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Surprising finding: Tree's leaves genetically different from its roots

Surprising finding: Tree's leaves genetically different from its roots | All About Science | Scoop.it

Black cottonwood trees (Populus trichocarpa) can clone themselves to produce offspring that are connected to their parents by the same root system. Now, after the first genome-wide analysis of a tree, it turns out that the connected clones have many genetic differences, even between tissues from the top and bottom of a single tree. The variation within a tree is as great as the variation across unrelated trees. Such somatic mutations — those that occur in cells other than sperm or eggs — are familiar to horticulturalists, who have long bred new plant varieties by grafting mutant branches onto ‘normal’ stocks. But until now, no one has catalogued the total number of somatic mutations in an individual plant.

 

In one tree, the top buds of the parent and offspring were genetically closer to each other than to their respective roots or lower branches. In another tree, the top bud was closer to the reference cottonwood genome than to any of the other tissues from the same individual.The tissue-specific mutations affected mainly genes involved in cell death, immune responses, metabolism, DNA binding and cell communication. Olds think that this may be because many of the mutations are harmful, and the tree reacts by destroying the mutated tissues or altering its metabolic pathways and the way it controls its genes, which leads to further mutations.

 

The findings have parallels to cancer studies, which have recently shown that separate parts of the same tumor can evolve independently and build up distinct genetic mutations, meaning that single biopsies give only a narrow view of the tumor’s diversity.


Via Dr. Stefan Gruenwald, Complexity Digest, Ganesh Bagler
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Scientists shed light on evolution of gene regulation | e! Science News

Scientists shed light on evolution of gene regulation | e! Science News | All About Science | Scoop.it
Scientists at Penn State have shed light on some of the processes that regulate genes -- such as the processes that ensure that proteins are produced at the correct time, place, and amount in an organism -- and they also have shed light on the...

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Urbanization could spell doom on some biodiversity hotspots by 2030

Urbanization could spell doom on some biodiversity hotspots by 2030 | All About Science | Scoop.it

City populations are expected to grow by five billion people and expand by 1.2 million square kilometers by 2030. Much of this expansion is forecast to occur in the tropics, which contain the bulk of the world's species. The new study attempts to quantify the impact of urbanization on the world's so-called "hotspots" — nearly three dozen areas with exceptionally high levels of species found no where else.

 

Using data from a variety of sources, researchers at Yale University, Texas A&M University, and Boston University developed a probabilistic model for estimating the impacts of urbanization on vegetation, carbon stocks, and threatened species. They found that by 2030, nearly three percent of hotspot areas will be urbanized, up from one percent in 2000. While the extent seems small, paving over marshes, forests, and grasslands could generate 1.38 billion tons of carbon emissions (5 billion tons of CO2) from direct land use change. Some 214 species currently listed as endangered and critically endangered and considered focal species by the Alliance for Zero Extinction (AZE) would be affected by urban expansion, including 20 — 15 of which are amphibians — that would experience complete urbanization of their habitat.

 

The biggest biodiversity impacts would occur in Africa and Europe, whereas the biggest increase in hotspot urbanization is forecast in Africa and Asia, specifically the Eastern Afromontane, the Guinean Forests of West Africa, the Western Ghats and Sri Lanka hotspots, according to the study.


Via Dr. Stefan Gruenwald, Beth Heller
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Flavoenzymes: Versatile catalysts in biosynthetic pathways

Riboflavin-based coenzymes, tightly bound to enzymes catalyzing substrate oxidations and reductions, enable an enormous range of chemical transformations in biosynthetic pathways.

Flavoenzymes catalyze substrate oxidations involving amine and alcohol oxidations and desaturations to olefins, the latter setting up Diels–Alder cyclizations in lovastatin and solanapyrone biosyntheses. Both C4a and N5 of the flavin coenzymes are sites for covalent adduct formation. For example, the reactivity of dihydroflavins with molecular oxygen leads to flavin-4a-OOH adducts which then carry out a diverse range of oxygen transfers, including Baeyer–Villiger type ring expansions, olefin epoxidations, halogenations via transient HOCl generation, and an oxidative Favorskii rerrangement during enterocin assembly.

Christopher T. Walsh and Timothy A. Wencewicz
Nat. Prod. Rep., 2012, Advance Article
DOI: 10.1039/C2NP20069D


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A First - Organbuilders: Scientists Make Progress in Tailor-Made Organs

A First - Organbuilders: Scientists Make Progress in Tailor-Made Organs | All About Science | Scoop.it
Tissue engineers have succeeded in making artificial organs that use a patient’s cells to become a living part of the body, with hope for eventual organ regeneration.

 

So far, only a few organs have been made and transplanted, and they are relatively simple, hollow ones — like bladders and Mr. Beyene’s windpipe, which was implanted in June 2011. But scientists around the world are using similar techniques with the goal of building more complex organs. At Wake Forest University in North Carolina, for example, where the bladders were developed, researchers are working on kidneys, livers and more. Labs in China and the Netherlands are among many working on blood vessels.

 

The work of these new body builders is far different from the efforts that produced artificial hearts decades ago. Those devices, which are still used temporarily by some patients awaiting transplants, are sophisticated machines, but in the end they are only that: machines.

Tissue engineers aim to produce something that is more human. They want to make organs with the cells, blood vessels and nerves to become a living, functioning part of the body. Some, like Dr. Macchiarini, want to go even further — to harness the body’s repair mechanisms so that it can remake a damaged organ on its own.

 

Researchers are making use of advances in knowledge of stem cells, basic cells that can be transformed into types that are specific to tissues like liver or lung. They are learning more about what they call scaffolds, compounds that act like mortar to hold cells in their proper place and that also play a major role in how cells are recruited for tissue repair.

 

Tissue engineers caution that the work they are doing is experimental and costly, and that the creation of complex organs is still a long way off. But they are increasingly optimistic about the possibilities.


Via Dr. Stefan Gruenwald
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The Biological Internet That Could One Day Program Artificial Organs

The Biological Internet That Could One Day Program Artificial Organs | All About Science | Scoop.it

Scientists have just found a way to use DNA to send massive amounts of data between cells, which means we soon may be able to give our cells incredibly complicated instructions.

 


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Breakthrough: Researchers create an animal entirely from stem cells

Breakthrough: Researchers create an animal entirely from stem cells | All About Science | Scoop.it

Biotechnology is getting into some pretty interesting territory these days. The latest breakthrough comes from Kyoto University where research scientists have, for the first time, created a mouse by using eggs and sperm produced by stem cells alone. The achievement once again shows the remarkable possibilities presented by regenerative technologies like stem cells — but also the unsettling potential for human births in which parents might not be required.


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Scientists discover 500MILLION year old bug brain fossil that could revolutionise understanding of insect evolution

Scientists discover 500MILLION year old bug brain fossil that could revolutionise understanding of insect evolution | All About Science | Scoop.it
Hailing the find in China a 'transformative discovery', experts said the 3in long fossil shows that insects evolved to have complex brains much earlier than previously thought.

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Application of synthetic biology in cyanobacteria and algae

by

Wang B, Wang J, Zhang W, Meldrum DR.

"Cyanobacteria and algae are becoming increasingly attractive cell factories for producing renewable biofuels and chemicals due to their ability to capture solar energy and CO(2) and their relatively simple genetic background for genetic manipulation. Increasing research efforts from the synthetic biology approach have been made in recent years to modify cyanobacteria and algae for various biotechnological applications. In this article, we critically review recent progresses in developing genetic tools for characterizing or manipulating cyanobacteria and algae, the applications of genetically modified strains for synthesizing renewable products such as biofuels and chemicals. In addition, the emergent challenges in the development and application of synthetic biology for cyanobacteria and algae are also discussed."

http://1.usa.gov/RiujLW


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Glaciers cracking in the presence of carbon dioxide

Glaciers cracking in the presence of carbon dioxide | All About Science | Scoop.it
(Phys.org)—The well-documented presence of excessive levels of carbon dioxide (CO2) in our atmosphere is causing global temperatures to rise and glaciers and ice caps to melt.

 

 

 

Read more, a MUST:

http://phys.org/news/2012-10-glaciers-presence-carbon-dioxide.html

 


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The original Twitter? Tiny electronic tags monitor birds’ social networks

The original Twitter? Tiny electronic tags monitor birds’ social networks | All About Science | Scoop.it

If two birds meet deep in the forest, does anybody hear? Until now, nobody did, unless an intrepid biologist was hiding underneath a bush and watching their behavior, or the birds happened to meet near a research monitoring station. But an electronic tag designed at the University of Washington can for the first time see when birds meet in the wild.

 

A new study led by a biologist at Scotland’s University of St. Andrews used the UW tags to see whether crows might learn to use tools from one another. The findings, published last week in Current Biology, supported the theory by showing an unexpected amount of social mobility, with the crows often spending time near birds outside their immediate family.

 

A study led by St. Andrews University in Scotland tagged New Caledonian crows to learn about their social behavior.

The study looked at crows in New Caledonia, an archipelago of islands in the South Pacific. The crows are famous for using different tools to extract prey from deadwood and vegetation. Biologists wondered whether the birds might learn by watching each other.

The results, as reported by St. Andrews, revealed “a surprising number of contacts” between non-related crows. During one week, the technology recorded more than 28,000 interactions among 34 crows. While core family units of New Caledonian crows contain only three members, the study found all the birds were connected to the larger social network.


Via Dr. Stefan Gruenwald
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Study Shows Some Turtles Urinate through Mouth

Study Shows Some Turtles Urinate through Mouth | All About Science | Scoop.it
A team of biologists led by Dr Yuen Ip of the National University of Singapore has discovered that Chinese soft-shelled turtles, Pelodiscus sinensis, effectively urinate through mouth.

 

Chinese soft-shelled turtles are exquisitely adapted to their aquatic lifestyle, sitting contentedly on the bottom of brackish muddy swamps or snorkelling at the surface to breath. They even immerse their heads in puddles when their swampy homes dry up. Why do these air-breathing turtles submerge their heads when they mainly depend on their lungs to breathe and are unlikely to breathe in water? Given that some fish excrete waste nitrogen as urea and expel the urea through their gills, the team wondered whether the turtles were plunging their heads into water to excrete waste urea through their mouths, where they have strange gill-like projections.


Via Dr. Stefan Gruenwald
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Genes for face shape identified

Genes for face shape identified | All About Science | Scoop.it
Scientists identify five genes that determine the form of the human face in a find that could lead to sketches based solely on DNA findings.

 

Understanding the genes that determine human facial shape could one day provide valuable information about person's appearance using just their DNA.

 

The discovery of five genes involved in facial form could have applications in forensics, say the authors of a study.

 

Virtually nothing was known about the genes responsible for facial shape in humans.

 

The study of almost 10,000 individuals is published in the journal Plos One.

 

Lead author Manfred Kayser from the Erasmus University Medical Center in Rotterdam, The Netherlands, said: "These are exciting first results that mark the beginning of the genetic understanding of human facial morphology.

 

"Perhaps some time it will be possible to draw a phantom portrait of a person solely from his or her DNA left behind, which provides interesting applications such as in forensics."

 

The researchers used magnetic resonance imaging (MRI) of people's heads together with portrait photographs to map facial landmarks, from which facial distances were estimated.

 

They then conducted what is known as a genome-wide association study, which is designed to search for small genetic variations that occur more frequently in people with particular facial types.

 

Prof Kayser and his colleagues identified five candidate genes associated with different facial shapes - known as PRDM16, PAX3, TP63, C5orf50, and COL17A1.

 

These associations mean the likelihood of a certain face shape can be estimated, and a full DNA-to-portrait mapping still remains a distant prospect.

 

But together with recent findings that suggest DNA can also be used to predict hair and eye colour and a 2010 study in which age can be inferred from blood, forensics is set to add a suite of powerful new DNA-based tools to its arsenal.


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A flash of blue light changes cellular activity — and understanding of disease

A flash of blue light changes cellular activity — and understanding of disease | All About Science | Scoop.it
With a milliseconds-long flash of blue light, Yale University researchers regulated a critical type of signaling molecule within cell membranes, another illustration of the power of light-based techniques to manipulate cell functions and thus to study mechanisms of disease. One of the most innovative new research approaches of recent years is called optogenetics or the use of genetically encoded probes to make cell functions sensitive to light. The team combined a plant protein that is sensitive to blue light with enzymes that catalyze the metabolism of signaling lipids within the cell membranes. When the complex was expressed in animal cells, scientists changed properties of cells such as their shape or ability to move simply by using blue light. By turning off the light, the researchers were able to rapidly reverse the changes they induced. They were also able to regulate activities within a region of a cell by illuminating the area.

Via Dr. Stefan Gruenwald, Julie Dunbar McTague
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'Extremophiles' Prove Their Worth

Scientists are "bio-prospecting" single-celled critters that live in the harshest environments on Earth for their hardy genes. But some question whether anyone should profit from Mother Nature.

Via Catherine Jackson
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A diamond exoplanet slightly bigger than Earth discovered around a sun-like star

A diamond exoplanet slightly bigger than Earth discovered around a sun-like star | All About Science | Scoop.it

Orbiting a star that is visible to the naked eye, astronomers have discovered a planet twice the size of our own made largely out of diamond. The rocky planet, called '55 Cancri e', orbits a sun-like star in the constellation of Cancer and is moving so fast that a year there lasts a mere 18 hours. Cancri e is about 40 light years, or 230 trillion miles away from Earth.

 

Discovered by a U.S.-Franco research team, its radius is twice that of Earth's but it is much more dense with a mass eight times greater. It is also incredibly hot, with temperatures on its surface reaching 3,900 degrees Fahrenheit (1,648 Celsius).

 

"The surface of this planet is likely covered in graphite and diamond rather than water and granite," said Nikku Madhusudhan, the Yale researcher whose findings are due to be published in the journal Astrophysical Journal Letters.

 

The study - with Olivier Mousis at the Institut de Recherche en Astrophysique et Planetologie in Toulose, France - estimates that at least a third of the planet's mass, the equivalent of about three Earth masses, could be diamond. Diamond planets have been spotted before but this is the first time one has been seen orbiting a sun-like star and studied in such detail.

 

"This is our first glimpse of a rocky world with a fundamentally different chemistry from Earth," Madhusudhan said, adding that the discovery of the carbon-rich planet meant distant rocky planets could no longer be assumed to have chemical constituents, interiors, atmospheres, or biologies similar to Earth. David Spergel, an astronomer at Princeton University, said it was relatively simple to work out the basic structure and history of a star once you know its mass and age.

 

"Planets are much more complex. This 'diamond-rich super-Earth' is likely just one example of the rich sets of discoveries that await us as we begin to explore planets around nearby stars."


Via Dr. Stefan Gruenwald
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Ingredient of life in space found! Enough water vapor in star cloud to fill 2,000 Earth's oceans

Ingredient of life in space found! Enough water vapor in star cloud to fill 2,000 Earth's oceans | All About Science | Scoop.it

A distant gas and dust cloud that is likely to collapse into a Sun-like star has enough water vapor to fill Earth’s oceans more than 2,000 times over. The discovery marks the first time scientists have detected water vapor in a “pre-stellar core”—the cold, dark clouds of gas and dust from which stars form.


“To produce that amount of vapor, there must be a lot of water ice in the cloud, more than three million frozen Earth oceans’ worth,” says Paola Caselli, a professor at the University of Leeds.

 

The discovery was made using the European Space Agency’s Herschel Space Observatory, in a pre-stellar core known as Lynds 1544, in the constellation of Taurus. Water has previously been detected outside of our Solar System as gas and ice coated onto tiny dust grains near sites of active star formation, and in proto-planetary discs capable of forming planetary systems. More than 2,000 Earth oceans-worth of water vapor were detected, liberated from icy dust grains by high-energy cosmic rays passing through the cloud. Some of the water vapor detected in L1544 will go into forming the star, but the rest will be incorporated into the surrounding disc, providing a rich water reservoir to feed potential new planets.

 

“Thanks to Herschel, we can now follow the ‘water trail’ from a molecular cloud in the interstellar medium, through the star formation process, to a planet like Earth where water is a crucial ingredient for life,” says ESA’s Herschel project scientist, Göran Pilbratt.


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Most extensive pictures ever of an organism's DNA mutation rates and processes

Most extensive pictures ever of an organism's DNA mutation rates and processes | All About Science | Scoop.it

Biologists and informaticists at Indiana University have produced one of the most extensive pictures ever of mutation processes in the DNA sequence of an organism, elucidating important new evolutionary information about the molecular nature of mutations and how fast those heritable changes occur. By analyzing the exact genomic changes in the model prokaryote Escherichia coli that had undergone over 200,000 generations of growth in the absence of natural selective pressures, the team led by IU College of Arts and Sciences Department of Biology professor Patricia L. Foster found that spontaneous mutation rates in E. coli DNA were actually three times lower than previously thought.


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A mammal lung, in 3D

A mammal lung, in 3D | All About Science | Scoop.it
A University of Iowa-led research team has created the most detailed, three-dimensional rendering of a key region of a mammal lung.

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NASA Discovers Far Off Galaxy that could be the Missing Link to the Evolution ... - Student Operated Press

NASA Discovers Far Off Galaxy that could be the Missing Link to the Evolution ... - Student Operated Press | All About Science | Scoop.it

TG DailyNASA Discovers Far Off Galaxy that could be the Missing Link to the Evolution ...Student Operated PressDiscovering hidden galaxies to NASA is like Christopher Columbus discovering America back in 1492.


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Seadiscovery.com - Polarstern Returnes from Central Arctic Expedition “IceArc“

Seadiscovery.com - Polarstern Returnes from Central Arctic Expedition “IceArc“ | All About Science | Scoop.it

Polarstern returned from the Central Arctic expedition “IceArc“ to Bremerhaven on 8 October 2012 after a good two months. 54 scientists and technicians from twelve different countries conducted research on the retreat of the sea ice and the consequences for the Arctic Ocean and its ecosystems over a period of two months in the High North. A number of new technologies were used for to film and photograph life in and below the ice down to a depth of 4400 meters. Since its departure from Tromsø (Norway) on 2 August 2012 Polarstern has traveled some 12,000 kilometers and conducted research at 306 stations. These included nine ice stations where the ship moored to an ice floe for several days to examine the ice, the water beneath it and the bottom of the sea. Many measurements were concerned with responses to the rapid retreat of the sea ice this summer. The researchers determined that the thick multiyear sea ice in the area of investigation had declined further. With the so-called EM-Bird (electromagnetic sensor to record the thickness of sea ice) an area of 3,500 kilometers of sea ice was measured from a helicopter. As early as July 2012 the Siberian shelves including the Laptev Sea were free from ice, whereas in the summer of 2011 Polarstern had still encountered multiyear ice in this region. This means that the volume of ice is greatly reduced by melting. The fresh water content of the sea surface has increased accordingly as a result of the melting ice. “The Arctic of the future will consist of thinner sea ice which will therefore survive the summer less frequently, will drift more quickly and permit more light to penetrate the ocean. This will lead to great changes in the composition of sea life“, says head of the expedition Prof. Dr. Antje Boetius, who manages the Helmholtz-Max-Planck Research Group for Deep-sea Ecology and Technology at the Alfred Wegener Institute.


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Indiacens A and B: Prenyl Indoles from the Myxobacterium Sandaracinus amylolyticus

Indiacens A and B: Prenyl Indoles from the Myxobacterium Sandaracinus amylolyticus | All About Science | Scoop.it

The gliding bacterium Sandaracinus amylolyticus, strain NOSO-4T, was recently characterized as the first representative of a new myxobacterial genus. A screening of the culture broth for antibiotically active metabolites followed by isolation and characterization revealed two unique 3-formylindol derivatives, indiacen A (1) and its chloro derivative indiacen B (2). Both are active against Gram-positive and Gram-negative bacteria as well as the fungus Mucor hiemalis. The biosynthetic origin of the isoprene-like side chain in 1 and 2 was studied by in vivo feeding experiments with 13C-labeled precursors.

Heinrich Steinmetz, Kathrin I. Mohr, Wiebke Zander, Rolf Jansen, Klaus Gerth, and Rolf Müller
J. Nat. Prod., Article ASAP
DOI: 10.1021/np300288b



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PLOS Genetics: The Non-Flagellar Type III Secretion System Evolved from the Bacterial Flagellum and Diversified into Host-Cell Adapted Systems (2012)

PLOS Genetics: The Non-Flagellar Type III Secretion System Evolved from the Bacterial Flagellum and Diversified into Host-Cell Adapted Systems (2012) | All About Science | Scoop.it

Type 3 secretion systems (T3SSs) are essential components of two complex bacterial machineries: the flagellum, which drives cell motility, and the non-flagellar T3SS (NF-T3SS), which delivers effectors into eukaryotic cells. Yet the origin, specialization, and diversification of these machineries remained unclear. We developed computational tools to identify homologous components of the two systems and to discriminate between them. Our analysis of >1,000 genomes identified 921 T3SSs, including 222 NF-T3SSs. Phylogenomic and comparative analyses of these systems argue that the NF-T3SS arose from an exaptation of the flagellum, i.e. the recruitment of part of the flagellum structure for the evolution of the new protein delivery function. This reconstructed chronology of the exaptation process proceeded in at least two steps. An intermediate ancestral form of NF-T3SS, whose descendants still exist in Myxococcales, lacked elements that are essential for motility and included a subset of NF-T3SS features. We argue that this ancestral version was involved in protein translocation. A second major step in the evolution of NF-T3SSs occurred via recruitment of secretins to the NF-T3SS, an event that occurred at least three times from different systems. In rhizobiales, a partial homologous gene replacement of the secretin resulted in two genes of complementary function. Acquisition of a secretin was followed by the rapid adaptation of the resulting NF-T3SSs to multiple, distinct eukaryotic cell envelopes where they became key in parasitic and mutualistic associations between prokaryotes and eukaryotes. Our work elucidates major steps of the evolutionary scenario leading to extant NF-T3SSs. It demonstrates how molecular evolution can convert one complex molecular machine into a second, equally complex machine by successive deletions, innovations, and recruitment from other molecular systems.


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