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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: [email protected].
    • 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

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2. Allen HK, Cloud-Hansen KA, Wolinski JM, Guan C, Greene S, Lu S, et al 2009 Resident microbiota of the Gypsy Moth midgut harbors antibiotic resistance determinants DNA Cell Biol. 28 109 117 10.1089/dna.2008.0812 19206998 http://dx.doi.org/10.1089/dna.2008.0812
3. Donato JJ, Moe LA, Converse BJ, Smart KD, Berklein FC, McManus PS, et al 2010 Metagenomics analysis of apple orchard soil revels antibiotic resistance genes encoding predicted bifunctional proteins Appl. Environ. Microbiol. 76 4396 4401 10.1128/AEM.01763-09 20453147 2897439 http://dx.doi.org/10.1128/AEM.01763-09
4. Foertsch J, Alexander B, Penberthy D 2000 Summer research opportunity programs (SROPs) for minority undergraduates: A longitudinal study of program outcomes 1986–1996 CUR Quarterly 20 114 119
5. Garfinkel DJ, Nester EW 1980 Agrobacterium tumefaciens mutants affected in crown gall tumorigenesis and octopine catabolism J. Bacteriol 144 732 743 6253441
6. Gillespie DE, Rondon MR, Williamson LL, Handelsman J 2005 Metagenomic libraries from uncultured microorganisms 261 279 Osborn AM, Smith CJ Molecular microbial ecology Taylor & Francis Group New York, NY
7. Jurkowski A, Reid AH, Labov JB 2007 Metagenomics: A call for bringing a new science into the classroom (while it’s still new) CBE Life. Sci. Educ. 6 260 265 10.1187/cbe.07-09-0075 18056294 http://dx.doi.org/10.1187/cbe.07-09-0075
8. Kelly T, Coleman EA, Fifer EK, Burns ER, Orr C, Nicholas RW 2006 Partners in research: Benefits of a summer research program J Cancer Educ. 21 243 247 10.1080/08858190701347853 http://dx.doi.org/10.1080/08858190701347853
9. Liles MR, Williamson LL, Rodbumrer J, Torsvik V, Goodman RM, Handelsman J 2008 Recovery, purification, and cloning of high molecular weight DNA from soil microorganisms Appl. Environ. Microbiol. 74 3302 3305 10.1128/AEM.02630-07 18359830 2394920 http://dx.doi.org/10.1128/AEM.02630-07
10. Louzada ES, Sonia de Rio H, Abell AJ, Peltz G, Persans MW 2008 Undergraduate research: A bridge to graduate education in agricultural biotechnology for Hispanics Hor Technology. 18 516 519
11. Marris E 2007 Program targets undergrads to make an early start on science Nat. Med. 13 1268 1268 10.1038/nm1107-1268 17987007 http://dx.doi.org/10.1038/nm1107-1268
12. National Research Council 2007 The new science of metagenomics: Revealing the secrets of our microbial planet NRC Committee on Metagenomics: Challenges and Functional Applications National Academies Press Washington, DC
13. Pfund CC, Maidl Pribbenow J, Branchaw S, Miller Lauffer, Handelsman J 2006 Professional skills. The merits of training mentors Science 311 473 474 10.1126/science.1123806 16439648 http://dx.doi.org/10.1126/science.1123806
14. Riesenfeld CS, Goodman RM, Handelsman J 2004 Uncultured soil bacteria are a reservoir of new antibiotic resistance genes Environ. Microbiol. 6 981 989 10.1111/j.1462-2920.2004.00664.x 15305923 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 al 2000 Cloning the soil metagenome: A strategy for accessing the genetic and functional diversity of uncultured microorganisms Appl. Environ. Microbiol. 66 2541 2547 10.1128/AEM.66.6.2541-2547.2000 10831436 http://dx.doi.org/10.1128/AEM.66.6.2541-2547.2000
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19. Turnbaugh PJ, Gordon JI 2008 An invitation to the marriage of metagenomics and metabolomics Cell 134 708 712 10.1016/j.cell.2008.08.025 18775300 http://dx.doi.org/10.1016/j.cell.2008.08.025

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2011-12-01
2019-05-26

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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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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