DECODING BACTERIAL GENOME WITH HIGH-THROUGHPUT SEQUENCING: GENES AND GENETIC MARKERS

Ph.DDOCTOR OF PHILOSOPH

Novel green and cost-effective preparation of acetylated lignin at high temperature without further separation

In order to realize the green and low-cost industrial production of acetylated lignin, this work proposes the heterogeneous reaction to acetylated lignin (ACAL) without catalysts and solvents at high temperature. The influence of reaction temperature and reaction time were investigated by IR, UV–vis, thermogravimetric analysis and water contact angle. Results showed that the optimum technological conditions were about 150 °C and 6 h. The degree of acetylation and the amount of residual phenolic hydroxyl groups of ACAL was 2.49 and 34.2%, respectively. Compared with conventional acetylated lignin, the ACAL had similar hydrophobicity with a water contact angle of 62.0°. The DTG peak of ACAL at about 200 °C reduced to 0.07 than the traditional acetylated lignin. The tensile strength and elongation of poly-lactic acid with 5 wt% ACAL increased to 64.03 MPa and 10.80%, respectively. ACAL revealed a great potential for mass production and applications owing to the eco-friendly and cost-effective modified method

Additional file 1: Table S1. of SpoTyping: fast and accurate in silico Mycobacterium spoligotyping from sequence reads

Spoligotype prediction and time performance of 161 Mtb isolates with SpoTyping in comparison with SpolPred. Table S2. Spoligotypes of 14 Mtb isolates determined from contigs obtained by de novo assembly, Velvet. Table S3. Actual length at different percentiles used as the read length for SpolPred spoligotype prediction of isolates sequenced on Illumina MiSeq. Table S4. Spoligotype prediction for Mtb isolates sequenced by Illumina MiSeq with SpoTyping in comparison with SpolPred. Table S5. Actual length at different percentiles used as the read length for SpolPred spoligotype prediction of isolates sequenced on Ion Torrent. Table S6. Spoligotype prediction for Mtb isolates sequenced by Ion Torrent with SpoTyping in comparison with SpolPred. Table S7. Statistics of time and accuracy of running SpoTyping on 50 iterations each for various down-sampling ratios of an H37Ra Mtb isolate. Table S8. Statistics of time and accuracy of running SpoTyping on 50 iterations each for various down-sampling ratios of a Beijing Mtb isolate. Table S9. Lineages of 14 discordant Mtb isolates by SpoTyping, experimentally reported and phylogenetic tree. (XLSX 55 kb

Additional file 4: Table S4. of In silico region of difference (RD) analysis of Mycobacterium tuberculosis complex from sequence reads using RD-Analyzer

Outputs from RD-Analyzer in the validation set of Mtb isolates. (XLS 107 kb

Additional file 1: Table S1. of In silico region of difference (RD) analysis of Mycobacterium tuberculosis complex from sequence reads using RD-Analyzer

Informative RD for MTC analysis and its characteristics. (XLS 25 kb

Whole-Genome Sequencing Analysis of Serially Isolated Multi-Drug and Extensively Drug Resistant Mycobacterium tuberculosis from Thai Patients.

Multi-drug and extensively drug-resistant tuberculosis (MDR and XDR-TB) are problems that threaten public health worldwide. Only some genetic markers associated with drug-resistant TB are known. Whole-genome sequencing (WGS) is a promising tool for distinguishing between re-infection and persistent infection in isolates taken at different times from a single patient, but has not yet been applied in MDR and XDR-TB. We aim to detect genetic markers associated with drug resistance and distinguish between reinfection and persistent infection from MDR and XDR-TB patients based on WGS analysis. Samples of Mycobacterium tuberculosis (n = 7), serially isolated from 2 MDR cases and 1 XDR-TB case, were retrieved from Siriraj Hospital, Bangkok. The WGS analysis used an Illumina Miseq sequencer. In cases of persistent infection, MDR-TB isolates differed at an average of 2 SNPs across the span of 2-9 months whereas in the case of reinfection, isolates differed at 61 SNPs across 2 years. Known genetic markers associated with resistance were detected from strains susceptible to streptomycin (2/7 isolates), p-aminosalicylic acid (3/7 isolates) and fluoroquinolone drugs. Among fluoroquinolone drugs, ofloxacin had the highest phenotype-genotype concordance (6/7 isolates), whereas gatifloxcain had the lowest (3/7 isolates). A putative candidate SNP in Rv2477c associated with kanamycin and amikacin resistance was suggested for further validation. WGS provided comprehensive results regarding molecular epidemiology, distinguishing between persistent infection and reinfection in M/XDR-TB and potentially can be used for detection of novel mutations associated with drug resistance