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Reflection Methods

Submitted by samihaalam on Wed, 12/13/2017 - 20:25

At the start of the Methods Project, I didn't really know what to expect. I was very not used to writing in small chunks. I was used to trying to stay up all night the night before an assignement was due and trying to finish assignment, especially writing ones. So, I expected this class in general to be challenging and new to me. And at first, I did struggle with writing a little bit every day. But, as the weeks went on, I improved. And, it was pretty helpful to write this way, because when the rough draft was due, the night before it was due, I was expecting a long night trying to complete it. But, I had discovered that since I wrote a little chucnk of the Methods project each day, I had already completed most of it, and I only mainly had to edit. This came as a surprise to me, as I had been so used to doing my writing one way, so I was surprised when this method worked out surprisingly well for this project. I think I will therefore try to continue this way, writing in small chucnks, every day for future assignments. 

Topics in Plant Bio Notes - Flowering III

Submitted by samihaalam on Sun, 12/10/2017 - 21:53

In plants, flower induction is when a plant has started floral production, and it is irreversible. More specifically, it is when the apical meristem starts to produce floral organs instead of stem or leaf organs. Plants become induced due to favorable conditions in the environment. Due to the irreversible nature of them, once induced, even if conditions then become non-inductive, the plants will continue to flower.

There is a critical day length in determining LDP or SDP in plants. LDP is promoted when day length exceeds a certain duration, while SDP is promoted when day length is less than the critical day length. Previously, it was a question of whether plants measure the length of day or the length of night. It turns out, plants really measure night length, or the length of darkness. This was demonstrated because in SDPs, they will flower when the length of day is less than a certain critical duration in a 24 hour cycle. In other words, the length of night must exceed a critical point for flowering to occur. In an experiment, the critical period of darkness exceeded the critical point, but it was also interrupted by a flash of light. This caused the flower to not bloom. For this reason, it would probably make more sense for SDPs to be called Long-Night plants instead. Conversely, LDPs flower when the day length exceeds a critical amount of time within a 24 hour cycle, or when the amount of night time and darkness is less than a critical period. This can be shown from experiments in which experimenters expose an LDP to a certain of night time that is too long, so it should not induce flowering. However, when a light is shined during the dark period, flowering occurs in these LDPs. Similarly, it would probably be more accurate to call these plants “Short-Night Plants”. Other experiments were done in both SDPs and LDPs, and it is now known that the dark period is the critical one, not the amount of light period. This is exceptionally noticeable in experiments where the entire days were less than 24 hours or longer than 24 hours. When less than 24 hours, there appeared to be about an even amount of light and darkness, but since it was less than 24 hours, it was a short cycle of each condition. This condition therefore induced the LDP into flowering while the SDP remained in its vegetative state, because the night length was less than the critical periods for both the SDPs and LDPs. When the days were over 24 hours, there was an extra long night time period. This led to he SDPs flowering and the LDPs remaining in their vegetative step. This also makes sense, because the night period would have exceeded the critical point for the SDPs and the LDPs. 

Topics in Plant Bio Notes - Flowering II

Submitted by samihaalam on Sun, 12/10/2017 - 13:59

Soybean flowering is controlled more by day length than the number of “days-to-flowering”. In other words, soybeans flower based on the length of days, instead of the “age” of the actual plants. This can be shown through the farming of soybeans. Regardless of when farmers plant their soybean crop, they will all have a relatively synchronized blooming in the autumn, suggesting that the length planted was not important to the plants.


There are two types of ways that plants can bloom: short day plants and long day plants. Short day plants bloom when the days are short, such as in the autumn and winter. This includes Morning Glories. Long day plants bloom when the days are long, such as in the summer. This includes the plant Henbane.

Photoperiodism is the ability of any organism to detect day length, not just plants. Humans and other mammals have this ability as well, as evidenced by our circadian rhythms. So, this is a common ability of organisms. There are different ways to categorize the photoperiodic response in plants specifically. There are short day plants and long day plants as described above. The short day plants more specifically flower only in short days (which is a qualitative SDP response) or are accelerated by short days (which is a quantitative SDP response). Another example of an SDP is the plant Cocklebur, which remains vegetative if the day is 16 hours long, but flowers if the days are 15 hours long. This seems to be an example of a qualitative SDP response. The long day plants more specifically flower only in long days (which is a qualitative LDP response) or their flowering is accelerated by long days (which is a quantitative LDP response). For example, the plant Lolium temulentum rye grass flowers when the day length is greater than 14 hours. This seems to be an example of a quantitative LDP response. There are also day-neutral plants (DNP) which are plants whose flowering is insensitive to day length.  

Topics in Plant Bio Notes - Flowering

Submitted by samihaalam on Sat, 12/09/2017 - 15:16

Flowering in plants needs to be a very strictly temporally regulated process. Flowering is officially when the plant moves from a vegetative state to a reproductive state. It needs to occur when the plant is large enough to "feed" the seed with photosynthates. There are several environmental conditions that need to be considered by flowers before they bloom. These include temperature, moisture, light, mate, and pollinator conditions. Plants at different latitudes thus experience  different day lengths. This, of course, has an effect on the cycles within the plants that occur at these different lattitudes. Day length changes because the Earth  is tilted and revolves around the Sun at this tilted angle. Therefore, a certain lattitude will get a certain amount of sunlight during one part of the year, but a few months later, the earth has rotated around the Sun and is at a tilt, and so it will get a different amount of the sunlight. 

Plants can be categorized by their photoperiodic responses. In 1906, a mutant tobacco plant was discovered that flowers in the winter and ust grows and grows in the summer, as opposed to flowering in the summer like normal tobacco plants. This mutant plant is called the Maryland Mammoth. It's unusual flowering ability is due to a recessive gene that is involved in short-day behavior in flowers. 


Topics in Plant Bio Notes - Light Perception II

Submitted by samihaalam on Sat, 12/09/2017 - 02:00

A phytochrome has two identical proteins that join together. Each of these proteins has two domains. One of these domains is the part that acts a photoreceptor. The structure that is specifically the photoreceptor is the chromophore, which captures light and undergoes conformational change. The other domain is the kinase domain, which triggers cellular responses. The phytochromes interconvert between an inactive and an active form. The Pr form abosorbs red light, and is synthesized in this form. This is the stable form of the protein. The Pfr form absorbs far-red light and is the active state of this protein. It is also the unstable protein and is degraded quickly, indicating that the active protein is fast-acting, with short effects in the plant cells. These responses include seed germination, control of flowering, and other various responses. After the Pfr form relays it effects, it is either slowly converted back to the Pr form in darkness in some plants, or it is sent to the lysosome to be destroyed. The red light being absorbed in the plant by the chromophore results in the the cis (Pr) isomer converting to the trans (Pfr) isomer. The response to light is transfered along the cell due to the movement of the phytochrome from the cytosol to the nucleus. When in the nucleus, phytochromes interact with to regulators of transcription. Therefore, light causes changes in gene expression. Phytochromes are not restricted to higher plants. The chromophore-binding region and signaling domain are highly conserved regions in prokaryotes, bacteria, and higher plants. Phytochromes are encoded by a multigene family, that has different functions in plant cells. They are responsive to different wavelengths and light intensities. PhyA activates a response to far-red light, while PhyB activates a response to red or white light. 

Elevator Speech

Submitted by samihaalam on Sat, 12/09/2017 - 00:26

Planarians exhibit the rare ability to regenerate their entire heads and central nervous system after being cut off. We also knew that an excess of salt can have a harmful effect on living tissues, so we wanted to observe the effects of different salt concentrations on the regenerative abilities of planarians. We cut the heads off of planarians, and then put the tails in different concentrations of salt. The control had no added salt, the low concentration had 1 gram of salt, and the high concentration had 2 grams of salt mixed into small water bottles. There were 3 planarians for each concentration. We measured the length of each planarian 3 days a week for 2 weeks. Our hypothesis was that higher salt concentrations would lead to a slower regeneration rate of the planarian head. Unfortunately, the planarians in both the low concentration and high concentration salt water died before we returned from Thanksgiving break, so we could not observe any growth in them. So, our results were inconclusive. Further studies at a lower, more precise concentration of salt are needed to fully observe the impact. 

Topics in Plant Bio Notes - Light Perception

Submitted by samihaalam on Fri, 12/08/2017 - 23:59

The mistletoe tree can get invaded by parasitic bushes. The Vikings used to think that these were a sign of good luck, ass they would be green plants in the winter, but they are in fact parasites. About 4000 biotrophic plant species are parasites. These plants have lost their ability to perform photosynthesis, and so they parasitize. For example, the species Striga can produce up to 500,000 seeds that sense roots of other plants, and germinate and grow towards. Plants convert sunlight into energy, which is processed through photosynthesis. Certain information is considered about the sunlight, such as he quantity, quality, direction, and photocycle about the sunlight. This leads to photomorphogenesis in the plant, which is all the different types of responses in the plant to the light. 

Photomorphogenesis is light-mediated regulation of plant growth and development. This involves the proccess of de-etioation, which is the transition from dark to light grown seedlings. It is characterized with the plant having short stems and there is an initiation of green leave and internodes. On the other hand, skotomorphogenesis is the development of the characteristic growth and appearance of plants grown in the absence of light. The plants in this category are characterized by etiolation, which is when th plants have exaggerated, long, spindly growth, pale color due to a lack of chlorophyll, and stunted leaves. Photoreceptors detect light of different wavelengths. A photoreceptor is a pigment in a protein that initiates a signal-transduction cascade when exposedd to light of a specific wavelength. Cryptochromes and phototropins respond to blue light. Phytochromes respond to red and far-red light and include phyA, phyB, phyC, phyD, and phyE. They can induce a photoreversible response. This means that red light stimulates growth, while far-red light inhibits growth in plants. This can be seen in lettuce seed germination. 

Elevator Speech Draft

Submitted by samihaalam on Thu, 12/07/2017 - 22:05

Planarians have a rare ability to regenerate their entire heads and central nervous system after being cut off. We also know that an excess of salt can have a deleterious effect on living tissues, so we wanted to observe the effects of different salt concentrations on the regenerative abilities of planarians. We cut the heads off of planarians, and then put the tails in different concentrations of salt. The control had no added salt, the low concentration had 1 gram of salt, and the high concentration had 2 grams of salt mixed into a small water bottle. There were 3 planarians for each concentration. We predicted that higher salt concentrations would lead to a slower regeneration rate of the planarian head. We measured the length of each planarian 3 days a week for two weeks.

We found that both the low and high salt concentrations resulted in the planarians dying. The lower salt concentration left the bodies mostly intact, but shriveled up, whereas the higher salt concentration left the bodies very disintegrated, often leaving the bodies in many small fragments. So, in the end, the results were mostly inconclusive, as the planarians died before we had a chance to see them grow at all. Further studies at a lower, more precise concentration of salt are needed to fully observe the impact. 

Topics in Plant Bio Notes - Plant Pathology Part III

Submitted by samihaalam on Sun, 12/03/2017 - 20:12

In biotrophic pathogens, they usually contain specialized feeding strutures to steal nutrients from host plants. For example, one of them is called a haustorium, which is a specialized absrobing structure. They only infect epidermal  cells, as that it as far as there penetration pegs go. A lot of distantly related pathogens have structures similar to this one, suggesting it evolved early on in evolutionary history. This also probably means that a lot of plants probably have evolved certain resistances to these kinds of structures. 

There can be a wide range of visible symptoms of disease in plants. For example, bacteria usually cause wilts becuase the infect the vascular system, the plant's system of water flowing through the entire organism. Cysts, knots, curls, and galls can also form due to the pathogens reprogramming the development of the host plant, and thus diverting water and nutrients away from certain parts of the plant they would normally go to. Galls are swellings near the root of plants. Another symptom that can occur is blights, which are yellowish-browish spotting, and can lead to cell death. For example, as previously mentioned, chestnut blights infect chestnut trees and kill them completely, leaving behind an orange ring around a canker. Before absolute death, the orange-y blights can be observed spreading around the canker. There can also just be visible colonies of certain bacteria and fungi. For example, the Tomato mosaic virus was named so because of the discolored patterning it causes on leaves on tomato plants.The patterning that is observed is the actual viral colonies. Powdery mildew leaves colonies that are patches of white on the plant. There are also just in general bacterial specks of darkening that are observed on tomatos. 

One type of effector molecules that influence interactions with the host plant are enzymes that degrade cell walls. An example of this is the bacteria Erwinia. These usually affect the cellulases and hemicellulases. They also exhibit quorum sensing, meaning that the pathogen will only secrete the effector molecule at certain population densities of the pahogen. So, the pathogens will only attack if there are a lot of the fellow pathogens around them. In other words, a high population density will cause a high concentration of effector molecules to be secreted. An example of this is in bacteria secreting a signal compound calle (N-acylhormoserine lactone). The bacteria enters the leaf through the stomata, as bacteria can only invade host plants through natural openings. At first, the concentration of bacteria in the host plant is low, and thus the concentration of N- acylhomoserine lactone is low. As more bacteria enter the host plant, the population density of the bacteria increases, and the N-acylhomoserine lactone concentration increases. This initiates the production of cell wall-degrading enzymes and similar effector molecules in the bacteria, which the bacteria secrete to outside of their own cells. When there are a lot of bacteria inside the plant cells, there is a lot of production of N-acylhomoserine lactone, and thus a lot of secretion of cell wall-degrading enzymes and similar effector molecules. This causes death of plant cells in the region where the bacteria invaded. This is thus a highly effective way that plant cell get invaded by these pathogens.  

Topics in Plant Bio Notes - Plant Pathology Part II

Submitted by samihaalam on Sun, 12/03/2017 - 01:46

There are different ways to classify plant pathogens. Necrotrophs kill plant tissue with toxins and break down cell walls. Examples of them include Botrytis and Erwinia. These types of pathogens tend to be generalists, meaning they target all plants in general, whichever plant they come in contact with. Biotrophs require that their host cells stay alive in order for them to complete a normal life cycle. They exhibit delayed senescence, or slower deterioation and eventual death,  as well as altered metabolism and development. These include powdery mildew, rusts, viruses, and nematodes. They are often highly specialized towards one particular host plant. Hemibiotrophs first live as biotrophs, then as necrorophs. An example of this includes the species Pseudomonas syringae. These are the three ways to classify pathogens.

These pathogens have three different pathways into plant cells. One method is through direct penetration. This involves the penetration peg on the pathogen piercing the cuticle layer and cell wall. The cuticle layer is a waxy covering on the cell surface, that is supposed to be thick and waxy to protect the cell. The cell wall of plants contains starch, which is also an incredibly thick and strong strucutre. The penetration peg must be able to get through both of these layers, so it must be incredibly strong. A second method is through penetration through natural openings in plant cells. An example of a natural opening in a plant is the stomata. One development in vascular plants that differentiate them from bryophytes is that vascular plants have stomata - openings on their leaves which allow for gas exchange. The plants have a vascular system to allow the transfer of gases, minerals, and water throughout the whole plant system, allowing them to be taller than the short, flat bryophytes. The stomata are a part of this system, as it is where gases enter and exit the system. However, as beneficial as these openings are, they also allow for potential pathogens and microorganisms to enter. The third way for pathogens to enter is through penetration through open wounds. Fungi can perform all three of these pathways, while bacteria can only go into existing openings or via insect vectors. Viruses and viroids usually enter through wounds made by insects. These are the three ways plants can be penetrated by invading pathogens. 


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