Topics in Plant Bio Notes - Cell Expansion and Walls II

Submitted by samihaalam on Tue, 11/21/2017 - 01:51

The cell wal is a very important feature in plant cells. It determines the mechanical strength of the cell, ascts as an exoskeletion controlling shape and allowing high turgot pressure to develop, and acts as a barrier by limiting the size of molecules that can reach the plasma membrane. Additionally, the cell wall can expand and change shape, whic controls the overrall shape of the cell. Plant cells walls are the most abundant source of organic carbon in nature. 

There are two cell walls in plants. The primary cell wall is forme by growing cells and is relatively unspecialized. It is the outermost cell wall layer. The primary cell wall includes the Zone of Cell Elongation and the Zone of Cell Division. 

The secondary cell wall is formed after cell growh has stopped and id highly specialized - both in structure and composition. This is determined by how the cell has differentiated. This is the next inner cell wall layer. This includes the Zone of Cell Differentiation and the mature cells layer. Plant cells also have a plasma membrane, on the inside of the secondary cell wall. 

It is very important for cells to keep ions, sugars, and metabolite levels controlled in their cells. The plasma membrane plays an important role in this. It is permeable to water, oxygen, and carbon dioxied, but other compounds need to actively transported  into the cells via protein channels. H+ is an exmple of an ion that needs to be actively transported across the membrane. A difference in H+ concentrations inside and outside the cell causes a pH gradient across the membrane. Proton gradients and electrical gradients are be harnessed to actively transport other molecules. 

Osmosis can help to change the size of the cell because the plasma membrane is permeable to water, but not solutes or ions dissolved in the water. This means that if there is a high concentration of ios inside the cell, osmosis will drive the water inside of the cell as well, to balance out the high amount of solutes. Thus, the cell will swell, as there will be a lot of water entering it. This movement of water causes turgor pressure. 

This turgor pressure happens due to the cell wall in plant cells. When the cell swells with water inside of the plasma membrane, the plasma membrane will eventually reach a point where it is fully stretched out and is pressed up against the secondary cell wall in the plants. The cell wall will push back against the cell, and won't allow more water to enter the cell. The plasma membrane and the cell wall pushing against each other causes a pressure called turgor pressure inside the cell. 

Water can enter the cell through simple diffusion, or it could enter the cell through aquaporins- portein channels that are selective for water specifically. If there is high turgor pressure in the cell, enzymes in the cell wall will work to loosen the cell wall sugars so that the cell wall itself is loosened, and thus the cell wall expands. There will be less pressure with an expanded cell wall because the plasma membrane will no longer be pressing up right against it. This will then allow for more water to enter the cell, as the turgor pressure has been reduceed due to the expanded cell wall. Thus, an uptake of water will cause plant cells to grow, due to turgor pressure. 

Limb devo 2

Submitted by daniellam on Mon, 11/20/2017 - 21:52

Hox is a turing model not a gradient model like Shh

Hox uses the turing model which forms alternating and repeating patterns using an activator and an inhibitor. The activator turns on itself and the inhibitor that is far away from the activator. Once the inhibitor is on, it turns off the activator as well as itself. These two interact to form a standing wave, showing areas where the activator is on (inhibitor off) and others where the inhibitor is on (activator off) (Bartlett 2017).

Digits form independently from Shh

Scientists found that the formation of fingers used the Turing model rather than the gradient model by removing Shh and Gli3 which both use the gradient model. What they found was that even after removing Shh and Gli3, fingers still formed. During development, Hox works by regulating this Turing model and increases the wavelength. The increase in wavelength allows for correct finger formation. Without this increase in wavelength, the spaces in between the fingers do not form properly and extra fingers can form. The scientists observed this phenomenon by removing Hox genes from developing mice embryos (Fig. 3). The hands with more Hox genes removed had more, thinner fingers with less space in between. After removing all of the Hox genes, they saw that there was only a stump (Sheth et al. 2012).

Trimyristin discussion perfect paragraph

Submitted by msgordon on Mon, 11/20/2017 - 19:31

In this lab, trimyristin and myristic acid was synthesized from nutmeg in the presence of tert butyl methyl ether, sodium hydroxide, ethanol, and hydrochloric acid through reflux, recrystallization and hydrolysis. The melting points of the once recrystallized and twice recrystallized trimyristin were found to be 40℃-43℃ and 42℃-44℃ respectively. The melting point of myristic acid was found to be 46℃-48℃. These values are well below the literature values (56℃-57℃ for both trimyristin and myristic acid) and suggest that there were impurities present in the recrystallized trimyristin and the hydrolysis product. Thus, it is possible that the products were contaminated with solvent as contaminants would interfere with the lattice structure, leading to a lower melting point. The percent recovery of crude trimyristin was found to be 16.67%. This was to be expected as trimyristin is only a component of nutmeg and thus the possible yield is limited. The percent recovery for the once recrystallized trimyristin was 95.8% while the percent recovery for the twice recrystallized was  60.7%. The percent recovery of the second recrystallization could have been improved by using less acetone to prevent the dissolution of product while it cooled. Another portion of this mass loss can be attributed to the loss of product during suction filtration. As 3 moles of myristic acid is generated for every mole of trimyristin, the theoretical yield of the reaction was found to be 0.055 grams, however the mass of the product was 0.039 grams. As a result, the percent yield of myristic acid was found to be 70.9%. This mass loss can be attributed to losing product that was dissolved in the sodium hydroxide and ethanol mixture, as well as not using enough hydrochloric acid to precipitate myristic acid out of the solution.


Submitted by msgordon on Mon, 11/20/2017 - 19:28

Chondrostei is comprised of Polyodontidae and Acipenseridae. Psephurus is a member of the Polyodon family that is presumed to be extinct - the last known specimen was caught in 2007. Was found in the middle - lower part of the Yangtze and associated bodies of water. Brought to extinction b/c of the three gorges dam and illegal fishing. Polyodon occurs in the Mississippi River, Missouri River, Ohio River and associated systems. It is a ram feeder and filters zooplankton out of water column w/ gill rakers. The paddles found in Polyodontidae specimens serve as electrosensory organs used to detect changes in electric fields. Similar to ampullae of Lorenzini, used to detect plankton.

Zebrafish lab intro

Submitted by cberg on Mon, 11/20/2017 - 18:33

In the paper Growth and metabolism of larval zebrafish; effects of swim training, it was discovered that once zebrafish hit a certain age it is more difficult for them to acclimate to chronic swimming because their rate of oxygen consumption does not adjust to conditions of hypoxia as readily. In this specific experiment, that age was 21 days old. The data found that fish who had reached this age had significantly higher routine oxygen consumption and mass-specific routine oxygen consumption values after 8 and 11 days of being trained to swim at various numbers of body lengths per second, when compared to fish only 96 hours or 9 days old.

We found this paper to be interesting because it compared metabolic rates of fish based on their age and stage of development. The findings applied to the experiment conducted in our lab because all fish we used were adults, and therefore greater than 21 days old. Therefore, because our fish would be less able to adjust to hypoxic conditions, it would be very possible to observe changes in their metabolic rate based on significant differences in their oxygen consumption over time. We decided to apply this knowledge towards an experiment in which we would examine the effects of gender socialization on adult zebrafish.


Submitted by dalon on Mon, 11/20/2017 - 08:56

To a 5 mL RB flask, 0.95 mL of propionic acid and 0.824 mL of n-propanol was added via pipet. To the RB flask, 4 drops of sulfuric acid were added and the mixture was thoroughly mixed by drawing the contents into a pipet and then releasing. After mixing, boiling chips were added to the RB flask. The RB flask was then connected to an air condenser and a side arm with the side arm pointing 45°downwards towards the sand-bath. The flask was lowered into the sand-bath and gently boiled for 15 minutes after the first water droplets were observed in the side arm. After 15 minutes, ½ of the contents in the sidearm were dropped back into the RB flask and the apparatus was lowered again and heated another 15 minutes. The sidearm was then again tipped until the upper phase of the side arm was in the flask, and the mixture was heated for another 15 minutes. At the end of the last 15 minute window, the apparatus was removed from the sand-bath and allowed to cool to room temperature for 12 minutes. After cooling, the mixture was removed from the flask into a centrifuge tube containing 1 mL of water via pipet and the two layers were mixed in the tube. The aqueous layer was then removed to liquid waste. To the centrifuge tube, 1 mL of saturated aqueous sodium bicarbonate was added and the layers were mixed again and the lower layer was removed. To the remaining mixture in the tube, 1 mL of saturated aqueous sodium chloride was added and mixed, and the lower layer was removed. The organic layer was then pipetted into a new vial and 4 spheres of anhydrous CaCl2 were added and swirled in the mixture. The vial was then left to sit for 5 minutes and after 5 minutes the remaining liquid was moved to a new vial. The odor of the product was then noted and an IR spectrum test was performed.


Limb devo

Submitted by daniellam on Sun, 11/19/2017 - 22:53

Scientists from Spain have discovered a way to not only increase the amount of fingers in mice but increase them to the point that they all connect to one another and form a stub for a hand. How is this possible? Fingers form from the hand during development in a wave-like fashion. If one imagines a standing wave with multiple peaks, in this case, the peaks pointing upward are the fingers and the spaces in between the peaks are the spaces in between the fingers. The spaces from the hand to the fingertips increases. This increase in space is due to a gene called Hox. Unlike its counterpart, Shh, which forms the identity of the fingers, Hox determines the number of digits formed. When there is a mutation in this gene (the gene stops working), extra fingers form on the hands (Sheth et al. 2012). 


Submitted by dalon on Sun, 11/19/2017 - 08:01

The reason the brain is so sensitive to changes in blood flow is because of the tight regulation of what goes in and out of the brain, which is maintained via the blood brain barrier. In order for molecules to move into the brain, they must pass via the endothelial cells. Gases and hydrophobic substances can cross via diffusion; however, substances such as carbohydrates and amino acids are dependent on mediated transport, and are selective for very specific molecules; therefore, any changes to which molecules are present in the blood at the time could impact the flow of molecules into the brain via the tightly regulated blood brain barrier; however, because the brain relies on glucose to function, there is a specific mechanism for glucose to cross the blood brain barrier. Glucose can readily cross the blood brain barrier by facilitated diffusion because transport proteins that carry the glucose are found in the cell membranes. Thus, glucose is carried over by GLUT-1 carriers, independent from the GLUT-4 carriers that rely on insulin. 

Ecology Assignment 5

Submitted by hamacdonald on Sat, 11/18/2017 - 21:19

Hailey MacDonald

Ecology 287

November 18th, 2017

Assignment A5


Part A (3 pts): Fig. 1 shows the relationship between local and regional species richness in a hypothetical region. Do you expect to observe this relationship between regional and local species richness in nature? Explain. (That is, if no, why not? If yes, why and under what circumstances?)


            I would not expect to observe this relationship between local and regional species richness in nature. The slope of the line produced in Figure 1 is higher than one meaning the local richness is higher than regional richness. It would not be possible to observe a higher local species richness than regional species richness because the total amount of species found in the local area also factors into the number of species in the regional area meaning the regional area would have to have a higher number of species richness.


Part B (6 pts): You are investigating patterns of species richness on two different continents to determine how local and regional species richness varies between them. Your two study areas are study area 1 and study area 2. For each study site, you sample the local species richness in a small area that is a subset of the entire site, and then find the regional species richness for the whole site. Your data are shown in Fig. 2. Which process, regional or local, is the dominant driver of the pattern in each study area? Explain your answer


            For Study area 1, regional processes appear to be the driving limiting local diversity. This is because the line forms a linear slope which means dispersal is limiting local richness growth. The regional richness is increasing at a steady rate and the local richness is slightly less. This means dispersal must be the issue because the species are not going to enough local areas to increase the local richness at the same rate as the regional richness.

            In the Study area 2, the driving limiting factor is local processes. This is what forms the horizontal line. The local processes most likely abiotic factors such as limited resources. These limit the local richness even with the addition of more species to the region.


Part C (3 pts): Now imagine you’re studying species richness on islands. Do you think the regional species richness on the mainland will affect how many species are predicted to be found on an island based on the equilibrium theory of island biogeography? Why or why not?

            I do think if the mainland has a higher species richness that the island will also have a high species richness and if the mainland has a lower species richness the island would similarly show lower species richness. The more species that exist on the mainland increases the chances that these species will immigrate to the island. The more species on the mainland competing for resources would likely encourage more species to immigrate to the island.


Amiids and Hiodons

Submitted by msgordon on Sat, 11/18/2017 - 20:36

Amiidae: sole living species: Amia calva. Found in slow waters with lots of vegetation. Generally found in eastern New England. Has vascularized swim bladder that allows it to breathe air (physostomous swim bladder). Males build nests in weedy areas —> clear weeds. Males then defend eggs and young. 

The Hiodons are the Mooneye fishes, found across North America. Have extremely large eyes, pectoral fins located at midline of body, whitish color. Hiodon tergius is found in NE.


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