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Anthony Atala: Printing a human kidney
Surgeon Anthony Atala demonstrates an early-stage experiment that could someday solve the organ-donor problem: a 3D printer that uses living cells to output a transplantable kidney. Using similar technology, Dr. Atala's young patient Luke Massella received an engineered bladder 10 years ago; we meet him onstage.
Foraminifera are found in all marine environments, they may be planktic or benthic in mode of life. The generally accepted classification of the foraminifera is based on that of Loeblich and Tappan (1964). The Order Foraminiferida (informally foraminifera) belongs to the Kingdom Protista, Subkingdom Protozoa, Phylum Sarcomastigophora, Subphylum Sarcodina, Superclass Rhizopoda, Class Granuloreticulosea. Unpicking this nomenclature tells us that foraminifera are testate (that is possessing a shell), protozoa, (single celled organisms characterised by the absence of tissues and organs), which possess granuloreticulose pseudopodia (these are thread-like extensions of the ectoplasm often including grains or tiny particles of various materials). Bi-directional cytoplasmic flow along these pseudopodia carries granules which may consist of symbiotic dinoflagellates, digestive vacuoles, mitochondria and vacuoles containing waste products; these processes are still not fully understood. In the planktic foraminifera Globigerinoides sacculifer dinoflagellate symbionts are transported out to the distal parts of rhizopodia in the morning and are returned back into the test at night. The name Foraminiferida is derived from the foramen, the connecting hole through the wall (septa) between each chamber.
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History of Study
The study of foraminifera has a long history, their first recorded "mention" is in Herodotus (fifth century BC) who noted that the limestone of the Egyptian pyramids contained the large benthic foraminifer Nummulites. In 1835 Dujardin recognised foraminifera as protozoa and shortly afterwards d'Orbigny produced the first classification. The famous 1872 HMS Challenger cruise , the first scientific oceanographic research expedition to sample the ocean floor collected so many samples that several scientists, including foraminiferologists such as H.B. Brady were still working on the material well in to the 1880's. Work on foraminifera continued throughout the 20th century, workers such as Cushman in the U.S.A and Subbotina in the Soviet Union developed the use of foraminifera as biostratigraphic tools. Later in the 20th century Loeblich and Tappan and Bolli carried out much pioneering work.
b) The protists are best defined in terms of what they are not: They are not procaryotes. They are mostly free-living and unicellular. They are not animals. They are not plants. They are not algae (though many argue that algae and protozoa ought to be grouped together). They are not fungi. They are not viruses.
c) Put another way: They typically do not have cell walls. They are not multicellular (or, if so, then colonial with minimal cellular differentiation). And, they are heterotrophs, not autotrophic (as are plants) but instead must eat other organisms (photosynthetic algae are an exception but we're avoiding lumping algae in with the protista in this discussion).
d) The need for the negative definition is to immediately focus your attention away from any consideration that protozoa should be considered a monophyletic taxon. This is because the protozoa consist of a number (actually the majority) of deeply rooted lineages found among the eucaryotes, including those that lead to the fungi, the plants, and the animals. Indeed, the take home message from the discussions presented thus far are that the niches open to unicellular eucaryotes must be numerous and long lived.
e) The majority of 16S rRNA genetic divergence (universal tree) found among eucaryotes is found within Protista. The evolutionary radiance (which presumably was associated with the16S rRNA genetic divergence) into the various niches occupied by protozoa therefore presumably occurred at or near the dawn of the eucaryotic cellular architecture. These niches have been sufficiently stable that they have maintained diverse protozoan lineages to the present.
f) As noted, some authors group together protozoa and microscopic algae. Think in this case of the algae as protozoa with chloroplasts. In this scheme the protista are "unicellular or colonial microorganisms that lack specialization into tissues." (p. 146, Talaro and Talaro, 1996) Here we will consider algae in a separate lecture, however.
g) In this lecture we will walk through descriptions of features associated with various protozoa. We will then progress to a discussion of diseases caused by protozoa. Since protozoan diseases can be very complicated and relevant, we will go through the life cycles of a few of the more important protozoan parasites including those causing malaria and giardiasis.
Huge Single-Celled Organisms Spotted at Record Breaking Six Miles Under Water
Mariana Trench Ocean single-celled organism world's largest xenophyophores
by Max Eddy | 12:41 pm, October 25th, 2011
If you haven’t heard of xenophyophores, you’re probably in good company. First thought to be sea sponges, these ocean dwellers have been tossed around taxanomically for nearly a century until finally settling into their role as the world’s largest single-celled organism. A recent expedition to the Mariana Trench by National Geographic spotted the strange creatures some six miles under the ocean, the greatest depth at which xenophyophores have been found.
Though they come in different shapes and sizes, xenophyophores are widely distributed throughout the world and can live in truly brutal conditions. This is partly due to their ability to eat sediment and tolerate high levels of heavy metals like uranium. In addition to their weird single-celled status, these creatures also secrete a kind of organic cement and build their bodies out of whatever is lying around nearby. Amazingly, they can grow to pretty spectacular sizes. The ones recently found in the Mariana were about four inches wide, and they were not even the largest on record.
IT’S past time to tell the truth about the state of the world’s coral reefs, the nurseries of tropical coastal fish stocks. They have become zombie ecosystems, neither dead nor truly alive in any functional sense, and on a trajectory to collapse within a human generation. There will be remnants here and there, but the global coral reef ecosystem — with its storehouse of biodiversity and fisheries supporting millions of the world’s poor — will cease to be.
Overfishing, ocean acidification and pollution are pushing coral reefs into oblivion. Each of those forces alone is fully capable of causing the global collapse of coral reefs; together, they assure it. The scientific evidence for this is compelling and unequivocal, but there seems to be a collective reluctance to accept the logical conclusion — that there is no hope of saving the global coral reef ecosystem.
What we hear instead is an airbrushed view of the crisis — a view endorsed by coral reef scientists, amplified by environmentalists and accepted by governments. Coral reefs, like rain forests, are a symbol of biodiversity. And, like rain forests, they are portrayed as existentially threatened — but salvageable. The message is: “There is yet hope.”
Indeed, this view is echoed in the “consensus statement” of the just-concluded International Coral Reef Symposium [ http://www.icrs2012.com/ ], which called “on all governments to ensure the future of coral reefs.” It was signed by more than 2,000 scientists, officials and conservationists.
This is less a conspiracy than a sort of institutional inertia. Governments don’t want to be blamed for disasters on their watch, conservationists apparently value hope over truth, and scientists often don’t see the reefs for the corals.
But by persisting in the false belief that coral reefs have a future, we grossly misallocate the funds needed to cope with the fallout from their collapse. Money isn’t spent to study what to do after the reefs are gone — on what sort of ecosystems will replace coral reefs and what opportunities there will be to nudge these into providing people with food and other useful ecosystem products and services. Nor is money spent to preserve some of the genetic resources of coral reefs by transferring them into systems that are not coral reefs. And money isn’t spent to make the economic structural adjustment that communities and industries that depend on coral reefs urgently need. We have focused too much on the state of the reefs rather than the rate of the processes killing them.
Overfishing, ocean acidification and pollution have two features in common. First, they are accelerating. They are growing broadly in line with global economic growth, so they can double in size every couple of decades. Second, they have extreme inertia — there is no real prospect of changing their trajectories in less than 20 to 50 years. In short, these forces are unstoppable and irreversible. And it is these two features — acceleration and inertia — that have blindsided us.
Overfishing can bring down reefs because fish are one of the key functional groups that hold reefs together. Detailed forensic studies of the global fish catch [ http://www.sciencedirect.com/science/article/pii/S0165783610002754 ] by Daniel Pauly’s lab at the University of British Columbia [ http://www.zoology.ubc.ca/person/~pauly ] confirm that global fishing pressure is still accelerating even as the global fish catch is declining. Overfishing is already damaging reefs worldwide, and it is set to double and double again over the next few decades.
Ocean acidification can also bring down reefs because it affects the corals themselves. Corals can make their calcareous skeletons only within a special range of temperature and acidity of the surrounding seawater. But the oceans are acidifying as they absorb increasing amounts of carbon dioxide from the atmosphere. Research led by Ove Hoegh-Guldberg [ http://www.sciencemag.org/content/318/5857/1737.abstract ] of the University of Queensland [ http://www.gci.uq.edu.au/ ] shows that corals will be pushed outside their temperature-acidity envelope in the next 20 to 30 years, absent effective international action on emissions.
We have less of a handle on pollution. We do know that nutrients, particularly nitrogenous ones, are increasing not only in coastal waters but also in the open ocean. This change is accelerating. And we know that coral reefs just can’t survive in nutrient-rich waters. These conditions only encourage the microbes and jellyfish that will replace coral reefs in coastal waters. We can say, though, with somewhat less certainty than for overfishing or ocean acidification that unstoppable pollution will force reefs beyond their survival envelope by midcentury.
This is not a story that gives me any pleasure to tell. But it needs to be told urgently and widely because it will be a disaster for the hundreds of millions of people in poor, tropical countries like Indonesia and the Philippines who depend on coral reefs for food. It will also threaten the tourism industry of rich countries with coral reefs, like the United States, Australia and Japan. Countries like Mexico and Thailand will have both their food security and tourism industries badly damaged. And, almost an afterthought, it will be a tragedy for global conservation as hot spots of biodiversity are destroyed.
What we will be left with is an algal-dominated hard ocean bottom, as the remains of the limestone reefs slowly break up, with lots of microbial life soaking up the sun’s energy by photosynthesis, few fish but lots of jellyfish grazing on the microbes. It will be slimy [ http://www.sciencemag.org/content/307/5716/1725.summary?sid=f6d73c58-81cf-4a59-85aa-a4a394b24ccd ] and look a lot like the ecosystems of the Precambrian era, which ended more than 500 million years ago and well before fish evolved.
Coral reefs will be the first, but certainly not the last, major ecosystem to succumb to the Anthropocene — the new geological epoch now emerging. That is why we need an enormous reallocation of research, government and environmental effort to understand what has happened so we can respond the next time we face a disaster of this magnitude. It will be no bad thing to learn how to do such ecological engineering now.
Ocean acidity increases surprise researchers In this file photo, fish swim amongst bleached coral near the Keppel Islands in the Great Barrier Reef, Australia. Ocean acidification has emerged as one of the biggest threats to coral reefs across the world. Extra carbon dioxide from the atmosphere has ended up in the world's oceans, increasing the acidity of the sea, scientists say. Reducing carbon emissions could help solve the problem. July 9, 2012 http://www.csmonitor.com/Science/2012/0709/Ocean-acidity-increases-surprise-researchers [with comments]
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US scientist: Ocean acidity major threat to reefs In this Jan. 23, 2006 file photo provided by Centre of Marine Studies, The University of Queensland, fish swim amongst bleached coral near the Keppel Islands in the Great Barrier Reef, Australia. Ocean acidification has emerged as one of the biggest threats to coral reefs across the world, acting as the "osteoporosis of the sea" and threatening everything from food security to tourism to livelihoods, the head of a U.S. scientific agency said Monday, July 9, 2012. 7/9/2012 http://www.msnbc.msn.com/id/48118757/ns/us_news-environment/ [with comments]
Scientists discover new trigger for immense North Atlantic Ocean spring plankton bloom The satellite image, with eddies clearly visible, shows chlorophyll concentration in the North Atlantic during the spring phytoplankton bloom. Scientists have long known that widespread springtime blooms take up enormous quantities of carbon dioxide, creating organic matter and emitting oxygen. The North Atlantic is an especially crucial region, responsible for more than 20 percent of the entire ocean’s uptake of human-generated carbon dioxide. New understanding of the underlying physical mechanisms of the annual blooms allows them to be represented more accurately in global models of the oceanic carbon cycle and improves the models' predictive capability. Courtesy of Bror Jonsson, Princeton University, and MODIS satellite data, NASA July 5, 2012 http://phys.org/news/2012-07-scientists-trigger-immense-north-atlantic.html [no comments yet]
Animals are already dissolving in Southern Ocean acid
18:00 25 November 2012 by Michael Marshall
In a small patch of the Southern Ocean, the shells of sea snails are dissolving. The finding is the first evidence that marine life is already suffering as a result of man-made ocean acidification.
"This is actually happening now," says Geraint Tarling [ http://www.antarctica.ac.uk/about_bas/contact/staff/profile/1e595b952fd7c6075438b02616174aa0 ] of the British Antarctic Survey in Cambridge, UK. He and colleagues captured free-swimming sea snails called pteropods from the Southern Ocean in early 2008 and found under an electron microscope that the outer layers of their hard shells bore signs of unusual corrosion.
As well as warming the planet, the carbon dioxide we emit is changing the chemistry of the ocean. CO2 dissolves in water to form carbonic acid, making the water less alkaline. The pH is currently dropping at about 0.1 per century, faster than any time in the last 300 million years [ http://www.newscientist.com/article/dn21534-oceans-acidifying-at-unprecedented-speed.html ].
The most vulnerable animals are those, like pteropods, that build their shells entirely from aragonite, a form of calcium carbonate that is very sensitive to extra acidity. By 2050, there will be a severe shortage of aragonite in much of the ocean.
Aragonite is still relatively plentiful in most of the ocean, but Tarling suspected that some regions might already be affected by shortages.
He visited the Southern Ocean near South Georgia where deep water wells up to the surface. This water is naturally low in aragonite, meaning the surface waters it supplies are naturally somewhat low in the mineral – although not so much so that it would normally be a problem. Add in the effect of ocean acidification, however, and Tarling found that the mineral was dangerously sparse at the surface.
Aragonite-depleted regions are still rare, but they will become widespread by 2050, says Tarling. The polar oceans will change fastest, with the tropics following a few decades after. "These pockets will start to get larger and larger until they meet," he says.
The only way to stop ocean acidification is to reduce our CO2 emissions, Tyrrell says. It has been suggested that we could add megatonnes of lime to the ocean to balance the extra acidity. However, Tyrrell says this is "probably not practical" because the amounts involved – and thus the costs – are enormous.
Antarctic marine wildlife is under threat, study finds
The research took place in the Southern Ocean
Pteropods are an important food source for fish and birds
A pteropod (Limacina helicina antarctica) showing acute levels of shell dissolution
25 November 2012 Last updated at 18:13
Marine snails in seas around Antarctica are being affected by ocean acidification, scientists have found.
An international team of researchers found that the snails' shells are being corroded.
Experts says the findings are significant for predicting the future impact of ocean acidification on marine life.
The results of the study are published in the journal Nature Geoscience.
The marine snails, called "pteropods", are an important link in the oceanic food chain as well as a good indicator of ecosystem health.
"They are a major grazer of phytoplankton and... a key prey item of a number of higher predators - larger plankton, fish, seabirds, whales," said Dr Geraint Tarling, Head of Ocean Ecosystems at the British Antarctic Survey (BAS) and co-author of the report.
The study was a combined project involving researchers from the BAS, the National Oceanic and Atmospheric Administration (NOAA), the US Woods Hole Oceanographic Institution and the University of East Anglia's school of Environmental Sciences.
Ocean acidification is a result of burning fossil fuels: some of the additional carbon dioxide in the atmosphere is absorbed into oceans.
This process alters the chemistry of the water, making it more acidic.
During a research cruise in the Southern Ocean in 2008, scientists assessed the corrosive effects of upwelled water on pteropod shells.
Upwelling occurs when winds push cold layers of deeper seawater from around 1,000m towards the surface layers.
Seawater from these depths is more corrosive to aragonite, the type of calcium carbonate that forms pteropod shells. The point at which this occurs is known as the "saturation horizon".
"Carbonates in shells dissolve more when temperatures are cold and pressure is high, which are the characteristic properties of the deep ocean," Dr Tarling explained.
Scientists found that the combined effect of increased ocean acidity and natural upwelling meant that in some areas of the Southern Ocean the saturation horizon was around just 200m - the upper layer of the ocean where pteropods live.
Dr Tarling explained the significance of these findings: "The snails do not necessarily die as a result of their shells dissolving, however it may increase their vulnerability to predation and infection, consequently having an impact to other parts of the food web."
He said that although upwelling sites are a natural phenomenon in the Southern Ocean, "instances where they bring the saturation horizon above 200m will become more frequent as ocean acidification intensifies in the coming years".
Interpreting the results
Dr Tarling said the study is "very much... a pilot study" and that it has provided an important body of work regarding "how pteropods will respond to future oceanic conditions".
To date there have been a number of laboratory studies predicting the effects of ocean acidification on marine organisms, but none assessing the impacts on live specimens in their natural environment.
"It took us several years even to develop a technique sensitive enough to look at the exterior of the shells under high-power scanning electron microscopes, since the shells are very thin and the dissolution pattern, subtle," commented Dr Tarling.
He went on: "We are now undertaking a much more comprehensive programme completely focussed on the effects of ocean acidification, not just on pteropods but to a wider range of organisms."
Ocean acidification caused by increased levels of carbon dioxide in the atmosphere is eating away at the shells of marine snails known as “sea butterflies”, the researchers said.
Shells of tiny sea snails are being eroded as more carbon dioxide is dissolved into seawater
Steve Connor Sunday 25 November 2012
Rising amounts of carbon dioxide dissolving in the ocean is causing the acid corrosion of tiny sea creatures that form the base of the marine food chain, scientists have discovered.
Ocean acidification caused by increased levels of carbon dioxide in the atmosphere is eating away at the shells of marine snails known as “sea butterflies”, the researchers said.
It is the first time that scientists have discovered the visibly acid-damaged shells of critically-important organisms living in the Southern Ocean off Antarctica. The researchers believe it could be a harbinger of worse things to come.
The sea butterflies, also known as pteropod snails, live in the surface layers of the open ocean, grow no bigger than a centimetre across and are part of the floating plankton on which all other fish and marine animals ultimately depend for their survival.
“Pteropods are an important food source for fish and birds as well as a good indicator of ecosystem health,” said Geraint Tarling of the British Antarctic Survey in Cambridge.
“The tiny snails do not necessarily die as a result of their shells dissolving, however it may increase their vulnerability to predation and infection, consequently having an impact on other parts of the food web,” Dr Tarling said.
In 2008, scientists on board a British scientific research vessel collected samples of pteropod snails from the Scotia Sea in the Atlantic sector of the Southern Ocean.
A microscopic analysis of a random sample of live pteropods revealed extensive acid erosion of their shells. It is the first documented case of acid damage to the shells of living wild pteropods, Dr Tarling said.
The scientists also found that the surrounding seawater had relatively low concentrations of a critically important calcium mineral called aragonite which the pteropods need for shell making. Aragonite concentrations fall when the seawater becomes less alkaline – and more acidic.
“The corrosive properties of the water caused shells of live animals to be severely dissolved and this demonstrates how vulnerable pteropods are,” said Nina Bednarsek, formerly of the British Antarctic Survey and now at the US National Oceanic and Atmospheric Administration.
“Ocean acidification resulting from the addition of human-induced carbon dioxide contributed to this dissolution,” said Dr Bednarsek, the lead author of the study, published in the journal Nature Geoscience.
The researchers found the damaged snails over areas of ocean “upwelling”, where cold, nutrient-rich deep water rises to the surface. Pteropods and other plankton congregate over upwelling spots because they are good sources of nutrients and food.
Upwelling is known to have a corrosive effect on marine shells because deep seawater is naturally rich in dissolved carbon dioxide and so, when it rises to the surface, it lowers the concentration of aragonite in the shallower layers of the ocean where pteropods live.
However, the researchers found that the increased concentration of carbon dioxide in the atmosphere, caused by the burning of fossil fuels, has tipped the aragonite balance in favour of the acidic corrosion of the pteropod shells in these upwelling areas.
“We know that the seawater becomes more corrosive to aragonite shells below a certain depth…which occurs around 1,000 metres depth,” Dr Bednarsek said.
“However, at one of our sampling sites, we discovered that this point was reached at 200 metres depth, through a combination of natural upwelling and ocean acidification. Marine snails – pteropods – live in this top layer of the ocean,” she said.
Dr Tarling said that computer modelling identified the role played by man-made carbon dioxide in the atmosphere which is causing the acidification of the oceans.
“If we had the carbon dioxide concentrations we had a century or more ago, the conditions wouldn’t have got to the corrosive state that we have observed,” said Dr Tarling.
If carbon dioxide concentrations continue to rise as expected in the coming decades, the areas of the ocean that will become corrosive to shelled creatures will spread over much wider areas, he added.
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