* NIH to retire all research chimpanzees

Fifty animals held in “reserve” by the US government will be sent to sanctuaries.

The US National Institutes of Health once maintained a colony of roughly 350 research chimpanzees. Two years after retiring most of its research chimpanzees, the US National Institutes of Health (NIH) is ceasing its chimp programme altogether, Nature has learned.

In a 16 November e-mail to the agency’s administrators, NIH director Francis Collins announced that the 50 NIH-owned animals that remain available for research will be sent to sanctuaries. The agency will also develop a plan for phasing out NIH support for the remaining chimps that are supported by, but not owned by, the NIH.

“I think this is the natural next step of what has been a very thoughtful five-year process of trying to come to terms with the benefits and risks of trying to perform research with these very special animals,” Collins said in an interview with Nature. “We reached a point where in that five years the need for research has essentially shrunk to zero. “

Many advocates of animal research are unhappy with the plan. “Given NIH’s primary mission to protect public health, it seems surprising,” says Frankie Trull, president of the Foundation for Biomedical Research in Washington DC.

The NIH retired about 310 chimpanzees in 2013, in line with recommendations from an internal advisory panel that drew on recommendations from the then-US Institute of Medicine (now the US National Academy of Medicine). The agency maintained a colony of 50 “reserve” animals that could only be used in cases where the research meets a very high bar, such as public-health emergencies

The US Fish and Wildlife Service (FWS) added a second, separate bar to chimp research in June, when it gave research chimps endangered-species protection. This prevents scientists from stressing chimps unless the FWS determines that the work would benefit wild chimpanzees. Researchers have, however, been able to continue some non-invasive behavioural research with the NIH chimps and others.

Trull sees the NIH’s latest move as inconsistent with the logic that drove it to keep a group of reserve chimps. “I don’t understand the decision of ‘we’re going to take that resource away forever’,” she says.

But Stephen Ross, an animal behaviour specialist who served on the 2013 advisory panel, says that from the beginning, the NIH considered retirement of the reserve animals to be an option if researchers were not using them. “It’s clear that chimpanzees are not a needed resource in the biomedical research world,” says Ross, who works at the Lincoln Park Zoo in Chicago, Illinois.

According to Collins, the NIH has received only one application since 2013 to use chimps in research; that application was later withdrawn. The FWS has not received any requests for research exemptions since the endangered-species protection took effect earlier this year.

The NIH’s first priority, Collins writes, will be to transfer 20 NIH-owned chimps from the Southwest National Primate Research Center in San Antonio, Texas, to Chimp Haven, a government-funded sanctuary in Keithville, Louisiana. Next will be the 139 chimps at a facility in Bastrop, Texas, which is owned by the University of Texas MD Anderson Cancer Center.

He told Nature that the NIH will also address the fate of 82 agency-supported chimps that are housed at the Southwest National Primate Research Center, although it has not made any decisions yet. NIH currently pays for these animals’ maintenance, but does not own them.

Collins has asked the NIH’s Division of Program Coordination, Planning and Strategic Initiatives to develop plans for this process. Few sanctuaries can accept research chimps, and many of the ones that can — including Chimp Haven — are nearly full. Collins says that Chimp Haven has, however, immediately opened 25 spots for retired NIH chimps.

The NIH decision essentially ends chimpanzee research at the MD Anderson’s Keeling Center for Comparative Medicine and Research in Bastrop, says the centre’s director, Christian Abee, because its chimps are owned by the government. The centre only performs behavioural and observational research.

“If these chimpanzees are moved to Chimp Haven, these facilities will be empty, while Chimp Haven will have to build more facilities,” says Abee, who notes that the NIH helped to pay for the construction of the Bastrop centre — and that MD Anderson has committed to spend US$500,000 on renovations to the centre, in part to accommodate some of the NIH’s 50 reserve chimps.

“This decision demonstrates a fundamental lack of understanding of the quality of care and the quality of life provided chimpanzees at the Keeling Center.”

Collins says that a 2013 law passed by Congress requires NIH to move chimps to federal sanctuaries, of which Chimp Haven is the only accredited facility. “Bastrop does have many positives and I’m sympathetic with their question,” he says. “But right at the moment we’re bound by the law.”

That law presents major problems for NIH, as Chimp Haven is nearly out of space. If the agency decides that more retirement facilities are needed, it will need to find the money to pay for them. Collins says that the NIH is still discussing how to house its retired chimps, especially since the animals’ eventual deaths will make sanctuary space unnecessary.

Animal-rights activists are thrilled by Collins’s move to retire the NIH chimp colony. “Experimenting on chimpanzees is ethically, scientifically and legally indefensible and we are relieved and happy that NIH is fulfilling its promise to finally end this dark legacy,” says Justin Goodman, director of laboratory investigations at the US organization People for the Ethical Treatment of Animals (PETA). “ We will continue to encourage the same considerations be made for all primates in laboratories.

The group has been pushing the NIH to end primate research. On 20 October, it delivered letters to about 100 people in Collins’s home neighbourhood, asking them to approach him to protest a set of experiments at the NIH that involve removing baby monkeys from their mothers to study stress in infants.

Allyson Bennett, a developmental psychobiologist at the University of Wisconsin–Madison, questions the decision to move them from research facilities to sanctuaries, which are not subject to the same strict oversight and welfare standards that govern NIH-supported centres. She adds that moving the animals to new facilities may create more stress for them.

And researchers who use chimps for conservation work — which may be allowable under the FWS rule — are furious about the NIH decision. Peter Walsh, a disease ecologist at the University of Cambridge, UK, has been leading an effort to develop an Ebola vaccine for wild chimps. He says that the FWS endangered-species protection has jeopardized his work at the University of Louisiana at Lafayette’s New Iberia Research Center, which houses chimps that are neither owned nor supported by the NIH.

The NIH decision further narrows the possibilities for conservation research, Walsh adds, in part because Gabon is the only country other than the United States that allows such work.

“There really is no other place to do conservation-related trials but the US biomed facilities,” he says. “A lot of wild chimps died in order to capture infants for originally stocking NIH’s own captive populations, and populations they have long supported financially. Now, the first time that NIH has ever been asked to give anything back to wild chimps, they cut and run.”

Nature doi:10.1038/nature.2015.18817  Nature  Original web page at Nature


‘Digital chimp’ trove preserves brains of retired apes

Decades of studies on chimpanzee brains and behaviour will be captured in an online resource. Panzee the chimpanzee was a skilled communicator that could tell untrained humans where to find hidden food by using gestures and vocalizations. Austin the chimp was particularly adept with a computer, and scientists have been scanning the animal’s genome for clues to its unusual cognitive abilities. Both apes lived at a language-research centre at Georgia State University in Atlanta, and both died several years ago — but they will live on in an online database of brain scans and behavioural data from nearly 250 chimpanzees.

Researchers hope to combine this trove, now in development, with a biobank of chimpanzee brains to enable scientists anywhere in the world to study the animals’ neurobiology. This push to repurpose old data is especially timely now that the US National Institutes of Health (NIH) has decided to retire its remaining research chimpanzees. The agency decommissioned more than 300 animals in 2013, but kept 50 available for research in case of a public-health emergency. Following an 18 November decision, this remaining population will also be sent to sanctuaries in the coming years. The NIH also hopes to retire another 82 chimps that it supports but does not own, says director Francis Collins.

“We were on a trajectory toward zero, and today’s the day we’re at zero,” says Jeffrey Kahn, a bioethicist at Johns Hopkins University in Baltimore, Maryland, who led a 2011 study on the NIH chimp colony for the Institute of Medicine. The NIH’s latest move, along with a decision in June by the US Fish and Wildlife Service to give research chimps endangered-species protections, effectively ends the possibility of biomedical research on the animals in the United States.

The retirement of the NIH chimps will also end non-invasive studies on the 139 NIH-owned animals at the University of Texas MD Anderson Cancer Center primate facility in Bastrop. Its director, Christian Abee, says that researchers have published more than 50 behavioural studies since 2012 using these animals. “There is no other alternative for cognitive research in chimpanzees,” he says. That makes the NIH-funded chimp database all the more important. “This is a very unique window of opportunity to make sure that there’s a legacy and a contribution from the lives they have lived,” says project leader Chet Sherwood, a biological anthropologist at George Washington University in Washington DC.

In the next few months, Sherwood’s team plans to launch a website with a database for researchers and an educational component for the public. The site will eventually include existing data on the chimps’ performance in behaviour and personality tests, scans of the primates’ brain structure and activity, and their pedigrees and some genetic information. Sherwood and his colleagues plan to model the website on that of the Human Connectome Project, an open-access collection of brain scans from 1,200 individuals that researchers can use to study the links between brain structure and activity and human traits. A chimp-brain biobank will help researchers to study the animals’ neurobiology.

The team is also collaborating with the Allen Brain Institute in Seattle, Washington, to create an atlas of gene expression in the chimp brain. Researchers who want to study chimp brains in more detail can request tissue and blood samples from the team, which has nearly 250 preserved organs stored at facilities in Washington DC and Atlanta.

But some scientists and advocates worry about the consequences of losing access to research chimps. Frankie Trull, director of the Foundation for Biomedical Research in Washington DC, which advocates for animal research, says that the US government may regret its decision if a public-health threat emerges that would be best studied in chimpanzees. Others caution that the dwindling number of research animals will make it difficult to develop therapies — such as vaccines against Ebola — for wild chimps, which would help both the animals and human beings.

In the meantime, the NIH is struggling to find homes for its newly retired chimps. By law, retired animals are sent to a federal sanctuary known as Chimp Haven in Keithville, Louisiana, but that facility has only 25 places available now. Nearly 310 NIH-owned animals need to be resettled, and Collins says that the agency is still evaluating its options — a situation that worries lawmakers.

On 20 November, two members of Congress sent the NIH a letter asking the agency for its plan to rehome the remaining chimps. “We want to make sure that for the sake of taxpayers and these much-abused chimpanzees, these delays are overcome immediately,” they wrote.

Although retired, the apes of Chimp Haven may one day re-enter research labs — posthumously. Sherwood’s team is drafting an agreement with the sanctuary to obtain the animals’ brains when they die; it also hopes to acquire organs from chimps in zoos and research facilities. “You can imagine 20 years from now, this ageing population won’t be here,” he says. “If we weren’t making the efforts today, there wouldn’t be a way to study neurobiology in chimpanzees.”

Nature 527, 422–423 (26 November 2015) doi:10.1038/527422a  Nature  Original web page at Nature


Monkey model discovery could spur CMV vaccine development

Cytomegalovirus (CMV) is the leading infectious cause of birth defects worldwide, but scientists have been frustrated in their efforts to develop a vaccine to protect against infections.

Among the most confounding problems is the lack of animal models that aptly mimic CMV passing from mother to unborn child, as it does in humans. Aside from guinea pigs, which have limited similarities to humans, no other mammals were known to pass the virus to their fetuses.

Now researchers at Duke Medicine have discovered that rhesus monkeys can, in fact, transmit the virus across the placenta to their unborn offspring. This finding, reported online October 19 in the Proceedings of the National Academy of Sciences, establishes the first primate model that researchers can use to study mother-to-fetus CMV infections and spur development of potential vaccine approaches.

“A huge impediment to CMV vaccine development has been our lack of ability to determine what immune responses would be needed to protect against mother-to-fetus transmission,” said senior author Sallie R. Permar, M.D., Ph.D., of the Duke Human Vaccine Institute. “This requires good animal models, where we can manipulate each arm of the immune system to evaluate its role in congenital infection.”

CMV is related to the herpes viruses that cause chicken pox and mononucleosis, and in most people, it results in mild to no symptoms of disease when they acquire an infection. However, in about a third of instances when women who have never been exposed to CMV contract the virus during pregnancy, they can pass an infection to the fetus. About a quarter of those infants will go on to have neurologic impairment.

The Centers for Disease Control and Prevention reports that about 5,000 children a year in the U.S. are born with permanent problems resulting from CMV infections, including deafness, blindness, seizures and cognitive delays.

“This is a situation of great concern and we need to work to prevent it,” Permar said. “After the rubella vaccine was developed in the 1960s, schools for the deaf and blind had to close their doors because there were far fewer children who had suffered congenital rubella infections and needed the services. That’s the kind of impact a CMV vaccine could have.”

Permar said simple approaches to vaccine development, such as creating a weakened virus to trigger immunity, have failed, because the virus has evolved alongside humans to elude the immune system. So having a non-human primate model — something of a higher order than guinea pigs — became imperative.

Permar said finding the mother-to-fetus transmission in the rhesus macaques became a hunt. She enlisted the help of co-senior author Amitinder Kaur of Tulane National Primate Research Center, an expert in CMV-specific immunity in rhesus macaques.

Most macaques are infected with the rhesus version of CMV before adulthood, yet their young are born without the hearing loss or neurological problems that human babies can acquire in utero. In an earlier study, coauthor Peter Barry of the University California at Davis found that infection of a macaque fetus directly through the abdomen resulted in a similar disease to that in humans. Permar and Kaur wanted know if the infection could pass through the placenta.

Using macaques at the New England Primate Research Center, Harvard Medical School, that were specially bred to be free of CMV and all herpes viruses, they depleted the CD4 “helper” T cells that play an important role in antibody responses. When infected with CMV a week later, all the animals passed the virus through the placenta, resulting in miscarriage in three of the four animals.

“This told us not only that the virus could be transmitted through the placenta, but that the mother’s immune system was playing an important role in the severity of the infection,” Permar said.

In a second experiment, Permar and Kaur infected CMV-negative animals with the virus, and left their immune systems intact. Among this group, CMV was transmitted to two of three offspring in utero, but the animals were born with no major neurological deficits — mimicking what often occurs in humans.

In a third control group of animals, the researchers studied females that had naturally been infected with CMV earlier in their lives, and depleted their CD4 helper T cells during pregnancy. The mothers had little to no circulating virus and the offspring appeared to be unaffected by the CD4 helper T cell depletion.

“In addition to establishing a primate model for congenital infection, we gained new information about the importance of the maternal immune system in protecting the fetus,” said lead author Kristy Bialas, a post-doctoral fellow at Duke. “Whereas CMV transmission among immune-competent mothers did not result in fetal disease, transmission in mothers with compromised T cell immunity led to severe fetal outcome.”

Permar said the next stage of research will be to determine whether neutralizing antibody responses would be enough to protect against transmission of severe disease, or whether a T-cell vaccine would be the better approach.  Science Daily  Original web page at Science Daily


What makes a leader? Clues from the animal kingdom

As the American media continues to buzz over who is more or less likely to secure the Republican and Democratic nominations for U.S. President, researchers in the journal Trends in Ecology & Evolution review some interesting perspectives on the nature of leadership. The experts from a wide range of disciplines examined patterns of leadership in a set of small-scale mammalian societies, including humans and other social mammals such as elephants and meerkats.

“While previous work has typically started with the premise that leadership is somehow intrinsically different or more complex in humans than in other mammals, we started without a perceived notion about whether this should be the case,” said Jennifer Smith of Mills College in Oakland, California. “By approaching this problem with an open mind and by developing comparable measures to compare vastly different societies, we revealed more similarities than previously appreciated between leadership in humans and non-humans.”

Chimpanzees travel together, capuchins cooperate in fights, and spotted hyenas cooperate in hunting, but the common ways that leaders promote those collective actions has remained mysterious, Smith and her colleagues say. It wasn’t clear just how much human leaders living in small-scale societies have in common with those in other mammalian societies either.

To consider this issue, a group of biologists, anthropologists, mathematicians, and psychologists gathered at the National Institute for Mathematical and Biological Synthesis. These experts reviewed the evidence for leadership in four domains–movement, food acquisition, within-group conflict mediation, and between-group interactions–to categorize patterns of leadership in five dimensions: distribution across individuals, emergence (achieved versus inherited), power, relative payoff to leadership, and generality across domains

Despite what those ongoing presidential primaries might lead one to think, the analysis by the scientific experts finds that leadership is generally achieved as individuals gain experience, in both humans and non-humans. There are notable exceptions to this rule: leadership is inherited rather than gained through experience among spotted hyenas and the Nootka, a Native Canadian tribe on the northwest coast of North America.

In comparison to other mammal species, human leaders aren’t so powerful after all. Leadership amongst other mammalian species tends to be more concentrated, with leaders that wield more power over the group.

Smith says the similarities probably reflect shared cognitive mechanisms governing dominance and subordination, alliance formation, and decision-making–humans are mammals after all. The differences may be explained in part by humans’ tendency to take on more specialized roles within society.

“Even in the least complex human societies, the scale of collective action is greater and presumably more critical for survival and reproduction than in most other mammalian societies,” Smith said.

The researchers now plan to further quantify the various dimensions identified in the new work. There’s still plenty more to learn. “As ambitious as our task was, we have only just scraped the surface in characterizing leadership across mammalian societies and some of the most exciting aspects of the project are still yet to come as biologists and anthropologists implement our novel scheme for additional taxa and societies,” Smith said.   Science Daily  Original web page at Science Daily


Immune responses provide clues for HIV vaccine development

Recent research has yielded new information about immune responses associated with–and potentially responsible for–protection from HIV infection, providing leads for new strategies to develop an HIV vaccine. Results from the RV144 trial, reported in 2009, provided the first signal of HIV vaccine efficacy: a 31 percent reduction in HIV infection among vaccinees. Since then, an international research consortium has been searching for molecular clues to explain why the vaccine showed this modest protective effect.

A new review outlines findings that hint at the types of immune responses a preventive HIV vaccine may need to induce. The article was co-authored by leaders in HIV vaccinology, including Anthony S. Fauci, M.D., director of the National Institute of Allergy and Infectious Diseases, part of the National Institutes of Health, and lead author Lawrence Corey, M.D., of the Fred Hutchinson Cancer Research Center.

Analyses of RV144 volunteers revealed that particular vaccine-induced immune responses, including production of certain antiviral antibodies and CD4+ T cell responses to HIV’s outer shell, or envelope, correlate with reduced HIV infection. Many RV144 vaccinees produced antibodies in the immunoglobulin G (IgG) family that bind to sites within part of the HIV envelope called V1V2. These antibodies were linked to protection against acquiring HIV. However, high levels of a different type of envelope-binding antibody belonging to the IgA family were associated with a lack of protection against HIV infection. Evidence suggests that IgA may block the protective action of IgG. Recently, monkey studies testing vaccine regimens different from those in RV144 have supported the notion that enhancing protective antibody activity may increase vaccine efficacy.

Guided by findings from human and monkey studies, researchers are working to improve upon the efficacy of the RV144 vaccine regimen. They are investigating strategies to increase the magnitude and durability of vaccine-induced immune responses associated with protection from HIV infection, as well as developing vaccines to elicit production of antibodies that are broadly neutralizing against a variety of HIV strains. As development of an effective HIV vaccine continues, efforts stemming from the modest success of the RV144 trial have “produced a momentum and series of immune targets that will hopefully lead to an effective global vaccine effort,” the authors conclude.  Science Daily  Original web page at Science Daily


* Genes linked with malaria’s virulence shared by apes, humans

The malaria parasite molecules associated with severe disease and death–those that allow the parasite to escape recognition by the immune system–have been shown to share key gene segments with chimp and gorilla malaria parasites, which are separated by several millions of years, according to a new study led by Harvard T.H. Chan School of Public Health. This new information about the origin and genetics of human malaria virulence factors could aid in basic understanding of the causes of malaria and provide targets for drugs and vaccines. The study will be published online October 12, 2015 in Nature Communications.

“The evolution of these key virulence determinants doesn’t occur in the same way as in other pathogens. Instead of gradually changing by mutation, like the flu virus, these malaria parasites exchange intact gene segments, like shuffling a deck of cards,” said Caroline Buckee, assistant professor of epidemiology at Harvard Chan School and senior author of the study.

Malaria kills more than 500,000 people a year, mostly children in Sub-Saharan Africa. Severe disease syndromes in human malaria–including severe malarial anemia, pregnancy-associated malaria, and cerebral malaria–have been linked with the malaria parasite’s ability to cause infected red blood cells to bind to the inner lining of blood vessels. This ability of the infected cells to adhere in this way–which is key to malaria’s virulence–is linked with certain genes called var genes.

Looking at hundreds of var sequence fragments using network analysis, the researchers discovered that short segments of these genes are shared across many different malaria parasites affecting humans, apes, and chimps. These segments are not recent adaptations, but rather reflect an ancient genomic structure.

“Astonishingly, we have found the very same shared sequence mosaics in these highly divergent species, implying that these short mosaic sequences, in spite of continual diversification, have an ancient origin,” Buckee said. “The origin of human malaria virulence factors is actually much older than previously thought.”  Science Daily  Original web page at  Science Daily


* Paralysis: Primates recover better than rodents

Monkeys and humans exhibit greater motor recovery than rats after similar spinal cord injury, according to a study conducted in Grégoire Courtine’s lab at EPFL. The study results have been published in Science Translational Medicine.

Spontaneous improvement occurs during the first six months after a spinal cord injury, allowing a hemiplegic patient to recover partial motor control. The researchers are using this observation to improve clinical trials and patient therapies. The neuronal mechanisms underlying this extensive recovery in primates are nearly absent in laboratory rats, according to the EPFL researchers.

“Research on rats is essential for developing regenerative therapies,” said Dr. Courtine, “but rodents show fundamental differences from primates in terms of neuronal reorganization and functional recovery.” The reason for this lies in differences in anatomy and function of the corticospinal tract, which are the fibers through which the cortex communicates with the spinal cord. In rats, the corticospinal tract is mainly located in the dorsal column and is restricted to one side of the spinal cord, whereas in monkeys and humans this pathway migrated to the lateral column, expand in size, and became bilateral.

“Because of these anatomical specificities, many fibers are spared after an injury,” said Dr. Courtine. “The corticospinal tract forms detour circuits around the lesion, restoring communication between the brain and the neuronal circuits that control the movement of the arms and legs. This neuroplasticity is minimal in rats.”

The more complex the movement required — such as grasping an object or walking along a horizontal ladder — the greater the differences between the two species. While rats recover the ability to walk on flat ground, they are no longer capable of picking up food or positioning their paws accurately. Monkeys and humans, on the other hand, recover fine motor control and the ability to grasp objects.

The difference is even more pronounced if the lesions are lateralized rather than symmetric, because the fibers are found on both sides of the spinal column in primates. These observations are consistent with those of more than 400 human patients with cervical lesions.

The identification of this primate-specific mechanism of recovery has major implications for future research. Using primate models rather than rat models will improve the design of therapies to repair the human spinal cord and increase the accuracy of predictive models of recovery.   Science Daily  Original web page at Science Daily


Chimpanzee personality linked to anatomy of brain structures

Chimpanzees’ personality traits are linked to the anatomy of specific brain structures, according to researchers at Georgia State University, The University of Texas MD Anderson Cancer Center and University of Copenhagen.

The findings, published online in the journal NeuroImage in August, reveal that both gray- matter volumes of various frontal cortex regions and gray-matter volume asymmetries (larger right versus left or vice versa) are associated with various personality traits. The results suggest the frontal cortex and asymmetries in this region of the brain play an important role in the neurobiological foundation of broad personality traits.

“Our results confirm the importance of neuroscientific approaches to the study of basic personalities and suggest that when compared to humans many of these associations are comparable in chimpanzees,” said Robert Latzman, assistant professor in the Department of Psychology at Georgia State.

The researchers studied 107 chimpanzees’ brains using magnetic resonance image (MRI) scans and also assessed each chimpanzee’s personality by using a 41-item personality questionnaire. They found chimpanzees who were rated as higher for the personality traits of openness and extraversion had greater gray-matter volumes in the anterior cingulate cortex in both hemispheres of the brain. Chimpanzees who were rated as higher on dominance had larger gray-matter volumes in the left anterior cingulate cortex and right prefrontal cortex. Chimpanzees who rated higher on reactivity/unpredictability had higher gray-matter volumes in the right mesial prefrontal cortex.

All chimpanzees received MRI scans during their annual physical examination. For the personality questionnaire, the chimpanzees were rated by staff members who had worked with the animals for an extended period and felt they had enough experience for an accurate rating. Each item consisted of a single trait with a behavioral definition and a scale ranging from “least descriptive of the chimpanzee” to “most descriptive of the chimpanzee.” The instrument consisted of five dimensions: extraversion, openness, agreeableness, dominance (opposite to the human trait of neuroticism) and reactivity/undependability (a dimension that includes content from the opposite side of the human traits of conscientiousness, agreeableness and extraversion.

Previous studies by this group suggest the existence of largely similar personality traits in humans and chimpanzees, but until this study, researchers had not explored the neuroanatomical basis of these traits in nonhuman primates.  Science Daily  Original web page at Science Daily


* Primates have been infected with viruses related to HIV for 16 million years

Disease-causing viruses engage their hosts in ongoing arms races: positive selection for antiviral genes increases host fitness and survival, and viruses in turn select for mutations that counteract the antiviral host factors. Studying such adaptive mutations can provide insights into the distant history of host-virus interactions. A study published on August 20th in PLOS Pathogens of antiviral gene sequences in African monkeys suggests that lentiviruses closely related to HIV have infected primates in Africa as far back as 16 million years.

Interested in the history of lentiviruses–the group of retroviruses to which HIV and its simian (monkey) relatives, the SIVs belong–Welkin Johnson, from Boston College, USA, and colleagues focused on an antiviral gene called TRIM5. TRIM5 is part of a group of antiviral genes called “restriction factors,” which have evolved to protect host cells from infection by viruses. Its product, the TRIM5 protein, interacts directly with the outer shell of lentivirus particles after they enter the host cells and prevents the virus from multiplying there. (The human version of TRIM5 does not interfere with–and therefore not protect against–HIV, but many monkeys have TRIM5 variants that do render HIV harmless and are therefore immune to HIV/AIDS.)

Because of its unique specificity for retroviruses (whereas other restriction factors often have broader antiviral activity), the researchers hypothesized that the evolution of TRIM5 in African monkeys should reveal selection by lentiviruses closely related to modern SIVs. To derive an evolutionary tree of the TRIM5 gene, they analyzed and compared its complete protein-coding DNA sequences from 22 African primate species. They identified a cluster of adaptive changes unique to the TRIM5 proteins of a subset of African monkeys–the Cercopithecinae, which include macaques, mangabeys, and baboons–that suggests that ancestral lentiviruses closely related to modern SIVs began colonizing primates in Africa as far back as 11-16 million years ago.

The scientists also generated a panel of (reconstructed) ancestral and existing TRIM5 genes (19 total), expressed them in cultured cell lines, and exposed the cells to 16 different retroviruses (lentiviruses and others) to see which TRIM5 versions conferred resistance to which viruses. These experiments confirmed that the observed cluster of adaptations resulted in resistance specifically to cercopithecine lentiviruses, but had no effect on restriction of other retroviruses, including lentiviruses of other, non-cercopithecine primates.

The researchers conclude “The correlation between lineage specific adaptations and ability to restrict viruses endemic to the same hosts supports the hypothesis that lentiviruses closely related to modern SIVs were present in Africa and infecting the ancestors of cercopithecine primates as far back as 16 million years ago, and provides insight into the evolution of TRIM5 specificity.”  Science Daily  Original web page at Science Daily


Major advance toward more effective, long-lasting flu vaccine

Scientists from The Scripps Research Institute (TSRI) and the Janssen Pharmaceutical Companies of Johnson & Johnson (Janssen) have found a way to induce antibodies to fight a wide range of influenza subtypes — work that could one day eliminate the need for repeated seasonal flu shots.

“This study shows that we’re moving in the right direction for a universal flu vaccine,” said Ian Wilson, Hansen Professor of Structural Biology and chair of the Department of Integrative Structural and Computational Biology at TSRI.

The study was part of TSRI’s long-term collaboration to strengthen research against infectious disease with the former Crucell Vaccine Institute, now known as Janssen Prevention Center and headquartered in Leiden, the Netherlands. The research was published online ahead of print on August 24 by the journal Science.

Seasonal flu typically causes more than 200,000 hospitalizations and 36,000 deaths every year in the United States, according to the U.S. Centers for Disease Control and Prevention. While a yearly flu shot provides some protection, subtypes not covered by the vaccine can emerge rapidly. This phenomenon was evident in the 2009 spread of the H1N1 (“swine flu”) subtype that killed an estimated 151,700 to 575,400 people worldwide.

In the last decade, several studies from TSRI, Janssen and other institutions have shown that some people are capable of making powerful antibodies that can fight many subtypes of influenza at once by targeting a site on the influenza virus that does not mutate rapidly. Unfortunately, these “broadly neutralizing antibodies,” or bnAbs, are rare.

Still, the tantalizing existence of broadly neutralizing antibodies led Janssen and TRSI to try creating an influenza vaccine specially designed to elicit them. Researchers zeroed in on a possible target: a protein on the surface of influenza, called hemagglutinin (HA). HA is present on all subtypes of influenza, providing the key viral “machinery” that enables the virus to enter cells. Most importantly, the long “stem” region of HA, which connects the virus to cells, plays such a crucial role that mutations at the site are unlikely to be passed on. “If the body can make an immune response against the HA stem, it’s difficult for the virus to escape,” Wilson explained.

To create antibodies against the HA stem, the research team looked to influenza’s own structure, specifically the universal recognition site of the broadly protective antibody CR9114 in the HA stem (described by Dreyfus et al., Science 2012). This vaccine candidate was designed, produced and tested by a team of scientists led by Jaap Goudsmit, head of the Janssen Prevention Center, the paper’s first author Antonietta Impagliazzo (responsible for the design) and co-senior author Katarina Radošević.

The effort represents the first time scientists have been able to cut off the variable head region of HA, designing features able to stabilize the conformation of the original protein, and at the same time faithfully mimicking the key broadly neutralizing site. The ultimate goal was to use this synthetic version of the HA stem in a vaccine to teach the body to make powerful antibodies against influenza virus, priming it to fight off a variety of flu strains.

The scientists then studied the response of rodent and nonhuman primate models given one of several candidate immunogens. They found that animals given one especially stable immunogen produced antibodies that could bind with HAs in many influenza subtypes, even neutralizing H5N1 viruses (“avian” or “bird” flu).

“This was the proof of principle,” said Wilson. “These tests showed that antibodies elicited against one influenza subtype could protect against a different subtype.”

Scientists at TSRI studied the structure of the immunogen at every point in the process. Using the imaging techniques of electron microscopy (led by TSRI Associate Professor Andrew Ward and postdoctoral fellow Ryan Hoffman) and x-ray crystallography (led by Wilson and TSRI Staff Scientist Xueyong Zhu), the team showed that the most promising candidate immunogen mimicked the HA stem and that antibodies could bind with the immunogen just as they would with a real virus.

With proof that an immunogen can elicit antibodies against the stem region, Wilson said the next step in this research is to see if the immunogen can do the same in humans.  Science Daily  Original web page at Science Daily


Chimpanzees found to survive in degraded and human-dominated habitats

A chimpanzee population in Uganda has been found to be three times larger than previously estimated, according to research published in the open access journal BMC Ecology. The study suggests that chimpanzees may adapt to degraded habitats better than expected, but also highlights the importance of new and more focused conservation strategies.

The protected Budongo and Bugoma Forest Reserves together compose approximately one quarter of the estimated total chimpanzee population in Uganda. The unprotected area between these two reserves is a human-dominated landscape comprising forest with villages, agricultural lands and natural grasslands.

At least 450 km2 of forest is estimated to have been lost between the Budongo and Bugoma Forests from 2000 to 2010. As a potential corridor for chimpanzees migrating between two protected areas, these fragmented landscapes could be vital for conservation, but few studies have examined the chimpanzee population of this corridor area.

Counting chimpanzee populations also presents a number of challenges. Direct monitoring is a lengthy process, counting nests can be inaccurate, while the use of camera traps and acoustic monitoring is still in its infancy.

The researchers spent 15 months carrying out ‘genetic censusing’ to provide an accurate method for counting chimpanzees in the corridor region. This involved collecting 865 chimpanzee fecal samples across 633 km2 and genetically analysing them to identify the presence of 182 different chimpanzees.

They then estimated the total population size of the area to be either 256 or 319 chimpanzees, depending on the calculation used. This suggests the presence of at least nine communities containing a minimum of eight to 33 individuals each. These figures are more than three times greater than a previous estimate of around 70 chimpanzees based on small-scale nest count surveys.

Lead author Maureen McCarthy from University of Southern California, USA, said: “Our results demonstrate a much larger population than previously estimated in this region. This is very surprising given the fragmentation of forests in this region and the high human population density. Chimpanzees, therefore, appear surprisingly resilient and can survive even in degraded habitats if they are not hunted. However, their future survival remains uncertain if protection is not afforded to them and habitat loss continues unabated.”

The authors say that it is highly improbable that these higher estimates are evidence of population growth since the time of the previous census. This is due to the long interval between chimpanzee births and the high rate of habitat loss throughout the region over the intervening years. The substantially higher estimates instead likely reflect the improved accuracy of the genetic censusing approach over previous estimates.

The surprising levels of chimpanzee survival in a fragmented human-dominated habitat are also likely aided by their behavioral flexibility. This includes incorporating new (often human-cultivated) foods into their diets and adopting more aggressive behaviors to mitigate human threats.

Maureen McCarthy adds: “Our study demonstrates that even unprotected and degraded habitats can have high conservation value. Though national parks and other protected areas are typically prioritized in conservation planning, unprotected areas should also be considered vital for conservation if they are highly valuable as wildlife corridors that harbor endangered species and maintain gene flow among larger populations of such species.”

The authors predict that a corridor enhancement project in this region would positively impact 30% of Uganda’s total chimpanzee population (including the chimpanzee populations of both Budongo and Bugoma Forests and the region between them).  Science Daily  Original web page at Science Daily


* Synthetic DNA vaccine against MERS induces immunity in animal study

A novel synthetic DNA vaccine can, for the first time, induce protective immunity against the Middle East Respiratory Syndrome (MERS) coronavirus in animal species, reported researchers from the Perelman School of Medicine at the University of Pennsylvania.

David B. Weiner, PhD, a professor of Pathology and Laboratory Medicine, and colleagues published their work in Science Translational Medicine (STM) this week. The experimental, preventive vaccine, given six weeks before exposure to the MERS virus, was found to fully protect rhesus macaques from disease. The vaccine also generated potentially protective antibodies in blood drawn from camels, the purported source of MERS transmission in the Middle East.

MERS is caused by an emerging human coronavirus, which is distinct from the SARS coronavirus. Since its identification in 2012, MERS has been linked to over 1,300 infections and close to 400 deaths. It has occurred in the Arabian Peninsula, Europe, and in the U.S.

The recent 2015 outbreak in South Korea was of great concern as the infection spread from a single patient to infect more than 181 people, resulting in hospital closings, severe economic impact, and more than 30 deaths. During this outbreak rapid human-to-human transmission was documented with in-hospital transmission the most common route of infection.

“The significant recent increase in MERS cases, coupled with the lack of effective antiviral therapies or vaccines to treat or prevent this infection, have raised significant concern,” Weiner said. “Accordingly the development of a vaccine for MERS remains a high priority.”

The vaccine was able to prevent MERS disease in the monkeys and offered benefit to 100 percent of the animals in this study in terms of minimizing symptoms. In addition, the vaccine induced antibodies that are linked with protection in camels, a species that is thought to be a major source of transmission to humans in the Middle East, showing that this vaccine could be deployed to break this link in the MERS transmission cycle. In the field, say the researchers, this vaccine could decrease person-to-person spread of infection in the event of an outbreak and help to protect health care workers or exposed individuals.

“This study was only possible by bringing together an international group of investigators with the necessary skills, including, the lab of Heinz Feldman at the NIH, Gary Kobinger from the Canadian government, scientists from Inovio who developed the plasmid delivery technology, along with Penn colleagues,” said first author Karuppiah Muthumani, PhD, a research assistant professor of Pathology and Laboratory Medicine. “This simple synthetic vaccine has the potential to overcome important production and deployment limitations, and what’s more, the vaccine is non-live, so does not pose a risk of spreading to unintended individuals.” Collaborators include researchers from the National Institute of Allergy and Infectious Disease, the Public Health Agency of Canada, Inovio Pharmaceuticals, the University of Washington, and the University of South Florida.  Science Daily  Original web page at Science Daily


Where commerce, conservation clash: Bushmeat trade grows with economy in 13-year study

Conservation laws also likely drove increased hunting on Bioko Island in Central Africa.

The bushmeat market in the city of Malabo is bustling–more so today than it was nearly two decades ago, when Gail Hearn, PhD, began what is now one of the region’s longest continuously running studies of commercial hunting activity. At the peak of recorded activity in 2010, on any given day more than 30 freshly killed primates, such as Bioko red-eared monkeys and drills, were brought to market and sold to shoppers seeking such high-priced delicacies.

Hearn’s team has now published its comprehensive results of 13 years of daily monitoring bushmeat market activity in the journal PLOS ONE. The researchers recorded more than 197,000 animal carcasses for sale during that time and analyzed market patterns in relation to political, economic and legal factors in the country of Equatorial Guinea in central Africa.

Among their notable findings: Bushmeat sales, a proxy for the level of wildlife hunting, increased steadily over the course of the study period, in tandem with increasing economic prosperity. Bushmeat hunting also rose in response to unenforced environmental conservation laws intended to limit the practice. The study and its findings are noteworthy both for the history of the long-running project and the conservation implications of the results.

The Bioko Biodiversity Protection Program (BBPP), a joint venture of Drexel University in Philadelphia and the National University of Equatorial Guinea (UNGE), is a comprehensive program for research, education and biodiversity protection on Bioko Island. Bioko, a volcanic island in the Gulf of Guinea, is located off the coast of Cameroon in central Africa and is part of the nation of Equatorial Guinea. Bioko’s tropical coastal and montane forests form a relatively understudied biodiversity hotspot, a critical site for numerous species of threatened and endangered monkeys, many of which are at risk because of commercial hunting

Hearn, now an emeritus professor at Drexel University, established BBPP in 1998 and led it until her retirement in 2014. BPPP is now led by Mary Katherine Gonder, PhD, an associate professor in Drexel’s College of Arts and Sciences. Since the start of BBPP, the steady daily monitoring of the commercial bushmeat trade in the capital city of Malabo has formed one of the strongest sources of tangible knowledge about threats to monkeys and other species in the island’s forests.

While Hearn, Gonder and their BBPP colleagues have shared selected data from their bushmeat market surveys with government officials and others over the years, their study’s publication this week is the first time that the full set of data from many years of monitoring–from October 1997 through September 2010–has been made publicly available.

“Every number represents an animal,” said Drew Cronin, PhD, lead author of the new study and a postdoctoral fellow in Gonder’s lab, who earned his doctorate at Drexel under Hearn. The count of carcasses in the bushmeat market creates an objective, comprehensible representation of the losses to Bioko’s forest ecosystem for those with the power to intervene to protect species at risk from overhunting. Their count included carcasses of over 35,200 monkeys; nearly 59,000 wild ungulates; over 4,100 birds; and over 80,900 rodents.

The dynamics in how many animals were sold in the bushmeat market over time, and under what economic, political and legal conditions, are as important as the raw numbers. These trends can inform management and enforcement efforts, both in Bioko and in other places where economic and legal considerations influence the trade and overconsumption of wildlife.

One major trend that Cronin and colleagues found is that bushmeat hunting and availability increased in parallel with economic growth during the 13-year monitoring period. Concurrent with that growth, the dominant method used to capture animals for bushmeat shifted from trapping to shotguns, contributing to more hunting of endangered monkeys, which are predominantly killed by shotgun, in the later years of the study.

Cronin notes that the relationship between economic growth and bushmeat sales on Bioko reflects the nature of bushmeat consumption there. “This bushmeat trade is being largely driven by urban consumers in Malabo who don’t need to eat wildlife to survive,” he said. “There has been a considerable amount of economic development on Bioko, which has resulted in readily accessible alternative protein sources, such as chicken, fish and pork, throughout much of the island, but especially in Malabo. Despite this, most of the valuable bushmeat is being brought to the city and sold.”

Another major finding is that the legal protections Equatorial Guinea enacted in 2007 to limit hunting and sales of primates, the species most highly threatened by the bushmeat trade on the island, were not upheld–and even backfired to the point where bushmeat hunting actually increased. Legal protections of species are necessary to limit hunting, Cronin noted, but that is not sufficient without strong governmental support and enforcement of those laws.  Science Daily  Original web page at Science Daily


New evidence of cultural diversification between neighboring chimpanzee communities

For centuries it has been thought that culture is what distinguishes humans from other animals, but over the past decade this idea has been repeatedly called into question. Cultural variation has been identified in a growing number of species in recent years, ranging from primates to cetaceans. Chimpanzees, our closest living relatives, show the most diverse cultures aside from humans, most notably, in their use of a wide variety of tools.

The method traditionally used to establish the presence of culture in wild animals compares behavioural variation across populations and excludes all behavioural patterns that can be explained by genetic or environmental differences across sites. Nevertheless, it is impossible to conclusively rule out the influence of genetics and environmental conditions in geographically distant populations.

To circumnavigate this problem, researchers, led by Dr. Kathelijne Koops, took a new approach. “We compared neighbouring chimpanzee groups living under similar environmental conditions, which allows for the investigation of fine scale cultural differences, whilst keeping genetics constant,” said Koops.

She and colleagues from Kyoto University and Freie Universität Berlin compared the length of tools used for ‘ant-dipping’ between two neighbouring chimpanzee communities, M-group and S-group, in the Kalinzu Forest, Uganda. Dipping for army ants is one of the hallmark examples of culture in chimpanzees and involves the use of a stick to extract the highly aggressive army ants from their underground nests.

Previous research has shown that ant-dipping tool length varied across chimpanzee study sites in relation to the army ant species (Dorylus spp.) that were present. So Koops compared the availability of the different species of army ants and the length of dipping tools used in the two adjacent chimpanzee communities.

The researchers found that M-group tools were significantly longer than S-group tools, despite identical army ant species availability. Considering the lack of ecological differences between the two communities, the tool length difference was concluded to be cultural. “Our findings highlight how cultural knowledge can generate small-scale cultural diversification in neighbouring groups,” said Koops.

“Given the close evolutionary relationship between chimpanzees and humans, insights into what drives cultural diversification in our closest living relatives will in turn shed light on how cultural differences emerge and are maintained between adjacent groups in human societies,” said Koops, who conducted the work at Cambridge University’s Division of Biological Anthropology and at Zurich University’s Anthropological Institute and Museum.

The research is published in the Nature journal Scientific Reports. Science Daily Original web page at Science Daily


Brain area found that may make humans unique

The brains of macaque monkeys do not integrate abstract information in the same way as human brains. Neuroscientists have identified an area of the brain that might give the human mind its unique abilities, including language. The area lit up in human, but not monkey, brains when they were presented with different types of abstract information.

The idea that integrating abstract information drives many of the human brain’s unique abilities has been around for decades. But a paper published in Current Biology, which directly compares activity in human and macaque monkey brains as they listen to simple auditory patterns, provides the first physical evidence that a specific area for such integration may exist in humans. Other studies that compare monkeys and humans have revealed differences in the brain’s anatomy, for example, but not differences that could explain where humans’ abstract abilities come from, say neuroscientists.

“This gives us a powerful clue about what is special about our minds,” says psychologist Gary Marcus at New York University. “Nothing is more important than understanding how we got to be how we are.”

A team of researchers headed by Stanislas Dehaene at the INSERM Cognitive Neuroimaging Unit at Gif-sur-Yvette near Paris, looked at changing patterns of activation in the brain as untrained monkeys and human adults listened to a simple sequence of tones, for example three identical tones followed by a different tone (like the famous four-note opening of Beethoven’s fifth symphony: da-da-da-DAH).

The researchers played several different sequences with this structure — known as AAAB — and other sequences to the subjects while they lay in a functional magnetic resonance imaging (fMRI) scanner. The fMRI technique picks up changes in blood flow in the brain that correlate with regional brain activity.

The team wanted to know whether the subjects of both species could recognize two different features of the sequences: the total number of tones, indicating an ability to count, and the way the tones repeat, indicating an ability to recognize this type of algebraic pattern.

In the first case, the string of tones might have been changed from AAAB to AAAAB for instance: the basic pattern stays the same but the number of tones changes. In the second case, the reverse is true: the tones might have been changed from AAAB to AAAA, but the number remains the same. The team also looked to see what happened when both features changed at the same time — for example going from AAAB to AAAAAA.

In both monkeys and humans, an area of the brain, part of which has been associated with numbers, lit up in the fMRI scanner when the subjects identified a change in the number of tones. Both species also registered the repetition pattern in specific brain areas, which are known to be equivalent in humans and monkeys. But only the human brains showed a unique response to the combined changes in number and sequence, in the form of intense activation in an additional brain area called the inferior frontal gyrus.

“It is like the monkey recognizes a pattern but does not realize it is interesting and take it no further — only humans take it on to the next level of analysis,” says Marcus.

The inferior frontal gyrus is a part of the cortex that is greatly expanded in humans compared with monkeys. Moreover, the inferior frontal gyrus in humans contains the Broca’s area, which processes language. And when Dehaene’s team read sentences to the humans, the language areas activated in each individual overlapped with those activated by the tone sequences.

But abstract information integration may be significant beyond language. “We had expected that humans have brain areas that put together information,” says cognitive biologist Tecumseh Fitch from the University of Vienna.“This type of computation may turn out to be also relevant to other characteristics that make humans unique, like music appreciation.”

Nature doi:10.1038/nature.2015.18051 Nature Original web page at Nature


Majority rules when baboons vote with their feet

At the Mpala Research Center in Kenya, field biologists get to know their study subjects. Observing the simultaneous interactions and decision-making of a 30-member troop of olive baboons was impossible before the advent of high-resolution GPS technology.

Olive baboon troops decide where to move democratically, despite their hierarchical social order, according to a new report in Science magazine by Smithsonian researchers and colleagues. At the Mpala Research Centre in Kenya, the team conducted the first-ever group-level GPS tracking study of primates, finding that any individual baboon can contribute to a troop’s collective movement.

‘Despite their social status, it’s not necessarily the biggest alpha males that influence where groups go,’ said Margaret Crofoot, research associate at Smithsonian Tropical Research Institute (STRI) and assistant professor of anthropology at University of California, Davis (UC Davis). ‘Our observations suggest that many or all group members can have a voice, even in highly stratified societies.’

Wild olive baboons (Papio anubis) live in strongly hierarchical troops. Dominant individuals displace subordinates when feeding or mating. However, analyzing the second-by-second GPS trajectories of each individual in a single troop revealed that neither a baboon’s rank nor their sex conferred leadership ability. Much to the scientists’ surprise, what emerged was almost identical to patterns previously predicted by theoretical models based on the movements of fish schools, bird flocks and insect swarms. Decision making in baboons is largely a shared process: individuals vote with their feet by choosing to lead or follow their troop-mates.

The study suggests that even in complex societies, there may be an evolutionary benefit in reducing conflict by following simple, egalitarian rules to determine collective motion. It also demonstrates the potential of using high-resolution GPS trackers to meet the challenge of accurately capturing the dynamics of social animal interactions in the wild.

‘Just ten years ago these questions seemed impossible to tackle,’ said Smithsonian post-doctoral fellow Damien Farine, based jointly at the University of Oxford and UC Davis. First, researchers trapped and fitted 25 members of a wild baboon troop with custom-designed GPS collars to record each individual’s location once per second for 14 days. The resulting 20 million GPS data points — representing the simultaneous, continuous movements of more than 80 percent of the group’s adults and subadults relative to each other — included not just collective movement decisions but also eating, hanging out and playtime.

Farine and co-first author Ariana Strandburg-Peshkin, a student at Princeton University, were tasked with extracting meaningful information from this glut of data. ‘We used some very creative computational analysis to isolate patterns of individual movement initiation attempts,’ said Farine. He and Strandburg-Peshkin wrote a program to calculate the relative movements of the baboons in pairs. Each individual’s movement away from the group could potentially ‘pull’ another one toward it. If the second individual did not follow, the movement initiator would return, ‘anchored’ by the decision of its neighbor. These simple behavioral rules have cumulative effects. If an individual’s movement decisions are unchallenged, it is likely to eventually be followed by a subgroup of other baboons, and eventually the whole troop.

Voting comes in if there is conflict about where to go, but this is also determined democratically. If multiple individuals initiate movements in similar directions, then the troop generally compromises by moving in the average of the angle of difference between individual choices. But if the angle of difference between the directions two individuals take differs greatly, the troop is less likely to follow — because when they do, they have to choose one direction over the other.

The baboons’ solution to the resulting conflict is surprisingly simple: they follow the majority. This majority rule means that they are more likely to follow the subgroup containing the greatest number of initiators, and as a result make a decision that suits the majority of the troop. ‘We are looking at are very broad patterns here,’ said Crofoot. ‘The next step will be to look at context to figure out what motivates individual baboons to initiate movement in the first place, and if some individuals can take advantage of certain situations to disproportionately influence the group.’  Science Daily  Original web page at Science Daily


Wild chimps teach scientists about gene that encodes HIV-fighting protein

Different people can vary substantially in their genetic susceptibility to viruses, including HIV. Although the biology that underlies this variation in humans is still being uncovered, it seems that we may be able to learn some key lessons from our closest cousins. A gene variant in chimpanzees in a Tanzanian wildlife preserve probably protects them from rapidly succumbing to the primate equivalent of HIV, Stanford University School of Medicine scientists report in the open access journal PLOS Biology, publishing May 28. The wild chimps inhabit Gombe Stream National Park, a 13.5 square mile preserve where they have been continuously observed from afar since famed primatologist Jane Goodall, Ph.D., began monitoring them more than 50 years ago.

A gene variant is a naturally occurring difference in the DNA sequence of a gene. Part of the chimp variant the scientists identified strongly resembles that of an analogous human variant known to slow the human immunodeficiency virus’ progression to AIDS. The gene in question is subject to evolutionary pressures that normally cause it to change rapidly over evolutionary time, resulting in many variants with diverse sequences. So the striking similarity of a section of the chimp and a section of the human variant implies two things, said Peter Parham, Ph.D., professor of structural biology and of microbiology and immunology. First, hominids have been fighting off HIV-like viruses at least since the two related species diverged some five million years ago. Second, because that particular section of the gene variant hasn’t changed much since then, it probably plays an important role in increased survival among those inheriting it.

‘Only a part of the chimp gene variant’s sequence looks a lot like the human one. That immediately tells us this is the important part of the gene,’ said Parham, the senior author of a study describing the findings. Unlocking this sequence’s significance could yield not only biological insights but also pharmaceutical or, someday, perhaps even gene-therapy applications that enhance HIV-infected people’s ability to avoid disease progression to AIDS, he said.

One of Parham’s research focuses is a set of three genes called the major histocompatibility complex. The MHC codes for proteins that help the immune system recognize foreign substances. These proteins sit on the surface of virtually every vertebrate cell, where they serve as display cases for peptides — small pieces of proteins — chopped out of proteins that once resided inside that cell. It’s the fate of all of a cell’s proteins to eventually be degraded into peptides, which get transported to the cell’s surface and encased in MHC proteins. This enables roving immune cells called T cells to inspect tissues and detect any peptides carved from proteins that are of foreign origin, such as those of a virus that has infected a cell, or have been altered, as in a cancerous cell. T cells often quickly mount an attack on cells bearing foreign or altered proteins.

In humans, HLA-B, one of the three genes in the MHC complex, is the blueprint for a protein that is the appropriate display case for a short peptide ‘tag’ from Gag, an HIV protein that manifests early in the course of infection. Studies have shown that HIV-infected people who carry a particular variant of this gene, known as HLA-B*57:01, resist progression to AIDS. Scientists think this is because the cell-surface protein encoded by the B*57:01 variant, which is present in about one in 10 people, displays its captive Gag peptide in a way that especially catches T cells’ attention. Although the virus can mutate so its Gag protein is invisible to T cells, it doesn’t get much time to do that — and even then, success comes at a cost, Parham said. The resulting virus can’t replicate as efficiently, so the disease can’t progress as quickly to the full-blown, symptomatic stage.

In the Gombe chimps, SIV is endemic. ‘About one in four animals is infected,’ Parham said. But the likelihood of infection isn’t distributed equally among them. The roughly 125 chimps occupying Gombe’s mountainous terrain during the study’s course lived in three geographically distinct communities. While the northern and central groups had low SIV-infection rates, that virus has a strong grip on the southern community. In this community, the newly discovered gene variant became more frequent over the study period, suggesting it may have been naturally selected for its capacity to enhance chimps’ survival to reproductive age and beyond. The Parham group’s genetic analysis supports that suggestion. The original thrust of the study, Parham said, was to compare the MHC diversity of wild versus captive chimp populations to see how real-world exposures to pathogens might affect relative frequencies of various versions of particular MHC genes.

Close human contact with the Gombe chimpanzees is prohibited, so obtaining genetic material from them wasn’t easy. Lead author Emily Wroblewski, Ph.D., a postdoctoral scholar in Parham’s lab, recruited her former Ph.D. adviser from the University of Minnesota, behavioral ecologist Anne Pusey, Ph.D., who had done her graduate work in Gombe in the 1970s under the direction of Goodall. Wroblewski, who herself had spent 1.5 years in the Gombe doing field work for her Ph.D. thesis, also brought in prominent SIV virologist Beatrice Hahn, M.D., now at the University of Pennsylvania. In 2000, Hahn developed methods for extracting DNA and RNA from chimp feces. Over the past 15 years, she has established a large collection of fecal samples, now housed in Philadelphia. Both Pusey, now at Duke University, and Hahn are co-authors of the study. Because the animals have been so carefully watched for so long, albeit always at a distance, each sample can be matched to a particular individual whose habits, maternal lineage and present social affiliations are known.

Wroblewski traveled to the Hahn lab, at the time in Birmingham, Ala.; coordinated the shipment of almost 300 fecal samples — at least two or three per chimp — from freezers in Hahn’s laboratory to Stanford; and returned to Parham’s lab, where she set up shop in one corner and began extracting DNA from the samples. Her DNA analysis permitted assessments of the chimps’ MHC genes’ status, and RNA analysis done by the Hahn lab enabled taking counts of SIV, which, like its cousin HIV, is an RNA virus.

Chimps have an MHC gene, PATR-B, which is functionally analogous to our HLA-B gene. The analysis found 11 different variants of PATR-B in the Gombe chimps, a surprisingly large number for such a tiny population. ‘Seven of these variants had never been seen in captive chimp populations,’ Wroblewski said. After analyzing the first few dozen samples, Wroblewski noticed that the southern community showed an increase in frequency over time of one hitherto unseen variant of PATR-B called B*06:03. Further analysis showed that a stretch of B*06:03 was nearly identical to a stretch on B*57:01, the human gene variant associated with slower AIDS progression. Notably, fecal samples from SIV-infected chimps with the B*06:03 version of PATR-B had lower SIV tallies than those from similarly infected chimps without that variant. ‘I found this to be quite exciting,’ said Wroblewski. ‘Fecal counts of SIV are a good proxy of viral load in the blood, which we have no easy way of measuring in Gombe chimps because we can’t draw blood from them.’  Science Daily  Original web page at Science Daily


Study suggests chimps have cognitive capacity for cooking

Many of the cognitive capacities that humans use for cooking — a preference for cooked food, the ability to understand the transformation of raw food into cooked food, and even the ability to save and transport food over distance for the purposes of cooking — are also shared with chimpanzees, new research suggests.

These days, cooking dinner requires no more thought than turning a knob on a stovetop, but for early humans the notion that — simply by applying heat or fire — foods could be transformed into something both tastier and easier to digest demanded huge cognitive insight — insights often believed to be limited to humans. A new study, co-authored by Felix Warneken, the John L. Loeb Associate Professor of the Social Sciences, and Alexandra Rosati ’05, currently a post-doctoral fellow in the Psychology Department at Yale University who will join the Department of Human Evolutionary Biology as an assistant professor at Harvard this summer, suggests that humans’ cognitive capacity for cooking are also share by chimpanzees. This includes a preference for cooked food, the ability to understand the transformation of raw food into cooked food, and even the ability to save and transport food over distance for the purposes of cooking.

The findings suggest that those abilities emerged early in human evolution, and that aside from control of fire, chimps may possess all the requisite cognitive skills to engage in cooking. The study is described in a June 3 paper in Proceedings of the Royal Society B. “It is an important question when cooking emerged in human evolution,” Warneken said. “We thought one way to get at this question is to investigate whether chimpanzees, in principle, have the critical cognitive capacities for cooking. If our closest evolutionary relative possesses these skills, it suggests that once early humans were able to use and control fire they could also use it for cooking.”

A number of earlier studies, particularly those led by Richard Wrangham, the Ruth Moore Professor of Biological Anthropology and Curator of Primate Behavioral Biology in the Peabody Museum of Archaeology and Ethnology, have hypothesized that cooking played a key role in human evolution by making food easier to digest and enabling early humans to extract more energy from their diet.

In trying to understand the evolutionary origins of cooking, however, those earlier studies largely focused on what is clearly a critical aspect of cooking — the control of fire. “People focus on the control of fire because that seems so salient, but even if you had a fire stick, several other insights are required before you can use it for cooking,” Rosati said. “Obviously, chimps can’t control fire, but we were trying to hypothesize about some of the other aspects of cooking, like the causal understanding that if you put this raw food on the fire it creates cooked food, or at the extreme end of our study, the ability to plan. What’s particularly interesting about cooking is it’s something we all do, but it involves a number of capacities that, even without the context of cooking, are thought to be uniquely human. That’s why we wanted to study this in chimpanzees.”

To get at those questions, Warneken and Rosati in the summer of 2011 travelled to the Jane Goodall Institute’s Tchimpounga Chimpanzee Sanctuary in Republic of Congo, where they conducted a series of experiments using wild-born chimpanzees to test whether they were capable of making the mental leaps necessary for cooking. Their first tests were dedicated to replicating the results of other studies: demonstrating that chimps preferred sweet potato that had been “cooked” — placed in a hot pan, without butter or oil, for one minute — to raw, and showing that the chimpanzees were more willing to pay a temporal cost, in the form of a minute-long wait, to obtain the preferred cooked food. Subsequent tests were aimed at gauging whether chimps truly grasped the transformation from raw food to cooked, and whether they would spontaneously attempt to “cook” items.

To explore those questions, researchers presented chimps with two devices — a “cooking device” that turned raw into cooked slices and a control device that left it unchanged. During the critical test, chimpanzees saw raw sweet potato go into both, but had choose one device before seeing its (possibly transformed) contents. Warneken and Rosati explain that nearly every chimp reliably picked the cooking device, suggesting they quickly understood the transformation that was at work. It was the last experiment, however, that truly revealed chimps’ capacity for cooking.

“We had done one season of testing and we thought what we had was interesting, but then we wondered if they might be able to hold on to the reward and actively choose to put it in the cooking device,” Warneken said. “That’s really tough because usually when chimps have food, they eat it.” “I thought there was no way they were going to do this,” Rosati added. “There is quite a lot of research that says animals have problems with self-control when it comes to possessing food, but we were leaving the sanctuary in a few days so we decided to try it.”

To their surprise, she said, a number of chimps, when given a raw piece of potato, chose to essentially cook it by placing it in the “cooking device” and receiving a cooked piece of food in return. “The first time one of the chimps did this, I was just amazed,” Rosati said. “I really had not anticipated it. When one of them did it, we thought maybe this one chimp is just a genius, but eventually about half of them did it.” The surprising result left Warneken and Rosati with a host of additional questions that would have to wait until they returned to the Congo the following summer.

Among those new questions was whether chimps’ apparent understanding of the cooking process extended to other foods. Just as chimps used the “cooking device” to transform raw sweet potato into cooked, tests showed that they did the same to carrots.


“The key thing here is that they had never seen carrot being put in these devices,” Rosati explained, “but they were still able to generalize that process.” They do not blindly try to cook everything, however. In another test, when chimps were given a piece of raw potato and a small piece of wood, the only put the potato in the cooker, suggesting they understood that only edible items could be cooked. “That shows they don’t simply view this as a trading situation,” Rosati said. “They’re not interested in putting any random thing in the cooking device. You might expect them to put both in because they’d get twice as much, but they really don’t care about the wood piece.”

In the final two experiments, Warneken and Rosati focused on one of the most pressing current questions in animal cognition — whether animals are capable of planning for the future. Though a handful of studies have suggested that chimps are capable of keeping tools for later use, “those studies are very different from cooking,” Rosati said. “A tool can be valuable because you can use it in the future, but you can’t eat it now. When it comes to cooking, you have something — food — that has intrinsic value.”

Despite that value, chimps were willing to transport food for the opportunity to cook it. When given pieces of raw potato on one side of an enclosure, a number of chimps showed a willingness to carry them four meters, to the cooking device on the opposite side. “In some cases, they actually carried it in their mouth, and you could see that sometimes they would eat it, almost by accident,” Rosati said. “This was a hard problem, so they were less likely to put it in the cooking device if they had to carry it, but the did succeed about half the time, so they were able to do it.”

To test whether chimps would save food in anticipation of cooking it later, over several test trials, chimpanzees were given food, but Warneken appeared with the cooking device only three minutes later. “At the beginning, this is a very difficult inference,” Rosati said. “But later on, they understood that he’s going to come back, so if they can hold onto the food for that three minutes, they can transform it into cooked food. In the control condition, they got the same amount of food, but he never showed up. If they didn’t think they were going to be able to cook the food, they ate it.”

To their surprise, Warneken and Rosati said, several of the chimps were able to perform the task, and two saved nearly every piece of raw food they were given for it to be cooked later. While the study supports the notion that cooking behavior emerged early in human history, Warneken and Rosati said it may also suggest a new account for humans’ control of fire.

“We can’t date the control of fire with cognition studies, but we can start to date these other skills that come into play for cooking,” Rosati said. “This type of comparative psychological evidence can tell us a great deal about our evolutionary past. I think it supports the idea that cooking emerged early in human evolution, because it suggests all the cognitive pieces were there, all we needed was control of fire.”

Though the assumption had long been that humans controlled fire before they began using it for cooking, Warneken and Rosati suggest that cooking may have given early humans a reason to control fire. “Why would early humans be motivated to control fire?” Rosati asked. “I think cooking might give you a reason. We know wild chimps will observe natural fire, and they even sometimes seek out and eat cooked food left behind by it. The evidence from our cognitive studies suggests that, even before controlling fire, early hominids understood it’s benefits and could reason about the outcomes of putting food on fire.”  Science Daily  Original web page at Science Daily


US government gives research chimps endangered-species protection

The decision will prohibit most research on captive animals. Wild and captive chimpanzees will now be treated equally under US law. Chimpanzee research in the United States may be nearly over. On 12 June, the US Fish and Wildlife Service (FWS) announced that it is categorizing captive chimpanzees as an endangered species subject to legal protections. The new rule will bar most invasive research on chimpanzees. Exceptions will be granted for work that would “benefit the species in the wild” or aid the chimpanzee’s propagation or survival, including work to improve chimp habitat and the management of wild populations.

The FWS proposed the rule in 2013 to close a loophole that exempted captive chimps from the Endangered Species Act protections that had already been given to their wild counterparts. Under the law, it is illegal to import or export an endangered animal, or to “harm, harass, kill [or] injure” one.

The new regulation will extend these limits to more than 700 chimps in US research laboratories, as well as animals in zoos or entertainment venues such as circuses. The FWS rule also makes it illegal to sell chimpanzee blood, cell lines or tissue across state lines without a permit.

The government’s decision to list captive chimps as endangered drew swift criticism from some science groups. “Practically speaking, [given] the process to get exceptions [for invasive research], I don’t expect chimps will be a viable option,” says Matt Bailey, executive vice president of the National Association for Biomedical Research in Washington DC.

Bailey’s group argues that medical research with chimpanzees benefits both humans and chimps, given that the two species are affected by many of the same diseases, and notes that captive research chimps have been bred for that purpose — making the connection to wild populations tenuous.

Unsurprisingly, animal-rights groups welcomed the government’s action. “This FWS decision continues momentum — adding another barrier to unnecessary and non-productive research purportedly to benefit humans,” Theodora Capaldo, president of the New England Anti-Vivisection Society in Boston, Massachusetts, said in a statement. “We stand on ethically and scientifically firmer ground as we move closer toward ending atrocities under the guise of ‘necessary’ research.”

Biomedical research on chimpanzees has already decreased drastically since the US National Institutes of Health announced in 2013 that it would retire more than 300 captive chimpanzees at its facilities. The agency has retained only 50 chimps, which had been available for invasive research that satisfies ethical considerations that it set out.

The NIH says that there are no active biomedical research projects with these animals. Going forward, the agency says, it  “will work with the Fish and Wildlife Service to comply with any implications of this ruling for future use of NIH-owned chimpanzees.”

The government action comes as chimpanzees are embroiled in another legal matter. The New York Supreme Court is currently considering whether two chimpanzees at Stony Brook University are “persons” illegally detained by the university. The court heard arguments last month on the matter, and a decision is expected this summer.

Nature doi:10.1038/nature.2015.17755  Natur  Original web page at Nature


For spider monkeys, social grooming comes with a cost

Social grooming, or helping others to stay clean and free of lice and other ecto-parasites, has long been associated with hygiene and good health in wild primates. In the process of picking out ecto-parasites, however, the groomers may be picking up internal ones, a new study finds. The results of the study on critically endangered brown spider monkeys show that physical contact is associated with the spread of several common gastrointestinal parasites. Social grooming, or helping others to stay clean and free of lice and other ecto-parasites, has long been associated with hygiene and good health in wild primates. In the process of picking out ecto-parasites, however, the groomers may be picking up internal ones, a new study finds.

The journal Philosophical Transactions of the Royal Society B published the results of the study on critically endangered brown spider monkeys, showing that physical contact is associated with the spread of several common gastrointestinal parasites. “Previously, it was generally assumed that animals are more likely to pick up these parasites from feces or other environmental sources,” says Thomas Gillespie, a disease ecologist at Emory University whose lab led the study. “Our research shows that the external surfaces of animals can serve as viable locations for development to infective stages of such parasites.”

Living in groups comes with costs and benefits. The benefits include more eyes, ears, noses and collective knowledge to hunt food sources and to avoid predators. The costs are competition for food and for mates. And growing evidence is revealing how group interactions affect the dynamics of disease transmission among social animals. “Breakthroughs in technology are allowing for more detailed network analyses, so that we can study the connection between sociality and health in ways that we couldn’t in the past,” Gillespie says. “We are working on models of health risk factors for different species of endangered primates, to try to ensure that disease does not finish them off, but our data could also have implications for people.”

The current study centered on a community of 16 brown spider monkeys in Hacienda San Juan, a patch of tropical rainforest in central Columbia. Spider monkeys are arboreal, spending most of their time in the trees. They swing from branch to branch through the canopy by their prehensile tails. Their communities split into smaller groups that later reconvene, a trait known as fission-fusion. “They basically hang out with whoever they want, and that changes often,” Gillespie says. This fission-fusion trait is associated with intelligence, he adds, and is also seen in chimpanzees, dolphins and humans.

While humans are far more complex, subdividing into groups bound by their families, churches, schools and workplaces, brown spider monkeys split into smaller groups primarily to search for food. “That enables them to cover more ground,” Gillespie explains. “They spend most of their day looking for ripe fruit, in between mating and playing.” The monkeys keep in contact with other members of the group through loud vocalizations. “They can really put on a show when they’ve found a fig tree full of fruit,” Gillespie says.

The interactions of fission-fusion animals are difficult to study in the wild because they are often on the move. For this study, the research team followed 12 individual spider monkeys of the community, collecting about 160 hours of data for each of them over the course of two years. The researchers recorded all social interactions that involved physical contact — including grooming, resting, embracing, mating and social play — and the duration of each interaction. They also collected a total of 166 fecal samples from the study group during the two-year period of the study and tested them for a variety of parasites.

The researchers used the data to diagram the contact and proximity networks, along with the levels of parasite infections, for each individual. The results showed no correlation between mere proximity and parasite infection, but a strong correlation between physical contact and infection. Specifically, infections with the roundworms Strongyloides and Trichostrongylus were associated with grooming interactions. “Our findings suggest that social grooming is the biggest risk for parasite transmission among this community of spider monkeys,” Gillespie says. “The groomer is removing matted fur and debris from another monkey, and some of that debris can contain active life stages of parasites that are not visible to the naked eye.”  Science Daily  Original web page at Science Daily


Alzheimer’s origins tied to rise of human intelligence

Alzheimer’s disease may have evolved alongside human intelligence, researchers report in a paper posted this month on BioRxiv. The study finds evidence that 50,000 to 200,000 years ago, natural selection drove changes in six genes involved in brain development. This may have helped to increase the connectivity of neurons, making modern humans smarter as they evolved from their hominid ancestors. But that new intellectual capacity was not without cost: the same genes are implicated in Alzheimer’s disease.

Kun Tang, a population geneticist at the Shanghai Institutes for Biological Sciences in China who led the research, speculates that the memory disorder developed as ageing brains struggled with new metabolic demands imposed by increasing intelligence. Humans are the only species known to develop Alzheimer’s; the disease is absent even in closely related primate species such as chimpanzees.

Tang and his colleagues searched modern human DNA for evidence of this ancient evolution. They examined the genomes of 90 people with African, Asian or European ancestry, looking for patterns of variation driven by changes in population size and natural selection. The analysis was tricky, because the two effects can mimic each other. To control for the effects of population changes ― thereby isolating the signatures of natural selection — the researchers estimated how population sizes changed over time. Then they identified genome segments that did not match up with the population history, revealing the DNA stretches that were most likely shaped by selection.

In this way, the researchers looked back at selection events that occurred up to 500,000 years ago, revealing the evolutionary forces that shaped the dawn of modern humans, thought to be around 200,000 years ago. Most previous methods for uncovering such changes reach back only about 30,000 years, says Stephen Schaffner, a computational biologist at the Broad Institute in Cambridge, Massachusetts.

The analytical approach that Tang’s team used is promising, he adds. “It’s treating all kinds of selection in a uniform framework, and it’s also treating different eras of selection in a more or less uniform way.” But Schaffner says that further research is needed to confirm that the method is broadly applicable. Still, even the most powerful genomic-analysis methods can be limited by the vagaries of history. Asian and European people descended from a small number of people who left Africa around 60,000 years ago, and that population bottleneck erased earlier patterns of genetic variation in Europeans. The genomes of African people allow researchers to look much further back in time, offering more information about the evolutionary changes that shaped humanity.

Nature doi:10.1038/nature.2015.17589  Nature  Original web page at Nature


Lowly ‘new girl’ chimps form stronger female bonds

Low-ranking ‘new girl’ chimpanzees seek out other gal pals with similar status, finds a new study. The results are based on 38 years’ worth of daily records for 53 adult females in Gombe National Park, Tanzania, where Jane Goodall first started studying chimpanzees in the 1960s. The researchers are still working out whether the low-ranking pairs are true buddies, friends of convenience, or merely acquaintances.

Unlike most primates, female chimps are loners compared to males. “They spend about half their time alone or with dependent kids,” said Duke University research scientist Steffen Foerster, who co-authored the study. “Chimpanzee females’ more solitary existence isn’t that surprising given their dispersal patterns,” said Duke evolutionary anthropology professor Anne Pusey. Male chimpanzees stay with the group they were born into their entire lives, forging strong social bonds with other males. Many females, on the other hand, leave their families behind and strike out on their own to join new groups.

Despite their reputation for being aloof, recent studies suggest that some pairs of female chimps hang out together more than others. But whether these females actively seek each other out, or merely cross paths by chance because they haunt the same spots, was unclear. “If two people live close together they might see each other often at the grocery store, for example,” Pusey said. “But the question is, do they also go and have coffee?”

To find out if some females forge stronger bonds than can be explained by chance encounters or range overlap alone, Foerster, Pusey and colleagues analyzed 38 years’ worth of daily records for 53 adult females in Gombe National Park, a 13.5-square-mile park in western Tanzania where Pusey began working with Jane Goodall more than 40 years ago. Over the decades, the females were spotted in more than 600 female-female pairs. For each pair, the researchers measured how much their ranges overlapped, how much time they spent together and how often they groomed each other, a chimp’s way of making friends and cementing social bonds.

Not surprisingly, mothers, daughters and sisters formed the strongest bonds. But among unrelated females — which made up more than 95 percent of the twosomes they studied — low-ranking females were more likely to seek each other out than females from other social ranks. The researchers are still working out whether the low-ranking pairs are true buddies, friends of convenience or merely acquaintances.

“It doesn’t necessarily mean that they like each other,” Foerster said. “The lowest-ranking females are the newest to arrive. When a female migrates into a new group, she starts at the bottom of the social ladder. It may be that they’re not really that into each other, but that they need to tolerate being in the same space,” he said. Or it could be that low-ranking females team up for support against harassment from higher-ranking females. “The resident females don’t make it easy for the new females — they chase them around,” Pusey said. Female bonding also could help offset the disadvantages of low rank by giving subordinate females greater ability to compete for food, or additional pairs of eyes and ears to help spot predators. Females with juvenile sons were also more likely to seek each other out, the researchers found, presumably to give the young males a start on developing the social skills they’ll need to thrive as adults. The study is part of a larger field of research on the importance of social networks for health and survival in primates and other animals, including humans.  Science Daily  Original web page at Science Daily


* Mountain gorillas stuck in genetic bottleneck

Kaboko, a mountain gorilla, had a rough start in life: in 2007, the three-year-old orphan was caught in a poacher’s snare in the Democratic Republic of the Congo. Rescuers, who were forced to amputate his hand to treat his injuries, gave him a name that means “one missing an arm” in a local language. Kaboko died in 2012, but his DNA lives on. Researchers have used genetic information from him and six other animals to construct the first complete genomic sequence for the mountain gorilla (Gorilla beringei beringei), which they report in Science along with the genome of the closely related eastern lowland gorilla (Gorilla beringei graueri). The data may help conservationists to improve the plight of the critically endangered mountain gorilla, which is found only in Central Africa. The genomes reveal that the genetic diversity of both subspecies has been declining for 100,000 years. That is surprising, says Ajit Varki, a molecular biologist at the University of California, San Diego. “You have animals that have no predators and easy sources of food — in a way they have everything going for them — and yet they have been heavily pressured,” he says. Some of that pressure is probably attributable to natural changes in the extent of Central Africa’s forests, and some to the emergence of humans, but Varki says the relative balance of these factors in the distant past is hard to determine.

The more recent impact of humans is clear. Heavy hunting caused the gorilla population to drop to fewer than 300 animals by the 1970s. The number has since risen to more than 800, thanks to conservation efforts promoted by primate researchers such as Dian Fossey. Still, the latest study reveals that genetic diversity of eastern gorillas remains low. The paired chromosomes of an individual mountain gorilla typically have the same DNA sequence for 34.5% of their length. The figure in eastern lowland gorillas is even higher, at 38.4%. Both subspecies have much lower genetic diversity than the western gorilla (Gorilla gorilla, 13.8% shared sequence) and even the children of human parents who are first cousins (11%). The gorilla is not the first non-human primate to have its complete genome sequenced — that was the chimpanzee (Pan troglodytes), in 2005. But mountain gorillas were among the most difficult primates to study. Unlike other great apes, no mountain gorillas live in captivity. In the wild, the animals are found in only two places: the Virunga Volcano Massif and the Bwindi Impenetrable Forest, two habitats some 30 kilometres apart that straddle the Democratic Republic of the Congo, Rwanda and Uganda.

Researchers spent six years waiting for permission to study mountain-gorilla blood samples collected by the charity Gorilla Doctors, which treats injured wild gorillas. The delay was caused by the strict paperwork required by the Convention on International Trade in Endangered Species of Wild Fauna and Flora, a treaty that governs the flow of such materials. But that long wait did have some benefits. “Technology and our knowledge of genomics were getting better during all that time,” says Peter Sudmant, a geneticist at the University of Washington in Seattle and a co-author of the study. As a result, the mountain-gorilla genome is of higher quality than previously published genomes of other gorilla subspecies. A complete mountain-gorilla genome will help conservationists to determine the degree to which genetic bottlenecks have increased the animals’ susceptibility to disease and reduced their ability to cope with environmental change. “On top of there being so few, these gorillas breed very slowly, and the population grows just about 1% a year,” says Damien Caillaud, a research scientist at the Dian Fossey Gorilla Fund International, a conservation group in Atlanta, Georgia. “That means if we’re not careful, the numbers could very easily go the other way.”

Nature doi:10.1038/nature.2015.17277  Nature   Original web page at Nature


Critically endangered monkey photographed in Congo’s newest national park, Ntokou-Pikounda

Two primatologists working in the forests of the Republic of Congo have returned from the field with a noteworthy prize: the first-ever photograph of the Bouvier’s red colobus monkey, a rare primate not seen for more than half a century and suspected to be extinct by some, according to WCS (the Wildlife Conservation Society). The elusive primate was recently photographed by independent researchers Lieven Devreese and Gaël Elie Gnondo Gobolo within Ntokou-Pikounda National Park, a 4,572-square-kilometer (1,765-square-mile) protected area created on advice from WCS in 2013 to safeguard gorillas, chimpanzees, elephants, and other species.

The field researchers set off in February 2015 to try to photograph Bouvier’s red colobus and establish the present distribution of this unique primate species in the Republic of Congo. Guided by local people familiar with red colobus vocalizations and behavior, the team found a group of red colobus in the swamp forests along the Bokiba River in the Ntokou-Pikounda National Park. “Our photos are the world’s first and confirm that the species is not extinct,” Devreese said. WCS helped in the search for Bouvier’s red colobus with logistical support and provided the unpublished survey records of red colobus monkeys in Northern Congo. “We’re very pleased indeed that Lieven and Gaël were able to achieve their objective of not only confirming that Bouvier’s red colobus still exists, but also managing to get a very clear close-up picture of a mother and infant,” said WCS’s Dr. Fiona Maisels. “Thankfully, many of these colobus monkeys live in the recently gazetted national park and are protected from threats such as logging, agriculture, and roads, all of which can lead to increased hunting.”

Bouvier’s red colobus (Piliocolobus bouvieri) is a species of monkey endemic to the Republic of Congo, about which virtually nothing is known. It has been considered a subspecies of a larger colobus taxonomic group in the past, but the most recent treatment lists it as a full species. The species was first described in 1887 and is only known from a couple of museum specimens collected from three localities over 100 years ago. The authors of a book written in 1949 mention that the species occurs in the swamp forests between the lower Likouala and Sangha Rivers, as well as along the Alima River farther to the south. The last unverified sightings of Bouvier’s red colobus monkey occurred in the 1970s. Recent surveys by WCS had previously recorded red colobus in what is now Ntokou-Pikounda National Park in 2007 and 2014, but they were very rarely encountered and no photograph had been taken. The new sighting and photograph confirm the presence of this threatened primate in Northern Congo. However, red colobus monkeys (there are several species) typically do not flee from humans but look down at them from the trees, an unfortunate behavioral characteristic that has led to them becoming very rare wherever hunters are active. They are highly threatened by the growing demand for bushmeat in the region, a trade that also threatens larger primates such as gorillas and chimpanzees. James Deutsch, Vice President for Conservation Strategy at WCS, commented: “Confirmation that Bouvier’s red colobus still thrives in the this area reminds us that there remain substantially intact wild places on Earth, and should re-energize all of us to save them before it is too late.”  Science Daily  Original web page at Science Daily


Female chimps more inclined to use tools when hunting

It was a discovery that changed what researchers knew about the hunting techniques of chimpanzees. In 2007, Jill Pruetz first reported savanna chimps at her research site in Fongoli, Senegal, were using tools to hunt prey. That alone was significant, but what also stood out to Pruetz was the fact that female chimps were the ones predominantly hunting with tools. It was a point some dismissed or criticized because of the small sample size, but the finding motivated the Iowa State University anthropology professor to learn more. In the years following, Pruetz and her research team have documented more than 300 tool-assisted hunts. Their results, published in the journal Royal Society Open Science, support the initial findings — female chimps hunt with tools more than males.

Generally, adult male chimps are the main hunters and capture prey by hand. Researchers observed both male and female chimps using tools, but more than half of the hunts — 175 compared to 130 — were by females. While males made up about 60 percent of the hunting group, only around 40 percent of the hunts were by males. “It’s just another example of diversity in chimp behavior that we keep finding the longer we study wild chimps,” Pruetz said. “It is more the exception than the rule that you’ll find some sort of different behavior, even though we’ve studied chimps extensively.” Both male and female chimps primarily pursued galagos, or bush babies, in tool-assisted hunts. Pruetz says the chimps used a spear-like tool to jab at the animal hiding in tree cavities. She added that one explanation for the sex difference in tool use is that male chimps tended to be more opportunistic. “What would often happen is the male would be in the vicinity of another chimp hunting with a tool, often a female, and the bush baby was able to escape the female and the male grabbed the bush baby as it fled,” Pruetz said.

The savanna chimps at Fongoli are the only non-human population to consistently hunt prey with tools. Why is that the case? Pruetz, Walvoord Professor of Liberal Arts & Sciences at Iowa State, says a better question may be why are chimps at other sites not using this technique? It may be that they never learned the technique, she said. Tool hunting also may be a result of social tolerance that doesn’t exist at other chimp sites. “At Fongoli, when a female or low-ranking male captures something, they’re allowed to keep it and eat it. At other sites, the alpha male or other dominant male will come along and take the prey. So there’s little benefit of hunting for females, if another chimp is just going to take their prey item.” The environment is another factor. Pruetz says there are no red colobus monkeys, the preferred prey of chimps at other sites, because of the dry conditions at Fongoli. The bush babies are more prevalent and prey that female chimps can access using tools.

Pruetz, a National Geographic Emerging Explorer, is often asked why the female’s use of tools is considered hunting rather than gathering. It’s a question that reflects stereotypes associated with female chimp behavior. The similarities to termite or ant fishing, which is sometimes used as a comparison for tool-assisted hunting, are superficial, she said. The behavior of the prey and effort required by the hunter is different. Fishing for termites is a very different activity than jabbing for a bush baby,” Pruetz said. “With fishing, termites grab on to a twig and don’t let go and the chimp eats the termites off the twig. When hunting, the bush baby tries to bite, escape or hide from the chimp. The chimps are really averse to being bitten by a bush baby.” While a bush baby is smaller than and not as fierce as a monkey, Pruetz says it is really no different than humans hunting doves instead of deer. Ultimately, the tool-assisted hunting allows female chimps, which may be less likely to run down prey, access to a nutritional food source, Pruetz said.  Science Daily  Original web page at Science Daily


Touch-sensing neurons are multitaskers

Two types of touch information — the feel of an object and the position of an animal’s limb — have long been thought to flow into the brain via different channels and be integrated in sophisticated processing regions. Now, with help from a specially devised mechanical exoskeleton that positioned monkeys’ hands in different postures, Johns Hopkins researchers have challenged that view. In a paper published in the April 22 issue of Neuron, they present evidence that the two types of information are integrated as soon as they reach the brain by sense-processing brain cells once thought to be incapable of such higher-order thought.

Past studies have indicated that the feel of an object against the skin and position information of the hands and fingers were processed separately in the sensory system’s first-line sense processors, and then passed along to more sophisticated brain regions to be integrated. But it was a challenge to reliably differentiate brain activity caused by the two inputs from one another and from the brain’s commands to muscles, says Manuel Gomez-Ramirez, Ph.D., an assistant research scientist at The Johns Hopkins University. To solve that problem, Steven Hsiao, Gomez-Ramirez’s late mentor, and his colleagues developed a machine that positions a monkey’s hand and delivers stimuli to its fingers.

In this experiment, then-graduate student Sung Soo Kim, Ph.D., now a research specialist at the Howard Hughes Medical Institute, trained monkeys to perform an unrelated visual task while their hands were manipulated by the machine, which moved their fingers slightly from side to side and up and down at precise angles. The machine also pressed a plastic bar to the monkeys’ fingertips in different orientations. By monitoring the monkeys’ brains in real time, the research group saw that the position and touch information were conveyed through the same cells in the somatosensory cortex. “This study changes our understanding of how position and touch signals are combined in the brain,” says Gomez-Ramirez. This information could be used in efforts to better integrate prostheses with patients’ brains so that they behave more like natural limbs, he notes. Holding objects and exploring the world with our hands requires integrating many sensory signals in the brain and continuously supplying this information to motor areas so that it can issue the appropriate commands for holding objects,” Gomez-Ramirez says. “Our understanding of how these processes occur is very limited, and Steve Hsiao spent a lot of time thinking about the problem and figuring out how to test it.”  Science Daily  Original web page at Science Daily


* Ebola whole virus vaccine shown effective, safe in primates

The vaccine, described today (March 26, 2015) in the journal Science, was developed by a group led by Yoshihiro Kawaoka, a University of Wisconsin-Madison expert on avian influenza, Ebola and other viruses of medical importance. It differs from other Ebola vaccines because as an inactivated whole virus vaccine, it primes the host immune system with the full complement of Ebola viral proteins and genes, potentially conferring greater protection. “In terms of efficacy, this affords excellent protection,” explains Kawaoka, a professor of pathobiological sciences in the UW-Madison School of Veterinary Medicine and who also holds a faculty appointment at the University of Tokyo. “It is also a very safe vaccine.” The vaccine was constructed on an experimental platform first devised in 2008 by Peter Halfmann, a research scientist in Kawaoka’s lab. The system allows researchers to safely work with the virus thanks to the deletion of a key gene known as VP30, which the Ebola virus uses to make a protein required for it to reproduce in host cells. Ebola virus has only eight genes and, like most viruses, depends on the molecular machinery of host cells to grow and become infectious.

By engineering monkey kidney cells to express the VP30 protein, the virus can be safely studied in the lab and be used as a basis for devising countermeasures like a whole virus vaccine. The vaccine reported by Kawaoka and his colleagues was additionally chemically inactivated using hydrogen peroxide, according to the new Science report. Ebola first emerged in 1976 in Sudan and Zaire. The current outbreak in West Africa has so far claimed more than 10,000 lives. There are no proven treatments or vaccines, although several vaccine platforms have been devised in recent years, four of which recently advanced to the clinical trial stage in humans. The new vaccine reported by Kawaoka has not been tested in people. However, the successful tests in nonhuman primates conducted at the National Institutes of Health (NIH) Rocky Mountain Laboratories, a biosafety level 4 facility in Hamilton, Montana, may prompt further tests and possibly clinical trials of the new vaccine. The work at Rocky Mountain Laboratories was conducted in collaboration with a group led by Heinz Feldmann of NIH. Those studies were conducted with cynomolgus macaques, which are very susceptible to Ebola. “It’s the best model,” Kawaoka says. “If you get protection with this model, it’s working.”  Science Daily  Original web page at Science Daily


Clues to aging from long-lived lemurs

When Jonas the lemur died in January, just five months short of his thirtieth birthday, he was the oldest of his kind. A primate called a fat-tailed dwarf lemur, Jonas belonged to a long-lived clan. Dwarf lemurs live two to three times longer than similar-sized animals. In a new study, Duke University researchers combed through more than 50 years of medical records on hundreds of dwarf lemurs and three other lemur species at the Duke Lemur Center for clues to their exceptional longevity. The conventional wisdom in longevity research is that smaller species live shorter lives than larger ones. For example, humans and whales can live to be over 100; yet the average lab mouse doesn’t live beyond its third birthday. The researchers found an exception to this pattern in a group of hamster-sized lemurs with a physiological quirk — they are able to put their bodies in standby mode.

How long the animals live and how fast they age correlates with the amount of time they spend in a state of suspended animation known as torpor, the data show. Hibernating lemurs live up to ten years longer than their non-hibernating cousins. Dwarf lemurs like Jonas were the most extreme examples in their study, spending up to half the year in deep hibernation in the wild. Dwarf lemurs go into a semi-hibernation state for three months or less in captivity, “but even that seems to confer added longevity,” said study co-author Sarah Zehr, a researcher at the Duke Lemur Center. Hibernating dwarf lemurs can reduce their heart rate from 200 to eight beats per minute. Breathing slows, and the animals’ internal thermostat shuts down. Instead of maintaining a steady body temperature, they warm up and cool down with the outside air. “Everything gets slower,” Zehr said

For most primates such vital statistics would be life-threatening, but for lemurs, they’re a way to conserve energy during times of year when food and water are in short supply. Hibernating lemurs not only live longer, they also stay healthier. While non-hibernators are able to reproduce for roughly six years after they reach maturity, hibernators continue to have kids for up to 14 years after maturity, the researchers found. Although all species they examined suffered from cataracts and other age-related eye diseases as they got older, the hibernators managed to stave off symptoms until much later in life. Some researchers have suggested that hibernators live longer and stay healthier simply because they avoid predators who may be looking for a snack. A lemur is much less likely to be eaten when it is curled up underground or snoozing in a tree. “But the fact that we see the same pattern in captivity, where they’re protected from predators, suggests that other factors are at work,” Zehr said. It may also be that torpor increases longevity by protecting cells against the buildup of oxidative damage that is a normal by-product of breathing and metabolism, said study co-author Marina Blanco. “If your body is not ‘working full time’ metabolically-speaking, you will age more slowly and live longer,” Blanco said. Because lemurs are more closely related to humans than mice are, the research may eventually help scientists identify “anti-aging” genes in humans. Science Daily Original web page at Science Daily


* Baboon friends swap gut germs

Baboons take turns grooming each other to make friends and cement social bonds. A new study finds that baboon friendships influence the microscopic bacteria in their guts. Previous studies have pointed to the food we eat, the drugs we take, genetics, even our house dust. Now, a new study in baboons suggests that relationships may play a role, too. The researchers studied social interactions, eating habits and bacteria in the feces of 48 wild baboons from two groups living near Mount Kilimanjaro in Kenya. Their findings appear in the March 16 issue of the journal eLife. “Poop contains a goldmine of data,” said Duke University biologist Jenny Tung, who co-authored the study. “Ninety-eight percent of the DNA in poop doesn’t come from the animal itself or the foods they eat — it’s bacterial.”

Using powerful sequencing machines to tease out each microbe’s unique genetic signature, the researchers identified the names and relative amounts of nearly 1,000 bacterial species thriving in the baboons’ bowels. The cast of characters includes relatively high levels of Firmicutes, Proteobacteria, Actinobacteria and Bacteroidetes — all of which are also commonly found in human guts. Baboons from the same troop had more similar gut microbes than baboons from different troops. The results are consistent with previous studies in humans showing that people who live together harbor similar gut germs. The connection has largely been attributed to couples and housemates eating many of the same foods in the same relative proportions, but Tung and co-author Elizabeth Archie of the University of Notre Dame and colleagues wondered if additional factors might be at play. To find out, the researchers recorded what the animals ate — a menu of grass seeds and stems, acacia seed pods, fruits and leaves.

They also noted when the baboons in each group hung out in close proximity to each other without physical contact, and measured how often they groomed each other. They found that, in both groups, baboons who groomed each other more often shared more similar sets of gut microbes. How friendly two baboons were to each other was a better predictor of how alike their gut bacterial communities were than whether they merely hung out in the same places, were related, or what they ate.

How fecal bacteria find their way from a baboon’s colon to her fur and from there to another baboon’s gut is unclear, but the researchers have a few ideas. “When baboons groom each other they’re combing through each other’s fur for parasites, dirt, dead skin. Sometimes they pull things off and put them in their mouths,” Archie said. “Males and females also spend a lot of time grooming close to the genital area during estrous,” Tung said. Hugging and cuddling and other forms of physical contact could play a role in allowing people to swap gut germs, too, the researchers say, especially after touching surfaces such as bathroom sinks and toilet handles. “This is another way that social relationships can influence your health,” Archie said. “Not only are relationships important for the transmission of harmful bacteria like the ones that cause pneumonia or strep throat, but they’re important for the transmission of microbes that are harmless or potentially good for you, too.”  Science Daily  Original web page at Science Daily


Gorilla origins of the last two AIDS virus lineages confirmed

Two of the four known groups of human AIDS viruses (HIV-1 groups O and P) have originated in western lowland gorillas, according to an international team of scientists from the Perelman School of Medicine at the University of Pennsylvania, the Institut de Recherche pour le Developpement, the University of Edinburgh, and others. The scientists led by Dr. Martine Peeters from the University of Montpellier conducted a comprehensive survey of simian immunodeficiency virus (SIV) infection in African gorillas. Beatrice Hahn, MD, a professor of Medicine and Microbiology, and others from Penn were part of the team, whose findings appear online this week in the Proceedings of the National Academy of Sciences. HIV-1, the virus that causes AIDS, has jumped species to infect humans on at least four separate occasions, generating four HIV-1 lineages — groups M, N, O, and P.

Previous research from this team found that groups M and N originated in geographically distinct chimpanzee communities in southern Cameroon, but the origins of groups O and P remained uncertain. The four cross-species transmissions have had very different outcomes in humans. Group M gave rise to the AIDS pandemic, infecting more than 40 million people worldwide by spreading across Africa and throughout the rest of the world. Groups N and P, at the other extreme, have only been found in a few individuals from Cameroon. However, group O, although not as widespread and prevalent as group M, has nonetheless infected about 100,000 people in west central Africa.

The team screened fecal samples from western lowland gorillas, eastern lowland gorillas, and mountain gorillas in Cameroon, Gabon, the Democratic Republic of Congo, and Uganda for evidence of SIVgor infection. They identified four field sites in southern Cameroon where western lowland gorillas harbor SIVgor. “Viral sequencing revealed a high degree of genetic diversity among the different gorilla samples,” explains Hahn. “Two of the gorilla virus lineages were particularly closely related to HIV-1 groups O and P. This told us that these two groups originated in western lowland gorillas.” “Understanding emerging disease origins is critical to gauge future human infection risks,” adds Dr. Peeters. “From this study and others that our team has conducted in the past it has become clear that both chimpanzees and gorillas harbor viruses that are capable of crossing the species barrier to humans and have the potential of cause major disease outbreaks.  Science Daily  Original web page at Science Daily