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Forkhead Box O3 (Foxo3) Anti-Aging Gene May Hold Key to Protect Inner Ear Hair Cells from Damage

Forkhead Box O3 (Foxo3) Anti-Aging Gene May Hold Key to Protect Inner Ear Hair Cells from Damage | Amazing Science |

Researchers have discovered that a protein implicated in human longevity may also play a role in restoring hearing after noise exposure. The findings, where were published in the journal Scientific Reports, could one day provide researchers with new tools to prevent hearing loss.


The study reveals that a gene called Forkhead Box O3 (Foxo3) appears to play a role in protecting outer hair cells in the inner ear from damage. The outer hair cells act as a biological sound amplifier and are critical to hearing. When exposed to loud noises, these cells undergo stress. In some individuals, these cells are able to recover, but in others the outer hair cells die, permanently impairing hearing. While hearing aids and other treatments can help recovered some range of hearing, there is currently no biological cure for hearing loss.


"While more than a hundred genes have been identified as being involved in childhood hearing loss, little is known about the genes that regulate hearing recovery after noise exposure," said Patricia White, Ph.D., a research associate professor in the University of Rochester Medical Center (URMC) Department of Neuroscience and lead author of the study. "Our study shows that Foxo3 could play an important role in determining which individuals might be more susceptible to noise-induced hearing loss."


Approximately one-third of people who reach retirement age have some degree of hearing loss, primarily due to noise exposure over their lifetimes. The problem is even more acute in the military, with upwards of 60 percent of individuals who have been deployed in forward areas experiencing hearing loss, making it the most common disability for combat veterans.


Foxo3 is known to play an important role in cell's stress response. For example, in the cardiovascular system, Foxo3 helps heart cells stay healthy by clearing away debris when the cells are damaged. Additionally, people with a genetic mutation that confers higher levels of Foxo3 protein have been shown to live longer.


White and her team carried out a series of experiments involving knock-out mice who were genetically engineered to lack the Foxo3 gene. The researchers found that, compared to normal mice, these animals were unable to recover hearing after being exposed to loud noises. The team also observed that during the experiment the Foxo3 knock-out mice lost most of their outer hair cells. In the normal mice, outer hair cell loss was not significant.


"Discovering that Foxo3 was important for the survival of outer hair cells is a significant advance," says senior author Patricia White. "We are also excited about the results because Foxo3 is a transcription factor, which regulates the expression of many target genes. We are currently investigating what its targets might be in the inner ear, and how they could act to protect the ear from damage."

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Viruses share genes with organisms across the three superkingdoms of life

Viruses share genes with organisms across the three superkingdoms of life | Amazing Science |

A new study finds that viruses share some genes exclusively with cells that are not their hosts. The study, reported in the journal Frontiers in Microbiology, adds to the evidence that viruses swap genes with a variety of cellular organisms and are agents of diversity, researchers say.


The study looked at protein structures in viruses and across all superkingdoms, or domains, of life: from the single-celled microbes known as bacteria and archaea, to eukaryotes, a group that includes animals, plants, fungi and all other living things.

"It is typical to define viruses in relation to their hosts, but this practice restricts our understanding of virus-cell interactions," said University of Illinois and COMSATS Institute of Information Technology researcher Arshan Nasir, who led the new research with Gustavo Caetano-Anolles, a professor of crop sciences and affiliate of the Carl R. Woese Institute for Genomic Biology at the U. of I., and Kyung Mo Kim, a senior scientist at the Korea Polar Research Institute, in Incheon, South Korea.


"Recent research has revealed that organisms can form partnerships with other organisms and live in communities. For example, many bacterial and archaeal species reside in and on the human body and constitute the human microbiota," Nasir said.


Viruses that infect archaea and bacteria, for example, are not known to infect eukarya. However, they may still interact in nonharmful ways with organisms they do not infect, the researchers said. "We wanted to investigate the genomes of viruses and cellular organisms to look for possible traces of gene transfer from viruses to cells, beyond what we already know about virus interactions with their hosts," Nasir said.


The team used a bioinformatics approach to analyze the genomes of organisms and the viruses that infect them. Rather than focusing on genetic sequences, which can change over the generations, the team examined the functional components of proteins, which they call folds. Each fold - and there are more than 1,400 of them across all domains of life - has a unique 3-D structure that performs a specific operation. Because folds are critical to protein function, they remain stable even as the sequences that code for them change as a result of mutations or other processes, the researchers said.

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Atomic structure of the entire mammalian mitochondrial complex I

Atomic structure of the entire mammalian mitochondrial complex I | Amazing Science |

Mitochondrial complex I (also known as NADH:ubiquinone oxidoreductase) contributes to cellular energy production by transferring electrons from NADH to ubiquinone coupled to proton translocation across the membrane1,2. It is the largest protein assembly of the respiratory chain with a total mass of 970 kilodaltons3. Scientists now present a nearly complete atomic structure of ovine (Ovis aries) mitochondrial complex I at 3.9 Å resolution, solved by cryo-electron microscopy with cross-linking and mass-spectrometry mapping experiments. All 14 conserved core subunits and 31 mitochondria-specific supernumerary subunits are resolved within the L-shaped molecule. The hydrophilic matrix arm comprises flavin mononucleotide and 8 iron–sulfur clusters involved in electron transfer, and the membrane arm contains 78 transmembrane helices, mostly contributed by antiporter-like subunits involved in proton translocation.


Supernumerary subunits form an interlinked, stabilizing shell around the conserved core. Tightly bound lipids (including cardiolipins) further stabilize interactions between the hydrophobic subunits. Subunits with possible regulatory roles contain additional cofactors, NADPH and two phosphopantetheine molecules, which are shown to be involved in inter-subunit interactions. The researchers observe two different conformations of the complex, which may be related to the conformationally driven coupling mechanism and to the active–deactive transition of the enzyme.


The obtained structure of the complex provides insight into the mechanism, assembly, maturation and dysfunction of mitochondrial complex I, and allows detailed molecular analysis of disease-causing mutations.

Via Imre Lengyel
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Here’s How Schooling Fish Coordinate Their Graceful, Mesmerizing Movements

Here’s How Schooling Fish Coordinate Their Graceful, Mesmerizing Movements | Amazing Science |

Humans tend to live in hierarchies, which rely on good leadership that ideally benefits the collective whole. There is little doubt that such systems are subject to frequent flaws, given that leaders may be vulnerable, corrupt, or self-interested. Even the most popular leaders have their detractors.


But most species of schooling fish and flocking birds do not have such problems. New research published in the journal PLOS Computational Biology finds that schooling fish switch their attention from neighbor to neighbor for seamless collective movement. The findings are helping scientists to design leaderless, self-organizing systems, such as swarms of drones.


The study focused on a common aquarium fish known as the rummy-nose tetra. When schooling, they can almost look like a single organism, given their coordinated movements. Each individual fish, however, has its own unique personality that can lead to relationship drama.


"While the movement of the fish gives the impression of the school as being very similar to a single organism, there are nonetheless conflicts within these groups: Rummy-nose tetras will still fight over food, or when mating," co-author Andrea Perna of the University of Roehampton in London told Seeker.


Despite the problems, fish do not drop out of 'school'. "Schooling is advantageous to each individual fish because they are less likely to be eaten by predators when they are in a school and because they can get information about food and about the environment from their neighbors,” she continued. “This is probably the main reason why they each individually decide to keep staying in the school."

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Big biology: The ’omes puzzle - Where once there was the genome, now there are thousands of ’omes

Big biology: The ’omes puzzle - Where once there was the genome, now there are thousands of ’omes | Amazing Science |

’Omics bashing is in fashion. In the past year, The New York Times and The Wall Street Journalhave run pieces poking fun at the proliferation of scientific words ending in -ome, which now number in the thousands. One scientist has created a bad­omics generator, which randomly adds the suffix to a list of biological terms and generates eerily plausible titles for scientific papers (example: ‘Sequencing the bacteriostaticome reveals insights into evolution and the environment’). Jonathan Eisen, a microbiologist at the University of California, Davis, regularly announces awards for unnecessary additions to the scientific vocabulary on his blog (recent winner: CircadiOmics, for genes involved in daily circadian rhythms).


Take the ’omics challenge: download our ’ome crossword.


Botanist Hans Winkler had no idea what he was starting back in 1920, when he proposed the term ‘genome’ to refer to a set of chromosomes. Other ’omes existed even then, such as biome (collection of living things) and rhizome (system of roots), many of them based on the Greek suffix ‘-ome’ — meaning, roughly, ‘having the nature of’. But it was the glamorization of ‘genome’ by megabuck initiatives such as the Human Genome Project that really set the trend in motion, says Alexa McCray, a linguist and medical informatician at Harvard Medical School in Boston, Massachusetts. “By virtue of that suffix, you are saying that you are part of a brand new exciting science.”


Researchers also recognize the marketing potential of an inspirational syllable, says Eisen. “People are saying that it’s its own field and that it deserves its own funding agency,” he says. But although some ’omes raise an eyebrow — museomics (sequencing projects on archived samples) and the tongue-in-cheek ciliomics (study of the wriggling hairlike projections on some cells) — scientists insist that at least some ’omes serve a good purpose. “Most of them will not make sense and some will make sense, so a balance should be in place,” says Eugene Kolker, chief data officer at Seattle Children’s Hospital in Washington, and founding editor of the journal Omics. “If we just laugh about different new terms, that’s not good.”


Ideally, branding an area as an ’ome helps to encourage big ideas, define research questions and inspire analytical approaches to tackle them (see ‘Hot or not’). “I think -ome is a very important suffix. It’s the clarion call of genomics,” says Mark Gerstein, a computational biologist at Yale University in New Haven, Connecticut. “It’s the idea of everything, it’s the thing we find inspiring.” Here, Nature takes a look at five up-and-coming ’omes that represent new vistas in science.

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Alzheimer's Tau protein forms toxic complexes with cell membranes

Alzheimer's Tau protein forms toxic complexes with cell membranes | Amazing Science |

The brains of patients with Alzheimer’s disease contain characteristic tangles inside neurons. These tangles are formed when a protein called Tau aggregates into twisted fibrils. As a result, the neurons’ transport systems disintegrate, essential nutrients can’t move through, and the cells begin to die, affecting the brain’s functions and giving rise to the disease’s symptoms.


Given its role in the pathology of Alzheimer’s disease, Tau protein has been extensively investigated. With several clinical trials of amyloid-targeting therapies failing recently, Tau has become one of the most actively pursued therapeutic targets for Alzheimer’s disease. However, questions still remain about how Tau spreads in the brain and kills neurons. The cell membrane has been shown to play a role in regulating Tau’s aggregation properties and physiological functions, but we still do not understand how the interplay between Tau and lipid membranes can lead to the loss of neurons seen in Alzheimer’s disease.


Now, the lab of Hilal Lashuel at EPFL, in collaboration with the lab of Thomas Walz at the Rockefeller University, found that individual Tau proteins interact with and disrupt the cell membrane of neurons. This disruption gives rise to highly stable complexes made up of several Tau proteins as well as fat molecules (phospholipids) from the membrane.


Subsequent studies showed that the protein/phospholipid complexes are more readily taken up by neurons compared to the fibril form of the protein, and induce toxicity in primary neurons of the hippocampus in vitro. The hippocampus is where memory is processed, and loss of hippocampal neurons is a classic symptom of Alzheimer’s disease. The complexes were detectable with an antibody (MC-1) that is used as a standard for detecting pathological conformations of Tau, meaning that they share some features of the pathological form of the protein.


“Our goal was to identify the sequence and structural factors that drive Tau interaction with membranes and the formation of these complexes so that we can develop strategies to interfere with their formation and block their toxicity,” says Nadine Ait Bouziad, the PhD student who led the study.

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A population of finches on the Galapagos has been discovered in the process of becoming a new species

A population of finches on the Galapagos has been discovered in the process of becoming a new species | Amazing Science |

This is the first example of speciation that scientists have been able to observe directly in the field. Researchers followed the entire population of finches on a tiny Galapagos island called Daphne Major, for many years, and so they were able to watch the speciation in progress.


The research was published in the journal Science. The group of finch species to which the Big Bird population belongs are collectively known as Darwin's finches and helped Charles Darwin to uncover the process of evolution by natural selection.


In 1981, the researchers noticed the arrival of a male of a non-native species, the large cactus finch. Professors Rosemary and Peter Grant noticed that this male proceeded to mate with a female of one of the local species, a medium ground finch, producing fertile young. Almost 40 years later, the progeny of that original mating are still being observed, and number around 30 individuals. "It's an extreme case of something we're coming to realise more generally over the years. Evolution in general can happen very quickly," said Prof Roger Butlin, a speciation expert who wasn't involved in the study.

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Just How Little Do We Know about the Ocean Floor?

Just How Little Do We Know about the Ocean Floor? | Amazing Science |
Less than 0.05 percent of the ocean floor has been mapped to a level of detail useful for detecting items such as airplane wreckage or the spires of undersea volcanic vents


Unlike mapping the land, we can’t measure the landscape of the sea floor directly from satellites using radar, because sea water blocks those radio waves. But satellites can use radar to measure the height of the sea’s surface very accurately. And if there are enough measurements to subtract the effects of waves and tides, satellites can actually measure bumps and dips in the sea surface that result from the underlying landscape of the ocean floor.


Where there’s a large underwater mountain or ridge, for example, the tiny local increase in gravity resulting from its mass pulls sea water into a slight bump above it. If instead there is an ocean trench, the weaker local gravity produces a comparative dip in the ocean surface.


Reading those bumps and dips in the sea’s surface is an astounding feat of precision measurement, involving lasers to track the trajectory of the measuring satellite and inevitably a lot of maths to process the data. The new map uses data from the Cryosat-2 and Jason-1 satellites and shows features not seen in earlier maps using data from older satellites. The previous global map of the ocean floor, created using the same techniques and published in 1997, had a resolution of about 20km.


So we do actually have a map of 100% of the ocean floor to a resolution of around 5km. From that, we can see the main features of its hidden landscape, such as the mid-ocean ridges and ocean trenches – and, in that sense, the ocean floor is certainly not “95% unexplored”. But that global map of the ocean floor is admittedly less detailed than maps of Mars, the Moon, or Venus, because of our planet’s watery veil.


NASA’s Magellan spacecraft mapped 98% of the surface of Venus to a resolution of around 100 meters. The entire Martian surface has also been mapped at that resolution and just over 60% of the Red Planet has now been mapped at around 20m resolution. Meanwhile, selenographers have mapped all of the lunar surface at around 100 meter resolution and now even at seven meter resolution.

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Zika virus-related nerve damage is caused by the body's immune response to the virus

Zika virus-related nerve damage is caused by the body's immune response to the virus | Amazing Science |

The immune system’s response to the Zika virus, rather than the virus itself, may be responsible for nerve-related complications of infection, according to a Yale study. This insight could lead to new ways of treating patients with Zika-related complications, such as Guillain-Barré syndrome, the researchers said.


In mice models lacking a key antiviral response, infection with Zika virus causes paralysis and death. To understand the mechanism, a research team led by immunobiologist Akiko Iwasaki examined the spread of infection in these mice.


The research team found that when the Zika infection spreads from the circulating blood into the brain, immune cells known as CD8 T cells flood the brain. While these T cells sharply limit the infection of nerve cells, they also trigger Zika-related paralysis, the researchers said.


The immune cells that are generated by infection start attacking our own neurons,” Iwasaki said. “The damage is not occurring through the virus infection, but rather the immune response to the virus.”


Immune-mediated nerve damage underlies Guillen-Barré syndrome, which affects some people infected with the Zika virus. The study findings suggest that suppressing the immune response might be an approach to treating the syndrome, which causes weakness, tingling, and, in rare cases, paralysis.


Read the full paper in Nature Microbiology.


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Researchers find the first methane-producing microbe that thrives in an oxygen-rich environment

Researchers find the first methane-producing microbe that thrives in an oxygen-rich environment | Amazing Science |

A study of a Lake Erie wetland suggests that scientists have vastly underestimated the number of places methane-producing microbes can survive—and, as a result, today’s global climate models may be misjudging the amount of methane being released into the atmosphere.


In the journal Nature Communications, researchers at The Ohio State University and their colleagues describe the discovery of the first known methane-producing microbe that is active in an oxygen-rich environment.


Oxygen is supposed to be toxic to such microbes, called methanogens, but the newly namedCandidatus Methanothrix paradoxum thrives in it. In fact, 80 percent of the methane in the wetland under study came from oxygenated soils. The microbe’s habitat extends from the deepest parts of a wetland, which are devoid of oxygen, all the way to surface soils.

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The Beautiful Intelligence of Bacteria and Other Microbes

The Beautiful Intelligence of Bacteria and Other Microbes | Amazing Science |

Bacterial biofilms and slime molds are more than crude patches of goo. Detailed time-lapse microscopy reveals how they sense and explore their surroundings.


Intelligence is not a quality to attribute lightly to microbes. There is no reason to think that bacteria, slime molds and similar single-cell forms of life have awareness, understanding or other capacities implicit in real intellect. But particularly when these cells commune in great numbers, their startling collective talents for solving problems and controlling their environment emerge. Those behaviors may be genetically encoded into these cells by billions of years of evolution, but in that sense the cells are not so different from robots programmed to respond in sophisticated ways to their environment. If we can speak of artificial intelligence for the latter, perhaps it’s not too outrageous to refer to the underappreciated cellular intelligence of the former.


Under the microscope, the incredible exercise of the cells’ collective intelligence reveals itself with spectacular beauty. Since 1983, Roberto Kolter, a professor of microbiology and immunobiology at Harvard Medical School and co-director of the Microbial Sciences Initiative, has led a laboratory that has studied these phenomena. In more recent years, it has also developed techniques for visualizing them. In the photographic essay book Life at the Edge of Sight: A Photographic Exploration of the Microbial World (Harvard University Press), released in September, Kolter and his co-author, Scott Chimileski, a research fellow and imaging specialist in his lab, offer an appreciation of microorganisms that is both scientific and artistic, and that gives a glimpse of the cellular wonders that are literally underfoot.


Imagery from the lab is also on display in the exhibition World in a Drop at the Harvard Museum of Natural History. That display will close in early January but will be followed by a broader exhibition, Microbial Life, scheduled to open in February, 2018.

Via Mariaschnee
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Acetabularia alga can grow to 10 cm (4 inches) and is a single cell

Acetabularia alga can grow to 10 cm (4 inches) and is a single cell | Amazing Science |

If I asked you what was the experimental basis for the central dogma of biology (DNA makes RNA makes Protein), you would be likely to mention the classical findings that the transforming principle was DNA (Avery et al.) or that phages transfer DNA to the host (Hershey & Chase). However, it is unlikely that you even have heard that the precept was earlier derived from studies with a unicellular marine alga, Acetabularia. If so, you would miss the remarkable biology that made it possible to carry out this work. Here is why: Acetabularia is such a large cell that it can be readily handled with one's hands.  It can be amputated into pieces that can be grafted together and its nucleus transplanted as easily as walking in the park.


Most cells are clearly too small for such luxuries. To enjoy them, we must turn to the outliers in range of sizes, that is, to giant cells. So, how big can cells get? The champion seems to be another a marine alga,Caulerpa, which can reach 3 meters in length. It is multinucleated, which seems almost like cheating (consider acellular slime molds, which can also reach enormous sizes, and othercoenocytic organisms). Incidentally, Caulerpas are edible and are called sea grapes in Okinawa (海葡萄 or umi-budō). Also multinucleated are the xenophyophores, foraminifera-like protists that live in the ocean at depths below 500 meters and reach 15 cm across (and which were mentionedhere earlier). Among the largest uninucleated single cells are the foraminifera called Nummulites, which can reach 5 cm in diameter, and a marine ameba called Gromia spherica.

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Twilight trick: Hybrid photoreceptor cell has been found in the eye of a deep-sea fish

Twilight trick: Hybrid photoreceptor cell has been found in the eye of a deep-sea fish | Amazing Science |
A new type of cell has been found in the eye of a deep-sea fish, and scientists say the discovery opens a new world of understanding about vision in a variety of light conditions.


Most vertebrates have a duplex retina comprising two photoreceptor types, rods for dim-light (scotopic) vision and cones for bright-light (photopic) and color vision. However, deep-sea fishes are only active in dim-light conditions; hence, most species have lost their cones in favor of a simplex retina composed exclusively of rods. Although the pearlsides, Maurolicus spp., have such a pure rod retina, their behavior is at odds with this oversimplified visual system. Contrary to other deep-sea fishes, pearlsides are mostly active during dusk and dawn close to the surface, where light levels are intermediate (twilight or mesopic) and require the use of both rod and cone photoreceptors.


A new study now elucidates this paradox by demonstrating that the pearlside retina does not have rod photoreceptors only. Instead, it is composed almost exclusively of transmuted cone photoreceptors. These transmuted cells combine the morphological characteristics of a rod photoreceptor with a cone opsin and a cone phototransduction cascade to form a unique photoreceptor type, a rod-like cone, specifically tuned to the light conditions of the pearlsides’ habitat (blue-shifted light at mesopic intensities). Combining properties of both rods and cones into a single cell type, instead of using two photoreceptor types that do not function at their full potential under mesopic conditions, is likely to be the most efficient and economical solution to optimize visual performance.


These results challenge the standing paradigm of the function and evolution of the vertebrate duplex retina and emphasize the need for a more comprehensive evaluation of visual systems in general.

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Scales, Feathers and Hair Have a Common Ancestor

Scales, Feathers and Hair Have a Common Ancestor | Amazing Science |

Reptiles have scales. Birds have feathers. Mammals have hair. How did they all get them?


For a long time scientists thought the spikes, plumage and fur characteristic of these groups originated independently of each other. But a study published Friday suggests that they all evolved from a common ancestor some 320 million years ago.


This ancient reptilian creature — which gave rise to dinosaurs, birds and mammals — is thought to have been covered in scale-like structures. What that creature looked like is not exactly known, but the scales on its skin developed from structures called placodes — tiny bumps of thick tissue found on the surface of developing embryos.


Scientists had previously found placodes on the embryos of birds and mammals, where they develop into feathers and hairs, but had never found the spots on a reptilian embryo before. The apparent lack of placodes in present-day reptiles fueled controversy about how these features first formed.


“People were fighting about the fact that reptiles either lost it, or birds and mammals independently developed them,” said Michel C. Milinkovitch, an evolutionary developmental biologist from the University of Geneva in Switzerland and an author of the new paper. “Now we are lucky enough to put this debate to rest, because we found the placodes in all reptiles: snakes, lizards and crocodiles.”


In their paper, published in the journal Science Advances, Dr. Milinkovitch and his team report the first findings of the anatomical structures in Nile crocodiles, bearded dragon lizards and corn snakes. They concluded that birds, mammals and reptiles all inherited their placodes from the same ancient reptilian ancestor.

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Boy Or Girl? It's In The Father's Genes, but the Gene is not Known Yet

Boy Or Girl? It's In The Father's Genes, but the Gene is not Known Yet | Amazing Science |
A study of hundreds of years of family trees suggests a man's genes play a role in him having sons or daughters. Men inherit a tendency to have more sons or more daughters from their parents. This means that a man with many brothers is more likely to have sons, while a man with many sisters is more likely to have daughters.


A Newcastle University study involving thousands of families is helping prospective parents work out whether they are likely to have sons or daughters.


The work by Corry Gellatly, a research scientist at the university, has shown that men inherit a tendency to have more sons or more daughters from their parents. This means that a man with many brothers is more likely to have sons, while a man with many sisters is more likely to have daughters.


The research involved a study of 927 family trees containing information on 556,387 people from North America and Europe going back to 1600. "The family tree study showed that whether you’re likely to have a boy or a girl is inherited. We now know that men are more likely to have sons if they have more brothers but are more likely to have daughters if they have more sisters.


However, in women, you just can’t predict it," Mr Gellatly explains. Men determine the sex of a baby depending on whether their sperm is carrying an X or Y chromosome. An X chromosome combines with the mother’s X chromosome to make a baby girl (XX) and a Y chromosome will combine with the mother’s to make a boy (XY).


The Newcastle University study suggests that an as-yet undiscovered gene controls whether a man’s sperm contains more X or more Y chromosomes, which affects the sex of his children. On a larger scale, the number of men with more X sperm compared to the number of men with more Y sperm affects the sex ratio of children born each year.

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Programming cells with computer-like logic

Programming cells with computer-like logic | Amazing Science |

Synthetic biologists are converting microbial cells into living devices that are able to perform useful tasks ranging from the production of drugs, fine chemicals and biofuels to detecting disease-causing agents and releasing therapeutic molecules inside the body. To accomplish this, they fit cells with artificial molecular machinery that can sense stimuli such as toxins in the environment, metabolite levels or inflammatory signals. Much like electronic circuits, these synthetic biological circuits can process information and make logic-guided decisions. Unlike their electronic counterparts, however, biological circuits must be fabricated from the molecular components that cells can produce, and they must operate in the crowded and ever-changing environment within each cell.


Similar to how computer scientists use logical language to have their programs make accurate AND, OR and NOT decisions towards a final goal, “Ribocomputing Devices” (stylized here in yellow) developed by a team at the Wyss Institute can now be used by synthetic biologists to sense and interpret multiple signals in cells and logically instruct their ribosomes (stylized in blue and green) to produce different proteins.


So far, synthetic biological circuits can only sense a handful of signals, giving them an incomplete picture of conditions in the host cell. They are also built out of several moving parts in the form of different types of molecules, such as DNAs, RNAs, and proteins, that must find, bind and work together to sense and process signals. Identifying molecules that cooperate well with one another is difficult and makes development of new biological circuits a time-consuming and often unpredictable process.


As reported in Nature, a team at Harvard’s Wyss Institute for Biologically Inspired Engineering is now presenting an all-in-one solution that imbues a molecule of ‘ribo’ nucleic acid or RNA with the capacity to sense multiple signals and make logical decisions to control protein production with high precision. The study’s approach resulted in a genetically encodable RNA nano-device that can perform an unprecedented 12-input logic operation to accurately regulate the expression of a fluorescent reporter protein in E. coli bacteria only when encountering a complex, user-prescribed profile of intra-cellular stimuli. Such programmable nano-devices may allow researchers to construct more sophisticated synthetic biological circuits, enabling them to analyze complex cellular environments efficiently and to respond accurately.


“We demonstrate that an RNA molecule can be engineered into a programmable and logically acting “Ribocomputing Device,” said Wyss Institute Core Faculty member Peng Yin, Ph.D., who led the study and is also Professor of Systems Biology at Harvard Medical School. “This breakthrough at the interface of nanotechnology and synthetic biology will enable us to design more reliable synthetic biological circuits that are much more conscious of the influences in their environment relevant to specific goals.”

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Digitally printed cyanobacteria can power small electronic devices

Digitally printed cyanobacteria can power small electronic devices | Amazing Science |

Researchers have used a simple inkjet printer to print a "bio-ink" of cyanobacteria onto a conductive surface, creating a biophotovoltaic cell. Unlike conventional photovoltaic cells that operate only when exposed to light, the cyanobacteria can generate an electric current both in the dark and in response to light. The researchers expect that the cell may serve as an environmentally friendly power supply for low-power devices such as biosensors, and can even be scaled up to print a bioenergy wallpaper.

The scientists, at Imperial College London and University of Cambridge, have published a paper on the new biophotovoltaic cell in a recent issue of Nature Communications. "Our biophotovoltaic device is biodegradable and in the future could serve as a disposable solar panel and battery that can decompose in our composts or gardens," coauthor Marin Sawa at University of Arts London and Imperial College London told "Cheap, accessible, environmentally friendly, biodegradable batteries without any heavy metals and plastics—this is what we and our environment really need but don't have just yet, and our work has shown that it is possible to have that."


In general, biophotovoltaic cells contain some type of cyanobacteria or algae that is phototrophic, meaning it converts light into energy. However, even in the dark these organisms continue to generate some energy by metabolizing their internal storage reserves. So when the organisms are connected to a non-biological electrode, they can function as either a "bio solar panel" when exposed to light or a "solar bio-battery" in the dark.


Currently one of the biggest challenges facing biophotovoltaic cells is producing them on a large scale. Typically, the organisms are deposited onto an electrode surface from a bulky liquid reservoir. In the new study, the researchers demonstrated that inkjet printing can be used to print both the carbon nanotube electrode surface and the cyanobacteria on top of it, while allowing the bacteria to remain fully viable. This approach not only allows the cells to be fabricated quickly, but the set-up is also more compact and allows for greater precision in cell design.


With these advantages, the inkjet-printed biophotovoltaic cells can generate a maximum current density that is 3-4 times higher than cells fabricated using conventional methods. To demonstrate, the researchers showed that nine connected cells can power a digital clock or generate flashes of light from an LED, illustrating the ability to produce short bursts of relatively high power. The researchers also showed that the cells can generate a continuous power output over the course of a 100-hour period consisting of light and dark cycles.


In the future, the researchers plan to develop thin-film biophotovoltaic (BPV) panels and also explore potential applications as integrated power supplies in the areas of point-of-care medical diagnostics and environmental monitoring, both of which benefit from disposable, environmentally friendly biosensors. Another potential application is a bioenergy wallpaper.

"The bioenergy wallpaper is a scaled-up application of our BPV system," Sawa said. "The wallpaper will have carbon-based conductive patterns with electron-producing cyanobacteria. It turns an interior surface into an energy harvester to drive low-power applications like LED lights and/or biosensors, which can, for example, monitor indoor air quality."

Via Mariaschnee
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DNA links male and female butterfly thought to be distinct species

DNA links male and female butterfly thought to be distinct species | Amazing Science |
Researchers recently discovered what was thought to be a distinct species of butterfly is actually the female of a species known to science for more than a century.


An international team of nine butterfly researchers from the U.S., Brazil, the U.K., Peru and Germany used DNA sequence data to associate the female sunburst cerulean-satyr, or Caeruleuptychia helios, an Amazonian brush-footed butterfly, with its male counterpart.


Males and females of this group look dramatically different from each other, a phenomenon known as sexual dimorphism, and the species was named and described in 1911 based on the brilliantly iridescent blue males. Rarer than the male, the brown female was considered another species and was recently named and placed in a different genus, Magneuptychia keltoumae.


A study correcting the classification error was published today in Insect Systematics and Evolution.


"Our study will serve as the basis for developing a firm understanding of true species diversity of this group and of Neotropical butterflies in general," said Shinichi Nakahara, the study's lead author and a research associate at the Florida Museum of Natural History's McGuire Center for Lepidoptera and Biodiversity at the University of Florida. "These findings are extremely valuable at a time when the biodiversity of the Neotropics is threatened since it will be impossible to recognize and document the region's unique elements of biodiversity after they are gone."


As part of the project, DNA bar codes—short, diagnostic gene sequences—were collected and analyzed for more than 300 species across the euptychiines group of butterflies.

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The Human Cell Atlas: an ambitious project to map all the cells in the human body gets officially under way

The Human Cell Atlas: an ambitious project to map all the cells in the human body gets officially under way | Amazing Science |

Our knowledge of the cells that make up the human body, and how they vary from person to person, or throughout development and in health or disease, is still very limited. Recently, a year after project planning began, more than 130 biologists, computational scientists, technologists and clinicians are reconvening in Rehovot, Israel, to kick the Human Cell Atlas initiative1 into full gear. This international collaboration between hundreds of scientists from dozens of universities and institutes — including the UK Wellcome Trust Sanger Institute, RIKEN in Japan, the Karolinska Institute in Stockholm and the Broad Institute of MIT and Harvard in Cambridge, Massachusetts — aims to create comprehensive reference maps of all human cells as a basis for research, diagnosis, monitoring and treatment.


On behalf of the Human Cell Atlas organizing committee, we outline here some of the key challenges faced in building such an atlas — and our proposed strategies. For more details on how the atlas will be built as an open global resource, see the white paper2 posted on the Human Cell Atlas website.


Cells have been characterized and classified with increasing precision since Robert Hooke first identified them under the microscope in the seventeenth century. But biologists have not yet determined all the molecular constituents of cells, nor have they established how all these constituents are associated with each other in tissues, systems and organs. As a result, there are many cell types we don’t know about. We also don’t know how all the cells in the body change from one state to another, which other cells they interact with or how they are altered during development.

Technology revolution 

New technologies offer an opportunity to build a systematic atlas at unprecedented resolution. These tools range from single-cell RNA sequencing to techniques for assessing a cell’s protein molecules and profiling the accessibility of the chromatin. For example, we can now determine the RNA profiles for millions of individual cells in parallel (see ‘From one to millions’). Protein composition and chromatin features can be studied in hundreds or thousands of individual cells, and mutations or other markers tracked to reconstruct cell lineages. We can also profile multiple variants of RNA and proteins in situ to map cells and their molecules to their locations in tissues.

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A dolphin’s forehead acts like an acoustic metamaterial

A dolphin’s forehead acts like an acoustic metamaterial | Amazing Science |

Echolocation beam controlled with deformable tissue is the trick many dolphins use.


A porpoise’s forehead acts like a ‘metamaterial’ to create the directional sound beam used by the marine mammals to detect and track prey, claim researchers in the US and China. The acoustics experts and biologists also found that the animals can adjust the acoustic properties of their foreheads to control the width of the beam. They believe that the structure of the porpoise forehead could inspire the development of new materials to control sound, with applications in underwater sonar and ultrasonic imaging.


Porpoises use directional acoustic waves as a sonar system to hunt. When first searching for prey they use a narrow beam of sound to scan the water. But as they close in on a target they dramatically increase the width of the beam, to keep it in their field of view.


Scientists have struggled to understand how porpoises produce, and control, this directional echolocation beam. Porpoises produce the sounds, or 'clicks', by forcing air through a structure in their blowhole called the phonic lips. But this sound source is smaller than the wavelength of the sound it produces, which should, in theory, make the acoustic beam hard to control. And the phonic lips emit sound in all directions, not just forwards.

Laurent's curator insight, November 24, 6:49 AM
20 years ago at Telecom ParisTech, our signal processing teacher showed us this amazing Nature miracle : how the nose of the dolphin shapes the ultrasonic impulse to make it super sharp therefore super efficient as a sonar signal !
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Fruit Fly Brains Could Help AI Perform Much Better Content Searches

Fruit Fly Brains Could Help AI Perform Much Better Content Searches | Amazing Science |
The neural architecture of a fruit fly brain is better at some types of searches than computers today.


The content you see on the internet is increasingly becoming tailored to you: Music based on your favorite jams, shopping suggestions corresponding to your recent purchases, and television shows similar to your most beloved episodes. These “similarity searches” drive custom content, and they’re pretty tricky to do correctly and quickly.


That is, for computers at least. Fruit flies, on the other hand, seem to be pretty good at them. A new study in the journal Science takes a look at how fruit flies quickly and efficiently sort out and identify different smells. Their neural architecture is so well-designed in fact, that it could hold the key to more effective similarity searches.


For brains, especially human brains, this kind of recognition isn’t too difficult, according to Saket Navlakha, assistant professor in Salk’s Integrative Biology Laboratory and lead author of the new paper. Many animals perform similarity searches all the time. “For example, you might see someone and be like, ‘That guy reminds me of my uncle.’ Or you might hear a song and be like, ‘That band sounds like Nirvana.’ Or you might smell a perfume and be like, ‘That smell reminds me of an orange,’” Navlakha explains.


He says in each of these instances we’re comparing new stimuli to an existing database of information stored in our brains. It would be much the same with animals in the wild — seeing a red berry may trigger a similarity search to other red berries to indicate that it might be poisonous. “It’s quite a general problem faced by many species,” says Navlakha.


The problem of categorizing and understanding new information is a little trickier for computers — you’ve likely received an automated suggestion for a movie or product that seemed way off base. That’s because when most computers analyze data to categorize items, they pare down the information to work more efficiently. Computers assign a kind of digital shorthand, called a “hash,” to each item. From there, hashes are compared and matched with other, similar hashes, a process known as called locality-sensitive hashing. The simplified hashes make searching through thousands, if not millions, of other items faster and easier.


Fruit flies, however, have a mechanism in their brains that performs similarity searches in a very different way. Specifically, they expand the stimuli information, as opposed to compressing and simplifying it. When fruit flies first sense an odor, 50 neurons fire in a combination unique to that smell. But instead of simplifying that information as computer programs would, the flies’ brains then send that information to a total of 2,000 neurons. With more neurons in play, the fly’s brain is able to give each smell a more unique label, meaning that it’s easier to categorize.


The flies then pare this information down to the top five percent or so of neural signals, effectively sorting out only the most salient information. This creates a pattern similar to a digital hash that the fly can then use to identify scents and respond accordingly.

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Whales switch from right to left-handed when diving for food

Whales switch from right to left-handed when diving for food | Amazing Science |

Ambidextrous behavior by “right-handed” blue whales has surprised scientists studying the huge creatures’ feeding habits.

Like many other animals, blue whales display laterality, or “handedness” – generally a bias towards the right. But a study using video cameras attached to the backs of whales has shown how they switch laterality when feeding.


Over a period of six years, the team attached suction “tags” fitted with video cameras, hydrophones and motion sensors to the backs of 63 blue whales off the coast of southern California. The tags were designed to detach after several hours and float to the surface, so they could be recovered and their data downloaded.


Blue whales are famous for their dramatic “lunge feeding” acrobatics close to the ocean surface. As they launch themselves upwards into swarms of the tiny crustaceans, called krill, on which they feed, the whales execute 360 degree barrel rolls. And according to the video evidence, they almost always roll to the left. This is in marked contrast to the way they normally feed at greater depths, when they execute 90-degree right-handed side rolls.


Rolling to the left while lunge feeding allows the blue whale’s dominant right eye to target smaller patches of krill more effectively, suggests US lead researcher Ari Friedlaender, at Oregon State University’s Marine Mammal Institute. “We were completely surprised by these findings, but when considering the means by which the whales attack smaller prey patches, the behaviour really seems to be effective, efficient, and in line with the mechanisms that drive their routine foraging behaviours,” he says. It was the first known example of an animal altering handedness to adjust to the context of a performed task.


Journal reference: Current Biology, DOI: 10.1016/j.cub.2017.10.023

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Schizophrenia originates early in pregnancy, 'mini-brain' research suggests

Schizophrenia originates early in pregnancy, 'mini-brain' research suggests | Amazing Science |
Symptoms of schizophrenia usually appear in adolescence or young adulthood, but new research reveals that the brain disease likely begins very early in development, toward the end of the first trimester of pregnancy. The finding opens up a new understanding of this devastating disease and the potential for new treatment possibilities in utero.

Recent research published in Translational Psychiatry by scientists from the Jacobs School of Medicine and Biomedical Sciences at the University at Buffalo and other institutions show that schizophrenia actually might have fetal beginnings. 

The findings provide powerful evidence that schizophrenia begins early in fetal development, said Michal K. Stachowiak, PhD, lead author and professor in the Department of Pathology and Anatomical Sciences at UB. "This disease has been mischaracterized for 4,000 years," he said, referring to the first time a disease believed to be schizophrenia was described in the 1550 BC Egyptian medical text, the Ebers Papyrus.
"After centuries of horrendous treatment, including even the jailing of patients, and after it has been characterized as everything from a disease of the spirit or moral values or caused by bad parental influence (a concept that appeared in psychiatric textbooks as recently as 1975) we finally now have evidence that schizophrenia is a disorder that results from a fundamental alteration in the formation and structure of the brain," Stachowiak said.

The research builds on previous work by Stachowiak and his colleagues showing that although hundreds of different genetic mutations may be responsible for schizophrenia in different patients, they all converge in a single faulty genomic pathway called the Integrative Nuclear FGFR 1 Signaling (INFS) pathway, which the UB researchers reported on earlier this year. But when and how dysregulation of that pathway occurred and how it affected brain development was unknown.

Via Miloš Bajčetić
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These are the world’s smartest fish

These are the world’s smartest fish | Amazing Science |

The East African cichlid fish Julidochromis transcriptus, a tiny fish no more than seven centimetres long, is able to recognize unfamiliar individuals just by looking at their eyes.


This stripped little fish lives hidden among rocks in Lake Tanganyika, one of the world oldest and largest freshwater lakes.


According to a recent study when another fish comes around, a simple look at the patterns around the eyes of the newcomer reveals if it is a friend or a stranger. Similar results have been found for another species living in this lake. The cichlid fishNeolamprologus pulcher uses face colour patterns to identify different individuals.


Another fish able to identify individuals by their faces is the Japanese rice fish (Oryzias latipes). A recent study showed that this little fish has evolved a complex way to deal with faces, similar to the way human process face patterns.


Humans and primates can easily identify any objects, even if they are upside down, but when it comes to faces, things get more complicated. “The neural pathway used for discriminating faces is different from other objects in mammals, and when faces are upside-down, our brain considers them as non-face objects and we cannot discriminate them as fast as right-up faces,” says Mu-Yun Wang at the University of Tokyo, Japan. And it seems like the brain of the Japanese rice fish works this way too.


“Medaka fish also delays face recognition when the faces are upside-down, and it is possible that they also have specific brain region for processing faces, just like us humans,” Wang says. “As research efforts continue, we are finding out more and more about the cognitive abilities of fish, and learning that there are many cases where the abilities of fish rival other vertebrates,” says Alex Jordan at the Max Planck Institute Department of Collective Behaviour in Konstanz, Germany.


“The long-held idea of a three-second memory for fish will slowly recede under the weight of evidence from studies like these as time goes on,” he adds.


But face recognition is just one of the many skills fish have.

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Growing kelp for biofuel: Researchers aim to harness potential

Growing kelp for biofuel: Researchers aim to harness potential | Amazing Science |

Sources of energy frequently in the limelight are solar, wind and hydropower.


Giant Kelp (Macrocystis pyrifera) is one of the fastest growing producers of biomass.  The open ocean is an immense, untapped region for collecting solar energy.  Giant kelp does not grow naturally in the open ocean because kelp normally needs an attachment at about 10-20 meters of depth and also needs key nutrients that are available in deep ocean water or near shore but not at the surface in the open ocean.  This concept proposes an economical system to provide a grid for attachment and access to nutrients, making it possible to farm kelp in the extensive regions of the open ocean.


If successful, this patented approach will grow kelp attached to large grids in the open ocean, each grid towed by inexpensive underwater drones.  These drones will maintain the grids near the surface during the day to gather sunlight for photosynthesis.  At night, the drones will take the grids down to the deeper, cold water where the kelp can absorb nutrients that are not adequate in the warmer surface waters.  These kelp farms will also be taken to deeper water during storms or to avoid passing ships.  Every three months, the drones will move the kelp farms to scheduled locations to rendezvous with harvesters.


Why grow giant kelp on farms in the open ocean?

  • does not compete with food production for agricultural land.
  • will not harm environmentally-sensitive areas, such as deserts or marine reserves.
  • does not use fresh water, pesticides, or artificial fertilizers (using, instead, abundant nutrients in deep water).
  • stores nutrients when they are available and uses them when needed.
  • is relatively easy to process into drop-in fuels because it has no lignin and little cellulose.
  • is one of the fastest-growing primary producers with elongation rates ~30 cm/day, and average photosynthetic efficiency in the range of 6-8%, much higher than terrestrial plant production at 1.8-2.2%.
  • stores over 1 Watt/m2 (averaged 24/7/365) of sunlight as chemical energy (~2.8 kg ash-free, dry weight per m2-year) , as observed in natural beds.
  • continues to grow year round especially if adequate nutrients are available, and the harvest is non-destructive so farms can be productive for years without replanting.


Why grow giant kelp on farms in the open ocean guided by underwater drones?

  • near shore areas with natural upwelling of nutrients won’t produce enough biomass to make a significant
     impact on the nation’s energy needs.
  • many natural kelp beds are in marine reserves, or in recreational or commercial areas.
  • the production underwater drones will be less expensive than one might expect because they will be made out of reinforced concrete and numerous subsystems are already available in production quantities (automated guidance & control, communications, batteries, pumps, sensors).
  • most importantly, kelp grown in the open ocean can utilize massive open ocean areas to supply an energy feedstock sufficient for the projected peak world population at the current U.S. per capita rate of energy consumption of ~9500W/person.


The Pacific Ocean offshore of the Western U.S. represents an immense, untapped solar collecting area and, if this effort is successful, will be the first deployment region for the commercial farm systems.  Fast-growing kelp produces biomass year round and could provide a transformational solution to the need for millions of tons of feedstock per year.

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