A bacterium that uses arsenic (and criticisms of the original paper)

Gammaproteobacteria GFAJ-1,
a bacterium capable of using arsenic as a component of its cell machinery (photo: NASA Astrobiology)

Left: Felisa Wolf-Simon, NASA astrobiology research fellow, processing
mud samples at Mono Lake. Right: Mono Lake, California (photos: NASA Astrobiology)
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Yesterday NASA made an exciting announcement in biology:

"Researchers conducting tests in the harsh environment of Mono Lake in California have discovered the first known microorganism on Earth able to thrive and reproduce using the toxic chemical arsenic. The microorganism substitutes arsenic for phosphorus in its cell components."

(From NASA Astrobiology)

This is a major finding, with important implications in the fields of astrobiology, microbiology and molecular biology, since P is one of the six elements so far believed to be essential to every life form. The Gammaproteobacteria GFAJ-1 is the first exception ever found to that rule. It was found in Mono Lake, California.

The discovery was published on the on line version of Science Magazine, and will soon be published on the regular paper edition. Pdfs of the article and support material can be accessed in my p-drive (a-cordoba. ONU students and faculty only).

In the following weeks, as we learn more about this discovery I'll bring new information into the classroom. In the meantime I want to provide links for you to start your own exploration of the topic:

• NASA announcement
• NASA Astrobiology
• National Public Radio (NPR)
• Wired Science
• CNN
• Discover Magazine
• Popular Science

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Update, March 21 2011

The news is exciting indeed, but there are detractors. Here I give them a voice (more updates will come if I find the sources)

Felisa Wolfe-Simon (of arsenic infamy) is no more convincing in person than in print
By Michael Eisen | March 18, 2011

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Update, June 01 2011

Science Magazine will publish a paper with criticisms to Wolfe-Simon et al.'s paper.  Click here to see the press release on Science Magazine News. (Link to the Science article will follow soon)

Click here for another Science Magazine News article on the criticism's to Wolf-Simon's paper.

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Lecture, chapter 3 - DNA, RNA, and proteins

Today, on chapter 3 we discussed the basic structure of nucleic acids, from the components of a nucleotide to the specialized regions in a eukaryotic chromosome. We also mentioned the central dogma of molecular biology and mentioned the several general and special cases of flow of genetic information.

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Module 1, lab 01b (section 1) Restriction enzyme digestion of lambda DNAGel electrophoresis

Today we ran the first agarose gel electrophoresis of the quarter. Students learned, or reinforced, how to load, run, take a picture of, and interpret an agarose gel.

The samples used in the gel were from the restriction enzyme digestion (RED) students set up yesterday: Lambda DNA undigested and digested with the restriction enzymes EcoRI, PstI, and HindIII. The ladder used was lambda DNA pre-digested with HindIII.

The picture below, shows the different bands of the HindIII digestion used as DNA ladder. Notice that there are 7 bands, one more than what it is specified in the lab guide. The 7th band is so faint that it is assumed to be invisible, but it was visible in most of the gels students ran. If visible, data from the 7th band should be included in the lab report.

All sizes in bp
(click on pic for full size image)
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Module 1, lab 02 (section 1) Size exclusion chromatography (SEC)

Column chromatography is a common technique used in molecular biology to purify large macromolecules, such as proteins, by separating the components of complex mixtures. A solvent (usually a buffer) and the molecules to be separated are passed through a resin of glass beads (column bed) whose specific characteristics vary depending on the type of chromatography.

Size exclusion chromatography (SEC) is a technique in which the molecules are separated by size. The glass beads in the resin have tiny pores. When the mix is applied to the column large molecules pass quickly around the beads, whereas smaller molecules enter the pores in the beads and pass through the column more slowly. The buffer and the molecules are collected in separate tubes (fractions), so that the earlier tubes get larger molecules and the later tubes get smaller molecules.

In this exercise you will separate a mix of hemoglobin (large molecule - 65,000 Daltons) and vitamin B12 (small molecule - 1,350 Daltons) using a SEC column.

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Module 1, labs 00 and 01 (section 1)Restriction enzyme digestion (RED) of lambda DNA

Micrograph and structure of a bacteriophage
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We started with a series of exercises to learn how to use a micropipette. Once students became familiar with the instrument we started with lab 1.

Lab 1 (module 1) - Restriction enzyme digestion (RED) of lambda DNA

Restriction enzymes are one of the most basic and important tools in molecular biology. They evolved in bacteria to attack and cut (cleave) foreign DNA, mostly from bacteriophages (viruses that "eat" bacteria). But hey have been isolated to be used in the lab, and are useful to cut any kind of DNA, not just viral.

Cleaving DNA is the first step in any technique that involves recombinant DNA technology. There are techniques that use special enzymes to paste (ligate) different fragments of DNA. For instance a gene can be ligated into a plasmid that can be inserted into bacteria to make many copies of it via bacterial reproduction (cloning), something we will do in a few weeks.

Today we used lambda DNA (DNA from the common lambda bacteriophage) as the substrate to be cleaved with three different restriction enzymes: EcoRI, HindIII, and PstI.

As a DNA marker, or DNA "ladder", we used a sample of lambda DNA pre-digested with HindIII.
Students will measure the distance bands in the gel migrated and will infer the size of the different bands based on such information.

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Biol 217, Winter 2010-11

Welcome to the Winter 2010-11 version of the Intro Molecular Biology (Biol 217) class.

Today we had our first official meeting, and due to several last minute registered students there has been a change in the meeting room. The class was originally scheduled to meet in Mathile 107, and indeed that's the room where we met today. But starting Friday we will meet in Meyer 128.

Today we reviewed the syllabus, explaining the grading scheme, some assignments (literature review paper and symposium presentation), and expectations in the class. We also went over the rationale of the class and how it explains the sequence of lectures that will be taught.

Reminders:

• Fall 2010 power point presentations are available on WebCT and the p-drive (under a-cordoba)
• This quarter's power point presentations will be made available as lectures are taught
• This blog can be used as a reference of the class progress; check it often, specially if you have missed class

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Module 1, labs 00 and 01 (section 2)Restriction enzyme digestion (RED) of lambda DNA

Today we had the firs lab meeting with section 2 in the class.

We went over the lab syllabus, distributed materials (lab notebooks, lab coats, and permanent markers), introduced the lab routines (where to find materials and how to behave in the lab), and spent a fair amount of time in the proper use of micropipettes.

We then performed lab 00, which allows students to practice pipetting techniques, and then we started lab 01, a restriction enzyme digestion.

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