Detection is key to the cure

raviolirookeryBiotechnology

Oct 2, 2013 (3 years and 11 months ago)

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Be a LifeSaver: Detection is the Key to a Cure


10
th
-
11
th

graders
,
Biomedical Fundamentals


In partial fulfillment of the requirements for


TTE596c

Summer 2012





SCENARIO




When you here the word “Cancer” what feelings do you experience? The
thought of you or someone
you know having cancer can be devastating. According to the American Cancer Society, half of all
men and one
-
third of all women in the US will develop cancer during their lifetimes. This means the
likelihood of one of the 100 pl
us forms cancer directly or indirectly affecting your life is very high.
Knowledge could be the key to survival.

In normal cells damage to DNA is either repaired or the cell dies. In cancerous cells this regulation
does not occur and the cell continues t
o divide uncontrollably. Normal cells are polite and will stop
multiplying when they touch another cell. Cancer cells are rude and will continue dividing to form
tumors. Sometimes the cancer cells migrate (metastasize) to other areas of the body and form
s new
tumors comprised of cloned cells from the original cancer cell.

Today, millions of people are living with cancer or have had cancer. The risk of developing many
types of cancer can be reduced by changes in a person’s lifestyle, for example, by stayin
g away from
tobacco, limiting time in the sun, being physically active, and healthy eating. There are also screening
tests that can be done for some types of cancers so they can be found as early as possible


while
they are small and before they have spre
ad. In general, the earlier a cancer is found and treated, the
better the chances are for living for many years. But is the same treatment the best for everyone?

You are a scientist that works in the Research and Development department at a well
-
known
biotechnology business

known for developing diagnostic tools for various cancers
.
A
person you love

has been

diagnosed with cancer and comes to you for advice on what type of treatment they should
undergo.

You are charged with developing a diagnostic too
l (probes and antibodies) to determine the
characteristics of your relative’s cancer so that you can suggest what the best treatments they should
consider.



Images?



Stage 1


Desired Results

Established Goals


Arizona Bioscience CTE
Standards & MC:

10.0

Demonstrate
understanding and knowledge
of cell biology techniques

10.1 Isolate and characterize cell
lines

10.4 Use microscopes

10.5 Perform cytological tests,
i.e. sectioning and staining

14.0 Demonstrate use of
bioinformatics resources

14.1
Identify databases for
sequence analysis (NCBI)

14.2 Utilize electronic
databases/websites (NCBI)

14.3 Identify unknown sequences

14.4 Recognize relationships
between sequences

15.0 Demonstrate
understanding and knowledge
of nucleic acid techniques

15
.1 Detect specific nucleic acid
sequences

15.8 Use sequence database


Arizona High School Life
Science Standards:

S4C2PO1 Analyze the
relationships among nucleic acids
(DNA, RNA), genes, and
Transfer



Student will be able to (SWBAT) use bioinformatics resources
(HUGO, NCBI, UCSC) to design probes and antibodies to enable
a diagnosis and recommendation of a
possible treatment of a
patient.



Student will be able to analyze cells us
ing a microscope to
evaluate characteristics involving presence of gene, mRNA and
protein production.


Meaning

Understandings



Bioinformatics involves using
online databases and
tools to
analyze nucleotide sequences,
RNA, and proteins.



Nucleotide

sequences
code for
mRNA and protein.



Probes can be designed to
target (recognize) specific
nucleotide sequences and
RNA.



Probes and antibodies are
used as diagnostic tools for
specific ca
ncers.



Probes and antibodies used in
identifying nucleotide
sequences are fluorescently
labeled to visually be seen
through a microscope.


Essential Questions

How do structures of biologically
important molecules (i.e. nucleic
acids
-
DNA & RNA, proteins)
account for their function?


Acquisition

chromosomes

S4C2PO2 Describe the molecular
basis of heredity,
in viruses and
living things, including DNA
replication and protein synthesis






Student will know that unique
nucleotide sequences of ~100
bp are needed to design a
probe.



Student will know that
nucleotide sequences and
mRNA are recognized by
probes and proteins by
antibodies.



Student will
know “Molecular
Biology Central Dogma”
(DNA

RNA

Protein)

and
variations
that
occur
.



Student will know how cell’s
communicate.




Student will use the
appropriate bioinformatics
resource (HUGO, NCBI,
UCSC) to accomplish a certain
task.



Students will analyze
slides
and distinguish between
cancerous and noncancerous
cells based on qualitative
microscopic observations (# of
gene copies, overexpressed
RNA, excess protein
production).






Stage 2
-

Assessments


Performance Task (in GRASPS format)


Goal:



Your challenge is to develop diagnostic probes and antibodies to help a relative
and their doctor
determine
the specific form of cancer they have and
what treatment they should be undergoing
.


Role:



You are a scientist in the Research and Development lab o
f a major biotechnology company.

Audience:



Your need to inform your relative and their doctor as to the genetic and molecular basis of the
cancer.

Situation:



The challenge involves using bioinformatics to design diagnostic tools in the form of probes and
a
ntibodies.

Product, Performance, and Purpose:



You will develop probes and antibodies specific to the DNA, mRNA, and proteins that are being
over expressed by you relative due to their
cancer.

Standards and Criteria for Success:



Your product must meet the f
ollowing standards:

o

Use HUGO to determine the official name of the gene of interest

o

Use a genome browser, NCBI or UCSC, to determine the gene sequence

o

Determine a probe specific to the gene of interest and produce a
FASTA

result sheet
verifying that the p
robe sequence is unique only to the gene of interest

o

Research and determine a possible protocol of treatment best suited for your relative.


Other Evidence: (quizzes, tests, prompts, work samples, labs, etc.)



Labs:

o

Using HUGO to Find Official Gene Name

o

Using NCBI or UCSC to Isolate the Gene

o

Designing a Probe for Detection of the Gene



Prompts:

o

Why, other than determining if a gene is present, is gene detection so important in
determining a form of treatment for patients?

o

Why is it important to determine t
he official name (acronym) of a gene?

o

Which gene browser did you prefer? Why?

o

What are the important aspects to keep in mind when designing a probe? How can you
increase probe specificity?


Student Self
-
Assessment and Reflection



Entries in Lab Books



Reflections in Journals



Peer Evaluations of Probes




UNIT MAP








Stage 3


Learning Plan



1.

Begin with the scenario and pose the question
, “What would you
do to save a loved one?” to hook the students into the
importance of research.
H

2.

Introduce the students to the Essential Question and discuss

the unit performance tasks

and rubric
.
W

3.

Ask st
udents brainstorm three questions: (1) What are the
key
concepts of the Central Dogma of Molecular Biology

and how

do they interact with each othe
r?

(2)
Wha
t is Cancer? (3) What
is Bioinformatics? Their responses will act as a pre
-
assessment
of prior knowledge and potential misconceptions.
R, E2

4.

Students view, “What is Cancer?”, video and select one of the
suggested cancer readings to review.
Stud
ents complete a
journal entry summarizing video and reading they selected. In
the entry they should include what they learned and what
questions they still have about cancer.
E

5.

Class discusses
results of
previous brainstorming

activity and
reflects on revisions that should be made to clear up any
misconceptions. Teacher addresses misconceptions not
resolved by students’ reflection.
E, R, E2

6.

Students think of someone they actually knew that has or had
cancer. The then complet
e the
HUGO online activity for

example gene (HER2) and for the gene they researched to get
the official name and acronym. Students can follow written
instructions or open video and follow along as they are working
through the process.
E, T

7.

Next students
will complete the Finding a Sequence Using
NCBI or UC
SC for their gene of interest.
Students can follow
written instructions or open video and follow along as they are
working through the process.
E, T

8.

Students perform a BLAST or BLAT with the FASTA form
created for their gene.
E

9.

Students analyze genes and determine the best probes based
on BLAST/BLAT following written instructions.
E

10.

Students peer
-
review another student’s work on Steps 7
-
9 and
discuss

areas of improvement if needed.
E2

11.

Students repeat steps 7
-
10

for RNA.
E

12.

Students reflect back on DNA and RNA sequences and write
relationships between the two in their journals.
E, R

13.

Students
show printout of and
explain their findings to the
teacher.
(Note: Teacher collects and reviews students’ results
of HUGO, Finding a Sequence Using NCBI or UCSC,
BLAST/BLAT, and probe design. Based on student
’s

explanation, teacher clears up misunderstandings or gaps on a
s
tudent
-
by
-
student

basis.
E2

14.

Students analyze teacher
-
prepared slides of HER2+ cancer
slides for DNA and RNA and write in their journal how the two
Pre
-
Assessments

What pre
-
assessments will you use to
check student’s prior knowledge,

skill
levels, and potential misconceptions?




Prompt: What are the key concepts
of the
Central Dogma of Molecular
Biology?



Prompt: What is Cancer?



Prompt
:
What is
Bioinformatics
?


Progress Monitoring

How will you monitor students’ progress
toward acquisition, meaning, and
transfer, during lesson events?




Student progress will be
monitored
through:



Verbal questioning of students
throughout activities.



Products of bioinformatics labs



Analysis of tissue slides.


slides compare and what that tells about the relationship
between DNA and RNA. (Teacher checks journal entri
es and
determines basis of class discussion to follow.)
E, R, E2

15.

Class discussion of alterations to Central Dogma that was
presented in a simplified form in previous year.
R

16.

Students are asked to reflect and answer the question, If a
treatment is found of a type of cancer, should everyone with
that cancer get that treatment? Why or Why not?

Student

writes reflection in their journal.

E, R

17.

Class discussion of why personalized

medicine comes into

play in this case and why knowledge is power.
E








What are potential rough spots and

student misunderstandings?


Common genetics misunderstandings
include the following
ideas:



Every aspect of the biology of an
organism can be predicted from its
genes.

o

It is much more complicated
involving expression of genes
and regulatory pathways.



The relationship between genes an
d

proteins as
one
-
gene

codes for one
protein.

o

In
actuality, one gene can
code for more than one
protein.



Genes are uninterrupted sections of
DNA that only code for a single
protein.

o

This negates the
understanding of introns and
exons.



The

sole function of genes is to code
for proteins, with the non
-
codin
g
remainder being "
junk DNA. "

o

However, it now appears that,
although protein
-
coding DNA
makes up barely 2% of the

human genome,

about 80% of
the bases in the genome may
be being expressed, so the
term "junk DNA" may be a
misnomer
.



The Central Dogma (DNA


RNA


Protein) no longer is the rule
.


o

Genes


Gene expression


Proteins


Metabolic
pathways


Sub
-
cellular
structures


Cells


Tissues


Organs


Organisms

o

Epigenetics
also
comes into
play
.



How will students get the feedback they
need
?



Verbal
Feedback (From Teacher &
Peers)



Writ
ten Feedback on Assessed Labs
Activities


• Are all three types of goals (acquisition, meaning, and transfer) addressed in the learning plan?

Yes


• Does the learning plan reflect principles of learning and best practic
es?

Yes


• Is there tight alignment with Stages 1 and 2?

Yes


• Is the plan likely to be engaging and effective for all students?

I hope so.





APPENDICES





3D Medical Animation
-
What is Cancer?



Hallmarks of Cancer



Hallmarks of Cancer: The Next Generation



Roots of Cancer



Understanding
C
ancer Video



HUGO Instructions



HUGO Instructional Video



Finding a Sequence

Using

NCBI & UCSC Instructions



Finding a Sequence Using NCBI & UCSC Video



DNA Probe Design Instructions



Bioinformatics Mindmap



Unit Rubric