Writing in Biology

In an effort to extend the expression data in Phytozome, we designed an experiment to study Bradi3g27407 gene expression under 5% glucose growth conditions. To explore this, we conducted an experiment to study expression levels in root samples in the presence and absence of 5% glucose. We chose root samples because that is where our gene is most expressed, as indicated by our results from the e-FP browser. We used 8 root samples (5cm, young) from Brachypodium distachyon plants, growing 4 experimental samples in MS medium plates containing 5% glucose and another 4 control samples in MS medium plates without 5% glucose. We grew the plants at optimum temperature and light conditions: 24℃ day, 18 ℃ night. We created primers for the reverse transcription reaction, using primer3 software, so that they flanked introns but bound to exon sequences. The forward primer was 5’-tacaaggggaagatcagggc-3’ and the reverse primer was 5’-ccgcttgatctccttctcca-3’. These were so that the length of the sequence between the primers (not including the intron sequence) was 321bp (Figure S3). In Figure S3, the texts highlighted in yellow are the exon sequences, that highlighted in green is the intron sequence and the texts with red font color are the primers.

This semester, I learned how to genotype zebrafish. I had never genotyped before, so performing the steps regularly helped me to understand the process better. I learned how to analyze and interpret fragment analysis data. Importantly, I became more comfortable with running gels. Its importance lies in the fact that we run gels so often in the lab and it is an essential skill to have.  I also performed some TOPO-cloning, chemical transformation, inoculation and plasmid extraction, alone for the first time. This gave me more confidence to execute these processes in the future. Presenting before other members of the lab allowed me to get a feel of what it is like to make a scientific presentation. I learned not just from my presentation but from everyone else’s presentation. The feedback I received played an enormous role in my learning process here.

        DNA evidence has dramatically expanded our knowledge of the human evolutionary tree. Since the discovery that genetic material could be recovered from ancient organisms in 1984 (Higuchi et al. 1984), the study of ancient DNA (aDNA) has advanced rapidly. Certain factors can complicate the collection and analysis of aDNA, such as advanced age, the surrounding environment, and the collection technique, which can lead to degradation via cross-linking, deamination of cytosine, and fragmentation, as well as contamination due to extraneous microbial DNA and exposure to modern human DNA during extraction. Despite these difficulties, the revelation that archaic DNA can be sequenced, in conjunction with the sequencing of the human genome less than twenty years later (2001), provided the foundation from which the field of human evolutionary genomics arose. The insights gained about humans closest extinct relatives, Neanderthals and Denisovans, has been particularly impactful. These archaic human populations branched off from the modern lineage early in the Middle Pleistocene, approximately 750,000 years ago, and then separated from each other around 390,000 years ago. Many modern humans carry DNA derived from these archaic populations due to interbreeding during the Late Pleistocene, a period spanning 126,000 to 12,000 years ago (Slon et al. 2018).  In just the last decade, genomes have been recovered from Neanderthals and Denisovans. This has resulted in the determination that Neanderthals account for between 1% and 4% of the ancestry of people outside sub-Saharan Africa (Green et al. 2010), and Denisovans contribute from 1% to 6% of the ancestry of people in island Southeast Asia and Oceania (Meyer et al. 2012). These genomes provide information about the phenotypes of archaic peoples, insight into interactions between them and modern humans, and evidence of their contribution to the biology of modern humans. 

    I enjoyed the proposal project, although my group did misjudge the due dates and had to quickly text and email each other to finish it. The methods project helped because it made us go into more detail, trying to be a specific as possible in our description and directions. And us having to speed up to finish this made us start somewhat earlier and quicker on the poster project. 

    The poster project was my favorite. I had never printed a poster here at UMass so that was exciting. My groups topic was interesting and it was fun making a survey and sending it out to people in my section of the marching band, who after taking the survey asked me questions on the topic. I was confident explaining and it was good practice for presenting, and just sharing science topics I was interested in was awesome. 

    Overall, I did enjoy this class. I felt that it was actually helpful, being that it was writing geared towards my career path. I had one of the better presentation groups I have ever had in  both high school and college in this class, and I am grateful for that. I like to think I did pretty okay overall, but I do admit, this class was one of the most challenging for me in college purely because EVERYTHING I had learned about writing was changed and I just do not enjoy writing in any context.

    Having to go from creative to scientific writing was also a tough transition. Every writing class I have had up until this semester stressed figurative, descriptive language and having to throw that all out the window made me questioning what was the point of learning that.   

    The methods project was not really new in the sense of following a method. I thought that it was really straight forward at the beginning. But, the amount of information that needed to be incorporated in order to achieve the expect result was a lot more than I thought. Someone can interpret your instructions in a way that is completely different than you meant them to be, even if you think you are being so clear. It really showed that attention to detail and specificity was really important and no one is a mind reader. 

Rosemary Harrison

Reflection on Writing in Biology:

    This class to be honest was a dreaded one, especially on a Friday for two and a half hours. I feel that every time I take a writing class, I just adds to the dread of writing. Trying to get in the habit of writing regularly was hard for me especially at the beginning of the semester, and there were time that I did forget, especially when I had exams and presentations in other classes. I did start to just keep a document open on my laptop to jot down ideas or notes from classes that I could turn into paragraphs every week, but sometimes it was tough to do. I don’t expect myself to continue to writing weekly, but I understand that doing that this semester was to build on scientific writing rather than creative writing. 

          In Approximate Bayesian computation with deep learning supports a third archaic introgression in Asia and Oceania, the authors use introgressions, defined as the transfer of genetic information from one species to another as a result of hybridization between them and repeated backcrossing, in the human lineage that have been identified using sequenced ancient genomes of Neanderthals and Denisovans to try to identify previously unknown groups. They built a demographic model based on deep learning in an Approximate Bayesian Computation framework to infer the evolutionary history of Eurasian populations including past introgression events in accordance with the current genetic evidence. In addition to the reported Neanderthal and Denisovan introgressions, their results supported a third introgression in all Asian and Oceanian populations from another archaic human population. The authors dubbed this group a “ghost ancestor”, and concluded the population was either related to the Neanderthal-Denisova clade or diverged early from the Denisova lineage. (Mondal et al. 2019)

Monozygotic (identical) twins develop from a single egg fertilized by a single sperm that divides and gives rise to two zygotes. Thus, monozygotic twins are genetically identical, in the sense that they possess identical DNA sequences, but they often differ somewhat in appearance, health, and behavior. The nature of these differences in the phenotypes of identical twins is not well understood, but recent evidence suggests that at least some of these differences may be due to epigenetic changes. In one study, Mario Fraga, at the Spanish National Cancer Center, and his colleagues examined 80 pairs of identical twins and compared the degree and location of their DNA methylation and histone acetylation. They found that DNA methylation and histone acetylation in identical twin pairs were similar early in life, but that older twin pairs had remarkable differences in their overall content and distribution of DNA methylation and histone acetylation. Furthermore, these differences affected gene expression in the twins. This research suggests that identical twins do differ epigenetically and that phenotypic differences between them may be caused by differential gene expression.

Early in the development of female mammals, one X chromosome in each cell is randomly inactivated to provide an equal expression of X-linked genes in males and females. Through this process, termed X inactivation, many genes on the inactivated X chromosome are permanently silenced and are not transcribed. Once a particular X chromosome is inactivated in a cell, that same X chromosome remains inactivated when the DNA is replicated, and the inactivation mark is passed on to daughter cells through mitosis. This phenomenon is responsible for the patchy distribution of black and orange pigment seen in tortoiseshell cats. X inactivation is a type of epigenetic effect because it results in a stable change in gene expression that is passed on to other cells.

Signal transduction, in a sensory processing sense, is the conversion of energy into a neural signal. It occurs in receptor cells located in sensory organs such as the ears, eyes, and hands. Receptor cells are responsive to certain types of energy, but not others. In the cochlea (inner ear) hair cells located in the basilar membrane have stereocilia, which are hair-like structures that touch the tectorial membrane. Sound vibration causes hair displacement and opens mechanically gated ion channels, which causes the cells to depolarize and release neurotransmitters. These cells do not fire action potentials. There are four different types of touch receptors: pain, touch, vibration, and stretch. These can be found subcutaneously all around the body. Each touch receptor type has a distinct pathway to the brain. The visual system detects both brightness and contrast. Photoreceptors perform signal transduction. There are two types of photoreceptors: scotopic (rods), which work in dim light, and photopic (cones), which govern vision of colors. The visual pathway crosses sides at the optic chiasm, so the right visual field is processed in the left occipital lobe, and vice versa.