bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biotic and abiotic stress distinctly drive the phyllosphere microbial community structure
Authors: Bhandari Rishi , Saez Alvaro Sanz , Leisner Courtney P. , Potnis Neha 
Published: October 2022

AbstractWhile the physiological and transcriptional response of the host to biotic and abiotic stresses have been intensely studied, little is known about the resilience of associated microbiomes and their contribution towards tolerance to these stresses. We evaluated the impact of one such abiotic stress, elevated tropospheric ozone (O3), under open-top chamber field conditions on host susceptibility and phyllosphere microbiome associated with pepper cultivars resistant and susceptible toXanthomonas. Pathogen challenge resulted in distinct microbial community structures in both cultivars under an ambient environment. Elevated O3alone affected microbial community structure associated with resistant cultivar but not the susceptible cultivar, indicating the role of host genotypic background in response to abiotic stress. Elevated O3did not influence overall host susceptibility but did increase disease severity on the resistant cultivar, indicating a possible compromise in the resistance. Interestingly, combined stress resulted in a shift in microbial composition and structure like that observed with pathogen challenge alone. It indicates the possible prioritization of community response towards the most significant stress and pathogen being most influential regardless of the cultivar. Despite community composition differences, overall functional redundancy was observed in the phyllosphere community. To gain insights into community-level interactions, network topology assessment indicated a stable network with enhanced taxon connectedness upon pathogen challenge. However, an observation of destabilized random network with a shift in hub taxa in the presence of combined stress warrants future studies on the consequences of such unstable microbial communities on host response to pathogens in the face of climate change.
On a mechanistic impact of transmembrane tetramerization in pathological activation of RTKs
Authors: Polyansky Anton A. , Efremov Roman G. 
Published: October 2022

AbstractConstitutive activation of receptor tyrosine kinases (RTKs) via different mutation has a strong impact into development of severe human disorders, including cancer. While pathological effect of such mutations can be common on the phenotypical level, mechanistic understanding of their contribution into the receptor activation depends on the exact molecular context. Mutations in transmembrane (TM) domains represent an interesting class of pathological modifications since they can directly affect a signal transduction pathway from the receptor to the kinase domains of RTKs. Here we propose a putative activation scenario of RTK, whereby TM mutations can also promote higher order oligomerization of the receptors that leads to the subsequent ligand-free activation. To illustrate this model with all-atom resolution for a previously characterized oncogenic TM mutation V536E in platelet-derived growth factor receptor alpha (PDGFRA), we use a computational modeling framework including sequence-based structure prediction and all-atom 1 µs molecular dynamics (MD) simulations in a model membrane for the predicted configuration of the PDGFRA TM tetramers. We show that in the course of MD simulations the mutant tetramer retains stable and compact configuration, which is strengthened by tight protein-protein interactions. In contrast, the wild type tetramer demonstrates looser packing and tendency to dissociate. Such a structural organization shapes the dynamics of TM helices in the oligomeric state. Specifically, the mutation affects the characteristic motions of mutated TM helical segments by introducing additional non-covalent crosslinks in the middle of the TM tetramer, which work as mechanical hinges. This leads to dynamic decoupling of the C-termini from the rigidified N-terminal parts and facilitates higher possible displacement between the C-termini of the mutant TM helical regions. This, in turn, can provide more freedom to downstream kinase domains in their mutual rearrangement. The observed structural and dynamic effects of the V536E mutations in the context of PDGFRA TM tetramer provide an interesting possibility that an effect of oncogenic TM mutations can go beyond alternating structure and dynamics of TM dimeric states and also promote formation of higher-order oligomers that may directly contribute into the ligand independent signaling of PDGFRA and other RTKs.
Re-evaluating homoploid reticulate evolution in the annual sunflowers
Authors: Owens Gregory L. , Huang Kaichi , Todesco Marco , Rieseberg Loren H. 
Published: October 2022

AbstractSunflowers of the genusHelianthusare models for hybridization research and contain three of the best studied examples of homoploid hybrid speciation. To understand the broader picture of hybridization within the annual sunflowers, we used whole genome resequencing to conduct a phylogenomic analysis and test for gene flow between lineages. We find that all annual sunflower species tested have evidence of admixture, suggesting hybridization was common during the radiation of the genus. Support for the major species tree decreases with recombination rate, consistent with hybridization and introgression contributing to discordant topologies. Admixture graphs found hybridization to be associated with the origins of the three putative hybrid species (H. anomalus, H. deserticola, andH. paradoxus). However, the hybridization events are more ancient than suggested by previous work. Furthermore,H. anomalusandH. deserticolaappear to have arisen from a single hybridization event involving an unexpected donor, rather than through multiple independent events as previously proposed. Using a broader data set that covers the wholeHelianthusgenus, including perennial species, we find that signals of introgression span the genus and beyond, suggesting highly divergent introgression and/or the sorting of ancient haplotypes. Thus,Helianthuscan be viewed as a syngameon in which largely reproductively isolated species are linked together by occasional or frequent gene flow.
Filtering microbial populations with a magnetic field
Authors: Nazareth Michelle , Kilinc Ece , Deamer David 
Published: October 2022

AbstractMagnetic fields strongly affect currents of electrically charged particles such as electrons, protons and other ions in solution. Because ionic currents of protons or sodium drive the rotation of bacterial flagella, it is possible that the motion of motile bacterial species will be affected if they swim through a strong magnetic field. We tested this prediction in mixed cultures of soil bacteria and observed that a magnetic field does in fact exert a filtering effect that alters the composition of the mixed population of motile species. We then monitored motility and growth to see if magnetic fields affected individual bacterial species (Vibrio, Enterobacter sp. andPseudomonas sp.) The same magnetic field had no observable effect on motility or growth. Although magnetic fields may have served as a selective factor in the evolution of certain species such as magnetotactic motile bacteria, they do not appear to have a direct effect on the ionic current driving flagellar rotation.
Elucidation of Global Trends in the Effects of VX-661 and VX-445 on the Expression of Clinical CFTR Variants
Authors: McKee Andrew G. , McDonald Eli F. , Penn Wesley D. , Kuntz Charles P. , Noguera Karen , Chamness Laura M. , Roushar Francis J. , Meiler Jens , Oliver Kathryn E. , Plate Lars , Schlebach Jonathan P. 
Published: October 2022

AbstractCystic fibrosis (CF) is a chronic genetic disease caused by mutations that compromise the expression and/ or function of the cystic fibrosis transmembrane conductance regulator chloride channel (CFTR). Most people with CF harbor a common misfolded CFTR variant (ΔF508), which can be rescued by combination therapies containing “corrector” compounds that restore its expression. Nevertheless, there are over 400 other CF variants that differ in their sensitivity to correctors for reasons that remain unclear. In this work, we utilize deep mutational scanning to quantitatively compare the effects of two FDA-approved correctors on the plasma membrane expression of 129 known CF variants, including 45 that are currently unclassified. Across 67 variants with attenuated expression, we find that VX-661-sensitive variants generally exhibit intermediate expression and feature mutations near its binding pocket in transmembrane domains (TMDs) 1, 2, 3, and 6. VX-445 also primarily rescues variants with intermediate expression but is instead uniquely effective towards mutations near its binding pocket in TMDs 10 & 11. Structural calculations suggest corrector binding provides similar stabilization to both sensitive and insensitive variants. These findings collectively suggest the mutation-specific effects of these compounds depend on the degree of variant destabilization and/ or the timing of cotranslational folding defects. Combining these correctors synergistically rescues variants with deficient and intermediate expression alike, presumably by doubling the total binding energy and suppressing defects at different stages of translation. These results provide an unprecedented overview of the properties of rare CFTR variants and establish new tools for CF pharmacology.
Non-viral gene editingin uterowith lipid nanoparticles complexed to mRNA
Authors: Gao Kewa , Li Jie , Song Hengyue , Han Hesong , Wang Yongheng , Yin Boyan , Farmer Diana L. , Murthy Niren , Wang Aijun 
Published: October 2022

AbstractNanoparticle-based drug delivery systems have the potential to revolutionize medicine but their low vascular permeability and rapid clearance by phagocytic cells have limited their medical impact. Nanoparticles delivered at thein uterostage have the potential to overcome these key limitations, due to the high rate of angiogenesis and cell division in fetal tissue, and the under-developed immune system. However, very little is known about nanoparticle drug delivery at the fetal stage of development. In this report, using Ai9 CRE reporter mice, we demonstrate that lipid nanoparticle (LNP) mRNA complexes can deliver mRNA for gene editing enzymesin uteroafter an intrahepatic injection, and can access and edit major organs, such as the heart, the liver, kidneys, lungs and the gastrointestinal tract with remarkable efficiency and low toxicity. In addition, we show here that Cas9 mRNA and sgRNA complexed to LNPs were able to edit the fetal organsin uteroafter an intrahepatic injection. These experiments demonstrate the possibility of non-viral delivery of gene editing enzymesin uteroand nanoparticle drug delivery has great potential for delivering macromolecules to organs outside of the liverin utero, which provides a promising strategy for treating a wide variety of devastating genetic diseases before birth.
Innate immune cell-intrinsic ketogenesis is dispensable for organismal metabolism and age-related inflammation
Authors: Goldberg Emily L. , Letian Anudari , Dlugos Tamara , Leveau Claire , Dixit Vishwa Deep 
Published: October 2022

AbstractAging is accompanied by chronic low-grade inflammation, but the mechanisms that allow this to persist are not well understood. Ketone bodies are alternative fuels produced when glucose is limited and improve indicators of healthspan in aging mouse models. Moreover, the most abundant ketone body, β-hydroxybutyrate (BHB), inhibits the NLRP3 inflammasome in myeloid cells, a key potentiator of age-related inflammation. Given that myeloid cells express ketogenic machinery, we hypothesized this pathway may serve as a metabolic checkpoint of inflammation. To test this hypothesis, we conditionally ablated ketogenesis by disrupting expression of the terminal enzyme required for ketogenesis, 3-Hydroxy-3-Methylglutaryl-CoA Lyase (HMGCL). By deleting HMGCL in the liver, we validated the functional targeting and establish that the liver is the only organ that can produce the life-sustaining quantities of ketone bodies required for survival during fasting or ketogenic diet feeding. Conditional ablation of HMGCL in neutrophils and macrophages had modest effects on body weight and glucose tolerance in agin, but worsened glucose homeostasis in myeloid cell specific Hmgcl deficient mice fed a high-fat diet. Our results suggest that during aging, liver derived circulating ketone bodies might be more important for deactivating NLRP3 inflammasome and controlling organismal metabolism.
An expandable FLP-ON::TIR1 system for precise spatiotemporal protein degradation inC. elegans
Authors: Xiao Yutong , Yee Callista , Martinez Michael A. Q. , Zhao Chris Z. , Zhang Wan , Shen Kang , Matus David Q. , Hammell Christopher 
Published: October 2022

AbstractThe auxin-inducible degradation system has been widely adopted in theC. elegansresearch community for its ability to empirically control the spatiotemporal expression of target proteins. This system can efficiently degradeauxin-inducibledegron (AID)-tagged proteins via the expression of a ligand-activatableAtTIR1 protein derived fromA. thalianathat adapts target proteins to the endogenousC. elegansproteosome. While broad expression ofAtTIR1 using strong, ubiquitous promoters can lead to rapid degradation of AID-tagged proteins, cell type-specific expression ofAtTIR1 using spatially restricted promoters often results in less efficient target protein degradation. To circumvent this limitation, we have developed a FLP/FRT3-based system that functions to reanimate a dormant, high-powered promoter that can drive sufficientAtTIR1expression in a cell type-specific manner. We benchmark the utility of this system by generating a number of tissue specific FLP-ON::TIR1 drivers to reveal genetically separable cell type-specific phenotypes for several target proteins. We also demonstrate that the FLP-ON::TIR1 system is compatible with enhanced degron epitopes. Finally, we provide an expandable toolkit utilizing the basic FLP-ON::TIR1 system that can be adapted to drive optimizedAtTIR1expression in any tissue or cell type of interest.
Engineered SMCHD1 and D4Z4 mutations reveal roles of D4Z4 heterochromatin disruption and feedforward DUX4 network activation in FSHD
Authors: Kong Xiangduo , Nguyen Nam Viet , Li Yumeng , Sakr Jasmine Shaaban , Williams Kate , Sharifi Sheila , Chau Jonathan , Bayrakci Altay , Mizuno Seiya , Takahashi Satoru , Kiyono Tohru , Tawil Rabi , Mortazavi Ali , Yokomori Kyoko 
Published: October 2022

AbstractFacioscapulohumeral dystrophy (FSHD) is commonly associated with contraction of D4Z4 repeats on chromosome 4q (FSHD1). Mutations in theSMCHD1gene are linked to both minor cases with no prominent repeat loss (FSHD2) and severe cases of FSHD1. Abnormal upregulation of the transcription factor DUX4, encoded in theD4Z4repeat, is believed to play a central role in FSHD. However, defining the disease mechanism has been hampered by the heterogeneity of patient-derived cells, difficulty to detect DUX4 in patient myocytes, and limited animal models because D4Z4 repeats are primate-specific. To overcome these limitations, we engineered isogenic human skeletal myoblast lines with D4Z4 and/orSMCHD1mutations. We found a highly synergistic effect of double mutations on triggering two key disease processes, D4Z4 heterochromatin disruption and cross-stimulation of DUX4 targets, such as histone H3.X/Y and LEUTX transcription factor. Thus, engineered human myocyte models provide unique insights into the molecular mechanisms underpinning FSHD.TeaserFSHD mutations cause D4Z4 heterochromatin disruption and feedforward DUX4 network activation.
Manipulating Oxalate Decarboxylase Provides the Basis of Antilithic Therapy by Acting on the Gut Microbiota
Authors: Wu Fang , Cheng Yuanyuan , Zhou Jianfu , Ye Peisen , Liu Xuehua , Zhang Lin , Lin Rongwu , Xiang Songtao , Liu Zhongqiu , Wang Caiyan 
Published: October 2022

ABSTRACTA high concentration of oxalate is associated with an increased risk of kidney calcium oxalate (CaOx) stones, and the degradation of exogenous oxalate mainly depends on oxalate-degrading enzymes from the intestinal microbiome. We found that Zinc Gluconate supplement to patients with CaOx kidney stones could significantly improve the abundance of oxalate metabolizing bacteria in human body through clinical experiments on the premise of simultaneous antibiotic treatment and the imbalance ofLactobacillusand OxDC was involved in CaOx kidney stones through clinical sample analysis. Then, we identified that Zn2+could be used as an external factor to improve the activity of OxDC and protectLactobacillus, achieved the preventive effect on rats with stones aggravated by antibiotics. Finally, by analyzing the three-dimensional structure of OxDC and somein vitroexperiments, we propose a hypothesis Zn2+increases the metabolism of oxalate in humans through its positive effects onLactobacillusand OxDC to reduce CaOx kidney stone symptoms in rats.IMPORTANCEUrinary stone disease is one of the most common urological disorders, and 70%-80% of urinary stones are calcium oxalate (CaOx) stones. We found the structural basis and metabolic mechanism by which oxalate decarboxylase metabolizes oxalate were elucidated, and Zn2+was illustrated to have therapeutic effects on CaOx stones by improving the tolerance of Lactobacillus to antibiotics. According to that, proper Zn2+levels in the diet, the consumption of more probiotic food and avoidance of the antibiotic overuse might be desirable measures for the prevention and treatment of kidney stones.Graphical Abstract
β-catenin-dependent endomesoderm specification appears to be a Bilateria-specific co-option
Authors: Lebedeva Tatiana , Boström Johan , Mörsdorf David , Niedermoser Isabell , Genikhovich Evgeny , Adameyko Igor , Genikhovich Grigory 
Published: October 2022

AbstractEndomesoderm specification based on a maternal β-catenin signal and axial patterning by interpreting a gradient of zygotic Wnt/β-catenin signalling was suggested to predate the split between Bilateria and their evolutionary sister Cnidaria. However, in Cnidaria, the roles of β-catenin signalling in both these processes have not been proven directly. Here, by tagging the endogenous β-catenin protein in the sea anemoneNematostella vectensis, we show that the oral-aboral axis in a cnidarian is indeed patterned by a gradient of β-catenin signalling. Unexpectedly, in a striking contrast to Bilateria,Nematostellaendoderm specification takes place opposite to the part of the embryo, where β-catenin is translocated into the nuclei. This suggests that β-catenin-dependent endomesoderm specification is a Bilateria-specific co-option, which may have linked endomesoderm specification with the subsequent posterior-anterior patterning.
Daily turnover of active giant virus infection during algal blooms revealed by single-cell transcriptomics
Authors: Hevroni Gur , Vincent Flora , Ku Chuan , Sheyn Uri , Vardi Assaf 
Published: October 2022

AbstractViruses are the most abundant biological entity in the ocean and play a significant role in shaping the marine ecosystem. The past two decades have revealed an outstanding diversity of giant viruses infecting protists across the tree of life and, in particular, algae that form massive blooms in the ocean. Virus-induced bloom demise significantly impacts marine ecology and biogeochemistry, as well as the associated microbial community. Nevertheless, little is known about the infection dynamics of these giant viruses in the natural environment and their role in regulating algal blooms. Here, we provide evidence for a daily life cycle of giant viral infection in algal blooms by processing the transcriptome of over 12,000 single algal cells during different phases of interaction with their giant viruses. We revealed that viral infection occurs already at the exponential phase of the bloom and that the timing of infection can determine the magnitude of the bloom but not the fraction of infected cells. We further revealed that the same proportion of infected cells are in the early phase of the viral replication program (13.5%) throughout several consecutive days of the bloom, suggesting that a daily turnover of infection is at play during the bloom and demise phases of the algal population. This may imply that a continuous source of virocell-associated metabolites diffuses throughout the bloom succession and could fuel the microbial food webs. Finally, we link single cell infection state to host physiology and show that infected cells remained calcified even in the late stage of infection, contradicting common observation of bulk population in which viral infection is directly linked with decalcification. Together, these results highlight the importance of studying host-virus dynamics in natural populations at a single-cell resolution, which can provide a fresh view of the dynamics and propagation of viral infection. This approach will enable quantification of the impact of marine viruses on microbial food webs.
Exploration of the sensitivity to macrocyclic lactones in the canine heartworm (Dirofilaria immitis) in Australia using phenotypic and genotypic approaches
Authors: Power Rosemonde Isabella , Šlapeta Jan 
Published: October 2022

AbstractCanine heartworm disease is a potentially deadly cardiopulmonary disease caused by the mosquito-borne filarial nematodeDirofilaria immitis. In Australia, the administration of macrocyclic lactone (ML) drugs has successfully reduced the prevalence ofD. immitisinfection. However, the recent re-emergence ofD. immitisin dogs in Queensland, Australia and the identification of ML-resistant isolates in the USA poses an important question of whether ML-resistance has emerged in this parasite in Australia. The aim of this study was to utilise phenotypic and genotypic approaches to examine the sensitivity to ML drugs inD. immitisin Australia. To do this, we surveyed 45 dogs from Queensland and New South Wales across 3 years (2019-2022) for the presence ofD. immitisinfection using an antigen test, quantitative Modified Knott’s test, and qPCR targeting bothD. immitisand theD. immitissymbiontWolbachia. A phenotype observed by utilising sequential quantification of microfilariae for 23/45 dogs was coupled with genetic testing of filtered microfilariae for SNPs previously associated with ML-resistance in isolates from the USA. Sixteen (16/45) dogs tested positive forD. immitisinfection despite reportedly receiving ‘rigorous’ heartworm prevention for 12 months prior to the study, according to the owners’ assessment. The phenotype and genotypic assays in this study did not unequivocally demonstrate the presence of ML-resistantD. immitisin Australia. Although the failure of 16 dogs to reduce microfilaremia by >90% after ML treatment was considered a suspect phenotype of ML-resistance, no genotypic evidence was discovered using the genetic SNP analysis. The traditional quantitative Modified Knott’s test can be substituted by qPCR targetingD. immitisor associatedWolbachiaendosymbiont DNA for a more rapid measurement of microfilariae levels. More definitive phenotypic evidence of resistance is critically needed before the usefulness of SNPs for the detection of ML-resistance in Australia can be properly assessed.