scholarly journals Environmental Variations in Mycobacterium ulcerans Transcriptome: Absence of Mycolactone Expression in Suboptimal Environments

Toxins ◽  
2019 ◽  
Vol 11 (3) ◽  
pp. 146
Author(s):  
Daniel Sanhueza ◽  
Jean-François Guégan ◽  
Heather Jordan ◽  
Christine Chevillon
Keyword(s):  
Culture Medium ◽  
Expression Profiles ◽  
Buruli Ulcer ◽  
Mycobacterium Ulcerans ◽  
Virulence Plasmid ◽  
Genomic Expression ◽  
Environmental Variations ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Buruli ulcer is a neglected tropical infectious disease, produced by the environmentally persistent pathogen Mycobacterium ulcerans (MU). Neither the ecological niche nor the exact mode of transmission of MU are completely elucidated. However, some environmental factors, such as the concentration in chitin and pH values, were reported to promote MU growth in vitro. We pursued this research using next generation sequencing (NGS) and mRNA sequencing to investigate potential changes in MU genomic expression profiles across in vitro environmental conditions known to be suitable for MU growth. Supplementing the growth culture medium in either chitin alone, calcium alone, or in both chitin and calcium significantly impacted the MU transcriptome and thus several metabolic pathways, such as, for instance, those involved in DNA synthesis or cell wall production. By contrast, some genes carried by the virulence plasmid and necessary for the production of the mycolactone toxin were expressed neither in control nor in any modified environments. We hypothesized that these genes are only expressed in stressful conditions. Our results describe important environmental determinants playing a role in the pathogenicity of MU, helping the understanding of its complex natural life cycle and encouraging further research using genomic approaches.

scholarly journals Recombinant Antibodies against Mycolactone

Toxins ◽  
2019 ◽  
Vol 11 (6) ◽  
pp. 346 ◽  
Author(s):  
Leslie Naranjo ◽  
Fortunato Ferrara ◽  
Nicolas Blanchard ◽  
Caroline Demangel ◽  
Sara D’Angelo ◽  
...  
Keyword(s):  
Structural Modification ◽  
Buruli Ulcer ◽  
Mycobacterium Ulcerans ◽  
Detection Methods ◽  
Yeast Display ◽  
Phage Antibody Library ◽  
Diagnostic Detection ◽  
Antigenic Targets ◽  
Generation Sequencing

In the past, it has proved challenging to generate antibodies against mycolactone, the primary lipidic toxin A of Mycobacterium ulcerans causing Buruli ulcer, due to its immunosuppressive properties. Here we show that in vitro display, comprising both phage and yeast display, can be used to select antibodies recognizing mycolactone from a large human naïve phage antibody library. Ten different antibodies were isolated, and hundreds more identified by next generation sequencing. These results indicate the value of in vitro display methods to generate antibodies against difficult antigenic targets such as toxins, which cannot be used for immunization unless inactivated by structural modification. The possibility to easily generate anti-mycolactone antibodies is an exciting prospect for the development of rapid and simple diagnostic/detection methods.

scholarly journals Triple oral beta-lactam containing therapy for Buruli ulcer treatment shortening

2018 ◽  
Author(s):  
María Pilar Arenaz Callao ◽  
Rubén González del Río ◽  
Ainhoa Lucía Quintana ◽  
Charles J. Thompson ◽  
Alfonso Mendoza-Losana ◽  
...  
Keyword(s):  
Inhibitory Concentration ◽  
Buruli Ulcer ◽  
Mycobacterium Ulcerans ◽  
Beta Lactam ◽  
Beta Lactams ◽  
Amoxicillin Clavulanate ◽  
Low Toxicity ◽  
Potential Use ◽  
Ulcer Treatment

ABSTRACTThe potential use of clinically approved beta-lactams for Buruli ulcer (BU) treatment was investigated with representative classes analyzed in vitro for activity against Mycobacterium ulcerans. Beta-lactams tested were effective alone and displayed a strong synergistic profile in combination with antibiotics currently used to treat BU, i.e. rifampicin and clarithromycin; this activity was further potentiated in the presence of the beta-lactamase inhibitor clavulanate. In addition, quadruple combinations of rifampicin, clarithromycin, clavulanate and beta-lactams resulted in multiplicative reductions in their minimal inhibitory concentration (MIC) values. The MIC of amoxicillin against a panel of clinical isolates decreased more than 200-fold within this quadruple combination. Amoxicillin/clavulanate formulations are readily available with clinical pedigree, low toxicity, and orally and pediatric available; thus, supporting its potential inclusion as a new anti-BU drug in current combination therapies.

scholarly journals First isolation of Mycobacterium ulcerans from Swabs and Fine-Needle-Aspiration Specimens in Togo.

2019 ◽  
Author(s):  
Tchalare Kondi Makagni ◽  
Maman Issaka ◽  
Piten Ebekalisai ◽  
Disse Kodjo ◽  
Essossimna A. Kadanga ◽  
...  
Keyword(s):  
Fine Needle Aspiration ◽  
Slow Growth ◽  
Buruli Ulcer ◽  
Needle Aspiration ◽  
Mycobacterium Ulcerans ◽  
Clinical Samples ◽  
Direct Examination ◽  
Fine Needle ◽  
Pcr Targeting

Abstract Background Buruli ulcer is a skin disease caused by a mycobacterium called Mycobacterium ulcerans . It is prevalent in more than 33 countries on several continents but West Africa is the most affected. The isolation in culture of the bacteria is difficult because of its slow growth and the facilities required. In Togo, studies have been done on the risk factors for Mycobacterium ulcerans infection and the detection of cases by the Ziehl-Neelsen and PCR technique on clinical and environmental samples, but to date no data of isolates from clinical samples are available. The purpose of this study was to perform an in vitro culture of M. ulcerans from swab and fine needle aspiration samples through the confirmation stages of direct examination and IS2404 -PCR. Method A total of 70 clinical samples from Togo and 10 clinical isolates from Benin are analyzed by the three techniques indicated in the diagnosis, in particular the direct examination of acid-fast bacilli (AFB) using the Ziehl-Neelsen staining, the PCR targeting the IS2404 sequence, and the culture after transport of the samples in a transport medium made of Middlebrook 7H9 medium supplemented with a mixture of PANTA and OADC and decontamination by the modified Petroff method. Results The application of the three techniques of diagnosis for clinical samples yielded 44.28% of positivity rates on direct examination of AFB, 35.71% on culture and 77.14% on qPCR IS2404 with a significantly higher rate for qPCR (0.0001). All samples positive for Ziehl-Neelsen staining and culture were also positive for qPCR. Conclusion : Our results show that the culture, despite it difficulty and the slow growth of the bacteria, can be carried out with recommended tools of the mycobacteria culture and a good method of decontamination of the samples can improve the positivity rates. Its realization will allow the assessment of the in vitro sensitivity to the antibiotics used in the treatment and the discovery of new strains of Mycobacterium ulcerans .

Machine Learning Perspective in Cancer Research

2021 ◽  
pp. 142-163
Author(s):  
Aman Sharma ◽  
Rinkle Rani
Keyword(s):  
Machine Learning ◽  
Cancer Research ◽  
Expression Profiles ◽  
Genetic Diseases ◽  
Cost Effective ◽  
Healthcare Sector ◽  
Diagnosis And Prognosis ◽  
Cost Effective Approach ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Advancement in genome sequencing technology has empowered researchers to think beyond their imagination. Researchers are trying their hard to fight against various genetic diseases like cancer. Artificial intelligence has empowered research in the healthcare sector. Moreover, the availability of opensource healthcare datasets has motivated the researchers to develop applications which can help in early diagnosis and prognosis of diseases. Further, next-generation sequencing (NGS) has helped to look into detailed intricacies of biological systems. It has provided an efficient and cost-effective approach with higher accuracy. The advent of microRNAs also known as small noncoding genes has begun the paradigm shift in oncological research. We are now able to profile expression profiles of RNAs using RNA-seq data. microRNA profiling has helped in uncovering their relationship in various genetic and biological processes. Here in this chapter, the authors present a review of the machine learning perspective in cancer research.

Genomic expression profiles in cumulus cells derived from germinal vesicle and MII mouse oocytes

2016 ◽  
Vol 28 (11) ◽  
pp. 1798 ◽  
Author(s):  
Li Shao ◽  
Ri-Cheng Chian ◽  
Yixin Xu ◽  
Zhengjie Yan ◽  
Yihui Zhang ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Expression Patterns ◽  
Germinal Vesicle ◽  
Cumulus Cells ◽  
Developmental Competence ◽  
Differentially Expressed ◽  
Genomic Expression ◽  
Oocyte Competence ◽  
Before And After

Cumulus cells (CCs) are distinct from other granulosa cells and the mutual communication between CCs and oocytes is essential for the establishment of oocyte competence. In the present study we assessed genomic expression profiles in mouse CCs before and after oocyte maturation in vitro. Microarray analysis revealed significant changes in gene expression in CCs between the germinal vesicle (GV) and metaphase II (MII) stages, with 2615 upregulated and 2808 downregulated genes. Genes related to epidermal growth factor, extracellular matrix (Ptgs2, Ereg, Tnfaip6 and Efemp1), mitochondrial metabolism (Fdx1 and Aifm2), gap junctions and the cell cycle (Gja1, Gja4, Ccnd2, Ccna2 and Ccnb2) were highlighted as being differentially expressed between the two development stages. Real-time polymerase chain reaction confirmed the validity and reproducibility of the results for the selected differentially expressed genes. Similar expression patterns were identified by western blot analysis for some functional proteins, including EFEMP1, FDX1, GJA1 and CCND2, followed by immunofluorescence localisation. These genes may be potential biomarkers for oocyte developmental competence following fertilisation and will be investigated further in future studies.

scholarly journals In Vitro Killing of Mycobacterium ulcerans by Acidified Nitrite

2004 ◽  
Vol 48 (8) ◽  
pp. 3130-3132 ◽  
Author(s):  
R. Phillips ◽  
S. Kuijper ◽  
N. Benjamin ◽  
M. Wansbrough-Jones ◽  
M. Wilks ◽  
...  
Keyword(s):  
Buruli Ulcer ◽  
Mycobacterium Ulcerans

ABSTRACT Mycobacterium ulcerans, which causes Buruli ulcer, was exposed to acidified nitrite or to acid alone for 10 or 20 min. Killing was rapid, and viable counts were reduced below detectable limits within 10 min of exposure to 40 mM acidified nitrite. M. ulcerans is highly susceptible to acidified nitrite in vitro.

scholarly journals Molecular characterization of Mycobacterium ulcerans DNA gyrase and identification of mutations reduced susceptibility against quinolones in vitro

2021 ◽  
Author(s):  
Hyun Kim ◽  
Shigtarou Mori ◽  
Tsuyoshi Kenri ◽  
Yasuhiko Suzuki
Keyword(s):  
Buruli Ulcer ◽  
Dna Gyrase ◽  
Resistance Mechanisms ◽  
Docking Studies ◽  
Mycobacterium Ulcerans ◽  
Amino Acid Residues ◽  
Wild Type Enzyme ◽  
Ulcer Disease

ABSTRACTBuruli ulcer disease is a neglected necrotizing and disabling cutaneous tropical illness caused by Mycobacterium ulcerans (Mul). Fluoroquinolone (FQ), used in the treatment of this disease, has been known to act by inhibiting the enzymatic activities of DNA gyrase; however, the detailed molecular basis of these characteristics and the FQ resistance mechanisms in Mul remains unknown. This study investigated the detailed molecular mechanism of Mul DNA gyrase and the contribution of FQ resistance in vitro using recombinant proteins from the Mul subsp. shinshuense and Agy99 strains with reduced sensitivity to FQs. The IC50 of FQs against Ala91Vla and Asp95Gly mutants of Mul shinshuense and Agy99 GyrA subunits were 3.7- to 42.0-fold higher than those against wild-type enzyme. Similarly, the CC25 was 10- to 210-fold higher than those for the WT enzyme. Furthermore, the interaction between the amino acid residues of WT/mutant Mul DNA gyrase and FQ side chains was assessed via molecular docking studies. This is the first detailed study showing the contribution of Mul DNA GyrA subunit mutations to reduce the susceptibility against FQs.

scholarly journals Enrichment of Food With Tannin Extracts Promotes Healthy Changes in the Human Gut Microbiota

2021 ◽  
Vol 12 ◽  
Author(s):  
Silvia Molino ◽  
Alberto Lerma-Aguilera ◽  
Nuria Jiménez-Hernández ◽  
María José Gosalbes ◽  
José Ángel Rufián-Henares ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Short Chain Fatty Acids ◽  
Human Gut ◽  
Human Gut Microbiota ◽  
Wood Extracts ◽  
Potential Benefits ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing ◽  
Booster Effect

Food and food bioactive components are major drivers of modulation of the human gut microbiota. Tannin extracts consist of a mix of bioactive compounds, which are already exploited in the food industry for their chemical and sensorial properties. The aim of our study was to explore the viability of associations between tannin wood extracts of different origin and food as gut microbiota modulators. 16S rRNA amplicon next-generation sequencing (NGS) was used to test the effects on the gut microbiota of tannin extracts from quebracho, chestnut, and tara associated with commercial food products with different composition in macronutrients. The different tannin-enriched and non-enriched foods were submitted to in vitro digestion and fermentation by the gut microbiota of healthy subjects. The profile of the short chain fatty acids (SCFAs) produced by the microbiota was also investigated. The presence of tannin extracts in food promoted an increase of the relative abundance of the genus Akkermansia, recognized as a marker of a healthy gut, and of various members of the Lachnospiraceae and Ruminococcaceae families, involved in SCFA production. The enrichment of foods with tannin extracts had a booster effect on the production of SCFAs, without altering the profile given by the foods alone. These preliminary results suggest a positive modulation of the gut microbiota with potential benefits for human health through the enrichment of foods with tannin extracts.

scholarly journals Shortening Buruli Ulcer Treatment with Combination Therapy Targeting the Respiratory Chain and Exploiting Mycobacterium ulcerans Gene Decay

2019 ◽  
Vol 63 (7) ◽  
Author(s):  
Paul J. Converse ◽  
Deepak V. Almeida ◽  
Sandeep Tyagi ◽  
Jian Xu ◽  
Eric L. Nuermberger
Keyword(s):  
Buruli Ulcer ◽  
Oxidase Inhibitor ◽  
Mycobacterium Ulcerans ◽  
Infection Model ◽  
Synergistic Activity ◽  
Content Type ◽  
Drug Regimens ◽  
Long Acting ◽  
Synthase Inhibitor

ABSTRACT Buruli ulcer is treatable with antibiotics. An 8-week course of rifampin (RIF) and either streptomycin (STR) or clarithromycin (CLR) cures over 90% of patients. However, STR requires injections and may be toxic, and CLR shares an adverse drug-drug interaction with RIF and may be poorly tolerated. Studies in a mouse footpad infection model showed that increasing the dose of RIF or using the long-acting rifamycin rifapentine (RPT), in combination with clofazimine (CFZ), a relatively well-tolerated antibiotic, can shorten treatment to 4 weeks. CFZ is reduced by a component of the electron transport chain (ETC) to produce reactive oxygen species toxic to bacteria. Synergistic activity of CFZ with other ETC-targeting drugs, the ATP synthase inhibitor bedaquiline (BDQ) and the bc1:aa3 oxidase inhibitor Q203 (now named telacebec), was recently described against Mycobacterium tuberculosis. Recognizing that M. tuberculosis mutants lacking the alternative bd oxidase are hypersusceptible to Q203 and that Mycobacterium ulcerans is a natural bd oxidase-deficient mutant, we tested the in vitro susceptibility of M. ulcerans to Q203 and evaluated the treatment-shortening potential of novel 3- and 4-drug regimens combining RPT, CFZ, Q203, and/or BDQ in a mouse footpad model. The MIC of Q203 was extremely low (0.000075 to 0.00015 μg/ml). Footpad swelling decreased more rapidly in mice treated with Q203-containing regimens than in mice treated with RIF and STR (RIF+STR) and RPT and CFZ (RPT+CFZ). Nearly all footpads were culture negative after only 2 weeks of treatment with regimens containing RPT, CFZ, and Q203. No relapse was detected after only 2 weeks of treatment in mice treated with any of the Q203-containing regimens. In contrast, 15% of mice receiving RIF+STR for 4 weeks relapsed. We conclude that it may be possible to cure patients with Buruli ulcer in 14 days or less using Q203-containing regimens rather than currently recommended 56-day regimens.

scholarly journals Cell-Free, Embryo-Specific sncRNA as a Molecular Biological Bridge between Patient Fertility and IVF Efficiency

2019 ◽  
Vol 20 (12) ◽  
pp. 2912 ◽  
Author(s):  
Angelika V. Timofeeva ◽  
Vitaliy V. Chagovets ◽  
Yulia S. Drapkina ◽  
Nataliya P. Makarova ◽  
Elena A. Kalinina ◽  
...  
Keyword(s):  
Embryo Development ◽  
Culture Media ◽  
Expression Profiles ◽  
Embryo Implantation ◽  
Human Reproduction ◽  
Vitro Fertilization ◽  
Small Noncoding Rnas ◽  
Polymerase Chain ◽  
Next Generation Sequencing Ngs

Small noncoding RNAs (sncRNAs) are key regulators of the majority of human reproduction events. Understanding their function in the context of gametogenesis and embryogenesis will allow insight into the possible causes of in vitro fertilization (IVF) implantation failure. The aim of this study was to analyze the sncRNA expression profile of the spent culture media on day 4 after fertilization and to reveal a relationship with the morphofunctional characteristics of gametes and resultant embryos, in particular, with the embryo development and implantation potential. Thereto, cell-free, embryo-specific sncRNAs were identified by next generation sequencing (NGS) and quantified by reverse transcription coupled with polymerase chain reaction (RT-PCR) in real-time. Significant differences in the expression level of let-7b-5p, let-7i-5p, piR020401, piR16735, piR19675, piR20326, and piR17716 were revealed between embryo groups of various morphological gradings. Statistically significant correlations were found between the expression profiles of piR16735 and piR020401 with the oocyte-cumulus complex number, let-7b-5p and piR020401 with metaphase II oocyte and two pronuclei embryo numbers, let-7i-5p and piR20497 with the spermatozoid count per milliliter of ejaculate, piR19675 with the percentage of linearly motile spermatozoids, let-7b-5p with the embryo development grade, and let-7i-5p with embryo implantation. According to partial least squares discriminant analysis (PLS-DA), the expression levels of let-7i-5p (Variable Importance in Projection score (VIP) = 1.6262), piR020401 (VIP = 1.45281), and piR20497 (VIP = 1.42765) have the strongest influences on the implantation outcome.

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