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Related Concept Videos

Genomics02:02

Genomics

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Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
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Genomic Imprinting and Inheritance02:30

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Diploid organisms inherit genetic material through chromosomes from both parents. Copies of the same gene are known as alleles. In most cases, both alleles are simultaneously expressed and allow various cellular processes to function optimally. If one of the alleles is missing or mutated, the expression of the other allele can compensate; however, this is not true for all genes.
The expression of some genes depends on which parent passed the gene to the offspring, through a phenomenon known as...
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Genome Size and the Evolution of New Genes03:21

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While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.
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Cis-regulatory Sequences02:02

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Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
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Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes02:16

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The present-day mitochondrial and chloroplast genomes have retained some of the characteristics of their ancestral prokaryotes and also have acquired new attributes during their evolution within eukaryotic cells. Like prokaryotic genomes, mitochondrial and chloroplast genomes neither bind with histone-like proteins nor show complex packaging into chromosome-like structures, as observed in eukaryotes. Unlike mitotic cell divisions observed in eukaryotic cells, mitochondria and chloroplasts...
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Sequences01:29

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Sequences are fundamental mathematical objects consisting of ordered lists of numbers that follow a specific rule or pattern. Sequences are critical in various mathematical concepts, including calculus, series, and number theory. They can model real-world phenomena such as population growth, financial investments, and physical processes like the diminishing height of a bouncing ball.Each number in a sequence is referred to as a term. Typically, the terms are denoted as a1, a2, a3,…, where...
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Ultra-long Read Sequencing for Whole Genomic DNA Analysis
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Salmonella Serotyping Using Whole Genome Sequencing.

George M Ibrahim1, Paul M Morin1

  • 1Microbiological Sciences Branch, Northeast Food and Feed Laboratory, United States Food & Drug Administration, Jamaica, NY, United States.

Frontiers in Microbiology
|January 9, 2019
PubMed
Summary

Whole Genome Sequencing (WGS) with SeqSero accurately predicts Salmonella serotypes, offering a powerful alternative to traditional methods for food safety and public health surveillance. This advancement aids in tracking foodborne illnesses and understanding pathogen characteristics.

Keywords:
Kauffmann White schemeSalmonellaSeqSerotraditional serologywhole genome sequencing

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Area of Science:

  • Microbiology
  • Genomics
  • Food Safety
  • Public Health

Background:

  • Traditional serology and the Kauffmann White Scheme (KWS) have been standard for Salmonella serotyping.
  • Whole Genome Sequencing (WGS) offers advanced pathogen characterization and improved traceback investigations for foodborne illnesses.
  • In silico tools like SISTR and SeqSero enable serovar prediction from WGS data.

Purpose of the Study:

  • To evaluate the accuracy of WGS-based serovar prediction using the SeqSero tool compared to traditional serological methods.
  • To assess the utility of WGS and SeqSero for public health surveillance and molecular epidemiology of Salmonella.

Main Methods:

  • Retrospective analysis of 1,041 Salmonella isolates from food, feed, and environmental samples collected between 1999 and 2017.
  • Serotyping of isolates using traditional serology and WGS with the in silico SeqSero tool.
  • Comparison of serotype predictions between WGS-based and traditional methods.

Main Results:

  • SeqSero accurately predicted identical Salmonella serotypes to traditional methods in 86.4% of isolates (899/1,041).
  • Discrepancies between SeqSero and traditional serotyping were observed in 7.7% of isolates (80/1,041).
  • No serotype prediction was possible for 5.9% of isolates (62/1,041).

Conclusions:

  • WGS and the SeqSero tool demonstrate high accuracy for Salmonella serotyping, serving as a viable alternative to traditional KWS.
  • WGS offers advantages in molecular detail and genetic characterization compared to traditional serotyping.
  • In silico WGS-based serotyping holds potential to replace traditional methods in public health surveillance.