The Curious J: A science blog

Exploring life, one atom at a time.


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Genetic Engineering Pt. II: Tools of the Trade

As introduced in my previous post, this is the second of a 3-part series on genetic engineering. The first post was a brief overview and introduction to genetic engineering; while this one will focus on the tools used, and explain the difference between artificial selection and genetic modification. The third and final post will cover some of the more controversial topics, such as personalized medicine and genetically modified organisms (GMOs).

Artificial Selection: How We Created Man’s Best Friend

In order to explain the differences between genetic modification and artificial selection, it’s easiest to look at specific examples. A prominent example of artificial selection is the animal that has touched so many hearts it’s been named “man’s best friend”- dogs. Dogs are especially interesting because they are believed to be the first animal ever domesticated, occurring even before agricultural animals such as cattle, and there are now several studies suggesting that dogs were independently domesticated  twice.

All dog breeds come from a common ancestor – the gray wolf. Genetic sequencing studies show how closely they are related. So how exactly did we get the chihuahua from the gray wolf? Through thousands of years of selective breeding, even as long as 30,000 years. Let’s start with the gray wolf meeting humans: it’s unknown whether humans sought out a relationship with wolves, if it was vise versa, or if it was a mutual “agreement”. However it happened, humans began to interact with wolves to the point where they were breeding them for specific qualities.

From the beginning of domestication, people recognized that if you cross two wolves that are docile than their offspring will have a high chance of being docile as well (versus breeding more aggressive wolves). If you continue this process, while also eliminating the aggressive wolves – let’s be honest, this occurred – than you would eventually, through several generations, have only docile wolves. If you continue this process while concentrating on a single characteristic at a time, such as size or coat-thickness, than eventually the wolves become so genetically different from their descendants that they became a new species: dogs.

For dogs, several characteristics were altered over thousands of years by repeatedly altering a trait at a time. In more modern times, such as with cattle and other agricultural animals, only a single trait or small set of traits is targeted for alteration, not allowing for speciation, or the separation of one species into two.

This same process is used for the domestication of plants. Although the exact date when wheat was first domesticated is still debated today, it is known that the wheat we consume today varies genetically from wild wheat due to years of selective breeding. Two traits in particular allowed humans to consume and to grow wheat: an increase in grain size and the development of non-shattering seeds. The former allows for easier cultivation of the seedlings and the latter prevents natural seed dispersal, so that humans can harvest the seeds at the optimal time. It’s believed that both of these traits occurred naturally, and humans took advantage of them by only selecting for plants with those qualities. Today, common wheat differs even greater from the wild ancestor through actual breeding programs. Wheat breeding programs around the world have artificially selected for traits that mostly confer a resistance to either a pest, disease or other environmental factor, creating a much more modern version of wheat.

For a further understanding of artificial selection, check out these links:

Genetic Modification: The Simple-ish Version

As mentioned in my previous post, genetic engineering, or modification, has been in practice since the 1970’s, when Boyer and Cohen first successfully recombined DNA into E. coli. Although the procedure Boyer and Cohen used, known as recombinant DNA technology, is still used today along with several other methods, there is a current shift into using CRISPR technology as the main tool for genetic alteration. Since this shift is occurring and there has been a focus on CRISPR, both by those that support genetic engineering and those that don’t, the rest of this post will have a major emphasis on CRISPR technology.

CRISPR stands for Clustered Regularly Inter-spaced Short Palindromic Repeats. Palindromic repeats are prokaryotic DNA containing short repetitions of base sequences, and in between the sequences are short segments of non-coding DNA (“spacer DNA”). One of the main components of CRISPR technology are CRISPR associated proteins, or Cas proteins, which are endonuclease enzymes – enzymes that will cut double-stranded DNA (dsDNA) – that are guided by RNA. CRISPR and Cas proteins are naturally found in several species of bacteria, and work as mechanisms of immunity by cleaving the DNA of invading pathogens, such as viruses. Although there are multiple Cas proteins, the Cas9 endonuclease found in Streptococcus pyogenes is currently the most efficient Cas protein, thus the current technology is known as CRISPR/Cas9. 

CRISPR/Cas9 technology is progressively getting more complicated with the addition of new information and modifications to the current methodology. However, the basic procedure that CRISPR/Cas9 performs remains the same. As mentioned, one of the main components of the technology is the Cas9 protein. The other component is a guiding RNA (gRNA). The gRNA is created so that it matches, or compliments, a DNA sequence within a genome. The gRNA will find that sequence and will hybridize to it. Next, the Cas9 protein uses that gRNA as a guide to find and bind to both the gRNA and to the DNA it’s hybridized to – binding to both strands of the DNA, not just the strand the gRNA is hybridized to. Finally, Cas9 will cleave both strands of the DNA. When the dsDNA is cleaved, the cell will detect there is a cut and when repairing the area, mutations will be introduced in a natural repair process. If the DNA encoded a gene, the introduction of a mutation will alter or silence the expression of that gene.

crspr_cas9

 

After gaining an idea of what the CRISPR/Cas9 system does, it makes sense that scientists are trying to use this tool as a way to silence and edit genes. The system can be modified to target specific genes by creating specific sequences of gRNA. Current studies are using the system in several new ways, including studying epigenetics – the study of how gene expression is effected by the environment, and the potential to target genes associated with cancer and Alzheimer’s, among other diseases. The first cancer-targeted CRISPR human trial has been green-lighted by the National Institute of Health, and may mark the beginning of a future where diseases are edited out of the genome.

Stick around for the next post, I’ll be covering further controversies associated with gene editing. And if you would like any further information on CRISPR/Cas9 technology, please check out the following links:

 

Author’s note: in an attempt to reach a wider audience, the processes of both artificial selection and genetic modification have been simplified. Before forming any opinions of either subject, I highly recommend doing further research on both topics. Thank you for reading. 

 

 

 


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The Invisible World of Microorganisms

As humans, it’s difficult to imagine the world in a scale that is different than our own, especially when that difference is significant, such as the expanse of the universe or the workings of a cell. That’s what makes microorganisms so interesting. There is an entire world among us and in us that is invisible to the naked eye. Now, not only are we aware of these hidden communities, but we use microorganisms in a wide range of industries, and we also know that the bacterial communities living inside our digestive tract (i.e. gut microflora) help keep us healthy. With all of this unseen activity among us, learning about microorganisms opens up our eyes and minds to an once-invisible world.

What is a microorganism anyway? 

The simplest definition of a microorganism, or microbe, is an organism that is too small to be seen by human vision, i.e. can only be seen with a microscope. Of course, microbes are much more complex and diverse than this definition implies. First of all, microbes can be single-cells or multicellular, and there are several categories of microbes: bacteria, archaea, fungi (includes yeasts, molds, and mushrooms), protista (algae and protozoa), and viruses.

Bacteria:
E. coli

Escherichia coli 
Archaea:
archaea
Pyrococcus furiosus
Fungi:
Fungi
Zygomycota rhizopus
Protista:
protista

Noctiluca scintillans
(Sea Sparkle; protozoa)
Viruses: 
Virus
Orthomyxovirus (Influenza)

Viruses are especially interesting in that it has long been debated whether viruses are “living” organisms are not, since they lack one of the seven characteristics of life: the ability to reproduce on their own [1]. Viruses need cells from other organisms in order to replicate, or reproduce. That is also why they are considered such a threat to health—they can move from cell to cell, replicating and usually killing the cells they inhabited along the way. As I’ll soon discuss though, viruses can be used for good.

Microbes are actually everywhere

Microbes can be found in any type of environment, including the human body. Since they can be found virtually everywhere, I’m only going to describe the more extreme habitats. Microbes living in these conditions are known as extremophilesTo start with, microbes can be found in the deepest parts of the ocean. When divers first discovered hydrothermal vents at the bottom of the ocean, they were surprised to find thriving communities of life there [2]. It turns out that microbes, especially archaea, are adept at surviving in extreme conditions; in this case those conditions are extreme pressure, and temperatures up to 350°C (662°F)! Microbes can also be found in the freezing temperatures of the arctic. On February 6, 2013 scientists first reported bacteria found a half-mile deep under the ice of Antarctica. In fact, since the arctic isn’t hospitable to other forms of life, bacterial communities dominate the biodiversity [3].

Radiation is scary for humans even at very low doses, but there are microorganisms that can withstand extremely high levels. These microbes exhibit “radio-resistance”: resistant to ionizing radiation [4]. A lethal dose of radiation for humans is approximately 4-10 gray (Gy), while these organisms can survive radiation of at least 1000 (Gy) (100x more than humans!) The most extreme example is Thermococcus gammatolerans, rightly named after its ability to survive 30,000 (Gy)!! [5]

And last, but certainly not least, there are astronaut microbes! When the unmanned lunar lander Surveyor 3 returned to earth, NASA scientists were surprised to find living Streptococcus mitis that had survived the 31 months in the vacuum of space [6].  Since then several microorganisms have been identified as having the ability to survive in space, and these include one of my favorite organisms (micro or macro): Tardigrades! Also known as “water bears”, because they literally look like little bears, these little guys are the ultimate extremophiles. Not only can they survive in space, they are also radio-resistant and can survive radiation levels up to 5,700 (Gy), as well as in temperatures below freezing and above boiling. To top it off, they can survive more than 10 years without food or water [7]. Basically, Tardigrades will outlive us all.

Some other not-so-common places that microbes are commonly found: bubbling tar, steam vents, boiling water, in soil and ice miles underground, and most likely in areas that humans have been unable to discover thus far [8].

Water Bear
 Tardigrade (Water Bear)

 

Humans and Microbes: A love-hate relationship

The term “human microbiota” is becoming increasingly well-known as we learn more about our close interactions with microorganisms, but as a short description: the human microbiota, or microflora, is the collective of microbes that live on the surface and in layers of the skin, the saliva and oral mucosa, in the conjunctiva (lines the inside of the eyelids), in the gastrointestinal tract, in the respiratory system, and in the vagina [9]. The interactions between the human body, the microbiota, and the environment are so complex that I’m not even going to go there; perhaps it will be its own future blog post. What I do want to discuss though, is how microbes are actually helping us!

Bacteria in our body play vital roles in keeping us healthy, they interact with and boost our immune systems and even combat pathogenic microbes (ones that cause disease). The bacteria on our skin act as an extra layer of protection against any bad guys getting in or on us. In a nut-shell, having these communities of good bacteria in and on our bodies helps prevent bad communities from moving in [10]. In fact, bacteria play such an important role in our health that there are approximately 10x more bacterial cells in our bodies than our own actual cells [11].

Microbes are also used to improve our health and combat diseases in more targeted ways. An example of this is the use of microbes as vehicles, or carriers, for medicine. Some bacterial strains are commonly used as “delivery capsules” for drugs that are normally toxic when taken alone. E. coli has been engineered to transport an enzyme specifically to cancer cells, without targeting and harming other cells [12]. Another example of this is using viruses to target cancer cells and deliver medicine. Recently a team from Massachusetts General Hospital and Harvard Medical School used Herpes Simplex Virus Type 1 (HSV-1) as vectors for targeting cancer cells [13]. Using viruses or other microbes as vehicles could eliminate more dangerous types of treatment such as chemotherapy. Microorganisms can also be genetically engineered to target tumors and specific areas of the body that are under attack from disease.

Other ways that microbes are helping us range from food production to toxic cleanup. Yeasts are commonly used for bread and beer production and various bacteria are used for cheese production. Microbes are also exploited for the compounds they make: including enzymes, vitamins, and antibiotics. For example, penicillin was originally isolated from the fungi Penicillium, and lactic acid is used as a food preservative. Microbes are also essential to agriculture and nutrient recycling. Microbes living in the soil break down nutrients that are found in their environment, and provide things like nitrogen to plants in a process called mineralization [14] (side note: bacteria also break down nutrients in the GI tract to help humans digest them better). As mentioned, microbes are also used for cleaning up environmental toxins, including oil spills. Some microorganisms actually use oil as fuel, so that they can be released into a contaminated area and, given enough time, the oil will be removed [15]. This is a promising approach to cleaning up other toxins found in soil and water in a relatively safe and hands-off way.

 

I could honestly go on and on about the wonders and curiosities of microorganisms, but for the sake of keeping at least some readers I’m going to stop here. I hope you enjoyed reading about these amazing organisms, and have a new-found or refreshed appreciation for the invisible world of microbes. Now I dare you to look at anything around you, even in the mirror, and not think about how many microorganisms are there…good luck, and welcome to my world.

 

Work Cited:

  1. http://infohost.nmt.edu/~klathrop/7characterisitcs_of_life.htm
  2. http://www.ucmp.berkeley.edu/fungi/fungi.html
  3. https://en.wikipedia.org/wiki/Archaea#Morphology
  4. http://www.microbeworld.org/types-of-microbes/bacteria/42-what-is-a-microbe-sp-828/types-of-microbes/138-bacteria
  5. https://microbewiki.kenyon.edu/index.php/Deep_sea_vent
  6. https://en.wikipedia.org/wiki/Antarctic_microorganism#Climate_and_habitat
  7.  http://morgana249.blogspot.com/2014/08/6-organisms-that-can-survive-fallout.html
  8. https://microbewiki.kenyon.edu/index.php/Thermococcus_gammatolerans
  9. http://www.panspermia.org/bacteria.htm
  10. https://en.wikipedia.org/wiki/Tardigrade
  11. http://www.livescience.com/29865-strangest-places-life-found.html
  12. https://en.wikipedia.org/wiki/Human_microbiota#Anatomical_areas
  13. http://www.scientificamerican.com/article/ultimate-social-network-bacteria-protects-health/
  14. http://schaechter.asmblog.org/schaechter/2014/07/microbial-to-human-cell-ratio-just-bragging-rights.html
  15. http://www.wpi.edu/Pubs/E-project/Available/E-project-040912-094932/unrestricted/Jared_Guttmann_Investigations_into_the_Current_Usage_of_Microbes_in_Medicine.pdf
  16. http://www.nature.com/cgt/journal/v9/n12/full/7700537a.html
  17. http://www.ext.colostate.edu/mg/gardennotes/212.html
  18. http://www.scientificamerican.com/article/how-microbes-helped-clean-bp-s-oil-spill/

Further Links: 

Wikipedia: Microorganisms  https://en.wikipedia.org/wiki/Microorganism
Fungi Information  http://www.ucmp.berkeley.edu/fungi/fungi.html
Archaea Information  https://en.wikipedia.org/wiki/Archaea#Morphology
Protista Information  http://www.microbeworld.org/types-of-microbes/protista
Virus Information  http://www.ucmp.berkeley.edu/alllife/virus.html 
Tardigrade Information  http://tardigrades.bio.unc.edu/