Microbes: Bacteria and Viruses

In my previous post I discussed about the misconceptions of science and in this post I guess I will write about what I actually study.

I get all types of science questions (not relevant to my field) asked to me because I am a biology student or a science student, and I'm supposedly to know the answer or have an explanation to all of them. I get questions about certain medical problems I never heard about, how certain pharmaceutical drugs are made, why the universe is the way it is and how it works; and the thing is I have no idea since I don't study these things even though it is science. The science I study is Microbiology.

Microbiology, as its name implies, is the study of microorganisms, single celled living things that are invisible to the naked eye and can only be seen with a microscope. There are many other subjects I have "touched up" on (chemistry, physics, etc.) and there are a lot of categories of microbes; however, the main focus of my major is bacteria and viruses. Many of the biology classes I take mainly deal with or is based upon bacteria and viruses. There is a huge emphasis on these two for many reasons.

Bacteria is definitely the most studied microbe due to it's abundance and importance in many fields including the food industry, medical industry, and use in other technology. Bacteria is found almost everywhere on earth: in cold environments, hot, dry, salty; there are bacteria that can live without oxygen (falcultative anaerobe) and some that are even killed by oxygen (obligate anaerobe). Our external body is covered in bacteria; in fact, we are more bacteria than human in that there are more bacteria cells on us than our own total cells. The bacteria that live on us is important and if they all died we would be in a lot of trouble; they defend us from foreign microbes and also produce certain vitamins our bodies can't make. Bacteria is used to make foods such as yogurt (probiotics, eg. Lactobacillus acidophilus), genetically engineered bacteria can make useful proteins such as insulin, they can also be employed for bio-remediation (cleaning waste with microbes, eg. Alcanivorax) and clean up waste such as oil spills.

Alcanivorax

Lactobacillus acidophilus

We have more bacterial cells on us than our own cells

Bacteria are also very important model organisms that have been studied extensively in order to better understand biological processes (such as cell division and food metabolism) that occurs within them and other organisms, like ourselves. They are simple, physically, when compared to complex, multi-organ organisms. We probably know more about the biology of bacteria than we do humans. In addition, bacteria cause some of the most deadliest diseases in the world (anthrax, tuberculosis, to name a few), it is important to study them so we know how to kill them.

Swine Flu Virus

Viruses, like bacteria, are also very well studied. They are vastly important in the medical field, causing many deadly diseases (ebola, AIDS, rabies, to name a few along with being able to cause cancers) and are not used in as many fields as bacteria. The interesting thing about viruses, compared to many of the other things studied in biology, is that they are not considered "alive" or living organisms by many biologists, some consider them alive. One of the main reason for this is because viruses are not made out of cells, all living things are made out of cells (whether single or many cells); a virus is very simple, most are just genetic information (DNA or RNA) wrapped around by proteins. Also, all known viruses cannot live or divide on its own, it needs to infect the cell of another organism in order to divide and make more of itself. They are considered to be infectious particles. Although they are not considered living they do have some characteristics of life such as producing more of itself (when it is in a cell) and being subject to natural selection (being able to adapt to struggles of environment, survive and evolve). Since viruses can inject foreign DNA into cells, they are possible candidates for gene therapy, fix broken genes, whether they serve a natural benefit to organisms is debatable.

For simplicity, I obviously haven't covered a lot or all there is to know about bacteria and viruses. There is way to much to put in one post; we are always learning new things about them which makes it always interesting.

Scientists... thoughts and how many of us really are

Typical looking "scientist"

Bill Nye

Steve Urkel, the geekiest kid I can think of

Kari Byron, Mythbuster (notice the white lab coat)

Einstein...

I know what many of you are thinking; scientists = white lab coat, likes math, brainy, geeky, non-religious, boring, non-sociable, high IQ, hates Art, always like to to use long complicated terms that no one understands...oh, and knows everything there is to know about any field of science. Okay, maybe you're only thinking a few of these things, or none, but the media sure portrays this. I will focus on the underlined ones.



Before I go on, I need to interrupt myself. Let  me make one thing clear, we all don't wear white lab coats and many rarely or NEVER do.



Back to topic, there are always these science shows, like Mythbusters and Bill Nye the Science Guy (I like these shows by the way), where the host(s) are talking about all types of experiments in anything science related. Science as in anything chemistry, physics, or biology related because these are the three basic sciences which these "science" shows never make clear of to people who don't know anything about science... and this is a very important concept! Anyways, there is no such thing as a person like that in the real academic world; a scientist that knows every freakin crap there is to know about every field of science who is always talking about chemistry one second and then next minute is yapping about biology and so on and so forth. At least I haven't met anyone like this so far in my life.

Three Main Sciences: Biology, Chemistry and Physics

In reality, people just focus on their field of study. How much exposure you get with various science fields, depend on your major. Usually biology majors are required to take some classes in chemistry and physics. Physics mostly take math and physics courses and sometimes chemistry, THEY ARE NOT required to take biology courses. The chemistry track is also similar to the physics one. So I guess in a way, biology majors are the more well rounded ones; however, this is just a broad view since each main science has many majors and divisions that intertwines with other fields (biochemistry for example).



Seeing these science shows, you would think that anyone that studies any field in science would like all of them, and that's just not the case. Me personally, I only like some topics in biology (it's a very huge/ diverse field as with the other basic sciences) and only a little bit of chemistry. Physics is only interesting to me when it is conceptual; once anything reaches to a complicated math level, I dislike it. If you go up to a physics professor and ask a question pertaining to biology in an upper division class, most likely they will be puzzled and not be able to help you and vice versa. As you can see from my first link (here it is again if you're too lazy to scroll up) each individual has their likes and dislikes in the sciences.

Usually biologists don't like physics and math; physicists and engineers (engineering is literally same as physics but I don't know why it's always separate) usually hate biology. Chemistry is an in betweener. Of course, there are those few that loves anything science, but hey, you can only major in one or a few.

Also we don't know everything there is to know about our field of study or major. There are many people who are extremely smart, but still there is no one that knows everything. Studying in any field of science, you  are expected to know a lot to be the best you can, but still you can't know everything. But really, that's how it is in any field of study, not just the sciences.



The term "scientist" is such an overused term outside the science community; it's rarely used amongst me and my fellow bio colleagues, I don't think chemists and physicists use the term much either. Yes, it is a broad term you use if you don't know a person's field of study in science, but, as I said before the media makes it seem like a scientist studies all fields of science. Basically, you don't hear anyone going around saying they are a "scientist", people will just say they are studying to be a physicist, biochemist, microbiologist, astronomer, geologist, or whatever it is that they study.

Fake...

Lastly, I have to bring up the white lab coat stuff again. It's only worn if  you are dealing with hazardous materials or if you don't want to get your clothes dirty with stains used in labs. Usually biologists and chemist wear these. Other types of scientists such as an astronomer or a geologist, probably never worn a white lab coat in their life since their work doesn't require it. Hell, have you ever seen Einstein in a white lab coat? He's a physicist.



I know I haven't talked about all the misconceptions I listed, but I think you get my point of how people studying a field in science are portrayed. inappropriately.

Oh, also, I love Art (Photography).

The Science of Life and Immortality

Why do we age and not live forever? Is immortality possible and does it exists?

Phoenix, Marvel Comics

Egyptian Phoenix (Bennu)

Chinese Phoenix (Fenghuang)

Most of us would think of a super human being or a god when we think of immortality. The media has portrayed immortality in a variety of ways; from a entity that ages but can’t die from physical injury or old age or one that stops aging at a particular stage and stays that way forever and cannot die no matter what. One popular immortal mythical creature portrayed in the media and many cultures around the world is the Phoenix; once it "dies" it rises from its ashes and lives again a new life. In either interpretations of immortality, it involves something supernatural. Although there are many ways to interpret immortality, I will focus on it at a cellular level; a cell that cannot die from aging but can die from other things such as starvation, physical trauma or pathogens (disease causing microbe).

First of all, why do we age? One major explanation or theory to why we age is that the telomeres in our cells shorten whenever it divides. Each one of our cells has DNA. Telomeres are DNA themselves, but are located at the end of the entire DNA molecule, or chromosome, and are composed of repeated sequences (repeated sequences meaning repeating in any of the 4 components of DNA: A, T, G, and C in a particular order, for instance in humans it is many repeats of just TTAGGG over and over again). The main purpose of telomeres is to protect our genes, our genetic information, from cleavage damage from cell division or other processes; when genes are destroyed they become cancerous or are unable to make useful proteins needed in life.


Cell division is important for growth, injury repair and many other things; whenever a cell divides its telomere gets cut and so does a portion of the lifetime; our cells that makes us age and therefore we age. When a cell divides, it needs to replicate its DNA so it can pass it on to its progeny cells, since the telomeres in DNA gets shorten during this process both progeny cells get a shorter DNA than their parent cell and therefore a shorter life. This is the reason why telomeres are at the end of the DNA so that it gets destroyed instead of DNA that stores useful information.

Telomeres indicated by red regions in  these chromosomes

If our cell’s DNA did not have telomeres, then it simply would not divide or our genes would be destroyed after only a couple divisions. According to the Hayflick Limit, a theory that states the number of times a cell can divide before it dies or stops dividing, a human cell can divide 50-70 times before it stops and dies. Basically, when the telomeres are gone and done with, so is the cell.  It is not clear to why our cells cannot retain the same telomere length we were born with and why it shortens after each cell division but we do know that is it not from a damaging process. As Dr. Bill Andrew describes it “it’s not a wear and tear mechanism, it’s simply due to the fact that our cells lack the ability to replicate the very ends of the chromosomes and is a passive process.”  Amazingly, your age can be estimated just by looking at the telomere lengths in your DNA.  One way in which the cell reverses this process is by an enzyme called telomerase, which elongates the ends of telomeres that have gotten shorter. However, as the cell gets older the activity of telomerase weakens.

Telomerase restoring the end of telomere.

So are there living things that are immune from the damaging processes of aging and can live forever (can’t die from old age)? Yes.

Cancer cells are a prime example of immortal living entities in biology, and yes they really are immortal especially if kept in a controlled laboratory environment where nutrients are constantly replaced, waste is constantly removed, and are kept from outside sources that can cause them trauma. Okay, so there's not supernatural stuff happening here, but it's still pretty damn amazing the fact that these cells can never age. The simple reason why cancer cells are immortal is because their telomeres don’t get shorten; they always have an overabundant supply of active telomerase. They can divide for an infinite number of times, defying the Hayflick Limit, never age and can live forever if they don’t get fatally injured or starve to death.  Not only are cancer cells immortal but they also divide rapidly. This is why they cause tumors, because they don’t die from aging and just keep on dividing infinitely to create a huge blobby mass.

Henrietta Lacks

One famous line of immortal cells used in research is the HeLa Cells, named after Henrietta Lacks who is the source of these cells. She died from cervical cancer in 1951; the cancer cells obtained from her, without her permission, have been dividing since her death and used in research labs all over the world. What makes these cells and other cancer cells more amazing is that they can survive outside of their source organism, unlike most normal cells that die shortly when taken out of the body.

The immortal HeLa Cells

Other examples of cells that don't show signs aging and can be immortal are sex cells and bacteria. In sex cells, it is almost the same biology behind cancer cells, their telomeres don't shorten due to active telomerase; however, I believe the mechanisms behind why these cells don't age is less known than cancer cells. In bacteria it is much different; MANY, BUT NOT ALL, bacteria have a single circular chromosome. When bacteria divide they replicate their entire chromosome and if there are no errors in the process, there is no loss of genetic material.

Egg and sperm

Bacteria

With the discovery and knowledge of telomeres and telomerase there are a lot of crazy things certain scientists are probably trying to do (this alone can be the topic of another post itself). Of course, one way benefit of this knowledge would be to treat cancer. In studies done with mice with cancer, taking away telomerase from the cancer cells caused the death of them. Next for us is to find a way to destroy tolemerase in human cancer cells. There's also this idea of how living forever may be possible. However; when I asked many of my friends if they wanted to live forever many of them said no.

How Disney Stars are Made

I write extremely LONG posts; I will be posting more shorter post starting from now. Anyways, with all my talk about genes and genetic engineering, I thought this was a funny video parody of Disney and what I've been talking about in my previous posts. The video is about how geneticists grow human beings in a lab with desirable traits of a super star. Imagine if there really were known genes that gave traits of great singing, dancing, and looking good; I can see some wanting their babies to be grown in these labs and, most likely, a lot of people banning the idea. Although a person may not be born with these traits, in a way, I do think stars in real life are "engineered" or instructed by their agents to act or look a certain way to be more famous and rich, which is a bit sad. Anyways, enjoy the video!

Time Out

I failed a very important test recently (no it wasn’t school or textbook related) and so I just want to devote this post to a free write of my feelings about blogging and any other thoughts I have compiled in the past few days. So failing this test has put me in a very despairing state. I’ve been ignoring all my friends that want to go play Tennis and do other fun things; the strange thing is that Tennis or any other physical outdoor activity is very therapeutic for me and I don’t even want to do any of them right now. I have been doing nothing but sit in front of the computer and eat loads and loads of junk food, particularly Twinkies. I’m really mad at myself for caving in under pressure and whenever I’m mad with myself and feel unworthy, to the point where I don’t want to do anything, I distant myself from the world and the people I know for a good amount of time. For me, during these times, I rather be alone so I can re-evaluate my life.

Why this post and not a post about Microbiology? Well, first off, I don’t really want to talk about those things right now and I think it’s important to just take a breather when you need it and do some self-reflection.

Anyways one thing I have been doing a lot the past few days, besides indulging in s***** food is reading on the net; random subjects from articles on Yahoo and mostly from other Blogs and I don’t really know why this was the only thing I’ve been doing. I was able to do this because I actually deactivated my Facebook and accounts on other social network sites. By doing that and reading, I realized that there is really not a lot of time spent on writing these days and expressing oneself or analyzing problems thoughtfully. It’s a lot of one sentence or one word statuses, watching videos on Youtube only to leave a f*** *** or other 4 letter curse words on comments of videos you don’t like, which I must admit I’m guilty of  from time to time. I even came across a Blog that discussed about how Blogs are becoming extinct now since it’s only older folks that are doing it and once they are gone so will Blogs.

At first, this was just a class requirement for a class that I didn’t want to be in; another boring and pointless activity. Initially, I was just going to post about biology issues, sound like a textbook with bare minimum lengths and be done with it because I thought Blogging was stupid. After reading other people’s Blogs, from classmates and other strangers on the internet, I really feel like Blogging is a form of an open diary where you post issues about your topic, of course, but also incorporate a bit of your thoughts. Besides expression, I realized that blogs can be a form of self-discovery and can be quite calming at times, something that is not done much with people these days. I bring up expression, because if we were to do essays in this class I don't think we would be able to do much of it due to confines of grading, not incorporating videos and pictures and writing about something we don't like.

Of course, at this point, I haven’t produced a lot of posts… well at least the amount required. However; I do spend a lot of time thinking about what my next topic should be. I also go back to my previous posts occasionally to read and work on the flow and correct any errors. Most importantly, I really try my best to research on my topic, refresh my memory so that I can make it easy to for people to comprehend and also thought provoking; try to avoid any fancy or complicated scientific terms so that it’s more relatable and less confusing, and steer away from many of the complicated processes or at least break it down straight to the point.

As I hinted on before, I was going to explain everything with my current knowledge and write without much thought; but after the class evaluations and everything it wasn’t going to happen anymore, which I’m kind of glad. By doing research on things I think I know about, I discover more interesting things and I feel like I want to explain it more with care as opposed to just randomly talking about it like nothing. In a way it made me ponder upon certain issues deeper instead of just recalling the scientific facts I’ve memorized about them.  

I don’t know how long this interest will allow me to Blog, if any, after this class but at this moment I think I’m getting the hang of Blogs. I realize that perhaps writing does have some benefits besides for school work. Anyways, I'm a bit glad I took some time out to do some self-reflection and evaluation.

Genes in the market

In my last post I gave a brief explanation on what genes are and touched up a bit on bioengineering and gene alteration in organisms; these organisms that result from such applications are called genetically modified organisms (GM or GMO) or transgenic. In most cases with GMOs, their original genes are not altered themselves but they have genes with desirable traits injected into their DNA. This application is used on a variety of organisms and the possibilities seem to be growing as fast as other technologies. Here we go over some of the uses of genetic engineering.

PLANTS

Plants, crops, fruits and veggies are among the most genetically modified organism today, especially since food is perhaps the most important commodity to us. GM produce grows faster and have a longer shelf life, this is very beneficial in countries where food source is scarce. This may also be helpful one day to help mass produce plants used for biofuels. The genes of desert plants, such as a cactus, can be inserted into a crop, a tomato, so that it can grow in areas that are either too dry or too hot for a normal tomato. GM plants can also be engineered to resist pests, herbicides. Even more interesting is that plants can be made to produce plastics, and human tissue. Who knows what other crazy things scientists will do with plants; bizarre colored fruits to weirdly shaped ones, to one tasting like another!

  

ANIMALS

Pets are also commonly engineered in a way to look more attractive or exotic to increase sales. One of the first genetically modified pet is the GloFish; which are zebrafishes made to have a variety of vibrant neon colors. Besides looks and appeal, this technology is making it possible for people that can't have certain pets be able to. Back in 2006, a company was able to produce cats and dogs that produced little (hypoallergenic) to no allergens. Though probably much more expensive, this may be a blessing for those who suffer from allergies from cats and dogs that really wants one. Of course, I don't advocate much of this, maybe the hypoallergenic cats and dogs a little, but if you are unhappy about GM animals perhaps you should report it to PETA.

Wild zebrafish

GM zebrafish, GloFish

Hypoallergenic cat

BACTERIA

Of the organisms I've mentioned, bacteria are the most easiest to genetically manipulate due to their simple structures and fast reproduction times. Also, many activists or other anti-GMO individuals wouldn't really care about bacteria being altered compared to plants, animals or "higher organisms". Most of the genetically engineered bacteria today are used to produce pharmaceutical drugs, vitamins used in multi-vitamin pills, and essential enzymes or proteins such as insulin. Others are made to be more efficient at producing certain foods, mainly in the dairy industry. As I mentioned in my other post, scientists have made glowing bacteria. I guess one purpose of this is BioArt, something I stumbled across while looking for links for this post. BioArt, as it's name implies, is artwork made out of life. Interesting. 

Various colored glowing bacteria on a petri dish

Genes: The instructions for our construction

I’m pretty sure most of us have heard of the term gene. We all have a basic idea of how we get it and what it does. Genes are hereditary; passed down to us from our parents and pretty much determine how each of us look and, to some extent, how we act. Genes have a huge influence on our lives and here I hope to break it down so that people can have a general understanding of what they are and appreciate them.

First let’s think of DNA, we have it in all our cells, which is a long double stranded structure consisting of four components: A, T, G and C. Each strand is made up of millions of A, T, G and C randomly lined up together. A gene is basically a portion of this DNA strand that “codes” for a particular protein. I say code because when proteins are made, a molecular machine must read all of the A, T, G and C within the sequence of a gene and it is the sequence or "code" that tells the molecular machine what type of protein to make.


Proteins are one of the major building blocks our body uses to build itself. The protein made from a gene could be a protein that makes your hair and nails such as keratin, or proteins that break down sugars in the foods that you eat, such as lactose in dairy products. As you can see from the example picture below, each gene is unique and differs by the protein it makes, it's length and the ordered sequence of the A, T, G and C within it; a gene length can be hundreds to thousands of all the four components lined up together. 

In short, although genes mostly associates with proteins and tangible biological processes, they do have an influence on our mental behaviors; however, the environment and culture we live in also plays a role in how we act. One plausible example in which genes can affect our mentality is when there is a defect in the gene(s) that produces serotonin, a neurotransmitter that regulates mood and sleep; without it a person will feel depressed. 


The important of all this? Well, this knowledge, genetic engineering, have been used in many applications such as the medical field. For instance, people who have Diabetes and lack insulin rely on genetically engineered bacteria to make the insulin for them. These bacteria have the insulin gene injected into their DNA so that they can make it. Gene therapy, in which a sufferer of a genetic disease can be cured by fixing their gene sequence or "code" that is broken. Basically, by inserting new genes, or instructions, or "codes" in an organism they can have a new "ability" (doing something that they naturally can't; eg. making a foreign protein). In a similar way, by fixing broken genes an "ability" can be restored.


There are also many other applications of genetic engineering that are quite controversial (and crazy). Plants have been genetically modified to last longer, become bigger, tastier and resistant to pests and herbicides. Those plumply big bright red tomatoes you see right next to those rotting ones that have been there for the same amount of time are probably genetically modified. Many pets have been modified to look more appealing and interesting. Labs have made glowing bacteria, and why the hell? I honestly don't know myself... okay maybe I do. Anyways, genes are basically the instructions for the construction of life and knowing these instructions allows for the manipulation of life in many ways.