Biology subjects

Chan, D. T. C.

Publications and source records attributed to Chan, D. T. C..

3 recordsLinked to original sources

bioRxiv2024

The genetic consequences of historic climate change on the contemporary population structure of a widespread temperate North American songbird

Studies of widely distributed species can offer insight regarding how past demographic events tied to historic glaciation and ongoing population genetic processes interact to shape contemporaneous patterns of biodiversity at a continental scale. In this study, we used whole-genome resequencing to investigate the current population structure and genetic signatures of past demographic events in the widespread migratory American goldfinch (Spinus tristis). In contrast to the low variation in mitochondrial genomes, a genome-wide panel of >4.5 million single nucleotide polymorphisms (SNPs) strongly supported the existence of eastern and western populations separated by western mountain ranges and additional population structuring within the western clade. Demographic modeling indicated that the eastern and western populations diverged approximately one million years ago, and both populations experienced subsequent population bottlenecks during the last glacial period. Species distribution models showed a severe contraction of suitable habitat for the American goldfinch during this period, with predicted discontinuities that are indicative of multiple, isolated glacial refugia that coincide with present-day population structure. This study highlights the power of genome-level sequencing approaches to deepen our understanding of evolutionary processes in nonmodel wild species and to contribute to efforts assessing how historic demographic events and contemporary factors might influence biodiversity.

evolutionary biology↗

bioRxiv2024

Pangenomic landscapes shape the genetic circuit performance in a Stutzerimonas biodesign toolkit

Engineering identical genetic circuits into different species typically results in large differences in performance due to the unique cellular environmental context of each host, a phenomenon known as the "chassis-effect". A better understanding of how genomic and physiological contexts underpin the chassis-effect will greatly improve biodesign strategies across diverse microorganisms. Here, we combined a pangenomics-based gene expression analysis with quantitative measurements of performance from an engineered genetic inverter device to uncover how genome structure and function relates to the observed chassis-effect across six closely related Stutzerimonas hosts. Our results reveal that genome architecture underpins divergent responses between our chosen non-model bacterial hosts to engineered genetic circuits. Specifically, differential expression of the core genome, gene clusters shared between all hosts, were found to be the main source of significant concordance to the observed genetic device performance, whereas specialty genes from respective accessory genomes were not significant. A data-driven investigation revealed that genes involved in denitrification and components of trans-membrane transporter proteins were among the most differentially expressed gene clusters in response to the genetic device. Our results show the chassis-effect can be traced along differences among genome-encoded functions that are mostly conserved and that these differences create a unique biodesign space among closely related species. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=87 SRC="FIGDIR/small/580380v2_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@173161dorg.highwire.dtl.DTLVardef@b0fdf3org.highwire.dtl.DTLVardef@1f09130org.highwire.dtl.DTLVardef@cc1eb3_HPS_FORMAT_FIGEXP M_FIG C_FIG

synthetic biology↗

bioRxiv2023

Revealing the chassis-effect on a broad-host-range genetic switch and its concordance with interspecies bacterial physiologies

Broad-host-range synthetic biology is an emerging frontier that aims to expand our current engineerable domain of microbial hosts for biodesign applications. As more novel species are brought to "model status", synthetic biologists are discovering that identically engineered genetic circuits can exhibit different performances depending on the organism it operates within, an observation referred to as the "chassis-effect". It remains a major challenge to uncover which genome encoded and physiological biological determinants will underpin chassis effects that govern the performance of engineered genetic devices. In this study, we compared model and novel bacterial hosts to ask whether phylogenomic relatedness or similarity in host physiology is a better predictor of toggle switch performance. This was accomplished using comparative framework based on multivariate statistical approaches to systematically demonstrate the chassis-effect and characterize the performance dynamics of a genetic toggle switch operating within six Gammaproteobacteria. Our results solidify the notion that genetic devices are significantly impacted by host-context. Furthermore, we formally determined that hosts exhibiting more similar metrics of growth and molecular physiology also exhibit more similar toggle switch performance, indicating that specific bacterial physiology underpins measurable chassis effects. The result of this study contributes to the field of broad-host-range synthetic biology by lending increased predictive power to the implementation of genetic devices in less-established microbial hosts.

synthetic biology↗