bluuebunny/crossref_metadata_2025_split huggingface dataset:
Time-dependent modulation of gut microbiome in response to systemic antifungal agents
Authors: Udawatte Nadeeka S. , Wook Kang S. , Wang Yue , Manzanero Silvia , Arumugam Thiruma V. , Seneviratne Chaminda J. 
Published: October 2020

AbstractThe effects of antifungal agents on the human microbiome can be challenging to study due to confounding factors such as the underlying disease states and concomitant use of antibiotics and other therapies. We elucidated longitudinal modification of gut microbiome in response to a short course (5 days) of antifungal treatment in healthy male Sprague-Dawley (SD) rats by sequencing 16S rRNA V1–V3 and ITS2 hypervariable regions. SD rats were randomized into a control group and three antifungal treated (AT) groups including Amphotericin B (AmB), voriconazole and, our novel antifungal drug candidate SM21 once per day for 5 consecutive days. Fecal samples were collected at three different time points (day 0, day 1 and day 5). Microbial communities of both bacteria and fungi were compared between conditions. In silico analysis of differential microbial abundance and the predictive functional domains of microbial communities was further done by inferring metabarcoding profiles from 16S data. AT animals exhibited significant change in bacteriome alphadiversity although no divergence in community structure (beta-diversity) was observed compared with respective control groups (day 0). Specific bacterial clades and taxa were longitudinally and significantly modified in the AT animals. The AT bacterium of AmB and SM21 was particularly enriched in probioticLactobacillusstrains includingL. reuteri. The key pathways overrepresented in the bacteriome under AT animals were linked to cellular processes, environment information processing and metabolism. Moreover, AT treated mycobiome diversity decreased longitudinally with insignificant variations along the time course; different fungal taxa dominating at different timepoints in a wave-like fashion. However, acute antifungal treatments could not alter healthy gut microbial community structure. Hence, the healthy gut microbiome is capable of resisting a major dysbiotic shift during a short course of antifungal treatment.
The Species-specific Acquisition and Diversification of a Novel Family of Killer Toxins in Budding Yeasts of the Saccharomycotina
Authors: Fredericks Lance R. , Lee Mark D. , Crabtree Angela M. , Boyer Josephine M. , Kizer Emily A. , Taggart Nathan T. , Hunter Samuel S. , Kennedy Courtney B. , Willmore Cody G. , Tebbe Nova M. , Harris Jade S. , Brocke Sarah N. , Rowley Paul A. 
Published: October 2020

AbstractKiller toxins are extracellular antifungal proteins that are produced by a wide variety of fungi, includingSaccharomycesyeasts. Although manySaccharomyceskiller toxins have been previously identified, their evolutionary origins remain uncertain given that many of the se genes have been mobilized by double-stranded RNA (dsRNA) viruses. A survey of yeasts from theSaccharomycesgenus has identified a novel killer toxin with a unique spectrum of activity produced bySaccharomyces paradoxus. The expression of this novel killer toxin is associated with the presence of a dsRNA totivirus and a satellite dsRNA. Genetic sequencing of the satellite dsRNA confirmed that it encodes a killer toxin with homology to the canonical ionophoric K1 toxin fromSaccharomyces cerevisiaeand has been named K1-like (K1L). Genomic homologs of K1L were identified in six non-Saccharomycesyeast species of the Saccharomycotina subphylum, predominantly in subtelomeric regions of the yeast genome. The sporadic distribution of these genes supports their acquisition by horizontal gene transfer followed by diversification, with evidence of gene amplification and positive natural selection. When ectopically expressed inS. cerevisiaefrom cloned cDNAs, both K1L and its homologs can inhibit the growth of competing yeast species, confirming the discovery of a new family of biologically active killer toxins. The phylogenetic relationship between K1L and its homologs suggests gene flow via dsRNAs and DNAs across taxonomic divisions to enable the acquisition of a diverse arsenal of killer toxins for use in niche competition.
Chronic hypoxia regulates Cytoplasmic Polyadenylation Element Binding Protein 2 alternative splicing to promote HIF1a translation
Authors: Mayo Emily M. , Stevens Shaun C. , Ali Anika N. , Moss Christina J. , Lund Sean P. , Nazario-Muñoz Gina S. , Permuth Jennifer B. , Westerheide Sandy D. , Chalfant Charles E. , Park Margaret A. 
Published: October 2020

AbstractHIF1 (Hypoxia-inducible Factor 1) is a transcription factor that plays a crucial role in the hypoxia stress response. However, chronic hypoxia exposure can cause irreversible physiological changes that can lead to pulmonary hypertension (PH), and the need for therapeutics to ameliorate these conditions is great and unmet. Previous studies in our lab have demonstrated that CPEB2 (cytoplasmic polyadenylation element binding protein 2) is a translational repressor of one of the HIF1 subunits: HIF1α. Our lab demonstrated that the alternatively spliced CPEB2A isoform of CPEB2 is a repressor of translation, while the CPEB2B isoform is a translational activator of HIF1α during hypoxia, suggesting a major regulatory role for CPEB2 AS in the pulmonary hypoxic response. Although it is well established that during hypoxia, HIF1α levels are dramatically upregulated due to a decrease in the degradation of this factor, we propose that during chronic hypoxia, the expression of HIF1α is maintained via a translational mechanism, likely alongside a decrease in proteolytic degradation. In this study we demonstrate that depletion of the CPEB2B splice isoform has an inhibitory effect on the translation of nascent HIF1α protein during chronic hypoxia, but not the acute phase. We further demonstrate this pathway is dependent on the initiation factor eIF3H. Finally, we show data that indicate CPEB2A and CPEB2B bind differentially to cytoplasmic polyadenylation element consensus sequences depending on the surrounding sequence context. These findings are important since they provide evidence for the potential of CPEB2 to act as a therapeutic target for treating chronic hypoxia-related pulmonary diseases.
Glutamatergic Control Of A Pattern-Generating Central Nucleus In A Gymnotiform Fish
Authors: Comas Virginia , Borde Michel 
Published: October 2020

ABSTRACTThe activity of pattern-generating networks (CPG) may change under the control exerted by various neurotransmitters and modulators to adapt its behavioral outputs to different environmental demands. Although the mechanisms underlying this control have been well established in invertebrates, most of their synaptic and cellular bases are not yet well understood in vertebrates.Gymnotus omarorum, a pulse-type gymnotiform electric fish, provides a well-suited vertebrate model to investigate these mechanisms.G. omarorumemits rhythmic and stereotyped electric organ discharges (EODs), which function in both perception and communication. The EOD is considered the behavioral output of an electromotor CPG which, modulated by descending influences, organizes adaptive electromotor behaviors in response to environmental and social challenges. The CPG is composed of electrotonically coupled intrinsic pacemaker cells, which pace the rhythm, and bulbospinal projecting relay cells that contribute to organize the pattern of the muscle-derived effector activation that produce the EOD. We used electrophysiological and pharmacological techniques in brainstem slices ofG. omarorumto investigate the underpinnings of the fast transmitter control of its electromotor CPG. We demonstrate that pacemaker, but not relay cells, are endowed with ionotropic and metabotropic glutamate receptors subtypes. We also show, for the first time in gymnotiformes, that glutamatergic control of the CPG likely involves both AMPA-NMDA receptors transmittingandonly-NMDA segregated synapses contacting pacemaker cells. Our data shed light on the fast neurotransmitter control of a vertebrate CPG that seems to exploit the kinetics of the involved postsynaptic receptors to command different behavioral outputs.NEW & NOTEWORTHYUnderpinnings of neuromodulation of pattern-generating central networks (CPG) have been well characterized in many species. The effects of fast neurotransmitter systems remain, however, poorly understood. This research usesin vitroelectrophysiological and pharmacological techniques to show that the neurotransmitter control of a vertebrate CPG in gymnotiform fish involve the convergence of only-NMDA and AMPA-NMDA glutamatergic synapses onto neurons that pace the rhythm. These inputs may organize different behavioral outputs according to their distinct functional properties.
Ethylenediaminetetraacetic acid promotes the accumulation of nitric oxide
Authors: Zhang Shizhong , Liu Shasha , Xiao Shenghui , Li Min , Huang Jinguang , Yan Kang , Yang Guodong , Zheng Chengchao , Wu Changai 
Published: October 2020

AbstractEthylenediaminetetraacetic acid (EDTA) is a well-established chelating agent used in industry, agriculture, food, and medicine. However, the analysis of an EDTA-sensitiveArabidopsis thalianamutant revealed that EDTA can significantly promote nitric oxide (NO) accumulation, indicating that EDTA has unexpected biological functions beyond its chelating activity. This finding challenges our current understanding about the effects of EDTA on biological systems.One Sentence SummaryAn analysis of ethylenediaminetetraacetic acid (EDTA)-sensitive mutants suggests that EDTA can promote the accumulation of nitric oxide.
Structural analysis of the master regulator Rns reveals a small molecule inhibitor of enterotoxigenicEscherichia colivirulence
Authors: Midgett Charles R , Talbot Kacey Marie , Day Jessica L. , Munson George P , Kull F Jon 
Published: October 2020

AbstractEnterotoxigenicEscherichia coli(ETEC) is a common cause of diarrheal disease worldwide and a frequent cause of travelers’ diarrhea. In addition to the production of enterotoxins, studies with human volunteers established ETEC virulence is dependent upon the production of proteinaceous adhesive pili for attaching to the intestinal wall. Although pilins are highly immunogenic, vaccines incorporating them have yet to be proven efficacious. An additional challenge for vaccines is the heterogeneity of ETEC pili, as 20 different pilus types have been identified. However, the expression of a significant number of pilus types is dependent upon Rns, an AraC family transcription factor. Furthermore, Rns also regulates the expression of the virulence factor CexE, an outer membrane coat protein. To determine how Rns functions and is regulated we solved its structure by X-ray crystallography to 3 Å resolution. Rns forms a dimer via its N-terminal domain and its structure is consistent with the dimer binding looped DNA. Our analyses also revealed a fatty acid, decanoic acid, bound within the Rns structure. Although Rns was not known to specifically bind small molecule ligands, biochemical analysis showed decanoic acid specifically stabilized Rns in a dose dependent manner. Lac reporter assays further showed that decanoic acid inhibits Rns function at both activated and repressed promoters. In situ, exogenous decanoic acid inhibited the expression of Rns-dependent CFA/I pili and CexE in different ETEC strains. Thus, our study reveals for the first time a naturally occurring small molecule ligand specifically inhibits Rns activity and potently suppresses the expression of ETEC virulence factors. Our findings provide an alternative approach to vaccines for inhibiting ETEC pathogenesis by using the Rns structure as a framework for rational drug design.
Bistable, biphasic regulation of PP2A-B55 accounts for the dynamics of mitotic substrate phosphorylation
Authors: Kamenz Julia , Gelens Lendert , Ferrell James E. 
Published: October 2020

SummaryThe phosphorylation of mitotic proteins is bistable, which contributes to the decisiveness of the transitions into and out of M phase. The bistability in substrate phosphorylation has been attributed to bistability in the activation of the cyclin-dependent kinase Cdk1. However, more recently it has been suggested that bistability also arises from positive feedback in the regulation of the Cdk1-counteracting phosphatase, PP2A-B55. Here, we demonstrate biochemically using Xenopus laevis egg extracts that the Cdk1-counteracting phosphatase PP2A-B55 functions as a bistable switch, even when the bistability of Cdk1 activation is suppressed. In addition, Cdk1 regulates PP2A-B55 in a biphasic manner; low concentrations of Cdk1 activate PP2A-B55 and high concentrations inactivate it. As a consequence of this incoherent feedforward regulation, PP2A-B55 activity rises concurrently with Cdk1 activity during interphase and suppresses substrate phosphorylation. PP2A-B55 activity is then sharply downregulated at the onset of mitosis. During mitotic exit Cdk1 activity initially falls with no obvious change in substrate phosphorylation; dephosphorylation then commences once PP2A-B55 spikes in activity. These findings suggest that changes in Cdk1 activity are permissive for mitotic entry and exit, but the changes in PP2A-B55 activity are the ultimate trigger.
First description of Hepatitis E virus in Australian rabbits
Authors: Jenckel Maria , Hall Robyn N. , Strive Tanja 
Published: October 2020

AbstractWe report the first detection of Hepatitis E virus in rabbits in Australia. While conducting metatranscriptomic sequencing of liver samples collected from domestic rabbits that had diedwe detected three samples positive for hepatitis E virus. Two viral genome sequences were obtained, which shared 96% nucleotide identity.
Airway bacterial and fungal microbiome in chronic obstructive pulmonary disease
Authors: Liu Haiyue , Liang Zhenyu , Cao Nannan , Tan Xilan , Liu Zuheng , Wang Fengyan , Yang Yuqiong , Li Chunxi , He Yan , Su Jin , Chen Rongchang , Wang Zhang , Zhou Hongwei 
Published: October 2020

AbstractBackgroundLittle is known about airway mycobiome, and its relationship with bacterial microbiome in chronic obstructive pulmonary disease (COPD).MethodsHere we report the first simultaneous characterization of sputum bacterial and fungal microbiome in 84 stable COPD and 29 healthy subjects, using 16S ribosomal DNA and fungal internal transcribed spacer DNA sequencing.ResultsAscomycota predominated over Basidiomycota in fungal microbiome both in COPD patients and healthy controls.Meyerozyma,Candida,AspergillusandSchizophyllumwere most abundant at the genus level. There was a significant inverse correlation between bacterial and fungal microbial diversity, both of which altered in opposite directions in COPD patients versus controls, and in frequent versus non-frequent exacerbators. An enhanced bacterial-fungal ecological interaction was observed in COPD patients, which was characterized by higher proportion of co-occurrence intrakingdom interactions and co-exclusive interkingdom interactions. In COPD, four mutually co-occurring fungal operational taxonomic units (OTUs) inCandida palmioleophila,Aspergillusand Sordariomycetes exhibited co-exclusive relationships with other fungal OTUs, which was specifically present in frequent exacerbators but not in non-frequent exacerbators. Conversely, the mutual co-occurrence interactions between bacterial OTUs inRothia mucilaginosa,Streptococcus,VeillonellaandPrevotella, showed up in non-frequent exacerbators but not in frequent exacerbators. The perturbed bacterial-fungal interactions in COPD were associated with increased airway inflammatory mediators such as IL-6 and IL-8.InterpretationThe disruption of airway bacterial-fungal community balance, characterized by the loss of commensal bacterial taxa and enriched pathogenic fungal taxa, is implicated in COPD. The airway mycobiome is an important cofactor mediating COPD pathogenic infection and host inflammation.Clinical Trial Registrationwww.clinicaltrials.gov(NCT 03240315).
Sphingolipid Containing Outer Membrane Vesicles Serve as a Delivery Vehicle to Limit Host Immune Response toPorphyromonas gingivalis
Authors: Rocha Fernanda G. , Ottenberg Gregory , Eure Zavier G. , Davey Mary E. , Gibson Frank C. 
Published: October 2020

ABSTRACTSphingolipids (SLs) are essential structural components of mammalian cell membranes. Our group recently determined that the oral anaerobePorphyromonas gingivalisdelivers its SLs to host cells, and that the ability ofP. gingivalisto synthesize SLs limits the elicited host inflammatory response during cellular infection. AsP. gingivalisrobustly produces outer membrane vesicles (OMVs), we hypothesized that OMVs serve as a delivery vehicle for SLs, that the SL status of the OMVs may impact cargo loading to OMVs, and that SL-containing OMVs limit elicited host inflammation similar to that observed by direct bacterial challenge. Transwell cell culture experiments determined that in comparison to the parent strain W83, the SL-null mutant elicited a hyper-inflammatory immune response from THP-1 macrophage-like cells with elevated TNF-α, IL-1β, and IL-6. Targeted assessment of Toll-like receptors (TLRs) identified elevated expression of TLR2, unchanged TLR4, and elevated expression of the adaptor molecules MyD88 and TRIF by SL-nullP. gingivalis.No significant differences in gingipain activity were observed in our infection models and both strains produced OMVs of similar size. Using comparative 2-dimensional gel electrophoresis we identified differences in the protein cargo of the OMVs between parent and SL-null strain. Importantly, use of purified OMVs recapitulated the cellular inflammatory response observed in the transwell system with whole bacteria. These findings provide new insights into the role of SLs inP. gingivalisOMV cargo assembly and expand our understanding of SL-OMVs as bacterial structures that modulate the host inflammatory response.
CRISPR/Cas12a mediated genome engineering in photosynthetic bacteria
Authors: Zhang Yang , Yuan Jifeng 
Published: October 2020

ABSTRACTPurple non-sulfur photosynthetic bacteria (PNSB) such asR. capsulatusserve as a versatile platform for fundamental studies and various biotechnological applications. In this study, we sought to develop the class II RNA-guided CRISPR/Cas12a system fromFrancisella novicidafor both genome editing and gene down-regulation inR. capsulatus. About 90% editing efficiency was achieved by using CRISPR/Cas12a driven by a strong promoter Ppucwhen targetingccoOornifHgene. When both genes were simultaneously targeted, the multiplex gene editing efficiency reached >63%. In addition, CRISPR interference using deactivated Cas12a was also evaluated using reporter genesgfpandlacZ, and the repression efficiency reached >80%. In summary, our work represents the first report to develop CRISPR/Cas12a mediated genome editing/transcriptional repression inR. capsulatus, which would greatly accelerate PNSB-related researches.IMPORTANCEPurple non-sulfur photosynthetic bacteria (PNSB) such asR. capsulatusserve as a versatile platform for fundamental studies and various biotechnological applications. However, lack of efficient gene editing tools remains a main obstacle for progressing in PNSB-related researches. Here, we developed CRISPR/Cas12a for genome editing via the non-homologous end joining (NHEJ) repair machinery inR. capsulatus. In addition, DNase-deactivated Cas12a was found to simultaneously suppress multiple targeted genes. Taken together, our work offers a new set of tools for efficient genome engineering in PNSB such asR. capsulatus.
Contact tracing and isolation reduces covid-19 incidence in a structured agent-based model
Authors: Low Marcus , Geffen Nathan 
Published: October 2020

AbstractBackgroundThe World Health Organization has identified contact tracing and isolation (CTI) as a key strategy to slow transmission of SARS-CoV-2. Structured agent-based models (ABMs) provide a means to investigate the efficacy of such strategies in heterogeneous populations and to explore the impact of factors such as changes in test turnaround times (TaT).MethodsWe developed a structured ABM to simulate key SARS-CoV-2 transmission and Covid-19 disease progression dynamics in populations of 10, 000 agents. We ran 10, 000 simulations of each of three scenarios: (1) No CTI with a TaT of two days, (2) CTI with a TaT of two days, and (3) CTI with a TaT of eight days. We conducted a secondary analysis in which TaT values were varied from two to 11. The primary outcome for all analyses was mean total infections.ResultsCTI reduced the mean number of infections from 5, 577 to 4, 157 (a relative reduction of 25.5%) when TaT was held steady at two days. CTI with a TaT of eight days resulted in a mean of 5, 163 infections (a relative reduction of 7.4% compared to no CTI and a TaT of two days). In the secondary analysis, every additional day added to the TaT increased the total number of infections – with the greatest increase in infections between four and five days, and the smallest increase between ten and 11 days.ConclusionsIn a structured ABM that simulates key dynamics of Covid-19 transmission and disease progression, CTI results in a substantial reduction in the mean number of total infections. The benefit is greater with shorter TaT times, but remained substantial even with TaTs of eight days. The results suggest that CTI may play a critical role in reducing the size of outbreaks and that TaTs should be kept as short as possible in order to maximise this benefit.