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Discussion Paragraph Bio 477H

Submitted by oringham on Wed, 02/14/2018 - 00:09

The rhodamine labeled f-actin did not appear in the composite image of the three different fluorophores due to the intensity of the fluorescence being too low to register. This could be due to photobleaching that had previously occurred in this specific area of the sample, or if the sample was not labeled adequately with enough fluorescent dye. Time-lapse data for all three fluorophores under the same condition revealed discrepancies in rate of decay and initial intensity for each fluorophore. A relative high initial intensity for DAPI labeled dsDNA can be explained by the relative high net local concentration of bright fluorophores. Each nucleus contains a high concentration of dsDNA, which when stained with DAPI, creates a large solid fluorescent region with overlapping fluorophores. This differs from both tubulin and f-actin, which are of tube like nature, and appear as porous regions of interest where background light can seep through and be analyzed, making the initial brightness in the region of interest inherently darker. This difference is also reflected in the rates of decay, where in samples where there is less light to be diminished, the rate of decay appears much slower as it approaches the plateau of photobleached darkness. Time-lapse data for fluorescein under stained tubules under different conditions demonstrated discrepancies in rate of decay and initial intensity for all three conditions. The relative low rate of decay and low initial intensity for the images taken with a neutral density filters and auto shutter can be explained by the effect of the neutral density filter. The collective effect of the neutral density filters decreases the intensity of the epi-illumination light path by a factor of 32. This in turn lowers the ability for the fluorophores to be excited, causing a low initial intensity and low excitation, which leads to a lower rate of decay. The auto shutter condition displays a lower rate of decay compared to the open shutter condition due to the lower exposure to light over time. When the shutter is left on automatic, the sample is only exposed to light during the time an image is snapped as opposed to the entire duration of the time lapse. This lessens the time window that fluorophores can covalently bond to oxygen and other elements, and less brightness is lost over time. The open shutter condition leaves the sample exposed to the epi-illumination light path during the entirety of the time-lapse, allowing more time for covalent bonds to form with fluorophores and thus lose more brightness intensity over time. This explains the high relative rate of decay.  

Methods Section

Submitted by mglater on Tue, 02/13/2018 - 20:54

The plant was located by entering the Durfee Conservatory via the West entrance. The plant was the closest in the left row along the aisle. To photograph the whole plant, the photographer stood by the entrance door and aimed his phone camera at the plant. He then walked backwards towards the right of the building until the whole plant could fit in the frame of the picture. The close-up picture of the flower was taken of the closest flower to the door along the aisle side of the plant. The phone was moved close to the flower in order to frame the flower in the image and the photo was taken. To provide a scale, another picture was taken with a “Dunkin Donuts” gift card held above the flower. The name of the plant was taken from a card on the pillar from which the plant was growing.

 

Endomycorrhizae vs Ectomycorrhizae

Submitted by brettconnoll on Mon, 02/12/2018 - 16:21

In many species of plants, there is a symbiotic relationship happening in the roots with a species of fungus. The fungi are put into a diverse group called mycorrhizae which means "fungus root" or "root fungus". The mycorrhizae help the plant by increasing surface area to the roots allowing for more nutrient absorption and in some instances even protecting the root. The fungi benefit from working with the plant by being supplied sugar that the plant makes from photosynthesis. There are also species of mycorrhizae that are parasitic and are not helpful to the plant because they just take away all of the plant's resources. The diverse group of mycorrhizae is broken up into two larger groups based off of their morphology: endomycorrhizae, ectomycorrhizae. Endomycorrhizae, also known as arbuscular mycorrhizae, forms along the outer surface of the root and exchanges nutrients with the plant by inserting itself inside the plant cells. The complex the mycorrhizae forms with the root cell is called an arbuscule. Ectomycorrhizae form on the external surface of the root and exchange nutrients through the cell walls of the root cells staying outside of the cells. The ectomycorrhizae forms a complex with the root cells called a Hartig net. Mycorrhizae are extremely important to the overall function of many species of plants it is a symbiotic relationship that not only helps run ecosystems but helps to power our agriculture.

Green Chemistry

Submitted by malberigi on Mon, 02/12/2018 - 12:54

Green chemistry is set of principals whose purpose is to guide and regulate the production and use of new chemical undertakings in all facets of human life.  These principals are as follows.  It is better to prevent waste than to treat or clean up waste after it has been created.  Synthetic methods should be designed to maximize the incorporation of all materials used in the process into the final product with as little waste as possible.  Wherever practical, synthetic methods should be designed to use and generate substances that possess little or no toxicity to human health and the environment.  Chemical products should be designed to affect their desired function while minimizing their toxicity.  The use of auxiliary substances (solvents, separation agents, etc.) should be made unnecessary wherever possible and innocuous when used.  Energy requirements of chemical processes should be recognized for their environmental and economic impacts and should be minimized.  If possible synthetic methods should be conducted at ambient temperature and pressure.  These principals set the guidelines used by chemical companies all over the world to allow for safe and environmentally friendly use and production of chemical products

Leaf Anatomy

Submitted by rmirley on Mon, 02/12/2018 - 00:13

A plant leaf is composed of several layers. On the outside of the leaf, both top and bottom, there is a waxy layer called the cuticle. This layer helps to prevent water loss from the leaf so that the plant can have more control over its transpiration rates. The next layer is the epidermis, which is also on the top and bottom of the leaf. This layer serves primarily for protection of the internal structures of the leaf. The next layer from the top is the palisade layer. This layer is denesly packed and is primarily used for photosynthesis. The final layer from the top is the spongy mesophyll layer. This layer is thick, but loosely packed together. While it has some photosynthetic function, its primary purpose is to facilitate the gas exhanges within the leaf.  

Movement of Water- Perfect Paragraph

Submitted by benjaminburk on Sun, 02/11/2018 - 21:22

Water is one the most presen organic molecules on the planet. It is a foundation of organic life, without it humans are unable to survive. Water is a required reactant for various metabolic reactions, so one would be safe to assume that it moves from cell to cell with ease. And this is true most of the time water simply diffuses across the a membrane via a process of simple diffussion , called osmosis. This process though the most well know form of water movement is not the only way water moves through cells. Other processes include bulk flow, which is the movement of water and solutes due to pressure potential. This occurs in the xylem and phloem of plants. This transport as stated previously is primarily used to move large amounts of water throughout  system.  There is also the process of active transport, which normally occur when transporting over a membrane with very low permeability. In general water moves throughout the body and from cell to cell in various ways and without these processes life as we know it would cesae to exist. 

Green Chemistry

Submitted by malberigi on Sun, 02/11/2018 - 17:55

Green chemistry is set of principals whose purpose is to guide and regulate the production and use of new chemical undertakings in all facets of human life.  These principals are as follows.  Prevention: it is better to prevent waste than to treat or clean up waste after it has been created.  Atom Economy, where synthetic methods should be designed to maximize the incorporation of all materials used in the process into the final product with as little waste as possible.  Less Hazardous Chemical Syntheses: where ever practical, synthetic methods should be designed to use and generate substances that possess little or no toxicity to human health and the environment.  Designing Safer Chemicals: chemical products should be designed to affect their desired function while minimizing their toxicity.  Safer Solvents and Auxiliaries: the use of auxiliary substances (solvents, separation agents, etc.) should be made unnecessary wherever possible and innocuous when used.  Design for Energy Efficiency: energy requirements of chemical processes should be recognized for their environmental and economic impacts and should be minimized.  If possible synthetic methods should be conducted at ambient temperature and pressure.  These principals set the guidelines used by chemical companies all over the world to allow for safe and environmentally friendly use and production of chemical products

Your Inner Fish

Submitted by crmckenzie on Fri, 02/09/2018 - 19:17

"Your Inner Fish" is the first episode of a documentary series about a vertebrae paleontologist named Neil Shubin. The focus of this episode is to discuss how humans evolved from fish. It considers Darwin's common ancestor theory and talks about how the same basic structure of forelimbs exists in both mammals and their fish-like ancestor. Birds and reptiles also share this common ancestor. There are significant similarities between the human embryo and the fish embryo. The portion of the human embryo that corresponds to gills in the fish embryo forms the lower jaw, middle ear, and voice box in humans. This correspondance represents the developments of evolution. A gene called hedgehog tells cells how to carry out events in a specific order during development. When this gene is overexpressed, it can result in extra fingers. When underexpressed, it can result in less than five fingers. The episode ends on the Tiktaalik, the missing link in the line of evolution between fish and humans. This is the creature that paleontologists have been searching for as it has the same forelimb pattern as humans.

 

What is Ethnonationlism?

Submitted by ameserole on Fri, 02/09/2018 - 12:27

Ethnonationalism is like nationalism in that it is a way to find sense and belonging within a group, but ethnonationalism emphasises the person’s ethnicity rather than where they live. These movements band people together based on their ethnicity regardless of their location. An example of this is seen during the fall of the Soviet Union, which encompassed many satellite countries near Russia such as Latvia, Estonia, and Lithuania. At the time they weren’t countries, but as the citizens began to see the Soviet Union fall, they began to identify with their region and ethnic identities rather than with the union they were a part of. Another example is Israel’s “right to return”, which grants every ethnically Jewish person the right to return to Israel, and be granted citizenship. This shows they identify with a place they may not live.

PP - Protein misfolding disease

Submitted by jonathanrubi on Fri, 02/09/2018 - 12:22

Protein misfolding can occur through a number of mechanisms and lead to a large variety of disease and misfunction. One pathway for protein misfolding and pathogenesis is improper degradation of proteins. Improper degradation occurs when proteins that are partially functional and can actually benefit cellular processes are degraded despite it being detrimental to the cell. This is seen in the case of cystic fibrosis, where a deletion of a phenylalanine in CFTR leads to partial functionality but is still targeted for degradation by CHIP, a molecular chaperone which ubiquitylates the protein. CFTR is an important membrane channel for the production of mucus, which is why this improper degradation is seen in a large number of cystic fibrosis patients.  Another way in which improper folding can lead to disease is through improper localization. Improper localization occurs when misfolded proteins cannot get to where they need to go, leading to not only a loss-of-function but potential toxicity if aggregated in the wrong place. One example of this is misfolded antitrypsin, which becomes retained in the ER of liver cells and accumulates, preventing synthesis of other proteins resulting in liver damage. Also, since antitrypsin does not get secreted to its proper location, it is unable to inhibit protease activity in the lungs leading to damage in the alveoli and emphysema. Another mechanism for pathogenesis as a result of protein misfolding is dominant-negative mutations. Dominant-negative mutations are characterized by mutant proteins that compromise the function of wild-type proteins, most often in a dimer or quaternary structure. An example of this process is seen in the connective tissue disorder epidermolysis bullosa simplex. When mutant forms of keratin proteins are present, they disrupt the function of the entire keratin composed filament, leading to fragile skin that blisters easily in response to minor friction. Gain of toxic function and amyloid accumulation are two other mechanisms for pathogenesis as a result of misfolding and play a big role in neurodegenerative disorders.

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