micro unit 2 part 2

what is MALDI-TOF MS?

Microorganisms in a colony can often be identified in less than 15 minutes; fast identification leads to more timely appropriate treatments.

genomic island

DNA segments that originated from another species. the qualities that are encoded could be: use of an energy source, acid tolerance, ability to cause disease

detecting specific nucleotide sequences

- tests can identify sequences unique to species or group (nucleic acid probes/ NAATs) - limitation is each test only finds only one possibility. - need to run multiple probes

who uses genome trakr

FDA

Classifying microorganisms

have shifted to ribosomal RNA sequencing. 16S used for bacteria. And 18S is Eukaryotic cell classification.

what current over arching system do we use to classify organisms?

the three domains of bacteria, archaea, Ekarya

3 ways of horizontal gene transfer

- transduction - transformation - conjugation

what is the three domain system?

Eukarya, Bacteria, Archaea

Phylogeny

Evolutionary history of a species or group of species.

when excision errors occur between chromosomal and F plasmid DNA, the new combined plasmid is called?

F prime plasmid

MGE (mobile genetic elements)

genes that are transferred are mostly nonessential but can allow for specific survival in conditions. most have narrow host range and conjugative plasmids carry all information out for transfer.

first genome published

haemophilus influenza

G+C content, the percentage of G-C pairs in DNA. how does this work?

if GC content differs by more than a few percent then the organisms are not related. similarity with GC content does not mean the two things are related.

what does a catalase test determine?

- determines catalase enzyme - can break down H2O2

why is CRISPR medically important?

- due to it lacking like molecular scossors,ccancrecognize specific sequences, cut the DNA and replace or leave the modified sequence.

way to identify organisms

- microscopic examination - culture characteristics - biochemical tests - nucleic acid analysis - patient symptoms

protein profiles

determined by MALDI-TOF. less than 15 minutes

what does phylogeny consider?

evolutionary relatedness

True or false: In bacterial conjugation, all F+ donor cells are high frequency recombinant (Hfr) cells.

false

what does characterizing different strains important for?

finding foodborne illness, forensic investigations of bioterrorism and diagnosing different diseases.

how do bacteria recognize and destroy foreign DNA that enters the cell?

- antibiotics -restriction endonuclease

what gene is most useful in determining the sequence of bacterial species?

16S rRNA

who uses pulsenet?

CDC

what is found in a bacteriophage ?

DNA or RNA genome and protein coat

In conjugation in E. coli, an Hfr cell refers to ______.

a cell in which the F plasmid has been integrated into the cell chromosome

open reading frame

a nucleotide longer than 300 base pairs. begins with start codon and ends with stop codon.

CRISPR/Cas9

a unique technology that enables geneticists and medical researchers to edit parts of the genome by removing, adding or altering sections of the DNA sequence

Metagenomics

analysis of total microbial genomes in environment. biggest challenge is the sheer amount of data being collected.

Some microorganisms can alter characteristics of certain surface proteins, allowing them to avoid detection by the host's immune system. This phenomenon is called?

antigenic variation

what strategy is used relies on a graphical method to determine an organism?

biochemical tests relying on dichotomous key

An origin of transfer is encoded by _______.

both mobilizable and conjugative plasmids

how can phage DNA be incorporated to infected?

can incorporate phage DNA directly into host DNA and become apart of host's genome. will be replicated and passed onto other cells. (prophage)

major examples of transposon transfer?

can yield vancomycin resistance to staph. aureus

bacteria that can take up things from an outside environment is considered what?

competent

The F or fertility plasmid contains genes that are required for bacterial _____.

conjugation

what does conjugation require?

contact between donor and recipient cell

microorganisms can be classified informally as well, examples?

lactic acid bacteria anoxygenic phototrophs, endospore formers, sulfate reducers

strategies to identify organisms

microscopic examination, culture characteristics, biochemical tests, nucleic acid analysis, patient symptoms

is WGS more or less advanced than RFLPS

more advanced

competent bacteria qualities (I.E. origin and frequency of competence)

most bacteria take up DNA regardless of origin / some only accept DNA from closely related bacteria. some species always competent while others become under certain conditions. F+ cells contain F plasmid while F- cells do not

recombinant cells contain what?

properties of each of the original strains from horizontal gene transfer

transposons characteristics?

provides a mechanisms for DNA to move. considered jumping genes because the gene can move from one are to the next within the cell.

DNA-DNA hybridization (DDH)

relatedness of organisms determined by similarity of nucleotide sequencing. Bacteria strains that are 70% similar are considered the same species.

Antibiograms

reveals differences in susceptibility to antimicrobial medication. - grown on agar - placed on laced antimicrobial agar - if cells susceptible then zones around them form

Taxomic Hierarchy

species, genus, family, order, class, phylum, kingdom, domain

core genome

the DNA of a species conserved across all genomes of the species.

what is the unit of species?

the most basic unit

serological testing

use antibodies to detect specific molecules. most useful surfaces include cell wall, capsule, flagella, pili

can certain types of phages insert their DNA into host chromosome?

yes

can resistance to medications spread quickly within bacterial populations?

yes, through r plasmids that are conjugated with large host range.

signal transduction

transmisson of information on the outside of cell to the inside of the cell.

Phenotypic methods

the tests methods have been largely replaced by methods that relay on DNA data. Phenotypic methods still important since it provides foundation for microbial identification.

conjugation is what?

the uptake of DNA via cell to cell contact

how is horizontal gene transfer used from scientists?

they use the HGT process to intentionally move DNA from one organism to another. those cells are called recombinant and have properties of both original strains

bacteria transfer via phage is called what?

transduction

bacterial transformation applies what method of gene transfer?

transformation

what transfer is naked DNA taken from environments?

transformation