View of the Abruzzo, Lazio and Molise National Park. Photo by Giorgio Bertorelle
The activities of Endemixit presented at the 81st national congress of the Italian Zoological Society 10.11.2022
The 81st congress of the Italian Zoological Society (UZI) was held between September 20th and 23rd, with several members of the team of the University of Trieste, where the congress took place being actively involved in the organizing committee. One of the three thematic symposia, entitled “Monitoring of biodiversity”, gave us the opportunity to highlight…
Updates on Bombina pachypus chromosomes microdissection
The first ChromSeq trial of Bombina pachypus is done! We isolated single chromosomes from cells fixed in metaphase using the technique of microdissection with an inverted microscope. The task was complicated by the large sized chromosomes of this species. Genetic material was then amplified using a Whole Genome Amplification kit and sequenced on a NovaSeq6000…
Endemixit in the primary school! 1.07.2022
Communication and dissemination are an important goal of the ENDEMIXIT project. We organized a teaching activity suitable for primary school pupils, and we enjoyed offering it to two fourth-grade classes in Ferrara. The session lasted about two hours and was structured in three parts. Initially, we provided the students with a presentation of the ENDEMIXIT…
Where are we now? Part 7 – Refinement of genome assemblies 25.05.22
We are finalizing the genome assembly of the Ponza grayling Hipparchia sbordonii, which is currently undergoing a manual refinement step. A comparative assessed of different de novo assembly strategies identified Canu as the best-performing algorithm: following different polishing and scaffolding steps, the genome assembly included 99 scaffolds (N50 = 10019938, L50 = 28 and BUSCO…
Studying the dark matter of the genome 09.05.2022
Transposable elements (TE) largely represent what is commonly referred to as the dark matter of the genome, a non-coding portion of the genome that has so far been considered only as “selfish”” or “junk” DNA.First discovered in maize plants by Barbara McClintock, TEs are repetitive DNA sequences with the ability to mobilize within a host…
Where are we now? Part 6 – Outreach
Our outreach activities have continued at full speed in the last months. Our journey full of scientific and dissemination efforts, challenges and successes have been constantly posted in this blog, Twitter and Instagram. An English and Italian glossary of relevant terms in evolutionary biology and conservation genetics has been created to help non-experts to better…
Where are we now? Part 5 – In vivo functional assays 30.03.2022
We completed the controlled crosses to explore in vivo the functional impact of genetic load on fitness in the Atlantic sturgeon. Twelve inbred and outbred families were successfully produced, reared, and tested for fitness markers such as survival, growth, and response to light (phototaxis, details in the post: Studying the phototactic response of our Adriatic…
Where are we now? Part 4 – In vitro functional assays 14.03.2022
We obtained oral biopsies of the Marsican brown bear (small population) and the European brown bear (here the large Slovakian population was used as a control) to proliferate fibroblasts (live cells) in laboratory. Cell cultures were successfully established and maintained. Standard canine cell cultures and the original brown bear cell cultures described above were used…
Where are we now? Part 3 – Genetic load estimates and its consequences 21.02.2022
Genomes can inform us on the amount of genetic load, i.e., the genetic variants that negatively affect survival and tend to accumulate during population’s contractions when closely related individuals breed. Estimating genetic load is not trivial as it requires knowledge on individual survival, which might be difficult to obtain in wild, elusive populations. Bioinformatics approaches…
Where are we now? Part 2 – Preliminary population genomics analyses 9.02.2022
As soon as we received the resequencing data from individuals of the large and small population, respectively, for each of the five target species (details in the post: Here comes the data! 06.05.2021), we started processing and analyzing it to study genomic variation patterns and reconstruct demographic histories. These steps require a reference genome for…
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