bluuebunny/crossref_metadata_2025_split huggingface dataset:
New Genotypes and Diversity ofOrientia tsutsugamushiIsolated from Scrub Typhus Patients in South Korea as Determined by Multilocus Sequence Typing
Authors: Hwang Joo-Hee , Kim Jeongsik , Sun In O , Lee Tae Hee , Chung Kyung Min , Lee Chang-Seop 
Published: August 2020

AbstractOrientia tsutsugamushi, an obligate intracellular organism, is the causative agent of scrub typhus, which is endemic in the Asia-Pacific region. No comparative studies on the genotypic properties ofO. tsutsugamushihave been performed using multilocus sequence typing (MLST) in South Korea. Here, we characterized 51 clinical isolates from Jeonju, in southwestern Korea, and we compared them to isolates from Thailand, Laos, and Japan. We also identified 10 new alleles and six novel sequence types. Overall, our results suggest that the relative genetic stability and the clonal populations ofO. tsutsugamushistrains in South Korea have remained mostly conserved.Author summaryScrub typhus is a life-threatening disease, caused by infection withO. tsutsugamushi, a Gram-negative intracellular bacterium. Approximately one million people are infected globally every year, especially in the Asia-Pacific region. Strains ofO. tsutsugamushiare typically distinguished serologically on the basis of sequences of the highly polymorphic 56-kDa outer membrane protein. Multilocus sequence typing (MLST) is a generic typing method that provides a unified bacterial isolate characterization approach that can be used for evolutionary and population studies of bacteria. In this study, we describe the development and application of a MLST scheme that was applied to 51O. tsutsugamushiisolates. We found 10 new alleles and six new STs, which yielded a total of sevenO. tsutsugamushiSTs in South Korea. Among seven different STs (ST 48, 93-98), ST 48 account for the largest proportion (49.0%) ofO. tsutsugamushiSTs in South Korea. With the exception of the appearance of six novel STs, the clonal populations have remained conserved but further study of population structure and evolutionary trends is warranted.
Ilomastat contributes to the survival of mouse after irradiation via promoting the recovery of hematopoietic system
Authors: Zhao Baoquan , Li Xiaoman , Li Xingzhou , Quan Dongqin , Zhang Fang , Hu Burong 
Published: August 2020

AbstractIlomastat, a broad-spectrum inhibitor of matrix metalloproteinases (MMPs), has drawn attentions for its function in alleviating radiation damage. However, the detailed mechanisms of Ilomastat’s protection from animal model remain not fully clear. In this study, the C57BL/6 mice were pre-administrated with Ilomastat or vihicle for 2 h, and then total body of mice were exposed to 6 Gy of γ-rays. The protective effect of Ilomastat on the hematopoietic system in the irradiated mice were investigated. We found that pretreatment with Ilomastat significantly reduced the level of TGF-β1 and TNF-α, and elevated the number of bone marrow (BM) mononuclear cells in the irradiated mice. Ilomastat pretreatment also increased the fraction of BM hematopoietic progenitor cells (HPCs) and hematopoietic stem cells (HSCs) at day 30 after irradiation, and protected the spleen of mouse from irradiation. These results suggest that Ilomastat promotes the recovery of hematopoietic injury in the irradiated mice, and thus contributes to the survival of mouse after irradiation.
The nitrogen-fixing symbiotic cyanobacterium,Nostoc punctiformecan regulate plant programmed cell death
Authors: Belton Samuel P. , McCabe Paul F. , Ng Carl K. Y. 
Published: August 2020

AbstractCyanobacteria such asNostocspp. can form nitrogen-fixing symbioses with a broad range of plant species. Unlike other plant-bacteria symbioses, little is understood about the immunological and developmental signalling events induced byNostoccyanobionts (symbiotic cyanobacteria). Here, we used suspension cell cultures to elucidate the early molecular mechanisms underpinning the association between cyanobionts and plants by studying the effects of conditioned medium (CM) fromNostoc punctiformecultures on plant programmed cell death (PCD), a typical immune response activated during incompatible interactions. We showed thatN. punctiforme-CM could suppress PCD induced by a temperature stress. Interestingly, this was preceded by significant transcriptional reprogramming, as evidenced by the differential regulation of a network of defence-associated genes, as well as genes implicated in regulating cell growth and differentiation. This work is the first to show that cyanobionts can regulate PCD in plants and provides a valuable transcriptome resource for the early immunological and developmental signalling events elicited byNostoccyanobionts.
Evolution of Chi motifs in Proteobacteria
Authors: Buton Angélique , Bobay Louis-Marie 
Published: August 2020

AbstractHomologous recombination is a key pathway found in nearly all bacterial taxa. The recombination complex allows bacteria to repair DNA double strand breaks but also promotes adaption through the exchange of DNA between cells. In Proteobacteria, this process is mediated by the RecBCD complex, which relies on the recognition of a DNA motif named Chi to initiate recombination. The Chi motif has been characterized inEscherichia coliand analogous sequences have been found in several other species from diverse families, suggesting that this mode of action is widespread across bacteria. However, the sequences of Chi-like motifs are known for only five bacterial species:E. coli, Haemophilus influenzae,Bacillus subtilis,Lactococcus lactisandStaphylococcus aureus. In this study we detected putative Chi motifs in a large dataset of Proteobacteria and we identified four additional motifs sharing high sequence similarity and similar properties to the Chi motif ofE. coliin 85 species of Proteobacteria. Most Chi motifs were detected inEnterobacteriaceaeand this motif appears well conserved in this family. However, we did not detect Chi motifs for the majority of Proteobacteria, suggesting that different motifs are used in these species. Altogether these results substantially expand our knowledge on the evolution of Chi motifs and on the recombination process in bacteria.
Mammalian deubiquitinating enzyme inhibitors displayin vitroandin vivoactivity against malaria parasites and potentiate artemisinin action
Authors: Simwela Nelson V. , Hughes Katie R. , Rennie Michael T. , Barrett Michael P. , Waters Andrew P. 
Published: August 2020

AbstractCurrent malaria control efforts rely significantly on artemisinin combinational therapies which have played massive roles in alleviating the global burden of the disease. Emergence of resistance to artemisinins is therefore, not just alarming but requires immediate intervention points such as development of new antimalarial drugs or improvement of the current drugs through adjuvant or combination therapies. Artemisinin resistance is primarily conferred by Kelch13 propeller mutations which are phenotypically characterised by generalised growth quiescence, altered haemoglobin trafficking and downstream enhanced activity of the parasite stress pathways through the ubiquitin proteasome system (UPS). Previous work on artemisinin resistance selection in a rodent model of malaria, which we and others have recently validated using reverse genetics, has also shown that mutations in deubiquitinating enzymes, DUBs (upstream UPS component) modulates susceptibility of malaria parasites to both artemisinin and chloroquine. The UPS or upstream protein trafficking pathways have, therefore, been proposed to be not just potential drug targets, but also possible intervention points to overcome artemisinin resistance. Here we report the activity of small molecule inhibitors targeting mammalian DUBs in malaria parasites. We show that generic DUB inhibitors can block intraerythrocytic development of malaria parasitesin vitroand possess antiparasitic activityin vivoand can be used in combination with additive effect. We also show that inhibition of these upstream components of the UPS can potentiate the activity of artemisininin vitroas well asin vivoto the extent that ART resistance can be overcome. Combinations of DUB inhibitors anticipated to target different DUB activities and downstream 20s proteasome inhibitors are even more effective at improving the potency of artemisinins than either inhibitors alone providing proof that targeting multiple UPS activities simultaneously could be an attractive approach to overcoming artemisinin resistance. These data further validate the parasite UPS as a target to both enhance artemisinin action and potentially overcome resistance. Lastly, we confirm that DUB inhibitors can be developed intoin vivoantimalarial drugs with promise for activity against all of human malaria and could thus further exploit their current pursuit as anticancer agents in rapid drug repurposing programs.Graphical abstract
A Strategy to Assess the Cellular Activity of E3 Ligases against Neo-Substrates using Electrophilic Probes
Authors: Pinch Benika J. , Buckley Dennis L. , Gleim Scott , Brittain Scott M. , Tandeske Laura , D’Alessandro Pier Luca , Harvey Edward P. , Hauseman Zachary J. , Schirle Markus , Sprague Elizabeth R. , Forrester William C. , Dovala Dustin , McGregor Lynn M. , Thoma Claudio R. 
Published: August 2020

ABSTRACTTargeted protein degradation is a rapidly developing therapeutic modality that promises lower dosing and enhanced selectivity as compared to traditional occupancy-driven inhibitors, and the potential to modulate historically intractable targets. While the well-characterized E3 ligases CRBN and VHL have been successfully redirected to degrade numerous proteins, there are approximately 600 predicted additional E3 family members that may offer improved activity, substrate selectivity, and/or tissue distribution; however, characterizing the potential applications of these many ligases for targeted protein degradation has proven challenging. Here, we report the development of an approach to evaluate the ability of recombinant E3 ligase components to support neo-substrate degradation. Bypassing the need for hit finding to identify specific E3 ligase binders, this approach makes use of simple chemistry for Covalent Functionalization Followed by E3 Electroporation into live cells (COFFEE). We demonstrate this method by electroporating recombinant VHL, covalently functionalized with JQ1 or dasatinib, to induce degradation of BRD4 or kinase targets, respectively. Furthermore, by applying COFFEE to SPSB2, a SOCS box and SPRY-domain E3 ligase that has not previously been redirected for targeted protein degradation, we validate this method as a powerful approach to define the activity of previously uncharacterized ubiquitin ligases against neo-substrates.
Ultra-Low Colcemid Doses Induce Microtubule Dysfunction as Revealed by Super-Resolution Microscopy
Authors: Rozario Ashley M , Duwé Sam , Elliott Cade , Hargreaves Riley B , Dedecker Peter , Whelan Donna R , Bell Toby D M 
Published: August 2020

ABSTRACTMicrotubule-interacting drugs, sometimes referred to as antimitotics, are used in cancer therapy to target and disrupt micro-tubules. However, their side effects require the development of safer drug regimens that still retain clinical efficacy. Currently, many questions remain regarding microtubule-interacting drugs at clinically relevant and ultra-low doses. Here, we use super-resolution microscopies (single molecule localization and optical fluctuation based) to reveal the initial microtubule dysfunctions caused by nanomolar concentrations of colcemid. Short exposure to 30 - 80 nM colcemid results in aberrant microtubule curvature while microtubule fragmentation is detected upon treatment with ≥100 nM colcemid. Remarkably, even ultra-low doses (5 hours at <20 nM) led to subtle but significant microtubule architecture remodeling and suppression of microtubule dynamics. These challenges to microtubule function represent less severe precursor perturbations compared to the established antimitotic effects of microtubule-interacting drugs, and therefore offer potential for improved understanding and design of anti-cancer agents.
DREAM represses distinct targets by cooperating with different THAP domain proteins
Authors: Gal Csenge , Carelli Francesco Nicola , Appert Alex , Cerrato Chiara , Huang Ni , Dong Yan , Murphy Jane , Ahringer Julie 
Published: August 2020

ABSTRACTThe DREAM (DP, Retinoblastoma [Rb]-like, E2F, and MuvB) complex controls cellular quiescence by repressing cell cycle and other genes, but its mechanism of action is unclear. Here we demonstrate that two C. elegans THAP domain proteins, LIN-15B and LIN-36, co-localize with DREAM and function by different mechanisms for repression of distinct sets of targets. LIN-36 represses classical cell cycle targets by promoting DREAM binding and gene body enrichment of H2A.Z, and we find that DREAM subunit EFL-1/E2F is specific for LIN-36 targets. In contrast, LIN-15B represses germline specific targets in the soma by facilitating H3K9me2 promoter marking. We further find that LIN-36 and LIN-15B differently regulate DREAM binding. In humans, THAP proteins have been implicated in cell cycle regulation by poorly understood mechanisms. We propose that THAP domain proteins are key mediators of Rb/DREAM function.
Kinetic analysis reveals the rates and mechanisms of protein aggregation in a multicellular organism
Authors: Sinnige Tessa , Meisl Georg , Michaels Thomas C. T. , Vendruscolo Michele , Knowles Tuomas P.J. , Morimoto Richard I. 
Published: August 2020

AbstractThe accumulation of insoluble protein aggregates containing amyloid fibrils has been observed in many different human protein misfolding diseases1,2, and their pathological features have been recapitulated in diverse model systems3.In vitrokinetic studies have provided a quantitative understanding of how the fundamental molecular level processes of nucleation and growth lead to amyloid formation4. However, it is not yet clear to what extent these basic biophysical processes translate to amyloid formationin vivo, given the complexity of the cellular and organismal environment. Here we show that the aggregation of a fluorescently tagged polyglutamine (polyQ) protein into µm-sized inclusions in the muscle tissue of livingC. eleganscan be quantitatively described by a molecular model where stochastic nucleation occurs independently in each cell, followed by rapid aggregate growth. Global fitting of the image-based aggregation kinetics reveals a nucleation rate corresponding to 0.01 h-1per cell at 1 mM intracellular protein concentration, and shows that the intrinsic stochasticity of nucleation accounts for a significant fraction of the observed animal-to-animal variation. Our results are consistent with observations for the aggregation of polyQ proteinsin vitro5and in cell culture6, and highlight how nucleation events control the overall progression of aggregation in the organism through the spatial confinement into individual cells. The key finding that the biophysical principles associated with protein aggregation in small volumes remain the governing factors, even in the complex environment of a living organism, will be critical for the interpretation ofin vivodata from a wide range of protein aggregation diseases.
PTEN Inhibition Ameliorates Muscle Degeneration and Improves Muscle Function in a Mouse Model of Duchenne Muscular Dystrophy
Authors: Yue Feng , Song Changyou , Huang Di , Narayanan Naagarajan , Qiu Jiamin , Jia Zhihao , Yuan Zhengrong , Oprescu Stephanie N , Roseguini Bruno T , Deng Meng , Kuang Shihuan 
Published: August 2020

AbstractDuchenne Muscular Dystrophy (DMD) is caused by mutation of the muscle membrane protein dystrophin and characterized by severe degeneration of myofibers, progressive muscle wasting and loss of mobility, ultimately cardiorespiratory failure and premature death. Here we report that skeletal muscle-specific knockout (KO) ofPhosphatase and tensin homolog(Pten) gene in an animal model of DMD (mdxmice) alleviates myofiber degeneration and restores muscle function without increasing tumor incidences. Specifically,PtenKO normalizes myofiber size and prevents muscular atrophy, and improves grip strength and exercise performance ofmdxmice.PtenKO also reduces fibrosis and inflammation; and ameliorates muscle pathology inmdxmice. Moreover, we found thatPtenKO upregulates extracellular matrix and basement membrane components positively correlated to wound healing, but suppresses negative regulators of wound healing and lipid biosynthesis; and restores the integrity of muscle basement membrane inmdxmice. Importantly, pharmacological inhibition of PTEN similarly ameliorates muscle pathology and improves muscle integrity and function inmdxmice. Our finding provides evidence that PTEN inhibition may represent a potential therapeutic strategy to restore muscle function in DMD.
Blocking palmitoylation ofToxoplasma gondiimyosin light chain 1 disrupts glideosome composition but has little impact on parasite motility
Authors: Rompikuntal Pramod K. , Foe Ian T. , Deng Bin , Bogyo Matthew , Ward Gary E. 
Published: August 2020

AbstractToxoplasma gondiiis a widespread apicomplexan parasite that causes severe disease in immunocompromised individuals and the developing fetus. Like other apicomplexans,T. gondiiuses an unusual form of gliding motility to invade cells of its hosts and to disseminate throughout the body during infection. It is well established that a myosin-based motor consisting of a Class XIVa heavy chain (TgMyoA) and two light chains (TgMLC1 and TgELC1/2) plays an important role in parasite motility. The ability of the motor to generate force at the parasite periphery is thought to be reliant upon its anchoring and immobilization within a peripheral membrane-bound compartment, the inner membrane complex (IMC). The motor does not insert into the IMC directly; rather, this interaction is believed to be mediated by the binding of TgMLC1 to the IMC-anchored protein, TgGAP45. The binding of TgMLC1 to TgGAP45 is therefore considered a key element in the force transduction machinery of the parasite. TgMLC1 is palmitoylated, and we show here that palmitoylation occurs on two N-terminal cysteine residues, C8 and C11. Mutations that block TgMLC1 palmitoylation disrupt the association of TgMLC1 with the membrane fraction of the parasite in phase partitioning experiments and completely block the binding of TgMLC1 to TgGAP45. Surprisingly, the loss of TgMLC1 binding to TgGAP45 in these mutant parasites has little effect on their ability to initiate or sustain movement. These results question a key tenet of the current model of apicomplexan motility and suggest that our understanding of gliding motility in this important group of human and animal pathogens is not yet complete.ImportanceGliding motility plays a central role in the life cycle ofT. gondiiand other apicomplexan parasites. The myosin motor thought to power motility is essential for virulence but distinctly different from the myosins found in humans. Consequently, an understanding of the mechanism(s) underlying parasite motility and the role played by this unusual myosin may reveal points of vulnerability that can be targeted for disease prevention and treatment. We show here that mutations that uncouple the motor from what is thought to be a key structural component of the motility machinery have little impact on parasite motility. This finding runs counter to predictions of the current, widely-held “linear motor” model of motility, highlighting the need for further studies to fully understand how apicomplexan parasites generate the forces necessary to move into, out of and between cells of the hosts they infect.
Bacterial gene essentiality under modeled microgravity
Authors: Burgos Emanuel , Vroom Madeline M. , Rotman Ella , Murphy-Belcaster Megan , Foster Jamie S. , Mandel Mark J. 
Published: August 2020

ABSTRACTThe health of eukaryotic hosts is tightly connected to relationships with symbiotic microorganisms, yet how these relationships develop and evolve during long-duration spaceflight is not well understood. In this study, we asked what bacterial genes are required for growth under modeled, or simulated, microgravity conditions compared to normal gravity controls. To conduct this study, we focused on the marine bacteriumVibrio fischeri, which forms a monospecific symbiosis with the Hawaiian bobtail squid,Euprymna scolopes. The symbiosis has been studied during spaceflight and in ground-based modeled microgravity conditions. We employed a library of over 40,000V. fischeritransposon mutants and compared the fitness of mutants in modeled microgravity compared to the gravity controls using transposon insertion sequencing (INSeq). We identified dozens of genes that exhibited fitness defects under both conditions, likely due to the controlled anaerobic environment, yet we identified relatively few genes with differential effects under modeled microgravity or gravity specifically: only mutants inrodAwere more depleted under modeled microgravity, and mutants in 12 genes exhibited greater depletion under gravity conditions. We additionally compared RNA-seq and INSeq data and determined that expression under microgravity was not predictive of the essentiality of a given gene. In summary, empirical determination of conditional gene essentiality identifies few microgravity-specific genes for environmental growth ofV. fischeri, suggesting that the condition of microgravity has a minimal impact on symbiont gene requirement.IMPORTANCEThere is substantial evidence that both the host immune system and microbial physiology are altered during space travel. It is difficult to discern the molecular mechanisms of these processes in a complex microbial consortium and during the short durations of experiments in space. By using a model organism that is amenable to high-throughput genetic approaches, we have determined thatV. fischeridoes not require a separate genetic repertoire for media growth in modeled microgravity versus gravity conditions. Our results argue that future studies on how this organism forms a specific and stable association with its animal host will not be confounded by growth effects in the environment. The identification of similar genetic requirements under modeled microgravity and gravity suggest that fitness pressures on microbiome growth in space may be similar to those on Earth and may not negatively impact their animal hosts during long-duration spaceflight.