Drafts

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)

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.

There are two types of processing: top-down and bottom-up control. Top-down processing is when the brain communicates to the organ based on previous experience. Bottom-up processing is the opposite, when information from the environment is relayed to the brain. The concept of attention is preferential processing of a subset of information from the environment. Endogenous attention is voluntary, top-down control that can be sustained over long periods of time. The main brain region involved is the frontoparietal networks. Exogenous attention is reflexive, bottom-up processing which ir rapid but quickly fades. It primarily uses modality-specific brain areas, such as the primary visual cortex or auditory cortex.

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. These sensory organs include the eyes and the ears. 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.

           In The genome of the offspring of a Neanderthal mother and a Denisovan father, the authors analyze the genome of ‘Denisova 11’, a bone fragment from Denisova Cave in Siberia.  They show that it comes from an individual who had a Neanderthal mother and a Denisovan father. The father, whose genome contains traces of Neanderthal ancestry, came from a population related to a later Denisovan found in the cave. The mother came from a population more closely related to Neanderthals who lived later in Europe than to an earlier Neanderthal found in Denisova Cave, indicating that migrations of Neanderthals between eastern and western Eurasia occurred sometime after 120,000 years ago. The finding of a first-generation Neanderthal–Denisovan offspring among the small number of archaic specimens sequenced to date allowed the authors to conclude that mixing between Late Pleistocene hominin groups was common when they met. (Slon et al. 2018)

Isopentyl acetate was synthesized in a 35.31% yield from isopentyl alcohol, acetic acid and concentrated sulfuric acid. The mixture of reactants was observed to have a putrid smell whilst the final product had a smell similar to that of bananas. There was also change in color from scarlet reactants to a brown product. These qualitative observations signal the occurrence of a chemical change. The identity and purity of final product was analyzed using IR spectroscopy. The IR spectrum of the final product showed peaks that were characteristic of an ester. A broad peak at 2960 cm^-1 shows the presence of an sp³ hybridized C-H bond. This type of bond is usually seen between 3300 and 2700 cm^-1. There is another large peak on the IR spectrum at 1743 cm^-1 which indicates a C=O bond or a carbonyl. This type of bond is usually seen between 1780 and 1650 cm^-1. These two peaks on their own could indicate the presence of a carboxylic acid or an ester, both of which have sp³ hybridized bonds and a carbonyl group. However, the lack of a broad peak between 3650 and 3200 cm^-1 shows that the final product is not a carboxylic acid because it does not contain a hydroxyl group. In addition, the IR spectrum of the final product shows a large peak at 1244 cm^-1, which is in the fingerprint region between 1250 and 1050 cm^-1. This large peak indicates a C-O bond, which is characteristic of an ester.

Into a 5 mL round-bottomed flask, isopentyl alcohol (1.2 mL), acetic acid (0.744 mL), 4 drops of concentrated sulfuric acid and 3 boiling chips were added. The solution was refluxed for 15 minute intervals for a total of 3 intervals or 45 minutes. After each interval, the organic phase was removed from the side arm of the flask and added to the solution. After refluxing, the contents of the round-bottomed flask were transferred to a centrifuge tube. The centrifuge tube was extracted with water (1 mL). This extraction process was repeated with sodium bicarbonate (1 mL) and sodium chloride (1 mL). 5 spheres of calcium chloride were added into a vial containing the organic phase. The mixture was transferred to a new vial and analyzed by infrared spectroscopy.

Trimyristin was isolated from nutmeg, and produced myristic acid. The trimyristin was recrystallized two times to collect it in the highest purity. The percent yield of the second recrystallization (83.29%) is higher than percent yield of the first recrystallization (71.88%). The melting points of the trimyristin after the first and second recrystallizations indicate the difference in purity between them. The melting point of trimyristin after the first recrystallization is 52-55 ºC, which is lower than the theoretical melting point of 56-57 ºC. A lower melting point indicates that there's are more impurities in the compound. The melting point of the trimyristin that was twice recrystallized also has a more narrow melting point range of 1 ºC, which demonstrates the homogeneity and purity of the substance. The melting point of myristic acid was observed at 53-54 ºC. The purity of the myristic acid is shown by the narrow melting point range. The theoretical melting point of myristic acid is 54.4 ºC. The myristic acid formed in this experiment is pure because it is close to this value. 

          Neanderthals and Denisovans were archaic human populations that 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). 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. 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.