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Summer Workshop in Metagenomics: One Week Plus Eight Students Equals Gigabases of Cloned DNA

    Authors: Carlos Rios-Velazquez1,*, Lynn L. Williamson2, Karen A. Cloud-Hansen2, Heather K. Allen3, Mathew D. McMahon2, Zakee L. Sabree4, Justin J. Donato5, Jo Handelsman6
    VIEW AFFILIATIONS HIDE AFFILIATIONS
    Affiliations: 1: Biology Department, University of Puerto Rico – Mayagüez, Mayagüez, Puerto Rico, 00681; 2: Department of Bacteriology, University of Wisconsin – Madison, Madison, WI, 53706; 3: Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, Ames, IA, 50010; 4: Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06516; 5: Department of Chemistry, University of St. Thomas, Saint Paul, MN, 55105; 6: Department of Molecular, Cellular, and Developmental Biology, Yale University New Haven, CT, 06511
    AUTHOR AND ARTICLE INFORMATION AUTHOR AND ARTICLE INFORMATION
    • Published 01 December 2011
    • Supplemental material available at http://jmbe.asm.org
    • *Corresponding author. Mailing address: Biology Department, University of Puerto Rico – Mayagüez, Call Box 9000, Mayagüez, Puerto Rico, 00681-9000. Phone: 787-832-4040. Fax: 787-834-3673. E-mail: carlos.rios5@upr.edu.
    • Copyright © 2011 American Society for Microbiology
    Source: J. Microbiol. Biol. Educ. December 2011 vol. 12 no. 2 120-126. doi:10.1128/jmbe.v12i2.177
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    Abstract:

    We designed a week-long laboratory workshop in metagenomics for a cohort of undergraduate student researchers. During this course, students learned and utilized molecular biology and microbiology techniques to construct a metagenomic library from Puerto Rican soil. Pre-and postworkshop assessments indicated student learning gains in technical knowledge, skills, and confidence in a research environment. Postworkshop construction of additional libraries demonstrated retention of research techniques by the students.

Key Concept Ranking

Rain Forest
0.4819027
Escherichia coli
0.47612292
Tropical Forest
0.4741636
Forest Soils
0.45780754
DNA
0.45061633
0.4819027

References & Citations

1. Alexander B, Foertsch J, Daffinrud S, Tapia R2000The “Spend a Summer with a Scientist” (SaS) program at Rice University: A study of program outcomes and essential elements 1991–1997CUR Quarterly20127133
2. Allen HK, Cloud-Hansen KA, Wolinski JM, Guan C, Greene S, Lu S, et al2009Resident microbiota of the Gypsy Moth midgut harbors antibiotic resistance determinantsDNA Cell Biol.2810911710.1089/dna.2008.081219206998 http://dx.doi.org/10.1089/dna.2008.0812
3. Donato JJ, Moe LA, Converse BJ, Smart KD, Berklein FC, McManus PS, et al2010Metagenomics analysis of apple orchard soil revels antibiotic resistance genes encoding predicted bifunctional proteinsAppl. Environ. Microbiol.764396440110.1128/AEM.01763-09204531472897439 http://dx.doi.org/10.1128/AEM.01763-09
4. Foertsch J, Alexander B, Penberthy D2000Summer research opportunity programs (SROPs) for minority undergraduates: A longitudinal study of program outcomes 1986–1996CUR Quarterly20114119
5. Garfinkel DJ, Nester EW1980Agrobacterium tumefaciens mutants affected in crown gall tumorigenesis and octopine catabolismJ. Bacteriol1447327436253441
6. Gillespie DE, Rondon MR, Williamson LL, Handelsman J2005Metagenomic libraries from uncultured microorganisms261279 Osborn AM, Smith CJMolecular microbial ecologyTaylor & Francis GroupNew York, NY
7. Jurkowski A, Reid AH, Labov JB2007Metagenomics: A call for bringing a new science into the classroom (while it’s still new)CBE Life. Sci. Educ.626026510.1187/cbe.07-09-007518056294 http://dx.doi.org/10.1187/cbe.07-09-0075
8. Kelly T, Coleman EA, Fifer EK, Burns ER, Orr C, Nicholas RW2006Partners in research: Benefits of a summer research programJ Cancer Educ.2124324710.1080/08858190701347853 http://dx.doi.org/10.1080/08858190701347853
9. Liles MR, Williamson LL, Rodbumrer J, Torsvik V, Goodman RM, Handelsman J2008Recovery, purification, and cloning of high molecular weight DNA from soil microorganismsAppl. Environ. Microbiol.743302330510.1128/AEM.02630-07183598302394920 http://dx.doi.org/10.1128/AEM.02630-07
10. Louzada ES, Sonia de Rio H, Abell AJ, Peltz G, Persans MW2008Undergraduate research: A bridge to graduate education in agricultural biotechnology for HispanicsHor Technology.18516519
11. Marris E2007Program targets undergrads to make an early start on scienceNat. Med.131268126810.1038/nm1107-126817987007 http://dx.doi.org/10.1038/nm1107-1268
12. National Research Council2007The new science of metagenomics: Revealing the secrets of our microbial planetNRC Committee on Metagenomics: Challenges and Functional ApplicationsNational Academies PressWashington, DC
13. Pfund CC, Maidl Pribbenow J, Branchaw S, Miller Lauffer, Handelsman J2006Professional skills. The merits of training mentorsScience31147347410.1126/science.112380616439648 http://dx.doi.org/10.1126/science.1123806
14. Riesenfeld CS, Goodman RM, Handelsman J2004Uncultured soil bacteria are a reservoir of new antibiotic resistance genesEnviron. Microbiol.698198910.1111/j.1462-2920.2004.00664.x15305923 http://dx.doi.org/10.1111/j.1462-2920.2004.00664.x
15. Rondon MR, August PR, Bettermann AD, Brady SF, Grossman TH, Liles MR, et al2000Cloning the soil metagenome: A strategy for accessing the genetic and functional diversity of uncultured microorganismsAppl. Environ. Microbiol.662541254710.1128/AEM.66.6.2541-2547.200010831436 http://dx.doi.org/10.1128/AEM.66.6.2541-2547.2000
16. Russell SH, Hancock MP, McCullough J2007Benefits of undergraduate research experiencesScience31654854910.1126/science.114038417463273 http://dx.doi.org/10.1126/science.1140384
17. Schloss PD, Handelsman J2005Metagenomics for studying unculturable microorganisms: Cutting the Gordian knotGenome Biol.622910.1186/gb-2005-6-8-229160868591273625 http://dx.doi.org/10.1186/gb-2005-6-8-229
18. Summers M, Hrabowski F2006Preparing minority scientists and engineersScience3111870187110.1126/science.112525716574853 http://dx.doi.org/10.1126/science.1125257
19. Turnbaugh PJ, Gordon JI2008An invitation to the marriage of metagenomics and metabolomicsCell13470871210.1016/j.cell.2008.08.02518775300 http://dx.doi.org/10.1016/j.cell.2008.08.025
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2011-12-01
2017-11-21

Abstract:

We designed a week-long laboratory workshop in metagenomics for a cohort of undergraduate student researchers. During this course, students learned and utilized molecular biology and microbiology techniques to construct a metagenomic library from Puerto Rican soil. Pre-and postworkshop assessments indicated student learning gains in technical knowledge, skills, and confidence in a research environment. Postworkshop construction of additional libraries demonstrated retention of research techniques by the students.

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FIG. 1

Students’ perception of knowledge and skills proficiency before (A) and after (B) library school.

Skills specifically addressed during library school are listed in type. Students were asked to rate their knowledge and skills in: 1) generation of small insert (<10kbp) metagenomic libraries; ; 5) cloning DNA fragments using the TOPO TA system; 6) cloning DNA fragments via traditional methods; ; 9) transformation of by electroporation; 10) transformation of by chemical methods; 11) restriction endonuclease digestion of DNA; 12) determination of optimal endonuclease concentration to generate small genomic fragments by incomplete digestion; 13) amplification of DNA fragments by PCR; 17) generation of recombinant DNA libraries from metagenomic libraries; 18) analysis of nucleotide and amino acid sequences; and 20) DNA sequencing. The scale used by the students to assess their level of knowledge or proficiency was high, intermediate, or low.

Source: J. Microbiol. Biol. Educ. December 2011 vol. 12 no. 2 120-126. doi:10.1128/jmbe.v12i2.177
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Image of FIG. 2

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FIG. 2

Dry forest library characterization.

Eighteen clones were chosen randomly to determine the presence of an insert via fosmid DNA purification, restriction endonuclease digestion, and gel electrophoresis. All but one clone contained insert DNA. Two molecular markers were used: 1 kb ladder (Promega Corporation, Madison WI) (lane 1) and Yeast Chromosome PFG Marker (New England BioLabs, Ipswich MA) (lane 2). The arrow indicates where linearized vector runs (approximately 7.5 kbp).

Source: J. Microbiol. Biol. Educ. December 2011 vol. 12 no. 2 120-126. doi:10.1128/jmbe.v12i2.177
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