Surveying Complex Samples for 3 Synthetic Elements by Targeted Enrichment
(2025) BINP50 20242Degree Projects in Bioinformatics
- Abstract
- Our ability to genetically engineer microorganisms is growing rapidly. We can perform small, precise modifications using techniques such as CRISPR-Cas9 to whole-virome synthesis and/or large genetic insertions. These advances reduces the threshold for synthetic biology to be employed maliciously. Preparations against pandemics or deliberate biological attacks currently rely on taxonomic identification of microorganisms and inference of their pathogenicity. In the modern landscape of bioengineering, taxonomic identification may be misleading as commonly benign microorganisms may be altered to increase their virulence and pathogenicity. Since modern bioengineering can fail to detect harmful microbes, there is a gap in the current... (More)
- Our ability to genetically engineer microorganisms is growing rapidly. We can perform small, precise modifications using techniques such as CRISPR-Cas9 to whole-virome synthesis and/or large genetic insertions. These advances reduces the threshold for synthetic biology to be employed maliciously. Preparations against pandemics or deliberate biological attacks currently rely on taxonomic identification of microorganisms and inference of their pathogenicity. In the modern landscape of bioengineering, taxonomic identification may be misleading as commonly benign microorganisms may be altered to increase their virulence and pathogenicity. Since modern bioengineering can fail to detect harmful microbes, there is a gap in the current methodology. In order to address this gap, this project aims to assess if in-solution hybridization (targeted enrichment) is a feasible approach to identify microorganisms by selectively enriching DNA elements that could indicate synthetic intervention. The approach utilizes a custom bait panel that targets plasmids and antibiotic resistance genes (ARGs). The bait panel was applied to a fecal sample set and a spike-in sample set (where a cell line, VERO E6, is mixed with a concoction of plasmid sequences). The enrichment outcome is preliminarily successful for initial DNA concentrations as low as 2.5e-5 ng. Background depletion works differently well depending on sample set, one of them yielding background sequence reduction from 90% to 10%. Continued experimentation should build upon the exploratory results achieved in this study by validating the results and continuing the optimization of the bait panel. (Less)
- Popular Abstract
- Biological weapons have been utilized long before humanity’s ability to genetically engineer microorganisms. The timeline goes something like; Dip arrowheads in poison, weaponize the plague and in modern times, genetically engineered microorganisms to become even more lethal. In this new age of bioengineering, we can no longer rely on the fact that mean-sounding microorganisms are more dangerous than others, such as anthrax (popularized by anthrax mail attacks of 2001). Instead, we need to look deeper at the genes that make some microorganisms dangerous. Any ordinary virus or bacteria can now potentially be weaponized by introducing genes leading to increased virulence or antibiotic resistance. An aspect of biological weaponry that is a... (More)
- Biological weapons have been utilized long before humanity’s ability to genetically engineer microorganisms. The timeline goes something like; Dip arrowheads in poison, weaponize the plague and in modern times, genetically engineered microorganisms to become even more lethal. In this new age of bioengineering, we can no longer rely on the fact that mean-sounding microorganisms are more dangerous than others, such as anthrax (popularized by anthrax mail attacks of 2001). Instead, we need to look deeper at the genes that make some microorganisms dangerous. Any ordinary virus or bacteria can now potentially be weaponized by introducing genes leading to increased virulence or antibiotic resistance. An aspect of biological weaponry that is a bit more subtle than dropping toxic bombs, is poisoning the water supply or introducing antibiotic resistances that become increasingly more difficult to combat. In this project, we try to get one step closer to identifying synthetic microorganisms, using a technology called targeted enrichment or in-solution hybridisation. This is a well-suited method for the task, as the signs of genetic intrusion may be subtle and drowned in the background noise generated by the remainder of the genetic sequences. Targeted enrichment is a method of fishing for sequences of interest. We started the project by defining what we are fishing for. We realized we should be looking for the vectors of genetic engineering. These are the rockets carrying the payload, if you will. If we can identify the rockets, perhaps we can also find the payloads. After having designed our fishing baits, we went to the lab and started fishing. After applying our method, we found that the baits caught something. By bioinformatically analysing the captured sequences, we found that some microorganisms were enriched hundreds of times their initial concentration. This pilot project was a success since we have established a baseline performance for an unoptimized bait panel. Scientists can now further the project by improving the baits and/or testing different experiments using our bait panel to further characterize its efficiency. (Less)
Please use this url to cite or link to this publication:
http://lup.lub.lu.se/student-papers/record/9184972
- author
- Bergman, Andrew
- supervisor
- organization
- course
- BINP50 20242
- year
- 2025
- type
- H2 - Master's Degree (Two Years)
- subject
- language
- English
- id
- 9184972
- date added to LUP
- 2025-02-12 13:35:18
- date last changed
- 2025-02-12 13:35:18
@misc{9184972,
abstract = {{Our ability to genetically engineer microorganisms is growing rapidly. We can perform small, precise modifications using techniques such as CRISPR-Cas9 to whole-virome synthesis and/or large genetic insertions. These advances reduces the threshold for synthetic biology to be employed maliciously. Preparations against pandemics or deliberate biological attacks currently rely on taxonomic identification of microorganisms and inference of their pathogenicity. In the modern landscape of bioengineering, taxonomic identification may be misleading as commonly benign microorganisms may be altered to increase their virulence and pathogenicity. Since modern bioengineering can fail to detect harmful microbes, there is a gap in the current methodology. In order to address this gap, this project aims to assess if in-solution hybridization (targeted enrichment) is a feasible approach to identify microorganisms by selectively enriching DNA elements that could indicate synthetic intervention. The approach utilizes a custom bait panel that targets plasmids and antibiotic resistance genes (ARGs). The bait panel was applied to a fecal sample set and a spike-in sample set (where a cell line, VERO E6, is mixed with a concoction of plasmid sequences). The enrichment outcome is preliminarily successful for initial DNA concentrations as low as 2.5e-5 ng. Background depletion works differently well depending on sample set, one of them yielding background sequence reduction from 90% to 10%. Continued experimentation should build upon the exploratory results achieved in this study by validating the results and continuing the optimization of the bait panel.}},
author = {{Bergman, Andrew}},
language = {{eng}},
note = {{Student Paper}},
title = {{Surveying Complex Samples for 3 Synthetic Elements by Targeted Enrichment}},
year = {{2025}},
}