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The study of proteins is important in fields like genetics, biochemical research, and medicine because the role they play in most if not all biological functions can be used to understand how diseases work, and more importantly how to treat them. The function of the protein comes from its structure, so an understanding of how the protein is built could shed some light on how it works. The goals of this lab were to successfully purify and crystallize the protein using methods such as chromatography, which is used to separate molecules by size; a Bradford Assay which determines the concentration of protein in collected solutions and subsequently the volume for the gel electrophoresis; an SDS-PAGE which confirms the presence of GFP protein in the solution; and finally handing drop vapor diffusion which ultimately crystallizes the protein. Throughout this lab, we feel as though we obtained an ample amount of 6xHis-GFP protein due to the bright green color of our eluate samples. Though we did not make a large GFP crystal, we successfully made scattered GFP crystals under 25% PEG 8000 precipitant concentration.

The structure of the human brain is one of the most complex organs in the body that is continuously researched for a deeper understanding of its function. Communication within the brain occurs between numerous neurons that transmit messages electrically within a neuron and chemically between neurons. Messages travel down a neuron from the dendrites that receive a message and then through the axon towards the synaptic cleft where the chemicals are dispensed. The synaptic cleft is a designated area for chemicals to be released from a neuron and transmitted to the next. Chemicals bind to the corresponding receptors of the upcoming neuron to be stimulated and continue its path throughout the brain. Chemicals such as serotonin and dopamine are transmitted throughout the brain via neurons. Serotonin relates to sleep, eating, and mood, which are critical for human well-being.

    It’s generally agreed upon that in order to close the achievement gap, we need to give opportunities to those who are poor, and are living in environments that pose a threat to their child’s education. The achievement gap is the gap in success in schools between high-income and low-income students. In my personal opinion, the reallocation of government spending (specifically demilitarization) to areas with poor education systems, would greatly increase educational opportunities, the quality of education, and create jobs for more teachers. During 2015 alone, the U.S spent roughly 600 billion dollars in military spendings. If we were to cut military spending in half, that would give education systems 300 billion more dollars to use, and still leave the military with 300 billion spending dollars. The large increase in educational spending will allow teachers to use better equipment, have more public resources at schools, and possibly even pay teachers a better salary. It’s important to note that the military also tends to “max out” on the budget in order to maintain the budget. For example, the military has lots of extra ‘disposable’ equipment that is bought in order to continually perpetuate this idea that the military “needs this amount of money” in order to continue functioning. The budgeting habits used by the military is constantly overlooked, yet when scrutinized it’s very apparent that the spendings are not being used efficiently. By allocating the taxpayers’ money elsewhere, we can generally increase the quality of education, and the achievement gap will eventually shrink due to better education systems.

Childhood for humans is considerably a lot longer than for other mammals including our closest living primate relatives. There is a long period of immaturity in humans even when taking into consideration our relatively long lifespans. However, stretching out the maturation may have given humans a unique evolutionary advantage. Humans and chimpanzees split off between six to seven million years ago and have been evolving separately ever since then. Early human fossils showed that humans had short growth periods which are a lot more similar to chimpanzees nowadays then modern-day humans. There is slow maturation in children nowadays that is linked to human’s emergence in society, this long period of maturation allows for an extended period of education. Humans are able to learn more and develop their brains better than other primates allowing them to “live slow and grow old.”

Sieve cells are called this because the tubes act as one continuous cell and are a collection of sieve tube elements. They tend to look empty, have very prominent joints, are very long and don’t have a nucleus (like xylem, but are living cells). They don’t have a cytoskeleton, have very few organelles (probably no Golgi, plastids or lignin; some ER, few mitochondria, have plasma membrane). Companion cells, ordinary cells that feed sieve cells and keep them alive, are next to sieve cells. A ‘sieve plate’ is the wall in between each sieve cell. Sieve plates contain special clotting proteins and polysaccharides which should only be released when the phloem is damaged. They are like slime and are very prominent; these are phloem clots that stop the flow of nutrients if the phloem is damaged. 

In class, we learned about different types of cytoskeletal filaments. We covered intermediate, actin, and microtubules. Intermediate filaments are only found in some animals, have a high tension capacity, and are made up of 8 tetramers stacked on top of each other. They have no directional polarity. Since they do not have polarity, they do not have any motor proteins. They also have no DNA triphosphate on them, so they are not dynamic filaments.

Actin filaments are highly dynamic and easily reorganized. They are 9 nanometers in diameter. Their subunits are called G actin and when in a polymer it is called F actin. A free actin subunit is bound to ATP while in the polymer it is bound to ADP instead. It also goes under a conformational change when incorporated into a filament. Actin has directional polarity where new subunits can be added or taken from each side. The plus end grows and shrinks faster than the minus end in that respect. 

Microtubules themselves have a negative charge and are 25-30 nanometers in diameter, forming hollow tubes, The subunit is a heterodimer of alpha tubulin and beta tubulin. It has directional polarity where the beta tubulin faces the plus end and alpha tubulin faces the minus end. Microtubules are dynamic and rearrange into mitotic spindle during mitosis or can form cilia for cell movement. With its polarity, it also has motor proteins going along it. Dyenin is a minus end motor protein and kinesis is a plus end motor protein. 

Thermogenin is a protein found in the inner mitochondrial membrane in the adipose tissue of some animals. It allows protons to flow from the intermembrane space to the mitochondrial matrix. If thermogenin is present in large quantities, it will decrease the rate of ATP synthesis but increase the rate of oxygen consumption, which is a measure of electron transport chain activity. This is because the proton gradient cannot form if protons are allowed to flow back to the matrix and cannot be built up in the intermembrane space, and this proton gradient is what powers the synthesis of ATP. On the contrary, oxygen consumption will increase since the electron transport chain will continue to pump protons into the intermembrane space in an attempt to form a gradient. Thermogenin allows for heat production without the production of ATP, so it is present in human infants and hibernating bears, animals that require heat but not much ATP.

Cancer vaccine immunotherapies exploit the cross-presentation function of the immune system that allows antigen-presenting cells (APCs), especially dendritic cells (DCs), to phagocytose extracellular tumor-associated antigens (TAAs) and display them with MHC class I molecules to CD8+ T cells. Typically, extracellular antigens are phagocytosed by APCs and presented through MHC class II to CD4+ T cells, while endogenous antigens are presented through MHC class I to CD8+ T cells. This ability to display injected extracellular TAAs on MHC I is crucial in the activation of CD8+ T cells and subsequent eradication of the tumor. There are currently two known routes in the immune system for this mechanism of cross-presentation: cytosolic and vacuolar (Immune Response 2014). In the cytosolic route, the extracellular antigen is phagocytosed and then actively transported to the cytosol, where it is cleaved by a proteasome, transported to the ER, loaded onto MHC class I, and displayed on the plasma membrane. In the vacuolar route, the extracellular antigen is phagocytosed and at the ER is incorporated into an early endosome with lysosomal enzymes and MHC class I, which subsequently displays the antigen on the plasma membrane (Immune Response 2014). Further research is necessary to understand specific pathways involved in this cross-presentation mechanism.

AT1g61610 is paralogous to AT4g21390, and AT4g21390 is gene B120, so it is homologous to gene B120 in Brachypodium distachyon, which is our gene of interest. AT1g61610 was found to have a Zinniacysteine protease 4 (ZCP4) promoter cis-element-like sequence 1000 b.p. upstream, and the ZCP4 promoter governs tracheary element differentiation (Pyo et al. 2007). This cis-element is known as tracheary-element-regulating-cis-element (TERE). 61 genes in Arabidopsis thaliana were found to include this cis-element 1000 b.p. upstream. These genes were Arabidopsis tracheary element differentiation related genes. Their functions include programmed cell death, cell wall biosynthesis and modification, lignification, phosphorylation, photosynthesis, and unclassified function. The presence of this cis-element-like sequence implicates AT1g61610 in the development of xylem, although nothing further is known to this end. Xylem are the vesicles in plants that transport water up from the roots to the leaves. The development of xylem includes lignification and secondary cell wall formation. This finding may help design experiments to elucidate the function of gene B120 in B. distachyon, which remains largely unknown.