Mapping short reads to a reference genome is an essential step in many next-generation sequencing (NGS) analyses. In plants with large genomes, a large fraction of the reads can align to multiple locations of the genome with equally good alignment scores. How to map these ambiguous reads to the genome is a challenging problem with big impacts on the downstream analysis. Traditionally, the default method is to assign an ambiguous read randomly to one of the many potential locations. In this study, we explore two alternative methods that are based on the hypothesis that the possibility of an ambiguous read being generated by a location is proportional to the total number of reads produced by that location: (1) the enrichment method that assigns an ambiguous read to the location that has produced the most reads among all the potential locations, (2) the probability method that assigns an ambiguous read to a location based on a probability proportional to the number of reads the location produces. We systematically compared the performance of the proposed methods with that of the default random method. Our results showed that the enrichment method produced better results than the default random method and the probability method in the discovery of single nucleotide polymorphisms (SNPs). Not only did it produce more SNP markers, but it also produced SNP markers with better quality, which was demonstrated using multiple mainstay genomic analyses, including genome-wide association studies (GWAS), minor allele distribution, population structure, and genomic prediction.
Detection methods for Vibrio cholerae and Vibrio parahaemolyticus which included the culture based approach with polymerase chain reaction (PCR) confirmation, PCR detection without enrichment and PCR with a pre-enrichment were developed and their performance evaluated. PCR assays targeted the SodB (V. cholerae species), Flae (V. parahaemolyticus species), 16S rRNA (Vibrio and Enterobacteriacea species) genes (Multiplex 1) and V. cholerae O1 and V. cholerae O139 rfb genes, ctxA (cholera toxin) gene and 16S rRNA gene (Multiplex 2). These methods were used to determine the occurrence of selected Vibrios in source water as well as in household container-stored water. The combination of filtration, enrichment and PCR method provided a sensitive and specific method for the detection of selected Vibrios in water samples. The PCR with a pre-enrichment method detected as few as 4–10 cfu/100 mL of selected Vibrios and PCR detection without the enrichment method detected as few as 40–100 cfu/100 mL of selected Vibrios. The inclusion of an enrichment period allows detection of culturable bacteria. As an application of the developed methods, V. cholerae and V. parahaemolyticus were detected in the source water used by the population and in the water-storage containers. The results indicate that Vibrio species in the containers could have originated from the source water and survive in biofilms inside the containers.
An airflow based, evaporative enrichment method for use in microfluidic paper-based assays. The method is used for fluid control in a multistep assay and as a technique to improve sensitivity in colorimetric detection assays.
Nutritionally exacting mutants of Cochliobolus sativus, a fungus with multinucleate, multicellular spores, were readily isolated by a filtration enrichment method. The method is similar to one described by Fries and is based upon the differential growth of auxotrophs and prototrophs in minimal medium. Most of the prototrophic propagules were removed by filtration. Propagules in the filtrate were concentrated by centrifugation, plated on complete medium, and subsequently tested for nutritional requirements.In comparative studies on four methods of isolation, namely, total isolation, mass transfer; total isolation, hyphal-tip transfer; filtration enrichment, mass transfer; and filtration enrichment, hyphal-tip transfer, the yield of auxotrophic mutants was 0, 0.04, 1.16, and 1.83%, respectively.
Sweet potato plants were treated with selenium (Se). Spraying Se on the sweet potato leaves was an effective Se enrichment method and proteins were extracted from the sweet potato stem. The structural characteristics of the protein were investigated. Fourier transform infrared spectroscopy (FT-IR) detected more signals from the Se-enriched sweet potato stem protein (SSP), and the number of forms of Se chemical bonds gradually increased with increasing Se content, such as the Se-O bond in high Se-enriched SSP, indicating altered secondary structures.Scanning electron microscopy-energy dispersive spectrometry (SEM-EDS) indicated more Se atoms in the Se-enriched SSPs (SSSPs). The DSC results revealed that Se enrichment enhanced the thermal stability of the samples. Moreover, selenomethionine (SeMet), selenocystine (SeCys2), and methylselenocysteine (MeSeCys) were determined to be the main Se forms in the SSSPs. Furthermore, the SSSPs showed relatively higher superoxide anion radical and DPPH radical scavenging activities than the blank, which indicates that SSSPs can be used as antioxidants. By recovering the proteins, the agricultural by-product—sweet potato stem can be further utilized, and the obtained Se-enriched proteins may contribute to human health.
In the present study, steam injection method (SIM) is implemented to a
hydrogen-enriched diesel engine in order to improve the levels of performance
and NO emissions. As hydrogen enrichment method increases effective
efficiency, NO emissions could be increased. However, the SIM is used to
control NO emissions and improve the engine performance. Due to these
positive effects, hydrogen enrichment and the SIM)are applied into a diesel
engine by using a two-zone combustion model for30% hydrogen enrichment of the
fuel volume and 20% steam ratio of the fuel mass at full load conditions. The
results obtained are compared with conventional diesel engine (D), steam
injected diesel engine (D+S20), hydrogen-enriched diesel engine (D+H30) and
hydrogen-enriched diesel engine with steam injection (D+H30+S20) in terms of
performance and NO emissions. In the results, the effective efficiency and
effective power improve up to 22.8% and %3.1, as NO emissions decrease up to
22.1%. Hence, the hydrogen enrichment with steam injection method is more
environmentally friendly with better performance.
An enrichment method to increase cell-free fetal DNA fraction and significantly reduce false negatives and test failures for non-invasive prenatal screening: a feasibility study
