Chapter 49
Proteomics and Genomics
Wojciech Rozek and Pawel S. Ciborowski
Questions
1.
What is proteomics?
2.
What is genomics?
3.
How does studying the proteome compare to studying the genome?
4.
Review the challenges in proteomics research?
5.
What is system biology?
6.
Explain in which cases SELDI-TOF technology will be more advantageous than LC-MS/MS and/or
MALDI-TOF.
7.
Review important factors in planning studies of clinical proteomics?
8.
Advantages and disadvantages in using protein arrays.
9.
What are biomarkers and how are they identified and validated for use in the clinical setting?
10. Describe strategies of sample prefractionation for genomic and proteomic analysis.
11. Mathematical models of the molecular pathways in cells will facilitate:
a. prediction of previously unknown interactions
b. combining genomic and proteomic data
c. discover novel proteins, cellular functions, and pathways
d. all of the above
12. Successful translation of results from laboratory to clinic depends on:
a. exploratory research studies
b. validation
c. prospective screening studies on large-scale population
d. all of the above
13. Weakness of 2-dimensional SDS-PAGE is:
a. lack of superior reproducibility
b. lack of protection of proteins from structural de-stabilization
c. inability of obtaining protein sequencing data
d. lack of superior methods of protein labeling
14. Major difficulty in proteomic studies of certain type of samples such as CSF is:
a. contamination with drugs penetrating through blood brain barrier
b. size and availability of the sample
c. lack of correlation with clinical diagnosis
d. contamination with red blood cells during spinal tap
15. Top-down approach in studies of systems biology is preferential over bottom-up approach because:
a. it provides more global view
b. it allows for faster conclusions which will lead to direct development of clinical tests
c. requires less sophisticated technology and instrumentation
d. both approaches are equal
49. Proteomics and Genomics
Wojciech Rozek and Pawel S. Ciborowski
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16. Major question to be addressed when considering application of genomics and proteomics to screening
and testing include selection of:
a. mouse species
b. non-radioactive reagents
c. reputable provider of proteomics and genomics technologies
d. conditions which are true reflections of in vivo biological function
17. Commercially available antibody arrays technology has many of the same problems observed with
genomics because of problems associated with:
a. data analysis, interpretation, storage, and retrieval
b. high background created by not well developed reagents
c. necessity of using radioactive materials
d. inaccuracy of chips readers
18. The best approach to determine the sensitivity and specificity of these methodologies, and to validate and
standardize these technologies?
a. to reduce “biological noise” in the samples and reduce number of replicates
b. to link data obtained from database searches to biological effects via fast computers
c. to develop a standard approach to understanding and communicating variability in ex-perimental data
d. none of the above
19. While planning proteomics experiments, a researcher should
a. have available all types of mass spectrometers
b. mandatory access to protein microarrays
c. be aware of strength and weaknesses of each technology
d. always be an expert in statistics and computer programming for solving problems associated with
bio informatics
20. Neuroproteomics analysis is most conclusive when
a. experiments are done using entire brain so that all cell types are used in one assay
b. only in vitro models are conclusive
c. selected types of cells from a brain are obtained and manipulated
d. two or more cell types are mixed together to facilitate interaction mimicking in vivo situation
49. Proteomics and Genomics
Wojciech Rozek and Pawel S. Ciborowski
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Answers
1.
What is proteomics?
The field of science using high throughput techniques to analyze proteins expressed under a certain set of
conditions within an individual cell or organism.
2.
What is genomics?
Field of science that combines genetics and molecular biology techniques to create genetic maps and DNA
sequences; analyze and organize genetic information into databases.
3.
How does studying the proteome compare to studying the genome?
Proteomics is a study of actual proteins, which are products of multi-step process: transcription, translation,
post-translational modification. Genomics is a study of genetic information, which may or may not produce
functional product – protein.
4.
Review the challenges in proteomics research?
The following factors can constitute challenge in proteomic studies: sample size (biopsy), sample availability
(brain tissue from healthy individual is not available), yield of protein after sample preparation, genetic
variation between individuals within group, sensitivity of analytical instrumentation, ability to separate
thousands of proteins and their forms in a highly reproducibly manner, throughput, fast and reliable data
analysis.
5.
What is system biology?
Field of science that studies the interactions between the components of biological systems and how these
interactions give rise to the function and behavior of that system.
6.
Explain in which cases SELDI-TOF technology will be more advantageous than LC-MS/MS and/or
MALDI-TOF.
SELDI-TOF technology platform is easy to use and facilitates fast screening of large number of samples. It is
very useful for profiling purposes. Limited sample preparation is necessary. LC-MS/MS is a low throughput
approach, however it provides more information about proteins including identification. Usually, requires multistep sample preparation.
7.
Review important factors in planning studies of clinical proteomics?
It is imperative in clinical proteomic to assembly a cohort of patients (samples) which represents well clinically
diagnosed diseased and control groups. Initial size of study group has to be larger from the planned end number.
Some individuals may be eliminated during studies due to unpredicted factors such as infection, trauma etc.
Samples (clinical material) obtained from patients have to be processed in uniformed manner to reduce
variability. Sample size should be sufficient for at least duplicate experiments.
8.
Advantages and disadvantages in using protein arrays.
Advantages: fast and relatively easy experiments using already well developed chip readers.
Disadvantage: protein arrays are limited to specific antibodies printed on the chip.
9.
What are biomarkers and how are they identified and validated for use in the clinical setting?
Biomarker can be any molecule, e.g. protein, carbohydrate, lipid, etc. which levels in diagnostic samples are
correlated with stage of disease. Biomarkers are usually identified by comparisons of samples obtained from a
population of healthy individuals with those obtained from diseased patients. For use in clinical setting, a
biomarker has to be measured reliably using a robust technique, e.g. ELISA.
49. Proteomics and Genomics
Wojciech Rozek and Pawel S. Ciborowski
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10. Describe strategies of sample prefractionation for genomic and proteomic analysis.
Sample preparation for genomic studies will have two main goals: yield of genetic material and preservation of
its stability. Sample preparation for proteomic studies will focus on elimination of proteolytic activity which
may degrade proteins, preventing protein degradation, preserving enzymatic activity when necessary, and
removal of genetic material which may increase background during analytical phase (removal nuclei for studies
of cytosolic fraction).
11.
d
12.
b
13.
a
14.
b
15.
d
16.
d
17.
d
18.
c
19.
c
20.
c