Perfect Paragraph

From the results of the melting point of the AE1, the identity of the unknown is 2-chlorobenzoic acid. The melting point for this compound was 143 degrees celsius and in the experiment protocol it was 142 degrees celsius. The less than two degree difference reaffirms that the unknown was a pure compound. The next step of calculating the percent recovery could have been caused by human error. During the extraction and filtration, it is possible that the solution did not become fully acidic by HCl before being left to cool, which would affect the product’s ability to recrystallize. In addition, this reasoning could also be applied to the OL1 recovery rate of 77.87%. The percentage could have been due to a lack of acidity or it could have been caused by the CaCl2 and NaHCO3 being unable to fully separate the compound from the solvent ether. The lack of acidity and insufficient separation of the compound would affect the amount of solute able to recrystallize and would further affect the recovery rate. The melting point of benzil was 95-96 degrees celsius, which is in the range of its known boiling point, therefore the compound is pure. The purified melting point reaffirms that the crystals were successfully purified because the melting point has less than a 2 degree celsius difference. The identity of compound AE1 is 2-chlorobenzoic acid and the identity of the compound in OL1 mixture is benzil.

The goal of this unit was to develop the ability to infer the genotype of various breeds of dogs at different genes. This was done by sequencing either the entire genome or, more practically, specific sequences containing desired single nucleotide polymorphisms (SNPs). There are many methods by which sequencing can be accomplished, but the most common method is Sanger sequencing. Sanger sequencing is run by amplifying desired DNA sequences in a solution containing regular deoxynucleotides (dNTPs) and a minimal amount of dideoxynucleotides (ddNTPs). These ddNTPs are structurally similar to typical nucleotides, but lack an OH group on the 3’ carbon that prevents the growth of the chain. As a result, sequences terminate at different lengths depending on the how early the ddNTP is added. The differently sized products of the amplification are then run through an agarose gel where they separate into bands. The distribution of the bands can then be used to read the sequence of the DNA.

Mammalian speciation expanded in two periods; 80-90 million years ago and 60-65 million years ago. For the 80-90 million years period, the theory for speciation is the super continent Pangea began to split apart and as the climate change so do niches. This may have led to some exctinctions that allowed small mammals to fill new niches and rise. 60-65 million years ago was the exctinction of the dinosaurs, which allowed for more environments, niches, and resourses for the early mammals to use.

Eutherians are a subclass of class Mammalia. The word eutheria comes from the Greek for "true" (Eu) and "wild beast" (Theria). Eutherians are unlike metatherians (marsupials) as they have a true placenta and give birth to more precocial young. The oldest eutherian fossil found so far is the Eomaia. It was found in China (Paleartic zoogeographical zone) and dates back to the Cretaceous period. It is though to be a small and insectivorous early mammal.

Eutherians all share some distinct characteristics. Eutherians follow a primitive dental formula with slight variation based on species. Both the upper and lower jaw have 3 incisors, 1 canine, 4 premolars, and 3 molars, with a premolar that is clearly different from the molar. Females have a chorloallantoic placenta, a vagina (some do have a cloaca), a cervic, a uterus, and ovaries (again with variation based on species) and males have a penis bone or baculum. 

The first step in establishing mutant lines, in any organism, is the induction of mutations. Here, I'll narrow down on just zebrafish, one of the many model organisms used for scientific investigation. There are a number of ways to create mutations. A highly effective one is CRISPR/Cas9. It involves the injection of guide RNAs, Cas9 protein and stop oligos into embryos at the single-cell stage. CRISPR/Cas9 gives a high level of specificity to mutation induction. A wide variety of mutations are induced; some can be innocous point mutations and others can be harmful insertions/deletions of varying lengths. The injected generation of fish is referred to as G₀ and they are mosaic organisms, meaning that different populations of cells have different genotypes (i.e. carry different mutations). To clean this up and have organisms with uniform genotypes across all cell populations, the G₀ adult zebrafish have to be outcrossed with wildtype fish. Ideally, the next generation of zebrafish (F₁) laid should have heterozygotes carrying one wild-type allele and one mutant allele, along with homozygotes carrying only wildtype alleles. Owing to the unpredictability of the process, all the embryos obtained from a cross could very well be wildtype. This might be an indication that the induced mutation did not go germline. By that, I mean that the gametes never picked up the mutation. To determine the alleles being carried by the progeny, a process called genotyping must be performed. That will be the discussion for the next segment. 

There are two categories of enzymes based on their kinetic features: Michaelis Menten and allosteric enzymes. Michaelis Menten enzymes display a hyperbolic curve when initial reaction rate is plotted against the concentration of the substrate, and they have kinetic parameters that are used to study their function. One parameter is the Km, which is the substrate concentration when the reaction rate is half its maximum. This value indicates how quickly an enzyme reaches maximum activity, and it can be considered a measure of affinity for particular substrates. On the other hand, Kcat is the turnover number that indicates how quickly an enzyme catalyzes a reaction once it’s bound to its substrate. The higher the Kcat, the faster the enzyme changes substrate to product once bound. These two parameters are compared to determine the specificity constant, Kcat/Km, which is the measure of an enzyme's overall catalytic efficiency. It takes into account both substrate binding and speed of product formation, so even if an enzyme's Kcat is low, if its Km is low, it can still be considered relatively efficient.

Modern horses have evolved to be adapted for environments very different to those the first equines lived in, and horses as we know them today look nothing like their earliest ancestors did when they first appeared. The first horse-like creature lived in North America and Europe about 54 million years ago, during the Eocene. Unlike modern horses, Hyracotherium boreale (also called Eohippus) was adapted for life in the woodlands and forests that dominated the Eocene. Hyracotherium was much smaller than the modern horse, and it had an arched back and raised hindquarters, a short snout, and a small cranium. It had short legs that ended in padded feet, four-toed forefeet and three-toed hind feet, and a functional hoof on each toe. Hyracotherium was a browsing animal that fed on shrubs, leaves, and branches, as evidenced by its low-crowned teeth and distinctive molars that were designed for grinding.

During the Oligocene, environmental changes occurred that started to change the local flora, and so about 33 million years ago Mesohippus bairdi appeared. Although also a forest browser, Mesohippus had a longer face and snout than Hyracotherium did, and had developed premolars that were more complex and had defined cusps. Mesohippus had three toes on both its fore and hind feet, as the fourth toe previously found on Hyracotherium was reduced to a vestigial nub, and unlike Hyracotherium Mesohippus had longer legs and a relatively straight and stiff spine that enabled it to run over hard ground.

Bone marrow derived cells are cells that originate from the bone marrow.  Cancer cells can release chemical signals that, upon reception by bone marrow derived cells, may recruit these cells as pro-tumor factors that help tumor growth and metastasis.  A crucial step to tumor metastasis is angiogenesis.  Once a tumor gains access to the blood stream, it can shed cells into circulation and they can implant in other places in the body and start new tumors.  One example cited by McAllister and Weinberg is that in mouse models of melanoma, lymphoma, lung carcinoma, and mammary carcinoma, the secretion by tumors of the inflammatory cytokine granulocyte-colony stimulating factor (G-CSF) recruits pro-tumor cells from the bone marrow into the blood stream.  It was also found that these bone marrow cells had distinct sets of genes that promote angiogenesis.  Another study cited by McAllister and Weinberg showed that the secretion of osteopontin by tumor cells induced pro-tumorigenic function in bone marrow cells by recruiting them to the tumor microenvironment.  The secretion of growth factors such as vascular endothelial growth factor-A by tumor cells also recruits bone marrow derived cells to the tumor microenvironment and elicits pro-tumorigenic function that aids in angiogenesis. 

When comparing the two figures there were many differences that could be observed not only with the pictures themselves but with the layout of the figure. When comparing the pictures, the first thing that stands out is that both the trees look very different, with the tree in the replica having pine needles and the tree in the original not having any form of  greenery or leaves at all. Another difference I noticed was that the tree in the replia didn't include the Ivy branches on the trunk while they were present in the original picture. The pictures also had very different backgrounds, the original had a grass with a small amount of snow in the background while the replica only has snow. The tree in the original also appears much larger than the tree in the replica. All of the photos in the replica also show where the tree is planted in the ground while for the original we only see this portion of the ground in 2 of the photos.

When comparing the structure of the figures, one thing that stands out is the labeling of the pictures which are labeled as Picture A,B,C,D in the original and labeled 1,2,3,4 in the replica. There are also no descriptions for the figure in the replica while the original contains these descriptions below their respective label.  The size of the photos is slightly different between the two, with the original having slightly taller pictures when compared to the replica. The arrows between the two figures also shared some differences, with the arrows for the Ivy all pointed to the same picture in the replica while there is one to each picture in the original. The arrows are also slightly  thicker in the replica when compared to the original. The labels the arrows pointing from are different with the original having Ivy Branches and tree and the replicate having Ivy and trees. These labels also have a slightly bigger font size than the labels used on the orginal.

The contents of the photos, specifically the tree and the background, are different in the two figures. The tree captured in figure 1 is thicker than the tree in figure 2. In addition, the tree in figure 1 is covered in moss. The tree in figure 2 does not have any moss on it. In figure 1, the tree has a rectangular black sign saying “Honey Locust,” whereas the tree in figure 2 does not have any sign on it. The surface of the tree in figure 1 is rough and uneven. The surface of the tree in figure 2 is more smooth in comparison. The background of both figures also differs. The Life Sciences Building appears larger in figure 2 than in figure 1. A gray fence lies behind the tree in figure 1, whereas in figure 2 there is no fence. All of the ground is covered with snow in figure 1. In contrast, the snow covers most of the ground but not all of it in figure 2. Both figures show another tree to the right of the interspecific interaction between the tree and moss. However, in figure 1 this tree to the right appears larger than the tree to the right in figure 2. The Integrated Science Building is present in both photos. But likewise, this building appears larger in figure 2 in comparison to figure 1. Overall there are 9 differences between the two figures in regards to the contents of the photos.