Our spring 2024 interns gave a fantastic update to their work with the Open Insulin and Barcoding the Harbor Projects. Thank you to the funders who made this work possible: The Chesapeake Bay Trust and the Baltimore City Department of Public Works.
Ulisses Santamaria is President of DMV Petri Dish, a nonprofit organization based in the DC area that aims to serve people working on the next big thing in their basements, living rooms, and garages through our helpful, innovative, and exciting science and tech community. He is an experienced researcher in neurological diseases, infectious disease, and immunology.
In this seminar, he provided some brief basics of genetic engineering and neurological diseases such as Alzheimer’s Disease, Parkinson’s Disease, Amyotrophic Lateral Sclerosis (ALS), and more. Then he took an in-depth look at clinical trials that attempted to use genetic engineering techniques to treat or cure these diseases.
On January 19, 2024, our winter interns delivered their presentations about the two research projects they worked on: Barcoding the Harbor and Open Insulin. Thanks to our interns for their fabulous talks:
Naomi Candado-Amador, University of Maryland College Park
Manal Ibrahim, UMBC
Joi Dixson, Notre Dame of Maryland University
Pearly, Gal-edd, University of Maryland College Park
Chiwe Iku, Bowie State University
Sarah Bishop, George Washington University
Joy Njuguna, UMBC
Nora E Jameson MPH MS is a transgender-nonbinary scientist, educator, DJ, and stand-up comedian who has worked at the bench for over 10 years doing biology and chemistry. After dropping out of a chemistry phd program with a MS thesis, and then a biomedical sciences PhD program, they decided to pursue their volunteer work and social justice work towards a profession in Public Health. They worked during the COVID19 Omicron wave as a COVID epidemiologist in Portland Oregon and they are now studying for their PhD in social epidemiology at the University of Maryland College Park-School of Public Health.
Their talk provided an introduction to the field of public health and CDC’s 10 essential public health services. They talked about their training in Public Health Practice and their time as a COVID epidemiologist in Portland OR and introduced the “People’s CDC” resource. They also talked about their current PhD field of study: epidemiology and their subspecialties including social epidemiology, non-cisgendered populations, violence prevention and gun violence.
Structural color occurs when light interacts with ordered nanostructures to generate bright, stable and angle-dependent colors. Structural coloration can be found throughout the tree of life, from butterflies to bacteria. Dr. Colin Ingham, CEO and founder of Hoekmine (Utrecht, Netherlands) discussed this fascinating topic and his efforts to use bacterial structural color to create sustainably colored biomaterials as sustainable replacements for bulk dyes and for artistic expression.
We’re delighted to welcome interns from MERIT Health Leadership Academy to learn basic techniques in genetic engineering and then to join our Open Insulin research project.
Bacteriophages (or phages) are arguably the oldest and most abundant entities on earth, yet their remarkable antibacterial activity has historically been fairly unexplored in the scientific community. However, interest in phages has rapidly increased in recent years, being prompted by both the emergence of antibiotic resistance and an increased demand for natural, non-chemical approaches to managing bacteria. This talk provided a brief history of phages, an overview of their mechanisms of action, and a discussion of the many ways the power of phages is being harnessed and used today, from human therapy to biodefense to food safety and beyond.
Our speaker, Joelle Woolston, is the VP of Lab Operations at Intralytix, Inc., a Maryland biotechnology company focused on the discovery, production and marketing of bacteriophage-based products to control bacterial pathogens in environmental, agricultural, food processing, and medical settings.
Maintaining soil quality is critical to feeding our growing world population. An important and sometimes overlooked aspect of soil is its microbial component. This talk by Dr. Harsh Bais of the University of Delaware highlights the importance of benign soil microbes on plant health.
Our bodies are home to trillions of microbes and while “germs” are often thought of things to be gotten rid of, most of our microbes don’t make us sick and are even important for our health. In this seminar, Dr. Noel Britton talks about the research into the human microbiome and what we know about the relationship between microbes and human immune system and how this partnership impacts human physiology, from digestion to brain health to drug metabolism. She discussed some of the ways researchers hope to leverage microbes as potential therapeutics for a wide range of health conditions and what you can do to keep your “marriage” with your microbes healthy.
If you’re puzzled by the plethora of information and advertisements about the microbiome, good bacteria, bad bacteria, probiotics and prebiotics, you aren’t alone. This talk answered some common questions about the human microbiome, including: “What even is the human microbiome anyway? Spoiler Alert: it’s more than just bacteria in your poop! How do you measure the microbiome? Are my microbes unique to me? How many microbes are living in and on me and how did they get there? What are these microbes doing for me and why does it matter?
Noel Britton, a postdoctoral researcher at Johns Hopkins University, presented her dissertation work on the human bacterial environment. Throughout the talk, she often referred to the idea of balance. She highlighted that bacteria are not always good or bad and that bacterial species keep one another in check.
The rapid increase in microbiome publications and general research in this field is due to technological advancements. These include DNA sequencing, next-generation sequencing, and pyrosequencing. The avalanche of scientific publications has even made its way into the general person’s daily life through microbiome-focused advertising and products. However, there is still much we have to learn. A microbiome means a collection of microbes and genes that share a common environment. In this presentation, we focused on the human body and its microbiome. The metagenome is the genetic material, while the microbiota refers to the organisms in this environment. Examples of microbiota include bacterial, fungal, and viral species. Microbiota research mainly focuses on bacterial bias rather than fungal or viral organisms.
You may be asking yourself how many microbes are in a person’s microbiome. There are likely more microbes in the human body than there are stars in the Milky Way. The estimated amount of microbes in a single person is one hundred trillion cells and this makes up 57% of the cells in the human body. Various types of microbial quantification methods center around the central dogma. The central dogma is a scientific theory that genetic information flows from DNA to RNA to proteins. As a result, different processes, ranging from microscopy to metabolomics, take advantage of the central dogma to quantify the number of cells in a microbiome. There are different body sample sites used for microbiology sampling like stool, swabs, biopsies, saliva, and urine. For each sample site, there are similar processing steps overall. These steps include DNA extraction, library prep for sequencing, sequencing, and DNA analysis.
In order to extract the DNA from a sample, you must create a solution via vortexing. Next, the solution is centrifuged. This allows for the removal and separation of noncellular debris at the bottom of the centrifuged mix. Researchers continue on working with the supernatant, which is the fluid on top that houses the microbes. The supernatant undergoes high heat exposure and physical beading to break microbe cell walls and extract DNA. Once the DNA is obtained, it is purified and washed for further experimentation.
In preparation for sequencing, adaptation and amplification occur, to ensure there is adequate data for sequencing. During the sequencing process, fragments of the DNA are put together to assemble the entire structure for later data processing. The adapters are removed and the taxonomy of the sample is classified. Similar data are grouped together in an OTU, or operational taxonomic unit. Now that this data is obtained, how can it be analyzed and what questions can it answer? Looking at the data researchers will focus on alpha versus beta diversity. Alpha diversity is the variation within a single sample/group while beta diversity is the dissimilarity between multiple samples/groups. Relative abundance, or the taxonomic composition of each group, is also an important factor for researchers. Researchers also rely on network and correlational analysis to piece together the relationships between the clinical symptoms of their patients along with the samples collected in order to develop a story for their data. In previous research, it has been determined that the phyla makeup mainly remains the same between patients, but the relative abundance and ratios of these groups vary between patients. Even in the case of the McFarlane twins, who are monozygotic twins and probiotic entrepreneurs, they share 100% of their DNA, but only 30% of their gut microbiota. The gut microbiome is a unique identifier between people and there is a possibility of harnessing it as a forensic tool.
Taking a step back, the majority of these studies focus on stool science for gut investigation. Nevertheless, researchers could really sample from anywhere on the human body since microbial communities cover the entire body. Studies depict that there is a similarity between what we commonly think of as good versus bad bacteria. It is truly the amount and ratio of these species and how they interact with one another which leads to beneficial or detrimental effects. Notably, different body sites have their own normal ratios of disease-causing bacteria. For example in the urinary tract, Candida species are normally considered healthy; however, excess amounts can lead to yeast infection. All this information begs the question of how we get our microbes in the first place. They can really come from anywhere. Even a fetus gets microbes from its parent, which go on to influence their immunity early in life. Babies receive additional microbes from the birth canal, breast milk, and their environment in the early stages of life. Microbes are even present on the body after death; though they do decline as the host begins to erode.
Stay tuned for the In Sickness and In Health seminar in which Noel returns to discuss what our microbes do for us and how we can best help them!