bluuebunny/crossref_metadata_2025_split huggingface dataset:
Antifungal effects of PC945, a novel inhaled triazole, onCandida albicans-infected immunocompromised mice
Authors: Nishimoto Yuki , Ito Kazuhiro , Kimura Genki , Lucas Kirstie A. , Daly Leah , Strong Pete , Kizawa Yasuo 
Published: July 2020

AbstractAlthoughCandida spp.are frequently detected in fungal cultures of respiratory secretions, their presence is normally assumed to reflect benign colonization. However, there is growing evidence thatCandida spp.are involved in the pathogenesis of respiratory diseases such as bronchiectasis and asthma. The aim of this study is to investigate thein vitroandin vivoeffects of a novel antifungal triazole, PC945, optimised for topical delivery, againstC. albicans. In temporarily neutropenic, immunocompromised mice,C. albicans(529L [ATCC®MYA4901™] strain), inoculated intranasally, induced acute lung injury and death, associated with higher fungal burden and cytokine induction in the lung. PC945 saline suspension, dosed intranasally once daily, starting one day post candida inoculation, dose-dependently (0.56 ~ 14 μg/mouse) improved survival rate and inhibited fungal load in the lung on Day 5 post inoculation. These effects by PC945 were 7 ~ 25-fold more potent than those of voriconazole, despite being of similarin vitroantifungal activity versus this strain. Furthermore, extended prophylaxis with low dose PC945 (0.56 μg/mouse) was found to inhibit fungal load more potently than the shorter treatment regimens, suggesting antifungal effects of PC945 accumulated on repeat dosing. In addition, antifungal susceptibility testing on 88 candida isolates(C. albicans, C. parapsilosis, C. tropicalis, C. lucitaniae, C. glabrata, C. guilliermondii)revealed that PC945 has potent effects onCandidaspecies broadly. Thus, PC945 has the potential to be a novel topical therapy for the treatment ofC. albicanspulmonary infection in humans.
Modal properties of fruit-rachilla system of the macaw palm
Authors: de Melo Villar Flora Maria , de Assis de Carvalho Pinto Francisco , Santos Fabio Lucio , de Queiroz Daniel Marçal , Pereira Mariana Ribeiro , Magalhães Valente Domingos Sárvio 
Published: July 2020

AbstractThe macaw palm has been domesticated due to its potential use in the production of biodiesel. One of the current challenges in this area is to determine the proper information and develop the technologies required for using macaw palm, allowing it to contribute to the sustainable production of feedstock for biodiesel industry. The principle of mechanical vibration can be employed for the detachment of fruits from a tree bunch, and it is therefore necessary to study the dynamic behavior of the macaw palm fruit-rachilla system during the vibration. Hence, the modal properties of the system were determined. A study on the dynamic behaviors was carried out using a deterministic finite element model, and the natural frequencies were obtained through a frequency-scanning test to evaluate the model. The mean relative error (MRE) between the measured and simulated natural frequencies was also used to evaluate the model. The natural frequencies, determined experimentally, varied between 26.21 and 33.45 Hz on average, whereas the simulated frequencies varied from 24.81 to 39.27 Hz. The overall MRE was 9.08%. Once the model was validated, a sensibility test showed that the density of fruit and the elasticity modulus are the parameters that most influence the natural frequencies of the fruit-rachilla system.
Cargo modulates the conformation of the nuclear pore in living cells
Authors: Pulupa Joan , Prior Harriet , Johnson Daniel S. , Simon Sanford M. 
Published: July 2020

AbstractWhile the static structure of the nuclear pore complex (NPC) continues to be refined with cryo-EM and x-ray crystallography, thein vivoconformational dynamics of the NPC remain under-explored. We developed sensors that report on the orientation of NPC components by rigidly conjugating mEGFP to different NPC proteins. Our studies show conformational changes to select domains of Nups within the inner ring (Nup54, Nup58, Nup62) when transport through the NPC is perturbed and no conformational changes to Nups elsewhere in the NPC. Our results suggest that select components of the NPC are flexible and undergo conformational changes upon engaging with cargo.
Flagellar structures from the bacteriumCaulobacter crescentusand implications for phage ϕCbK predation of multi-flagellin bacteria
Authors: Montemayor Eric J. , Ploscariu Nicoleta T. , Sanchez Juan C. , Parrell Daniel , Dillard Rebecca S. , Shebelut Conrad W. , Ke Zunlong , Guerrero-Ferreira Ricardo C. , Wright Elizabeth R. 
Published: July 2020

ABSTRACTCaulobacter crescentusis a gram-negative alpha-proteobacterium that commonly lives in oligotrophic fresh and salt-water environments.C. crescentusis a host to many bacteriophages, including ϕCbK and ϕCbK-like bacteriophages, which first adsorb to cells by interaction with the bacterial flagellum. It is commonly thought that the six paralogs of the flagellin gene present inC. crescentusare important for bacteriophage evasion. Here, we show that deletion of specific flagellins inC. crescentuscan indeed attenuate ϕCbK adsorption efficiency, although no single deletion completely ablates ϕCbK adsorption. Thus, bacteriophage ϕCbK likely recognizes a common motif amongst the six known flagellins inC. crescentuswith varying degrees of efficiency. Interestingly, we observe that most deletion strains still generate flagellar filaments, with the exception of a strain that contains only the most divergent flagellin, FljJ, or a strain that contains only FljN and FljO. To visualize the surface residues that are likely recognized by ϕCbK, we determined two high-resolution structures of the FljK filament, with and without an amino acid substitution that induces straightening of the filament. We observe post-translational modifications on conserved surface threonine residues of FljK that are likely O-linked glycans. The possibility of interplay between these modifications and ϕCbK adsorption is discussed. We also determined the structure of a filament composed of a heterogeneous mixture of FljK and FljL, the final resolution of which was limited to approximately 4.6 Å. Altogether, this work builds a platform for future investigation of how phage ϕCbK infectsC. crescentusat the molecular level.
Bro1 stimulates Vps4 activity to promote Intralumenal Vesicle Formation during Multivesicular Body biogenesis
Authors: Tseng Chun-Che , Dean Shirley , Davies Brian A. , Azmi Ishara F. , Pashkova Natalya , Payne Johanna A. , Staffenhagen Jennifer , West Matt , Piper Robert C. , Odorizzi Greg , Katzmann David J. 
Published: July 2020

AbstractEndosomal sorting complexes required for transport (ESCRT-0, -I, -II, -III) execute cargo sorting and intralumenal vesicle (ILV) formation during conversion of endosomes to multivesicular bodies (MVBs). The AAA-ATPase Vps4 regulates the ESCRT-III polymer to facilitate membrane remodeling and ILV scission during MVB biogenesis. Here we show that the conserved V domain of ESCRT-associated protein Bro1 (the yeast homolog of mammalian proteins ALIX and HD-PTP) directly stimulates Vps4. This activity is required for MVB cargo sorting. Furthermore, the Bro1 V domain alone supports Vps4/ESCRT-driven ILV formationin vivowithout efficient MVB cargo sorting. These results reveal a novel activity of the V domains of Bro1 homologs in licensing ESCRT-III-dependent ILV formation and suggest a role in coordinating cargo sorting with membrane remodeling during MVB sorting. Moreover, ubiquitin binding enhances V domain stimulation of Vps4 to promote ILV formation via the Bro1/Vps4/ESCRT-III axis, uncovering a novel role for ubiquitin during MVB biogenesis in addition to facilitating cargo recognition.SummaryCargo sorting is coordinated with intralumenal vesicle budding during ESCRT-mediated multivesicular body biogenesis. Bro1 V domain stimulates Vps4 to promote ESCRT-III-driven intralumenal vesicle formation in a manner required for this coordinated process.
Engineering DNA templated nonribosomal peptide synthesis
Authors: Huang Hsin-Mei , Stephan Philipp , Kries Hajo 
Published: July 2020

AbstractNanocontainers or macromolecular scaffolds for artificial biocatalytic cascades facilitate sequential enzyme reactions but diffusive escape of intermediates limits rate enhancement. Nonribosomal peptide synthetases (NRPS) naturally form gigantic assembly lines and prevent escape by covalently tethering intermediates. Here, we have built DNA-templated NRPS (DT-NRPS) by adding zinc finger tags to split NRPS modules. The zinc fingers direct the NRPS modules to 9-bp binding sites on a DNA strand, where they form a catalytically active enzyme cascade. DT-NRPS outperform previously reported DNA templated enzyme cascades in terms of DNA acceleration which demonstrates that covalent intermediate channeling is possible along the DNA template. Attachment of assembly line enzymes to a DNA scaffold is a promising catalytic strategy for the sequence-controlled biosynthesis of nonribosomal peptides and other polymers.
Characterising the hippocampal response to perception, construction and complexity
Authors: McCormick Cornelia , Dalton Marshall A. , Zeidman Peter , Maguire Eleanor A. 
Published: July 2020

ABSTRACTThe precise role played by the hippocampus in supporting cognitive functions such as episodic memory and future thinking is debated, but there is general agreement that it involves constructing representations comprised of numerous elements. Visual scenes have been deployed extensively in cognitive neuroscience because they are paradigmatic multi-element stimuli. However, questions remain about the specificity and nature of the hippocampal response to scenes. Here, we devised a paradigm in which we had participants search pairs of images for either colour or layout differences, thought to be associated with perceptual or spatial constructive processes respectively. Importantly, images depicted either naturalistic scenes or phase-scrambled versions of the same scenes, and were either simple or complex. Using this paradigm during functional MRI scanning, we addressed three questions: 1. Is the hippocampus recruited specifically during scene processing? 2. If the hippocampus is more active in response to scenes, does searching for colour or layout differences influence its activation? 3. Does the complexity of the scenes affect its response? We found that, compared to phase-scrambled versions of the scenes, the hippocampus was more responsive to scene stimuli. Moreover, a clear anatomical distinction was evident, with colour detection in scenes engaging the posterior hippocampus whereas layout detection in scenes recruited the anterior hippocampus. The complexity of the scenes did not influence hippocampal activity. These findings seem to align with perspectives that propose the hippocampus is especially attuned to scenes, and its involvement occurs irrespective of the cognitive process or the complexity of the scenes.
Mycobacterium tuberculosisevasion of Guanylate Binding Protein-mediated host defense in mice requires the ESX1 secretion system
Authors: Olive Andrew J. , Smith Clare M. , Baer Christina E. , Coers Jörn , Sassetti Christopher M. 
Published: July 2020

AbstractCell-intrinsic immune mechanisms control intracellular pathogens that infect eukaryotes. The intracellular pathogenMycobacterium tuberculosis(Mtb) evolved to withstand cell-autonomous immunity to cause persistent infections and disease. A potent inducer of cell-autonomous immunity is the lymphocyte-derived cytokine IFNγ. While the production of IFNγ by T cells is essential to protect againstMtb, it is not capable of fully eradicatingMtbinfection. This suggests thatMtbevades a subset of IFNγ-mediated antimicrobial responses, yet what mechanismsMtbresists remains unclear. The IFNγ-inducible Guanylate binding proteins (GBPs) are key host defense proteins able to control infections with intracellular pathogens. GBPs were previously shown to directly restrictMycobacterium bovisBCG yet their role duringMtbinfection has remained unknown. Here, we examine the importance of a cluster of five GBPs on mouse chromosome 3 in controlling Mycobacterial infection. WhileM. bovisBCG is directly restricted by GBPs, we find that the GBPs on chromosome 3 do not contribute to the control ofMtbreplication or the associated host response to infection. The differential effects of GBPs duringMtbversusM. bovisBCG infection is at least partially explained by the absence of the ESX1 secretion system fromM. bovisBCG, sinceMtbmutants lacking the ESX1 secretion system become similarly susceptible to GBP-mediated immune defense. Therefore, this specific genetic interaction between the murine host andMycobacteriareveals a novel function for the ESX1 virulence system in the evasion of GBP-mediated immunity.
A genome-wide CRISPR/Cas phenotypic screen for modulators of DUX4 cytotoxicity reveals screen complications
Authors: Ashoti Ator , Limone Francesco , van Kranenburg Melissa , Alemany Anna , Baak Mirna , Vivié Judith , Piccioni Federica , Creyghton Menno , Eggan Kevin , Geijsen Niels 
Published: July 2020

AbstractFacioscapulohumeral muscular dystrophy (FHSD), a fundamentally complex muscle disorder that thus far remains untreatable. As the name implies, FSHD starts in the muscles of the face and shoulder gridle. The main perturbator of the disease is the pioneer transcription factor DUX4, which is misexpressed in affected tissues due to a failure in epigenetic repressive mechanisms. In pursuit of unraveling the underlying mechanism of FSHD and finding potential therapeutic targets or treatment options, we performed an exhaustive genome-wide CRISPR/Cas9 phenotypic rescue screen to identify modulators of DUX4 cytotoxicity. We found no key effectors other than DUX4 itself, suggesting treatment efforts in FSHD should be directed towards its direct modulation.The screen did however reveal some rare and unexpected Cas9-induced genomic events, that may provide important considerations for planning future CRISPR/Cas9 knock-out screens.
ABO genetic variation in Neanderthals and Denisovans
Authors: Villanea Fernando A. , Huerta-Sanchez Emilia , Fox P. Keolu 
Published: July 2020

1AbstractVariation at the ABO locus was one of the earliest sources of data in the study of human population identity and history, and to this day remains widely genotyped due to its importance in blood and tissue transfusions. Here, we look at ABO blood type variants in our archaic relatives: Neanderthals and Denisovans. Our goal is to understand the genetic landscape of the ABO gene in archaic humans, and how it relates to modern human ABO variation. We found two derived Neanderthal variants of the O allele in the Siberian Neanderthals (O1 and O2), one of these variants is shared with an European Neanderthal, who is a heterozygote for this O1 variant and a rare cis-AB variant. The Denisovan individual is heterozygous for two ancestral variant of the O1 allele, similar to variants found widely in modern humans. Perhaps more surprisingly, the O2 allele variant found in Siberian Neanderthals can be found at low frequencies in modern Europeans and Southeast Asians, and the O1 allele variant found in Siberian and European Neanderthal is also found at very low frequency in modern East Asians. Our genetic distance analyses suggest both alleles survive in modern humans due to inbreeding with Neanderthals. We find that the sequence backgrounds of the surviving Neanderthal-like O alleles in modern humans retain a higher sequence divergence than other surviving Neanderthal genome fragments, supporting a view of balancing selection operating in the Neanderthal ABO alleles by retaining highly diverse haplotypes compared to portions of the genome evolving neutrally.
Erythrocyte CD55 facilitates the internalization ofPlasmodium falciparumparasites
Authors: Shakya Bikash , Patel Saurabh D. , Tani Yoshihiko , Egan Elizabeth S. 
Published: July 2020

AbstractInvasion of human erythrocytes by the malaria parasitePlasmodium falciparumis a multi-step process. Previously, a forward genetic screen forP. falciparumhost factors identified erythrocyte CD55 as essential for invasion, but its specific role and how it interfaces with the other factors that mediate this complex process are unknown. Using CRISPR-Cas9 editing, antibody-based inhibition, and live cell imaging, here we show that CD55 is specifically required for parasite internalization. Pre-invasion kinetics, erythrocyte deformability, and echinocytosis were not influenced by CD55, but entry was inhibited when CD55 was blocked or absent. Visualization of parasites attached to CD55-null erythrocytes point to a role for CD55 in progression of the moving junction. Our findings demonstrate that CD55 acts after discharge of the parasite’s rhoptry organelles, and plays a unique role relative to all other invasion receptors. As the requirement for CD55 is strain-transcendent, these results suggest that CD55 or its interacting partners may hold potential as therapeutic targets for malaria.
Nanopore direct RNA sequencing detects DUX4-activated repeats and isoforms in human muscle cells
Authors: Mitsuhashi Satomi , Nakagawa So , Frith Martin C , Mitsuhashi Hiroaki 
Published: July 2020

AbstractFacioscapulohumeral muscular dystrophy (FSHD) is an inherited muscle disease caused by misexpression of theDUX4gene in skeletal muscle. DUX4 is a transcription factor which is normally expressed in the cleavage-stage embryo and regulates gene expression involved in early embryonic development. Recent studies revealed that DUX4 also activates the transcription of repetitive elements such as endogenous retroviruses (ERVs), mammalian apparent LTR-retrotransposons (MaLRs), and pericentromeric satellite repeats (HSATII). DUX4-bound ERV sequences also create alternative promoters for genes or long non-coding RNAs (lncRNAs), producing fusion transcripts. To further understand transcriptional regulation by DUX4, we performed nanopore long-read direct RNA sequencing (dRNA-seq) of human muscle cells induced by DUX4, because long reads show whole isoforms with greater confidence. We successfully detected differential expression of known DUX4-induced genes, and discovered 61 differentially-expressed repeat loci, which are near DUX4-ChIP peaks. We also identified 247 gene-ERV fusion transcripts, of which 216 were not reported previously. In addition, long-read dRNA-seq clearly shows that RNA splicing is a common event in DUX4-activated ERV transcripts. Long-read analysis showed non-LTR transposons including Alu are also transcribed from LTRs. Our findings revealed further complexity of DUX4-induced ERV transcripts. This catalogue of DUX4-activated repetitive elements may provide useful information to elucidate the pathology of FSHD. Also, our results indicate that nanopore dRNA-seq has complementary strengths to conventional short read cDNA sequencing.
Sphingobiumsp. SYK-6 syringateO-demethylase gene is regulated by DesX, unlike other vanillate and syringate catabolic genes regulated by DesR
Authors: Araki Takuma , Tanatani Kenta , Kamimura Naofumi , Otsuka Yuichiro , Yamaguchi Muneyoshi , Nakamura Masaya , Masai Eiji 
Published: July 2020

ABSTRACTSyringate and vanillate are the major metabolites of lignin biodegradation. InSphingobiumsp. strain SYK-6, syringate is O demethylated to gallate by consecutive reactions catalyzed by DesA and LigM, and vanillate is O demethylated to protocatechuate by a reaction catalyzed by LigM. The gallate ring is cleaved by DesB, and protocatechuate is catabolized via the protocatechuate 4,5-cleavage pathway. The transcriptions ofdesA, ligM, anddesBare induced by syringate and vanillate, while that ofligManddesBare negatively regulated by the MarR-type transcriptional regulator DesR, which is not involved indesAregulation. Here we clarified the regulatory system fordesAtranscription by analyzing the IclR-type transcriptional regulatordesX, located downstream ofdesA. Quantitative reverse transcription (RT)-PCR analyses of adesXmutant indicates that the transcription ofdesAwas negatively regulated by DesX. In contrast, DesX was not involved in the regulation ofligManddesB. The ferulate catabolic genes (ferBA) under the control of a MarR-type transcriptional regulator FerC are located upstream ofdesA. RT-PCR analyses suggest that theferB-ferA-SLG_25010-desAgene cluster consists of theferBAoperon and the SLG_25010-desAoperon. Promoter assays reveal that a syringate- and vanillate-inducible promoter is located upstream of SLG_25010. Purified DesX bound to this promoter region, which overlaps with an 18-bp-inverted repeat sequence that appears to be essential for the DNA binding of DesX. Syringate and vanillate inhibited the DNA binding of DesX, indicating that these compounds are effector molecules of DesX.IMPORTANCESyringate is a major degradation product in the microbial and chemical degradation of syringyl lignin. Along with other low-molecular-weight aromatic compounds, syringate is produced by chemical lignin depolymerization. Converting this mixture into value-added chemicals using bacterial metabolism (i.e., biological funneling) is a promising option for lignin valorization. To construct an efficient microbial lignin conversion system, it is necessary to identify and characterize the genes involved in the uptake and catabolism of lignin-derived aromatic compounds and elucidate their transcriptional regulation. In this study, we found that the transcription ofdesA, encoding syringateO-demethylase in SYK-6, is regulated by an IclR-type of transcriptional regulator, DesX. The findings of this study, combined with our previous results ondesR(a MarR transcriptional regulator that controls the transcription ofligManddesB), provide an overall picture of the transcriptional regulatory systems for syringate and vanillate catabolism in SYK-6.
Performance of the BL03U beamline at SSRF
Authors: Sun Z. P. , Liu Z. H. , Liu Z. T. , Liu W. L. , Zhang F. Y. , Shen D. W. , Ye M. , Qiao S. 
Published: July 2020

The vacuum ultraviolet beamline BL03U with a photon energy range from 7 eV upwards has been constructed at the 3.5 GeV Shanghai Synchrotron Radiation Facility. Equipped with an APPLE-Knot undulator, this beamline is dedicated to angle-resolved photoemission spectroscopy. An energy-resolving power of higher than 4.6 × 104 has been achieved in the photon energy range 21.6–48 eV, which is almost the same as the theoretical estimation.
High-throughput in situ experimental phasing
Authors: Lawrence Joshua M. , Orlans Julien , Evans Gwyndaf , Orville Allen M. , Foadi James , Aller Pierre 
Published: July 2020

In this article, a new approach to experimental phasing for macromolecular crystallography (MX) at synchrotrons is introduced and described for the first time. It makes use of automated robotics applied to a multi-crystal framework in which human intervention is reduced to a minimum. Hundreds of samples are automatically soaked in heavy-atom solutions, using a Labcyte Inc. Echo 550 Liquid Handler, in a highly controlled and optimized fashion in order to generate derivatized and isomorphous crystals. Partial data sets obtained on MX beamlines using an in situ setup for data collection are processed with the aim of producing good-quality anomalous signal leading to successful experimental phasing.