Ear To The Ground

Genetic analysis of A/H1N1 flu virus finds a mixture of diverse parts, and support basis for concern about future mutations

Prior posts have noted that many of humankind's diseases were acquired from domesticated animals.  What is interesting about the recently emerged "swine flu" is its mixture of components, which suggests that monitoring of animal diseases, viruses, and bacteria may be mandatory to anticipate the emergence of new diseases that will impact humans.  It is still unclear if the virus "jumped" directly from pigs to humans or if it infected an intermediate host before jumping to humans.

The H1N1 (aka "swine flu" aka A/H1N1) virus combines old viruses in a new mix, as shown by recent genetic analysis.  [See http://www.sciencemag.org/cgi/content/abstract/1176225.] 

The components have apparently been circulating in human and swine populations for years, but A/H1N1 combines them in a unique manner.  The genetic analysis demonstrated that three of the virus' genes, including hemagglutinin (the H in H1N1), came from the 1918 "Spanish" influenza virus and has been present unchanged in pigs ever since.

However, A/H1N1 does not contain the genetic changes which are believed to have helped the 1918 flu and the H5N1 "avian flu" viruses to adapt to humans.  Thus, there is some other, as yet unknown, component that permits transmission from person to person. 

A study of the virus' neurminidase protein (the N in H1N1) also shows that the virus is sensitive to some drugs, but that parts of the protein which are important for vaccine development and antibody therapies are already changing.  Never a good sign for what the future may bring.  See http://www.biology-direct.com/content/4/1/18.  The closest relative of the virus' neurminidase protein is from a Eurasian swine flu virus that, it is believed, leaped from birds to pigs in about 1979.

Showing why concern about A/H1N1's future structure is justified, another recent report analyzed current viruses and virsues isolated from patients during the first two weeks of the outbreak, and found that there already have been changes on the outer surface of the neuraminidase protein.  The changes could interfere with antibodies against the virus as well as alter the effectiveness of future vaccines.  However, none of the changes have altered the parts of the protein targeted by the antiviral drugs Tamiflu and Relenza, among others.  See http://mendel.bii.a-star.edu.sg/SEQUENCES/H1N1/, which also contains images showing the interaction between the virus and various antiviral drugs.

Finally, here is an image of the neuraminidase protein.

The antiviral drug zanamivir (Relenza) is shown in green.  Regions where the new virus differs from the H5N1 avian flu and the 1918 H1N1 Spanish flu are shown in yellow.  Mutations occurring among different patients within the first weeks of the 2009 outbreak appear in red.

Alternative energy technologies that may, or may not, be on the horizon

Prior posts have noted a variety of technologies that MAY have promise sometime in the next decade, assuming they are perfected and are commercially viable.  In the area of photovoltaics, prior posts have noted a variety of technologies that hold the promise of improving conversion efficiency, utilizing a broader portion of the visible and invisible spectrum, and maximizing energy utilization during the day. 

An interesting synopsis of the potential of nano-engineering to produce substances that may boost alternative energy can be found at http://www.economist.com/sciencetechnology/displaystory.cfm?story_id=13941135.  One of the more interesting developments described is the vast increase in conversion efficiency of PV cells, though it is still far from being economic for general application.

Hydrogen storage has been one of the great barriers to the use of this fuel for vehicles.  What may help with storage and keep the cost reasonable?  Chicken feathers.  Not quite practical yet, to be kind.  But, a fun read.  See http://www.economist.com/sciencetechnology/displaystory.cfm?story_id=13941111.

Computer modeling supports supposition that Antarctic ozone hole may be key factor explaining why seas around Antarctica are absorbing less CO2

Recent research has indicated that the oceans surrounding Antarctica are not absorbing nearly as much planet-warming CO2 from the atmosphere as they did in previous decades.  This assessment has been subject to criticism.  [See https://www.sciencemag.org/cgi/content/full/319/5863/570b.]  In this research, scientists speculated that meteorological effects of the high-altitude ozone hole over Antarctica, including strengthening of winds at sea level, might be the cause for the decreased absorption.

 

In a newly published study, results of computer simulations bolster that conclusion.  See http://www.agu.org/pubs/crossref/2009/2009GL038227.shtml.  The researchers used climate models to compare two scenarios: one in which the stratosphere over Antarctica had no ozone hole from 1975 to 2004 and one in which the stratosphere had a hole like the one that has actually developed.  The average results of the two scenarios differ little from 1975 to 1986.  However, from 1987 onward, wind speeds over the high-latitude southern oceans were higher in the ozone-hole scenario than in the simulations that lacked an ozone hole.  Differences between the scenarios became larger with every passing year.  In the ozone-hole scenario, wind speeds in some areas were 60 percent higher in 2004 than they had been in 1975.

 

The researchers believe that the increase in wind speeds has triggered a series of real-world effects. First, the stronger winds stir the surface waters more effectively and boost the upwelling of waters from the deep — waters that include large amounts of dissolved CO2 from the decomposition of ocean life that died and sank to the depths.  As the surface waters become more enriched in CO2, they can absorb less carbon dioxide from the atmosphere, explaining the reduced uptake of that gas previously noted by scientists.  The simulation suggests that between 1987 and 2004, the southern oceans absorbed about 9 billion metric tons less CO2 than they would have without the ozone hole.  The increased concentrations of dissolved CO2 also boosted the ocean’s acidity in the ozone-hole scenario.  Surface water pH dropped (became more acidic) by about 0.02 units, about 10 percent of the change measured in oceans since the beginning of the Industrial Revolution.

 

For the next half century [the period that scientists estimate it will take for the ozone hole to "heal" after banning ozone-destroying chemicals; see http://uk.reuters.com/article/idUKL1671376220071016] reduced CO2 uptake in the southern oceans may exacerbate or speed the effects of climate change globally.

Exposure to traffic generated air pollution may increase the risk of rheumatoid arthritis

Prior posts have noted the variety of adverse health effects from traffic generated air pollutants, particularly from PM10 and PM2.5 particulate matter.  As noted in these prior posts, one of the effects seen is an increase in systemic inflammation.

Rheumatoid arthritis [see http://en.wikipedia.org/wiki/Rheumatoid_Arthritis] is a chronic, systemic inflammatory disorder that may affect many tissues and organs, but principally attacks the joints; it may progress such that there is destruction of the articular cartilage and ankylosis of the joints.  Genetic factors explain less than half of the cause of rheumatoid arthritis (RA).  Because traffic generated air pollution has been associated with a systemic inflammatory response, researchers examined the association between exposure to such pollution and RA.

They studied 90,297 U.S. women that are participants in the Nurses’ Health Study.  They used a geographic information system to determine distance to road at the residence in 2000 as an indicator of traffic pollution exposure.  Using Cox proportional hazard models, the researchers  examined the association of distance to road compared with the incident RA (1976–2004) with adjustment for a large number of potential confounders.

As a result, in models adjusted for age, calendar year, race, cigarette smoking, parity, lactation, menopausal status and hormone use, oral contraceptive use, body mass index, physical activity, and census-tract-level median income and house value, the analysis found an elevated risk of RA [hazard ratio (HR) = 1.31 ; 95% confidence interval (CI) , 0.98–1.74] in women living within 50 meters of a road, compared with those women living 200 meters or farther away.  They also observed this association in analyses among nonsmokers (HR = 1.62; 95% CI, 1.04–2.52), nonsmokers with rheumatoid factor (RF) -negative RA (HR = 1.77; 95%CI, 0.93–3.38), and nonsmokers with RF-positive RA (HR = 1.51; 95% CI, 0.82–2.77).  They found no elevations in risk in women living 50–200 meters from a road.

The researchers thus concluded that the observed association between exposure to traffic pollution and RA suggested that pollution from traffic in adulthood may be a newly identified environmental risk factor for RA.

The report can be found at http://www.ehponline.org/members/2009/0800503/0800503.pdf.

BPA to be considered by OEHHA's DART Committee for listing under California's Proposition 65

Prior posts have noted the nature and procedures related to Prop. 65.  The Developmental and Reproductive Toxicant Identification Committee of OEHHA’s Science Advisory Board identifies chemicals for addition to the list of chemicals known to the State to cause reproductive toxicity (California Health and Safety Code Section 25249.8).  Under Prop. 65 "reproductive toxicity" is a term of art that encompasses "chemicals" [another term of art] that cause birth defects and/or interference with male and/or female reproduction.

A public meeting of the DART Committee is scheduled to be held on Wednesday, July 15, 2009 in the Auditorium of the Elihu Harris State Building, 1515 Clay Street, Oakland, California.  On the Committee's agenda is consideration of the underlying data to support a listing of Bisphenol A as a reproductive toxicant.  The 120-page Hazard Identification Materials that will be considered by the Committee can be found at http://www.oehha.ca.gov/prop65/CRNR_notices/state_listing/pdf/dart090707_3.pdf.

On the day of the meeting, a link to the audiocast of the meeting will be posted on the OEHHA web site at http://www.oehha.ca.gov/prop65/whats_new/index.html.

OEHHA prioritizes chemicals for evaluation for listing under Prop. 65

Prior posts have discussed the nature and procedure of California's Proposition 65.  A recent meeting of the Carcinogen Identification Committee examined 38 chemicals to determine the priority with which OEHHA should address them as part of its Hazard Identification material preparation.  The CIC recommended that 9 be placed in the "high priority" category, 13 in the medium, and the balance in the low.  A transcript of the meeting can be found at http://www.oehha.ca.gov/prop65/public_meetings/pdf/cicMeetingTranscipt052909.pdf.

The Chemical Prioritizations are as folllows:

High	Medium	Low
Amphetamine and its salts	11-Aminoundecanoic acid	2-Amino-5-nitrothiazole
1,3-Dichloro-2-propanol	Aspartame**	Anthanthrene
Diisononyl phthalate (DINP)*	Dicofol	Benoxacor
2,6-Dimethyl-N-nitroso-morpholine	Diethanolamine (DEA)	2-Chloro-1,1,1-trifluoroethane
Fluoride and its salts	Hydroquinone	D & C Yellow #11
Haloperidol	Methoxychlor	N,N-Diethylthiourea
3-Monochloropropane-1,2-diol (3-MCPD)	Methyl ethyl ketoxime	1,3-Dinitropyrene
N-Nitrosohexamethyleneneimine	3-Nitrofluoranthene	Ethylnodiol diacetate
Perfluorooctanoic acid (PFOA) and its salts and transformation and degradation precursors	N-Nitrosoanabasine	Molybdenum trioxide
	Permethrin	Nitrofurantoin
	Tetrachlorvinphos	5-Nitro-o-toluidine
	Thiamethoxam	Rock wool
	Tris(1,3-dichloro-2-propyl) phosphate (TDCPP)	Triamterene
		Triclosan
		Triethanolamine (TEA)
		Vinylidene chloride

California Air Resources Board delays vote on carbon fee

A prior post noted that California was planning on imposing a fee on carbon emissions [and equivalents] to fund the State's GHG program.  [See 6/10/09 post.]  The ARB has now decided to delay adopting the fee, at least until the July 23 meeting of the Board.

For more details, see http://latimesblogs.latimes.com/greenspace/2009/06/carbon-fee-ab-32.html.

House Agriculture Committee seeks to stop EPA from evaluating indirect GHG effects of corn-based ethanol production

Prior posts have noted the nature of the life-cycle evaluation that EPA is undertaking to ascertain if ethanol meets the renewable fuels standards.  Prior posts have also noted that taking into account "indirect" effects, such as loss of rain forest due to conversion of the land to agricultural production to provide the inputs for ethanol production, would more likely than not result in ethanol not being classified as a renewable fuel.  EPA in May had introduced a rule to allow such an evaluation.  Well aware of the impact of such an evaluative approach on ethanol, the ethanol industry has been lobbying and complaining about EPA's method of calculation.  It now appears that the House Agriculture Committee has agreed amongst its members to prevent the use of such a calculation method for the next six years.

A good review of this issue, if a little dated, can be found at http://www.time.com/time/health/article/0,8599,1897549,00.html.

As noted in prior posts, one of the great shortcomings of all evaluations related to agriculture is the failure to assess the impact of increased emission of N2O due to bacterial production in response to fertilizer.  [See, for example, 4/14/09 post.] What is interesting about the debate over corn-based ethanol production is the complete absence of any awareness of this issue.  

Government of Virgin Islands is not entitled to sovereign immunity from counter-claims filed in CERCLA case

The Virgin Islands Department of Planning and Natural Resources (“DPNR”), acting as trustee for the natural resources of the Virgin Islands, and the Government of the Virgin Islands, as parens patriae, filed suit under CERCLA, as well as under territorial statutes and the common law, against numerous defendants in a case related to contaminants allegedly released from industrial facilities situated on St. Croix.  The defendants filed counter-claims; the governmental entities claimed sovereign immunity as a defense, and thus filed a FRCP 12(b)(6) motion to dismiss the counter-claims.

 

In Mathes et al v. Century Alumina Co., LLP, et al, 2009 U.S. Dist. LEXIS 52135 (D.V.I.: 6/19/09), the District Court addressed the motion.   The Court noted that CERCLA’s definition of “person” includes the Virgin Islands, and as such the statute contains an express waiver of sovereign immunity.  Plaintiffs contended that Congress lacked the authority to waive such immunity.  The Court noted that the U.S. Supreme Court had held that an immunity waiver under CERCLA as to the Federal government was appropriate, but had held that the 11th Amendment defeated such a waiver as to States; the only exception permitted was one such as that found in 14th Amendment (which was not at issue in the case).

 

The Court then noted the language of Art. IV, Section 3, Clause 2 of the Constitution, the so-called Territorial Clause:  “The Congress shall have power to dispose of and make all needful Rules and Regulations respecting the Territory or other Property belonging to the United States; and nothing in this Constitution shall be so construed as to Prejudice any Claims of the United States, or of any particular State.”  Congress thus had plenary powers over territories.  The Court noted that the Third Circuit had consistently held that although the Virgin Islands had some sovereign immunity, it existed solely per the Organic Act.  The Organic Act provides that the Virgin Islands have sovereign immunity only to the extent explicitly granted by Congress.  If Congress can grant, it can also take away.  As such, counter-claims under CERCLA were appropriate.

 

The Virgin Islands then argued that sovereign immunity barred the counter-claim for recoupment.  Citing to numerous Court of Appeals and U.S. Supreme Court case law, the District Court noted that a counterclaim sounds in recoupment if: “1) the claim arises from the same transaction or occurrence as the main claim; 2) it seeks relief of the same kind and nature as that sought by the main claim; and 3) the claim is defensive in nature and does not seek affirmative relief.”  This was the nature of the counter-claim; they alleged that the government was in some manner responsible for the initial contamination.  As such, where a state actor brings an action as a plaintiff, sovereign immunity generally will not impede a counter-claim for recoupment under such circumstances.  The District Court distinguished cases disallowing recoupment counter-claims by pointing out that those claims were based on post-contamination conduct, which was different from the governmental claims being made.

 

The government also argued that FRCP 13 prevented the counter-claims in view of the limited capacity of the DPNR in the case as trustee for natural resources.  The Court noted that case law made clear that the “opposing party” rule should not be applied mechanically, and that principles of equity and judicial economy mandated that all related claims be addressed together.

 

Thus, the motion to dismiss the counter-claims was denied.

Much to everyone's surprise, basking sharks go south for the winter

Basking sharks, the second largest fish, are commonly seen in temperate regions of the Atlantic and Pacific oceans.  Previous studies showed that basking sharks in the North Atlantic feed on plankton off the coast of New England during the late spring, summer and early fall.  The accepted thesis was that basking sharks were limited to temperate regions.  The 6-to-7-meter sharks disappear from view in the wintertime; some researchers have suggested that the sharks hibernate on the ocean floor.

Using satellite-based tagging technology, researchers found that basking sharks migrate to the tropical waters of the Caribbean when the weather in their temperate locales gets cold.  Although basking sharks usually swim near the ocean surface in the spring and summer, the sharks made their winter journeys at depths of 200 to 1,000 meters and stayed at those depths for weeks or months at a time.  Researchers believe that this may explain why no one spotted the sharks at their winter location. 

Why basking sharks make the trip is still unknown.  The waters off the coast of South Carolina, Georgia, and Florida would provide similar temperatures as the tropics and ample plankton for food, the researchers note.  Why they swim so far south in still not understood.  One theory is that basking sharks travel south to mate and give birth; however, neither a pregnant female nor a baby basking sharp has ever been seen.  The researchers speculate that the tropics could provide a good nursery location because of stable water temperatures and few predators.

The study can be found at http://www.mass.gov/Eoeea/docs/eea/press/curbio7233.pdf.