Does my breath smell?

It appears that Helicobacter pylori may be the cause of halitosis (aka 'bad breath') as well.

H. pylori is a very interesting bug. It appears to have first been identified in the 1800's, though the work didn't really go anywhere. The issue was readdressed in the early 80's, with the work of scientists Barry Marshall and J.R. Warren, who linked the organism to stomach ulcers. This was met with a fair bit of skepticism, but Marshall showed them (did he ever!) by drinking a flask of the bug and promptly coming down with a stomach ulcer. In addition to being a really stupid thing to do, it eventually earned them the Nobel Prize in 2005. There are also links between H. pylori and stomach cancer, which makes the issue of halitosis rather small potato's in the grand scheme of things. It's estimated that roughly 50% of the worlds population carries the organism, though only a percentage of those carriers ever present with any sort of symptoms.

Does this water taste funny to you?

Water from urine recycling machine broken in space station. $250 million dollar system? I think the Boy Scouts of America can do it for much less.

I hate Murphy ...

... and his stupid Law. So I have this manuscript that I'm revising and I've finished all but maybe 1/8th of it. So what goes and happens? Blue screen of death on my computer followed by a total crash (a little cursor blinking in the top corner, nothing else). All my data is on that computer, so now I have to wait for IT to recover my revised manuscript and new figures from their backups. So much for getting it finished today. Dang it.

J-E-T-S!

Jets! Jets! Jets! Jets!Jets defeat the previously unbeaten Titans.

Now, hopefully I pulled out a win in my fantasy football league. If I win, I get a berth in the playoffs.

ETA: Looks like I pulled out a 10 point win in fantasy football. Huzzah!

Yet another reason ...

... to stay a leg up in the scientific world.

The report, based on a global survey of experts and trends, was more pessimistic about America's global status than previous outlooks prepared every four years. It said that outcomes will depend in part on the actions of political leaders. "The next 20 years of transition to a new system are fraught with risks," it said.

Review #1

These reviews are taking a bit longer than I expected. Not that I've had much time myself to address the reviewer comments if I had gotten them sooner, so I guess no harm/no foul. At any rate, the work I had done during graduate school received a review requesting some minor edits: a change to the introduction; a change to a figure; a request for a figure; and more explanation on a third. Easily done, and very satisfying. According to the reviewers, the manuscript was well written, and the literature is adequately cited. That works for me. Now to get it turned around. I'm especially pleased because I have the work they requested, so I don't get into an ugly game of trying to do work I finished several years ago in my lab which doesn't deal in the slightest with pathogens.

Can't they just go to Lowes?

Spacewalkers loose toolbox.

The briefcase-sized tool bag drifted away from astronaut Heidemarie Stefanyshyn-Piper on Tuesday as she cleaned and lubed a gummed-up joint on a wing of solar panels on the space station.

Home Depot delivers too, right?

Open Letter to Cingular

Dear Cingular (AT&T),

You suck. You've been a pain in my rear several times. Mostly because of the stupid fact that even though I paid for my rollover minutes, you seem to have the ability to axe them whenever you want. However, the last straw was when, after 6 years of service with you guys, one of your customer service representatives reset my phone upgrade date two years back when I moved and changed my number (though I specifically asked if this would be a problem, and that I WOULD NOT do the number change if anything was going to get mucked up). That meant -- according to you folks -- that I had to go four years without getting a new phone ... or I could pay out the wazoo. Well, I wasn't about to pay out the wazoo, and your customer service didn't seem particularly keen on helping me sort out the issue either. So, I found someone else, and you lose a customer that you've had for the better half of a decade.

I'm sure you're crushed. As am I.

Eat poop,
Tom

Mars likely had an ocean ...

... which probably covered up to 33% of its surface.

The younger, inner shoreline is evidence that an ocean about 10 times the size of the Mediterranean Sea, or about the size of North America, existed on the northern plains of Mars a few billion years ago. The larger, more ancient shoreline that covered a third of Mars held an ocean about 20 times the size of the Mediterranean, the researchers estimate.

Where there is (was) water, there is (was) also the strong possibility of life.

If I ever fly Qantas airlines ...

... I want to avoid one particular plane. This one as a matter of fact.

A Qantas jetliner that was damaged by a midair explosion in July collided Tuesday with another of the airline's planes on an Australian airport tarmac, airline officials said.

Yes, I'm a tad bit superstitious. So either I avoid the plane, or the pilot (if the same yahoo was involved in both instances).

Janella Spears is an idiot

She truly is. I mean, really. REALLY. IS. AN. IDIOT.

Her family and bank officials told her it was all a scam, she said, and begged her to stop, but she persisted because she became obsessed with getting paid.

She lost over $400,000, burning through her husbands retirement. Her reply?

"The retirement he was dreaming of — cruising and going around and seeing America — is pretty much gone for him right now," she said.

Pretty much gone right now? Hopefully he has a shred of sanity left, otherwise his freedom will be pretty much gone for him after he kills you for your stupidity in an insane rage.

What a tool.

Enough! Just crown him Czar already ...

... and be done with it. You know that's what they want anyways.

Nebraska is for parents ...

... that don't want their teen-aged kids any longer. I personally know a couple of people who saw this coming, but who were derided on the internet for their speculation.

Nebraska's safe haven law was intended to allow parents to hand over an infant anonymously to a hospital without being prosecuted. Of the 34 children who have been dropped off at hospitals, officials said not one has been an infant.

All but six have been older than 10, according to a Nebraska Department of Health and Human Services analysis.

Bold emphasis mine. What a sad state of affairs.

Bioinformatics

So, for the microbiologists/molecular biologists/geneticists who read this blog (I know there are a couple), what programs/software do you use for sequence analysis/protein analysis/molecular biological applications?

Here's my list:

IN HOUSE

Geneious ($249 subscription/year)
Used: Daily
Official description:
Geneious Pro is an integrated, cross-platform bioinformatics software suite for manipulating, finding, sharing, and exploring biological data such as DNA sequences or proteins, phylogenies, 3D structure information, publications, etc. It features sequence alignment and phylogenetic analysis, contig assembly, primer design and restriction analysis, access to NCBI and UniProt, BLAST, protein structure viewing, automated PubMed searching, and more. It even includes an API for creating your own plugins.

What I use it for:
Geneious is the workhorse application for DNA sequence analysis (chromatogram/sequence quality) and editing (vector and quality trimming) in my laboratory. Geneious is also used for contig assembly of genes/organisms and for alignment of 16S sequences for downstream phylogeny analysis (see programs MEGA, DnaSP, DAMBE). It can also be used to construct quick phylogenetic trees for routine examination. The subscription package allows me to receive regular updates. The only other comparable software application that I’ve found that works well on Windows XP is Sequencher (2007 quote for purchase was $2975. Major updates would require another purchase).

Artemis (freeware)
Used: Moderately (several times a month)
Official description:
Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation. Artemis is written in Java, and is available for UNIX, GNU/Linux, BSD, Macintosh and MS Windows systems. It can read complete EMBL and GENBANK database entries or sequence in FASTA or raw format. Extra sequence features can be in EMBL, GENBANK or GFF format.

What I use it for:
Artemis is a valuable tool for examining completed genomes. Search by gene/sequence/functional category for items of interest. GenBank houses over 630 completed microbial genomes (631 as of 02/08/08).

MEGA ver4.0 (freeware)
Used: Moderately
Official description:
MEGA is an integrated tool for conducting automatic and manual sequence alignment, inferring phylogenetic trees, mining web-based databases, estimating rates of molecular evolution, and testing evolutionary hypotheses.

What I use it for:
MEGA is the primary phylogenetic tree building program. It constructs publication quality phylogenetic trees. It is used for molecular evolution and population genetic analysis. In terms of alignment data, MEGA is an established format and most programs export/import alignments in MEGA format. Geneious exports alignment data in MEGA format, allowing these two programs to be used in conjunction. MEGA also has a sequence editor for quick/minor alignment editing.

DnaSP (freeware)
Used: Infrequently/Rarely
Official description:
DnaSP, DNA Sequence Polymorphism, is a software package for the analysis of nucleotide polymorphism from aligned DNA sequence data. DnaSP can estimate several measures of DNA sequence variation within and between populations (in noncoding, synonymous or nonsynonymous sites, or in various sorts of codon positions), as well as linkage disequilibrium, recombination, gene flow and gene conversion parameters. DnaSP can also carry out several tests of neutrality: Hudson, Kreitman and Aguadé, Tajima, McDonald and Kreitman, Fu and Li, and Fu tests. Additionally, DnaSP can estimate the confidence intervals of some test-statistics by the coalescent. The results of the analyses are displayed on tabular and graphic form.

What I use it for:
DnaSP is primarily used to determine genotype numbers. Genotypes are based on SNP information derived from DNA sequencing (typically MLST – multi-locus sequence typing) closely related strains/isolates.

DAMBE (freeware)
Used: Infrequently/Rarely
Official description:
Data analysis in molecular biology and evolution. t is an integrated software package for retrieving, organizing, manipulating, aligning, and analyzing molecular sequence data. Allele frequency data can also be used by DAMBE for calculating genetic distances or phylogenetic reconstruction.

What I use it for:
DAMBE does not see frequent usage in the lab, but it is sometimes useful for determining genotype numbers (it ignores gapped sequences for example) from complex sequences.

TotalLab 120 DM ($6,000)
Used: Moderately
Official description:
The TL120 version in the TotalLab range is an advanced image analysis solution which offers an extensive range of features for the in-depth analysis of 1D electrophoresis gels and performing band pattern matching studies. TL120 DM is the TL120 analysis software complete with the DM database component so you can archive all your analysed results and perform cross experiment investigations.

What I use it for:
This program is integral for analysis of our ribosomal intergenic spacer analysis (RISA) data which is collected on a LiCor DNA sequencer. This allows us to look at archaea, eubacterial and fungal population patterns in a sample and then compare that gel image to other images/samples to construct a phylogenetic relationship between them. The DM option allows us to store this information in a database for comparison of data between experiments. This will enhance our ability to compare samples across time (date of analysis & time of collection) and space (place of collection).

ONLINE RESOURCES

NCBI (National Center for Biotechnology Information)
Site: http://www.ncbi.nlm.nih.gov/
Used: Daily
Official Description:
Established in 1988 as a national resource for molecular biology information, NCBI creates public databases, conducts research in computational biology, develops software tools for analyzing genome data, and disseminates biomedical information - all for the better understanding of molecular processes affecting human health and disease.

What I use it for:
PubMed serves as a primary reference search tool which is linked to the U.S. National Library of Medicine. NCBI houses several major databases, ranging from nucleotide and protein, to taxonomic and structure/function. NCBI also has databases dedicated to SNP (Single Nucleotide Polymorphim), EST (Expressed Sequence Tag), and GEO (Gene Expression Omnibus) analysis. Databases cover all forms of life, from eukaryotic (animal and plant) to prokaryotic (archaea and eubacterial). NCBI also serves the BLAST (Basic Local Alignment Search Tool) which is used to examine sequence similarity to other previously identified sequences (nucleotide or protein).

Ribosomal Database Project (Michigan State University, J.M. Tiedje)
Site: https://rdp.cme.msu.edu/
Used: Daily
Official Description:
The Ribosomal Database Project (RDP) provides ribosome related data and services to the scientific community, including online data analysis and aligned and annotated Bacterial small-subunit 16S rRNA sequences.

What I use it for:
Upon sequencing 16S clones, we use the RDP database to classify (Phylum/Class/Order/Family/Genus/Species) them for separation, for further phylogenetic analysis. The RDP also has sequence match functions which will identify closely related sequences which are useful when building phylogenetic trees (typically using MEGA).

Bellerophon
Site: http://foo.maths.uq.edu.au/~huber/bellerophon.pl
Used: Daily
Official Description:
Bellerophon is a program for detecting chimeric sequences in a multiple sequence dataset by comparative analysis. Bellerophon was specifically developed to detect 16S rRNA gene chimeras in PCR-clone libraries but can be applied to other gene datasets. A chimeric sequence, or chimera for short, is a sequence comprised of two or more phylogenetically distinct parent sequences. Chimeras are usually PCR artifacts thought to occur when a prematurely terminated amplicon reanneals to a foreign DNA strand and is copied to completion in the following PCR cycles. The point at which the chimeric sequence changes from one parent to the next is called the breakpoint or conversion point.

What I use it for:
Chimera detection in 16S sequences.

Farewell Phoenix Mars Lander ...

... you served us well. Hopefully this parting will be temporary and we'll see you again after the spring thaw.

Veterans Day

In Flanders Fields

In Flanders fields the poppies blow
Between the crosses, row on row,
That mark our place; and in the sky
The larks, still bravely singing, fly
Scarce heard amid the guns below.

We are the Dead. Short days ago
We lived, felt dawn, saw sunset glow,
Loved and were loved, and now we lie
In Flanders fields.

Take up our quarrel with the foe!
To you from failing hands, we throw
The torch-Be yours to hold it high!
If ye break faith with us who die
We shall not sleep, though
poppies grow
In Flanders fields.

by: Captain John D. McCrae

Open Letter to Tim Robbins

Tim,

Shut up. You're starting to look like an idiot.

Tom

Go vote!

It's too late to vote in the election for the Presidency of the United States, but you can make a difference in the life of a college student. It appears that there is a Blogging Scholarship (no, I'm not making it up) that pays out $10,000 to the winner (not making that up either). I voted for Brian Switek, author of Laelaps, and a student at Rutgers. There are several worthy candidates there, so go vote!

Sometimes ...

... you just can't make this stuff up. Really. Geocentrism (Thank God that the Earth is not moving).

Whiskey. Tango. Foxtrot?

Many people consider the Encyclopedia Britannica the FINAL AUTHORITY on all scientific matters.

Eh?

"The centrifugal force of Earth's rotation makes the planet bulge at the Equator. Because of this, Earth has the shape of an oblate spheroid, being flatter near the poles than near the Equator. Correspondingly, one degree of latitude is longer in high latitudes than it is in low ones." (Britannica vol. 4, p. 320).

Ordinary mortals cannot see this bulge however as it is visible only to the editors of the Britannica articles.

LOL.

Alas, I don't think this site is a spoof. I wish it were.

h/t to Mark Shea for the giggles.

Earth Four Hours From Destruction!

Ok, not really.

On the evening of Wednesday November 5, 2008 (for most of North America) a giant rocky body will pass through Earth's position in space less than 4 hours after Earth was there. If Earth were 3 hours and 40 minutes farther back in its orbit at that time, the collision would wipe out all life on Earth. In fact, it would render Earth's surface uninhabitable for millions of years.

Should the tabloids media run headlines like "Earth 4 Hours from Destruction"?

No, because there's a catch to this story. It's revealed by the question "What will the rocky body look like in our skies on the "eve of (near) destruction?" The answer is that the object will appear as bright as a first-quarter Moon. For a good reason — the object is the first-quarter Moon.