BSCI 222 St Leger Final

Stem cells

*Self-renew- make more cells indefinitely

*Differentiation- become other types of cells

*found in almost all tissues

*genetic factors can reverse differentiation & bring back pluripotency in somatic cells

Totipotent

can form an entire organism

pluripotent

embryonic stem cells

*can become any tissue type

multipotent

adult stem cells

*can become specific cell types

hematopoetic

give rise to all blood cells

*found in blood and bone marrow

iPS

induced pluripotent stem cells

*adult somatic cells reprogrammed to behave like embryonic cells and be pluripotent

*introduce master regulator genes (TFs, Oct4, Sox2, Klf4, c-Myc) to reprogram

*could be used to treat diseases and serious injuries to tissues

Brain Organoids

3D tissue cultures

*mimic human brain

*created from pluripotent stem cells

*as of Feb 2025, mini brains that resemble 40 day fetuses have been created

*tend to stay small bc lack of blood supply

Bio-Computing

Use of molecules, DNA & nano materials to create computing structures based on organic materials

Organoid Intelligence (OI)

using brain organoids to do the work of computers

Rat-Mice Chimeras

mix of rat and mice cells

DishBrain

*network of neurons connected to electrodes

*made from human induced pluripotent stem cells differentiated into neurons

*learned to play ping pong

Leber congenital amaurosis

defect in RPE65 gene

*genetic form of blindness

*starting to be treated with genetic engineering

Gene Therapy

*used to treat genetic disorders caused by nonfunctional gene

*delivers missing gene DNA to cells

Gene Therapy Steps

1) insert normal RNA into viral vector

2) virus infects cells cultured from patient

3) viral DNA inserts into chromosome

4) Inject cells into patient

CRISPR

Clustered Regularly Interspaced Short Palindromic Repeats

*made from immune system of bacteria against viruses

*Bacteria remembers viruses it fights, and puts it into CRISPR

*Remembrance is passed to daughter cells, so they know how to fight

CRISPR-Cas9

technique to precisely edit genome

*guide RNA (gRNA) guides Cas9 to target sequence, and Cas9 cuts the genome

Gene Editing

Gene Knockout- non-homologous end joining, leading to random mutations, leading to gene inactivation

Gene Knockin- donor DNA template used as a guide to insert new DNA by homologous directed repeats

Epigenetic Editing- catalytically inactive Cas9 protein (dCas9) fused to epigenetoc enzymes, that use Crispr to alter gene expression

Casgevy

cell based gene therapy

*approved for treating sickle cell in +12 yo

Ex Vivo Gene Therapy

blood stem cells collected fr patient, modiefied w/ CRISPR-Cas9 to correct mutation, and returned to patient in bone marrow transplant

Induced HbF Production

CRISPR disrupts a silencer that shuts off production of HbF

*HbF- fetal hemoglobin helps prevents sickling

Multiplex

providing multiple gRNAs so CRISPR attacks multiple sequences

Desktop DNA Printer

can synthesize 25 genes simultaneously

Xenotransplantation

A transplantation of an organ, tissue, or cells between two different species. ie. Pig->Human

*David Bennet Sr. = 1st person to have heart replaced by genetically altered pig at UMMC, survived 6 weeks

TIGRR lab

Thylacine Integrated Genetic Restoration Research lab

*trying to genetically restore & bring back extinct Tasmanian Tiger

*Only 5% genome difference fr dunnart mouse

Wooly Mammoths

99.6% similar DNA to Asian Elephants

*Crispr used to insert small ears, hair length, color, fat, and blood into Asian Elephant

*anticancer adaptations stop elephant cells from being reprogrammed into iPSCs

*by blocking all p53 in March 2024 they succeeded in making elephant iPSCs

Wooly Mice

gene edited mix of mutations modeled on woolly mammoths in mice

Dire Wolves

Extinct

*99.5% DNA w/ gray wolves

*Edited gray wolf at 20 sites to give a close resemblance to Dire Wolf

Synthetic Biology

writing & programming new DNA on the computer

*create genetic machines from scratch

*gain new insights how life works

Penultimate Biology

build synthetic cells that operate of chemically synthesized chromosomes

*eventually building life forms with new biological functions

Synthetic Cell

one that operates off a chemically synthesized genome

Minimal Bacterial Cell

bacterial cell that only has genes necessary & sufficient for continuous growth under ideal lab conditions

Mycoplasma Mycoides

Syn 3.0

*starting point for minimization

*can operate on 473 genes (half the # of wild bacteria)

*32% of the genes they couldn't identify the function, but are conserved in other species

Unknome

many human genes have unknown functions ~40-50%

Purpose of Minimal Cell

define genetic functions essential for life

*discover unknown functions that are essential

*defragging genome (organizing genes to align that work in common pathways)

*build complex cells with new functions

1st Complex Synthetic Organism

Sc2.0 designed it

*16 yeast chromosomes synthesized to run a yeast cell

*in a computer kept sequences that worked and cut what didn't

*freed codons to make de novo enzymes, biological therapeutics, functionalized biomaterials

*built in scrambling system to allow fast evolution

Synthetic Morphology

making artificial multicellular structures

*initially tweaking morphogens, segmentation genes, TFs, etc.

*create organisms never appeared in evolution

Morphospace

a representation of the possible form, shape, or structure of an organism

Xenobots

"living robots"

*synthetic living organisms spontaneously self assemble fr frog stem cells

*movement, self repair, & self replication

*AI can design most energy efficient configuration

Alpha Fold

program to predict how a protein will fold and it's function

*can make completely new proteins with properties never seen before

RFdiffusion

program that generates new proteins

*can make proteins w/ specific folds, or ones that nestle against the surface of another molecule (binding)

Chroma

diffusion network

*makes proteins that look like english alphabet

ProGen

protein language model

*designed millions of CRISPR protein sequences

Evo 2

focuses on genomes

*can write whole chromosomes and small genomes fr scratch

*includes regulatory sequences to control gene activation

Evo Designer Interface

predict the effects pf mutations in a gene & decipher other features of complex genome

Democratization of Biology

easy access, DIY at home gene editing technology

*website JOVE has videos on bioscience experiments

*Josiah Zayner sells DIY gene editing kits fr his kitchen

Biohacking

A radical do-it-yourself approach to experimenting with the human body for enhancement and augmentation.

Genespace

nonprofit promoting education in molecular bio for all ages

*fee of $100/month to experiment in the lab

*opened by Ellen Jorgensen (refuses to work with pathogens)

DNA arms race

China wants specified genetic weapons first because 90% of it's people are Han Chinese, so it would be very vulnerable if an opposing country got genetic weapons first

Germ-Line Therapy

enhancement gene therapy

*enhancing traits (intelligence or athletics)

*not legal due to ethics

Galton

founded eugenics (selective reproduction to "improve" humans)

*believed social worth = genetic worth (attractiveness, wealth, intelligence, mental illness)

WD Hamilton

primary theoretical inovator in modern evolutionary biology 1995

Eugenics

plan to breed "better" humans like racehorses

*influential 1905-WWII

*Harry Laughlin, Charles Davenport set up offices for eugenics a center for genetics research

*they were supported by Kellogg, Ford, & John Rockefeller

*Feared non white immigrants, interracial marriages, feeble minds, & promiscuity

Replacement Theory

false theory that white populations are being intentionally replaced by non-white people, which fed eugenics movement

*in the 20s eugenicists saw a threat from Asian immigrants & South East Europe

Johnson Reed Act

*1924 law severely restricted immigration

no more than 161,000 a year quotas for each European nation

*racist restrictions designed to stop southern and eastern European and Asian immigrants

*passed laws to block interracial marriages

Negative Eugenics

aimed to eliminate by sterilization/segregation those physically, mentally, or morally "unfit"

*1907 Indiana passed 1st sterilization law in the world

*started by targeting poor white people, by 1950s mostly women of color sterilized

*still hasn't completely gone away (2020 20 women involunatrily sterilized)

Geneticists Manifesto

1939

*23 geneticists demand improving genetic quality (supporting eugenics)

ZipCode

major predictor of life span in the USA

The Passing of the Great Race

Madison Grant's race eugenics book

*Hitler referred to it as his "bible"

*Nazi eugenics led to mass genocide

*FINALLY after WWII people rejected eugenics after disgust at the Nazis

Designer Babies

Lulu & Nana twin sisters

*2018 He Jiankui used CRISPR on the genome of 2 embryos to give HIV resistance

IVF

since 1978

*allows choice of embryo selection ie. one without genetic diseases like cystic fibrosis or Huntington's through

*Polygenic Screening- assesses one's risk of a condition

*can produce multiple viable embryos

*only produces 10-16 eggs

PRS

polygenic Risk Score

*can predict diseases, cancer, disorders, even IQ

*predictions are only probable not guarenteed

Athletic Factors

*Genes

*Environment

*Training

**Drive

NR2B Receptor

in hippocampus

*overexpression allows more efficient processing of neurotransmitter signals

*greatly increases memory but also sensitivity to pain

*many genetically beneficial modifications come with tradeoffs

The Human Genome Project

Goals:

1) Identify all human DNA genes

2) Determine the 3 billion nucleotide sequences of human DNA

3) store info in publicly accessible databases

How achieved:

1) DNA samples collected fr volunteers

2) DNA distributed to genome centers around world

3) mapping, sequencing, & analysis w/ specialized equipment

4) sequences placed in central database

Logic of Genome Sequencing

use sequence overlaps to align sequenced fragments

Contig

set of overlapping fragments that form a continuous stretch of DNA

Earth BioGenome Project

proposes to sequence the genomes of all the Earth's eukaryotic species by 2028

Syntenous

conserved segments in different genomes preserve their order ie. humans, platypus's and chickens have collinear regions on their genomes

Paedomorphic

retaining juvenile traits into adulthood

neoteny

ie. humans resemble a large baby African ape

Allometry

the growth of body parts at different rates, resulting in a change of body proportions

Proconsul

23 to 14 mya

*mixture of Old World monkey & ape

*possible ancestor to rest of apes

*loss of tail due to Alu insertion into TBXT

Sahelanthropus Tchadensis

7-6 mya

*discovered in Chad

*small brain, small canines, brow ridges of later hominids

*suggested close common ancestor to humans and chimps

*bipedal probable

Genetic Differences bt Humans & Chimps

*share 98.8% sequences

*differences 10x the differences than those between pairs of humans

*35M SNPs changes (10,000 changed protein coding genes)

*5M indels & chromosomal rearrangements

*30% of our proteins conserved, rest differ by 1-2 Amino Acids

Tick Tock of the Molecular Clock

rate of change of random mutations

Positive Selection

natural selection that increases the frequency of a favorable allele

*mutations that help reproduction & survival are more likely passed on

HARs

Human Accelerated Regions

*conserved regions on the human lineage that have been mutated by an abundance of substitutions compared to other species ie. chimps

*may influence gene regulation

*frozen throughout mammalian evolution (intense selective pressure), now sudden burst of change in human lineage

hCONDELs

Human Conserved Deletions

*regions of DNA not present in humans but are in other species ie. chimps

*may influence gene regulation

*can achieve rapid evolution/paedomorphism

*can keep juvenile body by losing genes that get to next developmental step

CNVs

Copy Number Variants

*differences in the # of copies of specific DNA sequences between individuals

*may influence protein amount

Katie Pollard

programmed, debugged, & ran computer code to identify human sequences that changed the most compared to chimp, mice, rat, & other genomes

HAR1

encodes a lncRNA

*involved in neurons that develop the cerebral cortex

*undergone 18 substitutions over 118 base stretch

*only 2 changed in 310MY that separates chickens fr apes

Lissencephaly

"Smooth brain"; condition where there is little to no gyri or sulci within cerebral cortex, making thoughts slow like a chimp's brain

HAR2

limb specific enhancer

*unlike chimp's expression in wrists & thumbs

Macroevolution

subtle changes in expression of developmental genes that over long periods of time dramatically change phenotypes

ZEB2

transcription factor

*by delaying expression, early human brain cells can stick together & multiply before specializing into mature nerve cells

*thus differences in cognitive ability come from timing of differentiation even before nerves form

Orthologs

homologous sequences found in different species & inferred to be descended from same ancestral sequence

Paralogs

homologous genes in the same species and arise from gene duplication

Synonymous Mutation

do not alter amino acid sequence of the protein

*often selectively neutral

Non-Synonymous Mutation

does alter the amino acid sequence of the protein

*more likely to undergo selection

Rate of Evolution

*differs in different types of DNA bc mutations occur at random, but they usually only persist in regions with least effect on function

*dN = rate of nonsynonymous

*dS = rate of synonymous

dN/dS = 1 neutral (genetic drift)

dN/dS < 1 negative selection (selection against changes)

dN/dS > 1 positive selection (Darwinian) (selection for changes in sequence)

ASPM

Abnormal Spindle-like Microcephaly associated gene

*regulates # times neuronal stem cells divide

*many amino acid changes in higher primates & additional in humans

*mutations cause microcephaly (smaller brain)

ARHGAP11B

human specific gene

*duplication of ARGHAP11A 5MYA

*regulated by ASPM

*mutations cause microcephaly

*expression gives mice expanded brains

FOXP2

pleiotropic

*transcriptional activator

*affects speech

*human version turns on 116 more genes than chimp FOXP2 in human brain organoids

AMY1

encodes salivary amylase

*higher copy # enhances starch digestion

Sexual Dimorphism

differences bt males & females of a species

*linked to male rivalry/competition

*leads to lrgr size, stronger canines, enhanced fight skills

Homo Erectus

chased prey to exhaustion leading to loss of fur

Alpha Tectorin

ear protein involved in hearing high frequencies

MYH16

2 base deletion 2.4 MYA led to massive jaws shrinking allowing for brains to grow x3

SEMG2

seminal protein gene

*correlates to levels of female promiscuity

Paleogenomics

Study of ancient DNA

*humans, neanderthals, & denisovans probably came fr H. erectus

Admixture Events

interbreeding & genetic exchange played role in emergences of new species repeatedly