Archive for April, 2010

Oral Flora

Posted by amanda on Saturday, April 17th, 2010

mouth

Mouth with probably over 240 species of bacteria inside
http://www.flickr.com/photos/mbaruzza_2/

It’s been an interesting week in the stratosphere with a fireball in Wisconsin caught on video and a giant ash plume from the eruption of Iceland’s Eyjafjallajökull volcano.

But I’m feeling a bit introspective. Published in The ISME Journal, researchers (including a couple from the J. Craig Venter Institute in Rockville and the Institute For Genome Sciences at the University of Maryland School of Medicine) finally determined the bacterial diversity of our mouths or at least of 10 lucky individuals.

The researchers collected 26 separate samples from different parts of each healthy person’s mouth and pooled them, collecting and amplifying the RNA sequences present. RNA (or ribonucleic acid) contains the important coding information from DNA. RNA is necessary to every living organism, transcribed from DNA and translated into protein. Without RNA, there would just be pieces of DNA code, unable to be read or to be used as a template to construct protein. By isolating and amplifying a specific piece of RNA present only in bacteria, scientists are able to determine specific species through deciphering the sequences. In this study, around 1000 sequences per mouth were analyzed.

So what did they find? Contrary to past estimates that the mouth harbors 500-700 different bacterial species, this study found about 240 belonging to 9 different phyla or groups. As you may expect, not every mouth is the same. Subject 4 had the greatest number of bacteria (lucky duck), and only around 50 different species were expected to be shared between any two individuals with 11 shared between all 10 of the people studied. If you’re really into species (and who isn’t?), the magic 11 are: Haemophilus parainfluenzae, Streptococcus oralis, Streptococcus sanguinis, Granulicatella adiacens, Veillonella parvula, Veillonella dispar, Rothia aeria, Actinomyces naeslundii, Actinomyces odontolyticus, Prevotella melaninogenica and Capnocytophaga gingivalis. Interestingly, although every subject had sequences belonging to the group of bacteria known as Neisseria, no single specific Neisseria species was shared across all subjects. Our mouth bacterial flora also appears to be very distinct from that found in our colon, confirming that these are very different environments (as if we didn’t know that already).

It’s already known that bacterial flora can be passed from mother to child. I wonder if this study had been conducted with healthy couples who kiss frequently, if they would find a more similar bacterial diversity than 10 strangers. But that study probably isn’t a strong candidate for NIH funding.

Antiwho?

Posted by amanda on Monday, April 12th, 2010

TARDIS

I spent the past two weeks in the well-known parental hell of daycare illness, swapping germs with my beloved sticky-handed, snotty-nosed daughter. As every working parent can attest, missing work first to nurse your child and then to nurse yourself is one of biggest downsides of parenting with career ambition. Watching Doctor Who reruns while in a medicine-induced haze kept me entertained, and now all I think about is traveling carefree through time and space. And this is why you, dear reader, get to hear about quarks and quantum theory.

In the early 20th century, there was a great revolution in physics with the birth of quantum mechanics, replacing classical mechanics as the description of motion on an atomic scale. Max Planck, the founder of quantum theory (and father of four…although I doubt they attended daycare), showed that electromagnetic radiation in a cavity can only be emitted in quantized form (the energy could only be in a multiple of a certain unit). Modern chemistry now relies on quantum mechanics for the description of most atomic and molecular phenomena.

Quantum field theory is used in particle physics and combines quantum mechanics with special relativity (theory on the structure of spacetime, ala Doctor Who). In the simplest of descriptions, quantum field theory tells us that all types of particles have antiparticles of the same mass but the opposite electric charge. Or that for all matter for any physical system describable in quantum field theory, there exists an antimatter analog. If we could describe you with quantum field theory, we would need to account for the existence of an antiyou. But not all is based on charge. For neutral atoms, an antiatom can also exist. Whereas a neutron is made up of quarks, an antineutron is made of antiquarks.

Yet we see very little antimatter. Look around and you see a lot of plain old matter, but where is the antimatter? We can see some examples, such as positively charged electrons (positrons in some radioactive decay) and antiprotons (present in cosmic rays) which can be used to form an antihydrogen atom. This lack of antimatter in our matter-filled universe is not completely understood but has been hypothesized to be caused by a temporary difference in physical laws for matter and antimatter occurring after the Big Bang (explained by a theory known as the CP violation). If there were complete symmetry, our universe would simply be an empty sea of radiation consisting of no matter at all.

Published recently in Science, researchers from something called the STAR Collaboration (made up of researchers from 54 separate institutions) describe how they formed and detected an antihypertriton, a variant of the heavy isotope of hydrogen called tritium. By using the Relativistic Heavy-Ion Collider (RHIC) at Brookhaven National Laboratory (BNL), they were able to briefly produce hot and dense matter (a quark gluon plasma) with an energy density similar to that of the universe a few microseconds after the Big Bang. In this process of extremely energetic heavy-ion collisions, they were able to create and observe the antihypertriton containing nine antiquarks (if you must know: four up, four down, and one “strange”). This is the first observation of an antimatter hypernucleus, an antinucleus with net strangeness. This research confirms our understanding of the existence of antimatter and helps scientists explore the dynamics of heavy ion collisions.

I’m secretly hoping that someday this research will help in creating the TARDIS.