Biology for Writers: What Scientists Do All Day

Hello, everyone! It’s the second Monday of the month, which must mean I’m doing a biology-for-writers post. Okay, so I know “what scientists do all day” doesn’t have that much to do with scientific topics of interest to writers, but it’s finals week and I wanted a post that would be quick to write but still informative. And hey, some of you might have scientist characters and be wondering what research looks like, or what different stages of academic science look like. (Science also happens in industry–pharmaceuticals, anyone?–but I’m most familiar with academia, so I’m going to focus on that!)

Life Stages of Academic Scientists

(I’m going to talk a little bit about this first, so I can talk about how research looks for the different stages of scientist in my next section.)

People don’t become scientists overnight. Especially in academia, there’s really a hierarchy, and you can find every stage of scientist working alongside each other in a lab.

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The first step is to get your undergraduate degree in a science field (which is where I’m at right now). If you’re an undergrad scientist, you’re probably taking a fairly heavy course load to complete all your general education, major, and elective courses in four years. Undergrad costs a lot, too (at least in the U.S.), so you might be working on the side to help cover that. If you think you want to go to grad school, you’re probably working in a lab, helping a grad student with their research and/or assisting with lab maintenance things (yes, someone has to wash the flasks and beakers). If you’re extra motivated, you might have your own research project, but you get a lot of help from the professor who runs your lab since you’re still so young and inexperienced. And the project can’t be too big, because you really don’t have that much lab time when you’re also taking four classes and working. But you do what you can to get you into grad school.

The next step is to get one or more graduate degrees. If you want to work in industry, or you don’t have enough research experience yet to get directly into a PhD program, you get your master of science degree first. If you want to teach at the college level and run a lab (i.e. be an academic scientist like your faculty mentor), you need a PhD (short for Doctor of Philosophy). Master’s programs usually take two to three years, and PhD programs in the biological sciences average around five years. You take some courses, but not as many as you did when you were an undergrad, and once you’ve selected a faculty advisor, you get right to work in their lab on your thesis project. In order to graduate with your degree, you need to write a thesis (basically a book on your research) and defend it orally to your faculty committee, who will then decide if you get your degree or not. In a PhD program, you also have to pass a comprehensive exam somewhere around halfway through your degree, which will determine if you get to go on to “candidacy” (full-time dissertation research) or not. Now I’ve gone into a lot of details, but basically grad students do a lot more research than undergrads, because their degree depends on it.

Say now you’ve gotten your master’s and your PhD, and after eleven years you’re finally out of university schooling. Phew! What happens next? Well, if their research is outstanding, some lucky souls get hired straight to faculty positions. Most go on to postdoctoral fellowships (“postdocs” for short). The postdoc is the most senior member of the lab save the faculty member who runs it, unless it’s a really big lab and has a professional lab manager who reports to the professor. Postdoc fellowships usually last one to three years, and they work full-time, similar to grad students except no classes and no thesis defending. As I understand it, this serves as a time to build up one’s resume before applying to become a faculty member.

The highest tier is your PI (primary investigator), the faculty member who runs the lab. They determine what is studied in the lab and who works under them doing their projects. They also teach classes and, when they’re young, try to get tenure (which is basically where your university can’t fire you because you’ve proved the quality of your work). I’ve heard there’s a lot of pressure on young faculty to publish a lot of research in order to get tenure. Older professors (like my PI), who already have tenure, can be more relaxed since they are freer to study whatever they might be interested in–contingent, of course, on the availability of funding. PIs manage all aspects of the lab, mostly from their offices, although mine sometimes comes in and reorganizes things in the freezers or teaches students techniques. They usually teach classes for undergrads and grad students, and write up research articles for publication in scientific journals.

What Science Looks Like (In a Laboratory)

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With some understanding of the academic science hierarchy, we can now get a general idea of what scientists actually do all day. Naturally, this depends on the discipline, in that different scientists do different things. A neuroscientist, for instance, might do behavioral experiments or brain dissections on mice. I have less idea what ecologists do, but my guess is they go into the field to at least collect their samples. When I worked in a seaweed lab, I used to go to the shore and collect seaweed sometimes. Now, as a rice geneticist/biochemist, I split my time roughly 85% lab/15% greenhouse. Some of the things I’ve done in my lab are in bullet points below.

  • Lab Maintenance
    • Washing dishes
    • Making tissue culture medium (think Petri dishes)
    • Disposing of biohazardous waste (seriously not a big deal–I’m only in a Biosafety Level 1 lab)
    • Cleaning up ethanol spills (also not a big deal–it’s basically handcleaner)
    • Preparing/organizing work surfaces (we put this paper on our prep room bench to absorb any spills)
  • Experimental Things
    • Collecting samples (read: cutting up rice leaves and putting them in tubes)
    • Subculturing tissue cultures (the medium dries out every so often)
    • Checking tissue cultures for bacterial contamination (things have to be sterile)
    • Extracting and quantifying biomolecules
    • Data analysis (Microsoft Excel, anyone?)
    • Checking raw data files for quality control (on lab computer)
    • Pouring salt water on plants (so I’m a little sadistic once in a while)
    • Planting seeds
  • Common Genetics/Biochemistry Lab Equipment
    • Petri dishes
    • Pipettes (used for EVERYTHING)
    • Disposable pipette tips
    • Microcentrifuge tubes
    • Boxes with little dividers for freezing things in tubes, and tube racks
    • Freezers (4, -20, and -80 Celsius)
    • Autoclave (a kind of steam sterilizer; usually common to multiple labs)
    • Heat/stir plate and stir bar magnets
    • Small spatulas, forceps, scalpels, razor blades, “scoopulas” (cross between spoon and spatula)
    • Beakers, flasks, graduated cylinders, other glassware
    • Test tubes (although I use these less than the microfuge tubes mentioned above)
    • Centrifuges, spectrophotometers, and other larger equipment
A pipette and Petri dish with medium (Image source)
A lady with some cool lab glassware. (Image source)

 

So that post was a little bit longer than I meant it to be, and it didn’t even include anything about specific techniques that are often used in biology. If there’s interest in a post about techniques, let me know in the comments and I’ll drum up something for next month!

That’s it for me this week! Did you find the day-to-day of science interesting? Do you think it will be helpful to you? Would you like to hear about techniques? Isn’t lab glassware awesome? (I’m going to be that person with chemistry-themed dishes someday!) Are you interested in becoming a scientist? Let me know in the comments!

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Biology for Writers: The Human Microbiome

Good morning, everyone! Happy Monday! It’s the second week of November (already!), so here I am with a quick post on a bioscience topic which may be of interest to some of the writers who read my blog (and don’t have that much background in science). Let’s get right to it!

The Overview

One of the biggest topics in science right now is the human microbiome. What is a microbiome, you ask? Well, it’s simply the entire set of microbes that inhabit the human body.

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Yes, that’s right–there are microbes in you, right now, and they’re even supposed to be there! As a matter of fact, there are more bacteria, archaea (basically extreme-environment microbes), and unicellular fungi in your body than there are human cells. Yes, you heard that right–we humans are more microbial than human. Blows your mind a little, doesn’t it?

So what do these microbes do for us? Are they good for anything, or do they just sit there? Well, my friends, I’m glad you asked. Let’s take a look at some of the parts of our bodies where our normal microbes are most influential.

The Mouth

We all know about dental plaque, and brushing our teeth so we don’t get it. (Seriously, I hope you all brush your teeth, ’cause plaque is disgusting.) But your mouth also contains 50-100 billion normal bacteria of at least 500 different species, mostly anaerobes, or bacteria that don’t require oxygen to live. (In fact, some anaerobes die when exposed to oxygen.) Streptococcus mutans and S. sanguinis, the organisms that cause plaque when they build up into a biofilm, are both “facultative anaerobes,” which means that they can either use oxygen or not depending on conditions in their environment (the mouth). Many other normal mouth bacteria can cause problems for the human host if there is bleeding in the mouth, or some other abnormal condition, bringing up an important point for the microbiome in general: Microbes that are normal inhabitants of our bodies (“normal flora” or “microbiota”) can be pathogenic if they are moved to a different spot or if something abnormal happens. These are called “opportunistic pathogens,” and we’ll see more of them as we move through the body.

The Gastrointestinal Tract

This is one of the places where the human microbiome is most important and best characterized; a lot of work has been done linking the gut microbiome composition to everything from diet to Parkinson’s disease. And gut microbes do a lot for us. For instance, we can’t digest vegetables without our gut microbes, and other microbes make vitamin K for us. That’s pretty darn helpful of them, don’t you think?

But when I say “gut microbiome,” what am I talking about? It turns out that not every part of the human body is colonized by microbes; accessory organs such as the liver and pancreas are sterile, and the stomach has a very low level of microbes due to the high acid content there (the stomach’s pH, a measure of its acidic content, is about 2–so very acidic). Not many things can survive the acidic environment of the stomach, which is why it’s great for digestion. One Helicobacter species, however, survives by burrowing into the stomach lining and secreting basic compounds, which neutralize the surrounding acid to create a neutral pH (good for life). This species can also cause stomach ulcers when it has lived in the stomach lining for a long time.

So if the stomach doesn’t have very many microbes, where is this gut microbiome I’ve been telling you about? Most of the gut microbiota live in the ileum (the last part of the small intestine) and in the colon (also known as the large intestine), where, as I mentioned, they help us digest our food, give us nutrients, and take up space so invaders can’t enter. This is known as a “mutualism,” in which both symbiotic partners benefit from their relationship. How do the bacteria benefit from us? Well, most parts of the body are at a neutral pH, which as I’ve already said is good for life, and they remain at a constant warm temperature, which allows microbes to grow.

I also just want to point out quickly that taking too many antibiotics can interrupt your gut microbes, and thus actually make you susceptible to sickness, since with space freed up by antibiotic treatment, pathogens can easily colonize your gut. Since this post is mainly about the microbiome, that’s all the space I can give to this extensive topic, but if you’re interested in learning more, feel free to comment below!

The Skin

The skin is one of our first defenses against microbes, since we are constantly sloughing off dead skin cells, but it is also colonized by many microbes. Similar to the gut microbiome, these take up space on your skin, preventing infection by pathogens. The skin microbiome also includes Staphylococcus aureus, an opportunistic pathogen which normally lives on the skin surface, but can cause problems when it penetrates deeper into the body. For instance, if you have a deep puncture wound, your normal S. aureus may get under your skin (literally) and cause nasty carbuncles and things when it infects you. So if you’re writing a novel and your character gets wounded, this is one thing that could follow that up if you want to give them extra torture be realistic about the consequences of wounding.

Find out More!

Here are some resources if you’d like to find out more about the human microbiome!

Human Microbiome Project–This would be a great resource if you want to find out some of the specific microbes that exist in each place on the human body (there are many, many more microbes than the ones I talked about today).

The Gut Microbiome in Health and Disease–A scientific paper about the gut microbiome. (Please note this is intended for a scientific audience, so it may be a bit dense.)

When Gut Bacteria Change Brain Function–An interesting general-audience article about how gut bacteria impact the brain.

I will continue to add more resources here as I find them! If you find interesting resources, feel free to let me know in the comments and I will consider adding them to this page.

That’s it for my first Biology for Writers post! Are you thinking of using the microbiome in your story? If so, how? Is there anything else you’d like to know about the microbiome? (I’m definitely not an expert, but I can point you to more resources if you’d like!) Are there other biology topics you’d like to see addressed in this monthly post series? Let me know in the comments!

Your Questions Answered, Part 2: General Biotechnology

Hi, everyone! Today I have Part 2 of a genetics/biotechnology/general life science post for you. You can check out Part 1 here. Again, thanks to H. Halverstadt for asking these fantastic questions! Let’s get right to it:

How do you think CRISPR and the gene drive will change the future of genetic engineering?

I am of the opinion that CRISPR is one of the most revolutionary advances in biotechnology of our time. The precision with which genes can be edited due to the specificity of the system is just incredible. I would certainly predict that its popularity (with scientists, not necessarily with the general public, especially the uninformed) will soar in the future, although at least for a short time, “conventional” genetic engineering will still be practiced. But given public outcry about GMOs (even if not warranted—a topic for another time), the ability to improve an organism without bringing in genes from another organism could be more popular and, indeed, simply easier, with fewer steps required.

The gene drive is more specific; I think it has a lot fewer potential applications than CRISPR. Whereas CRISPR can be used with most any current genetic engineering application, I really can’t think of an application for the gene drive that is really different from its current uses, combating insect-vector diseases and pesticide/herbicide resistance. They might try to tackle antibiotic resistance with it next, but I don’t think it will have broad-based applications after that. I would predict that CRISPR will be by far the more influential technique in future.

What gradual, irreversible changes to the human genome might happen?

My best idea is that, according to the principles of natural selection, any beneficial-to-survival changes made to a majority of people by genetic engineering (and propagated through the germ line) could eventually become fixed in the population. I’m going to stop there, since I don’t have quite the human or population genetics knowledge to go on.

Can you see cells from certain people being in high demand? What kind of people?

This is a very interesting question. First, instead of cells, I think we’d be talking about DNA sequences; why bother taking the whole cell if you can get just the DNA you want? I also assume here that the question is asking about acquiring copies of someone else’s DNA for non-gene-therapy genetic enhancement. In this case, I expect that genes from athletic people (there are some known genes related to athleticism—I know of one specific case in which a certain allele of one gene is associated with endurance running) and intelligent people (if such genes could be identified—to my knowledge there are none currently) might be popular for making “designer babies” and so forth.

What laws do you think might be passed to regulate genetic engineering?

I’m not as knowledgeable about the legal side of biotech, but currently, I know labeling laws for GMO foods are a big deal. A quick search revealed to me that GMOs are put through testing processes by a few federal agencies before being put on the market to determine their safety. It’s conceivable that a law prohibiting non-gene-therapy engineering of humans could be passed, although presumably not in the kind of society most sci-fi/dystopian writers who read this will be interested in. Besides that, I apologize, but I can’t come up with much.

Is inter-species gene editing something that is possible for humans?

Technically, yes. Ethically, it’s complicated. Personally, I don’t see this as acceptable, but I’m sure some bioethicist out there could make the case that improving human welfare by adding nonhuman genes would be worth the (hypothetical) cost in our humanity.  (A technical note: this seems to me to be less gene editing, and more transgenic expression. Gene editing is messing with a gene that’s already there; transgenics are organisms containing genes from other species.)

Do you see genetic engineering ever being something smart high school students can do in their kitchen?

Absolutely. In fact, this kind of thing is happening today among a DIY biologist or “biohacker” movement that believes science shouldn’t be for academia alone. So far, though, they’re not that scary; national and worldwide organizations like DIY Bio (https://diybio.org/) have been good about organizing events regarding safety and bioethics. It’s not being done to humans, or even vertebrate animals as far as I can tell; there are still too many ethical issues in that area. But yes, as long as you can afford the reagents and equipment, you can genetically engineer a plant or a (nonpathogenic) microbe. I believe even CRISPR is currently accessible for DIY biologists (though it costs about $500—I’m sure the price will go down as it becomes an established part of biotech).

If inter-species gene editing is possible for humans, how about humans and a different category of animals, like birds? 

Again, absolutely; you could put a plant gene in a human cell if you wanted, or vice versa. And I’ve read about glow-in-the-dark animals being created by expressing a jellyfish gene.

Please comment on the feasibility of these fantastical forms of genetic engineering. Winged humans, mermaids, elves, centaurs, giants, dwarves, humans able to breathe lower oxygen air. Do you think any other traits would bleed through? (Like for example, if winged humans had eagle genes, would they have other eagle traits as well?)

First, let me say that “dwarves” already exist; we know them as “midgets.” There are a variety fo forms of dwarfism, some dominant, some recessive, but none require genetic engineering. By “elves” I assume you mean basically humans with pointed ears. I expect this would most easily be done surgically.

As for “giants,” height is an extremely complex trait. It is quantitative, meaning that it follows a bell-curve distribution in the population, and there are currently thought to be about 700 genes that influence it. So engineering really tall people could be possible, but I suspect it would be inefficient in the incredible amount of effort it would take. Here is my source (http://time.com/4655634/genetics-height-tall-short/) for that, and I recommend you look up more detailed information on that trait if it’s something you’re interested in using in your story. I just don’t know enough about it to be of much help.

The others would be difficult, but theoretically doable in the far future given a masterful understanding of cellular physiology and probably lots of trial and error. For the humans with animal parts (winged, merpeople, centaurs), geneticists would need an almost perfectly complete understanding of development, which, once again, is incredibly complicated and controlled by many, many genes. It is possible that cells could be induced (“programmed”) to differentiate in such a way as to generate animal limbs on a human body, or to replace human limbs with animal ones, but this would also likely require detailed knowledge of the role of epigenetics in development, and complete knowledge of both human and animal development, which would simply take a very long time to achieve. And even then, it’s completely possible that scientists assembling and applying all this knowledge could miss something essential and make some terrible mistakes. Not to mention all the trial and error—what if a limb grew in the wrong place? etc. So, possible, but not probable to begin with, and would need to be masterfully executed.

The “bleeding through” of other traits mentioned in this question is, I would say, almost certainly not realistic. Giving someone wings will not automatically give them, say, sharp eyesight; that would be controlled by other genes (as well as environmental factors). It makes for interesting fiction, but as far as I know, there is no scientific basis for it.

As for the last one on the list, the pertinent process is cellular respiration. You would need to somehow increase the efficiency of this (again) complex process, which is only 39% efficient at capturing the energy in glucose into ATP (look up the basics of the process). I will say tentatively that this could be one of the more feasible things on this list, if only because cellular respiration is already fairly well understood (i.e. it’s not one of the great mysteries of our time) and preliminary studies could be carried out with bacterial or yeast cultures before progressing to human and mouse cultures, mouse trials, and finally human trials.

Here, to make a long answer longer, I want to make a general note about the approval process for human studies. I feel that the “evil scientist does unethical experiments on humans” trope is both overused and inaccurate. Every university, as far as I know, has an Institutional Review Board (IRB) that convenes solely for the purpose of evaluating and approving human-subject studies. This applies not only to clinical trials, but to interviews and surveys in psychology studies, and even to education studies that take class data and use it for research. Even if there is no perceptible risk at all, researchers are absolutely required to provide the subjects with knowledge about risks, so that they can be informed when they sign the form they must sign (even for a harmless survey!). This applies very much more to genetic engineering and so forth. Under this system, it’s very difficult to conduct an unethical study regarding human subjects, and unless social mores shifted in the future, it’s conceivable that the system will stay like this, making it difficult for any of these ideas to get off the ground, due to possible unforeseen consequences of the alterations.

If yes for the above, would reversal be possible, not just for the offspring but for the person in question? For example, if a winged human wanted to be a regular human again, would she be able to be one after extensive surgery and gene therapy?

I would say yes, although it’s completely a guess since I’m not a medical expert. The gene therapy might not even be necessary; though the genes might still be in the rest of her body, if they weren’t being expressed, she could be a “normal” human with nonhuman DNA, as long as her wings were removed. My bet is that the removal could be done with a surgical procedure (albeit complicated, probably, to remove the whole wing skeletal structure).

 

 

Karpechenko, Polyploidy, and Other Long Words

Greetings, everyone! It’s the second Saturday of the month already, and I am delighted to be here talking about one of my favorite science topics with you. As you may know, or may have guessed from reading my blog and noting the disproportionate amount of genetics posts, I am a genetics major, major DNA nerd, and plant biology minor. I’m going to bring all those things together in this post, so hold on to your hat and let’s have some fun!

As with many of my science posts, our topic today stems from a class I am taking (Evolutionary Genetics of Plants, in this case). My teacher told us a story, which I thought was cool, so I am now going to repeat it to you.

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The story was about this guy.

The guy in the picture above supplies the first of the long words in this post: his name, Georgii Dmitrievich Karpechenko. As you may have guessed, he was Russian. Specifically, he was a Russian botanist and plant cytologist (cell biologist) who did some interesting experiments with plant breeding. Let’s explore them.

Presumably, Karpechenko enjoyed both cabbages and radishes, or else he just wanted to contribute to improved agricultural productivity in his nation of limited farmland, or possibly both. Either way, he wanted to create a plant that produced a cabbage in the shoot and a radish in the root. The logical way to do this (his reasoning presumably went) was to cross a cabbage with a radish.

Here we have to back up a bit and get into some more long words. Cabbage and radish are different species, but not only that, they are in different genera (the first word of a scientific name); cabbage is Brassica oleracea and radish is Raphanus sativus. Usually, the definition of a species is “a population which is reproductively isolated (i.e. can’t breed) from others.” Of course, the only thing in science with no exceptions is that everything has an exception, and Karpechenko was indeed able to breed his cabbage and radish (for reasons we haven’t talked about in class yet) and produce a hybrid plant.

Well, unfortunately for Karpechenko, his hybrid didn’t look anything like either a cabbage or a radish. It was just a weed. Worse yet, it was a sterile weed; it produced seed pods, but no seeds. Fortunately for botany and genetics, though, Karpechenko didn’t give up on his experiments just yet. He kept observing his plants and noticed one day that a branch of one of them was producing seeds, even though the rest of this plant continued to be sterile. Furthermore, when he planted the seeds, they gave rise to fertile (if weedy) plants, and a new head-scratcher: how could this be?

Backing up again: The fertility of plants (or any organism, really) arises from a special cell division process called meiosis, which some may have learned about in high school biology. Most organisms are diploid, that is, they have two complete sets of chromosomes. For example, humans have 23 chromosomes in a set, and a total of 46 chromosomes in two sets. It works the same way for cabbage and radish; each has 9 chromosomes in a set, and 18 chromosomes total. This comes from reproductive biology; in any diploid organism, one of the sets of chromosomes comes from each parent. So in order to reproduce, plants (and animals, and fungi) have to produce haploid gametes, “sex cells” with only one set of chromosomes apiece. (In humans, we know them better as the sperm and the egg.) This is what meiosis is all about.

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A summary figure of meiosis. Note the homologous chromosomes separating into different cells; don’t worry about the different colors.

 

In order to reduce the chromosome set number, or “ploidy,” from diploid to haploid, chromosomes line up in matched (“homologous”) pairs and separate into two new cells (see the figure above). These cells then undergo further division to form gametes, the details of which we won’t worry about.

Now let’s think about Karpechenko’s sterile hybrid. This little weed had one set of chromosomes from cabbage and one set from radish, which enabled it to grow and function. However, when it came time for meiosis, it turned out that radish and cabbage chromosomes were different enough that they wouldn’t pair and divide into different cells, and no gametes were formed, which ultimately meant no seeds.

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Karpechenko’s experiments shown as seed pods. “Amphidiploid” is the same thing as tetraploid.

 

So what about that branch that became fertile? Well, it turns out that plants sometimes spontaneously undergo whole-genome duplications, in which, just as it sounds like, the entire genome of the plant is duplicated in the cell. (This happens routinely before cell division, but then it all divides into two cells. In whole-genome duplication, what happens is that the cell thinks it’s divided, but actually hasn’t, and now has four sets of chromosomes rather than two.) This happened in Karpechenko’s plant, in a branch precursor cell, and gave rise to a tetraploid branch, having four sets of chromosomes, two from radish and two from cabbage. Now, suddenly, all chromosomes had homologs to pair with in meiosis, and seeds could form.

Karpechenko had discovered polyploidy, the state of having more than two chromosome sets, which turns out to be a rather important phenomenon in plants. Besides generating greater genetic diversity, helpful to plant breeders, polyploidy results in more DNA, bigger nuclei, bigger cells, and eventually, bigger, more robust plants overall. It’s so useful that plant breeders sometimes induce polyploidy with chemicals to help in developing new varieties. Many important plants, such as wheat and canola, are polyploids.

What happened to Karpechenko himself? Well, in the early 20th century, the Soviet Union’s leadership was not big on genetics. In 1941, Karpechenko was arrested on a false charge and executed, but not before making a major contribution to botany and genetics.

What do you think? Have you heard of Karpechenko before? What about polyploidy? (Isn’t it cool?) Do you have any questions? Tell me in the comments!

The Synthetic Biology Equation: Engineering + Bioscience = The Future of Biotech

(Perhaps that title is a bit audacious; I don’t claim to be able to predict the future of anything. But it’s entirely possible that synth bio will play a big role in biotech in the future. Let’s explore that more below. . . .)

Good morning, everyone! I was traveling last week, which prevented my putting up this post on Saturday as usual, and I decided to postpone it till today.

One of the classes I took last semester was Biotechnology and Society, and I decided to write my final paper on synthetic biology after the teacher mentioned the first production of a self-replicating “man-made” cell by a group of scientists in California.

Before I dig into that a bit more, though, let me define synthetic biology (or synth bio for short): it is the full-scale application of engineering techniques to biological systems. How is it different from regular genetic engineering/GMO production, then? The answer lies in the scale of said engineering: for genetic engineering, it’s on the gene level, one or more genes plus regulatory elements (regulating the expression of the gene) within an organism. For synth bio, though, engineering is on the level of an entire chromosome or even a genome, either wholescale editing or rewriting from the ground up. Essentially, synth bio is genetic engineering on steroids.

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Stephane Leduc, author of La Biologie Synthetique

 

A little history: Synthetic biology was first conceived, if not put into practice, way back in 1912 when Stephane Leduc, a French scientist, published La Biologie Synthetique. In this book, Leduc stated that the consistent and controlled reproduction of natural processes seen in other sciences, like chemistry, was lacking in biology at his time. Synthetic biology couldn’t take off, though, without the development of molecular biology in the mid-1900s, starting with Crick and Watson’s discovery of DNA structure (a topic for another time). Then, the development of fast, easy sequencing sparked our current age of genomics, the study of whole genomes, and synthetic biology had all the tools it needed to become a practiced discipline.

This brings us up to recent developments. Just last year, a research group at the J. Craig Venter Institute, headed by Venter himself, succeeded in creating a self-replicating bacterium with a synthetic genome, the first of its kind. The bacterium, JCVI-syn3.0, has only what Venter’s team determined was the minimal genome necessary for life, a feat they accomplished by “mixing and matching” genes of the small bacterium Mycoplasma mycoides to find which ones a bacterium could live without. In future, Venter and his team see the use of similar synthetic bacteria not only to learn about life, but to engineer it for specific purposes, like biofuel production.

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A colony of JCVI-syn3.0

 

The question is: how synthetic is JCVI-syn3.0? Technically, it’s not really a man-made bacterium. Only the genome was man-made, and that was really only adapted from the genome of M. mycoides. The “shell” the genome was inserted into was simply a living bacterium with the genome removed. This is a big step for synthetic biology, but it has a long way to go before it is truly dictionary-definition synthetic.

What do you think? Have you heard of synthetic biology? Did you hear about the production of JCVI-syn3.0? Tell me in the comments!

Yakutian Horses and Pallas’s Cats: Adaptation to Extreme Environments

Good morning, all! It’s the second Saturday of the month, which means it’s time for a science post. This month, with winter approaching, I thought I would turn my attention to a couple of animals that are well adapted to cold environments: the Yakutian horse and the Pallas’s cat.

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The Yakutian horse is a breed of horse that lives in the Yakut region of Siberia; the Pallas’s cat is a species (Otocolobus manul) with a widespread range, from the Caspian Sea to northern India to China and Mongolia. Both these mammals show some common adaptations to cold environments, like small size (Yakutian horses are a bit smaller than most horses, and Pallas’s cats are only the size of a house cat) and long fur. According to the BBC, ancient woolly mammoths had similar adaptations, which enabled them to survive during the ice age.

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A new genomic study (reported by the same BBC article linked to above) has indicated that Yakutian horses evolved from Genghis Khan’s Mongolian horses in less than 800 years, basically the blink of an eye. Since they adapted to the harsh Siberian winters (with temperatures down to -94 degrees Fahrenheit), they’ve been indispensable to the Yakutian people, for food, clothing, and transportation.

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Pallas’s cats, in contrast, are wild. They live mostly in rocky areas at high altitudes (according to ARKive), and indeed, they’ve been found high up in the Himalayas where only snow leopards were thought to roam (see PBS’s “Nature: The Story of Cats”, episode 1). They’re active mostly at dawn and dusk, and hide in rock burrows the rest of the time to avoid predators. They’ve been known to inhabit burrows abandoned by other animals. To help them avoid predation, their fur changes color seasonally for camouflage.

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Here you can see just how fluffy the Pallas’s cat is.

 

That’s it for today! What do you think? Have you ever heard of these animals before? What do you think of them? Do you like winter as much as they do? Tell me in the comments!

Chlorophyll, Carotenoids, and Anthocyanins, Oh My (Why Leaves Fall in the Fall)

Well, it’s October, which means that here in New England, it must be leaf-peeper season. Drive up Interstate 93 anytime around now, and you’ll probably see hordes of license plates from more southerly states on cars packed in to see the leaves in the White Mountains. We residents refer to them fondly as “leaf-peepers” (and sometimes do some leaf-peeping ourselves).

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The White Mountains with fall colors.

 

So what does all this have to do with those three long words in the title of this post? Well, for my science post this week (which I normally do on a second Saturday, but I had a guest post  last week–check it out if you haven’t yet!), I thought it would be seasonally appropriate to talk about the biology behind leaf colors, the defining symbol of fall. And since I’m interested in plant biology, this is also right up my alley.

So during the spring and summer, leaves are green. This is because of Pigment #1 listed in the title: chlorophyll, the major photosynthetic pigment in plants. Chlorophyll is very important for exciting electrons and causing biochemical cascades and so forth, and all of that eventually leads to the plant producing its own glucose, which it can then use in respiration to essentially make energy for cellular mechanisms. So for most of the year, trees are green. Then why does it change in fall?

Well, in the fall, the weather starts getting colder, and the plant starts to go dormant in order to survive the winter. As the U.S. Forest Service explains, leaves are thin and contain a lot of water that could easily freeze in winter, so deciduous trees must get rid of them in order to survive each winter. And as nights get longer in the fall, the plant senses that it’s time to get rid of the chlorophyll, and Pigments #2 and #3, carotenoids and anthocyanins, show their colors, so to speak. Carotenoids, which are always present in leaves, cause yellow and orange colors. Anthocyanins, produced only in response to sugar buildup, cause reds and purples.

What affects leaf color? Well, you may have noticed it depends on the kind of tree. Oaks mainly have brown leaves (which, incidentally, don’t usually fall off until spring), beeches have lighter brown, and maples can be orange or red or other colors depending on the species.

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Maples in fall.

I found it interesting to learn that weather also affects the colors of leaves. Warm, sunny days cause buildups of sugars, and cool nights constrict the plant’s vessels, causing the sugars to stay in the leaves and the subsequent production of anthocyanins. Soil moisture can also affect leaf colors; if there’s a summer drought, for instance, color onset will be delayed a bit. The best colors occurs if there’s a warm, wet spring and good summer weather, according to the Forest Service.

One last question: what causes leaves to actually fall off? Starting early in the fall, xylem and phloem veins (veins that bring water and nutrients to leaves) start to close off, eventually leading the leaf to fall. The tree is left with only its winter-hardy tissue, giving it a better chance of surviving the winter. As an addendum, some trees actually have winter-hardy leaves that only fall due to old age. We know them as the evergreens: pines, spruces, hemlocks, and other trees with needle- or scale-like leaves. The waxy coatings on their leaves make them hardy enough to keep on photosynthesizing all winter long.

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Which is why people use evergreens as Christmas trees: they’re still green.

 Are your leaves turning colors yet? Have you ever thought about why they turn colors in the fall? Are you going to go “leaf-peeping” this fall? Tell me in the comments!

Class Project to Blog Post: A Word on Photosynthesis

Greetings! Once more, it is the second Saturday of the month, and I find myself scrambling to put together a post about science. Fortunately, I’m a genetics student two weeks into her third semester, and need not look too far for interesting topics.

Inspiration comes in various forms. Why shouldn’t it come in the forms of happy little houseplants?

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A jade plant, Crassula ovata.

I’ve kept jade plants for years. They’re a kind of succulent (a water-conserving plant with fleshy stems and leaves, something between a normal plant and a cactus) which, not surprisingly, grows well even when you forget to water it. Plus, every time a branch breaks off, if you stick it in a pot, you get a new plant. (I keep getting more of them that way.) They look cool, make great bonsai projects, and even flower once in a blue moon. And as this is a science post, not a gardening post, I bet you’ve already guessed that jade plants are also scientifically interesting.

All plants use photosynthesis to “fix” carbon dioxide into glucose, which can then be broken down in respiration to get energy. It’s more or less equivalent to making one’s own food. There are different ways of doing this; the most common is C3 photosynthesis, more or less the “normal” pathway. C4 photosynthesis is found most often in tropical plants, and involves some extras added to the C3 pathway to maximize carbon dioxide uptake in environments where the gas’s availability is limited. In both of these pathways, stomata (small openings in plants’ leaves) allow carbon dioxide into the plant.

Crassulacean acid metabolism, or CAM, photosynthesis adds on further to C4. It is found mostly in desert succulents like cacti and jade plants, and in fact was named after the jade plant’s family, Crassulaceae. In CAM photosynthesis, the stomata open only at night, when the temperature is lower and the water within the plant will evaporate less than it would during the day. The plant then takes in carbon dioxide, fixes it to an intermediate molecule, malate, and stores it to be processed during the day. This cool adaptation helps cacti and succulents survive in their desert environment.

One more note: I haven’t said anything about the first part of the title yet. Well, I’m taking genetics this semester, and I need to do an honors project on a gene that interests me. While poking around for genes involved in drought resistance in plants, I rediscovered CAM photosynthesis, which I learned about a few years ago and thought was really cool. There you are; inspiration from a class project. It really does come from various places.

(My source for this post was The Physiology of Flowering Plants: Their Growth and Development, third edition, by H.E. Street and Helgi Opik.)

Isn’t CAM photosynthesis cool? (If you don’t think so, I totally understand. I know lots of people probably don’t get why I’m a plant nerd.) Have you ever had a jade plant, or a cactus or something similar? If so, what was your experience with it? Tell me in the comments!

Are Allergies Genetic? (Said the Science Nerd)

Yes, yes, on second Saturdays of the month, everything I say is from science-nerd mode, isn’t it? Specifically biology-nerd mode. I suppose that’s what happens when one is a genetics student.

Really, though, a couple of things influenced me to ask myself this question. Number one, I am a genetics student; therefore, I am curious about genetics. Number two, I have allergies, as does everyone else in my family. We’ve been sneezing off the hook for about three months now. I am mostly allergic to pollen (a real letdown for a plant lover), but people in my family are allergic to all sorts of things: horses, corn, sheep, hazelnuts, cats, you name it. So I wondered: are allergies genetic?

I asked Google that question, and it was kind enough to direct me to this interesting article, which not only answered my original question, but added more to the answer. It turns out that allergies are genetic, passed from parent to child. They are also sex-related; for example, girls are more predisposed to have allergies if their mothers also have allergies, and vice versa for boys.

Another article points out that there are different kinds of “allergic diseases,” including eczema and asthma as well as hay fever (pollen allergy). And, like anything else, allergies are influenced by environmental factors, including air pollution, chemicals, and types of animals and plants in the area, as well as by genetics. (See this abstract for more.)

Well, this turned out to be a short post. There are some quick facts about allergy genetics for you!

What do you think? Do you have allergies or something similar, like asthma? If so, do your family members have it, too, and have you ever wondered whether it was genetic? Tell me in the comments!

Mosquitoes, Malaria, and Molecular Biology: How DNA can Help Kill a Disease

Happy second Saturday, everyone! It’s time for a science post. For today’s post, I visited the Science News website and browsed around for something interesting to talk about. There were a lot of options, but I settled on this one. All credit goes to the original authors.

I’m sure you’ve heard of malaria. It is commonly known to be rampant in third-world areas, particularly Africa. It’s caused by microorganisms of the genus Plasmodium, which have part of their life cycle in mosquitoes of the genus Anopheles. This makes it that much harder to eradicate, since any disease or parasite with what’s called an “animal vector” requires health workers to eliminate every animal that could carry the disease. Imagine trying to kill every one of the 30-40 malaria-transmitting Anopheles mosquito species in Africa, and you have some idea of why malaria is so hard to get rid of.

So essentially, to end the disease, end the mosquito. But how?

Using everyone’s favorite molecule, of course: DNA!

Scientists at Imperial College London have developed a “gene drive,” an engineered DNA molecule that disrupts genes’ activity by inserting itself into them, that is capable of sterilizing females of one Anopheles species. That could curb the reproduction of the mosquito, and thus the number of mosquitoes available to carry Plasmodium. 

 

 

Plasmodium, the malaria parasite. (Image from the CDC)

This is actually the second Anopheles gene drive to be developed by the same researchers. The other one (findings published 2015) aimed to prevent Anopheles from carrying Plasmodium. So far, both of them work, though neither has yet been released into the wild Anopheles population. But both have potential to help stop malaria.

There you have it: another manifestation of the current genetics revolution. (I must admit I am partial to blogging about said revolution, being a major DNA geek.) What do you think of these gene drives that might help eliminate malaria? Do you like DNA as much as I do? Share in the comments! Also, if you’d like to learn more about today’s topic, be sure to check out the links in the post!