Friday, September 30, 2011

Android Applications for Scientists (and other people too!)

If you're like me, you like to use your phone for its capabilities, including for work, and because it's shiny and you paid a lot of money for it.

I use an Android phone (no thank you, Apple) and am always interested in an application that could help me with my research or studying.  Unfortunately, the Android marketplace is cluttered with irrelevant applications, making finding useful applications difficult.

The following applications are presented as a summary of what I use.  Certainly there are more out there (please tell me!) and more are created every day, and I look forward to using these applications in the future:

Astrid Tasks:  Every morning as I'm walking into the building, I fill out my task list of things to do for the day.  I don't need anything fancy - I just need an application that is quick, easy, and simple.  Astrid is fantastic for putting together this list and for prioritizing my experiments and work.  Plus, it's got a handy widget (if you're into widgets, that is).  I would highly recommend this application for those who like to keep lists.

GoogleDocs: If you use Google for composing, sharing, or viewing documents, this application is fantastic because it will sync your computer and your phone to view the same documents.  Additionally, if you've got a big enough screen, it's not too horrible to actually compose in these documents.  I don't use this too often, but it's convenient  when I've got a document to get on my phone and my Dropbox happens to be full (see below).

Doodle:  Have you ever tried to schedule a meeting with faculty?  How about with multiple faculty?  Needless to say, it is a nightmare: herding cats as many would say.  Doodle attempts to make this a little bit easier by creating a spreadsheet which participants can then check off for their ability.  That one magical time spot that everyone checks is then the meeting time.  Doodle comes with several options for creating an event and then adding participants.  In my department, these things are really the best way to make sure that a meeting is really going to happen.

Dropbox:  If you're not already on Dropbox, seriously, sign up for it.  This program is the most useful thing I have every used.  Once installed on a few computers and on your phone, a folder is created - your Dropbox.  It acts just like a normal system folder and can be manipulated just like one too.  The great thing is that anything that is in your Dropbox can be accessed on any computer that has Dropbox installed and you can also access your files online.  This is so much better than carrying around a flash drive, and the syncing is instantaneous.  I could not recommend this program more.

handyCalc:  Usually, I'll use my crappy old calculator from high school to do the simple arithmetic needed for my experiments and notebook.  When I'm at my computer and can't find my calculator, I use handyCalc, mainly because I find it much easier to use than the standard calculator that came with my phone.  There are multiple iterations of calculators out there - from simple to mind-bogglingly complex.  This program will solve equations, create graphs, and perform simple addition and subtraction.  It works and I like it.

LinkedIn:  At a recent conference, I learned the importance of LinkedIn.  The seminar speaker asked everyone in the room to raise their hand if they were a member of LinkedIn.  I was the only person not to raise my hand.  LinkedIn is a Facebook for professionals - it can be helpful if you're looking for a job or want to make some contacts to look for a job in the future.  Being able to use it on my phone is convenient, too.

Pulse:  I like to read the news on my phone when I can't access a computer.  The best app I've found for this is the Pulse reader app.  Using this program, you can view tiles containing the top headlines from various websites, including numerous science-slanting websites.  The handy swipe-to-change-story feature is nice, and the entire interface is easy-to-use.  I also like using this while I'm walking because it's easy to pull up a short story that I can finish quickly and make myself feel like I accomplished something.

QuickOffice:  I'm not a big fan of paid applications - I am a poor graduate student after all. QuickOffice came preinstalled with my phone, and I must say that I am quite impressed with it.  It has the same features as the Microsoft Office suite (I can even view my PowerPoint slides on my phone!) and is really easy to use.  If you're not up for shelling out $15 (!), you can always opt for the Google Docs app, which I think is almost just as good, and you can't beat the price...

Google Reader: I use Google Reader religiously for keeping up on journal articles.  This handy little app presents my RSS feed conveniently and in my pocket so that I can keep up on my papers that I need to read.  Since I can't access the actual papers on my phone, I star the articles of interest and download on my computer when I'm connected to my university's network.

The Weather Channel:  I work in a lab with no windows.  Most of the time, I can't tell is there's a tornado outside or a beautiful sunny day.  Sometimes, that's for the best because then I'm not tempted to leave my benchtop and wander outside.  When I do have to go outside, however, it's nice to know the weather, and the Weather Channel app is convenient for quickly checking the weather.  Tons of functionality are included, such as animated weather maps.  There are a lot of weather applications out there, but I find this to be the most useful.

WTFSIMFD:  Hands down, my favorite food app.  WTFSIMFD provides you with a recipes that you should eat.  The app has a potty mouth, but it's amusing and endearing at the same time.  It also gives great recipes, you know, for when you're not in the lab or studying...

Just a roundup of what I find useful as a student and a scientist.  Maybe a followup post will be necessary when I find even more useful apps...

Saturday, September 24, 2011

Mendelian Genetics Part I

Gregor Mendel was an accomplished scientist, though he never would know this during his time. His studies of pea plants (as well as other organisms) laid the groundwork for the genetic breakthroughs that would come after his death. Mendel was a Augustinian monk that had ample time to experiment with his pea plants. The principles he was able to extract from his studies are the basics taught in high schools around the world.

 Mendel studied peas, but not just any peas. His peas were true-breeding, meaning that they self-fertilized and produced essentially clones of themselves.  Over the years of study, he bred plants with specific characteristics and then crossed different varieties of pea plants to test what their offspring would look like.

Importantly, Mendel considered discontinuous, contrasting traits: he only considered the traits that he could observe (such as color), came in a limited number of forms (green or yellow) and were easily distinguishable.  For these monohybrid crosses, Mendel considered seven different traits: seed shape (round versus wrinkled), seed color (yellow versus green), pod shape (full versus constricted), pod color (yellow versus green), flower color (violet versus white), flower position (axial versus terminal), and stem height (tall versus short).  Also important to Mendel's work was his use of mathematics and statistics to estimate the probabilities of a certain type of plant emerging from a certain type of pea plant cross.

The monohybrid cross is the consideration of one particular trait at a time.  For example, if looking at pea pod color, one might cross a yellow and a green pea plant and then determine how many of the offspring had yellow or green pea pods.  This type of cross is illustrated to the right in what's called a Punnett Square.  A Punnett square is a way of organizing the different traits expressed by the individuals being crossed.  The capitalized letters are the dominant traits, while the lower-cased letters are recessive.  Vertical columns traditionally represent females; horizontal, males.  Using the Punnett square, we can look at all the possible offspring that can emerge from a cross, which can then be used to determine probabilities associated with the offspring's traits.

From these monohybrid crosses, Mendel was able to make a few conclusions.  When he crossed two pea plants of distinct traits (the P1 generation, true-breeding variety) to produce progeny (the F1 generation) and then used the progeny to generate more progeny (the F2 generation), he found that the two parental traits were still present and unchanged.  This led to the hypothesis that each parent contributed equally to the inheritance of the "genetic determinants," which would have more technical and molecular definitions in the distant future.  These determinants were separated and segregated randomly to make gametes and produce the next generation of pea plants.

Mendel's principles from the monohybrid crosses can be summarized as follows:

  1. Hereditary determinants (unit factors) control traits that are in pairs in an individual.
  2. When two dissimilar unit factors for a trait are combined in one organism, one factor is dominant to the other recessive factor.
  3. When gametes are formed, the pair of unit factors separate and are equally likely to be separated into a gamete: the principle of segregation
In the next post, we'll examine dihybrid crosses and some more of the interesting findings from, of all things, pea plants.

Thursday, September 22, 2011

MAP Kinase Signaling

Cells exist in a very dynamic environment, not only on the inside of the cell membrane, but also on the outside.  Thus, cells must be able to interact with their outside environment and respond to stimuli appropriately.  One of the several signaling pathways involved in communication from the outside of the cell inward is the (very general) MAP kinase (MAPK) signaling pathway.  The cell uses the MAPK signaling pathway for several reasons, primarily to amplify signals.  Additionally, aberrant MAPK signaling is implicated in several types of cancers.

First, MAPK signifies mitogen activated protein kinase - a fancy word for a protein that responds to mitogens, or a molecule that stimulates mitosis.  Proteins of the MAPK family were discovered in 1989 in yeast, with ERK1 being the first mammalian MAPK signaling protein, involved in insulin signaling pathways (at the time at least...).

The MAPK signaling pathway is often called a cascade because the components in the pathway amplify a signal within the cell.  The three major components are:
  • MAPKKK / MEKK / MAP3K: The MAP kinase kinase kinase.  This protein phosphorylates MAP kinase kinase.  Several forms are found within the cell and their abundance is lower than that of MAPKK or MAPK; thus, MAPKKK isn't as involved in the amplification of signals.
  • MAPKK / MEK / MAP2K: The MAP kinase kinase.  MAPKK phosphorylates MAPK and is highly abundant within the cell, but its only substrate is MAPK.  Just a few phosphorylation events on MAPKK result in significant activation of MAPK.
  • MAPK / ERK: The MAP kinase.  MAPK is also abundant in the cell and has diverse substrates, including itself.
There are several pathways that involve MAPK signaling.  Two of the important ones are:
  1. The ERK pathway: growth factor stimulation of cell surface receptors (via receptor tyrosine kinases [RTKs]) causes activation of Ras, which activates Raf (MAPKKK) to activate MEK (MAPKK) and then ERK (MAPK).  ERK's several targets include Elk and Ets, which control cellular proliferation.
  2. The JNK pathway: Stress on the cell results in activation of several proteins, including Rho, which goes on to activate MEKK, then MEK, and JNK.  JNK's major targets include c-Jun, ATF2, and Elk1, which control proliferation and apoptosis.
One important consideration is the specificity of MAPK signaling.  Specificity can be achieved in several manners: protein components can only "fit" other specific protein components.  Additionally, the spacial organization of a cell can affect specificity, and this type of specificity is often controlled by scaffold proteins.  

MAPK signaling is essential for many cellular processes, including proliferation, apoptosis, embryonic development, and cancer progression.  Many intricacies of the pathways are still being worked out and will provide significant insight in the future.

Thursday, September 1, 2011

The Basics of Protein Translation

Proteins, a major constituent of the cell, have many diverse functions and are classically considered to be the "work horses" of the cell.  Additional molecules, such as RNAs and lipids, have shown importance in signaling and catalyzing chemical reactions; however, proteins remain an important part in the life of a cell.

Before proteins can perform their evolved functions, they must be synthesized within the cell.  The process of synthesizing a protein is critically important to the cell and, thus, is an energy-intensive process.  

The basic building blocks of a protein are amino acids, which come in twenty (and more) flavors.  These amino acids have different properties that afford proteins different structures and functions when the amino acids are polymerized together in distinct orders.  These amino acids can have distinct signaling roles when they exist as monomers as well (see this paper by Nobukuni et al for an example).  

Monomeric amino acids in the cellular environment do not randomly polymerize to form proteins.  In the first of several steps, tRNAs are charged: they are covalently linked to amino acids via aminoacyl tRNA synthetases.  These synthetases hold the very important role of attaching the appropriate amino acid to the appropriate tRNA.  Because inappropriate charging of tRNAs would lead to misincorporation of amino acids into a protein chain (wasting energy or leading to even bigger problems for the cell), sythetases are very specific.  In fact, some synthetases have an editing site, where they will catalyze the removal of incorrectly placed amino acids.

After tRNAs are charged with their appropriate amino acids, they are ready for interaction with the ribosome.  Ribosomes are large, complex molecules that merit their own post.  Briefly, ribosomes are composed of RNA and protein and are made of two distinct complexes: the large and small subunits (depending on the origin of the ribosome, the subunits have different sedimentation coefficients, so you might see 30S and 50S for bacteria or 60S and 40S for eukaryotes, for example).  Ribosomes catalyze the polymerization of amino acids into proteins.

In the first step of ribosome-mediated protein production, the small subunit of the ribosome combined with a tRNA for methionine (the amino acid that begins the protein chain) scans along the transcribed mRNA until it encounters a start site (ATG codon).  Here, the complex stops, and the charged tRNA with its amino acid comes into contact with the peptidyl transferase site (P) on the ribosome.  eIF2 (eukaryotic initiation factor 2), which was along for the ride, hydrolyzes GTP to GDP at this point such that the ribosome stops at the appropriate codon.

Next, the large subunit of the ribosome binds the small subunit, making a full ribosome that is ready for catalysis.

The tRNA that lines up with the mRNA's next codon then binds in the acceptor site (A), along with the help of eEF-1 (eukaryotic elongation factor-1), which hydrolyzes GTP to GDP.  At this point, the ribosome goes into action: using the peptidyl transferase center (PTC), it catalyzes the covalent linkage of the first and second amino acids.

The entire ribosome now moves along the mRNA in a process called translocation, which requires the help of EF-2 (and GTP hydrolysis).  The first tRNA is moved into the exit site (E), and the second tRNA moves into the P site, while the A site is open for another aminoacyl-tRNA.

The process repeats until the ribosome encounters a stop codon.  At this point, termination factors (TFs), which have structures similar to tRNAs and bind mRNAs but do not have amino acids, enter the acceptor site of the ribosome.  The ribosome then catalyzes the addition of water to the end of the amino acid chain, releasing it from the peptidyl transferase center and allowing it to leave the ribosome and begin folding into its native conformation.

While there are several details that I may have seemingly glazed over, this post should give a broad, simplified overview of translation.  Future posts will address the many details involved.

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