Saturday, August 17, 2024

 

Scientists map DNA of Lyme disease bacteria



In new data, researchers see potential for better vaccines.



The Graduate Center, CUNY





A team led by CUNY Graduate Center biologists has produced a genetic analysis of Lyme disease bacteria that may pave the way for improved diagnosis, treatment, and prevention of the tick-borne ailment.

Weigang Qiu, a professor of Biology at the CUNY Graduate Center and Hunter College, and an international team including lead author Saymon Akther, a former CUNY Graduate Center Biology Ph.D. student, mapped the complete genetic makeup of 47 strains of Lyme disease-related bacteria from around the world, creating a powerful tool for identifying the bacterial strains that infect patients. Researchers said this could enable more accurate diagnostic tests and treatments tailored to the bacteria causing each patient’s illness.

“By understanding how these bacteria evolve and exchange genetic material, we’re better equipped to monitor their spread and respond to their ability to cause disease in humans,” said Qiu, the corresponding author of the study.

The study was published in mBio journal.

Researchers said the genetic information uncovered in the study may help scientists develop more-effective vaccines against Lyme disease.

Lyme disease is the most common tick-borne illness in North America and Europe, affecting hundreds of thousands of people a year. The disease arises from bacteria belonging to the Borrelia burgdorferi sensu lato group, which infect people through the bite of infected ticks. Symptoms can include fever, headache, fatigue, and a characteristic skin rash. If left untreated, the infection can spread to joints, the heart, and the nervous system, causing more severe complications.

Case numbers are increasing steadily, with 476,000 new cases each year in the United States, and may grow faster with climate change, the authors of the study said.

The research team, led by scientists from the CUNY Graduate Center and Hunter College, Rutgers, Stony Brook, and more than a dozen other research institutions, sequenced the complete genomes of Lyme disease bacteria representing all 23 known species in the group. Most hadn’t been sequenced before the effort. The National Institutes of Health-funded project included many bacteria strains most associated with human infections and species not known to cause disease in humans.

By comparing these genomes, the researchers reconstructed the evolutionary history of Lyme disease bacteria, tracing the origins back millions of years. They discovered the bacteria likely originated before the breakup of the ancient supercontinent Pangea, explaining the current worldwide distribution.

The study also disclosed how these bacteria exchange genetic material in and between species. This process, known as recombination, allows the bacteria to rapidly evolve and adapt to new environments. The researchers identified specific hot spots in the bacterial genomes where this genetic exchange occurs most frequently, often involving genes that help the bacteria interact with their tick vectors and animal hosts.

To facilitate ongoing research, the team has developed web-based software tools (BorreliaBase.org) that allow scientists to compare Borrelia genomes and identify determinants of human pathogenicity.

Looking ahead, the researchers said they plan to expand their analysis to include more strains of Lyme disease bacteria, especially from understudied regions. They also aim to investigate the functions of genes unique to disease-causing strains, which could uncover new targets for therapeutic interventions. As Lyme disease expands its geographic range because of climate change, the research provides valuable tools and insights for combating this rising public health threat.

The study is supported by grants from NIH and an award from the Steven and Alexandra Cohen Foundation.

(DOI: 10.1128/mbio.01749-24).

 

About the Graduate Center of The City University of New York
The CUNY Graduate Center is a leader in public graduate education devoted to enhancing the public good through pioneering research, serious learning, and reasoned debate. The Graduate Center offers ambitious students nearly 50 doctoral and master’s programs of the highest caliber, taught by top faculty from throughout CUNY — the nation’s largest urban public university. Through its nearly 40 centers, institutes, initiatives, and the Advanced Science Research Center, the Graduate Center influences public policy and discourse and shapes innovation. The Graduate Center’s extensive public programs make it a home for culture and conversation. 

 

Blind cavefish have extraordinary taste buds



Cavefish increase the number and location of taste buds — to the head and chin, says UC biologist




University of Cincinnati

Blind cavefish 

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The blind cavefish

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Credit: Andrew Higley/UC Marketing + Brand





Over thousands of years, cavefish evolved and lost their vision, earning the moniker “the blind cavefish,” but some cavefish also developed an inordinate number of taste buds on the head and chin. 

In a new study, now published in the Nature journal Communications Biology, scientists at the University of Cincinnati have determined when the taste buds start to appear in areas beyond the oral cavity. The study was supported by the National Science Foundation. 

To begin, blind cavefish evolved in cave ponds in northeastern Mexico. They are pale pink and nearly translucent compared to their silvery counterparts that live in surface rivers and streams. While cavefish have the faintest outline of eye sockets, the surface fish have enormous round eyes that give them a perpetually surprised expression.

Despite the many obvious physical differences, the two fish are considered the same species.  

“Regression, such as the loss of eyesight and pigmentation, is a well-studied phenomenon, but the biological bases of constructive features are less well understood,” says the article’s senior author UC professor and biologist Joshua Gross, whose laboratory is dedicated to the study of evolution and development of cave-dwelling vertebrates.

Although scientists in the 1960s discovered that certain populations of blind cavefish had extra taste buds — on the head and chin — there was no further study of the developmental or genetic processes that explain this unusual trait, says Gross.

To determine when the extra taste buds appear, Gross and his research team looked at the species Astyanax mexicanus, including two separate cavefish populations that dwell in the Pachón and Tinaja caves in northwestern Mexico, known to have the additional taste buds. 

The research team found that the number of taste buds is similar to the surface fish from birth through 5 months of age. The taste buds then start to increase in number and appear on the head and chin in smatterings, well into adulthood, at approximately 18 months. 

Cavefish can live much longer than 18 months in nature and captivity, and the authors suspect even more taste buds continually accumulate as the fish get older.  

While timing of taste bud appearance was comparable for the Pachón and Tinaja cavefish populations, some differences were evident with respect to density and timing of expansion, says Gross. The other surprising discovery from this study, says Gross, is the genetic architecture of this trait: “Despite the complexity of this feature, it appears that more taste buds on the head are controlled mainly by only two regions of the genome.”  

The increase correlates with the time that the cavefish stop eating other live foods for sustenance and start to pursue other food sources, Gross says, such as bat guano. Equally fascinating, he says, is that the expansion may occur in other cave locations where there are no bat populations.   

With more taste buds, he says, the cavefish have a keener sense of taste, “which is likely an adaptive trait.”   

“It remains unclear what is the precise functional and adaptive relevance of this augmented taste system,” says Gross, which has led the team to begin new studies that focus on taste, by exposing the fish to different flavors such as sour, sweet and bitter.

The blind cavefish

Credit

Andrew Higley/UC Marketing + Brand

Surprise Finding in study of environmental bacteria could advance search for better antibiotics




Johns Hopkins Medicine
A fluorescent microscope image of Caulobacter crescentus cells stained to image their membranes 

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A fluorescent microscope image of Caulobacter crescentus cells stained to image their membranes.

 

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Credit: Erin Goley, Ph.D.




In what they labeled a “surprising” finding, Johns Hopkins Medicine researchers studying bacteria from freshwater lakes and soil say they have determined a protein’s essential role in maintaining the germ’s shape. Because the integrity of a bacterial cell’s “envelope” or enclosure is key to its survival, the finding could advance the search for new and better antibiotics.

The research, described August 15 in the journal mBio, suggests that loss of a protein called OpgH in a widely studied bacterium known as Caulobacter crescentus creates a cascade of activity that disrupts the bubble-like cell envelope protecting the bacterium, resulting in the cell’s death. OpgH is an enzyme that creates glucose-containing molecules known as osmoregulated periplasmic glucans, or OPGs, which fill up the gelatinous in-between spaces of the protective cell envelope.

“In our experiments, when we get rid of the protein OpgH in Caulobacter bacteria, which halts production of OPG sugar molecules, the bacteria can’t survive,” says senior study author Erin Goley, Ph.D., professor of biochemistry at the Johns Hopkins University School of Medicine.

While Caulobacter crescentus bacteria themselves are not generally thought to cause diseases, OPGs found abundantly in gram-negative bacteria — bacteria in an enclosed shell-like membrane — play a role in antibiotic resistance and disease outcomes.

As a result, efforts to better understand the role of the sugar molecules in gram-negative bacteria, including Caulobacter, are seen as a way to aid in the development of new drugs that target disease-causing bacteria that have OPGs, including BrucellaPseudomonas, Salmonella and E.coli.

If it’s true that the proteins that make or modify these sugar molecules are essential to bacterial survival, Goley notes, they could be good drug targets for antibiotics themselves. Or, in organisms where OPGs are not essential, a drug that targets some part of the OPG pathway might sensitize the cells to existing antibiotics, she says.

In this study, scientists used a molecular tool called an inducible promoter, dialing down the presence of the OpgH protein in Caulobacter to observe the effects on the shape of the bacteria cell and how loss of the OpgH protein affects a signaling pathway known as CenKR, which identifies and repairs problems in the cell envelope. They also manipulated the cell to make too much of the protein CenR, thus hyperactivating the CenKR pathway responsible for regulating the shape of the cell envelope.

After dialing up or down the OpgH or CenR proteins, scientists placed the bacteria cells on a pad of gel that prevented them from moving. Then, researchers used a specialized microscope to observe their shapes and activities.

“We found that they became misshapen as we dialed down the OpgH protein and halted production of sugar OPG molecules, or hyperactivated the CenKR signaling pathway that maintains the cell envelope,” Goley says.

“Then we also looked at where some of the molecular players that helped to grow the cell and keep the shape of the cell were located,” she says. “The molecular players were not in the correct locations, suggesting that OpgH and CenR are integral to maintaining the cell’s shape.”

Once the cell envelope loses its shape, all of the bacteria eventually burst open and die, Goley says.

“We established a model for how either depleting OPGs or activating the signaling pathway affects cell shape and growth,” Goley says.

While characterizing the sugar molecule’s role in Caulobacter’s cell structure is an important first step, Goley cautioned that “it will take some time to develop a complete picture about how they function across gram-negative species of bacteria.”

In Caulobacter, the sugar molecules resemble closed rings, and in E. Coli, they look like trees, with branches sticking off of chained structures. Understanding their shape and all of the decorations that associate with the molecules can help researchers characterize the cell envelope, she says.

“In the next phase of research, we hope to investigate all of the enzymes that make, decorate and break down these molecules — so we can get a full picture of their metabolism and how they maintain the cell envelope,” Goley says. “Once we uncover how these enzymes function, that’s great, because those are things drugs can target.”

Other scientists who contributed to this research include co-first authors Allison Daitch and Erika Smith, both recent doctoral graduates in Goley’s lab at Johns Hopkins Medicine, and now at the Biomedical Advanced Research and Development Authority at the U.S. Department of Health and Human Services and the National Institutes of Health, respectively.

Funding for the research was provided by the National Institute of General Medical Science (R35GM136221, T32GM007445).

DOI: 10.1128/mbio.01443-24

 

The bee’s knees: New tests created to find fake honey




Cranfield University
honey samples 

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Honey samples used to develop tests

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Credit: Cranfield University





Researchers led by Cranfield University have developed new ways to detect sugar syrup adulteration in honey, paving the way for fast and accurate tests to discover fake products.

There is growing consumer demand for honey, with £89.8 million worth of honey imported to the UK in 2023. But as a high-value product it is vulnerable to fraud, with syrups added to dilute the pure honey – a report from the European Commission in 2023 found 46% of 147 honey samples tested were likely to have been adulterated with cheap plant syrups.

Because honey’s characteristics vary due to sources of nectar, season of harvest and geography, it can be very difficult and complex to detect adulterated products. Authentication methods are costly and time consuming, and there is a growing appetite for reliable testing and the adoption of new rules to combat fraud.

Now scientists at Cranfield University have successfully tested two new methods to authenticate UK honey quickly and accurately.

Detecting fake honey without opening the jar

A research project led by Dr Maria Anastasiadi, Lecturer in Bioinformatics at Cranfield University, with the Food Standards Agency and the UK’s Science and Technology Facilities Council (STFC), used a specialist light analysis technique to detect fake honey without opening the jar.

Samples of UK honeys spiked with rice and sugar beet syrups were tested using the non-invasive Spatial Offset Raman Spectroscopy (SORS) method - developed originally at STFC’s Central Laser Facility (CLF) - more commonly used in pharmaceutical and security diagnostics. This proved highly accurate in detecting sugar syrups present in the honey. SORS rapidly identified the ‘fingerprint’ of each ingredient in the product, and the scientists combined this technique with machine learning to successfully detect and identify sugar syrups from various plant sources.

The analysis method is portable and easy to implement, making it an ideal screening tool for testing honey along the supply chain.

Dr Anastasiadi commented: “Honey is expensive, and in demand – and can be targeted by fraudsters which leaves genuine suppliers out of pocket and undermines consumers’ trust. This method is an effective, quick tool to identify suspicious samples of honey, helping the industry to protect consumers and verify supply chains.”

The paper Application of Spatial Offset Raman Spectroscopy (SORS) and Machine Learning for Sugar Syrup Adulteration Detection in UK Honey was published in Foods 2024, vol. 13.

DNA traces in honey used to decipher real from fake

DNA barcoding was used in a second study, in collaboration with the Food Standards Agency and the Institute for Global Food Security at Queen’s University of Belfast, to detect rice and corn syrups spiked in UK honey samples.

Scientists used 17 honey samples collected from bee farmers around the UK, representing different seasons and floral nectar sources, and bought four samples of UK honey from supermarkets and online retailers. The samples were then spiked with corn and rice syrups produced in a range of countries.

DNA barcoding – a method already used in food authentication to identify plant species in products – was effective in breaking down the composition of each sample, to successfully detect syrups even at 1% adulteration level.

“To date, DNA methods haven’t been widely used to examine honey authenticity,” commented Dr Anastasiadi. “But our study showed that this is a sensitive, reliable and robust way to detect adulteration and confirm the origins of syrups added to the honey.

“The large variation of honey composition makes it particularly difficult to authenticate. So having this consistent technique in the testing armoury could take the sting out of honey fraud.”

Sophie Dodd, who is completing her PhD on the topic of honey authentication at Cranfield University added, “It is vital to have samples of known origin and purity to validate the methods, so we want to extend our thanks to the Bee Farmers Association who we work closely with in our projects”.

The two methods developed can work together to increase chances of detecting exogenous sugar adulteration in honey.

The paper Detection of sugar syrup adulteration in UK honey using DNA barcoding was published in Food Control, vol. 167.

 

SORS testing (IMAGE)

Cranfield University

Researchers investigate parent perceptions of virtual learning




Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign
COVID testing 

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The current work was done as part of a larger research study aimed at examining the feasibility of using saliva-based testing in five K-12 schools in Illinois. 

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Credit: Christine Herman





In response to the COVID-19 pandemic, a majority of schools across the U.S. shifted to virtual learning. In a new study, published in Social Education Research, researchers conducted interviews with parents of students who attended middle or high schools to understand how virtual learning impacted their daily routines, stress levels, and the academic performance of the children.

The transition to virtual learning necessitated the creation of online lessons in a very short time period and with limited training of teachers. As a result, parents and students had to deal with unexpected changes in their home lives and learning environments.

“Virtual learning will not be limited to the pandemic, and we need to prepare for the future. We can see it becoming more popular, for example as a replacement for snow days. Therefore, we need to know how parents feel, so we can adjust how we approach virtual learning,” said W. Catherine Cheung, an assistant professor of physical therapy at Northern Illinois University.

The researchers recruited 20 parents initially as part of a larger research study aimed at examining the feasibility of using saliva-based testing in five K-12 schools in Illinois. The participants filled out questionnaires and participated in semi-structured interviews in the summer of 2021. The researchers then used constant comparative analysis and emergent coding to find patterns in the participants’ answers.

When the parents reflected on the impact of virtual learning, some agreed that its impact on their work schedule was a major source of stress. Additionally, they found it taxing to monitor their children to ensure that they completed their work. “It stopped me from doing a lot of things because I had to make sure that they were doing what they were supposed to. It was like I went back to school,” one parent stated. Virtual learning also caused financial stress, since the families had to buy more groceries and spend more on reliable internet.

The parents were also asked how their children responded to virtual learning, and many felt that the lack of social interaction had a negative effect on their children’s mental health. One parent shared, “I think that isolation had a significant impact on our kids. There’s very little time for socialization anyway and with having older kids, we don’t have the connections with [other] parents.”

Several parents also felt that in-person schooling was better for their children’s academic needs. One parent stated, “I saw that they were falling behind, their learning went down, and their concentration wasn’t there. It was very, very hard.” They were also concerned that their children’s academic performance would be affected once they returned to in-person schooling.

Notably, a few parents, whose children received special education services, reported having positive experiences with virtual learning. These parents were able to assist with their children’s needs better, with one parent reporting, “Remote learning was a great thing for [my child] because he has a neurological disability and has an issue with writing. It allowed him to be more successful at writing because of the format.”

“When we started the study, there were no data available on how the parents were dealing with the situation, outside of anecdotes,” said Rebecca Smith (CGD/IGOH), an associate professor of epidemiology at the University of Illinois Urbana-Champaign. “Now schools can consider different aspects of education, including the home situations of students. They need to think about what the students on the margins are going to need, rather than trust that they'll get taken care of.”

The study “Exploring Parent Perceptions of Virtual Learning in School: Learning During a Pandemic” can be found at https://doi.org/10.37256/ser.5220244572. The work was done in collaboration with Michaelene Ostrosky, Grayce Wicall Gauthier Professor of Education at Illinois.