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Histatin Your five inhibits adhesion associated with C. albicans in order to Rejuvinated Individual Oral Epithelium.
on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For permissions, please email [email protected] rapid development of Chromosome Conformation Capture (3C-based techniques), as well as imaging together with bioinformatics analyses, has been fundamental for unveiling that chromosomes are organized into the so-called topologically associating domains or TADs. While TADs appear as nested patterns in the 3C-based interaction matrices, the vast majority of available TAD callers are based on the hypothesis that TADs are individual and unrelated chromatin structures. Here we introduce TADpole, a computational tool designed to identify and analyze the entire hierarchy of TADs in intra-chromosomal interaction matrices. TADpole combines principal component analysis and constrained hierarchical clustering to provide a set of significant hierarchical chromatin levels in a genomic region of interest. TADpole is robust to data resolution, normalization strategy and sequencing depth. Domain borders defined by TADpole are enriched in main architectural proteins (CTCF and cohesin complex subunits) and in the histone mark H3K4me3, while their domain bodies, depending on their activation-state, are enriched in either H3K36me3 or H3K27me3, highlighting that TADpole is able to distinguish functional TAD units. Additionally, we demonstrate that TADpole's hierarchical annotation, together with the new DiffT score, allows for detecting significant topological differences on Capture Hi-C maps between wild-type and genetically engineered mouse. © The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.RNAs are post-transcriptionally modified by dedicated writer or eraser enzymes that add or remove specific modifications, respectively. Mass spectrometry (MS) of RNA is a useful tool to study the modification state of an oligonucleotide (ON) in a sensitive manner. Here, we developed an ion-pairing reagent free chromatography for positive ion detection of ONs by low- and high-resolution MS, which does not interfere with other types of small compound analyses done on the same instrument. We apply ON-MS to determine the ONs from an RNase T1 digest of in vitro transcribed tRNA, which are purified after ribozyme-fusion transcription by automated size exclusion chromatography. The thus produced tRNAValAAC is substrate of the human tRNA ADAT2/3 enzyme and we confirm the deamination of adenosine to inosine and the formation of tRNAValIACin vitro by ON-MS. Furthermore, low resolution ON-MS is used to monitor the demethylation of ONs containing 1-methyladenosine by bacterial AlkB in vitro. The power of high-resolution ON-MS is demonstrated by the detection and mapping of modified ONs from native total tRNA digested with RNase T1. Overall, we present an oligonucleotide MS method which is broadly applicable to monitor in vitro RNA (de-)modification processes and native RNA. © The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.Nanopore technology is a promising label-free detection method. However, challenges exist for its further application in sequencing, clinical diagnostics and ultra-sensitive single molecule detection. The development of DNA nanotechnology nonetheless provides possible solutions to current obstacles hindering nanopore sensing technologies. In this review, we summarize recent relevant research contributing to efforts for developing nanopore methods associated with DNA nanotechnology. For example, DNA carriers can capture specific targets at pre-designed sites and escort them from nanopores at suitable speeds, thereby greatly enhancing capability and resolution for the detection of specific target molecules. In addition, DNA origami structures can be constructed to fulfill various design specifications and one-pot assembly reactions, thus serving as functional nanopores. Moreover, based on DNA strand displacement, nanopores can also be utilized to characterize the outputs of DNA computing and to develop programmable smart diagnostic nanodevices. In summary, DNA assembly-based nanopore research can pave the way for the realization of impactful biological detection and diagnostic platforms via single-biomolecule analysis. © The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.OBJECTIVES Two commercially available lateral flow immunochromatographic assays (ICAs) for detection of the major carbapenemases were prospectively assessed for the detection of carbapenemases in Enterobacterales RESIST-4 O.K.N.V. (Coris BioConcept) and NG-Test CARBA 5 (NG Biotech). METHODS These two assays were performed prospectively on consecutive Enterobacterales suspected of producing a carbapenemase that were referred to the Belgian National Reference Center for Monitoring Antimicrobial Resistance in Gram-Negative Bacteria between March and June 2018. The intensity of the band corresponding to a carbapenemase for each test was compared using ImageJ software. RESULTS Of the 161 isolates tested, a carbapenemase was detected in 91 (60 OXA-48-like, 15 VIM, 9 KPC, 5 NDM, 1 IMP and 1 IMP + OXA-48); in the remaining 70, no carbapenemases were detected. For both tests, the results were 100% concordant with the results of the PCR-sequencing reference method. Two IMP producers were only detected by NG-Test CARBA 5 as IMP is not targeted by RESIST-4 O.K.N.V. The mean intensity of the OXA-48, VIM and NDM bands displayed by NG-Test CARBA 5 was 3 to 3.7 times higher than for RESIST-4 O.K.N.V., while the KPC band was on average 1.7 times more intense with RESIST-4 O.K.N.V. CONCLUSIONS RESIST-4 O.K.N.V. and NG-Test CARBA 5 are two efficient assays for identification of the major carbapenemases. NG-Test CARBA 5 offers the advantage of detecting IMP, which remains rare in Western countries. © The Author(s) 2020. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy.Double sleeve, bronchial and vascular reconstructions are challenging procedures indicated for centrally located tumours to avoid pneumonectomy. Traditionally, these resections have been performed by thoracotomy, but thanks to advances in imaging systems, better surgical instruments and the gained experience in video-assisted thoracic surgery (VATS), the scenario now is different. During the last decade, we have seen a rapid evolution of the uniportal VATS technique from simple lobectomies to advanced double sleeve bronchovascular procedures and carinal resections. The advantages of VATS over open surgery for major lung resections in terms of postoperative pain and morbidity, length of hospital stay and quality of life have prompted experienced surgeons to adopt uniportal VATS for cases requiring a sleeve resection. However, when a double bronchial and vascular sleeve resection is required, the adoption rate of minimally invasive surgery is still very low even for very experienced VATS surgeons. The difficulty of tumour mobilization, complexity of the suturing technique and the concern about possible uncontrolled massive bleeding during VATS are the main reasons for this low rate of adoption. In this article, we describe the technical aspects and tricks of this procedure when it is done by the uniportal VATS approach. © The Author(s) 2020. Published by Oxford University Press on behalf of the European Association for Cardio-Thoracic Surgery. All rights reserved.OBJECTIVES The aim of this study was to evaluate the feasibility and safety of fibre-optic confocal microscopy (FCM) using fluorescein sodium dye for the intraoperative location of conduction tissue regions during paediatric heart surgery. METHODS The pilot study included 6 patients undergoing elective surgery for the closure of isolated secundum atrial septal defect aged 30 days to 21 years. FCM imaging was integrated within the normal intraoperative protocol for atrial septal defect repair. Fluorescein sodium dye was applied on the arrested heart. FCM images were acquired at the atrioventricular node region, sinus node region and right ventricle (RV). Total imaging time was limited to 3 min. Any adverse events related to the study were recorded and analysed. Subjects received standard postoperative care. Trained reviewers (n = 9) classified, de-identified and randomized FCM images (n = 60) recorded from the patients as presenting striated, reticulated or indistinguishable microstructures. The reliability of reviewer agreement was assessed using Fleiss' kappa. RESULTS The FCM imaging instruments were integrated effectively into the cardiac surgery operating room. All adverse events found in the study were deemed expected and not related to FCM imaging. Reticulated myocardial microstructures were found during FCM imaging at atrioventricular node and sinus node regions, while striated microstructures were observed in RV. Reliability of agreement of reviewers classifying the FCM images was high (Fleiss' kappa 0.822). CONCLUSIONS FCM using fluorescein sodium dye was found to be safe for use during paediatric heart surgery. The study demonstrates the potential for FCM to be effective in identifying conduction tissue regions during congenital heart surgery. CLINICAL TRIAL REGISTRATION NUMBER NCT03189134. © The Author(s) 2020. Published by Oxford University Press on behalf of the European Association for Cardio-Thoracic Surgery. All rights reserved.OBJECTIVES Infections caused by vancomycin-resistant Enterococcus faecium (VREfm) represent a major public health concern due to limited treatment options. Among invasive isolates of VREfm, ST117, ST80 and ST78 represent the most frequently detected STs by MLST in Germany. In this study, we investigated the genetic diversity of isolates of VREfm recovered from different nosocomial outbreaks in Bavaria, Germany, by WGS. METHODS Between January 2018 and April 2019, 99 non-replicate isolates of VREfm originating from nosocomial outbreaks at eight different hospitals in Bavaria were investigated for genetic diversity by WGS. In detail, complex types (CTs) were identified by core-genome MLST. Furthermore, an SNP analysis was performed for all VREfm strains. RESULTS Most of the isolates of this study (76%) belonged to three major clonal groups, which occurred in at least three hospitals ST80/CT1065 vanB (n = 45; six hospitals), ST117/CT71 vanB (n = 11; four hospitals) and ST78/CT894like vanA (n = 19; three hospitals). Moreover, isolates of the predominant lineage ST80/CT1065 vanB showed a maximum difference of 36 SNPs as revealed by SNP analysis. CONCLUSIONS Whole-genome analysis of VREfm causing nosocomial outbreaks suggests the occurrence of few endemic clonal lineages in Bavarian hospital settings, namely ST80/CT1065 vanB, ST117/CT71 vanB and ST78/CT894like vanA. Further studies are needed for a better understanding of the factors affecting the successful spread of the above-mentioned lineages. © The Author(s) 2020. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For permissions, please email [email protected] G/U pairs are present in many RNAs, the lack of molecular studies to characterize the roles of multiple G/U pairs within a single RNA limits our understanding of their biological significance. From known RNA 3D structures, we observed that the probability a G/U will form a Watson-Crick (WC) base pair depends on sequence context. We analyzed 17 G/U pairs in the 359-nucleotide genome of Potato spindle tuber viroid (PSTVd), a circular non-coding RNA that replicates and spreads systemically in host plants. Most putative G/U base pairs were experimentally supported by selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE). Deep sequencing PSTVd genomes from plants inoculated with a cloned master sequence revealed naturally occurring variants, and showed that G/U pairs are maintained to the same extent as canonical WC base pairs. Comprehensive mutational analysis demonstrated that nearly all G/U pairs are critical for replication and/or systemic spread. Two selected G/U pairs were found to be required for PSTVd entry into, but not for exit from, the host vascular system.
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