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Scooped by Dr. Stefan Gruenwald!

Flies live 30 percent longer when AMPK is activated

Flies live 30 percent longer when AMPK is activated | Amazing Science |

Activating a specific gene in the intestines of a fruit fly made it live 30 percent longer, a team of biologists has reported.

The gene in question, AMPK, detects and reacts to fluctuations in the body to help modulate energy levels. The gene is also found in humans in low levels, leading the UCLA team to postulate in the open source journal Cell Reports that we could use it to learn about potentially delaying the ageing process.

Key to this statement is the fact that in the experiment on the Drosophila melanogaster fruit fly, the ageing process slowed throughout the insect's organs -- not just in the intestine where AMPK was activated.

The team behind the study is taking an approach similar to that ofbiogerontologist and SENS Foundation co-founder Aubrey de Grey, who argues that instead of attempting to modify our cells to combat disease, we must repair the molecular damage that happens as cells degrade. Among the cell death, cell divisions and mitochondria mutations that he cites as being cellular problems to combat, is "molecular garbage", a problem also flagged up by the UCLA team. In the body, we naturally discard of this molecular garbage through a process known as autophagy.

Autophagy allows any cells that are old or degrading to be shed, and AMPK is known to help activate that system. "However, the tissue-specific mechanisms involved are poorly understood," writes the UCLA team in Cell Reports. If we could better understand and harness its capabilities, they argue, we could go some way in slowing the aging process by tackling the molecular garbage problem prevalent in old age. It is molecular garbage and protein buildups that contribute to some of the biggest killer diseases in later years.

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Are 75% of Australia's living species still unknown?

Are 75% of Australia's living species still unknown? | Amazing Science |

Australia may be known for its unique plants and animals, but how many do we actually know about? Jo Harding is the manager of Bush Blitz, a program supported by federal and state government agencies and research institutions, which documents plants and animals around Australia, leading to the discovery of hundreds of new species.

Ms. Harding states: "There's estimated to be about 75 per cent of Australia's biodiversity that's largely unknown. So there's certainly a lot out there still to find. We've discovered 700 new species so far, that's over the last approximately four years, and we're still counting."

The word 'biodiversity' has a complex scientific definition, but generally speaking, it is used as a catch-all phrase for all plants, animals and other living organisms in a particular area, a spokeswoman for Bush Blitz said.

It covers all types of plants (including algae) and fungi as well as vertebrates (such as mammals, reptiles, fish and birds) and invertebrates (such as insects and octopuses) in both marine and land environments.

A recent CSIRO publication on biodiversity says the scientific definition "includes more than just organisms themselves". "Its definition includes the diversity of the genetic material within each species and the diversity of ecosystems that those species make up, as well as the ecological and evolutionary processes that keep them functioning and adapting," the publication said.

"Biodiversity is not simply a list of species, therefore. It includes the genetic and functional operations that keep the living world working, so emphasizing inter-dependence of the elements of nature."

Undescribed species are species that may have been found before, maybe in different areas or by different people, but which haven't been formally identified. It is then up to an expert to examine the specimen to ensure it really is an undescribed species. The expert will then write a description for the species. Once the description of the new species has been established and published, it is called a described specimen.

Ms Harding's claim that about 75 per cent of Australia's biodiversity is unknown is based on a 2009 report published by the federal environment department. It aggregates information from a large number of sources and previous studies to calculate the number of species already discovered and estimate the number of species yet to be discovered both around the world and in Australia.

It determined that Australia had 147,579 "accepted described species", 26 per cent of its estimated total Australian species.

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Lactic acid bacteria from the honey bees could be the source for efficient treatment of MRSA

Lactic acid bacteria from the honey bees could be the source for efficient treatment of MRSA | Amazing Science |

Could honeybees' most valuable contribution to mankind besides pollination services be alternative tools against infections? Today, due to the emerging antibiotic-resistant pathogens, we are facing a new era of searching for alternative tools against infections. Natural products such as honey have been applied against human's infections for millennia without sufficient scientific evidence. A unique lactic acid bacterial (LAB) microbiota was discovered by us, which is in symbiosis with honeybees and present in large amounts in fresh honey across the world. This work investigates if the LAB symbionts are the source to the unknown factors contributing to honey's properties.

Hence, a group of researchers at Lund University have tested the LAB against severe wound pathogens such as methicillin-resistant Staphylococcus aureus (MRSA), Pseudomonas aeruginosa and vancomycin-resistant Enterococcus (VRE) among others. They were able to demonstrate a strong antimicrobial activity from each symbiont and a synergistic effect, which counteracted all the tested pathogens. The mechanisms of action are partly shown by elucidating the production of active compounds such as proteins, fatty acids, anaesthetics, organic acids, volatiles and hydrogen peroxide. The team showed that the symbionts produce a myriad of active compounds that remain in variable amounts in mature honey. Further studies are now required to investigate if these symbionts have a potential in clinical applications as alternative tools against topical human and animal infections.

"Antibiotics are mostly one active substance, effective against only a narrow spectrum of bacteria. When used alive, these 13 lactic acid bacteria produce the right kind of antimicrobial compounds as needed, depending on the threat. It seems to have worked well for millions of years of protecting bees' health and honey against other harmful microorganisms. However, since store-bought honey doesn't contain the living lactic acid bacteria, many of its unique properties have been lost in recent times", explains Tobias Olofsson.

The next step is further studies to investigate wider clinical use against topical human infections as well as on animals. The findings have implications for developing countries, where fresh honey is easily available, but also for Western countries where antibiotic resistance is seriously increasing.

Reference: Lactic acid bacterial symbionts in honeybees – an unknown key to honey's antimicrobial and therapeutic activities

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New deep sea mushroom-shaped organisms discovered with similarities to 600 million year old extinct creatures

New deep sea mushroom-shaped organisms discovered with similarities to 600 million year old extinct creatures | Amazing Science |
Scientists discovered two new species of sea-dwelling, mushroom-shaped organisms, according to a study published September 3, 2014 in the open-access journal PLOS ONE by Jean Just from University of Copenhagen, Denmark, and colleagues.

Scientists classify organisms based on shared characteristics using a taxonomic rank, including kingdom, phylum, and species. In 1986, the authors of this study collected organisms at 400 and 1000 meters deep on the south-east Australian continental slope and only just recently isolated two types of mushroom-shaped organisms that they couldn't classify into an existing phylum.

The new organisms are multicellular and mostly non-symmetrical, with a dense layer of gelatinous material between the outer skin cell and inner stomach cell layers. The organisms were classified as two new species in a new genusDendrogramma enigmatica and Dendrogramma discoides, in the new family, Dendrogrammatidae. Scientists found similarities between the organisms and members of Ctenophora and Cnidaria and suggest that they may be related to one of these phyla. Scientists also found similarities to 600 million year-old Pre-Cambrian extinct life forms, suggested by some to be early but failed attempts at multi-cellular life.

The authors originally preserved the specimens in neutral formaldehyde and stored them in 80% ethanol, which makes them unsuitable for molecular analysis. However, they suggest attempting to secure new samples for further study, which may provide further insight into their relationship to other organisms.

Jørgen Olesen added: "New mushroom-shaped animals from the deep sea discovered which could not be placed in any recognized group of animals. Two species are recognized and current evidence suggest that they represent an early branch on the tree of life, with similarities to the 600 mill old extinct Ediacara fauna."

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Coffee Genome Sequenced and Annotated

Coffee Genome Sequenced and Annotated | Amazing Science |

The coffee genome has been sequenced for the first time, brewing up a better understanding of that flavor, aroma, and buzz we love (and need) so much. According to the findings, published in Science this week, the caffeine-producing enzymes in coffee evolved independently from those in tea and chocolate. 

“The coffee genome helps us understand what’s exciting about coffee -- other than that it wakes me up in the morning,” says SUNY Buffalo’s Victor Albert in a news release. “By looking at which families of genes expanded in the plant, and the relationship between the genome structure of coffee and other species, we were able to learn about coffee’s independent pathway in evolution, including -- excitingly -- the story of caffeine.”

Commonly known as robusta coffee, Coffea canephora makes up 30 percent of the coffee produced worldwide -- which totals 8.7 million tons a year or 2.25 billion cups a day. The less acidic-tasting Coffea arabica makes up most of the rest, but this lower caffeine variety has a more complicated genome. 

So, to derive a draft genome of Coffea canephora, a huge consortium led by Albert and researchers from the French Institute of Research for Development and the French National Sequencing Center pieced together DNA sequences and assembled a total length of 568.6 megabases -- that’s 80 percent of the plant’s 710-megabase genome.

After running a comparative genomics software on protein sequences from coffee, grape, tomato, and a flowering plant called Arabidopsis, the team identified 16,000 genes that originated from a single gene in their last common ancestor. They were also able to pinpoint adaptations in genes for disease resistance and caffeine production that were unique to coffee. Overall, the team isolated 25,574 protein-making genes in the Coffea canephora genome and 23 new genes that are only found in coffee.

The robusta coffee genome also revealed that the enzymes involved in coffee’s caffeine production -- called N-methyltransferases -- adapted independently from those in cacao and tea. That is, they didn’t inherit their caffeine-linked genes from a common ancestor: The ability to produce caffeine must have evolved at least twice, and long before we started depending on it.

But what good is caffeine for plants? It may protect the coffee plant from predators like leaf-eating bugs, and when their leaves fall on the ground, the high caffeine concentration stunts the growth of rival plants trying to develop near them. “Caffeine also habituates pollinators and makes them want to come back for more, which is what it does to us, too,”Albert tells Nature. Furthermore, over evolutionary time, the coffee genome wasn't triplicated or duplicated en masse. Instead, the team team thinks that the duplication of individual genes, including the caffeine ones, spurred innovations, Science explains.

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Scientists Uncover How Beautiful Color Patterns Develop in Zebrafish

Scientists Uncover How Beautiful Color Patterns Develop in Zebrafish | Amazing Science |

Scientists at the Max Planck Institute have discovered how pigment cells arise and interact to form the ‘zebra’ pattern in zebrafish.

The zebrafish, a small fresh water fish, owes its name to a striking pattern of blue stripes alternating with golden stripes. Three major pigment cell types, black cells, reflective silvery cells, and yellow cells emerge during growth in the skin of the tiny juvenile fish and arrange as a multilayered mosaic to compose the characteristic color pattern. While it was known that all three cell types have to interact to form proper stripes, the embryonic origin of the pigment cells that develop the stripes of the adult fish has remained a mystery up to now. Scientists of the Max Planck Institute for Developmental Biology in Tübingen have now discovered how these cells arise and behave to form the ‘zebra’ pattern. Their work may help to understand the development and evolution of the great diversity of striking patterns in the animal world.

New research by Nüsslein-Volhard’s laboratory published in Science shows that the yellow cells undergo dramatic changes in cell shape to tint the stripe pattern of zebrafish. “We were surprised to observe such cell behaviors, as these were totally unexpected from what we knew about color pattern formation”, says Prateek Mahalwar, first author of the study. The study builds on a previous work from the laboratory, which was published in June this year in Nature Cell Biology (NCB), tracing the cell behavior of silvery and black cells. Both studies describe diligent experiments to uncover the cellular events during stripe pattern formation. Individual juvenile fish carrying fluorescently labelled pigment cell precursors were imaged every day for up to three weeks to chart out the cellular behaviors. This enabled the scientists to trace the multiplication, migration and spreading of individual cells and their progeny over the entire patterning process of stripe formation in the living and growing animal. “We had to develop a very gentle procedure to be able to observe individual fish repeatedly over long periods of time. So we used a state of the art microscope which allowed us to reduce the adverse effects of fluorescence illumination to a minimum,” says Ajeet Singh, first author of the earlier NCB study.

Surprisingly, the analysis revealed that the three cell types reach the skin by completely different routes: A pluripotent cell population situated at the dorsal side of the embryo gives rise to larval yellow cells, which cover the skin of the embryo. These cells begin to multiply at the onset of metamorphosis when the fish is about two to three weeks old. However, the black and silvery cells come from a small set of stem cells associated with nerve nodes located close to the spinal cord in each segment. The black cells reach the skin migrating along the segmental nerves to appear in the stripe region, whereas the silvery cells pass through the longitudinal cleft that separates the musculature and then multiply and spread in the skin.

Brigitte Walderich, a co-author of the Science paper, who performed cell transplantations to trace the origin of yellow cells, explains: “My attempt was to create small clusters of fluorescently labelled cells in the embryo which could be followed during larval and juvenile stages to unravel growth and behavior of the yellow cells. We were surprised to discover that they divide and multiply as differentiated cells to cover the skin of the fish before the silvery and black cells arrive to form the stripes.”

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Herpes simplex virus type 1 and Alzheimer’s disease: Increasing evidence for a major role of the virus

Herpes simplex virus type 1 and Alzheimer’s disease: Increasing evidence for a major role of the virus | Amazing Science |

The concept of a viral role in Alzheimer’s disease (AD), specifically of herpes simplex virus type 1 (HSV1), was first proposed several decades ago (Ball, 1982Gannicliffe et al., 1986). Legitimizing the concept clearly depended on a positive answer to a number of test questions, the first of which was whether or not HSV1 is ever present in human brain. The subsequent discovery that HSV1 DNA resides in a high proportion of brains of elderly people in latent form (Jamieson et al., 1991)—both normals and AD patients—immediately made the concept more credible, but raised associated questions such as whether or not the virus is ever active in brain or is merely a passive resident there; whether on its own it is a causative factor in AD or it acts thus only with another factor, perhaps genetic; if active, what causes its activity; whether there is any link with the characteristic abnormal features of AD brains or their components, and whether, if indeed implicated in AD, antiviral agents would be useful for treating the disease. These questions were posed in a previous review (Wozniak and Itzhaki, 2010)—and strong evidence was presented that permitted the answer to each question to be “yes” or, very likely to be “yes”. The present review briefly summarizes the earlier evidence, and provides an update, which is especially timely in view of the subsequent steady increase in number of relevant publications.

Herpes simplex virus type 1 (HSV1), when present in brain of carriers of the type 4 allele of the apolipoprotein E gene (APOE), has been implicated as a major factor in Alzheimer’s disease (AD). It is proposed that virus is normally latent in many elderly brains but reactivates periodically (as in the peripheral nervous system) under certain conditions, for example stress, immunosuppression, and peripheral infection, causing cumulative damage and eventually development of AD.

Diverse approaches have provided data that explicitly support, directly or indirectly, these concepts. Several have confirmed HSV1 DNA presence in human brains, and the HSV1-APOE-ε4 association in AD. Further, studies on HSV1-infected APOE-transgenic mice have shown that APOE-e4 animals display a greater potential for viral damage. Reactivated HSV1 can cause direct and inflammatory damage, probably involving increased formation of beta amyloid (Aβ) and of AD-like tau (P-tau)—changes found to occur in HSV1-infected cell cultures.

Implicating HSV1 further in AD is the discovery that HSV1 DNA is specifically localized in amyloid plaques in AD. Other relevant, harmful effects of infection include the following: dynamic interactions between HSV1 and amyloid precursor protein (APP), which would affect both viral and APP transport; induction of toll-like receptors (TLRs) in HSV1-infected astrocyte cultures, which has been linked to the likely effects of reactivation of the virus in brain.

Several epidemiological studies have now shown, using serological data, an association between systemic infections and cognitive decline, with HSV1 particularly implicated. Genetic studies too have linked various pathways in AD with those occurring on HSV1 infection. In relation to the potential usage of antivirals to treat AD patients, acyclovir (ACV) is effective in reducing HSV1-induced AD-like changes in cell cultures, and valacyclovir, the bioactive form of ACV, might be most effective if combined with an antiviral that acts by a different mechanism, such as intravenous immunoglobulin (IVIG).

Krishan Maggon 's curator insight, September 2, 2014 6:48 PM

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Parasitic Plant Strangleweed Injects Host With Over 9,000 RNA Transcripts

Parasitic Plant Strangleweed Injects Host With Over 9,000 RNA Transcripts | Amazing Science |

Virginia Tech professor and Fralin Life Institute affiliate Jim Westwood has made a discovery about plant-to-plant communication: enormous amounts of genetic messages in the form of mRNA transcripts are transmitted from the parasitic plant Cuscuta (known more commonly as dodder and strangleweed) to its hosts.

Using Illumina next generation sequencing technologies to sequence the tissues of the host and an attached parasite, the team found that the number of genes that gets passed into the host depends on the identity of the host.  The tomato plant received 347 of the strangleweed’s mRNAs, whereas the Arabidopsis received an astonishing 9514 mRNAs.  When Arabidopsis plant receives this many mRNAs, the total genetic material of tissues in contact with the strangleweed is about 45% from the parasite.

The new quantitative result builds on Professor Westwood’s prior discovery of RNA transfer between the parasitic plant and its host plants.  In the prior study, Westwood found that when the strangleweed uses its haustorium (piercing appendage) to penetrate the stems of its host plants, it passes on its own RNA to the host, though only tens of mRNAs were identified.  The discovery challenged our understanding that mRNAs are mainly kept within cells.

But now the research team has quantified the extent to which the messages are passed.  mRNA stands for “messenger RNA” and are the snippets of genetic information that are created from DNA.  Typically an mRNA molecule is “read” by a molecule machine known as a ribosome and turned into a protein which carries out particular functions in the cell.  And usually, more mRNAs means more protein.  Therefore, the conversion from DNA to mRNA is one way to amplify or control the activation of a gene.

It is not yet clear what are the functions of the transmitted genes but bioinformatic analysis shows that hydrolase activity, metabolism and response to stimulus gene groups were among the most represented in those that crossed the species bridge.

Westwood has determined that the host plant may be receiving orders of a kind from the parasitic plant, such as lowering its natural defense system so that the strangleweed can more easily attack them.

The findings by Westwood, Professor of weed science, plant pathology and physiology at the College of Agriculture and Life Sciences, is even more surprising when considered against prior thought that mRNA is unstable, short-lived and fragile.

The discoveries also opens new avenues in the research of the eradication of parasitic plants such as broomrape and witchweed, two plants that pose serious threats to legumes and other crops.  This also has intriguing implications for increasing efficiency of yields.

Future plans include expansion of such research to other organismal domains, such as fungi and bacteria, also exchange the mRNA.  But the meaning and the outcome of the transmitted messages remain yet unclear and work must be done to find out what the plants are saying to each other.

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Chromatophagy, A New Cancer Therapy: Starve The Diseased Cell Until It Eats Its Own DNA

Chromatophagy, A New Cancer Therapy: Starve The Diseased Cell Until It Eats Its Own DNA | Amazing Science |

Nutritional starvation therapy is under intensive investigation because it provides a potentially lower toxicity with higher specificity than conventional cancer therapy. Autophagy, often triggered by starvation, represents an energy-saving, pro-survival cellular function; however, dysregulated autophagy could also lead to cell death, a process distinct from the classic caspase-dependent apoptosis.

A recent study shows how arginine starvation specifically kills tumor cells by a novel mechanism involving mitochondria dysfunction, reactive oxygen species generation, DNA leakage, and chromatin autophagy, where leaked DNA is captured by giant autophagosomes. 

Cells when stressed, whether cancerous or not, undergo a process of cellular suicide that involves controlled dismantling of its interior components such as proteins, DNA, and various compartments.  By far the most famous of such processes is “apoptosis”.  The authors in this study have found another, distinct process involving mitochondria dysfunction, reactive oxygen species (ROS) generation, DNA leakage, and chromatin autophagy.

The senior author, Professor Hsing-Jien Kung, both a cancer biology at UC Davis and  the Director of the National Health Research Institutes in Taipei, Taiwan, first discovered in 2009 the basic mechanism by which arginine shortage kills cancer cells.

“Traditional cancer therapies involve ‘poisoning‘ by toxic chemicals or ‘burning‘ by radiation cancer cells to death, which often have side effects,” according to Professor Kung. “An emerging strategy is to ‘starve’ cancer cells to death, taking advantage of the different metabolic requirements of normal and cancer cells. This approach is generally milder, but as this study illustrates, it also utilizes a different death mechanism, which may complement the killing effects of the conventional therapy.”

AdnanD's curator insight, August 29, 2014 12:29 PM

The perseverance of man kind ! 

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Blocking cell division with two synergistic chemical inhibitors

Blocking cell division with two synergistic chemical inhibitors | Amazing Science |

The cycle of cell division—one cell splitting itself into two—is a crucial and complex process managed by finely tuned molecular machines. When working properly, cell division assures healthy growth. When running out of control, it can usher in cancer.

Blocking cell division in disease has been the target of researchers hoping to induce the death of abnormal cells before they become cancerous tumors. Finding the right chemical compound to inhibit cell division gone awry has proved difficult: Target the cell cycle too broadly and healthy cells will also suffer, as when chemotherapy hits all cells that divide rapidly, not just cancerous ones. Narrow the sights too tightly and the misbehaving machine churns on.

Now a team led by Randall King of Harvard Medical School has shown how two chemical inhibitors working together act better than either one alone, shutting down the dividing cell by stalling mitosis, one step in the cycle during which the cell copies and then lines up chromosomes properly so each daughter cell has a complete set.

"Simultaneous disruption of multiple interactions in a protein machine may be an interesting way to go in terms of trying to design future therapeutic strategies," said King, HMS professor of cell biology. "You're basically targeting one step in the pathway, but there's a lot of complexity in that one step. The idea is to disable the biochemical or enzymatic function by simultaneously targeting multiple sites."

King discovered the two inhibitors 10 years ago, in the very first screen conducted at the Institute of Chemistry and Cell Biology-Longwood Screening Facility at HMS. It was an unbiased chemical screen, set up with no assumptions about what they might find. Especially in the era before the discovery of RNA interference and its usefulness in silencing genes, scientists needed chemical tools that would perturb biological processes in other ways, so they could understand in detail how the mechanisms they were examining worked.

King's goal in 2004 was to fish through all the identified candidates from these early screens for chemical compounds that would somehow illuminate the cell cycle pathway and perhaps stymie one of its protein machines: the anaphase-promoting complex/cyclosome (APC/C). This protein complex marks certain proteins for degradation by the proteasome, the cell's waste-disposal site, before it can progress through mitosis.

If the APC/C doesn't tag these proteins with a protein called ubiquitin, the proteasome doesn't recognize them, they don't get discarded and mitosis cannot proceed, stalling the cell cycle before it can properly segregate its chromosomes for faithful division.

In 2010 King and his colleagues published a paper in Cancer Cell that described in detail how one of the inhibitors, called tosyl-L-arginine methyl ester (TAME), weakens the interaction between the APC/C and its critical activating protein, Cdc20. Degradation is blocked, but only partially. That means the cell cycle is delayed briefly, but still continues toward mitotic exit.

Now the scientists have shown how another compound, also discovered in the original 2004 chemical screen, binds in a pocket on Cdc20 that normally recruits the targets of APC/C. Called apcin (for APC inhibitor), it also delays mitosis, but only by a little bit.

Together, TAME and apcin slow mitosis to a crawl. The cell dies before it can leave mitosis.

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Evolutionary history of honeybees revealed by genomics

Evolutionary history of honeybees revealed by genomics | Amazing Science |

In a study published in Nature Genetics, researchers from Uppsala University present the first global analysis of genome variation in honeybees. The findings show a surprisingly high level of genetic diversity in honeybees, and indicate that the species most probably originates from Asia, and not from Africa as previously thought.

The honeybee (Apis mellifera) is of crucial importance for humanity. One third of our food is dependent on the pollination of fruits, nuts and vegetables by bees and other insects. Extensive losses of honeybee colonies in recent years are a major cause for concern. Honeybees face threats from disease, climate change, and management practices. To combat these threats it is important to understand the evolutionary history of honeybees and how they are adapted to different environments across the world.

"We have used state-of-the-art high-throughput genomics to address these questions, and have identified high levels of genetic diversity in honeybees. In contrast to other domestic species, management of honeybees seems to have increased levels of genetic variation by mixing bees from different parts of the world. The findings may also indicate that high levels of inbreeding are not a major cause of global colony losses", says Matthew Webster, researcher at the department of Medical Biochemistry and Microbiology, Uppsala University.

Another unexpected result was that honeybees seem to be derived from an ancient lineage of cavity-nesting bees that arrived from Asia around 300,000 years ago and rapidly spread across Europe and Africa. This stands in contrast to previous research that suggests that honeybees originate from Africa.

Reference: A worldwide survey of genome sequence variation provides insight into the evolutionary history of the honeybee Apis mellifera, Nature Genetics, 2014.

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How lizards regenerate their tails: researchers discover genetic 'recipe'

How lizards regenerate their tails: researchers discover genetic 'recipe' | Amazing Science |

By understanding the secret of how lizards regenerate their tails, researchers may be able to develop ways to stimulate the regeneration of limbs in humans. Now, a team of researchers from Arizona State University is one step closer to solving that mystery. The scientists have discovered the genetic “recipe” for lizard tail regeneration, which may come down to using genetic ingredients in just the right mixture and amounts.

Other animals, such as salamanders, frog tadpoles and fish, can also regenerate their tails, with growth mostly at the tip. During tail regeneration, they all turn on genes in what is called the 'Wnt pathway’ – a process that is required to control stem cells in many organs, such as the brain, hair follicles and blood vessels. However, lizards have a unique pattern of tissue growth that is distributed throughout the tail.

"Regeneration is not an instant process," said Elizabeth Hutchins, a graduate student in ASU's molecular and cellular biology program and co-author of the paper. "In fact, it takes lizards more than 60 days to regenerate a functional tail. Lizards form a complex regenerating structure with cells growing into tissues at a number of sites along the tail.”

"We have identified one type of cell that is important for tissue regeneration," said Jeanne Wilson-Rawls, co-author and associate professor with ASU’s School of Life Sciences. "Just like in mice and humans, lizards have satellite cells that can grow and develop into skeletal muscle and other tissues."

"Using next-generation technologies to sequence all the genes expressed during regeneration, we have unlocked the mystery of what genes are needed to regrow the lizard tail," said Kusumi. "By following the genetic recipe for regeneration that is found in lizards, and then harnessing those same genes in human cells, it may be possible to regrow new cartilage, muscle or even spinal cord in the future."

The findings are published today in the journal PLOS ONE.

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Plants may use RNA language to communicate with each other, Virginia Tech researcher finds

Plants may use RNA language to communicate with each other, Virginia Tech researcher finds | Amazing Science |

A Virginia Tech scientist has discovered a potentially new form of plant communication, one that allows them to share an extraordinary amount of genetic information with one another. 

The finding by Jim Westwood, a professor of plant pathology, physiology, and weed science in the College of Agriculture and Life Sciences, throws open the door to a new arena of science that explores how plants communicate with each other on a molecular level. It also gives scientists new insight into ways to fight parasitic weeds that wreak havoc on food crops in some of the poorest parts of the world. His findings were published on Aug. 15 in the journal Science.

“The discovery of this novel form of inter-organism communication shows that this is happening a lot more than any one has previously realized,” said Westwood, who is an affiliated researcher with the Fralin Life Science Institute. “Now that we have found that they are sharing all this information, the next question is, ‘What exactly are they telling each other?’.” 

Westwood examined the relationship between a parasitic plant, dodder, and two host plants, Arabidopsis and tomatoes. In order to suck the moisture and nutrients out the host plants, dodder uses an appendage called a haustorium to penetrate the plant. Westwood previously broke new ground when he found that during this parasitic interaction, there is a transport of RNA between the two species. RNA translates information passed down from DNA, which is an organism’s blueprint. 

His new work expands this scope of this exchange and examines the mRNA, or messenger RNA, which sends messages within cells telling them which actions to take, such as which proteins to code. It was thought that mRNA was very fragile and short-lived, so transferring it between species was unimaginable. 

But Westwood found that during this parasitic relationship, thousands upon thousands of mRNA molecules were being exchanged between both plants, creating this open dialogue between the species that allows them to freely communicate. Through this exchange, the parasitic plants may be dictating what the host plant should do, such as lowering its defenses so that the parasitic plant can more easily attack it. Westwood’s next project is aimed at finding out exactly what the mRNA are saying.

“Parasitic plants such as witchweed and broomrape are serious problems for legumes and other crops that help feed some of the poorest regions in Africa and elsewhere,” said Julie Scholes, a professor at the University of Sheffield, U.K., who is familiar with Westwood’s work but was not part of this project. “In addition to shedding new light on host-parasite communication, Westwood’s findings have exciting implications for the design of novel control strategies based on disrupting the mRNA information that the parasite uses to reprogram the host." 

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Oxytricha trifallax breaks its own DNA into a quarter-million pieces and rapidly reassemble those for mating

Oxytricha trifallax breaks its own DNA into a quarter-million pieces and rapidly reassemble those for mating | Amazing Science |

Life can be so intricate and novel that even a single cell can pack a few surprises, according to a study led by Princeton University researchers. The pond-dwelling, single-celled organism Oxytricha trifallax has the remarkable ability to break its own DNA into nearly a quarter-million pieces and rapidly reassemble those pieces when it's time to mate, the researchers report in the journal Cell.

The organism internally stores its genome as thousands of scrambled, encrypted gene pieces. Upon mating with another of its kind, the organism rummages through these jumbled genes and DNA segments to piece together more than 225,000 tiny strands of DNA. This all happens in about 60 hours.

The organism's ability to take apart and quickly reassemble its own genes is unusually elaborate for any form of life, explained senior author Laura Landweber, a Princeton professor of ecology and evolutionary biology. That such intricacy exists in a seemingly simple organism accentuates the "true diversity of life on our planet," she said.

"It's one of nature's early attempts to become more complex despite staying small in the sense of being unicellular," Landweber said. "There are other examples of genomic jigsaw puzzles, but this one is a leader in terms of complexity. People might think that pond-dwelling organisms would be simple, but this shows how complex life can be, that it can reassemble all the building blocks of chromosomes."

From a practical standpoint, Oxytricha is a model organism that could provide a template for understanding how chromosomes in more complex animals such as humans break apart and reassemble, as can happen during the onset of cancer, Landweber said. While chromosome dynamics in cancer cells can be unpredictable and chaotic, Oxytricha presents an orderly step-by-step model of chromosome reconstruction, she said.

"It's basically bad when human chromosomes break apart and reassemble in a different order," Landweber said. "The process in Oxytricha recruits some of the same biological mechanisms that normally protect chromosomes from falling apart and uses them to do something creative and constructive instead."

Gertraud Burger, a professor of biochemistry at the University of Montreal, said that the "rampant and diligently orchestrated genome rearrangements that take place in this organism" demonstrate a unique layer of complexity for scientists to consider when it comes to studying an organism's genetics.

"This work illustrates in an impressive way that the genetic information of an organism can undergo substantial change before it is actually used for building the components of a living cell," said Burger, who is familiar with the work but had no role in it.

"Therefore, inferring an organism's make-up from the genome sequence alone can be a daunting task and maybe even impossible in certain instances," Burger said. "A few cases of minor rearrangements have been described in earlier work, but these are dilettantes compared to [this] system."

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Ultraviolet light-induced mutation drives many skin cancers and over 330 genes seem to be involved in the process

Ultraviolet light-induced mutation drives many skin cancers and over 330 genes seem to be involved in the process | Amazing Science |
Genes that cause cancer when mutated are known as oncogenes. Although KNSTRN hasn't been previously implicated as a cause of human cancers, the research suggests it may be one of the most commonly mutated oncogenes in the world.

"This previously unknown oncogene is activated by sunlight and drives the development of cutaneous squamous cell carcinomas," said Paul Khavari, MD, PhD, the Carl J. Herzog Professor in Dermatology in the School of Medicine and chair of the Department of Dermatology. "Our research shows that skin cancers arise differently from other cancers, and that a single mutation can cause genomic catastrophe."

Cutaneous squamous cell carcinoma is the second most common cancer in humans. More than 1 million new cases are diagnosed globally each year. The researchers found that a particular region of KNSTRN is mutated in about 20 percent of cutaneous squamous cell carcinomas and in about 5 percent of melanomas.

A paper describing the research will be published online Sept. 7, 2014 in Nature Genetics. Khavari, who is also a member of the Stanford Cancer Institute and chief of the dermatology service at the Veterans Affairs Palo Alto Health Care System, is the senior author of the paper. Postdoctoral scholar Carolyn Lee, MD, PhD, is the lead author.

Lee and Khavari made the discovery while investigating the genetic causes of cutaneous squamous cell carcinoma. They compared the DNA sequences of genes from the tumor cells with those of normal skin and looked for mutations that occurred only in the tumors. They found 336 candidate genes for further study, including some familiar culprits. The top two most commonly mutated genes were CDKN2A and TP53, which were already known to be associated with squamous cell carcinoma.

The third most commonly mutated gene, KNSTRN, was a surprise. It encodes a protein that helps to form the kinetochore -- a structure that serves as a kind of handle used to pull pairs of newly replicated chromosomes to either end of the cell during cell division. Sequestering the DNA at either end of the cell allows the cell to split along the middle to form two daughter cells, each with the proper complement of chromosomes.

If the chromosomes don't separate correctly, the daughter cells will have abnormal amounts of DNA. These cells with extra or missing chromosomes are known as aneuploid, and they are often severely dysfunctional. They tend to misread cellular cues and to behave erratically. Aneuploidy is a critical early step toward the development of many types of cancer.

The mutation in the KNSTRN gene was caused by the replacement of a single nucleotide, called a cytosine, with another, called a thymine, within a specific, short stretch of DNA. The swap is indicative of a cell's attempt to repair damage from high-energy ultraviolet rays, such as those found in sunlight.

"Mutations at this UV hotspot are not found in any of the other cancers we investigated," said Khavari. "They occur only in skin cancers." The researchers found the UV-induced KNSTRN mutation in about 20 percent of actinic keratoses -- a premalignant skin condition that often progresses to squamous cell carcinoma -- but never in 122 samples of normal skin, indicating the mutation is likely to be an early event in the development of squamous cell carcinomas.
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Plant genomics: Methods for obtaining large, phylogenomic data sets

Plant genomics: Methods for obtaining large, phylogenomic data sets | Amazing Science |

The use of next-generation sequencing (NGS) technologies in phylogenetic studies is in a state of continual development and improvement. Though the botanically-inclined have historically focused on markers from the chloroplast genome, the importance of incorporating nuclear data is becoming increasingly evident. Nuclear genes provide not only the potential to resolve relationships between closely related taxa, but also the means to disentangle hybridization and better understand incongruences caused by incomplete lineage sorting and introgression.

By harnessing the power of NGS—which has increased sequencing capacity by several orders of magnitude over the past few years—scientists are now able to easily sequence enormous amounts of DNA or RNA from any genome within an organism, a practice that is transforming many areas of plant biology.

A team of international scientists, led by researchers at Oregon State University, has utilized a recently developed method to assemble a phylogenomic data set containing hundreds of nuclear loci and plastomes for milkweeds.

"This approach, termed Hyb-Seq, uses targeted sequence capture via hybridization-based enrichment and has shown great promise for obtaining large nuclear data sets," explains Dr. Aaron Liston, principal investigator of the study. "Sequencing low-copy nuclear genes has traditionally required a large amount of effort for each gene. Hyb-Seq eliminates the need for PCR optimization and cloning—two time-consuming and sometimes problematic steps."

The protocol is freely available in the September issue of Applications in Plant SciencesWhile it would be ideal to simply sequence entire genomes for every organism being studied, this is not yet feasible across large numbers of species. The Hyb-Seq approach reduces genomic complexity of the organism-of-interest by targeting only a small portion of the total genome. This is achieved by hybridizing DNA or RNA probes to specific regions of the genome, then simply discarding the remaining, unwanted regions.

"The probe design was done bioinformatically by comparing our draft sequence of the milkweed genome and transcriptome (expressed genes) to another genome in the same family and to genes that are conserved across the asterids and the angiosperms," explains Liston. "This allowed us to eliminate duplicated genes that can complicate phylogenetic inference and select relatively conserved genes, so that they could be obtained from divergent milkweed species with a single probe set."

This approach enabled Liston and colleagues to sequence over 700 genes for 10 Asclepias species and two related genera. "Furthermore," says Liston, "we were able to assemble complete plastomes from the off-target reads."

"It is likely that as sequencing technology advances, it will be feasible in the next decade or so to sequence complete genomes routinely and inexpensively. However, until that time, the ability to sequence hundreds of genes at a time—as is possible with the Hyb-Seq method—represents a significant and exciting advance over previous methods."

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Humans are wiping out species a thousand times faster than nature can create new ones

Humans are wiping out species a thousand times faster than nature can create new ones | Amazing Science |

Sometimes extinction happens naturally. Other times humans are to blame. Given the many millions of plant and animal species that have ever existed, it’s tough to know exactly how to assign responsibility. But new research indicates that we have an alarmingly large role.

Humans are wiping out species at least 1,000 times faster than nature is creating new species, according to a new study in Conservation Biology (paid access only). And it’s getting much worse. In the future, plants and animal species will go extinct at 10,000 times the rate at which new species emerge, the researchers assert.

Looking at both fossils and genetic variation, the study found that nature snuffs out its own creations much more slowly than we’d realized—at a rate of only one species per every 10 million. Past estimates put the “normal background extinction rate”—the rate at which species would go extinct without human interference—at about 10 yearly extinctions for every 10 million species.

Since mankind hit the scene, however, more than 1,000 out of every 10 million species have been dying out each year. “We’ve known for 20 years that current rates of species extinctions are exceptionally high,” said Stuart Pimm, one of the co-authors and president of the nonprofit organization SavingSpecies. “This new study comes up with a better estimate of the normal background rate—how fast species would go extinct were it not for human actions. It’s lower than we thought, meaning that the current extinction crisis is much worse by comparison.”

Overall species’ diversity grows exponentially richer over time, as branches of news species diverge. The authors liken this to a person’s bank account. Think of your income as the number of new species, while your spending is those that go extinct. Every month when you get paid, your net worth jumps for a while, before spending whittles it down again. If your spending is constant, that monthly spike will rise over time as your salary increases—just as the number of new species should also rise over time. But the authors saw no such increase, implying that extinction is happening far too fast for the pace of new species creation to keep up.

Take birds, for instance. There are 10,000 species of birds, as Pimm explains in a blogpost. At nature’s rate of one extinction per 10 million species, the disappearance of a single bird species should therefore be a once-in-a-millennium event. However, since the year 1500, at least 140 birds have disappeared—including 13 species we only identified after they went extinct.

Paulo Gervasio's curator insight, September 10, 2014 2:39 AM

Why are we blaming ourselves for everything?  There is a biblical story about the tower of Babel.  I am sometimes reminded that maybe we are approaching the arrogance described in that story.  

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Good news: California blue whale numbers bounce back to near historic levels

Good news: California blue whale numbers bounce back to near historic levels | Amazing Science |

Researchers believe that California blue whales have recovered in numbers and the population has returned to sustainable levels.

Scientists say this is the only population of blue whales to have rebounded from the ravages of whaling.

The research team estimate that there are now 2,200 of these giant creatures on the eastern side of the Pacific Ocean. But concerns remain about their vulnerability to being struck by ships.

At up to 33 meters in length and weighing in at up to 190 tons, blue whales are the largest animals that ever lived on the planet. The California variety is often seen feeding close to the coast of the state, but they are found all the way from the Gulf of Alaska down to Costa Rica.

Writing in the journal, Marine Mammal Science, researchers from the University of Washington say the California blue whales are now at 97% of their historical levels. The team believes that a rise in population has slowed down as these whales have reached the capacity of what the ocean system can support.

One concern for the scientists at present are ship strikes. Most of these happen off the coast of California, and so worried are the authorities that they are now paying merchant shipping to slow down.

"Our perspective is that we'd rather there were no ship strikes at all, and they are over the legal limit," said Dr Branch.

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Cockatoos can learn from each other how to make and use tools - not by simply copying the action

Cockatoos can learn from each other how to make and use tools - not by simply copying the action | Amazing Science |

Figaro, a Goffin’s cockatoo (Cacatua goffini) housed at a research lab in Austria, stunned scientists a few years ago when he began spontaneously making stick tools from the wooden beams of his aviary. The Indonesian parrots are not known to use tools in the wild, yet Figaro confidently employed his sticks to rake in nuts outside his wire enclosure. Wondering if Figaro’s fellow cockatoos could learn by watching his methods, scientists set up experiments for a dozen of them. One group watched as Figaro used a stick to reach a nut placed inside an acrylic box with a wire-mesh front panel; others saw “ghost demonstrators”—magnets that were hidden beneath a table and that the researchers controlled—displace the treats. Each bird was then placed in front of the box, with a stick just like Figaro’s lying nearby.

The group of three males and three females that had watched Figaro also picked up the sticks, and made some efforts reminiscent of his actions. But only those three males, such as the one in the photo above, became proficient with the tool and successfully retrieved the nuts, the scientists report online today in the Proceedings of the Royal Society B. None of the females did so; nor did any of the birds, male or female, in the ghost demonstrator group. Because the latter group failed entirely, the study shows that the birds need living teachers, the scientists say. Intriguingly, the clever observers developed a better technique than Figaro’s for getting the treat. Thus, the cockatoos weren’t copying his exact actions, but emulating them—a distinction that implies some degree of creativity. Two of the successful cockatoos were later given a chance to make a tool of their own. One did so immediately (as in the video above), and the other succeeded after watching Figaro. It may be that by learning to use a tool, the birds are stimulated to make tools of their own, the scientists say.

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There are scenarios where chimpanzees are more intelligent than us: Chimps outplay humans in brain games

There are scenarios where chimpanzees are more intelligent than us: Chimps outplay humans in brain games | Amazing Science |

We humans assume we are the smartest of all creations. In a world with over 8.7 million species, only we have the ability to understand the inner workings of our body while also unraveling the mysteries of the universe. We are the geniuses, the philosophers, the artists, the poets and savants. We amuse at a dog playing ball, a dolphin jumping rings, or a monkey imitating man because we think of these as remarkable acts for animals that, we presume, aren’t smart as us. But what issmart? Is it just about having ideas, or being good at language and math?

In a recent study by psychologists Colin Camerer and Tetsuro Matsuzawa, chimps and humans played a strategy game – and unexpectedly, the chimps outplayed the humans.

Chimps are a scientist’s favorite model to understand human brain and behavior. Chimp and human DNAs overlap by a whopping 99 percent, which makes us closer to chimps than horses to zebras. Yet at some point, we evolved differently. Our behavior and personalities, molded to some extent by our distinct societies, are strikingly different from that of our fellow primates. Chimps are aggressive and status-hungry within their hierarchical societies, knit around a dominant alpha male. We are, perhaps, a little less so. So the question arises whether competitive behavior is hard-wired in them.

In the present study, chimp pairs or human pairs contested in a two-player video game. Each player simply had to choose between left and right squares on a touch-screen panel, while being blind to their rival’s choice. Player A, for instance, won, each time their choices matched, and player B won, if their choices did not. The opponent’s choice was displayed after every selection, and payoffs in the form of apple cubes or money were dispensed to the winner.

In Camerer’s experiment, it turned out that chimps played a near-ideal game, as their choices leaned closer to game theory equilibrium. Whereas, when humans played, their choices drifted farther off from theoretical predictions. Since the game is a test of how much the players recall of their opponent’s choice history, and how cleverly they maneuver by following choice patterns, the results suggest that chimps may have a superior memory and strategy, which help them perform better in a competition, than humans. In other words, chimps seem to have some sort of a knack when fighting peers in a face-off. 

Their exceptional working memory may be a key factor for chimps’ strategic skills. A movie clip, part of a study in 2007, impressively captures the eidetic memory of a 2-year old chimp as he played a memory masking game.  It makes jaws drop to see him memorize random numerical patterns within 200 milliseconds, about half the time it takes for the human eye to blink. Memory of such incredible precision is rare in human babies and close to absent in adults, save for fictitious characters like Sheldon Cooper.

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Eczema Fungus Found Everywhere Including Deep Hydrothermal Vents And Antarctic Soil

Eczema Fungus Found Everywhere Including Deep Hydrothermal Vents And Antarctic Soil | Amazing Science |

Professor Anthony Amend from the University of Hawaii at Manoa showed very recently that the fungus genus Malassezia is not only found on human skin with conditions such as dandruff and eczema, but has also been identified in marine environments such as deep-sea sediment, hydrothermal vents, corals, guts of lobster larvae, eel tissue, and Antarctica soils.

More remarkably, sequencing and tree building of species relatedness shows that the marine species and terrestrial (non-marine) species do not group together but “interdigitate”, or are spread randomly in the way they group together in their relatedness.  The evidence suggests that the marine and terrestrial forms have jumped repeatedly between habitats.

The data was obtained from a number of sources, most of them “environmental sequencing” projects around the world which aim to do simultaneous sequencing of all DNA found in a sample.  Done correctly the analysis yields in one try the identities of all organisms captured in a sample.

Prior to this analysis, it was thought that these fungus evolved to become optimally suited to mammalian skin.  But the careful analysis of environmental sequencing efforts overturned that belief.  One species could be spread out all over the globe, on land as well as in ocean.  One example is Malassezia restricta, found on human skin but also in extreme habitats such as arctic soil and hydrothermal vents. Marine animals also carry this fungus, including higher order seals and lower order fish, lobsters, and corals.

One criticism is that sequencing is bound to become contaminated especially with a fungus endemic to human skin.  However, the detection of completely novel species cannot be explained by contamination.  And moreover, RNA is a fairly unstable molecule, so in the cases where detection occurred for some of the samples in which there was sufficient time for degradation suggests that microbes were actively generating RNA.

While it is associated with many skin conditions it is unclear as of yet whether the fungus is a causal factor.  This is simply because disease etiology is a complex interplay of an individual immune system and disease agent.

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Modified yeast produces a range of opiates for the first time

Modified yeast produces a range of opiates for the first time | Amazing Science |

Yeast that can make opiates from other molecules raise the prospect of tanks of drug-producing microorganisms replacing open fields of opium poppies.

Severe pain? Reach for the yeast. Genetically engineered yeasts can now efficiently produce a range of opiates, including morphine and oxycodone. With growing anxieties about supplies of opium poppies, it could be just what the doctor ordered.

Opiates are primarily used as painkillers and cough suppressants, and many of the most widely used opiates can be produced only from opium poppies (Papaver somniferum). Demand for these drugs is booming. But of the poppies farmed to supply these drugs, some 50 per cent are grown on the Australian island of Tasmania, so poor growing seasons can affect availability.

As drug companies search for new places to grow poppiesChristina Smolkefrom Stanford University, California, and her colleagues have been looking at getting yeast to make these complex drugs from simple sugars.

Some opiates, like morphine, are made naturally by poppies. Others, like oxycodone, are produced by chemically altering one of the plant's natural alkaloid chemicals – in this case thebaine. Back in 2008, Smolke inserted a number of genes – including some from the opium poppy – into yeasts, and got them to turn simple sugar molecules into a complex precursor of opiates: salutaridine. Now, in her latest work, she has solved the other end of the pathway, engineering yeasts to take complex precursors like thebaine and synthesise the finished products, including oxycodone.

"This work gets us very close," says Smolke. All that's left is to combine the two stages in one strain of yeast, and solve the last few steps: getting the yeast to turn salutaridine into thebaine, completing the pathway from sugar to opiate product.

The benefits of yeast over poppies are manifold, Smolke says. She thinks that when the system is finished, a 1000-litre tank could produce as much morphine as a hectare of poppies. She believes the method, when completed, will also increase security. "It is difficult or impossible to secure many thousands of acres of poppy fields which are grown out in the open," she says. "Yeast will be grown in closed fermenters and can be kept in secure facilities."

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Core root growth mechanism identified: PLETHORA proteins and plant hormone auxin orchestrate root growth together

Core root growth mechanism identified: PLETHORA proteins and plant hormone auxin orchestrate root growth together | Amazing Science |

During plant growth, dividing cells in meristems must coordinate transitions from division to expansion and differentiation. Three distinct developmental zones are generated: the meristem, where the cell division takes place, and elongation and differentiation zones. At the same time, plants can rapidly adjust their direction of growth to adapt to environmental conditions.

In Arabidopsis thaliana roots, many aspects of zonation are controlled by the plant hormone auxin and auxin-induced PLETHORA transcription factors. Both show a graded distribution with a maximum near the root tip. In addition, auxin is also pivotal for tropic responses of the roots.

Ari Pekka Mähönen from the University of Helsinki, Finland, with his group and Dutch colleagues has found out with the help of experimentation and mathematical modelling how the two factors together regulate root growth.

"Cell division in the meristem is maintained by PLETHORA transcription factors. These proteins are solely transcribed in the stem cells, in a narrow region within the meristematic cells located in the tip of the root. So PLETHORA proteins are most abundant in the stem cells," Ari Pekka Mähönen, Research Fellow financed by the Academy of Finland says.

Outside the stem cells the amount of PLETHORA protein in the cells halves each time the cells divide. In the end there is so little PLETHORA left in the cells that they cannot stay in the dividing mode. This is when the cells start to elongate and differentiate.

Auxin is the factor taking care of many aspects of root growth. If there is enough PLETHORA in the root cells, auxin affects the rate of root cell division. If there is little or no PLETHORA in the cells, auxin regulates cell differentiation and elongation. In addition to this direct, rapid regulation, auxin also regulates cell division, expansion and differentiation indirectly and slowly by promoting PLETHORA transcription. This dual action of auxin keeps the structure and growth of the root very stable.

When PLETHORA levels gradually diminish starting from the root tip upwards, the cell division, elongation and differentiation zones are created. And this inner organisation stays even if the growth direction of the root changes.

"The gravity and other environmental factors can change the auxin content of the cells, and quite rapidly. This all affects the growth direction of the root. And of course it is important for the plant to maintain the organization while directing their roots there where water and nutrients most likely are to be found."

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21 Species of Metabolically Active Microbes In Hydrocarbon Lakes On Earth Boost Chances For Extraterrestrial Life

21 Species of Metabolically Active Microbes In Hydrocarbon Lakes On Earth Boost Chances For Extraterrestrial Life | Amazing Science |

In a ground-breaking discovery released by the journal Science, researchers have revealed microhabitats of metabolically active, thriving microbes living in the world’s largest asphalt lake, Pitch Lake, on the island of Trinidad in the Caribbean.  Asphalt lakes are large reservoirs of a sticky, black, viscous hydrocarbons (known as asphalt, bitumen or pitch) where no life was expected to be found.

The international team discovered the microbes in tiny water droplets recovered from the lake in 2011.  Each sample, measuring only one to three microliters, has the equivalent volume of approximately 1/50 of a conventional “drop” of water.

The team’s only United States-based researcher, Dirk Schulze-Makuch, is a professor at Washington University School of the Environment.  Using advanced sequencing technologies, the team extracted all the DNA of all organisms in each droplet simultaneously.  Reading through 12 microdroplets, they found 21 species of bacteria and archaebacteria.

Professor Schulze-Makuch explained that each water droplet seems representative of an entire ecosystem because of the observed diversity in bacteria and archaea.  Moreover, remarkably there was very little measurable ammonia or phosphates, both ingredients thought to be essential for life.

These microbes, the researchers report, are actively degrading oils in the lake, most likely to exploit it as a source of bioenergy.  One bioengineering implication of this discovery is to use these active microbes to clean up oil spills with as little impact to the environment as possible.

The water droplets also had an unusually high salt content.  By studying the isotope composition of droplets from Pitch Lake, the team was able to say that the microbes did not originate from surface waters that are part of the hydrologic cycle, but rather from much deeper, for example ancient underground seawater or another deep source of brine.

Professor Schulze-Makuch went on to explain that these microbes could mean life on other planets as well.  One well-known example is Saturn’s moon, Titan.  Its surface is characterized as being saturated with hydrocarbons, in liquid lakes on the ground and also in vapor form and liquid rain in the atmosphere.  Schulze-Makuch explains that this discovery has implications for astrobiology, the study of life on other planets.

Reference: Science 8 August 2014: Vol. 345 no. 6197 pp. 673-676

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More than just X and Y: miRNAs are responsible for sexual differences in fruit flies

More than just X and Y: miRNAs are responsible for sexual differences in fruit flies | Amazing Science |

Men and women differ in plenty of obvious ways, and scientists have long known that genetic differences buried deep within our DNA underlie these distinctions. In the past, most research has focused on understanding how the genes that encode proteins act as sex determinants. But Cold Spring Harbor Laboratory (CSHL) scientists have found that a subset of very small genes encoding short RNA molecules, called microRNAs (miRNAs), also play a key role in differentiating male and female tissues in the fruit fly.

A miRNA is a short segment of RNA that fine-tunes the activation of one or several protein-coding genes. miRNAs are able to silence the genes they target and, in doing so, orchestrate complex genetic programs that are the basis of development.

In work published in Genetics, a team of CSHL researchers and colleagues describe how miRNAs contribute to sexual differences in fruit flies. You've probably never noticed, but male and female flies differ visibly, just like other animals. For example, females are 25% larger than males with lighter pigmentation and more abdominal segments.

The team of researchers, including Delphine Fagegaltier, PhD, lead author on the study, and CSHL Professor and Howard Hughes Medical Institute Investigator Greg Hannon, identified distinct miRNA populations in male and female flies. "We found that the differences in miRNAs are important in shaping the structures that distinguish the two sexes," says Fagegaltier. "In fact, miRNAs regulate the very proteins that act as sex determinants during development."

The team found that miRNAs are essential for sex determination even after an animal has grown to adulthood. "They send signals that allow germ cells, i.e., eggs and sperm, to develop, ensuring fertility," Fagegaltier explains. "Removing one miRNA from mature, adult flies causes infertility." More than that, these flies begin to produce both male and female sex-determinants. "In a sense, once they have lost this miRNA, the flies become male and female at the same time," according to Fagegaltier. "It is amazing that the very smallest genes can have such a big effect on sexual identity."

Some miRNAs examined in the study, such as let-7, have been preserved by evolution because of their utility; humans and many other animals carry versions of them. "This is probably just the tip of the iceberg," says Fagegaltier. "There are likely many more miRNAs regulating sexual identity at the cellular and tissue level, but we still have a lot to learn about these differences in humans, and how they could contribute to developmental defects and disease."

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