unit 1 how to fight an infection. bioinformatics the collection, classification, storage, and...

Unit 1 How to Fight an Infection

Bioinformatics

• The collection, classification, storage, and analysis of biochemical and biological information using computers especially as applied in molecular genetics and genomics

• Sue and the outbreak of Neiserria meningitidis – We collected information from individuals to try to

track the infection

BLAST

• We identified the possible organisms infecting the college students with BLAST

• http://blast.ncbi.nlm.nih.gov/Blast.cgi– Provides you with a match to your sequence of

DNA.– The higher the percentage, the greater the match

that it is that organism.

ELISA

• Enzyme-linked immunosorbant assay– Quantitative and Qualitative results– http://www.sumanasinc.com/webcontent/animati

ons/content/ELISA.html

Attack of the Superbugs

• 1.2.2 - This activity investigates the mechanisms by which DNA from one bacterial cell is transferred to another bacterial cell.– This process is called CONJUGATION.

Attack of the Superbugs

• To see if we can induce conjugation making an antibiotic resistant bacterium

• We are using two strains of Escherichia coli– Strain 1 – has a gene on its DNA that codes for

streptomycin resistance– Strain 2 – has a gene found on the plasmid DNA

that codes for ampicillin resistance.

Results

• We had growth on three plates.

• If conjugation had not occurred, we would not have seen growth on the plate with strep and amp in it. Plasmid was conjugated.

Transduction and Transformation

• Transduction is the process by which DNA is transferred from one bacterium to another by a virus

• Bacterial transformation is the process by which bacterial cells take up naked DNA molecules from the surrounding media.– Not sure how this occurs.

Antibiotic Resistance

• Lab showed how bacteria can establish antibiotic resistance.

• Bad!

Hearing Loss

• Put a pic of the ear on your sheet with structures labeled– Sensionuerial vs conductive• Related to the use of Sue’s use of antibiotics due to

Neiserria meningitidis

• Conductive hearing problems are those that disrupt the conduction of sound through the outer and middle ear.

Conductive Hearing Loss

• Affects hearing before the sound reaches the cochlea and the nerve receptors of the inner ear.

Sensorineural deafness

• Sensorineural deafness is decreased hearing or hearing loss that occurs from damage to the inner ear, the auditory nerve, or the brain.

• Sensorineural hearing loss is most often due to a loss of hair cells (sensory receptors in the inner ear).

Treatment

• Cochlear Implant• Hearing Aid

Causes of Conduction Deafness

• Otitis Media• Middle ear infection• Chronic suppurative otitis media –

1.Peferation of the tympanic membrane

2. Bacterial infection

l

Otosclerosis

• Ossicles of the middle ear harden and become less able to vibrate.

Otosclerosis

• Approximately one-third of all persons with impaired hearing have this condition.

• Hereditary• Damage to the ossicles, e.g. by serious infection or

head injury. • Perforated (pierced) eardrum, which can be caused

by an untreated ear infection (chronic suppurative otitis media), head injury or a blow to the ear, or from poking something in your ear.

Interventions

• Hearing aids -usually effective for conductive hearing loss.

http://www.nlm.nih.gov/medlineplus/ency/imagepages/8685.htm

Vaccines – 3 major, out of 6

• Types of Vaccines– Attenuated – live virus, slightly weakened,

changed so that you get an immune response but not the disease

– Killed – virus is dead but still elicites an immune response

– Toxoid - vaccine is designed to trigger an immune response to a toxin produced by a bacterium or virus, not to the organism itself.

Unit 2 How To Screen What Is in Your Genes

Genetic Testing

• Genetic testing is the use of molecular methods to determine if someone has a genetic disorder, will develop one, or is a carrier of a genetic illness and involves sampling a person’s DNA and examining the chromosomes or genes for abnormalities.

• 2.1.1. Genetic Counselor• 2.1.2 Screening our own genes - PTC gene– PCR• http://www.sumanasinc.com/webcontent/animations/

content/pcr.html• Know the steps and the temps for each step

• 2.1.3 Restriction Enzymes– What are they– Sticky vs blunt- SNPs

2.2

• Gene Therapy– Gene therapy is the practice of inserting functional

genes into a person’s genome to replace faulty genes

– Viral Vectors vs Non-viral• Viral – can be engineered, enters cells easily but can

cause an immune response• Non-viral – plasmids, don’t enters cells as easily

2.3

• Reproductive Technology– in vitro fertilization (IVF) – preimplantation genetic diagnosis (PGD)

Unit 3 How to Conquer Cancer

3.1• Regulation in the cell cycle

• Proto-oncognes become oncogenes through a disruption in the cell cycle.

• Normally, cells will detect a mutation or that a certain point in the cell cycle has been disrupted and cause the cell to undergo apoptosis

• Oncogenes lead to cancerous cells

DNA Microarray - What Are They?

• Technology in which the activity (whether a gene is turned on or off) of thousands of genes can be measured.

• mRNA is attached to the wells• Conjucated with cDNA (complimentary) along

with a flourescent tag.• Color that is emited is detected.• Detects for the level of expression of mRNA

3.2 Cancer Screens and 3.3 Treating Cancer

• Why do we do screens?• How do we treat cancer?– Radiation– Chemotherapy– Biofeedback therapy

3.4 Building a Better Cancer Treatment

• Personalized Medicine– SNPS, haplotypes– How do you determine which medication to give

looking at SNPs?

Clinical Trials

• Random• Double Blind **• Orphan• Single Blind

Nanotechnology

• What can nanotechnology do?• How can we use it in cancer?

Unit 4 How To Prevail When Organs Fail

• GFP Lab– Why hdyrophobic column– Why CaCl2 and heat shock– Why lysozyme– Why binding buffer

ESRD and Organ Transplantation

• Know the tests that are used to diagnose ESRD

Kidney Vs Heart Transplant

• Both are used for patients that are ill and in need of an organ.

• Both must utilize tissue typing.• Both can have organ rejection.

Heart Transplant

More extreme of a surgery Kidney = laproscopicHeart = opening entire chest cavity

Blood has to be rerouted during surgery to a bypass machineKidney = just clamp the vessels to the kidney that is to

be removed Longer recovery time Needs to be performed ASAP vs wait time on a

kidney – WHY?

Transplantation of Other Tissues

Which of the following can we currently transplant?HeartIntestineKidneyLiverPancreasLungBone/TendonsCorneaSkin

• Which of the following organs is the only organ that can regenerate itself?– Heart– Intestine– Kidney– Liver– Pancreas– Lung

The Liver!

• A portion of a liver can be transplanted and can grow while the donor ‘s original liver can grow back to normal as well.

Those Involved

AnesthesiologistProvides medicine to put patient under during surgery

Transplant SurgeonSpecializes in the transplant of a certain organ

Preoperative NurseWorks with the surgeon handing her tools and provides

help when needed Pharmacist

Provides ant-rejection medication to patient after surgery

Xenotransplantation

• Using animal parts for humans– Plenty of animals, plenty of parts

• Problem – we can reject the organ (HLA)– Introduction of animal viruses into humans

• Problem – clone the animals – can lead to inferior structures

Tissue Engineering

• Using patients cells to grow organs and tissues in the lab– Could grow a replacement organ??– Bladder would be easier than intestines – due to

the multiple functions of intestines• What are some negatives?http://science.howstuffworks.com/genetic-science/cloned-organ-transplant.htm