#Researchers discover cancer markers may be visible early during human development Researchers at the Virginia Bioinformatics Institute have uncovered a link between the genomes of cells originating in the neural crest
and development of tumors a discovery that could lead to new ways to diagnose and treat cancer.
The new finding, recently published in Oncotarget, resolves why some cancer types share genomic and clinical features.
The discovery may also lead to new ways to diagnose and treat brain cancer, such as gliomas, medulloblastomas, and neuroblastomas;
and skin cancer, known as melanoma. More than 22,000 new cases of brain cancer and more than 73,000 new cases of skin cancer and were expected to arise in Americans in 2015, according to the National Cancer Institute.
To reveal when cancer-causing genomic changes occur, a research group led by Harold kipgarner, a professor in the departments of biological science, computer science,
and basic science at Virginia Tech Carilion Medical school, analyzed an often ignored part of the human genome repetitive DNA sequences referred to as microsatellites.
More than 1 million microsatellites exist in the human genome including in neural crest tissues, a thin layer of cells within an embryo that contains genetic instructions to build hundreds of cell types, from neurons to adrenal cells.
When cells migrate from the neural crest, researchers say the instructions may become garbled, causing cancer cells to emerge.
Neurological tumors, for example, may arise from glial cells that develop from the crest. Researchers with the institute Medical Informatics Systems division say cancer types can be found
or predicted from specific markers within these repetitive sequences, known as cancer-associated microsatellite loci, or CAML.
Long considered unk DNAOR ark matterwithin the genome because their function was unclear microsatellites are known for their role in certain diseases such as Fragile X and Huntington disease.
Garner group has shown that these regions can be informative about diseases ranging from cancer to autism spectrum disorder.
With more study, researchers believe interrelated hereditary and genetic traits of certain cancers can be traced to their common origin at the neural crest,
leading to potentially better therapies and easier tumor identification. The findings have been licensed to Genomeon, a company co-founded by Garner to develop new ways to assess cancer risk,
create diagnostics, and explore potential drug targets to help cancer patients p
#How chronic inflammation can lead to cancer Chronic inflammation caused by disease or exposure to dangerous chemicals has long been linked to cancer,
but exactly how this process takes place has remained unclear. Now, a precise mechanism by which chronic inflammation can lead to cancer has been uncovered by researchers at MIT a development that could lead to improved targets for preventing future tumors.
In a paper published in the Proceedings of the National Academy of Sciences, the researchers unveil how one of a battery of chemical warfare agents used by the immune system to fight off infection can itself create DNA mutations that lead to cancer.
As many as one in five cancers are believed to be caused or promoted by inflammation. These include mesothelioma,
a type of lung cancer caused by inflammation following chronic exposure to asbestos, and colon cancer in people with a history of inflammatory bowel disease, says Bogdan Fedeles,
a research associate in the Department of Biological engineering at MIT, and the paper lead author.
Innate immune response Inflammation is part of the body innate response to invading pathogens or potentially harmful irritants.
The immune system attacks the invader with a number of reactive molecules designed to neutralize it,
including hydrogen peroxide, nitric oxide and hypochlorous acid. However, these molecules can also cause collateral damage to healthy tissue around the infection site:
he presence of a foreign pathogen activates the immune response, which tries to fight off the bacteria,
but in this process it also damages some of the normal cells, Fedeles explains. Previous work by Peter Dedon, Steven Tannenbaum, Gerald Wogan,
and James Fox all professors of biological engineering at MIT had identified the presence of a lesion,
or site of damage in the structure of DNA, called 5-chlorocytosine (5clc) in the inflamed tissues of mice infected with the pathogen Helicobacter hepaticus.
This lesion, a damaged form of the normal DNA base cytosine, is caused by the reactive molecule hypochlorous acid the main ingredient in household bleach
which is generated by the immune system. The lesion 5clc, was present in remarkably high levels within the tissue,
says John Essigmann, the William R. 1956) and Betsy P. Leitch Professor in Residence Professor of Chemistry, Toxicology and Biological engineering at MIT,
who led the current research. hey found the lesions were very persistent in DNA, meaning we don have a repair system to take them out,
Essigmann says. n our field lesions that are persistent, if they are also mutagenic, are the kind of lesions that would initiate cancer,
he adds. DNA sequencing of a developing gastrointestinal tumor revealed two types of mutation: cytosine (C) bases changing to thymine (T) bases,
and adenine (A) bases changing to guanine (G) bases. Since 5clc had not yet been studied as a potentially carcinogenic mutagen,
the researchers decided to investigate the lesion further, in a bid to uncover if it is indeed mutagenic.
Using a technique previously developed in Essigmann laboratory, the researchers first placed the 5clc lesion at a specific site within the genome of a bacterial virus. They then replicated the virus within the cell.
The researchers found that, rather than always pairing with a guanine base as a cytosine would,
the 5clc instead paired with an adenine base around 5 percent of the time a medically relevant mutation frequency, according to Essigmann.
Damaged DNA The findings suggest that the immune system, when triggered by infection, fires hypochlorous acid at the site, damaging cytosines in the DNA of the surrounding healthy tissue.
This damage causes some of the cytosines to become 5clc. In addition, the researchers hypothesize that the hypochlorous acid also damages cytosines in the nucleotide pool,
which cells use as the reservoir of nucleotides that will become part of the DNA of replicating cells,
Essigmann says. o 5clc forms first in genomic DNA, and secondly it can form in the nucleotide pool,
meaning the nucleotides in the pool are mutagenic in themselves, he explains. his scenario would best explain the work of James Fox and his MIT colleagues on gastrointestinal cancer.
To confirm that 5clc is mutagenic in human DNA, the researchers replicated the genome containing the lesion with a variety of different types of polymerase,
the enzyme that assembles DNA, including human polymerases. n all cases we found that 5clc is mutagenic,
and causes the same kind of mutations seen within cells, Fedeles says. hat gave us confidence that this phenomenon would in fact happen in human cells containing high levels of 5clc.
What more the C-to-T mutation characteristic of 5clc is extremely common, and is present in more than 50 percent of mutagenic ignatures,
or patterns of DNA mutations, associated with cancerous tumors. e believe that in the context of inflammation-induced damage of DNA,
many of these C-to-T mutations may be caused by 5clc, possibly in correlation with other types of mutations as part of these mutational signatures,
Fedeles says. Yinsheng Wang, a principal investigator in the Department of chemistry at the University of California at Riverside who was involved not in the research,
says the paper provides a novel mechanistic link between chronic inflammation and cancer development. ith a combination of biochemical,
genetic, and structural biology approaches, the researchers have found that 5-chlorocytosine is intrinsically miscoding during DNA replication
and it could give rise to significant frequencies of C-to-T mutation, a type of mutation that is frequently observed in human cancers,
Wang says. Studies of tissue samples of patients suffering from inflammatory bowel disease have found significant levels of 5clc,
Fedeles adds. By comparing these levels with his team findings on how mutagenic 5clc is,
the researchers predict that accumulation of the lesions would increase the mutation rate of a cell up to 30-fold,
says Fedeles, who was honored with the prestigious Benjamin F. Trump award at the 2015 Aspen Cancer Conference for the research r
#Animal-eye view of the world revealed with new visual software New camera technology that reveals the world through the eyes of animals has been developed by University of Exeter researchers.
The details are published in the journal Methods in Ecology and Evolution. Borage family flowers (Echium angustifolium) as seen in human vision (left) and honeybee vision (right.
To humans the flowers are a fairly uniform purple, but bees can see two UV absorbent patches at the top of the flower.
Image courtesy of Jolyon Troscianko. The software, which converts digital photos to animal vision, can be used to analyse colours
and patterns and is particularly useful for the study of animal and plant signalling, camouflage and animal predation,
but could also prove useful for anyone wanting to measure colours accurately and objectively. The software has already been used by the Sensory Ecology group in a wide range of studies,
such as colour change in green shore crabs, tracking human female face colour changes through the ovulation cycle,
and determining the aspects of camouflage that protect nightjar clutches from being spotted by potential predators.
Dr Jolyon Troscianko from the Centre for Ecology and Conservation at the University of Exeter Penryn Campus said:
iewing the world through the eyes of another animal has now become much easier thanks to our new software. igital cameras are powerful tools for measuring colours
and patterns in nature but until now it has been surprisingly difficult to use digital photos to make accurate and reliable measurements of colour.
Our software allows us to calibrate images and convert them to animal vision, so that we can measure how the scene might look to humans
and nonhumans alike. e hope that other scientists will use this open access software to help with their digital image analysis. ntil now,
there has been no user friendly software programme that enables researchers to calibrate their images, incorporate multiple layers visible and UV channels-,convert to animal colour spaces,
and to measure images easily. Instead, researchers have needed to do much of this manually, including the sometimes complex programming and calculations involved.
This freely available open source software now offers a user friendly solution. Colour vision varies substantially across the animal kingdom,
and can even vary within a given species. Most humans and old-world monkeys have eyes sensitive to three colours;
red, green and blue, which is more than other mammals that are only sensitive to blue and yellow.
It is impossible for humans to imagine seeing the world in more than three primary colours,
but this is common in most birds, reptiles, amphibians and many insects that see in four or more.
Many of them can also see into the ultraviolet range, a world completely invisible to us without the use of full spectrum cameras.
So scientists studying these species need to measure UV to understand how these animals view the world.
Using a camera converted to full spectrum sensitivity one photograph taken through a visible-pass filter can be combined by the software with a second taken through an ultraviolet-pass filter.
The software can then generate functions to show the image through an animal eyes. The researchers have provided specific data on camera settings for commonly studied animals, such as humans, blue tits, peafowl, honey bees, ferrets and some fish.
Flowers often look particularly striking in UV because they are signalling to attract pollinators that can see in UV, such as bees.
UV is also often important for birds, reptiles and insects in their colourful sexual displays to attract mates.
Source: University of Exete i
#It takes a lot of nerve: Scientists make cells to aid peripheral nerve repair Scientists at the University of Newcastle,
UK, have used a combination of small molecules to turn cells isolated from human skin into Schwann cells the specialised cells that support nerves and play a role in nerve repair.
This new method generates large and pure populations of Schwann cells and hence is a promising step forward for the repair of peripheral nerve injuries.
This research has just been published in the scientific journal Development at http://dev. biologists. org/Currently,
nerve repair strategies involve taking grafts from patients and using these to repair their damaged peripheral nerves
but this approach has several disadvantages and can often itself cause nerve damage. Now Motoharu Sakaue together with Maya Sieber-Blum, Professor of Stem Cell Sciences at the Institute of Genetic Medicine in Newcastle, investigated the possibility of making Schwann cells,
which are known to promote nerve Repair to make these cells, the researchers isolated stem cells from adult skin
and coaxed them into Schwann cells by exposing them to small molecules. e observed that the bulge,
a region within hair follicles, contains skin stem cells that are intermixed with cells derived from the neural crest a tissue known to give rise to Schwann cells.
This observation raised the question whether these neural crest-derived cells are also stem cells
and whether they could be used to generate Schwann cellssaid Sieber-Blum. e then used pertinent small molecules to either enhance
or inhibit pathways that are active or inactive, respectively, in the embryo during Schwann cell differentiationshe said.
Using this approach, the scientists were able to generate large and highly pure populations of human Schwann cells.
showing that they could interact with nerves in vitro. he next step is to determine, for example in animal models of peripheral nerve injury,
This study identifies a biologically relevant and accessible source of cells that could be used for generating sufficient quantities of Schwann cells and thus offers great potential in the repair of peripheral nerve injuries r
#Important regulation of cell invaginations discovered Lack of microinvaginations in the cell membrane, caveolae, can cause serious diseases such as lipodystrophy and muscular dystrophy.
Researchers at Lund University in Sweden have discovered now a ain switchthat regulates the formation of these invaginations.
If this doesn work, the function of the cell is disturbed, resulting in diseases. Having too few invaginations is associated with atrial fibrillation.
A total absence of invaginations causes lipodystrophy and muscular dystrophy combined with fatal cardiac arrhythmia. he latter is an unpleasant disease
CGL4, which usually leads to death in the patient teenage years. Many children presumably also die from this disease during their first week of life,
without any diagnosis other than udden infant death syndrome'says Karl Swärd and Catarina Rippe, researchers at Lund University.
About ten different genes contribute to the formation of caveolae. Until recently it was known not how these genes are coordinated.
In a recently published study in the journal PLOS ONE (1), the researchers at Lund University reveal that a family of so-called transcription factors called yocardin family coactivatorsregulate the formation of invaginations.
This discovery helps us understand how cells work, and provides insight into how to combat diseases caused by a lack of caveolae.
Moreover, the discovery paves the way for further studies on the significance of caveolae for cancer
and renal diseases. hese transcription factors regulate the cellsability to move and therefore play an important role in metastasis,
for example says Karl Swärd who, together with colleagues at Lund University, is also investigating whether the regulatory mechanism is activated in the case of kidney disease h
#Perseid meteors to light up summer skies The evening of Wednesday 12 august into the morning of Thursday 13 august sees the annual maximum of the Perseid meteor shower.
which last passed near the Earth in 1992, leaves such debris in the Earth path.
Professor Mark Bailey, Director of Armagh Observatory, said he Perseid meteor shower is one of the best and most reliable meteor showers of the year.
#A new look at superfluidity MIT physicists have created a superfluid gas, the so-called Bose-Einstein condensate, for the first time in an extremely high magnetic field.
The magnetic field is a synthetic magnetic field, generated using laser beams, and is 100 times stronger than that of the world strongest magnets.
Within this magnetic field, the researchers could keep a gas superfluid for a tenth of a second just long enough for the team to observe it.
Superfluids are thought to flow endlessly, without losing energy, similar to electrons in a superconductor. Observing the behavior of superfluids
therefore may help scientists improve the quality of superconducting magnets and sensors, and develop energy-efficient methods for transporting electricity.
But superfluids are temperamental, and can disappear in a flash if atoms cannot be kept cold or confined.
to create and maintain a superfluid gas long enough to observe it at ultrahigh synthetic magnetic fields. oing to extremes is the way to make discoveries,
the John D. Macarthur Professor of Physics at MIT. e use ultracold atoms to map out
Ketterle team members include graduate students Colin Kennedy, William Cody Burton, and Woo Chang Chung. A superfluid with loops The team first used a combination of laser cooling and evaporative cooling methods,
The electric field of the laser beams creates what known as a periodic potential landscape, similar to an egg carton,
When charged particles are exposed to magnetic fields, their trajectories are bent into circular orbits, causing them to loop around and around.
The higher the magnetic field, the tighter a particle orbit becomes. However, to confine electrons to the microscopic scale of a crystalline material,
a magnetic field 100 times stronger than that of the strongest magnets in the world would be required.
their trajectories are unaffected normally by magnetic fields. Instead, the MIT group came up with a technique to generate a synthetic
ultrahigh magnetic field, using laser beams to push atoms around in tiny orbits, similar to the orbits of electrons under a real magnetic field.
On a flat lattice, atoms can easily move around from site to site. However, in a tilted lattice, the atoms would have to work against gravity.
In this scenario, atoms could only move with the help of laser beams. ow the laser beams could be used to make neutral atoms move around like electrons in a strong magnetic field
added Kennedy. Using laser beams, the group could make the atoms orbit, or loop around, in a radius as small as two lattice squares, similar to how particles would move in an extremely high magnetic field. nce we had the idea,
we were excited really about it, because of its simplicity. All we had to do was take two suitable laser beams
Kennedy says. ew perspectives to known physics After developing the tilting technique to simulate a high magnetic field,
which could make them lose their superfluid properties. t a complicated experiment, with a lot of laser beams, electronics,
and keep them cold some of it was painstaking work. In the end, the researchers were able to keep the superfluid gas stable for a tenth of a second.
During that time, the team took time-of-flight pictures of the distribution of atoms to capture the topology
Those images also reveal the structure of the magnetic field something that been known, but never directly visualized until now. he main accomplishment is that we were able to verify
Ketterle says. f we can get synthetic magnetic fields under even better control, our laboratory could do years of research on this topic.
For the expert, what it opens up is a new window into the quantum world,
where materials with new properties can be studied. Going forward, the team plans to carry out similar experiments
including quantum Hall physics and topological insulators. e are adding new perspectives to physics, Ketterle says. e are touching on the unknown,
#Machine teaching holds the power to illuminate human learning Human learning is a complex, sometimes mysterious process.
What if a fusion of computer science and psychology could help us understand more about how people learn,
That long-range goal is moving toward reality thanks to an effort led by professors in the University of Wisconsin-Madison departments of computer sciences, psychology and educational psychology.
Their collaborative research aims to break new ground in what computer scientist Jerry Zhu calls achine teachinga twist on the more familiar concept of machine learning. y hope is that machine teaching has an impact on the educational world.
It quite different from how people usually think about education, says Zhu. t will give us optimal, personalized lessons for real,
human students. achine learning is established a well subfield of computer science in which experts develop mathematical tools to help computers learn from data
and detect patterns. The machine learner (the computer) is like a student The goal of machine learning is to develop models that will prove useful in the future
when dealing with large, often unwieldly data sets. Practical tasks like speech recognition are aided by machine learning. Machine teaching turns this concept on its ear.
Rather than dealing with pools of data and not knowing at the outset what patterns might be revealed through analysis,
the researcher in a machine teaching arrangement already knows what knowledge he or she wants to impress upon the learner.
Machine teaching uses sophisticated mathematics to allow researchers to model actual human students and devise the best possible lessons for teaching them.
While the definition of estin a particular setting is up to the teacher one example could be identifying the smallest number of exercises needed for a particular student to grasp a concept.
Or, as Zhu puts it, an five really good questions teach the material, rather than 20?
hile this work is still in its early stages, it has immense potential to impact education.
Timothy T. Rogers, a professor of cognitive psychology at UW-Madison and one of Zhu collaborators, explains how computer science
and psychology come together. n order for the machine teaching approach to work, it needs a good model of how the learner behaves that is,
how the learner behavior changes with different kinds of learning or practice experiences, Rogers says. lso,
the model needs to be computational; it has to be able to make concrete, quantitative predictions about the learner behavior.?
Ultimately, we hope that the work can be used to help teachers develop lesson plans and curricula that promote learning in a wide variety of fields,
Rogers says, citing math, science and reading as examples. nd, just as important, the effort to bring cognitive models of learning to bear on real-world problems is bound to lead to important new advances in our understanding of how people learn generally. hu presented some of his research earlier this year in Austin, Texas, at the 29th annual
Conference on Artificial intelligence, organized by the Association for the Advancement of Artificial intelligence. A two-year seed grant from the UW-Madison Graduate school currently supports this work.
Future funding from outside sources will be sought. ith machine teaching it conceptually easy, but quite challenging to implement in the real world.
It a major undertaking, says Zhu. In addition to Zhu and Rogers, the UW research team includes computer sciences professors Michael Ferris, Bilge Mutlu andstephen Wright;
engineering professor Rob Nowak; psychology professor Martha Alibali; and educational psychology professorsmartina Rau and Percival Matthews. Machine teaching probes fundamental mathematical and scientific concepts.
In part because of that, the team research is open-ended at this stage h
#Scientists find a new way to manufacture graphene nanoribbons for future electronics There is no doubt that graphene is the key to the future of electronics.
It is the most significant material for developing new types of electronic devices because of its many extraordinary properties,
such as extraordinary strength (it is about 200 times stronger than steel by weight), almost transparent nature and conductivity of heat and electricity with great efficiency.
However, in order to use graphene in high-performance semiconductor electronics ultra-narrow strips of graphene are needed and scientists have struggled to create them.
Until now. Graphene nanoribbons grown using new method have desired properties of length width and smoothness of the edge.
However, they grow in random spots on germanium wafer in two different directions, which scientists have to control
in order to make electronics. Image credit: Arnold Research Group and Guisinger Research Group, news. wisc. eduscientists at University of Wisconsin-Madison have discovered now a method to grow these ultra-narrow strips, called nanoribbons, with desirable semiconducting
properties directly on a conventional germanium semiconductor wafer. This discovery is aimed at allowing manufacturers of electronics to develop the next-generation of electronic devices that will have much greater performance.
This technology is also likely to find applications in other industries as well, such as military, used in sensors that detect specific chemical
and biological species and photonic devices that manipulate light. Furthermore, this method of producing nanoribbons is complicated not overly it is scalable
and is compatible with current equipment used in semiconductor processing. In fact it is hard to put into words how significant this achievement is.
Professor Michael Arnold, one of the authors of the study, said raphene nanoribbons that can be grown directly on the surface of a semiconductor like germanium are more compatible with planar processing that used in the semiconductor industry,
and so there would be less of a barrier to integrating these really excellent materials into electronics in the futurewhere graphene could be in the future,
now mostly silicon is used, which is not as efficient in conducting electricity and dissipating heat.
However, to use graphene in such applications is not easy and that is why nanoribbons are needed.
They have to be extraordinary narrow they need to be less than 10 nanometres wide. They also must have smooth, well-defined rmchairedges in
which the carbon-carbon bonds are parallel to the length of the ribbon. Such nanoribbons can be manufactured by cutting larger sheets of graphene into ribbons.
But this technique is not perfect as produced ribbons have very rough edges. These graphene ribbons can also be produced by surface-assisted organic synthesis,
where molecular precursors react on a surface to polymerize nanoribbons. But resulting ribbon, although with smooth edges, is far too short for use in electronics.
But now scientists found a way to manufacture ultra-narrow nanoribbons with smooth straight edges directly on germanium wafers.
As scientists describe it, they are growing graphene in this shape via process called chemical vapour deposition.
Although described as a rather simple method, it is hard to explain it in a commonly understandable way.
Graphene is only one atom thick material, which conducts electricity and heat with such efficiency that it is likely to revolutionize electronics.
Image credit: Alexanderalus via Wikimedia, CC BY-SA 3. 0in this process scientists start with methane,
which adsorbs to the germanium surface and decomposes to form various hydrocarbons. Then these hydrocarbons react with each other
and form graphene on surface of the germanium wafer. Team of researchers made this discovery
when they were exploring dramatically slowing the growth rate of the graphene crystals by decreasing the amount of methane in the chemical vapour deposition chamber.
Scientists found that at a very slow growth rate graphene naturally grows into long nanoribbons on a specific crystal facet of germanium
and researchers only need to control this process to produce nanoribbons less than 10 nanometres wide.
Moreover these strips of graphene have very smooth, armchair edges and can be very narrow and very long, all of
which is needed for future generations of electronics. However, there are still some problems left to solve.
Using this process, graphene grows at completely random spots on the germanium wafer. Furthermore, strips are oriented in two different directions on the surface.
So now scientists will try to find a way to control the place where graphene starts growing
and to align the nanoribbons to the same direction
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