MRI, brain differences, and autism

MRI: Sagittal view of the brain. Photo courtesy of Wikipedia commons.

You may have read the news reports blaring the finding of an “autism test” that could lead to early and definitive diagnosis of autism. The new evaluation, which has proved worthy of its own name, the Lange-Lainhart test, uses magnetic resonance imaging (MRI) techniques to image brain areas to detect changes associated with autism.

I’ve been unable to find the complete paper, reported to have been published in Autism Research on Nov. 29; the journal has only papers through October available on its Website as of this writing. According to reports, however, the authors state that the new test was 94% accurate in identifying who was autistic and who wasn’t among 60 males tested. The participants in the study were ages  8 to 26; 30 were diagnosed with what the researchers call “high-functioning autism,” and 30 were typically developing.

The imaging technique the authors used involves tracing water diffusion along axons, the long connectors that link neurons to other neurons or tissues. This diffusion tensor imaging process yields an image that can highlight variations in the patterns of these connective pathways in different areas of the brain. This study focused on six brain areas associated with language, social, and emotional functioning, all of which are traditionally considered to be problematic among people with autism.

In the brains of non-autistic participants, the flow patterns were organized in a typical way that indicated connectivity among the brain regions. In the participants diagnosed with high-functioning autism, the flow was disorganized in a pattern common to the autistic group, indicating less connectivity and interaction and thus less exchange of information in the network. The researchers repeated the test on another, smaller set of participants, 12 with autism and 7 without, and produced similar results.

These findings imply that autistic brains may operate like a set of computer hardware components that cannot communicate very well with each other while still functioning perfectly well separately. There may be camera that captures a visual image without trouble or a microphone that captures a voice clearly, but the system lacks the network necessary to integrate the two inputs into a unified perception.

The news reports I’ve read on the study make a big deal out the prospect that this imaging breakthrough could lead to earlier diagnosis of autism, something that most experts believe is key to ameliorating some of its negative manifestations. But experts also urge the standard cautious optimism, and rightfully so.

For one thing, the participants in this study were ages 8 to 26, not within the time frame for early diagnosis of autism, and all of them were male. The study findings can’t tell us whether their brains present with these differences as a result of developing with autism, or whether they have autism because their brains are built this way. Before there can be talk of “early diagnosis” and linking these changes to manifestations of autism, we’d need studies showing these differences in much younger children. Further, given the frequent findings of differences between males and females on the spectrum, investigations involving autistic girls and women are necessary.

This study is not the first to use imaging to identify distinctions between autistic and non-autistic people. Other studies have also done so, finding pattern variations in the neuronal tracts of children with autism compared to children without it, in critical areas relevant to the clinical symptoms of autism.

While I find these results intriguing, I note one thing that no one seems to have commented on. In the reports I’ve read about this study, the researchers observe that currently, the only way to diagnose autism is based on a symptom checklist, questionnaires, screenings, and so on—any autism parents reading this will know that drill—and the ultimate call relies on the expertise of the medical professional conducting the evaluations. The implication of these comments is that we need some better, more unequivocal, less-subjective methods of identifying autistic people.

Yet, presumably the autistic boys and men they used for this study were diagnosed using just such subjective evaluation, and their autism diagnoses appear to have been confirmed in 94% of cases by similarities of MRI findings. In my mind, this outcome suggests that the process of subjective evaluation seems to be working pretty well. Of course, we’re a visual species and like our decisions to be given literally in black and white. Such MRI results may fulfill a need that has less to do with correct outcomes than it does with a dose of visual confirmation–and satisfaction.

Roll over eggs…it’s time for (unrolled) tobacco leaves

Tobacco leaf infected with Tobacco Mosaic Virus. Courtesy of Clemson University - USDA Cooperative Extension Slide Series

Timeline, 2008: If you’ve ever been asked about allergy to egg products before receiving a flu vaccine, you have had a little encounter with the facts of vaccine making. Flu viruses to produce the vaccine are painstakingly grown in chicken eggs because eggs make perfect little incubators for the bugs.

So…many…eggs

There are problems—in addition to the allergy issue—that arise with this approach. First of all, growing viruses for a million vaccine doses usually means using a million fertilized, 11-day-old eggs. For the entire population of the United States, 300 million eggs would be required. Second, the process requires months of preparation, meaning a slow turnaround time for vaccines against a fast-moving, fast-changing disease. Last, if there is anything wrong with the eggs themselves, such as contamination, the whole process is a waste and crucial vaccines are lost.

The day may come when we can forget about eggs and turn to leaves. Plants can contract viral disease just like animals do. In fact, an oft-used virus in some research fields is the tobacco mosaic virus, which, as its name implies, infects tobacco plants. It gives a patchy look to the leaves of infected plants, and researchers use this feature to determine whether the virus has taken hold.

Bitter little avatars of evil used for good?

Tobacco plants themselves, bitter little avatars of evil for their role in the health-related effects of smoking, serve a useful purpose in genetic research and have now enhanced their approval ratings for their potential in vaccine production. Plants have caught the eye of vaccine researchers for quite a while because they’re cheaper and easier to work with than animal incubators. Using plants for quick-turnaround vaccine production has been a goal, but a few problems have hindered progress.

To use a plant to make a protein to make a vaccine, researchers must first get the gene for the protein into the plant. Previous techniques involved tedious and time-consuming processes for inserting the gene into the plant genome. Then, clock ticking, there was the wait for the plant to grow and make the protein. Add in the Byzantine process of obtaining federal approval to use a genetically modified plant, and you’ve got the opposite of “rapid” on your hands.

One solution to this problem would simply be to get the gene into the plant cell cytoplasm for immediate use. It’s possible but involves meticulously injecting a solution with the gene sequence into each leaf. Once the gene solution is in, the plant will transcribe it—copy it into mRNA—in the cell cytoplasm and then build the desired protein based on the mRNA code. But there has been no way to take hand injection to the large-scale production of proteins, including for vaccines.

Age-old vacuum suction =  high-tech high-throughput

To solve this problem, researchers turned to one of our oldest technologies: vacuum suction. They grew tobacco plants to maturity and then clipped off the leaves, which they submerged in a solution. The solution was spiked with a nasty bug, Agrobacterium tumefaciens, a pathogen responsible for the growth of galls, or tumors, on plants. Anyone working in agriculture fears this bacterium, a known destroyer of grapes, pitted fruit trees, and nut trees. But it does have one useful feature for this kind of work: It can insert bits of its DNA into plant cells. The researchers tricked A. tumefaciens into inserting another bit of DNA instead, the code for the protein they wanted to make.

To get the solution close to the cells, the investigators had to get past air bubbles, and that’s where the vacuum came in. They placed the submerged leaves into a vacuum chamber and flipped a switch, and the activated chamber sucked all the air out of the leaves. When the vacuum was turned off, the solution flowed into the now-empty chambers of the leaf, allowing the A. tumefaciens-spiked solution to bathe the plant cells. After 4 days and a few basic protein-extraction steps, the research team had its protein batch. According to the team lead, “any protein” could be made using this process, opening up almost unlimited possibilities and applications for this approach.

Vaccines…or combating bioterrorism?

The technology has come far enough that a US company has taken steps toward manufacturing vaccines using tobacco leaves.  And it appears that the applications go beyond vaccines, as one news story has noted…the tobacco plants might also be used to produce antidotes to common agents of bioterrorism.

Beethoven died of lead poisoning–or did he?

Did lead kill Beethoven?

Timeline, 2005 and 2010: Literary folk have often noted the passion and emotion of Ludwig van Beethoven’s works. Lucy Honeychurch, the heroine of E.M. Forster’s A Room with a View, became “peevish” after playing Beethoven, and of course there’s the famous hooligan Alex from A Clockwork Orange, who was roused to stunning displays of violence after hearing “Ludwig van.” Given Beethoven’s own behavior, which was punctuated by violent rages, frequent sudden outbursts, and wandering the streets humming loudly, it’s not surprising that his music would communicate his passion.

A heavy metal influence?

A study in 2005 (news release here) yielded results that suggested that much of his anger, however, was attributable to the effects of heavy metal…specifically, lead. Beethoven became sick in his 20s (he also went deaf in his 20s), and suffered until his death at the age of 56 from a variety of illnesses, including chronic diarrhea and other stomach ailments. His death was lingering and painful, and some people thought that he had suffered from syphilis. Yet now many of his symptoms fit the classic description of slow lead poisoning. Among the effects of lead poisoning are irritability, aggressive behavior, headaches, and abdominal pain and cramping, all of which Beethoven experienced.

Doctor to businessmen to Sotheby’s to science

Some samples of the great composer’s hair and skull are available today for sophisticated testing for metals. A Viennese doctor apparently snagged a few fragments of his skull 142 years ago and the pieces eventually made their way through the family to a California businessman. The hairs were cut by a student soon after Beethoven died and ended up at a Sotheby’s auction. A few years ago, tests on the hairs suggested that Beethoven’s body harbored high levels of lead—hair accumulates and retains such toxins better than any other tissue—but because the testing method destroyed the hair, further tests were not completed.

Wobbling electrons solve the mystery?

Since that time, a powerful new X-ray technique has become available. The Department of Energy’s Argonne National Laboratory owns the X-ray. In the facility, subatomic particles fly through a tubular tunnel almost at the speed of light, emitting as they travel X-rays 100 times brighter than the sun’s surface. These X-rays can bounce off of the surface of even a tiny sample. As they bounce off of the sample, electrons wobble out of place, releasing energy in a pattern that is specific to the atom being bombarded.

Researchers were interested in Beethoven’s hair and skull pieces. The team that evaluated the samples actually works on developing bacteria that can take up heavy metals and render them relatively harmless; such organisms would be useful in environmental detoxification. They placed Beethoven’s hair in their high-powered X-ray. The electrons wobbled and the pattern indicated that Beethoven was simply full of lead. In fact, they reported that the poor man had about 60 parts per million of lead in his body, which is 100 times normal levels. It certainly was enough to make a person manifest the various symptoms that characterized most of Beethoven’s life.

The team also looked for a pattern that arsenic would emit, and they found none. This result seemed to exonerate Beethoven from having had syphilis, since arsenic would have been the treatment of choice for such an ailment.

Not so fast

At the time the study results were revealed, ideas about how did Beethoven built up so much lead abounded. Some suggested that  his body was less able than normal to rid itself of the heavy metal, through which he’d have been exposed by many channels. His stomach problems and temperament led him to consume much wine, and the vessels for drinking wine contained lead. In addition, his medicines probably were stored in lead-lined bottles or vials, and he may well have visited spas—for his health, ironically—at which he consumed or swam in mineral water containing lead. In one report, Beethoven’s poor doctor was identified as the likely culprit in his demise.

Fast-forward five years to 2010. A deeper analysis (news release here) of the bone fragments from Beethoven’s school indicated that his lead levels were not that spectacular. The bone is the reservoir for most of the lead the body takes up, and Beethoven’s bones simply didn’t have enough to have caused his various physical ailments. While the experts seemed to be in agreement that the results point away from lead, a new heavy metal mystery arose from the results. One skull fragment they tested had about 13 mcg of lead per gram of bone, nothing to write home about, while another sample turned up with 48 micrograms per gram, a much higher level. Nevertheless, we must look elsewhere for what killed one of the world’s greatest western composers. Ideas being tossed around include lupus and heart disease. What we do know is that he lived in terrible pain, both from his maladies and from the treatments designed to help, including pouring hot oil in his ears, according to one Beethoven scholar quoted in the New York Times.

Another wrongly accused suspect

Heavy metals have featured in other historical whodunits. For example, Napoleon reportedly died of stomach cancer during his exile on Elba, but one analysis showed that he actually died of slow arsenic poisoning, suggested to have been at the hand of his closest assistant. Then, much like Beethoven’s story, a later study showed that arsenic likely played no role in the great general’s death.

Think you're eating snapper? Think again

Grad students learn PCR, uncover fish fraud

It’s a great thing if you get your name published in the journal Nature, the pinnacle of publishing achievement for a biologist, while you’re still in school. Such was the fate of six graduate students participating in a course designed to teach them DNA extraction, amplification, and sequencing. They identified a real question to answer in the course of applying their techniques, and their results got them brief communication in Nature and national recognition. Not bad; I hope everyone also earned an “A.”

The group, led by professors Peter Marko and Amy Moran at the University of North Carolina-Chapel Hill, suspected that fish being sold as red snapper in markets in the U.S. were actually mislabeled, in violation of federal law. This kind of fraud is nothing new; marketers have in the past created “scallops” by cutting scalloped-shaped chunks from the wings of skates (part of the cartilaginous fish group), and have labeled the Patagonian toothfish as Chilean sea bass.

Protections can drive fraud

Such mislabeling has far-reaching implications, well beyond concerns about defrauding consumers of the fish they want. If fisheries and fish dealers are reporting their catches as red snapper or scallops or sea bass when they are, in fact, other marine species, then data on the abundance and distribution of all of these species will be misleading. Red snapper, Lutjanus campechanus, was placed under strict management in 1996, a move that gave incentive to the fishing industry and retailers to mislabel fish. Some experts suspect that many fish under heavy restriction end up with their names on a different species for market.

Who is responsible for the mislabeling? Fishermen pull in their catches and identify them on the boat or at the dock. The catch goes to a fish dealer, who is also responsible for reporting what species and how many of each species were caught. This report becomes the official number for the species. The dealer then sends the fish on to the retail market, where it is sold in stores and restaurants. Misidentification on the boat or dock is one reasonable possibility because some of the species identified in the North Carolina study frequent the same types of habitat, primarily offshore waters around coral reefs. These species, which include vermillion snapper and silk snapper, do look very much like red snapper, although there are some identifiable morphological differences.

One filet is just like the other?

So misidentification could be an honest mistake or purposeful change at the boat or dock, or it could be a willful relabeling at the restaurant or market. By the time a fish is processed, it consists essentially of a filet that is indistinguishable from that of other, similar fish. Hapless consumers end up paying twice as much for silk snapper, thinking they’re getting the pricier red snapper, instead.

But the DNA sequencing the North Carolina group performed not only turned up species closely related and very similar to red snapper, but also uncovered some sequences that have no identity with those of known species in gene databanks. In other words, fish of unknown identity are being caught, sold, and eaten as red snapper before we even have a chance to document what they are, their habitats, or their numbers.

Mislabeling is rampant

The grad students and professors also found that some of the fish being marketed as Atlantic red snapper were, in a few cases, from the other side of the planet, including the crimson snapper, which occurs in the Indo-West Pacific. All told, they found that 77% of the fish samples from stores in the eastern and midwestern U.S. were mislabeled as red snapper.

One way to prevent such mislabeling is to require identification of the country of origin of fish sold at market. The USDA has instituted such a program, although confusion will likely persist about fish caught in international waters. And the mislabeling isn’t only a U.S. phenomenon.

In the meantime, how do you know you’re getting red snapper? Some fish ecologists recommend avoiding it entirely because it still suffers from overfishing; however, one way to know your fish is to ask for it with the skin on, or completely intact. If you’ve got a smart phone, you can just look up the image and compare. Alternatively, you could just order the salad.

Polio vaccine-related polio

Polio virus bits in vaccine rarely join forces with other viruses, become infectious

[Note: some of the links in this piece are to New England Journal of Medicine papers. NEJM does not make its content freely available, so unfortunately, unless you have academic or other access, you'd have to pay per view to read the information. I fervently support a world in which scientific data and information are freely available, but...money is money.]

Worldwide, billions of polio vaccine doses have been administered, stopping a disease scourge that before the vaccine killed people–mostly children–by the thousands in a horrible, suffocating death (see “A brief history of polio and its effects,” below). The polio vaccination campaign has been enormously successful, coming close to the edge of eradicating wild-type polio.

But, as with any huge success, there have been clear negatives. In a few countries–15, to be exact–there have been 14 outbreaks of polio that researchers have traced to the vaccines themselves.  The total number of such cases as of 2009 was 383. The viral pieces in the vaccine–designed to attract an immune response without causing disease–occasionally recombine with other viruses to form an active version of the pathogen. Some kinds of viruses–flu viruses come to mind–can be notoriously tricky and agile that way.

Existing vaccine can prevent vaccine-related polio

Odd as it sounds, the existing vaccines can help prevent the spread of this vaccine-related form of polio. The recombined vaccine-related version tends to break out in populations that are underimmunized against the wild virus, as happened in Nigeria. Nigeria suspended its polio vaccination program in 2003 because rumors began to circulate that the vaccine was an anti-Muslim tactic intended to cause infertility. In 2009, the country experienced an outbreak of vaccine-derived virus, with at least 278 children affected. Experts have found that the existing vaccine can act against either the wild virus or the vaccine-derived form, both of which have equally severe effects. In other words, vaccinated children won’t get either.

Goal is eradication of virus and need for vaccine

Having come so close to total eradication before wild-type-associated cases plateaued between 1000 and 2000 annually in the 21st century, global health officials hold out the hope for two primary goals. They hope to eradicate wild-type polio transmission through a complete vaccination program, which, in turn, will keep vaccine-derived forms from spreading. Once that goal is achieved, they will have reached the final target: no more need for a polio vaccine.

As Dr. Bruce Aylward, Director of the Global Polio Eradication Initiative at WHO, noted: “These new findings suggest that if (vaccine-derived polio viruses) are allowed to circulate for a long enough time, eventually they can regain a similar capacity to spread and paralyse as wild polioviruses. This means that they should be subject to the same outbreak response measures as wild polioviruses. These results also underscore the need to eventually stop all (oral polio vaccine) use in routine immunization programmes after wild polioviruses have been eradicated, to ensure that all children are protected from all possible risks of polio in future.”

If that sounds nutty, it’s been done. Until the early 1970s, the smallpox vaccination was considered a routine vaccination. But smallpox was eradicated, and most people born after the early ’70s have never had to have the vaccine.

A brief history of polio and its effects

I bring you the following history of polio, paraphrased from information I received from a physician friend of mine who works in critical care:

The original polio virus outbreaks occurred before the modern intensive care unit had been invented and before mechanical ventilators were widely available. In 1947-1948, the polio epidemic raged through Europe and the United States, with many thousands of patients dying a horrible death due to respiratory paralysis. Slow asphyxiation is one of the worst ways to die, which is precisely why they simulate suffocation in torture methods such as water boarding. The sensation is unendurable.

In the early twentieth-century polio epidemics, they put breathing tubes down the throats of patients who were asphyxiating due to the respiratory paralysis caused by the polio virus. Because ventilators were unavailable, armies of medical students provided the mechanical respiratory assist to the patients by hand-squeezing a bag which was connected to the breathing tube, over and over and over, 16 times a minute, 24 hours each day, which drove air in and out of the patients’ lungs.  Eventually the iron lung was developed and became widely implemented to manage polio outbreaks. The iron lung subsequently gave way to the modern ventilator, which is another story.

Platypus spur you? Grab a scorpion

The most painful egg-laying mammal: the platypus

The duckbill platypus is an impossible-looking, risible creature that we don’t typically associate with horrific pain. In fact, besides its odd looks, its greatest claim to fame is that it’s a mammal that lays eggs. But that’s just because you’re not paying close enough attention. On the hind legs of the male platypus are two spurs that inject a venom so painful, the recipient human writhes for weeks after the encounter. In spite of the fact that platypuses (platypi?) and humans don’t hang out together much, platypus venom contains a specific peptide–a short protein strand–that can directly bind to receptors on our nerve cells that then send signals of screeching pain to our brains. Ouch.

Hurting? Reach for a scorpion

If you’ve ever experienced platypus-level pain and taken pain killers for it, you know that they have…well…side effects. It’s because they affect more than the pain pathways of the body. The search for pharmaceuticals that target only the pain pathway–and, unlike platypus venom, inhibit it–forms a large part of the “rational design” approach to drug development. In other words, you rationally try to design things that target only the pathway of interest. In this case, researchers reached for the scorpion.

Their decision has precedent. In ancient Chinese medical practice, scorpion venom has been used as a pain reliever, or analgesic. But as developed as the culture was, the ancient Chinese didn’t have modern protein analysis techniques to identify the very proteins that bind only to the pain receptors and inhibit their activity. Now, a team from Israel is doing exactly that: teasing apart the various proteins in scorpion venom and testing their ability to bind pain receptors in human nerve cells.

The next step? Mimicry

With proteins in-hand, the next step will be to create a synthetic mimic that influences only the receptors of interest. It’s a brave new world out there, one where we wrestle proteins from scorpion venom and then make copycat molecules to ease our pain.

For your consideration

Why do you think the platypus makes proteins in its venom that human pain receptors can recognize if humans generally haven’t targeted platypuses (platypi?) as prey over its evolution?

In the human body, a receptor may be able to bind each of two closely related molecules–as a hormone receptor does with closely related hormones–but one of the molecules activates the receptor, while the other molecule inhibits it. Taking this as a starting point, why do you think some proteins in scorpion venom–which often causes intense pain–have the potential effect of alleviating pain?

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