Latest Articles

  • Section: Neuroscience ; Topics: Neuroscience

    The Switchmaze: an open-design device for measuring motivation and drive switching in mice

    10.24072/pcjournal.416 - Peer Community Journal, Volume 4 (2024), article no. e48.

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    Animals need to switch between motivated behaviours, like drinking, feeding or social interaction, to meet environmental availability, internal needs and more complex ethological needs such as hiding future actions from competitors. Inflexible, repetitive behaviours are a hallmark of many neuropsychiatric disorders. However, how the brain orchestrates switching between the neural mechanisms controlling motivated behaviours, or drives, is unknown. This is partly due to a lack of appropriate measurement systems. We designed an automated extended home-cage, the Switchmaze, using open-source hardware and software. In this study, we use it to establish a behavioural assay of motivational switching in mice. Individual animals access the Switchmaze from the home-cage and choose between entering one of two chambers containing different goal objects or returning to the home-cage. Motivational switching is measured as a ratio of switching between chambers and continuous exploitation of one chamber. Behavioural transition analysis is used to further dissect altered motivational switching. As proof-of-concept, we show environmental manipulation, and targeted brain manipulation experiments which altered motivational switching without effect on traditional behavioural parameters. Chemogenetic inhibition of the prefrontal-hypothalamic axis increased the rate of motivation switching, highlighting the involvement of this pathway in drive switching. This work demonstrates the utility of open-design in understanding animal behaviour and its neural correlates.

  • Section: Mathematical & Computational Biology ; Topics: Genetics/genomics, Computer sciences

    Revisiting pangenome openness with k-mers

    10.24072/pcjournal.415 - Peer Community Journal, Volume 4 (2024), article no. e47.

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    Pangenomics is the study of related genomes collectively, usually from the same species or closely related taxa. Originally, pangenomes were defined for bacterial species. After the concept was extended to eukaryotic genomes, two definitions of pangenome evolved in parallel: the gene-based approach, which defines the pangenome as the union of all genes, and the sequence-based approach, which defines the pangenome as the set of all nonredundant genomic sequences. Estimating the total size of the pangenome for a given species has been subject of study since the very first mention of pangenomes. Traditionally, this is performed by predicting the ratio at which new genes are discovered, referred to as the openness of the species. Here, we abstract each genome as a set of items, which is entirely agnostic of the two approaches (gene-based, sequence-based). Genes are a viable option for items, but also other possibilities are feasible, e.g., genome sequence substrings of fixed length k (k-mers). In the present study, we investigate the use of k-mers to estimate the openness as an alternative to genes, and compare the results. An efficient implementation is also provided.

  • Dental calculus is an excellent source of information on the dietary patterns of past populations, including consumption of plant-based items. The detection of plant-derived residues such as alkaloids and their metabolites in dental calculus provides direct evidence of consumption by individuals within a population. We conducted a study on 41 individuals from Middenbeemster, a 19th century rural  Dutch archaeological site. Skeletal and dental analysis was performed to explore potential relationships between pathological lesions and presence of alkaloids. Dental calculus was analysed using ultra-high-performance liquid chromatography-tandem  mass spectrometry (UHPLC-ESI-MS/MS). We were able to detect nicotine, cotinine, caffeine, theophylline, and salicylic acid, suggesting the consumption of tea and coffee and smoking of tobacco on an individual scale, which is also confirmed by historic documentation and identification of pipe notches in the dentition. Nicotine and/or cotinine was present in 56% of individuals with at least one visible pipe notch. There is some influence of skeletal preservation on the detection of alkaloids, with higher quantities of compounds extracted from well-preserved individuals, and we observe a positive relationship between weight of the calculus sample and quantity of detected compounds, as well as between chronic maxillary sinusitis and the presence of multiple alkaloids. There are many limitations that will need to be addressed going forward with this type of analysis; we stress the need for more systematic research on the consumption of alkaloid-containing items and their subsequent concentration and preservation in dental calculus, in addition to how mode of consumption may affect concentrations in the dentition. Despite the limitations, this preliminary study illustrates many benefits of using calculus to target a variety of compounds that could have been consumed as medicine or diet. This method allows us to directly address specific individuals, which can be especially useful in individuals that are not always well-documented in historic documentation, such as rural populations, and especially children and women.

  • Section: Evolutionary Biology ; Topics: Evolution, Genetics/genomics, Population biology

    Does the seed fall far from the tree? Weak fine-scale genetic structure in a continuous Scots pine population

    10.24072/pcjournal.413 - Peer Community Journal, Volume 4 (2024), article no. e45.

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    Knowledge of fine-scale spatial genetic structure, i.e., the distribution of genetic diversity at short distances, is important in evolutionary research and in practical applications such as conservation and breeding programs. In trees, related individuals often grow close to each other due to limited seed and/or pollen dispersal. The extent of seed dispersal also limits the speed at which a tree species can spread to new areas. We studied the fine-scale spatial genetic structure of Scots pine (Pinus sylvestris) in two naturally regenerated sites located 20 km from each other in continuous south-eastern Finnish forest. We genotyped almost 500 adult trees for 150k SNPs using a custom made Affymetrix array. We detected some pairwise relatedness at short distances, but the average relatedness was low and decreased with increasing distance, as expected. Despite the clustering of related individuals, the sampling sites were not differentiated (FST = 0.0005). According to our results, Scots pine has a large neighborhood size (Nb = 1680–3210), but a relatively short gene dispersal distance (σg = 36.5–71.3 m). Knowledge of Scots pine fine-scale spatial genetic structure can be used to define suitable sampling distances for evolutionary studies and practical applications. Detailed empirical estimates of dispersal are necessary both in studying post-glacial recolonization and predicting the response of forest trees to climate change.

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