Journal

Literature suggests that scientific writing needs significant improvement at the moment (Jerde et al., 2004). Academic writing has been a problematic weakness for many students who want to develop their careers; no matter how good you are at collecting data, analysis or understanding complex topics, if you cannot write scientific articles, you will not be published and therefore limit your scientific career immensely. Data suggests that the most effecting way to improve writing is by integrating it into research (Jerde et al., 2004). For this reason our previous team, MSP-Maastricht 2020, decided to set up the journal initiative. They gathered research papers from as many iGEM teams as possible in order to simulate/imitate a real open access journal including aspects such as peer review. All of this was done in efforts to offer aspiring scientists, within the iGEM competition, a chance to familiarize themselves with the writing and publishing process. We maintain such intentions and have taken action to further improve last year’s efforts. As our 2020 team noticed that several teams had difficulty writing articles suitable for scientific journals, it was decided to not only organize/produce the journal, which in and of itself was time consuming and challenging, but also expand the scope of this year's journal initiative. This was achieved by offering academic writing workshops, as well as altering how we organized the peer review and setting up our own website external from the wiki.

Graph of population growth since 1700 — World population from 1700 to 2024 in Billions (Roser, Ritchie & Ortiz-Ospina, 2021)

Graph of meat production since 1961 per continent — Global meat production from 1961 to 2018 in Million tons (Ritchie & Roser, 2021).

Of course, it must not be underestimated that we took plenty of time to organize the journal itself. With the help of our peer who created an email sending program, we sent over 400 emails. We had to be consistently on top of the email to answer questions be it technical or organisational. Our initial form of contacting was by sending a message to all teams through Slack, approximately 150 through Instagram, and 35 through email. We created a template of how the paper should be formatted in order to make the journal more authentic.

Schematic of the methanogenesis process in the cow — Ruminant stomach compartments and methanogenesis (Zhao et al. 2020)

A total of five workshops were made. We realized that not every iGEM team has the privilege to receive academic writing training, even though we perceive academic writing as a major part of science and academia. Thus, a very big focus this year was to invest in education on scientific writing, and other skills such as referencing, and language use. Each workshop covered an important aspect of the writing and publishing process. At the same time, we contacted Joop Hoekstra, an expert in academic writing who worked in Maastricht University’s Language Center. He helped us develop each of these workshops, giving us feedback on making it engaging, accurate and useful. Additionally, for the peer review workshop, we contacted Roy Erkens, a biology professor from Maastricht University who is actively involved in science communication and publishing work He gave some insight on the peer review process from a scientist’s point of view talking about his experience, its importance and the changes that he has seen throughout his career.

Chart showing difference in the warming potency of CO2 and methane by showing circles with size corresponding to relative potency

On top of that, we changed the way we did the peer review. It was chosen to work with the Open Journaling System (OJS) compared to last year where our team organized it manually with the aim of making the process more authentic. Moreover, it also allows us to understand a new system that could be useful if the journal grows even more and micromanaging is no longer as feasible. This was challenging for all of us since we did not have guidance. Here is where some mistakes came into play: ___. This allowed us to learn and give advice to future

Graph showing methane parts per billion in the atmosphere, as well as delta C-13 isotope ratios in methane

Last but not least, we created a website in order for the team to have a single location in which information regarding our project could be accessible to other iGEM teams, potential sponsors, and other people interested in our work, a team website was created. The website was created using WordPress, which is an open-source content management system designed to rapidly create appealing websites. In WordPress, a number of plugins and templates were used to create the backbone of the website. Next, pages, content, and functionality such as the aforementioned OJS integration were added manually to suit the website to the specific needs of the team. Currently, the website has a team home page, a team members page, and a journal home page. The journal home page provides information to our journal initiative. The website offers forum functionality, which will be used for the journal’s peer review process.

Photograph of Asparagopsis Taxiformis in the ocean

The result of all this is the final version found below. We hope this product reflects the hard work of our team and all of the participants. We hope you enjoy it!

Structural formula of the chemical compound bromoform

Bromoform has the ability to inhibit a cobamine-dependent methyltransferase, which is required for the synthesis of methyl-coenzyme-M, the key enzyme in the final part of methanogenesis (Machando et al. 2016), ultimately reducing methane production if present in the cow rumen (Kinley et al. 2020). Image source: (Zhao et al. 2020) These methyl-coenzyme-M enzymes are present exclusively in methanogens (Zhu et al. 2021), whereof the archaeal genus Methanobreviacter is the most abundant and most studied (Danielsson et al. 2017).

Microscope image of methanogen microbes — Image source: Miller, 2015

Yet unfortunately, the life cycle of A.taxiformis consists of three life stages. Aquafarms have yet to grow the algae through all of these, meaning that the cycle could not be closed. This hinders the farming of the species on a global scale dramatically (Zhu et al. 2021).

Image depicting the discrepancy between required Asparagopsis Taxiformis feed and supplied Asparagopsis feed by showing differently sized circles depicting the two

In 2020, Thapa et al. identified the genes from different groups of A.taxiformis which are involved in the production of bromoform, as well as the genes involved in bromoform production in the algae Chondrus crispus, amongst others.

Schematic of the Mbb genes, which are involved in bromoform production — Three genes discovered in A. taxiformis by Thapa et al. (2020).

Schematic of the VHPO genes, which are involved in bromoform production — Two genes discovered in C. crispus by Thapa et al. (2020).

References

Britannica, T. Editors of Encyclopaedia (2019). Ruminant. Retrieved 16th June, 2021 from: https://www.britannica.com/animal/ruminant
Chagas, J.C., Ramin, M., & Krizsan, S.J. (2019). In Vitro Evaluation of Different Dietary Methane Mitigation Strategies. Animals, 9(12), 1120. doi:10.3390/ani9121120
Danielsson, R., Dicksved, J., Sun, L., Gonda, H., Müller, B., Schnürer, A., & Bertilsson, J. (2017). Methane production in dairy cows correlates with rumen methanogenic and bacterial community structure. Frontiers in microbiology, 8, 226.
Fletcher, S. E. M., & Schaefer, H. (2019). Rising methane: A new climate challenge. Science, 364(6444), 932-933.
Jackson, R. B., Saunois, M., Bousquet, P., Canadell, J. G., Poulter, B., Stavert, A. R., ... & Tsuruta, A. (2020). Increasing Anthropogenic Methane Emissions arise Equally from Agricultural and Fossil Fuel Sources. Environmental Research Letters, 15(7), 071002.
Kinley, R. D., Martinez-Fernandez, G., Matthews, M. K., de Nys, R., Magnusson, M., & Tomkins, N. W. (2020). Mitigating the Carbon Footprint and Improving Productivity of Ruminant Livestock Agriculture using a Red Seaweed. Journal of Cleaner Production, 120836. doi:10.1016/j.jclepro.2020.120836
Machado, L., Magnusson, M., Paul, N. A., Kinley, R., de Nys, R., & Tomkins, N. (2016). Identification of Bioactives from the Red Seaweed Asparagopsis taxiformis that Promote Anti-methanogenic Activity in vitro. Journal of Applied Phycology, 28(5), 3117–3126. doi:10.1007/s10811-016-0830-7
Machado, L., Tomkins, N., Magnusson, M., Midgley, D. J., de Nys, R., & Rosewarne, C. P. (2017). In vitro Response of Rumen Microbiota to the Anti-methanogenic Red Macroalga Asparagopsis taxiformis. Microbial ecology, 75(3), 811-818.
Matthews, C., Crispie, F., Lewis, E., Reid, M., O’Toole, P. W., & Cotter, P. D. (2018). The Rumen Microbiome: a Crucial Consideration when Optimising Milk and Meat Production and Nitrogen utilisation efficiency. Gut Microbes, 1–18. doi:10.1080/19490976.2018.1505176
Miller, T. (2015). Methanobrevibacter. Bergey's Manual Of Systematics Of Archaea And Bacteria, 1-14. https://doi.org/10.1002/9781118960608.gbm00496
Ritchie, H., & Roser, M. (2021). Meat and Dairy Production. Retrieved 7 July 2021, from https://ourworldindata.org/meat-production
Roser, M., Ritchie, H., & Ortiz-Ospina, E. (2021). World Population Growth. Retrieved 7 July 2021, from https://ourworldindata.org/world-population-growth
Thapa, H. R., Lin, Z., Yi, D., Smith, J. E., Schmidt, E. W., & Agarwal, V. (2020). Genetic and Biochemical Reconstitution of Bromoform Biosynthesis in Asparagopsis Lends insights into Seaweed Reactive Oxygen Species Enzymology. ACS Chemical Biology, 15(6), 1662-1670.
United Nations. (2021). Global Issues: Population. Retrieved 16th June, 2021 from: https://www.un.org/en/global-issues/population
Zhao, Y., Nan, X., Yang, L., Zheng, S., Jiang, L., & Xiong, B. (2020). A Review of Enteric Methane Emission Measurement Techniques in Ruminants. Animals, 10(6), 1004.
Zhu, P., Li, D., Yang, Q., Su, P., Wang, H., Heimann, K., & Zhang, W. (2021). Commercial Cultivation, Industrial Application, and Potential Halocarbon Biosynthesis Pathway of Asparagopsis sp. Algal Research, 56, 102319. https://doi.org/10.1016/j.algal.2021.102319

Team:MSP-Maastricht/Journal

Journal

References

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