening. Fecal immunochemical tests (FITs) are widely recommended and used as dichotomous tests for annual or biennial CRC screening, ignoring the quantitative information on fecal hemoglobin concentration above or below the positivity threshold.

MATERIALS AND METHODS

We aimed to assess and compare the ability of a single quantitative FIT and PRS to predict presence of advanced colorectal neoplasms (preclinical CRC or advanced adenoma) as a key indicator of CRC risk. A quantitative FIT (FOB Gold, Sentinel Diagnostics) was employed and a weighted PRS based on 140 common risk variants was determined among participants of screening colonoscopy in Germany. We compared areas under the curves (AUCs) of FIT and PRS for predicting presence of advanced colorectal neoplasm in the entire study population, and in subgroups defined by age, sex, family history of CRC, and history of colonoscopy.

RESULTS

A total of 3,025 participants aged 50-79 years were included, thereof 523 with advanced colorectal neoplasm and 2,502 participants without neoplasm. FIT clearly outperformed PRS in predicting presence of any advanced neoplasm in the entire study population (AUC 0.721, 95%CI 0.693-0.749 versus 0.591, 95%CI 0.564-0.617, p<0.0001), in younger (50-59 years) and older (60-79 years) participants, both sexes, those with and without a family history of CRC, and those with and without a previous colonoscopy (differences in AUC between 0.110 and 0.186, p=0.03 for those with previous colonoscopy and ≤0.005 for all other subgroups).

CONCLUSION

A single quantitative FIT, a low cost, easy-to-administer and universally available test, is more informative for CRC risk assessment than so far established PRS, irrespective of age, sex, family history, or history of colonoscopy.
Estimating the time-varying reproduction number for COVID-19 in South Africa during the first four waves using multiple measures of incidence for public and private sectors across four waves
Authors: Bingham Jeremy , Tempia Stefano , Moultrie Harry , Viboud Cecile , Jassat Waasila , Cohen Cheryl , Pulliam Juliet R.C.
Published: July 2022

Objectives

We aimed to quantify transmission trends in South Africa during the first four waves of the COVID-19 pandemic using estimates of the time-varying reproduction number (R) and to compare the robustness of R estimates based on three different data sources and using data from public and private sector service providers.

Methods

We estimated R from March 2020 through April 2022, nationally and by province, based on time series of rt-PCR-confirmed cases, hospitalizations, and hospital-associated deaths, using a method which models daily incidence as a weighted sum of past incidence. We also estimated R separately using public and private sector data.

Results

Nationally, the maximum case-based R following the introduction of lockdown measures was 1.55 (CI: 1.43-1.66), 1.56 (CI: 1.47-1.64), 1.46 (CI: 1.38-1.53) and 3.33 (CI: 2.84-3.97) during the first (Wuhan-Hu), second (Beta), third (Delta), and fourth (Omicron) waves respectively. Estimates based on the three data sources (cases, hospitalisations, deaths) were generally similar during the first three waves but case-based estimates were higher during the fourth wave. Public and private sector R estimates were generally similar except during the initial lockdowns and in case-based estimates during the fourth wave.

Discussion

Agreement between R estimates using different data sources during the first three waves suggests that data from any of these sources could be used in the early stages of a future pandemic. High R estimates for Omicron relative to earlier waves is interesting given a high level of exposure pre-Omicron. The agreement between public and private sector R estimates highlights the fact that clients of the public and private sectors did not experience two separate epidemics, except perhaps to a limited extent during the strictest lockdowns in the first wave.
miR-221/222 drive synovial fibroblast expansion and pathogenesis of TNF-mediated arthritis
Authors: Roumelioti Fani , Tzaferis Christos , Konstantopoulos Dimitris , Papadopoulou Dimitra , Prados Alejandro , Sakkou Maria , Liakos Anastasios , Chouvardas Panagiotis , Meletakos Theodore , Pandis Yiannis , Karagianni Niki , Denis Maria , Fousteri Maria , Armaka Marietta , Kollias George
Published: July 2022

MicroRNAs (miRNAs) constitute fine tuners of gene expression and are implicated in a variety of diseases spanning from inflammation to cancer. miRNA expression is deregulated in rheumatoid arthritis (RA), however, their specific role in key arthritogenic cells such as the synovial fibroblast (SF) remains elusive. We have shown in the past that the expression of the miR-221/222 cluster is upregulated in RA SFs. Here, we demonstrate that miR-221/222 activation is downstream of major inflammatory cytokines, such as TNF and IL-1β, which promote miR-221/222 expression independently. miR-221/222 expression in SFs from the huTNFtg mouse model of arthritis correlates with disease progression. Targeted transgenic overexpression of miR-221/222 in SFs of the huTNFtg mouse model led to further expansion of synovial fibroblasts and disease exacerbation. miR-221/222 overexpression altered the transcriptional profile of SFs igniting pathways involved in cell cycle progression and ECM regulation. Validated targets of miR-221/222 included p27 and p57 cell cycle inhibitors, as well as Smarca1 (a chromatin remodeling component). In contrast, complete genetic ablation of miR-221/222 in arthritic mice led to decreased proliferation of fibroblasts, reduced synovial expansion and attenuated disease. scATAC-seq data analysis revealed increased miR-221/222 gene activity in the pathogenic and activated clusters of the intermediate and lining compartment. Taken together, our results establish an SF-specific pathogenic role of the miR-221/222 cluster in arthritis and suggest that its therapeutic targeting in specific subpopulations should inform the design of novel fibroblast-targeted therapies for human disease.
Online media in dairy markets: a US dairy futures market study
Authors: Ortez Mario , Widmar Nicole Olynk , Mallory Mindy Lyn , Wolf Christopher Allen , Bir Courtney
Published: July 2022

Purpose

This article quantifies public sentiment for dairy products using online media and investigates potential relationships between online media, both volume and sentiment, and future prices of Class III milk.

Design/methodology/approach

Netbase, an online media listening platform, was used to quantify US generated online media sentiment and number of mentions regarding dairy products. Granger-causality tests and Impulse Response Functions (IRFs) were used to study relationships between online media derived data and dairy futures prices.

Findings

Milk and cheese have more mentions in online media than yogurt and ice cream. Online media net sentiment around milk was the lowest of the dairy products studied. Granger-causality tests showed that Class III milk price Granger-causes net sentiment of dairy as a whole and of fluid milk. Price additionally Granger-causes mentions of milk, ice cream and yogurt. Notably, milk and ice cream mentions Granger-cause the Class III milk price. IRF's reveals that increases in mentions have a positive, albeit small, effect on the Class III milk price that is statistically significant for ice cream, but not for milk. IRF's directionality of the relationship from price to online media derived data was mixed.

Originality/value

This is the first time that relationships between online media -volume and sentiment- and futures prices of an agricultural commodity are researched. Exploration of futures markets alongside online media advances the use of online media to glean insights in financial, along with food and agricultural markets.