bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inhibitory proteins block substrate access by occupying the active site cleft of Bacillus subtilis intramembrane protease SpoIVFB
Authors: Olenic Sandra , Heo Lim , Feig Michael , Kroos Lee 
Published: July 2021

AbstractIntramembrane proteases function in numerous signaling pathways that impact health, but knowledge about regulation of intramembrane proteolysis is limited. We examined inhibition of intramembrane metalloprotease SpoIVFB by proteins BofA and SpoIVFA. We found that BofA residues in and near a predicted transmembrane segment are required for SpoIVFB inhibition, and cross-linking experiments indicated that this transmembrane segment occupies the SpoIVFB active site cleft. SpoIVFA is also required for SpoIVFB inhibition. The inhibitory proteins block access of the substrate N-terminal Proregion to the membrane-embedded SpoIVFB active site, based on additional cross-linking experiments; however, the inhibitory proteins did not prevent interaction between the substrate C-terminal region and the SpoIVFB soluble domain. A structural model was built of SpoIVFB in complex with BofA and parts of SpoIVFA and substrate, using partial homology and constraints from cross-linking and co-evolutionary analyses. The model predicts that conserved BofA residues interact to stabilize a transmembrane segment and a membrane-embedded C-terminal region. SpoIVFA is predicted to bridge the BofA C-terminal region and SpoIVFB, forming a membrane-embedded inhibition complex. Our results reveal a novel mechanism of intramembrane protease inhibition with clear implications for relief from inhibition in vivo and design of inhibitors as potential therapeutics.
A Phosphorus-Limitation Induced, Functionally Conserved DUF506 Protein is a Repressor of Root Hair Elongation in Arabidopsis thaliana
Authors: Ying Sheng , Blancaflor Elison B. , Liao Fuqi , Scheible Wolf-Rüdiger 
Published: July 2021

ABSTRACTRoot hairs (RHs) function in nutrient and water acquisition, root metabolite exudation, soil anchorage and plant-microbe interactions. Longer or more abundant RHs are potential breeding traits for developing crops that are more resource-use efficient and can improve soil health. RH elongation is controlled by both environmental and endogenous factors. While many genes are known to promote RH elongation, relatively little is known about genes and mechanisms that constrain RH growth. Here we demonstrate that a DOMAIN OF UNKNOWN FUNCTION 506 (DUF506) protein, AT3G25240, negatively regulates Arabidopsis thaliana RH growth. The AT3G25240 gene is strongly and specifically induced during P-limitation. Mutants of this gene, which we call REPRESSOR OF EXCESSIVE ROOT HAIR ELONGATION 1 (RXR1), have much longer RHs, while over-expression of the gene results in much shorter RHs. RXR1 physically interacts with a Rab-GTPase (RXR2), and an rxr2 mutant phenocopies the rxr1 mutant. Overexpression of a Brachypodium distachyon RXR1 homolog resulted in repression of RH elongation in Brachypodium. Taken together, our results reveal a DUF506-GTPase module with a prominent role in repression of RH elongation that is conserved in monocots and dicots.
Larval zebrafish exhibit collective motion behaviors in constrained spaces
Authors: Zaki Haider , Lushi Enkeleida , Severi Kristen E. 
Published: July 2021

ABSTRACTCollective behavior may be elicited or can spontaneously emerge by a combination of interactions with the physical environment and conspecifics moving within that environment. To investigate the relative contributions of these factors in a small millimeter-scale swimming organism, we observed larval zebrafish, interacting at varying densities under circular confinement. Our aim was to understand the biological and physical mechanisms acting on these larvae as they swim together inside circular confinements. If left undisturbed, larval zebrafish swim intermittently in a burst and coast manner and are socially independent at this developmental stage, before shoaling behavioral onset. We report here our analysis of a new observation for this well-studied species: in circular confinement and at sufficiently high densities, the larvae collectively circle rapidly alongside the boundary. This is a new physical example of self-organization of mesoscale living active matter driven by boundaries and environment geometry. We believe this is a step forward toward using a prominent biological model system in a new interdisciplinary context to advance knowledge of the physics of social interactions.
Mutations in Drosophila tRNA processing factors cause phenotypes similar to Pontocerebellar Hypoplasia
Authors: Schmidt Casey A. , Min Lucy Y. , McVay Michelle H. , Giusto Joseph D. , Brown John C. , Salzler Harmony R. , Matera A. Gregory 
Published: July 2021

AbstractMature tRNAs are generated by multiple RNA processing events, which can include the excision of intervening sequences. The tRNA splicing endonuclease (TSEN) complex is responsible for cleaving these intron-containing pre-tRNA transcripts. In humans, TSEN copurifies with CLP1, an RNA kinase. Despite extensive work on CLP1, its in vivo connection to tRNA splicing remains unclear. Interestingly, mutations in CLP1 or TSEN genes cause neurological diseases in humans that are collectively termed Pontocerebellar Hypoplasia (PCH). In mice, loss of Clp1 kinase activity results in premature death, microcephaly and progressive loss of motor function. To determine if similar phenotypes are observed in Drosophila, we characterized mutations in crowded-by-cid (cbc), the CLP1 ortholog, as well as in the fly ortholog of human TSEN54. Analyses of organismal viability, larval locomotion and brain size revealed that mutations in both cbc and Tsen54 phenocopy those in mammals in several details. In addition to an overall reduction in brain lobe size, we also found increased cell death in mutant larval brains. Ubiquitous or tissue-specific knockdown of cbc in neurons and muscles reduced viability and locomotor function. These findings indicate that we can successfully model PCH in a genetically-tractable invertebrate.
Development of a fluorescent quantitative real-time polymerase chain reaction assay for the detection of novel-goose parvovirus in vivo
Authors: Ma Haibin , Li Yahui , Yang Junzheng 
Published: July 2021

AbstractObjectivesTo develop a sensitive, highly specific fluorescent quantitative real-time PCR assay for accurate detection and quantification of novel-goose parvovirus (N-GPV) in vitro and in vivo.MethodsSpecific primers was designed based on N-GPV inverted terminal repeats region; virus RNA (DFV, NDV, AIV, DHV-1, DHV-3) and virus DNA (MDPV, GPV, N-GPV) were extracted, cDNA (DFV, NDV, AIV, DHV-1, DHV-3) were prepared from viral RNAs using M-MLV Reverse Transcriptase, and prepared cDNA (DFV, NDV, AIV, DHV-1, DHV-3) and DNA (MDPV, GPV, N-GPV) amplified by real-time PCR; the sensitivity, specificity and reproducibility of established real-time PCR methods were evaluated, and finally we validated the reliability of real-time PCR methods in ducklings models in vivo.ResultsThe standard curve of established real-time PCR had a good linearity (slope was −0.3098, Y-intercept was 37.865, efficiency of standard curve was 0.995); the detection limit of established real-time PCR for N-GPV was 10 copies/reaction. The sensitivity of real-time PCR was 10 copies/μL, which was 1000 times higher than conventional gel-based PCR assay. The results of intra-assay CVs (0.04-0.74%) and inter-assay CVs (0.16-0.53%) showed that the real-time PCR assay had an excellent repeatability. This method also could efficiently detect viral load in heart, liver, spleen, lung, kidney, pancreas, bursa of Fabricius, brain, blood and excrement from ducklings models after N-GPV infection from 6h to 28 days, which could provided us a dynamic distribution observation of N-GPV viral load using this real-time PCR assay in vivo.ConclusionIn the study, we developed a high sensitive, specific and reproducible real-time PCR assay for N-GPV detection. The established real-time PCR assay was suitable for parvovirus detection and quantification simultaneously, no matter sample obtained from blood, internal organs or ileac contents; the present work may provide insight into the pathogenesis of N-GPV and will contributes to better understanding of this newly emerged novel GPV related virus in cherry valley ducks.
Differed cell division angle, position of cell proliferative area, and localization of ANGUSTIFOLIA3 in lateral organs
Authors: Kinoshita Ayaka , Naito Makiko , Tsukaya Hirokazu 
Published: July 2021

AbstractLeaf meristem is a cell proliferative zone present in the lateral organ primordia. In this study, we investigated how the proliferative zone affects the final morphology of the lateral organs. We examined how cell proliferative zones differ in the primordia of planar floral organs and polar auxin transport inhibitor (PATI)-treated leaves from normal foliage leaf primordia of Arabidopsis thaliana with a focus on the spatial accumulation pattern of ANGUSTIFOLIA3 (AN3), a key element for leaf meristem positioning. We found that organ shape changes by PATI treatment were correlated to the angle of the cell division plane relative to the leaf primordia axis in the leaf meristem (cell division angle), but not with leaf-meristem positioning, size of the leaf meristem, or the localization pattern of AN3 protein. In contrast, different shapes between sepals and petals compared with foliage leaves were associated with both altered meristem position associated with altered AN3 expression patterns and different distributions of cell division angles. These results suggest that lateral organ shapes are regulated via two aspects: position of meristem and cell division anglesSummary statementDifferent lateral organs with different morphology possess different properties of meristems; cell division angles, position of cell proliferative area and AN3 localization patterns.
Assessing the Effectiveness of Mycorrhizal Inoculation on the Biochemical Composition of the Different Species of Echinacea
Authors: Sharma Asha , Saini Ishan , Shankar Bandi Arpitha 
Published: July 2021

ABSTRACTThe information regarding the effect of the mycorrhizal inoculation on different Echinacea species is not available in detail. Therefore, here we determined the changes in the biochemical composition of echinacea as a result of mycorrhizal inoculation. This experiment was undertaken to assess the effect of the mycorrhizal association on biochemical properties of different echinacea species (E. angustifolia,E. purpurea, E. pallida). Here various echinacea species were inoculated with mycorrhiza to examine the species richness in different traits. The results established that biological traits (plant dry matter, chlorophyll content, carotenoid, N content, P content, K content) and physiological and mycorrhization characteristics (Root essential oil, ABTS Antioxidant, Ferric-Reducing Antioxidant, Total phenolic, AM Spore No., AM Root Colonization) both are higher under mycorrhizal association than the control plants of different echinacea species. E. purpurea showed greater results than the E. angustifolia and E. pallida. Among biochemical properties chlorophyll content, carotenoid and N, P, K were significantly higher underE. Purpurea than the E. angustifolia and E.pallida. Total dry matter was higher under E. angustifolia (49.23 g) and minimum dry matter was found under E. pallida (40.07 g). Physiological and mycorrhizal traits were significantly higher under E. purpurea than the other species. E. purpurea showed higher AM Spore No., AM Root Colonization 231.30, 78.70% respectively. Lowest physiological and mycorrhization characteristics were found under E. pallida. The result of mycorrhizal association was very effective for plant growth and increased bio-physicochemical properties than the control plants.
Selective whole genome amplification as a tool to enrich specimens with lowTreponema pallidumgenomic DNA copies for whole genome sequencing
Authors: Thurlow Charles M. , Joseph Sandeep J. , Ganova-Raeva Lilia , Katz Samantha S. , Pereira Lara , Chen Cheng , Debra Alyssa , Vilfort Kendra , Workowski Kimberly , Cohen Stephanie E. , Reno Hilary , Sun Yongcheng , Burroughs Mark , Sheth Mili , Chi Kai-Hua , Danavall Damien , Philip Susan S. , Cao Weiping , Kersh Ellen N. , Pillay Allan 
Published: July 2021

AbstractDownstream next generation sequencing (NGS) of the syphilis spirocheteTreponema pallidumsubspeciespallidum(T. pallidum) is hindered by low bacterial loads and the overwhelming presence of background metagenomic DNA in clinical specimens. In this study, we investigated selective whole genome amplification (SWGA) utilizing multiple displacement amplification (MDA) in conjunction with custom oligonucleotides with an increased specificity for theT. pallidumgenome, and the capture and removal of CpG-methylated host DNA using the NEBNext®Microbiome DNA Enrichment Kit followed by MDA with the REPLI-g Single Cell Kit as enrichment methods to improve the yields ofT. pallidumDNA in isolates and lesion specimens from syphilis patients. Sequencing was performed using the Illumina MiSeq v2 500 cycle or NovaSeq 6000 SP platform. These two enrichment methods led to 93-98% genome coverage at 5 reads/site in 5 clinical specimens from the United States and rabbit propagated isolates, containing >14T. pallidumgenomic copies/μl of sample for SWGA and >129 genomic copies/μl for CpG methylation capture with MDA. Variant analysis using sequencing data derived from SWGA-enriched specimens, showed that all 5 clinical strains had the A2058G mutation associated with azithromycin resistance. SWGA is a robust method that allows direct whole genome sequencing (WGS) of specimens containing very low numbers ofT. pallidum, which have been challenging until now.ImportanceSyphilis is a sexually transmitted, disseminated acute and chronic infection caused by the bacterial pathogenTreponema pallidumsubspeciespallidum. Primary syphilis typically presents as single or multiple mucocutaneous lesions, and if left untreated, can progress through multiple stages with varied clinical manifestations. Molecular studies often rely on direct amplification of DNA sequences from clinical specimens; however, this can be impacted by inadequate samples due to disease progression or timing of patients seeking clinical care. While genotyping has provided important data on circulating strains over the past two decades, WGS data is needed to better understand strain diversity, perform evolutionary tracing, and monitor antimicrobial resistance markers. The significance of our research is the development of a SWGA DNA enrichment method that expands the range of clinical specimens that can be directly sequenced to include samples with low numbers ofT. pallidum.
Screening and Identification of Lassa Virus Endonuclease-targeting Inhibitors from a Fragment-based Drug Development Library
Authors: Lan Xiaohao , Zhang Yueli , Liu Yang , Guo Jiao , Jia Xiaoying , Zhang Mengmeng , Cao Junyuan , Xiao Gengfu , Guo Yu , Wang Wei 
Published: July 2021

AbstractLassa virus (LASV) belongs to the Old World genus Mammarenavirus, family Arenaviridae, and order Bunyavirales. Arenavirus contains a segmented negative-sense RNA genome, which is in line with the bunyavirus and orthomyxoviruses. The segmented negative-sense RNA viruses utilize a cap-snatching strategy to provide primers cleavaged from the host capped mRNA for viral mRNA transcription. As a similar strategy and the conformational conservation shared with these viruses, the endonuclease (EN) would serve as an attractive target for developing broad-spectrum inhibitors. Using the LASV minigenome (MG) system, we screened a fragment-based drug development library and found three candidates (F1204, F1781, and F1597) inhibited MG activity. All three candidates also inhibited the prototype arenavirus Lymphocytic choriomeningitis virus (LCMV) MG activity. Furthermore, the investigation revealed that two benzotriazole compounds (F1204 and F1781) effectively inhibited authentic LCMV and severe fever with thrombocytopenia syndrome virus (SFTSV) infections. The combination of either compound with an arenavirus entry inhibitor had significant synergistic antiviral effects. Moreover, both F1204 and F1781 were found to exert the binding ability of LASV EN with binding affinity at the micromolar level. These findings provide a basis for developing benzotriazole compounds as potential candidates for the treatment of segmented negative-sense RNA virus infections.ImportanceCap-snatching is the mRNA transcription strategy shared by all the segmented, negative-sense RNA viruses. Using a fragment-based drug development (FBDD) library, we tried to screen out the backbone compound to inhibit the endonuclease activity and thus block this kind of virus infection. Two benzotriazole compounds, F1204 and F1781, were identified to inhibit the Lassa virus (LASV) minigenome activity by targeting the LASV EN.
Tributyltin exposure leads to increased adiposity and reduced abundance of leptogenic bacteria in the zebrafish intestine
Authors: de la Torre Canny Sol Gómez , Mueller Olaf , Craciunescu Camil V. , Blumberg Bruce , Rawls John F. 
Published: July 2021

ABSTRACTThe chemical obesogen tributyltin (TBT) is known to promote fat storage in adipose tissue through direct action on vertebrate cells. TBT also has direct toxic effects on microorganisms, raising the possibility that TBT may also promote fat storage in vertebrates by altering their microbiota. Here we show that exposure of conventionally-reared post-embryonic zebrafish to TBT results in increased adiposity, reduced body size, and altered intestinal microbiota composition including reduced relative abundance of Plesiomonas bacteria. To test if those microbiota alterations affected host adiposity, we exposed conventionally-reared zebrafish to intestinal bacterial strains representative of TBT-altered taxa. We found that introduction of a Plesiomonas strain into conventionally-reared zebrafish was sufficient to reduce adiposity and alter intestinal microbiota composition. Using new long-term gnotobiotic zebrafish husbandry methods, we found that colonization of germ-free zebrafish with Plesiomonas was sufficient to reduce host adiposity. Together these results show the leptogenic activity of Plesiomonas on zebrafish hosts, indicating that the ability of TBT to increase adiposity in vivo may be due in part to TBT-mediated modification of the abundance of leptogenic bacteria like Plesiomonas. These findings underscore how complex reciprocal interactions between animals and their microbial and chemical environments can influence energy balance and metabolic health.IMPORTANCEObesogens are environmental chemicals that promote fat storage and are generally thought to exert this effect directly on animal cells. Using zebrafish, we show that the obesogen tributyltin can also promote fat storage by acting upon intestinal microbiota via reduction of bacteria that are sufficient to reduce fat storage.
Small RNA profiling inMycobacteriuminsights into stress adapt ability
Authors: Chen Yingyu , Zhai Wenjun , Zhang Kailun , Zhu Tingting , Su Li , Bermudez Luiz , Chen Huanchun , Guo Aizhen 
Published: July 2021

AbstractMycobacteria would encounter a number of environment changes during infection, and respond to it using different mechanisms. sRNA is a posttranscriptionally regulatory system for the function of genes and has been investigated in many other bacteria. Here, we usedMycobacterium tuberculosisandMycobacterium bovisBCG infection models and sequenced the whole bacterial RNAs before and after host cells infection. Comparison of differential expressed sRNAs, by using GO and KEGG, and target predication, was carried out. Six pathogenically relevant stresses, drug resistance test, growth rate and morphology were used for screening and identify sRNAs. From these data, we identified a subset of sRNAs that are differentially expressed in multiple infection groups and stress conditions. We found that many of them were associated with lipid metabolism. Among them, ncBCG427, was significantly down-regulated when BCG entered into macrophages, and was associated with increase of biofilm formation and changed in drug susceptibility. Then, reduction of virulence possibility depends on regulating lipid metabolism.
Molecular mechanisms of stress-induced reactivation in mumps virus condensates
Authors: Zhang Xiaojie , Sridharan Sindhuja , Zagoriy Ievgeniia , Oegema Christina Eugster , Ching Cyan , Pflaesterer Tim , Fung Herman K. H. , Poser Ina , Müller Christoph W. , Hyman Anthony A. , Savitski Mikhail M. , Mahamid Julia 
Published: July 2021

SummaryMany viruses can establish long-term persistent infections in the human host and cause chronic diseases. Here we combine cell biology, whole-cell proteomics and cryo-electron tomography to uncover how cellular stress disrupts the host-virus equilibrium in persistent infection and induces viral replication, using a model of negative-stranded RNA viruses, the mumps virus. We show that phosphorylation of the largely disordered viral phosphoprotein coincides with increased partitioning of viral polymerase into pre-formed liquid-like condensates and the formation of a stable replication machinery. By obtaining the first atomic models for the authentic mumps virus nucleocapsid, we elucidate a concomitant conformational change that exposes the viral genome to its replication machinery. These events that occur within viral condensates upon stress, together with concerted down-regulation of the host antiviral defense, provide an environment that supports up-regulation of viral replication and constitute a stress-mediated switch that disrupts the host-virus equilibrium in persistent infection.In BriefA multi-scale approach uncovers molecular and structural basis of how cellular stress provokes activation of persistent viral infection mediated by biomolecular condensates.
A Massively Parallel Trafficking Assay Accurately Predicts Loss of Channel Function inKCNH2Variants
Authors: Ng Chai-Ann , Ullah Rizwan , Farr Jessica , Hill Adam P. , Kozek Krystian A. , Vanags Loren R. , Mitchell Devyn , Kroncke Brett M. , Vandenberg Jamie I. 
Published: July 2021

AbstractHigh throughput genomics has greatly facilitated identification of genetic variants. However, determining which variants contribute to disease causation is challenging with more than half of all missense variants now classified asvariants of uncertain significance(VUS). A VUS leaves patients and their clinicians unable to utilize the variant information in clinical decision-making. In long QT syndrome type 2,KCNH2channel function is directly associated with disease presentation. Therefore, functional phenotypingof KCNH2variants can provide direct evidence to aid variant classification. Here, we investigated the expression of all codon variants in exon 2 ofKCNH2using a massively parallel trafficking assay and for a subset of 458 single nucleotide variants compared the results with peak tail current density and gating using automated patch clamp electrophysiology. Trafficking could correctly classify loss of peak tail current density variants with an AUC reaching 0.94 compared to AUCs of 0.75 to 0.8 forin silicovariant classifiers. We suggest massively parallel trafficking assays can provide prospective and accurate functional assessment for all missense variants inKCNH2and most likely many other ion channels and membrane proteins.