Rhinovirus is a leading cause of the common cold, asthma attacks, and other respiratory illnesses. When the cold virus enters the nose, cells that line the airways, known as epithelial cells, respond and often clear the virus before it can replicate and trigger symptoms. But in other cases, individuals exposed to the virus get either mildly or seriously ill. A team of researchers, led by Ellen Foxman, set out to determine why.

The research team used epithelial cells from healthy human donors. The cells were derived from either the nasal passages or the lungs. They exposed both cell types, maintained under the same conditions in cell culture, to rhinovirus. To their surprise, the researchers observed a more robust antiviral response in nasal cells.

To investigate further, the researchers triggered the virus surveillance pathway — known as the RIG-I pathway — in both nasal and lung cells. They found that both cell types generated an antiviral response and a defense response against oxidative stress, a form of cell damage induced by viruses and other inhaled irritants such as cigarette smoke or tree pollen. In nasal cells, the antiviral response was stronger, but in bronchial cells, defense against oxidative stress was more pronounced.

In additional experiments, the research team found evidence for a tradeoff: The defense response against oxidative stress shut off antiviral defenses. To probe this further, the team exposed nasal cells to oxidative stress in the form of cigarette smoke, and then to the cold virus, and found that the nasal cells were more susceptible to the virus. “They survive the cigarette smoke but can’t fight the virus as well,” Foxman said. “And the virus grows better.”

This finding points to a delicate balance between the body’s different defense mechanisms, Foxman said. “Your airway lining protects against viruses but also other harmful substances that enter airways. The airway does pretty well if it encounters one stressor at a time. But when there are two different stressors, there’s a tradeoff,” Foxman explained. “What we found is that when your airway is trying to deal with another stress type, it can adapt but the cost is susceptibility to rhinovirus infection.”

The study, she said, shows a mechanistic link between environmental exposures and susceptibility to the common cold, and also may explain why smokers tend to be more susceptible to rhinovirus infection. The researchers hope the finding will lead to the discovery of new strategies to combat respiratory viruses, which cause an estimated 500 million colds and 2 million hospitalizations in the United States per year.

Other Yale authors are Valia T. Mihaylova, Yong Kong, Olga Fedorova, Lokesh Sharma, Charles S. Dela Cruz, Anna Marie Pyle, and Akiko Iwasaki.

This work was supported in part by the National Institutes of Health and the Howard Hughes Medical Institute. A.M.P. has a patent pending for RIG-I stimulation agent SLR-14.

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Materials provided by Yale University. Original written by Ziba Kashef. Note: Content may be edited for style and length.

A paper, published today in Nature Communications, seeks to shed new light on how these communities were formed, how people lived, and how they interacted with the local populations they supposedly came to dominate. The international team of geneticists, historians, and archaeologists led by Professor Patrick Geary of the Institute for Advanced Study and Professor Krishna Veeramah of Stony Brook University in the U.S., Professor Johannes Krause of the Max Planck Institute for the Science of Human History in Jena, Germany, and Professor David Caramelli of the University of Florence in Italy, have for the first time sequenced the genomes of entire ancient cemeteries — one in Hungary and one in Italy.

This research provides the clearest picture yet of the lives and population movements of communities associated with the Longobards, a barbarian people that ruled most of Italy for more than two hundred years after invading from the Roman Province of Pannonia (modern-day Hungary) in 568 C.E. The team’s data from the Hungarian cemetery, Szólád, almost doubles the number of ancient genomes obtained from a single ancient site to date. This in-depth genomic characterization allowed the team to examine the relationship between the genetic background of the community and the archaeological material left behind.

Professor Patrick Geary, of the Institute for Advanced Study, a senior author of the paper said, “Prior to this study, we would not have expected to observe such a strong relationship between genetic background and material culture. This appears to suggest that these particular communities contained a mix of individuals with different genetic backgrounds, that they were aware of these differences, and that it likely influenced their social identity.”

A somewhat surprising result was that in both cemeteries, individuals buried with elaborate grave goods, like swords and shields for the men and beaded necklaces and broaches for the women, tended to have a genetic ancestry associated with modern northern and central Europeans today, while grave goods in individuals with more southern European-looking genomes were much less abundant. The individuals with abundant grave goods also tended to consume more protein rich diets.

“What we have presented in this study is a unique cross-discipline framework for the future,” added Geary, “uniting experts from different disciplines to reinterpret and reconcile historical, genomic, isotopic, and archaeological evidence to enhance our knowledge of the past, compile new information on how populations move, how culture is transmitted, how to better understand identity, and new ways of understanding the complexity, heterogeneity, and malleability of Europe’s population in the past and the present.”

The approach also allowed researchers for the first time to reconstruct comprehensive genealogies of the people who were buried in these cemeteries, finding that family relations spanning multiple generations were likely key to establishing these communities. “It looks like both these cemeteries organized themselves around one or two large groups of biologically related kin, with the vast majority of these individuals being men” said Veeramah. “In addition, these related individuals tended to share the northern/central genetic ancestry associated with rich grave goods.”

The team concluded that it was unusual to see this genetic ancestry type in Hungary and certainly in Italy in the 6th century. “Though we really need more data, our current results are consistent with the idea of barbarians migrating from north of Danube and east of the Rhine, which would suggest we are observing the invasions previously described by the Romans,” said Veeramah. “It is also likely that social organization was based around large high-status male biological kinship groups, and these were key to establishing communities following the migration into Italy.”

Veeramah, Caramelli, Krause, and Geary stressed that these results represented mere snapshots of the period and that more work in other cemeteries in other regions is vital for truly understanding this period. “It could be that we look at some new cemeteries 50 km away or that are 100 years older or younger and find very different patterns of social organization. People are complicated now, and they almost certainly were during the Migration Period,” said Geary. “There are thousands of medieval cemeteries out there for us to look at. This is hopefully just the beginning of our work.”

The international team of 24 scholars joining Geary, Caramelli, Krause, and Veeramah in producing this paper include Carlos Eduardo G. Amorim and Dean Bobo of Stony Brook University; Stefania Vai, Alessandra Modi, and Martina Lari of Università degli Studi di Firenze; Cosimo Posth of the Max Planck Institute for the Science of Human History and University of Tübingen; István Koncz of Eötvös Loránd University; Susanne Hakenbeck of the University of Cambridge; Maria Cristina La Rocca of Università degli Studi di Padova; Balázs Mende of the Hungarian Academy of Sciences; Tivadar Vida of Eötvös Loránd University and the Hungarian Academy of Sciences; Walter Pohl of Österreichische Akadamie der Wissenschaften; Luisella Pejrani Baricco, Elena Bedini, and Caterina Giostra of Università Cattolica del Sacro Cuore; Paolo Francalacci of Università degli Studi di Sassari; Daniel Winger of Universität Rostock; Uta von Freeden of Deutsches Archäologisches Institut; and Silvia Ghirotto and Guido Barbujani of Università degli Studi di Ferrara.

The idea of creating such an interdisciplinary team originated eight years ago in the course of a faculty seminar at the University of California, Los Angeles, supported by a grant from the Andrew W. Mellon Foundation to transform research in the humanities. This work was supported by the National Science Foundation, the Anneliese Maier Research Award of the Alexander von Humboldt Foundation, the Max Planck Society, the German Federal Ministry for Education and Research, the Swedish Riksbankens Jubileumsfond, the Gerard B. Lambert Foundation, and the Italian Ministry for University and Research Department of Excellence Program. Additional funding was provided by the Director’s Office of the Institute for Advanced Study.

HIV-1 genome influences immune reaction

A Swiss research team led by the University of Zurich (UZH) and University Hospital Zurich (USZ) has been searching for these factors for years. Several have already been identified: For example, the virus load and the diversity of the viruses, the duration of the infection, and the ethnicity of the affected person can all influence the body’s immune response. “In our new study, we were able to identify another factor: The genome of the HI virus,” says Huldrych Günthard, deputy director of the Department of Infectious Diseases and Hospital Epidemiology at USZ.

Antibody response of transmission pairs

The starting point for the researchers was the data and biobanked blood samples of around 4,500 HIV-infected people, recorded in the Swiss HIV Cohort Study and the Zurich Primary HIV Infection Study. In total the researchers found 303 potential transmission pairs — i.e. pairs of patients for whom the similarity of the viruses’ genomic RNA indicated that they were probably infected with the same virus strain. “By comparing the immune response of these pairs of patients, we were able to show that the HI virus itself has an influence on the extent and specificity of the antibody reactions,” explains the study’s first author Roger Kouyos, research group leader at the Department of Infectious Diseases and Hospital Epidemiology at USZ.

Special envelope proteins provide broad protection

Antibodies acting against HIV bind to proteins found on the surface of the virus. These envelope proteins differ according to virus strain and subtype. The researchers therefore examined more closely a patient pair with very similar virus genomes and at the same time very strong activity of broadly neutralizing antibodies. “We discovered that there must be a special envelope protein that causes an efficient defense,” explains Alexandra Trkola, virologist and head of the Institute of Medical Virology at UZH.

Search for an ideal envelope protein continues

In order to be able to develop an effective vaccine against HIV-1, it is necessary to pinpoint the envelope proteins and virus strains that lead to the formation of broadly acting antibodies. It is therefore planned to widen the search. “We have found one candidate. Based on that, we now want to begin developing an immunogen ourselves,” adds Trkola.

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Involving a team of 40 scientists from 17 different nations, including Dr Alan Jamieson and Dr Thomas Linley from Newcastle University, UK, the expedition to the Atacama Trench has uncovered a wealth of information about life in one of the deepest places on earth.

Among the new discoveries are what the team believe to be three new species of snailfish.

Temporarily named ‘the pink, the blue and the purple Atacama Snailfish’, the footage shows the fish feeding and interacting in their secret world 7,500 metres below the surface.

These fish are part of the Liparidae family and do not conform to the preconceived stereotypical image of what a deep-sea fish should look like.

Instead of giant teeth and a menacing frame, the fishes that roam in the deepest parts of the ocean are small, translucent, bereft of scales — and highly adept at living where few other organisms can. The snailfish will be featured as part of the Challenger Conference 2018 which kicks off at Newcastle University from today and runs until Friday.

Dr Thomas Linley, from Newcastle University, said:

“There is something about the snailfish (fish of the family Liparidae) that allows them to adapt to living very deep. Beyond the reach of other fish they are free of competitors and predators.

“As the footage clearly shows, there are lots of invertebrate prey down there and the snailfish are the top predator, they seem to be quite active and look very well-fed.

“Their gelatinous structure means they are perfectly adapted to living at extreme pressure and in fact the hardest structures in their bodies are the bones in their inner ear which give them balance and their teeth. Without the extreme pressure and cold to support their bodies they are extremely fragile and melt rapidly when brought to the surface.”

Amazingly, the team did manage to catch one the new species of snailfish which followed its amphipod prey into one of the traps. The single specimen was in very good condition and, following careful preservation, is currently being described by the Newcastle team with the help of colleagues from the United States and the Natural History Museum, London.

Pioneering technology for exploration of the ultra-deep

The Hadal Trenches are one of the last great frontiers in marine science and the deepest places on Earth.

Mostly located around the Pacific rim in areas where tectonic plate collide and plunge, the seafloor reaches depths close to 11,000 metres (~7 miles) in some areas.

The Atacama Trench, a trench almost 6000 km long and more than 8000 m deep, runs along the west coast of South America.

Newcastle University scientists and engineers have been pioneering technology for the exploration of these ultra-deep environments for the last five years and have to date completed nearly 250 deployments of their novel ‘lander’ systems.

Using two full-ocean depth (11,000 m) capable landers equipped with HD cameras and traps the Newcastle team assessed the animals found within the trench.

Designed and developed at Newcastle University, the lander is dropped overboard, and free-falls to the ocean floor where it carries out a variety of monitoring and sampling tasks.

It can take four hours for a trap to sink to the bottom and after waiting an additional 12 to 24 hours, the researchers send an acoustic signal to the trap, which releases weights and the lander rises to the surface with the help of floatation.

This allows the team to catch fish specimens and take video footage of life at the bottom of the ocean.

On this latest expedition to the Atacama Trench in the SE Pacific off the coast of Peru and Chile, the team deployed their baited camera system 27 times from 2537 to the deepest point, Richard’s Deep, at just over 8000 metres.

More than 100 hours of video and 11,468 photographs were taken at the seabed.

As well as the snailfish, the team also filmed some astonishingly rare footage of long-legged isopods, known as Munnopsids, which are about the size of an adult hand.

These crustaceans have small bodies, extraordinarily long legs and swim backwards and upsides down, propelling themselves with paddles on their ventral side — their ‘tummies’ — before righting themselves on the seafloor and spreading their long walking legs out like a spider.

“We don’t know what species of munnopsid these are but it’s incredible to have caught them in action in their natural habitat — especially the flip they do as they switch from swimming to walking mode,” says Dr Linley.