Writing in Biology

In the phylogenetic tree created on the MAFFT program, there were 37 redundant entries removed, and about four natural groupings could be identified. There were no clear outliers on the tree (Figure 6). The Bradi1g72430 gene was found to be most closely related to a Oryza sativa gene, OSNPB_030183800. Within its natural grouping, the gene was most closely related to O. sativa and Brachypodium distachyon, then Arabidopsis thaliana genes (Figure 6).

Cross-sectioning of wildtype and mutant plant stems revealed mutant stems to have a smaller diameter than wild type, and based on the dyed sections, mutant plants seem to have thicker polysaccharide and lignin walls with smaller openings in the center of the stem.

The four mutant plant sequences obtained through Sanger sequencing were labeled S31-34. S31’s first quality base was the 50th base, while the last quality base was the 615th base. S32 had no quality bases. S33 and S34’s first quality bases were also the 50th base, while the last quality bases were the 600th and 620th bases respectively. The NCBI pairwise BLAST between the Sanger and reference genome sequences revealed one misalignment at the beginning of the sequence, but in between the beginning and end, the Sanger and reference sequences were perfectly aligned except at the 133rd position. This was confirmed to be the position of the NaN1898_Bd1_70884553_Het mutation, and it was located on the 133rd position of the chromatogram (Figure 5). On the chromatogram, there were two peaks, G and A, at the 133rd position, although the algorithm read it as A. This indicated a heterozygous mutation with a wild type G base and mutant A base, which is consistent with the NaN1898_Bd1_70884553_Het mutation. This mutation was at position 715 in the whole genome sequence.

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.

The amino acids in proteins are joined together by peptide bonds to form polypeptide chains; a protein consists of one or more polypeptide chains. Like nucleic acids, polypeptides have polarity under physiological conditions: one end (often called the amino end) has a free amino group (NH3+) and the other end (the carboxyl end) has a free carboxyl group (COO−). Proteins consist of 50 or more amino acids; some have as many as several thousand.

Like that of nucleic acids, the molecular structure of proteins has several levels of the organization. The primary structure of a protein is its sequence of amino acids. Through interactions between neighboring amino acids, a polypeptide chain folds and twists into a secondary structure. Two common secondary structures found in proteins are the beta (β) pleated sheet and the alpha (α) helix. Secondary structures interact and fold further to form a tertiary structure, which is the overall, three-dimensional shape of the protein. The secondary and tertiary structures of a protein are largely determined by the primary structure—the amino acid sequence—of the protein. Finally, some proteins consist of two or more polypeptide chains that associate to produce a quaternary structure. Many proteins have an additional level of organization defined by domains. A domain is a group of amino acids that forms a discrete functional unit within the protein. For example, there are several different types of protein domains that function in DNA binding.

This week I babysat my friends hamster, Cayenne. She is a Syrian Hamster. Cayenne is a large hamster so we nicknamed her Chubby. Everyday, I had to make sure she had enough food. Cayenne needs about 1/3 cup of hamster food everyday and every other day she can have fresh vegetables and fruits. To get her use to me, I wore gloves in case she would bite and gave her a sunflower seed as treats. I filled her water bottle and when I was down to about 1/4 full, I refilled it for her. Hamsters are nocturnal, so when I was in class I would cover her tank with a blanket and closed the blinds so she could sleep. Around 7 or 8pm she would start moving and then when she was fully awake by 9 or 10pm, I would take her out so she could run around in her hamster ball for about 45 minutes. After then, I would put her back in the tank so she could get some food and water. After that she spends all nigh on her wheel, which can get quite loud sometimes. Cayenne is asleep by the time I get up for class in the morning. 

Hummingbirds have adapted their digestive system in order to sufficiently support their high caloric intake. They use their newly ingested sugars as a fuel for flight. They are able to quickly digest sugars for immediate use. It takes a hummingbird about 40 minutes to turn food into fuel whereas it can take a human up to 40 hours to digest. This is partly due to their small digestive tracks and the absorption of nutrients across the intestine. They also have a high capacity for paracellular and transcellular movement of glucose.

Bird songs can be represented visually. With modern technology, sonograms can be created from the song recordings. However, before being able to read a sonogram, there are some teminology that must be used reviewed. In order to be familiar to birds’ vocalization, terms such as:  Amplitude (maximum energy), Fundamental tone, Frequency (number of complete cycles per unit of time), Glissando (bleeding of one tone into the next), Harmonic (a tone in the series of overtones produced by a fundamental tone), Hertz (one cycle per second), Modulation (form of a sound: carrier wave), Oscillograph (a device that records oscillations as a continuous graph), Overtone , Pitch (relative position of a tone in a scale, as determined by its frequency), Resonance (intensification and prolongation of a sound), Sinusoidal waveform (y=sin x), Sonogram (display of the frequency of a sound related to time), and Tone (distinct pitch and quality) are necessary for a better understanding of birds.

Birds have a special organ called the syrinx, that allow them to sing the way they sound. It is located on the trachea to produce sound. It is similar to the mammalian larynx but the way air is used is different. In the syrinx 100% of the air is converted to sound where the larynx only uses 2%. The vibrated air passes through the syringeal passageway to project on the tympaniform membrane. This vibration is the result of how birds can vocalizes. The syrinx is a complex organ itself but the muscle attached around it is also complex. There are layers of muscle structures to create fine adjustment of vibration. Sound produced by the syrinx can be filtered to change the loudness and the pitch. The experiment done to prove that sound travel faster than helium atmosphere showed sound produced in such atmosphere had different pitch and frequency than the sound produced in our normal atmosphere. The understanding of syrinx and physics of sound helped scientists to learn more about vocalization.