Bacteria contain enzymes called LanC that are capable of producing small proteins called lanthipeptides, which are characterized by the addition of a thiol group to a modified serine or threonine amino acid. Similar proteins — called LanC-like or LanCL — have been found in different eukaryotic cells for decades, but their function was unknown.

“LanCLs are found in nearly all higher organisms, including humans. Although scientists have worked on these proteins for over 20 years, we didn’t know their function. We had several hypotheses, which we kept ruling out based on our experiments,” said Wilfred van der Donk (MMG), a professor of chemistry and investigator of the Howard Hughes Medical Institute.

The first breakthrough came in 2015, when the Nair lab in the Department of Biochemistry solved the crystal structure of a LanC-containing protein in bacteria. The protein was bound to another enzyme called a kinase, which modifies proteins by adding a phosphate group. Inspired by this discovery, the researchers tested whether LanCL proteins were also binding to kinases in eukaryotic cells. “We saw that they were able to bind to many kinases, including AKT and mTOR, and all of a sudden the pieces of the puzzle started forming a picture,” van der Donk said.

The next piece fell into place in collaboration with Benjamin Davis, a professor of chemistry at the University of Oxford. The Davis group showed that eliminating a particular phosphate group in kinases causes them to become activated. Scientists had assumed that such processed proteins would be inactive. Together, the Illinois and Oxford groups were able to show that LanCL adds glutathione to kinases with eliminated phosphate groups, after which the kinases became deactivated. “We realized that when the LanCL proteins are absent, the cell has a big problem because there are active proteins floating around that need to be turned off,” van der Donk said.

The importance of these proteins became evident in mice that lacked them. “A third of the mice that lack these enzymes die when they are between four to six months old. They die suddenly without getting sick and we still don’t understand why,” said Jie Chen (GNDP), a professor of cell and developmental biology.

The researchers are interested in understanding the role of these proteins and making a complete list of all the possible targets of LanCLs. “When you have abnormal kinases, it can cause all kinds of problems, including cancer. LanCL proteins eliminate these damaged kinases and it is possible that they also affect other proteins that we are not aware of. We need to connect their cellular functions to the results we saw in the mice,” Chen said.

“This study is just the tip of the iceberg. Since these proteins are found everywhere, you can also imagine their effects in feedstock and the future of farming,” said Satish Nair (MME/MMG), Head of the Department of Biochemistry.

“This study was possible because of the persistence of our graduate students. Most of us would have given up long ago because the studies were initially going nowhere,” Nair said. “It also shows the importance of exploratory research, where you’re essentially just looking around. Although it is risky, it is great to see that there are rewards for students who stick it out,” van der Donk said.

Yet in that relatively short time span — 400 to 600 mouse generations — populations on the East and West Coasts have changed their body size and nest building behavior in nearly identical ways to adapt to similar environmental conditions, according to a new study by biologists at the University of California, Berkeley.

To make these adaptations — at least in the case of body size — mice in the Western United States evolved many of the same genetic changes as their cousins in the East, showing that evolution often works on the same genes in different populations when those populations are confronted with similar environmental conditions.

The study represents one of the first times scientists have tracked down the genetic changes underlying a complex adaptive trait in mammals, though similar studies have been conducted with laboratory insects, such as fruit flies, and in fish.

“The big take-home message from this paper is that there is some predictability to evolution, both at the organismal level and at the genetic level,” said study leader Michael Nachman, UC Berkeley professor of integrative biology and director of the campus’s Museum of Vertebrate Zoology. “We have shown that the same genes have been recruited independently in two different areas, all over very short evolutionary time. This is a good example of rapid evolutionary change over short times for a complex adaptive trait.”

The findings also have implications for mammals other than rodent pests.

“The mice we are studying are a reasonable model for thinking about human evolution as well, since humans have been in the Americas about as many generations as house mice,” Nachman said. “We found genes involved in mouse body size that had previously been implicated in metabolism and things like obesity in humans, so there also are parallels between humans and mice.”

Nachman and his colleagues were able to prove that these traits have a genetic cause — they resulted from nature, not nurture — by raising mice from different environments in the lab under the same environmental conditions. House mice from New York and Alberta, Canada, always produced bigger nests than mice from Florida and Arizona, even when nesting at the same temperature, while the northern mice were always bigger than the southern mice, despite being raised in similar conditions.

“We and many other people have studied natural populations for a long time and you can document differences among natural populations,” he said. “But in this case, we went one step further and took those animals into the lab and reared them for multiple generations so we could ask whether the differences we see in nature are due to the environment or due to genetics. By having a combination of animals in the wild and animals in the lab, we can tease out the genetic component to the traits that we are studying.”

The study appeared today in the journal PLOS Genetics.

Canadian mice vs. Arizona mice

Nachman and his team have been studying house mice in North and South America for several years to determine how they have adapted to different environments — physiologically and genetically — since arriving as stowaways aboard ships from Europe. His goal has been to link changes in physiology and instinctual behavior to changes in specific genes, to understand how multiple genes interact to create changes in complicated adaptations.

To date, most studies linking genetic change — genotype — to physiological change — phenotype — have involved relatively simple characteristics, such as changes in fur color with environment, or development of insecticide resistance.

House mice — Mus musculus domesticus, the ancestor of all laboratory mice used today — seemed a good subject since they exist in a wide variety of habitats throughout the Americas, including in the Andes at elevations above 4,000 meters (13,000 feet). Over the years, Nachman and his colleagues have collected hundreds of individual mice from Tierra del Fuego at the tip of South America to southern Canada and upstate New York, and from different elevations in Ecuador and Bolivia, and sequenced all the genes in their genomes.

Nachman said that he couldn’t help but notice that in the wild, northern mice — from Edmonton, Alberta, and Saratoga Springs, New York — tended to be larger than southern mice from Tucson, Arizona, and Gainesville, Florida, though it wasn’t always clear given that the mice differed in age, diet and health. Larger body size is a well-known adaptation to colder weather, referred to as Bergmann’s rule after the 19th century German biologist Carl Bergmann.

“Mice from 45 degrees north latitude are about 50% bigger than mice from the equator,” Nachman said. “A mouse from the equator is about 12 grams; a mouse from upstate New York is about 18 grams. That is a big difference. If we were talking about humans, that would be a 100-pound versus 150-pound person, on average.”

Northern mice also build bigger nests: about twice the size of southern mice.

To determine the genetic relationships among these mouse populations, his team collected 10 mice from 5 different sites in the West, about equally spaced from Tucson to Edmonton, sequenced their genes and compared them to the genes of mice his team had collected earlier along the East Coast from Gainesville to Saratoga Springs. He found that, though Northeastern mice and Northwestern mice had both developed larger bodies and built larger nests, they were not closely related. New York mice were more closely related to other Eastern mice than to Alberta mice, while Alberta mice were more closely related to other Western mice than to New York mice.

If Eastern and Western mice are two distinct populations that independently adapted to cold weather using the same strategy — larger size and larger nests — did their genes also change?

To find out, he and his colleagues established lab colonies with 41 individual mice from the extreme areas sampled: Edmonton (EDM) in the north and Tucson (TUC) in the south. Raising them in identical indoor conditions, the northern mice over five generations retained their larger body size and larger nest building behavior, showing that the behavioral and physiological changes were in fact encoded in their genetics. Three years ago, Nachman conducted similar experiments with mice from Saratoga Springs (SAR) and Gainesville (GAI), and found similar results from these Eastern populations.

“By bringing them into the common lab environment and keeping them there at a comfy room temperature for a few generations, we can conclude that any differences we see have a genetic basis,” he said.

They then conducted a genome-wide association study to identify which variant or allele of each gene in the genome had changed frequency along with the change in body mass. They’re still tracking the genetic causes of nest building.

Finding the genetic basis for Bergmann’s Rule

The researchers identified eight mutations in five genes associated with increased body size in the Edmonton mice.

“We found that of all those genes that we identified for body size, four of the five genes show strong signatures of natural selection in both the East and West,” he said. “That suggests that we found some genes that are contributing to this pattern, known as Bergmann’s Rule, which is actually one of the most widespread geographic patterns in the evolution of warm-blooded animals. We are starting to get at its genetic basis in this study.”

Combining these data with the results from Nachman’s previous study of house mice in New York and Florida, the researchers found a total of 16 genes that showed parallel evolution along the north-south gradient on both coasts, many of which are involved in regulating body temperature. For example, the gene Trpm2, which causes mice to avoid very high temperatures, showed genetic changes in southern populations.

While mice in the East and West exhibited evidence of independent evolution in many of the same genes, each region also harbored genetic adaptations not seen in the other region. In the West, for example, fur color varied with soil color: northern mice were a darker shade, consistent with trying to blend in on damper, darker soil. Eastern mice did not show such variation.

Nachman is continuing to study house mouse variation, and hopes eventually to employ CRISPR genome editing to alter genes in his mouse populations to confirm their involvement in traits such as body size.

“We’d like to edit some of these genes and see if we can take a mouse from Canada and turn it into a mouse that looks like a Tucson mouse, or vice versa,” he said.

The work was funded by the National Institutes of Health (RO1 GM074245, R01 GM127468). The NIH and The Jackson Laboratory also support Nachman’s development of new house mouse strains — SAR, GAI, EDM, TUC and a fifth strain, MAN, from Manaus, Brazil — that researchers can use in place of the inbred lab mouse — the most popular strain is called C57BL/6 — if they want greater genetic variation in their mouse studies.

“To understand diseases, a deep comprehension of the function of genetic variants is essential. With this data set, we can connect the data about changes to DNA sequence associated with a disease to genes and cell types that are important for disease pathogenesis,” said University of Tokyo Project Research Associate Mineto Ota, M.D., Ph.D., a clinical rheumatologist and expert in functional genomics. Ota is lead author of the study recently published in Cell. The project was completed with collaborators at RIKEN research institution and Chugai Pharmaceutical Co., Ltd.

Many prior research projects have compared the full genome sequences of patients with medical diagnoses to those of healthy people. Any DNA sequence variants identified in these genomewide association studies are then considered “associated” with the disease.

Many variants identified in association studies are not located in genes, the basic units of heredity, but rather in portions of DNA that regulate the “on” or “off” expression of genes. Most of the human genome is not genes, but this regulatory DNA. Experts might know that a portion of DNA is involved in gene regulation, but not understand exactly how or what it does or even what genes it regulates.

To uncover the function of regulatory DNA, a different type of genome study called expression quantitative trait loci (eQTL) analysis attempts to connect differences in DNA sequence to differences in gene expression. With eQTL data, researchers can make more informed guesses about the purpose of regulatory DNA sequences, how variants in the regulatory sequence might affect expression of the genes it regulates and how those differences in gene expression cause disease.

Other immune-focused eQTL studies have been performed, but prior research efforts included only healthy volunteers and examined a limited number of cell types.

“Inflammatory conditions create very different physical characteristics in immune cells compared to the same cells in a healthy condition. The genetic variants associated with immune conditions may only function in the diseased state, so for this type of genetic study, it was very important to get samples from real patients,” said Ota.

The research team sequenced the full genomes of 79 healthy volunteers and 337 patients diagnosed with any of 10 different categories of immune-mediated diseases, including rheumatoid arthritis, systemic lupus erythematosus and systemic sclerosis. All volunteers had Japanese ancestry.

Understanding immune-mediated diseases is challenging because although each disease is clinically distinct, there are many overlaps and patients with the same diagnosis may show very different symptoms.

“Due to all this diversity, there’s a limit to how much you can learn studying one immune-mediated disease at a time. But if we study 10 diseases together, it gives a bigger picture about these types of diseases,” Ota explained.

After completing full genome sequencing, researchers isolated 28 different types of immune-related cells from volunteers’ blood samples and measured gene expression in those cells.

The database created through this research was named the Immune Cell Gene Expression Atlas from the University of Tokyo (ImmuNexUT).

“We see that each immune cell type has distinctive eQTL results in the atlas, which can tell us how gene regulation differs between cell types and exactly which cell type is important for developing which disease,” said Ota.

ImmuNexUT is now the largest eQTL data set built using volunteers of East Asian ancestry.

“In this field so far, large-scale genomic and functional genomic studies have been mainly conducted with European donors, although population diversity is critical for precise understanding of the genomic functions. This eQTL atlas of Japanese subjects is also meaningful for overcoming this European-centric bias and further investigating the functions of DNA variants in combination with European data sets,” said Ota.

Researchers hope the ImmuNexUT database will continue to grow and eventually lead to better outcomes for patients.

“This discovery helps to increase our understanding of the mechanisms these bacteria use to evade our normal immune defenses,” says co-corresponding author Edmund Loh, researcher in the Department of Microbiology, Tumor and Cell Biology at Karolinska Institutet. “It could be an important piece of the puzzle in examining what turns this usually harmless bacterium into a lethal killer.”

Meningitis is an inflammation of the membranes surrounding the brain and the spinal cord. It can be caused by viruses, bacteria, fungi and parasites.

Bacterial meningitis is one of the most severe types and a major cause of death and disability in children worldwide. Several kinds of bacteria can cause the infection, including the respiratory pathogens Streptococcus pneumoniae and Haemophilus influenzae, which can be attributed to some 200,000 meningitis-caused deaths annually.

These two bacteria often reside in the nose and throat of healthy people without making them ill. In some cases they spread into the bloodstream and cause invasive diseases, but the reasons for this remain largely unknown.

In this study, the researchers set out to investigate the connection between temperature changes and survival of these bacteria in a laboratory setting. The experiments were prompted by another recent finding that linked the temperature sensing abilities of the bacterium N. meningitidis to invasive meningococcal disease.

One of the signs of an infection is elevated temperatures and fever, which typically boost our immune system’s ability to fight illness. In this study, however, the researchers found that both S. pneumoniae and H. influenzae activated stronger immune protections when challenged with higher temperatures.

They did so through mechanisms involving four specific so-called RNA thermosensors (RNATs), which are temperature-sensitive non-coding RNA molecules. These RNATs helped boost the production of bigger protective capsules and immune modulatory Factor H binding proteins, both of which help shield these bacteria from immune system attacks.

“Our results indicate that these temperature sensing RNATs create an additional layer of protection that helps the bacteria colonize their normal habitat in the nose and throat,” says the paper’s first author Hannes Eichner, PhD student at the same department. “Interestingly, we saw that these RNATs do not possess any sequence similarity, but all retain the same thermosensing ability, which indicates that these RNATs have evolved independently to sense the same temperature cue in the nasopharynx to avoid immune killing.”

More research is needed to understand exactly what triggers these pathogens to breach from the mucous membrane into the bloodstream and further into the brain. Future studies encompassing in vivo infection model are warranted to characterize the role of these RNATs during colonization and invasion, the researchers say.

The work was supported by grants from the Knut and Alice Wallenberg Foundation, the Swedish Foundation for Strategic Research, the Swedish Research Council, the Stockholm County Council and Karolinska Institutet.

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Hydrogen vehicles can refuel much more quickly and go farther without refueling than today’s electric vehicles, which use battery power. But one of the final hurdles to hydrogen power is securing a safe method for detecting hydrogen leaks.

A new study published in Nature Communications documents an inexpensive, spark-free, optical-based hydrogen sensor that is more sensitive — and faster — than previous models.

“Right now, most commercial hydrogen sensors detect the change of an electronic signal in active materials upon interaction with hydrogen gas, which can potentially induce hydrogen gas ignition by electrical sparking,” said Tho Nguyen, associate professor of physics in the Franklin College of Arts and Sciences, a co-principal investigator on the project. “Our spark-free optical-based hydrogen sensors detect the presence of hydrogen without electronics, making the process much safer.”

Not just for cars

Hydrogen power has many more applications than powering electric vehicles, and flammability mitigating technologies are critical. Robust sensors for hydrogen leak detection and concentration control are important in all stages of the hydrogen-based economy, including production, distribution, storage and utilization in petroleum processing and production, fertilizer, metallurgical applications, electronics, environmental sciences, and in health and safety-related fields.

The three key problems associated with hydrogen sensors are response time, sensitivity, and cost. Current mainstream technology for H2 optical sensors requires an expensive monochromator to record a spectrum, followed by analyzing a spectral shift comparison.

“With our intensity-based optical nano sensors, we go from detection of hydrogen at around 100 parts-per-million to 2 parts-per-million, at a cost of a few dollars for a sensing chip,” Tho said. “Our response time of .8 seconds is 20% faster than the best available optical device reported in the literature right now.”

How it works

The new optical device relies on the nanofabrication of a nanosphere template covered with a Palladium Cobalt alloy layer. Any hydrogen present is quickly absorbed, then detected by an LED. A silicon detector records the intensity of the light transmitted.

“All metals tend to absorb hydrogen, but by finding the suitable elements with a right balance in the alloy and engineering the nanostructure to amplify subtle changes in light transmission after hydrogen absorption, we were able to set a new benchmark for how fast and sensitive these sensors can be,” said George Larsen, a senior scientist at Savannah River National Laboratory and co-principal investigator on the project. “All while keeping the sensor platform as simple as possible.”

The research is primarily supported by the U.S. Department of Energy and the SRNL’s Laboratory Directed Research and Development Program.

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Materials provided by University of Georgia. Original written by Alan Flurry. Note: Content may be edited for style and length.