Drafts

The Rht gene is an inhibitor which stops a plant from growing. In a normal pathway, a gibberelin protein binds to the Rht gene and throws it away for degredation. Therefore, the plant is able to grow because gibberelin stops the inhibitor gene from inhibiting growth. When it comes to dwarfism, there is a defect or mutation in wheat that actually causes gibberelin to be ineffective. In dwarfs, because gibberelin is now inneffective, the Rht gene does not become inhibited and will thus be able to stop the wheat from growing. This is how dwarfism results in wheat

In rice however, there is a gene that is similar to Rht with the same function: it inhibits growing. With rice dwarfism, however, it is not that the gibberelin is ineffective, but that there is simply no gibberelin at all. This can be fixed however, by simply adding gibberelin which will then bind to the inhibitor and allow the rice to grow again. In wheat, this is not possible because the issue with the mutant is that gibberelin is rendered useless.

I'd heard of round up before but I never fully understood it and its use of GMOs. Round up relied on an edited pathway in plants that contained a single monomer that was altered in the pathway to produce three amino acids. The genetically modified plants were designed to have a new DNA sequence that yielded that same intermediate protein to produce the three amino acids but it was resistant to binding with the round up chemical that degraded the intermediate to prevent the amino acid synthesis. This meant that unedited plant genomes would produce a protein that round up would attack, killing the plant. The crops and plants of interest that the farmers grew were controlled GMOs that would not be affected by this deadly chemical because it could not bind to their intermediate proteins, but the amino acids were still successfully synthesized. This sounds great but I see potential problems this could cause. Firstly, if there is any possibility of cross-pollinating with a related species, this genetically modified sequence could find itself in an uncultivated species that could become very invasive with the use of the round up. Any transfer of the gene could cause superweeds that are immune to roundup. Also, this plathway is in many plants, making it an effective weed killer, but highly unspecialized. It could easily target species that do not compete with the crops when roundup goes deeper into the soil or runs off into streams, etc. This makes the roundup chemical highly dangerous in the use ouside a closed system like a greenhouse. Furthermore, the roundup company had a monopoly on the "roundup ready" species, meaning the genetically modified organisms that were resistant to roundup. This made the project extremely capitalistically driven, like a lot of projects, and shows a comflict of interests. They were selling the locks and the keys, which was an extremely successful business model and that high sale rate might have affected the attention to affect of roundup on the environment. People in charge would more apt to turn a blind eye until forced to look when great deals of money are involved. 

In general, plants glean four types of information from light: quantity, quality, direction, and photocycle. Plants can determine the level of irradiance, the wavelength of light they receive, its point of origin, and daily fluctuations in light using photoreceptors. Phytochromes are red/far-red light photoreceptors that play a role in germination, flowering, shade avoidance, and circadian rhythm entrainment. They are inactive as monomers, but when red light hits the plant, the chromophore of two phytochrome monomers will go through a cis-trans isomerization that leads to dimerization. Phytochromes are an exception among photoreceptors as their activation is reversible. For example, imbibed lettuce seeds can be induced to germinate by a pulse of red light, but when the flash of red light is followed by a flash of far-red light, germination is inhibited. Two other kinds of photoreceptors, both of which respond to blue and UV-A light, are cryptochromes and phototropins. Cryptochromes are responsible for de-etiolation, flowering, and circadian rhythm entrainment. When seeds germinate underground, they are said to undergo etiolation, by which they elongate, inhibit leaf growth, and do not produce chlorophyll. Upon breaching the surface of the ground, cryptochromes will detect blue and UV-A light, causing the seedling to become de-etiolated. That is, it will grow a short stem, produce leaves and internodes, and begin chlorophyll production. Phototropins are aptly named after one of the effects they have, phototropism. If the shoot apical meristem is exposed to blue and UV-A light, the plant will grow towards that light. Phototropins are also responsible for moving chloroplasts away from high irradiance light and moving them towards low irradiance light. Lastly, upon detecting blue light, they increase solute potential in guard cells, which causes the stomata to open. Though these are some of the important players in the light detection mechanisms of a plant, there are many other photoreceptors with functions ranging from UV protection to developmental control.

During extraction experiments, two compounds can be separated from each other by utilizing their solubility in two immiscible solvents.  The solvents are separated from each other because they each have their own density.  Therefore, the one with the larger density, would be the bottom layer.  Acid-base extraction utilizes acid-base reactions to alter the solubility of the acidic or basic compounds in the solvent in order to separate them.  During this lab, water is used as the aqueous solvent for the unknown carboxylic acid.  Tert-butyl methyl ether (TBME) was the either used that would contain the neutral compound.  The unknown carboxylic acid is highly soluble in the ether layer, therefore a base, NaHCO3,was added to the carboxylic acid to form a carboxylate which is water soluble and ether insoluble.  This separates with unknown neutral organic compound to the either layer as they both have low polarity and the unknown carboxylate which are both polar.  Because the water layer is denser, it would be found in the bottom of the test tube with the two solutions.  With the two layers determined, they can be separated and purified.  For the organic layer, some residual water can be found in the layer so NaCl is used to backwash the solution and remove any aqueous waste.  In addition, a drying agent, CaCl2, removes the last of the water.  In the aqueous layer containing the unknown carboxylate, HCl is used to turn the basic layer back into the carboxylic acid.  Both solutions utilize recrystallization to purify them. 

With the knowledge I gained in my botany class today, I returned home and was able to analyse the plants I keep in my room in a new light. I have a sunflower I cut from a plant kept in a small jar on the windowsill. Today in class, the professor explained to us the different types of infloresence in flowers. Infloresence is the structure and form that flowers take when they bloom on a flowering plant. Sunflowers are in the family Asteraceae which includes a very wide variety of flowers. These flowers present in the form of a captiulum which can be most closely compared to a dish. There are flowers along the outside which are usually sterile, and these are what are often presumed to be the only petals. However in the center of the flower, there are very small erect flowers arranged in the 'dish' known as disc flowers. These flowers produce the seeds for the plant, which is why sunflower seeds come from this dish-like area in the center of the flower. 

Immunotherapy is typically a treatment associated with cancer, but this therapy can actually be applied to many more ailments. Immunotherapy is essentially the activation, or suppression, of the immune system in order to help combat disease. Specifically, the reprogramming of CAR-T (chimeric antigen receptor T cells) to attack specific targets in the body holds many uses. In patients with autoimmune disorders, these CAR-Ts can be engineered to attack and destroy human immune cells that produce self-attacking antibodies. Other uses include combating inflammation, and even as treatments against donated organ rejection. The ability to tweak our immune systems manually, and either amplify or nullify responses, is an advance in medicine that cannot be overstated.

In the future, I’d like to use my biology degree to pursue a career in medicine. With that in mind, it is important that bioethics is considered when approaching life science in the real world. Bioethics is the ethics of medical and biological research. Ethics drive the way we are allowed to behave in different settings, and the science field is no exception. One article illustrates the consideration of bioethics, where five couples are currently lined up for CRISPR babies to avoid deafness. If you haven’t heard, the CRISPR-Cas9 system is a modern gene-editing technique that has not been well tested. It essentially causes a mutation in the germ-line cells, creating a heritable sequence for future generations. There are guidelines in place to make sure that CRISPR is not abused and tested on humans without proper conditions. One such condition is the inevitable death of some diseases. An example includes the editing of HIV-resistant infants. In this case, I think that the editing of infants to get rid of deafness is not life-threatening, so it should not be used and should be considered invasive, palliative surgery. However, moral guidelines may vary from country to country. Russia may have different protocols that may allow them to bypass this issue.

https://bioethics.com/archives/47444

Through out the past few decade various ways to sequence the genome had been invented. Originally the genome could only be sequenced in small portions and required mostly human oversight/work to set up the sequencing. This method of sequencing was time consuming and expensive. Today, next generation sequencing has revolutionized the way genomes are sequenced. Mass Parallel squencing is acomplished by sonicating a genome and ligating short, universal primers into the cut DNA strands. That is then poured over a "Chip" where individual fragments of DNA bind to unique positions by the primer that was just ligated on. Then synthesis begins on all the segments. A fluorescent ddNTP base pairs and is captured by a special camera. Next the ddNTP is altered so that the 3' end has an OH group where a new ddNTP molecule can bind. This process is repeated over and over again until all the strands are sequenced. Next, a program will run to match all the overlapping segments into one strand. It is convention to have atleast 30 overlapping sequences in one position to maintain accuracy of the sequencing. 30 overlapping segments would be known as having a depth of 30. 

In October of 2018, a frozen, headless macaque was placed in the UMass Taphonomy Lab and the taphonomic process of its decomposition was studied  Motion activated infrared cameras captured images of any organisms visiting the macaque throughout the process.  In addition, visits were made biweekly to record the progression of the decomposition.  Due to the time of year and weather patterns, the process of decomposition was unique in that insect activity was subsequent to animal activity.  Also, the wide variety of animals which fed the macaque cooperated in sharing the macaque as a food source.

Today, I had two classes. One in the morning and the other during early afternoon. After class today, I studied for my plant biology exam that is tomorrow during class. The exam covers the first eight lectures that we had in class and covers the topics of photosynthesis, different light receptors, plant pathogens and their defense sytem, and crop diversity. An interesting yet shocking fact I learned during one of the lectures is that undernutrition contributes to nearly half of all deaths in children under 5 and is widespread in Asia and Africa. Knowing that many children are dying from undernutrition is an important reason for studying the plants and crops that are produced to feed a population. Knowing how to effectively speed up the process of growing crops to feed a population who are being underfed can lead to a lower percentage of children under 5 being affected by undernutrition.