Same-sense mutation
A mutation which changes the nucleotide sequence of a codon but does not change the amino acid encoded due to the degeneracy of the genetic code. For example, both CCC and CCA encode proline.

Sanger sequencing
A method used to determine a DNA sequence based upon the incorporation of dideoxynucleotides.

Scaffolding proteins
Proteins which facilitate the assembly of a cell structure but are not included in the final structure. For example, phage encoded proteins that are required for procapsid assembly but are removed after the procapsid is constructed.

Score
To determine the presence or absence of a phenotype by testing for growth under different conditions (e.g., plus and minus an auxotrophic supplement or permissive and nonpermissive conditions). Usually done by replica plating or patching colonies onto each type of plate. Synonymous with "screen".

Screen
To determine the presence or absence of a phenotype by testing for growth under different conditions (e.g., plus and minus an auxotrophic supplement or permissive and nonpermissive conditions). Usually done by replica plating or patching colonies onto each type of plate. Synonymous with "score".

Secreted protein
A protein that is exported through the cytoplasmic membrane. Most secreted proteins have specific signal sequences that promote interaction with the export apparatus in the membrane.

Segregrate
See segregration below.

Segregration
The loss of one allele during cell division. For example, one allele maybe lost from because it fails to replicate or partition into one of the daughter cells.

Selectable marker
A mutation that confers a phenotype on a cell such that when grown on a certain medium only those cells with the mutation will grow. For example, the mutation rpsL1 makes cells resistant to the antibiotic streptomycin -- when grown on medium with streptomycin rpsL1 mutants will grow but rpsL+ cells will die.

Selected marker
An allele that allows growth under a particular selective condition.

Selective media
Growth media that only allow growth of mutant or recombinant cells with a particular phenotype grow. For example, media containing tetracycline would select for tetracycline resistant bacteria, preventing growth of parental tetracycline sensitive bacteria.

Selection
Conditions where only mutant or recombinant cells with a particular phenotype grow and divide.

SELEX
A method for isolation of high-affinity RNA- or DNA-protein interactions through successive rounds of selection for increased nucleic acid binding.

Selfish DNA
A DNA sequence that does not contribute to the fitness of an organism but is maintained in the genome because it promotes its own replication.

Serovars
Different strains of the same species of bacterium that can be distinguished by different reactions to certain antibodies (anti-sera). The name derives from the terms SEROlogical VARiety.

Sense strand
The strand of DNA that has the same nucleotide sequence as the mRNA (except the DNA has T where the RNA has U residues). Check out the supplemental resources for a diagram. Note that "sense strand" is sometimes used in different ways in the scientific literature, so it is critical to explicitly indicate what you mean when using this term.

Septum
The growth of the cell membrane and wall between opposite ends of a growing cell, ultimately separating the cell into two daughter cells.

Sexual PCR
PCR amplification in which similar, but not identical, DNA sequences are reassembled to obtain novel combinations of related, but variable sequences. When different combinations of a gene sequence are constructed, some of the resulting genes may possess improved characteristics. By repeating many rounds of PCR amplification and selection, an enormous amount of sequence variation can be obtained.

Shine-Delgarno sequence
A sequence in the mRNA which can pair with the ribosome facilitating the initiation of protein synthesis. (Named after the researchers who first described this sequence.)

Shotgun cloning
A cloning strategy that involves the insertion of random fragments of a large DNA molecule into a vector, resulting in a large number of different recombinant DNA molecules.

Shuttle vector
A vector that can replicate in the cells of more than one organism (e.g. in both E. coli and in yeast).

Sibs
An abbreviation for siblings.

Siblings
Two cells that arose by the division of a parent cell.

Sigma factor
A protein that functions as a subunit of bacterial RNA polymerases and is responsible for specificity of recognition of promoters. Different sigma factors allow recognition of different promoter sequences.

Signal transduction
Conditions that alter the conformation of a protein which regulates expression of other genes. Initially signal transduction was used to refer to extracellular conditions that alter the conformation of a membrane protein and cause it to relay the regulatory signal inside the cell, but more recently the term has been broadly applied to a variety of regulatory cascades.

Silent mutation
A mutation which changes the nucleotide sequence but does not cause a detectable change in the phenotype.

Similarity
Sequence identity between two nucleotide sequences. For example, 85% similarity means that 85 nucleotide positions out of 100 are identical in the two nucleotide sequences. Sequence similarity does not necessarily indicate that two sequences have common ancestry.

Single-strand DNA binding protein (ssb)
The small basic protein that has a high affinity for single-stranded DNA. Ssb protein protects single-stranded DNA from nuclease attack and inhibits it from reannealing into double-stranded DNA.

Site-directed mutagenesis
A method for introducing specific mutations at a defined site in a nucleotide sequence.

Site-specific recombination
Genetic exchange that occurs between particular, short DNA sequences. Site-specific recombination systems do not require RecA. Instead, each site-specific recombination system requires unique enzymes that catalyze the genetic exchange. Unlike RecA mediated recombination, site-specific recombination requires little sequence homology between the two DNA molecules. The best understood example is the integration of lambda into the E. coli chromosome by recombination between attP and attB catalyzed by the lambda integrase protein.

SNP
Defined regions of the genome where there are two or more nucleotide variations, each with 1% or greater prevalence in the population. SNPs can be used as genetic or physical markers.

SOS box
The operator sequence recognised by the LexA repressor protein.

SOS response
The coordinate induction of many genes in response to certain types of DNA damage. Many of the induced gene products facilitate repair of the damaged DNA, but the repair processes result in a high frequency of mistakes in the repaired DNA, a process often called error-prone repair. The SOS response in enteric bacteria is initiated by RecA protein, which becomes activated by DNA damage, and stimulates the autoproteolysis of several other proteins, including the LexA protein and the lambda cI repressor protein. The LexA protein is a global repressor that normally turns off expression of many other genes in the SOS regulon.

Southern blots
A method for detecting specific DNA fragments seperated on an agarose gel. DNA fragments are first seperated by electrophoresis through an agarose gel. After electrophoresis, the DNA in the gel is denatured by soaking the gel in an alkaline solution. Then a nitrocellulose or nylon membrane is layed on top of the agarose gel and absorbant paper is layered on top of the membrane. The aqueous solution passes from the agarose gel through the membrane into the absorbant paper by capillary action. The DNA moves with the aqueous solution but becomes trapped on the membrane. The DNA is then detected by annealing a labelled singlestranded DNA probe to the fragments of denatured DNA on the membrane, hybridization detected by autoradiography.

Specialized transduction
A method of gene transfer between bacteria in which a specific region of the bacterial donor DNA is carried by a phage. The host DNA carried by a specialized transducing phage arises by abbarent excision of a prophage. Thus, only regions of DNA adjacent to an integrated phage can be transferred by this method.

Spheroplast
Partial removal of the cell wall resulting in osmotically sensitive cells.

Spontaneous mutation
A mutation that occurs without known exposure to a mutagen.

Spore
A highly resistant, resting state of an organism. Under the proper condiditons s spore will germinate to form a viable, reproducing organism. Bacterial spores are often very resistant to heat and dessication.

Start (initiation) codon
The codon on mRNA where polypeptide synthesis is initiated. The most common start codon is AUG but sometimes GUG or rarely UUG can be used as a start codon.

Sticky (cohesive) ends
The two complementary single-stranded ends of a DNA duplex. For example, resulting from digestion with a Class II restriction endonuclease.

Stochastic
A random process; a process determined by a random distribution of probabilities.

Stop (nonsense) codon
A UAG, UAA. or UGA codons which is not representing any cognate aminoacyl tRNA in most organisms. When the ribosome encounters a stop codon in the mRNA, a termination factor interacts with the ribosome causing polypeptide synthesis to stop and the ribosome to dissociate from the mRNA.

Strain
An organism that is different from other organisms of the same species due to genetic differences. Strain is commonly used in two ways: (i) organisms of the same species that when initially isolated are found to have certain different properties (due to unknown mutations) are called different strains; (ii) derivatives of an organism that have distinct genotypes due to known mutations are called different strains.
Strand slippage
The denaturation and aberrant mispairing of a template strand during DNA replication. Results in frameshift mutations (see http://www.sci.sdsu.edu/~smaloy/MicrobialGenetics/topics/mutations/frame-shift.html).
Streptomycin
An antibiotic that inhibits protein synthesis in bacteria by binding to the S12 protein of the 30s ribosomal subunit and inhibiting translation. A high level of StrR can result from chromosomal mutations in the gene for the S12 protein (rpsL) which prevent streptomycin from binding to the ribosome. Only mutant ribosomes are StrR, so resistance to streptomycin is recessive to streptomycin sensitivity. Because streptomycin rapidly inhibits protein synthesis, when cells acquire the rpsL gene phenotypic expression is required before the cells become streptomycin resistant.

Stringency
Conditions affecting the hybridization of nucleotide sequences. Higher stringency conditions require more base pairing between the two sequences. Higher stringency conditions can be obtained by higher temperatures, highter salt concentrations, or addition of formamide.

Stringent response
The ability of a bacterium to limit the synthesis of tRNA and rRNA during amino acid starvation. The alarmones ppGpp and pppGpp are at least partially responsible for the stringent response. The concentrations of these alarmones are controlled by the relA and spoT gene products in E. coli.

Strong promoter
An efficient promoter that can direct synthesis of RNA transcripts at a relatively fast rate.

Structural gene
The portion of a gene encoding a functional polypeptide or RNA molecule.

DT>Structural protein

A protein which fulfill a purely structural role (i.e. not enzymatic). This includes phage capsid proteins, some ribosomal proteins, "histone-like" proteins, etc.

Stuffer fragment
The part of a lambda replacement vector that is removed during insertion of new DNA.

Substrate
A chemical recognized by an enzyme.

Substution mutation
A mutation that replaces one nucleotide in a DNA sequence with another nucleotide.

Subtraction library
A cDNA library that only contains those cDNAs that are expressed in a particular type of cell or tissue or under particular growth conditions. The cDNA common to all conditions is removed by hybridization with excess RNA from other cells (i.e. subtraction), leaving only the unique RNA behind.

Suicide plasmid
A plasmid that cannot replicate in a given host, used to force the; integration into host replicons of genetic determinants carried by the plasmid or phage. It is usually necessary to have a direct selection for the desired recombinants. See Allele exchange.

Supercoiled DNA
Double-stranded circular DNA in which either overwinding or underwinding of the duplex makes the circle twist. The conformation of a covalently closed-circular DNA molecule, which is coiled by torsional strain into the shape taken by a woundup elastic band.

Superinfection
The secondary infection by a phage in a cell already harbouring the same phage.

Superinfection exclusion
A process whereby the presence of one phage in a cell prevents the secondary infection by other. There are many different mechanisms of superinfection exclusion, including changes in cell surface receptors or the expression of a restriction system.

Suppression
The restoration (or partial restoration) of a wild-type phenotype by a second mutation. There are many different mechanisms of suppression (see the supplemental resources

Suppressor gene
A mutated gene which produces a product which reverses the effect of a previous specific mutation without actually correcting the original mutation in the DNA can be either intergenic or intragenic.

Suppressor mutation
A mutation that restores, partially or completely, the loss of function caused by another mutation. Many suppressor mutations are in genes encoding a transfer RNA species; the altered tRNA can recognise the original mutant codon and, during translation, insert an acceptable substitute amino acid into the polypeptide.

Suppressor tRNA
A mutant tRNA that recognizes a stop codon instead of the codon for the cognate amino acid. This property is sometimes, but not always, due to a base substitution in the anticodon.

Synapsis
The pairing of homologous chromosomes or of homologous chromosomal regions.

Synteny
Genes which occur in the same order on the chromosome of different species.

Sythetic lethal mutations
Two mutations are synthetically lethal if cells with either of the single mutations are viable but cells with both mutations are inviable. As with suppressor analysis, synthetic lethal mutations often indicate that the two mutations affect a single function or pathway.

Sythetic phenotype
A distinct phenotype that requires the presence of two mutations, and either of the mutations alone does not exhibit the same phenotype. Also note the defination of Synthetic lethal mutations.