Chapter 21 Helpful Hints!

Alright pretty people, my last blog. So many memories! Well, enjoy!

Ok, so I liked this video because it related genomics and proteomics to cancer, and we know cancer pretty well from previous chapters. He used proper terminology and explained genomics and proteomics in a nice simple way. Some of the terms he used were new to me, but after looking them up I found that they were just diseases. He clearly distinguished between proteomics and genomics. Lastly, he predicted how much information we could learn from genomics and proteomics in the future which was astonishing to me! This is a nice quick video to watch to learn a few facts about genomics and proteomics.

So, this video talked about transposons. It had very dramatic music in the background which was interesting. Anyway, yeah the video talked about transposons and the different types of transposons we have. He also talked about DNA fingerprinting and how people in families would have more similar transposons, than two random people. From there, he explained how two different species who are closely related have more similar transposons than less related species. He also talked about Alu, and how scientists have used it for all kinds of research. This is another short video to watch and pick up some quick easy facts. Enjoy!

Gene Families and Male Infertility?

I know, I know reading my title peeked your interest. You are wondering how could gene families and male infertility possibly be related? Luckily for you, I shall explain how the two are related. You're welcome.

So as this article explains, researchers from the University of California at San Francisco have found the head of the family of genes that have been linked to some male infertility cases. The gene which was name BOULE was found in mice, fleas, and humans. BOULE has been found to be involved in creating sperm during meiosis. As I previously said, BOULE was found to be the head of the gene family. Two descendants of BOULE that scientists have already discovered are DAZ and DAZL. Both DAZ and DAZL have been linked to male infertility.

In fact, 13% of male infertility cases are because of mutations in DAZ, yet strangely, the gene does not does not appear to be essential for sperm development. The exact role of DAZL is not yet known in humans, but in frogs it is fundamental in the development of both male and female germ cells. New studies show that BOULE may actually be required for mature sperm development. If defects in BOULE are proven to be what caused the male infertility, then gene therapy might be attempted to try and solve the male infertility problem.

People's Plasma Proteome

There I go with my clever alliterations for titles once again... I know you are super impressed so I shall give you a second to contain yourself... Ready? Off we go!

So plasma is on of the main components of blood. Some people even sell theirs for money! As this article explains, the human plasma proteome has the potential to revolutionize disease diagnosis and therapeutic monitoring. Not only is plasma a great specimen, but it also has the largest and deepest version of the human proteome. Plasma obviously contains plasma proteins, but it also contains proteins from all other tissues, many distinct immunoglobin sequences, and extraordinary range of proteins.

At the moment, only 289 proteins have been reported in plasma, but there are so many more to be found! Right now, the only thing limiting scientists in getting all of these proteins is technology. Currently, we do not have the needed technological insight to get all of the proteins. Fortunately, recent advances in survey techniques will yield at least double the amount proteins we can find. Many of the proteins that we can and will find are indicative of human disease, so these proteins will definitely help us in understanding and combating many diseases. Even with all of these discoveries, only a few proteins are used in routine clinical diagnosis, and the rate the FDA allows these protein tests has declined over the past few years. Despite all of this, hopefully we can find and understand new proteins so we can fight off and combat disease.

Chapter 20 Helpful Hints!

This is a nice virtual lecture on gene cloning.  He explains all of the steps in gene cloning and also talks about organism cloning. After lecturing with just notes on the board, he brings out several diagrams to help pull all of the ideas together. The lecturer also cracks a joke every now and again, which is always nice! He uses all of the proper terminology and asks/presents those sorts of application problems that we all know Dr. Weber loves putting on exams. The video is a nice, quick watch.

Ok so the speaker speaks kind of slowly but alas, what can one do? So despite the speaker's slow voice, he gives quality information. Now when I say the video breaks down genomics, I mean it really breaks down genomics. It gives  information like DNA stores information and basics like that. However, it builds on these basics so that one understands genomics just like one understands what a gene is. This video is one of the ones that really help you understand core concepts, so that all other aspects can be understood better. Enjoy!

Crazy Canola!!

Again, with my clever alliterations. People ask me all the time how I come up with them and I just don't even know... Anyhoo, now that you have collected yourself from the excitement of my title, we shall begin!

So genetically modified organisms (GMOs) are organisms that have changes in their DNA due to genetic engineering technologies. So when one thinks of these organisms, a laboratory environment probably comes to mind. However, as this article explains, GMOs are popping up in some unexpected places. In Langdon, North Dakota a couple ecologists saw a yellow canola plant growing near a parking lot. They picked some of the plants and after conducting some tests discovered that the canola was genetically modified!

Surprisingly, this isn't a rare find. North Dakota grows loads of the canola both conventional and genetically modified. It is a weed and its seeds are used to make canola oil. The canola's scientific name is Brassica napus var oleifera. What may shock you even more is the fact that  almost everywhere the ecologists and their colleagues went, they found more of the GM canola! They even found the transgenic canola in fields in the middle of nowhere.
So what does this mean to you and me? This means that transgenic plants are probably cross-breeding in the wild and swapping introduced genes. Depending on your views on GM foods, this could very easily frighten/worry you, or not affect you at all. Now GM canola has been found everywhere from Canada to Japan. However, this is the first time the plants have been found to evolve in this way. Ecologist Cindy Sagers of the University of Arkansas, explained that there are new combinations of transgenic traits and the best explanation for this would be that the traits are stable outside of cultivation and that they are evolving.
Most of the transgenic plant populations die out quickly without continual replenishment, but the canola plant is not having this problem. It is able to hybridize with at least 2, and possibly 8, different wild weed species in North America.
As of now, there is no evidence to say whether herbicide resistance genes will either increase or decrease in fitness. Weed scientist Carol Mallory-Smith of Oregon State University, explained that the biggest concern is whether or not these traits will increase invasiveness or weediness and traits such as drought tolerance, salt tolerance, heat or cold tolerance. This canola plant is not the first escaped transgenic population, and due to advancements in technology, it probably won't be the last

Gotcha GMOs!

Wow. You are just awestricken by my title. Short, sweet, terse (you like that SAT vocab, I know), to the point, yet attention grabbing. I'll give you a few moments to collect your thoughts. You ready? Off we go!

So as you know since we did a major lab on them, GMOs are genetically modified organisms. That be as it may, a genetically modified organism, is an organism whose genetic material has been changed, altered, or modified using genetic engineering techniques. This article talks about how people are new trends in detecting genetically modified organisms.
Food is necessary for life, so everyone eats. (Wow, what a groundbreaking statement.) Anyway, since everyone eats, one cannot go mess around with food and sell it to people. This could lead to many people dying. Hence, just like with other aspects of food, genetically modifying food has to be authorized and regulated.

 

Now as time goes on, the production of genetically modified organisms has been increasing. There are so many new technologies that allow for the development of GMOs, but at the same token, advancing technology is also accounting for the many news ways of detecting GMO. Most of the methods involving GMO involve Polymerase Chain Reaction (PCR). After reading that little tidbit I felt all scientific and connected because we know what that is and we have done this! Anyhoo, as I was saying, PCR is the preferred method in detecting GMO because it can detect even minute amounts of the transgene material in the foods we eat.

It was also interesting to learn about the other methods used to detect GMO, as we already know about PCR. One method is based on quartz crystal microbalance piezoelectric biosensors, dry reagent dipstick-type sensors and surface plasmon resonance sensors. That was a mouthful... Another method involves using visible/near-infrared (vis/NIR) spectroscopy or mass spectrometry combined with chemometrics techniques. Yet again, another mouthful. So yes, to combat the increasing amount of unauthorized GMO products being produced, authorities are exploring various methods to detect the GMO products.

Chapter 18 Helpful Hints!

I love Khan Academy! So this is a nice lecture on viruses! In true Khan Academy style, he breaks down everything there is to know about viruses. The video goes into the main different types of viruses, and the steps the virus takes from entry to release. There were also many situational example presented in the video, which I always like because many questions on the exam are situational. Always a nice lecture to watch or just even listen to when you have like 20 minutes.

Ok, well I know this video doesn't exactly use proper terminology, but I really liked it! I actually found this video for fun on my own time... Yeah I need to find things to do with my time. So I found this video and really liked it! This video was made for the masses so they had to I guess put many of the terms in layman's terms... For example, they referred to ribosomes as "peanuty" things. I took the improper use of terminology almost like a challenge to see that I knew all of the proper names! So, i really liked the video because the speaking was so simple but also gave such amazing visuals! Enjoy!

Viruses WERE Odd Little Things...

Awww did my title make you feel all warm and gooey inside but also made you want to read more? I know, I know. It's ok, it's ok. I understand! You ready? Off we go with some blogging!

Ok so once again viruses  have come to mind-blow us all. As we know, there is a huge debate on whether or not viruses are alive because they only contain the necessary components to reproduce, and can only do cell by invading another cell. Now viruses are generally tiny little guys, that will multiply and mess some stuff up. Please note how I said they are little things. Most viruses are much smaller than their host cells and almost fully rely on processes in the host cell to reproduce. Along came these viruses, as explained by this article, and they just kind of threw all of this previous knowledge to the wind! These things are huge! They also come chock full of lots of DNA which encodes for a bunch of proteins. One great example would be Cafeteria roenbergensis. Oh my gosh perfect time to make a joke about it being cafeteria and eating a lot so that's why it's big... But I won't. Oooh! Even better I can reference Urma!! Yeah I like that better!

Look at that an artist's rendition! I'll even give you an actual picture! Lucky you!!

Those lovely pictures were pictures of Cafeteria roenbergensis. Scientists nicknamed them CroV. Based on their size I think it's obvious what I would nickname them... So CroV is the marine largest virus known to man at the moment! It is even bigger than some bacteria! CroV has a genome of 730,000 base pairs, about 544 predicted genes, and about 22 of these genes codes for tRNA's. CroV also does something special because it takes care of its DNA just like our cells do. Many smaller viruses do not take care of their DNA in the least bit, and often exploit the mutations which occur. CroV takes care of its DNA, just like we do! Its genome encodes for DNA repair enzymes, which actively repair the virus's DNA. Scientists believe that the large size is an advantage because amoebae eat the virus and then it gets to work!
CroV falls into a class of viruses called "mimiviruses" or "giant-viruses". French scientists gave the name mimivirus because they thought the viruses were mimicking microbes. As time has gone on, scientists are finding more and more of these mimviruses all around the world, and the ocean is filled with them!

Persistent Pesky Plasmids....

You are just luh-ving the alliteration. I know, I know. I'll give you some time to simmer down.... You ready? Off we go!

Ok so this article talks about plasmids! It's kind of funny how we always learn about stuff on the BioLeague tests after the tests. I remember staring at the test and being like, "What on Earth is a plasmid..." Woe is me... But I digress! So back to the article... Yeah it talks about plasmids!

So there was a study which done to help more clearly identify the link between farm-generated animal waste and the dissemination of antibiotic resistance in microbial soil communities, by mobile genetic elements. The study used electromagnetic induction (EMI) surveying of a soil sampling that was broiler chicken farm assisted from a chicken-waste-impacted site and a not-so affected site. The EMI showed that there were differences between the two samples in pH and tetracycline resistance (Tc(R)) level in the culturable soil bacteria. Also,  several tet and erm genes were sparsely or highly present in the soil.

 Alright so here comes the interesting part. I know you're thinking, "And where are the plasmids..." So, in all of the aspects I mentioned above there really wasn't a huge difference in the marginally affected site and sites in the pristine regional forest sites. However, when the farm was operating, tet(L), tet(M), tet(O), erm(A), erm(B), and erm(C) genes were detected in the soil affected by waste. Two years after all waste was removed from the farm, tet(L), tet(M), tet(O), and erm(C) genes were still detected. Woah! If we removed them, how on earth could they still be there? Those sneaky little plasmids is how they are still there!
Being as though scientists are just constantly asking more questions, they delve even deeper and found out more information. Species of Bhargavaea, Sporosarcina, and Bacillus were the plasmid's hosts. The plasmid's mobilization (mob) gene was quantified to so they could estimte how much of it was in the soil. The ratio of tet(L) to mob changed from 34:1 at the beginning of the two years to 1:1 at the end of the two years.