The Best Laid (Body) Plans --- Discussion of Chapter 6 "Your Inner Fish"

Indeed all tetrapods have one head and four limbs arranged in two pairs, a tail and a variety of other gross morphological features. We, human beings, have the same basic body plan, too! (except the tail) But why? And where did this basic body plan come from? Chapter 6 of Your Inner Fish would give us the answer.

Here are some key terms in chapter 6. Let's discuss them one by one. :) 

I. Embryology:  The study of the development of an embryo from the fertilization of the ovum to the fetus stage. The study focuses on comparing different species at their early stage. By comparing, scientists are able to find the common structures of various species.

At the very early stage --- all look similar, almost the same. 

II. Germ layers:  Karl Ernst Von Baer, a Russian biologist and a founding father of embryology,  discovered that there are three layers in embryos (also known as germ layers). 

The endoderm is one of the germ layers formed during animal embryogenesis --- the process by which the embryo forms and develops. 

Cells migrating inward along the archenteron form the inner layer of the gastrula, which develops into the endoderm. Endoderm forms many of the inner structures of our bodies, including digestive tract and numerous glands that are associated with it. 

The mesoderm germ layer forms in the embryos of triploblastic animals. During gastrulation, some of the cells migrating inward contribute to the mesoderm, an additional layer between the endoderm and the ectoderm. The formation of a mesoderm led to the development of a coelom. Organs formed inside a coelom can freely move, grow, and develop independently of the body wall while fluid cushions and protects them from shocks. 

The mesoderm has several components which develop into tissues: intermediate mesoderm, paraxial mesoderm, lateral plate mesoderm, and chorda-mesoderm. The chorda-mesoderm develops into the notochord. The intermediate mesoderm develops into kidneys and gonads. The paraxial mesoderm develops into cartilage, skeletal muscle, and dermis. The lateral plate mesoderm develops into the circulatory system (including the heart and spleen), the wall of the gut, and wall of the human body. Also, it forms tissue in between skeleton and muscles. 

The ectoderm is the outer layer of the embryo, and it forms from the embryo's epiblast. The ectoderm develops into the surface ectoderm, neural crest, and the neural tube.

The surface ectoderm develops into: epidermis, hair, nails, lens of the eye, sebaceous glands, cornea, tooth enamel, the epithelium of the mouth and nose.
The neural crest of the ectoderm develops into: peripheral nervous system, adrenal medulla, melanocytes, facial cartilage, dentin of teeth.
The neural tube of the ectoderm develops into: brain, spinal cord, posterior pituitary, motor neurons, retina.

III. Organizer: 

In 1903, Hans Spemann discovered that some cells have the capacity to form a whole new individual on their own at the early stage of embryo. 

In 1920, Mangold discovered Organizer, which can direct other cells to form an entire body plan. Organizer could control the activity of the embryo. The importance of the organizer experiment is the discovery that a part of the mesoderm influences the ectoderm as the ectoderm differentiates into central nervous system tissue. 

All of the cells within a complex multicellular organism such as a human being contain the same DNA; however, the body of such anorganism is clearly composed of many different types of cells. What, then, makes a liver cell different from a skin or muscle cell? That is because the particular combination of genes that are turned on (expressed) or turned off (repressed) dictates cellular morphology (shape) and function. This process of gene expression is regulated by cues from both within and outside cells, and the interplay between these cues and the genome affects essentially all processes that occur during embryonic development and adult life. DNA interactions control and show how genes work. 

Mitosis and Meiosis

During today's class, we continued using the PRO microscope to observe either an onion root cell or an animal cell (whitefish). We need to find the different phases of mitosis when looking at these cells. For our group, we observed the onion root cell:

Interphase

Late Anaphase

Metaphase

Prophase

Telophase

After the lab, we had a lecture about mitosis and meiosis.

What's mitosis:
Mitosis produces two daughter cells that are identical to the parent cell. If the parent cell is haploid (N), then the daughter cells will be haploid. If the parent cell is diploid, the daughter cells will also be diploid.
N → N
2N → 2N
This type of cell division allows multicellular organisms to grow and repair damaged tissue.

The phases of Mitosis:

• Interphase (G1 and G2): Chromosomes are not easily visible because they are uncoiled
• G1 Interphase: The chromosomes have one chromatid.
• G2 Interphase: The chromosomes are replicated. Each one has two sister chromatids.
• Prophase: The chromosomes begin to coil. The spindle apparatus begins to form as centrosomes move apart.
• Metaphase: The chromosomes become aligned on a plane.
• Anaphase: The chromatids separate (The number of chromosomes doubles).
• Telophase: The nuclear membrane reappears. The chromosomes uncoil. The spindle apparatus breaks down. The cell divides into two.

What's Meiosis:

Meiosis produces daughter cells that have one half the number of chromosomes as the parent cell.
2N → N
Meiosis enables organisms to reproduce sexually. Gametes (sperm and eggs) are haploid.
Meiosis involves two divisions producing a total of four daughter cells.


The Phases of Meiosis: 

A cell undergoing meiosis will divide two times; the first division is meiosis 1 and the second is meiosis 2. The phases have the same names as those of mitosis. A number indicates the division number (1st or 2nd):
meiosis 1: prophase 1, metaphase 1, anaphase 1, and telophase 1
meiosis 2: prophase 2, metaphase 2, anaphase 2, and telophase 2
In the first meiotic division, the number of cells is doubled but the number of chromosomes is not. This results in 1/2 as many chromosomes per cell.
The second meiotic division is like mitosis; the number of chromosomes does not get reduced.

• Prophase I: Homologous chromosomes pair up and form tetrad
• Anaphase I: Spindle fibers move homologous chromosomes to opposite sides
• Telophase II: Nuclear membrane reforms, cytoplasm divides, 4 daughter cells formed
• Metaphase II: Chromosomes line up along equator, not in homologous pairs
• Prophase II: Crossing-over occurs
• Anaphase II: Chromatids separate
• Telophase I: Cytoplasm divides, 2 daughter cells are formed
• Metaphase I: Homologs line up alone equator

On the other hand, how could we control the system? Checkpoint is the master. Checkpoint stops the cell from going into the next phase. It stops the cell that it only allows the cell to live in a normal life style (nondividing).

Animal and Plant cells

During today's class, we learned how to use a really AWESOME microscope! By using this new microscope, we observed a dog flea and a plant cell. Also, we made our own slides --- cheek cells from our cheeks. With the help of such a pro microscope, we were able to observe the cells' structures
closely. It was a fun class! :)

A dog flea

Plant cell

Plant cell

Plant cell 

PRO microscope! 

Who is the father?

!! I started off my day with cuties!! :D

Look at them! SO CUTE!!

Aww.. adorable :) 

However, the picture reveals an essential question --- what is the genotype of the father? What does he look like in order to produce cuties like them?

And now, it's time to use genetics, our detective skill to figure out the genotype of the father.

As shown in the picture, the genotype of the mother is eebb, since she has yellow fur, brown nose,

brown eyelids and brown ears. 

The puppies have two different colors of fur. One color is black, and the other one is chocolate (in between yellow and black). There is no yellow color. Thus, for the fur color, the father should be EE so that the puppies would be heterozygous. Based on the pictures above, the puppies would have either black nose, black eyelids and black ears or brown nose, brown eyelids and brown ears. Thus, the genotype of the father would be Bb. In that way, the puppies would be either heterozygous or homozygous recessive. 

All in all, the genotype of the father would be EEBb. 

Sherlock Holmes --- !!GENETICS!! --- Part 6

Learning genetics can be fun! It helps us to improve our detective skills. WOW!                                                

For today's class, we refreshed our memories first by reviewing incomplete dominance, codominance and sex-linked genteics problems. We paired up in groups and went over several questions on the handouts that Mr. Quick gave us before the break. Then, we learnt a new concept about how to be Sherlock Holmes --- Pedigree. We learnt how to analyse a pedigree diagram, and how to determine whether the genetic problem is sex-linked or autosomal. In order to identify the genetic problem (it's sex-linked or autosomal), we always need to work backwards and detect the details on the diagram. 

Pedigree Symbols! Important! 

* For sex-linked problems, usually males have a higher chance of having it then females do. 

(males > females) 

* Autosomal means, all chromosomes except 23 [ NOT xx, xy] 

Once we determine whether the genetic problem is sex-linked or autosomal, we then need to determine whether it is dominant or recessive. To determine whether it is recessive or dominant, we need to calculate the percentage. For autosomal, if the percentage is higher than 25%, then it is dominant. If the percentage is lower than 25%, then it is recessive. However, I am not sure about how to determine the recessive and dominant part for sex-linked genetics problems. I need to work on that part.   

!!GENETICS!! --- Part 5

Cell Division --- Mitosis and Meiosis 

Mitosis is the process by which a cell has previously replicated each of its chromosomes. Separates the chromosomes in its cell nucleus into two identical sets of chromosomes, each set in its own new nucleus. It is generally followed immediately by cytokinesis, which divides the nuclei, cytoplasm, organelles, and cell membrane into two cells containing roughly equal shares of these cellular components. 

• Mitosis and cytokinesis together define the mitotic (M) phase of the cell cycle—the division of the mother cell into two daughter cells, genetically identical to each other and to their parent cell. 
• Mitosis occurs only in eukaryotic cells and the process varies in different species.
• Prokaryotic cells, which lack a nucleus, divide by a process called binary fission.
• The sequence of events is divided into stages corresponding to the completion of one set of activities and the start of the next. These stages are prophase, prometaphase, metaphase, anaphase and telophase. 
  
  
   

Meiosis is a special type of cell division necessary for sexual reproduction in eukaryotes. 

• The cells produced by meiosis are either gametes (the usual case in animals) or otherwise usually spores from which gametes are ultimately produced (the case in land plants). 
• In many organisms, including all animals and land plants, gametes are called sperm in males and egg cells or ova in females.
• Meiotic division occurs in two stages, meiosis I and meiosis II, dividing the cells once at each stage. The first stage begins with a diploid cell that has two copies of each type of chromosome, one from each the mother and father, called homologous chromosomes. All homologous chromosomes pair up and may exchange genetic material with each other in a process called crossing over. 
• In the second stage, each chromosome splits into two, with each half, called a sister chromatid, being separated into two new cells, which are still haploid. This occurs in both of the haploid cells formed in meiosis I. Therefore from each original cell, four genetically distinct haploid cells are produced. These cells can mature into gametes.
  

!! GENETICS!! --- Part 4

Monohybrid:

• A monohybrid cross is a mating between individuals who have different alleles at one genetic trait of interest. The character(s) being studied in a monohybrid cross are governed by two alleles for a single trait.
• To carry out such a cross, each parent is chosen to be homozygous or true breeding for a given trait. When a cross satisfies the conditions for a monohybrid cross, it is usually detected by a characteristic distribution of second-generation (F2) offspring that is sometimes called the monohybrid ratio.
• Monohybrid cross - a cross between parents that differ at a single gene pair (usually AA x aa)
• Monohybrid - the offspring of two parents that are homozygous for alternate alleles of a gene pair Remember!! --- a monohybrid cross is not the cross of two monohybrids.
• Generally, the monohybrid cross is used to determine the F2 generation from a pair of homozygous grandparents (one grandparent dominant, the other recessive), which results in an F1 generation that are all heterozygous. Crossing two heterozygous parents from the F1 generation results in an F2 generation that produces a 75% chance for the appearance of the dominant phenotype, of which two-thirds are heterozygous, and a 25% chance for the appearance of the recessive phenotype. 

  

* In the figure above, inheritance pattern of dominant (red) and recessive (white) phenotypes when each parent (1) is homozygous for either the dominant or recessive trait. All members of the F1 generation are heterozygous and share the same dominant phenotype (2), while the F2 generation exhibits a 3:1 ratio of dominant to recessive phenotypes (3).

Dihybrid:
A dihybrid cross is a cross between F1 offspring of two individuals that differ in two traits of particular interest. A dihybrid cross is often used to test for dominant and recessive genes in two separate characteristics.

*Two genes that are heterozygous mix together. When two genes that are heterozygous cross over, the phenotypical ratio is 9:3:1.  

!! GENETICS!! --- Part 3

Ch. 1 of Survival of the sickest

!! GENETICS!! --- Part 2

Solving genetics problems:
Step 1 (IMPORTANT!): Write down information
Step 2: Parent's genotype
Step 3: Gametes * Law of segregation
Step 4: Lay out information --- make info-squares
Step 5: Calculate ratios (Genotypic and phenotypic ratios)
We practiced some of the problems in class, and then we took a quiz. I got a 2 on the quiz. As I did not read the question carefully, I missed one point.

"Mathematic" Fitz way

"Shortcut" Quick way 

!! GENETICS!! --- Part 1

Gregor Johann Mendel (July 20, 1822 – January 6, 1884) was a German-speaking Silesian scientist who gained posthumous fame as the founder of the new science of genetics. Mendel demonstrated that the inheritance of certain traits in pea plants follows particular patterns, now referred to as the laws of Mendelian inheritance. These laws initiated the modern science of genetics.

Mendel's laws

• The principle of segregation (First Law): The two members of a gene pair (alleles) segregate (separate) from each other in the formation of gametes. Half the gametes carry one allele, and the other half carry the other allele.
• The principle of independent assortment (Second Law): Genes for different traits assort independently of one another in the formation of gametes.

Vocabulary

• Pure Line - a population that breeds true for a particular trait
• Phenotype - literally means "the form that is shown"; it is the outward, physical appearance of a particular trait
• Dominant - the allele that expresses itself at the expense of an alternate allele; the phenotype that is expressed in the F1 generation from the cross of two pure lines
• Recessive - an allele whose expression is suppressed in the presence of a dominant allele; the phenotype that disappears in the F1 generation from the cross of two pure lines and reappears in the F2 generation
• Allele - one alternative form of a given allelic pair; tall and dwarf are the alleles for the height of a pea plant; more than two alleles can exist for any specific gene, but only two of them will be found within any individual
• Allelic pair - the combination of two alleles which comprise the gene pair
• Homozygote - an individual which contains only one allele at the allelic pair
• Heterozygote - an individual which contains one of each member of the gene pair
• Genotype - the specific allelic combination for a certain gene or set of genes
• F1 - First generation offspring
• P - Parental generation
• Backcross - Offspring mating with parents 

* Somatic cell --- Body cell, anything but not sex cell. 

Cell division: meiosis/ 46 in total of chromosomes, 23 pairs

Operon System

• Operon system makes sure that there is no energy being wasted. Operon systems only exist in prokaryotes, since eukaryotes use TATA box for the control. There are two types of operon system: 1) repressible and 2) inducible. [Repressible---on to off/ Inducible---off to on] For the pGLO lab we did in class, it was an inducible operon system. Arabinose was brought into the system from an outside source, and it was added in front of the pGLO gene. Then, it produced protein to help it grow. Yet, overtime, the bacteria would not glow anymore due to the fact that the system would create arabinase that digests away the arabinose.  
  
  
  
  
  
  

  

  WOW! We created bacteria that glows in the dark

  
  
• Operon system is a genetic regulatory system found in bacteria and their viruses in which genes coding for functionally related proteins are clustered along the DNA. This system allows protein synthesis to be controlled coordinately in response to the needs of the cell. (By providing the means to produce proteins only when and where they are required). 
• A typical operon consists of a group of structural genes that code for enzymes involved in a metabolic pathway, such as the biosynthesis of an amino acid. These genes are located contiguously on a stretch of DNA and are under the control of one promoter (a short segment of DNA to which the RNA polymerase binds to initiate transcription). A single unit of messenger RNA (mRNA) is transcribed from the operon and is subsequently translated into separate proteins.
• The promoter is controlled by various regulatory elements that respond to environmental cues. The regulator protein can either block transcription, in which case it is referred to as a repressor protein; or as an activator protein it can stimulate transcription. Further regulation occurs in some operons: a molecule called an inducer can bind to the repressor, inactivating it; or a repressor may not be able to bind to the operator unless it is bound to another molecule, the corepressor. Some operons are under attenuator control, in which transcription is initiated but is halted before the mRNA is transcribed.
  
  
  
  
  

Protein Synthesis

Protein synthesis had three process: 1) Transcription from DNA to mRNA. 2) RNA processing happens where introns are cut off. Protective cap/ G-cap and poly-A-tail are added. 3) Translation of RNA to protein. Translation happens in the ribosome.   

DNA Replication

DNA replication is the process of producing two identical copies from one original DNA molecule. This biological process occurs in all living organisms, and is the basis for biological inheritance. DNA is composed of two strands and each strand of the original DNA molecule serves as template for the production of the complementary strand, a process referred to as semiconservative replication. Cellular proofreading and error-checking mechanisms ensure near perfect fidelity for DNA replication.

First of all, helicase unzips the strand and breaks hydrogen bonds. Secondly, RNA primase lays down RNA at the 3’ end. Thirdly, DNA poly III lays down DNA nucleotides on the leading and lagging strands. Last but not least, DNA poly I replaces the RNA with DNA, and ligase glues the lagging strand (Okazaki fragments) together.

The DNA structure

DNA has a double helix shape, which is like a ladder twisted into a spiral. Each step of the ladder is a pair of nucleotides. Speaking of nucleotides, it is a molecule made of deoxyribose, a kind of sugar with 5 carbon atoms, and a phosphate group made of phosphorus and oxygen, and nitrogenous base. There are four types of nucleotide: Adenine (A)/ Thymine (T)/ Cytosine (C)/ Guanine (G). The DNA ladder is made of two bases, one base coming from each leg. The bases connect in the middle: 'A' only pairs with 'T', and 'C' only pairs with 'G'. The bases are held together by hydrogen bonds. Adenine (A) and thymine (T) can pair up because they make two hydrogen bonds, and cytosine (C) and guanine (G) pair up to make three hydrogen bonds.