Chapter 16 Post

Hola! This chapter is all about simple patterns of inheritance. We all know about Gregor Mendel (aka the father of genetics) and his basic pea plant experiments, so I won't waste any time talking about that.


I found the section about sex determination pretty interesting. Humans have either two X chromosomes (if you're female) or one X and one Y chromosome (if you're male). But this isn't the case for all animals! How and why are sex chromosomes different? This article does a great job of explaining everything. Hermann Henking first studied wasp sperm cells in 1891. He observed that some cells had 12 chromosomes and other had only 11. He also noticed that the 12th chromosome acted different than the other 11. Puzzled, Henking called the 12th chromosome the "X element" because of its "unknown nature." 


Henking found that the "X element" couldn't be found in female grasshoppers and hypothesized that the "X element" must help determine the sex of insects. Over ten years later, Nettie Stevens studied numerous beetle species and their inheritance patterns. She also hypothesized that chromosomes had something to do with sex.


Besides the XX-XY system that we have, there are also the XX-XO and ZZ-ZW systems! 


XX-XO system

• Found in insects such as crickets and grasshoppers
• Females carry two X chromosomes (XX) and produce gametes with X chromosomes
• Males carry only one X chromosome (XO) and produce some gametes with X chromosomes, some gametes without sex chromosomes
• The number of X chromosomes determines maleness

ZZ-ZW system

• Found in birds, snakes and some insects
• Females carry the mismatched chromosome pair (ZW) 
• Males carry the identical pair (ZZ)
• Similar to humans' XX-XY system, except that females have the mismatched pair

The picture above shows the Punnett Squares of different sex determination patterns

Another topic in this chapter I found interesting were sex linked genes. The X chromosome of humans is a lot bigger than the Y chromosome. The X chromosome carries over 1000 genes while the Y chromosome carries less than 100 genes. That's a huge difference! It helps to explain why many genes are found on the X chromosome but not on the Y. These genes are called X-linked genes. The book mentioned Morgan's crosses of Drosophila melogaster and I decided to go on PubMed to research this more in-depth. This article describes how eye color mutants contribute to our knowledge of enzymatic pathways and vesicular transport. It also mentions the studies of mutations aiding organogenesis. In case you didn't know, organogenesis is the development and production of the organs of a plant or animal.

The eye (particularly of the Drosophila melanogaster) has one of the greatest experimental fields and phenotypes. The fly eye is comprised of unit-eyes called ommatidia. I looked it up, and each omnatidium has photoreceptor cells, in addition to support cells and pigment cells. Omnatidium structure is very complex, and any minor mutations will physically appear on the ommatidium. Studying eye mutants helps scientists to further understand signal transduction, cell polarity and programmed cell death.  Drosophila melanogaster is a great experimental system because of its multiple identifying genes.

One section of the chapter that I had to spend a little extra time studying was pedigree analysis. Pedigree analysis involves looking at a pedigree for a specific trait and analyzing it for multiple generations of a family. It takes some time and practice to understand a pedigree, but once you understand a few concepts, everything is a piece of cake!

The video above gives some great pedigree analysis practice. And if you look in the bottom corner, something may look familiar. Screencast-O-Matic! Haha I guess other people do use it. The lady in this video takes you step-by-step at looking at different pedigrees. What was great about this video is it starts really basic, and doesn't show a giant confusing pedigree. It only shows small pedigree sections, so you won't get confused. It also talks about the difference between autosomal and sex-linked traits on a pedigree. While doing the ConnectPlus homework, I had to determine the types of traits shown on different pedigrees. After reading the book, I wasn't sure which was which. But after watching this video, I understood the concept. It is a little on the long side, but it's a good quality video. Even if you understand pedigrees well, I would still recommend watching it because it's wonderful practice.

That's all for this chapter's post! 

Chapter 15 Post

Hello! Mysterious person, I'm Emily. Oh wait, you already knew that, silly me. Welcome to my blog, if you've never seen it before. It's called, "Em Fu The Science Guru!" Get it, like Bill Nye the Science Guy? I know what you're thinking, I'm a loser. But the truth is, I was trying to be creative, and at the time, it seemed like a catchy name. To be honest, I still really like it, no matter what anyone else says. After you read my blog post, you can check out my fishy (you can feed them!), or my scientific links, or my favorite scientific quote, if you'd like. But that's optional, you can if you have free time. So I think that's enough of an introduction to my blog. Now I will actually begin with the biology.


This article talks about two adults, uncle and niece, who have partial trisomy 8 and partial monosomy 21. This is due to a familial balanced translocation on their 8 and 21 chromosomes. A translocation is when one segment of a chromosome becomes attached to a different chromosome. There's two types of translocations:

• Simple translocation - when only one segment of a chromosome moves to a different one)
• Reciprocal translocation - two different chromosomes exchange pieces

Fluorescence in situ hybridisation (aka FISH) was used to specifically see the chromosomal breakpoints in a more accurate manner. The first patient reviewed (the uncle) had mild mental retardation and facial dysmophism, while the niece's symptoms were much more severe. She had severe epilepsy, however, she did not have the facial dysmorphism. Why? When the data was compared to other trisomy 8 cases, it was found that the phenotype of partial trisomy 8p was a lot more "variable." This means that the phenotypes are unpredictable, explaining why the uncle and niece had different symptoms. It's very unfortunate that translocations for these individuals caused mental retardation. 

This video talks all about mitosis, meiosis and sexual reproduction. It's from KhanAcademy, one of my favorite resources. Their videos are always really helpful. We all know about how a zygote is formed, all that basic stuff. One thing that I really loved was how he explained how zygotes actually become people. Most textbooks don't really go into that, so I found this really helpful. In addition, the speaker explained the basics of mitosis/meiosis in a very clear manner. He also talked about the topic of differentiation, which is how a zygote becomes a complex system of cells that make up our body! 


Genetic mutations are also explained by the speaker. Mutations seem really complicated, and don't get me wrong, they are! However, he talks about mutations in a way that makes everything seem so simple. I was so incredibly impressed by this video that I watched two more, linked below.


All About Mitosis
All About Meiosis

My next useful material is this animation that talks about the cell cycle. I liked all the useful facts it gave. Did you know it takes 10 hours to replicate all of the nuclear DNA in your body? I didn't know that. And one thing that was really cool was the apoptosis animation. The author, Barbara did a great job explaining everything. After the G1 phase, one of the identical daughter cells exits the cell cycle to become a specialized cell, and the other stays in the bone marrow (hello stem cell!) to go through the cell cycle again.


I also loved the simplicity of this animation. It isn't incredibly long, but you will get a lot of "aha" moments.

Chapter 14 Post

Hello! Mysterious person, I'm Emily. Oh wait, you already knew that, silly me. Welcome to my blog, if you've never seen it before. It's called, "Em Fu The Science Guru!" Get it, like Bill Nye the Science Guy? I know what you're thinking, I'm a loser. But the truth is, I was trying to be creative, and at the time, it seemed like a catchy name. To be honest, I still really like it, no matter what anyone else says. After you read my blog post, you can check out my fishy (you can feed them!), or my scientific links, or my favorite scientific quote, if you'd like. But that's optional, you can if you have free time. So I think that's enough of an introduction to my blog. Now I will actually begin with the biology, sigh. I'll try to make this as entertaining as I can for you.

So the title to this chapter is "Mutation, DNA Repair, and Cancer." Not too many know this, but I'm fascinated by cancer, and might even pursue oncology one day. Also, I love blood! No, not in a creepy vampire kind of way, but in a biological way. Learning about blood was one of my favorite parts of A&P, I found it really cool. Hematology and oncology are closely related, most doctors who pursue one of these specialities end up specializing in both. It's kind of like the relationship between Gynecology and Obstetrics. Most of the doctors in this field are OBGYNs. I would love to study hematology further, but most likely this would also involve going into oncology. Luckily, I have a great interest in oncology, and actually enjoyed this chapter.

Heading back to biology, the first section was all about mutations. Mutations are often associated with cancer, and are often seen as bad. However, mutations are a natural part of life, and contribute to evolution. So they can be good, and are actually necessary for a species to survive. There are a few different types of mutations, all causing different effects of polypeptides. It's super easy to get them confused, but I found Table 14.1 in the book to be really helpful. I'd suggest checking it out for quick review before an exam. Just so you know, this isn't one of my official useful materials. I just wanted to mention it, so you could check it out if you hadn't before.

The mutation type that fascinated me the most were frameshift mutations. They produce a completely different amino acid sequence because the reading frame is shifted over, changing the entire sequence downstream. When reading the book, I literally said, "whoa!," aloud. It's amazing how one addition/deletion of a single base can do so much. I decided to look into frameshift mutations as one of my useful materials. This article is titled, "Immunogenic peptides generated by frameshift mutations in DNA mismatch repair-deficient cancer cells." The authors wrote it in a very clear manner, unlike some PubMed articles that are impossible to comprehend. I'm sure you know what I'm talking about. The article states that the loss of DNA mismatch repair functions contribute to approximately 15% of human tumors. In cancer cells, there's an insertion or deletion at microsatellites. Microsatellites are repeating sequences of base pairs of DNA. Any mutations in coding microsatellites can be very bad, because genes can lose their function! Oh no! Frameshift mutations like these have been found recently. The authors found a "broad but comprehensive set of frameshift peptides that might be combined in a multivalent vaccine for MSI+ cancers." MSI stands for microsatellite instability, in case you were wondering. They identified and examined mutations in different genes, and found mutations that seemed similar to those found in cancer. Their research hopefully has brought us closer to finding a vaccine to MSI cancers. MSI cancers seem really interesting, and they connect frameshift mutations back to real-life. This article proved that frameshift mutations are incredibly dangerous and make a big difference.

After learning all about the consequences of mutations, I realized how vital DNA repair was! DNA repair allows us to live our lives by minimizing the occurence of mutations. One type of DNA repair is nucleotide excision repair (NER). I didn't understand it at first because the book's definition was a long run on sentence. After reading it a few times I understood it, but couldn't exactly picture it in my head. So I looked it up and found this diagram that does a pretty good job of illustrating all of the information. The book also had a diagram (showing NER in E. coli), but I understood this one a lot better. The illustrations could be better, but the point got across well. First, the damaged DNA gets distorted. Then, an enzyme complex finds the distortion and separate the DNA. Single-stranded binding proteins help to stabilize the strands and both sides are cleaved by an enzyme. Lastly, the damaged part is taken away and the empty space is filled by DNAP and sealed by DNA ligase. This diagram helped me realize that NER is actually quite simple after all!


The last section of the book was all about cancer! One topic I found quite interesting were types of cancer caused by viruses. The book specifically talked about the Rous sarcoma virus (RSV), and I decided to look more into it. This article gave a detailed description of RSV. RSV was the first virus shown to be able to cause cancer, called an oncogenic virus. A tumor from this virus is called a sarcoma, which is a connective tissue tumor. It's considered to be a retrovirus, it's genes are encoded in RNA instead of DNA, like HIV. RSV has four genes: gag encodes the capsid protein, pol encodes the reverse transcriptase protein, env encodes the envelope protein, and src which encodes a tyrosine kinase. Src is what makes RSV oncogenic, although it is not understood very well. As the article states, "the expression of this gene in some way...is able to transform cells in culture." A study was conducted on cells infected with RSV and it was found that they are temperature-sensitive, meaning that temperature changes can activate or denature the encoded protein, reversibly. In addition to it being a viral gene, it is also a proto-oncogene, called c-src. This is found in vertebrates and invertebrates, including humans! Ours in on chromosome 20, by the way. C-src has probably not changed much since the start of evolution because of how widely its found. Fortunately, Peyton Rous, the man who discovered RSV was awarded a nobel prize for his work, at the age of 87.


Thanks so much for reading by blog! I apologize for the length, but I hope you enjoyed reading it! 

Chapter 13 Post

Hello everyone! Long time no blog! This week's chapter is titled Gene Regulation. It focuses on regulation of transcription in bacteria, regulation of transcription in eukaryotes, and regulation of RNA processing and translation in eukaryotes.


This article from PubMed is about lac operon induction in Escherichia coli, a systematic comparison of IPTG and TMG induction and influence of the transacetylase LacA. The most frequently used expression systems in bacteria are based on the Escherichia coli lac promoter. Moreover, lac operon elements are used today in systems and synthetic biology. In a handful of cases the inducers IPTG or TMG are used. Here the author reported a comparison of lac promoter induction by TMG and IPTG which focuses on the aspects inducer uptake, population heterogeneity and a potential influence of the transacetylase, LacA. They provided induction curves in E. coli LJ110 and in isogenic lacY and lacA mutant strains and they showed that both inducers are substrates of the lactose permease at low inducer concentrations but can also enter cells independently of lactose permease if present at higher concentrations. Using a gfp reporter strain they compared TMG and IPTG induction at a single cell level and showed that bimodal induction with IPTG occurred at approximately ten-fold lower concentrations than with TMG. In addition, they observed that lac operon induction is influenced by the transacetylase, LacA. By comparing two Plac-gfp reporter strains with and without a lacA deletion they could show that in the lacA(+) strain the fluorescence level decreased after few hours while the fluorescence further increased in the lacA(-) strain. The results showed that through the activity of LacA the IPTG concentration can be reduced below an inducing threshold concentration, an influence that should be considered if low inducer amounts are used.


This article, titled, Clock Genes Might Control the Sleep We Need, focuses on Clock genes, which are long known to regulate our circadian rhythms, and also give clues to what makes sleep so persistent. Sleep is the one thing we can’t cheat. We lose it in our busy lives but yet our brains, surprisingly keep score – and force payback as soon as we lie down. And if it’s big, we sleep in, sometimes missing important activities. A clue has emerged from new research published in BioMed Central Neuroscience. Researchers have found that the expression of genes called “clock genes” are highly correlated with the need for sleep. It’s shown that clock genes regulate our 24-hour circadian rhythm – but researchers say these genes also appear to control the persistence of sleep. Researchers studied some mice that need a lot of sleep and those who need little sleep. They found that for mice the expression of clock genes increased the longer an animal stayed awake, and decreased when the animal was in recovery sleep.

The video above talks about the lac operon. It's a good animation about the process. As I was researching videos on YouTube, I was questioning the validity and trustworthiness of some videos. I ended choosing this one partly because it came from a textbook. Also, the animations are good and the information is detailed and clear. I like that the text is displayed at the side because reading information, in addition to hearing it, helps me learn better. I would suggest watching this video.