Tag Archives: University of Florida

Microbiology

AI-Powered Breakthrough for Improved At-Home Hepatitis and COVID-19 Testing

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Researchers at the University of Florida are using AI to develop an improved at-home test for diseases like hepatitis C and COVID-19. They have combined RT-LAMP and CRISPR technologies to create a simplified, one-pot reaction test called SPLENDID, which has demonstrated 97% accuracy for detecting SARS-CoV-2 and 95% accuracy for the most common strain of hepatitis C.

Going beyond pregnancy and COVID-19, the world could someday soon come to rely on at-home tests for many diseases thanks in part to AI-fueled improvements.

University of Florida (UF) scientists have used artificial intelligence tools to simplify a test that works for both hepatitis C and SARS-CoV-2, the virus that causes COVID-19. The simplified test happens in one small test tube in just a few minutes. With further refinement, it could come to doctor’s offices soon and, one day, even home tests that are as easy as a pregnancy test.

“We are trying to build a home-based test that is as reliable as a lab-based test,” said Piyush Jain, a UF professor of chemical engineering who led the latest research. “We are trying to make the test simple, eliminate the need for expensive equipment, and provide results in just 10 to 20 minutes.”

To accomplish those goals, Jain’s group is innovating on a system known as a one-pot reaction, because the entire test happens in one small test tube. These tests, based on a technology known as RT-LAMP, can amplify small portions of a virus’s genome and produce a visible signal when it detects the virus. Reading these tests can be as simple as looking for a blue color or using a small device that detects a change in the test tube.

The FDA has approved some at-home, one-pot tests for COVID-19, as a part of the emergency use authorization, but they have a relatively high false positive rate, meaning they aren’t as reliable as they could be.

“We are combining another technology called CRISPR to determine the difference between a false positive and a true positive,” Jain said.

CRISPR has become known in the biotech world for its ability to drive rapid genetic engineering improvements, which have the potential to one day cure inherited diseases by repairing genomes. Jain’s group relies on the CRISPR system’s ability to home in on particular genetic sequences. Only if the sequence for, say, the hepatitis virus is really present will the test show a positive result. 

The only problem? The RT-LAMP technology requires a temperature of 150 degrees F, while CRISPR works best at 100 degrees. That difference makes tests far more complicated requiring two separate reactions– too complicated for at-home use. Jain’s team has been trying to bridge this gap by developing a CRISPR system that can withstand higher temperatures.

From a heat-loving species of bacteria, the researchers recently discovered a CRISPR enzyme that thrives at 140 degrees. In their latest work, Jain’s group turned to AI tools to analyze this enzyme and discover how they could make it survive at 150 degrees. The AI programs suggested a few dozen changes to the enzyme, which Jain’s group tested in the lab. They eventually found four changes to the enzyme that let it work at 150 degrees.

“It’s very challenging for any human to do this kind of analysis on an enzyme. We didn’t have to spend years, we could make these improvements in months,” Jain said. “With everything working at the same temperature, now we are able to combine everything in a true one-pot reaction, we call SPLENDID.”

The team verified their simplified SPLENDID test on clinical samples from patients with hepatitis C or COVID-19. The test was 97% accurate for SARS-CoV-2 and 95% accurate for the most prevalent version of the hepatitis C virus found globally. Although it didn’t work well against all other less predominant versions of the hepatitis C virus, straightforward changes to the test should quickly improve its accuracy, Jain says. His team published their findings on May 8 in the journal Cell Reports Medicine.

The work was funded by the National Institute of Allergy and Infectious Diseases at the National Institutes of Health in hopes of developing simple tests for viruses like hepatitis C so they can be identified and treated early, when treatments work best. Jain’s group will now work to refine the test, improve its ability to distinguish between hepatitis C strains and verify it in hospital settings in hopes of one day providing at-home tests as well.

Reference: “Engineering highly thermostable Cas12b via de novo structural analyses for one-pot detection of nucleic acids” by Long T. Nguyen, Santosh R. Rananaware, Lilia G. Yang, Nicolas C. Macaluso, Julio E. Ocana-Ortiz, Katelyn S. Meister, Brianna L.M. Pizzano, Luke Samuel W. Sandoval, Raymond C. Hautamaki, Zoe R. Fang, Sara M. Joseph, Grace M. Shoemaker, Dylan R. Carman, Liwei Chang, Noah R. Rakestraw, Jon F. Zachary, Sebastian Guerra, Alberto Perez and Piyush K. Jain, 8 May 2023, Cell Reports Medicine.
DOI: 10.1016/j.xcrm.2023.101037

University of Florida

Microbiology

Scientists Discover New Probiotic That Could Protect Corals From a Mysterious and Devastating Disease

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Scientists from the Smithsonian’s National Museum of Natural History have discovered the first effective bacterial probiotic capable of treating and staving off stony coral tissue loss disease (SCTLD). This enigmatic disease has wreaked havoc on Florida’s coral reefs since 2014 and is swiftly permeating the Caribbean region.

The researchers’ findings were published in the journal Communications Biology. It presents a promising alternative to the currently used broad-spectrum antibiotic, amoxicillin. While amoxicillin is the only verified treatment for the disease so far, and it carries the potential risk of fostering antibiotic-resistant bacteria.

SCTLD afflicts at least two dozen species of so-called hard corals, which provide essential habitats for innumerable fishes and marine animals of economic and intrinsic value while also helping to defend coastlines from storm damage. Since its discovery in Florida in 2014, cases of SCTLD have been confirmed in at least 20 countries. The precise cause of the malady remains unknown but once a coral is infected, its colony of polyps can die within weeks.

“It just eats the coral tissue away,” said Valerie Paul, head scientist at the Smithsonian Marine Station at Fort Pierce, Florida, and senior author of the study. “The living tissue sloughs off and what is left behind is just a white calcium carbonate skeleton.”

Paul has been studying coral reefs for decades, but she said she decided to go “all in” on SCTLD in 2017 because it was so deadly, so poorly understood, and spreading so fast.

While probing how the disease is spread, Paul and a team including researchers from the University of Florida discovered that some fragments of great star coral (Montastraea cavernosa) swiftly developed SCTLD’s characteristic lesions and died, but other pieces never got sick at all.

Though the precise cause of SCTLD is unknown, the efficacy of antibiotics as a treatment suggested pathogenic bacteria were somehow involved in the progression of the disease.

For this reason, the researchers collected samples of the naturally occurring, non-pathogenic bacteria present on a pair of disease-resistant great star coral fragments for further testing. With these samples, the research team aimed to identify what, if any, naturally occurring microorganisms were protecting some great star corals from SCTLD.

 

First, the team tested the 222 bacterial strains from the disease-resistant corals for antibacterial properties using three strains of harmful bacteria previously isolated from corals infected with SCTLD. Paul and Blake Ushijima, lead author of the study and an assistant professor at the University of North Carolina Wilmington who was formerly a George Burch Fellow at Smithsonian Marine Station, found 83 strains with some antimicrobial activity, but one in particular, McH1-7, stood out.

The team then conducted chemical and genetic analyses to discover the compounds behind McH1-7’s antibiotic properties and the genes behind those compounds’ production. Finally, the researchers tested McH1-7 with live pieces of great star coral. These lab trials provided the final bit of decisive proof: McH1-7 stopped or slowed the progression of the disease in 68.2% of 22 infected coral fragments and even more notably prevented the sickness from spreading in all 12 transmission experiments, something antibiotics are unable to do.

Going forward, Paul said there is a need to work on improved delivery mechanisms if this probiotic is going to be used at scale in the field. Currently, the primary method of applying this coral probiotic is to essentially wrap the coral in a plastic bag to create a mini aquarium and then inject the helpful bacteria. Perhaps even more importantly, Paul said it remains to be seen whether the bacterial strain isolated from the great star coral will have the same curative and prophylactic effects for other species of coral.

The potential of this newly identified probiotic to help Florida’s embattled corals without the danger of inadvertently spawning antibiotic-resistant bacteria represents some urgently needed good news, Paul said.

“Between ocean acidification, coral bleaching, pollution and disease there are a lot of ways to kill coral,” Paul said. “We need to do everything we can to help them so they don’t disappear.”

Reference: “Chemical and genomic characterization of a potential probiotic treatment for stony coral tissue loss disease” by Blake Ushijima, Sarath P. Gunasekera, Julie L. Meyer, Jessica Tittl, Kelly A. Pitts, Sharon Thompson, Jennifer M. Sneed, Yousong Ding, Manyun Chen, L. Jay Houk, Greta S. Aeby, Claudia C. Häse and Valerie J. Paul, 6 April 2023, Communications Biology.
DOI: 10.1038/s42003-023-04590-y

This interdisciplinary research is part of the museum’s new Ocean Science Center, which aims to consolidate museum’s marine research expertise and vast collections into a collaborative center to expand understanding of the world’s oceans and enhance their conservation.

The study was funded by the Smithsonian, the Florida Department of Environmental Protection, the National Science Foundation, the National Oceanic and Atmospheric Administration and the National Institutes of Health.

Smithsonian

Microbiology

Invasion Alert: Disease Fears Raised Over New Mosquito Species Reported in Florida

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Another new mosquito species has made its way across the tropics into Florida, making a permanent home in at least three counties. Scientists are concerned because of the rate of new mosquitoes arriving in Florida and the potential for them to transmit mosquito-borne diseases.

A mosquito known only by its scientific name, Culex lactator, is the latest to establish in the Sunshine State, according to a new study published in the Journal of Medical Entomology by faculty at the UF/IFAS Florida Medical Entomology Laboratory (UF/IFAS FMEL).

This species was first discovered in Miami-Dade County in 2018 by UF/IFAS faculty while they hunted for other nonnative mosquitoes. Since then, thriving populations have been recorded in Miami-Dade, Collier, and Lee counties. Scientists are concerned there hasn’t been enough research on the species and their potential disease risk.

“There are about 90 mosquito species living in Florida, and that list is growing as new mosquito species are introduced to the state from elsewhere in the world,” said Lawrence Reeves, lead author of the study and an assistant professor and mosquito biologist at the UF/IFAS research center in Vero Beach.

Mosquitoes are among the most studied insects because they can transmit diseases. However, there are large gaps of knowledge, said Reeves.

“That’s particularly true for species from the tropical forests, where mosquitoes are diverse and understudied,” he said. “Introductions of new mosquito species like this are concerning because many of our greatest mosquito-related challenges are the result of nonnative mosquitoes, and in a case like this, it’s difficult to anticipate what to expect when we know so little about a mosquito species.”

Globally, there are more than 3,600 types of mosquitoes. When a new mosquito is found in Florida, it could be any of these species. Reeves and his team used DNA analysis and other tools to not only discover they had found a new mosquito species, but to identify it as Culex lactator.

Culex lactator is found in Central America and northern South America and is a member of the Culex group of mosquitoes. This group includes important species that transmit the West Nile and St. Louis encephalitis viruses, but it is unclear whether Culex lactator will contribute to the transmission of these viruses in Florida.

Every year, Florida faces challenges from mosquito-transmitted diseases like West Nile virus, eastern equine encephalitis virus, dengue virus, chikungunya virus and others, explained Reeves.

“It’s too early to know whether Culex lactator will exacerbate these challenges, but the implications are often difficult to predict because not all mosquito species are equally capable of transmitting a particular virus or other pathogen,” said Reeves.

Each mosquito-borne virus is transmitted by only certain mosquito species, said Reeves.

“We need to be vigilant for introductions of new mosquito species because each introduction comes with the possibility that the introduced species will facilitate the transmission of a mosquito-transmitted disease,” he said.

The initial specimens of Culex lactator were collected in 2018 from rural sites in southern Miami-Dade County, south of Florida City, followed by additional adult and immature specimens collected through 2022 in the same locations. Each set of mosquitoes were collected from traps set by associate professor Nathan Burkett-Cadena, doctoral student Kristin Sloyer and Reeves while looking for other recently introduced mosquitoes.

In 2022, scientists with the Collier Mosquito Control District and Lee County Mosquito Control District found Culex lactator in their counties, indicating that Culex lactator has likely spread from its initial point of introduction.

Currently, Culex lactator is known to live in Collier County – south and east of Naples – Lee County, west of Fort Myers, and in the Homestead area of Miami-Dade County, though it may have also spread elsewhere in the state, said Reeves.

“Culex lactator is physically similar to mosquito species already known from Florida. It looks like other more common mosquito species,” said Reeves. “Because of that similarity, the presence of Culex lactator in an area can be easy to miss.”

Reeves and his team stress it’s important to monitor for Culex lactator as it is likely to spread within the state into areas that are environmentally suitable.

Florida’s proximity to the tropics and climate conditions make it ideal for nonnative mosquito species. Scientists are concerned about the rate and frequency of new species establishing in Florida. As many as 17 nonnative mosquito species are established in the state. Researchers stress that the detections of nonnative mosquito species are increasingly frequent, with 11 of 17 nonnative species first reported in the past two decades, and six of these 17 detected in only the past five years, said Reeves.

The mosquitoes Aedes aegypti, Aedes albopictus, and Culex quinquefasciatus – among the most important disease vectors in the United States – like Culex lactator, are nonnative species, introduced from the tropics.

“Climate change may improve the chances of tropical mosquito species becoming established once they make it to Florida if the state becomes warmer,” adds Reeves. “Increasing storm frequency and intensity could also blow in more mosquitoes and other species from the Caribbean, Central America, and elsewhere.

Reference: “Culex (Phenacomyia) lactator (Diptera: Culicidae) in southern Florida, USA: a new subgenus and species country record” by Lawrence E Reeves, Kristin E Sloyer, Kara Tyler-Julian, Rebecca Heinig, Atom Rosales, Candelaria Domingo and Nathan D Burkett-Cadena, 22 March 2023, Journal of Medical Entomology.
DOI: 10.1093/jme/tjad023

University of Florida

Microbiology

New Portable Mosquito Repellent Device Passes U.S. Military Testing

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A device developed at the University of Florida for the U.S. military provides protection from mosquitos for an extended period and requires no heat, electricity, or skin contact.

Funded by the Department of Defense Deployed Warfighter Protection program, the controlled-release passive device was designed by Nagarajan Rajagopal, a PhD candidate and Dr. Christopher Batich in UF’s Department of Materials Science and Engineering in the Herbert Wertheim College of Engineering. It recently was tested successfully in a four-week semi-field study at the U.S. Department of Agriculture in Gainesville in a collaboration with Dr. Daniel Kline, Dr. Jerry Hogsette, and Adam Bowman from the USDA’s Center for Medical, Agricultural and Veterinary Entomology.

Results showed the controlled release of the repellent transfluthrin was effective in preventing multiple species of mosquitos from entering the testing site. Transfluthrin is an organic insecticide considered to be safe for humans and animals.

“Our device eliminates the need for applying topical repellents and for insecticides that are sprayed across an open area, which can contaminate surrounding plants or bodies of water and have a negative impact on beneficial pollinators like bees and butterflies,” Rajagopal said. “This is versatile, portable, easily deployed, and doesn’t require electricity or heat to activate the solution.”

Mosquitos are more than an annoying distraction for military personnel, as they can spread serious diseases and viruses like malaria, dengue virus, Zika, and West Nile virus. The DOD continually looks for ways to protect soldiers in the field from mosquito bites.

The controlled-release passive device is made up of a tube-shaped polypropylene plastic that is 2.5 centimeters long and holds two smaller tubes and cotton containing the repellent. The team attached 70 of the devices to the opening of a large military tent using fishing line and nothing to a similar control tent. Caged mosquitos were released at various points along the exterior of the tent, and almost all were killed or repelled within 24 hours, Rajagopal said.

He explained that while the field test showed the team’s prototype created a protective space from mosquitos for four weeks, the final product, which will be built through a 3D-printing process, could extend that period up to three months.

“We call our device passive because you don’t need to do anything to activate it,” he said. “It provides a sustained release of the insecticide over an extended period rather than just a spike at the beginning.”

Rajagopal said they are filing for a patent on the device, and the government is interested in further study, so that it can eventually be commercialized for the civilian market. USDA scientists believe there are more opportunities for its use by people who enjoy outdoor activities.

“While initially developed for tent-entrance protection, the personal protection device in various sizes and configurations has potential for other applications, including for hiking and fishing,” said Kline, a research entomologist with the USDA.

Kline added that they will evaluate other active ingredients in addition to transfluthrin to expand its potential.

“It doesn’t stop with mosquitos,” Rajagopal said. “We want to show that it will work with other insects, especially ticks, which pose a threat by causing Lyme disease.”

Reference: “Semi-field evaluation of a novel controlled release device using transfluthrin as spatial repellent to prevent entry of mosquitoes into military tents” by Nagarajan R. Rajagopal, Adam R. Bowman, Floyd J. Aldana, Christopher D. Batich, Jerome A. Hogsette and Daniel L.Kline, 13 January 2023, Current Research in Parasitology & Vector-Borne Diseases.
DOI: 10.1016/j.crpvbd.2023.100113

University of Florida

Microbiology

More Evidence Uncovered: Breast Milk of Those Vaccinated Against COVID-19 May Protect Infants

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The findings are another piece of evidence suggesting that the breast milk of those vaccinated against COVID-19 may help protect babies from the illness.

A new study from the University of Florida provides more evidence that the breast milk of people vaccinated against COVID-19 provides protection to infants too young to receive the vaccine.

This latest study follows up on findings published in 2021 showing that the breast milk of vaccinated people contained antibodies against SARS-CoV-2, the virus that causes COVID-19. The new study, published today (January 12) in the Journal of Perinatology, analyzed the stool of infants that consumed this breast milk and found SARS-CoV-2 antibodies there as well.

“Our first study showed there were SARS-CoV-2 antibodies in the breast milk, but we couldn’t say if those antibodies were getting through the babies’ gastrointestinal tract and possibly providing protection there,” said Joseph Larkin III, senior author of the study and an associate professor in the UF/IFAS department of microbiology and cell science.

Using a technique called a neutralization assay, the researchers showed that the antibodies found in the infants’ stool offered protection against the virus. The assay begins by isolating antibodies from the stool and adding them to a special line of cells that have the kind of receptors the SARS-CoV-2 virus uses to enter the cell. The researchers then introduce a SARS-CoV-2 pseudovirus, which acts like the virus that causes COVID-19 but is safer to use in the lab. The pseudovirus is fluorescent, so when it binds to a cell, the cell lights up.

“We saw that when the antibodies were present, there were fewer fluorescent cells compared to our controls where no antibodies were present,” said Lauren Stafford, one of the study’s first authors and a UF/IFAS College of Agricultural and Life Sciences doctoral student in Larkin’s lab.

“The antibodies run interference and don’t let the virus get to the cells,” Larkin added.

While the virus that causes COVID-19 is often thought of as mainly affecting the lungs, it can also invade the gut, which is why finding antibodies there is significant, the researchers said. 

“The antibodies ingested through breast milk may provide a protective coating in the infants’ mouths and gastrointestinal tract,” said Dr. Vivian Valcarce Luaces, the study’s other first author and a postdoctoral fellowship trainee in neonatology.

The study also measured and tested antibodies found in the mothers’ blood plasma and breast milk soon after vaccination and then again about six months later. The researchers found that the antibodies in the plasma and milk of vaccinated people were better able to neutralize the virus, though they also observed that antibody levels decreased at the six-month mark, which other vaccine studies have found as well.

Dr. Josef Neu, one of the study’s co-authors and a professor in the UF College of Medicine department of pediatrics, division of neonatology, said the first and second studies together give a more complete picture of how vaccinating against COVID-19 during pregnancy and breastfeeding may be protective for parent and child.

“In our research, we’re following the journey of the antibodies, from the time they are produced in mom after vaccination and now through the baby’s digestive system. The next question is whether those babies are less likely to get COVID-19,” Dr. Neu said.

The researchers say larger studies are needed to answer that question, as this latest study included 37 mothers and 25 infants, a relatively small number of participants.

However, this study adds to a growing body of research revealing how vaccination against COVID-19 during pregnancy and breastfeeding may protect newborns, the researchers say. Currently children under sixth months of age cannot receive the vaccine, so breast milk may be the only avenue for providing immunity.

Reference: “Detection of SARS-CoV-2 IgA and IgG in human milk and breastfeeding infant stool 6 months after maternal COVID-19 vaccination” by Lauren Stewart Stafford, Vivian Valcarce, Matthew Henry, Josef Neu, Leslie Parker, Martina Mueller, Valeria Vicuna, Taylor Gowen, Emilee Cato, Ivan Kosik, Jonathan Wilson Yewdell, Mark Atkinson, Nicole Cacho, Nan Li and Joseph Larkin III, 12 January 2023, Journal of Perinatology.
DOI: 10.1038/s41372-022-01581-5

The study was funded by grants from the Children’s Miracle Network and The Gerber Foundation.

The Centers for Disease Control and Prevention recommends COVID-19 vaccination for people who are pregnant, breastfeeding, trying to get pregnant or who may become pregnant in the future. According to the CDC, as of late November 2022, just over 70% of pregnant people in the United States had completed the primary series of COVID-19 vaccines, though only 14% had received the bivalent booster.

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