Download A golden fish reveals pigmentation loss in Europeans EG

Teacher Resource for:
SLC24A5, a Putative Cation Exchanger, Affects Pigmentation in
Zebrafish and Humans.
Table of Contents:
I.
GENERAL USE OF Science in the Classroom
a. Student Learning Goals (general)
b. Using this Resource
i. Learning Lens
ii. Learning Notes
iii. References
iv. Thought Questions
c. Suggestions for Classroom Use
II.
ARTICLE-SPECIFIC MATERIALS
a. Student Learning Goals (specific)
b. Connect to Learning Standards
c. Summary of the Article for the Teacher
d. Discussion Questions
e. Related Multimedia Resources from HHMI|BioInteractive
GENERAL USE OF Science in the Classroom
Student Learning Goals:
“One fundamental goal for K-12 science education is a scientifically literate person who
can understand the nature of scientific knowledge.”1
The U.S. National Academy of Sciences defines science as: “Any new finding requires
independent testing before it is accepted as scientific knowledge; a scientist is therefore
required to honestly and openly report results so that they can readily be repeated,
challenged, and built upon by other scientists. Proceeding in this way over centuries,
the community effort that we call science has developed an increasingly accurate
understanding of how the world works. To do so, it has had to reject all dogmatic claims
based on authority, insisting instead that there be reproducible evidence for any
scientific claim.”
An important student learning goal, central to any understanding of “the nature of
scientific knowledge,” is to give each student an appreciation of how science is done.
This includes knowing why:
 Scientists must be independent thinkers, who are free to dissent from what the
majority believes.
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Science can deal only with issues for which testable evidence can be obtained.
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All scientific understandings are built on previous work
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It is to be expected that one scientist’s conclusions will sometimes contradict the
conclusions of other scientists.
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Science is a never-ending venture, as the results from one study always lead to
more questions to investigate.
1
A Framework for K-12 Science Education, National Research Council, 2012
Using This Resource
Learning Lens:
The Learning Lens tool can be found on the right sidebar of each resource and is the
source of annotations. Click on the headings to highlight portions of the text of the
corresponding research article. A subsequent click on the highlighted text will produce
a text box containing more information about that particular piece of text. Below is an
example of the Glossary function of the Learning Lens.
An example of the resource with the Glossary, Previous Work, Author’s Experiments,
News and Policy Links, and References and Notes tools turned on. The Glossary tool
is in use.
Learning Notes:
Learning Notes accompany each figure and are designed to help students deconstruct
the methods and data analysis contained within each figure.
References:
The Reference section of each resource is annotated with a short statement about how
or why each reference relates to the current research study.
Thought Questions
Thought Questions are located above the Learning Lens in the right sidebar of each
resource. These questions were written to be universal and applicable to any primary
research paper. Thought questions do not have a single answer, or a correct answer
for that matter, and can be used to stimulate discussion among students.
Suggestions for Classroom Use:
In addition to the thought questions discussed above, other resources are provided for
use in the classroom. These can be found toward the end of the teacher guides
associated with each specific article and include:
1. Discussion questions specific to the article, related to the standards, and/or
associated with the figures.
2. Activities tied to the articles.
Some ways to use the Science in the Classroom articles:
1. Assign to student groups to read and discuss during class.
2. Assign small sections of the article to student groups to read and discuss during
class, with the expectation that they will present or use jigsaw to teach the entire
class what is in their part of the article.
3. Assign to individual students to complete during class or as homework.
4. Assign reading as an extra credit project.
Some ideas for interactive student engagement after reading the article:
1. Students write answers to discussion questions (for example, those linked to the
standards or those linked to the diagrams).
2. Go over the abstract, as well as information about the purpose and structure of
an abstract, and have students write their own abstracts for the articles in
language that could be understood by their peers.
3. Have students edit the article, or parts of the article, to a simpler reading level.
4. Have students, alone or in small groups, use the annotated list of references to
explain how the scientists who wrote this article built on the published work of at
least one independent group of scientists in making their discoveries. In the
process, did they produce data that supports the findings of the earlier
publication that they have cited in the text? In what way does this article support
the statement that scientific knowledge is built up as a “community effort”?
5. Use the article and discussion questions linked to the standards and the
diagrams for a teacher-led classroom discussion. The discussion can focus on
the nature of science and scientific research, as well as on the science in the
article itself.
6. Have students give a classroom presentation about the article, parts of the
article, or their answers to discussion questions.
ARTICLE-SPECIFIC MATERIALS
Connections to the nature of science from the article
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Approaches used to map and test slc24a5 as the golden gene have been around for
more than 10 years, but nobody had completed the work.
Although the effect of the human SLC24A5 allele on skin pigmentation is large, it
does not account for all skin color variation, even together with other known genes.
This paper required the expertise of many scientists from different fields using
different experimental approaches.
Conservation of certain traits, like pigmentation, in organisms other than humans
means these organisms can be used as models to understand human traits.
Large phenotypic differences can be caused by minor changes in gene sequence,
which in turn can change the protein amino acid sequence or the amount of gene
expression.
The study created a testable model for the role of calcium in melanosome function.
The importance of this scientific research
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Clarifies the origin of a common zebrafish mutant that is used to calibrate genetic
screens in vertebrate development.
Identifies a major polymorphism selected for in Europeans that results in lighter skin
pigmentation.
Highlights the merit of collaborative projects such as the human genome project and
HapMap project.
Highlights the relevance of model organisms to the study of human biology.
The actual science involved
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Positional cloning, gene knockdown, and gene rescue experiments to implicate a
particular gene as responsible for a trait.
Microscopy of fluorescently labeled proteins to determine their location in the cell.
The location of a protein helps determine its function.
Comparative genomics: Large-scale sequencing of genomes from geographically
isolated populations can help identify regions that are subject to a certain selective
pressure.
Importance of human test subjects in quantitative analyses: quantifying skin
pigmentation by measuring reflectance, and determining the frequency of genotypes
by genotyping admixed populations.
Connect to Learning Standards:
The National Academies of Science, Engineering, and Medicine Core Ideas of Life
Science
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Evolution and its underlying genetic mechanisms of inheritance and variability
are key to understanding both the unity and the diversity of life on Earth.
The Common Core English and Language Arts Standards
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ELA-Literacy.RST.11-12.4: Determine the meaning of symbols, key terms, and
other domain-specific words and phrases as they are used in a specific scientific
or technical context relevant to grades 11 and 12 texts and topics
ELA-Literacy.RST.11-12.7: Integrate and evaluate multiple sources of
information presented in diverse formats and media (e.g., quantitative data,
video, multimedia) in order to address a question or solve a problem
ELA-Literacy.RST.11-12.8: Evaluate the hypothesis, data, analysis, and
conclusions in a science or technical text, verifying the data when possible and
corroborating or challenging conclusions with other sources of information.
ELA-Literacy.RST.11-12.9: Synthesize information from a range of sources (e.g.,
texts, experiments, simulations) into a coherent understanding of a process,
phenomenon, or concept, resolving conflicting information when possible
The Common Core Statistics and Probability Standards
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Make inferences and justify conclusions from sample surveys, experiments and
observational studies
AP Biology Quantitative Skills
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Looking for trends or associations by determining linear regressions is a key
quantitative skill covered on the AP Biology exam.
Summary of the Article for the Teacher:
It is recommended that this not be used by students in place of reading the article.
General Overview:
Human skin color is a highly variable trait. Human skin cells contain the pigment
melanin, which gives skin its color. In general, individuals with lighter skin tones have
fewer, smaller, and less densely pigmented melanosomes, the melanin-producing
organelles, in their skin cells than individuals with darker skin tones.
To better understand the genetic origin of variation in human skin color, Rebecca
Lamason and colleagues turned to a model organism: the zebrafish (Danio rerio), which
also displays variations in skin color. They identified a gene (called golden) that, when
mutated, leads to more lightly pigmented, or golden, fish. Whereas wild-type zebrafish
have numerous dense, round-to-oval melanosomes in their skin cells, the melanosomes
of golden zebrafish are less numerous, smaller, and less densely pigmented. The
scientists searched for an ortholog (a corresponding gene of similar sequence and
function) of the golden gene in humans. The closest match was a gene called
SLC24A5. Like the golden gene, the SLC24A5 gene encodes a membrane protein that
affects melanosome production.
To determine the gene’s role in human skin color, the researchers searched for
polymorphisms within the gene. They identified one single-nucleotide polymorphism
with two alleles. The G allele, which encodes alanine, is found in most individuals in
African, Indigenous American, and East Asian populations (with an allele frequency of
93% to 100%), whereas the A allele, which encodes threonine, is found in EuropeanAmerican populations (frequency of 98.7% to 100%). They then studied two populations
of recently mixed ancestry, African-American and African-Caribbean, with a range of
skin colors to determine whether allele frequencies correlate with skin pigmentation.
Skin pigmentation was measured using reflectometry, which involves measuring the
amount of light reflected back by an individual’s skin to calculate the melanin index.
Individuals with a higher melanin index have darker skin.
Topics Covered:
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model organism genetics
organelle biology
gene identification
model building
human population genetics
protein function (ion pumps)
Methods used in the Research:
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electron microscopy of melanin-producing tissue
postitional cloning to identify mutated gene
gene knockdown, rescue experiments, and gene expression across tissues
flourescence microscopy for protein localization within cells
large-scale human genotyping
quantification of pigmentation
data analysis and statistics
Conclusions:
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The loss of slc24a5 function is responsible for the reduced pigmentation in golden
zebrafish.
The slc24a5 gene has an evolutionarily conserved function in fish and mammals
(including humans) where it affects melanin pigmentation.
The slc24a5 protein encodes a membrane protein that affects melanosome
formation and the production of melanin. It is probably an ion pump that maintains
ion homeostasis in melanosome organelles.
A human SLC24A5 gene variant that causes lighter skin pigmentation was under
evolutionary selection in ancestors of present-day Europeans.
The variation in human SLC24A5 explains more of the difference in skin
pigmentation between Europeans and Africans than any other gene identified to
date.
Areas of Further Study:
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How human SLC24A5 and other known pigmentation genes work together to
produce the diversity of human skin pigmentation.
The molecular function of the human SLC24A5 protein in melanosome organelles.
Other genes that could explain the remaining heritability of skin pigmentation in
humans (SLC24A5 only explains 25%!).
How skin pigmentation augments physiological processes relevant to human health
(for example the production of vitamin D).
Discussion Questions
1. Do you think the researchers started this project to understand human skin
pigmentation? Why or why not?
2. How did the authors use the genetic variation of another species to better
understand the trait of human skin color?
3. The slc24a5 gene encodes a membrane protein that affects the transport of cations
like sodium and calcium (Na+ and Ca2+) across the membrane. Why was it important
to find out where within the pigment cells of zebrafish the slc24a5 protein was
located?
4. Why did the authors study human populations of mixed ancestry?
5. Based on your background reading, what human ancestry most commonly has the
GG genotype and why? What ancestry most commonly has the AA genotype and
why?
6. How does the amount of melanin in the skin cells relate to skin color?
7. In Figure 6B, the distributions of skin melanin content for individuals of each
genotype overlap. What would you see if only one gene determined skin color?
What can this mean in terms of the number of genes that may be involved in skin
color?
8. What might be a physiological role or function for the range of skin pigmentation?
9. What do the results of this study tell us about the role of genes in determining skin
color?
10. The ancestral G allele of the SLC24A5 gene, which encodes alanine, is found in
most individuals in African, Indigenous American, and East Asian populations,
whereas the A allele, which encodes threonine, is found in European-American
populations.
11. The researchers found that both of these SLC24A5 alleles could restore
pigmentation in golden zebrafish. Because the A allele is associated with lighter skin
pigmentation, why do you think the allele could restore pigmentation in zebrafish?
12. Although the human SLC24A5 gene is only about 20 kb long, the region with
extensive loss of heterozygosity in Europeans (Figure 5) is about 150 kb long. What
is the significance of this difference in length?
13. What are some examples of other human traits that could be studied in model
organisms like zebrafish and mice? Are there any human traits that might be hard to
study in these organisms? How could these traits be studied?
Multimedia Resources from HHMI’s BioInteractive (www.BioInteractive.org)
Animations
How We Get Our Skin Color (http://www.hhmi.org/biointeractive/how-we-get-our-skincolor). This engaging animation shows how human skin cells produce the pigment
melanin and how the type, abundance, and distribution of melanin determines a
person’s unique skin color.
 Interactive Animation with Quiz: http://www.hhmi.org/biointeractive/how-we-getour-skin-color-interactive
Polymerase Chain Reaction (PCR) (http://www.hhmi.org/biointeractive/polymerasechain-reaction). Polymerase chain reaction, or PCR, is a technique for making many
copies of a specific DNA sequence. This animation shows how it works.
Related Topics
DNA Transcription. Using information from molecular research, this 3-D animation
shows how DNA is translated into RNA, an important step in the process of synthesizing
proteins.
 Advanced detail: http://www.hhmi.org/biointeractive/dna-transcription-advanceddetail
 Basic detail: http://www.hhmi.org/biointeractive/dna-transcription-basic-detail
Short Films
The Biology of Skin Color (http://www.hhmi.org/biointeractive/biology-skin-color). In
this film, anthropologist Dr. Nina Jablonski walks us through the evidence that the
different shades of skin color among human populations arose as adaptations to the
intensity of UV radiation in different parts of the world.
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Interactive Video with Quiz: http://www.hhmi.org/biointeractive/skin-colorinteractive-video
Film Guide: http://www.hhmi.org/biointeractive/film-guide-biology-skin-color
Virtual Labs
Bacterial Identification Virtual Lab (http://www.hhmi.org/biointeractive/bacterialidentification-virtual-lab). This virtual lab will familiarize you with the science and
techniques used to identify different types of bacteria based on their DNA sequences.
Classroom Activities
Data Point: Genetic Origin of Variation in Human Skin Color
(http://www.hhmi.org/biointeractive/genetic-origin-variation-human-skin-color). In this
short activity, students interpret and discuss a histogram from the annotated paper
Lamason et al. 2014. The accompanying educator guide includes discussion questions
on the characteristics of the histogram and what it shows.
Biochemistry and Cell Signaling Pathway of the Mc1r Gene
(http://www.hhmi.org/biointeractive/genetic-origin-variation-human-skin-color). An
advanced lesson that requires students to analyze partial DNA sequences of
the Mc1r gene and identify the effects of mutations on the MC1R protein pathway
Human Skin Color: Evidence for Selection
(http://www.hhmi.org/biointeractive/human-skin-color-evidence-selection). This case
study is based on the short film The Biology of Skin Color. Students use real data to
propose hypotheses, make predictions, and justify claims with evidence.
Related Topics
Using Genetic Crosses to Analyze a Stickleback Trait
(http://www.hhmi.org/biointeractive/using-genetic-crosses-analyze-stickleback-trait). A
hands-on activity in which students analyze the results of genetic crosses between
stickleback fish with different traits.
Interactive Tutorials (“Click and Learns”)
DNA Sequence Assembly (http://www.hhmi.org/biointeractive/dna-sequenceassembly). Learn the principles of how DNA is sequenced and assembled into whole
genomes using the Sanger method, shotgun sequencing, or ultra-deep sequencing.
Teacher Guides
Gene Expression (http://www.hhmi.org/biointeractive/teacher-guide-gene-expression).
This curriculum guide assists in filtering through the available resources from
BioInteractive and HHMI on topics related to gene expression, including RNA structure
and function, transcription, RNA processing, translation, and post-translational events.
DNA (http://www.hhmi.org/biointeractive/teacher-guide-dna). This curriculum guide
assists in filtering through the available resources from BioInteractive and HHMI on
topics related to DNA, including DNA structure and function, DNA replication, damage
to DNA, and eukaryotic chromosomal structure.
Image of the Week
Crystals and the Color of Skin (http://www.hhmi.org/biointeractive/crystals-and-colorskin). The panther chameleon alters the arrangement of tiny crystals in its skin to
change color.
Coloring the Past (http://www.hhmi.org/biointeractive/coloring-past). An electron
micrograph of tightly-packed melanosomes in a 55.4-million-year-old fossil bird feather
unearthed in Denmark.
Collections
Biology of Cells (http://www.hhmi.org/biointeractive/biology-cells). Resources for
teaching cell biology, including short films, animations, Click & Learn interactives, and
posters.
DNA (http://www.hhmi.org/biointeractive/dna-collection). A variety of engaging
animations, lecture clips, virtual labs, and other classroom resources teach key
concepts related to DNA’s structure and function.
Genetics (http://www.hhmi.org/biointeractive/genetics). resources for teaching
genetics, including short films, animations, Click & Learn interactives, and classroom
activities.
Evolution (http://www.hhmi.org/biointeractive/evolution-collection). Resources for
teaching evolution, from short films to Click & Learn interactives, and from lecture series
to classroom activities.
Organismal Biology http://www.hhmi.org/biointeractive/organismal-biology Resources
related to biology of organisms, including physiology, anatomy, infectious diseases, and
developmental biology.
Chemistry of Life http://www.hhmi.org/biointeractive/chemistry-life Resources related
to chemistry, biochemistry, and biological macromolecules such as DNA, RNA, proteins,
carbohydrates, and lipids.
Introductory Biology http://www.hhmi.org/biointeractive/introductory-biology
Multimedia resources that enhance college-level biology instruction. Short films,
stunning high-quality animations and data-rich virtual labs impart the thrill of discovery
and illuminate the scientific process.