Happy Earth Day!

Green glowing frogs detect pollution

Just came across this article from last December about engineering tadpoles to express green fluorescent protein when exposed to pollutants. A strength this approach has over more traditional techniques is that the tadpoles only respond to bioavailable forms of target toxins.

Since this is fluorescence not luminescence, the detection would require at minimum a special light source and a filter. My first thought when seeing this was to wonder how they detect the fluorescence. According to the researchers this turned out to be “nontrivial.”

"Tadpoles aren't just going to sit still while you measure them. They're usually off and running."

Product literature available at the website of the company the researchers founded, WatchFrog, says that the method can be used to detect hormonal disruptors and heavy metals.

It is a microbial world!

Researchers scouring the world's oceans have been forced to drastically revise estimates for the number of microbial species residing there after a census indicated up to one hundred times the expected diversity may be present.

Qiu 2010. Nature Online

Open access mandated by law

This is excellent news! The big funding bill Bush just signed into law includes the provision that all NIH funded research be made open access within 12 months of publication.

Read more here.

PCR

It is an exciting time to be following progress in the field of microbial ecology. While the awareness of the abundance of microscopic organisms is not new, the development of new methods to observe the microscopic world continue to deepen our understanding. Some of these methods have been described briefly on this blog. See the entry on 454 sequencing for example.

One of the most important techniques for modern microbial ecology and biology as a whole is the polymerase chain reaction or PCR. I suspect most of my modest readership is familiar with the technique, if any of you are not, it is something that you ought to take the time to learn about. A google search of the term PCR reveals a large number of pages devoted to explaining the technique. Many people have also developed diagrams and animations to aid in the understanding. The problem is, most of the good animations do not stand on their own. To make use of them, some background knowledge is needed.

The best animation I have seen on the web is this one. Go ahead and look at both the amplification animation and the interactive graph showing the number of copies of the target molecule present after each cycle.

Here are some things to keep in mind:

1. DNA is a double stranded molecule and the two strands are held together by hydrogen bonds. Each individual bond is weak, the strength of the bonding between the two strands arises from the sheer number of individual bonds present. Key point for PCR: The bonding that holds the double strand together is easily disrupted by heat. Thus the 95 deg C steps
2. DNA is made up of 4 nucleotides: adenine, thymine, cytosine and guanine attached to each other along a sugar-phosphate backbone. The hydrogen bonding between the two strands of the double stranded molecule are between these nucleotides. The pairing of the nucleotides is specific. Adenine always binds with thymine and guanine with cytosine. Key point for PCR: knowing the sequence of one of the strands of the double stranded DNA makes it possible to deduce the sequence of the opposite strand.
3. DNA polymerase is the enzyme required for PCR. The enzyme is capable of synthesizing double stranded DNA from single stranded DNA using the single strand as a template. The activity of this enzyme is specific in several ways. Most importantly for PCR:
• The nucleotide bases strung along the sugar-phosphate backbone of each DNA strand has directionality.^a and each of the two strands in the double stranded molecule are oriented in the opposite direction. DNA polymerase can elongate in only one direction. Key point for PCR: the DNA polymerase must elongate each of the two strands from opposite ends.^b
• DNA polymerase can not elongate single stranded DNA. A short fragment of double stranded DNA is needed. Key point for PCR: Small lengths of double stranded DNA need to be created flanking the region targeted for amplification (these are the primers).
4. The exponential nature of PCR amplification depends on multiple cycles of amplification involving both strands of the double stranded molecule. Key point for PCR: Two primers are needed.
   

The ingredients needed for a PCR reaction are:

• DNA polymerase - the enzyme.
• 2 primers - Small fragments of single stranded DNA. These are used to produce short regions of double stranded DNA flanking the sequence targeted for amplification.
  
• Free nucleotides - These must be in the form of nucleotide triphosphates. In this form, they provide the source of the bases needed to build new strands of DNA and the energy required to drive the reaction.
• Template - some DNA containing the region that is to be targeted.

When I teach people the basics of PCR, a question I use to assess comprehension is: How many cycles of amplification are needed to produce the first copies of the target fragment that are the correct length and why are are none produced prior to this cycle? If you can answer that question, you understand much of the basics of PCR.

There is much more to say about PCR but this post is already long enough so go enjoy the animation.

^aFor a better understanding of the structure of the DNA molecule itself see DNA is a polynucleotide by Larry Moran at Sandwalk.
^bSee here and here for an interesting exception to this rule on directionality.

Image from Flickr

Bacteria and the cost of oil

Oil is considered sour if it contains reduced sulfur compounds (sulfides) at concentrations of 1% or greater. High concentrations of sulfides in oil are problematic for a variety of reasons including:

• Hydrogen sulfide is extremely corrosive and can cause damage to the pipes used to transport oil.
  
• When complexed with other metals such as iron, the sulfides can form precipitates that restrict the flow of oil in the pipes.
  
• Sulfides are toxic and cause environmental and health problems in areas where sour oil is produced, processed or burned.

Removal of sulfides is costly and so refining costs for sour oil is significantly greater than for sweet oil.

Souring of oil is exacerbated by the common practice of pumping water into older oil fields to increase the pressure in the fields as a way to increase oil recovery. Depending on the source of the water used, this practice can introduce large quantities of sulfate (SO₄) into the oil/water mixture. Any oxygen present in the water when it is first pumped underground is rapidly consumed by microbial activity. Once the oxygen is gone, anaerobic microbes can contiune to extract energy from the organic mater present by using compounds other than oxygen as terminal electron acceptors. Sulfate reducing bacteria or SRBs are anaerobes that are able to use sulfate as an electron acceptor. The process results in the production of oxidized carbon compounds and reduced sulfur (sulfides). Biocides are often added to the water to inhibit microbial activity but this process is not efficient requiring enormous amounts of toxic compounds to be added to the water to have a lasting impact.

Thus, microbial activity in oil fields contributes the the cost of oil production. Microbial sulfide production is not limited to oil reservoirs. SRBs are also responsible for the 'rotten egg' smell associated with other anaerobic environments such as swamps and septic systems.

Kofi Annan's missed opportunity

Here is one of the many articles this week in overseas papers covering the announcement that the new organization, Alliance for a Green Revolution in Africa or AGRA led by the former UN chief Kofi Annan will attempt to engineer a green revolution in Africa without the aid of genetically modified (GM) crops. This decision is very short sighted.

From the article:

Conventional methods of farming have not yet been applied to the fullest extent in Africa. Simply working with conventional breeding, we can do a lot,' said Joseph De Vries, programme director with AGRA.

Yes, but, with GM crops, even more could be done. I understand that GM crops are controversial and many people find their use disturbing. However, on a continent where so many go hungry, closing the door completely on a technology that has the potential to improve the drought and pest resistance of important crops makes no sense. One of AGRA's primary goals is to improve "crop varieties for larger, more diverse, and more reliable harvests". How can anyone suggest that in this day and age, GM crops have no role to play in this endeavor?

The genie is out of the bottle. GM crops are here to stay. They should stay. On a planet with 6 billion people and counting, the potential they offer to increase yields, reduce chemical usage and expand arable land is too great to ignore.

The big challenge with the development of GM crops (and the aspect that I am most uncomfortable with) is that too many decisions about which traits to manipulate and what risks are worth taking are made by big agribusiness. This is where Annan's new organization could have played a constructive role. AGRA is headed by a former Secretary-General of the UN and bankrolled by the Gates and Rockefeller foundations to the tune of $150 million. Such an organization has the potential to be a powerful voice in the debate over the best use of GM crops for improving the quality of life and sustainability of agriculture in Africa.

By this decision, AGRA has removed itself a discussion that will occur whether they chose to participate or not.

Gecko/mussel hybrid velcro

This looks cool:

A reversible wet/dry adhesive inspired by mussels and geckos
Lee, Lee & Messersmith
Nature 448, 338-341 (19 July 2007)

From the abstract:

Researchers have attempted to capture these properties of gecko adhesive in synthetic mimics with nanoscale surface features reminiscent of setae; however, maintenance of adhesive performance over many cycles has been elusive and gecko adhesion is greatly diminished upon full immersion in water. Here we report a hybrid biologically inspired adhesive consisting of an array of nanofabricated polymer pillars coated with a thin layer of a synthetic polymer that mimics the wet adhesive proteins found in mussel holdfasts. Wet adhesion of the nanostructured polymer pillar arrays increased nearly 15-fold when coated with mussel-mimetic polymer. The system maintains its adhesive performance for over a thousand contact cycles in both dry and wet environments. This hybrid adhesive, which combines the salient design elements of both gecko and mussel adhesives, should be useful for reversible attachment to a variety of surfaces in any environment.

Check out the gecko images here: http://www.lclark.edu/~autumn/PNAS/

Stability - Diversity relationships

I mentioned in this post, my concerns about speculations by Xu et al on the role of the human host in the maintenance of a diverse gut microbial community. The proposed benefit to us is that the high diversity encouraged stability and assured that our guts continued to provide the desired services, but the mechanism by which we control diversity was not clear.

An article by Ives and Carpenter in a recent issue of the journal Science makes it clear that Xu et al. are in good company. Ives and Carpenter state that we lack of a good understanding of the relationship between diversity and stability in part because term stability is actually used in several related (but distinct) ways in the ecology literature.

Understanding the dynamics of complex systems such as the human gut is challenging. Here is the background knowledge Ives and Carpenter suggest is necessary for beginning to develop an understanding of the diversity/stability relationship:

Before designing an empirical study, it is necessary to know enough about the dynamics of an ecosystem and the environmental perturbations that impinge upon it to select appropriate definitions of stability; there will often be several appropriate definitions. These concepts also identify key features—we will refer to them as mechanisms—that together dictate stability. These mechanisms involve the strength of interactions among species, the mode in which species interact (whether they are competitors, predators, mutualists, etc.) that gives the food-web topology, and the ways in which species experience different types of environmental perturbations. Because both species interactions and environmental perturbations can drive fluctuations in species densities, these must be sorted out and quantified to understand their mechanistic roles in diversity-stability relationships.

And, here is a excerpt from the recommendations they make at the end of the paper:

The relationship between diversity and stability has interested ecologists since the inception of the discipline (35), and the absence of a resolution reflects the complexity of the problem. Much of the complexity derives from the multiplicity of diversity-stability relationships, depending on the definitions of diversity and stability and on the context in which an ecosystem is perturbed. We cannot expect a general conclusion about the diversity-stability relationship, and simply increasing the number of studies on different ecosystems will not generate one.

Rather than search for generalities in patterns of diversity-stability relationships, we recommend investigating mechanisms. A given diversity-stability relationship may be driven by multiple mechanisms, and the same mechanisms may evoke different diversity-stability relationships depending on the definitions of diversity and stability. We need more studies revealing exactly what these mechanisms are. This requires models joined to empirical studies that can reproduce, in a statistically robust way, not only a diversity-stability relationship but also the dynamics exhibited by a system.

The human gut community does exhibit characteristics of a stable system such as the ability to resist perturbations. So, what are the mechanisms that maintain the diversity, what is the diversity stability relationship and how do we go about studying it.

More on human guts

Yet another interesting open access gut microbe paper in PLoS Biology came out in June. This one describes patterns in the colonization of the intenstines of human infants. As mentioned in a previous post, we are born with a sterile intestinal tract and depend upon the ingestion of compatible microbes for the establishment of our gut community. This study used 16S rhibosomal DNA sequences to document changes in the structure and diversity of infant guts over the first year of life. As with the previous paper, Liza Gross wrote a nice summary article.

Some key points:

• 14 babies were followed (including one set of twins) for one year. Early the communities were quite different but by the end of the first year they had acquired a composition similar to that of the adult human.
• At one week of age, two babies delivered by cesarian had fewer total gut bacteria indicating that during natural child birth, the colonization begins during the birthing process.
• While broadly similar to each other and to the adult community, each infant had a distinct profile that persisted over time.
  

This paragraph from the end of the Gross summary provides a good overview of the most interesting findings:

The idiosyncratic nature of the early stages of colonization suggests that a baby’s initial bacterial profile largely results from incidental microbial encounters. The fact that some of the early stool samples matched their mother’s breast milk or vaginal sample supports this interpretation. Shared environment may also explain the coincidental appearance of microbes in the twins. The researchers explain the tendency of these communities to eventually converge by hypothesizing that the human–microbe symbiosis has likely evolved under strong selection and that certain well-adapted microbes repeatedly “win” the battle over the opportunistic early colonizers.

Selections from the final paragraph describes some of the future directions the work will take:

By comparing the surprising range of microbial profiles found in these healthy babies to the microbiota of infants born prematurely or with health problems, future studies can explore how diet, delivery method, or other factors might spell the difference between health and disease.

and that the approach used in the study will allow us to explore questions about

the environmental and genetic factors that shape and personalize the amazing “alien” ecosystem that lives within us.