Understanding the History of HIV

On Aetiology, Tara C. Smith explores the story of Gaetan Dugas, a man who was long blamed for precipitating the AIDS epidemic in the United States. The vilification of Dugas had nothing to do with science; instead he was dubbed “patient zero” in a misinterpretation of his study moniker “patient O” (for Outside). Dugas’ portrayal in the media turned him into a modern Typhoid Mary, but he was not an originator of the U.S. epidemic, as a 2007 molecular analysis proved and a new paper in Nature confirms. Smith writes “This is the real scandal and lingering tragedy of Dugas. His story was used to stoke fear of HIV-infected individuals, and especially gay men, as predators seeking to take others down with them.” Does science finally have the clout to revisit such an entrenched media narrative?

In other news, The Verge reports on a man who may hold the key to halting the spread of HIV and AIDS. Patient Z258, as he is known, exhibits natural immunity to “a whopping 98 percent of the de-clawed HIV virus strains the scientists generated in the lab.” Understanding the broadly neutralizing antibody that protects Z258 could lead to powerful new treatments for the disease.

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Genetic Modification as Medicine

On ERV, Abbie Smith provides an update on a pioneering treatment for hemophilia that uses viruses to insert missing genes in a patient’s DNA. Hemophilia results from from the mutation or deletion of a gene that makes a blood clotting agent called Factor IX; without it, hemophiliacs are at risk for uncontrolled bleeding. While Factor IX can be delivered pharmaceutically, utilizing viruses to modify patients’ DNA yields long-term improvements in natural Factor IX production. Abbie writes, “the amount of therapeutic Factor IX these patients needed (on average) dropped from 2613 IU/kg to 206. The people who got the ‘high’ dose of virus dropped that down to 92 IU/kg. They went from 15-16 ‘bleeding episodes’ a year, to one.” They also saved $2.5 million.

Next, Abbie revisits research on treating HIV by removing CCR5 receptors that the virus uses to enter white blood cells. Much excitement was generated in 2008 when the “Berlin Patient” was declared to be functionally cured of HIV after receiving bone marrow from a donor with a mutation that preludes manufacture of the CCR5 protein. Now scientists are considering using gene therapy to disable CCR5 production in HIV patients, but there’s a catch: some HIV quasispecies utilize other receptor proteins, and even a small population of such viruses can take over when a patient is not producing CCR5. For this reason, Abbie writes that this therapy may hold more promise as a vaccine for HIV than as a cure.

Meanwhile, HIV itself has been genetically modified to help some sufferers of acute lymphoblastic leukemia by training cytotoxic T cells to target cancerous B cells. Abbie writes, “for all the time HIV has stolen from people, from families, its nice to see it giving some time back.”

Supernova Flashes and Silver Linings

New research from the Weizmann Institute of Science reveals that “cells in our brain form little hexagonal grids that keep us oriented, map-like, in our surroundings.” Weizmann’s resident blogger describes this finding as “a pyrotechnic flash of insight that changes how we understand the brain to work.” Game developers delight; this discovery shows “that you can really apply mathematical models to understand how our mammalian brains get their bearings.” It may also have immediate implications for understanding human brain disorders such as vertigo. Meanwhile, on ERV, Abbie Smith explores a silver lining emerging from ongoing research into the viral scourge known as HIV. Abbie explains that HIV viruses genetically reprogrammed by scientists to “modify relapsed acute lymphoblastic leukemia (ALL) patients T-cells” are prolonging and possibly saving the lives of kids. Continued genetic modification could transform HIV into a powerful tool for fighting cancer and other diseases. Finally, on The Pump Handle, Elizabeth Grossman writes that rapid job growth in oil and gas industry is shining a light on some of the most dangerous jobs on the planet. Elizabeth writes, “Last year, 112 oil and gas industry workers were killed on the job and about 9,000 suffered non-fatal, work-related injuries and illnesses.” Hazards include toxic chemicals, respirable silica, and radiation exposure, not to mention “motor vehicle crashes, fires, electrocution and explosions.” But a new alliance between OSHA, NIOSH, and the National STEPS Network promises to fight for better workplace safety for these very important employees. Oh and for those not satisfied with a metaphor: some real supernova goodness from Ethan Siegel.

Genetic Drifters

On Pharyngula, PZ Myers criticizes the stubborn obfuscations of Michael Behe, who refuses to yield his illogical calculations. Behe says (rightly) that a certain mutation necessary for drug resistance in the malaria parasite has about a 1 in 1020 chance of occurring. But the mutation is also detected in 96% of malaria patients who respond well to the drug; it proliferated widely because, by itself, it had no impact on the parasite’s fitness. The parasite needed another mutation, occurring at a later date, to develop resistance to the drug. Behe rests his case for divine intervention on the basis of bad math; as PZ writes, “It was crude, stupid, and ridiculous when J. Random Creationist was doing it, and it’s even worse when a guy with a Ph.D. in biochemistry, who ought to know better, panders to the mob of creationists who don’t even grasp middle school mathematics by using fallacious operations in probability.” Meanwhile, Orac reports that one of the flu strains targeted by this year’s vaccine “has undergone what is referred to as ‘genetic drift,'” making the vaccine less effective than desired. Yet the vaccine still offers protection against about 57% of circulating strains. On Life Lines, Dr. Dolittle shares research that says consuming caffeine while pregnant can effect genes in the baby’s heart. In total, researchers “identified 124 genes and 849 transcripts that were altered by exposure to caffeine in utero.” And on ERV, Abbie Smith reviews the evolutionary trajectory of HIV, which may be tending toward a ‘truce’ with human hosts.

Life, Death, and ERVs

In a phenomenon known as Peto’s paradox, large mammals do not develop cancer more often than small mammals, despite having more cells that could go haywire. On Life Lines, Dr. Dolittle writes “Some researchers suggested that perhaps smaller animals developed more oxidative stress as a result of having higher metabolisms. Others proposed that perhaps larger animals have more genes that suppress tumors.” But a new hypothesis argues that large mammals have evolved to minimize the activity of ERVs, which are ancient viral elements integrated into our DNA. Active ERVs can cause cancer and possibly other diseases; mice exhibit about 3300 active ERVs, while humans exhibit about 350. On the blog known as ERV, Abbie Smith writes “some of the young ERVs in humans, the ones that can still code for a protein here and there, are reactivated in HIV+ patients.” Researchers are considering targeting these ERVs in order to combat HIV; as Abbie writes, “You could train the HIV+ individuals immune system to ‘see’ the ERV components in an HIV infected CD4+ T-cell, and BAM! Kill the HIV infected cell!” But she warns that other ERV components are expressed in many normal human cells, and teaching our immune system to target them might be a very bad idea.

Last Week on ResearchBlogging.org

Scientists use a ‘gene gun’ to insert a gene from a flowering plant called rockcress into the cells of wheat seeds. The genetically modified wheat became more resistant to a fungus called take-all, which in real life can cause “a 40-60% reduction in wheat yields.”

T-cells from six HIV+ patients were removed from their bodies, treated with a zinc-finger nuclease designed to snip a gene out of the cell’s DNA, and put back in the patients.  Removal of the gene mimics a naturally occurring mutation which confers resistance to the HIV virus.  But only 25% of the treated cells showed evidence of being successfully edited.

Researchers “use time-resolved X-ray microtomography to visualize the muscles and hinges in three-dimensions” of fly wings, modelling the complex physical processes that enable flies’ flight.

Even with the cost of building new energy storage infrastructure, wind energy will continue to offer a net gain of power.  Plus: wind produces enough surplus electricity to offer 72 hours of backup power (vs. 24 hours for solar panels).  Researchers say that the industry of onshore wind turbines can “double in size each year—and still maintain an energy surplus.”

Researchers cremated the remains of young piglets to investigate why there’s little evidence of high infant mortality in the archaeological record. To no avail.

Men in ‘traditional’ marriages (whose wives are not employed) are more likely to look negatively upon women in the workplace.

Regardless of the structural integrity of a shoulder (rotator cuff) repair, patients have improved function and reduced pain after surgery.

Stem cells are influenced by the rigidity of the substrate they grew up on: “spending 10 days on a particular bed leads to irreversible future differentiation of the stem cells into stiff-environment-loving bone or soft-loving fat cells.”  That could lead to considerable demand for a new scaffolding material “based on a biocompatible silk-alginate hydrogel” which can be made to varying standards of firmness.

By appearing to tap test subjects on the hand with a small hammer while playing the recorded sounds of a hammer tapping stone, researchers made people feel their hands were more stone-like (or numb).

A gene coincidentally named FAT10 ( for F Adjacent Transcript) actually “regulates lipid metabolism and longevity,” and model mice who lacked the gene were leaner, had a faster metabolism, and lived up to 20% longer.

Encapsulating immature pancreatic cells grown from human stem cells and implanting them under the skin of mice showed the cells could produce insulin whenever needed and reduce diabetic symptoms.

The CDC revised it autism prevalence rate upward again; in 2010 about 1 in 68 eight-year-olds had an autism spectrum disorder.

At age six, children award beneficial resources to members of their ‘in-group;’ at age eight they also assign harmful or negative resources to members of an ‘out-group.’

People with OCD were less likely than controls to believe they could influence a light bulb by pressing a space bar whenever they want. The light bulb blinked randomly on and off.

A virus affecting crickets not only sterilizes them, but makes them more eager to initiate courtship. Males perhaps uninhibited by the virus would start playing a courtship song for a female much sooner than their healthy peers.  Intimacy may be the virus’s way of spreading.

Within the ultrapure water purification system of a nuclear reactor, scientists found oligotrophic bacteria, including new species, growing in biofilms “visible to the naked eye” on ceramic filter surfaces.