Biology subjects

Bryk, J.

Publications and source records attributed to Bryk, J..

5 recordsLinked to original sources

bioRxiv2026

Genome-wide associations of host susceptibility to helminth and blood pathogens in spatially structured rodent populations

Parasites are ubiquitous drivers of host evolution by exerting strong selective pressure on natural populations. Understanding the genetic basis of host susceptibility to infection is important to know how host-pathogen interactions shape patterns of resistance and diversity in natural populations. We conducted a genome-wide association study (GWAS) to identify host genetic variants associated with infection by helminth and blood pathogens in spatially structured populations of Bank voles (Myodes glareolus; (Schreber, 1780). We genotyped 182 individuals sampled from ten sites in central Europe using quaddRAD sequencing, retaining 30,206 high-quality single-nucleotide polymorphisms (SNPs). Associations between SNP genotypes and parasite infection status were tested using mixed models controlling for relatedness, with host body mass included as a covariate. Across parasite taxa, we identified twelve SNPs exceeding genome-wide significance with the strongest signals detected for the intestinal nematode Heligmosomum mixtum. The variants identified are all intergenic, intronic, upstream or downstream of genes, with none predicted to alter coding sequences. These genes are not classical immunity genes but some are implicated in cytokine production, PI3K/AKT signalling and p38 MAPK pathway, suggesting that selective pressure from pathogens does not only act on known immunity genes, but on broader regulatory and metabolic networks. This finding suggests that variation in gene expression may be important for the differences in host susceptibility or resistance to parasitic infections.

evolutionary biology↗

bioRxiv2021

Identification and quantification of chimeric sequencing reads in a highly multiplexed RAD-seq protocol

Highly multiplexed approaches have become a common practice in genomic studies. They have improved the cost-effectiveness of genotyping hundreds of individuals by using combinatorially-barcoded adapters. These strategies, however, can potentially misassign reads to incorrect samples. Here we used a modified quaddRAD protocol to analyse the occurrence of index hopping and PCR chimeras in a series of experiments with up to a 100 multiplexed samples per sequencing lane (total n = 639). We created two types of sequencing libraries: four libraries of Type A, where PCR reactions were run on individual samples before multiplexing, and three libraries of Type B, where PCRs were run on pooled samples. We used fixed pairs of inner barcodes to identify chimeric reads. Type B libraries show a higher percentage of misassigned reads (1.15%) compared to Type A libraries (0.65%). We also quantify the commonly undetectable chimeric sequences that occur whenever multiplexed groups of samples with different outer barcodes are sequenced together on a single flow cell. Our results suggest that these types of chimeric sequences represent up to 1.56% and 1.29% of reads in Type A and B libraries, respectively. We review the source of such errors, provide recommendations for developing highly-multiplexed RAD-seq protocols and analysing the resulting data to minimise the generation of chimeric sequences, allow their quantification, and provide finer control over the number of PCR cycles necessary to generate enough input DNA for library preparation.

bioinformatics↗

bioRxiv2021

UNIGEMS: plasmids and parts to facilitate teaching on assembly, gene expression control and logic in E. coli

Synthetic biology is as an excellent vehicle for education, as it enables creative combination of engineering and molecular biology approaches for quantitative characterisations of the assembled constructs. However, there is a limited number of resources available for such applications in the educational context, where straightforward setup, easily measurable phenotypes and extensibility are of particular importance. To expand the availability of education-friendly resources to teach synthetic biology and genetic engineering, we developed Unigems, a set of 10 plasmids that enable out-of-the-box investigations of principles of gene expression control, as well as more complex designs a biological logic gate. The system uses a common high-copy plasmid backbone and a common set of primers to enable Gibson-assembly of PCR-generated or synthesised parts into a target vector. It currently has two reporter genes with either two constitutive (high- or low-level) or two inducible (lactose- or arabinose-) promoters, as well as a single-plasmid implementation of an AND logic gate. The Unigems system has already been employed in undergraduate teaching settings, during outreach events and for training of iGEM teams. All plasmids have been deposited in Addgene.

synthetic biology↗

bioRxiv2021

Apis mellifera cognition as a tool for scientific engagement

In addition to the crowdsourcing of experimental data, citizen science, and scientific engagement more broadly, serve as a bridge between researchers and the wider community. This serves to foster a greater understanding of the scientific method and science-based solutions generally. Apis mellifera (honeybees) are a well-established model for the study of learning and cognition and can serve as an engaging outreach system for this wider community. Here, we developed and implemented a protocol using well established honeybee conditioning protocols to safely study the effects of caffeine and dopamine on learning performance. Using this protocol, a group of high-school aged students as part of the Ryukyu Girls program demonstrated that caffeine, but not dopamine, significantly reduced the number of trials required for a successful conditioning response. This allowed these students to explore the scientific method in a relatable and engaging way. Simple SummaryGlobal scientific literacy can be improved through widespread and effective community engagement by researchers. We propose Apis mellifera (honeybee) as an public engagement tool due to widespread awareness of colony collapse and the bees importance in food production. Moreover, their cognitive abilities make for engaging experiments. Their relative ease of cultivation means that studies can be performed cost-effectively, especially when partnering with local aperists. Using a proxy for honeybee learning, a group of non-specialist high-school-aged participants obtained data suggesting that caffeine, but not dopamine, improved learning. This hands-on experience facilitated student understanding of the scientific method, factors that shape learning and the importance of learning for hive health.

animal behavior and cognition↗

bioRxiv2019

Population structure of Apodemus flavicollis and comparison to Apodemus sylvaticus in northern Poland based on whole-genome genotyping with RAD-seq

BackgroundMice of the genus Apodemus are one the most common mammals in the Palaearctic region. Despite their broad range and long history of ecological observations, there are no whole-genome data available for Apodemus, hindering our ability to further exploit the genus in evolutionary and ecological genomics context. ResultsHere we present results from the double-digest restriction site-associated DNA sequencing (ddRAD-seq) on 72 individuals of A. flavicollis and 10 A. sylvaticus from four populations, sampled across 500 km distance in northern Poland. Our data present clear genetic divergence of the two species, with average p-distance, based on 21377 common loci, of 1.51% and a mutation rate of 0.0011 - 0.0019 substitutions per site per million years. We provide a catalogue of 117 highly divergent loci that enable genetic differentiation of the two species in Poland and to a large degree of 20 unrelated samples from several European countries and Tunisia. We also show evidence of admixture between the three A. flavicollis populations but demonstrate that they have negligible average population structure, with largest pairwise FST < 0.086. ConclusionOur study demonstrates the feasibility of ddRAD-seq in Apodemus and provides the first insights into the population genomics of the species.

genomics↗