IST 444-Bioinformatics
Assignment 1: Using PubMed

Write a simple term search to find articles about HIV RNA dependent DNA polymerase. What search terms did you select?

Terms used: “HIV RNA dependent DNA polymerase”

Select the first 10 articles published in 2006 and send them to the clipboard. Save them as text. Score each for relevance(e.g. highly relevant, somewhat relevant, or irrelevant).

Article

Level of Relevance

1: Parkin NT, Gupta S, Chappey C, Petropoulos CJ.

 The K101P and K103R/V179D mutations in human immunodeficiency virus type 1

reverse transcriptase confer resistance to nonnucleoside reverse transcriptase inhibitors.

Antimicrob Agents Chemother. 2006 Jan;50(1):351-4.

PMID: 16377709 [PubMed - indexed for MEDLINE]

Somewhat relevant

 
2: Sabariegos R, Gimenez-Barcons M, Tapia N, Clotet B, Martinez MA.
 Sequence homology required by human immunodeficiency virus type 1 to escape from 
short interfering RNAs.
J Virol. 2006 Jan;80(2):571-7.
PMID: 16378959 [PubMed - indexed for MEDLINE]

Irrelevant

 
3: Toni TD, Masquelier B, Lazaro E, Dore-Mbami M, Ba-Gomis FO, Tea-Diop Y,
Kouakou K, Diby J, Sia E, Soppi S, Essien S, Schrive MH, Pinson P, Chenal H,
Fleury HJ.
 Characterization of nevirapine (NVP) resistance mutations and HIV type 1 subtype in women from Abidjan (Cote d'Ivoire) after NVP single-dose prophylaxis of HIV
type 1 mother-to-child transmission.
AIDS Res Hum Retroviruses. 2005 Dec;21(12):1031-4.
PMID: 16379606 [PubMed - indexed for MEDLINE]

Irrelevant

 
4: Mauss S.
 [Prevention and therapy of HIV-associated lipodystrophy syndrome and antiretroviral caused metabolic changes]
MMW Fortschr Med. 2005 Apr 25;147 Spec No 1:49-53. German.
PMID: 16385875 [PubMed - indexed for MEDLINE]

Somewhat relevant

 
5: Gianotti N, Galli L, Boeri E, Maillard M, Serra G, Ratti D, Gallotta G,
Vacchini D, Tremolada Y, Lazzarin A, Clementi M, Castagna A.
 In vivo dynamics of the K103N mutation following the withdrawal of non-nucleoside reverse transcriptase inhibitors in Human Immunodeficiency Virus-infected
patients.
New Microbiol. 2005 Oct;28(4):319-26.
PMID: 16386016 [PubMed - indexed for MEDLINE]

Highly Relevant

 
6: Ly N, Recordon-Pinson P, Phoung V, Srey C, Kruy LS, Koum K, Chhum V, Glaziou
P, Fleury HJ, Reynes JM.
 Characterization of mutations in HIV type 1 isolates from 144 Cambodian recently  infected patients and pregnant women naive to antiretroviral drugs.
AIDS Res Hum Retroviruses. 2005 Nov;21(11):971-6.
PMID: 16386116 [PubMed - indexed for MEDLINE]

Somewhat Relevant

 
7: Li XJ, Kusagawa S, Xia X, Yang C, Wang Q, Yokota Y, Hoshina Y, Onogi T,
Nohtomi K, Imamura Y, Shiino T, Yang R, Yamamoto N, Ben K, Takebe Y.
 Molecular epidemiology of the heterosexual HIV-1 transmission in Kunming, Yunnan 
Province of China suggests origin from the local IDU epidemic.
AIDS Res Hum Retroviruses. 2005 Nov;21(11):977-80.
PMID: 16386117 [PubMed - indexed for MEDLINE]

Irrelevant

 
8: Galegov GA.
 [Non-nucleoside inhibitors of reverse transcriptase in therapy of HIV-infection]
Antibiot Khimioter. 2005;50(4):23-6. Review. Russian. No abstract available.

PMID: 16392336 [PubMed - indexed for MEDLINE]

Highly Relevant

 
9: Goldschmidt V, Didierjean J, Ehresmann B, Ehresmann C, Isel C, Marquet R.
 Mg2+ dependency of HIV-1 reverse transcription, inhibition by nucleoside analogues and resistance.
Nucleic Acids Res. 2006 Jan 3;34(1):42-52. Print 2006.
PMID: 16394022 [PubMed - indexed for MEDLINE]

Somewhat relevant

 
10: Mohey R, Tolstrup M, Jorgensen LB, Moller BK, Black FT, Kjems J, Obel N.
 HIV-1 reverse transcriptase gene 103K/N and 184M/V combinations in tandem:
detection and quantification of HIV-1 populations in the CD45RO+ T-cell compartment by a double-ARMS real-time PCR assay.
J Acquir Immune Defic Syndr. 2006 Feb 1;41(2):160-7.
PMID: 16394847 [PubMed - indexed for MEDLINE]

Highly relevant

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Try your search delimited by quotation marks around “RNA dependent” “DNA polymerase” and “human immunodeficiency virus”. Try hyphens too. What are some differences and why?

“RNA dependent”

Yielded 3012 articles

“DNA polymerase”

Yielded 25, 257 articles

“human immunodeficiency virus”

Yielded 51, 297 articles

"HIV DNA polymerase"

Yielded 11 results

"RNA dependent DNA polymerase"

Yielded 490 results

The results above show that the more concise term you use in the search engine will give more concise results. This eliminates extra time to search through the articles manually.

What description do you get of your search when you click “Details”?  Is this what you expected?

 

There was a query translation of the search term: "RNA dependent DNA polymerase"[All Fields]

The result number: 490

The Database: PubMed

User Query: "RNA dependent DNA polymerase"

Search using all three of the Boolean operators (AND, OR, NOT).

 

When the Boolean operators were used, they yielded more specific results. These operators allow you to distinguish articles that are relevant and irrelevant. This is especially beneficial when time is of essence.

 

Demonstrate that you can search in PubMed using the parentheses to make an ordered series of searches.

 

          The terms, “HIV AND “RNA dependent and DNA polymerase” NOT treatment”

 

MESH

 

What is a descriptor? 
A descriptor is a main heading that helps to describe the subjects’ material/contents
A qualifier? 
A qualifier is a term often coupled with descriptors that allow grouping of words that pertain to the specific subject.
An entry term?
An entry term is a word similar to the term being searched. They are usually cross-references to descriptors. These terms are considered to be synonyms.

What is a MeSH tree?  Where on a MeSH tree is your term?

There are 15 total categories in the MeSH system. The descriptors are grouped by categories. Within each category, there are subcategories. This will show a physical branching. This is why the list is referred to as a tree. The term “Human Immunodeficiency Virus” was used in Pub Med.

What happens with “Find Exact Terms”? 

The search engine will scan through its articles looking for the terms entered in that particular order. This is more difficult to search for.

What happens with “Find terms with ALL fragments?”

The search engine will search for articles that have the search terms entered within the article itself, but it might not be in that consecutive order or related directly in the article.

What happens with “Find terms with ANY fragment?”

This results in articles that contain either one or more of the search terms entered. The articles might not have any relevance with another and this takes a long time to sort.

How many articles do you find using the MeSH terms instead of the terms you thought of?

            Using the search terms: “HIV and RNA-dependent DNA polymerase” 4,470 articles were found.

Score the first 10 articles published in 2006 for relevance to your search:

Articles

Level of Relevance

 
1: Yin J, Beerenwinkel N, Rahnenfuhrer J, Lengauer T.
 Model selection for mixtures of mutagenetic trees.
Stat Appl Genet Mol Biol. 2006;5:Article17. Epub 2006 Jun 23.
PMID: 17049028 [PubMed - indexed for MEDLINE]

Irrelevant

 
2: Gange SJ, Schneider MF, Grant RM, Liegler T, French A, Young M, Anastos K,
Wilson TE, Ponath C, Greenblatt R.
 Genotypic resistance and immunologic outcomes among HIV-1-infected women with viral failure.
J Acquir Immune Defic Syndr. 2006 Jan 1;41(1):68-74.
PMID: 16340476 [PubMed - indexed for MEDLINE]

Irrelevant

 
3: Saracino A, Monno L, Scudeller L, Cibelli DC, Tartaglia A, Punzi G, Torti C,
Lo Caputo S, Mazzotta F, Scotto G, Carosi G, Angarano G.
 Impact of unreported HIV-1 reverse transcriptase mutations on phenotypic
resistance to nucleoside and non-nucleoside inhibitors.
J Med Virol. 2006 Jan;78(1):9-17.
PMID: 16299731 [PubMed - indexed for MEDLINE]

Somewhat relevant

 
4: Sabariegos R, Gimenez-Barcons M, Tapia N, Clotet B, Martinez MA.
 Sequence homology required by human immunodeficiency virus type 1 to escape from 
short interfering RNAs.
J Virol. 2006 Jan;80(2):571-7.
PMID: 16378959 [PubMed - indexed for MEDLINE]

Somewhat relevant

 
5: Suzuki T, Moriyama K, Otsuka C, Loakes D, Negishi K.
 Template properties of mutagenic cytosine analogues in reverse transcription.
Nucleic Acids Res. 2006;34(22):6438-49. Epub 2006 Nov 27.
PMID: 17130163 [PubMed - indexed for MEDLINE]

Somewhat relevant

6: Mescalchin A, Wunsche W, Laufer SD, Grohmann D, Restle T, Sczakiel G.

 Specific binding of a hexanucleotide to HIV-1 reverse transcriptase: a novel class of bioactive molecules.

Nucleic Acids Res. 2006;34(19):5631-7. Epub 2006 Oct 12.

PMID: 17038335 [PubMed - indexed for MEDLINE]

Somewhat relevant

 
7: Montano SP, Cote ML, Roth MJ, Georgiadis MM.
 Crystal structures of oligonucleotides including the integrase processing site of the Moloney murine leukemia virus.
Nucleic Acids Res. 2006;34(19):5353-60. Epub 2006 Sep 26.
PMID: 17003051 [PubMed - indexed for MEDLINE]

Irrelevant

 
8: Feng JY, Myrick FT, Margot NA, Mulamba GB, Rimsky L, Borroto-Esoda K, Selmi B,
Canard B.
 Virologic and enzymatic studies revealing the mechanism of K65R- and Q151M-associated HIV-1 drug resistance towards emtricitabine and lamivudine.
Nucleosides Nucleotides Nucleic Acids. 2006;25(1):89-107.
PMID: 16440988 [PubMed - indexed for MEDLINE]

Irrelevant

 
9: Turkoski BB.
 Unraveling the mystery of HIV medications.
Orthop Nurs. 2006 Jan-Feb;25(1):51-6.
PMID: 16465115 [PubMed - indexed for MEDLINE]

Irrelevant

 
10: Trocello JM, Blanchet A, Bourdain F, Meyohas MC, Vidailhet M.
 [Resolution of choreic movements associated with HIV encephalitis with anti-retroviral therapy]
Rev Neurol (Paris). 2006 Jan;162(1):89-91. French.
PMID: 16446627 [PubMed - indexed for MEDLINE]

Irrelevant

 

Use related articles to find articles similar to those retrieved in #4.

How many articles do you find?

            When “related articles” is clicked, there are 3,863 articles available.

Score the first 10 articles in 2006 for relevance as above.

Articles

Level of Relevance

 
1: van der Laan MJ, Hubbard AE.
 Quantile-function based null distribution in resampling based multiple testing.
Stat Appl Genet Mol Biol. 2006;5:Article14. Epub 2006 May 21.
PMID: 17049025 [PubMed - indexed for MEDLINE]

Irrelevant

 
2: Gupta R, Auvinen P, Thomas A, Arjas E.
 Bayesian hierarchical model for correcting signal saturation in microarrays using pixel intensities.
Stat Appl Genet Mol Biol. 2006;5:Article20. Epub 2006 Aug 28.
PMID: 17049031 [PubMed - indexed for MEDLINE]

Irrelevant

 
3: Salzman P, Almudevar A.
 Using complexity for the estimation of Bayesian networks.
Stat Appl Genet Mol Biol. 2006;5:Article21. Epub 2006 Aug 31.
PMID: 17049032 [PubMed - indexed for MEDLINE]

Irrelevant

 
4: Kedzierska A, Husmeier D.
 A heuristic Bayesian method for segmenting DNA sequence alignments and detecting evidence for recombination and gene conversion.
Stat Appl Genet Mol Biol. 2006;5:Article27. Epub 2006 Oct 24.
PMID: 17140392 [PubMed - indexed for MEDLINE]

Somewhat relevant

 
5: Vittorio Luigi De Socio G, Simonetti S, Stagni G.
 Clinical improvement of psoriasis in an AIDS patient effectively treated with combination antiretroviral therapy.
Scand J Infect Dis. 2006;38(1):74-5.
PMID: 16338845 [PubMed - indexed for MEDLINE]

Irrelevant

 
6: Karlstrom O, Stahle L, Perrin L, Tegude H, Sonnerborg A.
 Efficacy of nelfinavir-based treatment in the central nervous system of HIV-1 infected patients.
Scand J Infect Dis. 2006;38(5):371-4.
PMID: 16709540 [PubMed - indexed for MEDLINE]

Irrelevant

 
7: Coleman T, Culkin C, Sierka D.
 Kidney transplants in HIV patients?
RN. 2006 Jan;69(1):33-8; quiz 39. Review. No abstract available.
PMID: 16441002 [PubMed - indexed for MEDLINE]

Irrelevant

 
8: Tardieu M.
 [Update on the neurological consequences of HIV-1 infection (2006)]
Rev Neurol (Paris). 2006 Jan;162(1):19-21. French. No abstract available.
PMID: 16446620 [PubMed - indexed for MEDLINE]

Irrelevant

 
9: Authier FJ, Gherardi RK.
 [Muscular complications of human immunodeficiency virus (HIV) infection in the era of effective anti-retroviral therapy]
Rev Neurol (Paris). 2006 Jan;162(1):71-81. Review. French.
PMID: 16446625 [PubMed - indexed for MEDLINE]

Irrelevant

 
10: Laurent-Coriat C, Tilikete C, Bouhour D, Boulliat J, Fleury J, Bernard M,
Vighetto A.
 [HIV infection presenting with bilateral optic neuropathy]
Rev Neurol (Paris). 2006 Jan;162(1):95-7. French.
PMID: 16446629 [PubMed - indexed for MEDLINE]

Irrelevant

 

Use the history function and combine the two searches.
Select the links for one or more of your articles.
Can you locate a “linkout” resource for HIV?

            The combination of the two searches leads to 1,066 articles.
                A “linkout” resource for HIV is:
                http://www.ncbi.nlm.nih.gov/sites/entrezDb=pubmed&Cmd=ShowDetailView&TermToSearch=17479950&ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVLinkOut

Find review articles on HIV RNA dependent DNA polymerase. Export 10 articles and rank for relevance as above. 

Articles

Level of Relevance

 
1: Held DM, Kissel JD, Patterson JT, Nickens DG, Burke DH.
 HIV-1 inactivation by nucleic acid aptamers.
Front Biosci. 2006 Jan 1;11:89-112. Review.
PMID: 16146716 [PubMed - indexed for MEDLINE]

Irrelevant

 
2: Olivero OA.
 Mechanisms of genotoxicity of nucleoside reverse transcriptase inhibitors.
Environ Mol Mutagen. 2007 Apr-May;48(3-4):215-23. Review.
PMID: 16395695 [PubMed - indexed for MEDLINE]

Somewhat relevant

 
3: Castro HC, Loureiro NI, Pujol-Luz M, Souza AM, Albuquerque MG, Santos DO,
Cabral LM, Frugulhetti IC, Rodrigues CR.
 HIV-1 reverse transcriptase: a therapeutical target in the spotlight.
Curr Med Chem. 2006;13(3):313-24. Review.
PMID: 16475939 [PubMed - indexed for MEDLINE]

Somewhat relevant

 
4: Boone LR.
 Next-generation HIV-1 non-nucleoside reverse transcriptase inhibitors.
Curr Opin Investig Drugs. 2006 Feb;7(2):128-35. Review.
PMID: 16499282 [PubMed - indexed for MEDLINE]

Somewhat relevant

 
5: Sato H, Yokoyama M.
 [RNA viruses and mutations]
Uirusu. 2005 Dec;55(2):221-9. Review. Japanese.
PMID: 16557007 [PubMed - indexed for MEDLINE]

Irrelevant

 
6: Tsai CH, Lee PY, Stollar V, Li ML.
 Antiviral therapy targeting viral polymerase.
Curr Pharm Des. 2006;12(11):1339-55. Review.
PMID: 16611119 [PubMed - indexed for MEDLINE]

Irrelevant

 
7: Fortin C, Joly V, Yeni P.
 Emerging reverse transcriptase inhibitors for the treatment of HIV infection in adults.
Expert Opin Emerg Drugs. 2006 May;11(2):217-30. Review.
PMID: 16634698 [PubMed - indexed for MEDLINE]

Somewhat relevant

 
8: Yin PD, Das D, Mitsuya H.
 Overcoming HIV drug resistance through rational drug design based on molecular, biochemical, and structural profiles of HIV resistance.
Cell Mol Life Sci. 2006 Aug;63(15):1706-24. Review.
PMID: 16715409 [PubMed - indexed for MEDLINE]

Irrelevant

 
9: Carvalho AP, Fernandes PA, Ramos MJ.
 Molecular insights into the mechanisms of HIV-1 reverse transcriptase resistance  to nucleoside analogs.
Mini Rev Med Chem. 2006 May;6(5):549-55. Review.
PMID: 16719829 [PubMed - indexed for MEDLINE]

Somewhat relevant

 
10: Menendez-Arias L, Matamoros T, Cases-Gonzalez CE.
 Insertions and deletions in HIV-1 reverse transcriptase: consequences for drug resistance and viral fitness.
Curr Pharm Des. 2006;12(15):1811-25. Review.
PMID: 16724949 [PubMed - indexed for MEDLINE]

Irrelevant

 

Find clinical trials on food allergies limited to human infants. Export 10 articles and rank for relevance and usefulness (1-10)

Articles

Level of Relevance and Usefulness (1-10)

1: Monti G, Bertino E, Muratore MC, Coscia A, Cresi F, Silvestro L, Fabris C,

Fortunato D, Giuffrida MG, Conti A.

 Efficacy of donkey's milk in treating highly problematic cow's milk allergic children: an in vivo and in vitro study.

Pediatr Allergy Immunol. 2007 May;18(3):258-64.

PMID: 17433003 [PubMed - indexed for MEDLINE]

Highly relevant 8

2: Jesenak M, Banovcin P.

 Atopy patch test in the diagnosis of food allergy in children with atopic dermatitis.

Acta Medica (Hradec Kralove). 2006;49(4):199-201. Review.

PMID: 17438830 [PubMed - indexed for MEDLINE]

Highly relevant 7

3: Kalach N, Soulaines P, Imad AS, Salloum A, Guerin S, de Boissieu D, Dupont C.

 Survey of prick test, total and specific age during food allergy in children.

Allerg Immunol (Paris). 2007 Feb;39(2):51-7.

PMID: 17441416 [PubMed - indexed for MEDLINE]

Highly relevant 8

4: Fussman C, Todem D, Forster J, Arshad H, Urbanek R, Karmaus W.

 Cow's milk exposure and asthma in a newborn cohort: repeated ascertainment indicates reverse causation.

J Asthma. 2007 Mar;44(2):99-105.

PMID: 17454323 [PubMed - indexed for MEDLINE]

Highly relevant 8

5: Simpson AB, Glutting J, Yousef E.

 Food allergy and asthma morbidity in children.

Pediatr Pulmonol. 2007 Jun;42(6):489-95.

PMID: 17469157 [PubMed - indexed for MEDLINE]

Highly relevant 7

6: Teitelbaum JE, Lagmay JP.

 Familiarity of pediatricians with different commercially available neonatal and infant formulas.

Clin Pediatr (Phila). 2007 Jun;46(5):418-23.

PMID: 17556738 [PubMed - indexed for MEDLINE]

Somewhat relevant 5

7: Mills EN, Mackie AR, Burney P, Beyer K, Frewer L, Madsen C, Botjes E, Crevel

RW, van Ree R.

The prevalence, cost and basis of food allergy across Europe.

Allergy. 2007 Jul;62(7):717-22.

PMID: 17573717 [PubMed - in process]

Somewhat relevant 5

8: Mullins RJ.

 Paediatric food allergy trends in a community-based specialist allergy practice,

1995-2006.

Med J Aust. 2007 Jun 18;186(12):618-21.

PMID: 17576175 [PubMed - indexed for MEDLINE]

Somewhat relevant 6

 

9: Chiang WC, Kidon MI, Liew WK, Goh A, Tang JP, Chay OM.

 The changing face of food hypersensitivity in an Asian community.

Clin Exp Allergy. 2007 Jul;37(7):1055-61.

PMID: 17581199 [PubMed - in process]

Somewhat relevant 4

10: Omata N, Ohshima Y, Yamada A, Yasutomi M, Tokuriki S, Mayumi M.

 A case of milk-protein-induced enterocolitis associated with enterotoxigenic E.coli and MRSA infections.

Eur J Pediatr. 2007 Jun 21; [Epub ahead of print]

PMID: 17582533 [PubMed – as supplied by publisher]

Irrelevant 2

 

Compare the precision and recall of these searches. What are some issues in assessing the performance of the searches?

            All of the searches gave adequate results. The MeSH and review articles on PubMed gave the most articles with the most relevance to the search terms.

Try Google with the same search term. What are some of the differences in what you hit? Number of hits?

When the same terms were used on google.com, approximately 1,120,000 articles were found.  The more concise terms used, the lesser the search results.

Try using some of the subfields in PubMed listed below:

Find Local or regional experts on HIV (Marshall, WVU, Ohio State, etc.)?

Articles

Li X, Stanton B, Feigelman S, Galbraith J.

 Unprotected sex among African-American adolescents: a three-year study.

J Natl Med Assoc. 2002 Sep;94(9):789-96.

PMID: 12392042 [PubMed - indexed for MEDLINE]

Kan H, Xie Z, Finkel MS.

 p38 MAP kinase-mediated negative inotropic effect of HIV gp120 on cardiac

myocytes.

Am J Physiol Cell Physiol. 2004 Jan;286(1):C1-7.

PMID: 14660488 [PubMed - indexed for MEDLINE]

Jones DJ, Beach SR, Forehand R, Foster SE.

 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]

Wu Y, Burns JJ, Stanton BF, Li X, Harris CV, Galbraith J, Wei L.

 Influence of prior sexual risk experience on response to intervention targeting

multiple risk behaviors among adolescents.

J Adolesc Health. 2005 Jan;36(1):56-63.

PMID: 15661597 [PubMed - indexed for MEDLINE]

Slain D, Amsden JR, Khakoo RA, Fisher MA, Lalka D, Hobbs GR.

 Effect of high-dose vitamin C on the steady-state pharmacokinetics of the

protease inhibitor indinavir in healthy volunteers.

Pharmacotherapy. 2005 Feb;25(2):165-70.

PMID: 15767232 [PubMed - indexed for MEDLINE]

Kan H, Xie Z, Finkel MS.

 iPLA2 inhibitor blocks negative inotropic effect of HIV gp120 on cardiac

myocytes.

J Mol Cell Cardiol. 2006 Jan;40(1):131-7. Epub 2005 Nov 28.

PMID: 16316660 [PubMed - indexed for MEDLINE]

                       

What was your search strategy?

These articles above were found using the terms “HIV at WVU.” They are articles about HIV projects that are being performed at WVU.

                        Search for a paper written by someone with your last name.

There were 4,165 articles written by people with the surname Hussain.

                        Search for a method used in a paper, such as rtPCR or PCR?

The technique, real time PCR, yielded 68,745 articles.  The technique, Western Blot, yielded 122,839 results.

Find a free full text article on HIV

                               High throughput functional analysis of HIV-1 env genes without cloning

Jennifer L Kirchherr, Xiaozhi Lu, Webster Kasongo, Victor Chalwe, Lawrence Mwananyanda, Rosemary M Musonda, Shi-Mao Xia, Richard M Scearce, Hua-Xin Liao, David C Montefiori, Barton F Haynes, and  Feng Gao

J Virol Methods. . Author manuscript; available in PMC 2007 August 13.

PMCID: 1948023

 

Find a paper on Canis familiaris published in Proceedings of the National Academy of Science USA.


Lysek DA, Schorn C, Nivon LG, Esteve-Moya V, Christen B, Calzolai L, von

Schroetter C, Fiorito F, Herrmann T, Guntert P, Wuthrich K.

 Prion protein NMR structures of cats, dogs, pigs, and sheep.

Proc Natl Acad Sci U S A. 2005 Jan 18;102(3):640-5. Epub 2005 Jan 12.

PMID: 15647367 [PubMed - indexed for MEDLINE]

 

Create a search strategy for your gene of interest. Tell me the gene, describe your strategy, and save it in your myNCBI. Use your search more than once during the course of the class to look for new papers.

For PubMed: FADD is the term that will be used initially. Once the true function of the gene is understood, more precise search terms can be chosen to further narrow articles.  Apoptosis will be one of the terms used once the search is narrowed.
For MeSH: FAS-associated via death domain AND apoptosis

 

Write a simple, non-technical summary of what your gene does in humans.

FADD is a gene that mediates the cell signals in apoptosis (programmed cell death). It interacts with the cell surface receptors.  A Fas-receptor and others help to bring the FADD gene to the site of apoptosis. The gene helps to cause the cascade of enzymes that will destroy the cell.