Tags Posts tagged with "DNA"

DNA

By Elof Axel Carlson

Elof Axel Carlson

The first time I heard DNA enter popular culture was hearing a record played by my son Anders. I heard the refrain, “Hey hey, hey hey! It’s DNA that made me that way.” Anders told me it was from a song called “Sheer Heart Attack” by the rock band Queen (1977).  

Since then that idea has spread from teenage rock fans to the public sphere, and in its modified form, I hear “It’s in my DNA” when a person feels passionately about an idea. Metaphors are part of how we speak but they are not always scientifically accurate. Before the era of DNA (that began with the publishing of the double helix model of DNA in 1953 by James Watson and Francis Crick), a different set of metaphors were in use going back to antiquity. 

Intense belief or fixed behaviors have been attributed to the intestines (I feel it in my gut), to the heart (I offer my heart-felt thanks), to the skeletal system (I feel it to the marrow of my bones), to the blood (royalty are blue bloods and a psychopath’s behavior reflects bad blood) and to the nervous system (argumentative personalities are called “hot headed”). 

Sumerians studied the shape of animal guts and livers to predict the future (haruspicy). Until the Renaissance the brain was thought to be the place where blood is cooled (hence the hot-headed belief). Thoreau was described by one contemporary as sucking the marrow out of life; and blood was considered the vital fluid of life. In the Renaissance the first human blood transfusions were given to provide youthful vigor by old men who believed in rejuvenation.  

When people say, “It’s in my DNA” for a behavior, they are conveying a deeply held belief that it is part of their personality as far back as they can remember or that it is innate. But the evidence for innate human social behaviors is often lacking. There are single gene effects of the nervous system that are well documented such as Huntington’s disease, which leads to dementia and paralysis with an onset usually in middle age. 

There are also family histories of psychosis and learning difficulties. The fragile X syndrome is one such well-documented condition that leads to low intelligence. But human social traits have lots of inputs from parents, siblings, playmates, neighborhoods, regional culture, ethnicity and national identity.  

Children growing up in poverty have different expectations than children whose parents are well off and send them to elite schools. Each generation uses, as best as it can, what it knows. Our knowledge of many important aspects of life and behavior is incomplete. Hence, we keep modifying our interpretations of how life works.  

Much of what is called evolutionary psychology or genetic determinism will be modified or abandoned in years to come as we learn how our genes use memories and other acquired knowledge to shape our personalities. For many cellular processes we know the flow of information from DNA (genes) to cell organelles to cellular function to tissue formation and to organ formation.  

That detailed interpretation of human behavior is not possible now for social traits. I would love to say, “It’s in my DNA” to write these Life Line columns, but my conscience would remind me that it is based on Freudian “wish fulfillment” and not careful experimentation down to the molecular level.

Elof Axel Carlson is a distinguished teaching professor emeritus in the Department of Biochemistry and Cell Biology at Stony Brook University.

Students take samples from Nissequogue River to analyze. Photo by Sara-Megan Walsh

By Sara-Megan Walsh

Hundreds of students from Smithtown to Northport got wet and dirty as they looked at what lurks beneath the surface of the Nissequogue River.

More than 400 students from 11 schools participated in “A Day in the Life” of the Nissequogue River Oct. 6, performing hands-on citizens scientific research and exploring the waterway’s health and ecosystem. The event was coordinated by Brookhaven National Laboratory, Central Pine Barrens Commission, Suffolk County Water Authority and New York State Department of Environmental Conservation.

Northport High School students analyze soil taken from the bottom of Nissequogue River. Photo by Sara-Megan Walsh

“’A Day in the Life’ helps students develop an appreciation for and knowledge of Long Island’s ecosystems and collect useful scientific data,” program coordinator Melissa Parrott said. “It connects students to their natural world to become stewards of water quality and Long Island’s diverse ecosystems.”

More than 50 students from Northport High School chemically analyzed the water conditions, marked tidal flow, and tracked aquatic species found near the headwaters of the Nissequogue in Caleb Smith State Park Preserve in Smithtown. Teens were excited to find and record various species of tadpoles and fish found using seine net, a fishing net that hangs vertically and is weighted to drag along the riverbed.

“It’s an outdoor educational setting that puts forth a tangible opportunity for students to experience science firsthand,” David Storch, chairman of science and technology education at Northport High School, said. “Here they learn how to sample, how to classify, how to organize, and how to develop experimental procedures in an open, inquiry-based environment. It’s the best education we can hope for.”

Kimberly Collins, co-director of the science research program at Northport High School, taught students how to use Oreo cookies and honey to bait ants for Cold Spring Harbor Laboratory’s Barcode Long Island. The project invites students to capture invertebrates, learn how to extract the insects’ DNA then have it sequenced to document and map diversity of different species.

Children from Harbor Country Day School examine a water sample. Photo by Sara-Megan Walsh

Further down river, Harbor Country Day School students explored the riverbed at Landing Avenue Park in Smithtown. Science teacher Kevin Hughes said the day was one of discovery for his fourth- to eighth-grade students.

“It’s all about letting them see and experience the Nissequogue River,” Hughes said. “At first, they’ll be a little hesitant to get their hands dirty, but by the end you’ll see they are completely engrossed and rolling around in it.”

The middle schoolers worked with Eric Young, program director at Sweetbriar Nature Center in Smithtown, to analyze water samples. All the data collected will be used in the classroom to teach students about topics such as salinity and water pollution. Then, it will be sent to BNL as part of a citizens’ research project, measuring the river’s health and water ecosystems.

Smithtown East seniors Aaron Min and Shrey Thaker have participated in this annual scientific study of the Nissequogue River at Short Beach in Smithtown for last three years. Carrying cameras around their necks, they photographed and documented their classmates findings.

“We see a lot of changes from year to year, from different types of animals and critters we get to see, or wildlife and plants,” Thaker said. “It’s really interesting to see how it changes over time and see what stays consistent over time as well. It’s also exciting to see our peers really get into it.”

Maria Zeitlin, a science research and college chemistry teacher at Smithtown High School East, divided students into four groups to test water oxygenation levels, document aquatic life forms, measure air temperature and wind speed, and compile an extensive physical description of wildlife and plants in the area.

Smithtown High School East students take a water and soil sample at Short Beach. Photo by Sara-Megan Walsh

The collected data will be brought back to the classroom and compared against previous years.

In this way, Zeitlin said the hands-on study of Nissequogue River serves as a lesson in live data collection. Students must learn to repeat procedures multiple times and use various scientific instruments to support their findings.

“Troubleshooting data collection is vital as a scientist that they can take into any area,” she said. “Data has to be reliable. So when someone says there’s climate change, someone can’t turn around and say it’s not true.”

The Smithtown East teacher highlighted that while scientific research can be conducted anywhere, there’s a second life lesson she hopes that her students and all others will take away  from their studies of the Nissequogue River.

“This site is their backyard; they live here,” Zeitlin said. “Instead of just coming to the beach, from this point forward they will never see the beach the same again. It’s not just a recreational site, but its teeming with life and science.”

By Elof Axel Carlson

Elof Axel Carlson

Science is a way of interpreting the universe in the era in which we live. One of the realities of our lives is that we do not know how much of the world we think we know is really incomplete.

Think of it this way — If you grew up when the American Revolutionary War was being fought, you would not know a lot. You would not know your body is composed of cells. You would not know that heredity is transmitted by genes located on chromosomes present in nuclei of cells because no one knew there were nuclei, chromosomes or genes.

You would also not know there are biochemical pathways that carry out your metabolism in cell organelles because no one then knew there was such a thing as metabolism, biochemical pathways or cell organelles. And you would not know that infectious diseases are associated with bacterial and viral infections nor would you know that your body is regulated by hormones. If you created a time line of scientific findings in the life sciences, the cell theory was introduced in 1838. Cells were named in 1665, but Robert Hooke thought they accounted for the buoyancy of cork bark. He drew them as empty boxes.

When Schleiden and Schwann described cells, they were filled with fluid; and Schwann thought nuclei were crystallizing baby cells being formed in a cell. The cell doctrine (all cells arise from pre-existing cells) did not come until Remak and Virchow presented evidence for it. Mitosis, or cell division, was not worked out until the late 1870s; and meiosis of reproductive cells (sperm and eggs) was not worked out until the 1990s.

Fertilization involving one sperm and one egg was first seen in 1876, while most cell organelles were worked out for their functions and structure after the invention of the electron microscope in the 1930s. There was no organic chemistry before Wöhler synthesized molecules like urea in 1823, and biochemical pathways were not worked out until the 1940s.

DNA was not known to be the chemical composition of genes until 1944, the structure of DNA was worked out in 1953, molecular biology was not named until 1938 and the germ theory was worked out in the 1870s and 1880s by Pasteur and by Koch, who both demonstrated bacteria specific for infectious diseases. Embryology was worked out in 1759 by Wolff, while hormones were first named and found in 1903 by Bayliss and Starling.

What the history of the life sciences reveals is how dependent science is on new tools to investigate life. Microscopes up to 30 power came from Hooke’s efforts in 1665. A better microscope by Leeuwenhoek distinguished living organisms (“animalcules”) at up to 500 power.

It was not until the 1830s that microscopes were able to overcome optical aberrations and not until the 1860s that a stain technology developed to see the contents of cells. This boosted observation to 2000 power. For the mid-20th century, cell fractionation made use of centrifuges and chromatography to separate organelles from their cells and work out their functions.

Experimental biology began in England with Harvey’s study in 1628 of the pumping action of the heart. Harvey was educated in Padua, Italy, where experimental science had been stressed by Galileo and his students who began applying it to the motion of the body relating bones and muscles to their functions. No one alive in 1750 (or earlier) could have predicted DNA, oxidative phosphorylation, the production of oxygen by plants, Mendel’s laws of heredity or the role of insulin in diabetes.

But what about the present? How complete is our knowledge of life processes? Are there major findings in the centuries to come that will make our present understanding look as quaint as reading the scientific literature in the 1700s?

We can describe what we would like to know based on our knowledge of the present and likely to be achievable. We cannot predict what may turn out to be new functions or structures in cells. At best (using what we do know) we can hope to create a synthetic cell that will be indistinguishable from the living cell from which it was chemically constructed. But that assumes the 300 or so genes in a synthetic cell will account for all the activities of the vague cytoplasm in which metabolism takes place.

For the level of viruses there are no such barriers and the polio virus has been synthesized artificially in cell-free test tubes in 2002 (an accomplishment of Eckard Wimmer at Stony Brook University).

Within a few years ongoing studies of bacteria and of yeast cells with artificial chromosomes, may resolve that question for the genome of a eukaryotic cell. I hope that an artificial cytoplasm will be worked out in that effort. That might be more of a challenge than presently assumed.

A murder mystery thousands of years old and a continent away is coming to Long Island, where middle school and high school students can look at a rare face from human history.

During the ice age, an arrow went through a man’s shoulder blade, nicked an artery that leaves the aorta and caused him to bleed to death. Some time after he died, weather conditions effectively freeze dried him, preserving him in a remarkably pristine state until German hikers found his five-foot, five-inch body protruding from a melting glacier in 1991. He was found in the Ötztal Alps (on the border between Austria and Italy) — hence the name Ötzi.

David Micklos, executive director of the DNA Learning Center, stands next to the only authorized replica of Ötzi outside of the South Tyrol Museum in Italy. Photo by Daniel Dunaief
Dave Micklos, executive director of the DNA Learning Center, stands next to the only authorized replica of Ötzi outside of the South Tyrol Museum in Italy. Photo by Daniel Dunaief

While Ötzi, as he is now called, remains preserved carefully in a special facility in Italy, a master craftsman and artist has created a painstaking replica of a 45-year-old man killed at over 10,000 feet that is now on display at the DNA Learning Center at Cold Spring Harbor Laboratory.

“Kids are fascinated by it,” said Dave Micklos, the executive director of the DNA Learning Center, who has shared the newest mummified celebrity with students for several weeks in advance of the official exhibit opening in the middle of February. “The story is quite fascinating: it’s an ancient murder mystery. We take it from the forensic slant: what is the biological evidence we can see on Ötzi’s body that tells us who he was and how he died.”

Ötzi, or the Iceman as he is also known, has become the subject of extensive investigation by scientists around the world, who have explored everything from the over 60 tattoos on his body, to the copper axe found next to him, to the contents of his stomach and intestines, which have helped tell the story about the last day of Ötzi’s life.

“It’s a story that’s been assembled, bit by bit,” Micklos said. “Each scientific investigation adds new twists to the story.”

The Learning Center came up with the idea to create a replica and proposed it to the South Tyrol Museum of Archeology in Bolzano, Italy. Eventually, the museum granted the center the rights to use the CT scans, which provide detailed anatomical features. Ultimately, artist and paleo-sculptor Gary Staab used the images and studied the Iceman himself.

Staab, who has recreated copies of extinct animals for museums around the world, used a three-dimensional printer and sculpting and painting techniques to create an exact replica of a man who probably didn’t know he was in immediate danger when he was hit, because he seemed to be taking a break, Micklos said. Staab built one layer at a time of a resin-based prototype, then worked on the skin through sculpting, molding and painting.

A close-up of Ötzi the Iceman mummy’s replica at the DNA Learning Center. Photo by Daniel Dunaief
A close-up of Ötzi the Iceman mummy’s replica at the DNA Learning Center. Photo by Daniel Dunaief

Nova produced a television feature called “Nova’s Iceman Reborn” on PBS that captures the process of combining art and science to make a replica of the rare and highly valued fossil, which viewers can stream online through the link https://www.pbs.org/nova.

Long Islanders can see the replica at the Learning Center, where they can ask a host of questions about a man born during the copper age — hence the copper axe — and about 2,500 years before Rome was founded. Visitors interested in seeing Ötzi need to purchase tickets, which cost $10, ahead of time through the Learning Center’s website at www.dnalc.org.

Ötzi’s entire genetic sequence is available online. The Learning Center is the first science center worldwide to focus on DNA and genetics.

The center is especially interested in helping students understand what DNA says about human evolution. In one experiment, students can compare their own DNA to Ötzi, a Neanderthal and another ancient hominid group, called the Denisovans. Students can see how similar modern DNA is to Ötzi and how different it is from the Neanderthals and Denisovans. The 5,200 year differences with Ötzi is “no time in DNA time,” Micklos said.

Ötzi’s genes reveal that he had atherosclerosis and the deposition of plaques on the inner walls of the arteries. Ötzi was a healthy, active, relatively long-lived man in the Paleolithic era, who ate a diet of natural, unprocessed foods, and yet he had heart disease. His heart condition came as a surprise to scientists.

A 3-D resin model of Ötzi’s head before being painted. Photo by Daniel Dunaief
A 3-D resin model of Ötzi’s head before being painted. Photo by Daniel Dunaief

In addition to his genes, Ötzi’s body left clues about his life, where he’d spent his last day and what he’d eaten. Scientists have explored the contents of each part of his digestive tract, which, remarkably, remained well preserved during those thousands of years.

Ötzi had eaten different kinds of ibex meat, which is a goat found in the mountains. The pollen that was in his system, which came from the air he inhaled and from the food he ate, were pieces of a puzzle that showed where he’d been. The pollen near the top of his digestive track came from coniferous trees, including relatives of spruces and pines, which came from higher altitudes. Stored deeper in his system was pollen from deciduous trees, like birch and hazel, which grew lower in the valleys.

In addition to the Ötzi replica, the Learning Center also has reproductions of the clothes he was wearing and the artifacts he was carrying, which included a couple of containers of birch bark sewn together with fibers.

The Learning Center is developing a program to help students from the age of 10 to 18 explore Ötzi, so students can ask what the artifacts tell them about neolithic time.

Micklos said students have shown a strong interest in this old replica.

“It’s a little bit morbid, but not too much, and it’s a little gruesome, but not too much,” he said. “Everybody loves a mummy,” he continued, citing the popularity of the mummy exhibit at the Metropolitan Museum of Art.

Suffolk County police car. File photo

Police say they used DNA to find a burglar who broke into a house a few months ago and assaulted the homeowner who found him.

The burglary occurred on Oct. 3, when the suspect entered a Huntington Station home around 7:40 p.m., according to the Suffolk County Police Department. After the owner discovered the intruder, police said, there was a struggle and the burglar told the victim he had a handgun. The burglar fled the scene afterward.

Police said detectives from the 2nd Squad recovered DNA evidence that was linked to 59-year-old Scott Lundquist of Huntington Station.

Lundquist was arrested on Friday afternoon and charged with first-degree burglary, third-degree assault and resisting arrest.

The defendant was listed as representing himself on the state court system’s database and could not be reached for comment.

 

by -
0 1122

By Elof Carlson

Fossils are relatively rare because most of the animals and plants that have died in nature have been eaten or decomposed. Fossils are often found in sedimentary rocks, and those dead organisms were buried after drowning, caught by volcanic ash, buried in a mudslide or sucked down by quicksand or some other event less likely than falling on a field or in the underbrush of a forest, or left as scattered bones by hungry predators. Only in the past few ten thousand years have humans buried their dead, improving the chances that their remains will someday be unearthed and studied by paleontologists.

DNAUntil the last half of the twentieth century, the only way to use human fossils to work out a historical association was through comparative anatomy and a variety of chemical and physical tools to determine the age of the sediments in which they were unearthed. The idea of a paleogenetics arose in 1963, with the use of that term by Linus Pauling and his colleagues, who studied the amino acid sequences in hemoglobin molecules of numerous organisms, from sipunculoid worms to humans, that use hemoglobin to carry oxygen to body tissues.

In 1964, the first sequence of fragments of the DNA of an extinct quagga were worked out using the skin of an extinct specimen in a museum. The quagga was an animal that looked like a chimera of giraffe and a zebra.

Once DNA sequencing was worked out, especially by Fred Sanger and his colleagues, viruses, bacteria, single-celled organisms, and then more complex worms and flies were sequenced. By 2000, the human genome was being worked out. Svante Pääbo and his colleagues are leaders in the working out of fossil human DNA.

This is what has been found so far. Four contenders for species status lived about 40,000 years ago. Three populations of humans arose after an initial origin in Africa. Of these three, the Neandertals (Homo neanderthalis) left Africa earlier than our own Homo sapiens. The Neandertals were named for the Neander river valley where they found in Germany. We were named by Linnaeus as Man (Homo) the Thinker (sapiens).

Two additional populations were found, one in western Siberia and the other in Indonesia. The Siberian humans are called Denisovans (Homo denisova). They were named for the Denis cave in which they were found and they also had an exit from Africa. The Indonesian humans are called Homo floresiensis and are named for the island Flores in Indonesia where they were found. Where they came from is not yet known. They are unusual for their small size, a Hobbit-like three- and-a-half feet tall.

The DNAs of three forms of humanity have been sequenced. The complete sequence of DNA of an organism’s cell is called a genome. The Indonesian form went extinct about 12,000 years ago, but no DNA has been extracted from their remains. Neandertals and Denisovans went extinct about 40,000 years ago.

Analysis of the three available genomes shows that most Europeans have about 4 percent Neandertal DNA. Living people in Melanesia and Australian aborigines have about 4 percent H. denisova DNA. About 17 percent of Denisovan DNA is from Neandertals. The human branch Homo bifurcated and one branch split into H. neanderthalis and H. denisova. The other branch from Homo produced us, H. sapiens. We are 99.7 percent alike for H. sapiens and H. neanderthalis.

Since we have 3 billion nucleotides to our genome, there remain 9 million mutations between us, most of it in our junk DNA. There are, nevertheless, hundreds of gene differences between our two species. It also means that where these populations came into contact, fertile matings occurred, and remain in our DNA from our ancestral “kissing cousins.”

Elof Axel Carlson is a distinguished teaching professor emeritus in the Department of Biochemistry and Cell Biology at Stony Brook University.

New DNA-based marker technology to aid town residents in securing property

Above, a view of the technology, called DNANet. Photo from Applied DNA Sciences

A new public safety pilot program in Huntington Station puts crime-fighting in the hands of residents by providing them with innovative DNA-based technology to mark up property susceptible to burglary.

Last week, Suffolk County Legislator William “Doc” Spencer (D-Centerport) was joined by County Executive Steve Bellone (D) and other elected officials in Huntington Station, where a new device manufactured by Stony Brook-based Applied DNA Sciences was introduced as part of a pilot program in the town. The kit called DNANet comes with a special marker that can be used to mark up to 100 valuables and assets in a home in an effort to keep track of goods if stolen or removed from the home.

“When I was approached last year by the scientists at Applied DNA Sciences with this unique technology, it was clear that it has great potential to be an effective tool in keeping communities safer,” Spencer stated in a press release. “Increasing public safety in Huntington Station and all of Suffolk County has always been a central focus of mine. Bringing in this resource will make this great community even better.”

Suffolk County is paying for the pilot program, which will cost $25,000.

The kits will be distributed to 500 homes in Huntington Station in areas with high burglary rates. Residents will be asked to perform in the study, mark up items and register them with the company.

The mark is not visible to the naked eye. A UV lamp will be needed to see the distinctive mark.

“You can’t see it [and] you can’t scratch it off,“ Spencer said in a phone interview Monday.

When items are stolen, burglars tend to trade the goods to pawn shops for quick cash. The new device will also force shop owners to carefully record data when items are pawned.

“Now it will be harder to pawn stolen goods,” Spencer said.

Once an item with the DNA code is run through the website’s database, it will match to a particular person and address. In the past, reuniting goods with an owner has proved to be difficult because there is no proof of ownership, according to Spencer. The mark would help prove ownership, he said.

Spencer hopes this new initiative will help increase item recoveries, theft convictions and decrease low level petit theft.

“This technology is another tool our police can use against crime,” Suffolk County Executive Steve Bellone said in a press release. “Our police will be able to address and solve theft of personal property with the information made available by DNAweb.”

According to Spencer, studies show the DNA mark has proven to last up to 350 years. Also if the owner sells an item, a call can be made to have the item removed from the database to prevent confusion.

The program is expected to begin in Huntington Station and Huntington shortly as officials wanted to focus in areas with high crime. The program will be evaluated after six months to see if there has been an improvement in recoveries and convictions. Residents who participate in the program can also put signs on their lawns alerting people the system is in use.

Once the evaluation is over, the Suffolk County Police Department will decide whether to recommend the program expand.