Source: UNIVERSITY OF PUERTO RICO AT MAYAGUEZ submitted to
GEOMICROBIOLOGICAL AND METAGENOMIC STUDIES (GEMS) OF PUERTO RICAN SOILS
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
TERMINATED
Funding Source
Reporting Frequency
Annual
Accession No.
0210361
Grant No.
2007-38422-18042
Project No.
PRE-2007-02386
Proposal No.
2007-02386
Multistate No.
(N/A)
Program Code
NJ
Project Start Date
Jul 1, 2007
Project End Date
Jun 30, 2011
Grant Year
2007
Project Director
Rios-Velazquez, C.
Recipient Organization
UNIVERSITY OF PUERTO RICO AT MAYAGUEZ
P. O. BOX 9000
MAYAGUEZ,PR 00681
Performing Department
BIOLOGY
Non Technical Summary
A. The genetic and biochemical potential of microbial-flora in Puerto Rican forests has not been explore. B. Lack of educational initiatives in emerging disciplines prevents Puerto Rican students to explore new careers. 1. To develop metagenomic libraries from forest, and search for novel activities and applications. 2. Expand studentsAE career opportunities involving them in emerging disciplines research, combined with natural resources conservation awareness.
Animal Health Component
100%
Research Effort Categories
Basic
(N/A)
Applied
100%
Developmental
(N/A)
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
90360993020100%
Goals / Objectives
The main objectives of the proposed project are: 1) Train students in genomics and to generate metagenomic libraries from different forest soils in Puerto Rico and determine their microbial diversity. We will teach the undergraduate students from the UPR how to perform metagenomic studies. The training that the students will receive in performing such studies, will promote the development of scientific research experimental skills such as experimental design, data collection, and analysis, specifically using state of the art, and up to date technology and techniques. Students will be able to generate, monitor and test the metagenomic libraries generated, and will be able to perform comparisons between the forests, specifically at microscopic level. 2) Develop and implement in the curriculum, an Introductory Course in Metagenomics at the UPRM and a course in Topics in Functional Genomics at the UPRH. 3) Train students to determine the bio-catalytic potential of the micro-flora represented in the metagenomic libraries, and test the production of any novel activities, bio-catalytic, biomineralization and/or antimicrobial agents. 4) Visits to fifteen rural elementary and high schools within Puerto Rico to teach soil microbiology and forest conservation to change the overall perception of the importance our forests. Our proposed project has a strong outreach component. We not only want to train our students in how to search for novel bio-catalytic activities in forests, but also, with the collaboration of the USDA Forest Service (International institute of Tropical Forestry), and the Animal and Plant Health Inspection Service (APHIS), teach the students the importance of natural resources conservation. This peer-teaching and mentoring approach will ensure the development of environmental responsible citizens, a society that knows and care.
Project Methods
The project plan of operation has been divided in two phases: The first phase involves a general orientation about the forests to be sampled: dry forest (Bosque Seco de Guanica), and El Yunque (rain forest), their importance, flora, fauna and the main aspects of conservation. The preliminary record of the microbial flora present in the forest soil samples will be completed by using vital dyes and fluorescent microscopy. Then, the isolation of DNA from the forest soil sample in Puerto Rico will be performed using various in situ (direct) and ex situ (indirect) methods. Once high quality DNA has been obtained, analyzed and quantified, the students will perform several methods to generate metagenomic libraries of low (5 to 20 kbp), and high molecular (20 to 100 kbp) weight size fragments. In order for the students to assay molecularly the forest soil diversity; rDNA gene-specific libraries [16S (bacteria and archaea) and 18S rDNA (fungi)] will be also generated. The PCR amplified products will be cloned into a special vector (pCR4-Topo), and the amplicons present in the libraries will be analyzed by genetic engineering techniques such as restriction analysis (RFLP, tRFLP, and ArDRA). This will allow a taxonomical, phylogenetical, and preliminary functional analysis of the soil samples, even if the microbes present in the soil can or cannot be cultivated. The next steps in the generation of metagenomic libraries involves the cloning of DNA fragments. Partial digestion of the DNA sample will be done using endonucleases, following size-fractionation by Pulse-Field Gel Electrophoresis. The gel slices containing the DNA of the appropriate size will be cut and ligated into Bacterial Artificial Chromosomes vectors, and transformed into Escherichia coli by means of recombinant DNA technology. The metagenomic clones (mgCLN) will be analyzed by colony-PCR, and mini-preps by Pulse Field Gel Electrophoresis. The second phase of the project involves monitoring the bioprospecting capabilities of the mgCLN by testing their ability to produce biomolecules with medical, biotechnological and geomicrobiological capabilities (mineralization). Also, the mgCLN will be screened for specific bio-catalytic activity by growing them in enriched or minimal culture media overlaid with top agar containing: exponentially specific microbial cultures of microbial pathogens (if screening for antimicrobial agents), contaminants such as xylene, or enzyme substrates such as starch, or cellulose, depending on the bio-catalytic activity of interest. The production of specific secondary metabolites will be screened by preparing culture extracts, using expression vectors and analyzing them by biochemical methods such as spectral absorption and high-pressure liquid chromatography (HPLC). In addition, a graduate student will be trained at the Univ. of Wisconsin-Madison to conduct more advanced experiments. A laboratory meeting will be organized twice a month in order to talk about experimental strategies, data, and to discuss scientific literature.

Progress 07/01/07 to 06/30/11

Outputs
A second no-cost extension was requested and approved for the NIFA-HSI project in order to allow completing the proposed support to GeMS alumni performing a Master degree in Bacteriology at UW-Madison, Miss Rosivette Santiago, and keep the research and disseminating activities. During the fourth year of the GeMS project, twenty five students (all of them Hispanics American) were trained on metagenomics, and to date a total of one hundred and two undergraduate students have been impacted from the project by participating actively in metagenomic research. Two new metagenomic libraries have been generated and many more are in process to be generated. A Yale Advisory Board in Metagenomics was formed focused in coordinating the Mastering metagenomics course-workshop in other Institutions. Two papers were published and one more accepted, and the first book in Puerto Rican research was published including an article in USDA-CSREES-GeMS metagenomic research. Thru the Puerto Rico college of Chemists, a short course in metagenomics was offered in the IUPAC 2011 World Chemistry Congress in Puerto Rico. During the fourth year, the project has been disseminated in more than 10 poster and 9 oral presentations locally and nationally. The interdisciplinary collaborations thru USDA-NIFA-GeMS have maintained and new proposals submitted as a team. the research performed at the labs at UPR-M and collaborators using the metagenomic libraries generated by the, putative genes involves in antibiotic resistant, degradation of caffeine, cellulose and urease have been found and in the process of identification. Finally, Miss Rosivette Santiago, the MS student supported by the USDA- NIFA--GeMS should complete her degree during the Fall of 2011. PRODUCTS: Two more metagenomics libraries from different environments has been developed by the students in the lab. One from a Coffee Bean plantation and another one from a riparian region mainly with bamboo plants. There are actual effort to keep generating more libraries from different regions from El Yunque and the Dry Forest. New clones activities has been detected from the metagenomic libraries generated through the USDA-CSREES-GeMS. This includes potential lipases, esterases and ureaseas. The topic of metagenomics is present in two of the assays chosen to be part of the first book of Puerto Rican Science. OUTCOMES: During the fourth year, four important and interdisciplinary collaborations have been maintained: in the Chemical Engineering at UPR-Mayaguez, at the Chemistry Department at UPR-Humacao, at the Chemistry Department at UPR-Cayey, at the Pontifical Catholic University Biology Department, and at the Sciences Department at Turabo University. Also, Mr. Nolberto Figueroa, a graduate student from Dr. Ortiz UPR-Mayaguez, Chemical Engineering, should be completing his MS degree this year. Besides searching for cellulases, laccases, esterases, lignine and caffeine degradative enzymes, he recently also found lipase activity in the tested clones. The 86% of the USDA-NIFA-GeMS graduated from the academic year 2010-2011 continue in a graduate program. While 57% of them will continue in PhD program at Harvard (Mr. Jose Cruz), UW-Madison (Angel Casanova) and Cornell (Mr. Jean Carlos Cruz), and UMDNJ-Rutgers (Mr. Moises De Jesus), 29% of the participants are in master programs and all of them has mentioned their plans to continue a PhD. From the students participating in the USDA-NIFA -GeMS, that have already graduated, 57% has continued a PhD in different areas in Science and Bioengineering, 38% began an MS degree in Sciences (with potential to continue PhD), and 7% an MD program. Miss Rosivette Santiago which received support from the USDA-NIFA -GeMS to complete a graduate degree, has completed her second year and a half at the Master's program in Bacteriology at UW-Madison. She has approved all the courses as well as the proposal. The experimental part is almost done, and she is expecting to finish this semester (Fall 2011). Miss Santiago has begun the process of applying for PhD programs in Microbiology at different graduate programs in USA. DISSEMINATION ACTIVITIES: A total of twenty two presentations of the project were done in local research activities, national congresses and symposiums during the fourth year of the project. The presentations included poster and oral presentations in places such as American Society for Microbiology, and the 46th ACS Junior Technical Meeting 31th Puerto Rico Interdisciplinary Scientific Meeting (PRISM), Semiannual, American Society for Microbiology Puerto Rico Branch, and the first Biology Program Research Symposium. Also, workshops and field trips were also organized, including the District Biology Honor Society BBB Convention, and finally in the IUPAC 2011 World Chemistry Congress in Puerto Rico, where a one special workshop was organized in Unraveling Activities with Applications in Biotechnology Thru Metagenomics. The activity was evaluated as excellent, and the College of Chemist is interested in repeated the workshop. This year again, the 'Fishing for Genes from Forests in Puerto Rico' workshop was offered to students participating in the 2011 Biotechnology for Educational Training in Teams through Research and Interdisciplinary Centers (BETTeR-IC+) Summer Camp at UPR-Mayaguez in Science, Technology, Environment and Community Service. This summer camp impacted 37 students and 17 schools distributed in 14 towns and cities in Puerto Rico different local schools high school. Also, a couple of talks were offered as part of two summer camps in Biotechnology at the Bioprocess Development and Training Complex (BDTC). A blog of the student's team from UPR-M that took the mastering metagenomic course at Yale during the summer was generated at our laboratory in order to present and discuss data and results: http://masteringmetagenomics.blogspot.com/. FUTURE INITIATIVES: We have been invited to bring a talk to the Annual Convention of the American Association of the Advancement of Science (AAAS), and also to coordinate a concurrent session in education to teacher, students from the elementary, intermediate and high school. The seminar and all four talk-workshops will incorporate metagenomics as emerging disciplines. The main topic of the convention is genes, environment and society, which apply completely with what we do at USDA-CSREES-GeMS. There are efforts to institutionalize a formal course and lab. in metagenomics at UPR-Mayaguez

Impacts
Thru USDA-NIFA-GeMS, different and diverse collaborative teams focused in metagenomics have been developed and as a result, research proposals have been prepared and submitted. One of them is a resubmission to NSF between UPR-Mayaguez, UPR-Humacao and UPR-Cayey using the knowledge of metagenomics. The second one involves collaboration between UPR-Mayaguez and the Pontifical Catholic University at Ponce. This also include the Metagenomics Advisory Board generated at Yale University (where Dr. Jo Handelsman's moved), where as a team we coordinate how to involves other institution and students to get into summer 'schools' in Mastering Metagenomics. Also, USDA-NIFA-GeMS developed important collaborations and partnerships with UW-Madison, Lawrence Berkeley National Laboratories, University of Connecticut, Yale University among others. The USDA-NIFA-GeMS has developed a generation of undergraduate and graduate students with the knowledge and active experience in metagenomics. This experience has impacted from secondary school to undergraduate and graduate programs, and also professional associations and the general public. The publication of the 'Puerto Rican Science: Anecdotes and Essays of a Puerto Rican Scientist' is an important example of that. The book will be used as a reference book in schools in Puerto Rico, and we have been participating in several radio stations interviews to talk about it.

Publications

  • Cruz, J.M., M. A. Ortega, J. C. Cruz, P. Ondina, R. Santiago, and Carlos Rios-Velazquez. 2010. Unraveling activities by functional-based approaches using metagenomic libraries from dry and rain forest soils in Puerto Rico Current Research, Technology and Education Topics in Applied Microbiology and Microbial Biotechnology.Vol. 2(2),1471-1478.
  • - Torres-Zapata, I., A. Gonzalez-Montalvo, C. Castro-Ruiz and C. Rios-Velazquez. 2010. Generation of large insert metagenomic libraries using indirect DNA extraction methods from benthic and ephemeral tropical hypersaline microbial mats. Current Research, Technology and Education Topics in Applied Microbiology and Microbial Biotechnology. Vol. 2 (2), 1569-1575.
  • - Carlos Rios-Velazquez, Lynn L. Williamson, Karen A. Cloud-Hansen, Heather K. Allen, Matthew D. McMahon, Zakee L. Sabree, Justin Donato, and Jo Handelsman. 2011. Summer Workshop in Metagenomics: One Week and Eight Students Equals Gigabases of New Information. (accepted)
  • - Carlos Rios-Velazquez. 2011. The API Model: engaging college students actively into learning basic concepts in metagenomics by collaborative and cooperative learning. In process to be re-submmitted
  • - Mayra Cancel and Lilliam Casillas-Hernandez. 2011. Conceptual Changes Through an Introductory metagenomic Course. In preparation.
  • - The Book entitled: 'Ciencia Boricua: Ensayos y anecdotas del cientifico puertorro'. (translated as 'Puerto Rican Science: Anecdotes and Essays of a Puerto Rican Scientist') is published. There was a press conference for the announcement on Sept. 22, 2011. There are two articles about metagenomics in the book from Carlos Rios-Velazquez and Lilliam Casillas.


Progress 07/01/09 to 06/30/10

Outputs
During the third year of the GeMS project, eighteen more students were trained on metagenomics, and several research skills and techniques by the project including one graduate student from the Chemical Engineering department at UPR-Mayaguez and one from the Turabo University. To date a total of fifty three undergraduate students have been impacted from the project. Besides UPR-M, a second introductory course was developed for undergraduate students at UPR-Humacao. During June 1st to 6th a workshop/short course entitled: "Unraveling the Ecological, Molecular and Biotechnological Potential of the Microbial Mats through Geomicrobiology and Metagenomics." was organized in Puerto Rico. The course impacted a total of 16 students from UPR-Mayaguez, UPR-Humacao, a teacher and a student from secondary school. The course included workshops, talks and demonstrations about metagenomics and Geomicrobiology and focus on the Cabo Rojo Salterns Microbial Mats. More than ten speakers from different disciplines participated in the short course. During the summer a total of 8 undergrads and one graduate student from UPR-M participated in the intensive workshop in metagenomics named as Library School at Yale University. This was an initiative funded by HHMI to Dr. jo Handelsman at Yale university, that emerged as USDA-CSREES-GeMS summer short course in metagenomics organized at UW-Madison. A Science and Technology CoHemis Conference was organized in Applied metagenomics where besides the invited speaker in Viral Metagenomics, two of the USDA-CSREES undergraduate participants from UPR-M were also main speakers. During the third year, the project has been disseminated not only to students, faculty and researchers at higher education institutions, and K-12 students and teachers, but also to the general public. In more than 26 poster and 10 oral presentations locally and nationally, three outstanding poster presentations in the Microbiological Sciences category has been also received. Thru the research performed at the labs at UPR-M and collaborators using the metagenomic libraries generated by the USDA-CSREES-GeMS, putative genes involves in antibiotic resistant, degradation of caffeine, cellulose and urease have been found and in the process of identification. Also, studies in the diversity on the metagenomic libraries are in progress and have been presented in general scientific meetings. One manuscript has been accepted for publication, two were submitted, and one is in preparation. Finally, a collaborative international proposal involved in the area of Human Microbiome is one of the impact of the project. PRODUCTS: After monitoring some of the metagenomic libraries generated through the USDA-CSREES-GeMS, we have been discovering and analyzing clones that have demonstrated biological activities with medical and biotechnological applications. Collaborators from the Chemical Engineering Department at UPR-M have found clones with putative activity in degrading caffeine and carboxy-methyl cellulose. OUTCOMES: During the third year, the collaborations has been maintained, especially those where the metagenomic libraries generated by the students are being used. For example, the graduate student Nolberto Figueroa definitively will use the results obtained through monitoring of the metagenomic libraries his thesis project. This is collaborations with the Chemical Engineering Department at UPR-Mayaguez with Dr. Patricia Ortiz. All the undergraduate students which participated in GeMS and graduated will continue PhD degrees in Sciences. During June 1st to 6th a workshop/short course entitled: Unraveling the Ecological, Molecular and Biotechnological Potential of the Microbial Mats through Geomicrobiology and Metagenomics. was organized in Puerto Rico. A total of 16 students were impacted by the course. Also, there was an average increase of 76 percent from a total of 25 skills, techniques and knowledge perceived to be acquired by the participants. The pre-post tests showed an increased in 28 percent in knowledge from all the participants. Mr. Jose Cruz and Mr. Jean C. Cruz were awarded individually as the Outstanding posters presentation at the Puerto Rico Society of Microbiologists Semi-Annual Meeting at the University of Puerto Rico - Humacao. Also, Mr. Jose Cruz was awarded with the Outstanding poster presentation at the Annual Biomedical Research Conference for Minority Students at Phoenix, Arizona. Miss Rosivette Santiago (her MS has been supported by the grant), has completed her first year at the Master's program in Microbiology at UW-Madison. She has approved all the course work and she is writing her research proposal. In the Yale University Library School: mastering metagenomics summer workshop, Miss Rosivette Santiago, which took the course initially as a GeMS student, became a mentor from UW-Madison. DISSEMINATION ACTIVITIES: A total of fourty one presentations of the project were done in local research activities, national congresses and symposiums during the third year of the project. The presentations included poster and oral presentations in places such as American Society for Microbiology, and the 45th ACS Junior Technical Meeting 30th Puerto Rico Interdisciplinary Scientific Meeting (PRISM), Northeast Alliance Poster Day and Puerto Rico Society of Microbiologists Semi-Annual Meeting among others. During the third year, more than 200 students, and 300 teachers and personnel from different professionals from the industry and medical related areas in Puerto Rico have been impacted by the project. Also, several workshops, and "open house" has been offered including a conference on the Ups and Down in Biotechnology to high school teachers that are currently part of the Title II-B "Mathematics and Science Partnership" grant from the Education Department. Finally, the "Fishing for Genes from Forests in Puerto Rico" workshop was offered to students and teachers participating in the 2009 Biotechnology for Educational Training in Teams through Research and Interdisciplinary Centers (BETTeR-IC plus) Summer Camp at UPR-Mayaguez. This summer camp also impacted 32 students and 12 high school teachers (local and international). As part of the Summer camp the participants also received talks about integration of Science Technology, Environment and Community Service using our research projects as models (emerging disciplines). The population of teachers and students impacted included especial education centers, and private and public schools. FUTURE INITIATIVES: A second no-cost extension was requested and approved for the project. This will allow completing the proposed support to USDA-CSREES-GeMS alumni performing a Master degree in Bacteriology at UW-Madison. Also, the participants will keep visiting some of the sites at the forests, and keep disseminating the results.

Impacts
The grant proposal submitted as a result of the success of the GeMS students' First Short Course in the Generation and Monitoring of Metagenomic Libraries at the Dr. Jo Handelsman's lab. Was accepted and as a result, one graduate student and eight undergrads from UPR-M participated in the same initiative at Yale University. The activity will continue every other summer including students from UPR-M and other educational institutions in PR and the United States. As an initial collaboration thru GeMS grant, one NSF and one NIH-AREA proposals were submitted as research collaborations between UPR-Mayaguez, UPR-Humacao and UPR-Cayey using the knowledge of metagenomics. Also, and international (Colombia, United Kingdom, and Puerto Rico) collaboration proposal entitled: Metagenomic and metabolomics analyses in individuals with metabolic syndrome: A comparative study in two populations, was also submitted to Colciencias in Colombia as a collaboration in a Human Microbiome initiative.

Publications

  • Jose M. Cruz, Manuel A. Ortega, Jean Cruz, Pedro Ondina, Rossivette Santiago, and Carlos Rios-Velazquez. 2010. Unraveling activities by functional-based approaches using metagenomic libraries from dry and rain forest soils in Puerto Rico. Current Research, Technology and Education Topics in Applied Microbiology and Microbial Biotechnology. Accepted
  • Carlos Rios-Velazquez, Lynn L. Williamson, Karen A. Cloud-Hansen, Heather K. Allen, Matthew D. McMahon, Zakee L. Sabree, Justin Donato, and Jo Handelsman. Summer Workshop in Metagenomics: One Week and Eight Students Equals Gigabases of New Information. Submitted in June, 2010.
  • Carlos Rios-Velazquez. The API Model: engaging college students actively into learning basic concepts in metagenomics by collaborative and cooperative learning. Submitted in August, 2010.


Progress 07/01/08 to 06/30/09

Outputs
During the second year of the GeMS project, sixteen more students were trained on metagenomics, and several research skills and techniques by the project including three students from the Chemistry department at UPR-Humacao, and one graduate student from the Chemical Engineering department at UPR-Mayaguez. To date a total of thirty eight undergraduate students have been impacted from the project. A Second team meeting for Geomicrobiological and Metagenomic Studies (GeMS) of Puerto Rican Soils (GeMS Team Meeting) took place February 7th-8th of 2009. The main topics covered included microbial diversity in soil, as well as wildlife diversity in forests, conservation, analysis of the libraries using in silico and molecular methods, and the development of libraries using indirect methods. A total of three faculty, and researchers from UPR-Mayaguez and UPR-Humacao as well as five graduate students and one personnel from the USA Fish and Wildlife Services participated as main speakers. A new introductory course was developed for undergraduate students entitled: Basic Concepts of Functional Genomics and Metagenomics. The two credit course was organized into six main areas: Genomes and Functional Genomics, Technology to dissect genomes and understand diversity, DNA extraction, Metagenomic library construction, Metagenomic models, and Metagenomic analysis of function and diversity. A total of twelve students from Biology, Industrial Microbiology and Biotechnology took the course. There was also a capstone activity for the students to integrate as a team the knowledge and skills learned in the course. The students assessed with highest score the course content (83%), format (92%), material presented (100%) and the professor's preparation (100%). A course with more credits and a separated lab was also suggested by the students. From a total of eighteen skills, the students developed complete or partially, sixteen of them with a score more than 83%. The capstone activity assessment ranged from 87% - 97%. Also, all the students mentioned that they will recommend the course to other cohorts. During the second year the outreach and dissemination program was continued and more than 300 students, teachers and more than 25 schools where directly and indirectly impacted by receiving the seminar and workshop about metagenomics. As many as twelve undergraduate research projects were and are actively in progress as part of searching for novel activities from the Metagenomic libraries generated during the first year of the GeMS project. These include searching for novel peptidases, lipases, estereases, antibiotics, and antibiotic resistance among others. The description of the activities as well as pictures of the participants can be seen at the USDA-CSREES GeMS webpage: http://www.cohemis.uprm.edu/gemspr/. PRODUCTS: Some of the faculty that has participated in the outreach program of GeMS has developed classes that have been incorporated as part of a academic unit in the curriculum. These educational products have been done at secondary school and college levels, as well as for students and teachers. Throughout the metagenomic libraries (last year product) several hundreds of bacterial clones have been identified that have demonstrated biological activities with medical and biotechnological applications. This includes genes involves in urease utilization, and antibiotic resistance, specifically and so far to tetracycline, ampicillin, and kanamycin. OUTCOMES: The first year for the project served to established new collaborations using the metagenomic libraries generated by the students. During the second year, some of the collaborations continued and other were initiated formally. For example, 1) the graduate student Nolberto Figueroa have been using the libraries to search for caffeine degradation among other complex substrates, 2) the graduate students Josue Malav a graduate students from the Biology department, and the undergraduate students from the Biotechnology program have been using the libraries to search for utilization of phenanthrene, naphthalene. These two collaborations are from the Chemical Engineering Department at UPR-Mayaguez with Dr. Patricia Ortiz, the Chemistry Department at UPR-Mayaguez with Dr. Felix Romn, Oscar Perales (ES&M) in the project involving Novel Magnetic Bio-Nano-Composite Sorbent for Removal of Toxic Metal Ions and Carcinogens from Pollute Waters. So, far, the students that has graduated, and previously participated in GeMS-CSREES project, 75% of them have chosen to continue advanced education, where 50% of them will continue with either an MD/PhD or a PhD in Sciences. Finally, as part of the dissemination activities, specifically the outreach program, the assessment (pre-post tests) has shown a gaining in knowledge of as much as 68% in students and as much as 53% in the secondary school teachers, after the workshop. DISSEMINATION ACTIVITIES: A total of twenty three presentations of the project were done in local research activities, national congresses and symposiums during the second year of the project. The presentations included poster and oral presentations in places such as American Society for Microbiology, the 2009 National Cooperative Soil Survey National Conference NRCS Soils, and the 44th ACS Junior Technical Meeting 29th Puerto Rico Interdisciplinary Scientific Meeting (PRISM) among others. During the second year, more than 350 students, 50 teachers and personnel from different pharmaceutical industries in Puerto Rico have been impacted by the project. Also, Dr. Rios-Velazquez and Dr. Casillas offered a workshop entitled "Fishing for Genes from Forests in Puerto Rico" to 200 students from several schools from Puerto Rico. The one day workshop consisted of a talk about Metagenomics followed by an interactive section using the "Fishing for Genes" activities. The activity was co-sponsored by "El Nuevo Dia" Newspaper in Puerto Rio. Finally, and as the last year, the "Fishing for Genes from Forests in Puerto Rico" workshop was offered to students and teachers participating in the Biotechnology for Educational Training in Teams through Research and Interdisciplinary Center (BETTeR-IC) Summer Camp at UPR-Mayaguez. This summer camp also included international teachers. FUTURE INITIATIVES: A non-cost extenson was requested and approved fr the project. During the summer of 2010, the GeMS participants will attend the University of Connecticut (UConn) in order to receive a workshop in Geomicrobiology by Dr. Pieter Visscher, the director of the Center for Integrative Geosciences at Uconn. The students will perform in situ experiments and will be exposed to state-of-the-art microbiological, and geochemical equipments and techniques. Also, the participants will visit the Dry Forest, and the El Yunque Tropical forest to present the experiments and the results obtained thru the project.

Impacts
Due to the success of the GeMS students' First Short Course in the Generation and Monitoring of Metagenomic Libraries at the Dr. Jo Handelsman's lab. at UW-Madison during summer of 2008, Dr. Haldelsman's submitted a grant proposal in order to keep doing these workshops during the summers to students from UPR-Mayaguez and UPR-Humacao. Also, as an initial collaboration thru GeMS proposal, an NSF proposal has been submitted as a research collaboration between UPR-Mayaguez, UPR-Humacao and UPR-Cayey using the knowledge of metagenomics. After participating in the workshop in metagenomics, a team of students from Upward Bound Science and Math program at Ponce Puerto Rico decided to a research project in the region and participate in a local scientific fair. The team obtained the first place of best project of the fair, as well as first place in applicability, presentation and poster set up. One of the students that began participated in the GeMS project, Miss Rosivette Santiago, graduated from UPR-Mayaguez last June of 2009, decided to apply for a Master's program in Microbiology at UW-Madison to continue research in the area of metagenomics. She considered that the experience in the program was decisive for her to continue graduate school, study at the USA, and continue in the metagenomics area.

Publications

  • A manuscript entitled: Summer Workshop in Metagenomics: One Week and Eight Students Equals Gigabases of New Information. Carlos Rios-Velazquez, Lynn L. Williamson, Karen A. Cloud-Hansen, Heather K. Allen, Matthew D. McMahon, Zakee L. Sabree, Justin Donato, and Jo Handelsman, was finished and will be submitted to Journal of Microbiology Education in October 2009.
  • A second manuscript entitled: Biol 4993: A new course in metagenomics by Carlos Rios-Velazquez, is in preparation and will be submitted in 2009-2010.
  • There is a GeMS blog that was generated by one of the participants (http:www.usdacsreesmetagenomics.wordpress.com) during the academic year 2008-2009, and has been used also for dissemination of the program, as well as a way for a dynamic interaction about the participants.
  • A progress report of the GeMS project was prepared for the Arst and Sciences Deanship of Research at UPR-Mayaguez during academic year 2008-2009.


Progress 07/01/07 to 06/30/08

Outputs
Even though the GeMS program provided stipends for only twelve students; to date the project staff trained a total of twenty-three students which have attended to the different research activities. The participants degrees represented included: Industrial Biotechnology, Industrial Microbiology and Microbiology, Biology, Agricultural Sciences, Wildlife management, and Marine Biology. As part of the conceptual and experimental training of the GeMS project, the students participated in the First Team Meeting on September 21st-22nd, 2007. The students received workshops on how to generate small size metagenomic libraries, and several seminars on natural Resources, Dry and Rainy Forests, Metagenome, Geomicrobiology, Aphis, and Soil. A total of nine experts and researchers discussed the topics actively with the students. During October of 2007, the students attended to a Science and Technology conference (http://cohemis.uprm.edu/scitecc/Scitecc07/scitecc07.html) organized by Dr. Rios-Velazquez, and sponsored by CoHemis and the USDA-CSREES. The main focus of the conference was: Bioprospecting: From the Environment to Synthetic Biology, to Technology-Base Enterprises: Unraveling a Universe of Microbial Life with Novel Activities and Potential Applications, where the GeMS collaborator, Dr. Tamas Torok, from LBNL was the main speaker. After the conference, the students had the opportunity to meet with him and talk about their projects. In May 2008, the GeMS participants visited the El Yunque National Rain and Tropical Forest, where they received a general orientation of the forest's natural resource by a guide. Soil samples were collected to generate the metagenomic libraries in Puerto Rico, and for the summer workshop at UW-Madison. During the summer of 2008 students from UPR-M and UPR-H participated in the First Short Course in the Generation and Monitoring of Metagenomic Libraries at the Dr. Jo Handelsmans lab. at UW-Madison where they learned other techniques on generating and monitoring metagenomic libraries. Also, the students received a seminar on Metagenomics by Dr. Jo Handelsman, and a workshop on the Criteria to consider at the moment to apply for graduate school. The workshop was organized and offered by Dr. Handelsman, Mrs. Lynn Williamson, as well as two PhD students (Mrs. Heather K. Allen, and Mr. Matt McMahon), and one post doctoral Scientist (Dr. Karen Cloud-Hansen). The description of the activities as well as pictures of the participants can be seen at the USDA-CSREES GeMS webpage: http://www.cohemis.uprm.edu/gemspr/. PRODUCTS: During year one, the GeMS students received training in the generation and construction of metagenomic libraries. A total of six metagenomic libraries from both forest consisting of a total of 852,270 clones, were generated by the GeMS's students. This is an important product because not only will be used for the students to continue their training and research, but also will be an important instrument to generate collaboration. After completing the libraries, each student was responsible to design a screening method for functionality. Students were introduced to the main biochemical tests currently used in the General Microbiology laboratory so they can start conducting experiments to test for lipases, and enzymes capable of degradation of complex sugars such as dextran. The students already started performing monitoring of other biocatalytic activities such as proteases, amylases, glycosidases, antimicrobial agents, antimicrobial resistant, presence of quitinases and cellulases, presence of stereases and anti fungic activity. The students have been able to integrate a metagenomic approach starting from soil DNA extraction, to screening method. At K-12 level, and in order to reinforce the knowledge about how to conduct a metagenomic approach a new activity, brochure and manipulative was designed and entitled Fishing for Genes. The activity consisted of a game named Lets go fishing (R) that simulates a Petri dish where each fish represents a colony that carries one specific gene. Once the student is able to fish a colony (the difficulty to catch the fish represents how difficult is to screen for one particular gene in a normal metagenomic study) it has to match each gene with it function looking for it in a cardboard. Depending on the function of the gene, the student matchs it possible origin (from the dry or the rain forest). In every school were the activity was done, a GeMS Lets go fishing (R) activity was given to the school. An important product of the GeMs-USDA-CSREES is a webpage where all the participants, goals, project objectives, collaborators, as well as the activities and achievements are described to the public: http://www.cohemis.uprm.edu/gemspr/. OUTCOMES: A total of twenty experimental skills related by techniques, technologies, and proficiency in using specialized equipment are part of the GeMS project. The knowledge and expertise on such skills have been assessed by the student's perception and a GeMS skills evaluation. Before the GeMS activities, around 20 percent of the specific GeMS propose research skills were previously known by the students. After attending and actively participating in different GeMS activities (workshops, SciTeCC, journal clubs, and lab work), there was an increase of 45 percent in understanding the techniques. From a total of twenty laboratory techniques, technologies and equipment operation; 85 percent (17/20 skills) were considered as mastered by the students after participating in the activities where 30 percent (6/20) was a complete to partial, mastering and 55 percent (11/20) intermediate. The GeMS outreach program has impacted more than 400 students and approximately 100 teachers during year one of the project. All the educational activities were assessed by pre post test that consisted in a ten multiple choice questions given to the participants before and after the Gene Fishing workshop. The results showed an increase in knowledge after the workshop in all the participants, ranging from 27 - 65 percent in students, and 0 - 43 percent in teachers. DISSEMINATION ACTIVITIES: A total of eleven presentations, oral (nine) and poster (two), have been done to disseminate the GeMS project at local (eleven) and National meetings. In one of the local activities, Dr. Rios-Velazquez was the main speaker in the Biotechnology day at UPR-Humacao. In collaboration with professionals from the USDA, NRCS agencies, a series of visits to ten rural schools and summer programs in the East-Central, South and Western part of Puerto Rico were accomplished. The visits consisted of a talk about soil conservation, followed by a short talk by Dr. Rios-Velazquez and Dr. Casillas about the GeMS program. Also, students participating from the Upward Bound (Regular and Science and math) and the BeTTER-IC Summer Camp which represent a total of three Schools from the South, and twenty-six Schools from the West regions of Puerto Rico, respectively, were introduced to the metagenomic topic. Also, Dr. Rios-Velazquez offered a workshop entitled Fishing for Genes from Forests in Puerto Rico to forty-four middle and high school teachers representing twenty-three of the schools of the East and Middle sections of Puerto Rico. The one day workshop consisted of a talk about Metagenomics followed by an interactive section using the Fishing for Genes activities. The activity was co-sponsored by the Department of Education. Finally, and during the Biotechnology for Educational Training in Teams through Research and Interdisciplinary Center (BETTeR-IC) Summer Camp at UPR-Mayaguez, twelve local and international teachers also received the talk Fishing for Genes from Forests in Puerto Rico. The BETTeR-IC Summer Camp is offered to local students and local and international teachers from secondary schools, where the participants discover biotechnology by visiting different interdisciplinary centers such as Engineering, Chemistry, Marine Biotechnology, and Microbial Biotechnology. FUTURE INITIATIVES: The GeMs-USDA-CSREES team plan to visit the Dry forest with the participants to explore more in details the ecology of the area, collect soil samples, and understand by talking with the guides, the importance of performing conservation of the area. Once, the students conclude the generation of the metagenomic libraries, and finish monitoring for specific activities, they will bring a seminar to the Tropical and Dry forests guides, so they can incorporate the knowledge acquired into the guides information that it is transmitted to the public. The GeMs-USDA-CSREES will continue visiting schools in Puerto Rico toshare and educate K-12 students about metagenomics, the research they are doing, and how important is the conservation of our natural resources.

Impacts
The metagenomic libraries generated by the students have allowed the development of new research collaborations with other disciplines and institutions. There are now new initiatives and research collaboration between our lab and 1) the Chemical Engineering Department at UPR-Mayaguez with Dr. Patricia Ortiz, using the libraries to search for hemi cellulosic activities, 2) the Physic department UPR-Humacao with Dr. Ezio Fasoli, searching for activities such as plasminogen activators, and epoxyhidrolases among other new activities, and 3) the Chemistry Department at UPR-Mayaguez with Dr. Felix Roman, Oscar Perales (ES&M) in the project involving Novel Magnetic Bio-Nano-Composite Sorbent for Removal of Toxic Metal Ions and Carcinogens from Pollute Waters. Also, the students have been using and applying the knowledge acquired thru GeMS research to other courses requirements. For example, they have selected in the seminar course, to use metagenomic as the main presentation topic. Finally, some of the teachers that received the seminar-workshop on metagenomics and Fishing for Genes, have incorporated the information and activity as part of the school or program curriculum. One example is Prof, Reynaldo Robles who teach research methods and special topics course at the Upward Bound Science and Math program at the Inter American University at Ponce.

Publications

  • The first USDA-CSREES team meeting was published in the Newsletter CoHemis Up Date. This Newsletter is distributed not only in Puerto Rico, but all Latin America and Spain due to the CoHemis Consortia. Vol 16. No. 1 2007. pg. 9 (http://cohemis.uprm.edu/news/update/update2007.pdf)
  • Just recently, a publication in the internet was done on the project at the SciencePR (http://74.125.45.132/searchq=cache:m6YpM-itzHYJ:www.cienciapr.org/+ metagenomics+of+Puerto+Rican+Soils+en+ciencia+pr&hl=en&ct=clnk&cd=1&g l=pr) September 2008.
  • Also, a publication in the internet was done as the emblematic projects from the departments and Arts and Science deanship at UPR-Mayaguez. (http://blogs.uprm.edu/artesyciencias/2008/10/). October of the academic year 2008-2009.
  • The activity and achievements during our summer visit to UW-Madison were published in: Department of Bacteriology, University of Wisconsin. Newsletter: Fall 2008. http://www.bact.wisc.edu/downloads/BactNewsletter08.pdf