(Roughly) Daily

Posts Tagged ‘virus

“The most outstanding feature of life’s history is a constant domination by bacteria”*…

Jennifer Kahn interviews biochemist Jennifer Doudna (who won the Noel Prize for the gene-editing engine Crispr) on her new focus– our microbiomes, tackling everything from immune disorders and mental illness to climate change—all by altering microbes in the digestive tract…

… what isn’t the microbiome responsible for? It’s been all the rage for the past few years, with scientists hoping it could help treat everything from immune disorders to mental illness. How exactly that will work is something we’re just starting to explore. This spring, the effort got a boost when UC Berkeley biochemist and gene-editing pioneer Jennifer Doudna, who won a Nobel Prize in 2020 for coinventing Crispr, joined the pursuit. Her first order of business, spearheaded by Berkeley’s Innovative Genomics Institute: fine-tuning our microbiome by genetically editing the microbes it contains while they’re still inside us to prevent and treat diseases like childhood asthma. (Full disclosure: I teach at Berkeley.) Oh, she also wants to slow climate change by doing the same thing in cows, which are collectively responsible for a shocking amount of greenhouse gas.

As someone who has written about genetic engineering in the past, I have to admit that my first reaction was: No way. The gut microbiome contains around 4,500 different kinds of bacteria plus untold viruses, and even fungi (so far: in practice we’ve only just started counting) in such massive quantities that it weighs close to half a pound. (Microbes are so tiny that 30 trillion bacteria would weigh roughly 1 ounce. So half a pound is a lot.)

Figuring out which ones are responsible for which ailments is tricky. First you need to know what’s causing the problem: like maybe something is producing too much of a particular inflammatory molecule. Then you have to figure out which microbe—or microbes—is doing that, and also which gene within that microbe. Then, in theory, you can fix it. Not in a petri dish, but in situ—meaning in our fully active, roiling, squishing stomach and intestines while they continue to do all the stuff they usually do.

Until recently, it would have seemed insane—not to mention literally impossible—to edit all the microbes belonging to a species within a vast ecosystem like our gut. And to be fair, Doudna and her collaborator, Jill Banfield, still don’t know quite how it will work. But they think it can be done, and in April, TED’s Audacious Project donated $70 million to support the effort. My own gut feeling (right?) was that this was either brilliant or terrifying, or possibly both at once. Brilliant because it had the potential to head off or treat diseases in an incredibly targeted and noninvasive way. Terrifying because, well, you know … releasing a bunch of inert viruses equipped with gene-editing machinery into the vital ecosystem that is our gut microbiome—what could go wrong? With that in mind, I invited Jennifer Doudna to my house for a chat about the future of microbiome medicine…

Fascinating– and encouraging: “Crispr Pioneer Jennifer Doudna Has the Guts to Take On the Microbiome,” in @WIRED.

(Image above: source)

* Stephen Jay Gould


As we investigate our intestines, we might spare a thought for Guido Pontecorvo; he died on this date in 1999. A geneticist, he discovered the process of genetic recombination in the common soil fungus Aspergillus— and as a result the parasexual cycle— in what became the model for the genetic studies in many other fungi. This cycle gives rise to genetic reassortment by means other than sexual reproduction; its discovery provided a method of genetically analyzing asexual fungi…. which, as noted above, populate our microbiomes.


Written by (Roughly) Daily

September 24, 2023 at 1:00 am

“There are more things in heaven and Earth, Horatio, than are dreamt of in your philosophy”*…

And some of them were recently found in the woods near Boston…

Researchers have unearthed a trove of wonders in the soil of a Massachusetts forest: an assortment of giant viruses unlike anything scientists had ever seen. The find suggests this group of relatively massive parasites has an even greater ecological diversity and evolutionary importance than researchers knew.

Giant viruses can exceed 2 micrometers in diameter, on par with some bacteria. They can also harbor immense genomes, which reach 2.5 megabases—larger than the genomes of far more complex organisms. Between the discovery of these impressively sized viruses in algae and the culturing of amoeba-infecting Mimiviruses, most of the research on the group has focused on viruses that inhabit freshwater environments. But DNA sequencing has long indicated that giant viruses are diverse and abundant elsewhere, too—especially in sediments and soils, which are estimated to host some 97% of all the viral particles on Earth. Indeed, genomic sequencing of the soils of Harvard Forest—a roughly 16-square-kilometer area west of Boston—indicated the presence of numerous, novel giant viruses.

Now, electron microscopy has allowed scientists to see what others had only sequenced. The diversity of forms was astounding, they report in a bioRxiv preprint. Not only did the researchers see the 20-sided icosahedral shapes they expected, they spotted ones with myriad modifications—tails, altered points, and multilayered or channeled structures abounded. There were even viruses with long tubular appendages, which the team dubbed “Gorgon” morphology [photo above]. Furthermore, many of these putative viral particles were coated with almost hairlike projections, which varied in length, thickness, density, and shape.

The findings suggest virologists have much to discover about how giant viruses interact with their host cells. That likely means the ecological roles these viruses play in soils—and elsewhere they’re found—are woefully underappreciated…

Microbes come in a variety of shapes, hinting at undiscovered ecological diversity: “Alien-looking viruses discovered in Massachusetts forest,” in @ScienceMagazine.

* Shakespeare, Hamlet

As we marvel at multifariousness (and note that viruses, while generally considered to be non-living and thus not considered microorganisms, are colloquially lumped in with microbes), we might spare a thought for Sidney Walter Fox; he died on this date in 1998.  A biochemist, he was responsible for a series of discoveries about the origin of life.  Fox believed in the process of abiogenesis, by which life spontaneously organized itself from the colloquially known “primordial soup,” poolings of various simple organic molecules that existed during the time before life on Earth.  In his experiments (which possessed, he believed, conditions like those of primordial Earth), he demonstrated that it is possible to create protein-like structures from inorganic molecules and thermal energy.  Dr. Fox went on to create microspheres that he said closely resembled bacterial cells and concluded that they could be similar to the earliest forms of life or protocells.


“The welfare and the future of our societies depend on our capacity to remain mobilized so as to improve the health of every mother and child”*…

Preparing for a world post Roe v Wade…

The red states poised to ban or severely limit abortion already tend to have limited access to health care, poor health outcomes and fewer safety net programs in place for mothers and children.

If the U.S. Supreme Court overturns Roe v. Wade, as it’s expected to, the ensuing increase in births will likely leave families in tough circumstances and strain systems that are already hanging by a thread.

“What we’re facing as a country is hundreds of thousands of births, probably disproportionately located in the states that have been most limited in what they do for pregnant women, infants and children. So this is the great paradox that we are dealing with,” said Sara Rosenbaum, a health law and policy professor at George Washington University. “We have not ever designed these programs for a world without Roe,” she added. “You need a child welfare system, the likes of which we’ve never seen.”…

A growing shortage of obstetricians, higher maternal mortality rates and worse health care outcomes generally, increased pressure on U.S. foster and adoption systems— it all bodes ill…

We know from focus on health outcomes that kids born into poverty, kids born into unstable social circumstances, tend to have higher incidence of early onset chronic diseases,” Shannon said. “We also know that when those children are raised in unstable circumstances and have to be cared for in foster care, the outcomes there are really sobering.

Richard Shannon, chief quality officer for Duke Health

Red states aren’t prepared for a post-Roe baby boom,” from Caitlin Owens (@caitlinnowens) in @axios.

* Jean Ping


As we contemplate care, we might sending healing birthday greetings to Thomas Huckle Weller; he was born on this date in 1915. A virologist, he developed a technique for cultivating poliomyelitis viruses in a test tube, using a combination of human embryonic skin and muscle tissue– which enabled the study of the virus “in the test tube,” a procedure that led to the development of polio vaccines. He was awarded the Nobel Prize in Physiology or Medicine in 1954.


“‘Life’ is of course a misnomer, since viruses, lacking the ability to eat or respire, are officially dead”*…

The human genome contains billions of pieces of information and around 22,000 genes, but not all of it is, strictly speaking, human. Eight percent of our DNA consists of remnants of ancient viruses, and another 40 percent is made up of repetitive strings of genetic letters that is also thought to have a viral origin. Those extensive viral regions are much more than evolutionary relics: They may be deeply involved with a wide range of diseases including multiple sclerosis, hemophilia, and amyotrophic lateral sclerosis (ALS), along with certain types of dementia and cancer.

For many years, biologists had little understanding of how that connection worked—so little that they came to refer to the viral part of our DNA as dark matter within the genome. “They just meant they didn’t know what it was or what it did,” explains Molly Gale Hammell, an associate professor at Cold Spring Harbor Laboratory. It became evident that the virus-related sections of the genetic code do not participate in the normal construction and regulation of the body. But in that case, how do they contribute to disease?

An early clue came from the pioneering geneticist Barbara McClintock, who spent much of her career at CSHL. In the 1940s, long before the decoding of the human genome, she realized that some stretches of our DNA behave like infectious invaders. These DNA chunks can move around through the genome, copying and pasting themselves wherever they see fit, which inspired McClintock to call them “jumping genes.” Her once-controversial idea earned her a Nobel Prize in 1983.

Geneticists have since determined that jumping genes originate in the viral portion of the genome. Many of these genes turn out to be benign or even helpful. “But some of the things are full-on parasites,” Hammell says, like infections embedded within our own DNA. All it takes to set these bad actors loose, she is finding, is a slip-up in the body’s mechanisms that normally prevent the genes from jumping around and causing harm…

Half of your genome started out as an infection; if left unchecked, some parts of it can turn deadly all over again: “The Non-Human Living Inside of You.”

See also: “The Wisdom of Pandemics– viruses are active agents, existing within rich lifeworlds. A safe future depends on understanding this evolutionary story.”

* “‘Life’ is of course a misnomer, since viruses, lacking the ability to eat or respire, are officially dead, which is in itself intriguing, showing as it does that the habit of predation can be taken up by clusters of molecules that are in no way alive.” – Barbara Ehrenreich, Living with a Wild God: A Nonbeliever’s Search for the Truth about Everything


As we check our baggage, we might send reforming birthday greetings to Abraham Flexner; he was born on this date in 1866.  The founding director of Princeton’s Institute for Advanced Studies, Flexner is best remembered for his pioneering work as a reformer of American higher education, especially medical education.  On the heels of his 1908 study, The American College, in which he effectively critiqued the university lecture as a method of instruction, he published the Flexner Report, which examined the state of American medical education and led to far-reaching reform in the training of doctors.  The report called on American medical schools to enact higher admission and graduation standards, and to adhere strictly to the protocols of mainstream science in their teaching and research.  While one unintended consequence of Flexner’s impactful advocacy was the reversion of American universities to male-only admittance programs to accommodate a smaller admission pool (female admissions picked up again only later the century), most historians agree with his biographer, Thomas Bonner, that Flexner was “the severest critic and the best friend American medicine ever had.”


Just when you were beginning to feel a little safer…

The Army News Service reports that, even as Microsoft itself is quietly declaring defeat on widely-reviled Vista and trying to shift attention to the can’t-be-soon-enough release of Windows 7, the U.S. Army is moving all of it’s PCs to Vista…

Army migrating computers to Vista
May 20, 2009
By Gary Sheftick and Delawese Fulton

WASHINGTON (Army News Service, May 20, 2009) — The Army is migrating
all of its Windows-based computers to Microsoft’s Vista operating
system to bolster Internet security and standardize its information

The systems change, which includes swapping Office 2003 for Office
2007, is set to be completed by Dec. 31.

The official release suggests that

First-time Vista users will discover added support for data
encryption, a new Windows Explorer, upgraded icons and navigation

… or not.

In any case, read the full piece here.

As we console ourselves that Trojan Horses have had a place in warfare since the time of Homer, we might recall that it was on this date in 1844 that Samuel F. B. Morse taped out the first message sent over the (first) “telegraph” line:  “What hath God wrought?”  Morse sent the famous message from the B&O’s Mount Clare Station in Baltimore to the Capitol Building. (The words were chosen by Annie Ellsworth, the daughter of the U.S. Patent Commissioner, from Numbers 23:23.)

The original Morse telegraph

Written by (Roughly) Daily

May 24, 2009 at 12:01 am

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