Writing in Biology

            Neanderthals are thought to have disappeared in Europe approximately 39,000–41,000 years ago but they have contributed 1–3% of the DNA of present-day people in Eurasia. In the study by Fu et al., DNA from a 37,000–42,000-year-old modern human from Peştera cu Oase, Romania was analyzed. Although the specimen contained small amounts of human DNA, an enrichment strategy was used to isolate sites that were distinct between Neanderthals and present-day humans. They found that on the order of 6–9% of the genome of the Oase individual is derived from Neanderthals, more than any other modern human sequenced to date. Three chromosomal segments of Neanderthal ancestry are over 50 centimorgans in size, indicating that this individual had a Neanderthal ancestor as recently as four to six generations back. However, the Oase individual did not share more alleles with later Europeans than with East Asians, suggesting that the Oase population did not contribute substantially to later humans in Europe.

Evolutionary development is a branch of biological study. Two lines of research in the field have developed across a span of twenty years since its conception. One branch of evolutionary development focuses on discrete and qualitative changes in phenotype. The other focuses on research done through investigating complex phenotypes though quantitative developmental phenomena. However, there is potential for the two to be used together in explaining processes and mechanisms of evolutionary development over time. In recent years, evolutionary development offers insight on specific molecular connections between genotype and morphology. Still, the importance of how the morphology interacts with the environment will make the final determination on the fitness of the genotype. Therefore, evolutionary development has a greater potential if it is broadened from the fine details of the genotype all the way to how those genotypes affect resource use (Irschick, Albertson et al, 2013).

Cichlids are a family of fish that include over 2000 species. They come in a variety of sizes with a range of habitats across continents from South America to Africa. Many of them are kept in aquariums as they are usually duable fish that come in a variety of colors. The species are known to take care of their eggs and incubate them and even take care of their fry. Depending on the species they have a variety of diets, some being herbavores while others are carnivorous. They are known to be able to adapt to environmental changes very quickly, making them good models for studying evolutionary development.

This was also from the talk I recently attended. The results showed that Lanthanides more specifically Lanthanum play a significant role in methanotrophs respiration. It was found that Lanthanum is critical for methanotrophs to help oxidize methane to methanol. It was found that when Lanthanum was available for cells the XoxF gene was upregulated and the MxaF gene was down regulated. Conversely when Lanthanum wasn’t available the XoxF gene was down regulated and the MxaF gene was upregulated. It was shown that bacteria could survive for a limited time in the formaldehyde by fixing the one carbon in the compound. When methanotrophs were grown in a co-culture with non-methanotrophs present methanol was produced. If the methanotrophs were grown in pure culture without non-methanotrophs present no methanol was produced, this shows that there is a connection between the two different organisms and both are needed for methanotrophs to go complete respiration. The conclusions that can be drawn from these results are that methanotrophs do heavily rely on the availability of Lanthanides in the environment. This also shows that Lanthanides may be commonly used when metabolizing one carbon molecules in other organisms that have yet to be studied. Based off of the results it can be concluded that XoxF is a regulatory gene within methanotrophs that help to with the uptake of Lanthanides. In the talk it was suggested that MxaF may have to do with calcium regulation. Additionally both XoxF and MxaF may be used for communication between methanotrophs and non-methanotrophs. Co-cultures are also essential for methanotrophs respiration. It is hypothesized that methanotrophs produce methanol which is then used by the non-methanotrophs. The non-methanotrophs produce a compound that binds to Lanthanum which the methanotrophs then used for respiration and to produce methanol making them co-dependent. The methanotrophs being able to live in formaldehyde suggests that it employs a TCA cycle during respiration. This study may have environmental applications because methanotrophs can be used to reduce methane sinks around the world. A suggested application was using methanotrophs to oxidize methane in sewage facilities and reduce atmospheric release.

This was a talk I recently attended. I enjoyed this talk and believe that it may have many environmental applications. The talk was about methanotrophs that live in lake Washington. These methanotrophs live in the sediment of the lake right at the bottom of the zone of oxygen diffusion. One thing that was focused on was the use of rare Earth metals in the energy production of methanotrophs. Little is known about these methanotrophs and how they methane to methanol. However from the findings of this study it seems like methanotrophs may be a viable solution to reducing methane sinks around the globe. The way that these methanotrophs were tested was by first obtaining samples from lake Washington. In this lake alone over 60 isolates have been identified in the area of sediment just where there is little oxygen that has diffused down. To map the respiration of the methanotrophs a full flux map was created. Bacterial cells were exposed to formaldehyde to see if they could continue respiration. Next components of the respiration pathway of methanotrophs were upregulated and downregulated by providing the methanotrophs with different compounds. This was used to test the effect that Lanthanides have on methanotroph respiration. Additionally the importance of a co-culture was tested by keeping methanotrophs and non-methanotrophs in the same and separate environments.

The results showed that many aspects play a role in how cells maintain a uniform rod shape as they grow. One result showed that there are two main ways that new cell wall is inserted into the cell. The first being that new cell wall is inserted in an oriented manor, which means that filaments travel around the radius of the cell and are oriented by cell radius rudders. The second is that new cell wall is inserted in an unoriented manor, this means that cell wall is inserted randomly by enzymes. Another result showed that when mreBCD was upregulated the cell rod width decreased and it became skinnier, if mreBCD was downregulated then the cell rod width increased and it became fatter. The salt shock showed that cells with upregulated mreBCD were able to maintain their rod form for a longer time than cells with lower levels. An additional result showed that when the cells were provided additional nutrients they were able to grow into a rod shape quicker. A similar result showed that when the cell was essentially tricked into thinking it had adequate nutrients it grew at the same rate showing that a kinase domain was responsible for sensing environmental nutrients.

    The way a student looks at the material of a course compared to the professor is very different. The way a teacher teaches the material by teaching the fundamentals and scaffolding that’s required in order to understand the material at a deeper level. That method of teaching shows that if the basic concepts are understood by the students, the students will remember and understand the material better by building off previous knowledge.. Albeit, while some students see the material under this light, and desire to understand how the material works, there are students who view the problems and see them as “obstacles” that need to be overcome. This means that these kinds of students see problems, and instead of thinking about “why it works”,  they think “how can I solve this problem in the easiest way possible”? For some material this method of thinking is more beneficial if a student knows the material they are learning is not a measure of their capabilities of understanding the material, but rather a measure of their intrinsic motivation to learn the material for an A. This method of “dodging” the content but still passing the course with an A is a flaw of the current education system, due to the fact that the system weighs two individuals who understand and retain the material at different levels, as equals.

          Ancient DNA has enabled us to answer long-standing questions about the relationship between archaic and modern humans. Admixture among archaic groups and between them and modern humans seems to have occurred whenever they came into geographic proximity. In that way, they were no different from groups of modern humans. Although most present-day human ancestry can be traced to African populations that dispersed into Eurasia ∼100,000 y ago, aDNA has allowed us to also determine which parts of our genomes are from archaic hominins that occupied Eurasia before modern humans. All non-African genomes carry small amounts of Neanderthal ancestry, and some carry an additional component of Denisovan ancestry. Because the paleoanthropological record of much of Asia is relatively poorly known, it is likely that more Neanderthal and Denisovan fossils will be found in this region. It is even possible that additional extinct groups of hominins will be identified using aDNA.

Fragile X Syndrome is a dominant X- linked syndrome, meaning it affects both men and women. Since men only have one x chromosome, it effects them more frequently and with more severity. In inheritance, the father passes on Fragile X only to the daughters since sons will recieve a Y chromosome from him. If the mother has Fragile X or acts as a carrier for it, there is a 50% chance her children will be affected by it.

The Fragile X mutation was discovered in 1943 by two scientists, Bell and Martin. The disease was originally named after them, but then was renamed after it was found to a sex-linked condition with a "fragile" site on the X chromorosome. The mutation that causes Fragile X is a CGG repeat on the X that extends more than normal. Normally, it repeats between 6 and 55 times. Anything over 55 repeats is considered Fragile X.

About 50% of women with Fragile X do not show any symptoms (long face, large ears, and flat feet). Also men and women who have between 55 and 200 CGG repeats have what is called "pre-mutation" Fragile X. Pre-mutation is incomplete Fragile X but can cause multiple issues like ovarian failure and Tremor Ataxia Syndrome. If someone has 200 or more CGG repeats, they have complete Fragile X. The greater the number of repeats, the greater the severity of the effects.

DISCUSSION

Across the various majors we surveyed, only 20% of the students had never heard of gene editing. Most of the 80% who had had a  major under the category of STEM (science, technology, engineering, and mathematics). Those in STEM, for the majority had gone over it in their required classes. Of those that were not STEM majors, they had learned about it from the news, social media, and general education requirements here at the University of Massachusetts. Overall, the population at the University of Massachusetts Amherst has some familiarity on the topic of gene editing on genetic disorders or medical practices in general to form some opinions. Major choice may limit the amount of in depth knowledge someone may have on the topic, but  today’s media (news sources, facebook, instagram, etc.), personal interest and internet access does give the population a general understanding.