IMSS BIOLOGY
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SUMMER 2013

(A) the population gene pool
(B) phenotypes
(C) an individual’s genotype
(D) allele frequencies in a species
This is because____________...
(Write answer in your notebook.)

• Phenotype is the physical expression of a trait.
• Such physical expression of traits depends on the genotype and the organism’s interactions with the environment.
• How would you categorize phenotypic traits? What are some examples?
Categories
Examples

• Genotypes produce different phenotypes in response to different environmental conditions.
commons.wikimedia.org

• Defined as “ability of individual genotypes to produce different phenotypes when exposed to different environmental conditions” (Pigliucci et al.
2006 and includes:
• ability to modify developmental pathways in response to specific environmental cues
• ability of individual organism to change its phenotypic state or activity (e.g. metabolism) in response to variations in environmental conditions.
• Genetic polymorphisms also exist that may or may not cause phenotypic variation.

• Seasonal polyphenism in butterflies
• Caste polyphenism in social insects
• Environmental sex determination in reptiles
• Predator-induced polyphenism in cladocerans (e.g. Daphnia)
• Phenotypic changes such as acclimation, learning, and immune response
Summer Fall

• Plasticity may be expressed at behavioral, biochemical, physiological, or developmental levels with different degrees of reversibility.
• Not always adaptive—some traits are plastic because of the physiology, biochemistry, or developmental biology of the organism.
• Type & degree of plasticity specific to individual traits and environmental conditions, e.g. a given trait is plastic in response to temperature, other traits are not.
• There is abundant genetic variation for plastic responses in natural populations—makes possible evolution of plasticity by natural selection (and other mechanisms).

(A) Genotype 1
(B) Genotype 2
• (C) Genotype 3
(D) They are all equivalent.

An example of genotypic reaction norms illustrating the concept of phenotypic plasticity.
Pigliucci M et al. J Exp Biol 2006;209:2362-2367
©2006 by The Company of Biologists Ltd

(A)
(B)
(E)
(C)
(D)

• Regulation of expression can occur at any stage in the
DNA-mRNA-protein pathway

• Modification of DNA may up or down regulate gene expression, e.g. chemical modification (“chemical tags”) of DNA, which includes
• DNA methylation – common mode of gene silencing; abnormal methylation patterns are involved in oncogenesis.
• Histone acetylation – allows transcription to proceed; histone deacetylation works with DNA methylation in gene silencing; also, signals DNA to be packed more densely, thus lowering gene expression.

CHEMICAL
TAG
METHYL GROUP
CHROMOSOME
DNA
HISTONE TAIL
GENE
HISTONE TAIL
DNA accessible, gene turned on
HISTONE
DNA hidden, gene turned off
Epigenomic Marks. The epigenome can mark DNA in t wo ways, both of which play a role in turning genes off or on. The first occurs when certain chemical tags called methyl groups attach t o the backbone of a DNA molecule .The second occurs when a variety of chemical tags attach t o the tails of hist ones, which are spool-like proteins that package DNA neatly into chromosomes.This action affects how tightly DNA is w ound around the hist ones.

• When gene is tightly wound around deactylated histones and highly methylated, gene expression is low.
• When gene is loosely wound around acetylated histones and unmethylated, gene expression is high.
• Gene control simulation: http://learn.genetics.utah.edu/content/epigenetics/ control/

• DNA is coiled around histones.
• Tightly coiled DNA is inaccessible to gene reading machinery.
• Methyl molecules bind to DNA and block access to genes.
• Acetyl molecules bind to histones and increase access to genes.
• View video tutorial: http://teach.genetics.utah.edu/content/epigenetics/

• Stably alters gene expression as cells divide and differentiate from embryonic stem cells  specific tissues.
• DNA methylation typically removed during zygote formation (“reprogramming”), then re-established through successive cell divisions during development.
• DNA methylation suppresses expression of harmful DNA sequences that have been incorporated over time (e.g., from retroviral genes).
• Involved in oncogenesis/carcinogenesis.
• Involved in genomic imprinting.

GENOMIC IMPRINTING
• For most genes, we inherit 2 functional copies—one from mom, one from dad.
• Imprinted genes are different— depending on gene, either copy from mom OR copy from dad is epigenetically silenced (occurs during egg & sperm formation).
• Environment has stronger effect on imprinted genes—only one active copy, no back up, so any epigenetic change has greater impact on gene expression.
• Improper imprinting  developmental defects, cancer, etc., e.g. Angelman syndrome (1 in 10,000)-abnormally silenced gene on Chromosome 15 from mother
• Demonstrated in insects, mammals, flowering plants (in mammals, ca. 1% of genes are imprinted).

GENOMIC IMPRINTING –
LIGERS AND TIGONS
• Lions and tigers can produce hybrid offspring in captivity.
• Offspring different depending on whether tiger or lion is the mom or dad:
• Male lion x female tiger  liger
(largest of big cats)
• Male tiger x female lion  tigon
(about same size as parents)
• Another example is horse x donkey
 mule or hinny

• http://learn.genetics.utah.edu/content/epigenetics/intro/

• Includes all the information, other than DNA sequence itself, that is heritable during cell division.
• While DNA sequences remain essentially unchanged throughout the lifetime of an organism, the epigenome changes immensely in response to internal or external environmental cues.

• Far-reaching impact http://systemsbio.ucsd.edu/

• Epigenetic “tags” present on parents’ epigenomes are passed down to offspring.
• Evidence is growing for transgenerational epigenetic inheritance, though mechanisms are not necessarily straightforward.
• Some examples…

• Wildtype and peloric variant are genetically identical—one epigenetic mutation has caused the difference in petal shape. This epimutation is passed on to offspring.

• Caterpillar attack of radish plants can generate defense phenotypes (distasteful chemicals and protective spines) that can last for multiple generations, even in absence of caterpillars.
• Involves DNA methylation, histone modifications, and small RNAs.

WATER FLEA (DAPHNIA)
• Female Daphnia respond to chemical signals from predators by growing protective helmets.
• Offspring of helmeted
Daphnia also born with helmets, even in absence of predator signals.
• Effect continues to next generation, although helmet size decreases.
http://www.nature.com/nature/journal/v401/n6748/fig_tab
/401060a0_F2.html

• Fungicide vinclozolin is used on crops, e.g. grapes.
Feeding vinclozolin to pregnant rats causes lifelong epigenetic changes in pups. As adults, male offpsring have low sperm counts, poor fertility, and several diseases (prostate and kidney disease).
Persists over multiple generations.
• Found abnormally hi levels of methyl tags on sperm DNA.

• Diethylstilbestrol (synthetic estrogen) was drug given to pregnant women to prevent miscarriages during mid-20 th C but discontinued because it caused rare vaginal cancer.
Also associated with increased risk of breast and reproductive cancers in daughters (and sons) and maternal granddaughters.
http://diethylstilbestrol.co.uk/
• Studies in mice suggest DES causes abnormal methylation of genes involved in uterine development; abnormalities present across multiple generations.

• The role of diet as an environmental factor in epigenetic change is area of active research.
• Nutrients from food are turned into methyl groups (along a metabolic pathway) that are ultimately attached to
DNA.

• Diets high in methyl-donating nutrients can rapidly alter gene expressions, especially during early development when epigenome is first being established.
• http://learn.genetics.utah.edu/content/epigenetic s/nutrition/

15 min.

• Factors from your environment, such as diet, physical activity, and stress level, influence the epigenome.

• Growing evidence for influence of mother’s diet on offspring’s epigenome.
• Agouti gene in mammals:
• Unmethylated  yellow fur, obese, prone to diabetes & cancer
• Methylated  brown, thin, low disease risk
• When pregnant yellow mice fed methyl-rich diet  pups were brown, thin, healthy for life

ENOUGH ABOUT MOM, HOW ABOUT DAD?
• Norbotten, Sweden – a small farming village with meticulous agricultural records back to 19 th C.
• Lars Bygren (1980s) uses the records to see how much food was available to parents and grandparents when they were kids.
• Discovered that famine/low food availability for paternal grandfathers when they were 9-12 yo associated with extended lifespan in grandchildren; early death associated with diabetes or heart disease in grandchildren of grandfathers who “gorged” themselves.

• Royal jelly is complex, protein-rich substance secreted from head glands of worker bees.
• The larva destined to be queen is fed lots of royal jelly inside a “queen cup.”
• All larvae genetically identical but royal jelly diet silences Dnmt3 gene which codes for enzyme involved in genome-wide silencing.
• When Dnmt3 gene is active, queen genes epigenetically silenced and larvae become workers.
• When royal jelly turns off Dnmt3 gene, queen genes are active and larva turns into queen.

• Increasing evidence shows the negative impact of environmental pollutants on the epigenome, e.g. BPA
• Pregnant yellow agouti females fed BPA  more yellow, unhealthy babies
• BPA-exposed moms fed methyl-rich diet  offspring predominantly brown (nutrient supplementation counteracted negative effects of BPA exposure)

• http://youtu.be/kp1bZEUgqVI

• Learn Genetics from University of Utah http://learn.genetics.utah.edu/content/epigenetics
/inheritance/
• National Human Genome Research Institute http://www.genome.gov/27532724
• NOVA ScienceNOW http://www.pbs.org/wgbh/nova/education/activiti es/3411_02_nsn.html

• Mechanism of evolutionary change that generates biological adaptation.
• Natural selection drives changes in the heritable components of phenotype that are mediated by differences in individual fitness.
• Phenotypes (thus genotypes) with the greatest reproductive success (highest fitness) are “favored” and become more common in the population.

THE CONCEPT OF FITNESS
• An individual’s fitness is the contribution that individual makes to the gene pool of next generation so depends on that individual’s survival and reproduction.
• The reproductive success of an individual indicates its fitness but is often difficult to measure, so proxies are more typically used, e.g.,
# matings, # offspring surviving to maturity.