Progress 09/01/21 to 08/31/24
Outputs
Target Audience:Throughout this project, our main target audiences were Agricultural Sciences and Farm Animal Health and Nutrition (FAHN) workforce trainees (university students) from diverse fields of study seeking higher-level skills in agricultural microbiome science. Through the direct activities of this project, we reached our target audience of graduate and undergraduate student trainees from different majors and departments, including plant science, soil science, food science (food safety), animal science, microbiology, and biology, and including about 45% of students coming from groups that are underrepresented in STEM, as follows: Students enrolled in 3 new undergraduate course-based research experience (CURE) courses and graduate research-based courses created by this project (38 students targeted: 23 undergraduates + 15 graduate students). Students enrolled in additional classes which used protocols or data or other materials from this project (220 students targeted: 180 undergraduates + 40 graduate students). Summer research Interns (48 students targeted: 25 Biology/Microbiology, or Chemistry, or Pre-Vet Program + 9 Computer Science/Math + 13 High School Research Student + 1 Graduate Intern). Graduate students involved in learning to create educational aids and materials (3 grad students targeted). In addition to students at Texas Tech, our direct activities targeted scientists broadly, at diverse career stages, through our trainee conference presentations delivered to scientists in fields such as nematology, entomology, microbiology, agronomy, crop science, soil science, animal science, neuroscience, and nutrition (19 presentations delivered at 3 local conferences, 1 regional conference, 5 national conferences, and 1 international conference). Target audiences also included educators, including the lead PD and Co-PDs as well as additional faculty/instructors in other Departments and Colleges at Texas Tech University, and Graduate Teaching Assistants. Specifically, our educational activities targeted the following instructors: Lead PD Dr. Amanda Brown, Department of Biological Sciences, Texas Tech University, Co-Project Directors Dr. Michael Ballou, Department of Veterinary Sciences, Texas Tech University; Dr. Marcos X. Sanchez-Plata, Department of Animal & Food Sciences, Texas Tech University; Dr. Sukhbir Singh, Department of Plant and Soil Science, Texas Tech University; and Collaborator Dr. Lindsey Slaughter, Department of Plant and Soil Science, Texas Tech University. Indirectly, the project targeted educators at any institution interested in building similar CUREs and graduate courses in advanced techniques in agricultural microbiome science who will be able to access and use our educational aids and curricular materials and protocols, hosted on the lab website. Finally, due to the nature of the research-based courses that we have developed, this project has produced a large amount of sequenced DNA/RNA data from 12 real agricultural microbiome projects/experiments. These outputs generated by the project target scientists and stakeholders who may use these datasets for biological inferences. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Throughout this project, the central objective was to provide opportunities for advanced training and professional development in agricultural microbiome science to (1) faculty advanced training, (2) teaching assistant training, (2) graduate student research training in the classroom, (3) undergraduate student training in research in course-based undergraduate experiences (CUREs), (4) undergraduate summer intern research training, and (5) others across disciplines associated with these educational experiences and programs. In addition to research training, many of the interns and CURE students, and all of the graduate students also gained valuable training in scientific communication through written reports, class and conference presentations, and participating in drafting manuscripts for publication. In total, training outcomes included formal classroom teaching in hands-on original research for 38 students, research training as summer internships for 48 students, and indirectly to students in other courses gaining training through integrating some of these new project-related course materials for 220 additional students. Three graduate students also gained trainings in pedagogy and interdisciplinary teaching in the process of assisting in developing course materials. The specific agricultural microbiome science trainings and trainees during the project were as follows: Year 1: Fall 2021: 9 undergraduates were taught in the project-funded "CURE Frontiers in Host-Microbe Genomics" course plus 3 graduates in "Advanced Frontiers in Host-Microbe Genomics" course. Class Project Training: (1) Testing gene expression changes in agricultural biofilm microbes under host- and no-host conditions using transcriptomics; (2) Testing plant species effects in endophytic microbiome recruitment in a common soil using metagenomics; (3) Testing pest insect bacteriome changes using amplicon sequencing; (4) Testing nematode-microbe interactions in irrigated crops using metagenomics. Some of the protocols, pedagogy, and materials developed from this CURE/Advanced course were also tested on 8 graduates in "Foundations of Microbiology Research" course, and 2 graduates in "Shotgun Metagenomics" course, and 1 graduate student in "Bioinformatics Research Seminar" course. Spring 2022: Some of the protocols, pedagogy, and materials developed from this CURE/Advanced course were also tested on 55 undergraduates and 5 graduates in "Microbiomes" (not a CURE). Similarly, some of this material was tested on 2 graduate students in "Genome Finishing Techniques" and "Metatranscriptomics". Summer 2022: 9 Interns in Biology/Microbiology/Chemistry/Pre-Vet: Kierra Hughes, Sushim Mishra, Micah Garner, Christina Kelley; Daniel Hsia, Joelle Jang, Ahmad Alard, Paris Balfour.1 High School Research Student: Jalaja Saireddy. Intern Project Training: Insect microbiome multi-omics; Plant-nematode-bacteria interaction genomics; Field-sampled pest and microbiome metagenomics; Effects of plant crop; genotype on endophytic microbiome genomics; Animal gut-brain axis microbiome manipulation; Rumen microbiota metatranscriptomics. Faculty Professional Development: PD Brown gained advanced pedagogy training through the STEM Teaching, Engagement & Pedagogy Program at Texas Tech. This program provided expert guidance on improving effectiveness of CURE-format courses. Year 2: Fall 2022: 5 undergraduates were taught in the project-funded "Microbiomes CURE" course and 7 graduates were taught in the "Microbiomes Research Methods" course. Class Project Training: (1) Testing the effects of warming and irrigation on soil microbiota associated with cotton using multiplex quantitative amplicon sequencing; (2) Testing microbiota effects on Salmonella abundance in chicken/poultry processing using quantitative amplicon sequencing; (3) Testing aphid-susceptible and aphid-resistant sorghum endophyte communities using metagenomics; (4) Testing the effects of viruses/phage on microbes in biofilm-forming insect gut microbiomes using Hi-C. Some of the protocols, pedagogy, and materials developed from this CURE/Advanced course were also tested on 3 graduates in "Foundations of Microbiology Research" course. Spring 2023: Some of the protocols, pedagogy, and materials developed from the CURE/Advanced course were tested on 57 undergraduates and 2 graduates in "Microbiomes" course, and 1 student in "Metatranscriptomics" course. Summer 2023: 8 Interns in Biology/Microbiology/Chemistry/Pre-Vet: Reanne De Souza, René Zambrano, Rylee Dallison, Chad Thornton, Angela Marentes, Kabuyi Ndaya, Logan Foster, Grayson Ressler. 6 Interns in Computer Science/Math: Zelepe Coulibaly, Alli Saenz, Ayobami Ajala, Isaac Doggett, Nathan Pierce, Sydney Rash. 7 High School Research Students: Zafeer Arefeen, Trista Arnold, Savanna He, Olivia Smith, Jason Ye, Bobby Stephens, Aaron Li. Intern Project Training: Animal gut-brain axis beneficial microbiome manipulation; Plant-nematode-bacteria interaction genomics; Effects of plant crop genotype on endophytic microbiome transcriptomics; Pest insect microbiome genomics and fluorescence in situ hybridization; Bioinformatic data-mining soil and animal microbiomes; Field-sampled pest and microbiome metagenomics. Year 3: Fall 2023: 7 undergraduates were taught in the project-funded "Microbiomes CURE" course and 1 graduates were taught in the "Microbiomes Research Methods" course. Class Project Training: (1) Testing arbuscular mycorrhizal fungi responses to climate change across 50 years in museum plants using amplicon sequencing; (2) Testing microbial exchanges between field-caught pest insects using quantitative amplicon sequencing; (3) Testing parasitic nematode diversity across geographic and soil conditions using amplicon sequencing. Fall 2023: 2 undergraduates were taught in the project-funded "Bioinformatics CURE" course and 4 graduates were taught in the "Bioinformatics of Agricultural Microbiomes" course. Class Project Training: (1) Bioinformatic analysis of gene expression changes in plants during drought; (2) Bioinformatic analysis of sorghum root exudate effects on nematodes and bacteria; (3) Bioinformatic analysis of animal gut microbiome spatial data from Hi-C; (4) Bioinformatic analysis of RNA-viruses within crop plant tissues. Some of the protocols, pedagogy, and materials developed from this CURE/Advanced course were also tested on 10 graduates in "Foundations of Microbiology Research" course. Spring 2024: Some of the protocols, pedagogy, and materials developed from this CURE/Advanced course were also tested on 68 undergraduates and 5 graduates in "Microbiomes" course. Similarly, some of this material was tested on 5 undergraduates in the Honors College Plus Projects. Summer 2024: 8 Interns in Biology/Microbiology/Chemistry/Pre-Vet: Emily Chacon, Emmalee Rose, Jessica Bailey, Linsey Hunter, Sydney Banovic, Angela Marentes, Faith Ruckey, Katheryne Avila Cortes. 3 Interns in Science/Math: Shanthan Sudhini, Gargi Pathak, Rohit Chabukswa. 5 High School Research Students: Mary Kim, Carolina Acosta, Jamie Kim, Shirley Chen, William Xie. 1 Graduate Intern Student: Aaliyah Lawson. Intern Project Training: Animal pathogen transcriptomics; Animal beneficial microbiome manipulation (antibiotic/probiotic); Plant-nematode-bacteria interaction genomics; Pest insect microbiome genomics; Rhizosphere community modeling; Genome-wide data-mining/bioinformatics for soil microbiomes; Field-sampled plant-pathogen data analysis. Faculty Professional Development: PD Brown gained additional high-level NGS training at the 2023 Genome Informatics Meeting at Cold Spring Harbor Laboratories, and cutting-edge interdisciplinary agricultural science and CURE teaching training through workshops at the International Congress of Entomology in 2024. How have the results been disseminated to communities of interest?Throughout this project, results have been disseminated in the following ways: Community Outreach and Involvement: We engaged in outreach to local High Schools to share the project features and recruit students as summer researchers. In total, 13 high school students worked in the lab during the project, learning about a wide range of agricultural microbiome genomics topics and techniques. Datasets, Curriculum Materials, and Protocols Shared on GitHub: We have deposited guides (wet lab and dry lab) and sample datasets onto our lab's GitHub repository. Datasets Shared on NCBI: We have been submitting raw and analyzed DNA and RNA sequence data on NCBI's SRA database and the GenBank nucleotide (nt) and genome databases. Conference Talks: Mentees associated with these projects and courses have presented 6 talks at general and specialized scientific meetings, as follows: Undergraduate, Reanne De Souza presented a talk titled "Analyzing antifungal activity in domesticated and wild banana plants and their extracted microbiomes" to a diverse general audience at the Texas Tech University Transformative Undergraduate Experiences Symposium Oct. 20-21, 2023, in Lubbock, TX. Graduate student Christian Guerrero, who worked closely with teams of summer interns associated with this project, presented a talk titled "Microbial modulation of aggression in crickets" at the Texas Branch American Society for Microbiology (ASM) Fall Meeting, Oct. 26-28, 2023, in Stephenville, TX, and a talk titled "Cricket microbiome modulation changes territorial-related aggression" at the International Congress of Entomology, Aug. 25-30, 2024, in Kyoto, Japan. Graduate students Taranjot Kaur and Shiva Aghdam and Era Sharma, who were in project-supported classes or train summer interns in the project, presented talks at the Texas Tech Annual Biology Student Symposium (TTABSS), Feb. 9-10, 2024, in Lubbock, TX, titled "Transcriptomic assessment of the effects of the sorghum root exudate, sorgoleone, on root-lesion nematodes", "Uncovering diverse roles of endophytic microbiomes in wild and cultivated bananas using metatranscriptomics", and "Development of an automated NCBI SRA mining tool for target discovery", respectively. Conference Poster Presentations: Mentees associated with these projects and courses have presented 13 posters at general and specialized scientific meetings, as follows: Undergraduate researcher Daniel Hsia together with other mentees presented two posters in 2023, titled "Analyzing Microbiome Changes in Wild and Domesticated Bananas using Metatranscriptomics" at the Texas Tech Annual Biology Student Symposium (TTABSS), Mar 31-Apr. 1, Lubbock, TX and at the 15th Annual TTU Undergraduate Research Conference, Apr 11-13, Lubbock, TX. Graduate student Amandeep Kaur and her mentee undergraduates presented 4 posters at conferences, including a poster titled "High prevalence of Wolbachia and Cardinium revealed in different geographical populations of plant-parasitic nematodes" at the Society of Nematologists Meeting, Aug. 4-9, 2024, in Park City, UT, and "Analysis of endosymbiont prevalence reveals unexpectedly widespread abundance in nematodes" and "Exploring bacterial endosymbionts Wolbachia and Cardinium in plant-parasitic nematodes" at the 16th Annual TTU Undergraduate Research Conference, Apr. 9-10, 2024, in Lubbock, TX, and "PCR screening of plant-parasitic nematode communities for Wolbachia" at the SACNAS National Diversity in STEM (NDiSTEM) Conference, Oct. 26-28, 2023, in Portland, OR. Graduate student McKinlee Salazar and her undergraduate mentees also presented 4 posters at conferences, including a poster titled "Complex multipartite microbial symbioses in treehoppers characterized with genomics and metatranscriptomics" at the International Congress of Entomology. Aug. 25-30, 2024, in Kyoto, Japan, a poster titled "Visualizing symbionts in tissue-sectioned treehoppers using fluorescence microscopy" at the SACNAS National Diversity in STEM (NDiSTEM) Conference, Oct. 26-28, 2023, in Portland, OR" a poster titled "Cooperation Between Symbiotic and Trophobiotic Partners of Membracids May Be Driven by Bacteria" at the 15th Annual TTU Undergraduate Research Conference, Apr 11-13, 2023, in Lubbock, TX, and a poster titled "Bacterial cooperation of temperate and neotropical treehoppers explored through FISH and metagenomics" at the LS-PAC Conference, Jul 21-23, 2023, in New Orleans, LA. Graduate student Taranjot Kaur, who was a student in one of our project-supported courses presented her work in two posters titled "Discovery of novel Wolbachia strain in Heterodera expands nematode host distribution" at the ASM Microbe meeting, Jun. 13-17, 2024, in Atlanta, GA, and "Transcriptome assessment of the effects of the sorghum root exudate, sorgoleone, on root-lesion nematodes" at the ASA, CSSA & SSSA International Annual Meeting, Oct. 29-Nov. 1, 2023, in St. Louis, MS. Undergraduate Niyati Babaria presented her project-related work in a poster titled "Imaging the microgeography of key behavior-modulating microbes in the gut-brain-axis" at the 15th Annual TTU Undergraduate Research Conference, Apr 11-13, 2023, in Lubbock, TX. 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: Although microbiomes are critical to plant, animal, and soil health and productivity, training programs in advanced agricultural microbiome analysis are severely lacking. Disruptions in animal, plant, and soil microbiome composition can severely impact production outcomes, incurring costs to farmers, whereas disease-protective microbiomes remain poorly understood. Most university-level training programs lack the capacity for preparing the future workforce in multi-disciplinary fields involving next-generation DNA/RNA sequencing (NGS). Throughout this 3-year project, our work addressed this need by developing and testing advanced training programs in agricultural microbiome science as follows: Objective 1: Create and test three course-based undergraduate research experiences (CUREs) associated with follow-up summer internships. Obj. 1.1 Develop detailed syllabi, content, cross-listings, and distribute recruitment materials. Obj. 1.2 Run the courses, assess student and TA feedback, and refine content; Select and train summer interns. Obj. 1.3 Analyze CURES, prepare research and educational manuscripts for publication and reports. Develop/negotiate plans for continuation. 1. Major Activities Accomplished: Six Courses Created: CURE Frontiers in Host-Microbe Genomics (9 undergrads), Advanced Frontiers in Host-Microbe Genomics (3 grads), Microbiomes CURE (12 undergrads), Microbiomes Research Methods (8 grads), Bioinformatics CURE (2 undergrads), Bioinformatics of Agricultural Microbiomes (4 grads) Additional Courses in which Project Materials Used: Microbiomes (180 undergrads), Advanced Microbiomes (12 grads), Foundations of Microbiology Research (21 grads), Metatranscriptomics (3 grads), Genome Finishing Techniques (2 grads), Shotgun Metagenomics (2 grads) Original Research Projects in Classes: Year 1: 4 projects on agricultural biofilms, endophytes, nematode-plant interactions, and pest insects. Year 2: 4 projects on soil warming, poultry microbiota, sorghum microbiomes, and gut viruses. Year 3: 7 projects on mycorrhizal fungi, plant pests, parasitic nematodes, gene expression, root exudates, spatial composition, and plant viruses. Interns: Year 1: Interns in Biology/Microbiology, or Chemistry, or Pre-Vet = 9. High School Research Student = 1. Year 2: Interns in Biology/Microbiology or Chemistry or Pre-Vet = 8. Interns in Computer Science/Math = 6. High School Students = 7. Year 3: Interns in Biology/Microbiology, or Chemistry, or Pre-Vet = 8. Interns in Science/Math = 3. High School Students = 5. Graduate Intern = 1. Internship Projects: Year 1: 7 projects on insect microbiomes, nematode genomics, pest metagenomes, crop microbiomes, gut-brain axis, and rumen microbiota. Year 2: 6 projects on animal gut, plant-bacteria genomics, crop metatranscriptomics, pest microbiomes, soil and animal microbiomes. Year 3: 7 projects on pathogen transcriptomics, microbiome manipulation, plant-nematode interactions, pest microbiomes; rhizospheres, data-mining, plant-pathogens. Recruitment Efforts: Co-PDs from diverse departments widely advertised each course across undergraduate and graduate student populations. Materials Created: We created and tested course syllabi, quizzes, questionnaires, lecture slides/activities, and Safety Training and Equipment Usage Guides. We also created guides to preparing Wet/Dry Lab Notebooks. We also created 27 specific step-by-step Wet/Dry Lab Protocol guides. Student and TA Feedback: Course evaluations included entry/exit quizzes, anonymous assessments, and a detailed questionnaire. Graduate Students Involved in Developing Materials: 3 2. Data Collected: Each project generated experimental data (e.g., genome and transcriptome sequences). Evaluations showed that most students found the courses highly valuable. Comments and criticisms were used to improve courses and materials. 3. Summary Statistics and Discussion of Results: Number of courses (syllabi) created by this project: 6 Total enrollment in new courses created by this project: 38 Number of summer interns involved in the project: 48 Number of students in other courses that integrated materials from this project: 220 Number of syllabi/lectures/protocol/guide documents created: 94 Number of different research projects performed by students: 31 Number of output datasets produced: 12 Total of Students Taught/Trained/Involved: 309 4. Key Outcomes: We provided cutting-edge training in agricultural microbiomes to 309 students (237 undergrads, 59 grads, 13 high school) including ~45% students from underrepresented groups in STEM. We created substantial educational materials for extending this program in the future. The CUREs and internships also generated a significant body of publishable research, including manuscripts in preparation. These results exceed our Proposal Expected Outcomes. Objective 2: Create and test a new Master of Science concentration in "Microbiome Sciences". Obj. 2.1 Develop program description, integrated course syllabi and cross-listings, and advertise and recruit the first cohorts into the program. Obj. 2.2 Run the MS concentration and assess feedback on the effectiveness in achieving objectives. 1. Major Activities Accomplished: We developed our Interdisciplinary Microbiome Science Masters program incorporating our advanced research-based courses (described above) with core curricula built from student meetings and assessments. The program was designed to include high-quality interdisciplinary integration, and using the expertise of all project Co-PDs. 2. Data Collected: We successfully advertised and recruited graduates from 5 Departments and assessed student career goals, deficiencies, and needs through meetings, questionnaires. 3. Summary Statistics and Discussion of Results: We tested course materials an interdisciplinary training effectiveness with 59 graduate students. We discussed and developed improvements in the classroom and for the logistics of administering the program. 4. Key Outcomes: Our MS program creates a transformative hands-on cutting-edge training experience for the FAHN workforce. We plan to integrate it with our new Institute for One Health Innovation - called the One Microbiome Center. As PD of this project, I have been a key member of the committee developing our One Microbiome institution. Objective 3: Prepare faculty with additional advanced trainings to help implement and improve these NGS-centered FANH trainings. Obj. 3.1 Identify advanced trainings for lead PD. Evaluate educational improvement outcomes. 1. Major Activities Accomplished: PD Brown gained advanced pedagogy training through the STEM Teaching, Engagement & Pedagogy Program at Texas Tech. This program provided expert guidance on improving effectiveness of CURE-format courses. Brown gained additional high-level NGS training at the 2023 Genome Informatics Meeting at Cold Spring Harbor Laboratories, and cutting-edge interdisciplinary agricultural science and CURE teaching training through workshops at the International Congress of Entomology in 2024. 2. Data Collected: Data from discussions and questionnaires following the introduction of new advanced lessons and techniques based on these professional development activities. 3. Summary Statistics and Discussion of Results: Student feedback following this training was positive, but suggested a need for more structure and step-by-step details in bioinformatics materials and additional time and mentoring from instructors. 4. Key Outcomes: The advanced trainings positively enhanced the quality of teaching. Data from students demonstrated the importance of budgeting sufficient time, funds, and teacher-to-student contact in these courses for future years. Through work associated with this project, PD Brown won two mentoring awards: The TTU Mortar Board Apple Polishing Award, and the Outstanding Faculty Mentor Award from the Center for Transformative Undergraduate Experiences.
Publications
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2024
Citation:
Guerrero CR (presenter), Brown AMV. Cricket microbiome modulation changes territorial-related aggression. International Congress of Entomology. Aug. 25-30, Kyoto, Japan.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2024
Citation:
Kaur T (presenter), Brown AMV. Transcriptomic assessment of the effects of the sorghum root exudate, sorgoleone, on root-lesion nematodes. Texas Tech Annual Biology Student Symposium (TTABSS), Feb. 9-10, Lubbock, TX.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2024
Citation:
Aghdam SA (presenter), Brown AMV. Uncovering diverse roles of endophytic microbiomes in wild and cultivated bananas using metatranscriptomics. Texas Tech Annual Biology Student Symposium (TTABSS), Feb. 9-10, Lubbock, TX.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2024
Citation:
Sharma E (presenter), Brown AMV. Development of an automated NCBI SRA mining tool for target discovery. Texas Tech Annual Biology Student Symposium (TTABSS), Feb. 9-10, Lubbock, TX.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
Guerrero CR (presenter), Brown AMV. Microbial modulation of aggression in crickets. Texas Branch American Society for Microbiology (ASM) Fall Meeting. Oct. 26-28, Stephenville, TX.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
De Souza R (presenter), Aghdam SA, Brown AMV. Analyzing antifungal activity in domesticated and wild banana plants and their extracted microbiomes. Texas Tech University Transformative Undergraduate Experiences (TrUE) Symposium Oct. 20-21, Lubbock, TX.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2024
Citation:
Kaur T (presenter), Brown AMV. Discovery of novel Wolbachia strain in Heterodera expands nematode host distribution. ASM Microbe, Jun. 13-17, Atlanta, GA.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2024
Citation:
Kaur A (presenter), Brown AMV. High prevalence of Wolbachia and Cardinium revealed in different geographical populations of plant-parasitic nematodes. Society of Nematologists Meeting, Aug. 4-9, Park City, UT.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2024
Citation:
Salazar MM, Pupo MT, Brown AMV (presenter). Complex multipartite microbial symbioses in treehoppers characterized with genomics and metatranscriptomics. International Congress of Entomology. Aug. 25-30, Kyoto, Japan.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2024
Citation:
Dallison R (presenter), Kaur A, Ruckey F, Brown AMV. Analysis of endosymbiont prevalence reveals unexpectedly widespread abundance in nematodes. 16th Annual TTU Undergraduate Research Conference, Apr. 9-10, Lubbock, TX.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2024
Citation:
Marentes A (presenter), Kaur A, Brown AMV. Exploring bacterial endosymbionts Wolbachia and Cardinium in plant-parasitic nematodes. 16th Annual TTU Undergraduate Research Conference, Apr. 9-10, Lubbock, TX.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
Kaur T (presenter), Brown AMV. Transcriptome assessment of the effects of the sorghum root exudate, sorgoleone, on root-lesion nematodes. ASA, CSSA & SSSA International Annual Meeting, Oct. 29-Nov. 1, St. Louis, MS.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
Ruckey F (presenter), Kaur A, Brown AMV. PCR screening of plant-parasitic nematode communities for Wolbachia. SACNAS National Diversity in STEM (NDiSTEM) Conference, Oct. 26-28, Portland, OR.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
Avila Cortes K (presenter), Ressler GW, Thornton C, Salazar MM, Brown AMV. Visualizing symbionts in tissue-sectioned treehoppers using fluorescence microscopy. SACNAS National Diversity in STEM (NDiSTEM) Conference, Oct. 26-28, Portland, OR.
|
Progress 09/01/22 to 08/31/23
Outputs
Target Audience:Our target audiences were FAHN workforce trainees seeking higher-level skills in agricultural microbiome science. Through the direct activities of the second year of this project, we provided this training to: 13 graduate students and 19 undergraduate students who we directly trained and engaged in formal laboratory instruction and original research experiences this year. The undergraduates included 5 undergraduates from the fall CURE Microbiomes class, 4 undergraduates who worked on this data through spring, 6 undergraduate summer interns, and 4 undergraduates who continued research from YR1 of the project. The graduates included 7 students from the fall "Advanced Methods in Microbiomes" class, 3 who enrolled in additional research classes related to this work in spring, and 3 additional graduate students who continued to work with us on thes projects from YR1. These students comprised trainees from different majors and departments, including plant science, soil science, food science (food safety), animal science, microbiology, and biology. Our student researchers and summer interns in this project also communicated their research at several conferences. Specifically, unergraduate students working with these datasets generated in these training modules presented five posters at conferences (5 local meetings and 1 national meeting), thus sharing their work and knowledge and training more broadly. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Training of graduate students in the classroom: This year, a new set of graduate students (both MS and PhD) from diverse programs across campus learned to use a wide range of molecular biology instruments and methodologies to isolate DNA and RNA from a variety of soil, plant, food, and animal samples. They gained new advanced skills in next-generation sequencing at all stages, from input nucleic acid normalization, ribosomal RNA depletion or differential cell disruption, to PCR and library preparation, assessment of libraries on the TapeStation and library normalization and pooling. For "dry lab" or bioinformatic training, these students learned basic unix/linux command line and bash shell scripting, then built effective analysis pipelines by writing bash for loops stringing together sets of commands for fastq filtering, read assembly or denoising, blast and bwa sequence searching and binning, diversity analysis, differential expression analysis, and many other standard approaches. Students also learned effective approaches at scientific literature searching and sequence database searching. Graduate students were trained in concepts of experimental design. Students were trained in presenting their outcomes effectively in class discussion and formal class presentations as well as a final short written documents. Students were also trained in ethical practices and proper use of lab notebooks and data organization. Training of undergraduates in the classroom: Undergraduate students obtained a unique experience that trained them in most of the same skills described above. Although it was sometimes challenging to keep these students at pace with the graduate students in the classroom, we have added extra guides for future years to ensure that these students get the most out of the learning experience without drifting behind in understanding or procedural steps. Training of summer intern students: Project-supported (and independently supported) summer undergraduate researchers, recruited specifically to continue working with the data and approaches in the classroom projects, were trained in similar skill sets described for graduate students, but with each team of 2 students being much more specialized in an area of skills (e.g., "omics frontiers" focusing on FISH and confocal microscopy and Hi-C, or "bioinformatics" focusing on writing for loops to test analysis pipelines and parameters, or "microbiomes" focusing on experimental design and processing specimens for sequencing). Professional development: Several students associated with the internships, data analyses, or classroom work with opportunities to present their work at conferences were trained in the skills of public presentation. How have the results been disseminated to communities of interest?Students and interns working with the class datasets have begun to present their findings at conferences. Specifically, two undergraduates (Daniel Hsia and Reanne De Souza) working on project-generated data presented this at a local research symposium: Poster: Hsia D (co-presenter), De Souza R (co-presenter), Aghdam SA, Brown AMV. Analyzing Microbiome Changes in Wild and Domesticated Bananas using Metatranscriptomics. Texas Tech Annual Biology Student Symposium (TTABSS), Mar 31-Apr. 1, 2023, Lubbock, TX. Another undergraduate (Niyati Babaria) presented the Hi-C project group work with a graduate student from the course (Christian Guerrero) at a local undergraduate symposium attended by diverse faculty and students from across campus: Poster: Babaria N (presenter), Guerrero C, Brown AMV. Imaging the microgeography of key behavior-modulating microbes in the gut-brain-axis. 15th Annual TTU Undergraduate Research Conference, Apr 11-13, 2023. Lubbock, TX. Two other teams presented course research findings at this conference: Poster: Balfour P (presenter), Salazar MM, Pupo MT, Brown AMV. Cooperation Between Symbiotic and Trophobiotic Partners of Membracids May Be Driven by Bacteria. 15th Annual TTU Undergraduate Research Conference, Apr 11-13, 2023, Lubbock, TX; and Poster: Hsia D (presenter), Aghdam SA, Brown AMV. Analyzing Microbiome Changes in Domesticated Bananas using Metatranscriptomics. 15th Annual TTU Undergraduate Research Conference, Apr 11-13, 2023, Lubbock, TX. A separate undergraduate (Chad Thornton) traveled to a conference to present data from this project: Poster: Thornton C (presenter), Salazar MM, Brown AMV. Bacterial cooperation of temperate and neotropical treehoppers explored through FISH and metagenomics. LS-PAC Conference, Jul 21-23, 2023, New Orleans, LA. We have begun to deposit guides (wet lab and dry lab) and sample datasets onto a GitHub repository. We will submit raw data on NCBI's SRA databases and assembled data (genomes/annotated genomes) on NCBI's GenBank. What do you plan to do during the next reporting period to accomplish the goals?Objective 1: Developing and running 3 CUREs and advanced graduate classes. 1.1 We will test our final new CURE course and cross-listed graduate-level course on bioinformatics in the year ahead, testing the course structure and effectiveness. We will test our advertising and outreach for this course. We will continue to analyze sequence data and educational effectiveness data from the first two years of this project. 1.2 In the year ahead, we will work as a team of co-PDs to review, revise, and formalize all stages of our CUREs and graduate classes. We will again consult TTU's experts at the TPDLC center for guidance and suggestions on optimizing pedagogical practices. We learned that the highly-involved nature of these courses functions better with an assigned TA per each ~8-10 students. Therefore, we will discuss with departments/Chairs how to move forward with arranging this support for these classes. Objective 2: Working to create and test a new Master of Science concentration in "Microbiome Sciences," 2.1 We will make a concerted effort as a team to overcome some of the initial slow-downs in pushing our MS program concentration into the curriculog/registrar formats for approval with the relevant Colleges and Departments on campus. In our testing of student interest thus far, it is clear that the course content and skills training will have broad appeal to the intended target MS students locally. In particular, based on previous enrollments and testing, we anticipate that the class ratio of graduate to undergraduate students may benefit from being closer to 50:50 than the ratio that we had originally envisioned (with 2/3 to ¾ undergraduates). Objective 3: Faculty training in Big Data, Multi-Omics, and NCBI-integrated software coding to help implement and improve these NGS-centered FANH training programs at TTU. 3.1 PD Brown and others have identified and will apply for the planned training workshops as per the proposal. Specifically, UC Davis has a remote-learning Metabolomics seminar/workshop each fall that team members will enroll in. Secondly, team members will participate in either remote or in-person Bioinformatics/Genomics workshops at Cold Spring Harbol Labs or NCBI in fall/spring of the final project year.
Impacts
What was accomplished under these goals?
IMPACT: Our project accomplishments in the second year focused on improving education in FANH fields of study through new "multidisciplinary learning by doing" course structures and programs. We created, taught, and assessed the effectiveness of undergraduate "CURE" courses (i.e. Course-based Undergraduate Research Experiences) that we ran alongside graduate experiential learning courses. The combined undergraduate-graduate enrollment facilitated a tiered "peer-to-peer" training model. Course content involved original, real-world experiments requiring students learn skills in agriculturally related molecular biology, genomic sequencing, and computational analysis (bioinformatics) to assess how microbes (bacteria, fungi, and viruses) within agriculturally important plants and animals function. We successfully planned, ran, and assessed a new paired course in Microbiomes, and planned another course in Bioinformatics (for the upcoming project period). The fall Microbiomes CURE (and paired graduate Microbiomes Research Methods course) were well-received and generated information to improve the next year's iteration. Students and trainees gained high-tech skills in solving real agricultural problems using interdisciplinary methods as described below. We also generated continuing interest in these research methods and projects and easily recruited summer interns to carry on futher work in these project areas. We analyzed MS student learning and interest for further developing our multidisciplinary MS Concencentration in Agricultual Microbiomes Sciences. Objective 1: To create and test three CUREs titled "Host-Microbe Genomic Frontiers", Objective 1.1 "Start-up phase": 1) Major activities: We finished testing and running our second CURE/grad course in Microbiomes and finished developing our third and final CURE/grad course in Bioinformatics. Course materials prepared and tested in our course included (1) regular course items like syllabi, quizzes, questionnaires, lecture slides, and lecture activities, and (2) specific laboratory resources like our Safety and Equipment use Guide, as well as step-by-step wet lab protocols such as "Experimental design and hypothesis testing", "Selecting the right sequencing targets", "Decontaminating surfaces and reagents for sequencing of microbiomes", "DNA and RNA isolation from plants, animals, soils, insects, mammals, cells, etc.", "Quantifying DNA/RNA on the Nanodrop and Qubit", "PCR and gel electrophoresis", "AMPure bead clean up and size selection", "Normalizing samples for library prep", "Amplicon library prep", "Shotgun metagenomic library prep", "Metatranscriptomic library prep", "Generating positive spike control for amplicon sequencing", "Hi-C library prep", "Lysis-Hi-C library prep", "Quality and quantity assessment of libraries on the TapeStation", "Normalizing libraries and pooling for sequencing". Course materials prepared and tested for dry lab work included "Guide for creating a unix environment", "Guide for working on servers", "Guide for developing an analysis pipeline", "Guide for analyzing amplicon data in QIIME2", "Guide for analyzing wgs data with MetaWRAP and basic scripts", "Guide for analyzing metatranscriptome data with SAMSA2, Kallisto, and DEseq2", "Guide for statistical tests and plots in R". 2) Data collected: N/A 3) Summary statistics: N/A 4) Key outcomes: The above materials were appreciated by students and have been shared among lab members, receiving positive feedback and great potential to be effective in the project goals of training the FANH workforce here and elsewhere. Objective 1.2 "Run the courses and assess feedback": 1) Major activities: In fall 2022, we tested the materials to ensure they were transferrable across project areas. Students performed experiments on microbiomes in poultry processing plant rinsates, dryland and irrigated cotton soil microbiomes, sorghum endophytic microbiomes across cultivars, and insect microbiome bacteria-phage interactions. The methodologies learned in these projects included DNA and RNA isolation, amplicon sequencing, metagenomic sequencing, and Hi-C/lysis-Hi-C. During the spring and summer of 2023, continuing research students (and summer interns) continued to analyze sequence data from the previous courses, including transcriptomic data from cattle rumen, ant-treehopper microbiomes, plant-parasitic nematode microbiomes, banana endophytic microbiomes, and environmental/plant biofilms. 2) Data collected: (1) Course Evaluations: we used several forms of evaluating our teaching effectiveness, including non-grade entry and exit quizzes, standardized anonymous university-led assesments of the course, and a specially designed and detailed "Feedback" questionnaire. The latter was highly informative, showing most students found the course highly valuable, with some example comments such as: "I think this course was awesome! I loved every second of it and experienced research firsthand in a class. It was so much fun and felt really great as a student that has never underwent research before" and "In the top three of any class I've taken at TTU. I really loved it" and "How they teach laboratory skills (pipetting, lab cleaning) from the beginning to assure we followed correctly the protocols." Several students suggested we could improve the dry lab section as follows: "I wish there was more of a step by step guide to the analysis plan like there was in the wet lab portion" and "Less time at the lab work and more time at the bioinformatics part of the course" and "Perhaps more structured dry lab." Students also commented on the need for a TA. Our department was not able to provide a TA due to high demand and limited supply this year. (2) Data generated: ~250 GB of project experimental sequence data was obtained from ~74 samples. 3) Summary statistics: We had 7 graduate students and 5 undergraduates in the Microbiomes CUREs course in fall, and 2 graduate students in the spring enrolled in an extension of another Microbiomes course that I teach, as well as 4 undergraduate research mentees and 1 graduate mentee in spring following up on the data gather in the fall courses. The graduate students came from diverse Departments/Colleges: Plant and Soil Sciences, Nutritional Sciences, Animal and Food Sciences, Microbiology, Biology, and Cell Biology. Most of the MS and PhD students involved in the program thus far have continued to interact with the field and with these initial projects. The project trained 6 summer interns (Logan Foster and Chad Thornton specializing on "omics frontiers", Reanne De Souza and Rylee Dallison specializing on "bioinformatics", and Faith Ruckey and Katheryne Avila specializing on "microbiomes"). Some of these interns gained independent fellowship or scholarship support. 4) Key outcomes: We have accumulated improved guides and materials and clearer strategies for making these training programs more effective. Overall, data analysis is underway for these numerous projects and we anticipate this will yield publications in the year ahead. Objective 2: To create and test a new Master of Science concentration in "Microbiome Sciences". Objective 2.1 "Start-up phase": 1) Major activities completed: ourMSprogramdescriptioncross-listed courses. 2) Data collected: We have continued to attract MS students from diverse disciplines. 3) Summary statistics and discussion: NA 4) Key outcomes: We hope to launch an official program in the year ahead. Objective 3: To prepare faculty with additional advanced trainings in ... and improve these NGS-centered FANH training programs at TTU. Objective 3.1 "Identify ideal training schedules and modes (in-person and remote); participate in trainings; evaluate educational improvement outcomes for students": 1) Major activities: PD Brown and Co-PDs have plans for training workshops in fall 2023.
Publications
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
2023 Hsia D (co-presenter), De Souza R (co-presenter), Aghdam SA, Brown AMV. Analyzing Microbiome Changes in Wild and Domesticated Bananas using Metatranscriptomics. Texas Tech Annual Biology Student Symposium (TTABSS), Mar 31-Apr. 1, Lubbock, TX.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
2023 Babaria N (presenter), Guerrero C, Brown AMV. Imaging the microgeography of key behavior-modulating microbes in the gut-brain-axis. 15th Annual TTU Undergraduate Research Conference, Apr 11-13, Lubbock, TX.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
2023 Balfour P (presenter), Salazar MM, Pupo MT, Brown AMV. Cooperation Between Symbiotic and Trophobiotic Partners of Membracids May Be Driven by Bacteria. 15th Annual TTU Undergraduate Research Conference, Apr 11-13, Lubbock, TX.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
2023 Hsia D (presenter), Aghdam SA, Brown AMV. Analyzing Microbiome Changes in Domesticated Bananas using Metatranscriptomics. 15th Annual TTU Undergraduate Research Conference, Apr 11-13, Lubbock, TX.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
2023 Thornton C (presenter), Salazar MM, Brown AMV. Bacterial cooperation of temperate and neotropical treehoppers explored through FISH and metagenomics. LS-PAC Conference, Jul 21-23, New Orleans, LA.
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Progress 09/01/21 to 08/31/22
Outputs
Target Audience:Our target audiences reached through the activities of the first year included 16 graduate students who we directly trained and engaged in formal classroom instruction, laboratory instruction, and original research experience. Three graduate students were also trained in instruction (mentoring and formal training) and course development or course material development. We also reached a target audience of 14 undergraduate students in the first year, to whom we delivered scientific knowledge (via lectures and hands-on research experiences). These students comprised trainees from different majors and departments, including plant science, soil science, food science (food safety), animal science, microbiology, and biology. Students in this list of 30 included 63% females, and many students from underrepresented minorities in STEM (including 3 students who were Black/African American, 11 who were Hispanic/Latinx, and most others were first-generation college students and/or from local/rural backgrounds). Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Training to PD: In the first year, the project provided training in pedagogical methods to PD Brown, both through working with Texas Tech's STEP program in developing and evaluating the courses, and through direct experiential learning of alternative teaching in these dynamic classes. Training to graduate student assistants involved in developing the CURE courses: So far, the project provided extensive training to one graduate student who was supported by project funds to work with the PD and co-PIs in developing detailed and effective experimental protocols and guides, as well as testing and optimizing hands-on sequencing activities together with students in the classrooms. These trainings provided highly relevant professional development in the area of agricultural science for this student, whose individual PhD research complemented with the goals of the class projects (rumen and animal metatranscriptomics). Training to graduates and undergraduate students involved in supporting the research aspects of the CURE courses: Several researchers (graduate and undergraduates in PD Brown's lab), who were already supported by other funds, participated in supervising and training students in some aspects of the classroom projects, providing a tiered-peer-mentoring structure. The activities of these students allowed one-on-one training to students in the classes, while also allowing the trainers to "learn through teaching". Research supports the value of learning through teaching others, especially during the formative phases of instructor training. Training to graduate students in the classroom: Graduate students learned to use a wide range of molecular biology instruments and methodologies to isolate DNA and RNA from a variety of plant and animal samples. They gained new advanced skills in next-generation sequencing at all stages, from input nucleic acid normalization, ribosomal RNA depletion or differential cell disruption, to PCR and library preparation, assessment of libraries on the Tapstation and library normalization and pooling. They learned basic unix/linux command line and bash shell scripting, then built effective analysis pipelines by writing bash for loops stringing together sets of commands for fastq filtering, read assembly or denoising, blast and bwa sequence searching and binning, diversity analysis, differential expression analysis, and many other standard approaches. Students learned effective approaches at scientific literature searching and sequence database searching. Graduate students also learned in-depth concepts in experimental design. Students were trained in presenting their outcomes effectively in class discussion and formal class presentations as well as a final short written documents. Students were also trained in ethical practices and proper use of lab notebooks and data organization. Training to undergraduates in the classroom: Undergraduate students learned most of the same skills described above, except that due to limitations of time and academic preparation, undergraduates were provided limited formal writing and peer-reviewed literature analysis training compared to graduate students. How have the results been disseminated to communities of interest?So far, the only dissemination of the project has been through the student participants' engagement directly in the courses. In the next years, we will disseminate the course materials, research data, and evaluations. What do you plan to do during the next reporting period to accomplish the goals?Objective 1: Developing and running 3 CUREs and advanced graduate classes. 1.1 We will continue to test the 2 CURES (Host-Microbe Genomic Frontiers, Plant and Animal Microbiomes) through the next years, while developing in the year ahead the final CURE titled "Bioinformatic Problem-Solving", developing its detailed syllabus, course content, and distribute recruitment materials (ads across departments). 1.2 We will continue to formalize student and TA feedback surveys and consult with TTU's TPLDC experts in assessments of pedagogical effectiveness. We will work as a team of co-PDs to solicit applications from undergraduates for summer internships, then select and train the first set of 6 summer interns, formalizing and running an impactful program in the three target areas of Genomics, Disease-protective Microbiomes, and Bioinformatics. Objective 2: Working to create and test a new Master of Science concentration in "Microbiome Sciences," 2.1 We were ahead of schedule with CUREs development, but this took time away from our planned efforts to fully develop our MS concentration. To some degree, COVID-19 slow-downs impacted all of the co-PD teaching and research programs in our first year, as well. In the project year ahead, we expect to be back on track in our goal to build a detailed MS program description, course-requirements or recommendations, integrated course syllabi and program cross-listings, and advertise and recruit the first cohorts into the program. Objective 3: Faculty training in Big Data, Multi-Omics, and NCBI-integrated software coding to help implement and improve these NGS-centered FANH training programs at TTU. 3.1 Again, due to slow-downs with teaching modality changes (to and from online/in-person) and slow-downs in our faculty team's research programs (especially with field work and supply chain issues and graduate student travel issues), we fell behind on moving forward with this sub-objective. However, with all of our labs and teaching returning to normal now, we anticipate advancing this goal to arrange for faculty advanced trainings at specific centers (Metabolomics at UC Davis, Bioinformatics at NCBI, and numerous others).
Impacts
What was accomplished under these goals?
IMPACT: Our project accomplishments in the first year focused on improving education in the area of food, agricultural, natural resources, and human sciences (FANH) through developing and testing a new model to modernize advanced higher education training centered on "multidisciplinary learning by doing". To achieve this goal we built two undergraduate "CURE" courses (i.e. Course-based Undergraduate Research Experiences) in conjunction with two novel graduate courses that center on a tiered peer-to-peer training model. Students in these courses gained real-world research skills in agriculturally related molecular biology, genomic sequencing, and computational analysis (bioinformatics) to assess how microbes (bacteria, fungi, and viruses) within agriculturally important plants and animals provide protection against diseases. The PD, co-PIs, and project-supported graduate student successfully planned, ran, and assessed our novel pilot program with outcomes including new curricula, original course content and syllabi, and evaluations of the teaching framework's effectiveness. Outcomes also include data (genomic sequences from agricultural microbiomes) gathered and analyzed by students that we will lead to publications in the coming year. So far, the courses directly engaged and trained 30 students (16 graduates and 14 undergraduates) in the process of developing hypotheses and experiments, and performing original genomics research. Trainees gained high-tech skills in solving real agricultural problems using interdisciplinary methods. Our dynamic course format creates a model that allows rapid acquisition of core competencies in cutting-edge tools while elevating students to become future trainers, thus, exponentially expanding the future genomics and bioinformatics-trained FANH workforce. Objective 1: To create and test three CUREs titled "Host-Microbe Genomic Frontiers", "Plant and Animal Microbiomes," "Bioinformatic Problem-Solving" associated with follow-up summer internship opportunities. Objective 1.1 "Start-up phase": 1) Major activities completed: We developed 2 of our 3 CUREs co-run with advanced graduate courses, including creation of detailed syllabi and full curriculum materials and lecture, lab, and computational teaching materials. We created and distributed recruitment materials. We successfully completed one formal CURE/grad course pairing in the fall semester (ahead of our original schedule) and invested in additional planning and more extensive advertising in Spring/Summer 2022 to launch the next courses in the Fall 2022 semester (which began in August 2022). 2) Data collected: (A) Syllabi and course materials for Host-Microbe Genomics Courses: Including detailed objectives and grading rubric guides and extensive slides and other documents to support the following class sessions: 7 formal lectures with interactive activities; 4 quizzes; 7 class sessions for laboratory projects plus additional out-of-class; 11 class sessions for bioinformatics including data mining and original analyses of class project results; 2 class sessions for student presentations; (B) Syllabi and course materials for Agricultural Microbiomes Courses: Including original slides and lab guides to support the creation of Project Plans, Analysis Plans, Wet Lab and Dry Lab Notebooks, Presentations, and following class sessions: 5 formal lectures with group learning activities; 21 class sessions and guides for laboratory projects and bioinformatics plus additional out-of-class trainings. 3) Summary statistics and discussion: Full materials were prepared and launched for 4 of the 6 proposed undergraduate and graduate courses. The initial materials were successful with positive student evaluations. 4) Key outcomes: Faculty and students involved in preparing and disseminating recruitment flyers across departments gained valuable knowledge and feedback to improve the effectiveness for future years. Classroom materials received much positive feedback showing great potential to be effective in the project goals of training the FANH workforce. Objective 1.2 "Run the courses and assess feedback": 1) Major activities completed: In the classes run in Fall 2021, we tested optimized detailed experimental protocols that we transferrable across projects and protocols specific to project areas. Students performed experiments in shotgun metagenomics (on plant-parasitic nematode communities and on two species of disease-protective plant endophyte communities), metatranscriptomics (on various species of plant- and animal-associated insects and on biofilms relevant to agriculture), and amplicon sequencing on symbiotic microbial consortia collected at local farms. During the Spring and Summer of 2022, with a project-supported PhD student, we developed the next paired CURE/grad course on Agricultural Microbiomes. 2) Data collected: (A) Student Evaluations: anonymous university poll (average of graduate/undergraduate courses): "Course a valuable learning experience" = 8.7/10, "Overall instructor effectiveness" = 8.5/10, "Instructor followed course objectives" = 8.9/10. Comments: "I enjoyed the opportunity to learn about microbial symbionts and see the whole process from data collection to the bioinformatic analysis." "Very good instructor!". In-class survey: "class provided invaluable hands-on skills", "could have more guidance on initial project design". (B): Participants: Fall 2021 undergraduates enrolled = 9; graduates enrolled 3; additional support students =2; Summer 2022 one graduate student involved in developing rumen metatranscriptomics protocols; Fall 2022 graduate students = 7, undergraduates = 5; (C) Data generated: ~300 GB of project experimental sequence data from ~120 samples. 3) Summary statistics and discussion: Overall, in the first project year, we are ahead of schedule in developing courses, recruiting students from diverse programs, and running and testing our courses. Data analyses from the first year will also serve as input for the third CURE: Bioinformatics which will be developed and implemented in the year ahead. 4) Key outcomes: This first phase of the project trained undergraduates and graduate students in advanced approaches and demonstrated the practical value of components of these novel courses training the future agricultural workforce in advanced genomics methods. Objective 2: To create and test a new Master of Science concentration in "Microbiome Sciences". Objective 2.1 "Start-up phase": 1) Major activities completed: We began to develop our MS program description, with these new cross-listed courses. 2) Data collected: We successfully advertised and recruit the first cohorts Fall 2022 graduates from Dept of Plant and Soil Sciences, Dept of Animal Sciences, Dept of Biological Sciences, & auditing graduate students = 2 (Biological Sciences). 3) Summary statistics and discussion: We discussed improvements and interests with the first cohort of graduate students in Fall 2021 and have prepared a survey for Fall 2022 graduate students. 4) Key outcomes: We have begun the process toward developing this program. Objective 3: To prepare faculty with additional advanced trainings in Big Data, Multi-Omics, and NCBI-integrated software coding to help implement and improve these NGS-centered FANH training programs at TTU. Objective 3.1 "Identify ideal training schedules and modes (in-person and remote); participate in trainings; evaluate educational improvement outcomes for students": 1) Major activities completed / experiments conducted: PD Brown was enrolled in the STEM Teaching, Engagement & Pedagogy (STEP) Program at TTU's Teaching, Learning, and Professional Development Center (TLPDC) throughout the first project year. This group met weekly for intensive training, workshops, and expert professional development guidance on improving effectiveness of classroom approaches including development of CURE-format courses.
Publications
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