BIO 115

The collection of microbial organsims within a community.

By sequencing the 16S rRna

Becuaes it is key for protein synthesis and conserved in all organsims.

2 regions: conserved regions and variable regions

Variable regions ideal for phylogenetic separation

In 16S rRNA amplicon sequencing -> amplification of bacterial 16S rRNA genes

In shotgun metagenomics -> No DNA amplification -> the entire genetic material is sequenced

There is high variation in the composition of the human microbiome between individuals at all body sites. However, the functions performed are constant across individuals.

Significant and long-lasting drop in microbiome diversity -> Antibiotic resistance persists in the microbiome after treatment

Dietary shifts induce changes in the microbiome in composition and diversity

There is a suggested connection between the microbiome, the gut and the brain. Western diet can negatively affect neurological functions.

Changes in the human microbiome can lead to dieseases

e.g. changes in the skin microbiome can lead to acne vulgaris, atopic dermatitis, psoriasis

Microbial imbalance inside the human body

Top-down approach -> Complex sample -> sequencing -> descriptive analysis -> correlation with health and disease

Bottom-up approach -> assembly of defined communities -> ecological dynamics -> evolutionary dynamics -> identify forces that lead to stable and healthy microbiomes

Oncogenes -> mutations lead to uncontrolled growth

Tumour suppressor genes -> mutation leads to damaged cells that are not killed or stopped in growth 

DNA repair genes -> mutation leads to DNA errors remaining unchecked

Increased chromosomal instability

Because mutational pathways differ -> giving raise to multiple lineages within a tumour. A tumour is an eco-system of interacting lineages with room for social interactions e.g. competition, cooperation etc.

Cell line A gives services to other cell lines -> tumour growth, metastasis, angioinvasion

Killing the cooperating cell lines results in a larger regression than killing selfish cell lines as the neutral cells are no longer provided with their services.

Diet

Radioactive radiation

Smoking

UV exposure

Infectious diseases

Chemical exposure

1) DNA double strand breaks: recombination during meiosis is beneficial for genetic shuffling -> can lead to chromosome instability in mitosis

2) Tissue regeneration - stem cells -> immortal cells -> high risk to acquire mutations

3) Inflammation -> helps to remove pathogens and repair damged tissue -> causes DNA damage -> increases risk of mutations

Because most people suffer from cancer after their reproductive period -> natural selection is absent or very weak.

There is no correlation between cancer incidences and body mass.

Large animals have much less cancer than they hypothetically shoud.

Large animals also have more copies of the tumour suppressor genes -> better DNA repair systems.

inadequate exposure to pathogens etc. -> insufficient immune priming

Individualized therapy that aims to predict, prevent and treat illnesses targeting to individual needs

Warrant delivery of targeted treatment to the right patient at the right time

Gene expression patterns of a particular tissue or organ, even single cell. Shows the expression level of certain genes -> biomarkers for diseases.

what proteins are produced in a tissue or organ -> biomarkers for disease

Proteins are often enzymes working together in a metabolic network -> biomarkers for disease

naturally occurring molecule -> by which a particular disease can be identified

Digital and standardized version of a patient's paper chart

Study of variation in the benefits / adverse effects of a drug among patients by analyzing their genomic profiles at the molecular level

1) Cystic fibrosis -> 1000 different mutations in the CFTR gene -> mutations are grouped in 6 classes -> specific drug combination depending on the mutational pattern

2) Cancer -> sequencing of the HLA genes -> sequencing of the tumour driver genes -> find drugs that treat the driver genes

State of disequilibrium -> trait that evolved in one environment is maladpative in another environment

integral part of evolution

can occur for cultural and genetic evolution

They happened in the context of selective pressure -> "adaptively relevant past environment"

humans (apes with adaptions)

- bipedal

- brain is 4 times larger