Search results for "Sequencing"
showing 10 items of 1087 documents
Genetic diversity of Dioscorea dumetorum (Kunth) Pax using Amplified Fragment Length Polymorphisms (AFLP) and cpDNA
2010
We have utilized Amplified Fragment Length Polymorphisms (AFLP) in conjunction with chloroplast DNA (cpDNA) sequence data to study the genetic diversity in 53 accessions of Dioscorea dumetorum from six countries in West and Central Africa. Our results provide a comparison of the two marker systems with regards to their applicability to differentiate intraspecific genotypes and the grouping of the accessions based on localities of collection. A total of 1052 AFLP fragments (of which 94.1% were polymorphic) produced from twelve primer combinations indicate a relatively high level of polymorphism among the accessions. Three major genetic groups that do not strictly follow a geographic distribu…
Analysis of S-allele genetic diversity in Sicilian almond germplasm comparing different molecular methods
2015
Italian almond germplasm is characterized by a wide diversity in several growing areas among which Sicily is one of the most important. Analysis with consensus and specific primers and DNA sequencing was performed to investigate S-RNase genetic diversity and to elucidate the homology rate within a genetic pool of 27 Italian accessions. Interestingly, some of the self-compatible cultivars did not show the presence of Sf allele. Amplicons from consensus and allele-specific PCR primers revealed a high level of variability. Sequencing of all the S-RNase amplicons derived from consensus primers allowed the identification of two new S-RNase alleles (S51 and S52). Surprisingly, despite the AA repl…
Molecular community and population studies of arbuscular mycorrhizal fungi (Glomeromycota)
2014
The arbuscular mycorrhizal symbiosis, which appeared at the same time as land plants, 460 million years ago, is a mutualistic beneficial association between most land plants, including those cultivated, and arbuscular mycorrhizal fungi (AMF). AMF, from the Glomeromycota phylum, are widespread soil microorganisms needing a photosynthetic host to complete their life cycle (obligate symbionts). The great potential of plant mineral nutrition improvement and crop production increased during this symbiosis, make AMF an asset in the context of an increase in the demand of world food crop production. The control of that symbiosis by ecology engineering in order to improve ecosystem services, especi…
The metabolic versatility of PAOs as an opportunity to obtain a highly P-enriched stream for further P-recovery
2015
The effects of two sequencing batch reactor operation strategies for phosphorus stream enrichment over the biological phosphorus removal performance have been studied. The objective of both strategies is of performing an extraction cycle in order to obtain a new stream highly enriched with phosphorus. In the 1st strategy the amount of influent volatile fatty acids (VFAs) is the same in each cycle; while in the 2nd strategy the influent VFAs concentration is increased during phosphorus extraction experiments. Despite the strong decrease of the stored poly-P inside the cells in both strategies after the recovery cycles, the ability of the systems to remove phosphorus was not affected. The P-r…
A catalog of HLA type, HLA expression, and neo-epitope candidates in human cancer cell lines
2014
Cancer cell lines are a tremendous resource for cancer biology and therapy development. These multipurpose tools are commonly used to examine the genetic origin of cancers, to identify potential novel tumor targets, such as tumor antigens for vaccine devel-opment, and utilized to screen potential therapies in preclinical studies. Mutations, gene expression, and drug sensitivity have been determined for many cell lines using next-generation sequencing (NGS). However, the human leukocyte antigen (HLA) type and HLA expression of tumor cell lines, characterizations necessary for the development of cancer vaccines, have remained largely incomplete and, such information, when available, has been …
Selective MicroRNA-Offset RNA Expression in Human Embryonic Stem Cells
2015
Small RNA molecules, including microRNAs (miRNAs), play critical roles in regulating pluri-potency, proliferation and differentiation of embryonic stem cells. miRNA-offset RNAs (moRNAs) are similar in length to miRNAs, align to miRNA precursor (pre-miRNA) loci and are therefore believed to derive from processing of the pre-miRNA hairpin sequence. Recent next generation sequencing (NGS) studies have reported the presence of moRNAs in human neurons and cancer cells and in several tissues in mouse, including pluripotent stem cells. In order to gain additional knowledge about human moRNAs and their putative development-related expression, we applied NGS of small RNAs in human embryonic stem cel…
kmcEx
2019
Memory-frugal and retrieval-efficient encoding of counted k-mers.
Start-Up of Chitosan-Assisted Anaerobic Sludge Bed Reactors Treating Light Oxygenated Solvents under Intermittent Operation
2021
Quality of the granular sludge developed during the start-up of anaerobic up-flow sludge bed reactors is of crucial importance to ensure the process feasibility of treating industrial wastewater such as those containing solvents. In this study, the microbial granule formation from suspended-growth biomass was investigated in two chitosan-assisted reactors. These reactors operated mimicking industrial sites working with night closures treating a mixture of ethanol, ethyl acetate, and 1-ethoxy-2-propanol. Each reactor operated under different hydrodynamic regimes typical from UASB (R1: <
TAF-ChIP: an ultra-low input approach for genome-wide chromatin immunoprecipitation assay
2019
The authors present a novel method for obtaining chromatin profiles from low cell numbers without prior nuclei isolation. The method is successfully implemented in generating epigenetic profile from 100 cells with high signal-to-noise ratio.
Genomics and Proteomics Analyses Revealed Novel Candidate Pesticidal Proteins in a Lepidopteran-Toxic Bacillus thuringiensis Strain
2020
Discovery and identification of novel insecticidal proteins in Bacillus thuringiensis (Bt) strains are of crucial importance for efficient biological control of pests and better management of insect resistance. In this study, the Bt strain KhF, toxic for Plodia interpunctella and Grapholita molesta larvae, underwent genomics and proteomics analyses to achieve a better understanding of the bases of its pathogenicity. The whole-genome sequencing results revealed that the KhF strain contained nine coding sequences with homologies to Bt insecticidal genes. The lepidopteran toxic mixture of spores and crystals of this Bt strain was subjected to liquid chromatography and tandem mass spectrometry …