Global ETD Search
Search theses and dissertations gathered from participating repositories worldwide. Every result links back to the library that holds it. No account is needed.
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Showing 1 to 20 of 73 for “"Miseq"”.
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Droplet digital PCR detection and next-generation sequencing of HIV-1 in breastmilk of breastfeeding women on antiretroviral treatment
… of viral variants in breastmilk using Illumina MiSeq next generation sequencing to inform transmission risk and efficacy of maternal ART clinical trials. HIV-negative breastmilk samples were spiked with 8E5 cells (a cell line where each cell contains one replication-defective HIV genome) at …
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High-throughput Amplicon Sequencing Optimization for Downstream Prediction Purposes
… a modified version of a commerical FDP assay, MiSeq FGx sequencing, genotype calling, and quality and ancestry inference assessments. The substantial dataset produced with this project will supply downstream applications in pigmentation and facial morphology prediction modeling. This work also …
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Understanding how microbial community contributes to wastewater treatment performance in constructed wetlands within Scotch whisky distilleries
… taxonomic results using ONT MinION and Illumina MiSeq. The research also examines spent lees treatment in mesocosms with various substrates and biochar, analysing biofilm diversity, microbial dynamics, and biochar's impact. Additionally, it assesses seasonal treatment performance and microbial …
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Dynamics of faecal bacterial populations in early infancy as determined by massively parallel sequencing
… specimens using quality controlled Illumina MiSeq sequencing data. Methods: We sampled infant meconium and maternal faecal specimens at birth, as well as two subsets of infant faecal specimens at 4-12 and 20-28 weeks of life. We extracted nucleic acid from faecal specimens using the automated …
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Estudio comparativo de herramientas bioinformáticas para el análisis metagenómico sobre el microbioma humano
… realizada con el software Wgsim con datos del MiSeq de Illumina, llevando a cabo una secuenciación paired-end. El análisis bioinformático se realizó con tres de los softwares más utilizados en la actualidad, que son: Gaia, Qiime2 y Mothur. Estos dos últimos son de código abierto por lo que para …
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Comparison of Potential Bioavailable Organic Carbon and Microbial Characterization of Two Carbon Amended Sites
… on relative abundance results from the Illumina MiSeq Sequencing of 16S rRNA genes showed large similarities among the samples within each site and the only observed differences occurred when comparing any sample to DV3, nearest to treatment.
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Genetic diversity of Entamoeba species, and the impact of the Madi Drop on the occurrence of Entamoeba among children in Vhembe, South Africa
… selected for Next-generation sequencing in the MiSeq platform based on the Entamoeba 18S rRNA gene, using a MiSeq v3 (600 cycles) kit. Data analysis was performed at Inqaba in-house developed data analysis. The phylogenetic trees were constructed to determine the species relatedness. Results: Of …
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Effect of Crude Oil on Light Attenuation and the Resulting Impacts on Marine Microbial Phototrophs and Heterotrophs
… 16S rRNA and psbA genes was also performed. Miseq Illumina sequencing analysis was performed to measure the abundance of bacteria and phototrophs. A qPCR was also performed to quantify phototrophs and HCB and UPLC analysis was done to quantify phototroph`s pigments. With continuous light, …
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The association between the oral and vaginal microbiome of young South African women
… and V4 16S sequencing was performed using MiSeq technology. The composition of the core oral microbiome of South African female adolescents was found to be similar to descriptive studies published in other populations. We additionally report a description the vaginal microbiome that is in …
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The genomic characterization of carbapenemase-producing Serratia marcescens at a tertiary hospital in South Africa
… for whole-genome sequencing using Illumina MiSeq, with the Nextera DNA Flex Library Preparation Kit. Sequence data was analysed in-house using srst2 and Tychus, and CRSM and control isolates were compared. Results Twenty-one CRSM and four control isolates were sequenced and analysed. …
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Characterization of Small Non-Coding RNAs in the Seminal Plasma of Beef Bulls with Predicted High and Low Fertility
… RNA preparation kit and sequenced on an Illumina MiSeq. Using the NCBI database of known human, porcine, mouse, and bovine miRNAs and known human piRNAs, expressed sequences were identified and mapped to the Bovine genome (Bta_4.6.1). A weighted FDR-corrected t-type test statistic was used to …
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De novo assembly of transcriptome and genome data from the Asia I mtCOI genetic clade of Bemisia tabaci
… bp paired-end reads generated on the Illumina MiSeq 2500 platform using Platanus. They were found to encode 41,981 PCGs and also contained 990 ncRNAs and repetitive elements (45.66%). A selection of 741 full-length genes were studied and found to contain larger intron sizes together with …
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Disentangling plant-microbe interactions under environmental change
… due to an inability to analyse poor quality MiSeq reads we find that drought application alongside C:N fertilisation has little effect on plant-microbial interactions for T. aestivum. In conclusion, high C:N treatments move mineralised N away from plant use and toward plant-host specific …
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Assessing Arbuscular Mycorrhizal Fungal community composition and diversity across a land-use gradient in Eastern Washington prairies
… pair NS31-AML2 and sequenced on the Illumina MiSeq platform using 300bp paired-end sequencing. Sequences were quality filtered and grouped into amplicon sequence variants (ASVs) using QIIME2. Taxonomy for the recovered AMF lineages was assigned using the MaarjAM database. Our results suggest …
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16S rRNA sequence analysis of silver carp microbial community in eDNA water samples
… through 16S rRNA sequencing on the Illumina MiSeq platform yielding 25 million reads and over 16,000 OTUs after initial clean up. Following analysis, there were multiple microbial groups, in particular 127 OTUs within the Fusobacteria phylum previously determined to be specialized to the gut …
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Characterizing the Microbiome of Scottish Freshwater Pearl Mussels (Margaritifera margaritifera): A Metabarcoding Analysis using Next-Generation Sequencing
… Technology) for full-length amplicons and MiSeq (Illumina) for short amplicons, enabling a comparative analysis of platform performance at the species level. Results revealed that the mussel microbiome was distinct from that of river water, with significant differences even at high …
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Field and laboratory evaluation of the interactions between pesticides and the gut microbiome in Honey Bees (Apis mellifera)
… 16S rRNA gene amplicon sequencing on Illumina MiSeq, respectively) in Chapter 1, and laboratory assays quantifying strain variation in the effects of pesticides on bacterial growth in Chapter 2. Field sampling of 20 hives across six sites in eastern Washington revealed that gut microbiome beta …
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The house dust microbiota in the Drakenstein Child Health Study
… was amplified and sequenced using the Illumina MiSeq platform to determine the bacterial taxonomic composition of the house dust samples. A custom python wrapper that meshes a set of tools integrated into a computationally efficient workflow, known as the YAP pipeline was used to classify 16S …
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Effects of seasonal changes on the depletion of microflora in natural wetlands in Northern KwaZulu Natal
… soil samples were analysed using the Illumina MiSeq sequencing. The bacteria were the most abundant >90% seasonally. The phyla Proteobacteria and Actinobacteria were the dominant phyla. The classes of Proteobacteria were all represented: Gamma-, Delta-, Alpha- and Betaproteobacteria. These …
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