bluuebunny/crossref_metadata_2025_split huggingface dataset:
Laccaria bicolor pectin methylesterases are involved in ectomycorrhiza development with Populus tremula x Populus tremuloides
Authors: Chowdhury Jamil , Kemppainen Minna , Delhomme Nicolas , Shutava Iryna , Zhou Jingjing , Takahashi Junko , Pardo Alejandro G. , Lundberg-Felten Judith 
Published: June 2022

SummaryThe development of ectomycorrhizal (ECM) symbioses between soil fungi and tree roots requires modification of root cell-walls. The pectin-mediated adhesion between adjacent root cells loosens to accommodate fungal hyphae in the Hartig Net, facilitating nutrient exchange between partners. We investigated the role of fungal pectin modifying enzymes in Laccaria bicolor for ECM formation with Populus tremula x Populus tremuloides.We combine transcriptomics of cell-wall related enzymes in both partners during ECM formation, immunolocalization of pectin (Homogalacturonan, HG) epitopes in different methylesterification states, pectin methylesterase (PME) activity assays and functional analyses of transgenic L. bicolor to uncover pectin modification mechanisms and the requirement of fungal pectin methylesterases (LbPMEs) for ECM formation.Immunolocalization identified remodelling of pectin towards de-esterified HG during ECM formation, which was accompanied by increased LbPME1 expression and PME activity. Overexpression or RNAi of the ECM-induced LbPME1 in transgenic L. bicolor lines led to reduced ECM formation. Hartig Nets formed with LbPME1 RNAi lines were shallower, whereas those formed with LbPME1 over-expressors were deeper.This suggests that LbPME1 plays a role in ECM formation potentially through HG-de-esterification, which initiates loosening of adjacent root cells to facilitate Hartig Net formation.
Validation of an RNase H2 activity assay suitable for clinical screening
Authors: Schulz Marian , Günther Claudia , Behrendt Rayk , Roers Axel 
Published: June 2022

AbstractAs the key enzyme mediating ribonucleotide excision repair, RNase H2 is essential for the removal of single ribonucleotides from DNA in order to prevent genome damage. Loss of RNase H2 activity directly contributes to the pathogenesis of autoinflammatory and autoimmune diseases and might further play a role in ageing and neurodegeneration. Moreover, RNase H2 activity is a potential diagnostic and prognostic marker in several types of cancer. Until today, no method for quantification of RNase H2 activity has been validated for the clinical setting. Herein, validation and benchmarks of a FRET-based whole-cell lysate RNase H2 activity assay are presented, including standard conditions and procedures to calculate standardized RNase H2 activity. Spanning a wide working range, the assay is applicable to various human cell or tissue samples with overall methodological assay variability from 8.6% to 16%. The assay readily detected reduced RNase H2 activity in lymphocytes of a patient with systemic sclerosis carrying a RNASEH2C variant. Implementation of larger control groups will help to assess the diagnostic and prognostic value of clinical screening for RNase H2 activity in the future.
Multiple ParA/MinD ATPases coordinate the positioning of disparate cargos in a bacterial cell
Authors: Pulianmackal Lisa T. , Limcaoco Jose Miguel I. , Ravi Keerthikka , Yang Sinyu , Zhang Jeffrey , Tran Mimi K. , O’Meara Matthew J. , Vecchiarelli Anthony G. 
Published: June 2022

SUMMARYIn eukaryotes, linear motor proteins govern intracellular transport and organization. In bacteria, where linear motors are absent, the ParA/MinD (A/D) family of ATPases spatially organize an array of genetic- and protein-based cellular cargos. ParA is well known to segregate plasmids and chromosomes, as is MinD for its role in divisome positioning. Less studied is the growing list of ParA/MinD-like ATPases found across prokaryotes and involved in the spatial organization of diverse protein-based organelles, such as Bacterial Microcompartments (BMCs), flagella, chemotaxis clusters, and conjugation machinery. Given the fundamental nature of these processes in both cell survival and pathogenesis, the positioning of these cargos has been independently investigated to varying degrees in several organisms. However, it remains unknown whether multiple A/D ATPases can coexist and coordinate the positioning of such a diverse set of fundamental cargos in the same cell. If so, what are the mechanistic commonalities, variation, and specificity determinants that govern the positioning reaction for each cargo? Here, we find that over a third of sequenced bacteria encode multiple A/D ATPases. Among these bacteria, we identified several human pathogens as well as the experimentally tractable organism, Halothiobacillus neapolitanus, which encodes seven A/D ATPases. We directly demonstrate that five of these A/D ATPases are each dedicated to the spatial regulation of a single cellular cargo: the chromosome, the divisome, the carboxysome BMC, the flagellum, and the chemotaxis cluster. We identify putative specificity determinants that allow each A/D ATPase to position its respective cargo. Finally, we show how the deletion of one A/D ATPase can have indirect effects on the inheritance of a cargo actively positioned by another A/D ATPase, stressing the importance of understanding how organelle trafficking, chromosome segregation, and cell division are coordinated in bacterial cells. Together, our data show how multiple A/D ATPases coexist and function to position a diverse set of fundamental cargos in the same bacterial cell. With this knowledge, we anticipate the design of minimal autonomous positioning systems for natural- and synthetic-cargos in bacteria for synthetic biology and biomedical applications.
Effects of floral symmetry and orientation on the consistency of pollinator’s entry angle
Authors: Jirgal Nina , Ohashi Kazuharu 
Published: June 2022

AbstractSince the publication of Sprengel’s (1793) observations, it has been considered that flowers with zygomorphic (or bilaterally symmetrical) corollas evolved to restrict the movement of pollinators into the flower by limiting the pollinator’s direction of approach. However, little empirical support has been accumulated so far, except Culbert and Forrest (2016) who found that zygomorphy reduced variance in pollinator’s flower entry angle. Our aim was to build on this work and observe whether floral symmetry or orientation had an effect on pollinator entry angle in a laboratory experiment using bumble bees, Bombus ignitus. Using nine different combinations of artificial flowers created from three symmetry types (radial, bilateral and disymmetrical) and three orientation types (upward, horizontal and downward), we tested the effects of these two floral aspects on the consistency of bee’s entry angle. Our results show that horizontal orientation significantly reduced the variance in entry angle, while symmetry had little effect. We also found no significant interactions between angle and symmetry in their effect on entry angle. Thus, our results suggest that horizontal orientation forces the bees to orient themselves relative to gravity rather than the corolla and stabilizes their flower entry. This stabilizing effect may have been mistaken for the effect of zygomorphic corolla as it is presented horizontally in most species. Consequently, we suggest that the evolution of horizontal orientation preceded that of zygomorphy as indicated by some authors, and that the reason behind the evolution of zygomorphy should be revisited.
No modular shape changes in the mandible of Andean white-eared opossum (Didelphis pernigra, Linnaeus, 1758)
Authors: Parés-Casanova P.M. 
Published: June 2022

AbstractMorphological integration and modularity are concepts that refer to the covariation level between the components of a structure. Species of the opossums, genus Didelphis, have been the object of several taxonomic and morphometric analyses but no study has so far analysed mandibular morphological integration and modularity at a species-level. The aim of this work was to check whether the body (corpus mandibulae, mandibular corpus) and the ramus (ramus mandibulae, ascending mandibular ramus) are separate modules in Didelphis pernigra using a two-dimensional geometric morphometric approach. For this purpose, a sample of hemimandibles from 36 D. pernigra (13 males and 23 females) was analysed using 17 landmarks in lateral view. The modularity hypothesis based on different developmental origins was tested, by using the RV coefficient. Later, the integration level was assessed applying a partial least-squares analysis (PLS). The underlying aim was to know whether the traditional division between mandibular body and ramus has a modular basis, as well as the morphological integration level between these two structures. Results reflected that landmarks integration was not uniform throughout the mandible but structured into two distinct modules: ramus and body. Results allow to conclude that allometry plays an important role in shape variation in this species, and that the hypotheses of two-module organization in males cannot be confirmed. Models that accurately represent the biting mechanics will strengthen our understanding of which variables are functionally relevant and how they are relevant to performances, not only masticatories.
Ivermectin for Treatment of Mild-to-Moderate COVID-19 in the Outpatient Setting: A Decentralized, Placebo-controlled, Randomized, Platform Clinical Trial
Authors:   Accelerating COVID-19 Therapeutic Interventions and Vaccines (ACTIV)-6 Study Group, Naggie Susanna 
Published: June 2022

AbstractBackgroundThe effectiveness of ivermectin to shorten symptom duration or prevent hospitalization among outpatients in the United States with mild-to-moderate symptomatic coronavirus disease 2019 (COVID-19) is unknown.ObjectiveWe evaluated the efficacy of ivermectin 400 µg/kg daily for 3 days compared with placebo for the treatment of early mild-to-moderate COVID-19.MethodsACTIV-6 is an ongoing, decentralized, double-blind, randomized, placebo-controlled platform trial to evaluate repurposed therapies in outpatients with mild-to-moderate COVID-19. Non-hospitalized adults age ≥30 years with confirmed COVID-19, experiencing ≥2 symptoms of acute infection for ≤7 days were randomized to receive ivermectin 400 µg/kg daily for 3 days or placebo. The main outcome measure was time to sustained recovery, defined as achieving at least 3 consecutive days without symptoms. Secondary outcomes included a composite of hospitalization or death by day 28.ResultsOf the 3457 participants who consented to be evaluated for inclusion in the ivermectin arm, 1591 were eligible for this study arm, randomized to receive ivermectin 400 µg/kg (n=817) or placebo (n=774), and received study drug. Of those enrolled, 47% reported receiving at least 2 doses of SARS-CoV-2 vaccination. The posterior probability for any improvement in time to recovery was 0.91 (hazard ratio 1.07, 95% credible interval 0.96–1.17). The posterior probability of this benefit exceeding 24 hours was less than 0.01, as measured by the difference in mean time unwell. Hospitalizations or deaths were uncommon (ivermectin [n=10]; placebo [n=9]). Ivermectin at 400 µg/kg was safe and without serious adverse events as compared with placebo (ivermectin [n=10]; placebo [n=9]).ConclusionsIvermectin dosed at 400 µg/kg daily for 3 days resulted in less than one day of shortening of symptoms and did not lower incidence of hospitalization or death among outpatients with COVID-19 in the United States during the delta and omicron variant time periods.Trial registrationClinicalTrials.gov Identifier: NCT04885530.
Backtracking of influenza polymerase upon consecutive incorporation of nucleoside analogue T1106 directly observed by high-resolution cryo-electron microscopy
Authors: Kouba Tomas , Dubankova Anna , Drncova Petra , Donati Elisa , Vidossich Pietro , Speranzini Valentina , Pflug Alex , Huchting Johanna , Meier Chris , De Vivo Marco , Cusack Stephen 
Published: June 2022

AbstractThe broad-spectrum antiviral pseudobase T705, a fluorinated pyrazinecarboxamide, is incorporated via its triphosphate form into nascent viral RNA by viral RNA-dependent RNA polymerases. Since it mimics guanine or adenine it can act as a mutagen, whereas consecutive incorporation leads to chain termination. Here we examine the structural basis for incorporation and stalling for the case of influenza polymerase, using T1106-TP, the nucleotide form of T1105, the de-fluoro analogue of T705. We used a specially designed template that allows single T1106-MP incorporation at a defined site followed by consecutive T1106-MP incorporation and stalling four nucleotides later, as demonstrated by biochemical analysis. A high-resolution cryoEM structure of influenza A/H7N9 polymerase, stalled after transcribing this template, revealed that the entire product-template duplex has backtracked by five nucleotides. Consequently, the singly incorporated T1106-MP resides at the +1 position and forms an unexpected wobble base-pair with a U in the template. The relative stability of the canonical and wobble T1106:U base-pairs in different contexts is investigated by molecular dynamics simulations. Using a different template and influenza B polymerase we also observe stalling after double incorporation of T1106-MP and structural analysis showed again that backtracking occurs, this time by four nucleotides. These results show that, at least in early elongation, consecutive T1106-MP incorporation into the product destabilises the proximal end of the product-template duplex, promoting irreversible backtracking until a more favourable overall configuration is achieved. These results give new insight into the unusual mechanism of chain termination by pyrazinecarboxamide base analogues.
The high diversity of Scedosporium and Lomentospora species and their prevalence in human-disturbed areas in Taiwan
Authors: Huang Yin-Tse , Fan Yun-Chen , Hung Tsu-Chun , Chen Chi-Yu , Sun Pei-Lun 
Published: June 2022

AbstractScedosporium and Lomentospora are important opportunistic pathogens causing localized or disseminated infection in humans. Understanding their environmental distribution is critical for public hygiene and clinical management. We carried out the first environmental survey in urbanized and natural regions in Taiwan. Overall, Scedosporium and Lomentospora species were recovered in 130 out of 271 soil samples (47.9%) across Taiwan. We morphologically and molecularly identified five Scedosporium species and one Lomentospora species. All four major clinical relevant species were isolated with high frequency, i.e. S. apiospermum (42.5%), S. boydii (27.5%), L. prolificans (15.0%), and S. aurantiacum (8.8%); two clinically minor species, S. dehoogii (5.6%) and S. haikouense (0.6%), had moderate incidence. These fungal species have high incidence in urban (48%) and hospital (67.4%) soil samples, and have limited distribution in samples from natural regions (5%). Multivariate analysis of the fungal composition revealed strong evidence of the preferential distribution of these fungi in urban and hospital regions compared to natural sites. In addition, strong evidence suggested that the distribution and abundance of these fungal species are highly heterogeneous in the environment; samples in vicinity often yield varied fungal communities. Our results indicated that these fungal species are prevalent in soil in Taiwan and their occurrences are associated with human activities. Hygiene sensitive places such as hospitals should be particularly aware of the high frequency of the clinical relevant species.
Crystal structures of glycoprotein D of equine alphaherpesviruses reveal potential binding sites to the entry receptor MHC-I
Authors: Kremling Viviane , Loll Bernhard , Pach Szymon , Dahmani Ismail , Weise Christoph , Wolber Gerhard , Chiantia Salvatore , Wahl Markus C. , Osterrieder Nikolaus , Azab Walid 
Published: June 2022

AbstractCell entry of most alphaherpesviruses is mediated by the binding of glycoprotein D (gD) to different cell surface receptors. Equine herpesvirus type 1 (EHV-1) and EHV-4 gDs interact with equine major histocompatibility complex I (MHC-I) to initiate entry into equine cells. We have characterized the gD-MHC-I interaction by solving the crystal structures of EHV-1 and EHV-4 gDs (gD1, gD4), performing protein-protein docking simulations, surface plasmon resonance (SPR) analysis, and biological assays. The structures of gD1 and gD4 revealed the existence of a common V-set immunoglobulin-like (IgV-like) core comparable to those of other gD homologs. Molecular modeling yielded plausible binding hypotheses and identified key residues (F213 and D261) that are important for virus binding. Altering the key residues resulted in impaired virus growth in cells, which highlights the important role of these residues in the gD-MHC-I interaction. Taken together, our results add to our understanding of the initial herpesvirus-cell interactions and will contribute to the targeted design of antiviral drugs and vaccine development.Author summaryEquine herpesvirus type 1 (EHV-1) and type 4 (EHV-4) are endemic in horses and cause great suffering as well as substantial economic losses to the equine industry. Current vaccines do not prevent infections and treatment is difficult. A prerequisite for vaccine and drug development is an in-depth understanding of the virus replication cycle, especially the virus entry process in order to block the infection at early stages. Entry of alphaherpesviruses into the host cell is mediated by a set of virus envelope glycoproteins including glycoprotein D (gD) that triggers the internalization of the virus particle. The structure of gD and the interaction with the entry receptor equine major histocompatibility complex class I (MHC-I) remains elusive. Here, we solved the crystal structures of gD1 and gD4 that allowed us to model virus-receptor interaction and to determine the key residues for virus entry. Alterations of these key residues impaired virus growth in cell culture. The overall structure of gD1 and gD4 shows classical features of other alphaherpesvirus gDs making it possible to gain further insights into human pathogens as well.
A Caenorhabditis elegans nck-1 and filamentous actin-regulating protein pathway mediates a key cellular defense against bacterial pore-forming proteins
Authors: Sitaram Anand , Yin Yunqiang , Zamaitis Tammy , Zhang Bo , Aroian Raffi V. 
Published: June 2022

AbstractPore-forming proteins (PFPs) comprise the largest single class of bacterial protein virulence factors and are expressed by many human and animal bacterial pathogens. Cells that are attacked by these virulence factors activate epithelial intrinsic cellular defenses (or INCEDs) to prevent the attendant cellular damage, cellular dysfunction, osmotic lysis, and organismal death. Several conserved PFP INCEDs have been identified using the nematode Caenorhabditis elegans and the nematicidal PFP Cry5B, including mitogen-activated protein kinase (MAPK) signaling pathways. Here we demonstrate that the gene nck-1, which has homologs from Drosophila to humans and links cell signaling with localized F-actin polymerization, is required for INCED against small-pore PFPs in C. elegans. Reduction/loss of nck-1 function results in C. elegans hypersensitivity to PFP attack, a hallmark of a gene required for INCEDs against PFPs. This requirement for nck-1-mediated INCED functions cell-autonomously in the intestine and is specific to PFPs but not other tested stresses. Genetic interaction experiments indicate that nck-1-mediated INCED against PFP attack is independent of the major MAPK PFP INCED pathways. Proteomics and cell biological and genetic studies further indicate that nck-1 functions with F-actin cytoskeleton modifying genes like arp2/3, erm-1, and dbn-1 and that nck-1/arp2/3 promote pore repair at the membrane surface and protect against PFP attack independent of p38 MAPK. Consistent with these findings, PFP attack causes significant changes in the amount of actin cytoskeletal proteins and in total amounts of F-actin in the target tissue, the intestine. nck-1 mutant animals appear to have lower F-actin levels than wild-type C. elegans. Studies on nck-1 and other F-actin regulating proteins have uncovered a new and important role of this pathway and the actin cytoskeleton in PFP INCED and protecting an intestinal epithelium in vivo against PFP attack.Author SummaryThe mechanism of action for a significant number of bacterial protein toxins is the formation of pores in the membrane of target cells. Host cells contain programmed defenses against such attacks. Here we use the model system of the roundworm Caenorhabditis elegans and crystal proteins produced by Bacillus thuringiensis to demonstrate a new defense pathway mediated by the activity of the NCK-1 protein. Consistent with its known function in mammalian cells, the NCK-1-mediated defense involves various actin-interacting proteins and affects the kinetics of pore repair. This pathway is novel in its independence from MAPK signaling. Furthermore, the NCK-1 activity is found to be generally needed for defense against multiple pore-forming proteins and yet is specific to defense against such proteins but not against other environmental stressors.
Gut microbiota modulation in response to combination of Escherichia coli Nissle 1917 and sugars: Lessons from comparative analysis of fecal microbiota of two healthy donors from 2019-2021
Authors: Bhowmik Debaleena , Heer Kiran , Kaur Manpreet , Raychaudhuri Saumya , Paul Sandip 
Published: June 2022

AbstractThe Escherichia coli Nissle 1917 strain (EcN) has shown its probiotic efficacy against many enteric pathogenic bacteria infecting human, including Vibrio cholerae, either alone or in combination with prebiotics. Understanding of these mechanisms of infection control requires the basic knowledge of probiotic mediated gut microbial community alterations especially in presence of different prebiotics. The present study has used the ex-vivo microbiota model and Next Generation Sequencing techniques to demonstrate the effect of EcN along with different sugars, namely glucose, galactose and starch, on the human gut microbiome community composition. The microbiome compositional changes have been observed at two different time-points, set one and a half years apart, in fecal slurries obtained from two donors. The study has indicated that the extent of microbiome alterations varies with different carbohydrate prebiotics and EcN probiotic and most of the alterations are broadly dependent upon the existing gut microbial community structure of the donors. The major distinct compositional changes have been found in the conditions where glucose and starch were administered, both with and without EcN, in spite of the inter-donor microbial community variation. Several of these microbiome component variations also remain consistent for both the time-points, including genus like Bacteroides, Prevotella and Lactobacillus. Altogether, the present study has shown the effectiveness of EcN along with glucose and starch towards specific changes of microbial community alterations independent of initial microbial composition. This type of model study can be implemented for hypothesis testing in case of therapeutic and prophylactic use of probiotic and prebiotic combinations.