Another perceptive in DNA expressing

Now there is one of the biggest challenges currently facing the fields of genomics and genetics, which Scientists from Australia and the United States bring into our concept of the three-dimensional structure of the genome.

DNA, roughly 3 metres is tightly folded into the nucleus of every cell in our body. This folding facilitates some genes to be ‘expressed’, or activated, while excluding others.

Genes consist of ‘exons’ and ‘introns’ the former being the sequences that code for protein and are expressed, and the latter being stretches of noncoding DNA in-between. As the genes are copied, or ‘transcribed’, from DNA into RNA, the intron sequences are cut or ‘spliced’ out and the remaining exons are strung together to form a sequence that encodes a protein. Depending on which exons are strung together, the same gene can generate different proteins.

Referring vast amounts of data from the ENCODE project*, Dr Tim Mercer and colleagues have examined the folding of the genome, finding that even within a gene, selected exons are easily exposed.

There will be new device to detect disease with drop of blood

Professor Eginald Farrow and his partners’ cutting-edge work with carbon nanotubes is the fore path to a new device, a prototype lab-on-a-chip that would someday enable a physician to detect disease or virus from just one drop of liquid, including blood.

The article entitled “Scalable nano-bioprobes with sub-cellular resolution for cell detection” will publish on July 15, 2013 but is available now online, describes how NJIT research professors Reginald Farrow and Alokik Kanwal, his former postdoctoral fellow, and their team have created a carbon nanotube-based device to noninvasively and quickly detect mobile single cells with the potential to maintain a high degree of spatial resolution.

In the article, the NJIT researchers evaluated three different types of cells using three different electrical probes. "It was an exploratory study and we don't want to say that we have a signature," Farrow added. "What we do say here is that these cells differ based on electrical properties. Establishing a signature, however, will take time, although we know that the distribution of electrical charges in a healthy cell changes markedly when it becomes sick."

Two Mutations produced an Evolutionary Leap 500 Million Years Ago

In a feat of "molecular time travel" the researchers resurrected and analyzed the functions of the ancestors of genes that play key roles in modern human reproduction, development, immunity and cancer. By re-creating the same DNA changes that occurred during those genes' ancient history, the team showed that two mutations set the stage for hormones like estrogen, testosterone and cortisol to take on their crucial present-day roles.

"Changes in just two letters of the genetic code in our deep evolutionary past caused a massive shift in the function of one protein and set in motion the evolution of our present-day hormonal and reproductive systems," said Joe Thornton, PhD, professor of human genetics and ecology & evolution at the University of Chicago, who led the study.

"If those two mutations had not happened, our bodies today would have to use different mechanisms to regulate pregnancy, libido, the response to stress, kidney function, inflammation, and the development of male and female characteristics at puberty," Thornton said.

The findings were published online June 24 in the Proceedings of the National Academy of Sciences.

Understanding how the genetic code of a protein determines its functions would allow biochemists to better design drugs and predict the effects of mutations on disease. Thornton said the discovery shows how evolutionary analysis of proteins' histories can advance this goal, Before the group's work, it was not previously known how the various steroid receptors in modern species distinguish estrogens from other hormones.

The team, which included researchers from the University of Oregon, Emory University and the Scripps Research Institute, studied the evolution of a family of proteins called steroid hormone receptors, which mediate the effects of hormones on reproduction, development and physiology. Without receptor proteins, these hormones cannot affect the body's cells.

Thornton's group traced how the ancestor of the entire receptor family -- which recognized only estrogens -- evolved into descendant proteins capable of recognizing other steroid hormones, such as testosterone, progesterone and the stress hormone cortisol.

To do so, the group used a gene "resurrection" strategy. They first inferred the genetic sequences of ancient receptor proteins, using computational methods to work their way back up the tree of life from a database of hundreds of present-day receptor sequences. They then biochemically synthesized these ancient DNA sequences and used molecular assays to determine the receptors' sensitivity to various hormones.
Thornton's team narrowed down the time range during which the capacity to recognize non-estrogen steroids evolved, to a period about 500 million years ago, before the dawn of vertebrate animals on Earth. They then identified the most important mutations that occurred during that interval by introducing them into the reconstructed ancestral proteins. By measuring how the mutations affected the receptor's structure and function, the team could re-create ancient molecular evolution in the laboratory.

They found that just two changes in the ancient receptor's gene sequence caused a 70,000-fold shift in preference away from estrogens toward other steroid hormones. The researchers also used biophysical techniques to identify the precise atomic-level mechanisms by which the mutations affected the protein's functions. Although only a few atoms in the protein were changed, this radically rewired the network of interactions between the receptor and the hormone, leading to a massive change in function.

"Our findings show that new molecular functions can evolve by sudden large leaps due to a few tiny changes in the genetic code," Thornton said. He pointed out that, along with the two key changes in the receptor, additional mutations, the precise effects of which are not yet known, were necessary for the full effects of hormone signaling on the body to evolve.

via DailyScience 

Puya chilensis

Puya chilensis is a kind of plant in very large bromeliad, native to the mountains of Chile. Bromeliads are spiky, mostly tropical, commonly New-World plants, the best-known of which is probably the pineapple. But while the pineapple is delicious, Puya chilensis is a bit more harmful.

Most bromeliads have firm, hard leaves, but Puya chilensis is sort of an extreme sample. Its leaves look sort of like aloe leaves, but in between them are huge, sharp spines that jut out past them. Most plants that have spines, like cacti, use them for protection, but it's theorized that Puya chilensis actually uses them for hunting.

This plant is sometimes known as a "sheep-eating" plant, which is not, strictly speaking, accurate: it is not a carnivorous plant like the well-known pitcher plant or Venus flytrap, as it doesn't actually digest animal matter. Instead, scientists believe that the spikes trap animals with thick fur, like sheep, which then starve to death, fall to the ground, and decompose at the base of the plant, providing highly rich, localized food for the plant. It's gruesome as hell.

It's not a particularly rare plant; it's in the news now because for the first time, horticulturists in England have coaxed it to bloom, 15 years after planting it. They've been feeding it liquid fertilizer, because, says one of the horticulturists, "feeding it on its natural diet might prove a bit problematic.

Brain drain and brain circulation

According to an article, a brain drain or human capital flight is an emigration of trained and talented individuals ("human capital") to other nations or jurisdictions, due to conflicts, lack of opportunity, health hazards where they are living or other reasons. Spokesmen for the Royal Society of London coined the expression “brain drain” to describe the outflow of scientists and technologists to Canada and the United States in the early 1950s. Its counterpart is brain gain in the areas to which talent migrates. Brain drain can occur either when individuals who study abroad and complete their education do not return to their home country, or when individuals educated in their home country emigrate for higher wages or better opportunities. This phenomenon is perhaps most problematic for developing nations, where it is widespread. In these countries, higher education and professional certification are often viewed as the surest path to escape from a troubled economy or difficult political situation. Brain drain can be described as “soft brain drain” which is the non-availability of research results from a country where the study was carried out. This could be due to a publication of the findings in an international journal to which health practitioners from the study country have little access. This is different from the physical movement of persons from the developing countries to northern nations “hard brain drain2”. 

In the article published in Perspective, the author looked into the problem of brain drain and showed what caused it and how to avoid and improve it. It had been included into database of oalib: http://goo.gl/58bnF.

Oalib

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Home messages affect fluency of speaking another language

Sometimes there are moments when people blurt out homeland languages while they are speaking with foreigners using foreign languages. Why they happen make people confused.

Shu Zhang, a Chinese native, teamed up with Columbia social psychologist Michael Morris and colleagues to figure out the problem. In a new study, they show that reminders of one’s homeland can hinder the ability to speak a new language. The findings could help explain why cultural immersion is the most effective way to learn a foreign tongue and why immigrants who settle within an ethnic enclave acculturate more slowly than those who surround themselves with friends from their new country.

Previous studies have shown that cultural icons such as landmarks and celebrities act like “magnets of meaning,” instantly activating a web of cultural associations in the mind and influencing our judgments and behavior, Morris says. In an earlier study, for example, he asked Chinese Americans to explain what was happening in a photograph of several fish, in which one fish swam slightly ahead of the others. Subjects first shown Chinese symbols, such as the Great Wall or a dragon, interpreted the fish as being chased. But individuals primed with American images of Marilyn Monroe or Superman, in contrast, tended to interpret the outlying fish as leading the others. This internally driven motivation is more typical of individualistic American values, some social psychologists say, whereas the more externally driven explanation of being pursued is more typical of Chinese culture.

Understanding how these subtle cultural cues affect language fluency could help employers design better job interviews, Morris says. For example, taking a Japanese job candidate out for sushi, although a well-meaning gesture, might not be the best way to help them shine.

“It’s quite striking that these effects were so robust,” says Mary Helen Immordino-Yang, a developmental psychologist at the University of Southern California in Los Angeles. They show that “we’re exquisitely attuned to cultural context,” she says, and that “even subtle cues like the ethnicity of the person we’re talking to” can affect language processing. The take-home message? “If one wants to acculturate rapidly, don’t move to an ethnic enclave neighborhood where you’ll be surrounded by people like yourself,” Morris says. Sometimes, a familiar face is the last thing you need to see.

Study shows that pesticide contamination kills up to 42 percent of water life

A study from US journal the Proceedings of the National Academy of Sciences, the first to compare regional biodiversity in polluted versus less polluted water presents Pesticides may kill off water insects and other small aquatic life by as much as 42 percent.

According to the study, freshwater invertebrates and aquatic insects were 42 percent less common in strongly contaminated areas in Europe compared to less polluted areas; and in Australia, a difference of 27 percent was found across regions.

The analysis involves in measurements of insecticides and fungicides, which are used often in agriculture and are typically well studied and heavily regulated.

However, little examination has been done to gauge their effect on the streams and rivers they end up in after it rains and the chemicals are washed off farmland and into watercourses.

“The current practice of risk assessment is like driving blind on the motorway,” said ecotoxicologist Matthias Liess, a study co-author.

Researchers said that Species that were particularly vulnerable to pesticides included dragonflies, stoneflies, mayflies and caddis flies.

The researchers warned that the threat pesticides pose to biodiversity has been underestimated, since experimental lab work and studies on artificial ecosystems often precede a pesticide’s market approval.

“The effects in Europe were detected at concentrations that current legislation considers environmentally protective,” said the study, calling for new approaches to better assess the ecological risks of pesticides.

Mystery of X-Ray Light from Black Holes Solved

According to a new study, astrophysicists from The Johns Hopkins University, NASA and the Rochester Institute of Technology did research that bridges the gap between theory and observation by demonstrating that gas spiraling toward a black hole inevitably results in X-ray emissions.

The paper suggests that as gas spirals toward a black hole through a formation called an accretion disk, it heats up to roughly 10 million degrees Celsius. The temperature in the main body of the disk is roughly 2,000 times hotter than the sun and emits low-energy or "soft" X-rays. However, observations also detect "hard" X-rays which produce up to 100 times higher energy levels.

Julian Krolik, professor of physics and astronomy in the Zanvyl Krieger School of Arts and Sciences, and his fellow scientists used a combination of supercomputer simulations and traditional hand-written calculations to uncover their findings. Supported by 40 years of theoretical progress, the team showed for the first time that high-energy light emission is not only possible, but is an inevitable outcome of gas being drawn into a black hole.

Breastfeeding benefits babies’ brains

Recently a new study by researchers from Brown University showed that breastfeeding improves brain development in infants.

Deoni, the research leader, and his team made experiments on 133 babies ranging in ages from 10 months to four years. All of the babies are the same in gestation times and socioeconomic statuses. The researchers divided the babies into three groups: those whose mothers reported they exclusively breastfed for at least three months, those fed a combination of breastmilk and formula, and those fed formula alone. The researchers compared the older kids to the younger kids to establish growth trajectories in white matter for each group.

The study showed that the exclusively breastfed group had the fastest growth in myelinated white matter of the three groups, with the increase in white matter volume becoming substantial by age 2. The group fed both breastmilk and formula had more growth than the exclusively formula-fed group, but less than the breastmilk-only group.

The study also looked at the effects of the duration of breastfeeding. The researchers compared babies who were breastfed for more than a year with those breastfed less than a year, and found significantly enhanced brain growth in the babies who were breastfed longer — especially in areas of the brain dealing with motor function.

People are likely to overestimate their accuracy of their judgments

In our daily life, we should make many judgments and we believe that these judgments are correct, even some are errors. These phenomenons called overprecison by scientists can have profound effects, increasing investors’ participation in investments, leading physicians to conclude quickly a diagnosis, even making people presenting dissenting views. Now, new research makes it acceptable that overprcision is a common and strong form of overconfidence driven, at least in part, by excessive certainty in the accuracy of our judgments

The new findings are published in Psychological Science, a journal of the Association for Psychological Science.

Research investigating overprecision typically involves asking people to put up with a 90% or above interval around a numerical estimate , such as the length of the Nile River -- but this doesn't always faithfully reflect the judgments we have to make in everyday life. We know, for example, that arriving 15 minutes late for a business meeting is not the same as arriving 15 minutes early, and that we ought to err on the side of arriving early.

Researchers design experiment that account for the asymmetric nature of many everyday judgments.

The results showed that participants adjusted their estimates in the direction of the anticipated payoff after receiving feedback about their accuracy, just as Mannes and Moore expected.

But they didn't adjust their estimates as much as they should have given their actual knowledge of local temperatures, suggesting that they were overly confident in their own powers of estimation.

The First Images of Molecules Breaking and Reforming Chemical Bonds

Microscopy is advancing in leaps and bounds these days. It was just last week that scientists produced the first image of a hydrogen atom’s orbital structure. Not to be outdone, Berkeley chemists have now captured a series of images showing molecules as they break and reform their chemical bonds. It looks almost... textbook.

Holy crap, is it incredible when scientists present actual, tangible visual evidence to reaffirm theoretical models. As any chemistry student knows, molecular bonds, or covalent bond structures, are typically represented in science class with a stick-like nomenclature. But as the work of Felix Fischer, Dimas de Oteyza and their Berkeley Lab colleagues beautifully demonstrates, these models are startlingly accurate.

And like so many good scientific discoveries, it all happened somewhat by accident.

The Berkeley scientists were actually working on a way to precisely assemble nanostructures made from graphene using a new cutting-edge approach to chemical reactions. They were trying to build a single-layer material in which carbon atoms are arranged in repeating, hexagonal patterns — but they needed to take a closer look to see what was happening at the single-atom level. So, they pulled out a powerful atomic force microscope — and what they saw was “amazing,” to quote Fischer.

In this image you can see the positions of individual atoms and bonds in a molecule having 26 carbon atoms and 14 hydrogen atoms structured as three connected benzene rings.

Specifically, they managed to capture the specific outcomes of the reactions themselves — a totally unexpected and happy consequence of the research.

“Nobody has ever taken direct, single-bond-resolved images of individual molecules, right before and immediately after a complex organic reaction,” Fischer noted through a release.

To create the image, the researchers used the fine tip of the non-contact atomic force microscope to “feel” or read the electrical forces produced by the molecules. Each time the tip moved near a molecule’s surface, it was deflected by the different charges. The resulting movements of the stylus were detected by a laser beam, which in turn provided the data required to produce an image of how the atoms and bonds were aligned. What’s more, they were also able to visualize the bonds between them.

Taking a look at the top image, you can see the original molecule at left before the reaction takes place. At right, the two most common final products of the reaction are shown. The clumps are about a billionth of a meter across (3 angstroms).

You can read the entire study at the journal Science: “Direct Imaging of Covalent Bond Structure in Single-Molecule Chemical Reactions.”

via io9

World's Oldest Primate Fossil Discovered

A tiny, beady-eyed, long-tailed primate with hand-like feet is now the world’s oldest known fossil primate skeleton. In a study to be released in the journal Nature this week, an international team of researchers describe their discovery of the Archicebus achilles and how it’s adding to what we understand about our own evolution.

The Archicebus achilles--named for its long tail and strange feet--was found in an ancient lakebed in China. The lack of oxygen at the bottom of the lake means that this specimen is remarkably complete and well-preserved. Recovered from sedimentary rock strata deposited in an ancient lake roughly 55 million years ago, this fossil is the oldest primate fossil, beating the previous record-holders--including Darwinius from Messel in Germany and Notharctus from the Bridger Basin in Wyoming --by 7 million years.

“It’s not just that it’s the oldest primate, but it turns out that this fossil tells us that primates had already been evolving for quite some time. This primate was already fairly advanced in terms of the evolutionary tree,” says Christopher Beard, a coauthor of the study and paleontologist from the Carnegie Museum of Natural History.

The Archicebus sits at a branch of the evolutionary tree, which goes in two directions: one toward living tarsiers—large-eyed night-dwelling small primates—and anthropoids, the monkeys, apes and humans, which have smaller eyes and are most active during the day.

This is the first time that we have had such a complete picture of the divergence between these two branches.

“Any time you find a specimen like this, it’s a bit special. It’s adding a lot of depth of history,” says John Flynn, another coauthor and curator for the American Museum of Natural History.

Given Archicebus’s size—weighing about an ounce and measuring 7 to 9 inches long including the tail—and its basal evolutionary position, this discover supports the idea that the common ancestor of both tarsiers and anthropoids were quite small. These two branches, anthropoids and tarsiers, have been thought to be evolutionarily linked for some time, and now scientists are starting to understand the age of that split.

Beyond its addition to our understanding of evolution, the ancient primate is also unique in its physique. One of the most curious characteristics of the Archicebus is its feet. Tarsiers tend to have elongated heel bones, which help give them leverage for their giant leaps. Anthropoids have feet specially designed for grasping—though humans are a bit of a special case, given our unique disposition of walking bipedally.

“I was convinced pretty early on by the foot of this creature, which looked like nothing else but a little marmoset, which is a type of monkey from South America. I was convinced this thing was going to be a very primitive anthropoid,” Beard says. “Here’s an animal that combines features that we’ve just never seen before in one fossil primate.”

But after the exhaustive analysis, it became clear that Archicebus was also closely linked to tarsiers.

To fully analyze the fragile fossil, researchers collaborated with the European Synchrotron Radiation Facility in Grenoble, France. Using a high-intensity X-ray beam, the Synchrotron scanned the fossil, producing high-resolution data. This data was then rendered into 3-D versions to be analyzed and compared with other primates, both living and fossilized.

The analysis and data-gathering was one of the longest and most extensive phases of the study. Researchers created a matrix that included data from more than 150 species and more than 2,000 different characteristics. All told, the process took 10 years and required collaboration from many institutions internationally. But the patience and practice is now finally paying off.

“[The Archicebus is like] what we find so often in paleontology, but we can never predict it, and that’s an animal that’s unlike everything else we’ve ever seen,” Beard says. “It’s a kind of hybrid or mosaic of different features that are found in different animals today, but never together in one. It’s truly a unique creature.”

via PopSci

Life-Producing Phosphorus Carried to Earth by Meteorites

We are wondering whether there is life living in outer space and researches are continuing to provide information about the question. Now new research from a team of scientists led by a University of South Florida astrobiologist now shows that one key element that produced life on Earth was carried here on meteorites.

In an article published in the new edition of the Proceedings of the National Academy of Sciences, USF Assistant Professor of Geology Matthew Pasek and researchers from the University of Washington and the Edinburg Centre for Carbon Innovation, revealed new findings that explain how the reactive phosphorus that was an essential component for creating the earliest life forms came to Earth.

The scientists found that during the Hadean and Archean eons -- the first of the four principal eons of Earth's earliest history -- the heavy bombardment of meteorites provided reactive phosphorus that when released in water could be incorporated into prebiotic molecules. The scientists documented the phosphorus in early Archean limestone, showing it was abundant some 3.5 billion years ago.

The scientists concluded that the meteorites delivered phosphorus in minerals that are not seen on the surface of Earth, and these minerals corroded in water to release phosphorus in a form seen only on the early Earth.

Via ScienceDaily

Artificial Magnetic Monopoles Discovered

A team of researchers from Cologne, Munich and Dresden have managed to create artificial magnetic monopoles. To do this, the scientists merged tiny magnetic whirls, so-called skyrmions. At the point of merging, the physicists were able to create a monopole, which has similar characteristics to a fundamental particle postulated by Paul Dirac in 1931. In addition to fundamental research, the monopoles may also have application potential. The question of whether magnetic whirls can be used in the production of computer components one day is currently being researched by a number of groups worldwide.

via ScienceDaily