There was a lot of mystery surrounding a disease which was rampaging through European Salmon farms, a disease which was wasting their hearts and muscles. Finally, through the use of Genome sleuthing, the mystery has been solved.

The disease is caused by a previously unknown virus. This identification does not mean that there is now also a cure for the disease, however it is a great step forward into solving the problem. Now that scientists have pinned down the disease and the genome, it is only a matter of time before a cure will be found.

“It’s a new virus. And with this information now in hand, we can make vaccines,” explained director of Columbia Univerity’s Center for Infection and Immunity, Ian Lipkin.

A couple of years ago, some Norwegion fisheries got into touch with Lipkin and asked for his aid in discovering what was going on in their Norwegion Salmon farms. They wanted to know what was causing the HSMI (Heart and Skeletal Muscle inflammation), the scientific name for an affliction which was identified in 1999 on one of their farms.

The fish which are infected are physically stunted, and have muscles so weak that they often have trouble swimming about, or even circulating blood around their bodies. This disease often results in death, so there is a great cause or concern. The reason there is so much concern is that the original outbreak was followed by 417 other in Norway and the United Kingdom, and every year there are more reports of the disease.. What is even more disturbing is that there have been reports of wild salmon being infected, which means that salmon which escape the farm are infecting the already low numbers of wild stocks. If something is not done to fix this problem, it could quite possibly spiral out of control, and have a devastating effect on not only local ecosystems but on the entire salmon market as we know it. “If the potential hosts are in close proximity, it goes through them like wildfire,” said Lipkin.

Lipkin and his team, which have already had great success in identifying mystery viruses, rigorously examined samples taken from infected salmon pens. They were looking for the DNA sequences which resemble sequences found in other viruses, and hopefully finding the HSMI-causing sequence. Lipkin compared the grueling process akin to solving a Sunday paper crossword. The researchers eventually found what they were looking for, and dubbed the virus piscine reovirus, or PRV. The virus was unveiled and explained in the issue of Public Library of Science one, published on the 9th of July.

Some viruses which are rather similar have been discovered on poultry farms, and cause muscle and heart disease in chickens. “Analogies between commercial poultry production and Atlantic salmon aquaculture may be informative,” The researchers wrote in the article. “Both poultry production and aquaculture confine animals at high density in conditions that are conducive to transmission of infectious agents.”

The results from these investigations might just be useful when the Obama administration comes up with its national policy for regulating aquaculture.

Researchers have finally been able to genetically map 85 different species of shark which are found in Indian waters.

The DNA mapping of these sharks is thought to be rather significant in terms of being able to identify the most threatened species. Now it will be easier to help manage programs to save them. The program is being headed by the Ministry of Earth Sciences, and is part of an ongoing survey and assessment plan for mapping deep sea species in the Indian Ocean.

India is currentlt the second largest shark fishing nation, many species of shark are killed for their fins, oil and their meat.

The actual genetic fingerprinting of the sharks was done by a team of scientists from the Central Marine Fisheries Research Institute in conjunction with the Kochi regional center of the National Bureau of Fish Genetic Resources in Lucknow.

The shark samples were collected in the Gujurat, Tuticorin, Conchin fisheries harbour and also the Neendakara fishing harbour. The researchers were performing the fingerprinting under the direction of the N.G.K. Pillai, of the Pelagic Fisheries Division of the Institute, along with the help of A. Gopalakrishnan of the bureau. Other members on the team included K.K. Bineesh, K.V. Akhilesh and K.A. Sajeela.

This genetic fingerprinting will greatly aid in the identification of the different shark species from tissue samples. Most shark species are found at a depth of around 250 meters and little is actually known about them. This project is aiming to change that, and bring the sharks into the public eye.

Researchers from Emory University have identified the first fish to have switched from ultraviolet vision to violet vision, i.e. the ability to see blue light. This fish in question – a type of scabbardfish – is also the first example of an animal where a deleted molecule has resulted in a change in visual spectrum.

Many species, including humans, have violet vision but our common vertebrate ancestor had UV-vision and could not sense the blue colour spectrum.

All fish studied before the scabbardfish have been found to have UV vision. The scabbardfish is believed to have switched from UV vision to violet vision by deleting the molecule at site 86 in the chain of amino acids that makes up the opsin protein.

“Normally, amino acid changes cause small structure changes, but in this case, a critical amino acid was deleted,” Yokoyama explains.

Vision is of particular interest to evolutionary geneticists since it is a comparatively straight-forward sensory system with a low number of genes involved. Human vision is for instance made possible by no more than four genes.

“It’s amazing, but you can mix together this small number of genes and detect a whole color spectrum,” says evolutionary geneticist and research team leader Shozo Yokoyama. “It’s just like a painting.”

In their study, the Emory researchers linked molecular evolution to functional changes and the possible environmental factors driving them.

“This multi-dimensional approach strengthens the case for the importance of adaptive evolution,” says Yokoyama. “Building on this framework will take studies of natural selection to the next level.”

The Scabbardfish spends most of its life at a depth of 25-100 meters and at these depths UV light is less intense then violet light, something which may have prompted the change in vision. Living deep down in the ocean will however not necessarily make you benefit from a vision switch; the Lampfish has for instance retained its UV vision – most likely because it swims up to the surface at night to feed on translucent crustaceans that are easier to locate if you have UV vision.

“The finding implies that we can find more examples of a similar switch to violet vision in different fish lineages,” says Yokoyama. “Comparing violet and UV pigments in fish living in different habitats will open an unprecedented opportunity to clarify the molecular basis of phenotypic adaptations, along with the genetics of UV and violet vision.”

The article has been published in the October 13 issue of Proceedings of the National Academy of Sciences.

http://www.pnas.org

In addition to evolutionary geneticist Shozo Yokoyama, the research team also included post-doctoral fellow in biology Takashi Tada and post-doctoral fellow in biology and computational chemistry Ahmet Altun.

Researchers at Woods Hole Oceanographic Institution (WHOI) and the University of South Carolina has managed to solve a conundrum that’s been puzzling marine scientists for roughly a decade – where does all the oceanic phosphonate come from?

Roughly a decade ago, phosphonate – a rare form of organic phosphorus – was discovered in marine organic matter. Not only were researchers baffled to find this rare form of phosphorus in the ocean; they were also flummoxed by the high concentrations in which it was found throughout the sea. No one could explain where it came from and why it could be found in such abundance.

That is, no one could explain it until now.

In 2006, biologist Sonya Dyhrman and her WHOI team commenced a field and laboratory study on a group of phytoplankton called Trichodesmium. Trichodesmium is a microscopic marine microbe found in ample amounts throughout warm tropical and subtropical waters where nutrients are scarce. The WHOI team were able to show that Trichodesmium uses phosphonate to support carbon and nitrogen fixation, and that a special set of genes have given them this capacity. This triggered Dyhrman’s curiosity – where did Trichodesmium get its phosphonate from in the first place?

To solve the mystery, Dyhrman partnered up with Claudia Benitez-Nelson, a marine geochemist with the University of South Carolina, and started analyzing various phytoplanktons using nuclear magnetic resonance.

“We’ve been fascinated by these phosphonate compounds for a while,” said Benitez-Nelson. “Sonya and I decided that something had to be producing them, and we had to start looking at all these organisms to figure out who it was.”

“After culturing several different kinds of phytoplankton and analyzing them using nuclear magnetic resonance (NMR) spectroscopy, we found high concentrations of phosphonate in cultures of a specific Trichodesmium species – in fact an average of 10 percent of the cellular phosphorus is in the form of phosphonate“, explained Dyhrman. “Ten percent may not sound like much, but this is the most phosphonate ever detected in a marine microbe.”

“When we first saw the phosphonate peak in the Trichodesmium culture, we were stunned, after a 10-year mystery it seemed ironic for Trichodesmium to both consume and produce this compound“, said Benitez-Nelson. “We ran it again. We grew them under different nutrient conditions and, sure enough, the results were the same.”

Since nitrogen is scarce in the open ocean, nitrogen fixing organisms like Trichodesmium are imperative to the marine food web. Trichodesmium phytoplankton will not only bring carbon into the food chain by absorbing it from the atmosphere like other phytoplankton; they will also provide the food chain with essential nitrogen due to their ability to absorb nitrogen gas from the air and transform it into a compound that other organisms can use.

“Not only does this solve a mystery about where these forms of phosphorus are coming from, but the fact that it is Trichodesmium has ramifications for how the phosphorus cycle is linked to the cycling of carbon and nitrogen and how those cycles will function in the future ocean,” said Dyhrman.

The Dyhrman and Benitez-Nelson study was recently published in the journal Nature Geoscience.

A team of scientists at the Michigan State University has found a new, more efficient method for cloning zebra fish.

“After the mouse, it is the most commonly used vertebrate in genetic studies,” said Jose Cibelli, an MSU professor of animal science and one of the paper’s co-authors. “It is used in cancer research and cardiovascular research because they have many of the same genes we have.”

Zebra fish is also used by scientists researching normal development and birth defects, as well as various human diseases and the functions of cell populations within organs.

Up until now, zebra fish cloning has had a low success rate, but the new Michigan method has changed this. The new method uses ovarian fluid from a Chinook salmon to keep the unfertilized egg alive.

“This worked well, because it kept the egg inactive for some time”, Cibelli explained. It gave us two or three hours to work with.

During the next step of the process, the Michigan researchers used a laser to remove DNA from the egg; a method borrowed from human in vitro fertilization. Next, the team devised a new, more efficient way of inserting the donor cells into the egg.

“The tricky part was finding a way to get into the egg,” Cibelli said. “We used the same entrance that sperm uses. There was only one spot on the egg, and we had to find it.”

You can find more information in the most recent issue of the journal Nature Methods.

The main author of the article “Novel Somatic Cell Nuclear Transfer Method in Zebra Fish,” is Kannika Siripattarapravat, a doctoral student in Cibelli’s Cellular Reprogramming Laboratory. Other authors include Patrick Venta, an associate professor of microbiology and molecular genetics, and C.C. Chang, a professor of pediatrics and human development.