scholarly journals Mechanism and resistance for antimycobacterial activity of a fluoroquinophenoxazine compound

2018 ◽  
Author(s):  
Pamela K. Garcia ◽  
Thirunavukkarasu Annamalai ◽  
Wenjie Wang ◽  
Raven Bell ◽  
Duc Le ◽  
...  
Keyword(s):  
Topoisomerase I ◽  
Antimycobacterial Activity ◽  
Mycobacterium Abscessus ◽  
Whole Genome Sequencing Data ◽  
Binding Property ◽  
Sequencing Data ◽  
Resistance Mutations ◽  
Colony Forming Units ◽  
Biophysical Analysis ◽  
Dna Binding Property

AbstractWe have previously reported the inhibition of bacterial topoisomerase I activity by a fluoroquinophenoxazine compound (FP-11g) with a 6-bipiperidinyl lipophilic side chain that exhibited promising antituberculosis activity (MIC = 2.5 μM againstMycobacterium tuberculosis, SI = 9.8). Here, we found that the compound is bactericidal towardsMycobacterium smegmatis, resulting in greater than 5 Log10reduction in colony-forming units [cfu]/mL following a 10 h incubation at 1.25 μM (4X MIC) concentration. Growth inhibition (MIC = 50 μM) and reduction in cfu could also be observed against a clinical isolate ofMycobacterium abscessus.Stepwise isolation of resistant mutants ofM. smegmatiswas conducted to explore the mechanism of resistance. Mutations in the resistant isolates were identified by direct comparison of whole-genome sequencing data from mutant and wild-type isolates. These include mutations in genes likely to affect the entry and retention of the compound. FP-11g inhibitsMtbtopoisomerase I andMtbgyrase with IC50of 0.24 and 31.5 μM, respectively. Biophysical analysis showed that FP-11g binds DNA as an intercalator but the IC50for inhibition ofMtbtopoisomerase I activity is >10 fold lower than the compound concentrations required for producing negatively supercoiled DNA during ligation of nicked circular DNA. Thus, the DNA-binding property of FP-11g may contribute to its antimycobacterial mechanism, but that alone cannot account for the observed inhibition of Mtb topoisomerase I.

scholarly journals Molecular epidemiological characteristics of Mycobacterium abscessus complex in non-cystic fibrosis patients in Japan and Taiwan

2021 ◽  
Author(s):  
Mitsunori Yoshida ◽  
Jung-Yien Chien ◽  
Kozo Morimoto ◽  
Takeshi Kinjo ◽  
Akio Aono ◽  
...  
Keyword(s):  
Cystic Fibrosis ◽  
Mycobacterium Abscessus ◽  
Whole Genome Sequencing Data ◽  
Sequencing Data ◽  
Genetic Characteristics ◽  
Genomic Epidemiology ◽  
Mycobacterium Abscessus Complex ◽  
Pre Treatment ◽  
Epidemiology Studies ◽  
Epidemiological Characteristics

Mycobacterium abscessus complex (MABC) is an emerging non-tuberculous mycobacterium (NTM). Specific MABC clones are reportedly spreading globally in cystic fibrosis (CF) patients, however, associated genomic epidemiology studies are lacking in East Asia. Analysis of whole-genome sequencing data for MABC isolates from 220 pre-treatment, non-CF patients in Japan and Taiwan revealed that 112/220, 105/220, and 3/220 were M. abscessus subsp. abscessus (ABS), M. abscessus subsp. massiliense (MAS), and M. abscessus subsp. bolletii (BOL), respectively. No significant differences in subspecies composition were noted based on location. Moreover, >50% of ABS and >70% of MAS were related to four predominant clones in the region. Known mutations conferring acquired macrolide resistance were rare (1.4%) and not enriched in the predominant clones. Conversely, the macrolide-susceptible erm(41) T28C mutation was significantly enriched in one predominant ABS clone. The most predominant ABS clone was genetically related to the dominant circulating clone (DCC). Hence, we have clarified the relationship between the predominant clones in Japan and Taiwan, and those reported in the international CF patient community. Our results provide insights regarding the genetic characteristics of globally dominant and area-specific strains isolated from patients with or without CF, as well as differences between globally spread and regionally-specific strains.

scholarly journals The genetic architecture of emerging fungicide resistance in populations of a global wheat pathogen

2020 ◽  
Author(s):  
Danilo Pereira ◽  
Bruce A. McDonald ◽  
Daniel Croll
Keyword(s):  
Fungicide Resistance ◽  
Genetic Architecture ◽  
Target Genes ◽  
Association Studies ◽  
Whole Genome Sequencing Data ◽  
Genome Wide Association Studies ◽  
Sequencing Data ◽  
Resistance Mutations ◽  
Evolutionary Trajectory ◽  
Trade Offs

AbstractContaining fungal diseases often depends on the application of fungicidal compounds. Fungicides can rapidly lose effectiveness due to the rise of resistant individuals in populations. However, the lack of knowledge about resistance mutations beyond known target genes challenges investigations into pathways to resistance. We used whole-genome sequencing data and association mapping to reveal the multilocus genetic architecture of fungicide resistance in a global panel of 159 isolates of Parastagonospora nodorum, an important fungal pathogen of wheat. We found significant differences in azole resistance among global field populations. The populations evolved distinctive combinations of resistance alleles which can interact synergistically. We identified 34 significantly associated SNPs located in close proximity to genes associated with fungicide resistance in other fungi, including an MFS transporter. Using fungal colony growth rates and melanin production at different temperatures as fitness proxies, we found no evidence that resistance was constrained by genetic trade-offs. Our study demonstrates how genome-wide association studies of a global collection of pathogen strains can recapitulate the emergence of fungicide resistance. The distinct complement of resistance mutations found among populations illustrates how the evolutionary trajectory of fungicide adaptation can be complex and challenging to predict.

scholarly journals Determination of MIC Distribution and Mechanisms of Decreased Susceptibility to Bedaquiline among Clinical Isolates of Mycobacterium abscessus

2018 ◽  
Vol 62 (7) ◽  
Author(s):  
Bing Li ◽  
Meiping Ye ◽  
Qi Guo ◽  
Zhemin Zhang ◽  
Shiyi Yang ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Efflux Pump ◽  
Mycobacterium Abscessus ◽  
Clinical Isolates ◽  
Whole Genome Sequencing Data ◽  
Pcr Analysis ◽  
Sequencing Data ◽  
Gene Encoding ◽  
Content Type

ABSTRACT Chemotherapeutic options against Mycobacterium abscessus infections are very limited. Bedaquiline, a new antituberculosis (anti-TB) drug, is effective for the treatment of multidrug-resistant TB. However, few data are available on bedaquiline for treatment of M. abscessus infections. In this study, we determined the profile for in vitro susceptibility of M. abscessus clinical isolates to bedaquiline and investigated the potential molecular mechanisms of decreased susceptibility. A total of 197 M. abscessus clinical isolates were collected from sputum and bronchoalveolar fluid of patients with lung infections. Standard broth microdilution test revealed that bedaquiline exhibited high in vitro killing activity against M. abscessus isolates, with a MIC 50 of 0.062 and a MIC 90 of 0.125 mg/liter. Whole-genome sequencing data showed that no nonsynonymous mutation occurred in atpE , the gene encoding the bedaquiline-targeted protein. However, of 6 strains with decreased susceptibility of bedaquiline (MIC = 0.5 to 1 mg/liter), 3 strains had nonsynonymous mutations in mab_4384 , the gene encoding the repressor of efflux pump MmpS5/MmpL5. Quantitative reverse transcription-PCR (qRT-PCR) analysis showed that the expression of MmpS5/MmpL5 in the group with decreased susceptibility to bedaquiline was significantly higher than in those with medium MICs (MIC = 0.125 to 0.5 mg/liter) or in the low-MIC group (MIC ≤ 0.062 mg/liter). Two isolates with increased MICs did not show overexpression of MmpS5/MmpL5, which could not be explained by known molecular mechanisms. This is the first report showing the association of MmpS5/MmpL5 with decreased bedaquiline susceptibility in M. abscessus clinical isolates and suggesting the presence of other, yet-to-be identified mechanisms for decreased bedaquiline susceptibility in M. abscessus .

Cytotoxic Activity and DNA Binding Property of New Aminopyrimidine Derivatives

2020 ◽  
Vol 17 (5) ◽  
pp. 640-654
Author(s):  
Hamidreza Akrami ◽  
Bibi Fatemeh Mirjalili ◽  
Omidreza Firuzi ◽  
Azadeh Hekmat ◽  
Ali Akbar Saboury ◽  
...  
Keyword(s):  
Cell Lines ◽  
Anticancer Agents ◽  
Lymphoblastic Leukemia ◽  
Cd Spectroscopy ◽  
Myelogenous Leukemia ◽  
Breast Adenocarcinoma ◽  
Binding Property ◽  
Anticancer Compounds ◽  
Calf Thymus ◽  
Dna Binding Property

Background: Chromene and anilinopyrimidine heterocyclics are attractive anticancer compounds that have inspired many researchers to design novel derivatives bearing improved anticancer activity. Methods: A series of pyrimidine-fused benzo[f]chromene derivatives 6a-x were synthesized as anticancer hybrids of 1H-benzo[f]chromenes and anilinopyrimidines. The inhibitory activity of the synthesized compounds 6a-x against cell viability of human chronic myelogenous leukemia (K562), human acute lymphoblastic leukemia (MOLT-4) and human breast adenocarcinoma (MCF-7) cell lines was evaluated using MTT assay. The interaction of the most promising compound with calf-thymus DNA was also studied using spectrometric titrations and Circular Dichroism (CD) spectroscopy. Results: Most compounds showed promising activity against tested cell lines. Among them, 2,4- dimethoxyanilino derivative 6g exhibited the best profile of activity against tested cell lines (IC50s = 1.6-6.1 μM) with no toxicity against NIH3T3 normal cell (IC50 >200 μM). The spectrometric studies exhibited that compound 6g binds to DNA strongly and may change DNA conformation significantly, presumably via a groove binding mechanism. Conclusion: The results of this study suggest that the prototype compound 6g can be considered as a novel lead compound for the design and discovery of novel anticancer agents.

scholarly journals Comparison of long-read sequencing technologies in interrogating bacteria and fly genomes

2021 ◽  
Author(s):  
Eric S Tvedte ◽  
Mark Gasser ◽  
Benjamin C Sparklin ◽  
Jane Michalski ◽  
Carl E Hjelmen ◽  
...  
Keyword(s):  
Bacterial Genome ◽  
Hybrid Approach ◽  
Cost Effective ◽  
Fruit Fly ◽  
Drosophila Ananassae ◽  
Whole Genome Sequencing Data ◽  
Sequencing Data ◽  
E Coli ◽  
Hybrid Approaches ◽  
Long Read

Abstract The newest generation of DNA sequencing technology is highlighted by the ability to generate sequence reads hundreds of kilobases in length. Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) have pioneered competitive long read platforms, with more recent work focused on improving sequencing throughput and per-base accuracy. We used whole-genome sequencing data produced by three PacBio protocols (Sequel II CLR, Sequel II HiFi, RS II) and two ONT protocols (Rapid Sequencing and Ligation Sequencing) to compare assemblies of the bacteria Escherichia coli and the fruit fly Drosophila ananassae. In both organisms tested, Sequel II assemblies had the highest consensus accuracy, even after accounting for differences in sequencing throughput. ONT and PacBio CLR had the longest reads sequenced compared to PacBio RS II and HiFi, and genome contiguity was highest when assembling these datasets. ONT Rapid Sequencing libraries had the fewest chimeric reads in addition to superior quantification of E. coli plasmids versus ligation-based libraries. The quality of assemblies can be enhanced by adopting hybrid approaches using Illumina libraries for bacterial genome assembly or polishing eukaryotic genome assemblies, and an ONT-Illumina hybrid approach would be more cost-effective for many users. Genome-wide DNA methylation could be detected using both technologies, however ONT libraries enabled the identification of a broader range of known E. coli methyltransferase recognition motifs in addition to undocumented D. ananassae motifs. The ideal choice of long read technology may depend on several factors including the question or hypothesis under examination. No single technology outperformed others in all metrics examined.

scholarly journals A 127 kb truncating deletion of PGRMC1 is a novel cause of X-linked isolated paediatric cataract

2021 ◽  
Author(s):  
Johanna L. Jones ◽  
Mark A. Corbett ◽  
Elise Yeaman ◽  
Duran Zhao ◽  
Jozef Gecz ◽  
...  
Keyword(s):  
Intellectual Disability ◽  
Protein Interactions ◽  
Cholesterol Biosynthesis ◽  
Crystalline Lens ◽  
Whole Genome Sequencing Data ◽  
Mendelian Disease ◽  
Cataract Formation ◽  
Sequencing Data ◽  
Zebrafish Model ◽  
Paediatric Cataract

AbstractInherited paediatric cataract is a rare Mendelian disease that results in visual impairment or blindness due to a clouding of the eye’s crystalline lens. Here we report an Australian family with isolated paediatric cataract, which we had previously mapped to Xq24. Linkage at Xq24–25 (LOD = 2.53) was confirmed, and the region refined with a denser marker map. In addition, two autosomal regions with suggestive evidence of linkage were observed. A segregating 127 kb deletion (chrX:g.118373226_118500408del) in the Xq24–25 linkage region was identified from whole-genome sequencing data. This deletion completely removed a commonly deleted long non-coding RNA gene LOC101928336 and truncated the protein coding progesterone receptor membrane component 1 (PGRMC1) gene following exon 1. A literature search revealed a report of two unrelated males with non-syndromic intellectual disability, as well as congenital cataract, who had contiguous gene deletions that accounted for their intellectual disability but also disrupted the PGRMC1 gene. A morpholino-induced pgrmc1 knockdown in a zebrafish model produced significant cataract formation, supporting a role for PGRMC1 in lens development and cataract formation. We hypothesise that the loss of PGRMC1 causes cataract through disrupted PGRMC1-CYP51A1 protein–protein interactions and altered cholesterol biosynthesis. The cause of paediatric cataract in this family is the truncating deletion of PGRMC1, which we report as a novel cataract gene.

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