R

hizobium leguminosarum. Like with Aa below, we'll simply refer to this bug here as Rl, because I'm not typing that out every single time. Rl is a soil organism which was first identified in 1889. These organisms are interesting because they pair up with legumes in a symbiotic relationship -- residing within root nodules -- and fix nitrogen. A portion of this nitrogen remains in the soil after the legumes are harvested, which cuts down on fertilizer costs. Because of this, you'll see legumes often used in crop rotations, rotating with other plants which do not fix nitrogen.

The nodulation process (formation of root nodules) is very intricate. The legumes release chemicals (flavinoids) which are sensed by the bacteria. In turn, the bacteria secrete chemicals (nod factors) which force the legume roots to undergo cell division and direct root hair growth. Eventually (with a few more steps) this forms the nodules in which the rhizobia reside.

Root Nodule.

I

sosphaera pallida. Isosphaera pallida is a species within the phylum Planctomycetes. The Planctomycetes are unique in that while they don't have a true nucleus, typically their DNA is enclosed within a double membrane (though this feature seems to be absent in Isosphaera. I. pallida is phototactic*, reproduces by budding, and displays gliding motility. Unlike most eubacteria, I. pallida (and other Planctomycetes) lack muramic acid -- a key component of peptidoglycan -- in their cell wall. It is therefore believed that these organisms went on their merry evolutionary way before peptidoglycan was ever heard of.

*I. pallida moves towards light sources.

S

hewanella putrefaciens. S. putrefaciens is a member of the Proteobacteria (Gamma class). It is a facultative anaerobe, and uses can use either iron or manganese as the terminal electron acceptor in electron transport (most organisms use oxygen). This organism derives its name due to the fact that it produces trimethylamines, which means it takes on a rotten fish smell. Yummy. Growing this organism will reveal that it has a pinkish color upon isolation. Another interesting tidbit is that this organism can also generate electricity.

People have also been unfortunate enough to find themselves infected with S. putrefaciens, though electrocution is not something they need to worry about.

T

hermotoga neapolitana. Another organism which has garnered a fair amount of buzz in bioenergy research circles. This hyperthermophilic organism can produce large amounts of hydrogen under anaerobic conditions (typically at around 80 degrees C). Like other organisms which have had their 15 minutes of fame, T. neapolitana is currently having its genome sequenced. The hope is that carbohydrates (generated/recovered as waste from other processes) can be fed to this organism so it can produce hydrogen for a variety of purposes (maybe hydrogen-fueled cars).

M

ethylococcus capsulatus. M. capsulatus is a methanotroph, which means it's able to use methane as their sole source of carbon and energy. This is useful as methane is a GHG that is approximately 26 times more problematic on a mole:mole basis than carbon dioxide. M. capsulatus uses methane by oxidizing it in a two step process, first to methanol, then to formaldehyde. The enzyme responsible for the first step of this process is methane monooxygenase (MMO) which comes in two forms, a soluble form (sMMO) and a particulate membrane form (pMMO). Different organisms may carry one or the other, or both (the organism in question, M. capsulatus encodes for both). Multiple labs have spent time studying M. capsulatus in the hopes that it can be exploited for methanol production.

M. capsulatus (Bath) has had its 3.3 Mb genome sequenced. As it's name suggests, M. capsulatus does possess a polysaccharide capsule, perhaps a tool to help it survive long periods of time in arid conditions.

Methylococcus capsulatus

A

ctinobacillus actinomycetemcomitans, which we will refer to simply as Aa from now on (because I'm not typing that out every damn time) is one of the "HACEK" grouping of Gram negative organisms that are all part of the normal human orophayngeal and/or urogenital flora. This organism (and the others) can, given the right circumstances, be found in association with endocarditis, bacteremia, and wound infections. Aa is a slow bugger to grow, often taking 48 to 72 hours, and forget about growing it on anything but enriched media. The most common infection associated with Aa is subacute bacterial endocarditis, though it is also blazing a trail in the area of periodontal disease as well. Aa has a decent sized virulence factor arsenal, including a leukotoxin, a PMN chemotaxis-inhibiting factor, resistance to complement killing, and bone resorption-inducing toxin.

S

erratia marcescens. S. marcescens is a Gram negative organism which belongs to the family Enterobacteriaceae. It can be pathogenic, most often found as a UTI, though it does also pose problems for immunocompromised individuals, especially those in a hospital setting -- leading to nosocomial infections. To make matters worse, S. marcesens has a habit of being antibiotic resistant, making it a very hard organism to clear. One of its hallmarks is that most isolates produce a reddish pigment called prodigiosin (see below), which assists in identification of the pesky bug.

From a historical, and religious, point of view, S. marcesens has been theorized to be the culprit in Eucharistic miracles involving bleeding hosts. However I'm not aware of it being confirmed in any such cases, if there have been any cases recently (of which I am also not aware).

Serratia marcesens

To Hell With Oil ... Where Is The Water?

Expect lots of droughts in the future.

At least 36 states expect to face water shortages within the next five years, according to a report from the U.S. Government Accountability Office. According to the National Drought Mitigation Center, several regions in particular have been hit hard: the Southeast, Southwest and the West. Texas, Georgia and South Carolina have suffered the worst droughts this year, the agency said.

This is obviously not a "Good Thing". With droughts come increases in food prices, which isn't something most people can handle right about now.

So, what can we do?

Water shortages don't have to remain a fact of modern life, drought experts say. Many offer the same solutions: Build better water delivery systems to accommodate population growth, develop more efficient uses of irrigation, and shift agriculture from the West to the East where it's easier and cheaper to water crops.

Infrastructure folks. More water storage capacity, both for on-farm and municipal use. I cannot stress the on-farm use enough either. I heard that costs in California for irrigation of a single acre in California is up from ~$30 last year to over $600 this year. If that report is true (if it was reported correctly AND I heard it correctly) that spells clusterf**k. Plus, it's about damn time we started working on inexpensive membrane technologies to desalinate sea water.

More Financial Crisis Victims

Pets.

In Arkansas, Cheryl Lang, a foreclosed-property inspector, found three dogs left locked in pet carriers in the back yard of a foreclosed home. Abandoned without food or water, the animals had died.

Whiskey! Tango! Foxtrot!

I've got to admit. This crisis still keeps me up at night, and puts a nice, tight knot in my stomach. I believe I'm very fortunate to have the job I do, and I'll do everything in my power to ensure that I continue to have it. Sometimes this world sucks.

Fair play

It appears that dogs can sense fair and unfair treatment.

To test the theory, Friederike Range and colleagues at the University of Vienna in Austria asked 33 trained dogs to extend a paw to a human.

The animals performed the trick virtually all of the time whether they were given a reward or not -- when alone or with another dog.

But the dogs' enthusiasm waned when they saw other dogs being rewarded but received nothing themselves.

Dogs that were ignored extended their paws much less often, doing so in only 13 out of 30 trials. They also showed more stress, such as licking or scratching themselves.

"They are clearly unhappy with the unfair situation", Range told New Scientist magazine. She also suspects that this sensitivity might stretch beyond food to more abstract things like praise and attention.

When we first adopted Kode, our Norwegian Elkhound mix, Max, became sullen and withdrawn. Then he took a very dominant approach towards Kode. We've tried our best to love equally on all three dogs we have, and things have definitely improved. Perhaps I spent too much time with Kode (who was undernourished and definitely skittish but still attention starved) when we first got him. Nowadays Kode looks to Max for cues, and Max is secure in his "alpha" role (I say "alpha" role because his owners are the dominant species in the house and they all know it).

Idiot

The title says it all really (MSNBC), guess it's Chicago politics as usual (CNN).

On November 5, Blagojevich allegedly told an advisor, "I've got this thing and it's [expletive] golden, and, uh, uh, I'm just not giving it up for [expletive] nothing. I'm not gonna do it."

What a tool.

Currently ...

Listening ToJeff Buckley - Sketches For My Sweetheart The Drunk.

Released post humously, this album has many a lyrical gem on it. My favorite song on the album is "Everybody Here Wants You". If you ever want to hear the love song to end all love songs, this is it.

Puppy cuteness

This is Kode, our most recent adoptee.

Linkage

Sol Light - Creators of the LightCap

Hello Ubuntu

The new computer arrived, but in the meantime I've been given a to-be-scrapped computer to use as a testbed for my "linux project". What I'm hoping to do is build a linux cluster. At first it'll just be two computers, but I hope to expand it as things go to surplus.

Why? Because with the amount of information we'll be acquiring (especially once we start 454 sequencing in earnest), I'll need the computing power for processing the data. I'd like a 64 bit computer, but from a Windows standpoint that means using Vista, and the government doesn't currently allow Vista on their computers without seeking exceptions ... and that paperwork is a bit of a pain. Besides, several of my programs don't work on Vista yet, which means I'd need to keep an XP machine around anyways (rendering the above moot). *sigh*

Anyways, if I cluster a couple of linux machines, I can achieve (I believe) similar results. So, anyone build a cluster recently? Also, what bioinformatic tools do you use regularly on linux? I've already installed Geneious and the Bio-Linux base programs (which is mostly Emboss) and Artemis.

ASM General Meeting

I'm putting the finishing touches on my ASM abstract for the 2009 General Meeting in Killadelphia. I hope everyone else is getting their abstracts done, the deadline is about a month away.

First Casualty of Global Warming?

Rare breed of possum may be extinct due to global warming.

Experts fear climate change is to blame for the disappearance of the highly vulnerable strain thanks to a temperature rise of up to 1.5 degrees Fahrenheit.

Currently ...

Listening ToUNKLE - Psyence Fiction

Societies, Memberships, and Fees

You know, I don't have a problem belonging to Societies. As a matter of fact, they're pretty much essential in my line of business. Stick around long enough, publish regularly in their journals, and do a fair bit of networking and in about a decade you get someone to nominate you for Fellow. In my business, becoming a Fellow in a Society is a big deal. It shows that you're regarded very highly by your peers, which shows that you've had what they refer to as "impact". That's a key word in my business ... impact.

Unfortunately, you don't just pick ONE society, you have to pick several ... because, being a Fellow in multiple societies is much better than being a Fellow in just one. Problem is, societies cost money. And they all want their money in December.

So here I am looking at what it's going to cost me, and I'm looking at a bill which will come in at around $500. That's money that I could use for Christmas shopping, holiday travel, and whatnot.

But it's tax deductible! Well, yes and no. Yes, it is ... but only if you meet a certain threshold, which last year the wife and I did not reach. It's doubtful we'll reach it again this year.

*sigh*

Well, time to ante up.

Always look on the bright side of life ...

... such as, we can expect a nuclear or biological terrorist attack within the next five years. Hey, at least we have five years and it's not going to happen tomorrow!