Precision Microbiome Engineering Research

PreMiEr DEI Book Club: Racism, Not Race | Ch. 7 - 8
2023-10-17 12:00 - 13:00 (America/New_York)
Fall DEI Book Club: Racism, Not Race, by Joseph Graves, Jr.
On Tuesday, October 17th, we will discuss Chapters 7 & 8.

PreMiEr Seminar Series: Dr. Dongyang (Sunny) Deng
2023-10-12 12:00 - 13:00
PreMiEr-sponsored seminar hosted by North Carolina North Carolina Agricultural and Technical State University.
Speaker: Dongyang (Sunny) Deng, Associate Professor, College of Science and Technology
Assessment of Health and Safety Hazards in African American Low-Income Communities of Greensboro
The research project, based in low-income areas of Greensboro, presents a detailed protocol aimed at understanding the correlation between housing conditions and health. Through meticulous sampling procedures, the study evaluates the health status of selected housing units by measuring factors such as temperature, humidity, carbon dioxide levels, metal particulates, dust, and other air contaminants. This comprehensive approach not only seeks to provide empirical data on living conditions but also incorporates educational interventions. The ultimate goal is to enhance the living environment, ensuring it is both safer and healthier for residents.
Click here to register!

PreMiEr Seminar Series: Dr. Anthony Fodor
2023-10-05 12:00 - 13:00
PreMiEr-sponsored seminar hosted by University of North Carolina at Charlotte.
Speaker: Anthony Fodor, Professor, College of Computing & Informatics, PreMiEr Associate Director
Adventures with the Poisson distribution: on simplicity and reproducibility in microbial analyses
Abstract
In this talk, we explore ways in which simple algorithms can sometimes outperform more complex ones in metagenomics pipelines. We present recent results where straight-forward classical statistical approaches to differential analysis can out-perform more recently developed negative-binomial based methods. We show that data normalizations based on simple or “naïve” proportions can have some attractive properties when compared to more sophisticated, but more complex, compositionally aware transformations. And we explore how one-parameter models based on the Poisson distribution can provide reasonable null error models for 16S-based ASVs and WGS approaches to taxonomic classification. As recent controversies highlight, analysis of metagenomic data can often get bogged down in complexity. Adopting simpler methods where possible has the potential to yield more easily interpretable results that are less likely to be the result of arbitrary choices made in data analysis pipelines.
Click here to register!

PreMiEr DEI Book Club: Racism, Not Race | Ch. 5 - 6
2023-10-03 12:00 - 13:00
Fall DEI Book Club: Racism, Not Race, by Joseph Graves, Jr.
On Tuesday, October 3rd, we will discuss Chapters 5 & 6.

PreMiEr Seminar Series: Dr. Benjamin Callahan
2023-09-28 12:00 - 13:00
PreMiEr-sponsored seminar hosted by North Carolina State University.
Speaker: Benjamin Callahan, Associate Professor, College of Veterinary Medicine
Topic: Microbiome or not? Measuring low biomass environments in placentas, feline bile, and cancer.
Click here to register!

PreMiEr Seminar Series: Dr. Karis Boyd-Sinkler
2023-09-21 12:00 - 13:00
PreMiEr-sponsored seminar hosted by Duke University.
Speaker: Karis Boyd-Sinkler, Director of Diversity, Equity, & Inclusion and Adjunct Assistant Professor at Duke University’s Pratt School of Engineering
Click here to register!

PreMiEr DEI Book Club: Racism, Not Race | Ch. 3 - 4
2023-09-19 12:00 - 13:00
Fall DEI Book Club: Racism, Not Race, by Joseph Graves, Jr.
On Tuesday, September 19th, we will discuss Chapters 3 & 4.

PreMiEr Seminar Series: Dr. Jill Stewart
2023-09-14 12:00 - 13:00
PreMiEr-sponsored seminar hosted by University of North Carolina at Chapel Hill.
Speaker: Jill Stewart, Philip C. Singer Distinguished Professor, Department of Environmental Sciences and Engineering
Seminar Abstract: Environmental Antimicrobial Resistance (AMR) in the Built Environment
Antimicrobial resistance is an increasing threat to public health and modern medicine. Clinical cases of antimicrobial resistance are on the rise. However, the environmental dimensions of resistance remain poorly understood. Building on previous research to understand the evolution and ecology of resistance, we aim to develop tools and recommendations for antibiotic resistance in the built environment where humans spend most their time. Specifically, we aim to (1) establish reproducible methods to identify and prioritize antibiotic resistance genes and their biological meaning in the built environment; (2) expand sampling of key indicators and signatures to study the evolutionary ecology of resistance in these systems; and (3) evaluate the critical ability of resistance to move among humans, animals, and the built environment and potential risks to human health. We seek to work collaboratively with other PreMiEr Center projects, including sharing samples and methodological insights. Together this work will advance capabilities to study environmental dimensions of antimicrobial resistance and will contribute knowledge, recommendations, and products to advance the global fight against resistant infections.
Click here to register!

PreMiEr Seminar Series: Dr. Misty Thomas
2023-09-07 12:00 - 13:00
PreMiEr-sponsored seminar hosted by North Carolina Agricultural and Technical State University.
Speaker: Misty Thomas, Associate Professor of Biology
Click here to register!

PreMiEr DEI Book Club: Racism, Not Race | Intro - Ch. 2
2023-09-05 12:00 - 13:00
Fall DEI Book Club: Racism, Not Race, by Joseph Graves, Jr.
On Tuesday, September 5th, we will discuss the Introduction through Chapter 2.

PreMiEr Scholars Leadership Council (SLC) Monthly Meeting
2023-08-30 12:00 - 13:00
SLC leadership invites all scholars associated with PreMiEr to attend a meeting to discuss issues related to students, post-docs, and research staff, and to learn about opportunities and initiatives within the center.
Please check your emails for the Zoom meeting link

Summer Research Experiences for Undergraduates (REU) Poster Presentations
2023-07-27 10:00 - 12:30
Please join us through the Zoom link provided in emails and the PreMiEr Newsletter for the final poster presentations of our inaugural class of REU participants!

PreMiEr REU & RET Lunch & Learn
2023-07-18 12:00 - 13:00, 2023-07-11 12:00 - 13:00
All members of PreMiEr are welcome! Check your email for details.

Scholars Leadership Council Meeting
2023-07-12 14:00 - 15:00, 2023-04-25 10:00 - 11:30
Meeting for scholars associated with PreMiEr, including undergraduate students, graduate students, post-docs, research staff, and lab managers.
ERC-funded scholars and SLC leadership are required to attend.
Other PreMiEr-associated scholars are welcome to attend.
Please see your email invitation from the SLC Chair, Ivory Blakley, for the Zoom link.

PreMiEr Innovation Bootcamp
2023-06-01 09:00 - 17:00
William (Bill) Walker, PreMiEr’s Innovation Ecosystem Director will be leading an Innovation Bootcamp on June 1, 2023 from 9:00 AM to 5:00 PM ET.

PreMiEr NSF Site Visit
2023-05-19
All day visit from representatives of the National Science Foundation (NSF). All PreMiEr faculty, staff, and scholars are encouraged to attend.

Social & Ethical Implications of Microbiome Engineering Journal Club
2023-05-10 15:00 - 16:00
PreMiEr Scholars Leadership Council Chair and UNC Charlotte researcher Ivory Blakley leads a discussion on a topic TBD.
Open to PreMiEr faculty and scholars. Contact Sharon Stauffer for a calendar invitation, or show just up! Please see your emails or newsletter for the zoom link.

SLC-sponsored Poster Review Session
2023-05-10 13:00 - 14:00
Share your posters for the NSF site visit with Visual Design specialist Dr. Eric Monson and get feedback!
Check your emails or newsletter for the Zoom link.

SLC-sponsored Poster Review Session
2023-05-08 15:00 - 16:00
Share your posters for the NSF site visit with peers and get feedback!
Check your emails or newsletter for the Zoom link.

PreMiEr Contaminant Review
2023-05-04 12:00 - 13:00
Join a discussion led by Dr. Anthony Fodor, Lead of the Data Analytics Core, concerning reducing contaminants in sequence libraries. Dr. Fodor will talk about two recent publications:
Contamination source modeling with SCRuB improves cancer phenotype prediction from microbiome data: https://www.nature.com/articles/s41587-023-01696-w
Contamination in Low Microbial Biomass Microbiome Studies: Issues and Recommendations: https://pubmed.ncbi.nlm.nih.gov/30497919/
This is an important event within PreMiEr to begin creating best practices in the sampling and analyses of built environment microbiomes and all researchers involved in collecting data of that type are strongly encouraged to attend.
Please check your emails or PreMiEr Newsletter for the Zoom link.

DCI Event : "Science as Mastery" Viewing and Discussion
2023-04-27 12:00 - 13:00
Please join us on April 27, 12-1 PM on zoom for a conversation on the new AAAS documentary entitled “Science as Mastery: A Story about Race and Power”.
The documentary has a duration of ~30 minutes so we will watch the documentary together and then Joe and Karis will lead a discussion in the remaining time.
https://sciencereligiondialogue.org/resources/science-as-mastery-a-story-about-race-power/
From the AAAS Website – “This AAAS DoSER original short film, “Science as Mastery: A Story about Race and Power,” explores the intersection of the history of race, religion, and science as it relates to social structures and civil movements. Grounded in expert interviews, the film begins with the religious arguments surrounding the 16th-century slave trade and ends with the backlash to the Genome Project in the 21st-century, explaining how religious and scientific arguments of the past supported and shaped racist movements such as polygenism and eugenics. This challenging and moving short film opens the door for discussions of scientific racism of the past and present, the use of religion and science as social tools, the continuing impact of eugenics in society, and the challenges of societal progress in the face of these histories.”

Social & Ethical Implications of Microbiome Engineering Journal Club
2023-04-19 15:00 - 16:00
Topic: Race as a “ghost” variable in microbiome research – continued
Facilitator: Andrew Hardwick, Graduate Student Research Assistant for PreMiEr SEI Core. In addition, Andrew is a PhD student in Public Administration, a Research Assistant at the Genetic Engineering and Society (GES) Center at NC State and a Fellow in Cohort 2 of the AgBioFEWS graduate training program.
Summary: In our previous SEI Journal Club in March, we had discussed the existence of race as a “ghost” variable in microbiome research. “Ghost” variables are instances where variables like socially defined race are assumed to be biological and act as a proxy for a number of variables that affect microbiome research like red-lining or environmental racism. We continue this discussion by looking at the executive summary of the NASEM Report “Using Population Descriptors in Genetics and Genomics Research: A New Framework for an Evolving Field”. This report provides multiple recommendations to replace the use of ghost variables with more appropriate descriptors. In this upcoming Journal Club we will review the reports recommendations and how we can apply them in our own work.
Open to PreMiEr faculty and scholars. Contact Sharon Stauffer for a calendar invitation, or just show up! Please see your emails or newsletter for the zoom link.
Link to the NASEM Report: https://nap.nationalacademies.org/catalog/26902/using-population-descriptors-in-genetics-and-genomics-research-a-new Note: You will not be expected to read the entire report, but please review the executive summary
Supplement to NASEM Report – Webinar Link: https://www.nationalacademies.org/event/03-17-2023/use-of-race-ethnicity-and-ancestry-as-population-descriptors-in-genomics-research-report-release-webinar
See also: Past SEI Journal Club articles and discussions
The purpose of the PreMiEr SEI Journal Club is to build a community that is exposed to and thinking about the societal implications of microbiome engineering, so that we can begin to think about ways to integrate these aspects into the technology development. Another purpose—to get to know each other better as colleagues in PreMiEr!
All PreMiEr affiliated faculty, students and staff are welcome to attend. We will start with an informal 5-10 minute presentation of the article. We will then have an open discussion about how the societal and ethical aspects in the article may relate to PreMiEr’s natural science or engineering research, work, or scholarship.

Effective Academic Posters - Sponsored by the PreMiEr SLC
2023-04-18 14:00 - 15:00
Scholars are invited to a virtual training session with Dr. Eric Monson, Data Visualization Analyst from Duke University Libraries, to learn best practices for the creation of posters, figures, and the presentation of data.
This experience is Part 1 of 2, the second of which will offer critiques of posters to be presented at the NSF Site Visit.
All PreMiEr scholars are invited to attend.
Please check your emails for the Zoom invite.

SLC Discord Training Session
2023-03-30 16:00 - 16:30
Introductory session for PreMiEr scholars (undergraduates, graduate students, post-docs, research staff, and lab managers) to learn how to use discord for intra-ERC communications. See your emails from SLC Chair Ivory Blakley for Zoom link.

Scholars Leadership Council Meeting
2023-03-24 16:00 - 17:00
The next meeting of the PreMiEr SLC will be on Friday, the 24th of March, at 4pm, by zoom (please check your email or the weekly newsletter for the link).
These meetings are not strictly required (except for leaders), but attending is highly encouraged for all members.

Social & Ethical Implications of Microbiome Engineering Journal Club
2023-03-15 15:00 - 16:00
Dr. Joseph Graves Jr., PreMiEr Associate Director at N.C. A&T, leads a discussion on the topic of Race as a “ghost” variable in microbiome research.
The publication to be discussed will be Chasing Ghosts: Race, Racism, and the Future of Microbiome Research.
Additional reading: The Misguided History of Racial Medicine.
Open to PreMiEr faculty and scholars. Contact Sharon Stauffer for a calendar invitation, or just show up! Please see your emails or newsletter for the zoom link.

Social & Ethical Implications of Microbiome Engineering Journal Club
2023-02-15 15:00 - 16:00
UNC Chapel Hill researcher Dr. Joe Brown leads a discussion of the paper “Reporting individual results for biomonitoring and environmental exposures: lessons learned from environmental communication case studies“.
Open to PreMiEr faculty and scholars. Contact Sharon Stauffer to for a calendar invitation, or just show up! Please see your emails or newsletter for the zoom link.

SLC Meeting
2023-02-10 12:00 - 13:00
A meeting of the PreMiEr Scholars Leadership Council. All students, post-docs, and research staff associated with PreMiEr are invited to attend. Please check your email for the Zoom link.
