Mixotrophy

Open access mandated by law

2007-12-27T16:32:00.000-05:00

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

2007-08-09T11:20:00.000-04:00

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:

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
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.
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).

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

2007-08-08T12:00:00.000-04:00

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

2007-07-19T12:10:00.000-04:00

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

2007-07-18T20:35:00.000-04:00

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

2007-07-18T12:47:00.000-04:00

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 knowenough about the dynamics of an ecosystem and the environmentalperturbations that impinge upon it to select appropriate definitionsof stability; there will often be several appropriate definitions.These concepts also identify key features—we will referto them as mechanisms—that together dictate stability.These mechanisms involve the strength of interactions amongspecies, the mode in which species interact (whether they arecompetitors, predators, mutualists, etc.) that gives the food-webtopology, and the ways in which species experience differenttypes of environmental perturbations. Because both species interactionsand environmental perturbations can drive fluctuations in speciesdensities, these must be sorted out and quantified to understandtheir 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 interestedecologists since the inception of the discipline (35), and theabsence of a resolution reflects the complexity of the problem.Much of the complexity derives from the multiplicity of diversity-stabilityrelationships, depending on the definitions of diversity andstability and on the context in which an ecosystem is perturbed.We cannot expect a general conclusion about the diversity-stabilityrelationship, and simply increasing the number of studies ondifferent ecosystems will not generate one.
Rather than search for generalities in patterns of diversity-stabilityrelationships, we recommend investigating mechanisms. A givendiversity-stability relationship may be driven by multiple mechanisms,and the same mechanisms may evoke different diversity-stabilityrelationships depending on the definitions of diversity andstability. We need more studies revealing exactly what thesemechanisms are. This requires models joined to empirical studiesthat can reproduce, in a statistically robust way, not onlya diversity-stability relationship but also the dynamics exhibitedby 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

2007-07-09T20:20:00.000-04:00

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.

Bacteriorhodopsin phototrophy

2007-07-07T09:20:00.000-04:00

Classification of the metabolic capabilities of microbes can be challenging. With few exceptions, macroorganisms are either photosynthesizing primary producers (photo-autotrophs) or consumers (organotrophs or more commonly, heterotrophs).

For microbes, the story is more complicated. In addition to phototrophy, microbes can be chemo- or litho-trophs meaning they are able to derive energy from the oxidation of inorganic compounds such as reduced sulfur. If they can use light or chemical energy to fix carbon, then they are considered autotrophs. If the energy they acquire can be used to synthesize ATP but not to fix carbon, they are dependent on external sources of organic carbon making them mixotrophs.

An example of a phototrophic mixotroph is pictured above. These are salt loving haloarchaea in salt production ponds near (in?) San Francisco. The red color is due to the transmembrane protein bacteriorhodopsin. Using this protein some haloarchaea can harness sunlight to pump protons across their cell membrane. This establishes a proton gradient across the membrane. This gradient can be used to generate ATP.

There is a large number of scientific papers on bacteriorhodopsin because of its relative simplicity, it has become a model system for the study of membrane associated ion pumps.

Image from here http://www.sfgate.com/cgi-bin/article.cgi?file=/chronicle/archive/2001/03/13/MN152047.DTL

These salt ponds are near San Francisco. If you want another view of the bay area ponds follow this link, select the satellite map and zoom way in. I tried this for a few of the other places I know these salt production ponds exist but the satellite images did not provide good enough resolution. An example is Bon Aire in the Netherlands Antillies

Friday dog post?

2007-07-06T10:50:00.000-04:00

This one is for ERV

This photo won us a years supply of dog food at a local fundraiser a few years ago. The muzzle has gotten whiter since then. It may be due to the fact that he now shares the house with two young kids.

In The Bay 3 July 2007 II

2007-07-05T21:32:00.000-04:00

Another diatom this time. Striatella unipunctata in girdle view. These cells form chains with adjacent cells often attached by the corner as seen at the top if this image.

400x phase contrast image.

This week at the CSA

2007-07-05T20:45:00.000-04:00

Just back from the local CSA. Here is some of what we picked up:

Find one near you

Sustainable education

2007-07-05T12:19:00.000-04:00

The most recent issue of the journal Nature has a review (behind a subscription barrier) of a new book: Degrees that Matter: Climate Change and the University by Ann Rappaport & Sarah Hammond Creighton. I have not read the book but some of the information is interesting.

The book documents a 15 year effort by Tufts University that began in 1991 to reduce its energy consumption. From the review:

The central observation from Degrees that Matter is that universities are in a unique position to offer leadership on climate change and carbon emissions through their educational, research and wider roles in society.

The conclusion is a bit disheartening:

The bad news is that despite the intense programme, carbon emissions at Tufts — both net and normalized — seem to have increased over time. The university as a whole has become more energy intensive, with the consequence that it will not meet its Kyoto target. This should, however, be set against other higher-education institutions, where the rate of increase over similar time periods is much greater and the reversal of trends, if at all, much slower. A large part of the increase is due to growing demands from personal equipment.

I assume the "personal equipment" are computers which consume an enormous amount of energy.

In the Bay 3 July 2007

2007-07-04T09:50:00.000-04:00

Since I wrote about marine cilliates in my previous post, I thought I'd try to find some for this edition of In The Bay.

This is a group of Vorticella or Vorticella-like stalked cillates. As you watch the movie you can see the feeding current they are creating with their cillia. About 21 seconds into the movie (6 seconds from the end) the whole colony retracts. This is a defensive mechanism and occurs extremely fast.

Cilliate kleptoplasty

2007-06-30T14:55:00.000-04:00

Chloroplasts, like mitochondria, have their own chromosomal DNA. This is, of course, evidence for the endosymbiotic theory of the origin of chloroplasts. It is also useful because it allows researchers to use the DNA to identify the source of the chloroplasts present in kleptoplastic organisms. This is a fairly standard method and is the way that Gast et al 2007 determined the source of the chloroplasts in the Antartic dinoflagellates discussed in a previous post.

In a paper (pdf) a few years ago in Limnology and Oceanography, McManus et al. used the chloroplasts present in the kleptoplastic tide-pool ciliates, Strombidium oculatum and Strombidium styliferseen to help reveal an interesting life history. The chloroplasts were from the large multicellular macroalgae Enteromorpha clathrata which raised the question of how these unicellular cilliates were able to acquire macroalgal chloroplasts.

McManus et al. found that the cilliates don't appear to be grazing directly on the large strands of the mature algae but on the small motile reproductive cells, called zoospores, mature algal strands release.

In addition to chloroplasts, the zoospores contain a pigmented eyespot. As the photo above (from the paper's figure 1) demonstrates, the kleptoplastic cilliates contain a pigmented eyespot similar to the ones possessed by the zoospores. This suggests that the Strombidium cilliates also owe their phototaxic abilities to the alga cells they ingest.

Some other interesting points about these cilliates:

They are tidal organisms and live by the rhythm of the tides, becoming active during low tide when tidal pools are calm, and then attach to surfaces and encyst during high tide, presumably to prevent them from being washed out to sea and away from their food.
They appear to be obligate mixotrophs, unable to grow in the dark or in the absence of algal food.

Complete reference:
McManus, G. B., H. Zhang, and S. Lin. 2004. Marine planktonic ciliates that prey on macroalgae and enslave their chloroplasts. Limnol. Oceanogr. 49:308-313.

8 random facts meme

2007-06-26T20:30:00.000-04:00

I have been tagged by John Dennehy (aka the Evilutionary biologist) in this 8 random facts meme. The rules are:

We have to post these rules before we give you the facts.
Players start with eight random facts/habits about themselves.
People who are tagged need to write their own blog about their eight things and post these rules.
At the end of your blog, you need to choose eight people to get tagged and list their names.
Don’t forget to leave them a comment telling them they’re tagged, and to read your blog.

1. When I saw I'd been tagged for this, my first though was: how big a population of facts do I need to generate in order to make sure that the list of 8 will seem random?

2. I own more that one microscope.

3. I have never known what I wanted to be when I grow up (I still don't).

4. I love the change of seasons and do my best to never complain about the weather.

5. There is a definite trend in the size of the organisms I've studies since college: penguins > tilapia > phytoplankon > bacteria ... ?

6. My dog's name is Larry

7. I live on an island off the the coast (if Spalding Grey can say that about Manhattan, I can say it about Aquidneck Island)

8. I am pretty sure this is not a random list but we'll have to check with Larry to be certain.

So many people have already done this so for the last part, I'll steal this from Tara: anyone who's not been hit already, feel free to consider yourself tagged.

In the Bay 24 Jun 2007

2007-06-25T14:30:00.000-04:00

Dactyliosolen fragilissimus, a chain forming diatom, one of the most abundant species of phytoplankton in the bay.

Building a better biofuel

2007-06-21T21:40:00.000-04:00

Biofuels offer the promise of reducing our dependence on fossil fuels. The most widely used biofuel is ethanol made by the biological fermentation of corn. This process is not as green as many would like to believe because a substantial amount of energy (in the form of fossil fuel) is used in the production process. So ,the net gain is not great. Also, ethanol itself is not a terribly good fuel as it is very volatile, is not very energy dense and absorbs water.

A better biofuel would be one that does not rely on an important food crop, has a higher energy density and can be produced with as little energy input as possible. In todays issue of Nature, Román-Leshkov et al present a letter in which they report on a process by which the are able to produce 2,5-dimethylfuran (DMF) from the sugar fructose.

DMF is a better fuel than ethanol and interest in it is not new. What is new in this report is the ability to produce DMF in an industrial process requiring much less energy than previously reported methods.

The environmental impacts of this material have not been well studied and the source of fructose for the production of DMF remains an important issue but this type of innovative thinking has a place in our efforts to move away from dependence on fossil fuels.

Complete citation:
Roman-Leshkov, Y., C. J. Barrett, Z. Y. Liu, and J. A. Dumesic. 2007. Production of dimethylfuran for liquid fuels from biomass-derived carbohydrates. Nature 447:982-985.

Cow burps and global warming

2007-06-21T12:40:00.000-04:00

Methane is a greenhouse gas and methane released into the atmosphere contributes to global climate change. Compared to CO₂, relatively little methane is released but it is ~ 20 times more effective at absorbing energy than CO₂ so its contribution is significant. There are both human influenced and natural sources of methane. These including rice patties, swamp gasses, termites and ruminants such as cows.

My friend (and a reader of this blog) Marek Kirs send me this link to a story on NPR about attempts to reduce the amount of methane produced by cows. The idea is to adjust the types of food they eat or even manipulate their gut microbial community to eliminate the methanogenic organisms responsible for the gas production.

One of the points the researchers make is that the production of methane is the result of incomplete oxidation of food eaten by the cows. So, the elimination of methanogenesis could result in increases production of meat and milk from these animals. Cattle food conversion ration are around 12%, and any increases would likely be small but the idea is to have enough of an increase to offset any increased cost to the producers.

Gut bacteria metabolic diversity

2007-06-20T09:30:00.000-04:00

Another paper exploring microbial diversity of the human gut has been released in PLoS Biology. It is open source so go read it for yourself! There is also a summary article on the data intended for a lay audience. The data presented in the paper is very interesting. They sequenced the genomes of two gut bacteria, Bacteroides vulgatus and Bacteroides distasonis, and contrasted their metabolic potential (the genes present in the genome) with the well studied species Bacteroides thetaiotaomicron. This comparison does provide some evidence that niche specialization plays a role in maintaining the diversity of the gut microbiota.

The importance of studying the gut microbiota is summed up nicely in the beginning of the author summary:

"Our microbial partners provide us with certain features that we have not had to evolve on our own. In this sense, we should consider ourselves to be a supraorganism whose genetic landscape includes both our own genome as well as the genomes of our resident microbes, and whose physiologic features are a synthesis of human and microbial metabolic traits."

I would have worded the first sentence differently as saying 'have not had to" sounds a bit too teleological to me.

I am also troubled by their use (later in the introduction) of the term "top-down selection" in reference to host driven selective forces that they argue are responsible for maintaining a high degree of functional redundancy in the gut community. I am not aware that the term top-down selection, as used by the broader ecology community, is considered a force for the maintenance of ecosystem stability.

The end of the paper lists a set open questions that it would be very nice to have answers to:

"Do we share an identifiable core “microbiome”? If there is such a core, how does the shell of diversity that surrounds the core influence our individual physiologic properties? How is the human microbiome evolving (within and between individuals) over varying time scales as a function of our changing diets, lifestyle, and biosphere? Finally, how should we define members of the microbiome when microbes possess pan-genomes (all genes present in any of the strains of a species) with varying degrees of “openness” to acquisition of genes from other microbes?"

Bacterial predators

2007-06-17T16:30:00.000-04:00

With the rise of antibiotic resistance in important bacterial pathogens, attention is being focused on alternative treatments for bacterial infections. The most prominent among these is phage therapy. Another potential antimicrobial agent is the predatory bacteria Bdellovibrio and related species

I am not sure how likely it is that these bacteria will ever find use as therapeutic agents, but they are pretty amazing organisms and they definitely have the potential to be used in this way.

Bdellovibrio have a truly predatory life style. They require specific species of gram negative bacteria to grow. The cells are small and highly motile. When they encounter a susceptible host cell, they attach themselves to the outer surface of the cell, bore a hole in the cell wall and push themselves into the periplasmic space (the space between the outer membrane and cytoplasmic membrane of gram negative bacteria). Once there the cell is killed and its contents consumed. Bdellovibrio reproduces within the cell and once the contents of the prey are consumed, the daughter cells will burst out of the shell of the dead prey cell and head off to find other targets.

454

2007-06-14T21:15:00.000-04:00

DNA sequencing has revolutionized biology. Not too long ago obtaining the sequence of an individual gene was a big deal. Now sequencing entire genomes is becoming routine. To obtain the sequence of an organism's entire genome, the genome is broken into fragments and many many fragments are sequenced individually using a PCR based method. In the standard process, the sequence generated from each fragment is about 500 to 1,000 bases long. To generate the sequence of the genome, computers are used to align all of the data and identify contiguous sequences that can then be assembled. In order to be confident in the data (errors are made in the process), the entire genome is sequenced multiple times. At least 4 to 5 x coverage is considered necessary for good data.

A typical bacterial genome of 3.5 mega-bases sequenced to 5x coverage amounts to over 21,000 individual sequencing runs. For organisms (such as humans) which have multiple chromosomes each chromosome is sequenced individually. With about 3 billion bases in the human genome and 10x coverage, the data contained in the human genome project represents an enormous amount of sequencing and alignment effort.

A relatively new innovation called 454 sequencing has sped up the process. 454 is still based on PCR but it is much faster as the sequence is read as the PCR progresses. The trade off to the increased speed is that each individual read is somewhat shorter making assembly more challenging.

One 454 application that is becoming more and more widespread is the sequencing of multiple strains of a species of bacteria. In this type of application the genome of one strain is already known. The assembly of the genome of each successive strain is facilitated by the use of the original strains sequence as a template.

454 sequencing was used to determine James Watson's genome. The whole genome was assembled in two months at a cost of $1 million. The assembly was almost certainly accelerated by aligning short reads of Watson's DNA with the pre-existing human genome sequence.

image from the tutorial found on 454 life sciences web page

Kleptoplasty

2007-06-11T21:45:00.000-04:00

Kleptoplasty is a wonderful term. It is used to describe the behavior of a group of organisms that are able to ingest algal cells and degrade the cells, but not the chloroplasts contained within the cells. The chloroplasts remain functional for some period of time during which the photosynthetic products generated by the sequestered chloroplasts are utilized by the new 'host'.

On the left is a figure from a paper by Gast et al. in the journal Enviornmental Microbiology from earlier this year showing a kleptoplastic dinoflagellate isolated from the Ross Sea in Antartica (the paper is in a free issue of the journal so go read the whole thing).

In addition to being a very interesting behavior from an ecological perspective, kleptoplasty is of evolutionary interest because the capacity to grow autotrophically by photosynthesis arose within dinoflagellates by the retention of chloroplasts from ingested algal cells. This ability appears to have arisen multiple times within dinoflagellates because not all contain chloroplasts from the same type of algal cell.

African deforestation

2007-06-10T16:05:00.000-04:00

The rainforest of the Congo Basin in Central Africa is the second largest in the world. It covers millions of square kilometers and spans 6 different countries (including Gabon where I spent 2 years). As with other tropical rain forests this region is home to substantial biodiversity. Here in the US we hear a great deal about deforestation in the Amazon, less is heard about the African rainforests.

The most recent issue of the journal Science contains a brief report documenting the extent of deforestation and increases in commercial logging in the Congo Basin. The information was acquired by analyzing almost 30 years of satellite data for changes in forest cover and the appearance of new logging roads. The objectives of the report were to highlight the lack of good data on the extent of deforestation in the Congo Basin, present the data acquired from the available satellite data and demonstrate the value of the satellite data as a tool to assess changes in land use and document the extent of logging.

*added on edit: Here is some more information about the article and here is the figure from the paper showing the extent of the deforestation. Note how much of the area still has >75% forest cover.

adopt a cheetah

2007-06-09T07:38:00.000-04:00

A recent report in Proceeding of the Royal Society describes the genetic relationship among cheetah litter mates. They found that almost half the litters were comprised kittens of mixed paternity. Female cheetah parole a territory of 300-400 km² and this allows them to interact with more than one male during a single reproductive cycle. This is a behavior that they share with the common cat. A summary of the paper can be found here.

One finding that struck me was that within the 47 litters surveyed, they found 3 instances of adoption by mother cheetahs of unrelated kittens. This finding has been described previously and there are several ideas as to the potential selective advantage this behavior. My first question is given the huge territories these cats parole, how on earth do the new mothers find orphaned kittens?

Plant-bacteria communication

2007-06-07T20:32:00.000-04:00

In a previous post I mentioned that the nitrogen fixation performed by leguminous plants is the result of a symbiosis between the plants and bacteria. In this relationship, the plants create an environment within their roots (called nodules) where the bacteria take up residence. In exchange for energy provided by the plant, the bacteria fix atmospheric nitrogen that is then made available to the plant. Allowing bacteria access to the interior of the root is a potentially risky act on the part of the plant. So, a mechanism to exclude all bacteria except for the desired nitrogen fixer has developed and the symbiotic relationships are species specific. Each plant has specific bacterial symbionts. In the early stages of the establishment of the root nodule, signals are exchanged between the plant roots and bacteria in the soil. First, the plants release phytochemicals that attract the desired bacteria. The target bacteria are attracted by the phytochemicals and these chemicals induce the bacteria to release their own compounds called nod factors. The nod factors, in turn are sensed by the plant. Detection of the appropriate nod factor will induce the plant to initiate the process of allowing the bacteria access to the interior of the root where the nodule will form.

In the latest PNAS, Fox et al. report that many common pesticides inhibit the formation of root nodules by interfering with communications between the plants and bacteria.

While the significance of this in the environment is not known, it has the potential to be of concern because the use of crop rotations that include plants (such as soy or alfalfa) that are capable of enriching the nitrogen content of the soil is one important way to reduce the use of fertilizer (and energy) in modern agriculture.