MSTP Practice Questions

June 7, 2014

  1. Identify five genes reported to be strongly associated with Alzheimer’s disease,as identified by Genome Wide Association Studies (GWAS).Cite one literature reference for each gene.
  1. Name three scientists who are very productive in terms of publication in the fields of Alzheimer’s disease research and report their total number of publications.
  1. Name one University of Pittsburgh scientist who has received an NIH-funded research R01 grant for work on Alzheimer’s disease and retrieve his/her grant abstract(s).
  1. Imagine the following text is the abstract taken from your manuscript. Name three journals you could target to publish your paper and report the most similar published paper to your abstract.

Interleukin 7(IL-7) has been demonstrated to provide signals, via theIL-7receptor, which are required at many stages of lymphocyte development and play a role in maintaininghomeostasisof T cells in the periphery as well.IL-7 receptor is composed of two different cytokine receptor subunits, IL-7 receptor alpha chain and the common gamma chain.These two subunits are shared with other cytokine receptors: IL-7 receptor alpha chain is also a subunit of the functional thymicstromallymphopoiesisreceptor, while common gamma chain is a component of functional receptor complexes forIL-2,IL-4,IL-7,IL-9,IL-15andIL-21.The developmental processes governed by IL-7 receptor signaling include initiation ofcell proliferation, protection from apoptoticcell death, and the induction of lineage-specific events (i.e.,gene rearrangementin antigen receptor loci).We have previously shown thatcell survivalsignalingmediated byIL-7-drivenupregulationof an anti-apoptotic protein,Bcl-2, is important forT cell development.We have also demonstrated thatBcl-2expression in peripheral T cells is directly regulated by IL-7 receptor signaling.Dysfunction of IL-7 receptor subunits (either IL-7 receptor alpha or common gamma chains) causes profoundimmunodeficiencyin both humans and mice, highlighting the central roleIL-7plays inlymphopoiesis.Conversely, supra-physiological levels ofIL-7lead to dramatic alterations inmouselymphocyte development, culminating in themalignant transformationof lymphocytes.Although progress has been made in identifying the intracellular mediators of IL-7 receptor signaling that regulate these developmental and transforming processes, significant gaps remain.We will focus not only on positivesignal transduction pathways, but also on the negative regulation of activatedsignalingvia IL-7 receptors.We will also investigate the role of IL-7 receptor signaling in vivo by introducing IL-7 receptor alpha mutants.The goal of this project is to elucidate thesignaling pathwaysdownstream of IL-7 receptor that drive specific steps in lymphocyte development.

  1. (a) Locate two online databases on microRNA targets, and report their URLs.

(b) Identify one database that store all HIV inhibiting siRNA data and cite its URL.

(c) Cite a paper offering a step-by-step guide for analyzingChIP-seq data.

  1. Search for dog genome sequence and answer the following questions:

(a)What is the RefSeq accession number for the Chromosome 6 genome sequence?

(b)What is the size (nucleotide base pairs) for Chromosome 6?

  1. You have a protein with the peptide sequence GPDGMPVIYHGHTLTTKIKFSDVLHTIKE
  2. Identify the human gene associated w/this sequence
  3. Where is its chromosomal location?
  4. Name two neighboring genes, one from its 5’ side and the other from 3’ side
  5. How many splice variants (isoforms) have been reported for this gene according to UCSC and Refseq?
  6. Pick one transcript (isoform) from the UCSC Genes and submit its
  7. mRNA sequence in FASTA format
  8. Protein (amino acid ) sequence(s) in FASTA format
  9. 1000 bp 5’ upstream potential promoter sequence

8.Identify the human protein containing this short peptide sequence to answer the following questions: GVMCVESVNREMSPLVDNIALWMT

(a)What is its biological function?

(b)What % identity is shared with its homologous mouse gene and protein?

(c)What is its calculated PI and molecular wt?

(d)Which region of this protein is most hydrophobic?

(e)Locate five experimentally verified Ser/Thr/Tyr phosphorylation sites in this protein.

(f)How many protein domains are reported to be present in it?

(g)Find the amino acid location of its largest domain.

(h)Name five interacting human protein partners.

(i)Name five interacting yeast protein partners.

(j)Name two biological pathways associated with this protein.

(k)Name two cell lines where it is over expressed and two where it is under expressed.

(l)Name one drug that down regulate its expression and one drug that up regulate its expression.