Category Archives: DNA

Growing up, Brandon Tong longed for a brother or sister. Raised by a devoted single mother, Dung (known as Donna) working two jobs to keep the family afloat, he struggled to make friends.

[Mum] worked very hard to support me, Brandon, now 26 and from San Diego, told The Mirror. She owned a dollar store and also worked repairing watches. She juggled so much.

But as an only child, Brandon sometimes felt isolated.

He said: I was unbelievably lonely when I was a child. A brother or sister was pretty much all I wanted. But mum wasnt really dating or anything so another child never came.

I thought it would be really cool to have a brother.

And when he was at school, Brandons loneliness was even more acute.

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I was a bit lacking in social skills. I didnt really know how to make friends and I was the kid who got picked on, he recalled.

Being raised by a strong woman, Brandon never knew much about his dad. He had a few photos of his father holding him as a baby, and received birthday cards for a few years. But the cards stopped around the time he was in primary school.

Luckily, he slowly came out of his shell as he reached adolescence. But even with some friends by his side, Brandon still struggled at school.

School never went well for me. I had a big social anxiety problem and never got my high school diploma, he said.

Brandon decided to drop out of school at 17, before working part time in retail and as a sushi chef. In time, he went back to college, hoping things would be different. But when he was put on academic probation, he knew this path wasnt for him.

Thats when I joined the army, he said. My lifes been a lot better since.

And from there, things finally started to fall into place. While stationed in Korea, Brandon met his now-wife, Viktoria. The pair married in 2018 and moved across the country to San Diego, where she is from.

Happy with his lot, Brandon was never particularly interested in tracking down his biological father.

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My wife was always bothered by it but I wasnt very curious, he said.

But one day, the pair saw a TV advert for a home DNA test kit and had an idea.

I was interested to find out more about the scientific side of things, like which diseases I might be susceptible to and my ethnicity. So me and my wife got a package deal and bought two kits at the same time.

The kits arrived and Brandon and Viktoria did their swabs. When the results came back, Brandon wasnt particularly surprised.

It told me I was mostly Vietnamese with some Chinese heritage but I pretty much expected that, he said.

It wasnt until Brandon logged onto his account on the 23&Me website to fill in details about health conditions that he discovered something incredible.

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When he clicked on his profile, Brandon had a relative listed, who had also taken a home DNA test - his half brother, who shared a biological father.

I was so shocked. I didnt know if it was real. I did remember my Mum saying something about my dad starting a new life but it never crossed my mind that it would be possible to meet any siblings, he said.

After the initial shock wore off, Brandon started having doubts

I was hesitant to reach out to him. I didnt feel like it was natural and I didnt think it would be something he wanted to do, he said.

Meanwhile, he and Viktoria took a belated honeymoon trip to Europe, travelling across the continent. But when he landed in Barcelona, he got another surprise.

My brother actually messaged me. I got it right as I turned on my phone when we got off the flight. I was like, Oh my God, he wants to talk to me.

His name was Ben, he was 16 and living on the other side of the country in Massachusetts, where Brandon had lived when he was very young.

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We were talking online for a long time. He didnt know much about his family either. He was excited about turning 18 so he could start doing his own thing, Brandon said.

When Brandon told his mum about the wonderful news, she was over the moon.

I think she was more excited than me, he joked.

Do you have a long lost family story? Did you discover a family member late in life? Send your stories to jessica.taylor@reachplc.com

With the coronavirus pandemic scuppering plans around the world, and while they waited for Ben to turn 18, the half brothers had to put their plans to meet on hold.

But just last week, Ben was travelling through San Diego with some friends and arranged to meet Brandon and Viktoria for the day.

Finally meeting his half brother for the first time, Brandon admitted it was a bit strange.

He said: Initially it was a little awkward but when we sat down to brunch, we realised we had plenty to talk about and catch up on.

We hung out for the entire day and Viktoria and I showed him the sights and drove him around.

Sadly, Ben was just passing through and could only stay for the day, but now the pair have met, theyre not letting each other go again.

Were definitely staying in touch. Its just a case of figuring out who travels to see the other one, Brandon said.

After the whirlwind of the last few years, Brandon still cant quite believe he met his brother through an online DNA kit.

Its like something out of a movie. I cant believe its real, he joked.

When Ben gets older, well have a bit more freedom to meet up, but were definitely going to see each other again.

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'I bought home DNA kit and discovered family secret that changed my life forever' - The Mirror

Nucleic acids are the organic materials present in all organisms in the form of DNA or RNA. These nucleic acids are formed by the combination of nitrogenous bases, sugar molecules and the phosphate groups that are linked by different bonds in a series of sequences. The DNA structure defines the basic genetic makeup of our body. In fact, it defines the genetic makeup of nearly all life on earth.

Table of Contents

Read on to explore DNA meaning, structure, function, DNA discovery and diagram in complete detail.

What is DNA?

DNAis a group of molecules that is responsible for carrying and transmitting the hereditary materials or the genetic instructions from parents to offsprings.

This is also true for viruses as most of these entities have either RNA or DNA as their genetic material.For instance, some viruses may have RNA as their genetic material, while others have DNA as the genetic material. TheHuman Immunodeficiency Virus (HIV) contains RNA, which is then converted into DNA after attaching itself to the host cell.

Apart from being responsible for the inheritance of genetic information in all living beings, DNA also plays a crucial role in the production of proteins. Nuclear DNA is the DNA contained within the nucleus of every cell in a eukaryotic organism. It codes for the majority of the organisms genomes while themitochondrial DNA and plastid DNA handles the rest.

The DNA present in the mitochondria of the cell is termed as mitochondrial DNA. It is inherited from the mother to the child. In humans, there are approximately 16,000 base pairs of mitochondrial DNA. Similarly, plastids have their own DNA and they play an essential role in photosynthesis.

Also Read:Difference between gene and DNA

DNA is known as Deoxyribonucleic Acid. Itis an organic compound that has a unique molecular structure. It is found in all prokaryotic cells and eukaryotic cells.

There are three different DNA types:

Who Discovered DNA?

DNA was first recognized and identified by the Swiss biologist, Johannes Friedrich Miescher in 1869 during his research on white blood cells.

The double helix structure of a DNA molecule was later discovered through the experimental data by James Watson and Francis Crick. Finally, it was proved that DNA is responsible for storing the genetic information in living organisms.

Also Read:Difference between deoxyribose and ribose

DNA Diagram

The following diagram explains the DNA structure representing the different parts of the DNA. DNA comprises a sugar-phosphate backbone and the nucleotide bases (guanine, cytosine, adenine and thymine).

DNA Diagram representing the DNA Structure

DNA Structure

The DNA structure can be thought of like a twisted ladder. This structure is described as a double-helix, as illustrated in the figure above. It is a nucleic acid, and all nucleic acids are made up of nucleotides.The DNA molecule is composed of units called nucleotides, and each nucleotide is composed of three different components, such as sugar, phosphate groups and nitrogen bases.

The basic building blocks of DNA are nucleotides, which are composed of a sugar group, a phosphate group, and a nitrogen base. The sugar and phosphate groups link the nucleotides together to form each strand of DNA. Adenine (A), Thymine (T), Guanine (G) and Cytosine (C) are four types of nitrogen bases.

These 4 Nitrogenous bases pair together in the following way: AwithT, and Cwith G. These base pairs are essential for the DNAs double helix structure, which resembles a twisted ladder.

The order of the nitrogenous bases determines the genetic code or the DNAs instructions.

Components of DNA Structure

Among the three components of DNA structure, sugar is the one which forms the backbone of the DNA molecule. It is also called deoxyribose. The nitrogenous bases of the opposite strands form hydrogen bonds, forming a ladder-like structure.

DNA Structure Backbone

The DNA molecule consists of 4 nitrogen bases, namely adenine (A), thymine (T), cytosine (C) and Guanine (G) which ultimately forms the structure of a nucleotide. The A and G are purines and the C and T are pyrimidines.

The two strands of DNA run in opposite directions. These strands are held together by the hydrogen bond that is present between the two complementary bases. The strands are helically twisted, where each strand forms a right-handed coil and ten nucleotides make up a single turn.

The pitch of each helix is 3.4 nm. Hence, the distance between two consecutive base pairs (i.e., hydrogen-bonded bases of the opposite strands) is 0.34 nm.

The DNA coils up, forming chromosomes, and each chromosome has a single molecule of DNA in it. Overall, human beings have around twenty-three pairs of chromosomes in the nucleus of cells. DNA also plays an essential role in the process of cell division.

Also Read:DNA Packaging

Chargaffs Rule

Erwin Chargaff, a biochemist, discovered that the number of nitrogenous bases in the DNAwas present in equal quantities. The amount of A is equal to T, whereas the amount of C is equal to G.

A=T; C=G

In other words, the DNA of any cell from any organism should have a 1:1 ratio of purine and pyrimidine bases.

DNA Replication

DNA replication is an importantprocess that occurs during cell division. It is alsoknown assemi-conservative replication, during which DNA makes a copy of itself.

DNA replication takes place in three stages :

The replication of DNA begins at a point known as the origin of replication. The two DNA strands are separated by the DNA helicase. This forms the replication fork.

DNA polymerase III reads the nucleotides on the template strand and makes a new strand by adding complementary nucleotides one after the other. For eg., if it reads an Adenine on the template strand, it will add a Thymine on the complementary strand.

While adding nucleotides to the lagging strand, gaps are formed between the strands. These gaps are known as Okazaki fragments. These gaps or nicks are sealed by ligase.

The termination sequence present opposite to the origin of replication terminates the replication process. The TUS protein (terminus utilization substance) binds to terminator sequence and halts DNA polymerase movement. It induces termination.

Also Read:DNA Replication

DNA Function

DNA is the genetic material which carries all the hereditary information. Genes are the small segments of DNA, consisting mostly of 250 2 million base pairs. A gene code for a polypeptide molecule, where three nitrogenous bases sequence stands for one amino acid.

Polypeptide chains are further folded in secondary, tertiary and quaternary structure to form different proteins. As every organism contains many genes in their DNA, different types of proteins can be formed. Proteins are the main functional and structural molecules in most of the organisms. Apart from storing genetic information, DNA is involved in:

Also Read:r-factor

Why DNA is called a Polynucleotide Molecule?

The DNA is called a polynucleotide because the DNA molecule is composed of nucleotides deoxyadenylate (A) deoxyguanylate (G) deoxycytidylate (C)and deoxythymidylate (T), which are combined to create long chains called a polynucleotide. As per theDNA structure, the DNA consists of two chains of the polynucleotides.

Also Read:Genetic Material

For more detailed information on DNA meaning, diagram, its types, DNA structure and function, or any other related topics, explore @ BYJUS Biology.

DNA is a double helical structure composed of nucleotides. The two helices are joined together by hydrogen bonds. The DNA also bears a sugar-phosphate backbone.

The three different types of DNA include:

Z-DNA is a left-handed double helix. The helix winds to the left in a zig-zag manner. On the contrary, A and B-DNA are right-handed DNA.

The functions of DNA include:

B-DNA is found in humans. It is a right-handed double-helical structure.

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What Is DNA?- Meaning, DNA Types, Structure and Functions

Jul 31st 2021

EVERYTHING ON Earth is made of atoms, most of which are closely packed together in the form of minerals. Life has its uses for mineralsask a coral reefbut its essence lies in atoms arranged as distinct molecules and the way they interact.

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Biological molecules are distinctive in various ways. One is that they can be very large indeed. The simple inorganic molecules that make up the air and the oceans typically contain only a few atoms, and often just two or three. Many biological molecules contain thousands. A few contain billions. These molecules are not just large, they are also precisely structured. Furthermore, those structures can be recreated with atom-by-atom accuracy.

These distinctly lifelike qualities stem from the fact that biological molecules have purposes bestowed on them by evolution. For example, life needs molecules which can catalyse chemical reactions and molecules which can store and transmit the genetic information needed to make those catalysts. Those requirements are met by two sorts of large molecule: proteins, which do most of the catalysis, as well as much else, and nucleic acids, which mostly store and transmit information.

Nucleic acids and proteins are both linear polymers; long, unbranched strings of similar-looking components, like paper chains at a childs party or beads on a necklace. In both cases the range of component monomersthe paper-chain links, or the beadsis limited. Nucleic acids are made from just five different monomers, known as nucleotides; proteins are typically made from 20 different varieties of amino acid. In both cases the assembly of the chains takes place one link at a time using a specific type of chemical reaction. Nucleotides are strung together using what are called ester bonds; proteins using what are called peptide bonds.

This linear, modular approach means that the same machinery can make lots of different molecules. All that is required is a system which can catalyse the addition of a new monomer to the lengthening chain, a way of telling that system which sort of monomer to add next, and a certain dogged persistence. A typical human protein is about 400 amino acids long; some are a lot longer. Molecules of DNA, one of lifes two types of nucleic acid, are far longer still. The shortest DNA molecules found in humans are about 17,000 nucleotides long; the longest consist of over 100m.

The order in which those nucleotides appear determines what information is stored in the DNA. The order of the various amino acids determines the shape of the protein created from them by controlling the way in which the chain folds itself up. The process can create a remarkable number of shapes and capabilities, all of which are dependent on just the order of the amino acids.

The fact that both proteins and DNA are ordered modular chains does not just reflect the ease with which such molecules can be made. It is also what makes possible the single most important thing anyone needs to know about molecular biology. The order of nucleotides in specific DNA sequencesgenesdetermines the order of amino acids in specific proteins.

In DNA the system which catalyses the creation of a new polymer is a mechanism called a DNA polymerase which is made of a number of protein subunits. It gets its instructions as to which sort of nucleotide to add next from a pre-existing piece of DNA used as a template.

The four different nucleotides used in DNA differ in the chemical base that they carry; the bases are adenine (A), cytosine (C), guanine (G) and thymine (T). One of the findings which led Francis Crick and James Watson to their double-helix model of DNA in 1953 was that DNA always contains the same number of Cs as Gs, and As as Ts.

A nucleotide carrying guanine can loosely pair itself to one on another DNA strand carrying cytosine; nucleotides carrying adenine and thymine can do likewise. This is the basis of the double helix, which consists of two DNA molecules wrapped around each other. Where one has a thymine the other has an adenine, and where one has a guanine the other has a cytosine; the attraction between these paired bases holds the two strands together. It also explains why there are the same number of Gs as there are Cs and As as Ts.

The end of the paper in which that structure was unveiled boasts one of the greatest understated asides of all time: It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material. Unzip the double helix and each of the two strands provides a template for remaking the other. When a polymerase comes across a T on the existing strand it adds an A, and vice versa; it swaps Gs for Cs in a similar way.

Copying DNA this way produces two double helices both containing the same sequence of base pairsthat is, the same information. When one of the new double helices goes into an egg or sperm cell all the information recorded on it, the Watson-and-Crick genetic material, gets passed on to the next generation.

What is more, if the message changesperhaps because of a mutation in which a stray bit of cosmic radiation turns an A into a Gthe new sequence can normally be copied just as well as the old one could. The fact that how reproducible a bit of DNA is does not depend on what it says allows mutations to persist long enough for evolution to find those which confer benefits. Steven Benner, a biochemist, sums this fundamental and vital property of DNA up with the natty acronym COSMIC LOPER: Capable Of Searching Mutation-space Independent of Concern over Loss of Properties Essential for Replication. Without a COSMIC-LOPER way of storing a genome, life in anything like its Earthly form could not exist.

The manufacture of proteins also requires a system to catalyse the addition of the next monomer to the lengthening chain and a way of knowing which monomer to add next. This time the catalyst is a complex piece of molecular machinery called a ribosome and the what-monomer-next cheat-sheet is an edited copy of some of the sequence information stored in the genomes nucleotides.

This process requires an intermediary: RNA, a nucleic acid very closely related to DNA but which does not form double helices and has a fifth base, called uracil (U), instead of DNAs thymine. First a system called an RNA polymerase uses a DNA sequence as a template for making a piece of RNA in the same way as a DNA polymerase makes a new strand in replication. That transcript is then tidied up into what is called a messenger RNA (mRNA).

This message is then read by the ribosome. Every triplet of letters in the mRNA tells the translation mechanism which of the different varieties of amino acid to add next. The relationship between these various nucleotide triplets and the amino acids they refer to is the genetic code, which is why the triplets are called codons.

Decoding an mRNA to make a protein is a lot more complex than just matching a new nucleotide to an existing one, as DNA and RNA polymerases do. As a result the ribosome is a much larger and more complex piece of molecular machinery. While the DNA polymerase is made just of proteins, the ribosome has some RNA mixed into it too, and uses other little bits of the stuff, tRNAs, to recognise the codons and add the appropriate amino acids. As the chain lengthens, the attractions and repulsions between its various amino acids lead it to fold into the shape required (though other proteins, called chaperonins, sometimes help).

In humans the genome has more than 21,000 DNA sequences which describe proteins, and human cells have the ability to edit the RNA made from some of those sequences to produced a number of different mRNAs, allowing them to make at least four times that many proteins and maybe ten times as many. In Escherichia coli, the bacterium most studied in laboratories, the genome describes just 4,285 different proteins. But that is still enough to provide all the proteins used in the ribosomes and the various polymerases, to catalyse all the reactions that build up the other molecules the bacterium needssuch as those which make up its outer surfaceand to break down the food it uses to provide the energy which drives everything else.

In a happily growing E. coli there are some 3m individual protein molecules, making up 55% of the organisms dry mass. There are just 300,000 RNA moleculesmostly tRNAs by number and mostly ribosomal RNA by weightwhich make up 20% of the dry mass. The millions of molecules involved in making the membranes and the cell wall which define the outer surface of the cell account for 15% of the dry mass. Everything elsethe pool of molecules involved in generating energy from food and storing it, the components needed to build the bigger molecules, various other gubbins and the DNA itselftogether make up the last 10%.

It is worth remembering, though, that there is one last vital molecule, and that is the one present in the greatest quantity. The dry mass of a cell as measured in the lab is just a third of the total mass it has when alive. The remaining two-thirds is good old H2O, the solvent in which everything else sits and which allows most of the necessary chemistry to take place. Big complex molecules are the unique and wonderful stuff of life. But life needs its water, too.

This article appeared in the Schools brief section of the print edition under the headline "Chains and reactions"

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Biology brief: How DNA and proteins work - The Economist

To assess conservation needs in certain areas, researchers first need to find out what animals call the region home. This task is often accomplished using trail cameras, but gaining a big picture view of a habitat is challenging when relying on literal snapshots.

As species continue to decline at a rapid pace globally, researchers need non-invasive tools that can swiftly determine which critters lurk close by, reports Michael Le Page for New Scientist.

Now, two research teams from the University of Copenhagen and Queen Mary University of London are working on a method that filters DNA from the air to detect which animals are near, reports Erik Stokstad for Science. Both studies were published this week on the preprint server bioRxiv, awaiting peer-review. The results demonstrate how environmental DNA (eDNA) can be used to detect terrestrial animals.

Theres more than just spores; there are cells and hair and all kinds of interesting things that float through the air, Julie Lockwood, a molecular ecologist at Rutgers University not involved in either study, tells Science.

Previously, Elizabeth Clare, a molecular ecologist now based at York University, published a study in the journal PeerJ detailing how eDNA from naked mole rats could be detected from air samples obtained in a laboratory setting, Science reports. To see if scientists could apply this tech to real-world situations, Clare and her team at the Queen Mary University tested air samples from 15 locations at the Hamerton Zoo Park in Huntingdonshire, United Kingdom. The air from indoor and outdoor enclosures were sampled using a pump and filter for 30 minutes each.

Seventy-two samples were sequenced using the polymerase chain reaction technique (PCR), a method used to amplify segments of DNA collected on the air filters. From the samples, the research team was able to identify 17 species of animals that lived within the zoo enclosures or roamed around it, such as deer and hedgehogs. Some of the DNA collected came from the zoo residents meaty meals, including chicken, cow, or pig. In total, the team determined 25 species of birds and mammals.

The researchers at the University of Copenhagen had a similar experiment where they went to the Copenhagen Zoo and vacuumed air from three different locations for anywhere between 30 minutes to 30 hours, New Scientist reports. Using the eDNA collected on the filters, the team detected animals up to 300 meters away from the vacuum pump. The method the team used to filter DNA was so sensitive that when the scientists sampled an enclosed area, DNA from guppies swimming in tanks were also picked up. A total of 49 species of vertebrae were detected, Science reports.

Similar methods were previously used to detect species in aquatic settings. The technique identified eDNA from rare species like the great crested newt and olm, an aquatic salamander, New Scientist reports.

Scientists suspect the method may detect animals in hard-to-reach or see areas, such as dry environments, caves, or burrows. However, the method still needs some finetuning. Researchers still need to evaluate how far eDNA may travel in the air depending on its environment, how different animals shed DNA, and how eDNA can be contaminated, Science reports.

Despite the unknowns, various scientists are planning on using the method to monitor wildlife, Clare tells New Scientist.

The ability to detect so many species in air samples using DNA is a huge leap. It represents an exciting potential addition to the toolbox, Matthew Barnes, an ecologist at Texas Tech University who was not involved with the study, tells Science.

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Researchers Vacuum DNA From the Air to See What Animals Are Near - Smithsonian Magazine

Yavier Ruiz-Velez was arrested in connection with three car thefts following the identification of his DNA

NORTH HAVEN, Conn. After almost a year, police arrested Yavier Ruiz-Velez in connection with three car thefts after a forensic investigation linking DNA evidence to the stolen vehicles.

On September 13, 2020 a Wayland Street resident reported his 2020 Jeep Gladiator was stolen from his driveway.

The victim reported that he left the keys inside the vehicle when he parked. Police say when he attempted to leave for work in the morning, the Jeep was gone.

The Jeep was recovered in East Hartford over a week later on September 22 and processed by North Haven Officers.

Police say DNA collected from the Jeep matched two other recovered stolen vehicles, one from East Hartford, and one from Rocky Hill.

Investigators, with the efforts of the Connecticut Forensic Laboratory, identified 21-year-old Ruiz-Velez as a suspect.

He was charged Wednesday with larceny in the first degree.

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Nearly a year later, DNA leads to arrest of alleged car thief - FOX 61

Emily Leproust, CEO and cofounder of the buzzy biotech startup Twist Bioscience, is an industrialist on the nanoscale. I remind everyone at Twist, we are a manufacturing company, she says. We manufacture DNA.

Twist is part of the young industry of synthetic biology, in which living organisms are the product and a biology lab is the factory floor. By manufacturing strands of DNAassembling the genetic code of life from its basic componentsscientists are creating organisms the likes of which the world has never seen. And these new life forms can be decidedly useful: Biologists have produced yeast cells that excrete pharmaceuticals and algae that brew jet fuel.

DNA Factory: Twist Biosciences machine builds DNA strands inside 600-nanometer wells on a silicon plate.Photo: Twist Bioscience

This burgeoning business sector has been hampered by the labor-intensive nature of DNA assembly, a painstaking process requiring trained personnel. Now, nimble startups are competing to fashion automated DNA assembly lines that would make Henry Ford proud, using techniques copied from the fabs that make computer chips. As their innovations bring down the cost of constructing DNA strands, these entrepreneurs are aiming for a low price point, which they say will cause a market boom. Twist Bioscience, which will begin commercial operations at its San Francisco headquarters in 2016, is a leading contender in that race to the bottom.

Genetic material is composed of molecules called nucleobases; the four types of bases in DNA are identified by the letters A, C, G, and T. The order of these letters serves as a code that instructs an organism how to build its cells and carry on the functions of life. In human beings, this code is about 3.2 billion letters long, while the yeast used in baking and beer brewing has a code of about 12million letters. If you tweak the order of the letters, you tweak the organisms instructions. Synthetic biologists have written new snippets of code and inserted them into yeast DNA, causing the microbe to churn out, for example, the omega-3 fatty acids found in fish oil supplements or the aromatic oils normally produced by roses.

Constructing a strand of DNA isnt complicated; in fact its a routine procedure performed in labs all over the world. But that procedure is typically carried out by hand, says Twists Leproust: Microbiology is manual labor. You have a Ph.D. student moving liquid from one test tube to the next all day long. So she and her cofounders invented a machine that automates the construction process.

The heart of the machine is a silicon plate pocked with 10,000 tiny wells, which are etched using the same photolithography techniques perfected by computer chip manufacturers. A different strand of DNA can be constructed in each 600-nanometerwide well. The machine does the exact same chemistry as a Ph.D. student would do, Leproust says, only in a volume thats 100 times smaller.

Twist isnt selling its machine but rather its DNA manufacturing services, which are aimed at researchers and startups seeking new genetic modifications that might prove useful. In 2015 the company began production runs for select customers; 2016 will see Twists full commercial launch. DNA assembly is priced on a cost-per-base model, and Leproust says her companys 10-cents-per-base starting price is already the best in the industry. But shes aiming for a 2-cent price point: Thats the point at which researchers can significantly scale experiments and will no longer be limited by the cost of DNA, she says. Today, customers typically order DNA strands of 300 to 1,800 bases in length, Leproust says.

Another synthetic-biology startup in the San Francisco area, Zymergen, offers customers a broader set of services. The company not only constructs DNA snippets on the cheap, it also inserts that DNA into microbes and monitors the outcome. Chief science officer Zach Serber explains that the results can inform the next round of DNA design, letting customers iterate quickly as they look for their ideal organism. You cast a wide net, Serber says, and when you find a variation that improves the microbes performance, then you double down.

Such setups have led to excited talk of a synthetic-biology industry based on organism fabs. But the promise of mass-produced DNA doesnt impress Rob Carlson, a biotech consultant and managing director of the BioEconomy Capital venture fund. I dont understand the business model, he says.

Carlson is skeptical that cheap DNA assembly will lead to a proliferation of startups with ideas for profitable microbes. So you can make and test a whole bunch more DNAbut thats not the hard part, he argues. Going from test tube to bench scale to commercial scale, thats 90 percent of cost. For a startup to build a business around a yeast that cranks out a pharmaceutical, for example, it must manage massive tanks full of microbes. Reducing the cost of the initial DNA manufacturing would only give the company pocket money, Carlson says: Hooray, they get to buy beer, or more pizza on Friday.

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DNA Manufacturing Enters the Age of Mass Production - IEEE Spectrum

The urgency to remember a dangerous experience requires the brain to make a series of potentially dangerous moves: Neurons and other brain cells snap open their DNA in numerous locations more than previously realized, according to a new study to provide quick access to genetic instructions for the mechanisms of memory storage.

The extent of these DNA double-strand breaks (DSBs) in multiple key brain regions is surprising and concerning, says study senior author Li-Huei Tsai, Picower Professor of Neuroscience at MIT and director of The Picower Institute for Learning and Memory, because while the breaks are routinely repaired, that process may become more flawed and fragile with age. Tsai's lab has shown that lingering DSBs are associated with neurodegeneration and cognitive decline and that repair mechanisms can falter.

"We wanted to understand exactly how widespread and extensive this natural activity is in the brain upon memory formation because that can give us insight into how genomic instability could undermine brain health down the road," says Tsai, who is also a professor in the Department of Brain and Cognitive Sciences and a leader of MIT's Aging Brain Initiative. "Clearly, memory formation is an urgent priority for healthy brain function, but these new results showing that several types of brain cells break their DNA in so many places to quickly express genes is still striking."

In 2015, Tsai's lab provided the first demonstration that neuronal activity caused DSBs and that they induced rapid gene expression. But those findings, mostly made in lab preparations of neurons, did not capture the full extent of the activity in the context of memory formation in a behaving animal, and did not investigate what happened in cells other than neurons.

In the new study published July 1 in PLOS ONE, lead author and former graduate student Ryan Stott and co-author and former research technician Oleg Kritsky sought to investigate the full landscape of DSB activity in learning and memory. To do so, they gave mice little electrical zaps to the feet when they entered a box, to condition a fear memory of that context. They then used several methods to assess DSBs and gene expression in the brains of the mice over the next half-hour, particularly among a variety of cell types in the prefrontal cortex and hippocampus, two regions essential for the formation and storage of conditioned fear memories. They also made measurements in the brains of mice that did not experience the foot shock to establish a baseline of activity for comparison.

The creation of a fear memory doubled the number of DSBs among neurons in the hippocampus and the prefrontal cortex, affecting more than 300 genes in each region. Among 206 affected genes common to both regions, the researchers then looked at what those genes do. Many were associated with the function of the connections neurons make with each other, called synapses. This makes sense because learning arises when neurons change their connections (a phenomenon called "synaptic plasticity") and memories are formed when groups of neurons connect together into ensembles called engrams.

"Many genes essential for neuronal function and memory formation, and significantly more of them than expected based on previous observations in cultured neurons are potentially hotspots of DSB formation," the authors wrote in the study.

In another analysis, the researchers confirmed through measurements of RNA that the increase in DSBs indeed correlated closely with increased transcription and expression of affected genes, including ones affecting synapse function, as quickly as 10-30 minutes after the foot shock exposure.

"Overall, we find transcriptional changes are more strongly associated with [DSBs] in the brain than anticipated," they wrote. "Previously we observed 20 gene-associated [DSB] loci following stimulation of cultured neurons, while in the hippocampus and prefrontal cortex we see more than 100-150 gene associated [DSB] loci that are transcriptionally induced."

In the analysis of gene expression, the neuroscientists looked at not only neurons but also non-neuronal brain cells, or glia, and found that they also showed changes in expression of hundreds of genes after fear conditioning. Glia called astrocytes are known to be involved in fear learning, for instance, and they showed significant DSB and gene expression changes after fear conditioning.

Among the most important functions of genes associated with fear conditioning-related DSBs in glia was the response to hormones. The researchers therefore looked to see which hormones might be particularly involved and discovered that it was glutocortocoids, which are secreted in response to stress. Sure enough, the study data showed that in glia, many of the DSBs that occurred following fear conditioning occurred at genomic sites related to glutocortocoid receptors. Further tests revealed that directly stimulating those hormone receptors could trigger the same DSBs that fear conditioning did and that blocking the receptors could prevent transcription of key genes after fear conditioning.

Tsai says the finding that glia are so deeply involved in establishing memories from fear conditioning is an important surprise of the new study.

"The ability of glia to mount a robust transcriptional response to glutocorticoids suggest that glia may have a much larger role to play in the response to stress and its impact on the brain during learning than previously appreciated," she and her co-authors wrote.

More research will have to be done to prove that the DSBs required for forming and storing fear memories are a threat to later brain health, but the new study only adds to evidence that it may be the case, the authors say.

"Overall we have identified sites of DSBs at genes important for neuronal and glial functions, suggesting that impaired DNA repair of these recurrent DNA breaks which are generated as part of brain activity could result in genomic instability that contribute to aging and disease in the brain," they wrote.

The National Institutes of Health, The Glenn Foundation for Medical Research, and the JPB Foundation provided funding for the research.

Reprinted with permission of MIT News. Read the original article.

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Making memories actually involves breaking our DNA, study shows - Big Think

His DNA did not match that from the hair on the glasses.

In 1998, a new sheriffs deputy took over the investigation into the killings and turned his attention to Mr. Perry, prompted in part by a woman who said she had heard Mr. Perry say that he was going to kill Harold Swain.

Mr. Perry was arrested in 2000. At his trial, prosecutors relied in part on the womans testimony, and also on statements that investigators said Mr. Perry had made during unrecorded interviews. According to his lawyers, the jury did not learn that the woman who had testified against him had received $12,000 in reward money.

Mr. Perry was convicted in 2003 of two counts of homicide, and prosecutors agreed not to request the death penalty if Mr. Perry gave up his right to appeal. He did, and was sentenced instead to two consecutive life terms.

The fact that they sought the death penalty on a case with incredibly weak evidence, and involving extensive misconduct, is an indictment on the death penalty, said Clare Gilbert, the executive director of the Georgia Innocence Project, which worked on the case for years. Thank God Dennis Perry wasnt executed before anybody found this out.

After Mr. Perrys conviction, the case continued to draw outside attention. It had been featured on the television show Unsolved Mysteries in 1988, and was highlighted on the program again in 2010. In 2018, the case was covered and investigated on the third season of Undisclosed, a podcast about wrongful convictions, and the law firm King & Spalding began representing Mr. Perry.

In 2020, the case was the subject of an award-winning investigation by The Atlanta Journal-Constitution. That article cast doubt on an alibi that had been used by Erik Sparre, another man who had been investigated in connection with the killings.

The reporting spurred the Georgia Innocence Project to get a hair sample from Mr. Sparres mother, to see whether it matched the DNA from the glasses closely enough to suggest that a relative of hers had been at the church on the night of the killings.

Originally posted here:
After Two Decades and a DNA Test, Charges Are Dropped in Georgia Killings - The New York Times

Who are you? Where are you from? How we identify ourselves is at the core of what it means to be human, and the chance to get easy, quick and affordable answers to these questions has prompted the genetic testing market to be worth almost a $1 billion a year.

The best DNA test kits give you detailed, personalised reports on what, exactly? Where your ancestors came from? Actually, no. They tell you where your DNA is from today, which can help you research your genetic ancestry and your ethnicity, but they certainly dont provide the quick-fix you might think. Heres how DNA tests work, their pros and cons, and how to choose the right one for you.

Deoxyribonucleic acid (DNA) is two long molecules that carry genetic instructions for cells to work and reproduce. DNA is in all living things. Its arranged in a double helix of two strands that wind around each other. Sections of those strands are called genes, which determine particular characteristics. DNA exists in the nucleus of every cell as chromosomes. There are 46 chromosomes in each cell, 23 from each parent.

However, exactly how DNA is inherited is random. People in the same family even twin brothers can inherit different segments of DNA from their parents. Cousins share some DNA and if you sign-up to a DNA testing companys cousin-matching service you can see your genetic matches pop-up. Get to third cousins and DNA is not much use. Go back several generations and you may share zero DNA with some of your ancestors.

DNA test kits collect your saliva or cheek swabs, which you then post to a laboratory, which extracts your DNA. Essentially, you spit in a tube or swab each cheek twice with a cotton swab. What you get back either in the mail or more likely online is information that appears to show where your ancestors came from. In short, a breakdown of your genetic ancestry; your ethnicity.

But DNA test kits dont tell you where your ancestors are from. Human history is the history of migration so trying to place your genetic ancestors in a geographic location is inherently problematic.

So how does the process work? Segments of your genome are cross-referenced with others in a database, loosely assigning different bits of your DNA to geographic locations. Companies tend to use reference samples of people that have four grandparents in that region, too, and similar DNA samples from a particular location are clustered. This helps produce a likely connection to a place over long time periods, but a lot of assumptions are made. Your results may not be unique.

Nevertheless, youll be sent information and visuals on the general populations and regions your DNA contains links to. For example, you might learn that youre 81% European, 9% Asian, but within that data you might be told that youre 41% English and 40% Welsh, for example. These are estimates based on the size of the companys databases, and the algorithms and statistical techniques they use.

You might also be told that youre related to specific other people that have also done a DNA test with that company, with cousin-matching the most common product.

Leading genetic companies in the industry include AncestryDNA, LivingDNA, Family Tree, MyHeritage and 23andMe. Once youve done one test and got the results back you can generally upload your raw DNA data to another testing company to take advantage of their databases and algorithms.

Thats because the results youre going to get will vary. Over time the various companies databases are getting bigger and therefore better, with data from new locations added, while the reference populations used for particular regions also get larger and more reliable. Algorithms, software and AI are also improving. This is why the results you get from a DNA test kit today are much more detailed than they were when they first became available a decade ago and theyll be better in the future.

Its also worth knowing that until recently DNA testing companies have best served people with European ancestry, simply because theyre been most popular in North America and Europe.

There are three different tests for genetic genealogy, each of which will reveal different data about your ancestry:

Autosomal (atDNA): this is by far the most common and most useful DNA test for ancestry and is often just called family finder or simply your ancestry. It can give anyone their ancestors up to about seven generations back and is useful for cousin-matching. Its therefore used by all DNA testing companies as the default offering.

Chromosome (yDNA): this test uses the Y-chromosome, which is only found in men and passed down the paternal line. The mutations in a mans yDNA can link him to a genetic population with whom he shares a common ancestor.

Mitochondrial (mtDNA): this one traces your maternal ancestors. It can be taken by anyone. The mutations in your mtDNA can link you to a genetic population with whom you share a common ancestor.

Many DNA testing kits offer genetic readouts on your ancestry as an entry-level product within a wider offering designed to help you investigate your individual family history. It also matches your DNA to new customers, so it can give you new information years after that initial cheek swab you did.

Here are the basic differences between the most popular services all of which offer autosomal testing as a default but head over to our best DNA test kits article for full details:

AncestryDNA: Uses a saliva test and has a database of 20 million the largest of all and gives access to 30 billion genealogy records for family tree research.

Living DNA: uses a cheek swab and has a database of one million. It claims to have data from across Africa so promises better results for African Americans and European Africans. It also specialises in British ancestry.

Family Tree DNA: uses a cheek swab and has a database of 1.4 million so its not the best for cousin-matching. For an additional fee, you can have your DNA cross-referenced with its yDNA and mtDNA databases, too.

MyHeritage DNA: uses a cheek swab and has a database of 4.5 million. It also offers access to 12 billion historical records and syncs everything with your family tree research.

23andMe: costs $99, uses a saliva test and has a database of 12 million the second-largest. Its thus good for cousin-matching, 23andMe also offers health results.

DNA test kits aren't a scam, but you need to know their limitations and realise that theyre actually a spin-off of much broader ambitions. For example, researchers are using anonymised DNA test results to create maps of human migration patterns, but also to develop personalized and population-based healthcare, partly by identifying people at risk from genetic conditions. For population-genetic modelling the growth of DNA test kits is great news.

However, what DNA test kits dont do is give simple, quick and 100% reliable information about where a specific individuals ancestors came from. So if youre researching your family tree, by all means get a DNA test kit and feed the results into your own research. But if youre only after a quick DNA-based sense of identity confirmation of your own unique heritage and ancestral roots DNA test kits are not going to give you enough accuracy for that.

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DNA test kits for ancestry: how they work and how to choose the right one for you - TechRadar

Changes in policy would help broaden work that DNA labs are doing to identify the remains of missing service members, said a Lawton native who has been involved in DNA identification projects across the globe for decades.

What DNA labs can do is being hindered by policy, said Ed Huffine, one of the leaders in DNA technology that is greatly speeding the identification of remains in locations ranging from the World Trade Center in the aftermath of 9-11, to mass grave sites in Bosnia.

The sites share a common thread: the use of nuclear DNA to identify remains, rather than the less specific and more costly mitochondrial DNA. But, the nuclear DNA testing in common use in other countries isnt in common use by the U.S. military because of policy, Huffine said, adding while the military is directed to provide the fullest possible accounting in remains, their own policies violate that. That must be changed.

Huffine said the two types of DNA mitochondrial and nuclear are important in identifying human remains because of their characteristics. When a dead person begins to decay, DNA begins to slowly fall apart. Mitochondrial DNA is more likely to be present after the nuclear DNA has decayed. But, because it is not unique to a person, it cannot stand alone in the identification process.

It needs other forms of identification to collaborate, he said, of things such as forensic evidence found with the body.

For example: human remains are found at the site of a plane crash in Vietnam and if you identify the type of plane and who was flying on it, that narrows down the identity of remains. Using nuclear DNA at the same crash site would allow you to compare it to the relatives of a missing person, providing an identity.

Huffine, who worked for the Armed Forces DNA Laboratory in the mid-1990s, said skeletal remains tested by that lab relied on mitochondrial DNA, the same technique still being used today.

Huffines views on DNA testing were shaped by the years he spent in Bosnia, beginning in 1999, to help identify the estimated 8,000 victims of 1995s Srebrenica massacre.

They had tens of thousands of missing and mitochondrial simply would not work, he said, of the number of unidentified remains and the relations of families of missing people. Mitochondrial would not be able to assist that much. And, mitochondrial takes far more time to get results and is far more expensive.

Instead, scientists there refined the process of obtaining nuclear DNA from skeletal remains, then began mass testing. At the same time, the group went through the country to retrieve DNA samples from living relatives. They created a data base and created a computer program to match living relatives with DNA found in remains. It was a powerful new tool: testers matched seven identifications over seven years with the old system, while they were able to do hundreds of matches a month with nuclear DNA.

That was the first example of large-scale, Huffine said, of a DNA technique used to identify thousands of remains. That has since become the template, except for the U.S. military, which still relies on mitochondrial DNA.

Huffine said its a realization that frustrates him and the families of missing service members. He said hes certain of the viability of nuclear DNA because he saw it work in Bosnia, and the testing he used there is primitive compared to what can be done today.

DNA technology is rapidly advancing. Military rules are not, he said, of the unwillingness to adopt a testing technique so successful, it is even accepted as court evidence. They (scientists) are handicapped.

Huffine cited a specific incident: the accidental bombing of a U.S. POW camp in Tokyo toward the end of World War II. Seventy prisoners died and today, about half the remains have been identified through mitochondrial testing that relies on matches to immediate relatives (parents, siblings, children). Nuclear DNA testing could use relatives of second or third degree to help identify the remain. Huffine said the system is set up for failure.

If you were to completely disregard that, do the system the rest of the world is using, you could identify these individuals very quickly, he said.

Finally identifying remains decades after a loved one has gone missing in war is crucial for families, Huffine said, adding closure comes from knowing the remains are family, and knowing what happened.

They have a greater peace, a greater understanding of the last few days a loved ones been through, he said.

And, thats why Huffine continues along with family organizations to push the U.S. military to adopt the nuclear DNA testing system.

Weve begun to see incremental changes, he said, of a bureaucracy that is sometimes difficult to move. One way to do it is more publicity, more getting the points out there, the points of the success of nuclear-led system that is identifying people. The needle can be moved.

Thats important when you realize 78,000 to 80,000 World War II service members still are listed as missing.

For Huffine, the process of identifying long-missing family members is important on multiple levels, built from personal experience and his early career.

His first DNA-related job was with the Federal Aviation Administration in its national site in Oklahoma City after he graduated from the University of Oklahoma. His four years there focused primarily on the remains from airplane crashes, explaining that testing a pilots DNA could help prove the cause of a crash (ensuring substance abuse was not a factor).

Then, he left the FAA to work with the Armed Forces lab in Washington, D.C. It was there he received a call from home that his father was missing.

He went out driving and never came home, Huffine said. They didnt find his body for a few days. It gave me, somewhat, a feeling for having a missing person in the family. That became imbedded in me, the impact of a missing soldier, the impact on the family. Oftentimes, Id go to their funeral services, just to see the impact on the families.

He also saw the weight DNA could have on the judicial system. He was part of the project that identified the remains of the victims of Argentinas Dirty War, when death squads killed thousands in the mid-1970s to early 1980s.

Because we knew who these people (victims) had been seen in the presence of, there were thousands of charges of crimes against humanity, he said. It shows power of DNA testing, finding the truth decades after it happened.

Giving the family news, their loved one is found and they are dead, is some of the worst news you can give a family. But, it does release them. You have a body and a site they can go to and remember, and go on with their lives.

Link:
Lawton native argues that military has to change DNA testing policy for service remains - The Lawton Constitution