Mia Brown
Bioinformatics
Assignment 1: PubMed
1) Created a My NCBI account:
a. Username: brown297
b. Password: bishop
2) Did a term search to find articles about HIV RNA dependent DNA polymerase by using HIV RNA
dependent DNA polymerase as the search term.
a. Found 10 articles published in 2006 on HIV RNA dependent DNA polymerase:
i. Detection assays for HIV proteins. Curr Protoc Immunol. 2006 Jan;Chapter
12:Unit 12.5.PMID: 18432967 [PubMed - indexed for MEDLINE]
ii. Inferring protein-protein interactions in viral proteins by co-evolution of
conserved side chains. Genome Inform. 2006;17(1):23-35.PMID: 17503353
[PubMed - indexed for MEDLINE]
iii. HIV-1 reverse transcriptase pausing at bulky 2' adducts is relieved by deletion
of the RNase H domain.RNA Biol. 2006 Oct;3(4):163-9.PMID: 17396357
[PubMed - indexed for MEDLINE]
iv. Antiretroviral efficacy and virological profile of a
zidovudine/lamivudine/tenofovir disoproxil fumarate combination therapy in
antiretroviral-naive patients. Antivir Ther. 2006;11(6):827-30.PMID: 17310827
[PubMed - indexed for MEDLINE]
v. A randomized trial to evaluate continuation versus discontinuation of
lamivudine in individuals failing a lamivudine-containing regimen: the COLATE
trial. Antivir Ther. 2006;11(6):761-70. PMID: 17310820 [PubMed - indexed for
MEDLINE]
vi. Rare selection of the K65R mutation in antiretroviral-naive patients failing a
first-line abacavir/ lamivudine-containing HAART regimen. Antivir Ther.
2006;11(6):701-5. PMID: 17310814 [PubMed - indexed for MEDLINE]
vii. Impact of HIV-1 reverse transcriptase polymorphism at codons 211 and 228 on
virological response to didanosine. Antivir Ther. 2006;11(6):693-9. PMID:
17310813 [PubMed - indexed for MEDLINE]
viii. Lamivudine and indinavir/ritonavir maintenance therapy in highly pretreated
HIV-infected patients (Vista ANRS 109). Antivir Ther. 2006;11(7):889-99. PMID:
17302251 [PubMed - indexed for MEDLINE]
ix. Primary resistance of human immunodeficiency virus type 1 in a reference
center in Recife, Pernambuco, Brazil. Mem Inst Oswaldo Cruz. 2006
Dec;101(8):845-9. PMID: 17293977 [PubMed - indexed for MEDLINE]
x. Inhibition of human immunodeficiency virus type-1 reverse transcriptase by a
novel peptide derived from the viral integrase. Arch Biochem Biophys. 2007
Feb 15;458(2):202-12. Epub 2006 Dec 28. PMID: 17257575 [PubMed - indexed
for MEDLINE]
b. Article relevancy:
i. Relevant Articles: I-iii
ii. Somewhat Relevant Articles: iv, x
iii. Irrelevant Articles: v-ix
c. Did a term search delimited by quotation marks around “RNA dependent” “DNA
polymerase” and “HIV” and also used hyphens as a second attempt.
i. Results for quotation marks: As a result for adding the quotation marks around
the individual terms, only two articles were available. The quotation marks were
able to better define the selection criteria where it only searched for items
concerning RNA dependence, DNA polymerase, and HIV and as a result, it
limited the number of articles relevant to each search term.
1. Highly selective action of triphosphate metabolite of 4'-ethynyl D4T: a
novel anti-HIV compound against HIV-1 RT.
2. Differential susceptibility of HIV-1 reverse transcriptase to inhibition
by RNA aptamers in enzymatic reactions monitoring specific steps
during genome replication.
ii. Results for using hyphens: When using hyphens instead of quotation marks, the
search engine seemed to have consider HIV-RNA dependent-DNA polymerase as
a single term instead of search for each individual term if we were to use
quotations or not at all. It gave the following message and 18 articles were
retrieved:
Your search for ("2006"[Publication Date] : "2006"[Publication Date]) AND (HIVRNA dependent-DNA polymerase) retrieved no results.
However, a search for ("2006"[Publication Date] "2006"[Publication Date])
AND (hbv rna dependent dna polymerase) retrieved the following items.
d. Description of search when clicking “Details” when using quotation marks versus
hyphens.
i. Details using quotation marks: This what I expected because the quotation
marks were used to define the search to individual terms. The details indicated
that the search did search for each individual terms throughout the database.
ii. Details using hyphens: This is what I expected because the hyphens treated the
terms as a two terms linked together. Not only did it search the terms linked
together as a single term, it automatically changed HIV to HBV. The query was
not able to search it properly.
3)
e. Search using all three of the Boolean operators (AND, OR, NOT).
i. ("2006"[Publication Date] : "2006"[Publication Date]) AND (HIV OR RNA
dependent AND DNA polymerase) there were 1247 articles retrieved.
ii. ("2006"[Publication Date] : "2006"[Publication Date]) AND (HIV AND RNA
polymerase NOT DNA dependent) there were 211 articles retrieved.
f. Demonstrating searching PubMed using the parentheses to an ordered series of
searches:
i. ("2006"[PDAT] : "2006"[PDAT]) AND ("HIV"[All Fields] AND "RNA dependent"[All
Fields] OR "DNA polymerase"[All Fields]) gave 962 articles.
MeSH terms:
a. What is a descriptor? A descriptor is a main heading that characterizes the subject
matter or content.
b. A qualifier? A qualifier is used with descriptors and afford a means of grouping together
those documents concerned with a particular aspect of a subject.
c. An entry term? An entry term is a synonym or closely related term that is a crossreference to descriptors. Generally, entry vocabulary may be used interchangeably with
preferred descriptors for searching of PubMed. Thus, the entry vocabulary is a means by
4)
5)
6)
7)
8)
9)
which the MeSH thesaurus can be enriched to the advantage of both the online user
and the user of the printed bibliography.
A written strategy for the same HIV RNA dependent DNA polymerase search using MeSH
headings related to the term on the Main Heading.
Using “Related Articles”
Using “limits”
Comparing precision
Googling
a. When Googling for HIV RNA dependent DNA polymerase the search returned many
articles that had the whole term listed:
i. Results 1 - 10 of about 1,510,000 for HIV RNA dependent DNA
polymerase.
b. When Googling for “HIV” AND “RNA dependent” OR “DNA polymerase” the search
returned articles that may have the specific terms:
i. Results 1 - 10 of about 373,000 for “HIV” AND “RNA dependent” OR
“DNA polymerase”.
Using some of the subfields in PubMed listed below.
a. Finding local or regional experts on HIV (Marshall, WVU, Ohio State etc.? with your own
search strategy.
i. HIV expert located in Morgantown, WV Department of Psychology, Life Sciences
Building, West Virginia University, P.O. Box 6040, Morgantown, West Virginia
26506, USA. deborah.jones@mail.wvu.edu. This search method was by using
the term HIV AND West Virginia in the search engine box.
Self-reported health in HIV-positive African American women: the role of
family stress and depressive symptoms. J Behav Med. 2003 Dec;26(6):577-99.
PMID: 14677213 [PubMed - indexed for MEDLINE]
b. Finding a paper written by someone with your last name.
i. Golden Delicious Apple search by co-author Mark Brown from the Appalachian
Fruit Research Station, Agricultural Research Service, U. S. Department of
Agriculture, Kearneysville, West Virginia 25430, USA. wjanisie@afrs.udsa.gov
entitled Fate of Escherichia coli O157:H7 on fresh-cut apple tissue and its
potential for transmission by fruit flies. This search method was by typing in
Golden Delicious Apples AND Fruit Flies in the search engine and then the
Advanced search was clicked and Author was defined to search by the last name
of Brown.
c. Finding a paper with a method such as rtPCR or PCR.
i. “RTPCR Method/Assay” search gave a few papers one listed as Real-time PCR
assay for rapid detection and quantification of Campylobacter jejuni on
chicken rinses from poultry processing plant. Mol Cell Probes. 2007
Jun;21(3):177-81. Epub 2006 Nov 14. PMID: 17223308 [PubMed - indexed for
MEDLINE]. This search method involved putting the method into quotation
marks and also listing an additional word such as assay or method.
d. Finding a free full text article on HIV
i. Free full text article on HIV listed 32183 articles. One entitled Gynaecological
morbidity among HIV positive pregnant women in Cameroon. Reprod Health.
2008 Jul 3;5(1):3. [Epub ahead of print] PMID: 18598359 [PubMed - as supplied
by publisher]. This search method involved listing HIV in the search box but
then also clicking the tab “limits” and asking the search to be for full free texts.
e. Finding a paper on Canis familiaris published in Proceedings of the National Academy of
Science USA
10) My Gene of Interest
a. Gene name: Metallothionein(MT)
b. Gene function: Cheung et al. [1] conducted studies on metal concentrations and
metallothionein (MT) gene expression in the Tilapia fish cell line liver tissues. MT has
been used as a biomarker of metal contaminations in polluted waters. MT is a small
metal-binding protein that regulates cellular response to essential metals (Zn2+, Cu2+)
and non-essential metal ions (Cd2+, Hg2+) [1]. However, only a few studies reported the
study of other fish cell lines for this particular gene and its regulation by heavy metal
ions in fish cell lines such as Zebrafish and Goldfish. The fish hepatoma cell line (PLHC-1)
is a tool used to study cytotoxicity, but MT expression in this cell like has not been
characterized. Cheung et al. [1] has reported that the metallothionein gene becomes
activated once exposed to metals and induces mRNA expression levels.
c. Search Strategy: Using the search box to search for the term Metallothionein AND
PLHC-1 (this indicates no results) or metallothionein AND fish (gives 225 articles)