Significant portions of plasmid DNA samples functionally survived suborbital flight — as well as atmospheric reentry — while riding on the outside of the research rocket’s payload

© 2014 Peter Free

Citation — to study

Cora S. Thiel,  Svantje Tauber, Andreas Schütte, Burkhard Schmitz, Harald Nuesse, Ralf Moeller, and Oliver Ullrich, Functional Activity of Plasmid DNA after Entry into the Atmosphere of Earth Investigated by a New Biomarker Stability Assay for Ballistic Spaceflight Experiments, PLoS ONE 9(11): e112979, DOI:10.1371/journal.pone.0112979 (26 November 2014)

Citation — to press release

University of Zurich, DNA survives critical entry into Earth’s atmosphere, Mediadesk – University of Zurich (26 November 2014)

Playing with “what if” yields a surprising result

While preparing an experiment to see how gravitational changes affect gene expression from DNA carried inside the payload of a sounding (research) rocket, the research team wondered what might happen if they put some of the plasmid DNA at various locations on the outside of the suborbital rocket.

From the press release:

Applied to the outer shell of the payload section of a rocket using pipettes, small, double-stranded DNA molecules flew into space from Earth and back again.

After the launch, space flight, re-entry into Earth’s atmosphere and landing, the so-called plasmid DNA molecules were still found on all the application points on the rocket . . . .

For the most part, the DNA salvaged was even still able to transfer genetic information to bacterial and connective tissue cells.

“This study provides experimental evidence that the DNA’s genetic information is essentially capable of surviving the extreme conditions of space and the re-entry into Earth’s dense atmosphere,” says study head Professor Oliver Ullrich . . . .

“The results show that it is by no means unlikely that, despite all the safety precautions, space ships could also carry terrestrial DNA to their landing site. We need to have this under control in the search for extraterrestrial life.”

© 2014 University of Zurich, DNA survives critical entry into Earth’s atmosphere, Mediadesk – University of Zurich (26 November 2014) (extracts)

As quantified in the paper’s abstract:

[A]rtificial plasmid DNA carrying a fluorescent marker . . . and an antibiotic resistance cassette (kanamycin/neomycin) was attached on different positions of rocket exterior;

(i) circular every 90 degree on the outer surface concentrical of the payload,

(ii) in the grooves of screw heads located in between the surface application sites,

and

(iii) on the surface of the bottom side of the payload.

Temperature measurements showed two major peaks at 118 and 130°C during the 780 seconds lasting flight on the inside of the recovery module, while outer gas temperatures of more than 1000°C were estimated on the sample application locations.

Subsequent analyses showed that DNA could be recovered from all application sites with a maximum of 53% in the grooves of the screw heads.

We could further show that up to 35% of DNA retained its full biological function, i.e., mediating antibiotic resistance in bacteria and fluorescent marker expression in eukariotic cells.

© 2014 Cora S. Thiel,  Svantje Tauber, Andreas Schütte, Burkhard Schmitz, Harald Nuesse, Ralf Moeller, and Oliver Ullrich, Functional Activity of Plasmid DNA after Entry into the Atmosphere of Earth Investigated by a New Biomarker Stability Assay for Ballistic Spaceflight Experiments, PLoS ONE 9(11): e112979, DOI:10.1371/journal.pone.0112979 (26 November 2014) (extracts, underlines added)

Caveat

These findings would be still more persuasive, if they are replicated after (for example) 6 months of an orbital mission and its subsequent reentry.

Keep in mind, also, that external temperatures (during reentry) are estimates.

The moral? — A treasure trove for science fiction writers

If (as it seems) it is possible to carry Earth’s contaminating DNA outward into space — then — external origin DNA-like material could conceivably make it through our atmosphere to contaminate or populate the Earth.

What fun — and all from a clever research team playing around with a seemingly low probability idea.

Wind tunnel tests indicate that adding trailer skirts and bobtails to tractor trailers could reduce aerodynamic drag by 19 to 25 percent — a 25 percent reduction in drag represents about a 13 percent savings in fuel — at present, only 3 to 4 percent of American trucks use the devices

© 2014 Peter Free

Citation — to scientific conference presentation abstract

Jason Ortega and Kambiz Salari, Aerodynamics of Drag Reduction Devices for Semi-Trucks, American Physical Society Division of Fluid Dynamics — 67th Annual Meeting of the APS Division of Fluid Dynamics 59(20) (24 November 2014)

Citation — to press release

American Physical Society Division of Fluid Dynamics, How to Save Billions of Gallons of Gasoline, NewsWise (25 November 2014)

Wind tunnel testing validates what a very small minority of truckers are already doing

From the conference abstract:

An increasing number of semi-trucks throughout the United States are being retrofitted with aerodynamic drag reduction devices to improve the vehicle fuel economy. Such devices typically include both trailer skirts and boattails to mitigate trailer underbody drag and base drag, respectively.

In this experimental study, the wind-averaged drag coefficient is measured for a detailed 1/8th scale semi-truck model.

A number of trailer skirt and boattail device configurations are considered, as well as the effects of the boattail deflection angle. The results of this study demonstrate that a combination of a trailer skirt and boattail reduces the aerodynamic drag of a semi-truck by as much as 25%.

© 2014 Jason Ortega and Kambiz Salari, Aerodynamics of Drag Reduction Devices for Semi-Trucks, American Physical Society Division of Fluid Dynamics — 67th Annual Meeting of the APS Division of Fluid Dynamics 59(20) (24 November 2014) (extracts)

From the press release:

Fluid dynamicists Kambiz Salari and Jason Ortega ran aerodynamic tests on a detailed 1/8 scale model of a semi-truck in the wind tunnel facilities at NASA’s Ames Research Center at Moffett Federal Airfield in California.

The truck was tested in various configurations. In some, it was outfitted with trailer skirts, which are panels affixed along the lower side edges of a trailer that reduce drag resulting from airflow interacting with wheels and other structures under the body of the trailer; in others, a boat tail fairing, a device affixed to the back of the trailer that decreases drag by reducing the trailer wake size, was added. In still other tests, the truck was rigged with both of the drag-reducing devices (or with neither one).

Salari and Ortega found that adding both of the devices — which are currently used in combination on about three to four percent of the nation’s semi-trucks — reduced the aerodynamic drag by as much as 25 percent, which represents about a 13 percent decrease in fuel consumption.

“Even a minor improvement in a truck’s fuel economy has a significant impact on its yearly fuel consumption,” Salari said.

“For example, 19 percent improvement in fuel economy, which we can achieve, translates to 6.5 billion gallons of diesel fuel saved per year and 66 million fewer tons of carbon dioxide emission into the atmosphere. For diesel fuel costing $3.96 per gallon, the savings is about $26 billion.”

© 2014 American Physical Society Division of Fluid Dynamics, How to Save Billions of Gallons of Gasoline, NewsWise (25 November 2014) (extracts)

The moral? — Simple concepts, apparently big results

If the one-eighth scale results hold for full size tractor trailers, this represents an important advance in reducing trucking’s environmental footprint.

Digoxin probably contraindicated in atrial fibrillation without heart failure — a California Kaiser Permanente study

© 2014 Peter Free

25 November 2014

Citation — to study

James V. Freeman, Kristi Reynolds, Margaret Fang, Natalia Udaltsova, Anthony Steimle, Niela K. Pomernacki, Leila H. Borowsky, Teresa N. Harrison, Daniel E. Singer, and Alan S. Go, Digoxin and Risk of Death in Adults with Atrial Fibrillation: The ATRIA-CVRN Study, Circulation: Arrhythmia and Electrophysiology, DOI: 10.1161/CIRCEP.114.002292 (online before print, 20 November 2014)

Citation — to press release

Cyrus Hedayati and Janet Byron, Digoxin Associated With Higher Risk of Death and Hospitalization in Adults With Atrial Fibrillation and No Heart Failure, Kaiser Permanente (21 November 2014)

Demonstrating the analytical power of an HMO that tracks what it does

California’s Kaiser Permanente decided to investigate whether using digoxin to treat atrial fibrillation in the absence of heart failure was actually a good idea. The study ran from 01 January 2006 through 30 June 2009.

The research team looked at outcomes among 14,787 patients, who demonstrated atrial fibrillation, but no signs of heart failure:

During the study period, 4,858, or 17.8 percent, of the participants initiated digoxin use.

There were 1,140 deaths among the study cohort, with a significantly higher rate of death in digoxin users compared with non-users (8.3 vs. 4.9 per 100 person years).

At the same time, there were 8,456 hospitalizations for any cause, and the rate of hospitalization was higher for patients who received digoxin compared with those who did not (60.1 vs. 37.2 per 100 person years).

Cyrus Hedayati and Janet Byron, Digoxin Associated With Higher Risk of Death and Hospitalization in Adults With Atrial Fibrillation and No Heart Failure, Kaiser Permanente (21 November 2014)

In more scientific phraseology:

Digoxin remains commonly used for rate control in atrial fibrillation, but very limited data exist supporting this practice and some studies have shown an association with adverse outcomes.

We performed a retrospective cohort study of 14,787 age, gender and high-dimensional propensity score-matched adults with incident atrial fibrillation and no prior heart failure or digoxin use in the AnTicoagulation and Risk factors In Atrial fibrillation-Cardiovascular Research Network (ATRIA-CVRN) Study . . . .

We examined the independent association between newly initiated digoxin and the risks of death and hospitalization using extended Cox regression.

During a median 1.17 . . . years of follow-up among matched patients with atrial fibrillation, incident digoxin use was associated with higher rates of death (8.3 vs. 4.9 per 100 person-years . . .) and hospitalization (60.1 vs. 37.2 per 100 person-years . . . ).

Incident digoxin use was independently associated with a 71% higher risk of death (hazard ratio [HR] 1.71 . . . ) and a 63% higher risk of hospitalization (HR 1.63 . . .).

In adults with atrial fibrillation, digoxin use was independently associated with higher risks of death and hospitalization.

Given other available rate control options, digoxin should be used with caution in the management of atrial fibrillation.

James V. Freeman, Kristi Reynolds, Margaret Fang, Natalia Udaltsova, Anthony Steimle, Niela K. Pomernacki, Leila H. Borowsky, Teresa N. Harrison, Daniel E. Singer, and Alan S. Go, Digoxin and Risk of Death in Adults with Atrial Fibrillation: The ATRIA-CVRN Study, Circulation: Arrhythmia and Electrophysiology, DOI: 10.1161/CIRCEP.114.002292 (online before print, 20 November 2014) (at Abstract) (extracts)

Ponder the numbers

71 percent more likely to die and 63 percent more likely to be hospitalized are very big numbers in medicine. This is not a patient sample size or result that can be easily ignored.

The moral? — A showstopper

The authors’ conclusion, less diplomatically paraphrased, would be — “If you prescribe digoxin for atrial fibrillation in the absence of heart failure, you better darn well have some scientifically intelligible reason for doing so.”

Guess how likely that is going to be, unless and until a rebuttal study arrives.

Could inhibiting or functionally removing the brain’s suprachiasmatic nucleus improve memory in elderly people — who have chronic problems sleeping? — A finding in Siberian hamsters hints “maybe”

© 2014 Peter Free

Citation — to study

Fabian Fernandez, Derek Lu, Phong Ha, Patricia Costacurta, Renee Chavez, H. Craig Heller, and Norman F. Ruby, Dysrhythmia in the suprachiasmatic nucleus inhibits memory processing, Science 346(6211): 854-857, DOI: 10.1126/science.1259652 (14 November 2014)

Citation — to press release

Bjorn Carey, Stanford biologists explore link between memory deficit and misfiring circadian clock, Stanford University (17 November 2014)

Method and findings

From the abstract:

Chronic circadian dysfunction impairs declarative memory in humans . . . . [H]uman dysrhythmia occurs while SCN [suprachiasmatic nucleus] circuitry is genetically and neurologically intact.

Siberian hamsters (Phodopus sungorus) are particularly well suited for translational studies because they can be made arrhythmic by a one-time photic [light] treatment that severely impairs spatial and recognition memory.

We found that once animals are made arrhythmic, subsequent SCN ablation [destruction] completely rescues memory processing.

© 2014 Fabian Fernandez, Derek Lu, Phong Ha, Patricia Costacurta, Renee Chavez, H. Craig Heller, and Norman F. Ruby, Dysrhythmia in the suprachiasmatic nucleus inhibits memory processing, Science 346(6211): 854-857, DOI: 10.1126/science.1259652 (14 November 2014) (at Abstract) (extracts)

More detail

From Bjorn Carey’s excellent press release:

[T]hey trained Siberian hamsters in a standard learning and memory task, which involved familiarizing them with two objects and then, some time later, changing up one of the objects and seeing if the rodents noticed. On the whole, the animals excelled at the test.

Once the animals had mastered the task, the researchers exposed them to light at odd intervals, which threw off their circadian rhythms. The arrhythmic hamsters were then given the same memory task, and failed miserably.

Next, the researchers surgically removed each hamsters’ SCN . . . and gave the memory test a third time . . . . [T]he animals performed the test as well as they had at the beginning of the experiment.

Elderly people with neurodegenerative memory deficiencies also often complain of poor sleep, which can be associated with weakened circadian timing.

The new work suggests that rather than repairing the systems responsible for a misfiring SCN, it might be more productive to simply remove it from the equation.

“The more I investigate it, the idea of shutting off the SCN as a way of restoring memory ability in humans seems more provocative and possibly doable,” Ruby said. “If you are treating a a neurodegenerative brain, rather than fixing the circadian clock, it might be easier to just pharmacologically shut down the SCN.”

© 2014 Bjorn Carey, Stanford biologists explore link between memory deficit and misfiring circadian clock, Stanford University (17 November 2014) (extracts)

Caveat

Without a gram of belittlement intended, the suprachiasmatic nucleus probably controls a good deal more than we recognize. Taking it out of the “circuit” may create more problems than it solves.

I am also not convinced that there is a substantial subset among the elderly population, who simply have a circadian rhythm problem that is not accompanied by a wider neuro-degenerative one. The latter might itself account for the inability to drag an even adequately formed memory out of storage in useable form.

The moral? — Excellent work and a promising avenue of further investigation

My caveats may be completely wrong and are not intended to slight the worth of this clever study.

Comparing actual past ecological niches — to those predicted by backward looking climate models — has apparently demonstrated that existing models move species too far south — during the Last Glacial Maximum

© 2014 Peter Free

Citation — to study

Edward Byrd Davis, Jenny L. McGuire, and John D. Orcutt, Ecological niche models of mammalian glacial refugia show consistent bias, Ecography 37(11): 1133–1138, DOI: 10.1111/ecog.01294 (November 2014)

Citation — to press release

Jim Barlow, Fossils cast doubt on climate-change projections on habitats, University of Oregon (18 November 2014)

Past animal biology appears to have known something that we don’t

From the abstract:

Ecological niche models (ENMs) are crucial tools for anticipating range shifts driven by climate change. As hypotheses of future biotic change, they can be difficult to test using independent data.

The fossil record is the best way to assess the ability of ENMs to correctly predict range shifts because it provides empirical ranges under novel climate conditions.

We tested the performance of ENMs using fossil distributions from the Last Glacial Maximum (LGM, ∼21 000 yr ago).

We compared hindcast [backward looking] ENM LGM distribution hypotheses for five species of small mammals, drawn from the published literature, to the known LGM fossil record for those species and found a consistent southern prediction bias in the ENMs.

This bias urges caution in interpreting future range predictions, and we suggest that the Pleistocene and Holocene fossil record should be used as an additional resource for calibrating niche modelling for conservation planning.

© 2014 Edward Byrd Davis, Jenny L. McGuire, and John D. Orcutt, Ecological niche models of mammalian glacial refugia show consistent bias, Ecography 37(11): 1133–1138, DOI: 10.1111/ecog.01294 (November 2014) (at Abstract) (paragraph split)

Thus,

Blarina brevicauda (northern short-tailed shrew),

Martes americana (American pine marten),

Glaucomys sabrinus (northern flying squirrel),

Glaucomys volans (southern flying squirrel),

and

Myodes gapperi (Gapper’s or southern red backed vole) —

all lived farther north (and closer to the ice) than anticipated by niche-predicting models.

Why the error?

The authors suggest that:

In the end, we propose four possible causes for these patterns of biased prediction:

1) [M]odern distributions may not reflect the full range of environmental conditions in which a species can survive and, taken alone, serve as poor predictors of their potential distributions under other climate regimes.

2) The environmental tolerances of mammalian species can evolve fast enough to have changed since the LGM [Last Glacial Maximum], so modern distributions are poor predictors of deeper time distributions, but may still be good predictors of shallow time responses to climate change.

3) The problem lies with the general circulation models (GCMs) used to reconstruct LGM climate, so the reconstructed ranges are biased southwards because of incorrect temperature and/or precipitation values near the continental glaciers.

4) The models used to hindcast ranges are based on correlations between climatic variables and occurrence data in modern ecosystems.

[C]hanging distribution and relationships between climatic variables mean that modern ecosystems may not be appropriate analogs for alternative climatic regimes, such as those that existed during the LGM and that may result from future warming.

© 2014 Edward Byrd Davis, Jenny L. McGuire, and John D. Orcutt, Ecological niche models of mammalian glacial refugia show consistent bias, Ecography 37(11): 1133–1138, DOI: 10.1111/ecog.01294 (November 2014) (at Discussion, second to last paragraph) (extracts)

The moral? — We don’t know “squat”

Which is why I occasionally get irritated with the high levels of certainty that some modelers seem to extrapolate from their concocted guesses about (a) climate change and (b) its past and future effects on all manner of things.

Just because we know that warming is occurring (and generally why) does not mean that we can (today) reliably predict its consequences under complex past or future conditions.