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Two Scientists

June 26, 2019

This summer has been tough for me, with the passing of two scientists I knew well. The first is my father, the physicist John Slonczewski, 1929-2019. As Wikipedia helpfully says, “Not to be confused with Joan Slonczewski.”

Back in the 70s, John wrote the Britannica article on magnetism. A lifetime theoretical physicist at IBM, John invented equations for magnetic effects that are now used in all of our thumb drives and mobile devices. A video at the Computer History Museum describes his work.

John received the International IEEE Magnetics Society award for prediction of the spin transfer torque effect in magnetic thin films. He also received the 2013 Oliver E. Buckley Condensed Matter Physics Prize for a lifetime of work including MRAM, Magnetoresistive Random Access Memory. This kind of memory is the only kind that does not “wear out” and is non-volatile (does not go away when power is off).

Nominated for a Nobel, John was better known to us over the years for his fun-loving adventures with family, especially beloved Esther.


My second heartbreak this summer was the loss of our Bacteria Lab graduate Sean Bush, 1994-2019, third-year medical student at Wright State who passed in a bicycle accident.

At Kenyon, Sean was a preternatural computer whiz who installed our lab’s supercomputer node that formed the foundation of our our current Bacteria Lab, our past six publications. He was also the most compassionate human on Earth, readily sharing his gifts with students ranging from Bacteria Lab to Wiggin Street Elementary.

He was still running our computer from med school, where he was on track to become a neurosurgeon. In life though you never know what’s round the corner, and Sean lived every moment as if it were the most important.

Spider-Toxin Franken-Fungus Fights Malaria

May 30, 2019

Where to begin, with this “Frankenstein of the week” story? The recluse spider, whose brew of toxins perhaps earns it an overly bad rep? True, humans occasionally pick up the Hybrid toxin, its name perhaps inspired by a Marvel superhero.This image has an empty alt attribute; its file name is 27840_400x400.jpgMalaria is arguably the world’s most debilitating microbial disease, for human and animal death and morbidity, as well as economic impact. Every few decades another antimalarial med or insecticide is spread across the malaria belts of Africa and Asia, only to fail a decade later as resistant pathogens arise. Spread by the Anopheles mosquito, the parasite invades red blood cells, crowding the blood with Plasmodium parasites, and spreading to the bite of new mosquitoes.

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The latest entrant into our malaria arms race is the fungus, Metarhizium pingshaense. This previously obscure fungus is known for attacking mosquitoes. Here we see a hapless Anopheles mosquito dying a gruesome death, thanks to fungal attack. The fungus paints the mosquito green, from a plasmid (DNA circle) that genetically engineered the fungus to express green fluorescent protein (GFP). GFP originally comes from a jellyfish, carried by a bacterial plasmid—before the GFP gene got immortalized by Roger Tsien and others, engineered into a rainbow of variously-colored fluorescent proteins.

So can we enlist Metarhizium as a weapon against the mosquito that carries killer plasmodiums? As vicious as the fungus appears, apparently it’s not strong enough to dent the vast mosquito population. But researchers don’t give up easily. Brian Lovett, entomologist at University of Maryland, teamed up with Etienne Bilgo, Sante/Centre Muraz in Burkina Faso (and a host of others) to engineer a fungus that produces the spider toxin.

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Here, Etienne Bilgo is part of a team that tested the ability of a genetically engineered fungus to kill mosquitoes that can spread malaria.

How did they make the fungus-plasmid-spider-Hybrid hybrid? That feat was reported by Paula Calabria and her team at the Butantan Institute, São Paulo, Brasil. (You can see how badly people all over the world want to fight malaria.) First, they undertook some molecular sleuthing to identify the spider gene that encodes two toxins from spider venom. The genes were spliced together to encode “Hybrid” toxin. Originally their idea was to generate an anti-venom agent to treat people poisoned by a spider bite. The hybrid toxin would be used to raise antibodies that could neutralize spider toxins.

But other researchers found another use for this toxin, which effectively destroys an insect when expressed within the insect’s hemolymph (blood-like fluid). The gene encoding the Hybrid toxin was introduced into the fungal cells by use of a plasmid vector, a circle of DNA into which the Hybrid gene was spliced using restriction enzyme-cut DNA.

How to get the fungus into the mosquitoes? The recombinant fungus was suspended in sesame oil and spread onto black sheets within experimental living quarters. The mosquitoes were infected and died, or left few offspring. Moreover, the infected insects released fungal “conidia,” the spores that grow new fungi. It remains to be seen if this new virulent Franken-fungus can persist in the environment and effectively control malaria mosquitoes. And–avoid killing other insects the ecosystem needs.

Carbon Comes Home

May 22, 2019

Any serious plan to solve the carbon problem, to stop global warming before the planet cooks, must include carbon capture. That’s because, even as we replace CO2-releasing energy technologies, it won’t be enough: The CO2 up their already will continue to bake the planet, with irreparable harm for ocean food chains. What will it take to stop?

Somehow we must take CO2 out of the air and put it somewhere. But who trusts pumping a gas down into the Earth? A better way is to build the carbon into carbonate (carbon-oxygen) materials that are inert, and even usable for building construction. This was a premise of The Highest Frontier, where carbon is reacted into “carb” that (ironically) builds the tall seawalls that protect coastal cities.

Project team hand weaving new carbon fiber architecture

Materials such as carbon fiber, and more are being invented.

This MIT lab claims to suck carbon into construction while releasing oxygen, like plants do. But building anything requires input of energy from somewhere. Can building carbon fiber be carbon-neutral?

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Carbon Engineering thinks they have a comprehensive plan for carbon removal, and they’re starting now, with a plant in Texas. Their plan impressed the New York Times.

So how does it work? Inject base (hydroxide) into air with fans, and precipitate the CO2 into carbonate. (Where does the hydroxide come from? Takes energy to make.)

Calcium carbonate (Where does the calcium come from?) is then packed into pellets, converted into calcium oxide, or pumped into the earth.  All these processes can store CO2, but they all cost energy from somewhere.

Ultraphyte thinks it’s great to start somewhere—but do the math on your thermodynamics. The laws of energy and entropy are unforgiving.

Phage to the Rescue

May 15, 2019

A bacteriophage (virus that infects bacteria) may have cured a patient dying of multidrug-resistant bacteria.This image has an empty alt attribute; its file name is superbug-1-97bc22a41648c21f57606b6d37dc27403f73879c-s600-c85.jpg


The patient, Isabelle Carnell-Holdaway of Faversham, UK, had a lung transplant, as a result of cystic fibrosis, a condition in which the cilia lining the lungs are paralyzed and bacteria build up. The lung transplant required suppression of the immune system. So a multi-drug resistant bacterium grew and spread throughout her body. The bacterium, Mycobacterium abscessus, is related to those that cause tuberculosis and leprosy—a really nasty pathogen.

But Isabelle’s mother had heard of “phage therapy,” an experimental treatment in which bacteriophages attack a pathogen.

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The phages have to be very specific to the bacterial species, which they inject with their DNA to program the cell to make more phage particles. The idea of phage therapy goes way back to the early twentieth century, as dramatized in Sinclair Lewis’s novel Arrowsmith. But no full-scale trials have ever been conducted. There were always antibiotics that worked more simply, and had a broader spectrum of activity.

The problem was, where to find a phage that would specifically infect M. abscessus? Doctors turned to Graham Hatfull, a professor at University of Pittsburgh who has worked with large teams of undergraduates to isolate new phages. This project, which now reaches students all over the world, is called the Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES).

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Hatfull searched his collection of ten thousand undergraduate-discovered phages. In the collection he discovered three phages that could attack the specific pathogen that had infected Isabelle. One of the three phages, called Phage Muddy, had been discovered from a rotting eggplant. That gives you some idea of what phage discovery is like.

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Since no one know which phage would actually work (destroy the infectious bacteria despite Isabelle’s suppressed immune system) she was treated with a combination of all three phages. This was kind of a “Hail Mary” attempt, something you do only when all other treatments have failed.
Isabelle’s infection receded surprisingly fast, then cleared up almost entirely. While the story is not done yet, it looks like phages gave her a miraculous life extension. Time to revisit Arrowsmith.

Newborn Genetic Diagnosis—Guinness World Record

May 5, 2019

In 2003, the Human Genome Project claimed completion of the first DNA sequence of “the” human genome. Just fifteen years later, hospitals can sequence an entire baby’s genome literally overnight. Typically 19 hours, at the Rady Children’s Institute for Genomic Medicine, holder of the Guinness World Record, up there with the world’s largest origami rhinoceros and the most balloons popped by a dog.

Why is it important to sequence the DNA of a newborn? 
4%, that is 1 in 25 newborn children has a genetic defect. Think about it—How many people you know have this in themselves or their families?

For treatment, the first days, even hours, are crucial. The sooner therapy can start, the greater the chance that an infant can have a normal life. This is true for certain conditions, such as phenylketonuria (PKU), cystic fibrosis, immune deficiencies, and tendencies for early cancer. PKI has always had a simple biochemical test, required by law at birth. But what of thousands of other conditions? Sadly, many of those still have no cure. But increasingly, knowing the defect early means help is on the way.

To sequence a genome and get useful information that fast requires chip technology and enormous computing power.

First, there is Illumina DNA sequencing, in which fragments of DNA are stuck to special “start” sequences at either end of the double strand. A DNA polymerase enzyme extends each strand, by fitting nucleotides to its complement. Eventually, all the short sequences are read and assembled into a whole genome.

Next, a computational pipeline that screens the three million base pairs and sifts out the likely errors that might have significance. Surprisingly, the fast majority of mutations have no effect at all on our health; even some “lethal” ones, whose compensatory mechanism may be unknown. Each of us has about 150 mutations not present in our parents. So, finding the lethal one may be quite a trick.

Studies show that genome sequencing can actually save money, as well as lives, by enabling treatment before a condition does irreparable damage.
So in the future, should we screen all newborns for entire genomes at birth, not just PKU?

That is another question, with many complex considerations.

CRISPR for Cancer?

April 28, 2019

CRISPR, the gene editing tool that sounds like something out of a fridge, is now talked about for every genetic disease and just entered a clinical trials to treat cancer.

What is it?  In a cell, a complex of proteins and RNA that can cut a gene, in some cases cutting out one gene and splicing in another. Big business, leading to mega patent disputes. Yet it all started from a relatively modest NSF grant to Jennifer Doudna about bacterial DNA.

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As Ultraphyte presented before: CRISPR stands for
Clustered (short DNA sequences)
Interspaced (with bits inbetween)
Palindromic (read the same forwards and back)

So where did this DNA-editing machine come from? It evolved over millions of years in bacteria, as a bacterium’s immune system. The clusters of short repeated sequences appear in the bacterial DNA. Each short sequence has been copied from the viral genome of a previously infecting virus.

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Some generations before, a bacteriophage (bacteria-infecting virus) injected its DNA into the cell. The DNA sequence was recognized as foreign by the CAS complex, which is 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.

Now what molecular biologists are doing is to engineer the CAS complex (and related protein machines, from different bacteria). Incredibly, the CAS machine has been made to work inside a human cell, where it can snip and edit one gene. The CAS needs to be engineered for extreme accuracy, to cut only one place in a large human genome, and to avoid “off-target effects” (unknown other ways it could mess with a genome). For example, at Duke University researchers have found a way to modify the shape of the RNA part of the machine so as to make the cutting more specific to the DNA sequence. This is really important when you are trying to fix one gene out of 3 billion base pairs.

The first clinical trial for cancer has been approved,  at the University of Pennsylvania, for treatment of multiple myeloma. Multiple myeloma occurs in white blood cells called B lymphocytes, or B cells. These B cells develop in the bone marrow, and certain clones proliferate when stimulated by an antigen to make antibodies. Then these antibody-producing cells develop into plasma cells, which are supposed to produce antibodies in the blood to combat infection. But when regulation fails, too many plasma cells are made, and they make abnormal antibodies that clog the blood.

Normally, the body needs to make T lymphocytes to regulate the B cells, but in multiple myeloma this regulation fails. So the aim of CRISPR therapy is to restore the patient’s own T cell regulation. This is done by:

–Remove some of patient’s own T cells for engineering (by autologous donation, giving cells back to oneself afterward)

–Giving the patient’s T cells a gene called TCR that recognizes a cancer surface protein called NY-ESO-1, found on myeloma cells. Now the T cells will be able to recognize and eliminate the cancer cells.

–To give the gene to the cells require a vector DNA called a lentivector. This lentivector was engineered from a lentivirus, originally the same HIV virus that causes AIDS. Ultraphyte has discussed lentivirus before; and The Highest Frontier shows lentiviruses as a future everyday therapy like aspiring. Amazingly, lentiviruses are now a standard approach for developing new cures.

–Use CRISPR to edit three other genes of the T cells, altering their function to enable these engineered T cells to attack the myeloma cells.

If that all sounds like a mouthful, it is. The result could be a miracle cure for an incurable illness. As you might imagine, though, as such cures become routine, increasing complexity means increasing development costs, and costs to your insurer. Something to think about as we develop these cures: Who will be able to afford them?

Galápagos–Volcanoes Young and Old

April 14, 2019

The Galápagos islands are an unfinished project of volcano building, perhaps going on for the past 90 million years. A plate of mantle moves southeast above a magma chamber that fountains new rock, creating new land. The result provides the equivalent of a testing ground for evolution of new species.

Here on Isabela Island, Punto Moreno, we clambered over a relatively young lava field, just 300 years since it solidified. Much of it remains smooth and black, barely a trace of soil. Only the marine iguanas, which long ago evolved black coloration to hide against the rock, here can be seen like drops of lava come alive to slither down and hunt for algae.

The lava still has the “ropy” texture of molten rock flowing down the mountain.

An old lava tube had collapsed, from where a flow of lava cooled and solidified on the outside, leaving molten rock to continue flowing out the middle.

During the flow, the various metals within the rock separated out by density, especially iron oxide. The separations led to layers of color, particularly red iron, and yellow.

Different islands formed from different offshoots of the magma chamber–where the metals had already separated. The lava forming Rábida Island had 80% iron, which oxidized to red and crumbled into red grains of sand. Here too the animals must adjust.