From Publishing to People
A brief look at recent, published research in states adjacent to the Great Lakes and thoughts on how to find more
Communication is fundamental to scientific research. When I was teaching, I often included the dissemination of findings and conclusions as a final step to the scientific method. Within the context of the method, this helps to feed into the questions and hypothesis of others. It is also crucial from a practical standpoint, as has been painfully evident for many in the scientific community who have seen funding recently sequestered. It is debatable whether more effective communication and engagement with the public might have averted such a scenario, but it is less controversial that this is necessary for finding our way forward.
Sharing research findings can take many (and increasingly diverse) forms, but traditional mainstay has been the peer-reviewed publication in an academic or trade journal. I personally have a complex relationship with this part of the scientific ecosystem (more on that another time), but today I’d like to focus on this vehicle for showcasing new research. That is because it can also provide a window into not only what research is being done, but who and where - it can be used as a tool to find interesting work in biotechnology and synthetic biology in your area.
Finding interesting new research in biotechnology and synthetic biology that is happening in your area can help take you from reading publications to connecting with the people behind the work. Whether you are an ‘active-duty’ scientist, a professional, and educator, or a teacher, each new publication from our region is an opportunity to connect with the corresponding author - to help build your own version of a regional synthetic biology network. While this can also be done on a global scale, there are advantageous to local connections. Maybe you can have one of the lead researchers stop by your classroom, library, or place of business to give a short talk.
Another gem from ChatGPT, to illustrate how academic publishing can build community
One of the best places to start your search of the literature is PubMed, a database of life-science related research hosted by the National Center for Biotechnology Information (NCBI), part of the NIH’s national library of medicine. This will take you directly to primary research, which can sometimes be hard to digest if you don’t have the appropriate technical background. Still, it can give you a direct glimpse into the types of problems being addressed and the tools typically employed in doing so. I would recommend selecting the ‘Advanced Search’ function and adding the term for your state or favorite institution to the ‘Affiliation’ field. This will narrow your search to those publications that feature at least one author with an affiliation in the state of your choice.
For your convenience, here are links to search for biotechnology or synthetic biology publications in the past year with authors that are affiliated in Ohio, Michigan, Illinois, Indiana, or Wisconsin.
One of the first things you might notice from this search is the preponderance of papers that have several dozen authors. Collaboration is increasingly important in research. Just as a single data point does not define a project, so too does a single researcher seldom make important contributions to the scientific community. It also makes sense that we would see such results given our search parameters - a paper that has 50 authors needs only 1 of them to have a Midwest affiliation to show up in this search. When selecting a search result, it is worth expanding the ‘author affiliations’ section to get a sense for the contributions and involvement of scientists in our region.
Another theme I notice with this particular search is a high number of papers that appear to be focused around a treatment or medicine, usually from scientists employed in private industry. This can be helpful to better understand the bioeconomy landscape in your region or state. If you are a student, this might be a window into the activities of potential future employers!
I’d like to highlight a few recent publications I found through this search that I think are particularly interesting. In another post, I may dive deeper into this or others - in fact, going through the exercise of writing a summary of a compelling or exciting research publication is a great way to deepen your understanding of the science while building writing experience. It is an exercise I often challenged students with, particularly in the biotechnology journal club I used to teach, in which they had to adapt published research into press release style summaries, like the kinda you might find at EurekAlert! (which is itself another great resource for surveying recent breakthroughs)
Here are some recent publications to sample, for your reading pleasure or as an exercise for your studnets:
Muñoz KA, Ulrich RJ, Vasan AK, Sinclair M, Wen PC, Holmes JR, Lee HY, Hung CC, Fields CJ, Tajkhorshid E, Lau GW, Hergenrother PJ. A Gram-negative-selective antibiotic that spares the gut microbiome. Nature. 2024 Jun;630(8016):429-436. doi: 10.1038/s41586-024-07502-0. Epub 2024 May 29. PMID: 38811738.
Exciting development of a ‘silver-bullet’ antibiotic, which preferentially targets pathogenic gram-negative species. The importance of this type of work is underscored by the growing problem of antibiotic resistance in pathogenic bacteria, which represents a looming public health crisis that could make COVID seem tame!
This represents work done across multiple departments at the University of Illinois at Urbana-Champaign. The university has filed patents on the compounds described herein, and has also published an associated press release.
Trettel DS, Hoang Y, Vecchiarelli AG, Gonzalez-Esquer CR. A robust synthetic biology toolkit to advance carboxysome study and redesign. bioRxiv [Preprint]. 2024 Oct 8:2024.10.08.617227. doi: 10.1101/2024.10.08.617227. PMID: 39416180; PMCID: PMC11482911.
A nice example of a paper which affiliations across states - the one relevant for this post is Dr. Vecchiarelli at the University of Michigan. His lab focuses on how bacteria are organized on a subcellular level - with manipulation or re-engineering of such organization key to producing desired behaviors.
This paper provides a way to do just that with carboxysomes, which are large protein complexes that function as bacterial organelles. These giant protein assemblies feature an outer shell that sequesters carbon assimilation enzymatic activity inside. Optimizing carbon assimilation is important for combating climate change - beyond this, I can think of several other pathways that could benefit from this type of engineered compartmentalization.
If you enjoyed those, I’d recommend some further reading:
Rapp JT, Bremer BJ, Romero PA. Self-driving laboratories to autonomously navigate the protein fitness landscape. Nat Chem Eng. 2024 Jan;1(1):97-107. doi: 10.1038/s44286-023-00002-4. Epub 2024 Jan 11. PMID: 38468718; PMCID: PMC10926838. An excellent paper from the Romero Lab (which has since relocated from Wisconsin to Duke, NC).
Ipoutcha T, Racharaks R, Huttelmaier S, Wilson CJ, Ozer EA, Hartmann EM. A synthetic biology approach to assemble and reboot clinically relevant Pseudomonas aeruginosa tailed phages. Microbiol Spectr. 2024 Mar 5;12(3):e0289723. doi: 10.1128/spectrum.02897-23. Epub 2024 Jan 31. PMID: 38294230; PMCID: PMC10913387.
Tseng YJ, Krans A, Malik I, Deng X, Yildirim E, Ovunc S, Tank EMH, Jansen-West K, Kaufhold R, Gomez NB, Sher R, Petrucelli L, Barmada SJ, Todd PK. Ribosomal quality control factors inhibit repeat-associated non-AUG translation from GC-rich repeats. Nucleic Acids Res. 2024 Jun 10;52(10):5928-5949. doi: 10.1093/nar/gkae137. PMID: 38412259; PMCID: PMC11162809.
Chamberlain AR, Huynh L, Huang W, Taylor DJ, Harris ME. The specificity landscape of bacterial ribonuclease P. J Biol Chem. 2024 Jan;300(1):105498. doi: 10.1016/j.jbc.2023.105498. Epub 2023 Nov 25. PMID: 38013087; PMCID: PMC10731613.
Xue Y, Zhang Y, Zhong Y, Du S, Hou X, Li W, Li H, Wang S, Wang C, Yan J, Kang DD, Deng B, McComb DW, Irvine DJ, Weiss R, Dong Y. LNP-RNA-engineered adipose stem cells for accelerated diabetic wound healing. Nat Commun. 2024 Jan 25;15(1):739. doi: 10.1038/s41467-024-45094-5. PMID: 38272900; PMCID: PMC10811230.
Do you have a favorite recent bioscience breakthrough, academic or commercial, in the Midwest? Is there a neat method for finding this work that I didn’t highlight? Please share these in the comments below, and share this post with your colleagues. A brief programming note: there was no post last week, and I may start to post on a biweekly (or semi-monthly, twice a month) basis going forward due to scheduling constraints.
Devin Camenares
Editor, GLSB Bulletin.