Ebola: Reports from the front lines

Dr. Noah Rosenberg “Ebola was never the only killer here, and our ability to appropriately diagnose and treat these patients is woefully limited.”

Alpert Medical School professors Michael Smit and Noah Rosenberg are in Sierra Leone and Liberia respectively, treating Ebola patients. There are some signs of a slowdown in the epidemic, but the doctors emphasize that the virus must be fought “until the last case.”

PROVIDENCE, R.I. [Brown University] — In a limited sense, two Brown University medical professors who have been fighting Ebola in West Africa this winter have good news to report. They have seen some signs of slowing disease transmission. But the broader reality of what Ebola has done in Sierra Leone and Liberia is grim, according to Drs. Michael Smit and Noah Rosenberg.

Ebola shouldn’t just be contained, they note: It must be treated until all cases are resolved.

Smit, assistant professor of pediatrics and a physician at Hasbro Children’s Hospital, arrived in Sierra Leone Dec. 3, 2014, and will remain there through Jan. 18. Rosenberg, clinical assistant professor of emergency medicine and a Lifespan doctor, arrived in Liberia in mid-December and will stay until Jan. 27. They answered questions for medical science writer David Orenstein about what they are doing and seeing, and what people back in the States need to know.

Please describe a typical day.

NR: I arrive at 7 a.m. and meet with the overnight doctor and nurses to discuss our patients. My team pulls on full personal protective equipment and enters the high-risk area. We examine each patient, inquire about their current symptoms, give routine supportive medications and IV fluids if needed. We take blood to test for Ebola. We remove our equipment while being intermittently sprayed with chlorine. Rounds repeat in the afternoon and we often make an additional trip for a new admission. In the evening we meet with the night team and then rest to return in the morning.

Dr. Michael Smit “The effect of the epidemic goes far beyond those infected with Ebola virus. ... The economic impact on the country is devastating.

MS: I am the medical team leader of one of four medical teams at the Mateneh Ebola Treatment Center (ETC). Our days differ depending on which shift we are working. When working the early shift, we eat breakfast around 7 a.m. and drive to the ETC. We change into our work uniforms of scrubs and rubber boots at the ETC. At 7:30 we receive signout on the patients from the overnight team. We then assign personnel to conduct the nursing rounds, physician rounds, admissions, and discharges. During the heat of the day, we try to limit time in the high-risk area in personal protective equipment (PPE) to one hour. We deliver meals, administer medications, place intravenous catheters, and draw blood for laboratory tests. We triage admissions as they come through the ambulance bay. We also process discharges. These include survivors discharged home and deaths transferred to the morgue. At the end of the shift, we sign out the patients to the oncoming team, change back into our civilian clothes, and go back to the compound to eat. The late and overnight shifts are the same as the early shift for the most part.

What do you observe and hear about the status of the epidemic where you are?

NR: The exponential growth of the epidemic is clearly over in Liberia, but sporadic outbreaks are likely to continue until every case has been eliminated from West Africa, which may take months. Most of our new admissions now test negative for Ebola; they frequently die nonetheless. This may seem counterintuitive, but Ebola was never the only killer here, and our ability to appropriately diagnose and treat these patients is woefully limited.

MS: It is difficult to assess the status of the epidemic from here. We have limited access to the Internet, so our updates of what is happening are intermittent. As for what we observe, after a slow start from our opening in mid-December, we saw a steady increase in cases in our district in Bombali. Over the last week, admissions have decreased. The reason for this is not clear. We hope that it reflects a reduction in transmission, but we cannot assume this given the complexities of case identification and transport here.

What do people in the United States most need to know, based on what you are experiencing?

NR: Before the epidemic Liberia suffered from a large disease burden and severely limited health care system. Decades of civil war, sparked by inequality and tension between descendants of indigenous West Africans and freed slaves, wrecked the infrastructure and economy. Not only was the U.S.A. responsible for the founding of Liberia, but many of the struggles here today have their origins in the slave trade. Ebola will soon fade from the news but the epidemic has only worsened an already grave condition. We have a special responsibility to Liberia and it deserves our sustained attention.

MS: People in the United States need to know that the epidemic here is far from over. Even in a situation with diminished transmission, the United States needs to send personnel and resources here to combat Ebola until the last case. The effect of the epidemic goes far beyond those infected with Ebola virus. The schools here in Sierra Leone have been closed for months. Teen pregnancy is increasing as a result. The economic impact on the country is devastating, with some estimates setting the economy back 10 years. Also, people in the United States need to know about the dedication and resilience of the local and international healthcare workers who are fighting the epidemic, often under challenging physical and emotional conditions.

Source: Brown University

WHO contemplates reforms after admitting missteps on Ebola

World Health Organization (WHO) Director-General Margaret Chan addresses the media during a special meeting on Ebola in Geneva on Jan. 25, 2015. Photo by Pierre Albouy/REUTERS.

In a special session on Sunday, the World Health Organization debated how to reform itself after acknowledging the organization had botched its response to the 2014 Ebola emergency. 

“The Ebola outbreak revealed some inadequacies and shortcomings in this organization’s administrative, managerial, and technical infrastructures,” WHO Director-General Margaret Chan said. At its headquarters in Geneva, Chan presented a series of proposals aimed at ending the current outbreak, as well as reinforcing preparedness globally and guaranteeing the WHO’s ability to address future large-scale outbreaks. 

She stressed the need to streamline recruitment for emergencies, as the current process is “too slow” and emphasized the need for a “one WHO” approach that employs universal operating procedures and tools for responding to emergencies. According to Chan, the current rules for reporting outbreaks – International Health Regulations (IHR) – created to prevent national health emergencies from becoming global crises, are too thin. But the largest lesson she and others at WHO learned during the outbreak fight was that well-trained, and appropriately paid health care workers, are essential to stemming the spread of disease. 

To date there have been more than 21,000 Ebola cases and over 8,400 deaths. “The volatile microbial world will always deliver surprises, Chan said. “Never again should the world be caught by surprise, unprepared.”

Source: WHO

Cold virus replicates better at cooler temperatures

Artist's rendering of a rhinovirus (stock illustration). Credit: © fotoliaxrender / Fotolia

The common cold virus can reproduce itself more efficiently in the cooler temperatures found inside the nose than at core body temperature, according to a new Yale-led study. This finding may confirm the popular yet contested notion that people are more likely to catch a cold in cool-weather conditions.

Researchers have long known that the most frequent cause of the common cold, the rhinovirus, replicates more readily in the slightly cooler environment of the nasal cavity than in the warmer lungs. However, the focus of prior studies has been on how body temperature influenced the virus as opposed to the immune system, said study senior author and Yale professor of immunobiology Akiko Iwasaki.

To investigate the relationship between temperature and immune response, Iwasaki and an interdisciplinary team of Yale researchers spearheaded by Ellen Foxman, a postdoctoral fellow in Iwasaki's lab, examined the cells taken from the airways of mice. They compared the immune response to rhinovirus when cells were incubated at 37 degrees Celsius, or core body temperature, and at the cooler 33 degrees Celsius. "We found that the innate immune response to the rhinovirus is impaired at the lower body temperature compared to the core body temperature," Iwasaki said.

The study also strongly suggested that the varying temperatures influenced the immune response rather than the virus itself. Researchers observed viral replication in airway cells from mice with genetic deficiencies in the immune system sensors that detect virus and in the antiviral response. They found that with these immune deficiencies, the virus was able to replicate at the higher temperature. "That proves it's not just virus intrinsic, but it's the host's response that's the major contributor," Iwasaki explained.

Although the research was conducted on mouse cells, it offers clues that may benefit people, including the roughly 20% of us who harbor rhinovirus in our noses at any given time. "In general, the lower the temperature, it seems the lower the innate immune response to viruses," noted Iwasaki. In other words, the research may give credence to the old wives' tale that people should keep warm, and even cover their noses, to avoid catching colds.

Yale researchers also hope to apply this insight into how temperature affects immune response to other conditions, such as childhood asthma. While the common cold is no more than a nuisance for many people, it can cause severe breathing problems for children with asthma, noted Foxman. Future research may probe the immune response to rhinovirus-induced asthma.

The study was published in the Proceedings of the National Academy of Sciences.

Source: Yale University

Volunteers can now help scientists seek Ebola cure in their (computer's) spare time

The Scripps Research Institute’s Professor Erica Ollmann Saphire is leading the new effort against Ebola. Credit: Photo courtesy of The Scripps Research Institute.

Although some medical therapies show promise as treatments for Ebola, scientists are still looking urgently for a definitive cure.

For the first time, anyone with access to a computer or Android-based mobile device can help scientists perform this critical research -- no financial contribution, passport or PhD necessary. In fact, volunteers can be asleep, traveling or on a coffee break when they help researchers search for an Ebola cure.

Beginning today, anyone can download a safe and free app that will put their devices to work when the machines would otherwise be idle. With their collective processing power, the computers will form a virtual supercomputer to help The Scripps Research Institute (TSRI) screen millions of chemical compounds to identify new drug leads for treating Ebola. 

Meanwhile, the devices will remain fully available for normal use by their owners.

This citizen science effort is possible through a partnership with IBM's (NYSE: IBM) World Community Grid, which has been making similar data-driven health and sustainability initiatives possible for 10 years as a free, philanthropic service to the science community. 

The "Outsmart Ebola Together" volunteer computing project announced today is being run by the Ollmann Saphire laboratory at TSRI, which has mapped the structures and vulnerabilities of the proteins comprising the Ebola virus.

The best candidate compounds that emerge from this crowdsourced effort will be physically tested in the lab to pinpoint their effectiveness against real virus infection. The most promising compounds will then be modified to perform even better, at lower concentrations, and with fewer side effects. Subsequent drug trials could ultimately lead to an approved medicine.

Crowdsourcing this citizen science effort will dramatically accelerate the process of identifying a cure. The speed and scale of a drug search is essential, as this particularly lethal disease continues to spread and mutate. Once believed to be less of a widespread public health risk than other communicable diseases because of its existence in mainly isolated regions, Ebola now carries a higher risk of spreading farther because people are more mobile than ever before.

"Our molecular images of the Ebola virus are like enemy reconnaissance," said Dr. Erica Ollmann Saphire of TSRI, one of the largest private biomedical research institutes in the United States. "These images show us where the virus is vulnerable and the targets we need to hit. In the Outsmart Ebola Together project, we will be able to harness World Community 

Grid's virtual supercomputing power to find the drugs we need to aim at these targets."

IBM's World Community Grid has successfully run other projects that search for drug candidates for both high- and low-profile diseases -- such as AIDS, cancer, malaria, Dengue fever, and influenza. It has enabled multiple breakthroughs, such as helping the Chiba Cancer Center in Japan discover seven new drug candidates to fight childhood neuroblastoma. The IBM-managed program also hosts projects that have led to important scientific advances in renewable energy and water purification technology.

"It is a privilege to partner with The Scripps Research Institute to advance the process of identifying an Ebola cure," said Stanley S. Litow, IBM's vice president of Corporate Citizenship and president of the IBM International Foundation. "It is only fitting that IBM's World Community Grid 10-year anniversary of accomplishments coincide with the launch of perhaps one of the most critical scientific and humanitarian efforts."

Conceived and managed by IBM, and powered by IBM's reliable and secure SoftLayer cloud technology, World Community Grid provides computing power to scientists by harnessing the unused, surplus cycle time of volunteers' computers and mobile devices. The software receives, completes, and returns small computational assignments to scientists. The combined power contributed by hundreds of thousands of volunteers has created one of the fastest virtual supercomputers on the planet, advancing scientific work by hundreds of years.

Nearly three million computers and mobile devices used by more than 680,000 people and 460 institutions from 80 countries have contributed virtual supercomputing power for vitally important projects on World Community Grid over the last 10 years. Since the program's inception, World Community Grid volunteers have powered more than 20 research projects, donating more than one million years of computing time to scientific research, and enabled important scientific advances in health and sustainability. IBM invites researchers to submit research project proposals to receive this free resource, and invites members of the public to donate their unused computing power to these efforts at worldcommunitygrid.org.

TSRI also invites members of the public to support Dr. Saphire's crowdfunding campaign at www.crowdrise.com/CUREEBOLA to secure resources needed to analyze the enormous volume of data generated by Outsmart Ebola Together.

The software used for screenings in the Outsmart Ebola Together project is called AutoDock and AutoDock VINA, developed by the Olson laboratory at TSRI.

World Community Grid is enabled by software developed in 2002 by Berkeley Open Infrastructure for Network Computing (BOINC) at the University of California, Berkeley and with support from the National Science Foundation. The BOINC project choreographs the technical aspects of volunteer computing.

Source: Scripps Research Institute

New tool for exploring cells in 3D created

The new software can generate editable models of mid-size biological structures such as this one of HIV. Credit: Image created by Graham Johnson and Ludovic Autin of The Scripps Research Institute

Researchers can now explore viruses, bacteria and components of the human body in more detail than ever before with software developed at The Scripps Research Institute (TSRI).

In a study published online ahead of print December 1 by the journal Nature Methods, the researchers demonstrated how the software, called cellPACK, can be used to model viruses such as HIV.

"We hope to ultimately increase scientists' ability to target any disease," said Art Olson, professor and Anderson Research Chair at TSRI who is senior author of the new study.

Putting cellPACK to the Test

The cellPACK software solves a major problem in structural biology. Although scientists have developed techniques to study relatively large structures, such as cells, and very small structures, such as proteins, it has been harder to visualize structures in the medium "mesoscale" range.

With cellPACK, researchers can quickly and efficiently process the data they've collected on smaller structures to assemble models in this mid-size range. Previously, researchers had to create these models by hand, which took weeks or months compared with just hours in cellPACK.

As a demonstration of the software's power, the authors of the new study created a model of HIV showing how outer "spike" proteins are distributed on the surface of the immature virus.

The new model put to the test a conclusion made by HIV researchers from super-resolution microscopic studies -- that the distribution of the spike proteins on the surface of the immature virus is random. But by using cellPACK to generate thousands of models, testing alternative hypotheses, the researchers found that the distribution was not random. "We demonstrated that their interpretation of the distribution did not match that hypothesis," said Olson.

A Team Effort

The cellPACK software began as the thesis project of a TSRI graduate student, Graham Johnson, now a QB3 faculty fellow at the University of California, San Francisco (UCSF) who continues to contribute to the project. Johnson had more 15 years' experience as a medical illustrator, and he wanted to create an easy way to visualize mesoscale structures. cellPACK is an expansion of Johnson's autoPACK software, which maps out the density of materials -- from concrete in a building to red blood cells in an artery.

The researchers see cellPACK as a community effort, and they have made the autoPACK and cellPACK software free and open source. Thousands of people have already downloaded the software from http://www.autopack.org.

"With the creation of cellPACK, Dr. Olson and his colleagues have addressed the challenge of integrating biological data from different sources and across multiple scales into virtual models that can simulate biologically relevant molecular interactions within a cell," said Veersamy Ravichandran, PhD, of the National Institutes of Health's National Institute of General Medical Sciences, which partially funded the research. "This user-friendly tool provides a new platform for data analysis and simulation in a collaborative manner between laboratories."

As new information comes in from the scientific community, researchers will tweak the software so it can model new shapes. "Making it open source makes it more powerful," said Olson. "The software right now is usable and very useful, but it's really a tool for the future."

Source: Scripps Research Institute

Up to 80 million bacteria sealed with a kiss

Couple about to kiss (stock image). As many as 80 million bacteria are transferred during a 10 second kiss, according to research published in the open access journal Microbiome.

As many as 80 million bacteria are transferred during a 10 second kiss, according to research published in the open access journal Microbiome. The study also found that partners who kiss each other at least nine times a day share similar communities of oral bacteria.

The ecosystem of more than 100 trillion microorganisms that live in our bodies -- the microbiome -- is essential for the digestion of food, synthesizing nutrients, and preventing disease. It is shaped by genetics, diet, and age, but also the individuals with whom we interact. With the mouth playing host to more than 700 varieties of bacteria, the oral microbiota also appear to be influenced by those closest to us.

Researchers from Micropia and TNO in the Netherlands studied 21 couples, asking them to fill out questionnaires on their kissing behaviour including their average intimate kiss frequency. They then took swab samples to investigate the composition of their oral microbiota on the tongue and in their saliva.

The results showed that when couples intimately kiss at relatively high frequencies their salivary microbiota become similar. On average it was found that at least nine intimate kisses per day led to couples having significantly shared salivary microbiota.

Lead author Remco Kort, from TNO's Microbiology and Systems Biology department and adviser to the Micropia museum of microbes, said: "Intimate kissing involving full tongue contact and saliva exchange appears to be a courtship behavior unique to humans and is common in over 90% of known cultures. Interestingly, the current explanations for the function of intimate kissing in humans include an important role for the microbiota present in the oral cavity, although to our knowledge, the exact effects of intimate kissing on the oral microbiota have never been studied. We wanted to find out the extent to which partners share their oral microbiota, and it turns out, the more a couple kiss, the more similar they are."

In a controlled kissing experiment to quantify the transfer of bacteria, a member of each of the couples had a probiotic drink containing specific varieties of bacteria including Lactobacillus and Bifidobacteria. After an intimate kiss, the researchers found that the quantity of probiotic bacteria in the receiver's saliva rose threefold, and calculated that in total 80 million bacteria would have been transferred during a 10 second kiss.

The study also suggests an important role for other mechanisms that select oral microbiota, resulting from a shared lifestyle, dietary and personal care habits, and this is especially the case for microbiota on the tongue. The researchers found that while tongue microbiota were more similar among partners than unrelated individuals, their similarity did not change with more frequent kissing, in contrast to the findings on the saliva microbiota.

Commenting on the kissing questionnaire results, the researchers say that an interesting but separate finding was that 74% of the men reported higher intimate kiss frequencies than the women of the same couple. This resulted in a reported average of ten kisses per day from the males, twice that of the female reported average of five per day.

To calculate the number of bacteria transferred in a kiss, the authors relied on average transfer values and a number of assumptions related to bacterial transfer, the kiss contact surface, and the value for average saliva volume.

Source: BioMed Central

How llamas' unusual antibodies might help in the fight against HIV/AIDS

Llamas contribute to the fight against AIDS. Credit: Nika Stropakke, CC-BY

Most vaccines work by inducing an immune response characterized by neutralizing antibodies against the respective pathogen. An effective HIV vaccine has remained elusive so far, but researchers have continued to make progress, often employing innovative methods. A study published on December 18th in PLOS Pathogens reports that a combination of antibodies from llamas can neutralize (destroy) a wide range of circulating HIV viruses.

After initial disappointment that HIV vaccine candidates were unable to elicit neutralizing antibodies, researchers found that some HIV-infected individuals did produce such antibodies. The current challenge is therefore to find safe and effective vaccine formulations (as opposed to HIV infection) that trigger the development of neutralizing antibodies that can recognize and prevent infection with all or most circulating HIV subtypes.

Many known neutralizing antibodies are directed against a specific part of the virus that binds to the CD4 receptor on the human target cells, and structural biology studies indicated that the site is a narrow groove. Antibodies in most mammals are relatively large proteins made up of two copies of two different individual parts (or chains), and bulkiness might be one reason why neutralizing antibodies are rare. Llamas are a notable exception: besides the common four-chain antibodies they also produce smaller ones made up of only two of the four chains. Robin Weiss, an HIV expert, and Theo Verrips, a llama antibody expert, therefore started working with this unconventional research animal.

Laura McCoy (working with Weiss at University College London, UK) led an international group of researchers to test immunization protocols and the resulting immune response in llamas. Having previously identified one particular HIV neutralizing llama antibody, for this study the researchers immunized two additional llamas and identified a total of three new neutralizing antibodies. The four HIV neutralizing llama antibodies target different parts of the CD4-binding site of the virus, and the researchers could show that when used in combination, rather than interfering with each other, they are more potent and can neutralize all of the 60 different HIV strains tested.

To understand how the llama immunization--which included two sets of four sequential vaccine injections per animal--worked, the researchers sequenced many copies of antibody-coding genes from blood cells collected after the first set of immunizations and after a further four rounds of vaccination. They also looked at the "naïve" antibody repertoire from seven llamas that had not been vaccinated. The results suggest that the neutralizing antibodies were not part of the pre-immunization repertoire, nor were they detectable after the first vaccination round. Rather, they were generated as immune cells repeatedly encountered the vaccine and responded by maturing specific antibodies that can recognize it.

While it is encouraging that broadly neutralizing antibodies were found in all of the immunized llamas, they are present only at low concentrations in the blood, and so fail to meet the goal for a protective HIV vaccine. Nonetheless, the researchers conclude that the llama model has allowed them to examine the generation of four broadly neutralizing antibodies induced by vaccination, which has not been possible in any other species.

Source: PLOS.

The shape of infectious prions

Structural changes were located in the prion protein N-terminus, where a novel reorganization of the beta sheet (in yellow) was observed. In the background, the X-ray diffraction pattern of the crystal composed by the complex prion protein-Nanoboy.

Prions are unique infective agents -- unlike viruses, bacteria, fungi and other parasites, prions do not contain either DNA or RNA. Despite their seemingly simple structure, they can propagate their pathological effects like wildfire, by "infecting" normal proteins. PrPSc (the pathological form of the prion protein) can induce normal prion proteins (PrPC) to acquire the wrong conformation and convert into further disease-causing agents.

"When they are healthy, they look like tiny spheres; when they are malignant, they appear as cubes" stated Giuseppe Legname, principal investigator of the Prion Biology Laboratory at the Scuola Internazionale Superiore di Studi Avanzati (SISSA) in Trieste, when describing prion proteins. Prions are "misfolded" proteins that cause a group of incurable neurodegenerative diseases, including spongiform encephalopathies (for example, mad cow diseases) and Creutzfeldt-Jakob disease. Legname and coworkers have recently published a detailed analysis of the early mechanisms of misfolding. Their research has just been published in the Journal of the American Chemical Society, the most authoritative scientific journal in the field.

"For the first time, our experimental study has investigated the structural elements leading to the disease-causing conversion" explains Legname. "With the help of X-rays, we observed some synthetic prion proteins engineered in our lab by applying a new approach -- we used nanobodies, i.e. small proteins that act as a scaffolding and induce prions to stabilize their structure." Legname and colleagues reported that misfolding originates in a specific part of the protein named "N-terminal." "The prion protein consists of two subunits. The C-terminal has a clearly defined and well-known structure, whereas the unstructured N-terminal is disordered, and still largely unknown. This is the very area where the early prion pathological misfolding occurs" adds Legname. "The looser conformation of the N-terminal likely determines a dynamic structure, which can thus change the protein shape."

"Works like ours are the first, important steps to understand the mechanisms underlying the pathogenic effect of prions" concludes Legname. "Elucidating the misfolding process is essential to the future development of drugs and therapeutic strategies against incurable neurodegenerative diseases."

Source: Sissa Medialab

Bacteria could be rich source for making terpenes

Odoriferous terpene metabolites: A phylogenetic tree of terpene synthases shows the synthases (bold face or underlined) found by researchers in Japan and at Brown University using bacterial sequences. Credit: Image courtesy of Brown University

If you've ever enjoyed the scent of a pine forest or sniffed a freshly cut basil leaf, then you're familiar with terpenes. The compounds are responsible for the essential oils of plants and the resins of trees. Since the discovery of terpenes more than 150 years ago, scientists have isolated some 50,000 different terpene compounds derived from plants and fungi. Bacteria and other microorganisms are known to make terpenes too, but they've received much less study.

New research at Brown University, published in the Proceedings of the National Academy of Sciences, shows that the genetic capacity of bacteria to make terpenes is widespread. 

Using a specialized technique to sift through genomic databases for a variety of bacteria, the researchers found 262 gene sequences that likely code for terpene synthases -- enzymes that catalyze the production terpenes. The researchers then used several of those enzymes to isolate 13 previously unidentified bacterial terpenes.

The findings suggest that bacteria "represent a fertile source for discovery of new natural products," the researchers write.

David Cane, a professor of chemistry at Brown and one of the authors on the new paper, began working about 15 years ago to understand how bacteria make terpenes.

"At that time, the first genomic sequences of certain classes of bacteria were just beginning to come out," he said. "We had this idea that maybe you could find the enzymes responsible for making terpenes by looking at the sequences of the genes that were being discovered."

To do that, Cane searched through the genome data gathered for a group of bacteria called Streptomyces, looking for sequences similar those known to produce terpene synthases in plants and fungi. Eventually, he found that Streptomyces did indeed have genes encoding terpene synthases and that those enzymes could be used to make terpenes.

The verified bacterial sequences found by Cane and others enabled researchers to refine subsequent searches for additional terpene synthase genes. "Instead of using plant sequences or fungal sequences as your search query, we can now use bacterial sequences, which should yield a greater degree of similarity," he said. "So now we're fishing in the right waters with the right kind of bait, and you can find more matches."

This latest paper made use of the third generation of iterative searches and a powerful search technique developed by Haruo Ikeda of Kitasato University in Japan. Previous work had identified 140 probable sequences for terpene synthases. This latest work expanded that to 262.

The next step was to verify that these sequences did indeed code for enzymes capable of making terpenes. Testing all 262 wasn't practical, so the team chose a few they thought might give them the best chance of finding terpene compounds that hadn't previously been identified. They looked for sequences that didn't seem to fit clearly into previously known categories of terpenes.

After they had selected a few, the team made use of a genetically engineered Streptomyces bacterium as a bio-refinery to generate the terpene products.

"What Professor Ikeda did, in collaboration with us, is develop a variant of a very well-studied Streptomyces system," Cane said. "He eliminated the genes that were responsible for making most of its native products, but he left behind all of the capacity to provide the starting materials and handle the accumulation of products."

By taking some of the gene sequences they found and splicing them into their test organism, the researchers could let the organisms generate the product using the instructions from the newly introduced gene. Using this method, they were able to make 13 previously unknown terpenes, their structures verified by mass spectrometry and nuclear magnetic resonance spectroscopy.

"It's a big step forward in the area in that it provides a paradigm for how one could go about discovering many new substances," Cane said. "It's a good example of how one can use sequence analysis to identify genes of interest and then apply molecular genetic and microbiological techniques to produce the chemical substances of interest."

The work also suggests that there may be many new terpene products as yet undiscovered hiding in the genomes of bacteria.

Source: Brown University

Genetic factors behind surviving or dying from Ebola shown in mouse study

In an emerging disease research lab at the University of Washington, Chris Williams, a research scientist who specializes in microbiology laboratory robotics, programs a piece of equipment that can be programmed to performs many lab tasks. Credit: Brian Donohue

A newly developed mouse model suggests that genetic factors are behind the mild-to-deadly range of reactions to the Ebola virus.

People exposed to Ebola vary in how the virus affects them. Some completely resist the disease, others suffer moderate to severe illness and recover, while those who are most susceptible succumb to bleeding, organ failure and shock.

In earlier studies of populations of people who have contracted Ebola, these differences are not related to any specific changes in the Ebola virus itself that made it more or less dangerous; instead, the body's attempts to fight infection seems to determine disease severity.

In the Oct. 30 edition of Science, scientists describe strains of laboratory mice bred to test the role of an individual's genetic makeup in the course of Ebola disease. Systems biologists and virologists Angela Rasmussen and Michael Katze from the Katze Laboratory at the University of Washington Department of Microbiology led the study in collaboration with the National Institutes of Health's Rocky Mountain Laboratories in Montana and University of North Carolina at Chapel Hill.

Research on Ebola prevention and treatment has been hindered by the lack of a mouse model that replicates the main characteristics of human Ebola hemorrhagic fever. The researchers had originally obtained this genetically diverse group of inbred laboratory mice to study locations on mouse genomes associated with influenza severity.

The research was conducted in a highly secure, state-of-the-art biocontainment safety level 4 laboratory in Hamilton, Mont. The scientists examined mice that they infected with a mouse form of the same species of Ebola virus causing the 2014 West Africa outbreak. The study was done in full compliance with federal, state, and local safety and biosecurity regulations. This type of virus has been used several times before in research studies. Nothing was done to change the virus.

Interestingly, conventional laboratory mice previously infected with this virus died, but did not develop symptoms of Ebola hemorrhagic fever.

In the present study, all the mice lost weight in the first few days after infection. Nineteen percent of the mice were unfazed. They not only survived, but also fully regained their lost weight within two weeks. They had no gross pathological evidence of disease. Their livers looked normal.

Eleven percent were partially resistant and less than half of these died. Seventy percent of the mice had a greater than 50 percent mortality. Nineteen percent of this last group had liver inflammation without classic symptoms of Ebola, and thirty-four percent had blood that took too long to clot, a hallmark of fatal Ebola hemorrhagic fever in humans. Those mice also had internal bleeding, swollen spleens and changes in liver color and texture.

The scientists correlated disease outcomes and variations in mortality rates to specific genetic lines of mice.

"The frequency of different manifestations of the disease across the lines of these mice screened so far are similar in variety and proportion to the spectrum of clinical disease observed in the 2014 West African outbreak," Rasmussen said.

While acknowledging that recent Ebola survivors may have had immunity to this or a related virus that saved them during this epidemic, Katze said, "Our data suggest that genetic factors play a significant role in disease outcome."

In general, when virus infection frenzied the genes involved in promoting blood vessel inflammation and cell death, serious or fatal disease followed. On the other hand, survivors experienced more activity in genes that order blood vessel repair and the production of infection-fighting white blood cells.

The scientists note that certain specialized types of cells in the liver could also have limited virus reproduction and put a damper on systemic inflammation and blood clotting problems in resistant mice. Susceptible mice had widespread liver infection, which may explain why they had more virus in their bodies and poorly regulated blood coagulation. The researchers also noticed that spleens in the resistant and susceptible mice took alternate routes to try to ward off infection.

"We hope that medical researchers will be able to rapidly apply these findings to candidate therapeutics and vaccines," Katze said. They believe this mouse model can be promptly implemented to find genetic markers, conduct meticulous studies on how symptoms originate and take hold, and evaluate drugs and that have broad spectrum anti-viral activities against all Zaire ebolaviruses, including the one responsible for the current West African epidemic.

Source: University of Washington Health Sciences/UW Medicine

For tiger populations, a new threat

This is an Amur tiger photographed by camera trap. Credit: WCS Russia Program

Along with the pressures of habitat loss, poaching and depletion of prey species, a new threat to tiger populations in the wild has surfaced in the form of disease, specifically, canine distemper virus (CDV). According to a new study from the Wildlife Conservation Society (WCS) and its partners, CDV has the potential to be a significant driver in pushing the animals toward extinction.

While CDV has recently been shown to lead to the deaths of individual tigers, its long-term impacts on tiger populations had never before been studied.

The authors evaluated these impacts on the Amur tiger population in Russia's Sikhote-Alin Biosphere Zapovednik (SABZ), where tiger numbers declined from 38 individuals to 9 in the years 2007 to 2012. In 2009 and 2010, six adult tigers died or disappeared from the reserve, and CDV was confirmed in two dead tigers -- leading scientists to believe that CDV likely played a role in the overall decline of the population. Joint investigations of CDV have been an ongoing focus of WCS and Russian scientists at Sikhote-Alin Zapovednik and veterinarians at the regional Primorye Agricultural College since its first appearance in tigers in 2003.

A key finding of this study: Modeling shows that smaller populations of tigers were found to be more vulnerable to extinction by CDV. Populations consisting of 25 individuals were 1.65 times more likely to decline in the next 50 years when CDV was present. The results are profoundly disturbing for global wild tigers given that in most sites where wild tigers persist they are limited to populations of less than 25 adult breeding individuals.

The scientists used computer modeling to simulate the effects of CDV infection on isolated tiger populations of various sizes and through a series of transmission scenarios. These included tiger-to-tiger transmission and transmission through predation on CDV-infected domestic dogs and/or infected wild carnivores (such as foxes, raccoon dogs and badgers). High and low-risk scenarios for the model were created based on variation in the prevalence of CDV and the tigers' contact with sources of exposure.

Results showed that CDV infection increased the 50-year extinction probability of tigers in SABZ as much as 55.8 percent compared to CDV-free populations of equivalent size.

"Although we knew that individual tigers had died from CDV in the wild, we wanted to understand the risk the virus presents to whole populations," said WCS veterinarian Martin Gilbert. "Tigers are elusive, however, and studying the long-term impact of risk factors is very challenging. Our model, based on tiger ecology data collected over 20 years in SABZ, explored the different ways that tigers might be exposed to the virus and how these impact the extinction risk to tiger populations over the long term."

WCS Russia Program Director Dale Miquelle said, "Tigers face an array of threats throughout their range, from poaching to competition with humans for space and for food. 

Consequently, many tiger populations have become smaller and more fragmented, making them much more susceptible to diseases such as CDV. While we must continue to focus on the primary threats of poaching and habitat destruction, we now must also be prepared to deal with the appearance of such diseases in the future."

Priorities for future research, according to the authors, include identifying the domestic and wild carnivore species that contribute to the CDV reservoir, and those that are the most likely sources of infection for tigers. Tigers are too rare to sustain the virus in the long term, so CDV must rely on more abundant carnivore species to persist in the environment. 

Understanding the structure of the CDV reservoir will be a critical first step in identifying measures that might prevent or control future outbreaks. In addition, since we now know that small tiger populations are at greater risk to diseases such as CDV than larger populations, conservation strategies focusing on connectedness between populations become all the more important. "Estimating the potential impact of canine distemper virus on the Amur tiger population (Panthera tigris altaica) in Russia," appears in the current online edition of PloSONE. Authors include: Martin Gilbert of WCS and Boyd Orr Centre for Population and Ecosystem Health at the University of Glasgow; Dale G. Miquelle of WCS; John M. Goodrich of Panthera; Richard Reeve, Sarah Cleaveland and Louise Matthews of Boyd Orr Centre for Population and Ecosystem Health at the University of Glasgow; and Damien Joly of WCS and Metabiota.

This study was made possible through generous support from Morris Animal Foundation, Zoo Boise Conservation Fund, AZA Tiger Species Survival Plan Tiger Conservation Campaign, and the Biotechnology and Biological Sciences Research Council.

"Morris Animal Foundation is thankful to Dr. Miquelle and his team for helping protect the Amur Tigers," said Diane Brown, DVM, PhD, DACVP and Chief Scientific Officer for Morris Animal Foundation. "Our Foundation values their hard work and dedication to this study and we look forward to many more partnerships with the Wildlife Conservation Society."

Source: Wildlife Conservation Society

Experimental Ebola vaccine appears safe, prompts immune response

A 39-year-old woman, the first participant enrolled in VRC 207, receives a dose of the investigational NIAID/GSK Ebola vaccine at the NIH Clinical Center in Bethesda, Md. on September 2. Credit: NIAID

An experimental vaccine to prevent Ebola virus disease was well-tolerated and produced immune system responses in all 20 healthy adults who received it in a Phase 1 clinical trial conducted by researchers from the National Institutes of Health. The candidate vaccine, which was co-developed by the NIH's National Institute of Allergy and Infectious Diseases (NIAID) and GlaxoSmithKline (GSK), was tested at the NIH Clinical Center in Bethesda, Maryland. The interim results are reported online in advance of print in the New England Journal of Medicine.

"The unprecedented scale of the current Ebola outbreak in West Africa has intensified efforts to develop safe and effective vaccines, which may play a role in bringing this epidemic to an end and undoubtedly will be critically important in preventing future large outbreaks," said NIAID Director Anthony S. Fauci, M.D. "Based on these positive results from the first human trial of this candidate vaccine, we are continuing our accelerated plan for larger trials to determine if the vaccine is efficacious in preventing Ebola infection."

The candidate NIAID/GSK Ebola vaccine was developed collaboratively by scientists at the NIAID Vaccine Research Center (VRC) and at Okairos, a biotechnology company acquired by GSK. It contains segments of Ebola virus genetic material from two virus species, Sudan and Zaire. The Ebola virus genetic material is delivered by a carrier virus (chimpanzee-derived adenovirus 3 or cAd 3) that causes a common cold in chimpanzees but causes no illness in humans. The candidate vaccine does not contain Ebola virus and cannot cause Ebola virus disease.

The trial enrolled volunteers between the ages of 18 and 50. Ten volunteers received an intramuscular injection of vaccine at a lower dose and 10 received the same vaccine at a higher dose. At two weeks and four weeks following vaccination, the researchers tested the volunteers' blood to determine if anti-Ebola antibodies were generated. All 20 volunteers developed such antibodies within four weeks of receiving the vaccine. Antibody levels were higher in those who received the higher dose vaccine.

The investigators also analyzed the research participants' blood to learn whether the vaccine prompted production of immune system cells called T cells. A recent study by VRC scientist Nancy J. Sullivan, Ph.D., and colleagues showed that non-human primates inoculated with the candidate NIAID/GSK vaccine developed both antibody and T-cell responses, and that these were sufficient to protect vaccinated animals from disease when they were later exposed to high levels of Ebola virus.

The experimental NIAID/GSK vaccine did induce a T-cell response in many of the volunteers, including production of CD8 T cells, which may be an important part of immune protection against Ebola viruses. Four weeks after vaccination, CD8 T cells were detected in two volunteers who had received the lower dose vaccine and in seven of those who had received the higher dose.

"We know from previous studies in non-human primates that CD8 T cells played a crucial role in protecting animals that had been vaccinated with this NIAID/GSK vaccine and then exposed to otherwise lethal amounts of Ebola virus," said Julie E. Ledgerwood, D.O., a VRC researcher and the trial's principal investigator. "The size and quality of the CD8 T cell response we saw in this trial are similar to that observed in non-human primates vaccinated with the candidate vaccine."

There were no serious adverse effects observed in any of the volunteers, although two people who received the higher dose vaccine did develop a briefly lasting fever within a day of vaccination.

Source: NIH/National Institute of Allergy and Infectious Diseases

Parasites and the evolution of primate culture

Chimpanzees (stock image). A new study examines the ‘costs’ of innovation, and learning from others. Credit: © shiruikage / Fotolia

Learning from others and innovation have undoubtedly helped advance civilization. But these behaviours can carry costs as well as benefits. And a new study by an international team of evolutionary biologists sheds light on how one particular cost -- increased exposure to parasites -- may affect cultural evolution in non-human primates.

The results, published Dec. 3, 2014 in the journal Proceedings of the Royal Society B, suggest that species with members that learn from others suffer from a wider variety of socially transmitted parasites, while innovative, exploratory species suffer from a wider variety of parasites transmitted through the environment, such as in the soil or water.

"We tend to focus on innovation and learning from others as a good thing, but their costs have received relatively little attention," says McGill University biologist Simon Reader, co-author of the study. "Here, we uncover evidence that socially transmitted pathogen burdens rise with learning from others -- perhaps because close interaction is needed for such learning -- and environmentally transmitted pathogen burdens rise with exploratory behaviour such as innovation and extractive foraging."

Chimpanzees, for example, live in groups and have a wide range of such behaviours, such as digging for food underground or eating new kinds of insects.. Previously, studies have not been able to determine whether costly parasites force primates to engage in more exploratory behaviour -- by diversifying food sources, for example -- or whether exploratory behaviour leads to their having more parasites, Reader notes. "Our results support the idea that exploratory and social behaviours expose primates to specific kinds of parasites."

"The findings also lead to questions about how people and other primates have developed solutions to minimize these parasite costs -- such as eating medicinal plants -- and may help us better understand how the processes underlying human culture arose," Reader says.
The research team, led by Collin McCabe of Harvard University and Charles Nunn of Duke University, based their analyses on databases obtained by surveying thousands of articles on primate behaviour and parasites.

Funding for the research was provided by the National Science Foundation, the Natural Sciences and Engineering Research Council of Canada, and the Netherlands Organisation for Scientific Research.

Source: McGill University

Using power of computers to harness human genome may provide clues into Ebola virus

Ramaswamy Narayanan, Ph.D., professor in the Charles E. Schmidt College of Science at Florida Atlantic University.

Ramaswamy Narayanan, Ph.D., professor in the Charles E. Schmidt College of Science at Florida Atlantic University, is working to blend the power of computers with biology to use the human genome to remove much of the guesswork involved in discovering cures for diseases.

In an article titled "Ebola-Associated Genes in the Human Genome: Implications for Novel Targets," published in the current MedCrave Online Journal of Proteomics and Bioinformatics, Narayanan describes how key genes that are present in our cells could be used to develop drugs for this disease.

"Bioinformatics is a powerful tool to help us understand biological data," said Narayanan whose research has focused in this field for more than a decade. "We are mining the human genome for Ebola virus association to develop an understanding of the human proteins involved in this disease for subsequent research and development, and to potentially create a pipeline of targets that we can test and evaluate."

Ebola virus disease is a major healthcare challenge facing the globe today and if left unchecked could become a pandemic. A limited knowledgebase exists about the Ebola virus and companies are hastening to develop vaccines and other forms to treat and cure the virus. There are no FDA-approved drugs, and developing vaccines or antibodies and testing them in clinical trials is an arduous process that takes considerable time. Currently, patients infected with Ebola are only able to receive supportive care such as fluid replacement, nutritional support, pain control, and blood pressure maintenance. In some cases, patients may be fortunate enough to be treated with experimental drugs.

Narayanan's work has helped to identify numerous FDA-approved drugs already used for many other diseases including anti-inflammatory drugs, anticoagulants, cancer, HIV, statins and hormones, which could potentially be used to add to the current supportive care for patients with the Ebola virus.

"With the high mortality rate of this disease, the world urgently needs new ways to treat patients," said Narayanan. "The ability to use drugs that are already approved by the FDA could provide clinicians with more options to treat Ebola patients, rather than just relying on supportive measures like fluid replacement or antibiotics."

According to the World Health Organization (WHO), Ebola virus disease (EVD) is a severe, often fatal illness in humans. The virus is transmitted to people from wild animals and spreads in the human population through human-to-human transmissions. The evolving knowledge of this disease is prompting appropriate attention locally and globally. The 2014 Ebola epidemic has affected multiple countries in West Africa with some cases observed in Europe and the United States.

Source: Florida Atlantic University

Nanotechnology against malaria parasites

After maturation, malaria parasites (yellow) are leaving an infected red blood cell and are efficiently blocked by nanomimics (blue). Credit: Fig: modified by University of Basel with permission from ACS

Malaria parasites invade human red blood cells, they then disrupt them and infect others. Researchers at the University of Basel and the Swiss Tropical and Public Health Institute have now developed so-called nanomimics of host cell membranes that trick the parasites. This could lead to novel treatment and vaccination strategies in the fight against malaria and other infectious diseases. Their research results have been published in the scientific journal ACS Nano.

For many infectious diseases no vaccine currently exists. In addition, resistance against currently used drugs is spreading rapidly. To fight these diseases, innovative strategies using new mechanisms of action are needed. The malaria parasite Plasmodium falciparum that is transmitted by the Anopheles mosquito is such an example. Malaria is still responsible for more than 600,000 deaths annually, especially affecting children in Africa (WHO, 2012).
Artificial bubbles with receptors

Malaria parasites normally invade human red blood cells in which they hide and reproduce. They then make the host cell burst and infect new cells. Using nanomimics, this cycle can now be effectively disrupted: The egressing parasites now bind to the nanomimics instead of the red blood cells.

Researchers of groups led by Prof. Wolfgang Meier, Prof. Cornelia Palivan (both at the University of Basel) and Prof. Hans-Peter Beck (Swiss TPH) have successfully designed and tested host cell nanomimics. For this, they developed a simple procedure to produce polymer vesicles -- small artificial bubbles -- with host cell receptors on the surface. The preparation of such polymer vesicles with water-soluble host receptors was done by using a mixture of two different block copolymers. In aqueous solution, the nanomimics spontaneously form by self-assembly.

Blocking parasites efficiently

Usually, the malaria parasites destroy their host cells after 48 hours and then infect new red blood cells. At this stage, they have to bind specific host cell receptors. Nanomimics are now able to bind the egressing parasites, thus blocking the invasion of new cells. The parasites are no longer able to invade host cells, however, they are fully accessible to the immune system.

The researchers examined the interaction of nanomimics with malaria parasites in detail by using fluorescence and electron microscopy. A large number of nanomimics were able to bind to the parasites and the reduction of infection through the nanomimics was 100-fold higher when compared to a soluble form of the host cell receptors. In other words: In order to block all parasites, a 100 times higher concentration of soluble host cell receptors is needed, than when the receptors are presented on the surface of nanomimics.

"Our results could lead to new alternative treatment and vaccines strategies in the future," says Adrian Najer first-author of the study. Since many other pathogens use the same host cell receptor for invasion, the nanomimics might also be used against other infectious diseases. The research project was funded by the Swiss National Science Foundation and the NCCR "Molecular Systems Engineering."

Source: University of Basel