Scientists don’t know the exact molecular nature of the epigenetic information that one generation transmits to the next. The list of candidate carriers includes proteins, noncoding RNA and the histones around which DNA winds itself. Or it could be modifications to the DNA itself that somehow get replicated when cells divide.

Now, a Harvard Medical School team has written a new chapter in the epigenetics story, with their discovery of a new position for an epigenetic modification to DNA that potentially carries heritable epigenetic information.

Over the past 20 years, a growing body of evidence has implicated chemical marks that are added to the DNA.  The best studied modifications scientists have found occur when a methyl group marks the C. More ancient organisms have other modifications, including methylation of the A.

Yang Shi, HMS professor of cell biology, overturned dogma in the field in 2004 when he showed that methylation of histones is not static. Adding a methyl group to histones—the spool around which the DNA double helix wraps to form chromosomes—can help turn a gene on or off; so does removing a methyl group. The discovery of enzymes that specifically remove methyl groups highlights the dynamic nature of histone methylation regulation, a process that is critical for stem cell biology, development and differentiation, and when it goes awry, can lead to many human diseases. Their surprising discovery was made in C. elegans, a transparent roundworm that is a widely studied model organism.

Scientists previously thought that C. elegans simply had no DNA methylation because their C letters showed no signs of the methyl modification that other animals have. It is also unknown how they can transmit epigenetic modifications across generations.

Shi’s team reports that C. elegans does in fact carry DNA methylation, but not on the C position. They found epigenetic modifications to adenine at the same location previously thought to exist only in more primitive organisms.

They also identified the enzymes that act to methylate and demethylate the A. Further bolstering their case, they showed that a transgenerational epigenetic inheritance system in C. elegans, which displays a generationally progressive reduced fertility, also progressively accumulates A methylations.

“We have identified what we think is a fundamental new layer of regulation that occurs in animals,” said Eric Greer, formerly a postdoctoral fellow in the Shi lab and now HMS assistant professor of pediatrics at Boston Children’s Hospital. “We’re excited about this because this is a modification that hasn’t previously been shown to occur in Metazoa, of which humans and worms are members.”

The more common C modification may overshadow the A modification in more recently evolved animals, said co-lead author Andres Blanco, an HMS postdoctoral fellow in pediatrics in the Shi lab.

“Maybe it’s not the dominant form of DNA methylation, but maybe it has a smaller role that is nonetheless extremely important,” he said. Harvard Medical School

Much like a finger leaves its own unique print to help identify a person, researchers are now discovering that skull fractures leave certain signatures that can help investigators better determine what caused the injury.

Implications from the Michigan State University research could help with the determination of truth in child abuse cases, potentially resulting in very different outcomes.

Until now, multiple skull fractures meant several points of impact to the head and often were thought to suggest child abuse.

Roger Haut, a University Distinguished Professor in biomechanics, and Todd Fenton, a forensic anthropologist, have now proven this theory false. They’ve found that a single blow to the head not only causes one fracture, but may also cause several, unconnected fractures in the skull. Additionally, they’ve discovered that not all fractures start at the point of impact – some actually may begin in a remote location and travel back toward the impact site.

“It’s a bit like smashing raw hamburger into a patty on the grill,” Haut said. “When you press down on the meat to flatten it, all the edges crack. That’s what can happen when a head injury occurs.”

Because piglet skulls have similar mechanical properties as infant human skulls – meaning they bend and break in similar ways – Haut and Fenton used the already deceased specimens in their research and found they were able to classify the different fracture patterns with a high degree of accuracy.

“Our impact scenarios on the piglet skulls gave us about an 82 percent accuracy rate, while on the older skulls, it improved to about 95 percent,” Fenton said.

To help them get to this level of accuracy, both researchers teamed up with Anil Jain, a University Distinguished Professor in computer science and engineering at MSU, to develop a mathematical algorithm to help classify the fractures.

“A major issue in child death cases is you never really know what happened,” Haut said. “The prosecutor may have one idea, the medical examiner another, and the defendant a completely different scenario.”

Fenton and Haut’s close relationship with medical examiners often results in them being called upon in certain, hard-to-determine cases. They’ve used this new knowledge to help solve these cases, but both are also looking to use Jain’s algorithm in an online resource that will provide even more assistance to investigators.

The team is currently developing a database, or Fracture Printing Interface, that will allow forensic anthropologists and investigators to upload human fracture patterns from different abuse cases and help them determine what most likely caused an injury.

Michigan State University

Researchers funded by the National Institutes of Health Genotype-Tissue Expression (GTEx) project have created a new and much-anticipated data resource to help establish how differences in an individual’s genomic make-up can affect gene activity and contribute to disease. The new resource will enable scientists to examine the underlying genomics of many different human tissues and cells at the same time, and promises to open new avenues to the study and understanding of human biology.

GTEx investigators reported initial findings from a two-year pilot study in several papers. These efforts provide new insights into how genomic variants – inherited spelling differences in the DNA code – control how, when and how much genes are turned on and off in different tissues, and can predispose people to diseases such as cancer, heart disease and diabetes.

‘GTEx was designed to sample as many tissues as possible from a large number of individuals in order to understand the causal effects of genes and variants, and which tissues contribute to predisposition to disease,’ said Emmanouil Dermitzakis, Ph.D., professor of genetics at the University of Geneva Faculty of Medicine, Switzerland, and a corresponding author on the main Science paper. ‘The number of tissues examined in GTEx provides an unprecedented depth of genomic variation. It gives us unique insights into how people differ in gene expression in tissues and organs.’

In the main paper, researchers analysed the gene activity readouts of more than 1,600 tissue samples collected from 175 individuals and 43 different tissues types. One way that researchers evaluate gene activity is to measure RNA, which is the readout from the genome’s DNA instructions. Investigators focused much of their analyses on samples from the nine most available tissue types: fat, heart, lung, skeletal muscle, skin, thyroid, blood, and tibial artery and nerve.

The genomic blueprint of every cell is the same, but what makes a kidney cell different from a liver cell is the set of genes that are turned on (expressed) and off over time and the level at which those genes are expressed. GTEx investigators used a methodology – expression quantitative trait locus (eQTL) analysis – to gauge how variants affect gene expression activity. An eQTL is an association between a variant at a specific genomic location and the level of activity of a gene in a particular tissue. One of the goals of GTEx is to identify eQTLs for all genes and assess whether or not their effects are shared among multiple tissues.

Investigators discovered a set of variants with common activity among the different tissue types. In fact, about half of the eQTLs for protein-coding genes were active in all nine tissues. They identified approximately 900 to 2,200 eQTL genes – genes linked to nearby genomic variants – for each of the nine tissues studied, and 6,486 eQTL genes across all the tissues. ‘We didn’t know how specific this regulation would be in different tissues,’ said co-corresponding author Kristin Ardlie, Ph.D., who directs the GTEx Laboratory Data Analysis and Coordination Center at the Broad Institute of MIT and Harvard in Cambridge, Massachusetts. ‘The analysis showed a large number of variants whose effects are common across tissues, and at the same time, there are subsets of variants whose effects are tissue-specific.’

Comparing tissue-specific eQTLs with genetic disease associations might help provide insights into which tissues are the most relevant to a disease. The researchers also found a great deal of eQTL sharing among tissues, which can help explain how genomic variants affect the different tissues in which they are active. National Human Genome research Institute

Diagnosing a heart attack can require multiple tests using expensive equipment. But not everyone has access to such techniques, especially in remote or low-income areas. Now scientists have developed a simple, thermometer-like device that could help doctors diagnose heart attacks with minimal materials and cost.

Sangmin Jeon and colleagues note that one way to tell whether someone has had a heart attack involves measuring the level of a protein called troponin in the person’s blood. The protein’s concentration rises when blood is cut off from the heart, and the muscle is damaged. Today, detecting troponin requires bulky, expensive instruments and is often not practical for point-of-care use or in low-income areas. Yet three-quarters of the deaths related to cardiovascular disease occur in low- and middle-income countries. Early diagnosis could help curb these numbers, so Jeon’s team set out to make a sensitive, more accessible test.

Inspired by the simplicity of alcohol and mercury thermometers, the researchers created a similarly straightforward way to detect troponin. It involves a few easy steps, a glass vial, specialized nanoparticles, a drop of ink and a skinny tube. When human serum with troponin — even at a minute concentration — is mixed with the nanoparticles and put in the vial, the ink climbs up a protruding tube and can be read with the naked eye, just like a thermometer. American Chemical Society

Researchers discovered a new mechanism of how fluorescent proteins can change colour. It enables the microscopic visualization of individual cells in their three-dimensional environment in living organisms.

Researchers at ETH Zurich’s Department of Biosystems Science and Engineering in Basel have developed a new microscopy technique that enables for the first time to selectively visualize individual cells within the complex, three-dimensional tissue of a living organism. The researchers have thus succeeded in capturing spectacular microscopic images, such as in the nervous system of a zebrafish larva, a preferred model organism for research. Motor neurons in the spinal cord can be seen in the researchers’ images; at the same time, a single neuron with all its extensions is highlighted in another colour.
An observation by William Dempsey, post-doc in the group of ETH professor Periklis Pantazis, led to the new application. He worked with a special class of fluorescent proteins that change colour when irradiated with laser light of a specific wavelength. One such ‘chameleon protein’ is called Dendra 2, which normally emits green light when illuminated with blue light. The emission of Dendra 2 is however shifted into the red when it is irradiated by intensive violet or ultraviolet (UV) laser light.

Dempsey and Pantazis specifically discovered that when Dendra 2 is irradiated by both a blue and a red laser at the same time, the protein’s colour can also change to red. For this dual-colour illumination low intensity laser light is sufficient. In contrast to high intensity violet or UV irradiation it does not damage living cells.

ETH professor Pantazis and his colleagues then had an idea of how this finding could be deployed in light microscopy. Fluorescent proteins can be used to make whole cells, precise cell structures or single molecules visible. For the first time, the ETH researcher’s discovery permits a single cell or group of molecules located within a desirable part of a living organism to be highlighted with one colour, while all the other cells or molecules remain visible with another colour.

The research group showed that when used individually, two different laser beams cannot change a chameleon protein’s colour. But when the two beams are combined and directed in a way that they meet at a certain point on the object, then the proteins in focus change colour. In contrast, the proteins that are not activated at the same time by the two lasers retain their original colour.
The researchers have developed a simple and inexpensive colour filter, which can be used with the conventional confocal laser microscopes that are found in many biomedical research institutes. When mounted between the laser source and object, the filter divides the laser light into separate blue and red beams that are directed on to a small focal point on the object.

In the case of the zebrafish larva, which is transparent and therefore well suited for microscopy, the ETH researchers used Dendra 2 to colour neurons. They then focused the combined laser beam’s focal point on the cell body of a single neuron in a live, anesthetized zebrafish. The local Dendra 2 molecules became red, spread throughout the entire cell and dyed the cell extensions. All other cells, even in the immediate vicinity of the targeted cell, remained green.
The ability to make individual neurons visible could be of great importance, for example, in the precise mapping of the brain, according to Pantazis. Since the method is suitable for individual cell targeting in living organisms, it could also be used to examine dynamic processes; for example, what happens to individual cells or a group of molecules when researchers treat an organism with active pharmaceutical ingredients. Embryo development could also be examined in more detail. “Our method allows for a three-dimensional analysis in an elegant manner,” explains Pantazis. “This is a very nice example of how you can take a result from basic research and use it to provide a solution for a technically challenging issue.” Pantazis hopes the technique will be used more broadly in biomedical research in the future and is in talks with microscope manufacturers to implement this technology.
wavelength of light. ETH Zurich