Human Genetics Final Exam

Forward (Hypothesis-Generating)

Random Mutagenesis (Classical genetics) or Chemical Genetics (diverse small molecules) —> Phenotype of Interest —> Gene or Proteins of Interest

Reverse (Hypothesis-Based)

Targeted Mutagenesis/ Targeted Molecules —> Gene/Protein of Interest —> Phenotype of Interest

In situ Hybridization

exposed to a “probe” based on a specific sequence, labeled probe binds to matching sequence, location of bound probe can be seen by microcrope

Antibody staining

immunostaining to detect protein

use adaptive immune system to create custom antibodies to a protein of your choice

Mutagenesis

Mutagenesis screens using “mutagens” to introduce changes in the genome, which might lead to phenotypic changes

Exogenous (older methods)

• Radiation: X-rays, Ionizing radiation, UV,

• Alkylating agents: ethyl methanesulfonate (EMS), ethylnitrosourea (ENU)

Endogenous (newer methods)

• zinc finger nucleases (ZNF)

• transcription activator-like effector nucleases (TALEN)

• clustered regularly interspaced short palindromic repeats/Cas proteins (CRISPR)

Transcriptomics

• Bulk RNA-seq provide the average measurement for all the cells

✓It does not provide insights into the stochastic nature of gene expression

• Single-cell RNA-seq allows the measurement of the distribution of expression levels for each gene across a population of cells

zygote

fertilized egg

embryology

traditional name of the study of that phase of an organism that exists between fertilization and birth

invagination

involution

ingression

delamination

epiboly

Stages of Developmen

Fertilization • Zygotic genome activation

Cleavage • Lineage segregation • Blastocyst formation & Peri-implantation

Gastrulation

Organogenesis

fertalization

Zygotic genome activation

Clevage

is a series of extremely rapid mitotic divisions that immediately follow fertilization

Blastomeres

During cleavage, the enormous volume of zygote cytoplasm is divided into numerous smaller cells called

blastocyst

By the end of cleavage, the blastomeres have usually formed a sphere, known as

Rotational cleavage

What type of cleavage occurs in humans and most mammals?

Late Cleavage / 1st Fate

Hippo Pathway

y is the switch that translates where a cell sits into what lineage it adopts

Inner Cell Mass

Hippo Pathway- On

Completely surrounded by neighbors (No apical domain)

Cell–cell contact activates Hippo pathway

Trophoectoderm

Hippo Pathway- OFF

✓Exposed to the outside environment → form anapical domain

✓Apical domain contains a complex that inhibits the Hippo pathway

2nd Fate Decision: Epiblast vs Primitive Endoderm (PrE)

✓ Happens within the ICM, after TE/ICM is already set

✓ FGF4/ERK signaling drives this decision

✓ Epiblast becomes the embryonic tissues; PrE becomes yolk sac derivatives

Totipotent

Can differentiate into all possible cell types

Pluripotent

Can differentiate into any of the three germ layers

Multipotent

Can differentiate into a limited number of cell types within a specific lineage or tissue

Gastrulation

Two cell split

2 chorions, 2 amnions

Inner Cell Mass split

2 chorions, 1 amnion

Epiblast split

1 chorion, 1 amnion

Anterior-Posterior

important for defining the head/brain

2 signaling centers

A-P split

1. Anterior Visceral Endoderm (AVE) an anterior hypoblast population

2. Henson’s node (“the organizer”)

AVE and node activity set up gradients

BMP, Wnt, FGF

Their antagonists - Dkk 1, Cerberus, lefty-1

BMP, Wnt, FGF

secreted signaling molecules

Bone morphogenetic proteins (BMPs)

Hox gene

helpful in A-P axis formation and creating somites

Zone of Polarizing Activity (ZPA )

is a region of posterior limb bud mesenchyme in the limb field

Shh (sonic hedgehog)

involved in digit formation (based on time and gradient)

Hox regulatory evolution

Left and Right Axis Formation

Cilia on the Henson’s node

Nodal Pathway and nodal flow

Leftward direction (breaking symmetry)

vesicular particles (containing Sonic hedgehog, RA, Ca+)
Neonatal Primary Ciliary Dyskinesia

Hominids

Chimpanzees and Gorillas are also classed as Hominids • Modern humans share a common ancestor with chimps ~8 mya

biped

able to walk on two feet

No major consensus - but overall it likely wasn't a single environment, but rather the instability and variability of the environment over time

Australopithecines

1. adapting to a diet of nuts and seeds by evolving huge teeth and powerful jaw muscles

2. taller and capable of making tools out of stone

Encephalization

big brain

Homo erectus

migrated out of Africa using land bridge

“Denisovan” and “Neanderthal”

Named after cave systems

Out-of-Africa

“Individuals from African ancestry populations harbour the greatest numbers of variant sites, as predicted by the out-of Africa model of human origins

introgression

inbreeding with Neandertals

The Agricultural Revolution

• Starting around 11,000 years ago, Homo sapiens started to select, breed, and domesticate plants and

animals

• The development of agriculture occurred many times independently

Selection Coefficents

Calculating Relative Fitness

More on selection coefficients

chi-squared

(o-e)2/e

population genetics

is the study of allele and gene frequency distribution and change within populations, driven by fo

modern synthesis

Conditions for Hardy Weinberg Principle

Inbreeding depression

This inbreeding may lower the population’s ability to survive and reproduce, a phenomenon called inbreeding depressio

Genetic Hitchhiking

Gene flow

homogenizing force

ex. adaptive introgression

Pharmacogenetics

The field of research that studies how a person’s genetic makeup impacts how they respond to drugs

precision medicine

What can effect a drug response?

Pharmacokinetics

What the body does to the drug

Pharmacodynamics

What the drug does to the body

Drugs generally produce their effects by interacting with specific proteins, primarily receptorsDetoxification

Detoxification

Phase I

modification

e.g. hydroxylation by cytochrome P450 enzymes

‣ Modifies drug molecule by adding/exposing functional groups ‣ Typically makes drug polar and more water soluble

Phase II

conjugation

e.g. glutathione group added by a glutathione S-transferasP

‣ Drug molecule is coupled to a large chemical group ‣ This further increases water solubility and polarity, often making the metabolite unable to pass through cell membranes

Glutathione S-transferases and UDP-glucuronosyltransferases

Phase III

excretion

e.g. removal from the body via ABC transporters

‣ Transporters move metabolites from cells into urine, bile, intestine

Predicting Metabolizing Types

Metabolizer Phenotypes

Presence / Absence PCR-based Tests

PCR than gel visualization or not

PCR Repeat Length

PCR and visualize size fragments

Quantitative PCR

does allow copy number to be assessed

Quantitative Fluorescent PCR

Interpreting QF-PCR Aneuploidy Data