Tag: Laboratory Animal Science

Mice are one of the most commonly used laboratory organisms, widely used to study everything from autism to infectious diseases. Yet genomic studies in mice have lagged behind those in humans.

“Genome-wide association studies — matching genes to diseases and other traits — have been a big deal in human genetics for the past decade,” said Abraham Palmer, PhD, professor of psychiatry at University of California San Diego School of Medicine. “But progress hasn’t been so great in animal genetics. That’s because researchers have mostly been using crosses between inbred strains, making it impossible to pinpoint specific genomic regions or individual genes associated with a trait. In addition, we didn’t previously have good ways of genotyping animals in a cost-efficient way.”

Now, in a study published July 4, 2016 in Nature Genetics, Palmer’s team used 1,200 outbred mice, which are more similar to a natural population, to test a new cost-effective technique to search for specific genes linked with 66 different physical and behavioral traits.

“This is a system that could be used to discover genes associated with any complex trait a researcher is interested in, in any animal model,” Palmer said. “We can look at any trait and rapidly develop hypotheses about specific genes. It’s like genome-wide association studies in humans, but less expensive. And we can look at certain traits that we can’t in humans.”

Previously, only large regions of a chromosome could be associated with a particular mouse trait or behavior. Palmer’s method takes advantage of the superior mixing that is present in an outbred population to help drill down to specific genes using two steps: genotype-by-sequencing, which sequences about one percent of the mouse genome; and RNA sequencing, which identifies only genes turned “on” in a particular tissue, such as the brain.

With this approach, the researchers found numerous associations between genes and the traits they are associated with. For example, they report that the mouse gene Azi2 is associated with the effects methamphetamines have on body movements, and that mouse gene Zmynd11 is associated with anxiety-like behavior. The findings may be clinically relevant, as humans have analogous genes, Palmer said.

Next, the team will engineer mice that specifically lack these genes to determine if the associations are truly causal and to better understand the underlying mechanisms.

“This study has been extremely gratifying since this is the first time these two genes have been identified as playing roles in psychological conditions,” Palmer said. “And now we can think about targeting these genes or the proteins they encode with novel therapeutics.”

https://www.sciencedaily.com/ Science Daily

https://www.sciencedaily.com/releases/2016/07/160704145736.htm  Original web page at Science Daily

Australian bill provokes rush of protests ahead of parliamentary deadline.

Nicholas Price works to understand the brain’s fundamental functions, with a view towards developing a bionic eye. The neuroscientist uses marmosets and macaques in his experiments at Monash University’s Biomedicine Discovery Institute in Melbourne. In late January, he was shocked to discover a bill before the Australian Parliament that calls for a ban on the import of non-human primates for medical research.

Australia’s three main breeding colonies of research primates consist of several hundred macaques, marmosets and baboons. Regular imports of the animals are vital to maintain the genetic diversity of these colonies, says Price.

Senator Lee Rhiannon, a member of the Greens party, introduced the bill on 17 September last year as an amendment to Australia’s federal Environment Protection and Biodiversity Conservation Act. But because the Senate committee that deals with this piece of legislation is not usually of interest to those in the medical research community, the amendment almost slipped under the community’s radar, says Price. By the time he heard about the proposed ban, from another researcher, the window for public comment was days away from closing, though it was later extended.

As soon as they found out, Price and his Monash colleagues James Bourne and Marcello Rosa began e-mailing researchers around the world. Several institutions rushed to submit statements opposing the bill, including the Federation of European Neuroscience Societies (FENS), the Society for Neuroscience, headquartered in Washington DC, and the Basel Declaration Society, which promotes the open, transparent and ethical use of animals in research. Australia’s National Health and Medical Research Council and the Australasian Neuroscience Society also sent statements of opposition to the Senate committee.

Animal research, including that on non-human primates, “continues to be the basis for medical advances that have extended our life expectancy”, says the FENS statement, submitted on 4 February. The Society for Neuroscience’s statement, dated the same day, says that the proposed legislation would lead to “the loss of critical research resources that will be devastating for Australian science”. The committee is now in the process of considering the bill, and will report on it on 1 March, as a prelude to an eventual Senate vote.

Rhiannon, who trained as a zoologist, told Nature that the Greens are not calling for a ban on non-human primates being used in research. “There’s certainly a live debate but it’s not the party position,” she says. She calls the bill a “modest” way to improve the welfare of research animals, and, when she launched the bill last year, spoke at length about the “the cruelty during their capture, confinement and transportation”.

Price and Bourne say that cutting off access to the genetic diversity required to maintain the monkey colonies would eventually spell the end of Australian research on non-human primates. “After a while you’ll get genetic inbreeding,” says Price, “and that can lead to exacerbation of health problems that you may not be able to see until you’re a few generations down the track.” He regards non-human primate research as one of the country’s major sources of scientific innovation.

In introducing the bill, Rhiannon also said that it would ensure that Australia “does not participate in the unethical trade of wild-caught primates for use in experimentation for the research industry”. But Australian regulations already prohibit the use of wild-caught primates in medical research, says Bourne, who is chairman of the National Non-human Primate Breeding and Research Facility Board. “They have to be certified from a registered and accredited breeding facility in another country.”

Rhiannon introduced a similar bill in 2012 that never made it to a Senate vote before Parliament was dissolved ahead of a federal election. The latest bill may face a similar challenge with an election required by January 2017 at the latest. But Rhiannon says that even if it doesn’t get passed into legislation anytime soon, the bill is a way to highlight that there is a problem with the use of non-human primates, without going so far as to call for banning such research entirely.

Price says that the events have convinced him of a need to be more public about the importance of his work. “If we can demonstrate the value and outcomes, especially in medical research, then we feel that the majority of the public would be very supportive.”

Nature doi:10.1038/nature.2016.19419

http://www.nature.com/news/index.html  Nature

http://www.nature.com/news/proposal-to-ban-imported-monkeys-catches-scientists-off-guard-1.19419  Original web page at Nature

Mice are sensitive to minor changes in food, bedding and light exposure.

It’s no secret that therapies that look promising in mice rarely work in people. But too often, experimental treatments that succeed in one mouse population do not even work in other mice, suggesting that many rodent studies may be flawed from the start.

“We say mice are simpler, but I think the problem is deeper than that,” says Caroline Zeiss, a veterinary neuropathologist at Yale University in New Haven, Connecticut. Researchers rarely report on subtle environmental factors such as their mice’s food, bedding or exposure to light; as a result, conditions vary widely across labs despite an enormous body of research showing that these factors can significantly affect the animals’ biology.

“It’s sort of surprising how many people are surprised by the extent of the variation” between mice that receive different care, says Cory Brayton, a pathologist at Johns Hopkins University in Baltimore, Maryland. At a meeting on mouse models at the Wellcome Genome Campus in Hinxton, UK, on 9–11 February, she and others explored the many biological factors that prevent mouse studies from being reproduced.

Christopher Colwell, a neuroscientist at the University of California, Los Angeles, has first-hand experience with these issues. He and a colleague studied autism in the same genetically modified mouse line, but obtained different results on the same behaviour tests. Eventually they worked out why: Colwell, who studies circadian rhythms, keeps his mice dark in the daytime to trick their body clocks into thinking day is night, so that the nocturnal animals are more alert when tested during the day. His colleague does not.

Colwell notes that disregarding mouse circadian rhythms could bias many behaviour experiments. Most humans would not perform well on social and cognitive tests either if made to do them in the middle of the night, he adds.

Nutrition can also determine whether a mouse study succeeds or fails, yet Brayton says that many researchers cannot even say where their animals’ feed comes from. Some mouse foods contain oestrogens and endocrine-disrupting chemicals that can affect research on cancer, among other diseases. And the high-fat, high-sugar food used in obesity studies goes rancid quickly; when it does, mice may stop eating and lose weight without researchers realizing why.

Food choices can also alter a mouse’s gut microbiome. Catherine Hagan Gillespie, a veterinary pathologist at the Jackson Laboratory in Sacramento, California, has found that species of bacteria in the gut vary widely between mice from different vendors. In another, unpublished, study, she found that mice with different assortments of gut bacteria showed different anxiety levels in behavioural tests.

But few behavioural scientists think about running microbiology assessments, says Hagan Gillespie. Even when they do, the extra work involved can increase the complexity and cost of the study. Yet the mouse microbiome is sensitive to a wide array of factors, such as air quality, maternal stress and immune function.

Differences in the gut microbiome may explain why mice with the same genetic mutation can have different characteristics, or phenotypes, says George Weinstock, associate director for microbial genomics at the Jackson Lab’s site in Farmington, Connecticut. Jackson Lab, which breeds and supplies mice for use in studies around the world, tightly controls factors such as the type and quantity of food and the pH of water that animals receive. Even so, it finds differences between the mice at its three sites. Weinstock says that the company has begun researching ways to standardize its customers’ experiments by providing special food and care instructions for the mice that it provides.

But even when improved mice and food are available, some researchers resist using them out of concern that it will affect their results, says Graham Tobin, former technical director of the mouse-diet vendor Teklad in Alconbury, UK. Yet he argues that standardizing results across labs is worth this inconvenience to individual scientists. Tobin also notes that researchers rarely resist adopting other new technologies — such as improved DNA sequencers — that can throw older data into question.

Zeiss says that the competitive nature of science might increase researchers’ resistance to changing how they consider animals in research design. If scientists have to treat their animals at the right point in the experiment, analyse both clinical and biomarker changes, include old mice and both sexes to ensure that results are representative of broad populations, and control environmental variables, each experiment will take much longer and they’re probably not going to be able to publish as much, she says.

The US National Institutes of Health (NIH) has taken steps to address some of these problems. Some of its institutes require certain animal trials to be replicated before a therapy can move into clinical trials, but the NIH says that it has no plans to require this agency-wide. And in 2014, the NIH began requiring researchers to include female animals in studies, and started to give out supplementary grants to researchers who complained about the cost. But the agency has not issued any specific grants or supplements to study other confounding factors.

That is disappointing to those who would like to see researchers control — or at least report — factors such as the strain of mice used and the type of environment they are raised in. This would allow researchers to perform metanalyses of published literature that could identify any confounding factors. “The information and the wisdom is out there,” says Zeiss, “but studies get funded without necessarily a lot of attention to that.”

Nature doi:10.1038/nature.2016.19335

http://www.nature.com/news/index.html  Nature

http://www.nature.com/news/a-mouse-s-house-may-ruin-experiments-1.19335  Original web page at Nature

A running joke among health researchers is that everything has been cured — in mice. However that may not be always true. The failure of experimental drugs that had once looked promising could have been prevented with better animal studies, according to a re-examination of past clinical trials. “I hear too many stories about patients who have used their one shot at getting into a trial on a drug that didn’t have enough legs to begin with, and that’s a tragedy,” says Steve Perrin, an amyotrophic lateral sclerosis (ALS) researcher who led the work. Perrin, chief scientific officer of the ALS Therapy Development Institute in Cambridge, Massachusetts, used mice with symptoms similar to ALS to test more than 100 compounds that had previously been identified as candidate drugs. Most — including eight that had shown promise in previous mouse work but ultimately failed in humans trials — failed to slow the progressive, fatal degenerative disease, also called Lou Gehrig’s disease or motor neuron disease. Perrin argues that positive results seen in previous mouse trials were spurious, probably resulting from poorly conducted studies. In a Comment published today in Nature, he is urging researchers to boost the quality of animal studies by better characterizing and understanding how mouse models correspond to human disease, minimizing result-muddling variation between animals, and using statistical models to guide study design. “The recommendations could have a profound positive impact on translational research, strongly improving the quality of preclinical studies,” says Adriano Chiò, a neurologist at the University of Turin in Italy. Perrin found that one type of mouse model for ALS, in which animals express a mutant version of the protein TDP43, differs in key ways from the human disease. For example, TDP43 mice usually died of bowel obstructions, whereas humans with the disease tend to succumb to muscle wasting, which often results in the inability to breathe. He further found that although the first generation of TDP43 mice had been reported to die within 200 days, later generations bred from those originals lived for up to 400 days without signs of disease.

Other researchers have highlighted problems with reproducibility of animal studies in cancer. Neurobiologist Caterina Bendotti of the Mario Negri Institute for Pharmacological Research in Milan, Italy, agrees that the issues Perrin describes are not unique to his field: “The poor reproducibility of preclinical results, particularly in animal models, goes beyond ALS,” she says. Irreproducible preclinical results can lead to a massive waste of time and money in clinical trials. Chiò points to the example of a 2008 study in mice and 44 humans with ALS, which suggested that therapeutic lithium might slow the disease. The metal is already used as a drug to treat mental disorders including schizophrenia, so it is available cheaply, and people with ALS began administering it to themselves. Perrin’s and Bendotti’s groups both tried to replicate the original results, and found that they could not — but not before clinical trials began to test the effect. Ultimately, five trials involving more than 1,000 people with ALS in five countries found no benefit, Chiò says, and the initial mouse results were never duplicated. Untreated animals in the original study survived for 20 days less than those in other mouse studies, suggesting that there may have been some anomaly with these animals. “It is our stringent responsibility to avoid a new lithium saga, and Perrin’s recommendations go exactly in this direction,” Chiò says. Other researchers say they agree broadly with Perrin, but that they would also like to see the data from his group’s experiments, and that it may not be necessary to find a positive animal result to progress to a human trial. “Many ALS researchers would say that if there is other preclinical evidence that a drug might work, it may be sufficient to go into human trials,” says neurologist Leonard van den Berg, director of the NetherlandsALSCenter at University Medical Center Utrecht. But work to discover how relevant animal models are to human disease — such as Perrin’s studies on TDP43 mice — is expensive and unrewarding for researchers and their teams. Perrin argues that they must be funded specifically, perhaps by private–public collaborations. “Somebody has to do this, or else we’re wasting precious resources,” says Perrin.

Nature doi:10.1038/nature.2014.14938

http://www.nature.com/news/index.html Nature

April 15, 2014

http://www.nature.com/news/misleading-mouse-studies-waste-medical-resources-1.14938  Original web page at Nature

Although muscle cells did not reduce in size or number in mice lacking a protective antioxidant protein, they were weaker than normal muscle cells, researchers from the Barshop Institute for Longevity and Aging Studies at The University of Texas Health Science Center San Antonio found. The scientists, who are faculty in the university’s School of Medicine, are studying how oxidative stress in cells impacts sarcopenia — a loss of muscle mass and strength that occurs in all humans as they age. The antioxidant protein is called SOD1. The researchers developed mice that did not have SOD1 in their muscles, though it was still present in other types of cells. Then they asked the question: Is lack of SOD1 at the muscle enough to cause atrophy? Surprisingly, the total muscle mass in this mouse was larger. “We think that lack of SOD1 could be priming the muscle to use all of its survival skills,” said Holly Van Remmen, Ph.D., professor of cellular and structural biology in the School of Medicine and associate director for basic research at the Barshop Institute. “The muscle knows things aren’t quite right. Its rescue mechanisms are pulled into play.” But even though the muscles were not atrophied, they were still weak.

Sarcopenia in people has two components: loss of muscle mass and loss of function (weakness). This study supports the idea that oxidative stress has a role in these detrimental effects. If a way can be found to curb the effects, then healthier, more productive aging could result, Dr. Van Remmen said. The oxidative stress theory of aging holds that oxidation from molecules called “free radicals” causes damage to cells over time, resulting in sarcopenia and other decline. The study is described in The FASEB Journal. Future research will assess whether limiting oxidative stress can effect muscle regeneration, Dr. Van Remmen said.

Science Daily
September 3, 2013

Original web page at Science Daily