Biological Diversity

In recent conversations I've had with biologists at a plant breeding symposium at UMN and other local events, I've come across people using the term "diversity" in rather distinctively different ways.

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A researcher was described how low diversity soybeans were, as an argument for the fast-neutron mutagenesis project he was working on to develop new useful diversity. I didn't believe soybeans to be a low diversity crop, as there are so many wild and weedy forms available in the center of diversity for the species in China. He then made some comment about the limited diversity brought to the United States from Asia...  which made me wonder why he would limit himself to what is locally available, when strains from the whole world are available with some effort.

The closing keynote speaker was later discussing his 34 year career of soybean breeding and started off by describing the great diversity available in soybeans for breeders to work with. I then realized that the first researcher and I had been using different measures of diversity. He was using "diversity" to mean what was commonly available locally (definition #1 below), while I (and the keynote speaker) were using "diversity" to mean the range of genotypes available worldwide (definition #2 below).

Population genotype structures:
Local: AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAABB
World: AAAAAAAAAAAAAAAAAAAAAAAAAAAAABBCDEFGHIJKLMN

1. Range of genotypes locally available. The population approximates just genotype A, so under this definition the crop species has a very low diversity.

2. Range of genotypes in a species. The population includes 14 distinct genotypes (ABCDEFGHIJKLMN), so under this definition the crop species has a very high diversity.

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At another event, a speaker was talking about how some regions of the genome for his study plant species had very low diversity and that this indicated recent introgression from a related species because the rest of the genome had a very high diversity.

I commented that I would have to look into the math behind it to better grasp what he was talking about.  He shrugged off the need for this and said the region was determined as having low diversity using a hidden-markov-model (HMM) approach.

I pondered on his statement. The HMM approach is used to identify transitions between states as you move along the axis of a dataset. In the case of the speaker's research, the HMM would calculate the most probably coordinates in the genome for transitions from high diversity to low diversity and back. Unfortunately, this still doesn't explain what he meant by "diversity". As the speaker was talking about a region of the genome having lower diversity than average for the species(individual?), there are two ways I can interpret his use of "diversity".

3. The amount of heterozygosity within an individual. A highly inbred individual will have a very low "diversity", while a highly outbred hybrid individual will have a very high "diversity".

4. The variation in haplotypes across a population. Haplotypes are distinct coordinately traveling regions of genetic information. The more haplotypes in a region, the more diverse the population is. A You would need to sequence a relatively large number of individuals to get a glimpse at the sort of data this analysis would require.

I have the feeling he was using "diversity" to mean a change in some measure across the genome of an individual (definition #3 above), rather than a measure of the population of the species (definition #4 above).

If he meant "diversity" like definition #3 above, then I would interpret a region of the genome with much lower level of heterozygosity to indicate a recent loss-of-heterozygosity (LOH) event, such as a damaged chromosome region being repaired by replacement with sequence from the intact other homolog to the chromosome. If he meant "diversity" like definition #4 above, then I would interpret such a region to indicate a recent selective sweep. In neither case does the data suggest to me there has been an introgression from an unspecified near relative with a higher propensity to self.

I really wish I had been able to get more clarity from the speaker about what he meant. I also wish he hadn't dismissed my interest in his project so quickly.

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The meaning of even commonly used words can drift between different groups of speakers. In science it is very important to be clear in what you mean by the terms you use, even for the words that don't seem to be jargon.


References:

1. HMM: en.wikipedia.org/wiki/Hidden_Markov_model
2. Haplotypes: en.wikipedia.org/wiki/Haplotype

Astrobiology : The basics of life.

Life as we know it is composed of three basic types of chemical compounds: nucleic acids (DNA & RNA), proteins, and lipids. One aspect of the study of abiogenesis (the origin of life) has been to determine how the basic compounds could have been formed from simple chemical precursors that we already know can be formed from simple physical and chemical processes.

One of the first experiments in to examine how the basic biomolecules could have been formed was performed in 1952 and is known as the Miller-Urey experiment. In this experiment, a selection of simple reducing gases was repeatedly condensed and boiled while being exposed to electric sparks. The experiment was setup to mimic the conditions of the early atmosphere here on Earth. The reducing gases are those that would have been generated from geologic processes before living things started adding oxygen to the mix. The sparks represented lightening, which was thought of as a plausible energy source that could drive the reactions to generate interesting chemistry.

The experiment was able to produce hydrogen cyanide (HCN), formaldehyde (CH₂O), and other simple molecules. These molecules then reacted to form over 40 different amino acids, in sufficient amounts to color the condensed liquid pink after a day. Several variations of the experiment have been done that produce different mixes of small biomolecules, including all the purines and pyrimidines used in the bases of RNA/DNA as well as the ribose sugars used to construct nucleotides.

Most of these experiments required the presence of ammonia (NH₄) and methane (CH₃) to produce interesting biomolecules. This is a problem, because these gases are now thought to be relatively rare in the early atmosphere because of their absence in the volcanic gas emissions that would have contributed heavily to the early atmosphere.

A new set of conditions has been identified (Patel, Nature 2015) that is able to generate the precursors to amino acids, nucleic acids (sugars and purines/pyrimidines), and lipids. The key components were hydrogen cyanide (HCN) and hydrogen sulfide (HS) from the atmosphere and ultraviolet light from the sun interacting in a water (H₂O) bath. The process was sped up by the presence of dissolved copper ions. Interestingly, the proposed reactions generate all the basic compounds used in our type of life, but also don't generate many other simple compounds that our type of life doesn't use.

I consider this topic to be part of astrobiology because the same basic physical processes which are studied in research into abiogenesis here on Earth have also been playing out at sites throughout the universe. The same basic compounds of life have been generated on wet worlds wherever they are found. This not only suggests that life may be ubiquitous through the universe, but that when life is found on planets like ours that it may also be composed of similar basic types of molecules.

Lots of other simple chemicals have been identified in space using spectroscopy. These have also been generated through common physical and chemical processes and may represent the basic chemicals found in other types of life that started in environments distinct from our own.


References

1. Miller-Urey experiment: en.wikipedia.org/wiki/Miller%E2%80%93Urey_experiment
2. Recent analysis of Miller-Urey: www.ncbi.nlm.nih.gov/pubmed/23340907
3. Patel, Nature 2015: http://www.nature.com/nchem/journal/v7/n4/full/nchem.2202.html
4. Molecules in space: en.wikipedia.org/wiki/List_of_interstellar_and_circumstellar_molecules

Convergence on the Seaside

Cakile maritima flowers.

I found this plant growing on the beach on a trip to southern California two years ago. The four-petaled flower and shape of the seed pods told me it was in the family Brassicacea, like the wild radishes which are common in the region. The thick and succulent leaves, however, indicated this plant was unlike any plant in the family I had seen before. I collected a few seed pods, hoping to later identify the plant.

After periodic internet searches over the last two years, whenever I found myself thinking about the plant, I finally found an image of a flower with the right shape and color that also grows in beach habitats above the high-water line. I've identified the plant as Cakile maritima (European Sea-Rocket). It and the related C. edentula (American Sea-Rocket) and C. lanceolata (Coastal Sea-Rocket) have small seed pods which contain one or two seeds and are dispersed by floating in water. The pods and leaves differ in shape between the species, but they are otherwise very similar.

C. maritima seed pods.

The species in this genus are generally described as edible, with leaves tasting spicy like horseradish. The plant I found had leaves which tasted mostly sweet. This may be just because I chose young leaves to taste, or I might have lucked onto a plant that was mild instead of hot. Hopefully the seeds I've stored will germinate so I can find out. Either way, I see it as an interesting plant to develop for the salad garden.

Sea-Rocket is commonly described as edible, but it doesn't seem it was ever a major crop. I've found one reference to it being grown in a garden in 1596-1599, but it isn't clear if was grown for vegetable or botanical use.

Another interesting beach-side plant in the Brassicaceae is Crambe maritima (Sea-Kale). Both plants have succulent leaves and dry fruit that effectively float and disperse their seeds. I find interesting that the two species evolved convergently from related ancestors to similar forms in the shared environment of European coastlines.

Sea-Kale appears to have been commercially harvested in Roman times and was cultivated in Europe from around the 1600s, but went out of fashion around the time of WWII.

References:

• Cakile maritima (Sea-Rocket)
• en.wikipedia.org/wiki/Cakile_maritima
• Biology of: onlinelibrary.wiley.com/doi/10.1111/j.1365-2745.2006.01131.x/full
• 1596-1599 garden: books.google.com/books?id=nmwZAAAAYAAJ&pg=PA28#v=onepage 
• Crambe maritima (Sea-Kale)
• en.wikipedia.org/wiki/Crambe_maritima
• edible: www.eattheweeds.com/sea-kale/

Biology in the Snow

All through this deep Minnesota winter, I've been trying to think of some observations or discussion I could have about the biology of snow.

There are lots of interesting little things to learn about how living things deal with snow. Some plants grow roots into snow-banks to extract nitrogen before it is delivered to other plants in melt-water. Various bugs are specialized to deal with the cold and are active in and on snow. There are plants that heat themselves up in spring, melting away snow, so their flowers can get pollinated. I find these and many other things to be very interesting...  but it is difficult to go out and examine biology in the snow so I can have some direct observations to talk about.

The one exception is the observation of tracks in new snow. The photo at left shows the track left from a mouse scampering from near my front door (at right) to the top of my deck stairway (at left). As it bounded along, its larger hind feet landed ahead of the smaller front feet. This track doesn't tell a great deal, but it does highlight the amazing energetic feat of a tiny little rodent running around in the cold snow instead of freezing into a solid little mouse-cube.

You can learn a lot about what the animals are doing by reading their tracks.

A persistent mouse track-highway has revealed a well-used path between a rock-pile shelter and the base of a near-by blue spruce, where the mice are presumably foraging.

Other tracks have revealed the under-snow explorations of short-tailed voles. Many of these tracks become very obvious when the snow begins to melt. Long arcing paths are left as they forage for seeds and other tasty plant bits.

One time, I found tracks from a mouse bounding along the top of the snow crossing over the tracks left by a burrowing vole. The two rodents have very distinct methods of getting around in the snow. Mice hurry along from shelter to shelter, while voles tunnel along under the snow's surface. Both strategies minimize their exposure to cold wind.

Recently, the tracks of two coyotes revealed how they sauntered through the yard while one playfully ran around the other. I knew coyotes were in the neighborhood because we saw one crossing the road a few miles away, but I had never seen or heard them in the yard.

I've found the unique impression formed when an owl or crow lands heavily in the snow while trying to capture a burrowing vole.

Unfortunately, tracks in the snow can be very hard to photograph. You're trying to capture a white impression in white snow. The tracks are plain to see in 3D, but the 2D images from a camera are usually unclear. The mouse-track image above took several tries and then further post-processing to highlight the tracks that were immediately visible in person. Even after that work, I'm still pretty sure that the photo only turned out because the footprints were clearing away the snow to reveal the darker colored decking material beneath.

So, until I can figure out a good way to capture the images for presentation and discussion, all I can do is suggest you pay attention to the tracks being left all around you in the snow.

References:

• Snow-roots: www.academia.edu/2517365/New_nitrogen_uptake_strategy_specialized_snow_roots
• Snow-bugs: www.microscopy-uk.org.uk/mag/indexmag.html?http://www.microscopy-uk.org.uk/mag/artjan99/basnow.html
• Skunk Cabbage: www.damninteresting.com/warm-blooded-plants/

Publish or Perish

Most of my biology-focused posts have been about topics related to garden projects I've done or have been thinking about. The subject of gardening does account for much of the biology I spend my free-time thinking about, especially now in the middle of a winter-bound Minnesota. It is also far easier to examine the growth and interactions of living things in the garden than it is to go on expeditions or develop lab protocols to explore the diversity of biological topics.

I've avoided talking in detail about the biology I do at work because the work is on-going and to publicize it here might detract from the process of publishing the work in more formal contexts once the projects reach usable conclusions. Sometimes a key result can be quickly replicated once the idea behind it has been developed, so talking about results too early can be asking for some competitor to beat you to publication. I've defended my thesis and dealt with graduate school bureaucracy sufficiently to be awarded my PhD. I can now refer to myself as "Darren Abbey, PhD" in professional contexts. (I can also refer to myself as "The Doctor" (Dr. Who?) in certain social contexts.)

Along the way, I've written or contributed to several research publications. The following list is the publications I've been received name credit for my contributions, from oldest to most recent.

1. Gale CA, Leonard MD, Finley KR, Christensen L, McClellan M, Abbey D, Kurischko C, Bensen E, Tzafrir I, Kauffman S, Becker J, Berman J. (2009) SLA2 mutations cause SWE1-mediated cell cycle phenotypes in Candida albicans and Saccharomyces cerevisiae. Microbiology. 155(Pt 12):3847-59. [PMID: 19778960]
    
2. Forche A, Abbey D, Pisithkul T, Weinzierl MA, Ringstrom T, Bruck D, Petersen K, Berman J. (2011) Stress alters rates and types of loss of heterozygosity in Candida albicans. MBio. 2(4). [PMID: 21791579]
    
3. Abbey D, Hickman M, Gresham D, Berman J. (2012) High-Resolution SNP/CGH Microarrays Reveal the Accumulation of Loss of Heterozygosity in Commonly Used Candida albicans Strains. G3 (Bethesda). 1(7):523-30. Erratum in: G3 (Bethesda). 2(11):1473. [PMID: 22384363]
    
4. Hickman MA, Zeng G, Forche A, Hirakawa MP, Abbey D, Harrison BD, Wang YM, Su CH, Bennett RJ, Wang Y, Berman J. (2013) The 'obligate diploid' Candida albicans forms mating-competent haploids. Nature. 494(7435):55-9. [PMID: 23364695]
    
5. Abbey DA, Funt J, Lurie-Weinberger MN, Thompson DA, Regev A, Myers CL, Berman J. (2014) YMAP: a pipeline for visualization of copy number variation and loss of heterozygosity in eukaryotic pathogens. Genome Med. 6(11):100. [PMID: 25505934]
    
6. Ford CB, Funt JM, Abbey D, Issi L, Guiducci C, Martinez DA, Delorey T, Li BY, White TC, Cuomo C, Rao RP, Berman J, Thompson DA, Regev A. (2015) The evolution of drug resistance in clinical isolates of Candida albicans. Elife. 4. [PMID: 25646566]
    

I've also got a couple others in the pipeline. For one I'm looking for a target journal, for the other I'm still deciding exactly how to present the results. I'll let you know more details once they're further along the way to publication.

The projects a grad student works on depends on a mix of the lab they end up in and their personal style of problem solving. I ended up in a Candida albicans lab and brought to it a heavy computational approach. The mix between the two is the realm of computational biology, the topic I find myself most connected to.

The academic life can readily be described as, "Publish or Perish". With six name papers from my time in grad school, I've done alright. Now I just have to figure out the next step.

The Color of Cotton

1. www.perunaturtex.com/scientif.htm

Ever since I first heard about it, I've been interested in naturally colored cotton (also known as "color grown cotton"). The cotton plants most people are familiar with produce a pure white fiber, which can then be dyed to match any desired color. Naturally colored cotton, on the other hand, is grown with color straight from the plant.

There is archaeological evidence for the existence of cotton in various shades of yellow, brown, green, and red. The pre-Columbian Peruvian textile at left is supposedly made from colored cotton without the processing of additional dyes. There are also reports of a naturally colored blue cotton, but the internet has provided minimal evidence for this.

The majority of commercially grown cotton belongs to the species Gossypium hirsutum. Varieties of this cotton species can be found in light brown and green, but the other colors are generally nowhere to be found.

2. Inheritance of different fiber colors in cotton.

During a recent web search, I came across an image of a very dark brown naturally colored cotton. The image also shows a nice orange cotton, in addition to the more typically seen tan and light brown colors. Seed for these varieties aren't generally available, however, but they can be accessed from different seed collections (such as GRIN) if you can show you have some worthwhile research, education, or other public good rationale for having them.

These more interesting colors are seen in relatively wild varieties of a second cotton species, G. barbadense. G. hirsutem and G. barbadense don't naturally cross in the wild due to different timing of pollen maturation and other mechanisms. These are all easily circumvented by directed hybridization efforts. The resulting F1 hybrids grow well and are fertile, though fertility issues do arise in some F2 generation plants. These issues wouldn't interfere greatly with the intentional recombination of pigment alleles from both species, which I think has interesting potential to create new interesting colored varieties.

After I've done some further experiments with growing the cotton lines I already have in Minnesota, I might request some of the interesting colored forms from the collections.

3. Cotton and I.

...wait, growing cotton in Minnesota (red star)? ...a thousand miles north of where cotton is grown in the USA (green regions)?

A few years ago, on a whim, I planted some cotton seeds I had come across in south Texas. Cotton is typically described as needing a long and hot growing season to mature. I don't know how the production of my plants compared to similar plants in the South, but their production was dramatically higher than I expected up here in the North. After the first hard freeze of winter, I broke the plants off at their base and hung them to dry in the garage. A few weeks later, the cotton fibers had completed drying and were easy to collect. This process might not be something that can be scaled up to a proper crop, but it might. Further research is needed.

References:

1. www.perunaturtex.com/scientif.htm
2. Dark brown cotton: www.scielo.br/scielo.php?pid=S1984-70332014000400008&script=sci_arttext
3. GRIN: www.ars-grin.gov/npgs/orders.html
4. Crossing: www.ogtr.gov.au/internet/ogtr/publishing.nsf/content/cotton-3/$FILE/biologycotton08.pdf

The Case of the Marvelous Meiosis

1. Meiosis in male (A) and female (B).

The typical story of meiosis is described in detail in many a biology textbook. It all starts with a diploid somatic cell. The chromosomes duplicate and homologs align along the cell's mid-line. The aligned chromosome doublets crossover and then the doublets are divided into two new cells (Meiosis I). The chromosome doublets align along the mid-lines and the new cells divide again (Meiosis II) to produce the final gametes. This model well matches the process of spermatogenesis (Fig 1A), which was used as a model to study and understand the process. Oogenesis follows basically the same process, except that each division is asymmetric. The result is one large gamete (Fig 1B) and two or three non-viable cell fragments with the extra chromosomes.

2. Meiosis in male (A) and female (B) Caninae group roses.

Roses in the group Caninae (Dog Roses) do a peculiar version of the process. The basic example is tetraploid, but produces haploid male (Fig 2A) and triploid female (Fig 2B) gametes. During meiosis I, two homologs for each chromosome align to form a bivalent and the rest remain as monovalents. The monovalents are lost during spermatogenesis, but retained during oogenesis. This system is referred to as "permanent odd polyploidy".  It even works with extra uneven chromosome copies. The extras form monovalents and are discarded or retained just like the red and blue chromosomes in Figure 2. This system allows fertility to be maintained even with odd chromosome counts that would normally make a plant sterile.

I came across this peculiar variant of meiosis while researching what complications might develop in a cross between Rosa pomifera (4n, group Caninae) and R. rugosa (2n). Both parent species have relatively large fruit. My initial plan was to hybridize the two species, generating at least one F1 plant, then allow them to self and screen many F2 progeny plants for increased fruit size.

That the two roses are not very closely related and both species have numerous smaller-fruited relatives suggests their large fruit was evolved separately. This is useful for a breeding project as it means that different mutations accumulated as each plant developed large fruit. Those separate mutations can possibly be recombined via hybridization to generate a progeny plant with even larger fruit.

I expect the project of domesticating roses as [more of] a fruit will take decades. It should be an amusing hobby and I expect to have enough time left to see some nice results.

References:

1. Meiosis: en.wikipedia.org/wiki/Meiosis
2. Rose groups: en.wikipedia.org/wiki/List_of_Rosa_species
3. Dog rose meiosis:
1. www.nature.com/hdy/journal/v101/n4/abs/hdy200863a.html
2. www.ncbi.nlm.nih.gov/pubmed/24685720