Precision Microbiome Engineering Research

PreMiEr SLC Journal Club
2024-09-05 12:00 - 13:00 (America/New_York)
The PreMiEr Scholar’s Leadership Council invites all scholars in the ERC (undergraduates, graduate students, postdocs, and research staff) to join in a spirited discussion and analysis of a published manuscript of relevance to the center’s vision and mission. Please check your emails or contact Megan Lott (melott@unc.edu) with any questions or for the Zoom link.

PreMiEr Fall 2024 Seminar Series | Dr. Karis Boyd-Sinkler
2024-08-29 12:00 - 13:00
The NSF Engineering Research Center for Precision Microbiome Engineering (PreMiEr) invites you to the next installment of the PreMiEr Fall 2024 Seminar Series on August 29th from Noon to 1pm on Zoom:
Dr. Karis Boyd-Sinkler
Co-Director of Diversity and Inclusion for
the NSF Engineering Research Center for
Precision Microbiome Engineering (PreMiEr)
Duke University
Unlocking Mental Resilience: Balancing Stress and Academic Pressure
This presentation aims to explore strategies to help build mental resilience while navigating the varying challenges of higher education. We will delve into the science of stress, its effects on mental well-being, and the balance between healthy motivation and overwhelming pressure. Attendees will learn practical tools for stress management, including mindfulness techniques, time management strategies, and self-compassion practices, all aimed at fostering a balanced and sustainable approach to academic success. The session encourages a proactive and inclusive discussion on how to create academic environments that promote resilience, reduce burnout, and help individuals thrive amidst pressure.
This series is open to the public, but non-PreMiEr members must register to receive the Zoom link. You need register only once for the entire series.
Register at https://duke.qualtrics.com/jfe/form/SV_0Pzn6Zv6XjNwKlE

Fall Workshop Series - Biology & Microbiomes
2024-08-26 13:00 - 16:00
For PreMiEr members and affiliates – check your emails and newsletter for instructions to register.
Taught by Dr. Misty Thomas of N.C. A&T, this workshop is intended to give a broad overview of biological topics related to microbiome research. The intended audience is PreMiEr members with expertise outside of biology or microbiology, or those looking for a refresher on those topics.
Virtual (Zoom) | 1 – 4 pm.
Registration closes: August 21

Summer REU and RET Final Presentations
2024-07-19 09:00 - 12:00
Members of PreMiEr are cordially invited to attend the virtual final presentations of our summer 2024 Research Experiences for Teachers (RET) and Research Experiences for Undergraduates (REU) participants!
9:00 am | RET participants – Lesson plan presentations
10:15 am | REU participants – Research presentations
11:15 am | Breakout room conversations with participants
A Zoom invitation will be sent to your email.

Duke University Graduate Boot Camp (Virtual)
2024-06-26 16:00 - 17:30
Presented by PreMiEr, ATHENA, and the Pratt School of Engineering:
For students interested in pursuing a Master’s or PhD in Engineering and/or Computer Science.
Virtual Session
4pm – 5:30 EST
Insights: Get information to help you decide if graduate school is right for you
Funding: Learn about graduate admissions, funding opportunities, and how to develop a strong application
Connections: Meet faculty and graduate students in your areas of research interest.
Apply by June 21st: duke.is/GradCamp6-2024

PreMiEr REU Journal Club
2024-06-13 12:00 - 13:00
Led by the PreMiEr postdoctoral scholar Dr. Megan Lott, this series targeted to members of the PreMiEr REU program and any interested ERC scholars or faculty explores published manuscripts of interest to the mission and goals of PreMiEr.
Non-REU participants interested in joining should contact Dr. Megan Lott, melott@unc.edu, for details.

PreMiEr REU: Innovation Lunch and Learn
2024-06-11 12:00 - 13:00
Led by the PreMiEr Director of the Innovation Ecosystem, Dr. Ibrahim Mohedas, this series targeted to members of the PreMiEr REU program and any interested ERC scholars or faculty explores aspects of technology development and translation in a relaxed environment.
Non-REU participants interested in joining should contact Dr. Megan Lott, melott@unc.edu, for details.

PreMiEr REU Boot Camp: Day 3
2024-06-07 09:30 - 17:00
PreMiEr Research Experiences for Undergraduates (REU) Boot Camp Day 2. Non-REU participants from within PreMiEr are welcome to attend. Anyone from the ERC interested in attending one or more of the sessions either online or in person should contact Dr. Megan Lott, Lott, melott@unc.edu for details.
9:30 AM DCI in Science and Engineering (Dr. Karis Boyd-Sinkler via Zoom)
10:00 AM Introduction to Data Analytics (Dr. Anthony Fodor via Zoom)
11:00 AM Scientific Reading and Writing (Dr. Megan Lott)
1:30 PM REU Evaluation (Dr. Glenda Kelly)

PreMiEr REU Boot Camp: Day 2
2024-06-06 09:30 - 17:00
PreMiEr Research Experiences for Undergraduates (REU) Boot Camp Day 2. Non-REU participants from within PreMiEr are welcome to attend. Anyone from the ERC interested in attending one or more of the sessions either online or in person should contact Dr. Megan Lott, Lott, melott@unc.edu for details.
9:30 AM Biology and Microbiomes (Dr. David Singleton)
10:30 AM Ethics and Comprehension in PreMiEr Research Areas (Dr. Joseph Graves via Zoom)
11:15 AM Hands-on Scanning Electron Microscope Demo (Dr. Holly Leddy)

PreMiEr REU Boot Camp: Day 1
2024-06-05 09:30 - 17:00
PreMiEr Research Experiences for Undergraduates (REU) Boot Camp Day 1. Non-REU participants from within PreMiEr are welcome to attend. Anyone from the ERC interested in attending one or more of the sessions either online or in person should contact Dr. Megan Lott, Lott, melott@unc.edu for details.
9:30 AM Welcome (Dr. Kristen Rhinehardt)
10:00 AM Introduction to PreMiEr (Dr. Jill Stewart)
11:00 AM Meet the Mentors (On Zoom, with Breakout Rooms)
2:00 PM Introduction to Microbiology (Dr. Mizpha Fernander)

PreMiEr REU: NSF GFRP Workshop Session 1
2024-06-04 12:00 - 13:00
For PreMiEr Research Experiences for Undergraduates (REU) and interested scholars, a panel discussion on the NSF Graduate Research Fellowship Program (GRFP) hosted by current PreMiEr graduate students.
Non-REU participants should reach out to Dr. Megan Lott, melott@unc.edu, if they are interested in attending.

PreMiEr NSF Site Visit and Evaluation
2024-05-30 08:00 - 17:30
PreMiEr faculty and scholars are required to attend the Year 1 NSF Site Visit and Evaluation.

PreMiEr Annual Meeting
2024-05-29 10:00 - 17:00
PreMiEr Members are invited to the second Annual Meeting of the PreMiEr ERC at Duke University.

PreMiEr Spring 2024 Seminar Series - Dr. Shalani Prasad
2024-04-04 12:00 - 13:00
Please join the NSF Engineering Research Center for Precision Microbiome Engineering (PreMiEr) and host Duke University for a talk by Dr. Shalani Prasad of the University of Texas – Dallas.
Title:Non-invasive tracking host inflammatory response due to infection and chronic disease
Abstract: Inflammation is a biological response of the immune system that can be triggered by a variety of factors, including pathogens, damaged cells and toxic compounds. These factors may induce acute and/or chronic inflammatory responses in multiple organs, potentially leading to tissue damage or disease. Both infectious and non-infectious agents and cell damage activate inflammatory cells and trigger inflammatory signaling pathways. Hence, there is a widespread interest in designing technologies that will enable tracking of the human body’s inflammatory response due to non-infectious and infectious triggers.
In this work we demonstrate the viability of passive perspiration, a functional biofluid toward tracking the human body’s inflammatory response. Cytokines are biomarkers that orchestrate the manifestation and progression of an infection/inflammatory event. Hence, noninvasive, real-time monitoring of cytokines can be pivotal in assessing the progression of infection/inflammatory event, which may be feasible through monitoring of host immune markers in eccrine sweat. This work is the first experimental proof demonstrating the ability to detect inflammation/infection such as fever, FLU directly from passively expressed sweat in human subjects using a wearable “SWEATSENSER” device. The developed SWEATSENSER device demonstrates stable, real-time monitoring of inflammatory cytokines in passive sweat.
We have expanded the tracking of Inflammation to chronic disease with inflammatory bowel disease being the disease model. This work demonstrates the first proof-of-feasibility of multiplexed cytokine and inflammatory marker detection in passively expressed eccrine sweat in a wearable form-factor that can be utilized toward better management of inflammatory bowel disease.
Open to the public, but registration is required for non-PreMiEr members.
Non-PreMiEr members can register for the seminar series through this link.

PreMiEr Spring 2024 Seminar Series - Currently Cancelled
2024-03-21 12:00 - 13:00

PreMiEr Spring 2024 Seminar Series - Dr. Yun Shen
2024-02-29 12:00 - 13:00
Please join the NSF Engineering Research Center for Precision Microbiome Engineering (PreMiEr) and host institution Duke University for a talk from Dr. Yun Shen of George Washington University.
Environmental behaviors of pathogens in complex environments and challenges to engineering interventions
Understanding the transmission of bacterial and viral pathogens in engineered water systems is of great importance to protect public health. In our study, we investigated the fate of several key pathogens in drinking water and wastewater environments. Specifically, we have 1) elucidated the physiological and transcriptional responses of Legionella pneumophila, a ubiquitous opportunistic pathogen in drinking water, to different reactive oxygen species (ROS) widely adapted in water treatment. We found that L. pneumophila exhibited resistance to ROS, and different ROS targeted on different cell components of L. pneumophila. 2) We examined the abundance and diversity of viral vesicles from wastewater. Viral vesicles are persistent clusters of viruses cloaked in vesicles released from humans and animals, and they are the dominant forms of some human viruses. We found several human viruses, including norovirus, rotavirus, astrovirus, and Sapporo virus, were associated with viral vesicles in wastewater. 3) We further investigated the persistence of viral vesicles in simulated soil environment that receives treated wastewater. Remarkably, our study demonstrated that viral vesicles exhibit greater persistence compared to free viruses in soil, underscoring the significance of detecting and controlling these vesicles in wastewater and agricultural systems. The outcomes of our study will provide insights on optimization of wastewater treatment strategies and mitigation of health risks caused by environmental pathogens.
Open to the public, but registration required for non-PreMiEr members.
Non-PreMiEr members can register for the seminar series through this link.

PreMiEr Scholars Leadership Council (SLC) Monthly Meeting
2024-02-19 15:00 - 16:00
All PreMiEr-associated scholars (undergraduates, graduate students, post-docs, and research staff) are invited to attend the monthly meetings of the Scholars Leadership Council (SLC), an organization led by and for the scholars that comprise the ERC. Please check your emails from SLC Chair Jorden Rabasco for the Zoom link.
PreMiEr-supported scholars are expected to be active members of the SLC.

PreMiEr Spring 2024 Seminar Series - Dr. Karthik Anantharaman
2024-02-15 12:00 - 13:00
Please join the NSF Engineering Research Center for Precision Microbiome Engineering (PreMiEr) and host institution The University of North Carolina at Charlotte for a talk from Dr. Karthik Anantharaman of the University of Wisconsin – Madison.
(Re)defining the roles of phage in microbiomes
Viruses that infect microbes (typically referred to as bacteriophages, or phages) are amongst the most abundant biological entities in all ecosystems. By infecting and lysing microbial populations, phages can affect community composition and function which can directly impact ecosystems, biogeochemistry, and human health and disease. Increasing use of sequencing approaches such as metagenomics has allowed the generation of massive quantities of ‘viral dark matter’ from microbiomes, which refers to viruses, viral genomes, and proteins which are poorly characterized. In this talk, I will present novel techniques developed in our laboratory including the use of machine and deep learning approaches to study phage ecology in microbiomes. Our approaches allow for the study of phage at multiple resolutions and enable prediction of phage-microbe metabolic interactions at the scale of entire communities in human and environmental systems. Overall, these approaches have diverse applications ranging from engineering viruses, microbiomes, and ecosystems, to phage therapy.
Open to the public, but registration required for non-PreMiEr members.
Non-PreMiEr members can register for the seminar series through this link.

PreMiEr Spring 2024 Seminar Series - Dr. Nathan Crook
2024-02-01 12:00 - 13:00
Please join the NSF Engineering Research Center for Precision Microbiome Engineering (PreMiEr) for a seminar by Dr. Nathan Crook of North Carolina State University.
Accelerated Engineering of Nonmodel Microbes
Microbial communities are present in a diverse range of important habitats, including the built environment, the human gut, and the plant root. In these environments, microbial communities utilize available nutrients and produce molecules that have important impacts on their surroundings. Unfortunately, many of the mechanisms that underlie these important behaviors remain mysterious, which limits our ability to modify these communities when something goes wrong, or to enhance the performance of the environment they inhabit. Genetic modification, such as knockout, knock-down, or overexpression greatly facilitates the elucidation of these mechanisms, but this ability is absent in the majority of bacteria living in important microbial communities. In this talk, I will discuss the Crook Lab’s recent efforts to enable genetic engineering in nonmodel bacteria. I will first describe a cell-free approach to “disguise” incoming foreign DNA and its application to intractable gut commensals. Then, I will discuss the development of a genetic toolkit for engineering the maize root microbiome. Finally, I will introduce our new efforts to engineer and study built-environment-derived Enterobacter ludwigii.
Open to the public, but registration required for non-PreMiEr members.
Non-PreMiEr members can register for the seminar series through this link.

PreMiEr Scholar Research-in-Progress Discussions - Limited to PreMiEr Members only
2024-01-25 12:00 - 13:00
PreMiEr scholars actively involved in research share their data, findings, and problems with other members of PreMiEr.

PreMiEr Scholars Leadership Council (SLC) Meeting
2024-01-19 10:00 - 11:00
All PreMiEr scholars (undergraduates, graduate students, post-docs, and research staff) are invited and encouraged to join the next meeting of the SLC.
Please check your email from an invitation from the SLC Chair, Jorden Rabasco, for the Zoom link.

PreMiEr Spring 2024 Seminar Series - Drs. Connie Syharat, Arash Zaghi, and Marisa Chrysochoou
2024-01-18 12:00 - 13:00
Please join the NSF Engineering Research Center for Precision Microbiome Engineering (PreMiEr) and host institution Duke University for a talk from Drs. Connie Syharat, Arash Zaghi, and Marisa Chrysochoou of the University of Connecticut.
Reframing Neurodiversity in Higher Education
A growing body of literature suggests that neurodiverse learners may possess assets that are highly desirable within STEM disciplines. Even so, despite the potential of neurodiverse individuals to contribute to innovation, neurodiverse students, such as those with attention deficit hyperactivity disorder (ADHD), autism, or dyslexia, remain highly underrepresented in STEM majors, and in higher education overall. This talk will argue that the predominant perception of neurodiversity as a disability limits the participation of neurodiverse students in higher education, ultimately impacting the diversity and creativity of the workforce. Instead, a strengths-based perspective of neurodiversity will be presented that may be integrated within STEM education in particular, as well as in higher education overall, as we present our vision for a transformative education system that moves beyond mere accommodation of learning differences and empowers all students to leverage their unique strengths.
Open to the public, but registration required for non-PreMiEr members.
Non-PreMiEr members can register for the seminar series through this link.

PreMiEr SLC December Meeting
2023-12-18 13:00 - 14:00
All students, post-docs, and research staff affiliated with PreMiEr are invited and encouraged to join the next meeting of the ERC’s Scholars Leadership Council. Please check your email for an invitation from Chair, Jorden Rabasco, for the link.

CFCI/PreMiEr Accelerator Pitch Day - Final Presentations
2023-12-07 16:00 - 17:30
PreMiEr Members are invited to join Innovation Ecosystem director Dr. Ibrahim Mohedas and the Christensen Family Center for Innovation at Duke University for the final presentation of the participants of the inaugural CFCI/PreMiEr Accelerator Workshop.
Five teams of scholars and faculty mentors have been working to develop an idea into a product and this event is their final presentation. All members of the ERC are invited and encouraged to attend. Please see your email or PreMiEr Weekly Newsletter for details of the Zoom meeting.

PreMiEr DEI Book Club: Racism, Not Race | Ch. 11 - Conclusions
2023-11-28 12:00 - 13:00
Fall DEI Book Club: Racism, Not Race, by Joseph Graves, Jr.
On Tuesday, November 28th, we will discuss Chapter 11 & Conclusions.

PreMiEr Seminar Series: Drs. Cynthia Gibas and Jessica Schlueter
2023-11-16 12:00 - 13:00
PreMiEr-sponsored seminar hosted by University of North Carolina at Charlotte.
Speakers: Drs. Cynthia Gibas, Professor, and Jessica Schlueter, Associate Professor of Bioinformatics and Genomics
Adventures in Wastewater Monitoring
Wastewater surveillance has become an established part of US public health infrastructure via the National Wastewater Surveillance System and its network of collection sites in all 50 states. Wastewater based epidemiology has become a powerful tool for public health to monitor circulating and emerging viral variants. As a medium, wastewater is a complex mixed matrix, making the deconvolution of wastewater samples more difficult as there is a scarcity of benchmarked tools for metagenomic samples. We have created a gold-standard dataset constructed from synthetic viral controls spiked into a wastewater RNA matrix and sequenced on the Oxford Nanopore Technologies platform. We compare the performance of seven of the most commonly used deconvolution tools in identifying SARS-CoV-2 variants present in these mixtures. But there’s more to find in wastewater than just viruses and bacteria. Protein biomarkers of exposure and infection are accessible via fecal samples, and we have recently demonstrated that specific human antibodies can be detected in community wastewater. This assay has the potential to provide population-level data about the susceptibility component of the epidemiological SEIR model at a much lower cost than traditional serology.
Click here to register!

PreMiEr DEI Book Club: Racism, Not Race | Ch. 11 - Conclusions
2023-11-14 12:00 - 13:00
Fall DEI Book Club: Racism, Not Race, by Joseph Graves, Jr.
On Tuesday, November 14th, we will discuss Chapter 11 & Conclusions.

PreMiEr Seminar Series: Andrew Hardwick
2023-11-09 12:00 - 13:00
PreMiEr-sponsored seminar hosted by North Carolina State University.
Speaker: Andrew Hardwick, Graduate Student and PreMiEr Scholar
Ghosts in The Built Environment – Evaluating the Use of Socially Defined Variables in Microbiome Research
Halloween may have passed, but ghosts still linger. Ghost variables are cases where socially defined variables like race and sex/gender are improperly used to study and create narratives about socially defined groups. The narratives people use matter with stories having the power to shape the development of future healthcare policy and scientific funding. This research project evaluates the use of different socially defined variables correctly and incorrectly in the context of the built environment to map out their prevalence in a network that spans academia, funding agencies, and the news. This talk will focus on the methods developed to systematically study the use of ghost variables in the built environment and some preliminary results so far.
Click here to register!

PreMiEr Seminar Series: Dr. Nicole Rockey
2023-11-02 12:00 - 13:00
PreMiEr-sponsored seminar hosted by Duke University.
Speaker: Nicole Rockey, Assistant Professor, Pratt School of Engineering
Virus persistence and treatment – implications for infectious disease transmission in the built environment
Infectious diseases from emerging and endemic pathogens continue to cause significant morbidity and mortality worldwide. Recent global changes, including urbanization, climate change, and population growth, have altered the infectious disease landscape. These changes increase disease spread and risk of viral emergence. My research seeks to better understand risks from viral pathogens and identify effective strategies to limit their spread in the built environment. In this talk, I will discuss work investigating alternative molecular and predictive modeling approaches for estimating virus fate through disinfection and developing virus monitoring strategies in water treatment settings. I will also highlight research employing animal models to assess influenza virus transmission and controlled bench-scale approaches to study the persistence and spread of respiratory viruses. This work ultimately assesses the impact of engineering interventions (e.g., ventilation) on influenza virus transmission in close-contact scenarios. Overarching aims of our work are focused on establishing transmission risks in the built environment and informing engineering interventions that will aid in building robust, sustainable responses to microbial threats.
Click here to register!

PreMiEr DEI Book Club: Racism, Not Race | Ch. 9 - 10
2023-10-31 12:00 - 13:00
Fall DEI Book Club: Racism, Not Race, by Joseph Graves, Jr.
On Tuesday, October 31st, we will discuss Chapters 9 & 10.
