Fossils of land animals from the Antilles, including mammals and amphibians, have their closest relatives in South America. The crossing of the Caribbean Sea from South America was therefore possible, but how?

As swimming across the continent must be ruled out, given that several hundred kilometres separate the South American continent from the Antilles, the dispersal of this fauna has been attributed either to natural rafts coming out of the continent’s flooded rivers, or to the existence of land bridges that are now submerged.

A scientific project involving geologists, palaeontologists and geophysicists1 is now solving some of the mysteries related to these terrestrial species in the Antilles. The researchers have reconstructed the geography of the northern Lesser Antilles over the last 40 million years and have shown that the movements of the tectonic plates at the junction between the Lesser Antilles, the Greater Antilles and the Aves Ridge (an underwater mountain), have several times given birth to archipelagos and islands quite close to each other, which were then swallowed up in the course of time.

In addition to tectonic movements, the glacial-interglacial cycles for 1.5 million years (Quaternary) have favoured the appearance and disappearance of archipelagos. Indeed, during these cycles, the sea level decreases or increases according to the storage of water in the ice caps or their melting (the duration of these cycles is about 100,000 years). The formation of these archipelagos could thus have favoured terrestrial connections between the Aves Ridge, the Greater Antilles and the Lesser Antilles.

Scientists will now extend their studies southward, between Guadeloupe and South America, to reconstruct the past geography of the entire Caribbean Plate, in order to define more precisely the nature of the terrestrial species’ dispersal paths between the Americas.

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The researchers from UNSW’s Kirby Institute, the Peter Doherty Institute for Infection and Immunity, and the University of Sydney have identified an ‘immune correlate’ of vaccine protection. This has the potential to dramatically cut development times for new vaccines, by measuring neutralising antibody levels as a ‘proxy’ for immune protection from COVID-19.

“Neutralising antibodies are tiny Y-shaped proteins produced by our body in response to infection or vaccination. They bind to the virus, reducing its ability to infect,” says Dr Deborah Cromer from the Kirby Institute.

“While we have known for some time that neutralising antibodies are likely to be a critical part of our immune response to COVID-19, we haven’t known how much antibody you need for immunity. Our work is the strongest evidence to date to show that specific antibody levels translate to high levels of protection from disease.”

The researchers analysed data from seven COVID-19 vaccines to examine the how the response measured soon after vaccination correlated with protection. They then used statistical analysis to define the specific relationship between immune response and protection. Their analysis was remarkably accurate and was able to predict the efficacy of a new vaccine.

Dr Cromer said that this finding has the potential to change the way we conduct COVID-19 vaccine trials in the future.

“Antibody immune levels are much easier to measure than directly measuring vaccine efficacy over time. So, by measuring antibody levels across the range of new vaccine candidates during early phases of clinical trials, we can better determine whether a vaccine should be used to prevent COVID-19.”

Vaccine boosters likely to be required within a year

Another crucial application of this analysis is its ability to predict immunity over time. The researchers predict that immunity to COVID-19 from vaccination will wane significantly within a year, with the level of neutralising antibodies in the blood dropping over the first few months following infection or vaccination.

“Vaccination works very well to prevent both symptoms and severe disease in the short to medium term, but efficacy is predicted to decline over the first few months for most of these vaccines,” says Dr David Khoury, also from the Kirby Institute.

“However, it is very important to understand the difference between immunity against infection and protection from developing severe disease. Our study found that a 6-fold lower level of antibodies is required to protect against severe disease. So even though our analysis predicts that we will start losing immunity to mild infection in the first year after vaccination, protection from severe infection should be longer lived,” says Dr Khoury.

“But ultimately, for optimal protection against moderate disease and transmission of COVID-19, these findings suggest we may be looking at annual vaccine boosters, just like what we have with the flu vaccine.”

Applying the model in the real word

A major global challenge is the evolution of the virus and the emergence of new variants. There is a growing concern, based on laboratory studies, that antibodies developed against the dominant strains are less effective at neutralising these new variants.

“An added advantage of our work is that allows us to predict how protective an immune response will be against different variants,” says Professor Jamie Triccas from the University of Sydney’s Marie Bashir Institute and Faculty of Medicine and Health.

“This analysis shows a very good correlation between the immune response — which is very easy to test for — and the efficacy of a vaccine in preventing infection, which is incredibly hard to test for. This means we can predict how protective an immune response will be against different variants, without having to determine efficacy against each variant in large and costly clinical trials.

“This work can facilitate decision making by providing the necessary data much earlier on in the vaccine development pipeline and in a far more efficient way.”

A limitation of this study is that it analyses the relationship between early immune responses to infection and vaccination and protection from infection (the data that is currently available), and uses this relationship to project how immunity will change in the future and in the response to different viral variants. Future studies should aim to confirm these predictions as data becomes available.

The engineered strain of the gut bacteria E. coli senses pH and glows when it encounters acidosis, an acidic condition that often occurs during flareups of inflammatory bowel diseases like colitis, ileitis and Crohn’s disease.

Researchers at the University of Colorado (CU) School of Medicine used the Rice-created organism in a mouse model of Crohn’s disease to show acidosis activates a signature set of genes. The corresponding genetic signature in humans has previously been observed during active inflammation in Crohn’s disease patients. The results are available online in the Proceedings of the National Academy of Sciences.

Study co-author Jeffrey Tabor, whose lab engineered the pH-sensing bacterium, said it could be reprogrammed to make colors that show up in the toilet instead of the fluorescent tags used in the CU School of Medicine experiments.

“We think it could be added to food and programmed to turn toilet water blue to warn patients when a flareup is just beginning,” said Tabor, an associate professor of bioengineering in Rice’s Brown School of Engineering.

Over their 3.5 billion-year history, bacteria have evolved countless specific and sensitive genetic circuits to sense their surroundings. Tabor and colleagues developed a biohacking toolkit that allows them to mix and match the inputs and outputs of these bacterial sensors. The pH-sensing circuit was discovered by Rice Ph.D. student Kathryn Brink in a 2019 demonstration of the plug-and-play toolkit.

PNAS study co-authors Sean Colgan, the director of the CU School of Medicine’s mucosal inflammation program, and Ian Cartwright, a postdoctoral fellow in Colgan’s lab, read about the pH sensor and contacted Tabor to see if it could be adapted for use in a mouse model of Crohn’s disease.

“It turns out that measuring pH within the intestine through noninvasive ways is quite difficult,” said Colgan, the Levine-Kern Professor of Medicine and Immunology in the CU School of Medicine.

So Brink spent a few weeks splicing the necessary sensor circuits into an organism and sent it to Colgan’s lab.

“Normally, the pH in your intestines is around seven, which is neutral, but you get a lot of inflammation in Crohn’s disease, and pH goes to something like three, which is very acidic,” Tabor said.

Colgan and colleagues have studied the genes that are turned on and off under such conditions and “needed a tool to measure pH in the intestine to show that the things they were observing in in vitro experiments were also really happening in a live animal,” Tabor said.

“Colonizing this bacterial strain was the perfect biological tool to monitor acidosis during active inflammation,” Colgan said. “Correlating intestinal gene expression with the bacterial pH sensing bacteria proved to be a useful and valuable set of biomarkers for active inflammation in the intestine.”

Tabor said he believes the pH-sensing bacterium could potentially be advanced for human clinical trials in several years.

Tabor’s work was supported by the Welch Foundation (C-1856) and the National Science Foundation (1553317).

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Materials provided by Rice University. Original written by Jade Boyd. Note: Content may be edited for style and length.

Marine biodiversity, the diversity of life in the seas and oceans, supports ecosystem services of immense societal benefits. However, climate change and human activities have been adversely affecting marine biodiversity for many decades, resulting in population decline, community shifts, and species loss and extinction. Developing effective means to mitigate this rapid biodiversity loss is vital.

Scientists from Hokkaido University have identified and characterised regions in the Eastern Bering Sea where biodiversity has been protected from the effects of climate change. Their work was published in the journal Global Change Biology.

Conservation is one of the many approaches by which we have been able to protect biodiversity in various environments from climate change, pollution and human encroachment. Conservation hinges on the identification of areas where the maximum amount of biodiversity is preserved. One such area are refugia, regions that are relatively buffered from the impacts of ongoing climatic changes, which provide favorable habitats for species when the surrounding environment becomes inhospitable.

The scientists tracked the distribution of 159 marine species in the Eastern Bering Sea, off the coast of Alaska, from data collected by the National Oceanic and Atmospheric Administration (NOAA) between 1990 and 2018. Using statistical analysis, they attempted to find regions where there existed persistently high species richness and a stable marine community over a longer period of time. They also, separately, mapped out the changes in climate across the Eastern Bering Sea over the same period.

The scientists identified two distinct refugia in the fishery-rich waters of the Eastern Bering Sea. These regions covered less than 10% of the total study area but harbored 91% of the species analyzed. Most significantly, among the species sheltered in these refugia, commercially important fish and crabs were present in high numbers — indicating that these refugia conserved high-value resources in addition to supporting high species diversity and community stability. Moreover, these refugia overlapped with regions of high climatic stability over time, where trends in seasonal sea surface temperatures and winter sea ice conditions remained largely unchanged.

Climate buffering and high productivity within the Eastern Bering Sea refugia potentially permit the persistence of stable communities and high biodiversity as well as cushion marine communities from the impacts of fishing. “These biodiversity refugia, albeit small, will be increasingly crucial for preserving communities in this climate-exposed and continually exploited marine ecosystem,” says Irene D. Alabia, the lead author of the paper. “At a larger scale, this underpins the need and urgency to identify and manage marine biodiversity refugia to maintain climate-resilient marine ecosystems and fisheries.”

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