Dear Readers,

For those of you who are hesitating and still planning to take your MCAT, let me say one thing: JUST DO IT!

I haven’t been able to add any sciency postings mostly due to the fact that I was slaving and studying for the MCATs early mornings and late at night, then work in between. It’s pretty tough (the schedule) but I definitely think that the MCAT is doable (as in, you can do really well!)

Let me give you a little history of my quest for taking the MCAT.

I actually wanted to go to medschool for a really long time, as in when I was 4 years old. Of course, at that age I didn’t know what it’ll take to be admitted into a medical school. My undergraduate years were a little tough. A combination of friends, people dying, boyfriends, and a research mentor who was really tough on me made me a little paranoid. I definitely developed a lot of anxiety and had a hard time doing well on my exams even if I studied a month in advance. It was strange, I can’t really explain it, but basically my scores out of college isn’t on par to the current average/expectations as noted in the AMCAS website.

Due to this negative thinking that I cannot do it, made me even more depressed about myself and my abilities. It pretty much smashed my dreams. I went on working other jobs but I always looked back and wanted to go ahead and take the MCAT, then apply to medical school. So after many years of doing that, I finally went on forward. I saved enough money to pay for a prep course. I committed as much time as I could to the course and studied as much as I could (about 5 hours a day for 3 months straight). I have tried studying on and off for two years prior to this but the outcome was never an improvement (thats why I went on with just studying for 3 months straight).

It’s not easy to work 40 hours a week plus other time needed to help my family with things. I pretty much did not have a social life and I started to feel very alone. Again, the sadness fills the air and I became very depressed. Yes, I cried. Several times actually. The worst thing I did to myself was when I kept Facebook-stalking all of my friends who I see have done something extraordinary with their lives. I kept looking at pictures of current parties, events, and other social gatherings that I am clearly missing out because of this stupid damned MCAT I have to take.

At one point I canceled my test date and said, oh I’ll take it in another 6 months. Then I was advised by friends and family that I should just go ahead and do it since I’ll only be suffering more of this aggravation for another 6 months if I don’t do it now! So , $400 dollars later,  I signed back into the next available MCAT test date. I basically had to check every day of every week (any time I had) to see if another test date in September opened up. When it did, I signed up right away! (People do back out of the test date when it nears the test date, but I definitely recommend signing up ahead of time so it forces you to maintain your study schedule towards your goal).

I haven’t received my score yet, and I’m not sure how confident I feel about my score. All I know is I am very relieved that I took this big step towards doing what I really want to do with my life. It’s been many years, but at least I know I have accomplished a goal that I set myself out to do it regardless of whatever obstacle that was in my way.

I was told by many doctors, principal investigators, faculty members, that if you really want to become a doctor, you will be able to get there. Someone is bound to accept you with your obvious passion, persistence, and determination. I look forward to hearing any of your stories good or bad. It’ll totally help with my uneasiness and whoever else out there reading this blog.

This post is getting way too long now, so I’ll stop here and I’ll post my study schedule on here on a different post.

Thanks again for stopping by.

All right, it is likely that you may need to repeat the same PCR reaction about oh I don’t know how many times before you can get enough of what you want. I have been told, but was resilient to admit that contamination can and WILL occur if you don’t take precautions.

• Do not talk while you do your PCR.
• Do not wave stuff around your PCR tube or samples or Primers or any of the solutions you’re working on because a spec of dust can cause a strange band in your result after you go and analyze your reaction.
• Do not stoop over or lean over to look into your PCR tubes, instead tilt the tubes toward you so you can pipet into it.
• Mix every solution really well and make sure to centrifuge it down so that there is no residual solution on the side of your tubes or in your cap. I recently lost a lot of DNA because of residual solution in my cap.
• Make sure everything that you use is autoclaved and as clean as can be.
• Consider running a gradient PCR, which means the same reaction mix, but at varying temperature (+/- 0.2 to 1.0 C) to assess the best annealing temperature for your primers
• Clean up your PCR by doing a Gel PCR purification or use a kit such as Qiagen MinElute PCR Purification, or Qiaquick PCR Purification (depending on the size of your sequence and of what base pairs you are trying to remove) to clean up your PCR. Keep in mind that gel purification is likely to lower your actual concentration of amplified sequence.  In other words, if you have a wee bit to begin with, it might not be worth it to do the clean up.

All in all, be very very mindful of what you are doing. Read your protocols way before you do your experiment and have the necessary calculations ready BEFORE you do your experiment.

Good luck and happy experimenting!

What is it?

PCR stands for Polymerase chain reaction. It is used for various reasons but it’s main purpose as the name suggests is to amplify DNA. How it can be applied in science is countless. The DNA sample will amplify exponentially based upon the number of thermal cycles (n) you have set, which can be calculated as 2ⁿ.

What you’ll need for PCR

1. DNA strand containing your sequence of interest
2. Forward and Reverse Primers : about 18-20 base pair oligonucleotide that marks the point where your amplification of that desired sequence to occur. The forward primer fixes itself from the 3′ end to the 5′ end of your template DNA. The reverse primer fixes itself from the 3′ end to the 5′ end of your other template DNA. This way, the DNA polymerase that you use can recognize the 5′ end and replicates your DNA sequence from 5′ to 3’5.  In order to have good yield, you will need to have a “good” set of primers. There are certain things you would need to look for: too high or too low of a G-C content can affect your experiment, annealing temperatures, mispriming likelihood, 5′ overhang, hairpin formation, size of your interested sequence.
3. ddNTPs – these are dATP, dCTP, dGTP, dTTP – a pool of these in your sample will allow the DNA polymerase to use them to amplify your sequences
4. DNA polymerase – usually Taq polymerase
5. thermocycler – a convenient machine that will automatically change it’s temperature, time, cycles based upon what you ask it to do

Nowadays, you can easily purchase a ready mix from companies such as Kapa Biosystems which has everything you need aside from your primer and obviously your DNA sample in solution. There are different ready mixes that are made catered to your needs such as your sample size, your starting temperature, and compatibility with your polymerase. To fully grasp what you will need, you’ll most likely need to read into research articles on the specific specie, strain, and gene of interest. People who have published something are likely to have successful data, thus by comparing protocols or materials and methods, you can whip up one that is best for you.

What are all the different temperatures and time mean?

The most standard form of set up seen is:

Denature: 95 C for 2 min

—cycle begins—-

Denature: 95 for 15 seconds

Annealing Temperature: 50-60 for 15 seconds

Extension: 72 for 15 seconds

—cycle ends—

Extension: 72 for 10 minutes

Store PCR product in 4

Denature Step

DNA is double stranded, thus it will take high temperature to denature the double stranded into two single stranded DNA by breaking apart the hydrogen bonds between the base pairs that hold the double stranded DNA together. Too high of a temperature though, can possibly break the backbone of the DNA, held together by phosphodiester bonds, and thus prevents you from getting an amplified DNA PCR product!

Annealing Step

The annealing temperature is speaking of the annealing or the connection of the primer to that of your, now, single stranded DNA. Every primer has a preferred annealing temperature that you can get either from the manufacturer or within the program that you used to create your primer sequence. The temperature you choose for the annealing temperature should be around that recommended temperature. To optimize, you can try doing a + 2 degrees of the recommended or to run a gradient PCR, which means you just run different PCR reactions with

different annealing temperatures. In doing so, you can see which temperature is the best for you.

Extension

Extension is the time in which your DNA polymerase will work on adding complimentary nucleotide to your DNA sequence.

This completes your first cycle. Thus, the second and the following cycles will repeat the process starting at 95 C for 15 sec until the number of cycles have finished. As you can see, your number of amplifications will simply be 2ⁿ try plugging and chugging to see if it

works for you!

Things to consider

• These settings are pretty standard. The variance is usually the number of cycles used and the primer annealing temperature. Keep in mind that by increasing the number of cycles, it is possible that the number of mutations within the sequences are higher. This is because DNA polymerase has an error of its own.
• The amount of reagents used, including your DNA can also affect your PCR product amplification. Simply because you may run out of one of the reagents and thus cannot continue.
• Primer dimers can be a by product from your PCR. This usually happens when the primer curls up and binds to itself
• Hairpin structures are similar to primer dimers, but this time it is of the DNA itself

Goodluck!

This can you be YOU!

Science isn’t for everyone, but curiosity is likely the drive to get you started into thinking about doing research.

1. I think networking is key to get yourself noticed.
2. Your passion and dedication will have you liked.
3. Your resume and credentials determine whether or not you will get paid.

For High School Students:

I commend you on your interest in science so early, but here are some things you can do.

1. Talk to your science teacher and see if he/she know of anyone or any place you can apply to do a science project/report with
2. Check out local/distant universities for high school students opportunities (Some programs are more rigorous than others, so research!)

For Undergraduates:

Royce Hall - UCLA - Los Angeles, CA

1. Determine what kind of experiments/laboratory you are interested in working in.
2. Check work-study websites for list of jobs in laboratory OR Check for faculty members (best if they are your professor)
3. Research on what the lab does: either read up on the faculty on their website, you will usually see their full name and a list of their publications
4. Go to: http://www.ncbi.nlm.nih.gov/pubmed/ and try to get their paper, using your university wifi/LAN (you usually get free access to articles) OR Google Scholar
5. Read the abstract and methods to see what they study (reading the abstract) and what they do (methods)
6. Get your resume and cover letter ready – cater it to the lab of choice (don’t be super generic, they will know you mass emailed it)
7. If you got a hit on your work study page – send an email with your cover letter, resume, and write a professional (short, simple, and to the point) email to the professor/lab of interest
8. Wait for a reply
9. If you are bold – go directly to the professor’s office and talk to them. I know this sounds crazy, but I know a guy who did this. He’s a doctor and  post-doc right now at Stanford. (So, don’t be discouraged!)
10. Try looking at internships in companies (this is highly recommended for those who are interested in getting into research immediately after college)
11. If it didn’t work out, repeat and try again! (or ask an upperclassman friend – that’s what I did)

For College Graduates:

This is a little bit more challenging since your GPA, experience, and who you know become a lot more important if you have graduated for a few years.

1. If you graduated for a few years, try picking up a lab course at a JC and get to know your professor. Chat it up and see if they can help you out.
2. If you just graduated, you still have the career center and perhaps do what is recommended for the “For Undergraduates” listed above
3. If you have friends who are in grad school, ask them to mass email your information, resume, research interest to their peers. There are usually a mailing list for grad students/post-docs who might be interested in seeing if they can get a volunteer interested in doing research
4. Emailing professors and seeing them directly may also help. For me, I knew someone who was a post-doc and he sent out my resume to the post-doc mailing list and that’s how I got my foot in the door.
5. Try looking up companies who would like to hire newly grads, Genentech does it (http://www.gene.com/gene/careers/interns_coops.html) I’m sure other companies do too.

Internships

1. A lot of big name companies like Amgen, Genentech, BioRad, etc. are pretty big in offering internships. The higher your credentials, the more likely you will get accepted. Of course, there is always an exception! Who you know and your luck all play a big role in this.

Opportunities come and go, often time surprises you. I hope this will help you on your way to satiate your thirst for research. I truly hope you the best. One thing you really got to know is that, science seldom goes the way you expect it to be. Just remember to keep and open mind and allow yourself to be surprised!

This topic pops up a lot when talking about the nervous system. It is this action potential that allows us to have any sort of feelings in our senses! No kiddin’. So, I hope this will help it stick in your mind!

Our neurons work by an all or nothing method. This means, the action potential is either relaying info to and from your central to your peripheral nervous system and vice versa. In other words, you touch a hot stove, the hotness stimulates your peripheral nervous system which sends a signal to your brain (central nervous system), which gets your neurons to send out a signal to other nearby neurons to eventually get to the part of the brain that tells you “yes, it is hot!”

The function of the action potential is simply causing the release of a neurotransmitter into the synaptic cleft. The synaptic cleft is this guy right over there. It is the spacing between an axon and a dendrite.

There exists a potential difference between the inside of the neuron and its outside or the extracellular space. This difference is -70 mV. The neuron has a semipermeable plasma membrane that has similar characteristics of all other plasma membrane. The interesting thing is, the inside of the neuron is more negative than the outside of the neuron. Hence, the potential difference cannot be 0 mV. Neurons maintain this more negative inside by selective permeability of ions via the sodium potassium ATPase channel.

The insides of the Neuron:

• high POTASSIUM (K+)
• low SODIUM (Na+)
• The opposite is true for the outside of the neuron.

Sodium Potassium ATPase

This channel are present in other parts of the body as well such as in muscles. Know that this channel’s purpose is to pump out 3 Sodium out of the cell for ever 2 Potassium that enters with the usage of 1 ATP. ATP is needed because the sodium and potassium are going against their gradients.

How does an Action Potential start?

The action potential is triggered when the stimulus causes a depolarization. The axon end at the synapse will get an excitation by the stimulus sent from the other neuron firing from its dendrite. When the axon is excited, it becomes more positive and eventually will reach a threshold of around -55 or -40 mV. (Recall the resting potential is -70 mV)

So:

• depolarization –> excitatory –> more positive–>reach threshold of -50mV = action potential

• hyperpolarization –> inhibitory–> more negative –> goes back to resting potential and beyond

How does the action potential continue?

This is where some can be confused. The movement of the sodium and potassium in and out of the neuron happens in an electrochemical gradient. What this means is, instead of looking of the concentration of the ion, we’re talking about the overall charge of the environment inside and outside of the neuron.

So this is the sequence of events that happens after the threshold has been reached!

1. Sodium channel opens up. Since the outside of the cell is more positive than the inside of the cell, the sodium ions will move into the cell (or neuron) because sodium is positive. Thus, the sodium is moving with the electrochemical gradient.

Note: The influx of sodium into the cell will bring the potential in the cell to about 35-40mV (see picture). The inside of the cell is now positive instead of the -70mV (resting) or -50mV (threshold).

2. Sodium channel closes.

3. Potassium channel opens. Now that the inside of the cell is at positive (35-40mV), the positively charged potassium will move out of the cell. Again, the potassium is following its electrochemical gradient.

Note: The efflux of potassium will repolarize the cell. Often times, the potassium will efflux enough to cause a hyperpolarization (meaning that the inside of the cell is more negative than what it’s resting potential was). Based on the image, say its about -90mV.

Hyperpolarization is important because it gives the potassium channel time to close.

Can multiple action potential happen at the same time?

No. The action potential once started needs to be completed before it can accept another stimulus to cause another action potential. Once an initiation in an action potential occurs, a refractory period is observed. There are two types:

1. Absolute refractory period means there is absolutely no stimuli, no matter how strong, will cause another action potential. This is reasoned by the fact that the action potential initiation is dependent on the sodium channel opening. Also, the neuron or cell needs to, at least be at its resting potential or in hyperpolarization in order for it to go about its second stimuli.

2. Relative refractory period means the duration of an action potential that may be able to be depolarized again because of another stimuli. Usually, this will be seen after hyperpolarization.

Take home

Remember that while the potassium and sodium are moving along its electrochemical gradient, it is going against its ion concentration gradient thus needs ATP to allow the channels to open.

I felt silly after realizing what I thought would be water soluble, wasn’t. So, I decided to look into finding a general rule to go by and lucky me, I found info on that as well as their exceptions. I’m not certain though if these are the ONLY exceptions, that’s always going to be hard to pin point since our understanding of science is still fairly primitive.

What’s the difference among solute, solvent, solution, and solubility?

Solubility means the how well something (solute) can dissolve in something else (solvent). Usually, we call the disolvee, the solute since it is less (mnemonic acute and solute). The disolver is the one usually with greater volume, so that’s called the solvent. Together, the solvent and solute combine give you a solution.

For example, we can add salt, NaCl, a (solute) into water H2O (solvent). If we put the NaCl into our water, it will dissolve by breaking into its elements Na and Cl. The feasibility of them dissolving (solubility) is about —. Other examples of solutes in water are sugar, food coloring, alcohol, etc.

What aren’t water soluble and the exception?

1. Metal oxides are NOT soluble in water EXCEPT alkali metal oxides and oxides with Ba, Ca, and Sr.

• oxides – those with oxygen (O)
• metal oxides – metal with O
• alkali metal oxides – alkali metal + O

2. Hydroxides (-OH) are NOT soluble, EXCEPT if it were with alkali metals or Ba, Ca, and Sr

3. All sulfate salts ARE soluble EXCEPT ones with Ba, Ca, Sr

See the periodic table for more info on the elements.

We have previously discussed the structure of our bone macroscopically, and we have discussed how strong compact bones are compared to cartilage bones. However, we have yet to delve into why our bones are strong. Hence, this post is focused on further explaining the bone matrix, how bones are formed, and the concept of bone remodeling or resorption.

Bone Matrix

The bone matrix is composed of both organic and inorganic materials. Organic be it carbon containing molecules such as collagen and proteins. Inorganic be it free flowing ions like minerals such as sodium, magnesium, and phosphate.

the Haversian systems or osteons are ordered in the bone matrix. As shown in the figure on the left, the osteon is used to describe the lamellae which circulate around the the Haversian canal. The separation between the lamellae is called lacunae, which is interconnected by canaliculi.

Haversian canal – contains the blood vessels, nerve, and lymph that provides the bone nutrients with interaction with the canaliculi

Lacunae – houses osteocytes (mature bone cells)

Canaliculi – small canals that allow nutrient and wastes exchange between themselves and the Haversian canals.

Ossification (Bone Formation)

Bone formation occurs in two ways: endochondral (endo-inside chondral-cartilage) ossification and intramembranous (intra – within) ossification.

Endochondral Ossification

In our pervious post, we briefly mentioned that the bones in our body were once cartilage. The process in which the cartilage hardens is called endochondral ossification.

Intramembranous Ossification

Intramembranous ossification is another way in which bones are formed. It occurs in undifferentiated embryonic connective tissue (mesenchymal tissue) which becomes bone.

Bone Remodeling or Bone Resorption

Our bone is constantly being broken down and built back up by these cells called: osteoclasts and osteoblasts (used in ossification).

Bone resorption is best described as the breakdown of the bone by osteoclasts which causes bone minerals (calcium and phosphate) to be released into the blood. Bone resorption can occur anywhere and it can happen during exercising or seen in patients with periodontitis. Stimulation of blood resorption is detected by the calcium receptors in the blood, which is monitored by the parathyroid. With low levels of calcium in the blood, parathyroid hormone is secreted from the parathyroid gland to encourage bone resorption.

You’ve guessed it, our body is smart. So smart, that as it notices bone resorption occurs, ossification takes over. Of course, there are situations in which our body loses its imbalance, such as in patients with osteoporosis (increased osteoclast resorption and decrease bone formation). Therefore, it is encouraged for growing children, well all of us, to consume adequate amounts of calcium rich foods (MILK!) to help with bone formation. The logic is, I presume, with high levels of calcium in our system, it is less likely the need of our parathyroid gland to secrete the parathyroid hormone to encourage bone resorption or breaking down our bone to sustain the desired level of calcium in our blood.

The overall function of the musculoskeletal system is simply to provided us with movements and structure of our form. In this post we will focus on the skeletal system covering the macroscopic and microscopic bone structure, bone formation, and bone remodeling. Related posts soon to come are: Microscopic Structure of the Skeletal System: What makes our bones Strong?; Joints; Skeletal, Smooth, and Cardiac Muscle.

Skeletal System:

Our skeletal system can be identified into the axial and appendicular section. Axial skeleton categorizes the skull, spine, and ribcage. Appendicular skeleton section comprises of the arms, legs, pelvic area. I usually remember it as: axial skeleton is within the mid axis of our body, while the appendicular skeleton is anything that deals with the appendages or extension from our body.

This article will focus on: what is tested in the MCAT, how are the questions asked, how is it scored?

Just in case you guys didn’t know, the MCAT is the medical college admissions test and its pretty much THE test you need to take in order to apply to medical school in the US (exceptions are to some international schools).The MCAT requires you to have a basic understanding of the sciences (General Chemistry, Organic Chemistry, Physics, Biology) and it requires that you have a good reading comprehension. Oh, you’ll also need to know how to write!

The test IS multiple choice, but it is NOT like a regular multiple choice. The questions are often tied up to a passage. This means that a passage (literally 4-5 paragraphs of stuff) is presented. From this passage and your basic knowledge, you need to derive with the equations as well as a way to answer the questions preceding the passage. It is kind of like a reading comprehension with science terms. Of course, you’re not a doctor yet, so the passages will never be anything that requires you to diagnose the problem. Then, there are some questions that are not attached with a passage.

In the verbal section questions are always pertaining to the passage. There are no analogies nor fill in the blanks. It is straight up, read and answer the questions pertaining to what you just read. To me, this verbal section is the easiest to do on the exam since the answer is right there in front of you. To practice for it, I would have to say – lots of practice!

Er go…

MCAT BREAKDOWN

(based from American Medical College Application Service)

Physical Sciences – 70 mins for 52 questions (scored 1-15)

Verbal (Reading Comprehension) – 6o mins for 40 questions (scored 1-15)

Writing – two 30 min essays (scored J-T, with T being highest)

Biological Sciences – 70 mins for 52 questions (scored 1-15)

You will have a 10 min break or so in between these sections. You can get a free practice test #3 through the AAMC website.

How is it scored?

Like any other standardized test, your results are deeply reflected among those who took the test on that day.

The average, according to Kaplan is 24 (8 per section), with no indication of the standard deviation.

The Beginning

In search for the right profession for yourself is probably the hardest thing to do (for most people). I have been dilly-dandling for quite some time and finally decided that I’m just going to go through with taking the MCAT before giving up on medical school all together. I wanted this page to be dedicated solely on my process, thoughts, and how I plan to attack the MCAT. Sort of like a reach out for those who are willing to listen. I mean, I can totally share the excitement for the entire route to being an MD fo-sho!

I have visited plenty other MCAT blogs and forums. Most of them are very very very very stressful of a read. Mostly because it’s so negative and demeaning. I do not believe that a person who wants to become a doctor should be afraid of the process of being a doctor. (easy to say..)

The first step to even moving on towards the idea of becoming a doctor, is definitely, the commitment and willingness to pull through – regardless of whatever hardship you may encounter. If you think about it, your willingness to be responsible for another person’s life or well being is far greater and far more hefty than taking the MCAT, applying and going through medical school.

It took me three years upon graduation to plan for the MCAT is solely based upon financial reasons, and eh..a little cowardliness.  However, the armor is on and I’m ready to rumble!

Happy MCAT-ing.

“Nucleic acid” is found within the name of DNA (Deoxyribose nucleic acid) and RNA (Ribose nucleic acid), but aren’t DNA & RNA made up of nucleotides?

NUCLEOSIDE :

is the ribose or deoxyribose sugar bound with a nitrogenous base (purine or pyrimidine) without the attachment of a phosphate group

NUCLEOTIDE

is made of:

1. Five carbon sugar also known as a pentose (pent = five) sugar. This pentose, or five carbon sugar, may either be deoxyribose or ribose. The difference between the two is at the 2nd carbon of the five ring structure. If there is NO “OH” or hydroxyl group attached to that 2nd carbon, it is called a deoxyribose. If there is an “OH” or hydroxyl group attached, it is called a ribose.

2. A tri-phosphate group attached at the 5’ carbon of the pentose

3. A base attached at the 1’ carbon atom of the pentose. This base isn’t just any base, it is a Nitrogen containing ring structure, and can be either purines or pyrimidines.

Purines (found in both RNA and DNA)

Adenine

Guanine

Pyrimidines (in DNA)

Cytosine

Thymine (not in RNA)

Uracil 
(found in RNA)

Examples of nucleotides in DNA are: dAMP, dGMP, dCMP, dTMP.

dATP isn’t considered a nucleotide because there are three phosphate groups instead of one.

Examples of nucleotides in RNA are AMP, GMP, CMP, TMP.

Note: d = deoxy (describing the sugar, ribose), AMP = adenosine mono phosphate, GMP = guanine mono phosphate, CMP = cytosine mono phosphate, TMP = thymine mono phosphate Nucleic Acid

NUCLEIC ACID

This is a sequence of nucleotides covalently bound together. The result is an alternating sugar to phosphate sequence found as the backbone of the DNA or RNA strand. Since each nucleotides are acidic, it is rational to say that a series of these nucleotides would give you an acidic polymer (nucleic acid).

Quick Review: What is the structural difference between RNA and DNA?

Viruses

Viruses, viroids, and prions are all acellular pathogens. They are not within any kingdom and carry their own significant characteristics.

1. obligate intracellular parasite – require a host to cause damage
2. filterable – small enough to be filtrated
3. contains an outer protein coat and inner genome
4. has only 1 kind of nucleic acid (RNA or DNA, but never both)
5. lacks metabolic abilities

Viruses can be found either inside a cell (intracellular) or outside of a cell (extracellular). If it is found extracellular, the virus is called a virion. A virion contains a protein coating called a capsid, which surrounds the core of the virus containing the nucleic acid (either DNA or RNA).  Together with the capsid and the DNA or RNA core is called a nucleocapsid.  Some virions also contain an envelope which is made up of a phospholipid membrane. Both the capsid and the envelope are important in protection and providing shape to the virus.

Continue Reading »

Recombinant DNA technology entails modifying the genomes of organisms.

Things needed:

mutagen – anything physical or chemical that causes mutations in an organism

reverse transcriptase - these enzymes were discovered from retrovirses and its effects on DNA. Using reverse transcriptase, scientists are able to make DNA out of RNA.  These DNA are called complementary DNA or cDNA. After making cDNA from eukaryotic mRNA, scientists are able to input cDNA into the genome of the prokaryotic DNA. One main reason why this is useful is that prokaryotes are not able to excise or remove the introns (junk DNA or noncoding sequences) of DNA in eukaryotes. Since eukaryotes mRNA are already processed and had removed the introns, the newly made cDNA would also be free from introns!

Continue Reading »

Quick DNA Overview

Double helix deoxyribosenucleic acid

Deoxyribosenucleic acid, as you know in humans and in other eukaryotic organisms codes our chromosomes and makes us the way we are!

Similarly, in prokaryotes, like bacteria, DNA makes up their genetic code or in other words what they are.  This includes their function and their appearance.

Universally, DNA contains purines (adenosine, guanine) and pyrimidines (cysteine, thymine, uracil (found in RNA)).  These guys are the bases, in which three of it together will code for a codon, that signifies an amino acid. A sequence of these codons assist with making up a peptide chain. As you know, peptides together, after having been rearranged into a 3D structure is a protein.

As you can see in the picture, DNA’s backbone is connected by phosphodiester bonds (I can get into this later and why its called what its called). These bonds help create the phosphate backbone of DNA. Since phosphate groups (PO₄^-) are negatively charged, a chunk of PO₄^- used as the backbone of the DNA will make the DNA a highly negative molecule.

As you already know, DNA is a double helix. The two strands are antiparallel. Basically, DNA strands are replicated from what is called the 5′ (five prime) end to the 3′ end (I’ll break it down in another post).

5′——-TAG———>3′

3′<—–ATC———–5′

The bases (T, A, G, C) are connected to each other by weak hydrogen bonds.

Continue Reading »

Similar to Gram stain, acid fast stain, and flagellar stain, capsule and spore stain are used to differentiate between microbes.

Capsule

Purpose: Our immune system contains neutrophils and macrophages that fight against foreign bodies or antigens. Capsules, which contains mucoid polysaccharides or polypeptides, protects bacterial cells against our immune system (macrophage and neutrophils). Capsules are also resistant to stains, hence capsule stain techniques are staining around the cell and not the cell wall or membrane directly (different from Gram and Acid fast stains).

Acidic or Negative Stain – used to stain the background

• Nigrosin
• Congo Red
• India Ink

In this first step, there is NO heat fixing because it will cause the cells to shrink, which will give a false reading of a white halo around the cells.  This may cause a misrepresentation of a capsule.

Cytoplasm, basic stain

• Maneval’s
• Carbol fuschin

The unstained, halo, seen between the stain in cells are the capsule.

Continue Reading »

Eukaryotic microbes consists of: protists, animals, fungi and plants.

In this post, we will be looking at fungi (mostly molds and yeast), protozoan, and helminths.

Fungi are organized into two categories:

Ascomycotina (sac-like fungi such as penicillium, aspergillus, yeast) and zygomycotina (molds such as rhizopus stolonifer)

Fungal Anatomy

Yeast: Candida albicans

Yeast

asexual reproduction- budding

Molds

asexual reproduction

• sporangiospores (sac) zygomyces
• chlamydospores (walled in)
• conidiospores (no sac) ascomyces

Mold: Rizopus zygospore. Zygospore is where the cytoplasm of two mating strain fuses.

Mold: Ascomycotina: Aspergillus conidiophores

Molds: Penicillium: Conidiophore and Conidia

Please see the following pages for Protozoan Anatomy and Helminths

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There are various ways in assessing DNA and its components. One widely used is electrophoresis, which utilizes electricity to measure the length of DNA fragments. This mechanism can be used for identification either for unknown diseases or human DNA, determining an inherited disease or finding cures for such diseases (National Health Museum).

What is Electrophoresis?

How is DNA assessed?

See image for specific column for details. The ladder is usually placed nearest the right or left side of the gel. Conducted by Kendall McCarthy, Chloe Yap, and Amy Truong

HOW TO READ THE RESULTS

The Gel was ran at approximately 113-117 volts.

Every ladder has its own defined or known measurements of DNA (usually measured in base pairs). In this ladder, there are 8 segments seen, which are measured at:

(*farthest from the well at middle of photo)

570 bp = 0.570kbp*
725 bp = 0.725 kbp
2027 bp = 2.027 kbp
2322 bp = 2.322 kbp
3000 bp = 3.000 kbp
6557 bp = 6.557 kbp
9416 bp = 9.416 kbp
23,130 bp = 23.130 kbp**

(**closest to the wells at the bottom of the photo)

Closest to the wells (bottom of the photograph is the higher DNA fragments). Remember, the larger the DNA segments, the greater the bp, the slower it will travel due to its inefficiency in traveling through the lattice matrix of the Agarous Gel.

As you can see, each column has a few or none (blank column) segments. It is expected that the blank has none considering there shouldn’t have been any DNA in there, if there were any sort of contamination in the blank, any band shown in the blank would then be disregarded in the other columns as well. However, usually, we would have to redo because it is dependent upon how the contamination occurred (ex: not changing tips).

As you can see in our unknown, there are 3 bands that are arranged similar to the bands found in BCV. It is then “presumed,” from this procedure that the unknown virus is BVC. In lab, we would consider to do other techniques to assess for the true congruency between BCV ad the unknown virus. Assuming that unknown virus is BCV is not classified as truly conclusive. However, for the sake of this experiment, it is.

Measuring the band segments is simple, you literally try to extrapolate the bands according to the ladder. In a rough estimation, we found:

CPV: 650 bp and 2322 bp

BCV: 650 bp; 2322 bp; and 3000bp

MIOV: 2027 bp

Unknown: 650 bp; 2322 bp; and 3000bp

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The differences between eukaryotes and prokaryotes are described within the last two former posts. The following table is a reflection and minor edited table found on Pg. 87 of Microbiology with Diseases by Taxonomy, 2nd edition, by Robert Bauman., in Table 3.4 and 3.5.

Click Image to Zoom: Refer to Table 3.4 in the textbook or previous posts for details of organelle functions

Click to Magnify: Refer to Table 3.5 on Pg. 87 of the textbook

Prokaryotes, as mentioned earlier are cells containing NO nucleus. I will write a post on the major differences of prokaryotes and eukaryotes later.

In microbiology, there are plenty of research under bacteriology (study of bacteria). In this post, we will focus on bacteria (which is made up of eubacteria & archaebacteria).

Relative size of bacteria (measured in micrometer µm)

• mycoplasma – bactera like (no cell wall) ~0.4 µm
• genitalium – acts as a contaminant in labs ~0.4µm
• Haemophilus influenza f (considered as a true bacteria)~0.2um
• Staphylococcus aureus* ~ 0.9 µm
• Escherichia coli* ~ 1.5 µm
• Bacillus megaterium ~4.0 µm

*Note: both are used as controls in Gram’s stain

Based upon these numbers we can say that bacteria are really tiny! Continue Reading »