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July 22, 2014

Could a bacterium’s defense against bacterial viruses be used to protect a human cell from HIV?

A lot is in the news about people who seemed to be “cured” of HIV (the virus causing AIDS) yet two years later, the virus returns. That’s because the HIV virus hides a DNA copy of its RNA within the human cell’s own DNA chromosomes. The latently infected cells circulate in the bloodstream, undetected, because the hidden viral DNA looks the same as host DNA, to the immune system.

But what if we could cut the embedded DNA copy of HIV’s genome–out of the host cell DNA?

Amazingly, a way to do that has been reported, using a molecular machine used by bacteria to defend themselves from bacterial viruses. This defense is called CRISPR (clustered regularly interspaced short palindromic repeats). It is named for the clusters of short repeated sequences that appear in DNA of the bacterium. Each short sequence has been copied from the viral genome of a previously infecting virus. The genome of the previously infecting virus got recognized by the CAS complex–a protein/RNA machine that makes RNA copies of the infecting DNA sequence. The CAS RNA copies then cause the cell to (1) degrade the viral genomic DNA; (2) make short copies of viral sequence and insert them into host. These short copies (the “palindromic repeats” of CRISPR) then serve to generate future CAS RNAs that recognize the virus when it infects again–a kind of bacterial immune system.

For biotechnology, the CAS machine turns out to be an amazing way to edit vertebrate genomes. We can cut out a gene, for example a cancerous gene. So now, the PNAS researchers report using CAS to edit a small part of an integrated HIV genome, and prevent the integrated viral sequence from generating new phage particles. So far, this has been done in tissue culture. It will remain to be seen whether a delivery method can enable use of CRISPR/CAS to prevent HIV virus production in humans.


Robot Caregivers

July 20, 2014

Fiction writers used to assume that robots would take us to the stars, or Antarctica, or other future adventures. But today the fastest growing use of robots may be that of caregivers for the elderly. Here in this NYT opinion, a physician argues that robots will be a good thing. Two kinds of robots–one, what you might expect, a robot that takes vital signs and is improbably named GiraffPlus. Another kind however is designed purely for “compassion.” Provides endless patience and limitless consideration, in the absence of that distantly located child with his/her own family.

The author argues that the time has come, and that companion robots will indeed be a good thing. We’ve already seen Robot and Frank, the infinitely self-sacrificing  robotic companion. Perhaps its work reflecting how far we want to go down this road? The physician suggests that, with our high geriatric ratio and our declining personal patience, the road already has no exit.

Antarctica for Ultraphyte

July 9, 2014


Announcing the fall adventure–yes, it’s true, Ultraphyte is going to Antarctica. The expedition will be led by experienced Antarctic explorer Rachael Morgan-Kiss, of Miami University of Ohio. And yes, I’ll be posting Youtube videos (McMurdo Station has good internet. When the 200-mile winds aren’t blowing.)

Morgan-Kiss has a National Science Foundation grant to study eukaryotic microbes conducting photosynthesis–kinds of algae. See great video of her researchWe’ll conduct most of our field work in the Lake Bonney region, including a look at the curious Blood Falls.

Antarctic algae are one of the least understood partners in the global carbon cycle. The more we know about the carbon cycle, the better we can predict climate change. Furthermore, Antarctic climate change is the heavyweight when it comes to long-term impact on sea level.

We’ll get to identify new kinds of algae, with interesting cute little shapes, as well as culture them in the laboratory. Yes, they’re very green.

Getting to Antarctica, and trained to work there, is a major task in itself. Only a few thousand people officially work there, and one assumes that doctors and dentists (and their technology) are scarce. So I have to spend the summer going the round of doctors, opticians, and dentists to fill out a mega-page form. Including EKG stress test–Ultraphyte is in decent shape, from weekly 20-miles running and biking.

Will Antarctica make it into Blood Star Frontier? Yes, toward the end–and will take center stage in book 3, Sun Ice Frontier. Next spring at ICFA and Wiscon, I hope to have more to say about it; and trade  notes with Antarctic traveler Stan Robinson.

Ebola–One Plane Away

July 2, 2014

While we fret over childish court rulings, and homeless children dare to cross our borders, the spread of Ebola virus gets buried. For true heroism, nothing beats Doctors Without Borders–for months, the main source of care and treatment in a growing epidemic. So far the disease has struck Guinea, Liberia and Sierra Leone. Most of our Google news feeds relegate the disease below the first screen on our monitors. But experts say it’s just one plane flight away from Paris. Yes, a place that “matters” (sarcasm).

What makes Ebola virus so deadly? An RNA virus, Ebola has a relatively simple structure, just eight genes encoding proteins. The small RNA  is coiled within a flexible tubular protein capsid. The main host cells the virus can infect are white blood cells, liver cells, and endothelial cells–cells that line the blood vessels. That’s quite a deadly combination. By infecting the white blood cells, the Ebola virus disrupts the immune system, avoiding effective defense. Also, the cells carry the virus through the blood, all throughout the body. When the endothelial cells get infected, the blood vessels leak. More from my post in April.


Disco Clam

June 26, 2014

With so much strife in the world, it’s a relief to know that scientists have solved one of nature’s great mysteries: the disco clam. The disco clam, Ctenoides ales, appears to flash lightning bolts within its mouth. Young scientist Lindsey Dougherty at Berkeley has figured out the mechanism of this light display. Note that her research on this project involved “high speed video, transmission electron microscopy, spectrometry, energy dispersive x-ray spectroscopy and computer modeling.” Funded by the National Science Foundation, among several conservation organizations.

So how does it work? Not bioluminescence; that is, there is no biological light organ that emits its own light, like a firefly or the jellyfish Aequorea. Instead, the lip of the clam grows to form a narrow edge that scatters light–only from one side. The edge contains miniature balls of silica (glass) that efficiently reflect and scatter light. So as the lip moves the light appears to flash on and off, like the facets of a disco ball.

Does the clam use this flashing for anything useful? The next stage of research is to figure out if clams use the light signals to communicate. Great possibilities for science fiction.

The Sloths are Coming

June 23, 2014

Appropriately, this story took three years to crawl into my consciousness. The world’s slowest creature, the sloth, turns out to be the cutest.

A fascinating question: What kind of selective pressure favors slowness? Avoiding energy loss? The faster you move, the less efficient you are. We all know that from everyday experience–the faster you try to clear the table, the more likely you drop a dish.

Anyway, these lucky sloths at the Aviarios Sloth Sanctuary in Costa Rica don’t seem to have such problems.

The absolute opposite of Costa Rica’s awesome soccer team.

Bionic Pancreas

June 16, 2014

Our bodies are machines; and one failed part can mean we never wake up. So now we try to replace a failing part with something we design. The classic case is diabetes, in which the pancreas fails to produce insulin on demand. In this case, the father of an insulin-dependent boy designed an artificial insulin regulator.

It’s actually not the whole pancreas, which has many functions besides insulin. But the device monitors blood sugar and readjusts the hormone levels. Blood sugar monitors already exist; what is new about the “bionic pancreas” is that it not only monitors the sugar, it responds by pumping insulin (lowers glucose) or glucagon (raises glucose) as needed.

Will we see more and more of such devices? The current device (still in testing) addresses a life-threatening condition; for an entire lifetime, the patient must monitor their own glucose 24/7, every moment of the day. It will be interesting to see, though, how many such devices begin to augment our bodies, picking up for failing functions–or adding new ones.


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