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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

Genome Size and the Evolution of New Genes

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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

Cis-regulatory Sequences

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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

Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes

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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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Cluster Sampling Method01:20

Cluster Sampling Method

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Appropriate sampling methods ensure that samples are drawn without bias and accurately represent the population. Because measuring the entire population in a study is not practical, researchers use samples to represent the population of interest.
To choose a cluster sample, divide the population into clusters (groups) and then randomly select some of the clusters. All the members from these clusters are in the cluster sample. For example, if you randomly sample four departments from your...
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Genome-wide Gene Deletions in Streptococcus sanguinis by High Throughput PCR
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Genome-wide Gene Deletions in Streptococcus sanguinis by High Throughput PCR

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Genomic sequence investigation Streptococcus pyogenes clusters in England (2010-2015).

J M Coelho1, G Kapatai1, A Jironkin2

  • 1Bacterial Reference Department, Public Health England, London, UK.

Clinical Microbiology and Infection : the Official Publication of the European Society of Clinical Microbiology and Infectious Diseases
|April 27, 2018
PubMed
Summary
This summary is machine-generated.

Genomic sequencing accurately distinguished Streptococcus pyogenes (group A streptococcus) outbreaks in healthcare settings. This analysis confirmed or excluded cases and identified staff colonization and environmental contamination with outbreak strains.

Keywords:
ClustersEnglandGenomic sequenceInvestigationStreptococcus pyogenes

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Area of Science:

  • Microbiology
  • Genomics
  • Epidemiology

Background:

  • Streptococcus pyogenes (group A streptococcus) outbreaks pose significant risks in healthcare settings, particularly in elderly care and maternity wards.
  • Effective outbreak investigation relies on accurate methods to link cases and identify transmission routes.

Purpose of the Study:

  • To analyze genomic differences between epidemiologically related and unrelated Streptococcus pyogenes isolates from healthcare outbreaks.
  • To assess the utility of genomic sequencing in distinguishing outbreak strains from sporadic infections.

Main Methods:

  • Genomic sequencing and bioinformatics analysis of 134 S. pyogenes isolates from 21 outbreaks (2010-2015).
  • Phylogenetic analysis, single nucleotide polymorphism (SNP) comparison, and statistical outlier detection.
  • Comparison of isolates from patients, healthcare workers, and environmental samples within and between outbreaks.

Main Results:

  • Genomic sequences of epidemiologically linked isolates were highly conserved (0-1 SNP difference).
  • Healthcare worker colonization and environmental contamination with outbreak strains were identified in several instances.
  • Genomic SNP analysis successfully excluded ten isolates from defined epidemiological outbreaks.

Conclusions:

  • Genomic discrimination is a valuable tool for assisting in Streptococcus pyogenes outbreak investigations.
  • Genomic data can confirm or exclude cases from epidemiologically defined outbreaks.
  • The study demonstrated healthcare worker colonization and environmental contamination as potential transmission sources.