Microbes in soil can work with plants to fight off disease

http://www.the-scientist.com/?articles.view/articleNo/33703/title/Fighting-Microbes-with-Microbes/

It is a very interesting article, albeit long. A summary:

There are 30,000 species of microbes in soil samples, vs 10K in humans. Current ag methods kill most but not all microbes, creating a vacuum for opportunistics.

Tomato plants communicate via a fungal network in the soil. Infected plants grown in the presence of this fungus warn neighbors about the disease, inducing the plant to produce disease fighting proteins.

A beneficial bacteria B subtilis establishes itself in the soil by blocking plant defenses, producing an antimicrobial at the same time, which may protect the plants roots while it is establishing. Other plants that were infected with bad bacteria Pseudomonas produced a sugar food source for B subtilis to encourage it's colonization of the roots. This triggered the plant to produce defensive chemicals. They worked together! Progeny of plants that were grown with B subtilis had better defense systems even if B subtilis wasn't around - it lasts across generations.

Plants grown under drought conditions had more bacteria that enhance growth and photosynthesis, enabling the plant to better withstand drought.

In infected plants, B subtilis colonization induced the plant to close its stomata (the pores in the leaves that allow gas exchange), which would prevent further infection (this particular disease can enter the plant through the stomata).

Microbial communities that were more genetically distinct resisted establishment of pathogens better - there was no niche for the pathogen. However, some communities with "too many" species were less able to ward off pathogens - they were not working synergistically in this case. You can imagine there may be a way to encourage certain beneficial microbial communities to best help the plant.

Of the plots sampled, a plot planted with a mixture of grasses and herbs had the strongest microbial community for fighting off disease.

You can draw a comparison between using antibiotics and the effect on your gut microbes, and the use of fungicides and insecticides on the soil microbes. Studies suggest that crop rotation, tilling and fertilizing are better ways to establish a strong soil microbial community.

Rapeseed seed meal can help beneficial bacteria streptomyces colonize soil and prevent root rot and help the plant grow as much as introducing streptomyces itself. A combination of seedmeals was better able to resist colonization by pathogens, because they contain different glucosinolates that break down, producing a variety of anti pathogen chemicals.

Cultivating healthy soil and hence, microbial communities, can help plants reduce disease, growing better, and curtailing the reliance on blunt-force chemicals.

* * *

I think this research is very interesting because it shows how little we understand about nature. I am not a fan of the cover-all techniques we use in a lot of modern science and I think science is really going to move in the direction of using what nature has already provided via microbes. Microbes are the next big thing!

So many hobbies!

This was a very busy weekend. In fact, most of my weekends lately seem to be this busy.

This weekend, I wrapped up koji growing for my sake, miso AND shoyu projects. The sake is going very well and I expect it to be a great success. The miso and shoyu, however, are total experiments because of course I went off recipe and used spent grains from brewing instead of more traditional grains for koji. As a result, the grains were too wet I think for really good koji growth. Something was definitely happening, just not sure what. I think it would be cool to be able to sequence some of these home ferments and see what is actually going on in there. Towards the end, I think some yeasts started going to work in the spent grain koji, as it acquired a sort of sharp, alcoholic smell. Well, only thing to do is wait! The sweet miso will be ready in 4 to 6 weeks, the salty miso in some amount of months, and the shoyu in... a year! I tend to think that the salt will prohibit more ethanol production, but thats just a hunch.

ALSO, I am engaging in an expt with my fishtank. The poor fish have been lethargic and have had their dorsal fins down for quite a while. I have switched to a canister filter because I wanted to try to boost my plant growth, by reducing the surface turbulence and trapping the CO2 the fish produce in the tank. My oxygen is suffering, however, because I woke up this morning to heavily breathing fish with dark red gills. Turn on the air stone and they were fine in 15, but it was a little scary. Not sure if I should add more light so that the plants do a better job photosynthesizing - is CO2 still the limiting reagent, or is it light? I think there is a lot of confusion about this on the forums. People inject CO2 into their tanks but then have surface turbulence, which I would think would cause the CO2 to degas and regain equilibrium with the environment. Goldfish are really dirty, so I would think they would produce plenty of CO2. I don't really know though.

Anyway, I think my fish have some sort of parasite, they flash and yawn and twitch. PraziPro didn't clear it up so I thought maybe it is Trichodina? The stupid Petsmart and Petco here didn't have the Malachite Green + Formalin product I was looking for, so I ended up with this herbal stuff. Hopefully it works anyway because I hear the Malachite can stain the sealant in the aquarium. Weird. The herbal thing probably won't work but I guess its worth a shot since it's not an emergency. I turned the air stone back on for the treatment, to make the fish comfortable as well. The plants will just have to wait.

In other news, I have yet to start my presentation for Biophysical Society, which is in 2 weeks. And I also need to finish my design for Threadless so maybe I can win and go to Japan!!! Unlikely, but its worth a shot! Busy busy!

Post-Vacation Grad School Blues

Having recently returned from my vacation (as in, yesterday), I am confronted with the typical post-vacation work-related feet-dragging. There is certain prevalence of the idea that vacation is supposed to "recharge" you for work, that you will return ready to kick science-butt with renewed energy. Instead of being recharged, however, I find myself wondering: who are these people that are recharged after vacation? Does this really exist?

I think for the majority of graduate students, this vacation recharge is a myth.

Case in point.

However, maybe there are people that are truly rearing to go after they get back from vacation. I think that my PI is probably one of them. He let us in on this little secret of his when he told us that he spent a lot of time thinking about the philosophy of graduate school while on his most recent vacation in Mexico. Sitting on a beach, thinking about how best to mold these young minds into great hypothesis-driven, problem-crushing, publication-writing machines. This is a man who obviously enjoys his job.

...

Of course, it is probably unfair to say that most graduate students fall into the "I'm on vacation, so we're NOT talking about lab" category. I have known some fantastic grad students who remain truly curious about all things science, even while Science slowly erodes their hopes and dreams on a daily basis. They stay upbeat, read journal articles for fun at night, etc. I believe these are the people that are going to make great professors someday.

For the rest of us, it's not to say that maybe we won't be useful scientists or even great professors. I think the issue is more about the work mindset that is necessary to succeed in graduate school. For instance, I now cook as soon as I come home from school, in part because it allows me to achieve something on a shorter timescale. Many of graduate school's successes (for me anyway) are few and far between. It is difficult to celebrate an attractive gel when you have yet to get your first paper published.

For students like me, graduate school is a long and tiresome process. It is a journey. When I was a first-year, I was told by a senior grad student that graduate school is a marathon, not a sprint, and that many of his classmates were no longer there because they didn't have this particular brand of perseverance. This same student also told me that you stay in graduate school either because you love your project, or your professor. If you love both, obviously that is the ideal situation. Of course, I didn't take him very seriously at the time, but it's true that when your project is giving you grief, the only thing that really pushes you to continue with any fervor is your professor. And when your professor is a true pain to work with, genuine interest in the project is the only thing that keeps you there.

So, while I know I don't quite have the right blend of working style and personal attributes to really soar in graduate school, I know it is temporary. And I know the journey will teach me the skills and knowledge to land a career where I may experience that recharged, go-get-em attitude... when I come back from vacation :)

Kanye and Jay and Elsevier

OBSESSED with this song! Gonna be in Paris in less than a month. "I'm in France, I'm just sayin"

Reading this article about the future of academic journals. Knowledge should be freely accessible. How do we move forward as a society otherwise? I get miffed when I run into an article I can't read in entirety because the University's subscriptions don't cover it. Just try and stop progress, b**ches! That sh*t cray. Elsevier, show me why you deserve it all!

BTW that panther at the end with the statue in the background, that imagery is EPIC. Like, wolf t-shirt epic.

Yesterday I went to the future and here I am!!

Here is a crazy article about baby universes popping out of old static high-entropy universes, like alpha particles popping out of nuclei. This doesn't seem that far-fetched to me. After all, the whole entropy thing is very interesting. We started out in our universe with very low entropy, everything ordered, and entropy can't help but get higher. So this baby universe idea sort of explains how it got low in the first place, but THEN where did the original static timeless universe come from? So, apparently this Sean Carroll guy is pretty cool. This all jives with my current viewing of the Cosmos series, which is AWESOME.

This sort of reminds me of a drunken conversation I had with a physicist in Vienna. He said anything that goes against entropy is considered to be life. We were arguing about whether viruses are alive. As a biochemist, I sort of see how this is a very convenient argument, but I STILL don't think viruses are alive. They wouldn't be working against entropy if they didn't have any cells full of established life machinery to infect and they would eventually succumb to entropy themselves.

Marine Reserve Success!

Researchers found that marine reserves around the world are indeed successful in both raising the number and sizes of fishes within the protected boundary. The same data does not seem to extend to macrofauna, however. The success of any given reserve is also dependent on proximity to large human populations and how the local culture regards law enforcement. Remote areas with little poaching are much more successful in repopulating.


This map shows the locations of protected marine environments that encompass corals. Note the size of the dots is not an indication of the size of the reserves. In some cases, they are very small.

I found this map on THIS page which is a review of the global state of coral reefs from NOAA. I havent read it, but it looks good. By good, I mean comprehensive, not feel-good. Right.

Fishes Use Gills for Ion Exchange, Oxygen Secondary!

I stumbled upon (not literally) this Science commentary that says that fish may have evolved their gills initially as agents for ion exchange. The researchers, and I'm not sure how animal friendly this is, put fish into little boxes that separated their back ends from their front ends and measured ion levels and oxygen levels in the separate compartments. Little fishes are able to exchange ions and oxygen through their thin skin, and the idea was that as the fish age, the gills would start to exchange ions and oxygen faster than the back end of the fish. The gills exchanged ions earlier in development than oxygen, so the researchers are saying that this indicates that they were evolved for this function. This is not really a very compelling argument and the researchers are talking about doing future work with gene expression to see which set of machinery is expressed in development first, but still... That doesnt quite make the argument either, because when something appears in development earlier isnt necessarily correlated with earlier evolution.

It is apparently hard to take pictures of baby fishes because there are no good pictures out there. Fish gills were too gross and drawings are boring. Here is another hit I got with baby fishes though :)

Extraterrestrial FISHES?!?!?

Apparently, people are thinking that Europa, the icy moon of Jupiter, could possibly support macroorganisms like fishes! The story is that there is likely liquid water underneath the ice-shell, and because life on earth can live to about -50 C, why couldn't there be life there? The water may also be warmed because it is thought that the gravitational force of Jupiter could cause enough flux to keep the core of Europa molten. The ice patterns on the surface indicate great tidal forces, and besides the cracking, the surface being so smooth and crater-less, scientists also figure that the ice is constantly turning over and able to introduce oxygen into the liquid water underneath. And if the core of Europa is molten, you could imagine there being structures like the midatlantic oceanic ridge, with black smokers and whatnot spewing out all sorts of chemicals from the mantle. And we all know that life eats that shit up (literally! har har).

I would also like to point out, though, that oxygen is toxic to most forms of life, and maybe you could get a macroorganism that would subsist on "breathing" something else. Oxygen just serves as an electron acceptor and microorganisms on our planet can "breathe" other things like Fe(III), and SO4 or CO2, which I guess also involve oxygen, but whatever...

Apparently the folks at NASA were so excited at the idea of liquid water on Europa that they purposefully crashed their Galileo probe into Jupiter, rather than potentially contaminate Europa. Unfortunately, though, the next probe that heads in that direction might be a ways off because of the technological challenges, like needing its own power source.

Honey > Sugar

I recently learned in the class I am taking on microbial diversity, by the great microbiologist Norm Pace, about the superiority of honey over sugar as a sweetener in regard to your Teeth! Tooth plaque results from biofilms formed by a common mouth microbe, Streptococcus mutans. This microbe produces a polysaccharide as part of the biofilm and can't use honey as a substrate in the transesterification reaction because it contains the monosaccharides frusctose and glucose, as opposed to the disaccharide in sugar, sucrose. Sucrose is the only known substrate of the polysaccharide-producing enzyme, dextransucrase. S. mutans is considered to be the largest threat to dental health because of this plaque formation, in addition to the lactic acid it forms as a metabolic product.


There was also a study that showed that people that chewed on a study-formulated manuka honey chew had lower levels of plaque and gingivitis than people who chewed sugarless gum. So honey not only can prevent plaque formation, but it appears it can reduce it! However, the study was done specifically with Manuka honey, which is honey produced by bees who collect nectar from Manuka (Tea Tree) bushes in New Zealand, the antimicrobial properties of which are measured with a seemingly meaningless unit called "Unique Manuka Factor." I could spin off into a Tea Tree oil tangent, but I won't.

Honey has long been used as an anti-microbial, however, with the advent of clinical antibiotics, its use has decreased. One study (Pubmed link) I found that showed that 30-100% honey solutions inhibited the growth of various kinds of bacteria. New honey works better than old honey. AND honey is as effective on wounds as clinical antibiotics. It appears as though its antimicrobial properties stem primarily from the presence of glucose oxidase(GOD), which catalyzes the oxidation of beta-D-glucose into D-glucono-1,5-lactone, a side product of which is hydrogen peroxide. (You would think that having an enzyme that acted upon glucose would reduce the sweetness of sugar, and oxidized product is apparently a little sour)


In addition, it appears that microbes and fungi can't grow in honey because of it's low (0.5-0.7) water activity. This low water activity just means that the water in the honey has a lower vapor pressure than that of pure water, and apparently many bacteria need a water of activity of around 0.9 and fungi, 0.7. I guess this is also why people salt meat, as it lowers the water activity of the meat to around .95.

I presume that these organisms need a certain water activity for osmotic reasons, and this "water activity" variable is something that food scientists made up, even though there are already purer measurements that could be used to explain this phenomenon instead. This seems like something that happens in science, different divisions have their own units of measurement that they like to talk about. I think a standardization in terms of units would be helpful for getting other scientists to understand, because the divisions in science are becoming more blurry and everything makes more sense anyway if you think about it in a multidisciplinary way.

So, anyway, eat honey!

And now, the Center of the Galaxy!!!

The center of the galaxy is a giant black hole that is hiding inside of "Sagittarius A," which is this glowy spot in infrared and radio waves because of the heat emitted from matter "accreting" into the black hole. Accreting means growing bigger, which I don't really get, I guess things get bigger when they heat up? Maybe matter is accelerating towards the black hole, heating up and expanding before disappearing? No clue there. Well anyway, this picture is pretty awesome, I got it from the Sweet Astronomy Picture of the Day. While we are on the subject, I would also like to point out that the center of the galaxy is in the constellation of my astrological sign, Sagittarius, which we COULD say, if we were being sassy, either explains my massive ego OR that my heart is actually a black hole. Or that astrology is silly.

There is also this cool video that was on the APOD site:


I can't really watch videos very well on my computer anymore because all browsers on the Mac hate me, BUT what I can tell you is that it has this cool part where it shows the orbits of the closest stars around the black hole, including this star which gets 17 light-hours away from it!!! (Recall here that earth is 8 light-minutes from the sun) Well, anyway, I think the whole thing is pretty mind-expanding.

The Oceans, they are a-changin'

A gross sea slime produced by algae blooms is bogging down sad sea birds, forcing them onto the beaches where they die of predation or hypothermia. Such algae blooms are produced when there are unusually high local levels of nutrients; basically when things are out of whack. SO, what is up? There have always been algae blooms in the ocean, part of the cyclical nature of life, however this appears to be different. That's all. And THEN, a giant algae monster raises from the sea and consumes the plastic continent!!!

This reminds me... People talk about metabolic engineering of bacteria, I specifically talk about making organisms that eat plastic and oil and whatnot (& turn them into diamonds, but thats not really very practical (although it would make for an attractive beach!)). But of course theres the whole question of introduction of engineered organisms into the environment, and gene transfer between bacteria and archaea is really rather easy, so is something like this REALLY ok?! I don't know...

Pictures of Atomic Bonds Using Atomic Force Microscopy

Awesome. I'm depressed and I still think its awesome.

Science article for those who have access.

Gizmodo article.

As a side note: Grad school is depressing.

Eh heh.

Sorry I am so lazy. :-/

I read "Into the Wild." If I ever get the ambition, I will write about it. Talk about escapist fantasies, man.

In the sciencey bits, I am reading about CML, which is some sort of leukemia, and I can't remember what the other letters stand for, but it results from a chromosomal translocation that fuses two genes together (called the Philadelphia Chromosome, I remember that much). This sort of thing usually happens from RADIATION EXPOSURE. Anyway, this particular fusion results in a constitutively active kinase, which basically means that the gene has been truncated by the fusion, and it used to be self-inhibited, and now it is active all the time, turning all sorts of shit on, like a naughty toddler or something.

And suddenly, I am distracted by The Beatles "Something" that is playing right now, because I am all sentimental lately. Something of an honest confusing love song. (I do not suggest watching the video, it takes away from the lyrics, I think)

ANYWAYS. Um, so theres this kinase running amuck, that is normally involved in regulating the cell cycle and inhibiting the apoptotic pathway (which leads to CELL DEATH) upon DNA damage (that might occur upon radiation exposure). So you see, the kinase normally is involved in killing off sick cells that have DNA damage and may turn cancerous. When it is doing things wrongly, the cells don't die, and they proliferate uncontrollably, and in this case, you get all sorts of crazy unnecessary blood cells being made in the bone marrow, and I'm not really sure of the mechanism, but it eventually leads to death.

SOOOOOO, this is a success story, because someone figured, Dude, let's just inhibit the kinase. And they were able to develop/find a specific enough inhibitor that you are just inhibiting this particular kinase and not all the other ones that have to do other normal things. BTW, kinases are responsible for putting a phosphate group on particular amino acids on proteins. (I really am so out of touch with what terms laymen know, so this probably makes no sense to anyone outside the field. But oh well, thats what Wikipedia is for.) So, they actually have a super awesome, specific drug for this form of cancer. Honestly, if you were to get a cancer, I would choose this one. Cancers are a**-scary, but its nice that this one makes so much sense.

IN ANY CASE, one of the people involved in this whole saga, Jean Wang, is coming to give a talk next week and that is why I'm learning about sh*t, because I have to, because I'm on a training grant and this is what is expected of me. But it's pretty cool.

In other news, my car developed a nasty brake fluid leak and I think I am getting ripped off by the car mechanic man, but there is not much I can do about that now.

In some even more remote news, that is related to escapist fantasies, I am daydreaming about flying away to Munich, because it is less than $400 to get there, see. But this whole paying for expensive car repairs thing is not very conducive to that sort of thing. Ah well.

I might also mention that citing so many wikipedia articles is bad form for a scientist, but honestly, we all look at wikipedia. YOU MUST TRUST IN YOUR FELLOW MAN.

Another Reason to Go Organic

That is, if you have to eat meat, or other animal products. Here is a synopsis of a Scientific American podcast about how flies are transferring antibiotic-resistant microbes from factory farms to US. Apparently 70% of antibiotics used in our country are applied to livestock. So, really, this antibiotic resistance problem is more about factory farms, which totally makes sense, because they are unnecessarily giving antibiotics to animals before they get sick, just so they can grow more of them in a small area. Duh.

This is interesting to me, because I am working on a project that may lead to the development of new antibiotics - but I assumed they were only for people, because they would prevent disease associated with certain bugs, not actually kill them. You would think this sort of antibiotic would be less useful for factory farmers. You can imagine at some point all our traditional antibiotics failing, and you would have bug-specific antibiotics that would be used for preventing disease in humans. This could potentially be a good thing, because then the farmers would be unable to overcrowd. Maybe.

I just think its weird how people have to deal with the consequences of farming practices with their health. Doesn't seem as worth it anymore, does it?

And Now... You are Reading the Blog of a Shiny PhD Candidate! BAM!

That's right. I have been out of commission for the past several weeks because I was studying for my oral comprehensive exam, which is something that all second year grad students have to do. Basically, you write a proposal for your research, and then you get locked in a room with three professors and you tell them about your research. And they proceed to ask you WHATEVER THEY WANT about your project or about biochemistry or chemistry in general (in my case... Presumably not if you were an English major, har har). So NOWWWW I am all fancy and am feeling pretty smart because the whole thing really went very well and I was done in an hour, which is pretty fricking quick if you ask me. ANYWAY. It was awesome. I kicked its ass. And it is such a huge relief and I am so happy that it is finally over. The morning after, I woke up in the middle of the night thinking about kinetics, dP/dt = ... and I realized, I don't have to care about kinetics anymore. HA! Take that Kinetics! And now I can go back to doing things I used to like to do, there is such a feeling of freedom, and I am excited about my research as well, so Everything is all Really quite great right now!!!! HOORAY!!

I will say that the entire orals experience was really quite horrible, weeks and weeks of dread and counting down, and I got sick and had a headache for like 5 days, and THEN I got strep throat, and then Phillippe got sick and died (thats for another post), and everything was all sucky in the world and I wasn't sure if I was going to make it, I couldn't even consider how I was going to do, and I was SOOO sick of studying, but I had to, just because I don't even know what I would do if I failed. But now I did it and it is GREAT.

ARGH TINY MACHINES RIPPING INTO ME!!!

HOLY FREAKING HELL. Some crazy MFers have decided to make a little magnet-controlled gripper guy that closes its FIST of DEATH on cells or other things when the temp or other chemical conditions change. Be sure to watch the video on the above linked site where the gripper MERCILESSLY RIPS a chunk of some suspiciously-BLOODY-looking substance off. GRUESOME.

Crazy Silica Crystals

In keeping with my theme of posting National Geographic News, which you could easily read yourself on National Geographic, thus rendering my blog entirely obsolete, here are some cool Silica crystals that are all super curvy and "organic." This is tricksey, because it means that when people find curvy looking fossils on rocks (like from Mars), it could just be mineral crystals after all, and not life. Curtains! In addition, I am in a crystallography lab, and so crystals are kind of cool, yes?

Creepy Mummified Dead Girl

This mummy of a little girl who died in 1920 freaks me out. Her dad was a taxidermist and embalmer and was apparently "an artist" at the job, and used zinc salts, in addition to other normal embalming things, which account for the insane state of preservation. From National Geographic, "Formalin, now widely used by embalmers, is a mixture of formaldehyde and water that kills bacteria. Salafia was one of the first to use this for embalming bodies. Alcohol, along with the arid conditions in the catacombs, would have dried Rosalia's body and allowed it to mummify. Glycerin would have kept her body from drying out too much, and salicylic acid would have prevented the growth of fungi." Makes sense to me!

On another note, I used to say that I wanted to be petrified when I died and then shot off into space all Han Solo like, encased in my stone. But I guess this is a pretty good way to be preserved. Or, whatever, I'll just go back into the circle of life and be immortal that way. Some day, you may EAT one of my molecules!

Clouds are Gross

SOOOOO. What we thought were nice fluffy, pure clouds of delicious, clean water vapor are actually full of disgusting bacteria. Not that there is anything really wrong with bacteria, and it is everywhere, just that I never expected it to be in clouds. APPARENTLY, the bacteria have taken to the skies and use clouds to travel and colonize other places on earth. AND, say in a region with a lot of plants, the bacteria go up into the clouds and may have an effect in nucleating rain drops and causing rain. SO, all your rain dancing bull shit won't help one bit if you kill all the plants. This can lead to a sort of vicious cycle in deforested or over-chemicaled fields, where the bacterial load is decreased, so there are not as many airborne bacteria, so there is no rain, etc etc etc. I mean, its all pretty cool, but still, when I went skydiving, I went through a cloud, and maybe someone should have told me about this first so I could have least kept my mouth shut while going through it. It felt cool and misty, but I didn't know that was because of all the billions of little mushy bacteria that were running into me, and not just water droplets. Oh well.

Also, life has been difficult and busy lately and I don't have time to peruse the internets like I used to. Maybe I never really had the time in the first place.

A Word of Warning from Endangered Species

This article from the National Geographic Magazine is definitely worth the read. It is a sad (to me) story about the Endangered Species Act, the challenges it has faced in the past and must overcome in the future.

And definitely make sure to check out the stunning photo gallery that accompanies the article, which includes pictures of the ocelot, the extinct dusky seaside sparrow, and the yellowfin madtom, among others. I don't say 'stunning' lightly, and maybe you might not experience the same feeling, but the diversity on earth is mind-blowing to me (and sad when threatened, which is all the time now).

I would also like to mention that the article says that the building of the Kennedy Space Center overtook critical habitat of the now-extinct dusky seaside sparrow. For shame, Science.