Unit 3 and 4 terms

Genome

All of the genetic information in chromosomes. Includes genes encoding proteins, RNA, and regulatory sequences, and noncoding DNA

Genomics

Discipline of mapping, sequencing, analyzing, and comparing genomes

How are genomes generated?

1. Sample preparation

2. DNA sequencing

3. Genome assembly

4. Genome annotation

Annotation

Determining a genes “identity”. Major bottleneck in genomics.

Bioinformatics

Storing and analyzing sequences and structures of nucleic acids and proteins

Functional Genomics

Discipline that attempts to describe what DNA and genes (and the proteins they encode) actually do, or what the function of particular DNA sequence is

Virus

Genetic element that can multiply only in a living (host) cell

Obligate intracellular parasite

Needs host cell for energy, metabolic intermediates, proteins synthesis

Virion

A virus particle outside its host

Naked virus

Have no outer layer (only capsid and nucleic acid)

Enveloped virus

Have an outer layer consisting of a phospholipid bilayer(from host cell membrane) and viral proteins (contains capsid, nucleic acid, glycoprotein, and envelope)

Nucleocapsid

Nucleic acid + proteins in enveloped viruses

Capsid

The protein shell that surrounds the genome of a virus

Burst size

the expected number of virons produced by one infected cell over its life-time

Helical symmetry

Rod-shaped length determined by length of nucleic acid. Width determined by size and packaging of capsomeres

Icosahedral symmetry

(spherical - also a naked viron) most efficient arrangement of subunits in a closed shell. Requires fewest capsomeres (subunit that makes up the protein coat)

Titer

Number of infection virons per volume of fluid

Plaques

Clear zones of cell lysis that develop on lawns of host cells where successful viral infection occurs

Synthetic biology (SynBio)

Assembling DNA pieces into new genetics elements

Genetic engineering

Using in vitro techniques to alter genes in the laboratory

Heterologous expression

the process of introducing a gene or gene fragment from one species into a host organism that does not naturally have that gene

Polymerase chain reaction (PCR)

Enables researchers to quickly generate many copies of a single DNA sequences

Taq polymerase

Thermostable DNA polymerase named after the thermophilic bacterium Thermus aquaticus

In vitro

Outside of a living organism

How can new genes can be expressed in an organism

1. Introducing a plasmid containing those genes (molecular cloning)

2. Inserting them into an organism’s genome (I.e. genome engineering)

Expression vector

A plasmid or virus designed to express large quantities of a specific gene of interest

Homologous recombination

Swaps out foreign genes with original gene based on sequence similarity. Almost always a part of genome engineering

CRISPR (clustered regularly interspaced short palindromic repeats)

Derived from DNA fragments of bacteriophages that previously infected the prokaryote so that prokaryotes can attack similar viruses that attack in the future

Cas9

A microbial enzyme that cuts at those specific sequences, so that if it comes across a virus with that sequence, it cuts and destroys it

Reporter gene

Encodes proteins easy to detect and assay (ex GFP or beta-galactosidase)

Reporter gene fusion

Coding sequence from reporter is fused with part of a “native gene” to form hybrid gene

Green fluorescent proteins (GFP)

Protein found in Aequorea Victoria jellyfish that exhibits green fluorescence when exposed to UV light

Attenuated vaccine

Contains live microorganisms that have been weakened so they cannot cause disease. It stimulates a strong immune response and often provides long-lasting immunity. Examples include vaccines for measles, mumps, and rubella (MMR) and oral polio vaccine.

Vector vaccines

Made by adding pathogenic genes to a harmless virus, enabling the immune system to recognize and develop immunity against those pathogens

Probiotics

Live microorganisms that may provide health benefits when consumed, generally by improving or restoring the gut microbiota

Where did life originate?

Hydrothermal systems in an RNA world

Stromatolites

Fossilized microbial formations found in rocks 3.5 billion years old

Endosymbiotic theory

Posits that some eukaryotic cell organelles, such as mitochondria and plastids, evolved from free-living prokaryotes

Homologous recombination

Requiring short flanking segments of similar sequence

Nonhomologous recombination

Does not require high similarity

Gene family

A set of several similar genes, formed by duplication of a single original gene, and generally with similar biochemical functions

Homologous genes (Homologs)

Genes that all descended from single ancestral gene

Orthologs

Homologous genes sharing same function

Paralogs

Single ancestral gene diverges to many different function in many different organisms

Core genome

Genes shared by all members of a group (ex. All strains of the same species

Pan genome

Core genome plus genes not shared by all strains

Average nucleotide identity (ANI)

Very common metric. Little less stringent than 16S because there is more genetic information

Ecological diversity

Microbial interactions between organisms and their environment

Phylogenetic diversity

Evolutionary relationships between organisms

Functional diversity

describes the organism's role such as competitiveness among organisms, cooccurrence of species, and community assembly in the community and ecosystem

Why are metabolic and ecological traits shared by divergent organisms?

Gene loss, convergent evolution, horizontal gene transfer

Gene loss

A trait is present in a common ancestor is lost during divergence over time

Proteobacteria

Gram-negative bacteria that are separated into 5 classes (alpha-,beta-,gamma-,delta-,epsilonproteobacteria)

Alphaproteobacteria

Capable of growth under low levels of nutrients. Examples include Rickettsia, Rhizobia, and Wolbachia

Rickettsia

Obligate intracellular parasites which are rod shaped bacteria that are transmitted to humans via insect and tick bites. Causes typhus and rocky mountain spotted fever.

Rhizobia

Infects the roots of legumes, creating a symbiotic relationship.This bacteria from root nodules that are sites of nitrogen fixation that convert nitrogen gas to ammonia.

Wolbachia

Common infectious bacterial genus that live inside insect host. In Aedes aegypti mosquito they can transmit dengue, Zika, etc. This bacteria stops viruses from replicating inside the mosquitoes that transmit the disease

Betaproteobacteria

Often use nutrients that diffuse away from anaerobic decomposition of organic matter. Examples include Burkholderia, Neisseria, and Zoogloea

Gammaproteobacteria

facultatively anaerobic, gram negative bacteria that live the intestinal tract of humans an other animals. Contain fimbriae and include vibrio, escherichia, and salmonella.

Deltaproteobacteria

Contain Bdellovibrio that attaches to other gram-negative to penetrate outer layer. Once inside, the cell will elongate into a tight spiral that fragments into individual cells. Host cell eventually lyses to release contents

Epsilonproteobacteria

Typically gram-negative rods that are helical or curved. This includes campylobacter and helicobacter

Consortium

Intimate two-membered microbial association

Diazotrophs

Bacteria and Archaea that fix gaseous nitrogen in the atmosphere into a more usable form such as ammonia

Diatom-diazotroph associations (DDAs)

Symbiotic relationship between diatoms (unicellular eukaryotic algae) and cyanobacteria. Bacteria provide the host with nitrogen while host provide carbon and other nutrients

Methanotrophs

Prokaryotes that metabolize methane as their source of carbon and chemical energy. Can be bacteria or archaea

Helminths

Muticellular, chemoheterotrophic animals that obtain nutrients by ingestion through a mouth

Mycosis/mycoses

Fungal disease(s) that are generally chronic because fungi grow slowly. They are difficult to treat because drugs that effect fungal cells also affects animal cells

Systemic mycoses

Deep within the body, often caused by fungi that live in soil with in soil with spores transmitted by inhalation

Subcutaneous mycoses

Beneath the skin by direct implantation of spores into a puncture wound

Cutanous mycoses

Infect epidermis, hair, and nails