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BTEC 3301 S15 ResearchProject

By Azzah2 Apr 27, 2015 994 Words
BTEC
 3301
 Spring
 2015
 
Research
 Project
 Description
 

 
For
  your
  research
  project,
  you
  will
  research
  a
  human
  genetic
  disease
  through
  the
  application
  of
 
bioinformatics
 methods
 to
 understand
 the
 disease,
 and
 current
 and
 future
 treatment
 regimes.
 

 
You
  will
  complete
  the
  project
  as
  a
  series
  of
  five
  tasks.
  Each
  task
  will
  be
  assigned
  to
  you
  following
  the
 
completion
 of
 the
 related
 topic
 in
 class.
 You
 will
 turn
 in
 a
 1-­‐2
 page
 report
 for
 each
 task.
 Please
 remember
 
that
 this
 is
 a
 research
 report,
 so
 do
 not
 submit
 a
 list
 of
 one/two-­‐line
 short
 answers.
 You
 should
 write
 full
 
paragraphs
 to
 concisely
 describe
 the
 tasks
 accomplished.
 I
 am
 more
 interested
 in
 your
 interpretation
 of
 the
 
results
 than
 the
 results
 themselves,
 so
 be
 sure
 to
 describe
 in
 detail
 your
 evaluation
 of
 the
 task,
 and
 when
 
appropriate
 the
 statistical
 and
 biological
 significance
 of
 each
 result.
 

 
Please
 be
 sure
 to
 give
 web-­‐links
 (URL
 pointers)
 to
 the
 disease,
 gene,
 bioinformatics
 tools
 and
 all
 references
 
and
 web
 sites
 used
 in
 your
 bibliography
 or
 as
 footnotes
 in
 your
 submitted
 task-­‐reports.
 Also
 please
 be
 sure
 
to
  put
  any
  copied
  material
  in
  quotes
  with
  complete
  reference
  or
  URL
  pointer
  to
  the
  source
  of
  the
  material
 
copied
 in
 your
 paper.
 Failure
 to
 properly
 reference
 source
 material,
 even
 from
 the
 Internet,
 is
 plagiarism
 
and
 is
 considered
 academic
 dishonesty.
 
 

 
IMPORTANT
  NOTE:
  if
  you
  need
  assistance
  with
  writing
  your
  task
  reports
  in
  terms
  of
  writing
  skills
 
related
 to
 logical
 organization
 of
 the
 material,
 vocabulary,
 expression
 of
 thoughts,
 language,
 grammar,
 
and
 other
 general
 tips
 on
 writing
 research
 papers/reports.
 Please
 consult
 the
 UH
 Writing
 Center.
 

 
SUBMISSION
 DETAILS
 
You
 will
 use
 TURNITIN
 LINKs
 on
 BBLearn
 to
 submit
 your
 reports
 for
 each
 task.
 The
 link
 will
 be
 provided
 
on
 the
 Blackboard
 Learn
 Page
 closer
 to
 the
 submission
 deadlines.
 

 
Task
 1:
 Disease
 Fact-­‐Sheet
 
1) You
  will
  be
  assigned
  a
  single
  gene,
  Mendelian
  disease
  from
  one
  of
  the
  Disease
  databases
  (Genes
 
and
  Diseases,
  Genetics
  Home
  Reference,
  Gene
  Reviews,
  or
  Online
  Inheritance
  in
  Man
  (OMIM),
  or
 
Gene
 Cards.
 
 
2) Your
  task
  is
  to
  create
  a
  disease
  fact
  that
  will
  briefly
  describe
  what
  is
  known
  about
  the
  genetic
 
variations
  that
  cause
  that
  disease.
  Provide
  at
  least
  one
  mutation/deletion/duplication
  in
  the
  gene
 
for
  the
  disease
  that
  is
  causative
  of
  the
  disease.
  Provide
  a
  basic
  description
  of
  the
  disease
  and
  its
 
symptons
 (reference
 the
 URL
 to
 OMIM
 or
 Gene
 Reviews
 entry
 for
 your
 disease).
 Is
 there
 a
 classical
 
(pre-­‐genetic)
  differential
  diagnosis
  of
  the
  disease
  or
  treatment
  of
  the
  disease?
  What
  is
  the
  world
 
and
 ethnic
 distribution
 of
 the
 disease
 gene?
 
3) Complete
 a
 2
 page
 report.
 Page
 1
 will
 be
 the
 FACT
 SHEET,
 and
 page
 2
 will
 include
 your
 bibliography,
 
and
 details
 of
 any
 searches
 conducted
 on
 PubMED/WoS/Google
 Scholar.
 

 
Task
 2:
 Sequence
 Retrieval
 
 
1) Retrieve
  the
  genomic
  and/or
  mRNA
  sequence
  for
  the
  gene
  (normal).
  Review
  the
  Gene
  record
  (if
 
available)
 in
 Entrez
 Gene
 and
 determine
 the
 structure
 and
 function
 of
 the
 gene.
 
2) Search
  the
  database
  to
  see
  if
  the
  corresponding
  genomic/mRNA
  sequence
  is
  available
  for
  the
 
mutant/abnormal/disease.
 If
 yes,
 retrieve
 the
 sequence
 and
 save
 it
 as
 the
 “mutant
 sequence”.
 If
 not,
 
create
 a
 mutant
 sequence
 based
 on
 the
 genetic
 mutation.
 
3) Retrieve
 the
 corresponding
 protein
 sequence.
 
1

4) Turn
 in
 a
 ½
 -­‐
 1
 page
 report
 on
 your
 search
 strategy
 for
 find
 the
 sequences,
 and
 list
 the
 AC#s
 of
 the
 
DNA
 and
 protein
 sequences.
 

 
Task
 3:
 Sequence
 Analysis
 
 
1) Analyze
  the
  gene
  sequence
  to
  determine
  number
  of
  exons/introns,
  mRNA
  transcripts
  and
  other
 
features.
 
2) Search
  for
  the
  protein
  in
  UNIPROT
  or
  SWISSPROT.
  Identify
  the
  domains?
  Does
  the
  protein
  have
  a
 
well-­‐understood
 biological
 function.
 You
 can
 check
 the
 biological
 functions
 of
 your
 protein
 choice
 by
 
examining
  the
  Gene
  Ontology
  terms
  in
  the
  UniProt
  entry
  for
  your
  protein.
  How
  do
  the
  domains
 
relate
 to
 the
 function
 of
 the
 protein.
 
3) Turn
 in
 a
 1
 –
 2
 page
 report
 on
 you're
 the
 structure/features
 of
 the
 DNA
 and
 protein
 sequences.
 

 
Task
 4:
 Sequence
 Alignment
 
1) Perform
  a
  pairwise
  alignment
  of
  the
  abnormal
  sequence
  with
  the
  normal
  sequence
  (gene
  and/or
 
protein).
 Justify
 the
 your
 choice
 of
 the
 tool,
 parameters
 and
 explain
 the
 results.
 
2) Turn
 in
 a
 1½
 -­‐
 2
 page
 report
 describing
 the
 method
 used
 and
 explaining
 your
 results.
 

 
Task
 5:
 Discussion
 

 
1) Prepare
 a
 1-­‐page
 summary
 of
 your
 research
 (Tasks
 1-­‐4)
 on
 the
 gene
 and
 the
 inferences
 you
 made
 
from
 the
 sequence
 analysis.
 The
 summary
 should
 discuss:
 What
 is
 the
 causative
 genetic
 disorder?
 
How
  does
  the
  mutated
  sequence
  compare
  to
  the
  normal?
  Did
  you
  find
  the
  mutation?
  Is
  it
  in
  a
 
functionally
 or
 structurally
 important
 site?
 It
 is
 critical
 that
 you
 describe
 how
 the
 genetic
 variation
 
may
 cause
 the
 disease.
 For
 example,
 is
 it
 by:
 
 
Ø A
 mutation
 within
 the
 coding
 region
 of
 the
 protein
 
Ø A
 mutation
 altering
 gene
 expression
 by
 affecting
 the
 promoter
 
Ø A
 mutation
 altering
 gene
 expression
 by
 affecting
 a
 transcription
 factor
 binding
 site
 
Ø A
 mutation
 altering
 gene
 expression
 indirectly
 by
 mutating
 a
 transcription
 factor
 itself
 
Ø A
 mutation
 altering
 copy
 number,
 hence
 changing
 gene
 expression
 levels
 
Ø A
 mutation
 altering
 other
 regulatory
 sites
 (miRNA
 targets)
 
Ø A
 mutation
 altering
 splice
 signals
 
Ø Etc.
 …
 
Often
 there
 will
 be
 several
 types
 of
 mutations
 that
 can
 cause
 the
 disease.
 Please
 comment
 on
 at
 least
 
ONE
  type
  that
  is
  known
  for
  the
  disease.
  Justify
  the
  variation
  as
  a
  potential
  cause
  of
  the
  disease
  by
 
supporting
 it
 with
 the
 sequence
 analysis
 you
 did
 in
 Task
 3-­‐4.
 Are
 there
 any
 genetic
 tests
 available
 for
 
the
 disease
 and/or
 any
 potential
 treatments.
 Are
 there
 any
 novel
 diagnostics
 that
 have
 resulted
 from
 
knowing
 the
 genetics?
 Is
 there
 any
 novel
 understanding
 of
 the
 disease
 that
 has
 lead
 to
 novel
 therapy
 
based
 on
 genetic
 knowledge.
 
 

 
References:
  (Use
  RefWorks
  to
  manage
  your
  citations
  and
  create
  your
  reference
  LIST
  in
  reports).
  Your
 
bibliography
 can
 include:
 
Ø Citations
 of
 articles
 
 
Ø Website
 for
 Tools
 
Ø Note
 you
 can
 also
 cite
 the
 ORIGINAL
 RESEARCH
 PAPER
 describing
 the
 tool
 or
 database
 

 

2

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