#12 The DNA Vacuum, Genetic Clues to Lost Senses and Saving Megadiverse Colombia
The new eDNA and the vacuum to capture it, genetic links to COVID symptoms and the integral role the second most biodiverse country plays in the future.
š§¹The DNA Vacuum
How Scientists Vacuumed Animal DNA out of the Airā¦
In December 2020, Elizabeth Clare collected āair samplesā from Hamerton Zoo Park in England. Using a small vacuum pump outside of animal enclosures with a small flexible tube attached DNA could be sucked out of thin air. This method has been dreamt about for over a decade, the ability to find airborne genetic material has the potential to remove more invasive and intrusive DNA collection methods. DNA that has been collected from water samples can be used to identify and track numerous aquatic species such as salmon and sharks. Scientists knew that they could use environmental DNA (eDNA) from the air to identify and track land based species, two seperate groups have no achieved this using vacuums.
Clare got the idea from a previous experiment, where she sampled air outside of the naked mole ratās burrow. At the zoo, the team collected 72 samples from 20 different locations running the vacuum pump for 30 minute periods. The pump filter could then be removed with the material trapped inside being analysed in the lab.
Meanwhile, a University of Copenhagen based team unknowingly chased the same idea. Kristine Bohmann, shown above, and colleagues set out to trap airborne DNA at the Copenhagen Zoo using tiny fans as well as experimenting with vacuums. Both techniques were deemed suitable, following testing by which the two contraptions were run for between 30 minutes and 30 hours.
Using zoos to test their techniques was done by both research groups. This is because DNA found in their samples could be cross referenced with the known animals in the zoo, therefore allowing them to test not only the concentration of a particular animals DNA, but the distance travelled in relation to others. Bohmann and the Copenhagen based team were able to identify 49 different vertebrate species. They detected animals such as Okapis, Dumerilās ground boa as well as fish that was used as food.
The Hamerton zoo identified 25 species including zoo residents as well as some native species such as the European hedgehog, domesticated dogs, mice and even mild traces of human DNA.
Utilising these techniques could be a non-invasive way of identifying, tracking and locating endangered animals, a slight step up from the camera trap. However in the wild, applications could be more difficult due to the dispersion of airborne eDNA as well as environmental factors such as wind and weather. However, this proof of principle study shows accuracy and potential and will likely evolve as has aquatic eDNA sampling over the past decade.
š·No Smell With COVIDā¦
Genetic Clues as to Why Some Lose Taste and Smell with COVIDā¦
A loss of smell or taste following a positive COVID test has been a common and well known side effect since the start of the pandemic. Scientists across the globe have researched the cause and future implications of these symptoms with roughly 700,000 to 1.6 million people in the US having either lost, or seen alterations to their sense of smell following the COVID-19 infection.
Scientists may have found a genetic link that is associated with these COVID-19 symptoms. This genetic link may be a clue as to help us better understand why these symptoms occur. Lead study author Adam Auton said that āThe loss-of-smell symptom of COVID-19 has been one of the notable ways that people have been able to distinguish a SARS-CoV-2 infection from common flu,ā. However the the underlying mechanisms is still largely unknown.
The study was conducted by 23andMe, a company that does genetic research as well as an insight into your personal family tree. Scientists identified a certain locus in the area of two genes that are āexpressedā in the humans nasal cavity. This could show us why certain individuals lose smell or taste after COVID-19. Auton went on to say that āAs far as weāre aware, this finding is the first genetic link to this symptom and may provide insight into how the virus is interacting with our bodies,ā.
So how was this research conducted? The research relied on self-reported data from more than 1 million research participants through 23andMe. 69,841 people reported having tested positive for COVID and out of those participants roughly 68% reported a change to their sense of smell or taste as a symptom. Following this data, a genome wide association study was conducted. The loss of smell and taste was more common in the people who tested positive than those who reported flu like symptoms, yet tested negative.
When scientists then ācontrastedā the data of people who reported a loss of taste or smell after COVID 19 with those who said they didnāt experience the symptoms after testing positive, they found the genetic locus āin the vicinityā of the two genes. However, this is still a vague statement at this point with the researchers saying that how the two genes āare involved in this process is unclearā. However, these genes may play a role in the physiology of infected cells and the resulting functional impairment that contributes to loss of ability to smell.
Auton says that the research conducted so far is āvery much a first stepā and that numerous āfollow up studies will be needed to understand the underlying biologyā.
šØš“Saving the Megadiverse Colombia
Using Genomics to Save the Biodiversity in Colombiaā¦
Columbia is the second most biodiverse country in the world with more bird, amphibian, butterfly and frog species than anywhere else in the world. Roughly 14% of all species living in Colombia are endemic species. In 2019, Colombia joined the Earth Biogenome Project (EPB) in the aim to help sequence the genomes of all of the eukaryotic life on earth. This international collaboration between governments and the private sector will integrate research with sustainable strategies to develop Colombiaās bioeconomy, whilst maintaining its rich culture.
A combination of factors has helped to preserve Colombiaās biodiversity so far with much of it inaccessible and resultantly understudied. Following the 2016 peace agreement, the country has begun to open up likely harmful industries such as timber, mining and agriculture. These all threaten the unique ecosystems that have been hidden in Colombiaās rainforest, and could accelerate biodiversity loss.
An international research team says that joining the EBP and launching the proposed National Bioeconomy Strategy will have numerous positive outcomes for Colombia. Not only is there potential for the scheme to preserve biological wealth, but the scheme could even lead to the discovery of new species with the potential to aid human medicine and health.
Dr Huddart, Senior Research Associate in UEA's School of Biological Sciences, said that "We are at the beginning of an exciting new era of molecular research, where technological advances mean we can potentially sequence species DNA in the field cost-effectively and in real-time.ā Colombiaās NBS is a plan focused on the long term, post conflict brining about a multi disciplinary approach to value their biological resources.
The goal of the EPB is to essentially sequence all 1.8 million names species of animals, plants, fungi and single celled organisms. With Colombia not only being so diverse, but so large, the country is key in bringing success to this project. The sequencing project could provide discovery of novel molecules with potentially health, industry and food benefits that could have unknown potential in the modern world.
Earth is estimated to lose roughly 50% of the current biodiversity by the end of this century without action against climate change occurring. A digital DNA library could generate effective tools for preventing this loss in biodiversity, tacking pathogen spread, enhancing services and much more.
Weekly Topics
šļø Environmental
Solid waste systems reach environmental goals
Global chemical pollution exceeds safe limits for humanity
Coral populations gravely affected by climate change
š¦Marine
Enormous breeding colony of ice fish
Deep sea fish with transparent headā¦
Sponge cells hint at origins of nervous system
š¼ Conservation
Effectiveness of protection areas in safeguarding biodiversity
Swiss gold imports from Brazilā¦
š¦ Disease and Illness
New model to identify biological markers
Link shows causal link between deficiency in Parkinsonās disease gene and reduced immunoaging
New heart cell may provide cluesā¦
š· COVID
Omicron causes less severe illness in animal models
Biology unlikely to drive ethnic differences in COVID-19 risk
Structural Biology identifies new information to accelerate structure-based drug design
š§Ŗ Biochemistry
Protein mediates non-genetic inheritance of growth strategies
Lifespan and myriad functions of mRNA
We might not know half of our cells?
š¬ Evolution
Human DNA from 2000 year old headliceā¦
Female dolphins have what similar to humans?
š§¬ Genetics
Hidden gem enables gene editing with small but mighty system
Modelling how cells choose their fates
š· Weekly Camera Roll
Click on the text below to keep readingā¦
Thank you for reading! Please consider sharing to friends, family and classmates!
šReference List
š§¹The DNA Vacuum
Jude Colman, Science News. (2022) https://www.sciencenews.org/article/animal-dna-air-scientist-vacuum-first-time-zoo
E. Clare et al. Measuring biodiversity from DNA in the air. Current Biology. Published online January 6, 2022. doi: 10.1016/ j.cub.2021.11.064. C. Lynggaard et al. Airborne environmental DNA for terrestrial vertebrate community monitoring. Current Biology. Published online January 6, 2022. doi: 10.1016/j.cub.2021.12.014.
š·No Smell With COVIDā¦
Sarah Sloat (2022) https://www.nbcnews.com/science/science-news/genetic-risk-factor-found-covid-19-smell-taste-loss-researchers-say-rcna11996
Shelton, J.F., Shastri, A.J., Fletez-Brant, K. et al. The UGT2A1/UGT2A2 locus is associated with COVID-19-related loss of smell or taste. Nat Genet (2022). https://doi.org/10.1038/s41588-021-00986-w
šØš“Saving Megadiverse Colombia
University of East Anglia. "Saving species through genomics in megadiverse Colombia." ScienceDaily. ScienceDaily, 18 January 2022. <www.sciencedaily.com/releases/2022/01/220118104117.htm>.
Joseph E. A. Huddart, Andrew J. Crawford, Arturo L. Luna-Tapia, Silvia Restrepo, Federica Di Palma. EBP-Colombia and the bioeconomy: Genomics in the service of biodiversity conservation and sustainable development. Proceedings of the National Academy of Sciences, 2022; 119 (4): e2115641119 DOI: 10.1073/pnas.2115641119