3.0

DNA

The genetic material of the phage that is injected into the host cell.

Protein structure

The head and tail of the phage that remain attached to the outside of the host cell.

Cytoplasm

The fluid inside the host cell where the phage DNA enters.

Linear DNA

The initial form of the phage DNA before it circularizes.

Circularize

The process of the linear phage DNA forming a circular shape.

Lysis

The breaking open of the host cell, releasing new phage particles.

Early genes

Genes that are transcribed and translated first after the phage DNA enters the host cell.

Late genes

Genes that are expressed after the early genes and encode the structural proteins of the new phage particles.

Virions

Fully formed phage particles.

Copy-number

The total number of molecules of a specific protein found in a single virion particle.

Burst size

The number of phage particles produced from a single infected cell upon lysis.

Virulent phages

Phages that only use the lytic cycle to reproduce.

Lysogenic cycle

A life cycle of temperate phages where the phage genome becomes stably maintained within the host cell.

Prophage

The phage genome within the host cell during the lysogenic cycle.

Homologous recombination

The process by which a prophage integrates into the host chromosome.

Genetic switch

A set of genes and regulatory sequences that control the decision of a temperate phage to enter the lytic or lysogenic cycle.

Plasmid

A small, circular DNA molecule that can replicate independently of the host chromosome.

Excise

The process by which a prophage is removed from the host chromosome and enters the lytic cycle.

Plaques

Clear or cloudy areas on a bacterial lawn caused by the growth of phages.1. Plaque morphology:The appearance or "morphology" of a plaque, which can be clear or cloudy.

Temperate phages

Phages that have the ability to enter a lysogenic cycle and integrate their DNA into the host genome.

Lysogens

Bacterial cells that have integrated phage DNA into their own genome and can pass it on to daughter cells.

Clear plaques

Plaques produced by lytic phages, which are transparent and indicate the lysis of bacterial cells.

Turbid plaques

Plaques produced by temperate phages, which are cloudy and indicate the presence of lysogens.

Genomic information

Information about the genetic makeup of an organism, which can help distinguish between different phage behaviors.

Host range

The range of bacterial types that a particular phage can infect.

Host specificity

The ability of a phage to recognize and infect a specific host bacterium.

Receptor

A molecule on the host's cell wall that the phage can recognize and bind to.

Host transcription and translation systems

The cellular machinery of the host that the phage needs to interact with for successful infection.

Host range mutants

Phages that have undergone mutations that alter their ability to infect certain bacterial hosts.

Global phage population turnover

The constant turnover of the entire global phage population in a matter of days.

Selective pressure

The pressure for bacterial hosts to become insensitive to phage infection.

CoevolutionThe process of phages and hosts evolving together

The process of phages and hosts evolving together to ensure successful replication.

Insensitivity mechanisms

Various mechanisms by which bacteria can become insensitive to phage infection, including loss or alteration of host receptors, host restriction-modification systems, superinfection immunity, CRISPR systems, and surface exclusion.

Superinfection immunity

The ability of a lysogen to resist infection from an invading phage by repressing the invader's lytic genes.1. Immunity repressor protein:A protein that binds to the DNA of phages attempting to infect a lysogen and represses the expression of lytic genes, granting the lysogen immunity.

Superinfection

The attempt of a phage to infect a lysogen.

Exclusion

When prophage-encoded proteins alter the host cell surface to prevent other phages from infecting and injecting their DNA.

Bacterial resistance

The insensitivity of a host cell to phage infection due to mutation or loss of the phage receptor or through the action of bacterial defense systems.

Restriction system

A bacterial defense system that cuts double-stranded DNA at specific base pair sequences using endonucleases.

Abortive infection

A mechanism where infected cells sacrifice themselves to prevent phage multiplication, usually through the degradation of the antitoxin, leading to the release of the toxin and cell death.

CRISPR

Clustered Regularly-Interspaced Palindromic Repeats, a prokaryotic defense system that uses short spacer sequences to prevent phage infection.

CRISPR-Cas system

The system that uses CRISPR arrays and Cas proteins to provide acquired immunity against phages.

Antirestriction genes

Genes encoded by phages to counteract bacterial restriction systems.

Anti-CRISPR genes

Genes encoded by phages to counteract the CRISPR-Cas system.

Phage genomics

The study of phage genomes and their genetic connections.

SEA-PHAGES program

A program that focuses on studying phages that infect specific bacterial hosts to deepen our knowledge of phage genomics.

Mapping

Determining the relative positions of genes or other genetic markers on a chromosome.

Characterized

Describing or identifying the properties or features of something.

Gene structure

The organization and arrangement of DNA sequences that make up a gene.

Gene organization

The specific order and arrangement of genes within a genome.

Gene regulation

The control of gene expression, determining when and to what extent a gene is active.

Gene function

The specific role or purpose of a gene in an organism.

Genetic diversity

The variety of genetic material within a population or species.

Phage genetics

The study of genetic principles and mechanisms in bacteriophages.

Antibiotic resistance

The ability of bacteria to withstand the effects of antibiotics, rendering them ineffective.

Therapeutic use

The application of a substance or treatment for the purpose of treating or curing a disease or medical condition.

Phage typing

A method of identifying and classifying bacteria based on their susceptibility to specific bacteriophages.

Reporter phages

Bacteriophages engineered to carry a reporter gene, allowing for the detection of specific bacteria or antibiotic susceptibility.

Vector systems

Tools or methods used to introduce foreign DNA into a host organism.

Microbial computers

Systems that use genetically engineered bacteria or bacteriophages to perform computational tasks.

Mutant construction

The creation of organisms with specific genetic mutations for research purposes.

Transposon delivery

The transfer of transposons (mobile genetic elements) into a host organism for genetic manipulation.

Viral diversity

The range of different viruses present in a population or environment.

Biosphere

The regions of the Earth occupied by living organisms.