ewinter's blog

There are five major functions of sleep as defined by neuroscientists. These are energy conservation, reinforcement of ecological niche, body restoration, brain restoration, and memory consolidation. There are four major brain regions that are responsible for sleep. The basal forebrain causes slow wave sleep via GABAergic projections to the hypothalamus. The brainstem, specifically the reticular formation, activates forebrain to wakefulness via acetylcholine and norepinephrine. The pons induces REM sleep via GABAergic and glycinergic projections to the spinal motor neurons to suppress motor activity. The hypothalamus coordinates the circadian rhythm and switches between states of sleep via hypocretin projections to the other three brain regions aforementioned.

There are three major classes of hormones. Peptide hormones are small protein molecules. Their mechanism of action is binding to G-protein coupled receptors for fast effects. An example of an amine is acetylcholine. Amines are modified amino acids. Their mechanism of action is the same as peptides. Common amines include epinephrine and norepinephrine. Steroids are derivatives of cholesterol. Their mechanism of action includes diffusing across the cell membrane and binding to cytosolic receptors. They affect gene expression by contributing to chromatin remodeling. Cortisol is a well known steroid that regulates glucose levels and promotes learning during stressful situations.

There are three types of signaling in neuroscience. Neurocrine signaling, also known as synaptic transmission, is when neurotransmitters are released by a presynaptic neuron into the synapse, and bind to the postsynaptic neuron. The presynaptic neuron fires an action potential for the neurotransmitters to be released, and to postsynaptic neuron depolarizes when the neurotransmitters bind. Endocrine signaling is when endocrine glands release hormones into the bloodstream. Hormones may have differing effects, and effect any cell type that expresses their receptor. This type of signaling results in slower, widespread effects. The third type of signaling is neuroendocrine signaling. This is when neurons integrate postsynaptic potentials, fire action potentials, and release hormones into the bloodstream.

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.

The bright bands on the gel indicate that DNA was successfully extracted. This was expected, despite some worry about self complementation due to the “any th” value of 8.16 in the primer3 output. We do not know why lane number 2 on the TE gel did not show a band. We recall loading sample into this lane. It is possible that something in the DNA extraction protocol failed, so no DNA of large band size was extracted. We preferentially chose mutants from the TE gel to send for sequencing because TE stabilizes DNA. All three of the trustworthy sequence results confirmed that the mutant plants were homozygous for the NaN1793 mutation.

By looking at the gels, we decided to extract M1 from H20 because it did not show up on TE. We then chose to take M2, M6, and M7 from the TE gel. After purifying the DNA from the gel using the gel extraction protocol. The concentration of M1 was 30.2 ng/uL. The concentration of M2 was 37.3 ng/uL. The concentration of M6 is 24.1 ng/uL. The concentration of M7 is 25.1 ng/uL. The A260/280 ratios are all near 2.0. This is usually considered pure for RNA. In this case, the fact that they are consistent across all four samples is a good indicator that we have pure DNA.

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). 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.

In my opinion, the writing is very clear. In each of the four sections outlined above, the writing is organized by bullet points with one sentence following. This length of writing seems suitable for a poster. The figures are high resolution, notably the picture of the immunohistochemical expression of PD-L1 in squamous cell carcinoma. No raw data is shown. The only data shown includes four odds ratios with confidence intervals and P-values. The data for the figures is not displayed in its own chart. The bar graphs serve to visually engage the viewer to the results. Without reading the text, the viewer can see the PD-L1 expression levels in tumor cells and lymphocytes, and how this varies across tumor type.  

I believe that the poster has an attractive design. I like the use of the light blue background for the text on the sides, with the figures in the middle of the poster. The poster is easy to follow, with four headings: ‘Introduction,’ ‘Design,’ ‘Results,’ and ‘Conclusions,’ clearly marked, and flowing in this order from top left to bottom right. I like how the ‘Conclusions’ section is simply one sentence, serving as the discussion. It reads “our results provide further support for the rationale of using immune checkpoint inhibition in patients with penile SCC, especially in those with high-grade tumors.” Sometimes when I read literature, I struggle to figure out exactly what is so great about the paper. This one line does an excellent job of phrasing the significance of the paper in an understandable way. It also is a great hook, because if I were to walk up to this poster at a poster session, I may skip straight to the conclusion before deciding if I want to engage the authors or spend time studying the poster. In this case, I definitely decided that this is worth my time, which is important for the authors.  

When T cells are activated, there are both stimulatory and inhibitory pathways that are activated. CD28 is the activating cytokine. It binds to CD80 and CD86 receptors on antigen-presenting cells. CTLA-4 is homologous to CD28. In fact, it binds CD80 and CD86 receptors with much greater avidity than CD28. Therefore, after some time, the T cell response will be inhibited. In immunotherapy, it has been shown by James P. Allison that blocking the CTLA-4 inhibitory mechanism leads to improved cancer treatment. James Allison won the 2018 Nobel Prize in Physiology and Medicine for this discovery.