Category Archives: DNA

Montgomery County police released this sketch of the man who is believed to have raped five women between June 2010 and September 2012. The sketch was drawn based on characteristics found in DNA evidence the rapist left behind. (Courtesy Montgomery County Police Department)

WASHINGTON DNA left behind by a rapist who attacked five women in Montgomery County, Maryland, has provided police with what could provide a breakthrough in the unsolved cases: a sketch depicting what the unidentified man might look like.

Investigators believe the same attacker broke into the homes of the women and raped them between June 2010 and Sept. 2, 2012. He raped one of the women twice six months apart.

Police collected DNA from three of the cases the samples matched, identifying a single attacker. Police believe the same man was responsible for the other attacks because in each case he broke into the homes or sneaked in through an open door or window. Most of the women were attacked after midnight. The women ranged in ages from 37 to 95; most lived in the Germantown area.

In one case, the attacker wore a distinctive red hat with embroidered white vines and leaves.

The forensic evidence has never matched other samples submitted to law enforcement databases and police dont know if the man is still in the area, said spokesman Officer Rick Goodale.

A process called phenotyping, which determines physical characteristics based on DNA, found that the attacker was primarily of Western African descent. He likely had brown to dark brown skin and brown or hazel eyes. His hair was black and he likely had no freckles. The process can also suggest the shape of the mans face but cannot not depict height, weight or age.

Investigators hope that someone in the community might recognize the man in the sketch.

It might be the final piece of the puzzle that detectives need to solve this case, Goodale said.

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Police release sketch of Montgomery Co. rapist drawn from DNA evidence - WTOP

Pennsylvania lawmakers moved closer this week to mandating that DNA samples be collected from people who have been convicted of crimes, something supporters predict will help solve serious crimes.

The state House voted 157-32 for a bill that would require cheek swabs from those convicted of any first-degree misdemeanor and a list of 15 second-degree misdemeanors. Current law requires testing for those convicted of felonies and certain other offenses. Pennsylvania classifies as first-degree misdemeanors many crimes that are felonies in other states.

It was sent to the state Senate, where a nearly identical proposal is pending. A Senate Republican aide said Friday one of the bills could get a final vote before lawmakers adjourn for the summer.

"Not only will some crimes be solved, serial offenders would be stopped before they could reoffend, and innocent people would be ruled out of suspicion in cases where their DNA does not match what's found at the scene," said Tom Dymek, an aide to House Judiciary Chairman Ron Marsico, R-Dauphin, the bill's prime sponsor.

Gov. Tom Wolf, a Democrat, opposes the bill in its current form, saying it would test for too many minor offenses, and its costs are not funded. A fiscal note for the House bill estimated the additional testing would eventually cost more than $3 million annually, based on an estimate of 40,000 offenders.

"Gov. Wolf believes we should expand DNA collection to combat violent crime," said his press secretary, J.J. Abbott. "However, this bill expands the law to include more than 100 misdemeanors, including many offenses that are non-violent in nature such as retail theft and littering."

The Senate will likely consider amending the proposal to remove a few of the less serious misdemeanors, said Mike Stoll, chief of staff to Sen. Tom Killion, R-Delaware, sponsor of the Senate bill .

"The list can't be reduced that much, or you defeat the purpose of it," Stoll said.

Previous efforts in recent years to expand DNA sampling in Pennsylvania have failed, partly because of opposition to collecting the genetic material upon arrest. The current proposal is limited to those who have been convicted. The House bill also would not authorize testing of prisoners already in jail, only the newly convicted.

Marsico "just wanted to make sure that the due process and the civil liberties rights of people, he thought they were best preserved by doing it post-conviction, where there's been a finding of guilt," Dymek said.

The expanded testing would go into effect in December 2019, which means the financial impact won't be felt by the state police and local crime labs for more than two years.

"This is a proven way of solving crimes and protecting victims," said Greg Rowe, legislative director for the state association of district attorneys. "When it comes to protecting victims, and when it comes to apprehending violent criminals, there's no price tag."

A spokeswoman for the state chapter of the American Civil Liberties Union said the organization was opposed, calling the expanded list of offenses excessive.

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Pennsylvania Legislature eyes wider DNA sampling of convicts - Newsworks.org

DNA is all the same chemical

The stringy stuff in the test tube is DNA. But you can't tell which one of these organisms it came from just by looking at it. That's because DNA looks exactly the same in every organism on Earth.

All living things have DNA. And whether it comes from you, a pea plant, or your pet rat, it's all the same molecule. It's the order of the letters in the code that makes each organism different.

The order of building blocks in a strand of DNA makes up a "sequence." We can read a DNA sequence like letters in a book. In fact, we know the sequence of the entire human genomeall 3 billion letters. That's enough information to fill roughly 1,000 200-page books!

Contained within the 3 billion letters of the human genome are about 21,000 genes. Most of our known genes code for proteins, but some code for RNA molecules.

All humans have the same genes arranged in the same order. And more than 99.9% of our DNA sequence is the same. But the few differences between us (all 1.4 million of them!) are enough to make each one of us unique. On average, a human gene will have 1-3 bases that differ from person to person. These differences can change the shape and function of a protein, or they can change how much protein is made, when it's made, or where it's made.

APA format:

Genetic Science Learning Center. (2016, March 1) What are DNA and Genes?. Retrieved June 22, 2017, from http://learn.genetics.utah.edu/content/basics/dna

CSE format:

What are DNA and Genes? [Internet]. Salt Lake City (UT): Genetic Science Learning Center; 2016 [cited 2017 Jun 22] Available from http://learn.genetics.utah.edu/content/basics/dna

Chicago format:

Genetic Science Learning Center. "What are DNA and Genes?." Learn.Genetics.March 1, 2016. Accessed June 22, 2017. http://learn.genetics.utah.edu/content/basics/dna.

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What are DNA and Genes?

The structure of DNA and RNA. DNA is a double helix, while RNA is a single helix. Both have sets of nucleotides that contain genetic information.

Deoxyribonucleic acid or DNA is a molecule that contains the instructions an organism needs to develop, live and reproduce. These instructions are found inside every cell, and are passed down from parents to their children.

DNA is made up of molecules called nucleotides. Each nucleotide contains a phosphate group, a sugar group and a nitrogen base. The four types of nitrogen bases are adenine (A), thymine (T), guanine (G) and cytosine (C). The order of these bases is what determines DNA's instructions, or genetic code. Similar to the way the order of letters in the alphabet can be used to form a word, the order of nitrogen bases in a DNA sequence forms genes, which in the language of the cell, tells cells how to make proteins. Another type of nucleic acid, ribonucleic acid, or RNA, translates genetic information from DNA into proteins.

The entire human genome contains about3 billion bases and about 20,000 genes.

Nucleotides are attached together to form two long strands that spiral to create a structure called a double helix. If you think of the double helix structure as a ladder, the phosphate and sugar molecules would be the sides, while the bases would be the rungs. The bases on one strand pair with the bases on another strand: adenine pairs with thymine, and guanine pairs with cytosine.

DNA molecules are long so long, in fact, that they can't fit into cells without the right packaging. To fit inside cells, DNA is coiled tightly to form structures we call chromosomes. Each chromosome contains a single DNA molecule. Humans have 23 pairs of chromosomes, which are found inside the cell's nucleus.

DNA was first observed by a German biochemist named Frederich Miescher in 1869. But for many years, researchers did not realize the importance of this molecule. It was not until 1953 that James Watson, Francis Crick, Maurice Wilkins and Rosalind Franklin figured out the structure of DNA a double helix which they realized could carry biological information. Watson, Crick and Wilkins were awarded the Nobel Prize in Medicine in 1962 "for their discoveries concerning the molecular structure of nucleic acids and its significance for information transfer in living material." [Related: Unraveling the Human Genome: 6 Molecular Milestones]

DNA sequencing is technology that allows researchers to determine the order of bases in a DNA sequence. The technology can be used to determine the order of bases in genes, chromosomes, or an entire genome. In 2000, researchers completed the first full sequence of the human genome.

Your DNA contains information about your heritage, and can sometimes reveal whether you're at risk for certain diseases. DNA tests, or genetic tests, are used for a variety of reasons, including to diagnose genetic disorders, to determine whether a person is a carrier of a genetic mutation that they could pass on to their children, and to examine whether a person is at risk for a genetic disease. For instance, mutations in the BRCA1 and BRCA2 genes are known to increase the risk of breast and ovarian cancer, and analysis of these genes in a genetic test can reveal whether a person has these mutations.

Genetic test results can have implications for a person's health, and the tests are often provided along with genetic counseling to help individuals understand the results and consequences of the test.

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DNA: Definition, Structure & Discovery | What Is DNA?

June 23, 2017 The jellyfish glow helped focus laser beams on proteins. Credit: University of York

Scientists at the University of York have used florescent proteins from jellyfish to help shed new light on how DNA replicates.

Using these proteins, originally found in jellyfish to make them glow, the team where able to focus laser beams on the brightly lit proteins and track them inside a bacteria that normally lives inside the human gut.

This allowed scientists to watch the molecular machinery of DNA as it replicated inside a cell one molecule at a time. It revealed for the first time that only one component of this process, called DnaB helicase, remains stable - like a molecular anchor to the process.

In most cells, whether human or bacterial, a new cell is created after an existing cell divides in two. This means that a copy of the original sequence of genes coded in its DNA must be precisely copied and placed into the new cell.

This is thought to be a process that occurs slowly and methodically at set points in time. New research at the University of York, in collaboration with the University of Oxford and McGill University Canada, however, has now tracked this replication process in real-time and shown that it is far more dynamic than the textbooks suggest, occurring instead through a 'stuttering-like process' in short bursts.

Pioneering

Professor Mark Leake, Chair of Biological Physics at the University of York, said: "We pioneered a new method of light microscopy which allowed us to see this fascinating replication process occur molecule-by-molecule.

"We were surprised to find, however, that rather than the organised and methodical way that we expected this process to unfold, it instead happened in a 'stuttering' action, much like driving too slowly in high gear of a car. The big question, of course, was why the cell performs an essential process in such an unstable way?

"The stuttering action provide 'checkpoints' at various stages of the DNA copying process to make sure there is no errors made and, if there is, correct them before it is too late. This means that the cells can pause to fix an error in a small fragment of the DNA rather than attempt an unmanageable correction in one complete and huge strand of it.

"Although the process looks inelegant and almost random, it is actually highly efficient."

Human health

The process of DNA replication is fundamental to all life and the way errors in the process are resolved is especially important to human health. Errors can give rise to forms of cancer and become more prevalent in an ageing population.

This work will help scientists not only understand more fully the basic building blocks of life but potentially also provides new insights into a range of health conditions as well as even shedding new light on how human ageing can give rise to diseases associated with errors in copying the DNA from cell to cell.

Research was conducted using the DNA of Escherichia coli cell, bacteria, but However, the next stage of this research will investigate the same process in more complex cells, ultimately including those from humans.

The research, 'Frequent exchange of DNA polymerase during bacterial chromosome replication', was supported by the BBSRC and is published in the journal,eLife.

Explore further: Excessive DNA replication and its potential use against cancer

More information: Thomas R Beattie et al. Frequent exchange of the DNA polymerase during bacterial chromosome replication, eLife (2017). DOI: 10.7554/eLife.21763

Journal reference: eLife

Provided by: University of York

DNA over-replication is a phenomenon that can have devastating consequences for proliferating cells. When parts of the genome are duplicated more than once, cells suffer from 'genomic instability' (alterations to the structure, ...

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Fresh insights into the structures that contain our genetic material could explain how the body's cells stay healthy.

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Sometimes, when a science experiment doesn't work out, unexpected opportunities open up.

Scientists at the University of York have used florescent proteins from jellyfish to help shed new light on how DNA replicates.

It's one of the tiniest organisms on Earth, but also one of the most abundant. And now, the microscopic marine bacteria called Prochlorococcus can add one more superlative to its list of attributes: It evolves new kinds of ...

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Jellyfish fluorescence shines new light on DNA copying - Phys.Org

June 23, 2017 by Bennett Mcintosh A depiction of the double helical structure of DNA. Its four coding units (A, T, C, G) are color-coded in pink, orange, purple and yellow. Credit: NHGRI

A host of proteins and other molecules sit on the strands of our DNA, controlling which genes are read out and used by cells and which remain silent. This aggregation of genetic material and controlling molecules, called chromatin, makes up the chromosomes in our cell nuclei; its control over which genes are expressed or not is what determines the difference between a skin cell and a neuron, and often between a healthy cell and a cancerous one.

Parts of the genome are only loosely coiled in the nucleus, allowing cells to access the genes inside, but large sections are compacted very densely, preventing the genes form being read until their region of the genome is unfolded again. These compacted regions, known as heterochromatin, are formed by a protein known as HP1 and similar proteins, but exactly how HP1 segregates this off-limits DNA from the rest of the nucleus has been largely a mystery, until now.

In a new study by UC San Francisco researchers published in the journal Nature on June 22, 2017, what looked at first like a failed experiment instead revealed the intriguing possibility that HP1 binds to stretches of DNA and pulls it into droplets that shield the genetic material inside from the molecular machinery of the nucleus that reads and translates the genome.

"This provides a very simple explanation for how cells prevent access to genes," said Geeta Narlikar, PhD, professor of biochemistry and biophysics and senior author of the study.

'Bad News' Led to New Discovery

Narlikar's graduate student Adam Larson was trying to purify HP1, and noticed that the liquid in his samples was growing cloudy. For protein scientists, this is typically bad news, said Narlikar: it suggests that proteins that should dissolve in water are instead clumping together into a useless mass.

But Larson thought the clumps might actually be useful. After all, previous work had shown that the role of HP1 is to sequester long strands of DNA into very small volumes. What if this was exactly the sort of clumping he was seeing in the tube?

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Larson took his samples to the lab across the hall from Narlikar's, where Roger Cooke, PhD, professor emeritus of biochemistry and biophysics, helped him examine under the microscope what could have been just a tangled molecular mess. Instead, Larson and Cooke saw clouds of delicate droplets floating around in the water, like a freshly shaken mix of oil and vinegar.

HP1 had a reputation as a difficult protein to work with get any solution too concentrated, and the protein would clump out. But if the protein was supposed to clump, said Narlikar, "a lot of things we couldn't explain started to make sense."

Narlikar speculates that other scientists may have seen the same cloudiness before, but thinking it was simply a ruined sample, never pursued it like Larson did. "It demonstrates the power of curiosity-driven research," she said.

Rapidly Compacting DNA

To see how and why the HP1 formed droplets, the team produced different mutant versions of the protein, watching which separated out. By watching which parts of the protein were important for forming droplets, and using X-rays to monitor changes in the protein's shape, the team found that the protein nearly doubles in length when small phosphate residues are added in cetain locations. "The molecule literally opens up," said Narlikar. "I was surprised at the size of the change."

This opening-up exposes electrically charged regions of the protein, which stick together, turning dissolved pairs of proteins into long chains that clump together into droplets. Just as balsamic vinegar's dark and flavorful molecules don't seep into the oil of a salad dressing without some extra effort by the chef, the molecules for reading DNA don't seep into the HP1 droplets.

The fact that such a drastic change in shape comes from such a small modification may allow the cell to tightly regulate where and when HP1 silences genes, said Narlikar. The changes come quickly and robustly too using a technology employed by Sy Redding, PhD a Sandler Fellow, the team created a "curtain" of DNA molecules pulled straight by fluid flowing around them, then added HP1 and watched the protein compress the DNA into tiny droplets, folding it up against the flow.

"People have been seeing for over a hundred years that you get these dense regions of DNA in the nucleus," said Madeline Keenen, the Ph.D. student who ran the curtain experiment. "Now we're seeing the actual mechanism."

Explore further: Researchers find new mechanism for genome regulation

More information: Adam G. Larson et al. Liquid droplet formation by HP1 suggests a role for phase separation in heterochromatin, Nature (2017). DOI: 10.1038/nature22822

The same mechanisms that quickly separate mixtures of oil and water are at play when controlling the organization in an unusual part of our DNA called heterochromatin, according to a new study by researchers at the Department ...

Inside the cell, DNA is tightly coiled and packed with several proteins into a structure called "chromatin", which allows DNA to fit in the cell while also preventing genes from being expressed at the wrong time. Guided by ...

The textbook description of chromatin, the condensed form DNA takes when it is not in use, consists of rigid building-blocks called nucleosomes, which act as spindles on which inactive DNA can be spooled and archived. But ...

Scientists at The Scripps Research Institute (TSRI) have solved a cellular mystery that may have important implications for fundamental biology and diseases like ALS. Their new research suggests that RNA may be the secret ...

Dartmouth researchers have found that some proteins turn into liquid droplets on the way to becoming toxic solids implicated in neurodegenerative diseases and other genetic disorders.

Led by professor Ludo Van Den Bosch (VIB-KU Leuven), scientists from Belgium, the UK and the US have identified new processes that form protein "clumps" that are characteristic of amyotrophic lateral sclerosis (ALS) and frontotemporal ...

Humans belong to a select club of species that enjoy crisp color vision in daylight, thanks to a small spot in the center of the retina at the back of the eye. Other club members include monkeys and apes, various fish and ...

Toxins produced by three different species of fungus growing indoors on wallpaper may become aerosolized, and easily inhaled. The findings, which likely have implications for "sick building syndrome," were published in Applied ...

Marine seismic surveys used in petroleum exploration could cause a two to three-fold increase in mortality of adult and larval zooplankton, new research published in leading science journal Nature Ecology and Evolution has ...

Sometimes, when a science experiment doesn't work out, unexpected opportunities open up.

Scientists at the University of York have used florescent proteins from jellyfish to help shed new light on how DNA replicates.

It's one of the tiniest organisms on Earth, but also one of the most abundant. And now, the microscopic marine bacteria called Prochlorococcus can add one more superlative to its list of attributes: It evolves new kinds of ...

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From strands to dropletsnew insights into DNA control - Phys.Org

James Opelton Bradley is charged with first-degree murder in the presumed death of his missing coworker, Shannon Rippy Van Newkirk, who vanished April 5, 2014.

WILMINGTON -- DNA, computer searches and letters written from jail by the defendant were presented to the jury in the ninth day of testimony Friday in the murder trial of James Opelton Bradley.

Bradley, 54, of Wilmington is charged with first-degree murder in the presumed death of his missing coworker Shannon Rippy Van Newkirk, 53, of Wilmington, who vanished April 5, 2014.

Investigators testified Bradley told police three different stories in the days after Van Newkirk went missing -- initially denying he saw her on the day she was last seen and then ultimately saying he'd picked her up from her house that day. When a discussion they were having became "heated," she ran from his truck near Greenfield Lake, investigators said Bradley told them.

Three weeks later, when police searched land in Hampstead owned by Bradleys employer, they unearthed the body of Elisha Tucker, 33, another missing Wilmington woman whod last been seen in August 2013. Despite the fact that Van Newkirks body was never been found, Bradley is being tried in her presumed death.

A trial in Tuckers killing has yet to be set, but prosecutors said they will seek the death penalty in that case. Bradley has a previous murder conviction for killing his 8-year-old stepdaughter in 1988. The jury learned of that prior conviction after the prosecution successfully argued it be admissible.

On Friday, Sharon Hinton, a DNA analyst with the N.C. State Crime Laboratory, told the jury that she was unable to locate Van Newkirks DNA on any of the items she tested from Bradleys apartment or vehicle.

But, Hinton said, she was able to extract a full DNA profile for Elisha Tucker from at least one stain from the carpet padding in Bradleys Chevy Tahoe. The probability of it being anyone else's DNA other than Tucker's was 1 in 359 trillion, she said. That stain, however, did not test positive for blood.

FBI computer examiner Rich Novelli testified that on April 20, 2014 -- four days after his last interview with police -- Bradley searched online for information on cellphone pinging and visited a webpage that explained how cellphones are tracked. Novelli said Bradley also searched for the StarNews.

Additionally, Jurors each read a copy of two letters. One was addressed to a relative's daughter and the other was to a friend. The contents of the letters were not discussed before court took an early recess.

Testimony in the case resumes Monday.

Reporter F.T. Norton can be reached at 910-343-2070 or Fran.Norton@StarNewsOnline.com.

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Dead Wilmington woman's DNA found in Bradley's truck - News ... - StarNewsOnline.com

A Lincoln judge has given the OK for the Nebraska Department of Correctional Services to use reasonable force to collect DNA from an inmate refusing to give it voluntarily.

It was the fifth time the state prison system had sought permission to use force to get DNA samples from the 78 inmates who still hadn't provided it to prison staff as of February.

The other motions were in Omaha cases. One since has led to new charges against Brandon Weathers in connection to serial rapes of four women in 2002 and 2004.

DNA can be an important tool used to solve crimes or lead to suspects.

The Nebraska Attorney General's office recently asked a Lincoln judge for an order to allow a Phoenix police officer to get an additional DNA sample from an inmate at the Nebraska State Penitentiary.

After the inmate went to prison in September for a sex assault in Douglas County, his DNA sample was collected.

In December, the Nebraska State Patrol Crime Laboratory matched his DNA, which was uploaded into the Combined DNA Index System, to DNA on a toothbrush taken from a Phoenix home in 2010 by investigators looking into the homicide of a man who had been shot dead in a car outside, according to court records.

State law says a person who had been convicted of a felony or other specified offense as of July 15, 2010, who did not have a sample in the state DNA Sample Bank, was required to have one collected at his or her own expense. The law also applied to people already serving a sentence.

Still, some inmates refused to comply.

In the Lincoln case, Assistant Nebraska Attorney General Kale Burdick said prison employees notified Reuben J. Reyes of his obligation to provide his DNA in April 2013, about two months after he went to prison, and again this May.

Reyes refused, Burdick said in the motion filed June 14.

The same day, Lancaster County District Judge Lori Maret authorized the use of force to get it from the man serving a 20- to 25-year sentence for attempted first-degree assault and use of a firearm to commit a felony for pointing a .380 handgun at his cousin and firing once into the air, then twice more in his cousin's direction, in 2012.

Lincoln police said one of the rounds hit an apartment building. Another hit a car.

Reyes later pleaded no contest.

By Monday, state prisons spokeswoman Dawn-Renee Smith said the number of inmates who hadn't provided DNA was down to six.

She said she couldn't provide a list of the inmates' names because the information is related to their conduct in prison and protected by state statute.

Earlier this month, Corrections Director Scott Frakes said he is committed to collecting DNA samples from every incarcerated person to be in full compliance with state statute.

By policy, inmates who have not provided a DNA sample are ordered to submit it monthly and get written up for each refusal. Misconduct reports that result are referred to the institutional disciplinary committee.

Repeated refusals can lead to up to 90 days of lost good time.

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Use of force may be applied to collect DNA samples from inmates ... - Beatrice Daily Sun

One of the DNA nanomachines and the shapes it can switch between.

Song et al.

DNA-based computers are one step closer to full realisation following the creation of simple DNA machines that can switch between two shapes with only a single trigger.

The switching ability, which is fully reversible, means that information is being relayed at a molecular level transferred between DNA structural units in a manner than is both self-sustaining and controllable.

Lead researcher Yonggang Ke of the Wallace H. Coulter Department of Biomedical Engineering at Georgia Tech, US, says the micromachines can be used to either relay specific pieces of information through a DNA-constructed system, or to amplify a signal emanating from another part of it.

In the field of DNA-based computing, the DNA contains the information, but the molecules are floating around in solution, Ke says.

Whats new here is that we are linking the parts together in a physical machine.

Ke and colleagues constructed two different nanomachines, each comprising a number of artificial DNA double helixes stacked on each other, in two orientations, providing strength and stability.

The completed design looks rather like an accordion, or a foldable trellis.

One extra strand at the edge of each machine is attached, and functions as a trigger. When activated it compels the first DNA strand of the machine array to contract (or expand, depending on its initial state). This in turn transfers energy to the next strand, causing it to move in the same way, and so on, a little like dominoes falling.

The machines, fully built, are just a few hundred nanometres long slightly smaller than an influenza virus. To see them, Ke and colleagues used a powerful imaging technique known as atomic force microscopy.

Constructing machines on a nanometric scale would seem to require some impossibly fine hand-eye coordination on the part of the molecular engineers, but the compulsion of DNAs chemical structures to automatically bond means that, in solution, they seek out the complimentary strands of their neighbours, making construction a guided, rather than mechanical, process.

Although the machines built by Ke and his colleagues are very simple, they provide a powerful pathway towards construction of more complex structures. In research published in the journal Science, the team include blueprints for rectangles, cubes and tubes built by the same process.

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DNA nanomachines can transmit information - Cosmos

Doctors at Zuckerberg San Francisco General Hospital could not figure out what was wrong with the 29-year-old man sitting before them. An otherwise healthy construction worker from Nicaragua, the patient was suffering from a splitting headache, double vision and ringing in his ears. Part of his face was also numb. The cause could have been anythingfrom an infection to a stroke, a tumor or some kind of autoimmune disease. The Emergency Department (ED) staff took a magnetic resonance imaging scan of the mans brain, performed a spinal tap and completed a series of other tests that did not turn up any obvious reason for the swelling in his braina condition that is formally known as encephalitis.

Most likely, it was some kind of infection. But what kind? Nineteen standard tests are available to help clinicians try to pin down the source of encephalitis, but they test for the presence of only the most common infections; more than 60 percent of cases go unsolved each year. Physicians looked in the patients cerebrospinal fluid (which surrounds the brain and protects it) for evidence of Lyme disease, syphilis and valley fever, among other things. Nothing matched. So the S.F. General ED staff settled on the most likely culprit as a diagnosis: a form of tuberculosis (TB) that causes brain inflammation but cannot always be detected with typical tests. Doctors gave the man a prescription for some steroids to reduce the swelling plus some anti-TB drugs and sent him home.

Soon he was back, however, with the same symptoms. This time the physicians assumed the man, whose life was chaotic, had not been taking his drugs properly. (Even people with regular jobs and schedules often find taking TB medications fairly difficult.) The ED staff sent him away with another prescription but he returned again and againeven after he could prove that he was taking his medication correctly and on time. The drugs helped briefly after each visit, but the symptoms always returned. During that year his medical bills reached $580,000. Finally, S.F. General turned to an experimental test that is designed to uncover the source of virtually any neurological infection.

The test is the brainchild of researchers at the nearby University of California, San Francisco, led by neurologist Michael Wilson, biochemist Joseph DeRisi and infectious disease expert Charles Chiu. The group uses genetic-sequencing technology to identify mystery illnesses in people with encephalitis or meningitis (inflammation of the meninges, the membranes around the brain and spinal cord). This so-called metagenomic test analyzes all the DNA and RNA found in a sample of cerebrospinal fluid (meta means beyond in Greek). So any DNA or RNA that does not belong to the patientincluding that from viruses, bacteria, parasites or fungishows up in the results.

Done correctly, metagenomic testing could radically change the way infections of the brain are diagnosed. An element of circular logic underlies most standard infectious disease tests. Doctors order individual tests for each bug they suspect might be causing the problem. But how do they know what is causing the problem if they have not yet done the test? Metagenomic sequencing, in contrast, casts the broadest possible net, which allows it to pick up unexpected or previously unknown pathogens. Were looking at everything at once, which has the potential of replacing the myriad of lab tests with a single test, Chiu says.

The U.C. San Francisco team ran a sample of the mans cerebrospinal fluid through their investigative diagnostic procedure. Thats when we found the worm, Wilson says. Genetic sequencing and analysis revealed DNA from the kind of tapeworm found in pigs. The patient did not get better on TB drugs because he did not have TBhe had tapeworms living in his brain.

In Nicaragua and other developing countries tapeworm infections are common, and the larvae can migrate into the braina condition called neurocysticercosis. Usually the infection causes seizures as well as large brain cysts that are obvious on an MRI. This man had neither, however, which had led the medical staff to dismiss neurocysticercosis as a possibility. When this guy first presented, they absolutely thought of it, Wilson says. But when they scanned him in his brain and spinal cord, there were no cysts. He would improve briefly, because the steroids they gave him temporarily reduced the swelling in his brain, but the TB drugs were useless, so he would soon relapse again. Now that they knew the cause, the team started him right away on anti-worm drugs, which cannot eliminate the infection but will keep it under control. Its very treatable, Wilson says. Hes doing great.

The construction worker is one of nearly 300 patients who has participated since June 2016 in a metagenomic sequencing study based at U.C. San Francisco. Participants consist of anyone who has been admitted to one of eight medical centers, mostly in California, with an apparent neurological infection and no clear diagnosis. Metagenomic sequencing is done alongside traditional testing, for a head-to-head comparison.

Wilson and colleagues hope to prove their test, which will be more widely available this summer for about $2,400, can be an efficient and reliable solution for the sorts of medical mysteries that befuddle doctors, aggravate patients and can run up huge medical bills. The challenge is in making sense of the output, Chiu says. Sequencing does not produce a yes or no answer. The group developed a standard set of procedures to make it easy for an infectious disease doctor to pinpoint what the most likely bug might be.

On July 1 the U.C. San Francisco group will begin offering this test as a custom-ordered service to a broader group of people so that hospitals and labs in the U.S., and eventually anywhere in the world, can send cerebrospinal fluid for analysis. They plan to eventually expand their metagenomic testing to include pneumonia (infection of the lungs) and sepsis (infection of the bloodstream)two other ailments that often cause diagnostic dilemmas.

A similar metagenomic test for pneumonia, developed by researchers at the University of Utah, Arup Laboratories and start-up IDbyDNA, is also expected to debut this summer. In both cases the teams first do extensive work to make it easier for physicians to understand the complex and ambiguous genomic information garnered by the test.

These two tests will be the first commercially available metagenomic tests for infection in the U.S., but they are part of a growing trend. Two academic groups in Europe recently introduced tests for sepsis. And researchers at computational geneticist Pardis Sabetis lab at Harvard University are currently running a study on a similar test for encephalitis, says Anne Piantadosi, an infectious disease physician at Massachusetts General Hospital and a postdoctoral research fellow with the Sabeti group. She envisions a time in the next few years when future clinicians will be able to look back say, That was a really big improvement in how we diagnose infections.

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Brain-Invading Tapeworm That Eluded Doctors Spotted by New DNA Test - Scientific American