Drafts

Species on earth usually follow a similar growth pattern which scientists have been able to observe and quantify. In general, a species will experience a higher growth rate when at lower population densities until it reaches a plateau at its carrying capacity. The carrying capacity is the number of individuals an environment can sustain indefinitely. The most basic way to describe this model is through a logistic growth curve. It begins exponential and levels out. However, this is not the full story in real life. What tends to happen is a population will overshoot the carrying capacity when times are good and population growth rates are positive. When this happens the environment imply cannot sustain this population and the species feels the impact via two factors. Decreased birth rates from less food and possible increased emigration to other suitable ranges. The growth rate then decreases and the population may undershoot the carrying capacity at which point the cycle may repeat. Populations that over-and-under shoot by very little can be described as dampened oscillations.

An unfortunate problem some species face is the allee effect of population growth. The trend most observed in the wild is when population density is low for a certain area, the growth rate is high because the environment can sustain more individuals than currently present. However, consider a small population that is very dispersed and therefore partially isolated from each other. When it comes time to breed they may not be able to find a mate in time and therefore not produce any young. This is the allee effect. Low population densities mixed with isolation produces a decreased growth rate. This effect can drive many species to extinction fairly quick as it's hard to recover when a population size becomes so small so fast.

Species on earth usually follow a similar growth pattern which scientists have been able to observe and quantify. In general, a species will experience a higher growth rate when at lower population densities until it reaches a plateau at its carrying capacity. The carrying capacity is the number of individuals an environment can sustain indefinitely. The most basic way to describe this model is through a logistic growth curve. It begins exponential and levels out. However, this is not the full story in real life. What tends to happen is a population will overshoot the carrying capacity when times are good and population growth rates are positive. When this happens the environment imply cannot sustain this population and the species feels the impact via two factors. Decreased birth rates from less food and possible increased emigration to other suitable ranges. The growth rate then decreases and the population may undershoot the carrying capacity at which point the cycle may repeat. Populations that over-and-under shoot by very little can be described as dampened oscillations.

An unfortunate problem some species face is the allee effect of population growth. The trend most observed in the wild is when population density is low for a certain area, the growth rate is high because the environment can sustain more individuals than currently present. However, consider a small population that is very dispersed and therefore partially isolated from each other. When it comes time to breed they may not be able to find a mate in time and therefore not produce any young. This is the allee effect. Low population densities mixed with isolation produces a decreased growth rate. This effect can drive many species to extinction fairly quick as it's hard to recover when a population size becomes so small so fast.

Viruses are genetic material inside a protein coat. To be more specific, there  is a caspid, and some viruses can have an envelope which is outside of the capsid. It is interesting to know that viruses are actually not alive, not like bacteria. They contain DNA and RNA. Bacteriophage, is the process of viruses infecting bacteria. There are fiive phases of virus replikcation. The first is attachment, in which the virus attaches to host. The second is entry, when the viral genetic material enters the host. Thirdly, there is the synthesis of new viral particles, it uses host machinery to build new viral genetic mterial and protein coats. Almost there, but second lastly, assembly of viral particles. and lastly, there is an explosion, which is a burse/release from the host

There are many different plant cell types, but there are a few unique types that distinguish plants from animals. Meristem cells are found in the root apical, shoot apical, leaf bud, and vascular cambium meristems of plant, and are the regions of new plant cell synthesis. Undifferentiated cells in the meristems will turn into leaves, flowers, roots, xylem, phloem, and other plant organs depending on internal and external stimuli. Xylem and phloem are the vessels through which water and sugar flow, respectively. Xylem are dead cells, consisting of thin tracheids and large vessels, transporting water from root to shoot. Phloem are live cells, comporting two cell types joined together via branched plasmodesmata. The sieve element is largely devoid of organelles and even lacks a nucleus, leaving it mostly hollow, which allows for the transfer of nutrient laden liquid throughout the plant. The companion cell is linked to the sieve element and provides it with the cellular products it cannot make itself. Root hairs are epidermal cells found on roots that extend via tip growth in order to increase root surface area, allowing for more water and nutrient absorbance. Pollen is the plant equivalent of animal sperm and serves to fertilize female plant gametes. It is made up of two, sometimes three, nuclei of two types, vegetative and generative. The vegetative nuclei is responsible for the growth of the pollen tube, which extends into the stigma of the plant in order to allow for the male gametes produced by the generative nuclei to fertilize the egg and the endosperm. Stomata and trichomes are specialized structures found on any aerial plant surface. Stomata are openings that allow for gas exchange and are regulated by guard cells who open and close in response to blue light. Trichomes come in two forms, glandular and non-glandular, and more than one type of trichome can be found on a plant. The glandular form releases chemicals when burst that can deter predators or attract pollinators. The non-glandular form can be used as physical defence, trapping the predator on the plant, where it will die of thirst. Additionally, the non-glandular form provides an increased boundary layer that minimizes airflow around the aerial parts of the plant, thus decreasing water evaporation.

Experiment 1: Neuromuscular SHIRPA

The scores increased significantly from week 3 to week 24, indicating a decrease in muscle usage. The adult C22 mice were the most affected and C3-PMP mice were intermediate. The things that were most noticeable were in tremor, gait and tail elevation and escape strength. (Figure 1)

Experiment 2: Electrophysiology. 

    The mean NCV was lower in C3-PMP mice and in C22 mice. Than in wt mice. C22 mice had a lower amplitude compared to C3-PMP mice and wt. The mean CNAP was decreased significantly from 3 to 48 weeks in C22 mice. But not in C3-PMP mice. (table 1)

Experiment 3: Histology and morphology

    In the C3 and CC22 and had numerous inappropriately thinly myelinated and unmyelinated fibers at 3 weeks compared to the control. The number of normally myelinated fibers increased in C3 and C22. There were more inappropriately myelinated in the motor branch compared to the peroneal nerve (Figure 3). Many amyelinated and thinly myelinated fibers and small diameter fibers that were hyper myelinated were found in both strains. There were occasional atrophic fibers and loss of Schwann cells at all ages of the C3 and C22 mice. All abnormalities were more frequent in C22 mice compared to the C3 PMP mice (figure 4). Macrophages were seen in C22 but not in C3 mice, which implies axonal damage. There were no regenerative fibers not identified with either the CC22 or C33 model(figure 3). 

Putting it all together:

    In adults, a higher neuromuscular SHIRPA score was associated with a lower number of fibers and lower CMAP amplitudes. Lower MNCV is associated with higher SHIRPA scores and lower number of axons. (figure 5)

Prep work: The mice were first genotyped to confirm mice’s genotype. The mice that were used for this experiment were created using cc22 mice in a C57BL/6J x CBA/Ca background, which have 7 copies of the human PMP22 gene. The CC22 mice were then backcrossed with wild type for ten generations. The researchers then isolated mice with milder phenotype and reduced PMP22 compared to the CC22 mice (3 or 4 copies instead of 7), and had a more stable genotype. All 3 types, The mild phenotype, C3-PMP, wt, and C22 were used for the experiment.

Experiment 1: neuromuscular SHIRPA

    In this experiment, the mice were assessed for neuromuscular function using the SHIRPA protocol. SHIRPA protocol contains 19 items to check for, such as body tremors and spontaneous activity as well as tail elevation. Using the items, the mice were each given a score from 0 to 43. 

Experiment 2: Electrophysiology

    In this experiment, mice were anesthetized and the sciatic nerve and caudal nerves were studied on an EMG machine to study motor conductivity. The electrodes were placed at the medial ankle and at the sciatic notch. Wave pulses were delivered and CMAP amplitudes were recorded the MNCVs were calculated. The needle electrode was inserted again to study the caudal nerve and CNAP and NCV were recorded

Experiment 3: Histology and Morphology

.     Mice were deeply anesthetized, blood was flushed shout and the body was preserved. Then the peroneal, femoral, and lumbar nerves were physically removed and fixed in formaldehyde overnight.  The samples were then processed into the resin, and light and electron microscopy were performed on the samples. The samples were stained using thionine and acridine orange for light microscopy and stained with methanolic uranyl acetate and lead citrate for electron microscopy. Morphology was performed by fitting the nerve to the stage and cross-section of the nerve were analyzed. 

Post experiment: Statistics. 

The data was gathered from the experiment were analyzed using descriptive statistics. The differences between the different mice were evaluated using the unpaired t-test.

The goal of the research was to study the pathology of myelin and axon in PMP22 overexpressing mice, a mouse model often used for CMT1A. The research question that is asked in the research is what is the change to the mice’s muscle tone, electrophysiology, and histology in the course of 1.5 years?

The experiment showed that the phenotype that is measured through noninvasive measures is indicative of certain morphology of the cells in mice and that the disease gets worse both in behavior and in morphology, histology, and pathology as the mice age. In addition, the C3 mice, in general, had less severe symptoms compared to the C22 mice but had symptoms whereas the control did not have any symptoms. In general, the C3 mice would be the better model for CMT1A.

The impact of this research on the disease is the creation of new model of CMT1A mice, which have a relatively more mild symptoms, and as a result would be more effective model compared to C22 model. This is important because the severity of C22 mice means that the treatment that work in C22 model would less likely be able to work in humans because humans generally do not have symptoms that severe. By having a less severe model, it will allow better replication in humans, saving time and money. 

Today scientists know that actin, a protein structure in the cell, and myosin, motors running on actin structures, produce the phenomena known as cytoplasmic streaming (CS). CS is the movement of vesicles, organelles, and other cargos through the cell. This movement has been observed for a long time, however, scientists wanted to isolate exactly which structures in the cell facilitated this movement. In order to know how something works in biology, it's broken, usually in one of two ways. Either add a drug/compound to disrupt the processes, or genetically modify a specific gene. In this case, scientists used the drug approach. There were three factors scientists believed may be associated with CS, Actin, microtubules, and protein synthesis. Drugs inhibiting each respective factor were introduced. CS stopped in the Actin trial only. To verify the other two factors weren't important for CS a mix of drugs was added and in both when the actin inhibitor was introduced, CS stopped. 

Plants and animals owe their regenerative and replaceable properties to a class of cells known as stem cells. Plants specifically have 4 types of stem cells, also called meristems, scientists have identified and studied. First, is the shoot apical meristem (SAM). SAM's can be found at the tips of growing shoots as small translucent clumps. They're encased by a protective cover of the differentiated cells they've recently produced as to prevent any damage. Second, are auxiliary meristems. These meristems determine the sites of leaf growth and leaf categorization. If off the main shoot there is a leaf and an auxiliary meristem between the two, this leaf can be classified as a simple leaf. A shoot next to an auxiliary meristem next to a branch with leaves classifies the branched leaves as compound leaves, where each individual leaf is a leaflet. A shoot next to an auxiliary meristem next to a branch off of which smaller branches appear with leaves is classified as a doubly compounded leaf. Third, is root apical meristems (RAM). RAM's appear at root tips with a hard shell protecting the absolute tip. This is because, unlike the SAM, the roots are more susceptible to damage. Similar to the SAM's these cells grow the roots out while also producing more meristematic cells. Fourth is cambium cells. There are two cell types that fall under the cambium denomination; the cork cambium, and the vascular cambium. The cork cambium includes the bark and phloem on a plant near the outside. The vascular cambium includes some of the phloem and xylem cells on the inside of the plant.

When deciding on a topic for my research proposal, I began with going to the Umass Amherst Libraries page. While on this page, I thought about the different kinds of projects that I could construct. I wanted to choose a topic that I would be able to replicate and write a methods for. I decided to search for eye colors in populations. I thought it might be interesting to do a proposal project analyzing the percentage of certain eye colors in the Umass population. I searched through the given options and looked for an article that had a literature review. I chose an article called, “A pupil center detection algorithm based on eye color pixels differences.” I felt that this topic would be relevant to my research proposal. I clicked on the link and was directed to a page on the Umass libraries with the entire article.