Sniffs, pees and poos

Well, firstly, I need to apologize for being so quiet on the blogger world. I had SO much to absorb on arrival in Europe, and France was a little bit of a culture shock for me.   I am now settled in, and will resume a fairly regular blog of - as I write in my introduction in May 2013, "thoughts about all things dog, biological, microbiological, daily sniffs that seem unusual and needing some extra attention or investigation".  See, in France, or where we were from October to December, Banyuls-sur-Mer, the dogs roam the streets, come up to you and sniff your butt while you are on a leash, and then if you offer to play, very few have any concept of what that means.  Then, you can also poop and pee anywhere and everywhere. Much to ALRs disappointment, I have now got into the habit of squatting to pee in the middle of a walkway, not problem. Privacy, whats that?! When in France do as the French do, right?! ALR still picks up my poo, but people think it funny, as there is a full time employee, who drives around on his motorcycle, vacuuming up poop.

Now talking about poo, did you know that dogs align themselves to the Earths magnetic field when its stable, and they are free to poo off leash?!  When the magnetic field is unstable, such as during a solar flare, dogs may become confused (Hart et al., 2013). How about peeing?...it seems there is now a "Law of Urination", which demonstrates that regardless of their size, all mammals pee for about 21 seconds (Yang et al., 2013).

The first author hanging out with me

And now I am thinking about sniffing, and the French gastronomy. There was a recent interesting paper (Antony-Babu et al., 2013, Environ Microbiol. 2013 doi: 10.1111/1462-2920.12294) on the microbiology of truffles that showed that the microbial diversity differs inside and on the outside of truffles, and changes over time. Its not clear whether the microbes are specifically selected by the truffles, or whether the microbes are just enjoying the truffle environment.  One day, maybe I can sniff out some truffles for ALR as I have an acute sense of smell for apples, but also other goodies.

While trying to figure out the French dog culture,  I have been watching how the French dogs wag their tails, and found this general explanation for dog wagging (Siniscalchi et al., 2013). Turns out, a wag to the left suggest negative emotion with increased anxiety such as higher heart rate, while a wag to the right it more positive, and calming. Seems most dogs dont use this for communication, but can be explained as a result of the asymmetry of the brain, much like right-handed and left-handedness are.

Plate tectonics

Its interesting what we take so for granted-- plate tectonics, was once only a theory and as hotly debated as global warming and climate change is still today. The historical development of formulating of the plate tectonics ideas is very nicely documented in this article ..."How plate tectonics clicked". For me, volcanic eruptions, deep-sea vents, earthquakes, provide us of the humbling realization we live on a very active, living and sometimes volatile planet, unlike our dead friend Mars.  See, 50 years ago this week, two geologists Vine and Matthews, reported in Nature magazine that they thought that the alternating magnetic polarities in ocean rocks was evidence for seafloor spreading as continents were being pushed apart.  Mars on the other hand, has no magnetic field- or tectonics.  However, we may all have our origins from Mars as Dr Steven Benner presented at the recent Goldschmidt meeting in Italy see link Earth life "may have come from Mars".

If I had it all over again, I think I would like to be a search and rescue dog, not to search for life on Mars, but to help during natural disasters from tectonic plate movements.  I really like working. I am already a registered therapy dog, so could provide comfort, but I like finding things.. like tomatoes. Maybe while in France I can be trained to smell for truffles.

Munching on methane

Just over two weeks before we head to Europe on sabbatical. Dr. Dave is prepping my documentation. I had a rabies shot, 2 weeks ago or so, I have a new name tag, and I have to go back to see Dr. Dave for my wellness exam, before the USDA signs off on my medical certificate.  Phew.

Mufasa and I at a water fountain in Mosier

 In the meantime I met a young Leonberger, Mufasa, and we played and shared some water.  I tried to tell Mufasa about a recent discovery that was reported in Nature Geosciences journal. Because I still smell skunky when I get wet, it reminded of the article by Saito et al., 2013, DOI: 10.1038/NGEO1893 in Nature Geoscience that I read recently. Recall in a previous blog I made the analogy of the skunk tail-a plume- and then the skunk spray- also a plume ... with deep-sea hydrothermal plumes. Well, a new  hydrothermal plume with very high iron was discovered in the Southern Atlantic. In our oceans iron is a very important micronutrient in photosynthesis and nitrogen fixation, so estimating how much iron exists in our oceans has important implications, even for such factors as global climate. Much of this iron is derived as seawater circulates through the Earth's crust and is again released as hydrothermal fluid at deep-sea vents. Because we haven't studied many of the global deep-sea vents, and especially not the slow spreading ones like those in the southern Atlantic ocean, helium-3 concentrations have been used as a proxy (tracer) for hydrothermal activity in our oceans. Now what Saito et al found from iron  measurements in the plume that they discovered was that the helium proxy potentially grossly underestimates the hydrothermal input of iron into our global iron biogeochemical cycle. Other approaches for estimating iron, like models, in concert with helium measurements will in the future provide greater insights into the global fluxes of iron in our oceans. Unfortunately Mufasa wasnt really interested in this. I guess he's just 18 months old, so too young to understand ...

But just to illustrate how little we know about global biogeochemical cycles, Haroon et al., report  in Nature 500:567-570, the discovery of a novel archaeal lineage that couples anaerobic oxidation of methane (AOM) to nitrate reduction. AOM is a very important global biogeochemical process, as it reduces the release of the potent greenhouse gas, methane. Although the process has been known to occur for over 35 years, it has only recently been shown how microbes can do this energetically difficult task. And they can do this in a number of ways.. by coupling sulfate reduction to methane oxidation sometimes alone, or sometimes in collaboration with each other, or through through AOM coupled to denitrification. But if that isn't complex enough, Haroon et al show that yet another archaeon can also enjoy 'eating' methane with others by directly coupling AOM to nitrate reduction.   If ammonia is also present they get a little help from a bacterial anaerobic ammonia oxidizer friend, who keeps the other denitrifier (who is able to couple AOM to denitrification) at bay.  I do wonder if I have AOMs in my gut?  Probably not.

Recently, I have also been bossing my friend Albie around, training him how to clean faces. First you have to calm the subject. Then gently reach up to their face, but dont let them pull back. Here Albie, let me show you how.

Two other papers of note: Nature 500:541, Richness of human gut microbiome correlates with metabolic markers, and companion paper Nature 500:585, Dietary intervention impact on gut microbial gene richness.

Plumes and in memory of Jim Cowen

I know I was going to elaborate on the viruses publication... but so much has happened. So for now, I need to talk about plumes. Hydrothermal plumes, the beautiful tail (plume) of a skunk, the plume of odor that a skunk emits, the plume that a dead fish or old apple emits... and leads me to their loveliness.  You see, Jim Cowen studied hydrothermal plumes. I have never met him, but I believe he was a Leonberger soul, and ALR says he was, so he was. He also understood that, the further you got from the source, the geochemistry was diluted, but the microbes also really directing some of the dilution. I wish I learnt that from him, when I sniffed the beautiful black and white 'cat' that didnt run from me... He also looked deeper into why rocks, water, microbes and life are so carefully playing together in a beautiful interconnected web. Oh my, I tried to understand why 'cats' are cats and got one BIG blast in my face and in my mouth, no dilution... until ALR at 2AM put the antiskunk potion together, to dilute out the SKUNK.   The 'cat' was a SkUNK! You see, I think Jim knew, the really interesting things at deep-sea hydrothermal vents occurred in the hydrothermal plumes, not the deep super-heated water, not the crazy actively forming rocks/chimneys, but the diluted plumes.   The plumes tell a story of water traveled through different crevasses in the deep- rock interior, surfacing and intermingling with a cacophony of microbes that again change that story that might be written in the chemistry of the travels that the water has gone. These are the conduits of recycling and replenishing very important elements into our planet. 


So few scientists have that broad, yet detailed perspective of how the mechanics of our planet work.  I have tried-- but see where that got me- STINKY TINKY.  If only I had stayed a distance, observed the skunk,  I may have gained a deeper insight into the ways of plumes, which are in some ways like smoke stacks. And Jim, did, in a very quite and modest unassuming way, he showed how important cycles like methane oxidation, manganese oxidation and iron oxidation, all transform our ocean chemistry. He didnt get 'skunked', we all respected and enjoyed all he had to offer. He was generous with his time, kind in his ways and loved the water, like me. I have webbed feet (from my Newfoundland ancestry), and I think I was a water animal in some past life. But being skunked, the smell is intensified when I am wet, so, life has not been as good recently for me.  But especially not, as we have lost a great colleague, and water friend, a gentle soul. Jim Cowen passed away recently.  He fought a battle against cancer... quietly. I will miss not having ever met him, but ALR was very fortunate to have, early on in her career, and he made a very positive imprint on her life.
Thank-you Jim for YOU.

more microbes than cells in our bodies ??!

Today I walked a bit with ALR downtown. We stopped at one bus station... when a woman was quite curious.. but a little nervous about my size. ALR asked... "Do you want to say Hello"... the woman was nervous so I put on my best calmest, non-confrontational no eye contact, non-committal stance. And slowly she warmed to me, and slowly let me even investigate her face with a light purple lipstick and purple eye shadow to accentuate her lovely black skin.

This week in Nature "Insights into the phylogeny and coding potential of microbial dark matter", Rinke et al., sequenced about 200 single-cell genomes of 29 major and mostly uncharacterized branches in the Tree of Life.  But more interesting to me - sorry Rinke et al.. - was the National Public Radio  discussion of our personal microbiome.   You see, I am aware that in humans.. there are more microbes on your body than cells in your body, and well...  if you look after you personal microbial family, like I look after all my friends and people, and my person, ALR, then we will all be healthier.  When I was young, I was diagnosed with inflammatory bowel disease.   I think we're still not clear if it was an extreme infestation of Clostridium difficile or my microbiome showing an allergic response to something... like stress..  Now ALR's PhD thesis was on a nicer microbe called Clostridium acetobutylicum, so she knows something about this obligate anaerobic group of Bacteria, but she also understands how allergies or stress can imbalance the microbial ecosystem of our bodies. And together over the years she and I have managed whatever microbial imbalance I was born with. I clearly don't do well with grains, although I love chicken, any amounts will set the bowels moving... so ALR makes me eat only certain things, unless I sneak in something here or there. I do love vegetables. Broccoli, brussel sprouts, berries, apples.. cherries, oranges, bananas... so maybe in some past life I was a vegan.

So on this matter of the microbiome...  let me tell you about another recent paper in Nature. magazine. . "Antibiotic treatment expands the resistance reservoir and ecological network of the phage metagenome", Modi et al. July 11 2013, Nature. 499:219
Ok.. later. I need to sniff here a bit. more interesting for now. May be some dog who has no good intentions!

Happy Birthday Nelson! 18 July

I am a bit busy today, swimming, and staying cool in the Oregon sun, but I hear it can get quite a bit hotter in South Africa. I hope one day I can meet you , Nelson Mandela. I think you and I would be great friends. Dogs ... you know .. only see good in people. We believe, some day we dogs win  over people and other dogs. Nelson, -you did the same, and after many dog lives, much sacrifice, you almost miraculously..  helped transition South Africa... Trust is something we dogs know a lot about. And Nelson, you were able to provide that leadership to help build trust in humanity and forgiveness.   I think they still need a lot more Mandelas and Leonbergers. in the world.  I hear there is only one Leonberger family in Cape Town.   But maybe it's because we get confused with lions.

Happy Birthday Nelson.!  I do hope I can meet you some day, My ALR would also like to. When asked who she most admires in this world.. you are first, and then me. So... seems we have to meet! Licks.

I know you will always be there.
Tinka

What Dogmatix and I had in common this past week

Well- like Dogmatix, in the movie version of "Astérix et Obélix: God save Britannia", I couldn't go to China with my person. Dogmatix didnt go with Obelix to London. But like Asterix and Obelix, we will no doubt hear some of the China adventures in my blogspot.   You see.. my person's grandfather lived in Shanghai for a while in the early 1900's.. and when her very very best friend died, her mom, my person had just landed in Beijing, China. And her hosts were very kind and generous to her during that time.  So, there are strong bonds for my person in China.  I don't think there is a Leonberger in China, but my person did see an English sheep dog in Kunming, Yunnan Province.  Must be one lonely sheepdog! Not many sheep there.. goats and pigs is all I hear about. 

While my person, Anna-Louise (ALR from now on), was in China I had a blast.. with my friends Frank and Felix.  I was reminded of Dr Seuss who once said... "Today was good, today was fun, tomorrow will be another one". I had to do that to stay optimistic, and maybe you can do so too if you feel sad....

This post has no science citation, but a movie recommendation. If you were a kid and adult growing up reading the adventures of Asterix and Obelix, I think you will appreciate the new movie with Gerard Depardieu, Catherine Deneuve and others "Astérix et Obélix: Au service de Sa Majesté" or "Astérix et Obélix: God save Britannia".  About friends, Obelix says to Asterix, translated from French,  " You have no right to decide what's good for me".. "you said I am a burden and that you sacrifice everything for me... its a sacrifice if you get nothing in return. But..you do get something in return, you get a friend, me, Obelix".

Talking about friends and Britannia, I may have a new British friend called Jessie (below). Well.. aloof Brit Jessie, will maybe warm to me, even though I am female, I have a bit of a tomboy personality. See ya in Europe Jessie. I am quite a soccer star. I play defense.