Not surprisngly, Ebola outcomes may be tied to our genes

Ebola Virus

In mice, genetics dictates Ebola infection outcomes
[Via Ars Technica]

The outcome of Ebola infections often depends on a patient’s access to sophisticated medical care. But there’s the possibility that it could be influenced by genetics as well. That suggestion comes from the authors of a new paper that looked at what happens when genetically diverse groups of mice were exposed to the virus. As it turns out, the results ranged from losing a bit of weight to complete mortality.

The work doesn’t seem to have been inspired by looking for insight into the progression of hemorrhagic fever in humans. Instead, the researchers involved appear to have been frustrated by the fact that the most convenient research mammal, the mouse, doesn’t experience the symptoms typical of Ebola infections in humans: no problems with blood coagulation, no hemorrhages, and no shock. So they decided to see if they could find a mouse strain that did show these symptoms (and would thus enable convenient studies).

To do so, they started with something called the Collaborative Cross collection. Most of the mouse strains used in research have been inbred until all members of the strain are genetically identical. There are, however, differences between strains; C57 mice are genetically distinct from 129 mice. So it’s possible to see very different things happen if you do the same experiment in different strains.


Very interesting way to find an animal model for Ebola. They looked at a lot of mouse strains to see how they would react.

And  they saw a huge range, from mice that showed no effects to mice that died without symptoms to mice that had similar symptoms as humans,

It will be interesting to see just what is going on, especially since different gene expression patterns were seen. This suggest that epigenetic processes may also be involved.

Whales may only taste salt


The loss of taste genes in cetaceans
[Via BioMed Central - Latest articles]

Background: Five basic taste modalities, sour, sweet, bitter, salt and umami, can be distinguished by humans and are fundamental for physical and ecological adaptations in mammals. Molecular genetic studies of the receptor genes for these tastes have been conducted in terrestrial mammals; however, little is known about the evolution and adaptation of these genes in marine mammals. Results: Here, all five basic taste modalities, sour, sweet, bitter, salt and umami, were investigated in cetaceans. The sequence characteristics and evolutionary analyses of taste receptor genes suggested that nearly all cetaceans may have lost all taste modalities except for that of salt. Conclusions: This is the first study to comprehensively examine the five basic taste modalities in cetaceans with extensive taxa sampling. Our results suggest that cetaceans have lost four of the basic taste modalities including sour, sweet, umami, and most of the ability to sense bitter tastes. The integrity of the candidate salt taste receptor genes in all the cetaceans examined may be because of their function in Na+ reabsorption, which is key to osmoregulation and aquatic adaptation.


Must be a boring world of food for them. 

Could eating disorders be auto-immune diseases brought on by gut bacteria?


Molecular Origins Of Eating Disorders Found In Gut Microbe |
[Via  Neomatica]

The incidence of eating disorders (EDs) such as bulimia and anorexia nervosa somewhere between 5 to 10% of the population but there is very little understanding of the biological mechanism that is the source of the disease. Given that mood disorders such as depression and schizophrenia have roots in biochemical imbalances, there is speculation that eating disorders can be traced to a similar cause.

Now researchers at the French Institute of Health and Medical Research and the University of Rouen in France have found strong evidence that a protein made by intestinal bacteria are a causative agent for the disorders. Specifically, antibodies made by the host against this protein cross-react with a mammalian satiety hormone. The severity of symptoms in ED patients was also found to correlate with levels of the neutralizing antibodies. The researchers believe that this understanding will ultimately lead to a chemical therapeutic strategies to correct eating disorders.


Interesting paper (Which is Open Access). Our intestinal bacteria might be responsible for human behavior we generally think of as mental rather than physical.

People with eating disorders (such as bulimia, anorexia) have circulating antibodies to a known human protein – α-melanocyte-stimulating hormone (α-MSH).

The levels of auto-antibodies to α-MSH correlate with severity of disease. α-MSH also influences anxiety and stress. And α-MSH is known to affect eating behavior, binding to important parts of the brain.

So, how do these auto-antibodies arise? One theory about all auto-antibodies is that they arise from exposure to external, such as bacterial, proteins. The body generates antibodies to these proteins that cross eact with self proteins in the person.

The authors did a database search for bacterial proteins, along with ones from viruses, fungi and archea, that had at least 5 consecutive amino acids in common with α-MSH.

They found a hit in ClpB – a heat-shock disaggregation chaperone protein – from the common gut bacteria Esherichia coli. 

The authors showed that  anti-ClpB antibodies could be found in people with  eating disorders and that these antibodies crossreacted with α-MSH.

Their experiments in mice indicate that this protein may well be involved in weight loss. Antibodies that crossreacted with α-MSH could be raised  following exposure to purified ClpB..

These antibodies has an inhibitory effect on α-MSH activity. There was a decrease in the food intakes for mice  exposed to ClpB.  

And they showed that the presence of E. coli in the guts of mice resulted in similar effects on eating behavior. The mice also developed anti-ClpB antibodies that crossreacted with α-MSH.

Yet mice with E. coli lacking the ClpB gene did not show eating behavior changes. And no auto-antibodies.

The extent of the effects in mice were often short-lived. While this could be due to differences in the murine and human immune systems, it suggests something more complex going on.

Because exposure to purified CLpB protein or to E. coli producing ClpB had different effects on the immune system and different effects on eating.

This  may have something to do with the type of antibodies raised and their affinity for α-MSH. Low affinity IgG antibodies against α-MSH correlated with weight gain while high affinity IgM correlated with weight loss.

It may not simply be the presence of auto antibodies but the type of auto antibodies.

Thus, as science almost always does, there are more questions.

It is interesting that ClpB is a stress related protein for E. coli, helping deal with protein stability when the environment the bacteria is in comes under attack. 

Because α-MSH is also related to stress and anxiety in humans.

From the paper:

Although such functional similarity might be coincidental, it may also suggest a phylogenetic link in development of coordinated responses to stress in bacteria and the mammalian host. Furthermore, such a link would implicate bacterial stress-activated proteins in the pathophysiology of stress-related diseases in humans

Proteins like ClpB are also found in a lot of other bacteria, so it may not be directly from E. coli the problems arise. In fact, several bacteria involved in intestinal disease such as Salmonella or Shigella may be more likely possibilities.

It makes some sense – someone has a bout of nausea, illness, diarrhea and vomiting from food poisoning, then develops antibodies that reinforce behavior that involves eating.

Examining other possible auto-antibodes that could be derived from exposure to intestinal flora and that affect eating problems sure seems like a nice place to spend a career. 

From the paper:

Although such functional similarity might be coincidental, it may also suggest a phylogenetic link in development of coordinated responses to stress in bacteria and the mammalian host. Furthermore, such a link would implicate bacterial stress-activated proteins in the pathophysiology of stress-related diseases in humans

Ebola not very contagious and hard to get


No, Seriously, How Contagious Is Ebola? : Shots – Health News : NPR
[Via Health News : NPR]

Holy moly! There’s a case of Ebola in the U.S.!

That first reaction was understandable. There’s no question the disease is scary. The World Health Organization now estimates that the virus has killed about 70 percent of people infected in West Africa.

The Ebola case in Dallas is the first one diagnosed outside Africa, the Centers for Disease Control and Prevention said Tuesday. And the health care system in Texas didn’t quarantine the man right away. He was sick with Ebola — and contagious — for four days before he was admitted to the hospital.


This is an important number to get out. It’s R0 is 2.  It represents the basic reproduction number. Someone with Ebola infects 2 others.

This is quite low (measles has an R0 of about 18) and can be dealt with using public health protocols.

It is not easy to get Ebola. Simple isolation can stop an epidemic. Only 50% of the people would need vaccines for herd immunity to work. We need >94% immunized to protect against pertussis or measles.

Vaccines are on the way. Add in useful therapies like anti-virals and there should be little to worry about. 

Tom Lehrer demonstrates that what many call traditional today was once radical

(h/t to my mother who not only turned me on to Tom Lehrer but whose own inability to follow the New Math I was being taught often resulted in exasperated rants but helped me learn as I tried to explain it to her. plus ça change, plus c’est la même chose)

Parents complaining about  the math being taught to their children seems to be a constant refrain probably  going back to Hammurabi.

It continues today. Anyone with a sense of humor, a sense of history and who grew up in the 60s should get a smile on their face and a wry shake of the head.

For those following the contretemps of Erick Erickson’s rant about current math approaches 9my bold)

The traditional method of subtracting, borrowing and carrying numbers, is derisively called the “Granny Method.” The new method makes no freaking sense to either my third grader or my wife.


This is maddening and angering and frustrating. This is why so many parents are so upset. They cannot help their children. The math makes no sense and seems to offer no practical purpose other than it is new. The teachers privately concede the uselessness of it.

As we can see from the video above – a Tom Lehrer song from the early 60s  bemoaning the very approach of borrowing in subtractions that Erick claims is traditional – what was radical 50 years ago is now just the way it is supposed to be.

It is the Granny method because it was actually first taught to people who are now grandparents. Then it was the radical New Math.

His second paragraph could probably be reused by parents in every generation ever. I know that it could have come right out of the mouth of any parent when I was a child. To this day my mother and I laugh about number lines and negative numbers.. 

But all the problem is demonstrating is simply another strategy for subtracting, one that we actually all pretty much use in our heads to figure out things like change back, etc. – I gave him $5 for a $3.62 coffee. $3.62 to $4 is $0.38 and 4 to 5 is $1 so i should get back $1.38. Nobody uses the granny method on their head to figure that out.

It is humorous that what he learned as a child is now the traditional way, not the radical New Math it was depicted at the time.

What Erick sees as traditional was actually once so radical that satirical songs could be written about it. People laughed at what he now thinks is traditional. I bet his parents ranted about the very thing he now sees as traditional.

And I bet that Erik’s daughter will be bemoaning the way her children are being taught math rather than the traditional way of counting up subtraction.

The more things change, the more they stay the same.

Understanding chemistry using fully relativistic quantum calculations

baker test

Making a chemical with electrons that move at 80% the speed of light
[Via Ars Technica]

Sometimes, getting exactly the result you predict is more exciting than it sounds. Last week, Science published a paper about creating chemical compounds with element 106, Seaborgium. A quick glance at the abstract showed that this chemical behaved similarly to the one made of Sg’s lighter cousin, tungsten. That sounds a bit dull—in fact I skipped covering it last week for precisely this reason—until you find out that you wouldn’t necessarily expect this result.

Admittedly, just getting the experiment done at all is pretty impressive. The isotope of seaborgium used, 265Sg, has a half-life of only 16 seconds. It has to be produced in a particle accelerator, which means it’s normally rather energetic and part of a cloud of energetic debris. So, the technique involved slowing it down and separating it, letting it undergo a chemical reaction, and only then could they characterize something about the resulting chemical’s behavior.

In this case, the researchers reacted it with carbon monoxide to form Sg(CO)6. The resulting chemical stuck to a silicon dioxide surface briefly before the Sg decayed, allowing a very basic characterization of its chemical behavior. And, as noted above, it behaved similarly to the tungsten version of the same compound.


Yep, the only way to understand the chemistry of some of these unusual elements is to include ‘unreal’ quantum effects on particles moving at almost light speed.

Here, the proper chemistry could only be determined by realizing that the electrons of Seaborgium are moving (if we can use that word) at 80% light speed. In hydrogen, the electrons travel at about 1% the speed of light.

Relativistic quantum mechanics are responsible for many weird things in the physics world. They are invading the chemical world. 

What is cool – Seaborgium (element #106) is named after Glenn Seaborg who proposed an island of stability up around element #115. Understanding the chemistry of seaborgium may help us get there.

Seaborg is one of the greats of the 20th century, not only discovering plutonium and figuring out how to isolate it, his work redrew the Periodic table. He patented americium which helped him in his old age. He worked hard for arms control, ran the Atomic Energy Commission and, as chancellor of UC Berkeley  he relaxed control of political speech in the lat 50s.

The pictire above is from the Baker test at Bikini atoll, the first underwater explosion that resulted in so much radioactive contamination that further tests were canceled. Glenn Seaborg called it the first atomic disaster.

West Coast climate more affected by ocean than by air

 Malibu Beach, California

Changing Winds Explain Most Pacific Coast Warming 
[Via SFCC]

Changes in winds over the eastern Pacific Ocean explain most of the warming trend along the West Coast of North America in the last century, according to a new analysis published in the Proceedings of the National Academy of Sciences.

Similar atmospheric shifts are known to drive fluctuations in Pacific climate over decades in the form of the Pacific Decadal Oscillation (PDO), a long-recognized pattern of seesawing ocean temperatures. The new research indicates that similar changes in regional pressure and winds can also drive trends in sea surface and coastal air temperatures that extend over a century or more.

This study used independently measured ocean and land-surface air temperature records from 1900 to 2012 to confirm an already well-documented increase of approximately 0.5 to 1 degree Celsius in the northeast Pacific Ocean and nearby land areas. What’s especially interesting and new about this work is that independently measured atmospheric sea level pressures over the past century show that circulation changes account for nearly all of the year to year, decade to decade, and century long surface temperature changes in the northeast Pacific Ocean and West Coast states since 1900.


A nice discussion from the authors of their research all over the news about West Coast warming. Here is the relevant graph:


First, you do not see the same sort of temperature trend for West Coast temperatures as seen globally. One of the benefits of living on a coast – the oceans modulate the temperatures. As shown in this paper. This is not new and has been known for some time.

What is new is that almost all of this can be modeled using ocean-driven winds, not by direct impacts of greenhouse gas emissions into the atmosphere.

It has been known for a long time that coastal temperatures have not risen as rapidly an interior temperatures. The question was, was any effect due to direct emissions of greenhouse gases? The model the authors present indicate that West Coast air temperature change fits best with changing wind patterns than with CO2 release.

As the authors state:

This study used independently measured ocean and land-surface air temperature records from 1900 to 2012 to confirm an already well-documented increase of approximately 0.5 to 1 degree Celsius in the northeast Pacific Ocean and nearby land areas. What’s especially interesting and new about this work is that independently measured atmospheric sea level pressures over the past century show that circulation changes account for nearly all of the year to year, decade to decade, and century long surface temperature changes in the northeast Pacific Ocean and West Coast states since 1900.

Changes in winds explain most of the temperature differences, most of which took place before 1940. And the winds are determined by ocean currents and ocean temperatures. 

They make the point that regional variation is not the same as global. While at a global level, we can see changes, at more granular levels, such as regions, other factors can dominate. It is not surprising that being near an ocean can ameliorate temperature changes since this is one reason people like living near oceans – it is not nearly as hot or as cold as living inland.

So, the change in wind patterns explains most of the atmospheric temperature variability for parts of the West Coast. But what is causing the wind patterns to change? As the authors state:

This study shows that atmospheric circulation changes, essentially changes in winds, were the proximate cause for West Coast/NE Pacific temperature changes from 1900 to 2012. If anthropogenic effects were important for NE Pacific / west coast warming from 1900 to 2012, they likely occurred through an indirect circulation pathway that that is not well simulated by current global climate models. The more we understand the regional climate dynamics discussed in this research the better we can understand how they may interact with human-caused climate change, and what the combined effect on the region’s climate may be.

Indirect pathways in ocean circulation  are what we would expect from anthropogenic release of CO2 into the atmosphere. We are not putting the CO2 or heat directly into the ocean. We do know that the ocean is soaking up a lot of atmospheric heat. 90% of the additional heat is being stored in the oceans.

This will likely have an effect on ocean circulation and thus atmospheric properties, but an indirect one rather than the direct effect.

Getting a better idea of the effects on ocean circulation patterns will help inform us a lot, not only at the regional level but at the global.

We really do not have a great idea of all the drivers behind these ocean changes (such as El Nino or the Pacific Decadal Oscillation), although we are gaining a better understanding all the time.The oceans are the greatest heat sink we have but since we do not live there, we do not have as much data as we have with atmospheric data. 

Understanding this as fast as possible will make for better models. That is what science does.


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