To help researchers operating under tight budget constraints, a research team at the Georgia Institute of Technology has developed OpenCell, a three-in-one laboratory device for DNA extraction procedures.

The OpenCell device, described in the open-source journal PLOS One, combines the functionalities of a bead homogenizer, a microcentrifuge, and a vortex mixer into one compact, open-source solution, addressing the significant financial challenges associated with traditional extraction methods. The battery powered OpenCell can fit into a backpack, making it ideal for fieldwork or use in locations with limited access to electricity.

According to the researchers, DNA extraction procedures often require multiple expensive instruments, making them inaccessible to budget-constrained laboratories and educational institutions, particularly in low-and-middle-income countries.

The device was developed in the laboratory of Saad Bhamla, assistant professor in Georgia Tech’s School of Chemical and Biomolecular Engineering. The other authors of the PLOS One paper include undergraduates Aryan Gupta and Justin Yu, Bioengineering PhD alumnus Elio Challita, and Janet Standeven, program director of Georgia Tech’s Frugal Science Academy.

Frugal Science Innovations

The origins of OpenCell date back to 2017, when Bhamla started working with students at Lambert High School in Suwanee, Georgia, as part of synthetic biology program led by Standeven, who was a high school teacher there. Bhamla helped students develop an electroporator costing less than a dollar with barbecue lighter technology. This led to a string of low-cost innovations and the creation of the Frugal Science Academy.

Gupta, who is lead author of the OpenCell project paper, studied at Lambert under Standeven where he needed to extract DNA for a project involving E. coli. Now finishing his junior year as an electrical engineering major, Gupta was inspired to attend Georgia Tech as a result of the collaboration with Bhamla and now works in his lab as an undergraduate researcher.

“We wanted to figure out how to use 3D printing and low-cost technologies to help solve the problem of how expensive many lab devices are, especially when you’re on a high school budget,” Gupta said. “Our main goal to make science easier and more accessible for more people.”

Low-cost Technology

Leveraging the wide accessibility of 3D printing and off-the-shelf components, the OpenCell device can be manufactured and assembled at a unit cost of less than $50, offering an accessible alternative to expensive laboratory equipment that can cost upwards of $4000.

In the study published in PLOS One, OpenCell demonstrated great effectiveness at isolating DNA from Spinacia oleracea (spinach). "These results highlight the device's potential for downstream applications such as Polymerase Chain Reaction (PCR) amplification, opening doors for research in a wide range of fields,” Bhamla said.

OpenCell’s design uses modular attachments that magnetically connect to a central rotating brushless motor, enabling efficient bead homogenization, vortex mixing, and centrifugation within a single unit. Its compact size and lightweight design contribute to its easy portability, and its battery power enables use for more than an hour in the field.

OpenCell incorporates multiple redundant safety features to protect the device and its users. But the researchers note that its 3D-printed construction, while cost-effective, is less durable than commercial devices. Therefore, regular monitoring and maintenance of components such as the motor hub and gears are necessary.

"The affordability of OpenCell makes it a game-changer for laboratories operating on tight budgets, democratizing access to essential equipment and accelerating scientific progress," said Standeven, who recently led a DNA extraction and barcoding workshop with the OpenCell device for 25 high school teachers in Pathum Thani, Thailand.

CITATION: Aryan Gupta, Justin Yu, Elio Challita, Janet Standeven, Saad Bhamla, “OpenCell: A low-cost, open-source, 3-in-1 device for DNA extraction,” PLOS One, https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0298857, 2024

Georgia’s saltwater marshes — living where the land meets the ocean — stretch along the state’s entire 100-mile coastline. These rich ecosystems are largely dominated by just one plant: grass.

Known as cordgrass, the plant is an ecosystem engineer, providing habitats for wildlife, naturally cleaning water as it moves from inland to the sea, and holding the shoreline together so it doesn’t collapse. Cordgrass even protects human communities from tidal surges.

Understanding how these plants stay healthy is of crucial ecological importance. For example, one known plant stressor prevalent in marsh soils is the dissolved sulfur compound, sulfide, which is produced and consumed by bacteria. But while the Georgia coastline boasts a rich tradition of ecological research, understanding the nuanced ways bacteria interact with plants in these ecosystems has been elusive. Thanks to recent advances in genomic technology, Georgia Tech biologists have begun to reveal never-before-seen ecological processes.

The team’s work was published in Nature Communications. 

Joel Kostka, the Tom and Marie Patton Distinguished Professor and associate chair for Research in the School of Biological Sciences, and Jose Luis Rolando, a postdoctoral fellow, set out to investigate the relationship between the cordgrass Spartina alterniflora and the microbial communities that inhabit their roots, identifying the bacteria and their roles.

“Just like humans have gut microbes that keep us healthy, plants depend on microbes in their tissues for health, immunity, metabolism, and nutrient uptake,” Kostka said. “While we’ve known about the reactions that drive nutrient and carbon cycling in the marsh for a long time, there’s not as much data on the role of microbes in ecosystem functioning.”

Out in the Marsh

A major way that plants get their nutrients is through nitrogen fixation, a process in which bacteria convert nitrogen into a form that plants can use. In marshes, this role has mostly been attributed to heterotrophs, or bacteria that grow and get their energy from organic carbon. Bacteria that consume the plant toxin sulfide are chemoautotrophs, using energy from sulfide oxidation to fuel the uptake of carbon dioxide to make their own organic carbon for growth.

“Through previous work, we knew that Spartina alterniflora has sulfur bacteria in its roots and that there are two types: sulfur-oxidizing bacteria, which use sulfide as an energy source, and sulfate reducers, which respire sulfate and produce sulfide, a known toxin for plants,” Rolando said. “We wanted to know more about the role these different sulfur bacteria play in the nitrogen cycle.”

Kostka and Rolando headed to Sapelo Island, Georgia, where they have regularly conducted fieldwork in the salt marshes. Wading into the marsh, shovels and buckets in hand, the researchers and their students collected cordgrass along with the muddy sediment samples that cling to their roots. Back at the field lab, the team gathered around a basin filled with creek water and carefully washed the grass, gently separating the plant roots.

Next, they used a special technique involving heavier versions of chemical elements that occur in nature as tracers to track the microbial processes. They also analyzed the DNA and RNA of the microbes living in different compartments of the plants.

Using a sequencing technology known as shotgun metagenomics, they were able to retrieve the DNA from the whole microbial community and reconstruct genomes from newly discovered organisms. Similarly, untargeted RNA sequencing of the microbial community allowed them to assess which microbial species and specific functions were active in close association with plant roots.

Using this combination of techniques, they found that chemoautotrophic sulfur-oxidizing bacteria were also involved in nitrogen fixation. Not only did these bacteria help plants by detoxifying the root zone, but they also played a crucial role in providing nitrogen to the plants. This dual role of the bacteria in sulfur cycling and nitrogen fixation highlights their importance in coastal ecosystems and their contribution to plant health and growth.

"Plants growing in areas with high levels of sulfide accumulation tend to be smaller and less healthy," said Rolando. "However, we found that the microbial communities within Spartina roots help to detoxify the sulfide, enhancing plant health and resilience."

Local to Global Significance

Cordgrasses aren’t just the main player in Georgia marshes; they also dominate marsh landscapes across the entire Southeast, including the Carolinas and the Gulf Coast. Moreover, the researchers found that the same bacteria are associated with cordgrass, mangrove, and seagrass roots in coastal ecosystems across the planet.

"Much of the shoreline in tropical and temperate climates is covered by coastal wetlands,” Rolando said. “These areas likely harbor similar microbial symbioses, which means that these interactions impact ecosystem functioning on a global scale."  

Looking ahead, the researchers plan to further explore the details of how marsh plants and microbes exchange nitrogen and carbon, using state-of-the-art microscopy techniques coupled with ultra-high-resolution mass spectrometry to confirm their findings at the single-cell level.

"Science follows technology, and we were excited to use the latest genomic methods to see which types of bacteria were there and active,” Kostka said. “There's still much to learn about the intricate relationships between plants and microbes in coastal ecosystems, and we are beginning to uncover the extent of the microbial complexity that keeps marshes healthy.”

Citation: Rolando, J.L., Kolton, M., Song, T. et al. Sulfur oxidation and reduction are coupled to nitrogen fixation in the roots of the salt marsh foundation plant Spartina alterniflora. Nat Commun 15, 3607 (2024).

DOI: https://doi.org/10.1038/s41467-024-47646-1

Funding: This work was supported in part by an institutional grant (NA18OAR4170084) to the Georgia Sea Grant College Program from the National Sea Grant Office, National Oceanic and Atmospheric Administration, US Department of Commerce, and by a grant from the National Science Foundation (DEB 1754756).

Biomedical engineer Annabelle Singer has spent the past decade developing a noninvasive therapy for Alzheimer’s disease that uses flickering lights and rhythmic tones to modulate brain waves. Now she has discovered that the technique, known as flicker, also could benefit patients with a host of other neurological disorders, from epilepsy to multiple sclerosis.

Previously, Singer and her collaborators demonstrated that the lights and sounds, delivered to patients through goggles and headphones, have beneficial effects. Flicker has been successful in animal studies and in early human feasibility trials, where it was tested for safety, tolerance, and patient adherence.

Now, thanks to a clinical trial for people with epilepsy, the researchers quantified flicker’s effects with unprecedented precision. They also made an unexpected, but encouraging, discovery: The treatment reduced interictal epileptiform discharges (IEDs) in the brain.

These large, intermittent electrophysiological events are observed between seizures in people with epilepsy. They appear as sharp spikes on an EEG readout.

“What’s interesting about these IEDs is that they don’t just occur in epilepsy,” said Singer, McCamish Foundation Early Career Professor in the Wallace H. Coulter Department of Biomedical Engineering at Georgia Tech and Emory University. “They occur in autism, multiple sclerosis, Alzheimer’s, and other neurological disorders, too.” And IEDs disrupt normal brain function, causing memory impairment.

Singer and her team published their findings recently in Nature Communications.

The Rhythm in Our Heads

Inside the brain are elaborate symphonies of electrical activity: brain waves, or oscillations, that compose our memories, thoughts, and emotions. Singer wants to modulate those oscillations for therapeutic purposes. 

At specific frequencies of light and sound, the flicker treatment can induce gamma oscillations in mice. This helps the brain recruit microglia, cells responsible for removing beta amyloid, which is believed to play a central role in Alzheimer’s pathology. Part of the work is in recording what’s happening in the brain during treatment to verify how it’s working.

The patients in the trial were under the care of physician Jon Willie at the Emory University Hospital Epilepsy Monitoring Unit. (Willie, co-corresponding author of the study with Singer, is now at Washington University in St. Louis.) They were awaiting surgery to remove an area of the brain where seizures occur. Before that could happen, they had to undergo intracranial seizure monitoring — recording electrodes are placed in the brain to pinpoint the seizure onset zone and determine exactly which tissue should be removed. Then, patients and their care team wait for a seizure to happen. It can take days.

“In human studies, we’ve used noninvasive methods like functional MRI or scalp EEG, but they have real downsides in terms of resolution,” Singer said. “Working with these patients was a game changer. These are people with treatment-resistant epilepsy, which means that drugs aren’t working for them.”

Pathway to Healing

Singer’s team recruited 19 patients. Lead author of the study, Lou Blanpain, a former Ph.D. student in Singer’s lab and now a medical student at Emory, went from patient to patient with the flicker stimulation and recording equipment.

“Because these patients already had recording probes implanted for clinical reasons, we were able to record directly from the brain,” Singer said. “We’ve never been able to get recordings of this quality during flicker treatment before.”

As the researchers expected, flicker modulated the visual and auditory brain regions that respond strongly to stimuli. But it also reached deeper, into the medial temporal lobe and prefrontal cortex, brain regions crucial for memory. And across the brain, in regions Singer hadn’t fully explored before, she found IEDs were decreasing. 

“That has important implications for whether flicker is therapeutically relevant for people with Alzheimer’s, but also in general if we want to target anything beyond the primary sensory regions,” she said. “All of this points to the potential use of flicker in a lot of different contexts. Going forward, we’re definitely going to look at other conditions and other potential implications.”

Citation: Lou T. Blanpain, Eric R. Cole, Emily Chen, James K. Park, Michael Y. Walelign, Robert E. Gross, Brian T. Cabaniss, Jon T. Willie, Annabelle C. Singer. “Multisensory Flicker Modulates Widespread Brain Networks and Reduces Interictal Epileptiform Discharges,” Nature Communications. 

Funding: National Institutes of Health (R01 NS109226, RF1NS109226, RF1AG078736, R01 MH120194, P41 EB018783, MH12019), DARPA, McCamish Foundation, Packard Foundation.

Competing interests: Annabelle Singer owns shares in Cognito Therapeutics, which aims to develop gamma stimulation-related products. These conflicts are managed by Georgia Tech’s Office of Research Integrity Assurance.

James T. Stroud has been named an Early Career Fellow by the Ecological Society of America.

He joins the ranks of nine newly appointed ESA Fellows and ten 2024-2028 ESA Early Career Fellows, elected for "advancing the science of ecology and showing promise for continuing contributions" and recently confirmed by the organization's Governing Board.

Stroud, an Elizabeth Smithgall Watts Early Career Assistant Professor in the School of Biological Sciences, is an integrative evolutionary ecologist who investigates how ecological and evolutionary processes may underlie patterns of biological diversity at the macro-scale.

He primarily studies lizards and his research is highly multidisciplinary, combining field studies with macro-ecological and evolutionary comparative analyses. Stroud’s current interests are particularly focused on measuring natural selection in the wild, often taking advantage of non-native lizards as natural experiments in ecology and evolution.

Earlier this month, Stroud presented his recent work at the inaugural College of Sciences Frontiers in Science: Climate Action Conference and Symposium, joining more than 20 faculty experts and 100 stakeholders from across all six colleges at Georgia Tech to discuss climate change, challenges, and solutions.

Stroud joined the Georgia Tech faculty in August 2023. He earned a Ph.D. in Ecology and Evolution from Florida International University.

"I am thrilled to recognize the exceptional contributions of our newly selected Fellows and Early Career Fellows,” says ESA President Shahid Naeem. “Their groundbreaking research, unwavering commitment to mentoring and teaching and advocacy for sound science in management and policy decisions have not only advanced ecological science but also inspired positive change within our community and beyond. We celebrate their achievements and eagerly anticipate the profound impacts they will continue to make in their careers."

ESA will formally acknowledge and celebrate its new Fellows for their exceptional achievements during a ceremony at ESA’s 2024 Annual Meeting in Long Beach, California.

About ESA Fellowships

ESA established its Fellows program in 2012 with the goal of honoring its members and supporting their competitiveness and advancement to leadership positions in the Society, at their institutions, and in broader society. Past ESA Fellows and Early Career Fellows are listed on the ESA Fellows page.

About ESA

The Ecological Society of America, founded in 1915, is the world’s largest community of professional ecologists and a trusted source of ecological knowledge, committed to advancing the understanding of life on Earth. The 8,000 member Society publishes six journals and a membership bulletin and broadly shares ecological information through policy, media outreach, and education initiatives. The Society’s Annual Meeting attracts 4,000 attendees and features the most recent advances in ecological science. Visit the ESA website at https://www.esa.org.

From her home more than 800 miles away, Georgia Tech online master's student Jasmine Tata is monitoring fish in aquariums at Georgia Tech.

The University System of Georgia Board of Regents has approved a new Neuroscience and Neurotechnology Ph.D. Program at Georgia Tech.

The interdisciplinary degree is a joint effort across the Colleges of Sciences, Computing, and Engineering. The program expects to enroll its first graduate students in Fall 2025, pending approval by the Southern Association of Colleges and Schools Commission on Colleges.

The Institute Curriculum Committee has also approved a new Minor in Neuroscience, set to become available in the Georgia Tech 2024-2025 Catalog.