A coral reef infested with cyanobacteria (dark). Photo courtesy of Jennifer Smith.
Seaweed may be a drug out of place
In the pristine waters of Pu’uhonua o H’onauau National Historical Park off the Kona coast of Hawaii, a kind of seaweed consisting of blue-green cyanobacteria is considered a pest and bane to indigenous corals, which are smothered and killed by the rubbery, bulbous bacterial colonies.
But almost nothing nasty in nature is without its upside, a fact underscored again in findings by researchers at UC San Diego’s Scripps Institution of Oceanography and the Skaggs School of Pharmacy and Pharmaceutical Sciences, who found that the cyanobacterium – Leptolyngbya crossbyana – produces chemical compounds that may provide the basis for new anti-inflammatory medicines and anti-bacterial treatments.
Writing in the journal Chemistry & Biology, Hyukjae Choi, a postdoctoral researcher in the laboratory of William Gerwick and colleagues report that L. crossbyana secretes natural products known as honaucins, chemical compounds that control how and where the tiny algae grows and spreads.
If researchers can translate that natural talent into therapeutic drugs or treatments, they might be able to prevent at least some types of bacterial infections in humans or treat inflammation-related conditions like acne and arthritis.
“I think this finding is a nice illustration of how we need to look more deeply in our environment because even nuisance pests, as it turns out, are not just pests,” said Gerwick. “It’s a long road to go from this early-stage discovery to application in the clinic but it’s the only road if we want new and more efficacious medicines.”
You can read the entire UC San Diego news release here.
“Birth of DNA (Epigenetics)” by Zdenko Herceg
Deciphering DNA’s hidden code
Reading the genetic “Book of Life” is not easy, an observation scientists learn all of the time. Consider the well-known nucleobases that comprise DNA. There are only four: adenine, thymine, guanine and cytosine (plus uracil, which is found in RNA). It turns out, however, that cytosine comes in two modified forms: 5-methylcytosine (5-mc) and 5-hydroxymethlcytosine (5-hmC). The versions look almost alike, but affect genes in very different ways.
In a paper published in the journal Cell today, researchers at the University of Chicago, the Ludwig Institute for Cancer Research at UC San Diego and Emory University describe a new technique for reading the particular differences in cytosine, an achievement that has ramifications for better understanding fundamental life processes.
These two modifications of cytosine “regulate gene expression that has broad impact on stem cell development, various human diseases such as cancer, and potentially neurodegenerative disease,” said Chuan He, a professor of chemistry at the University of Chicago. “They may even shape the development of the human brain.”
He, with Bing Ren, PhD, head of the Laboratory of Gene Regulation at the Ludwig Institute for Cancer Research at UC San Diego, and colleagues developed a method called TAB-Seq that directly measures 5-hmC and produced the first map of the entire genome of 5-hmC at single-base resolution. Ren applied TAB-Seq to human embryonic stem cells; Peng Jin of Emory applied the method to mouse embryonic stem cells.
The work is expected to have a significant impact upon the field of epigenetics, which looks at changes in gene expression caused by factors other than alterations in the actual DNA. 5-mC and 5-hmC appear to be major epigenetic players. 5-mC is generally found on genes that are turned off; it helps silence genes that aren’t supposed to be turned on. Conversely, 5-hmC appears to be abundant on active genes, especially in brain cells.
“This is a major breakthrough in that TAB-Seq allows precise mapping of all 5-hydroxymethylcytosine sites in a mammalian genome using well-established, next-generation DNA sequencing methods,” said Joseph Ecker, a professor at the Salk Institute for Biological Studies, who was not involved in the Cell study. “The study showed very clearly that deriving useful knowledge about this poorly understood epigenetic regulator requires determination of the exact locations of 5-hmC with base-level accuracy. I expect that their new method will immediately become widely adopted.”
Bacillus subtilis
A big step writ small
Microbial colonies are tiny cities of life. Understanding how they work – their integrated chemistry, genomics and phenotypes – has long been a sort of “holy grail” among microbiologists.
A step in that direction is reported this week by Pieter C. Dorrestein, PhD, associate professor at the UC San Diego Skaggs School of Pharmacy and Pharmaceutical Sciences, and colleagues in a paper published in the Proceedings of the National Academy of Sciences.
The scientists describe a new, highly sensitive, broadly applicable and cost-effective technique using mass spectrometry to profile the metabolic activity of live microbes directly from a Petri dish without any sample preparation.
Though most people will never see it at work, the new visualization platform is a significant advance in understanding the space and time dynamics of interacting microbial colonies and communities. It’s a big step writ small, akin perhaps to the qualitative difference between studying a dinosaur fossil and watching a whole herd of frolicking sauropods.
Why Omega-3 Oils Help at the Cellular Level
Findings suggest possibility of boosting their health benefit
For the first time, researchers at the University of California, San Diego have peered inside a living mouse cell and mapped the processes that power the celebrated health benefits of omega-3 fatty acids. More profoundly, they say their findings suggest it may be possible to manipulate these processes to short-circuit inflammation before it begins, or at least help to resolve inflammation before it becomes detrimental.
The work is published in the May 14, 2012 online Early Edition of the Proceedings of the National Academy of Sciences.
The therapeutic benefits of omega-3 fatty acids, which are abundant in certain fish oils, have long been known, dating back to at least the 1950s, when cod liver oil was found to be effective in treating ailments like eczema and arthritis. In the 1980s, scientists reported that Eskimos eating a fish-rich diet enjoyed better coronary health than counterparts consuming mainland foods.
“There have been tons of epidemiological studies linking health benefits to omega-3 oils, but not a lot of deep science,” said Edward A. Dennis, PhD, distinguished professor of pharmacology, chemistry and biochemistry. “This is the first comprehensive study of what fish oils actually do inside a cell.”
The scientists fed mouse macrophages – a kind of white blood cell – three different kinds of fatty acid: eicosapentaenoic acid (EPA), docosahexaenoic acid (DHA) and arachidonic acid (AA). EPA and DHA are major polyunsaturated omega-3 fatty acids, essential to a broad range of cellular and bodily functions, and the primary ingredient in commercial fish oil dietary supplements. AA is a polyunsaturated omega-6 fatty acid prevalent in the human diet.
Powdered casein protein.
Mystery solved: The casein of the missing kinase
In 1883, a Swedish chemist named Olof Hammarsten discovered that milk proteins called caseins contain not just the known building blocks of proteins, but also the chemical phosphate. It was the first hint that phosphates – which are now considered critical regulators of protein function -are tacked onto proteins.
Today, scientists know that enzymes called kinases can control protein function by attaching phosphates to proteins produced inside cells. Hundreds of kinases have been discovered and characterized, but the kinase that phosphorylates casein remained unknown -until now.
Howard Hughes Medical Institute (HHMI) scientists, led by Jack E. Dixon, PhD, professor of pharmacology, cellular and molecular medicine, chemistry and biochemistry at UC San Diego, have identified and isolated the elusive enzyme. In a study published online May 10, 2012, in Science Express, they report that they have uncovered the enzyme that transfers phosphate not only to milk proteins like casein, but also to proteins found in bones and teeth enamel.
“We solved this scientific puzzle that dates back to the 19th century,” said Dixon, who is HHMI vice president and chief scientific officer. “We also ended up stumbling onto this connection between this kinase and biomineralization.”
Dixon studies kinases, the enzymes that add phosphates to proteins, and phophatases, which remove phosphates. While most kinases are located within the cell, in the 1980s researchers started reporting that they’d detected kinase activity, such as phosphorylated proteins, outside of cells. In 2008, Kenneth Irvine, an HHMI investigator at Rutgers, was studying a protein called four-jointed, which is important in the development of fruit flies. Irvine demonstrated that four-jointed had kinase activity, even though the protein was unlike any other traditional kinase. Moreover, the protein localized to the Golgi apparatus, a compartment within the cell where proteins are sorted and packaged.
“It was not clear to us that any of the approximately 580 traditional kinases had signal sequences which would allow them to end up in the same cellular compartment as casein, which was known to be secreted,” says Dixon. So, Dixon, in collaboration with Nick Grishin, an HHMI investigator at the University of Texas Southwestern Medical Center, searched databases of protein sequences to find human proteins that resembled four-jointed. They identified a family of proteins - so little studied that its only name was Fam20 (for family 20) - with sequence similarity to four-jointed, and found that the Fam20 A, B, and C proteins had amino acid sequences that would direct them to same part of the Golgi apparatus as the casein protein. Fam20C phosphorylated casein and many peptides on a specific amino acid sequence motif.
But discovering that Fam20C is the kinase that acts on casein wasn’t the end of the story. As Dixon’s group looked through the scientific literature, they found that mutations in Fam20C had previously been found in patients with Raine syndrome, a rare and fatal disease in which developing bones become too dense. To understand this link between Fam20C and Raine syndrome, Dixon developed cell lines that produce Fam20C containing mutations that affect the same amino acids that had been implicated in the disease.
“It turns out that every single one of these mutations inactivated the kinase and prevented it from being secreted,” says Dixon. And the targeted amino acid sequence that the researchers had nailed down earlier wasn’t just found in casein—it was found in dental matrix protein, osteopontin, and bone sialophosphoprotein, among others. All these proteins are involved in enamel and bone formation.
“In the end, what we’ve discovered isn’t just the casein kinase,” Dixon says. “It’s a whole new branch on the kinase tree, a branch that seems to play very important roles in bone and teeth formation.”
Phosphates are often used by proteins to bind calcium, a key ingredient of bones, teeth, and milk. So Dixon thinks the phosphorylation by Fam20C generates a calcium-binding site that is critical in the formation of bone and teeth. When the kinase is mutated, the bones or teeth don’t develop correctly.
Next on the scientists’ to-do list is uncovering the functions of the other Fam20 proteins—Fam20A and Fam20B, as well as working out the exact mechanism by which Fam20C works.
“This is the end of one scientific mystery,” says Dixon, “but it also opens up a whole new area of kinase biology for us to explore.”
This report courtesy of HHMI.
River of dreams
The hippocampus is a region of the mammalian brain involved in learning and memory. In this confocal microscopy image of an adult mouse’s hippocampus by Sandra Dieni of the Institute of Anatomy and Cell Biology at Albert-Ludwigs University in Germany, reactive astroglia (star-shaped cells that support neurons in the brain, here colored pale yellow) have proliferated and enlarged in response to neuronal activity over time.
Enlightened science
Ablation in medicine means to remove tissue by various means, such as cutting, chipping or vaporizing, to eliminate a threat to health. Cellular ablation is a more particular endeavor: Cells are selectively destroyed to better understand their lineage and function.
Researchers have some clever tools to do this. A laser, for example, can focus upon a single cell in Caenorhabditis elegans, a tiny worm and proven model organism. Or genetically coded reagents, such as enzymes or cytotoxic molecules, can be introduced into targeted cells to induce apoptosis or programmed cell death.
The problem with the latter approach, which has been used in organisms other than C. elegans, is that chemical reagents may accumulate in tissues other than the targeted cells, causing non-specific toxicity. In other words, healthy cells near the target can also die.
In a paper published online this week in the Proceedings of the National Academy of Sciences, Yishi Jin, PhD, a professor in the division of biological sciences and Howard Hughes Medical Institute investigator, and Roger Tsien, PhD, professor of pharmacology, chemistry and biochemistry Howard Hughes Medical Institute investigator, and Nobel laureate describe, with colleagues, using a tiny, light-activated molecule to effectively kill single neurons in a nematode without any apparent collateral effect.
The molecule is called a mini-singlet oxygen generator or miniSOG. It’s a radically re-engineered light-absorbing protein from the cress plant Arabidopsis thaliana that, when exposed to blue light, produces abundant quantities of singlet oxygen. The researchers in Jin’s lab targeted the expression of miniSOG to mitochondria, and observed that the expressing cells die quickly upon blue light illumination, without affecting neighboring tissues.
“We believe that singlet oxygen generated by miniSOG (genetically introduced into the mitochondria of the targeted neuron) destroys the integrity of the mitochondria, which releases toxic molecules that lead to the death of the cell,” said Jin. “The dead neuron is then cleared away by nearby cells, most likely through phagocytosis.”
While the findings may be a boon to basic research, Tsien said they are unlikely to have direct value for developing human treatments because the method requires gene therapy, which is not yet practical enough.
“Plus it needs blue light, which doesn’t penetrate very far through organisms as thick as ourselves. However, we are separately working on synthetic injectable molecules (not minSOG) that would home in on cancer cells and kill them with red or near-infrared light, which penetrate mammalian tissues much better than blue light. But even red or near-infrared would mostly have to be applied by endoscopes or during surgery.”
Unfolding secrets
While much has been written about The Human Genome Project over the years, the full story may just now be unfolding. Literally.
Inside each normal, nucleated cell, a lot of DNA is tightly packed. Uncoiled, it would stretch almost nine feet. Magnified 1,000 times to better see it, the length would be three kilometers – the equivalent distance of the Lincoln Memorial to the capital of Washington, D.C.
In a paper published today in the journal Nature, Bing Ren, PhD, head of the Laboratory of Gene Regulation at the Ludwig Institute for Cancer Research at UC San Diego, and colleagues describe for the first time how different parts of DNA are actually folded next to each other inside a cell’s nucleus.
You can read the Ludwig Institute’s news release here or here. We asked Jesse Dixon, a biomedical graduate student in Ren’s lab and the paper’s first author, to elaborate further.
Question: Why is it important to know where genes are positioned within the nucleus?
Answer: One thing that we know is there are between 20 and 30 thousand genes in the human genome, but in any one cell, only a subset of them are turned on. We know that one important factor in deciding which of the genes in the genome are turned on in any one cell is where they are positioned in the nucleus, and where they are positioned relative to other parts of the genome. For example, we know that there are certain regions of the genome that are called enhancers, and these act like switches that turn on genes. The trick is that the enhancer that is responsible for turning on a gene may not be located right next to the gene, and in fact may be some distance away, almost like a light switch that turns on the lights in another room.
So we know that at least one of the ways that these enhancers work is that they are brought in close physical proximity to the gene they regulate by bending the DNA and causing a large loop to form in the genome. This “looping” allows the enhancer to work in turning on its target gene. So it is this kind of physical association of different parts of the genome that can play a critical role in deciding which genes a cell turns on, which is what we were hoping to learn something about in our study.
Q: You call these identified regions “topological domains.” What do they look like? Does their structure explain how they work?
A: With regards to what the topological domains look like, we can’t say for certain, but it is something that we are interested in. What we know from what we have found is that the topological domains are regions of the genome that are tightly self-associated. It’s as if these domains are parts of our genome that are wound up like a ball of yarn, and that our genome is composed of many of these domains, over and over again, but that each of the domains appears to be relatively separate from each of the neighboring domains, like many balls of yarn linked together.
Q: What’s the significance of your finding that these domains are highly conserved and appear ancient in origin?
A: We think the finding that these domains are conserved in evolution is really interesting. In the case of humans and mice, these are organisms that are believed to be separated by 65 million years of evolution, yet we can see that in the parts of the human and mouse genomes that are analogous to each other, the structures can be remarkably similar.
In addition, there was another group that showed recently that the genome of fruit flies, which are even further away on the evolutionary tree, are arranged with a similar topological domain structure. Exactly what all this means isn’t entirely clear, but it suggests that this strategy of organizing genomes into topological domains was something that was hit on very early in animal evolution, and appears to be something that has been retained quite strongly. This suggests that this is an effective way for animals to organize their genomes. Perhaps by segregating our genome into these domains, it is easier to regulate the function of different regions of the genome. We are hoping that as we learn more about how these domains function, this may allow us to make better predictions about why they have been retained so well in evolution, and this may tell us something about how we and other organisms have evolved our genomes.
Q: How are these findings likely to be used by other researchers?
A: We hope our paper will be a good resource for other scientists studying genome function. For example, what we have done is to essentially create large-scale maps of how the genome is folding up in embryonic stem cells and differentiated cells. As I mentioned earlier, we know that the way that certain genes may be turned on are via these long range “loopings” between enhancers and distant genes.
We hope these maps of how the genome is folding up and interacting may give researchers clues about which regions of the genome may regulate which genes, and this is important for understanding how any particular gene is normally regulated, and how that regulation may be altered in disease.
Biomedical science by the (very big) numbers
Almost daily, it seems that health science researchers in San Diego, the United States and around the world report or announce a novel technology, process, approach, means or method for measuring, mapping and monitoring human health.
The goal, of course, is to translate this ever-growing amount of newly derived health data into tangible treatments and cures, a feat that increasingly appears as overwhelming as the amount of data.
That point was made abundantly clear recently when the National Science Foundation announced solicitations for its “Big Data” project, a joint effort with the National Institutes of Health to develop and advance the scientific and technological means of managing, extracting, analyzing and visualizing huge, diverse, distributed and heterogeneous data sets.
In other words, making sense and use of raw information for real-world ills.
It’s a massive undertaking, says Lucila Ohno-Machado, MD, PhD, the founding chief of UC San Diego’s Division of Biomedical Informatics and a key player in this type of effort. Speaking about the White House event that announced the project, Ohno-Machado said:
“Every day Americans go to clinics and hospitals and their data are recorded for treatment, but are not consistently used to make new discoveries or improve healthcare. By developing a means of using these data without compromising patient privacy, we may accelerate science and improve care for all.”
There are a number of obstacles to overcome, says Wendy Chapman, PhD, associate professor at the Division of Biomedical Informatics and director of dissemination for iDASH, an acronym for integrating Data for Analysis, Anonymization and Sharing, the latest additon to the National Center for Biomedical Computing funded by the NIH. iDASH’s explicit goal is to focus on ways of advancing methods for anonymizing and sharing research data. It is based on a platform that matches high security and privacy levels with massive, scalable storage and calculating power.
For example:
Today, most data (which is mostly non-clinical) resides in repositories governed by limited data use agreements among the biomedical researchers and institutions most likely to find benefit in the material. In the future, these databases will need to be annotated and managed using reliable patient informed consent systems and a certified trust network developed as part of iDASH and SCANNER, which stands for Scalable National Network for Effectiveness Research, a project funded by the Agency for Healthcare Research on Quality. There will be incentives for securely sharing information so that effective science can be done at its fullest and fastest.
Today, the system is indisputably incomplete. Computer scientists are looking for data; biomedical and behavioral scientists are looking for analytics. The amount of data stored out there is huge, but the high-performance computing required to crunch the numbers effectively is limited to just a few institutions.
One of those institutions is UC San Diego, which is home to both the San Diego Supercomputer Center and the California Institute for Telecommunications and Information Technology, or Calit2.
In this image, courtesy of Arshad Desai, a one-cell C. elegans embryo is shown undergoing mitosis. Microtubules are depicted red, chromosomes in blue, centromeres in green.
Add, subtract, divide equals life
Centromeres are regions of DNA and proteins on each chromosome that both link together sister chromatids and ensure accurate chromosome segregation and distribution during cell division or mitosis. When centromeres don’t work right, the result can be catastrophic. Indeed, aberrant division and chromosomal instability are hallmarks of cancer cells, especially the most aggressive types.
Yet despite their existential importance – “Chromosome segregation is the key event of cell division and fundamental to understanding life,” said Arshad Desai, PhD, professor of Cellular and Molecular Medicine at UC San Diego – centromeres remain imperfectly understood more than a century after German biologist Walther Flemming first described them.
In a letter published today in the advance online edition of the journal Nature, Desai, who is also an investigator at the Ludwig Institute for Cancer Research at UC San Diego, and colleagues fill in some critical details, describing the germline transcription process that defines centromeres in Caenorhabditis elegans, a nematode whose similar molecular mechanisms make it a model for human biology.
“How does a chromosomal region know it is a centromere and how is that information maintained. That’s the topic of our paper,” said Desai.
The work goes beyond simply advancing basic scientific understanding. Current cancer drugs like taxol and vinca alkaloids work by perturbing cell division. The problem is that these drugs can be toxic in non-dividing cells, such as neurons. A better understanding of how centromeres form and function could lead to more finely tuned or different ways for perturbing cell division.
Perhaps more significantly, said Desai, understanding centromeres will help in designing artificial chromosomes. “We currently rely on viruses for stable delivery of genetic information,” Desai said. “But this has the disadvantage that viruses integrate at random into genomes, which can negatively impact the patient.”
An artificial chromosome, with all of the genetic information tucked into the appropriate places, would preclude the need for viral vectors. And, said Desai, “the major limitation to designing true artificial chromosomes is our lack of understanding of centromeres.”
