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Biology subjects

Zhang, A. Y.

Publications and source records attributed to Zhang, A. Y..

3 recordsLinked to original sources

Cities as evolutionary incubators for the global spread of the Spotted Lanternfly

Habitat destruction and invasive species pose two of the greatest global threats to biodiversity. These factors do not operate in isolation, and nowhere is their interaction more apparent than in urban environments. Urban organisms rapidly evolve under novel ecological circumstances where they also encounter anthropogenic opportunities for range expansion. Here, we examine the role of urbanization in the invasive success of an emerging global pest, the Spotted Lanternfly, during colonization and expansion. We demonstrate that the invasive population in the United States has undergone three sequential bottlenecks, resulting in significantly reduced genetic diversity and elevated inbreeding. The success of this invasive population may be in part attributable to adaptation in the native range prior to the invasion: we detect divergence between urban and rural lanternflies in Shanghai, China, (the invasion origin) in genes related to stress response, metabolism, and detoxification pathways. Additionally, we detect genomic signatures of selection in the invasive population suggesting adaptive refinement as the invasion progresses. This study provides evidence of adaptive evolution in response to urbanization despite substantial loss of genetic diversity, and implicates adaptive responses to pesticide application, dietary shifts, and climate in the invasive success of the Spotted Lanternfly.

evolutionary biology↗

Melanin Nanoparticles as an Alternative to Natural Melanin in Retinal Pigment Epithelium Cells and Their Therapeutic Effects against Age-Related Macular Degeneration

Melanin is a natural pigment that is widely distributed in many parts of the human body, such as the skin and retinal pigment epithelium (RPE) in eyes. In contrast to skin melanin, which is being constantly synthesized by the epidermal melanocytes, melanin in the RPE does not regenerate. Melanin is known to function as a potential radical scavenger and photoprotective agent. However, the protective effects of melanin against oxidative stress decline with increasing age. This phenomenon has been significantly correlated with the pathogenesis of age-related macular degeneration (AMD). To increase the potential antioxidant and photoprotective characteristics of the melanin, we designed a new strategy by replenishment of melanin using PEGylated-synthetic melanin nanoparticles (MNPs) in the RPE for the treatment of AMD. We performed experiments using AMD-like cellular and mouse models and demonstrated that MNPs are safe, biocompatible, and selectively target reactive oxygen species (ROS) with powerful antioxidant properties. MNPs can traffic and accumulate in the RPE and are exclusively located in cytosol, but not the nucleus and mitochondria of the cells, for up to three months after a single-dose intravitreal (IVT) injection. Our findings demonstrate, for the first time, that MNPs are able to substitute for natural melanin in the RPE of eyes and suggest the potential efficacy of MNPs as a natural radical scavenger against oxidative stress in ROS-related diseases, such as AMD. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=88 SRC="FIGDIR/small/481315v2_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@18929e6org.highwire.dtl.DTLVardef@1dc929org.highwire.dtl.DTLVardef@181c8c2org.highwire.dtl.DTLVardef@1a36eab_HPS_FORMAT_FIGEXP M_FIG C_FIG Intracellular trafficking showing that PEGylated-synthetic melanin nanoparticles (MNPs) reach their target and are stable in the retinal pigment epithelial cells for up to 3 months via a single-dose intravitreal (IVT) injection.

molecular biology↗

A data-driven approach to characterising intron signal in RNA-seq data

RNA-seq datasets can contain millions of intron reads per sequenced library that are typically removed from downstream analysis. Only reads overlapping annotated exons are considered to be informative since mature mRNA is assumed to be the major component sequenced, especially when examining poly(A) RNA samples. In this paper, we demonstrate that intron reads are informative and that pre-mRNA is the major source of intron signal. Making use of pre-mRNA signal, our index method combines differential expression analyses from intron and exon counts to categorise changes observed in each count set, giving additional genes with evidence of transcriptional changes when compared to a classic approach. Considering the importance of intron retention in some biological systems, another novel method, superintronic, looks for evidence of intron retention after accounting for the presence of pre-mRNA signal. The results presented here overcomes deficiencies and biases in previous works related to intron reads by exploring multiple sources for intron reads simultaneously using a data-driven approach, and provides a broad overview into how intron reads can be utilised in relation to multiple aspects of transcriptional biology.

bioinformatics↗