Genomics  

Like other exponential technologies, genetics is becoming more affordable, more available, and is making new innovations possible. Along with curing ailments and genetic disorders, such technology may also help make us more than human. 

DNA can tell us what percentage of our ancestors came from which part of the world, or the likelihood of developing diabetes. But humanity means more than matching up 23 pairs of chromosomes. Our appearance and susceptibility to disease are not major differences, but minute variations called SNPs (single nucleotide polymorphisms). Like any technology, as genetics advances, it becomes more affordable, more available, and leads to innovations that take us in new directions.

Custom Genetics

In Boston in 2013, researchers were able to grow a human ear on the back of a lab rat. It was grown from living cells over a wire mesh. Physicians are already capable of growing us new corneas from our own cells. Our own DNA can grow us whatever we want, and any concerns about immune system rejection and a lifetime of immunosuppressant drugs no longer applies. Genetic advancement means doing it quickly, easily, and reliably, and even the idea of clones as personal organ banks is outdated.

Home Genetics

DNA testing kits for home use are already available. From a few hundred to a few thousand dollars, people can determine their own family risk of 23 different medical conditions. Critics might deride the tests as unreliable, but as awareness spreads, the market grows, and so will the quality, affordability, and scope of these tests.

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Computing and Engineering

Mapping thousands of combinations of nucleotides and other components of DNA would not be possible without computers. Leaps forward in genetics will not happen without more programmers and data analysts. Engineering is another field that is constantly advancing by leaps and bounds. Engineers pave the way forward to help humankind produce the best results and have the best impact we can. Online schools make it possible for virtually anyone with internet access to become accredited in computer science, or earn an online master’s in civil engineering, depending on what field you prefer. These are few specific degrees that can be earned from home but these ones are great examples. Self-paced study means students earn degrees as quickly as possible or at their leisure. Startling discoveries may come not from government labs and universities, but bright people working with their own digital models of the human genome.

Transhumanism

Being more than our genes allow is one of the dreams of genetic scientists. In a laboratory, certain enzymes are used to cut and splice DNA. As we perfect manipulating genes, the pursuit of health and eternal youth will lead us to improved health, treatments, and longevity. Man-made viruses, Frankenstein's monster, and other shortfalls lie ahead, but if genetics keeps pace with computing, or even close, stronger and healthier bodies and minds are a goal that is well within sight.

By Rachelle Wilber

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Genomics  

Genetic testing provides benefits for individuals and families by identifying increased risks of disease, potential interventions when disease is present, and also to determine the efficacy of ongoing treatments.

DNA testing is often associated with determining the parentage of a child and the guilt or innocence of a defendant in criminal cases. However, genetic testing provides benefits for individuals and families by identifying increased risks of disease, potential interventions when disease is present, and also to determine the efficacy of ongoing treatments.

Family Planning

Genetic testing, which includes analysis of DNA, RNA, enzymes and proteins, can be an important resource for family planning. Couples may benefit from genetic testing to determine if they are carriers for certain gene mutations that are identified with increased likelihood of developing disease. A specialist at Courtagen Life Sciences can also help with gene sequencing. While an individual carrier may not exhibit symptoms of a disease, their offspring will inherit genes that may lead to the development of symptoms of the disease. 

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Prenatal Diagnosis

Prenatal diagnosis through DNA testing is performed on the fetus to determine the presence of disease or changes in the fetus' genes and chromosomes that may indicate disorders before birth. Amniocentesis, one type of fetal genetic testing, is performed in vitro by obtaining a sample of amniotic fluid, typically after 15 weeks of pregnancy. Prenatal testing may indicate genetic abnormalities responsible for diseases such as Down Syndrome. Chrorionic Villus Sampling, performed after the 10th week of pregnancy, uses material from the placenta to test for genetic abnormalities.

Early Detection of Disease

Newborns in developed countries typically receive DNA testing within one to two days after birth to screen for certain illnesses or health risks. Determining health vulnerabilities early provides a better outcome when treatment strategies can be applied before symptoms are prevalent. Additionally, when genetic mutations or abnormalities have been identified early, monitoring changes over time may indicate the development of disease that otherwise may go undetected. 

Personalized Medicine

Pharmacogenomics, a type of DNA testing associated with personalized medicine, provides benefits when treatment for disease has already been implemented. Information about an individual’s potential reaction and response to certain types of pharmaceutical interventions may determine changes in treatment protocols. While one treatment may prove beneficial to one individual, the same treatment may prove ineffective or detrimental for someone else depending on his or her unique genetic makeup.

As new developments in DNA testing continue to inform scientists and medical professionals about the causes of serious diseases such as Diabetes and Alzheimer’s, increased opportunities arise for individuals and families to take a more proactive approach to disease prevention and health maintenance.

By Rachelle Wilber

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 Genetic Engineering  

Researchers have developed a way to program DNA in such a way that genes can be turned on or off in living cells. The new tool can affect two different genes at the same time, an advance that will allow scientists to treat even the most complex genetic disorders.

Bioengineers at Stanford and other universities have developed a sort of programmable genetic code that allows them to preferentially activate or deactivate genes in living cells.

The research is published in the current issue of Cell, and could help usher in a new generation of gene therapies.

The technique is an adaptation of CRISPR, itself a relatively new genetic tool that makes use of a natural defense mechanism that bacteria evolved over millions of years to slice up infectious virus DNA.

Standard CRISPR consists of two components: a short RNA that matches a particular spot in the genome, and a protein called Cas9 that snips the DNA in that location. For the purposes of gene editing, scientists can control where the protein snips the genome, insert a new gene into the cut and patch it back together.

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Inserting new genetic code, however, is just one way to influence how the genome is expressed. Another involves telling the cell how much or how little to activate a particular gene, thus controlling how much protein a cell produces from that gene and altering its behavior.

"We could eventually synthesize tens of thousands of RNA molecules to control the genome over a whole organism."

It's this action that Lei Stanley Qi, an assistant professor of bioengineering and of chemical and systems biology at Stanford, and his colleagues aim to manipulate.

In the new work, the researchers describe how they have designed the CRISPR molecule to include a second piece of information on the RNA, instructing the molecule to either increase (upregulate) or decrease (downregulate) a target gene's activity, or turn it on/off entirely.

They also designed it so that it could affect two different genes at once. In a cell, the order or degree in which multiple genes are activated can produce different metabolic products.

"It's like driving a car. You control the wheel to control direction, and the engine to control the speed, and how you balance the two determines how the car moves," Qi said. "We can do the same thing in the cell by up- or downregulating genes, and produce different outcomes."

To prove the principle, the scientists used the technique to take control of a yeast metabolic pathway, turning genes on and off in various orders to produce four different end products. They then tested it on two mammalian genes that are important in cell mobility, and were able to control the cell's direction and how fast it moved.

The ability to control genes is an attractive approach in designing genetic therapies for complex diseases that involve multiple genes, Qi said, and the new system may overcome several of the challenges of existing experimental therapies.

"Our technique allows us to directly control multiple specific genes and pathways in the genome without expressing new transgenes or uncontrolled behaviors, such as producing too much of a protein, or doing so in the wrong cells," Qi said.

Next, Qi plans to test the technique in mice and refine the delivery method. Currently the scientists use a virus to insert the molecule into a cell, but he would eventually like to simply inject the molecules into an organism's blood. "I'm optimistic because everything about this system comes naturally from cells, and should be compatible with any organism."


SOURCE  Stanford University

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 Biotech  

Scientists have used DNA as a smart adhesive for 3D printing.  The method may lead to 3D printed tissues and self-assembling organs in the future.

The “source code” for life in humans, plants, animals and some microbes, DNA is the molecular computer that controls how life develops. But now researchers report an initial study showing that the strands can also act as a glue to bind together 3D printed materials that could someday be used to grow tissues and organs in the lab.

This first-of-its-kind demonstration of the inexpensive process is published in the new journal ACS Biomaterials Science & Engineering.

Andrew Ellington and colleagues explain that although researchers have used nucleic acids such as DNA to assemble objects, most of these are nano-sized — so tiny that humans can’t see them with the naked eye. This is the case with DNA origami.  Making the structures into larger, visible objects is cost-prohibitive.

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The current methods of working with DNA also do not allow for much control or flexibility in the types of materials that are created. Overcoming these challenges could potentially have a big payoff — the ability to make tissues to repair injuries or even to create organs for the thousands of patients in need of organ transplants. With this in mind, Ellington’s group set out to create a larger, more affordable material held together with DNA.

The researchers developed DNA-coated nanoparticles made of either polystyrene or polyacrylamide. DNA binding adhered these inexpensive nanoparticles to each other, forming gel-like materials that they could extrude from a modified MakerBot Replicator 3D Printer.

For this study, the 3D printer was modified for printing microparticle-based gels by directing the print head to extrude a suspension provided via a programmable syringe pump. By actuating the print head while controlling the dispense rate of the syringe pump, the 3D printer directed the extrusion of a colloidal gel into 3D shapes.

"The ability to control the macroscale shape, the microscale topology by DNA computation-mediated self-assembly, and the ability to choose the chemistry of the “dumb” substrate material is a unique combination of features for tissue engineering."

The materials were easy to see and could be manipulated without a microscope. The DNA adhesive also allowed the researchers to control how these gels came together. They showed that human cells could grow in the gels, which is the first step toward the ultimate goal of using the materials as scaffolds for growing tissues.

Given the progress that has been made in the DNA nanotechnology community, such programmability may provide an interesting avenue for creating new materials with programmed structure at the microscale.

Future work will focus on controlling the self-assembly process using the properties of both DNA hybridization and DNA circuitry in order to test the effects of different self-assembly processes. By working from the nanoscale to the microscale, to the macroscale, in the future, structures may be self-assembled based on how the seed cells within it are established.

"The ability to control the macroscale shape, the microscale topology by DNA computation-mediated self-assembly, and the ability to choose the chemistry of the “dumb” substrate material is a unique combination of features for tissue engineering," write the study authors.


SOURCE  American Chemical Society 

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 Main Label  

NIH researchers have found that the biological machinery that builds DNA can insert molecules into the DNA strand that are damaged as a result of environmental exposures. These damaged molecules trigger cell death that produces some human diseases, according to the researchers.

By using a new imaging technique, National Institutes of Health (NIH) scientists have found that the biological machinery that builds DNA can insert molecules into the DNA strand that are damaged as a result of environmental exposures. These damaged molecules trigger cell death that produces some human diseases, according to the researchers.

The work, appearing in the journal Nature, provides a possible explanation for how one type of DNA damage may lead to cancer, diabetes, hypertension, cardiovascular and lung disease, and Alzheimer’s disease.

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Time-lapse crystallography was used by National Institute of Environmental Health Sciences (NIEHS) researchers to determine that DNA polymerase, the enzyme responsible for assembling the nucleotides or building blocks of DNA, incorporates nucleotides with a specific kind of damage into the DNA strand. Time-lapse crystallography is a technique that takes snapshots of biochemical reactions occurring in cells.

Samuel Wilson, M.D., senior NIEHS researcher on the team, explained that the damage is caused by oxidative stress, or the generation of free oxygen molecules, in response to environmental factors, such as ultraviolet exposure, diet, and chemical compounds in paints, plastics, and other consumer products. He said scientists suspected that the DNA polymerase was inserting nucleotides that were damaged by carrying an additional oxygen atom.

“When one of these oxidized nucleotides is placed into the DNA strand, it can’t pair with the opposing nucleotide as usual, which leaves a gap in the DNA,” Wilson said. “Until this paper, no one had actually seen how the polymerase did it or understood the downstream implications.”

"Until this paper, no one had actually seen how the polymerase did it or understood the downstream implications."

Wilson and his colleagues saw the process in real time, by forming crystal complexes made of DNA, polymerase, and oxidized nucleotides, and capturing snapshots at different time points through time-lapse crystallography. The procedure not only uncovered the stages of nucleotide insertion, but indicated that the new DNA stopped the DNA repair machinery from sealing the gap. This fissure in the DNA prevented further DNA repair and replication, or caused an immediate double-strand break.

“The damaged nucleotide site is akin to a missing plank in a train track,” Wilson said. “When the engine hits it, the train jumps the track, and all of the box cars collide.”

Large numbers of these pileups and double-strand breaks are lethal to the cell, serving as a jumping off point for the development of disease. However, it can be a good thing if you are a researcher trying to destroy a cancer cell.

“One of the characteristics of cancer cells is that they tend to have more oxidative stress than normal cells,” said Bret Freudenthal, Ph.D., lead author of the paper and postdoctoral fellow in Wilson’s group. “Cancer cells address the issue by using an enzyme that removes oxidized nucleotides that otherwise would be inserted into the genome by DNA polymerases. Research performed by other groups determined if you inhibit this enzyme, you can preferentially kill cancer cells.”

Wilson and Freudenthal stressed that the quantities of oxidized nucleotides in the nucleotide pool are usually under tight control, but if they accumulate and start to outnumber undamaged nucleotides, the DNA polymerase adds more of them to the strand.

Molecules that inhibit oxidation, known as antioxidants, reduce the level of oxidized nucleotides, and may help prevent some diseases.



SOURCE  NIH

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 Cell Biology  

Another discovery has been made that will cause textbooks to be rewritten. New research reveals that when missing critical components, cells can adapt and make copies of their DNA in an other way.

New research shows that cells are more resilient in taking care of their DNA than scientists originally thought. Even when missing critical components, cells can adapt and make copies of their DNA in an alternative way.

In a study published in Cell Reports, a team of researchers at Michigan State University showed that cells can grow normally without a crucial component needed to duplicate their DNA.

“Our genetic information is stored in DNA, which has to be continuously monitored for damage and copied for growth,” said Kefei Yu, MSU Professor. “If the cell is unable to make copies of its DNA or if it overlooks mistakes in its structure, it can lead to cell death or the production of cancerous cells.”

The study shows that cells are much more flexible in managing their DNA — when they lack the gadgets required to replicate DNA, they adapt and use other tools instead.

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But the study shows that cells are much more flexible in managing their DNA than we thought. When they lack the gadgets required to replicate DNA, they adapt and use other tools instead.

These tools are a family of proteins called DNA Ligases, which are needed for a variety of processes associated with DNA. There are several forms of these ligases, and the consensus among scientists has been that they each have specific roles that don’t really overlap.

Belonging to this family of ligases is DNA Ligase I, which is thought to be critical for making copies of DNA and hence essential for growth. However, the researchers have shown that DNA Ligase I is actually not needed in some cells.

“This suggests that cells are much more flexible in the way they make more of their DNA,” Yu said. “It might be that these ligases can substitute for each other when one of them is missing.”

The researchers took out DNA Ligase I in a type of mouse cells and examined how the cells would respond to the challenge of losing a supposedly essential component for making copies of DNA.

To their surprise, they saw that these cells could grow just fine, indicating that they were still managing to make more DNA without DNA Ligase I. They even saw that these ‘handicapped’ cells were able to fix induced damages in the DNA as well.

“Our next question is whether this phenomenon is unique to this specific type of cell, or if it’s generally true to a variety of other cells, including those of humans,” Yu said. “We’re interested in finding out how exactly the cell’s adapting.”

If the replacement of DNA Ligase I is in fact a general rule among many types of cells, then textbooks will have to be rewritten, and scientists will have to start working toward a better explanation of how DNA is maintained and copied in the cell – two processes that are essential to the viability of life.


SOURCE  Michigan State University

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 Cancer  

Research by scientists at the University of Exeter has shown that cells demonstrate remarkable flexibility and versatility when it comes to how they divide — a finding with potential links to the underlying causes of many cancers.

New research by scientists at the University of Exeter has shown that cells demonstrate remarkable flexibility and versatility when it comes to how they divide - a finding with potential links to the underlying causes of many cancers.

The study, published in Developmental Cell, describes a number of routes to the formation of a microtubule spindle – the tracks along which DNA moves when a cell divides in order to make two genetically identical cells.

In order to understand the phenomenon, the authors, including Biosciences researchers Dr. James Wakefield, PhD student Daniel Hayward and Experimental Officer in Image Analysis, Dr. Jeremy Metz, combined highly detailed microscopy and image analysis with genetic and protein manipulation of fruit fly embryos.

The innovative research not only describes how the cell can use each pathway in a complementary way, but also that removal of one pathway leads to the cell increasing its use of the others. The researchers also identified that a central molecular complex – Augmin – was needed for all of these routes.

The authors were the first to identify that each of four pathways of spindle formation could occur in fruit fly embryos.

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It was previously thought that, in order for chromosomes – packages containing DNA – to line up and be correctly separated, microtubules have to extend from specific microtubule-organising centres in the cell, called centrosomes. However, this study found that microtubules could additionally develop from the chromosomes themselves, or at arbitrary sites throughout the main body of the cell, if the centrosomes were missing.

All of these routes to spindle formation appeared to be dependent on Augmin - a protein complex responsible for amplifying the number of microtubules in the cell.

Dr. Wakefield said of the project "We have all these different spindle formation pathways working in humans. Because the cell is flexible in which pathway it uses to make the spindle, individuals who are genetically compromised in one pathway may well grow and develop normally. But it will mean they have fewer routes to spindle formation, theoretically predisposing them to errors in cell division as they age."

The group are currently investigating cancer links in light of these findings.


SOURCE  University of Exeter

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 Nanomedicine  

As part of an international research project, a team of researchers has developed a DNA clamp that can detect mutations at the DNA level with greater efficiency than methods currently in use. Their work could facilitate rapid screening of those diseases that have a genetic basis, such as cancer, and provide new tools for more advanced nanotechnology.

An increasing number of genetic mutations have been identified as risk factors for the development of cancer and many other diseases. Several research groups have attempted to develop rapid and inexpensive screening methods for detecting these mutations.

Now a team of researchers has developed a DNA clamp that can detect mutations at the DNA level with greater efficiency than methods currently in use. Their work could facilitate rapid screening of those diseases that have a genetic basis, such as cancer, and provide new tools for more advanced nanotechnology.

Image Source - ACS Nano

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"The results of our study have considerable implications in the area of diagnostics and therapeutics,” says Professor Francesco Ricci, “because the DNA clamp can be adapted to provide a fluorescent signal in the presence of DNA sequences having mutations with high risk for certain types cancer. The advantage of our fluorescence clamp, compared to other detection methods, is that it allows distinguishing between mutant and non-mutant DNA with much greater efficiency. This information is critical because it tells patients which cancer(s) they are at risk for or have.”

The results of this research is published this month in the journal ACS Nano.

"Nature is a constant source of inspiration in the development of technologies,” says Professor Alexis Vallée-Bélisle. “For example, in addition to revolutionizing our understanding of how life works, the discovery of the DNA double helix by Watson, Crick and Franklin in 1953 also inspired the development of many diagnostic tests that use the strong affinity between two complementary DNA strands to detect mutations.”

"However, it is also known that DNA can adopt many other architectures, including triple helices, which are obtained in DNA sequences rich in purine (A, G) and pyrimidine (T, C) bases,” says the researcher Andrea Idili, first author of the study. “Inspired by these natural triple helices, we developed a DNA-based clamp to form a triple helix whose specificity is ten times greater than a double helix allows.”

"Beyond the obvious applications in the diagnosis of genetic diseases, I believe this work will pave the way for new applications related in the area of DNA-based nanostructures and nanomachines," notes Professor Kevin Plaxco, University of California, Santa Barbara. "Such nanomachines could ultimately have a major impact on many aspects of healthcare in the future."

The researchers also found that their clamp-switch strategy could also be used to engineer highly specific structure-switching biosensors using more complex recognition elements including aptamers and proteins.

"The next step is to test the clamp on human samples, and if it is successful, it will begin the process of commercialization," concludes Professor Vallée-Bélisle.


SOURCE  University of Montreal

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 Genomics  

Scientists found that there is a second code hiding within DNA. The discovery of what are being called "duons" has major implications for how scientists and physicians interpret a patient’s genome and will open new doors to the diagnosis and treatment of disease.

R esearchers have discovered a second code hiding within DNA. This second code contains information that changes how scientists read the instructions contained in DNA and interpret mutations to make sense of health and disease.

A research team led by Dr. John Stamatoyannopoulos, University of Washington associate professor of genome sciences and of medicine, made the discovery. The findings were reported in the journal Science.

The work is part of the Encyclopedia of DNA Elements Project, also known as ENCODE. The National Human Genome Research Institute funded the multi-year, international effort. ENCODE aims to discover where and how the directions for biological functions are stored in the human genome.

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Since the genetic code was deciphered in the 1960s, scientists have assumed that it was used exclusively to write information about proteins. The University of Washington scientists were stunned to discover that genomes use the genetic code to write two separate languages. One describes how proteins are made, and the other instructs the cell on how genes are controlled. One language is written on top of the other, which is why the second language remained hidden for so long.

“For over 40 years we have assumed that DNA changes affecting the genetic code solely impact how proteins are made,” said Stamatoyannopoulos. “Now we know that this basic assumption about reading the human genome missed half of the picture. These new findings highlight that DNA is an incredibly powerful information storage device, which nature has fully exploited in unexpected ways.”

The genetic code uses a 64-letter alphabet called codons. The UW team discovered that some codons, which they called duons, can have two meanings, one related to protein sequence, and one related to gene control. These two meanings seem to have evolved in concert with each other. The gene control instructions appear to help stabilize certain beneficial features of proteins and how they are made.

The discovery of duons has major implications for how scientists and physicians interpret a patient’s genome and will open new doors to the diagnosis and treatment of disease.

“The fact that the genetic code can simultaneously write two kinds of information means that many DNA changes that appear to alter protein sequences may actually cause disease by disrupting gene control programs or even both mechanisms simultaneously,” said Stamatoyannopoulos.

The research (and the way it has been presented)  has a critical response so far, but it could lead to new discoveries and treatments for disease.


SOURCE  University of Washington

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 Aging  

A UCLA study has uncovered a biological clock embedded in our genomes that may shed light on why our bodies age and how we can slow the process. The findings could offer valuable insights into cancer and stem cell research.

An American scientist has discovered an internal body clock based on DNA that measures the biological age of our tissues and organs.

This clock shows that while many healthy tissues age at the same rate as the body as a whole, some of them age much faster or slower. The age of diseased organs varied hugely, with some many tens of years "older" than healthy tissue in the same person, according to the clock.

Researchers say that unravelling the mechanisms behind the clock will help them understand the ageing process and hopefully lead to drugs and other interventions that slow it down.

Therapies that counteract natural ageing are attracting huge interest from scientists because they target the single most important risk factor for scores of incurable diseases that strike in old age.

The research has been published in the journal Genome Biology.

"Ultimately, it would be very exciting to develop therapy interventions to reset the clock and hopefully keep us young," said Steve Horvath, professor of genetics and biostatistics at the University of California in Los Angeles.

Horvath showed that the biological clock was reset to zero when cells plucked from an adult were reprogrammed back to a stem-cell-like state.

Horvath looked at the DNA of nearly 8,000 samples of 51 different healthy and cancerous cells and tissues. Specifically, he looked at how methylation, a natural process that chemically modifies DNA, varied with age.

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Horvath found that the methylation of 353 DNA markers varied consistently with age and could be used as a biological clock. The clock ticked fastest in the years up to around age 20, then slowed down to a steadier rate. Whether the DNA changes cause ageing or are caused by ageing is an unknown that scientists are now keen to work out.

"Does this relate to something that keeps track of age, or is a consequence of age? I really don't know," Horvath told the Guardian. "The development of grey hair is a marker of ageing, but nobody would say it causes ageing," he said.

The clock has already revealed some intriguing results. Tests on healthy heart tissue showed that its biological age – how worn out it appears to be – was around nine years younger than expected. Female breast tissue aged faster than the rest of the body, on average appearing two years older.

Diseased tissues also aged at different rates, with cancers speeding up the clock by an average of 36 years. Some brain cancer tissues taken from children had a biological age of more than 80 years.

"Female breast tissue, even healthy tissue, seems to be older than other tissues of the human body. That's interesting in the light that breast cancer is the most common cancer in women. Also, age is one of the primary risk factors of cancer, so these types of results could explain why cancer of the breast is so common," Horvath said.

Healthy tissue surrounding a breast tumour was on average 12 years older than the rest of the woman's body, the scientist's tests revealed.

"It provides a proof of concept that one can reset the clock," said Horvath. The scientist now wants to run tests to see how neurodegenerative and infectious diseases affect, or are affected by, the biological clock.

Horvath discovered that the clock’s rate speeds up or slows down depending on a person’s age.

“The clock’s ticking rate isn’t constant,” he explained. “It ticks much faster when we’re born and growing from children into teenagers, then slows to a constant rate when we reach 20.”

In an unexpected finding, the cells of children with progeria, a genetic disorder that causes premature aging, appeared normal and reflected their true chronological age.

SOURCE  The Guardian, UCLA via Newswise

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 Forensic Science  

Since 2000 the number of Biobanks worldwide has increased by one third.  With DNA evidence increasingly being used in criminal cases, Elizebeth Coakley raises questions about biobanks' access and use of private genetic data.

While forensic science, at least by name, has been around for a long period of time, it has only recently become reliant on DNA evidence. Previously, evidence presented by people identifying as forensic scientists had been acquired through a number of means—testimony by dentists, footprint experts, mental health professionals.

In an episode of Frontline called “The Real CSI”, which first aired in April of 2012, the documentary crew reveals lapses in real science in forensic science, resulting in the false imprisonment of a shocking number of individuals.

The episode is startling in its discussion of the overly-simplistic process of obtaining a document certifying one as a forensic science expert—it is perhaps because of this coming under fire for faulty means of conviction and misrepresentation of degrees that forensic science has seen a shift to irrefutable DNA evidence.

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Such is the accuracy of DNA evidence that positive identification, arrests, and prosecution double in the presence of such evidence. Such is the accuracy of DNA evidence that all 50 states have at least one criminal conviction which demands the use of DNA evidence. And with new technology comes new problems—in 2011, the National Institute of Justice revealed that backlogged samples were as high as 100,000. The increase in genetic testing had led to a test bank so overburdened that it was slow and prone to errors.

The solution, in part, was an increase in the number and size of biobanks handling genetic testing storage. Facilities such as this assist in the storage of human tissue, serum, plasma, urine, and blood, and require extreme consideration of temperature. Though such banks have been around for at least 50 years, the industry has seen tremendous growth—1/3 of existing banks have been built since 2000.

With the invention and inclusion of facilities that manage sample storage by way of machine, it is no wonder that forensic science is making a name for itself as a reputable one, positively contributing to the capture and persecution of many criminals. But it is sparking debate too—are medical biobanks used for forensic purposes subject to the same privacy considerations as those focused on disease and population?

The answer seems to be a resounding no. While it may seem unfair to disregard the rights of donors for forensic use, the basic right to privacy is sometimes secondary to another—in this case, violent criminal investigation and conviction. And, though access to DNA databases held in biobanks has the potential to encourage reluctance of individuals to contribute DNA or perhaps perpetuates the idea that donors are simply being used to solve crimes—it works.

By Elizebeth Coakley

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Author Bio - Elizebeth Coakley is a freelance writer with a background in life science research. When she's not trying to explain cytometers, you can find her binge-watching The Walking Dead.

 Biological Computation  

Chemists from North Carolina State University have performed a DNA-based logic-gate operation within a human cell. The research may pave the way to more complicated computations in live cells, as well as new methods of disease detection and treatment.

Chemists from North Carolina State University have performed a DNA-based logic-gate operation within a human cell. The research may pave the way to more complicated computations in live cells, as well as new methods of disease detection and treatment.

Their results appear in the Journal of the American Chemical Society.

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Logic gates are the means by which computers “compute,” as sets of them are combined in different ways to enable computers to ultimately perform tasks like addition or subtraction. In DNA computing, these gates are created by combining different strands of DNA, rather than a series of transistors. However, thus far DNA computation events have typically taken place in a test tube, rather than in living cells.

NC State chemist Alex Deiters and graduate student James Hemphill wanted to see if a DNA-based logic gate could detect the presence of specific microRNAs in human cells. The researchers utilized a DNA-based logic gate known as an “AND” gate that was engineered to respond to the presence of two specific microRNAs – known as miRNA-21 and miRNA-122.

Just as computer operations utilize different inputs to create a particular output, the researchers’ DNA-based Boolean logic gate was activated only when both miRNA-21 and miRNA-122 “inputs” were present in cells. If they were present, the gate generated an “output” by releasing a fluorescent molecule.

Deiters believes that use of these logic gates could lead to more accurate tests and treatments for human disease, especially cancer.

“The fluorescent molecule we used in this logic-gate design could be useful as a marker that identifies a cancer cell,” he says. “Or, instead of directing the gate to release a fluorescent molecule in the presence of particular microRNAs, we could attach therapeutic agents that are released to treat the disease itself.”



SOURCE  \NC State

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 Evolution  

A research team led by a University of Chicago scientist has discovered two key mutations that sparked a hormonal revolution 500 million years ago.

Evolution, it seems, sometimes jumps instead of crawls.

A research team led by a University of Chicago scientist has discovered two key mutations that sparked a hormonal revolution 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.

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"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 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.


SOURCE  University of Chicago

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