Category: PastSeminar

 

The Microbes in Space seminar, co-sponsored by the Maryland Branch of the American Society for Microbiology, highlighted projects conducted in space relating to microbiology. Seminar attendees were joined by Dr. Jennifer Kerr of Notre Dame of Maryland University to present on some key studies happening in space and her own lab’s research.

Kerr first highlighted the many hazards spaceflight has on the human body. These dangers include radiation which damages DNA and lack of gravity which leads to mineral and bone loss. Therefore it is quite astonishing how certain microorganisms can withstand these obstacles, in particular tardigrades. Also known as water bears or moss piglets, tardigrades are tiny and cute invertebrates which prefer to live in water. They are well known for cryptobiosis, Latin for “hidden life”. Cryptobiosis is when there are no signs of metabolic activity, but the organism is still alive. In this state these animals only maintain 0.01% of normal metabolic activity which lets them handle extreme environments. Tardigrades shrivel up and go into what is known as the tun state during this dormancy period. There are also variations of cryptobiosis that tardigrades partake in. For instance, tardigrades in the tun state could survive 125 years without water (anhydrobiosis).

Tardigrade space research began in 2007 with the NASA Foton-M3 Mission studying radiation’s effects on these tiny critters. In a 2019 study, tardigrades in the tun state accidentally crash landed on the moon! Now, is it likely that there is a colony of tardigrades on the moon since there is no water on the moon and those tardigrades arrived in the tun state? Well, a 2021 study investigated tardigrade survival in such high-speed crashes. It was found that moss piglets could survive the impact, but not the shock pressure withstood, so it is unlikely that there is a tardigrade colony on the moon.

Aside from cute water bears, there are also more general microbiome studies happening in space. Specifically, these studies depict how contact surfaces around the International Space Station (ISS) have changed in response to the astronauts who come and go on the Space Station. The microbiomes of crewmembers may influence the microbial composition of ISS habitable surfaces. This is important in managing disease control and preventing contaminants from breaking certain hardware on the ISS. It was found that an astronaut’s microbiome contributes to roughly 55% of the environmental surface microbiome. These findings were not startling, yet it was importantly confirmed that the majority of these were safe and typical bacteria that already exists on the skin. However some were classified as opportunistic pathogens. Opportunistic pathogens have the potential to cause disease, but are unlikely to do so when kept in check by other bacteria or if the person’s immune system is properly functioning. Furthermore, this microbiome snapshot was maintained for a few weeks even after the particular astronaut had left. However this micro-diversity encountered turnover when a new astronaut arrived at the space station and was in constant interplay.

Not only did the microbiomes on ISS surfaces change, even the astronauts who lived there had notable shifts in their own microbial environments. In particular there were 347 bacterial species identified. This varied based on sample sites from the saliva, ears, skin, and nostrils. There were 12 top genera with the highest relative abundance identified across these astronaut samples. Mainly differences were seen in skin samples when astronauts were in flight to and from the Space Station. In the mouth, there were some key, but minimal changes. For instance, saliva had the largest change in composition of bacteria but relative abundance (which is the overall number of bacterial species) stayed the same. One potentially concerning finding with the saliva organisms was that some of them sampled displayed antimicrobial resistant gene markers. The reasoning is unknown, but further research is ongoing.

The NASA Biomedical Engineering for Exploration Space Tech (BEEST) lab is researching health care for exploration. Their goal is to train astronauts in non-invasive treatment of dental cavities. Seminar attendees were also shown a light-hearted video on how astronauts brush their teeth in space. Something as simple as brushing their teeth is even more important in space. There has never been an astronaut who is a dentist, so having preventative care and training is important. Astronauts are even taught techniques up to tooth extraction.

A healthy microbiome is known to be in eubiosis while an unbalanced one is in dysbiosis. For example, the reason that too much sugar leads to tooth decay is because bacteria in the mouth feed on this excess sugar. It causes them to grow more and create more acid. This excess acid leads to a pH shift in which creates a habitable environment for more hardy bacteria to in turn create more acid. This acid also destroys tooth enamel. This leads to cavities and even more body-based diseases. For instance, the dangerous bacteria from the mouth can move through blood to other bodily systems and clog arteries. Maintaining oral hygiene is of utmost priority in space.

This human-microbial research ties back to Dr. Jennifer Kerr’s research at Notre Dame. She is an oral microbiologist and studies teeth in space. Her work centers around Streptococcus mutans. Her lab hopes to help astronauts identify a cavity and use a handheld microwave device to kill the bacteria. Astonighly when this gadget is held to the mouth for only a minute, 99% of the S. mutans are killed. However, in the case of a cavity, demineralization still remains. In order to remineralize it, the astronaut’s body needs to be given the appropriate starting material and the pH has to come back to neutral. This research is still ongoing, but it could have profound impacts, not only on human health in space but even on Earth. According to the Global Burden of Disease Study “oral diseases affect close to 3.5 billion people worldwide” which is why this research and its findings will be so consequential to the world of dentistry and the science and medical communities as a whole.
 

Co-sponsored by the Maryland Branch of the American Society for Microbiology.

Last fall, with the promise of historic federal and state investments for community recovery, among other important initiatives, Baltimore City announced its Digital Equity Framework – a plan to permanently close its digital divide within the next eight years. Free public Wi-Fi in outdoor community gathering places has been announced as part of the plan, as has connecting our Rec Centers. The grand vision is a municipally owned fiber infrastructure serving all locations in the city. But this ambitious goal won’t be met by technology solutions alone.

Chris Ritzo presented to us about how the city is beginning this work and we discussed the Internet, Wi-Fi, and the power of human networks and community based solutions to combat inequities.

The seminar began with some background information and definitions. The Digital Divide is the gap between those with access to engage online and it disproportionately affects minorities and prevents equal technological access Digital Equity, on the other hand, differs from equality in that it acknowledges systemic barriers in place to hinder others. Lastly Digital Inclusion aims to involve all communities even those most disadvantaged. In order to achieve Digital Inclusion, there are five pillars which must be fulfilled. These include: affordable internet services, access to digital training, quality tech support, access to internet devices, and participation collaboration in the internet sphere. With online school and the overall shift online due to the COVID-19 pandemic, the Divide Divide problem has been further exacerbated and solutions for it become even more pressing.

Throughout the seminar there was active discussion from participants. A question was raised by one attendee on why internet within the City is worse than outside of it, even from the same provider. Another proposed this is because it is harder to lay underground lines in the City. Furthermore, Chris spoke to the disconnect between marketing and engineering sides at companies which also contributes to these problems. Another person highlighted the recent news of a sexual assault that occurred in the Facebook Metaverse. The victim had received responses along the lines of “if you don’t like it then don’t join”. Chris mentioned how this current event ties back to the definition of Digital Inclusion and how moderating community norms is important in addition to creating these novel tools. He also suggested a book, Behind the Screen by Sarah Roberts, identifying the problematic issues of social media. Around the ongoing purchase of Twitter by Elon Musk, Ritzo highlighted Twitter and other social media networks’ claims to support free speech, but how they can never be truly utopian since the judgment lies within the corporation with an end goal of data mining and advertising to its users.

The seminar moved on to discuss technical aspects of getting access to the Internet. For instance, a router helps us connect wired/wirelessly to a laptop onto the Internet. This router also protects us and our data to some extent via firewall. First Mile is the idea of democratizing internet setup. In this concept, individuals can also set up Wi-Fi services, not just big corporations. The seminar also touched upon running speed tests. Chris said speed is important, but not the only thing that matters. It was recommended to survey nearby Wi-Fi channels, buy an extender, and understand the channel overlaps of your current network and where it should be. There were also online sites provided to see how crowded the channels are in your neighborhood. In the same vein, conduct basic latency tests, in particular latency under load also known as bufferbloat, to determine where your internet stands as it buffers in the case there is too much data.

Overall, data mechanics surrounding internet accessibility maintains a key driver in creating a community based solution to this problem. Science and technology will benefit greatly when there is contribution and inclusion in which there is equitable and diverse representation across the Internet.

A plant geneticist’s discussion on alternative methods of bioengineering.

Sebastion Cocioba discussed using sugars as a means of selection in molecular cloning and plant genetic engineering, removing antibiotics and herbicides from the equation entirely.

A plant geneticist’s discussion on alternative methods of bioengineering, Sebastion Cocioba discussed using sugars as a means of selection in molecular cloning and plant genetic engineering, removing antibiotics and herbicides from the equation entirely. He is a plant biotechnology researcher with a focus on the production of commercially and industrially valuable plant species. He is an owner of New York Botanics, LLC, a plant biotech R&D laboratory with a specialization in orchid micropropagation, a founder of Binomica Labs (https://binomicalabs.org/), and a leader in the open science movement.

Follow him at: https://twitter.com/atinygreencell.
Join the Petalsmiths Plant Engineering Research Party on Facebook: https://www.facebook.com/groups/390697141974598

Cocioba spoke to us from a converted bedroom turned microbiology lab space and discussed his informal thesis dissertation. Like many of our talks, Cocioba began his discussion on antibiotics. Antibiotics are chemicals that prevent bacterial growth. We can isolate and harvest these compounds to cure diseases. However, antibiotic dosage is key. Through diluted exposure, bacteria gain resistance and antibiotic therapies become antiquated. Additionally, there are many ways this resistance takes place, such as transduction (bacteriophage viral infection), conjugation (bacterial sex), and transformation (free-floating DNA pickup from the environment). These horizontal gene transfer methods are all ways that antibiotic resistance spreads aside from normal cell lineage passage.

It’s not all bad news though. We can use these genetic transfer methods to our advantage. For instance, transformation is the foundation for molecular cloning. Bacterial DNA comes in the form of circular fragments known as plasmids. Naturally occurring plasmids can be used to artificially recreate traits. Plasmids with genes of interest are put into the environment and uptaken by bacteria. The code of the plasmid then hijacks the bacterial machinery to produce our desired protein. However, there is never a 100% chance of plasmid uptake by the bacteria. We don’t want to move forward with an experiment without knowing that our bacteria has the desired result we are looking for, so how do we confirm this? This is where the initial discussion about antibiotics comes into play. Adding antibiotic resistance genes to these plasmids in addition to the gene of interest can be used to screen and confirm gene uptake. The media is laced with antibiotics. Any bacterial colonies that grow in the presence of antibiotics are the ones with successful plasmid uptake. We can harvest these cells for further analysis.

Coming from a home lab, Cocioba aimed to create a way to select for gene uptake without using antibiotics. Out of pure fortune, he landed on sugar gene research. Interestingly, lab strains of Escherichia coli cannot break down sucrose on their own. Cocioba developed a way to take advantage of this metabolization inability as a selection marker. He gave E. coli in his experiments the metabolic component to digest sucrose via a plasmid. Thus in theory when bacteria survive on sucrose media, it is because the cell is consuming the sugar. This means plasmid uptake was successful and the gene of interest is present as well. Cocioba replaced the antibiotic resistance gene on a plasmid with the gene to aid in sucrose breakdown, and it worked! He developed a way to screen for plasmid uptake into bacteria without using antibiotics.

In the past, archaea were thought to be the same as bacteria. Although both are single-celled organisms, archaea fall under a different category of life. However, we can still translate between the two. Haloarchaea is an extremophile, meaning it lives in extreme conditions. They cannot survive without high salt levels. Additionally, haloarchaea is incapable of metabolizing sucrose entirely. Cocioba applied the same bacterial screening solution to archaea. He encouraged plasmid uptake into haloarchaea, so that the specimen metabolizes sucrose in extremely salty environments. This means that our sample is pure due to the high salinity (no autoclave needed). They also use different machinery which hinders them from pathogenic transfer in a normal environment. Due to their intolerance for low saline environments, these cells will literally explode down the drain and allow for safe disposal. This is a great solution for DIY bio!

He then switched gears to discuss Agrobacterium tumefaciens, a soil bacteria normally found all over plants. He compared A. tumefaciens to a shark in the water. Whenever the bacteria sense “plant blood”, it springs into action. The bacterium locates the wound site and injects itself into the plant cell. Making its way to the nucleus, this bacteria begins to genetically engineer the plant. A. tumefaciens works in two ways. It programs the plant to create a carbohydrate that only the bacteria can use and to build a fortress around the bacteria protecting itself. A. tumefaciens infection can be pinpointed by the presence of “plant tumors”. Notably, genetically modified A. tumefaciens can input their DNA into a plant this way as a form of plant genetic engineering.

This brings us from the microscopic to the macroscopic scale ending with plants. Many plant cells can regenerate via shoots (somatic embryogenesis). But how do we screen out the transgenics that have our gene of interest from the ones that don’t after A. tumefaciens infection? We can apply the sugar-bacteria solution from before here for plants too. Mannose is a sugar that plants naturally cannot metabolize, but if they were given a supplemental gene, they can. We have the sugars for selection and the mechanism to get them into plants; now we just have to test it. Plasmid molecular cloning with the gene of interest is done in E. coli and Haloarchaea. Then these are transformed into A. tumefaciens. Swapping the sugar genes in between to ultimately prepare for plant infection. Further refinements to the process speed things along. Ruby betalain from beets is used as a potent pigment to differentiate transgenic plant tissue (bright red) from normal variations (lime green). Vanilla and other pantry staple spices agitate the plant cells to encourage A. tumefaciens infection. This whole process is organic but still transgenic and revolves around sugar all the way down.

Ever wonder where shrimp come from? Shrimp farming is harder than you might think! Agriculture and aquaculture farmers need to understand how many plants and animals they are growing on land or in the water to make decisions on their farms. For aqua-farmers, counting shrimp is a major challenge because their animals are grown in murky water and the farmers are blindfolded to how many shrimp they have. Minnowtech aims to help the farmers by counting their shrimp using sonar and doing the math behind their behavior, providing aqua-farmers with the information they need to manage their farms efficiently. In this seminar, Dr. Suzan Shahrestani of Minnowtech tells us how shrimp and other seafood get to your dinner plate, and how Minnowtech is striving to make that process easier for farmers.

Aquaculture is a fairly new field in farming. Dr. Shahrestani touched on the different types of aqua-farming from oysters, salmon, yellowtail, tilapia, and even seaweed as well as the sophisticated engineering solutions developed for each. Minnowtech aims to make aquaculture more efficient and sustainable through technology integration.

Dr. Shahrestani pointed out that other types of meat are inefficient in comparison to fish. This is because other forms of meat like chicken, pork, and beef require much more feed to just grow. Cows, in particular, eat the most. They also release the most energy before ending up on our plates. Ultimately, hamburgers are more expensive to the environment than fish sticks due to the increased methane output and feed required to raise the same amount of meat. Furthermore, fish use less energy by being buoyant in water as opposed to land animals which are weighed down further by gravity.

Energy efficiency isn’t the only benefit of aquaculture. For instance, aquaculture allows further growth in less space (i.e. vertical farming). However, aquaculture presents its own problems by being in the water. It is harder to calculate crop quantity in the water. In general, science on land is easier rather than in the water. Electronics and data collection in marine environments is a tricky area to navigate, but thanks to naval research (i.e. sonar radar) these technologies can be repurposed for commercial uses.

The challenge with shrimp farming is that hundreds of thousands of animals grow in turbid water. There is no way to see below the surface even with cameras to judge the quality and yield of their crop. Minnowtech’s solution is to use sonar devices to see into the murky water. The company’s initial deployment and testing started in Hawaii and the team has taken trips around the world to apply their solution to real-life situations. The majority of shrimp farming happens at backyard farms in Southeast Asia and Central America. Due to the small-scale nature of these farms, Minnowtech’s work is even more important and impactful for the lives of these farmers.

Dr. Shahrestani concluded her talk by touching on her dissertation research in which she studied counting jellyfish. Through the IMET Ratcliffe Environmental Entrepreneur Fellowship (REEF) program she transitioned her dissertation work to an aquaculture industry-level startup and co-founded Minnowtech. Countless prototypes ultimately led to Minnowtech’s BRS-1 which is now on the market and you can check out here: https://minnowtech.com/.

Computer-aided drug design (CADD) methods have made a significant impact on the discovery and development of new drugs for treating disease. Our speakers, Alexander MacKerell and Paul Shapiro, Professors of Pharmaceutical Sciences at the University of Maryland School of Medicine, provided us with an an overview of CADD approaches and their applications in designing new drugs that target enzymes involved in cancer and inflammation.

You may have heard of bioprinting, where cells and biomaterials can be printed to create custom organs and tissues. But did you know that bioprinting can be achieved through the same techniques used to get graphics printed on a t-shirt? This talk on bioprinting discusses unique strategies to bioprint at home!

What is a trash wheel? What role do they play in protecting Baltimore’s harbor and wildlife from pollution? Adam Lindquist, the director of Healthy Harbor, answered all of our questions about our trash-intercepting, googly-eyed neighbors and the rest of Healthy Harbor’s initiatives!

Mango Materials is a San Francisco-based company that manufactures biodegradable materials using bacteria that feed on waste biogas (methane). The company’s end product is a naturally occurring polyhydroxyalkanoate (PHA) polymer that can biodegrade in many different environments. Since 2012, Mango has developed PHA that can be used to create textile fibers as a polyester replacement and that can be used to create injection molded packaging for the cosmetics industry.

This talk by Dr. Anne Schauer-Gimenez, Vice President of Customer Engagement and co-founder, discussed the journey from methane to end-product application, end-of-life biodegradability, and next steps for the company as it transitions to commercialization.

Thanks to Dr. Nick Wohlgemuth, a virologist at St. Jude’s Children’s Research hospital, for a fantastic seminar on the epidemiology and natural history of the SARS-CoV-2 virus, what the emergence of variants means for the vaccines, and how to tell if someone is protected.