Sunday, May 28, 2017

Reflection For Week of May 22-26 -- Genius Hour Update #3

Phew, a lot has happened this week, and all of it has been interesting!  First, when I came back from the weekend and looked at my mini plates to see if the bacteria had grown blue, they had not!  Given that the methylene blue (MB) was supposed to kill the bacteria and it appeared that the bacteria were actually metabolizing it, I decided it would be good to test this phenomenon again.  I made up two plates with half of the agar blue and half of it normal, and one plate (accidentally, BECCA!) that was more of a marbled look.  I then put blue bacteria from my original MB resistant plate on one of the half-and-half plates, blue bacteria from my original MB stock plate on the other half-and-half plate, and stock bacteria from the tube on the marbled plate.  When I checked after 24 hours, all of the bacteria had grown on any agar that was without MB.  When it came to bacteria growing on the MB, however, results varied.  The resistant E. coli had grown a bit on the MB agar, but none of the stock bacteria had grown on the MB agar, regardless of whether it was from the tube or from the original MB stock plate.  I am not sure as to why this happened.  It is the original desired result, but it’s weird that it didn’t happen originally, and only worked on the stock bacteria this time.  I will keep researching and see if I can think of anything that differed in this trial from the last one.  At 72 hours, the results were the same on the two half-and-half plates, but the growth on the marbled plate had changed.  Not only did it now have mold, there were also now big and large colonies all over the plate.  Each colony was a different shade of blue, depending on the amount of MB available for it to pull up in the agar.  The colonies in the dark blue part were very blue, whereas the ones in the lighter blue area were lighter blue.  Even the colonies that grew in a basically normal agar grew with a blue tint, because they drew MB from the agar close by, I’m assuming.  This confirmed that the bacteria seem to be somehow metabolizing the MB.  When researching why/how they might be doing this, I found an article that said they may be reducing MB into a colorless form.  I’m a little confused as to why/how they are doing this since MB was supposed to kill them...but I will keep researching.  In the meantime, I also made a liquid environment for my bacteria to see if we can see anything further with that.  I added MB to one of the flasks, and it would be amazing if I showed up Monday to find the liquid clear, or at least a lighter shade of blue.  Lastly, today I tried to do an oil immersion in order to better see the E. coli, but wasn’t able to see anything.  I repeated the procedure with stock bacteria from the tube and was successful, so I will try it again on Monday with the blue bacteria, this time somehow suspending it in liquid, because that worked well with the stock E. coli.  

Sunday, May 21, 2017

Reflection for Week of May 15-19th -- Genius Hour Update #2

This week I ran my experiment, and, as with most experiments, there were some definite hiccups.  I plated my bacteria on Tuesday and started my experiment, using a blue binder divider over a small, white light to create the desired blue light effect.  I was worried that the light might die overnight, but it turned out this should not have been my primary concern.  When I came into school the next morning, the light was completely fine, but the stock bacteria was not.  There was absolutely nothing growing on any of the stock plates, even on the control plate, so Mrs. Cole helped me make up a new batch of stock bacteria, and I re-plated.  When I checked the next morning, the stock bacteria was growing no problem, perhaps too well.  The bacteria growing under the blue light showed absolutely no signs of growth inhibition, and I was hoping to at least see a little less bacteria on those plates than on the control plates, but both were basically full-on lawns.  With the methylene blue, the story was a little different.  There was definitely not the large-scale growth inhibition I was hoping to see, but both the stock and antibiotic resistant plates with the compound were made up of very defined dots of colonies, rather than the complete coating that happened on the blue light plates. Overall, in response to my question, I would say the methylene blue worked better, although, with the available equipment, neither method is an effective way of combating antibiotic resistance bacteria.
Additionally, all of the colonies except one large one were blue, and so had obviously taken-up the dye.  Mrs. Cole and I thought it would be interesting to see if the bacteria continues to grow blue if it is plated on a normal plate of agar, so I took some of the methylene blue bacteria and plated it on some mini plates to leave in the incubator over the weekend.  I’m looking forward to seeing how that goes!

Saturday, May 13, 2017

Reflection for Week of May 8-12th -- Genius Hour Update #1

So, I, per usual, have run through a number of ideas in order to arrive at my final one.  I started out looking at comparing the effectiveness of natural remedies to the effectiveness of modern medicine.  I found a study looking specifically at the effectiveness of green tea and a modern heart medicine at lowering heart rate, and was thinking perhaps I could use something like ginger as well, or maybe compare different teas, but then I stumbled on a new and more interesting idea.  In researching other natural remedies, I found that sage and rosemary both have active ingredients that serve as neuroprotectors and help enhance memory.  I was thinking I could use the mice, expose them to the two different plants, and see if that exposure decreased the time it took for them to get through a maze.  But then I decided that I didn’t want to deal with the increased numbers of variables that using animals brings.  At home, having run through several different ideas, I was feeling a little desperate, and asked my dad at breakfast if he could think of anything.  He mentioned phototherapy having a positive effect on metabolism, so I came into school that morning and looked up phototherapy.  I found a study that detailed how blue light kills antibiotic-resistant bacteria, then stumbled on another than detailed how the compound methylene blue does the same thing.  What it seems no one has done, however, is compare the effectiveness of the two, so that’s what I will be looking at.  

Now that I have my question (which will be more effective), I have begun looking at my procedure and laying it out.  I plan using plates with antibiotic resistant E. coli and stock bacteria.  I will have a control with no substance present (with one plate antibiotic-resistant, one plate stock bacteria), two plates with antibiotics, two plates with methylene blue, and one exposed to blue light. I'm doing pretty well drafting up my procedure, and am hoping to start this week. I guess the only problem with that is that I don't know how long it's going to take...Away, I'm really looking forward to this!   

Sunday, April 30, 2017

Reflection for Week of April 24-28th

This week was a mashup of material from Domains 5, 6, and 7, because we finished up all of our AP Bio learning for the test (the learning never really stops!).  We covered neurons very basically, took an introductory look at communities and ecosystems, and did a lab on transpiration.  
Monday we looked over the transpiration lab, answering basic questions about our thoughts on how the number of stomata and the environment of a plant affect the plant’s rate of transpiration.  We also looked at the stomata on leaves by using nail polish to obtain an imprint of sorts of the leaf's surface.  For homework,  we completed a POGIL on neuron structure (Domain 6, specifically 6.6 mostly), which was a bit difficult in places, because I think it is designed as more of a review tool and assumes you know certain things, like the parts of a neuron.  With a little help from the internet, however, I feel good about the material.  
Tuesday was lab day #1.  We set up our lab with our chosen variable (plant type for my group) and made initial observations of the amount of water in the tube.  We came in throughout the day for the next 48 or so hours to check our water levels in order to track each plant’s rate of transpiration.  Homework for Tuesday night was a Mr. Anderson vodcast BBECPO, or the organization of life.  This one was on communities (Domain 7) which wasn’t too difficult to understand, although I felt a little confused on the difference between species composition and species diversity at first.  
Wednesday was lab day #2.  We completed observations and then discussed both the neuron packet and the communities packet.  The homework was another Mr. Anderson BBECPO vodcast, this time on ecosystems.  This one talked about how different populations interact in food chains and how this determines the carrying capacity of each population, as well as how to measure life in a place using primary productivity (Domain 7).  I feel like I understand this well, but perhaps am missing the purpose of primary productivity and why it exists.  I will, of course, ask Mrs. Cole.  

Friday was a wrap up day, with work on the lab and ecosystems occurring.  This mishmash of stuff all relates well to the big picture of biology and our course this year, with it being like looking at the forest rather than the trees (well, neurons were more like the trees, but the Domain 7 stuff is more like the forest).  Neurons allow us to interact with and be aware of our world and our body, which is comprised of all of the molecules we learned about in unit 2, and which is controlled by DNA as learned in Unit 4, and which runs using the energy processes we learned about in Unit 3.  An organism's ability to interact with its environment is what determines its success, as we learned in Unit 1.  The study of BBECPO is how all of this comes together and is organized, and so is a perfect ending for our exam portion of the course.  

Thursday, April 20, 2017

Reflection for Week of April 10-14th

HEART WEEK!  Aaaaaaaaaand...wait for it...somehow I didn’t end up unconscious on the floor or with my face in the sink!  Yay me!  
We started off the week preparing for our actual dissection days by watching a really cool, but also really gross, video on heart transplant.  I think I was more disgusted watching that than by actually cutting the deer heart open myself.  The guy narrating was rather weird, and very aggressive when it came to mimicking heart surgery.  I hope no surgeon ever performs heart surgery on me as aggressively as he did on that poor pig heart; it was disturbing.  
Tuesday was the first heart day, and we all gathered around to watch Mrs. Cole identify the parts of the heart and do a bit of dissection.  And then it was our turn.  We worked to identify the different parts of the heart, like the apex, the pulmonary artery, and the aorta, and then began the dissection.  With the heart cut open, we were able to see the left and right ventricles and atria and the valves that separate them, as well as the heart strings.  We measured the sides of the ventricles, and found that the left ventricle wall was 1.5 times as great as that of the right ventricle!  That makes sense though, with it having to send blood to the entire body (6.6).  But still, wow!
This week we also reviewed Vodcasts 5.1 and 5.2, which dealt with gene regulation and development (5.1-5.2).  While much of this material makes sense, it was a lot of new ideas all at once, and when we discoed, we were discoing 4.12 as well as these two, so we didn’t get to spend a lot of time on any one thing. I am feeling rather overwhelmed and have a TON of questions (what's new haha).  I’ve already gone over everything once over break, and am still feeling this way, so I really need to work on that.  The concepts I need to work on are understanding how positioning happens (hox genes versus the simple order of genes: do both of these affect position?), neurulation and organogenesis, how positioning works in plants, and secondary growth.  While I largely understand the rest of the concepts, I need to work on the specifics; I do not know them well enough to be tested on them or be able to apply them to anything.  I will work on that and will have a list of questions to ask Mrs. Cole when we get back (be ready haha).  
The work we did this week connects to the overall course because the heart is the kind of like the powerhouse of the body and the process of circulation requires key concepts we learned earlier in the year like bulk flow, diffusion, and gradients.  The pumping the heart does is how we move molecules that we learned about in unit 2 around our body in order to supply our bodies with the energy that we learned about in unit 3.  Our four chamber heart is the result of evolution, as discussed in unit 1, and is coded for by our DNA, which we learned about in unit 4.  Gene regulation and development also deal with all of the units, because our DNA plays a crucial role in both, and both code for molecules discussed in unit 2 that provide the energy we learned about in unit 3.  

Sunday, April 9, 2017

Reflection for Week of April 3-7

This week, we began domain 5, Regulation, which I think will be a very interesting unit, once I get a handle on the info (little overwhelmed currently).  So far, we have looked into the regulation of genes and development (5.1-5.2), and how organisms maintain homeostasis in a variety of areas (5.3-5.5).  All of these topics are super fascinating, albeit it complex.  I definitely could happily take an entire course on either of these topics studied so far.  
The week began with a look at stickleback fish, which I found intriguing and felt pretty good on.  The only mutations we had discussed up until now are those that affect an expressed gene and create a new allele.  This packet looked at what can happen if a gene that isn’t directly expressed is mutated: a regulatory gene.  Here, the proteins that binds to the regulatory gene will no longer be able to do so, and then the regulatory gene will no longer be able to go and “turn on” the coding gene.  A major point the packet made was that there are different regulatory genes to turn on a coding gene in different parts of an organism, and therefore a gene may be expressed in one part of an organism but not another.  Through this packet, I also learned that a gene can be expressed in two different parts of the body but through different proteins, due to intron editing.  We had learned that this was possible earlier in Unit 4, but this really brought the idea together for me.  This packet, and this unit so far, has been really doing that for me: bringing together bits and pieces of other units that I didn’t understand the reasoning behind and answering all my questions.  
Wednesday through Friday we worked on a cooperative handout on physiology of animals and plants.  My group researched gas exchange, which, as it turns out, is pretty interesting.  Not going to lie, I wasn’t super enthused when I first started.  I feel very solid on the parts I researched, but I definitely need to read over and solidify the rest of the the presentation.  Friday, we all looked over other groups’ handouts.  This is where the whole, “I can’t read and listen to and talk to people at the same time” and “I process things rather slowly” thing became incredibly evident.  I read the first handout pretty thoroughly and feel well versed on nutrition, but the rest of them, wellllllll...Basically I had to blast through those and make some comments, but I didn’t get to take things in.  So yeah, gotta go back and look those over, especially circulation, so that, even if I pass out or throw up later this week, I will at least theoretically understand everything I was supposed to be learning through dissection before I hit my head off the counter/find solace in the toilet.  (To be clear, I’m planning on neither of those things happening, but I also want to acknowledge the worse, and very possible, case scenarios.)
Lastly, we had several vodcasts to do this week, and wow, these threw me for a loop.  I didn’t reeeeeally understand large portions of Vodcast 4.12, and then Vodcast 5.1 hit.  5.1 built upon Vodcast 4.12, so it was like, DOUBLE WHAMMY, you didn’t really understand the first one, well here’s another one, haha!  But that’s my fault for not clarifying parts of 4.12 that I didn’t understand, and I know that looking these two lessons over and asking questions will get me right back on track, so I'm not majorly worried.  Vodcast 5.2 explored how both plants and animals go from being two gametes to a zygote to a fully developed organism, and I actually feel pretty good on these ideas overall.  Sure, I need to focus a little more on the details and fully understanding them, but I feel that I have a pretty good start, because I took the time to process the vodcast as I was doing it, rather than rushing through like I had to with 4.12 and 5.1, due to a time crunch.  I will take the time to go back and revisit those two over vacation, for sure, and hopefully sooner, but probably not, because I will be focusing on studying for our test Thursday.  
As I mentioned earlier, the information we have been learning in this unit has really been some of the missing puzzle pieces from other units, and I think it fits seamlessly.  In the stickleback packet, we went back to unit one and evolution, this time learning the "why" behind the "what."  This idea of regulatory genes wraps into units four, when talking about genetics, and unit two, when talking about the proteins that are both needed to turn on the regulatory genes and that are produced when regulatory genes activate coding genes.  Our work with homeostatic regulatory systems also ties in closely with all of these units, as well as unit three.  Nutrition is a regulatory system that is especially closely aligned with unit three.  And development, as discussed in 5.2, also wraps into all of the units, with evolution being a result of differences in development, often times caused by genes, and not enough of a life molecule, like a protein, being present.  All of this needs energy.  

Saturday, April 1, 2017

Reflection for Week of March 27-31

This week focused on diving deeper into genetics and patterns of inheritance, and solidifying our use of Chi Square Tests with respect to genetics (4.5-4.10).  We began Monday with our big fruit fly virtual lab, and continued it into Tuesday and Wednesday.  This dealt with largely basic Mendelian patterns, as well as X-linked genes and homozygous fatal phenotypes (4.5 and a bit of 4.6), and was my favorite part of the week (although the simulation of the flies hatching really grossed me out).  This lab was largely review of material from sophomore year in a new setting, but we also learned lots of new material this week via vodcasts.  Vodcast 4.10 dealt with extending our understanding of how traits can be expressed and passed down, with patterns like epistasis and pleiotropy, as well as penetrance and expressivity.  Vodcast 4.11 focused on human genetic conditions like Tay Sachs and Huntington’s, and whether they were autosomal or sex-linked, and dominant or recessive.  Vodcast 4.12 focused on gene regulation in prokaryotes and eukaryotes, and how this leads to differentiation in eukaryotes and efficiency in both pro- and eukaryotes.  
I think I did well with the material this week.  I understood the fly lab, and really enjoyed trying to figure out what kinds of traits I was dealing with.  My Cross #4 was rather disappointing, however, because it was the same X-linked recessive pattern as Cross #3.  I had to cut my loses though, as I was running short on time this week.  That seems to have become a prevalent theme in my life.  Anyway, I also feel pretty good on Vodcasts 4.10 and 4.11, but 4.12 was almost entirely new material and was a doozy for my brain.  I think with some serious looking over, Mr. Anderson videos, and questions for Mrs. Cole, I’ll feel good with it next week.  I also felt very good on the majority of the Genetics Problems Set #2, but I definitely need to wrap my head around the whole gene mapping thing a little better.  Based on Mr. Anderson’s video, I thought that all the frequencies would add up exactly, but then they didn’t, so I was confused for a bit.  It makes more sense this way though, as I was having a hard time seeing how frequencies could be translated directly into distances.  I will look at the fungus lab again tomorrow, as I think that will also help me understand gene mapping.  
As I said last week, the purpose of DNA is to code for the genes that comprise us, and with the material this week, we now know the majority of our traits are not Mendelian.  Understanding how genes are expressed and what acts on them (parents, environment) is key to understanding how populations evolve and are acted upon, as was studied in Unit One, how the body synthesizes the proteins, carbs, lipids, and nucleic acid as discussed in Unit Two, and how our body is able to create and store energy, as was looked at in Unit Three.  Because of how important genes are, gene regulation is absolutely imperative to understanding life.  This is how we get different organisms, how we don’t all look the same, how we change over our lifetimes.  This is a field that is incredibly relevant right now (not that all of biology isn’t), and that makes it so, so interesting.  We never know what we might learn next.