Week Four: Introduction to Microbiology

Introduction to Microbiology

I.               Microbiology

a.     The study of microbes

b.     2 Types

                                               i.     Medical

1.     Host response

2.     Diagnosis

3.     Pathogens

                                              ii.     Non-medical

1.     Animal

2.     Plant

3.     Industrial

c.      Microbes

                                               i.     Bacteria

1.     1-8µ in size

2.     Phenotype classification

a.     External structures

                                                                                                     i.     Flagella

1.     Movement with chemical signals

2.     Highly antigenic

                                                                                                    ii.     Pili

1.     Fimbria

2.     Thin, more numerous, for sticking to stuff

                                                                                                  iii.     Capsule

1.     Very virulent

2.     Non antigenic

3.     No host immune response

b.     Shapes

                                                                                                     i.     Cocci – round

                                                                                                    ii.     Baccili – rod

                                                                                                  iii.     Coccobacilli – very short rods

                                                                                                  iv.     Spirochaetes – spiral or coiled

                                                                                                    v.     Vibrios – commas

c.      Gram staining

                                                                                                     i.     Discovered by Gram

1.     Peptidoglycan – thick in gram +, thin in gram -

a.     Positive=violet

b.     Negative=pink

2.     Acid fast – pink

3.     Non acid fast - green

d.     Culture characteristics

                                                                                                     i.     Hemolysis

                                                                                                    ii.     Pigment

e.     Biotyping

                                                                                                     i.     Biochemical reactions

f.      Serotyping

                                                                                                     i.     Antibody and antigen reactions

g.     Antibiogram

                                                                                                     i.     Antibiotic discs

h.     Phage typing

                                                                                                     i.     Outdated

i.       Genotypic classification

                                                                                                     i.     through genetic differences

                                                                                                    ii.     PCR

                                                                                                  iii.     Rickettsia

1.     Must live in cells

2.     Behave like viruses

3.     Gram negative

                                                                                                  iv.     Genus species- Genus capitalized, species lowercase, all italicized

                                              ii.     Viruses

1.     Needs electron microscopy

a.     Not a cell

b.     May have lipid envelope over protein coat

c.      Strictly intracellular

d.     DNA or RNA

e.     Use cells to replicate

f.      CMI effective

                                            iii.     Protozoa

1.     Single cell

2.     Parasite

3.     Mostly free living

                                            iv.     Helminths

1.     Worms

2.     Macroscopic

                                              v.     Fungi

1.     Yeasts

a.     Oval, round, budding

b.     Rigid cell wall

2.     Molds

a.     Rigid cell wall

b.     Fillamentous

                                            vi.     Microbe Human Host Relationships

1.     Commensals – normal flora

2.     48-72 hours commensals change completely

3.     Short term commensals that become infectious

Week Four: Biotechnology and Genomics

I.               Biotechnology and Genomics

a.     Vocabulary

                                               i.     ADA – adenosine deaminase deficiency

                                              ii.     SCID – severe combined immunodeficiency disease

                                            iii.     Etiological determinants – Factor that causes a disease

b.     Biomarkers

                                               i.     Disease presents overt symptoms and biomarkers

                                              ii.     Any substance that can tell us about the disease state is a biomarker

1.     Metabolites, nucleic acids, proteins, antibodies

                                            iii.     Nucleic acids

1.     Analyze with probes, hybridization

2.     Using a target sequence

3.     Amplification (PCR)

4.     Denature +renature

5.     Probe

a.     ssDNA –radioactive, fluorescent, enzyme, etc.

b.     Complement to the probe

                                            iv.     PCR

1.     2 primers, opposite direction

2.     Amplify DNA via DNA polymerase and dNTPs

a.     Denature

b.     Anneal primers

c.      Extend

d.     Geometric amplification

e.     Impure DNA okay

f.      Assay time<1 day

g.     Gel electrophoresis

                                              v.     Gene chips

1.     Quickly analyze thousands of samples

2.     Mark DNA, scan for pattern

3.     Strain typing

a.     More sensitive diagnosis

                                            vi.     Recombinant DNA

1.     Vectors used to carry target

2.     Autonomous

a.     Viruses

b.     Plasmids

3.     Steps

a.     Isolate DNA

b.     Mix DNA

c.      Ligate DNA

d.     Ligate DNA

e.     Transform host

4.     Applications

a.     Produce hormones and vaccines

b.     GM (genetically modified)

c.      Protein content

5.     Animal recombination

a.     Relies on in vitro fertilizations

b.     Some proteins need to be in the right cell to fold properly

c.      Milk proteins – “Pharming” pharmaceutical farming

c.      Gene therapy

                                               i.     Deficiency

1.     How to get genes where they need to be?

2.     ADA

a.     Ex vivo approach

b.     Single gene

c.      Constitutive

d.     Amount not precise

e.     Lymphocytes easy targets

                                              ii.     Curing acquired

1.     Cancer

2.     HIV

                                            iii.     DNA Vaccines

1.     Introduce DNA encoding for a vaccine

d.     Genomics

                                               i.     Genome – the entire DNA sequence

                                              ii.     Genomics vs. Genetics

1.     Genes vs. entire genome

                                            iii.     Genome projects

1.     Massive sequencing

a.     Usually involves many people and companies

b.     Sequenced 3.2 billion base pairs from 1990-2003

                                            iv.     RNA + Protein expression

1.     Transcriptionomics

2.     Proteomics

                                              v.     Effects

1.     Describe genes

2.     Develop diagnostics

3.     Treat and cure

a.     Disease has a genetic basis

                                                                                                     i.     Mono/polygenic

                                                                                                    ii.     Epigenetic