ZFN, TALEN, and CRISPR/Cas systems help scientists dissect the vast amount of information accumulated through the Genomic Revolution.
The Genomic Revolution has promised to advance medicine and biotechnology by providing scientists with enormous amounts of data that can be converted into useful information.
Over 10 years ago, the Human Genome Project produced the first draft of the more than 3 billion base pairs of DNA that make up the genetic code in each of our cells.
More recent efforts like the 1000 Genomes and HapMap Projects have since focused on identifying the differences within these billions of base pairs of DNA between individuals, while genome-wide association studies have pinpointed specific sequences that determine health and disease. The ENCODE Project and other studies have annotated chromatin states, regulatory elements, transcription factor binding sites, and other epigenetic states throughout the genome.
Dozens of other species have since undergone similar analyses, with the number of sequenced genomes continuously growing. Collectively, these efforts have generated an incredibly rich source of data that promises to aid our understanding of the function and evolution of any genome. However, until recently, scientists have been lacking the tools necessary to interrogate the structure and function of these elements.
While conventional genetic engineering methods could be used to add extra genes to cells, they cannot be easily used to modify the sequences or control the expression of genes that already exist within these genomes. These types of tools are necessary to determine not only the function of genes, but also the role of genetic variants and regulatory elements. They can also be used to overcome longstanding challenges in the field of gene therapy. Without these technologies, it has been difficult—and in some cases impossible—for scientists to capitalize on the Genomic Revolution.
Bottlenose dolphins use auditory (or echoic) information to recognize their environments, and many studies have described their echolocation perception abilities. However, relatively few systematic studies have examined their visual perception. A team of scientists now tested dolphins on a visual-matching task using two-dimensional geometric forms including various features. Based on error patterns, they used multidimensional scaling to analyze perceptual similarities among stimuli. In addition to dolphins, they conducted comparable tests with terrestrial species: chimpanzees were tested on a computer-controlled matching task and humans were tested on a rating task. The overall perceptual similarities among stimuli in dolphins were similar to those in the two species of primates. These results clearly indicate that the visual world is perceived similarly by the three species of mammals, even though each has adapted to a different environment and has differing degrees of dependence on vision.
Because dolphins have adapted to an underwater environment, they have developed a perceptual system that differs considerably from that of terrestrial mammals such as primates. One strikingly different aspect of the perceptual system of dolphins is echolocation1,. They can recognize shapes, materials, and the texture of objects using this form of biological sonar. Many echolocation studies on cetaceans have been conducted both in the laboratory and in the wild4. A few studies have investigated dolphins' ability to use cross-modal integration through vision–echolocation matching5, 6,. In these studies, dolphins were very accurate in matching three-dimensional complex objects using information gathered via echolocation. On the other hand, these results indirectly suggest that dolphins may also visually discriminate complex objects. Dolphins (e.g., bottlenose dolphins) have poorer in-air and underwater visual acuity (12.6 min of visual angle from a distance of 2.5 m) than that of primates10. Nevertheless, they still visually recognize and discriminate human gestural signs11, 12, 13, mirror images of themselves14, 15, numbers of objects16, three-dimensional objects4, 17, and two-dimensional forms17, 18. Moreover, researchers have used visual stimuli to study the basic features of the vision and various cognitive abilities of dolphins17, 18.
Discovering planets outside our Solar System has raised hopes that we may one day contact alien lifeforms. But will this ever happen?
Two possibilities exist: either we are alone in the Universe or we are not. Both are equally terrifying.” So said sci-fi author Arthur C Clarke. We’ve been fascinated by the idea life may exist elsewhere, and for over 50 years the Search for Extra Terrestrial Intelligence (Seti) has been scanning the galaxy for messages from an alien civilisation to no avail.
But the discovery of planets outside our solar system, or exoplanets, has raised hopes that efforts to contact alien lifeforms may one day succeed. BBC’s Horizon joined the planet hunters who discovered a new world called Gliese 581 c. To date, it is one of the most Earth-like planets found around another star, and it may have habitats capable of supporting life.
In humans, a tiny area in the center of the retina called the fovea is critically important to viewing fine details. Densely packed with cone photoreceptor cells, it is used while reading, driving and gazing at objects of interest. Some animals have a similar feature in their eyes, but researchers believed that among mammals the fovea was unique to primates — until now.
University of Pennsylvania vision scientists report that dogs, too, have an area of their retina that strongly resembles the human fovea. What’s more, this retinal region is susceptible to genetic blinding diseases in dogs just as it is in humans.
“It’s incredible that in 2014 we can still make an anatomical discovery in a species that we’ve been looking at for the past 20,000 years and that, in addition, this has high clinical relevance to humans,” said William Beltran, an assistant professor of ophthalmology in Penn’s School of Veterinary Medicine.
The word “fovea” comes from the Latin meaning “pit,” owing to the fact that in humans and many other primates, the inner layers of the retina are thin in this area, while the outer layers are packed with cone photoreceptor cells. It is believed that this inner layer thinning allows the foveal cone cells privileged access to light.
It is known that dogs have what is called an area centralis, a region around the center of the retina with a relative increase in cone photoreceptor cell density. But dogs lack the pit formation that humans have, and, before this study, it was believed that the increase in cone photoreceptor cell density didn’t come close to matching what is seen in primates. Prior to this study, the highest reported density in dogs was 29,000 cones per square millimeter compared to more than 100,000 cones per square millimeter seen in the human and macaque foveas.
It turns out that previous studies in dogs had missed a miniscule region of increased cell density. In this study, while examining the retina of a dog with a mutation that causes a disease akin to a form of X-linked retinal degeneration in humans, the Penn researchers noticed a thinning of the retinal layer that contains photoreceptor cells.
Zeroing in on this region, they examined retinas of normal dogs using advanced imaging techniques, including confocal scanning laser ophthalmoscopy, optical coherence tomography and two-photon microscopy. By enabling the scientists to visualize different layers of the retina, these techniques allowed them to identify a small area of peak cone density and then estimate cone numbers by counting the cells in this unique area.
Based on their observations, the researchers found that cone densities reached more than 120,000 cells per square millimeter in a never-before-described fovea-like region within the area centralis — a density on par with that of primate foveas.
Human patients with macular degeneration experience a loss of photoreceptor cells — the rods and cones that process light — at or near the fovea, resulting in a devastating loss of central vision. To see whether the fovea-like region was similarly affected in dogs, the Penn researchers used the same techniques they had employed to study normal dogs to examine animals that had mutations in two genes (BEST1 and RPGR) that can lead to macular degeneration in humans.
In both cases, the onset of disease affected the fovea-like region in dogs in a very similar way to how the diseases present in humans -- with central retinal lesions appearing earlier than lesions in the peripheral retina.
Thirty years ago, the states with the deepest poverty were all clustered in dixie. But the rest of the country has been playing catchup.
So how did poverty stop being a Southern specialty? You've had, deindustrialization in the Midwest and Northeast. And you've had fast growing Hispanic populations, which tend to be poorer, in California, Nevada, Arizona, and Colorado (as well as North Carolina and Georgia, which could explain their presence on the list above). Meanwhile, the Southeast has made some economic progress by attracting foreign manufacturing, among other efforts.
"For Regional Geography, I ask that all my students take an online quizzes before coming to class because it is very difficult to intelligently discuss European issues if you don’t know the countries of Europe, where they are and what other countries are on their borders. Quizzes and knowing places doesn’t define geography, but if geography were English literature, knowing about places could be described as the alphabet–before you write a sonnet or critique an essay, you better know your ABC’s and basic grammar. Given that, I like the Lizard Point Geography quizzes, Sheppard Software quizzes and those from Click that ‘Hood; they are simple, straightforward and comprehensive."
Illumina, Inc. announced Tuesday that its new HiSeq X Ten Sequencing System has broken the “sound barrier” of human genomics by enabling the $1,000 genome. “This platform includes dramatic technology breakthroughs that enable researchers to undertake studies of unprecedented scale by providing the throughput to sequence tens of thousands of human whole genomes in a single year in a single lab,” Illumina stated.
Initial customers for the HiSeq X Ten System, which will ship in Q1 2014, include Macrogen, based in Seoul, South Korea and its CLIA laboratory in Rockville, Maryland, the Broad Institute in Cambridge, Massachusetts, and the Garvan Institute of Medical Research in Sydney, Australia.
“For the first time, it looks like it will be possible to deliver the $1,000 genome, which is tremendously exciting,” said Eric Lander, founding director of the Broad Institute and a professor of biology at MIT. “The HiSeq X Ten should give us the ability to analyze complete genomic information from huge sample populations. Over the next few years, we have an opportunity to learn as much about the genetics of human disease as we have learned in the history of medicine.”
“The HiSeq X Ten is an ideal platform for scientists and institutions focused on the discovery of genotypic variation to enable a deeper understanding of human biology and genetic disease,” Illumina stated. “It can sequence tens of thousands of samples annually with high-quality, high-coverage sequencing, delivering a comprehensive catalog of human variation within and outside coding regions.”
HiSeq X Ten utilizes a number of advanced design features to generate massive throughput. Patterned flow cells, which contain billions of nanowells at fixed locations, combined with a new clustering chemistry deliver a significant increase in data density (6 billion clusters per run). Using state-of-the art optics and faster chemistry, HiSeq X Ten can process sequencing flow cells more quickly than ever before — generating a 10x increase in daily throughput when compared to current HiSeq 2500 performance.
The HiSeq X Ten is sold as a set of 10 or more ultra-high throughput sequencing systems, each generating up to 1.8 terabases (Tb) of sequencing data in less than three days or up to 600 gigabases (Gb) per day, per system, providing the throughput to sequence tens of thousands of high-quality, high-coverage genomes per year.
Illumina Introduces the HiSeq X™ Ten Sequencing System
"Dr. Martin Luther King Jr. once stated,"A man who won't die for something is not fit to live." Arrested over twenty times, stabbed in the chest, his house firebombed and, ultimately shot and killed, King embodied the idea that equality and the African American Civil Rights Movement were worth dying for.He was a husband and father to four children as persecution and death threats filled his days, yet his example was one of nonviolent, civil disobedience.Had he not been assassinated, King would have celebrated his 85th birthday on January 15th."
Over the last five years we have published our end of year review of the best free icon sets for designers and developers. So, as 2013 begins to close we have just finished reviewing, compiling and categorizing our latest review. This really is the best one ever!
The icons have all been split into categories: There is a fantastic selection of web icon fonts, versatile & general sets, and thin & line sets, we also have an obligatory section for flat icons, which have been trending this year, and we also small sections for mini icons, mobile-specific icons,payment services & ecommerce sets, and finally some top-notch social icons.
The recent emergence of Massive Open Online Courses, commonly known as MOOCs, is revolutionizing the online education world and is having a profound impact on higher education. With the growing adoption of MOOCs, the number of MOOC providers has also increased many folds. Below is a comprehensive and up-to-date list of MOOC providers; might be helpful to all interested.
A team of interdisciplinary researchers have created "smart" holograms that can monitor health conditions or diagnose diseases, by changing color in the presence of disease indicators in a person's breath or bodily fluids. When developed into a portable medical test, these responsive holograms could make testing for medical conditions and monitoring one's health very easy, the scientists claim.
A person would just have to check the hologram's color against a chart or use a camera phone to read the results. As these holographic sensors don't require batteries, electricity or lasers to function, it's possible to create inexpensive portable tests for healthcare workers to use or people to self-administer, that could help them potentially diagnose diseases in their earliest stages.
"We often see holograms on banknotes, credit cards, as security features, or artwork," Ali Yetisen, a PhD student at the University of Cambridge, UK, who led the research, tells Gizmag. "However, these type of holograms do not response when they encounter a health condition indicator such as glucose or blood electrolytes. We have developed techniques to make these holograms 'smart,' so that they can respond to a wide range of disease markers."
The holographic sensors are made out of hydrogels (a highly absorbent material) that are doped with silver nanoparticles. These silver nanoparticles are then organized into three-dimensional holograms of predetermined shapes using a multi-megawatt laser. The final sensors resemble the iridescent hardened forewings of beetles, and normally diffract light in a green color.
However, when the holographic sensor is exposed to a person's breath, urine, tears or a drop of their blood or saliva, the hydrogel in the sensor, which is sensitive to specific disease indicators, reacts if any of them are present. The hydrogel either swells or shrinks, causing a change in the hologram's color in the entire visible spectrum. It's the first time, the researchers claim, that they've been able to achieve such a result with a colorimetric sensor.
"It's pretty much like a butterfly wing," says Dr. Haider Butt, a Lecturer in Micro Engineering and Nanotechnology, at the University of Birmingham and a co-author of the study. "But this is a butterfly wing that changes color depending on the solution we dip it in."
A new technology developed at the Massachusetts General Hospital Center for Systems Biology allows simultaneous analysis of hundreds of cancer-related protein markers from miniscule patient samples gathered through minimally invasive methods.
Minimally invasive techniques – such as fine-needle aspiration or circulating tumor cell analysis – are increasingly employed to track treatment response over time in clinical trials, as such tests can be simple and cheap to perform. Fine needle aspirates are also much less invasive than core biopsies or surgical biopsies, since very small needles are used. The challenge has been to comprehensively analyze the very few cells that are obtained via this method. "What this study sought to achieve was to vastly expand the information that we can obtain from just a few cells," explains Cesar Castro, MD, of the MGH Cancer Centerand CSB, a co-author of the Science Translational Medicine paper. "Instead of trying to procure more tissue to study, we shrank the analysis process so that it could now be performed on a few cells.”
Up until now, pathologists have been able to examine only a handful of protein markers at a time for tumor analyses. But with this new technology, researchers at CSB have demonstrated the ability to look at hundreds of markers simultaneously down to the single-cell level. "We are no longer limited by the scant cell quantities procured through minimally invasive procedures," says Castro. "Rather, the bottleneck will now be our own understanding of the various pathways involved in disease progression and drug target modulation."
The novel method centers on an approach known as DNA-barcoded antibody sensing, in which unique DNA sequences are attached to antibodies against known cancer marker proteins. The DNA 'barcodes' are linked the antibodies with a special type of glue that breaks apart when exposed to light. When mixed with a tumor sample, the antibodies seek out and bind to their targets; then a light pulse releases the unique DNA barcodes of bound antibodies that are subsequently tagged with fluorescently-labeled complementary barcodes. The tagged barcodes can be detected and quantified via imaging, revealing which markers are present in the sample.
After initially demonstrating and validating the technique's feasibility in cell lines and single cells, the team went on to test it on samples from patients with lung cancer. The technology was able to reflect the great heterogeneity – differences in features such as cell-surface protein expression – of cells within a single tumor and to reveal significant differences in protein expression between tumors that appeared identical under the microscope. Examination of cells taken at various time points from participants in a clinical trial of a targeted therapy drug revealed marker patterns that distinguished those who did and did not respond to treatment.
When a person suffers a broken bone, treatment calls for the surgeon to insert screws and plates to help bond the broken sections and enable the fracture to heal. These “fixation devices” are usually made of metal alloys.
But metal devices may have disadvantages: Because they are stiff and unyielding, they can cause stress to underlying bone. They also pose an increased risk of infection and poor wound healing. In some cases, the metal implants must be removed following fracture healing, necessitating a second surgery. Resorbable fixation devices, made of synthetic polymers, avoid some of these problems but may pose a risk of inflammatory reactions and are difficult to implant.
Now, using pure silk protein derived from silkworm cocoons, a team of investigators from Tufts University School of Engineering and Beth Israel Deaconess Medical Center (BIDMC) has developed surgical plates and screws that may not only offer improved bone remodeling following injury, but importantly, can also be absorbed by the body over time, eliminating the need for surgical removal of the devices.
The findings, demonstrated in vitro and in a rodent model, are described in the March 4 issue of Nature Communications. “Unlike metal, the composition of silk protein may be similar to bone composition,” says co-senior author Samuel Lin, MD, of the Division of Plastic and Reconstructive Surgery at BIDMC and Associate Professor of Surgery at Harvard Medical School. “Silk materials are extremely robust. They maintain structural stability under very high temperatures and withstand other extreme conditions, and they can be readily sterilized.”
"The Digital Scholarship Lab at the University of Richmond has created an enhanced version of the Atlas of the Historical Geography of the United States, which was published in 1932. The atlas, which took dozens of researchers to assemble, used maps to illustrate a variety of political, demographic and economic concepts."
Finding Materials: This site is designed for geography students and teachers to find interesting, current supplemental materials. To search for place-specific posts, browse this interactive map. To search for thematic posts, see http://geographyeducation.org/thematic/ (organized by the APHG curriculum). Also you can search for a keyword by clicking on the filter tab above.
'The nuts and bolts that make up search engine optimization all hold the frame together, and that frame is content.
However, it’s much bigger than that.Without those nuts and bolts, such as inbound links, social signals, microformats, and citations, the content itself is nothing more than a pile sheet metal that can’t do anything.
As we continue to explore the ways that content can help with SEO, it’s important to note that even the infographic below by Fat is only one side of the content equation'.
An improved assistive technology system for the blind that uses sonification (visualization using sounds) has been developed byUniversidad Carlos III de Madrid (UC3M) researchers, with the goal of replacing costly, bulky current systems.
How it works: Called Assistive Technology for Autonomous Displacement (ATAD), the system includes a stereo vision processor measures the difference of images captured by two cameras that are placed slightly apart (for image depth data) and calculates the distance to each point in the scene.
Then it transmits the information to the user by means of a sound code that gives information regarding the position and distance to the different obstacles, using a small audio stereo amplifier and bone-conduction headphones.
“To represent height, the synthesizer emits up to eight different tones,” said co-developer Pablo Revuelta Sanz, who described the system in a doctoral thesis. In addition, the sounds are laterally located, so that something on the left sounds louder on that side, and vice versa.
Six profiles, ranging from one that is very simple, with a sound alarm that only works when one is going to crash into an obstacle, to others that describe the scene with 64 simultaneous sounds can be chosen.”
The prototype system was tested on 28 individuals, including sighted individuals, persons with limited vision, and blind persons. The final system was tested on eight blind persons in real environments.
According to Revuelta, “the aim of the system is to complement a cane or a guide dog, and not in any way replace them.” The estimated price of 250 euros is “very economical compared with other systems that are currently on the market.”
Revuelta Sanz, Pablo, ATAD: Assistive Technology for an Autonomous Displacement, UC3M Thesis, 2013
Most people think of Google Maps in terms of finding a place or business, or getting directions from one point to another. Others use the satellite images and terrain mapping features. But there are tons of other uses out there for Google maps.
From mapping the weather and news to mapping things that aren't maps at all, like paintings or magazines, Google Maps has a lot to offer. And there are free tools available out there for those who want to use the Google Maps API without doing a bunch of coding. Here are more than 100 of the best mashups and tools out there right now.
After spending hours online at different websites, you tend to pick up discernable trends in design. Advancing W3C specifications coupled with modern web browsers have opened the door toa new era of digital design. Here are 20 growing trends listed for the year 2014. Many have already been set in motion while others are just beginning to dawn. New trends are fun to check out and see how long they stick around. When browsing websites in 2014 keep your eyes peeled for any of these UI/UX trends in action.
40 Web Design Conferences To Look Forward To In 2014