Get latest biomedical research news compilation here

Monday, February 1, 2016

CRISPR Editing of Human Embryos Approved in the U.K.

Preserving the distinction between research purposes and clinical applications, the Human Fertilisation and Embryology Authority (HFEA), a U.K. regulatory body, has approved the use of CRISPR gene editing on human embryos. The HFEA indicated that its approval was specific to an application tendered by researchers at the Francis Crick Institute, who could begin their work “within the next few months,” provided they also secure the approval of a local ethics body.

The Crick’s research, which will be led by Kathy Niakan, Ph.D., is aimed at understanding the genes human embryos need to develop successfully. Details of the prop
osed work appeared in September 2015, when the Crick researchers submitted their application to the HFEA.

"To provide further fundamental insights into early human development, we are proposing to test the function of genes using gene editing and transfection approaches that are currently permitted under the HFE Act 2008,” said Dr. Niakan at the time. “We also propose to use new methods based on CRIPSR/Cas9, which allows very specific alterations to be made to the genome. By applying more precise and efficient methods in our research we hope to require fewer embryos and be more successful than the other methods currently used.”

In response to the current announcement, Paul Nurse, Ph.D., director of the Crick, noted that Dr. Niakan's proposed research is “important for understanding how a healthy human embryo develops. It will enhance our understanding of IVF success rates,” he continued, “by looking at the very earliest stage of human development—one to seven days." During this stage of development, a single cell gives rise to around 250 cells. In the Crick’s investigations, development will be stopped at this point and the embryos destroyed.

In line with HFEA regulations, any donated embryos will be used for research purposes only and cannot be used in treatment. These embryos will be donated by patients who have given their informed consent to the donation of embryos that are surplus to their IVF treatment.

The current announcement follows HFEA deliberations that were detailed in the minutes of a meeting that took place on January 14. The minutes indicate the kinds of questions that were raised by proposed use of the CRISPR/Cas9 technique:

“One of the peer reviewers had suggested using alternative techniques for gene disruption, such as gene expression knock-down using RNA interference (shRNA), instead of CRISPR/Cas9,” the minutes read. “However the Committee was satisfied that CRISPR/Cas9 had, in other studies, produced results suggesting that it was a highly efficient and targeted method of gene disruption, potentially superior to other techniques that were available.”

The minutes also described the aims of the Crick’s research:

Determine the relationship between the cellular and molecular properties of human preimplantation embryos and human embryonic stem cell lines.
Establish defined, animal product–free conditions for the derivation of pluripotent human embryonic stem cell lines, ultimately leading to Good Manufacturing Practice–compatible approaches.
Establish and characterize human extraembryonic stem cell lines.
It is with respect to the first aim that the CRISPR technique is most directly relevant. This technique, the researchers say, will allow functionally testing of the requirement of human-specific genes during embryonic development.

“Our recently published RNA sequencing data demonstrate several genes and signaling pathways that are specifically expressed during human embryo development, compared with mouse,” the researchers indicated. “Many of our candidate regulatory genes are also expressed in [human embryonic stem cell (hESC)] lines. Therefore, gene-editing approaches will be optimized in hESC lines, prior to experiments using embryos. However, while we showed that hESC have a related gene expression state to the epiblast in the embryo, they are far from identical, which means that ultimately, we need to test the function of genes directly in the human embryo to determine if they are necessary for development.”

Initially, the Crick’s research will focus on the Oct4 regulatory factor, deficiencies of which are associated with the inability to generate embryonic stem cells in mice. According to the Crick team, there is evidence of temporal distinctions in the expression dynamics of OCT4/Oct4 between humans and mice. “It is therefore important to functionally test the requirement of factors such as OCT4 in human embryogenesis, to directly test conserved versus specific roles compared to the mouse,” say the researchers. “As OCT4 is likely to play a role, this gene will also serve as a first proof of concept.”

Following OCT4, the researchers will focus on human-specific epiblast enriched genes, such as KLF17, which the Crick team we recently identified. The Crick team also looks forward to investigating several human-specific factor, whose expression is absent in any of the pluripotent stem cell lines established to date, such as ARGFX.


Sunday, October 25, 2015

Neuroscientists decode the brain activity of the worm

Head of a roundworm whose nerve cells have been genetically modified to glow under the microscope.
Credit: Image courtesy of Research Institute of Molecular Pathology

Manuel Zimmer and his team at the Research Institute of Molecular Pathology (IMP) present new findings on the brain activity of the roundworm Caenorhabditis elegans. The scientists were able to show that brain cells (neurons), organized in a brain-wide network, albeit exerting different functions, coordinate with each other in a collective manner. They could also directly link these coordinated activities in the worm's brain to the processes that generate behavior. The results of the study are presented in the current issue of the journal Cell.

One of the major goals of neuroscience is to unravel how the brain functions in its entirety and how it generates behavior. The biggest challenge in solving this puzzle is represented by the sheer complexity of nervous systems. A mouse brain, for example, consists of millions of neurons linked to each other in a highly complex manner. In contrast to that, the nematode Caenorhabditis elegans is equipped with a nervous system comprised of only 302 neurons. Due to its easy handling and its developmental properties, this tiny, transparent worm has become one of the most important model organisms for basic research. For almost 30 years, the list of connections between individual neurons has been known. Despite the low number of neurons, its neuronal networks possesse a high degree of complexity and sophisticated behavioral output; the worm thus represents an animal of choice to study brain function.

Interplay of neuronal groups in brain-wide networks

Researchers have mostly concentrated on studying the functions of single or a handful of neural cells and some of their interactions to explain behavior such as movements. For the worm, it has been known how some single neurons function as isolated units within the network, but it remained unknown how they work together as a group. Manuel Zimmer, a group leader at the IMP, wanted to address this unsolved question in his research. Together with his team, he combined two state-of-the-art technologies for the current study: first, the scientists used 3D microscopy techniques to simultaneously and rapidly measure different regions of the brain; second, they used worms genetically engineered with a fluorescent protein that caused the worm's neurons to flash when they were active. "This combination was brilliant for us, as it allowed a brain-wide single-cell resolution of our recordings in real time," Zimmer explains the advantages of this approach.

Reading the worm's mind

Zimmer and his team tested the animals' reaction to stimuli from outside when they were trying to find food. Under the microscope, a fascinating picture was revealed to the researchers: "We saw that most of the neurons are constantly active and coordinate with each other in a brain-wide manner. They act as an ensemble," explains postdoctoral scientist Saul Kato, who spearheaded the study together with Harris Kaplan and Tina Schrödel, graduate students in the Zimmer laboratory. The animals were immobilized for these experiments, their reactions therefore representing intentions as opposed to reflecting actual movement.

With a different technique of microscopy, set up for freely moving worms, the scientists were able to detect the neurons that initiate movement. There was a direct correlation between the activity of certain networks and the impulse for movements; thus Zimmer and his co-workers could literally watch the worms think. These network activities not only represented short movements, but also their assembly into longer lasting behavioral strategies such as foraging. "This is something that no one has managed to do before," Zimmer points out. Suggestions of similar patterns of neural activity have been found in higher animals, but so far only a fraction of neurons in sub-regions of the brain could be examined at the same time. Zimmer and his colleagues are therefore confident that their results represent basic principles of brain function, even though the worm is only distantly related to mammals.

Investigation of molecular mechanisms

Many questions in the area of neurobiology remain largely unsolved, such as how decisions are made or whether the brain operates in a formal algorithmic manner, like a computer. In the next phase of research, Manuel Zimmer intends to analyze the molecular mechanisms underlying the processes he investigated. "It would also be interesting to have a closer look at long lasting brain states such as sleep and waking," he says, laying out his ambitious plans for the future.

Research Institute of Molecular Pathology. | Sciencedirect

Kato et al. Global Brain Dynamics Embed the Motor Command Sequence of Caenorhabditis elegans. Cell, October 2015 DOI: 10.1016/j.cell.2015.09.034

Deep-sea bacteria could help neutralize greenhouse gas!!

Deep-sea bacteria could help neutralize greenhouse gas.
Credit: Image courtesy of University of Florida

A type of bacteria plucked from the bottom of the ocean could be put to work neutralizing large amounts of industrial carbon dioxide in the Earth’s atmosphere, a group of University of Florida researchers has found.

Carbon dioxide, a major contributor to the buildup of atmospheric greenhouse gases, can be captured and neutralized in a process known as sequestration. Most atmospheric carbon dioxide is produced from fossil fuel combustion, a waste known as flue gas. But converting the carbon dioxide into a harmless compound requires a durable, heat-tolerant enzyme. That’s where the bacterium studied by UF Health researchers comes into play. The bacterium -- Thiomicrospira crunogena -- produces carbonic anhydrase, an enzyme that helps remove carbon dioxide in organisms.

So what makes the deep-sea bacterium so attractive? It lives near hydrothermal vents, so the enzyme it produces is accustomed to high temperatures. That’s exactly what’s needed for the enzyme to work during the process of reducing industrial carbon dioxide, said Robert McKenna, Ph.D., a professor of biochemistry and molecular biology in the UF College of Medicine, a part of UF Health.

“This little critter has evolved to deal with those extreme temperature and pressure problems. It has already adapted to some of the conditions it would face in an industrial setting,” he said.
The findings by the McKenna group, which included graduate research assistants Brian Mahon and Avni Bhatt, were published recently in the journals Acta Crystallographica D: Biological Crystallography and Chemical Engineering Science.

The chemistry of sequestering works this way: The enzyme, carbonic anhydrase, catalyzes a chemical reaction between carbon dioxide and water. The carbon dioxide interacts with the enzyme, converting the greenhouse gas into bicarbonate. The bicarbonate can then be further processed into products such as baking soda and chalk.

In an industrial setting, the UF researchers believe the carbonic anhydrase could be captured this way: The carbonic anhydrase would be immobilized with solvent inside a reactor vessel that serves as a large purification column. Flue gas would be passed through the solvent, with the carbonic anhydrase converting the carbon dioxide into bicarbonate.

Neutralizing industrial quantities of carbon dioxide can require a significant amount of carbonic anhydrase, so McKenna’s group found a way to produce the enzyme without repeatedly harvesting it from the sea floor. The enzyme can be produced in a laboratory using a genetically engineered version of the common E. coli bacteria. So far, the UF Health researchers have produced several milligrams of the carbonic anhydrase, though Bhatt said much larger quantities would be needed to neutralize carbon dioxide on an industrial scale.

That’s just one of the challenges researchers face before the enzyme could be put to use against carbon dioxide in real-world settings. While it has good heat tolerance, the enzyme studied by McKenna’s team isn’t particularly efficient.

“You want it to do the reaction faster and more efficiently,” Bhatt said. “The fact that it has such a high thermal stability makes it a good candidate for further study.”

Ideally, Bhatt said, more research will produce a variant of the enzyme that is both heat-tolerant and fast-acting enough that it can be used in industrial settings. Next, they want to study ways to increase the enzyme’s stability and longevity, which are important issues to be addressed before the enzyme could be put into widespread industrial use.

While carbonic anhydrase’s ability to neutralize carbon dioxide has been widely studied by McKenna and other scientists around the world for some time, finding the best enzyme and putting it to work in an efficient and affordable carbon sequestration system has been challenging. Still, McKenna said he is encouraged by the prospect of discoveries that could ultimately benefit the planet.

“It shows that it’s physically possible to take known enzymes such as carbonic anhydrase and utilize them to pull carbon dioxide out of flue gas,” he said.

The study was funded by grant GM25154 from the National Institutes of Health and grant NSF-MCB-0643713 from the National Science Foundation.

Video description

Source:  University of Florida. | By: Doug Bennett.

Probable Biomarker for Premature Death

This schematic summarizes an investigation of the biology of GlycA, a known biomarker for short-term mortality. They reveal GlycA's long-term behavior in apparently healthy patients: it is stable for >10 years and associated with chronic low-grade inflammation. Accordingly, GlycA predicts death from infection up to 14 years in the future.
Credit: Ritchie et al./Cell Systems 2015

A single blood test could reveal whether an otherwise healthy person is unusually likely to die of pneumonia or sepsis within the next 14 years. Based on an analysis of 10,000 individuals, researchers have identified a molecular byproduct of inflammation, called GlycA, which seems to predict premature death due to infections.

The findings, published October 22 in Cell Systems, suggest that high GlycA levels in the blood indicate a state of chronic inflammation that may arise from low-level chronic infection or an overactive immune response. That inflammation damages the body, which likely renders individuals more susceptible to severe infections.

"As biomedical researchers, we want to help people, and there are few more important things I can think of than identifying apparently healthy individuals who might actually be at increased risk of disease and death," said co-senior author Michael Inouye, of the University of Melbourne, in Australia. "We want to short-circuit that risk, and to do that we need to understand what this blood biomarker of disease risk is actually telling us."

Inouye and his colleagues note that additional studies are needed to uncover the mechanisms involved in GlycA's link to inflammation and premature death, and whether testing for GlycA levels in the clinic might someday be warranted.

"We still have a lot of work ahead to understand if we can modify the risk in some way," said co-senior author Johannes Kettunen, of the University of Oulu and the National Institute for Health and Welfare, in Finland. "I personally would not want to know I was at elevated risk of death or disease due to this marker if there was nothing that could be done about it."

For example, to plan a course of treatment, researchers need to know whether high GlycA is the result of a chronic, low-level microbial infection or an aberrant reaction of the body's own inflammatory response.

The findings will likely form the foundation for numerous other studies that will investigate the role of GlycA in the body. "The more high-quality genomics data we have, linked health records and long-term follow-up, the better our models and predictions will be," Inouye says. "This study is an example of the progress that can be made when altruistic research volunteers, clinicians, technologists, and data scientists work together, but we have the potential to do much more, and large-scale strategic inter-disciplinary initiatives are vitally needed."

Cell Press. | Sciencedirect

Ritchie et al. The biomarker GlycA is associated with chronic inflammation and predicts long-term risk of severe infection. Cell Systems, October 2015 DOI: 10.1016/j.cels.2015.09.007

Saturday, October 24, 2015

Antioxidant use may promote spread of cancer

Picture source:
Metastasis, the process by which cancer cells disseminate from their primary site to other parts of the body, leads to the death of most cancer patients. New research suggests that when antioxidants were administered to lab mice, their cancer spread more quickly than in mice that did not get antioxidants.

A team of scientists at the Children's Research Institute at UT Southwestern (CRI) has made a discovery that suggests cancer cells benefit more from antioxidants than normal cells, raising concerns about the use of dietary antioxidants by patients with cancer. The studies were conducted in specialized mice that had been transplanted with melanoma cells from patients. Prior studies had shown that the metastasis of human melanoma cells in these mice is predictive of their metastasis in patients.

Metastasis, the process by which cancer cells disseminate from their primary site to other parts of the body, leads to the death of most cancer patients. The CRI team found that when antioxidants were administered to the mice, the cancer spread more quickly than in mice that did not get antioxidants. The study was published online today in Nature.

It has long been known that the spread of cancer cells from one part of the body to another is an inefficient process in which the vast majority of cancer cells that enter the blood fail to survive.

"We discovered that metastasizing melanoma cells experience very high levels of oxidative stress, which leads to the death of most metastasizing cells," said Dr. Sean Morrison, CRI Director and Mary McDermott Cook Chair in Pediatric Genetics at UT Southwestern Medical Center. "Administration of antioxidants to the mice allowed more of the metastasizing melanoma cells to survive, increasing metastatic disease burden."

"The idea that antioxidants are good for you has been so strong that there have been clinical trials done in which cancer patients were administered antioxidants," added Dr. Morrison, who is also a CPRIT Scholar in Cancer Research and a Howard Hughes Medical Institute Investigator. "Some of those trials had to be stopped because the patients getting the antioxidants were dying faster. Our data suggest the reason for this: cancer cells benefit more from antioxidants than normal cells do."

Healthy people who do not have cancer may very well benefit from antioxidants that can help reduce damage from highly reactive oxidative molecules generated by normal metabolism. While the study's results have not yet been tested in people, they raise the possibility that cancer should be treated with pro-oxidants and that cancer patients should not supplement their diet with large doses of antioxidants.

"This finding also opens up the possibility that when treating cancer, we should test whether increasing oxidative stress through the use of pro-oxidants would prevent metastasis," said Dr. Morrison. "One potential approach is to target the folate pathway that melanoma cells use to survive oxidative stress, which would increase the level of oxidative stress in the cancer cells."

UT Southwestern Medical Center.

Elena Piskounova, Michalis Agathocleous, Malea M. Murphy, Zeping Hu, Sara E. Huddlestun, Zhiyu Zhao, A. Marilyn Leitch, Timothy M. Johnson, Ralph J. DeBerardinis, Sean J. Morrison. Oxidative stress inhibits distant metastasis by human melanoma cells. Nature, 2015; DOI: 10.1038/nature15726

Deep sea methane metabolizing organism discovered

The production and consumption of methane by microorganisms play a major role in the global carbon cycle. Although these processes can occur in a range of environments, from animal guts to the deep ocean, these metabolisms are confined to the Archaea. Evans et al. used metagenomics to assemble two nearly complete archaeal genomes from deep groundwater methanogens (see the Perspective by Lloyd). The two reconstructed genomes are members of the recently described Bathyarchaeota and not the phylum to which all previously known methane-metabolizing archaea belonged.

Textbooks on methane-metabolising organisms might have to be rewritten after researchers in a University of Queensland-led international project on 23 October announced the discovery of two new organisms.

Deputy Head of UQ's Australian Centre for Ecogenomics in the School of Chemistry and Molecular Biosciences Associate Professor Gene Tyson said these new organisms played an unknown role in greenhouse gas emissions and consumption.

"We sampled the microorganisms in the water from a deep coal seam aquifer 600m below the earth's surface in the Surat Basin, near Roma, Queensland, and reconstructed genomes of organisms able to perform methane metabolism," Associate Professor Tyson said.

"Traditionally, these type of methane-metabolising organisms occur within a single cluster of microorganisms called Euryarchaeota. "This makes us wonder how many other types of methane-metabolising microorganisms are out there?"

Dr Tyson's group discovered novel methane metabolising organisms belonging to a group of microorganisms, called the Bathyarchaeota - an evolutionarily diverse group of microorganisms found in a wide range of environments, including deep-ocean and freshwater sediments.

"To use an analogy, the finding is like knowing about black and brown bears, and then coming across a giant panda," Dr Tyson said.
"They have some basic characteristics in common, but in other ways these they are fundamentally different.
"The significance of the research is that it expands our knowledge of diversity of life on Earth and suggests we are missing other organisms involved in carbon cycling and methane production."
The discovery of the novel methane-metabolising microorganisms was made using techniques that sequence DNA on a large scale and assemble these sequences into genomes using advanced computational tools, many of which were developed at The Australian Centre for Ecogenomics over the past 24 months.
The research, titled Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics, was published in Science.

"Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics." Science 23 October 2015: DOI: 10.1126/science.aac7745

Source: University of Queensland | Phys.

Cellular damage control system helps plants tough it out

Plants Naturally Recycle Chloroplasts

In plants, chloroplasts can accumulate high levels of toxic singlet oxygen, a reactive oxygen species formed during photosynthesis. In these cells, most of the chloroplasts (green organelles) and mitochondria (red organelles) appear healthy. However, the chloroplast in the top left of the image is being selectively degraded and is interacting with the central vacuole (blue). Salk scientists reveal how this strategy to degrade singlet oxygen-damaged chloroplasts may help a cell avoid any further oxidative damage during photosynthesis.
Credit: Salk Institute
As food demands rise to unprecedented levels, farmers are in a race against time to grow plants that can withstand environmental challenges--infestation, climate change and more. Now, new research at the Salk Institute, published in Science on October 23, 2015, reveals details into a fundamental mechanism of how plants manage their energy intake, which could potentially be harnessed to improve yield.

"Plants are unique in that they are stuck wherever they germinate, so they must use a variety of ways to deal with environmental challenges," says Joanne Chory, senior author of the paper and director of Salk's Plant Molecular and Cellular Biology Laboratory. "Understanding the techniques plants use to cope with stress can help us to engineer stronger crops with improved yield to face our growing food shortage."

Plants have cellular organelles akin to tiny solar panels in each leaf. These microscopic structures, called chloroplasts, convert sunlight into chemical energy to enable the plant to grow. The command center of the cell, the nucleus, occasionally sends out signals to destroy all of the 50-100 chloroplasts in the cell, such as in autumn when leaves turn brown and drop off. However, the Salk team found how the plant nucleus begins to degrade and reuse the materials of select, malfunctioning chloroplasts--a mechanism that had been suspected but never shown until now.

"We've discovered a new pathway that lets a cell do a quality control check on the chloroplasts," says Jesse Woodson, Salk staff scientist and first author of the paper. Chloroplasts are full of enzymes, proteins and other materials that the plant can otherwise use if the chloroplast is defective (for example, creating toxic materials) or not needed.

While studying a mutant version of the model plant Arabidopsis, the team noticed the plant was making defective chloroplasts that created a reactive, toxic molecule called singlet oxygen that accumulated in the cells. The team noticed that the cells were marking the damaged chloroplasts for degradation with a protein tag called ubiquitin, which is used in organisms from yeast to humans to modify the function of a protein. Under closer investigation, the team observed that a protein called PUB4 was initiating the tagging.

"Damaged chloroplasts were being coated in this ubiquitin protein," says Woodson. "We think this is fundamentally different than the cell-wide signal, because the cell wants to continue doing photosynthesis, but has some bad chloroplasts to target and remove."

While PUB4 had been tied to cell death in other work, the Salk team showed that this protein initiates the degradation of chloroplasts by placing ubiquitin tags to mark the organelle for cellular recycling. This process, says Woodson, is like labeling defective solar panels to break them down for other materials.

"Understanding the basic biology of plants like this selective chloroplast degradation leads us a step closer to learning how to control chloroplasts and design crops that are more resistant to stressors," says Chory, who is also a Howard Hughes Medical Institute investigator and holder of the Howard H. and Maryam R. Newman Chair in Plant Biology. For example, if a plant is growing in an environment that is fairly relaxed, one could potentially reduce the degradation of chloroplasts to boost the growth of the plant. Or, if the environment contained a lot of sun, spurring on the breakdown and regeneration of chloroplasts could help the plant thrive.

Interestingly, chloroplasts could help us understand our brains as well. Neurons have energy-generating organelles similar to chloroplasts called mitochondria. "Recently it's become apparent that mitochondria are selectively degraded in the cell and that bad mitochondria accumulation could lead to disease like Parkinson's and maybe Alzheimer's," says Woodson. "Cells, whether plant or animal, learn how to degrade defunct energy organelles selectively to survive."

By better understanding this process in chloroplasts, the Salk team may be able to also glean insight into how the cells handle misbehaving mitochondria. "So far it seems like it might be a parallel process," Woodson adds. "We're hoping with our molecular and genetic tools available for plants we can continue to uncover general concepts on how cells do these quality control checks on organelles and learn something about neurodegenerative disease as well."

Salk Institute. | Sciencedirect

Jesse D. Woodson, Matthew S. Joens, Andrew B. Sinson, Jonathan Gilkerson, Patrice A. Salomé, Detlef Weigel, James A. Fitzpatrick, and Joanne Chory. Ubiquitin facilitates a quality-control pathway that removes damaged chloroplasts. Science, 23 October 2015: 450-454 DOI: 10.1126/science.aac7444