Faculty/Mentor Information: Nirmal Singh

Academic Institution/Laboratory: MassBay Community College

Department/Division: Department of Biotechnology, Genomics & Biomanufacturing; Center for Therapeutics and Genomics Training

Co-mentor(s)/Team members: Dennis M. Walsh

Appointment period: 5/1/2027 to 7/1/2027

Work mode: on-site

Primary location: Wellesley, MA

Project Title: Integrating Molecular Biology, Genomics, and Gene Therapy to Advance Therapeutic Biomanufacturing

Project summary: The Therapeutics Research Experience provides a hands-on, research-driven learning opportunity modeled after undergraduate research programs. Students work collaboratively in small teams on diverse projects, including biologics production, biomanufacturing processes, genome analysis, and RNA-based therapeutics.

Leveraging the advanced facilities at MassBay’s Centers for Therapeutics and Genomics Training (CTGT) and Biomanufacturing Education and Workforce Training (CBEWT), students gain access to state-of-the-art equipment and industry-standard techniques. Through guided laboratory work, they develop a thorough understanding of therapeutic product development, employing cutting-edge genetic tools for gene expression analysis and mastering quality assurance practices essential to biomanufacturing.

The course also incorporates workshops, case studies, and industry lab tours that cultivate key professional skills such as ethics, communication, and teamwork, preparing students for careers in the field. This integrated approach nurtures both technical expertise and critical thinking vital for success in biotechnology and pharmaceutical research.
Designed for students pursuing careers or advanced study in biotechnology and therapeutics, the program concludes with presentations where students effectively communicate their research findings. Enrollment requires foundational coursework in biotechnology and approval from the program director. With 12 hours of weekly lab work over 8 to 12 weeks, the course emphasizes experiential learning and workforce readiness, reflecting MassBay’s commitment to developing skilled life sciences professionals.

Technical description: The Therapeutics Research Experience is a comprehensive, hands-on course designed to immerse students in advanced biotechnological research focused on therapeutics development. This program engages students in collaborative research projects that span critical areas such as biologics production, biomanufacturing processes, genome analysis, and RNA-based therapeutics. By working in small teams, students gain practical experience in experimental design, data collection, and analysis within a real-world research environment.

Students utilize the cutting-edge facilities at MassBay’s Centers for Therapeutics and Genomics Training (CTGT) and Biomanufacturing Education and Workforce Training (CBEWT), which provide access to industry-standard equipment and technologies. These include advanced genetic tools such as CRISPR for gene editing, next-generation sequencing platforms for genomic analysis, and techniques for stem cell culture and differentiation. The course emphasizes the development of proficiency in biomanufacturing workflows, including quality assurance and compliance with current Good Manufacturing Practices (cGMP).

Training includes operation of sophisticated instrumentation used in the production and analysis of therapeutic agents, along with instruction in laboratory safety and regulatory standards. Students are also introduced to data analysis software and bioinformatics tools essential for interpreting complex genomic and molecular data.

Beyond technical skills, the course integrates professional development through scientific communication, ethics, and teamwork, preparing students for the collaborative nature of biotechnology industries. Industry lab tours and case studies further contextualize the research experience, highlighting regulatory frameworks and workforce expectations.

By the conclusion of the program, students are expected to demonstrate competency in conducting therapeutic research, critically evaluating data, and effectively presenting their findings. This course serves as a rigorous training ground for students aspiring to careers or advanced studies in Life sciences, biotechnology, pharmaceutical development, and related fields, combining theoretical knowledge with practical skills essential for success in the evolving life sciences sector.

Expected student deliverables: Students are expected to deliver a range of work that demonstrates their research skills and understanding. This includes detailed laboratory notebooks documenting experiments and procedures, data sets generated from their research activities, and comprehensive research reports analyzing their findings. Additionally, students will prepare and deliver oral presentations or poster presentations to communicate their results clearly and professionally. Depending on the project, students may also produce prototypes or experimental models related to therapeutics development. These deliverables collectively showcase students’ scientific technical proficiency, critical thinking, and communication abilities.

Description of work environment: The work environment in the Therapeutics Research Experience course is highly collaborative, with students working in small research teams typically consisting of 3-5 members. Students engage in both independent and group tasks, fostering teamwork, communication, and problem-solving skills. The course requires approximately 12 hours of laboratory work per week (8-12 weeks), complemented by discussions, data analysis, and preparation of presentations. This structure simulates real-world research settings, preparing students for professional scientific environments.

Does this project allow for continuation remotely after summer 2027?: No

Required skills/background of student: Students should have completed foundational courses in biotechnology and biomanufacturing and have permission from the program director. They need basic lab skills, knowledge of biomanufacturing processes, and experience using biotech equipment. Students should be able to work well in teams, communicate clearly, analyze data critically, and understand ethics and regulatory rules in biotechnology.

Helpful skills/background (but not required): Helpful but not required skills or background include experience with advanced genetic tools like CRISPR, knowledge of next-generation sequencing, familiarity with stem cell culture, understanding of quality assurance and regulatory standards, and prior exposure to research methodologies and experimental design. Skills in scientific communication and some soft skills for teamwork and presentations are also beneficial.

Training provided: Training provided includes hands-on experience with biomanufacturing equipment and advanced biotech instruments, use of genetic analysis tools like CRISPR and sequencing technologies, lab methods such as stem cell culture and differentiation, quality assurance and safety protocols including cGMP compliance, and software for data analysis. The course also covers research techniques, experimental design, and professional skills like scientific communication and ethical practices

Security clearance or background check required?: NA

Age restrictions?: NA

Other restrictions?: NA

Housing: On Campus/Off Campus: NA

Approximate housing cost per week: NA

Public transportation: NA

Meal Plan Available/Not Available: NA

If available, approximate meal plan price range per week: NA

Nearby restaurant/grocery Store: NA

Ideal candidate profile: The ideal candidate is a motivated student with foundational knowledge in life sciences, biotechnology and biomanufacturing, strong analytical skills, and a keen interest in therapeutics, molecular biology research. They should be collaborative, detail-oriented, and eager to develop both technical and professional skills in a hands-on laboratory environment.

How will you evaluate applicants?: NA

Anything else applicants should know?: NA

Briefly describe your experience mentoring undergraduates: As Chair of the Biotechnology, Genomics, and Biomanufacturing programs at MassBay Community College and Director of the Center for Therapeutics and Genomics Training, I have extensive experience mentoring undergraduate students. Over the past decade, I have guided students through coursework and hands-on research in cell and gene therapy, molecular biology, genomics, and biomanufacturing. My mentorship focuses on developing technical skills, critical thinking, scientific communication, and professional growth.

I provide individualized guidance, facilitate collaborative lab work, and create opportunities for students to present research findings. I have also developed curricula that integrate current industry practices and technologies to prepare students for careers in biotechnology. Through partnerships with research institutions and industry, I expand internship and experiential learning opportunities for students.

Faculty/Mentor Information: John Barthell

Academic Institution/Laboratory: University of Central Oklahoma

 Department/Division: Department of Biology - Division of Academic Affairs

Co-mentor(s)/Team members: Dr. Matthew Parks at the University of Central Oklahoma (UCO)

Appointment period: 6/7/2027 to 7/30/2027

Work mode: On-Site

Primary location: Field research in Lesvos, Greece with laboratory work at UCO

Project Title: Integrative Biological Studies of Plant-Pollinator Dynamics in an Island Ecosystem

Project summary: This program allows students to be exposed to multiple subdisciplines of research in the Biological Sciences that offer insights into the effects of environmental (thermal) stress on pollinators (bees). The research includes an international venue: Kalloni, Greece, on the Northeast Aegean Island of Lesvos. Lesvos was the home of Aristotle during the 4th Century BCE while he studied terrestrial and marine organisms there. Hypotheses will be tested on the impact of stress on (1) learning, (2) foraging dynamics, (3) physiological outcomes, and (4) the genetic basis for these stress responses. The study system takes advantage of an excellent organismal study system: honey bee and native carpenter bee species native to Greece. The student participant would work alongside seven other students participating in a National Science Foundation (NSF) funded Research Experiences for Undergraduates (REU) program as well as several senior personnel (two from the University of Central Oklahoma) that include at least three other US institutions as well as with Greek colleagues at the University of the Aegean at Mytilene. Formal training in Responsible and Ethical Conduct in Research is included in a one-week training period at the University of Central Oklahoma (UCO) prior to departing for Greece. After field-based research at the outset of the program in Greece, the student would then participate in laboratory research and a symposium at UCO (presenting results of the study) with the option of presenting those results at a national conference (Society for Integrative and Comparative Biology in Los Angeles, California, the first week of January of 2028).

Technical description: Hypotheses will be broken into four predictive areas that test the effects of environmental stress (primarily temperature) in a Mediterranean bee guild: (1) Non-Apis (honey bee) species will vary in their stimulus responses in accordance with their foraging (host plant preference) characteristics (the student gains hands-on experience in using behavioral conditioning methods); (2) pollinator guilds will compensate for nectar availability and optimal foraging temperature (experience with AI-based field and laboratory instrumentation will be gained by the student in this part of the study); (3) phenotypes (as ecophysiological expressions) will reflect spatial and temporal foraging niches of bee species in correlation with their respective life history strategies (the student will gain laboratory experience in measuring desiccation, CTmax, HSP70 expression, and other useful laboratory skills); (4) genomic and molecular systems underlying these phenotypes will be explored (molecular skills will be gained by the student and these can inform career interests in agriculture and conservation biology). The research will begin in an international setting (Lesvos, Greece) wherein a guild of native bee species will be used to test the aforementioned predictions; the project will progress to laboratory studies on the UCO campus. The results will have clear implications for pollination systems in the United States wherein at least one of these species (the honey bee) contributes to billions of dollars worth of agricultural crops each year.

Expected student deliverables: The student will be expected to produce two poster presentations, one for a local audience (at the host institution) and another for a national meeting (the annual conference of the Society for Integrative and Comparative Biology). The data collected and presented during the study will be published as abstracts and/or articles. The student will also contribute to a self-survey that explores the impact of the program on the ability of the student to work and think like a scientist.

Description of work environment: The training and work environment(s) will occur at the University of Central Oklahoma (UCO) and on the Northeast Aegean Island of Lesvos. At UCO the student will learn to think about science as a process and be trained in field methodologies (e.g., field insect collection methods) and in Responsible and Ethical Conduct in Research in preparation for research in Kalloni, Greece. Two researchers (Barthell and Parks) representing UCO will be the primary mentors for the student. However, additional Senior Personnel members from the NSF REU collaborative (at least three more from the US and two in Greece) will contribute to the broader context of the research. REU student participants (seven) will be selected as the primary student cohort with the Goldwater student participant introduced into the same research context, thereby maximizing exposure to an international and research-intensive collaborative. Working hours may be irregular (not to exceed 40 per week) in nature due to the availability of study organisms but will accommodate the laboratory and/or field interests of the participant. In addition, the student will experience cultural and historical features of the very historic island of Lesvos, including visits to museums and ancient research sites (visited by Aristotle and Theophrastus in the 4th Century BCE) such as Kalloni Bay (the place of Aristotle's early marine biological studies) and Sigri (near the second largest petrified forest known in the world). Faculty-student (mentoring) and student-student (co-working on projects) interactions are frequent and professional progress of the student will be monitored with regular, narrative-based essays.

Required skills/background of student: The student should have had an introductory course in the Biological Sciences or a related discipline that provides a basis for understanding research in biological systems. An aptitude for field and/or laboratory studies is also expected but it is understood that early-stage college or university students will apply to the program and can still benefit from and gain career momentum in a scientific discipline.

Helpful skills/background (but not required): While quantitative training (e.g., statistics) is helpful, the early training period of the experience (in Oklahoma) includes discussion of experimental design; other students who have this experience (along with the mentorship of the Senior Personnel) facilitate learning this subject during the research experience itself.

Training provided: The student will receive (1) RECR training, (2) instruction in experimental design pursuant to the scientific process, (3) field and laboratory methods training specific to testing each of four predictions, and (4) experience in writing and presenting scientific studies.

Security clearance or background check required?: No

Age restrictions?: No

Other restrictions?: No

Housing: On Campus/Off Campus: On (UCO) and off Campus (Lesvos, Greece).

Approximate housing cost per week: $400.00

Public transportation: No

Meal Plan Available/Not Available: Yes (included in lodging, above).

Nearby restaurant/grocery Store: Yes

Ideal candidate profile: The ideal student participant would have an interest in pursuing a career in research related to the Biological Sciences.

How will you evaluate applicants?: Criteria include (1) GPA with transcript (to verify a scientific discipline), (2) a statement on previous research experience, (3) an essay on why participating in the program is important to his/her career, and (4) recommendations from two professionals who know the candidate.

Anything else applicants should know?: All students should know that sensitivity to the culture of the host country (Greece) and compliance with its laws are imperative to completing the research experience (a Memorandum of Understanding outlines this and other issues more precisely). The program stipend will be used to cover lodging and travel costs, including to Greece. The estimated cost for travel to Greece is $2,500.

Briefly describe your experience mentoring undergraduates: I have worked with over 100 students in the NSF REU program over the last 20 years (since 2006). I have worked (separately) for 30 years with over a dozen undergraduates on mentored research experiences at my own institution (UCO) as well.

This experience includes working with students in the field, museum, and laboratory.

Faculty/Mentor Information: Mark Running

Academic Institution/Laboratory: University of Louisville

Department/Division: Biology

Co-mentor(s)/Team members: Esiosa Adewale, Chelsea Pipkin

Appointment period: 6/1/2027 to 8/7/2027

Work mode: On-site

Primary location: Louisville, KY

Project Title: MINDY genes in Arabidopsis and moss

Project summary: Proteins are the most versatile molecules in our body, as in all living things, and it is critical that we make the right ones at the right time. It is also critical that we get rid of proteins we no longer need, but how we do that is still unknown, especially because how it happens varies among different proteins that are being destroyed. A recently discovered set of genes, known as MINDY genes, play unique roles in this process, but how they function is not known. They are present in both animals and plants, though, underscoring their importance across different life forms. We aim to understand how they work in two very different plants, a flowering weed and a simple moss. Part of how we will do this is by seeing where and when MINDY genes are expressed, what happens when MINDY genes do not work, and what other genes MINDY interacts with. Together, these will lend insight into how MINDY genes function in other organisms, including humans.

Technical description: MINDY proteins are recently discovered proteins whose sequence suggests they play a role in protein degradation. Remarkably, they are found in both plants and animals, and the plant MINDY genes have not been characterized at all. What sets them apart from other genes involved in protein degradation is that, in plants, some of them appear to be membrane-associated, while some are not. We are interested in elucidating their function in a both Arabidopsis, a model flowering plant species, and the moss Physcomitrella patens, representing an early-arising clade of plants that's useful for evolutionary studies. Several parallel approaches will be used to elucidate their function. First we will use genetic tools to reduce the function of MINDY genes, alone and in combination, to assess their biological role in growth, development, and stress responses. This will also uncover unique and redundant function of each MINDY gene present. We will also test whether the mislocalization of the MINDY genes, by removing or adding their subcellular localization signals, affect their function. We will use molecular approaches to examine gene expression patterns and timing, and we will use a biochemical approach to identify MINDY interacting and target proteins.

Expected student deliverables: The students will present a poster at the University of Louisville Summer Research Showcase at the end of the summer term, and may have additional opportunities for presentations and publications, especially in The Cardinal Edge Undergraduate Research Journal.

Description of work environment: The lab currently consists of the PI, two PhD students, one research Masters student, and five undergraduates. There are opportunities for both independent and collaborative work, with many undergraduates transitioning to independent work after a brief training period. The lab operates on a full-time basis of 40 hours a week, with flexibility for working on nights and weekends if convenient.

Required skills/background of student: Freshman biology and chemistry sequence, exposure to lab procedures in a classroom setting

Helpful skills/background (but not required): Familiarity with molecular techniques, familiarity with literature searches

Training provided: Training will include standard molecular techniques (DNA/RNA isolation, protein isolation, cloning, primer design, PCR, etc.), along with required instrumentation, as well as microscopy. Chemical and Biological safety training, record keeping/notebook keeping, and ethics training are provided.

Security clearance or background check required?: No

Age restrictions?: 18+

Other restrictions?: No

Housing: On Campus/Off Campus: Both on campus and off campus housing is available for students participating in formal summer programs

Approximate housing cost per week: $1200

Public transportation: Yes

Meal Plan Available/Not Available: Yes

Nearby restaurant/grocery Store: Yes

Ideal candidate profile: The ideal candidate is motivated, interested in molecular genetics research, and able to transition to independent work.

How will you evaluate applicants?: Applicants will be evaluated based on potential to benefit the most from the experience. Basic biology/chemistry coursework and course lab experience and references will be strongly considered.

Briefly describe your experience mentoring undergraduates: I have mentored over 150 undergraduates in my 15 years at UofL. My mentees have been co-authors and have gone on to become Goldwater Scholars and Fulbright Scholars and have been admitted to top medical and graduate schools.

Faculty/Mentor Information: Emily Blythe

Academic Institution/Laboratory: University of Minnesota, Twin Cities

Department/Division: Genetics, Cell Biology and Development

Co-mentor(s)/Team members: Dr. Zachary Baker (postdoc)

Appointment period: 6/1/2027 to 8/7/2027

Work mode: On-site

Primary location: Minneapolis, MN

Project Title: Spatial regulation of TGF-β signaling

Project summary: Essentially every biological process depends on a cell’s ability to accurately detect and respond to cues from its environment and from other cells. Much of this information processing begins at the plasma membrane, where cellular receptors bind cues and then direct the cell’s response. Rather than acting only at the cell surface, many receptors also move to different locations inside of the cell, and this movement can change the messages that they transmit. In this project, we will examine how the movement of the transforming growth factor β receptor (TGFBR) impacts its signaling. TGFBR is an important receptor that regulates growth and healing. Using mutated versions of the receptor that go to specific places inside of the cell, we will ask whether receptor location affects how the cell turns on specific genes in response to TGFBR stimulation. This project will provide hands-on experience in cell culture, molecular biology techniques, and data analysis.

Technical description: Cells process external stimuli through receptor-mediated signaling pathways that initiate at the plasma membrane and continue from intracellular compartments such as endosomes. This compartmentalization gives rise to “spatial encoding,” a phenomenon whereby receptor signaling elicits distinct downstream outcomes depending on its subcellular origin. While spatial encoding is well-characterized for some families of receptors, it remains highly controversial for transforming growth factor β receptors (TGFBRs), a family of transmembrane kinases that mediate proliferation, differentiation, and tissue repair. This fundamental gap in our understanding of how spatial organization encodes specificity limits our ability to precisely modulate these pathways for therapeutic and engineering applications. The goal of this project is to elucidate the spatial logic of TGFBR-mediated signaling in a simple cell culture model system. We will focus on canonical TGFBR signaling, which proceeds via receptor-mediated phosphorylation of the transcription factor Smad. To precisely control the spatiotemporal activation of TGFBRs, we will adapt an existing minimal TGFBR system that is activated by light rather than ligand (optoTGFBR). By targeting optoTGFBRs to specific subcellular compartments, including the plasma membrane and endosomes, we will interrogate how TGFBR localization impacts downstream Smad signaling. Specifically, we will assess whether each optoTGFBR mediates Smad phosphorylation and subsequent Smad-dependent transcriptional activation using western blots and reporter assays. This project will provide hands-on experience in cell culture, molecular biology techniques, plate-reader based cellular assays, and data analysis. Additionally, the student will present their findings at the end of the summer at the University of Minnesota Summer Undergraduate Research Expo.

Expected student deliverables: The student will give a final oral presentation in our weekly group meeting and present a poster at the UMN Summer Undergraduate Research Expo (SURE) in early August.

Description of work environment: The Blythe lab is a small, collaborative team currently made up of two postdocs, one graduate student, one researcher, and one undergraduate. The student will work closely in the lab with Dr. Zach Baker on the proposed project throughout the internship. Additionally, every week the student will attend a one hour group meeting and a one hour one-on-one meeting with Prof. Blythe. The student will be expected to work full-time (~40 hours), and night and weekend work is not permitted.

Required skills/background of student: Minimum one college-level biology course including a laboratory - Minimum one college-level chemistry course including a laboratory - Interest in cell biology research - Good organizational skills

Helpful skills/background (but not required): Coursework in cell biology and/or biochemistry - Experience reading primary scientific literature - Prior experience in a research lab environment

Training provided: Laboratory safety training - Wet laboratory skills: cell culture and molecular biology techniques - Data analysis and visualization - Scientific communication: oral and poster presentations - Scientific literature comprehension

Security clearance or background check required?: No

Age restrictions?: 18+

Other restrictions?: No

Housing: On Campus/Off Campus: On-campus intern housing available (fully furnished with kitchen), and lots of off-campus summer sublets are available within walking distance.

Approximate housing cost per week:On-campus $300/week, off-campus $200-400/week

Public transportation: Yes

Meal Plan Available/Not Available: Not available

Nearby restaurant/grocery Store: Yes, restaurants and grocery stores are both within walking distance and accessible by public transit

Ideal candidate profile: The ideal student will be excited to engage in laboratory research and already have a basic understanding of cell biology through their coursework. We are looking for someone who is curious, collaborative, and responsible.

How will you evaluate applicants?: 1. Coursework: Does the student have a basic understanding of cell biology? Has the student been exposed to a laboratory environment through their coursework? 2. Statement quality: Does the student express an interest in research that is compatible with our project (cell biology / cell signaling)? Is the student able to communicate their background and goals effectively? 3. References: Does the student have a track record of being responsible, collaborative, engaged, and curious?

Anything else applicants should know?: NA

Briefly describe your experience mentoring undergraduates: I started my lab at UMN in early 2025. I currently have one undergraduate student in my lab, and I have extensive experience in undergraduate classroom and laboratory teaching. Additionally, Dr. Zach Baker, who will be the student's mentor in the lab, taught an undergraduate laboratory course at Bemidji State University in fall 2025.

Faculty/Mentor Information: Rebecca Simmons

Academic Institution/Laboratory: University of North Dakota

Department/Division: Biology

Co-mentor(s)/Team members: none

Appointment period: 6/1/2027 to 8/7/2027

Work mode: Either On-site, Hybrid, or Remote

Primary location: Grand forks

Project Title: Pollinator and Microbial Communities in the Northern Great Plains

Project summary: North Dakota is the largest producer of honey in the US; both native and commercial pollinator species are central to the success of agriculture in the region. Despite their importance, pollinators are experiencing declining numbers both in the region and nationwide. These declines are caused by many factors including, habitat destruction, pesticide/herbicide use, and diseases; loss of these species are a threat to economic growth in the region and national food security. While there are efforts to document the decline in pollinator species in the region, these surveys do not address the hidden diversity within pollinators themselves-microbes found in pollinator digestive tracts. In healthy individuals, these microorganisms synthesize vitamins, aid in honey production and provide other vital functions. To document and compare microsymbionts between pollinator species, students will collect and identify pollinators. Students will remove pollinator digestive systems which will be used to extract, amplify and sequence both pollinator and microsymbiont DNA. Students will then analyze resulting Illumina sequence data to identify species-specific and shared symbionts.

Technical description: We will use PCR to amplify mitochondrial DNA to identify native pollinators; we will use Sanger sequencing methods to visualize these amplicons. We will use BLAST via GenBank to match sequences to pollinator species. We will collect pollinators in different landscapes throughout the state. We will use metabarcoding approaches to document the microbial communities and the plants that pollinators visit. We perform two rounds of PCR to amplify the 16S subunit and chloroplast genes. We then attach adapter sequences using PCR to create libraries for MiSeq runs that are performed at the UND Genomics core. We use bioinformatic approaches to match these sequences to the Silva database and to plant species.

Expected student deliverables: Students will present this work at a campus poster session and at the Annual Meeting of the Entomological Society of America. Students will also be co-authors on resulting publications.

Description of work environment: I typically host one other full time undergraduate student through our REU program and three part time students. We work as a team. Students typically work 30-40 hours per week.

Required skills/background of student: None

Helpful skills/background (but not required): Basic molecular approaches (PCR, gel electrophoresis), coding in R

Training provided: Lab methods, lab safety, analytical approaches in Mothur and Rstudio

Security clearance or background check required? Yes, criminal background check

Age restrictions?: Yes, 18 years

Other restrictions?: No

Housing: On Campus/Off Campus: Either is possible

Approximate housing cost per week: $250

Public transportation: Yes

Meal Plan Available/Not Available: Available

If available, approximate meal plan price range per week: $300

Nearby restaurant/grocery Store: No

Ideal candidate profile: I like working with students that want to do research and enjoy working in a collaborative setting.

How will you evaluate applicants?: Statement quality, prior research and interest in this work.

Anything else applicants should know?: No

Briefly describe your experience mentoring undergraduates: I have mentored 132 students. I also was awarded the Best Research Mentor/Late Career from the Council of Undergraduate Research in 2025.

Faculty/Mentor Information: Sascha Duttke

Academic Institution/Laboratory: Washington State University, Pullman

Department/Division: School of Molecular Biosciences

Co-mentor(s)/Team members: Mackenzie Meyer, Oluwadamilola Joy Olanrewaju, Marina Savenkova

Appointment period: 6/1/2027 to 8/7/2027

Work mode: On-site

Primary location: Pullman, WA

Project Title: Exploring the "Unkn-ome" through curiosity-driven inquiry

Project summary: The regulation of gene expression is a central control point for nearly all cellular processes. However, despite the massive accumulation of genomic data over the last decade and modern AI models, identifying the generalizable principles that explain how DNA specifies gene output remains a largely speculative. As evidenced by our laboratory’s recent discovery of a novel spatial code in DNA (Duttke et al., 2024, Nature), the current limitation to scientific breakthrough is often not a lack of data, but a lack of transformative ideas and the people willing to pursue them. By re-analyzing existing datasets through a new conceptual lens, we overturned the long-standing paradigm that transcription factors act as fixed activators or repressors, revealing instead a critical position-dependency that explains why predicting gene activity from sequence alone has remained elusive. This project pursues the hypothesis that decoding the "unkn-ome"—the vast gaps in our genomic knowledge—requires fresh conceptual frameworks rather than more raw data. Undergraduates are uniquely suited for this work; their fresh perspectives, unburdened by established disciplinary biases, allow them to ask the seemingly "naïve" but fundamental questions that lead to serendipitous discovery. Supported by a plethora of available data and generative AI to bridge technical gaps, students will develop and test their own spatial grammar hypotheses. Our goal is to mentor independent scientists who recognize that in the era of Big Data, the most valuable tool is not a faster sequencer, but a creative and curious mind.

Technical description: The trajectory of biological research is increasingly defined by data-intensive methodologies. Traditionally, entering this field required a rigid apprenticeship model where trainees spent months to years acquiring computational expertise before participating in meaningful research. While rigorous, this structure often delays time-to-contribution and discouraged students and PIs from pursuing "out-of-the-box" ideas that fall outside established lab paradigms. This project utilizes the mentored use of generative artificial intelligence (AI) to fundamentally shift how technical prerequisites are acquired (Call et al., PloS Biology 2026). Rather than requiring students to master complex coding syntax before beginning their inquiry, we employ an "on-question" learning model. Students engage immediately in hypothesis-driven research, learning technical syntax iteratively as the project demands. Importantly, while AI is used as a bridge for technical gaps and troubleshoot syntax, the student remains in the driver’s seat. This democratization of technical skill allows undergraduates to focus on the biological "why" rather than the technical "how," significantly reducing the barrier to entry for high-level genomic analysis. By lowering the technical burden of execution, this project enables undergraduates to pursue serendipitous discoveries that might have previously been dismissed as too time-demanding or biologically unlikely. Notably, this approach requires immense upfront mentoring. But once hypothesis and experimental design are clear, AI severely reduced the burden of troubleshooting syntax. The research workflow involves: 1. Mentored re-analysis of existing omics data (e.g., PRO-seq or csRNA-seq) to test their novel hypotheses. 2. Iterative hypothesis refinement based on data-driven observations. 3. Results: hypothesis falsification (valuable negative data) or discovery of DNA regulatory principles, such as new regulators, motifs, or spatial configurations in the human genome or associated with specific diseases. 4. Assisted experimental validation utilizing our lab’s infrastructure in genome editing and transcriptomics. To execute this, students utilize the WSU Kamiak high-performance computing cluster, which remains accessible to them even after their physical tenure in the lab ends, fostering long-term scientific engagement. This approach is particularly effective for exploring the "unkn-ome"—the gaps in our genomic knowledge—where fresh perspectives are often more valuable than traditional biases. The efficacy of this model is evident from our discoveries. Despite leading a small lab to allow proper mentoring and oversight, we uncovered a spatial code or grammar in our DNA (Duttke et al., 2024, Nature) and recently, an undergraduate identified a novel autoregulatory syntax prevalent in several cancer-driver genes using this framework. We are thus at the beginning of an undergraduate research renaissance and a new era of undergraduate contribution to science. Moreover, this model lowers the hurdles towards learning and pursuing big data analysis, a sought-after skill in both academia and industry, and offers undergraduates to pursue authentic research. Aside from curiosity and willingness to learn, no requirements are needed.

Expected student deliverables: An experimental design flow chart with the key steps from hypothesis to expected results. An annotated and documented Jupyter Notebook with the code used to address their question: A set of Python/pandas scripts (developed via the "on-question" AI-mentored model) used to re-analyze nascent transcriptomics datasets (PRO-seq/csRNA-seq). A poster or oral presentation for the WSU Undergraduate Research Symposium or a national venue such as ABRCMS. A written summary of findings formatted as a publication-ready "Results" section. As seen in our lab’s history, high-achieving students often to contribute toward peer-reviewed manuscripts.

Description of work environment: The Duttke Lab at WSU Pullman provides a vibrant, inclusive, and highly collaborative R1 research environment designed to foster elite scientific achievement. Since 2023, our undergraduates have secured first-author publications in Nature Plants and BMC Genomics, co-authored Nature and Development papers, and won prestigious honors including the Barry Goldwater Scholarship, NSF GRFP, and Washington Opportunity Fellowships. To date, 100% of our undergraduate alumni have transitioned into PhD or MD/PhD programs. Team structure: Students join a diverse team of approximately 10 members from different background and experiences, including a senior scientific assistant, 4 graduate students, and 4 fellow undergraduates. Collaborative synergy: We utilize a "Wet Lab" and "Dry Lab" pairing system. Students often specialize in one track but collaborate closely with a peer in the other to ensure a holistic understanding of the project from bench to data. Mentoring framework: Following NCFDD guidelines, members are supported by a multi-layered mentoring network, have weekly 1-on-1 meetings with the PI to discuss question, monthly review of Tailored/Individual Development Plans, daily guidance from a "Research Mentor" (peer or grad student), and biweekly "Accountability Buddy" meetings over ice cream to foster a sense of belonging. Hours & flexibility: During the semester, undergraduate students typically commit 8-10 hours per week. During the summer, students are immersed in full-time research. Our use of the Kamiak high-performance computing cluster allows for flexible, hybrid work where students can continue their analysis remotely.

Required skills/background of student: Curiosity, interest in gene regulation, willingness to learn data analysis and drive their own project

Helpful skills/background (but not required): Basic understanding of molecular biology basic knowledge in DNA and gene regulation

Training provided: Experimental design: Students are trained to move beyond technical execution to become architects of their own research. They learn to identify gaps in genomic knowledge (the "unkn-ome"), formulate testable hypotheses based on the "spatial grammar" paradigm, and design rigorous controls for both computational and, time permitting, "wet lab" validation experiments. Responsible conduct & use of Generative AI: Given our lab’s reliance on the "on-question " learning model, students receive specific training on the ethical and responsible use of AI in research. This includes: • Validation & verification: Learning to treat AI-generated code as a draft that requires rigorous testing and line-by-line validation. • Prompt engineering & logic: Developing the ability to decompose complex biological questions into logical prompts. • AI ethics: Discussions on the limitations of AI, potential biases in training data, and the importance of maintaining scientific integrity and transparency when using assistive tools in data analysis (Call et al., submitted). Computational data analysis: Hands-on training in the Linux command line and Python 3 (pandas). Students learn to navigate the Kamiak High-Performance Computing (HPC) cluster to manage big-data genomics workflows, shifting the focus from the technical "how" to the biological "why." Safety & ethics: Comprehensive WSU laboratory safety training and workshops on the Responsible Conduct of Research (RCR) and scientific ethics are covered both in lab and during the WSU undergraduate summer training. Professional development: Students receive individualized guidance on drafting competitive fellowship applications (Goldwater, NSF GRFP) and preparing for graduate/medical school interviews, following the NCFDD mentoring guidelines. In addition, WSU hosts programs for all summer students including graduate school information sessions, weekly workshops on topics like laboratory safety, research documentation, scientific ethics, literature searches, as well as guidance on preparing and presenting research findings. The Office of Undergraduate Research hosts a summer research poster symposium, providing students an opportunity to showcase their work and expand their network. These activities enhance students' professional development and foster connections beyond the lab. Commitment: I will continue to mentor and sponsor students post their tenure.

Security clearance or background check required?: No

Age restrictions?: 16+

Other restrictions?: No

Housing: On Campus/Off Campus: All non-WSU undergraduate students who are on campus for summer research experiences (e.g. REU’s, typically 50 – 70) stay in one of WSU’s residence halls.  In 2026 they will stay in Global Scholars (air conditioning, laundry facilities, etc).  This will provide the Goldwater interns with a peer network.  They will be able to interact with their peers in the residence hall, but they will also be able to attend weekly brown bag workshops with their peers.  All students will be able to present their research at the Summer Research Symposium.

Approximate housing cost per week: The rates for Summer 2026 are $40.50 per person per night for double occupancy and $44 per person per night for single occupancy or $283.50 per week for double occupancy and $308 per week for single occupancy.

Public transportation: Yes, Pullman Transit With a WSU ID card, student’s can ride the bus for free. We are a small town and most things are accessible by bus or walking. We also have a lab bicycle that visitors often borrow

Meal Plan Available/Not Available: Regular meal plans are not available during the summer, but the mini-meal plan is available. There are dining options available on campus including Compton Union Building (CUB) Food Court Carlita’s and Freshens CUB food court Hillside Café and Northside Café (campus dining center) Starbucks (located on the ground floor of the Spark building) Lighty Espresso (also has food options) There is also a shared kitchen option in the residence hall which include oven, microwave, refrigerator, and sink. Basic cooking utensils are provided by the Office of Undergraduate Research.

If available, approximate meal plan price range per week: The mini meal plan is available during summer and costs $250, which includes a fee of $50 and $200 to use in Dining Dollars, which can be used during the summer at on campus dining locations. Mini meal plan holders receive a 25% discount.

Nearby restaurant/grocery Store: Pullman is a small town and all grocery stores are accessible. In Pullman, there are four large grocery store options: Rosauers, Safeway, Grocery Store Outlet, and Walmart. There are also smaller specialty stores such as Shin’s Asian Market and PNW Halal Meats.

Ideal candidate profile: The ideal candidate is fascinated by how DNA encodes life or cellular processes and excited to learn. They should be curious and willing to give computational biology a try.

How will you evaluate applicants?: I will employ a comprehensive evaluation strategy that monitors both immediate technical growth and long-term professional trajectory. Regular discussions, goal setting, and feedback are the cornerstones used to assess students' progress during their time in the laboratory. • Weekly 1-on-1s: I use these meetings to pivot quickly if a student encounters technical hurdles in their "on-question" learning. • IDP-Based Growth: Based on each student's Individual Development Plan (IDP), we evaluate and discuss specific learning outcomes and progress toward personal or professional goals. This ensures the research experience is tailored to their unique aspirations, whether they are aiming for a PhD, MD-PhD, or a career in biotech. I assess the quality of the student’s intellectual contributions through tangible milestones: • Computational competency: Evaluation of the student's ability to use generative AI responsibly to build and validate data analysis pipelines on the Kamiak HPC cluster. • Conceptual ownership: Assessing the student's ability to move from following a protocol to identifying novel patterns in the "unkn-ome." • Scientific communication: Success is measured by the student's ability to present their findings at the WSU Summer Research Poster Symposium (SURCA) or national conferences such as ABRCMS. The ultimate metric of success however is the student’s trajectory after leaving the lab. Following their stay, I offer students' continued involvement in research and mentorship.

Anything else applicants should know?: It's also OK to come out of this not wanting to pursue computational/big data biology. That is also important to finding your role in academia.

Briefly describe your experience mentoring undergraduates: Since starting my research group in 2023, I have prioritized the development of undergraduate scientists as the cornerstone of my laboratory- they are the future of science. My mentoring experience is defined by a commitment to moving students from technical assistance to conceptual ownership, a philosophy recognized by the WSU Honors College Undergraduate Mentorship Award (2023) and the WSU "Mindful Mentor Award" (2024) and the SMB excellence in Research Award (2025). 3/3 past undergraduates transitioned into PhD or MD-PhD programs at elite institutions. Other notable outcomes include: • Publications: Undergraduates in my lab have secured first-author publications in Nature Plants and BMC Genomics, as well as co-authorships in Nature and Development. • Fellowships: My mentees have successfully competed for national fellowships including the Barry Goldwater Scholarship, the NSF Graduate Research Fellowship (GRFP), and the Washington Opportunity Fellowship. All undergraduate also have WSU-internal fellowships. • National recognition: Students have won awards at the WSU undergraduate symposium (SURCA) and national venues like ABRCMS. As a mentor for programs such as T32, NIH ESTEEMED-MIRA or MARCS, I am dedicated to providing inclusive, curiosity-driven training that empowers the next generation of scientific leaders.

Faculty/Mentor Information: Alan Goodman

Academic Institution/Laboratory: Washington State University

Department/Division: School of Molecular Biosciences

Co-mentor(s)/Team members: Mary Sanchez-Lanier

Appointment period: 6/1/2027 to 8/7/2027

Work mode: On-site

Primary location: Pullman, WA

Project Title: Host responses to pathogenic infections using Drosophila melanogaster

Project summary: Innate immunity refers to the initial response of the body upon exposure to invading organisms. Innate immunity acts as a bridge for the activation of the adaptive immune response. Indeed, the innate surveillance of pathogen-associated molecules to trigger an immune response is an ancient form of host defense. However, if innate imunity is hyperactivated, it can cause autoimmune disease. On the other hand, if the innate immune response does not function during an infection, the host can succumb to the infection. Together, innate immune signaling must be finely tuned so that it can provide a sufficient response against pathogenic infection, yet not be constitutively or hyperactive in such a way that autoinflammatory or autoimmune disease results. The innate immune response is initiated through the activation of pattern recognition receptors (PRRs) that recognize conserved pathogen motifs called pathogen-associated molecular patterns (PAMPs). Our lab uses the fruit fly as a model organism to decipher innate immune responses to microbial infection. The fruit fly does not have an adaptive immune response, so its innate immune response is the sole response to curb pathogen infection. We use the fruit fly to student vector-borne diseases such as mosquito viruses and Coxiella burnetii.

Technical description: Students will infect Drosophila melanogaster fruit flies with different strains of virus or bacteria. They will measure mortality rates and virus or bacterial replication over time. They will extract total RNA from flies for processing to cDNA and subsequent qRT-PCR. The qRT-PCR will measure levels of host genes to show how the host responds to infection. Students will then use cell culture to overexpress genes of interest and perform infections in cells to confirm the role of the gene of interest during infection. Cells will be lysed and the protein extract will be analyzed by western blot to determine how proteins downstream of the gene of interest are activated. Finally, students will infect mutant fruit flies that lacks the gene of interest to further define the role of the gene during infection. Depending on the precise type of virus or bacteria used in the student's project, they will also infect fruit flies with mutant strains of the virus or bacteria to determine if proteins from the pathogen interact with the gene of interest that was identified and characterized. Data from biological replicates will be analyzed for statistical differences among control and variable groups using Graphpad Prism. Figures will be generated using graphed data for presentation.

Expected student deliverables: Students will be required to submit monthly written progress reports on their work in the lab and present a research poster at the WSU Summer Research Symposium.

Description of work environment: Our group is currently composed of two graduate students and seven undergraduate students. We expect to hire a postdoctoral fellow and lab manager when funding becomes available.

Required skills/background of student: Undergraduate courses in microbiology, biochemistry, chemistry, physics, and calculus. Undergraduate lab course.

Helpful skills/background (but not required): Undergraduate lab experience, pipetting, cell culture

Training provided: We will teach fruit fly husbandry and injection, cell culture, nucleic acid extraction, qRT-PCR, western blotting. Data analysis using Graphpad Prism.

Security clearance or background check required?: No

Age restrictions?: No

Other restrictions?: No

Housing: On Campus/Off Campus: All non-WSU undergraduate students who are on campus for summer research experiences (e.g. REU’s, typically 50 – 70) stay in one of WSU’s residence halls. In 2026 they will stay in Global Scholars (air conditioning, laundry facilities, etc). This will provide the Goldwater interns with a peer network. They will be able to interact with their peers in the residence hall, but they will also be able to attend weekly brown bag workshops with their peers. All students will be able to present their research at the Summer Research Symposium.

Approximate housing cost per week: The rates for Summer 2026 are $40.50 per person per night for double occupancy and $44 per person per night for single occupancy or $283.50 per week for double occupancy and $308 per week for single occupancy.

Public transportation: Yes, Pullman Transit With a WSU ID card, student’s can ride the bus for free. We are a small town and most things are accessible by bus or walking.

Meal Plan Available/Not Available: Regular meal plans are not available during the summer, but the mini-meal plan is available. There are dining options available on campus including Compton Union Building (CUB) Food Court Carlita’s and Freshens CUB food court Hillside Café and Northside Café (campus dining center) Starbucks (located on the ground floor of the Spark building) Lighty Espresso (also has food options) There is also a shared kitchen option in the residence hall which include oven, microwave, refrigerator, and sink. Basic cooking utensils are provided by the Office of Undergraduate Research.

If available, approximate meal plan price range per week: The mini meal plan is available during summer and costs $250, which includes a fee of $50 and $200 to use in Dining Dollars, which can be used during the summer at on campus dining locations. Mini meal plan holders receive a 25% discount.

Nearby restaurant/grocery Store: Pullman is a small town and all grocery stores are accessible. In Pullman, there are four large grocery store options: Rosauers, Safeway, Grocery Store Outlet, and Walmart. There are also smaller specialty stores such as Shin’s Asian Market and PNW Halal Meats.

Ideal candidate profile: The ideal candidate will be able to work independently after learning the experimental techniques in our lab. They will be self-motivated to complete their experiments and learn from others in the lab.

How will you evaluate applicants?: I will look for strong aptitude from grades in STEM courses, the quality of their written statement, and prior research skills that are similar to those in our lab.

Anything else applicants should know?: Our lab is part of the EschLEAD undergraduate research program at WSU (https://vetmed.wsu.edu/education/undergraduate-degrees/eschlead-program/). Students who do summer research in our lab will have the opportunity to take part in all EschLEAD events at WSU.

Briefly describe your experience mentoring undergraduates: Including current and former students/lab members, I have advised 10 graduate students, 36 undergraduate students, five high school students, three lab technicians, and two post-doctoral fellows. The students have attended 30 conferences and received nearly 60 research awards. Not including students in my own lab, I have served on 29 Ph.D. thesis committees, five Professional Science Master’s committees, and seven undergraduate Honors thesis committees. I have also mentored four Goldwater Scholars and was nominated for the Goldwater Scholars Faculty Mentor Award from the Council on Undergraduate Research.