Progress 08/15/22 to 08/14/23
Outputs
Target Audience:Target Audiences: The target audience of this project is undergraduate and graduate students in Puerto Rico whom are considering a degree in Biology, and Agro-Environmental Biology/Agriculture. I was able to reach 18 graduate and undergraduate students with funding from this project. I was able to incorporte Next Generation Sequencing via Oxford Nanopore Flongle sequencing as part of the Insect Taxonomy Course and introduced students to coding in Linux and R as part of the Insect Morphology graduate course. As part of graduate research courses I trained 4 seperate graduate students apart from the other 18 how to build NGS libraries for Illumina Sequencing. This allowed them to work towards completeing their masters projects on time. Changes/Problems:The main difficulties this last year was the ossified nature of the way in which we can teach coureses. There is no coordination this last year with the first year graduate students. This makes it extremely difficult to teach them the bioinformatics (Linux, R, and python) that they need to learn in order to work with next generation sequencing data. They need to learn coding through immersion, and without this it just does not stick for them. My suggestions to the Biology Department going forward are to coordinate a time slot to teach the in coming graduate students as a cohort so that they can finish their classes within the first year and allow the faculty interested in teach graduate courese the ability to tag-team teach short immersion based courese in bioinformatics, NGS library building, and CRISPR so that they can recieve the training they need and get credit for it in order to graduate. The biology department has started to have the incoming first year graduate students all TA at the same time so hopefully future efforts will allow us to teach immersion based courses that are time intensive, but needed in order to recieve the needed information and learn these difficult skills that are equivalent or similar in nature to learning a foreign language. What opportunities for training and professional development has the project provided?Training activities: The best training activities we did this last year was perfect a number of different DNA extraction protocols as well as build next generation sequencing (NGS) libraries for sequencing. The students whom were able to stay in the lab did get a lot out of their NGS training. This type of training is not taught in the laboratories on campus so the students were excited to recieve the training. Professional development: I organized a meeting with students to go over the NSF-GRFP for my senior undergraduate students. In addition to this effort students were encouraged to reach out to top labs in their are of interest to enquire aboutopenings in those labs for potential PhD students. They were also encouraged to apply to those same graduate schools and be aware of the upcoming deadlines and if the GRE was needed. How have the results been disseminated to communities of interest?Mostly the students in the lab end up pushing eachother to do better so if they see that one of their peers is applying to a PhD program then the others get interested as well. What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
IMPACT: The major impact that we had this year was to complete several large amplicon and draft genome sequencing projects. We built libraries for approximatley 40 draft weevil genomes from Puerto Rico as well as another 40 draft genomes for the Auchenorhyncha: Nogodinidae: Colpopterini clade. We also completed 90 amplicon library sequencing of the millipede microbiome project. We have been also able to sequence 15 draft Peripattus juanensis genomes as part of a population genomic study, the first of its kind for Onychophora. 1) Major activities completed / experiments conducted; The major activities we conducted were related to undergraduate and graduate student research projects. There were four major research projects that students were able to complete last year; Nogodinidae phylogenomics ongoing sequencing work; continuing weevil alpha taxonomy and draft genome sequencing of weevils from Puerto Rico; annotation of the Arecerus fasciculatus genome; Peripattus juanensis population genomic sequencing; 18s and 16s millipede microbiome amplicon sequencing; development of a low cost illumina amplicon sequencing protocol for individual museum specimens. 2) Data collected; The results from keeping the lab up and running are really quite good. The students feel a bit intimidated from applying to PhD programs as many of them feel underprepared. Continuing to work on these laboratory projects during quarantine has kept their skills sharp and boosted their confidence. I have three students whom plan to apply to PhD programs this next year, one of whom is an undergraduate student. All of the students have in the lab are not dropping out of college and all plan to graduate. 3) Summary statistics and discussion of results: We have been able keep all fourof the MS students I have now to complete the data collection phase of their MS research which will give them the skillsets they need to go forward with their careers. 4) Key outcomes or other accomplishments realized: A change in knowledge: the most significan change in knowledge of my students over the past year was learning how to build next generation genomic libraries for sequencing on the Illumina platform as well as how to work with PacBio Sequel data from low input libraries. A change in action: This has allowed the students to feel confident that they are well prepared for working in the top labs associated with their research interests. A change in condition: The boost in confidence in compotency in next generation sequencing has opened doors for the most interested students whom plan to apply for PhD programs in some of the top labs in the country.
Publications
|
Progress 08/15/18 to 08/14/23
Outputs
Target Audience: The target audience of this project is undergraduate and graduate students in Puerto Rico whom are considering a degree in Biology, and Agro-Environmental Biology/Agriculture. I was able to reach 18 graduate and undergraduate students with funding from this project. I was able to incorporte Next Generation Sequencing via Oxford Nanopore Flongle sequencing as part of the Insect Taxonomy Course and introduced students to coding in Linux and R as part of the Insect Morphology graduate course. As part of graduate research courses I trained 4 seperate graduate students apart from the other 18 how to build NGS libraries for Illumina Sequencing. This allowed them to work towards completeing their masters projects on time. ? Changes/Problems: The main difficulties this last year was the ossified nature of the way in which we can teach coureses. There is no coordination this last year with the first year graduate students. This makes it extremely difficult to teach them the bioinformatics (Linux, R, and python) that they need to learn in order to work with next generation sequencing data. They need to learn coding through immersion, and without this it just does not stick for them. My suggestions to the Biology Department going forward are to coordinate a time slot to teach the in coming graduate students as a cohort so that they can finish their classes within the first year and allow the faculty interested in teach graduate courese the ability to tag-team teach short immersion based courese in bioinformatics, NGS library building, and CRISPR so that they can recieve the training they need and get credit for it in order to graduate. The biology department has started to have the incoming first year graduate students all TA at the same time so hopefully future efforts will allow us to teach immersion based courses that are time intensive, but needed in order to recieve the needed information and learn these difficult skills that are equivalent or similar in nature to learning a foreign language. In addition to that the CID that processes all of our grants has no central administration oversight so it it completely disorganized. They purposefully left this account open so I could not submit my final report until they had completely audited the grant which took them more than a year, this is the reason why the fina report is so late, I could not submit the final reportu until they completed this process then when they were ready they blame the PI for being late. What opportunities for training and professional development has the project provided? excited to recieve the training. Professional development: I organized a meeting with students to go over the NSF-GRFP for my senior undergraduate students. In addition to this effort students were encouraged to reach out to top labs in their are of interest to enquire about openings in those labs for potential PhD students. They were also encouraged to apply to those same graduate schools and be aware of the upcoming deadlines and if the GRE was needed. How have the results been disseminated to communities of interest? Mostly the students in the lab end up pushing eachother to do better so if they see that one of their peers is applying to a PhD program then the others get interested as well. ? What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
IMPACT: The major impact that we had this year was to complete several large amplicon and draft genome sequencing projects. We built libraries for approximatley 40 draft weevil genomes from Puerto Rico as well as another 40 draft genomes for the Auchenorhyncha: Nogodinidae: Colpopterini clade. We also completed 90 amplicon library sequencing of the millipede microbiome project. We have been also able to sequence 15 draft Peripattus juanensis genomes as part of a population genomic study, the first of its kind for Onychophora. 1) Major activities completed / experiments conducted; The major activities we conducted were related to undergraduate and graduate student research projects. There were four major research projects that students were able to complete last year; Nogodinidae phylogenomics ongoing sequencing work; continuing weevil alpha taxonomy and draft genome sequencing of weevils from Puerto Rico; annotation of the Arecerus fasciculatus genome; Peripattus juanensis population genomic sequencing; 18s and 16s millipede microbiome amplicon sequencing; development of a low cost illumina amplicon sequencing protocol for individual museum specimens. 2) Data collected; The results from keeping the lab up and running are really quite good. The students feel a bit intimidated from applying to PhD programs as many of them feel underprepared. Continuing to work on these laboratory projects during quarantine has kept their skills sharp and boosted their confidence. I have three students whom plan to apply to PhD programs this next year, one of whom is an undergraduate student. All of the students have in the lab are not dropping out of college and all plan to graduate. 3) Summary statistics and discussion of results: We have been able keep all four of the MS students I have now to complete the data collection phase of their MS research which will give them the skillsets they need to go forward with their careers. 4) Key outcomes or other accomplishments realized: A change in knowledge: the most significan change in knowledge of my students over the past year was learning how to build next generation genomic libraries for sequencing on the Illumina platform as well as how to work with PacBio Sequel data from low input libraries. A change in action: This has allowed the students to feel confident that they are well prepared for working in the top labs associated with their research interests. A change in condition: The boost in confidence in compotency in next generation sequencing has opened doors for the most interested students whom plan to apply for PhD programs in some of the top labs in the country.
Publications
|
Progress 08/15/21 to 08/14/22
Outputs
Target Audience:Target Audiences: The target audience of this project is undergraduate and gradaute students in Puerto Rico whom are considering a degree in Biology, and Agro-Environmental Biology/Agriculture. The last year was difficult to reach a broad audience becuase of COVID however I was able to keep my lab up and running which helped the most dedicated students. Efforts: The lab was made available for students to come in and use the lab during the 2020 year. We took some basic precautions such as temperature and hand sanitizer etc. This helped keep the projects going from the previous year and keep the most interested students working in the lab so that they could finish their projects and momentum towards graduation and applying for PhD programs.This helped keep the projects going from the previous year. I am happy to report that we had one of our undergraduates publish his first joural article as well as be accepted into the PhD program at Arizona State University (ASU) PhD program in Evolutionary Biology at theBiodesign Center for Mechanisms of Evolutioncs to studymicrobial Eukaryotes using phylogenomics. Phylogenomics was a specific subject that was enhanced greatly and supported by NIFA-HSI in my lab, so this effort may have helped our student in securing our student a PhDposition in a prestegious program at ASU. So our efforts here at UPRM with funding via the NIFA-HSIare starting to pay off. Changes/Problems:The COVID pandemic greatly impacted the program. For instance we were not able to go to international conferences. Instead I have encouraged students to communicate directly with labs that they are interested for PhD programs and offered to use travel funds for them to visit labs of potential PhD programs. This seems like a better use of their time as at their stage of career development the most important part of the conference is networking. So I simply encouraged them to communicate directly. This strategy has so far been effective with our first student interested in PhD programs being able to get accepted. I hope that remaining five masters studetns will be alble to replicate these results.Second the university is cancelling a lot of the special problems classes which is how I was able to teach the genomics course. The cancelation means that I will have to find another way to reach more students by encorporating the material from the Genomics course directly into existing courses. What opportunities for training and professional development has the project provided?Training activities: The best training activities we did this last year was perfect a number of different DNA extraction protocols as well as build next generation sequencing (NGS) libraries for sequencing. The students whom were able to stay in the lab did get a lot out of their NGS training. This type of training is not taught in the laboratories on campus so the students wereexcited to recieve the training. Professional development:I organized a meeting with students to go over the NSF-GRFP for my senior undergraduate students. In addition to this effort students were encouraged to reach out to top labs in their are of interest to enquire about openings in those labs for potential PhD students. They were also encouraged to apply to those same graduate schools and be aware of the upcoming deadlines and if the GRE was needed. How have the results been disseminated to communities of interest?Mostly the students in the lab end up pushing eachother to do better so if they see that one of their peers is applying to a PhD program then the others get interested as well. We also plan on developing Youtube videos for our laboratory protocols that are in Spanish as well as Youtube videos of our collecting trips that should be of interest to a broader community. What do you plan to do during the next reporting period to accomplish the goals?I have three major priorities for the final year of this project. The first one being to complete any unfinished lab work for undergraduate and graduate student projects. This will help them grauduate on time and allow them to apply to PhD programs if they so choose. The second goal is to develop a Youtube channel that has a combination of laboratory protocols, field trips, and interviews with other scientists. This will help reach a larger target audience here in Puerto Rico as well as other people interested in Entomology and Evolutionary Biology. Last will be to apply for funding to various funding agencies using the research progress that we have made over the last three years of this program. This will keep the program we have built here alive which will benefit local students here at Mayaguez greatly.
Impacts
What was accomplished under these goals?
IMPACT: The major impact that we had this year was fully sequencing the genome of the coffee beanweevil (Araecerus fasciculatus) as part of a graduate student research project. This project will have a significant impact on researchers interested in genomic resources pertaining to Coleoptera as it will be the first Anthribidae to have it's genome fully sequenced. We are currenlty writing up the paper from this project and hope to submit it later this year. 1) Major activities completed / experiments conducted; The major activities we conducted were related to undergraduate and graduate student research projects. There were four major research projects that students were able to complete last year; Sequencing the coffee bean weevil genome; Cosmopolites sordidus paper submitted and accepted with revisions; Nogodinidae phylogenomics ongoing sequencing work; continuing weevil alpha taxonomy. 2) Data collected; The results from keeping the lab up and running are really quite good. The students feel a bit intimidated from applying to PhD programs as many of them feel underprepared. Continuing to work on these laboratory projects during quarantine has kept their skills sharp and boosted their confidence. I have three students whom plan to apply to PhD programs this next year, one of whom is an undergraduate student. All of the students have in the lab are not dropping out of college and all plan to graduate. 3) Summary statistics and discussion of results: This last year do to quarantine the sample size is rather small 5undergraduates and 4graduate students. That said I had my first undergraduate research accepted into a PhD program. 4) Key outcomes or other accomplishments realized: A change in knowledge: the most significan change in knowledge of my students over the past year was learning how to build next generation genomic libraries for sequencing on the Illumina platform as well as how to work with PacBio Sequel data from low input libraries. A change in action: This has allowed the students to feel confident that they are well prepared for working in the top labs associated with their research interests. A change in condition: The boost in confidence in compotency in next generation sequencing has opened doors for the most interested students whom plan to apply for PhD programs in some of the top labs in the country.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2022
Citation:
Alex R. Van Dam, Javier O. Covas Orizondo, Athena W. Lam, Duane D. McKenna, Matthew H. Van Dam. Metagenomic clustering reveals microbial contamination as an essential consideration in ultraconserved element design for phylogenomics with insect museum specimens. 2022. Ecology and Evolution. 12(3) e8625.
- Type:
Journal Articles
Status:
Accepted
Year Published:
2022
Citation:
J. Geli-Cruz, Alexander J. Ropelewski, Carlos J. Santos-Flores, Mat�as J. Cafaro, Alexander J. Ropelewski, Alex Van Dam. Benchmarking assembly free nanopore read mappers to classify complex millipede gut microbiota via Oxford Nanopore Sequencing Technology. Journal of Biological Methods. 2022.
- Type:
Journal Articles
Status:
Under Review
Year Published:
2022
Citation:
Alfredo Rodriguez Ruiz, Alex R. Van Dam. Genome Announcement: Metagenomic binning of PacBio HiFi data reveals a complete genome of Cosmopolites sordidus (Germar) (Coleopterea: Curculionidae, Dryophthorinae) the most damaging arthropod pest of bananas and plantains. PeerJ. 2022
|
Progress 08/15/20 to 08/14/21
Outputs
Target Audience:Target Audiences: The target audience of this project is undergraduate and gradaute students in Puerto Rico whom are considering a degree in Biology, and Agro-Environmental Biology/Agriculture. The last year was difficult to reach a broad audience becuase of COVID however I was able to keep my lab up and running which helped the most dedicated students. Efforts: The lab was made available for students to come in and use the lab during the 2020 year. We took some basic precautions such as temperature and hand sanitizer etc. This helped keep the projects going from the previous year and keep the most interested students working in the lab so that they could finish their projects and momentum towards graduation and applying for PhD programs. Changes/Problems:The COVID pandemic greatly impacted the program. For instance we were not able to go to international conferences. Instead I have encouraged students to communicate directly with labs that they are interested for PhD programs and offered to use travel funds for them to visit labs of potential PhD programs. This seems like a better use of their time as at their stage of career development the most important part of the conference is networking. So I simply encouraged them to communicate directly. Second the university is cancelling a lot of the special problems classes which is how I was able to teach the genomics course. The cancelation means that I will have to find another way to reach more students by encorporating the material from the Genomics course directly into existing courses. What opportunities for training and professional development has the project provided?Training activities: The best training activities we did this last year was perfect a number of different DNA extraction protocols as well as build next generation sequencing (NGS) libraries for sequencing. The students whom were able to stay in the lab did get a lot out of their NGS training. This type of training is nottaught in the laboratories on campus so the students were excited to recieve the training. Professional development?I organized a meeting with students to go over the NSF-GRFP for my senior undergraduate students. In addition to this effort students were encouraged to reach out to top labs in their are of interest to enquire about openings in those labs for potential PhD students. They were also encouraged to apply to those same graduate schools and be aware of the upcoming deadlines and if the GRE was needed. How have the results been disseminated to communities of interest?Mostly the students in the lab end up pushing eachother to do better so if they see that one of their peers is applying to a PhD program then the others get interested as well. We also plan on developing Youtube videos for our laboratory protocols that are in Spanish as well as Youtube videos of our collecting trips that should be of interest to a broader community. What do you plan to do during the next reporting period to accomplish the goals?I have three major priorities for the final year of this project. The first one being to complete any unfinished lab work for undergraduate and graduate student projects. This will help them grauduate on time and allow them to apply to PhD programs if they so choose. The second goal is to develop a Youtube channel that has a combination of laboratory protocols, field trips, and interviews with other scientists. This will help reach a larger target audience here in Puerto Rico as well as other people interested in Entomology and Evolutionary Biology. Last will be to apply for funding to various funding agencies using the research progress that we have made over the last three years of this program. This will keep the program we have built here alive which will benefit local students here at Mayaguez greatly.
Impacts
What was accomplished under these goals?
IMPACT:The major impact that we had this year was fully sequencing the genome of the Plantain Weevil (Cosmopolites sordidus) the worlds most damagaing beetle pest of banannas an plantains, as part of an undergraduate research project. This pilot project will have a significant impact on researchers interested in genomic resources pertaining to Coleoptera. It also proves on a small budget we can successfully fully sequence an arthropod genome as part of an undergraduate education. We are currenlty writing up the paper from this project and hope to submit it later this year. This project can serve as a novel method to develop a core genomics course for our undergraduate students in Puerto Rico and mainland US in the future to say nothing about the scientific impact of producing these valuable genomic resources for the scientific community. 1) Major activities completed / experiments conducted;The major activities we conducted were related to undergraduate and graduate student research projects. There were fourmajor research projects that students were able to complete last year; Sequencing the plantain weevil genome; Scolopendramorpha phylogenomics; Nogodinidae phylogenomics; weevil alpha taxonomy. 2) Data collected; The results from keeping the lab up and running are really quite good. The students feel a bit intimidated from applying to PhD programs as many of them feel underprepared. Continuing to work on these laboratory projects during quarantine has kept their skills sharp and boosted their confidence. I have three students whom plan to apply to PhD programs this next year, one of whom is an undergraduate student. All of the students have in the lab are not dropping out of college and all plan to graduate. 3) Summary statistics and discussion of results: This last year do to quarantine the sample size is rather small 7 undergraduates and 3 graduate students. However one of the graduate students graduated and finished his thesis, the other two continue to work towards graduation. 4) Key outcomes or other accomplishments realized: A change in knowledge:the most significan change in knowledge of my students over the past year was learning how to build next generation genomic libraries for sequencing on the Illumina platform. A change in action:This has allowed the students to feel confident that they are well prepared for working in the top labs associated with their research interests. A change in condition:The boos in confidence in compotency in next generation sequencing has opened doors for the most interested students whom plan to apply for PhD programs in some of the top labs in the country.
Publications
- Type:
Journal Articles
Status:
Accepted
Year Published:
2021
Citation:
ALFREDO RODRIGUEZ RUIZ AND ALEX R. VAN DAM (2021) A NEW SPECIES OF DECUANELLUS OSELLA (COLEOPTERA: CURCULIONIDAE: MOLYTINAE: LYMANTINI) FROM MARICAO STATE FOREST, PUERTO RICO. The Coleopterists Bulletin.
|
Progress 08/15/19 to 08/14/20
Outputs
Target Audience:The target audience are Puerto Rican students at the Masters and Bachelors level whom are interested in Entomology and related fields. Last year there was participation of 4graduate students and 1undergraduates in the Bioinformatics and genomics projects funded by this grant. Additionally 10 undergraduates and 4graduate students participated taxonomy related projects including species descriptions of new species of weevils from Puerto Rico. Changes/Problems:Due to the COVID pandemic I was not able to hold the short course that I had planned for the summer. I plan to modify the material that I have and at least teach the bioinformatics portion of the course as an e-course. This way students in PR from other parts of the island have the ability to learn the bioinformatics portion of the planned course. The other change that I would like to make is to have a lot more guest speakers. If the COVID epidemic continues it might make sense to send students to their top PhD program picks recruitment sessions or interview at potential labs so that they can get to know future majro professors a bit more before they apply. This could give the students a better chance at getting into the program that is their top choice and the best fit for them. What opportunities for training and professional development has the project provided?Training Activities: The training activities this year were primarily in the laboratory where I helped the students gain proficiency in building genomic libraries from scratch. These training activities includeded DNA sonication, size selection, and adapter ligation. I also helped the students learn how to describe new species using classical taxonomy techniques. These skillsets included taking auto-montage photographs, classic morphometrics, and scientific illustration. Professional development: We had a guest speaker whom was from Finland talk about his experiences moving from Cuba to Finland to complete his PhD there. We also had a small symposium where students presented the taxonomic work they were doing in the lab to eachother. How have the results been disseminated to communities of interest?Primarily we have beeen depositing the data that we have generated in public databases. I hope to construct an online bioinformatics course for Puerto Rican students in the upcoming year. What do you plan to do during the next reporting period to accomplish the goals?In order to reach a broader audience I will have to develop the in person bioinformatics course as an interactive online course instead due to the COVID pandemic. The other thing that we need to do is to have more potential schools and labs give lab talks as most of the conferences were closed last year. By having more skype interviews with collaborative labs it will keep the idea of PhD programs present in the student's minds and give them a chance to hear other Entomologists perspective on career paths. This will greatly increase their professional development by giving them more ideas about potential PhD programs.
Impacts
What was accomplished under these goals?
IMPACT:The major accomplishment this was establishing the lab's ability to build high quality genome-libraries from museum specimens, and training students to become proficient in genome library construction. Students successfully built 16 genomic libraries in our laboratory without outside assistance from other facilities. These libraries are from local and exotic weevils to Puerto Rico, and will be used in a forthcoming work on weevil phylogenomics. Additionally PI and an undergraduate student successfully constructed and sequenced a HI-C library of the plantain weevil that will be used in conjunction with PacBio sequencing this year to build a chromosome scale genome of the Plantain weevil. The Plantain weevil is one of the most damaging pests globally of bananas and plantains so this will certainly be a feather in our cap as well as for the HSI program if successful. 1) Major activities completed / experiments conducted; Hard Skill Sets: I was able to train my four graduate and one undergraduate student in Illumina library construction using hands on laboratory training. Thses libraries were also successfully sequenced. We built these libraries from scratch and delivered them ready to sequence. This is a new accomplishment for our lab to deliver and sequence home produced libraries from scratch without any outside assistance. The investment in the Covaris ultrasonicator paid off dividends as we were able to construct 11 draft genomes using these libraries that we built in the lab. Soft Skill Sets: One of the bigger accomplishments this year was continuation of the projects that we started during the Insect Taxonomy class. One of my undergraduate students is close to completeing a species description of a new species of weevil from Maricao Puerto Rico. We hope to submit this publication later this year. Additionally one of my masters students is also close to submitting a new species description of a Anthribidae weevil from Puerto Rico that he started during the Insect Taxonomy class. One of my hopes for the class is to teach the students how to describe species, and we seem to be starting to hitting our stride in that respect as we have several new taxonomic species descriptions in the works. 2) Data collected: I collected data on the students ability to complete laboratory work including building genomic libraries from start to finish. My four graduate students and one undergraduate are now completely fluent in the laboratory methods needed to build successful genomic libraries. 3) Summary statistics and discussion of results: 100% of the students whom have been dedicated and involved in the laboratory work are getting quite good at building genomic libraries and performing DNA extractions with efficiency and reproducability. This is certainly a confidence booster for them that they have a highly marketable skill set that will help carry them forward at the PhD level when they graduate. 4) Key outcomes or other accomplishments realized: A change in knowledge: Hard Skills: As 100% of the students did not have prior experience building genomic libraries from scratch the last year was successful in building up their hard skillsets. They also greatly improved their scientific illustration abilities and species description skillset for classical taxonomy. Soft Skillsets: Students learned how species descriptions is not descriptive science but hypothesis testing. They also learned how to stack multiple projects in order to flesh out their CVs. For example the four students in my lab help eachother out with their projects and farm out specific skillsets to help further larger projects. This is a skill that collaboration leads to a fuller resume with more publications and is a very important soft skill to be learned. Going it alone is more difficult and leads to fewer publications where as collaboration makes life easier and will give them more publications in the end. Directed Laboratory Research: In terms of research outcomes we are much closer to publishing a higher level phylogeny of the Scolopendroidea, Cryptorhynchinae, and Cosmopolites sordidus genome. These three projects still require more work to finish them but they should be completed this upcoming year. My students also got to meet a visiting scientist from Finland whom is originally from Cuba and now completeing his PhD in systematics at Turku University in Finland. This was a good experience for my students as they got his perspective on the PhD path in Europe which gives them additional resources and ideas for how to complete their journey to the PhD.
Publications
|
Progress 08/15/18 to 08/14/19
Outputs
Target Audience:The target audience are Puerto Rican students at the Masters and Bachelors level whom are interested in Entomology and related fields. Las year there was participation of 19graduate students and 10 undergraduates in the Bioinformatics projects funded by this grant. Additionally 10 undergraduates and 6 graduate students participated in a next generation sequencing library construction course as part of a new Arthropod Genomics Course. Changes/Problems:While this project had many successes in the first year we also had a number of setbacks as well. One of the biggest unexpected hurddles of this project is just how long it takes to order reagents for doing lab work here in Puerto Rico. This pushed back being able to show students laboratory work back about six months. The CID at UPRM does not always process the pruchase requests or payment requests from vendors adding to the difficulty in ordering reagents. I also ran into some trouble validating the primers for the meta-barcoding study that was inteneded as a masters project and as an introduction for the undergraduates. Since the long-range PCR seems to be very sensitive to PCR inhibitors I don't think it will make for a good introductory experience for the undergraduates. That said I think if I am able to purchase some equipment to do ultrasonication which is highly repeatable. The metabarcoding project will remain a masters student project but I am abandoning it as a way to teach undergraduates as it is just too difficult for undergraduates. Teachign graduate and undergraduate students genomic library construction techniques is not currently offered at UPRM. Having an ultrasonicator will allow us to use sample with even small amounts of starting material, and it will make teaching undergraduates genomic library preparations techniques considerably easier with more consistent results. With phylogenomics we only need about 10% genome coverage with a draft genome assembly to find enough universal markers thorughout different related insect genomes to reconstruct a phylogeny using maximum likelihood techniques. I think also by making the graduate course also open to undergraduates will alos greatly increase participation as few undegraduates sign up for graduate courese as it requires more permissions. This will make for a six week short course that has a much higher probability of success. It will also improve their bioinformatic skills to have them meet for consecutive days during the work week without many days on inactivity as the semester system has. I will be applying for a change in the budget to purchase an ultrasonicator so that we can run the short course next summer, pending approval of course. I would like to discuss these changes with the HSI program and will be following up with e-mail/phone conversations. What opportunities for training and professional development has the project provided?Training Activities: One of the best things that has happened this year is the growth and development of the advanced undergraduates and graduate students have been able to train new and incoming undergraduates in my lab in DNA extraction techniques and sorting of arthropod specimens from leaf litter samples. It was really good to see the students who have hung in there over the last year take leadership roles in passing down their knowledge to the newer members of my lab. Professional development: This last year I was able to take one of my masters student's to the USDA-HSI/AAHHE conference. I think it was a good experience for the student to see the diversity of research being done at other universities as well as make conections at other universities of interest. How have the results been disseminated to communities of interest?So far results from our research have been disseminated as publications in scientific journals and data sets on NCBI. That said I would like to develop more outreach activities at the collection to K-12 students. I have a new masters student in my lab, as part of his masters thesis he will be developing educational displays about arthropods aimed at elementary school children. We hope to interact more with the local elementary schools and find out how this affects their attitudes towards arthropods. What do you plan to do during the next reporting period to accomplish the goals?We had a number of successes over the semester. Probably the biggest one was exceeding the number of graduate students that we aimed to reach in the first year. We also assembled a large number of genomes (11 in total assembled from novel data generated the previous summer), and produced 12 new genomic data sets from weevils, and libraries for one chromosome level genome for the plantain weevil. That said there could be a lot of improvements made in their ability to make leaps of knowledge in their bioinformatic abilities at the masters level. One of the biggest problems was the gaps in days between classes having only meetings twice a week for 4 hours. I think the laboratory course would work much better as a 4-6 week short course during the summer where they meet five days a week with 6 hours a day of class time. As coding is essentially like learning new language one of the best ways to do this is through emersion. I think a summer coding "genomics/bioinformatics-bootcamp" would be much more effective at helping students to learning bioinformatics and genomics. Essentially programming is learning a new language and the best way to do this is through emersion. I think a summer course would also give a lot more undergraduates the opportunity to develop their coding skills. There are a number of other universities that run their core introductory bioinformatics course in this way. Currently no such course is offered at UPRM. As students often don't have enough time during the week to dedicate to multiple laboratory sessions per-week, summer is the perfect time to offer this course. I think this would raise undergraduate attendance significantly. The students also greatly prefered the combination of the laboratory and bioinformatics classes combined together. Probably the best way that this course would work, would be for the students to participate in library preparations in the first week of the course, the middle three weeks a bioinformatics bootcamp, the final week they analyse the data they generated the first week. This would make for a very compact six week short course. In terms of the Entomological taxonomic training that will still take place as a semester long course each year and in my laboratory throughout the year will continue as planned.
Impacts
What was accomplished under these goals?
Impact: During the last year, 19graduate students and 10 undergraduates were trained genomic laboratory methods and in genome and transcriptome bioinformatic assembly. 12of those graduate students recieved training in phylogenomics, and training in genomic laboratory methods as part of courses offered at UPRM. Other students enrolled in insect morphometric class that focused on using massive morphological data sets from museum specimens.Our collaboration withe the Pittsburgh Supercomputing Center (PSC) was very helpful and allowed for students to get a legitimate experience doing some fairly memory intensive bioinformatic computing. 1) Major activities completed / experiments conducted; Hard Skill Sets: During the first semester of last year I taught two graduate courses, Insect Morphology and Systematic Biology. in the Insect Morphology Class I encrorporated elements where the students were able to perform morphometric analyses on sample insect data sets using iDigBio. The class was taught mostly in the R programming language and linux. Students learned how to find specimen record data as well as images from museum records and perform morphometric analyses using R packages using the specimens that they downloaded images of. They also developed skills in the R programming language to perform statistical tests for significant differences between specimens. These morphometric and statistical knowledge of R have a wide range of applications. For example they can not only be used to help identify morphological differences between species but also for differences in quantitative traits caused by disease or genetic variablitiy within a population. In the Insect Genomics course we focused on both the laboratory techniques and bioinformatics involved in next generation sequencing and genome assembly of arthropods. Students were also recieved training in high molecular weight DNA extractions. I was also able to train graduate students in class on genomic DNA library construction for next generation sequencing. Finally we were able to learn how to take the raw next generation sequencing data and complete genome reconstruction. This bioinformatics portion of the class again used linux command line scripting and programs. The students really liked this class as it contained both the laboratory and bioinformatics methods. Soft Skill Sets: The major goal of developing softkills sets was to simulate in a learning environment the day to to day team based problem solving and hypothesis formation where insect taxonomy and genomics intersect with agriculture and biotechnology. The hope was to give the students small projects at the end of each course that they could work on as a team and implement many of the hardskills that they learned to solve a novel problem they had not yet seen before. Being faced with a novel problem and forming hypotheses and experiments in order to solve that problem is an important milestone between an undergraduate or graduate student who reaches the masters level or not. In genomics one of the biggest hurdles to this is having enough basic coding ability to know where to look or how to breakdown the data into managable chunks in a stepwise process in order to complete a task. Most of the students were able to formulate their own solutions which gave them added confidence to be able to use genomics in their future research. Specific Research Objectives: The students in my laboratory continued with a variety of projects that involved both genomics and classical morphology. For example we are in the process of describing some new species of weevils from Puerto Rico. We also produced genomic libraries for 12 genomic libraries for Cryptorhinchinae weevils. Additionally we produced genomic libraries for Cylas formicarius (the sweet potato weevil) and Cosmopolites sordidus (the plantain weevil). We were also able to make two Hi-C genomic libraries for C. sordidus and are in the process getting these libraries sequenced to produce a chromosome level genome assembly of the C. sordidus. During the Fall semester of 2018 I held fair and open recruitment call for the masters student scholarship. This student will be responsible for conducting research on the differential expression of seed weevils (Bruchidae) on bean pests here in Puerto Rico. I was able to find a Puerto Rican student who wanted the masters student (Anjel Castro) whom is highly qualified to fill the position and he will be starting in my lab this August to conduct this research. I have also been trying to develop strategies to get more graduate students to pursue a PhD in Entomology and related fields as it is a challange here to get our masters student to pursue these positions. One thing that the students all agreed upon was that at our lab meetings I had guest skype talks from a scientist at the USDA and they found this skype talk very helpful to identify what was key to their career track success in science. It was eye opening to me to see the large impact that this skype talk had on the students and we plan to have many more of these in the future. 2) Data collected: I collected data on the students ability to complete their bioinformatic course work and whether or not they are able to improve key bioinformati competency related to genomics. 3) Summary statistics and discussion of results: Of the 19 graduate students whom participated in the courses supported by this program 100% of them developed basic liunx compotency and bioinformatic competency. That said only 8 of the students were able use what they had learned and able to make jumps ahead in their ability to solve novel bioinformatic problems completely independantly. All students were able to complete all of their required projects but needed additional assistance from the instructor to do so. At the masters level all the students should have been able to use what they had learned to jump ahead and solve novel problems. The reasons for this is that the class structure of the semester system is not condusive to learning bioinformatics. Students often needed refreshers every week to go over what we had learned last week in terms of coding ability. 4) Key outcomes or other accomplishments realized: A change in knowledge: Hard Skills: The graduate students whom atteneded the classes and laboratory work supported by this project showed markedley improved skills in genomics and bioinformatics and how this relates to Entomology. 100% of the students had little to zero coding experience prior to joining these class and afterwards they were fairly compotent in the overall data processing approach needed to carry out a basic genome assembly and phylogenomic analyses. Soft Skills: Students whom participated in my courses did to improve their confidence with next generation sequencing technology. The students who participated in my laboratory research got the most benefit from hearing about other successful scientists career paths so that they could begin to see patterns that led to their success. Directed Laboratory Research: Students whom participated in directed laboratory research did see a marked increase in their Entomological knowledge. They also developed the laboratory skills needed to be successful researcher in the field of genomics and phylogenomics related to arthropods. They propbably got the most benefit as well in their soft skill sets in terms of our laboratory meetings when we had skype interviews from FANH Scientist as they could begin to see how important getting a PhD is to the overall success at landing a career in science. Actually seeing multiple examples or role models seemed to have the biggest impact on the graduate students even more so than developing new skills. In order to change this condition more globally at our university I want to start involving more laboratories with NGS directed research and hopefully this will help other lab's students to succeed as well.
Publications
- Type:
Journal Articles
Status:
Submitted
Year Published:
2019
Citation:
Massini Espino, M., A.M. Mychajliw, J.N. Almonte, M.E. Allentoft, A.R. Van Dam. 2019. Raptor pellets as archives of invasion histories: phylogeographic insights from the first black rat, Rattus rattus, mitochondrial genome in the Caribbean. The Holocene.
|
|