Science

In a study published online this week in Nature, an international team of researchers report the first complete sequence of the Atlantic cod genome and an unexpected discovery of the unique immune system of this important species.

Led by researchers from the University of Oslo, a consortium of Norwegian universities and aquaculture institutions turned to 454 Sequencing Systems from Roche (SIX: RO, ROG; OTCQX: RHHBY) to obtain a comprehensive de novo assembly of the highly complex cod genome at a fraction of the time and cost of traditional sequencing methods. Strikingly, the researchers found that Atlantic cod has lost genes that are essential for a critical component of its immune system. The findings call to question fundamental ideas on the evolution of the immune system in all vertebrate species.

"The overall aim of this initiative was to obtain the entire genome sequence of the Atlantic cod utilizing cutting edge sequencing technology," said study lead Professor Kjetill S. Jakobsen from the Centre for Ecological and Evolutionary Synthesis, University of Oslo. "We had not expected to find that the Atlantic cod had lost such a crucial component of its immune system." Despite lacking genes essential for the function of the major histocompatibility (MHC) II pathway, the Atlantic cod appears to function normally and relies on an increased number of MHC I genes and Toll-like receptor genes for its immune response. This finding will potentially allow for the development of more targeted vaccine development — aiding disease management and the process of domestication of Atlantic cod.

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CLOSED AREA 1

TUESDAY 8/2/2011: YT Update for 8/2: 39 boats reported 337 tows from 8/1 thru 8/2

YT catch was: MEDIUM: T1

LOW: A1,B1,C1,D1,E1,I1,J1,K1,M1,N1,O1,P1,Q1,S1,V1,W1,Z1,AA1,BB1, CC1,FF1,GG1

NO DATA: F1,G1,H1,L1,R1,X1,Y1,DD1,EE1, HH1,LL1,JJ1,KK1

Cell T1 had some high YT catch.

Next report 8/3.

Thank you!

Read the complete advisory from SMAST.

 

 

 

 

 

Over 200 scallop vessels have signed up to participate in this year’s University of Massachusetts School for Marine Science and Technology (SMAST) Yellowtail Flounder Bycatch Avoidance Program.  Participants in the program range from North Carolina to Massachusetts and include owner-operated vessels as well as vessels from larger fleets.  The program is endorsed by the Fisheries Survival Fund, which represents the vast majority of full-time Atlantic scallop fishermen from Maine to Virginia.

The SMAST Yellowtail Flounder Bycatch Avoidance Program is ready to start at the opening of Closed Areas I and II on August 1st at 12:01am.  The scallop management actions, Amendment 15 and Framework 22, were published in the Federal Register on July 21st authorizing vessels to harvest their allocations from the Georges Bank closed areas.  All vessels were allocated two 18,000 lb. trips to the areas with 75% of the effort in Closed Area I and 25% of the effort in Closed Area II.  The fleet must operate under a Total Allowable Catch of yellowtail flounder set at 201 mt. (~306,000 lb.).  Reaching this catch limit on yellowtail flounder will force a closure of both areas to all scallop fishing.

The program uses data collected by active fishermen on the location and amount of yellowtail and scallop catch.  SMAST sends a summary of the information back to the fleet each day to provide a real-time update of bycatch hotspots.

The program began in 2010 in the Nantucket Lightship area with 122 participants.  The fleet was able to harvest their full allocation of scallops, worth ~$40 million, while only catching 32% of the yellowtail flounder Total Allowable Catch.  With over half of the fleet participating in the program in 2011, SMAST is optimistic that the scallop fleet will be able to harvest their full allocation of scallops from the Georges Bank access areas.  The value of the 2011 access area scallop fishery could be as high as $125 million.

Listen to SMAST's Cate O'Keefe and Greg DeCelles describe the Yellowtail Flounder Bycatch Avoidance Program

Read the Standard-Times editorial:  SMAST, scallopers develop another model program

 

 

 

 

 

Reduced catches of small oceanic prey fish like sardines and anchovies may be required in some ocean areas in order to protect the larger predators that rely on these species for food, the first major study of the ecosystem effects of fishing forage species concludes.

“Forage species such as anchovy, sardine, herring, mackerel and krill often are the main food source for larger predatory fish, marine mammals and seabirds,” said Dr. Tony Smith, a scientist with Australia’s Commonwealth Scientific and Industrial Research Organization (CSIRO’s) and lead author of the paper. “They account for more than 30 percent of global fisheries production for use directly as human food and indirectly in livestock feeds, and demand is rising.”

Previous studies have raised concerns about the flow-on effects on seabirds of forage fishing off Peru and South Africa and in the North Sea, and of rising krill catches on whales in the Southern Ocean. “We found forage fishing had large impacts in the five areas studied,” Smith said. “In this study we used three different types of models to examine the broader ecosystem effects when forage fish are harvested at levels that maximize sustainable yields. We found forage fishing had large impacts in the five areas studied – the northern Humboldt, southern Benguela and California currents, North Sea and south-east Australia. These impacts were both positive and negative, and varied across forage species, ecological groups and ecosystems.”

Read the complete story from Global Adventures.

 

 

 

 

 

 

There’s been some buzz lately from luminaries like Senator John Kerry and Legal Seafoods’ Roger Berkowitz about new methods for measuring fish populations using acoustic remote sensing that are being pioneered by a group of scientists from MIT and Northeastern University and that may have the potential application for dramatically improving fisheries science and management. Talking Fish had a chance to find out more about this initiative through a visit last week to the group’s lab – and it was very exciting!

Getting real time, accurate fish population data is a weak spot in fisheries management science. Fisheries data coming from fishermen has problems with quality control and bias; fisheries data from the government’s trawl surveys is expensive, episodic, and selectively samples small swaths of the ecosystem. The data issue is nonetheless hyper-critical since the fisheries stock assessment models on which all fishery management decisions are based, even the best ones, are only as good as the data inputs.  Given data limitations, the current ability to cost-effectively and accurately understand what is happening to fish populations in response to management changes and environmental or other factors is characteristically uncertain.

Many fishermen say that the scientists don’t see as many fish as the fishermen do. There are legitimate and sound reasons why scientists and fishermen see different abundances of fish; it doesn’t mean the science is “bad.” In fact, it is quite good in New England. The trend lines for stock biomass are accurate in projecting relative upward or downward changes in overall stock abundances. But these differing perspectives as to what fishermen and scientists “see” out on  the water does produce a confidence gap that is a major problem and science uncertainties force managers to set lower catch limits than might otherwise be possible.

Read the complete article from Talking Fish.

 

 

 

 

 

JUNEAU – July 18, 2011 — A new study of genetically modified salmon shows they can breed with their wild counterparts.

That raises concerns that escaped farmed fish could weaken wild stocks. It’s not an immediate threat to Alaska species, though it could be to commercial sales.

The study was conducted at the Memorial University of Newfoundland, on Canada’s eastern seaboard.

Graduate student Darek Moreau says he and other researchers worked with what are called growth hormone transgenic Atlantic salmon. Those have an added Chinook, or king salmon gene, that speeds their growth.

Moreau says modified males were exposed to male and female wild salmon in a laboratory simulation of natural spawning conditions.

"So we basically put these fish together and allowed them to do what they do that time of the year and recorded the results. … We found the transgenics had a much reduced breeding performance but they did, in fact, show an interest in breeding and the ability to breed," Moreau says.

The research, published in the scientific journal Evolutionary Applications, is the first to show this type of genetically engineered salmon can interbreed with wild fish.

Moreau says the study should raise concerns about the possible release of modified salmon through accidents at fish farms.

"If there was a significant number of escapes that occurred in succession over many years, there’s certainly the potential for there to be some harm," Moreau says.

 

Read the complete story from NPR's Affiliate in Alaska

 

 

 

 

 

EAST BAY — Chris Deacutis, chief scientist for the Narragansett Bay Estuary Program (NBEP) at the URI Bay Campus, has been working on the issue of excess nutrients (nitrogen) and the low oxygen issue in the upper half of Narragansett Bay for over 10 years.

Today things are better, but Bay advocates are still combating nutrients in the Bay that create algae blooms (which actually create oxygen). But as algae decays it uses oxygen and reduces the oxygen level in the water, often times well below the levels that fish need. This low oxygen level has occurred in Greenwich Bay in the summer as well as in other parts of the Bay.

With a prevailing southwest summer wind in Narragansett Bay, Greenwich Bay (particularly East Greenwich Cove), does not get flushed and low oxygen levels are more prominent there, according to the NBEP, which measures oxygen levels in the Bay. “The famous menhaden fish kill of August 2003 was clearly caused by a sever hypoxia (actually anoxic — no oxygen) events that centered on western Greenwich Bay,” said Dr. Deacutis.

The NBEP eliminated the East Passage, the Mt. Hope Bay and the lower Bay from measurement because oxygen levels in these areas are good. The channel in the east passage acts as a conduit for flushing and mixing. Oxygen levels in deep water off Warwick Neck mix well too, due to the water passing from the east to the west passage and back. Water at Quonset Point and south have good oxygen levels as well.

According to the NBEP blog, “Marine animals breathe oxygen, too, and when oxygen levels drop below 3mg/L there is not enough oxygen to go around. Creatures that live on the bottom of the bay such as oysters, littlenecks and marine worms are at a greater risk during hypoxic events because they cannot move to a different area. Schooling fish such as menhaden are also affected by hypoxia because they are often chased into coves by predators such as striped bass and the school will use up the oxygen faster than it can be produced by photosynthesis or mixed into the water at the surface from the air.”

 

Read the complete story from The East Bay RI

 

 

 

 

July 18, 2011 (CNN) — Massive global greenhouse gas pollution is changing the chemistry of the world's oceans so much that scientists now predict it could severely damage shellfish populations and the nations that depend on the harvests if significant action isn't taken.

A new study from the Woods Hole Oceanographic Institution in Massachusetts shows that ocean acidification is becoming a very serious problem. The study was published in July online in the journal Fish and Fisheries.

"What the study found was that in the next 10 to 50 years many countries are going to see impacts, particularly countries that are heavily reliant on clams and oysters and mussels, and will not be able to adapt by shifting to other foods or aquaculture methods," said Jackie Savitz, senior scientist and chief strategist for the international ocean conservation and advocacy organization Oceana.

 

Read the complete story from CNN

Off the coast of San Juan Island, greenlings doze on ledges 400 feet down. Sculpins snuggle into reefs scattered with scallops. Crabs camouflaged with feathery hydroids creep past crimson sea cucumbers.

It's a world invisible to us, at depths divers seldom venture. But a series of expeditions mounted this summer by the environmental group Oceana is bringing some of these scenes into focus for what may be the first time.

"No one has ever seen what the sea floor looks like in some of these areas," said project leader Geoff Shester. Working on the cheap, the team outfitted small ROVs (remotely-operated vehicles) with the type of video cameras skiers strap to their helmets. Operators guided the craft with joysticks and oohed and aahed as images flashed across their shipboard monitors.

Read the complete story from The Seattle Times.

 

 

 

 

Writing in Quadrant magazine, the Australian journal of ideas, literature, poetry and historical and political debate,  Dr.Walter Starck observes that before "the ascendancy of environmentalism, the scientific ideal was an objective, evidence-based, value-neutral search for truth. Basic research, aimed only at better understanding the world in which we live, was pursued with considerable success. Over recent decades, however, basic research in natural history has been largely supplanted by studies predicated on environmental concerns. As a consequence, acquisition of new understanding of the nature and functioning of the natural world has declined. In addition, much of the research into purported environmental problems suffers from bias and distortion arising from adherence to faith-based notions of environmental correctness."  Dr. Starck holds a  PhD in marine science from the Institute of Marine Science at the University of Miami. He was a pioneer in the study of coral reef biology and the development of undersea technology.

This shift in emphasis from basic research to environmentalism began innocuously in the 1960s and 1970s when an expanding scientific community began to outgrow its funding, and competition for research grants became stronger. At the same time, government was also coming to realise that scientific research was a black hole that could devour any amount of funding and always be hungry for more. Moreover, much of the research appeared to be highly esoteric with little prospect of ever yielding anything of practical or even intellectual value. Governments started to demand a greater consideration of utility.

For those schooled in the ideal of basic research, finding practical relevance was not always easy. Coincidentally, environmental concerns were on the rise in public awareness and were gaining political traction. Grant-seekers found that with a little imagination some environmental aspect could be suggested to attend to the basic research one actually wanted to pursue. Initially this worked to advantage; but competition soon demanded something stronger. Grant applications began to shift their focus to environmental concerns themselves with basic research receiving diminishing attention.

An environmental problem suitable for grant-seeking is not as easy to find as it might seem. It needs to be one that has credibility as a problem or, better still, public perception as being one. It also needs to be one that is not already over-subscribed by competing researchers. It further needs to appear both solvable and important enough to warrant considerable expense to do so. Preferably it should be something that involves a human cause, as this not only makes it amenable to correction but provides a dimension of moral rectitude as well. The moral aspect always goes down well politically and makes any criticism look shabby.

Just any old problem won’t do. Most are too hard, too unimportant or too uncertain to attract significant research funding. This limitation was met by manufacturing new ones. An early and highly successful effort in eco-threat manufacture here in Australia was the great crown-of-thorns starfish plague.

Population explosions of the coral-eating crown-of-thorns starfish on the Great Barrier Reef first came to scientific and public attention in the late 1960s. The starfish threat was soon deemed by academic “experts” to be unprecedented, even though earlier scientific research and underwater exploration on the reef which might have found any earlier outbreaks were almost non-existent. Once a few such outbreaks had been found, the “problem” was deemed to be on a scale which threatened the entire reef. It was even predicted that unless something was done (that is, generous funding for research) the reef would be killed and then wash away, causing massive coastal erosion as well.

When it was discovered that the triton’s trumpet shell was a natural predator of the crown-of-thorns starfish, it was immediately concluded that shell collectors were to blame for the starfish outbreaks. That trumpet shells are never abundant enough anywhere to control an outbreak of starfish and most of the reefs involved had never been subjected to shell collecting was ignored.

Although a geologist found good evidence for ongoing earlier crown-of-thorns outbreaks in the form of varying amounts of their distinctive skeletal elements at different levels in the reef sediments, this too was simply ignored. As far as the crown-of-thorns bandwagon was concerned, the science was quickly settled: the starfish plague had to be unprecedented and somehow caused by humans. All that was needed to solve the problem was more funding for research.

The Great Barrier Reef is a national icon and the success of the starfish threat in releasing government purse strings founded a substantial new industry for the region. “Saving” the reef from various purported threats has continued for almost half a century. This has entailed a total expenditure in the hundreds of millions of dollars with no real threat ever being confirmed and, of course, no solution ever being found. As old threats lose credibility and public concern fades, new ones always seem to be found.

Following the starfish plague, overfishing became a major concern. This generated more millions in research and culminated in the creation of a vast complicated array of green zones comprising about a third of the entire region where the already highly restricted fishing activity is prohibited entirely. While there is voluminous evidence to refute the existence of a threat from overfishing, just one fact alone demonstrates the utter absurdity of this claim.

Read the complete story from Quadrant Online.