A Miniature, Aquatic World

Last year (2015), I had the pleasure of performing field work in Nome, Alaska with a professor named Dr. Derek Taylor. Dr. Taylor had devised a brilliant set of experiments to study animals local to the tundras of Alaska. We arrived at the end of July and stayed for approximately one week. While there, we witnessed environments unscathed by the touch of man. We beheld landscapes that seemed as though they were painted into existence, holding beasts of great magnificence and power. We heard muskoxen snort in discontent, warning that we were too close.

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-Photo taken by Mr. Bill Nichols of the University at Buffalo)

Despite all of the obvious wonders around us, we were there for something else entirely. Global climate change shifts aquatic ecosystems as the borders of bodies of water are altered rapidly. This is especially so for freshwater environments. These environments are the homes to a number of zooplankton* species.

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-Left – Daphnia, Top Right – Heterocope, Bottom Right – Chaoborus)

While in Alaska, we collected zooplankton samples from a variety of locations. The samples were gathered from numerous freshwater sources using D-nets or throw-nets depending on the depth of the water. D-nets are attached to a long wooden handle, whereas throw nets are thrown and then reeled back in, allowing the net to catch these tiny organisms as it passes. Samples were generally preserved using ethanol solutions or by drying them out. They would later be kept in freezers to maintain the integrity of their nucleotide sequences (see previous post – April 19th, 2016).

Dr. Taylor once told me that despite their small size, if one were to only consider the mass of zooplankton on our planet, the outlines of all of the major bodies of water would still be visible from space. This thought is truly astonishing and goes to show that there is an entire world of organisms that most people do not even consider.

These zooplankton are also a major component of the freshwater and saltwater ecosystems that they reside in. They can range from keystone predators to primary consumers that simply eat the algae in these waters. They are a major food source to countless organisms as they play their role in the food web.

Taking this a step further, there are viruses that are specifically adapted to infect individual species of zooplankton. These viruses can be extremely diverse and found in most (or all) types of zooplankton. Their tremendous numbers and quickly changing DNA makes them difficult, yet interesting to study. One method of doing so is known as metagenomics.

For a metagenomic analysis, a researcher sequences all of the genetic material in a given sample. In this case, it would be everything within a certain volume of water. This type of analysis then requires the researcher to take all of this data and compare it to known databases in order to find out which segments of DNA or RNA* are coming from which organisms (some viruses store their genetic information in the form of the molecule RNA, instead of DNA). This can be tricky since certain viruses are so new and underrepresented that they do not share high sequence similarity to anything in public databases. In our samples, I rarely saw viral segments of DNA/RNA that matched with known viruses to a degree of greater than 70%.

These zooplankton and their viruses have a massive impact on a number of organisms in their food webs. In this area of research, there are interesting stories around every corner. One just needs to ask the right questions.

 

Terminology Definitions*

Plankton – The aggregate of passively floating, drifting, or somewhat motile organisms occurring in a body of water, primarily comprising microscopic algae and protozoa

Zooplankton – The aggregate of animal or animal-like organisms in plankton, as protozoans

RNA – Acronym for Ribonucleic Acid – any of a class of single-stranded molecules transcribed from DNA in the cell nucleus or in the mitochondrion or chloroplast, containing along the strand a linear sequence of nucleotide bases that is complementary to the DNA strand from which it is transcribed: the composition of the RNA molecule is identical with that of DNA except for the substitution of the sugar ribose for deoxyribose and the substitution of the nucleotide base uracil for thymine.

Definitions from Dictionary.com

 

There are more pictures of our trip to Alaska in the Photography section of this blog.

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What are Structural Variants and Why Do they Matter?

After spending some time in my Ph.D. program at the University at Buffalo, I ended up in the laboratory of a man by the name of Dr. Omer Gokcumen. In this lab, we study Evolutionary Biology. In particular, Dr. Gokcumen is a specialist with regards to what are known as structural variants. To understand what this means, we need to understand the basics.

All living organisms on this planet have a biological “blueprint.” This blueprint involves a particular coding system that utilizes four different nucleotides in a molecule known as deoxyribose nucleic acid, or DNA for short. These four nucleotides are Adenine (A), Thymine (T), Cytosine (C), and Guanine (G). Each molecule of DNA consists of two strands that are connected by these nucleotides. A always pairs with T and C always pairs with G.

A mutation is a change in this code. The best studied mutations are ones that cause a single nucleotide to change from one to the other. For example, a Thymine could be placed where there should be an Adenine. These are called point mutations.

It should be noted that a single set of DNA “blueprints,” referred to as a genome collectively, is approximately 3 billion bases (nucleotides) in length in humans. This means that there are 3 billion A’s, T’s, C’s, and G’s in a single set. Each human has two sets. One of these sets comes from your mother, while the other set comes from your father. Despite this vast number of bases, if a single change is made in the wrong place, the effects can be tremendous. For example, sickle cell anemia, a life threatening blood disorder, is caused by a single point mutation. Conversely, a mutation could have no effect whatsoever.

Not all changes to the genetic code are caused by point mutations. This is where structural variants come into play. Structural variants involve taking an entire segment of this code and altering it in some way. The segment can be deleted out, duplicated, moved elsewhere (translocation), or flipped backwards (transversion). When these alterations cause a change in the number of times you see a particular DNA segment in the genome, the result is referred to as a copy number variant (CNV).

(Click the Picture to Enlarge – Figure from tutorhelpdesk.com (4))

When compared to single nucleotide variants (SNVs), which are caused by point mutations, these structural variants often seem to have a much greater effect on the human genome. In fact, according to one study (2), structural variants affect a minimum of seven times more human nucleotides than SNVs do! Despite this astonishing figure, the majority of research has been focused on SNVs. Why might this be?

The answer is simple; it’s easier. The current method of sequencing and mapping DNA involves cutting the DNA into small portions and then comparing it to the reference sequence. This means that if you have segments of DNA that have been moved, duplicated, or deleted, these small portions might not align to where they are supposed to be (i.e. where they originally came from in the genome prior to being cut up). One new study stated that 40 to 50 percent of CNVs have not been recognized yet (3)! This leaves much of the genome a mystery. Luckily, new technologies that utilize longer DNA sequence reads may solve this problem.

Structural variants are involved in a number of disorders including spinal muscular dystrophy, which is the result of a deletion. We must understand the cause of these diseases if we hope to one day fully remedy them. A number of these alterations could have also been involved in what made our lineage unique throughout our evolutionary history. For example, certain duplication and deletion events have been linked to body morphology (shape) and brain development in humans.

This is why the work done in laboratories that focus on structural variation is so important. We cannot hope to understand human genetics without a proper understanding of this type of variation. That is why I spend my time in the Gokcumen lab working on the discovery and understanding of SVs.

 

Works Cited

  1. Alkan, C. et al. (2011) Genome structural variation discovery and genotyping. Nat. Rev. Genet., 12, 363–376
  2. Conrad, D. F., Pinto, D., Redon, R., Feuk, L., Gokcumen, O., Zhang, Y., … & Fitzgerald, T. (2010). Origins and functional impact of copy number variation in the human genome.Nature464(7289), 704-712
  3. Huddleston, J., & Eichler, E. E. (2016). An Incomplete Understanding of Human Genetic Variation.Genetics202(4), 1251-1254
  4. Modification of Chromosome Structure. (n.d.). Retrieved May 27, 2016, from http://www.tutorhelpdesk.com/homeworkhelp/Biology-/Modification-Chromosome-Structure-Assignment-Help.html

 

Survival of the Fittest? Not Always…

Imagine, if you will, this hypothetical scenario. It is not too long after the origin of life, and a population of organisms emerges. These organisms are the best adapted, compared to other species of organisms, to their particular environment. They have the potential to expand throughout the world. If left to their own devices, in this hypothetical situation, this population would continue adapting to their environments. By April 5th, 2016, this population of organisms would have evolved to the point that each individual would be that of tremendous intellect. In this scenario, they would have understood the world enough to create renewable energy sources to prevent themselves from altering their environment in detrimental fashions. They would have been a species of nonviolence, living in peace and harmony without concern or hatred over trivial matters. While progression toward complexity is not always the case in evolution, these magnificent beings could have become a reality with their roots residing in this population of primitive organisms. This is the potential power of selection. Now consider that this population of well adapted organisms found themselves in a small body of water that dried up, killing all of them. This then allowed for a species of violent, semi-intelligent primates to rule the world. This is the power of genetic drift.

The process of Natural Selection is commonly referred to as “survival of the fittest.” This states that the organisms best adapted to their particular environment are the ones that are more likely to produce viable offspring, affecting the allelic frequencies in their population. This concept generally increases the frequency of beneficial alleles and decreases the frequency of detrimental alleles. This is selection.

 

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However, genetic drift involves changes in allelic frequency due to chance events. Not every event throughout evolutionary history was a direct result of selective pressures. In other words, new alleles that would have been beneficial could very well have been wiped from existence before ever being propagated if the organism carrying said allele is killed prior to reproduction.

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The interplay between these two mechanisms seems simple enough, but it is still discussed at great lengths today. Population geneticists often seem to feel that certain evolutionary biologists overplay the power of selection, stating that chance events have had a much larger role in shaping the organisms around us today. This would mean that there isn’t an adaptive reason for every trait that ends up reaching high frequencies in populations.

It is important to note that these chance events have greater effects on a particular population if the number of individuals in that population is lower. Consider a group of three puppies being sold. In this group of dogs, each one is a different breed. For this example, we will say that there is one Chihuahua, one Maltese, and one Pomeranian. Now imagine that one of these dogs is randomly adopted. This would affect the diversity of puppies there in a much greater fashion than if there were twenty of each type of dog. This is a simple way of considering the effect of genetic drift on groups with different population sizes.

So when asking yourself how a particular trait is adaptive for the population that it resides in, one must consider the fact that it might not be adaptive at all.

 

Terminology Definitions

Allele – one of two or more alternative forms of a gene that arise by mutation and are found at the same place on a chromosome.

Definition from Google.com