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Biology subjects

Lili, L.

Publications and source records attributed to Lili, L..

3 recordsLinked to original sources

Saracatinib, a Selective Src Kinase Inhibitor, Blocks Fibrotic Responses in In Vitro, In Vivo and Ex Vivo Models of Pulmonary Fibrosis

Idiopathic Pulmonary Fibrosis (IPF) is a chronic, progressive, and often fatal disorder. Two FDA approved anti-fibrotic drugs, nintedanib and pirfenidone, slow the rate of decline in lung function, but responses are variable and side effects are common. Using an in-silico data-driven approach, we identified a robust connection between the transcriptomic perturbations in IPF disease and those induced by saracatinib, a selective Src kinase inhibitor, originally developed for oncological indications. Based on these observations, we hypothesized that saracatinib would be effective at attenuating pulmonary fibrosis. We investigated the anti-fibrotic efficacy of saracatinib relative to nintedanib and pirfenidone in three preclinical models: (i) in vitro in normal human lung fibroblasts (NHLFs); (ii) in vivo in bleomycin and recombinant adenovirus transforming growth factor-beta (Ad-TGF-{beta}) murine models of pulmonary fibrosis; and (iii) ex vivo in precision cut lung slices from these mouse models. In each model, the effectiveness of saracatinib in blocking fibrogenic responses was equal or superior to nintedanib and pirfenidone.

systems biology↗

A wipe-based stool collection and preservation kit for microbiome community profiling

While a range of methods for stool collection exist, many require complicated, self-directed protocols and stool transfer. In this study, we introduce and validate a novel, wipe-based approach to fecal sample collection and stabilization for metagenomics analysis. A total of 72 samples were collected across four different preservation types: freezing at -20{degrees}C, room temperature storage, a commercial DNA preservation kit, and DESS (dimethyl sulfoxide, ethylenediaminetetraacetic acid, sodium chloride) solution. These samples were sequenced and analyzed for taxonomic abundance metrics, metabolic pathway classification, and diversity analysis. Overall, the DESS wipe results validated the use of a wipe-based capture method to collect stool samples for microbiome analysis, showing an R2 of 0.96 for species across all kingdoms, as well as exhibiting a maintenance of Shannon diversity (3.1-3.3) and species richness (151-159) compared to frozen samples. Moreover, DESS showed comparable performance to the commercially available preservation kit (R2 of 0.98), and samples consistently clustered by subject across each method. Future studies will be needed to further explore sample processing options and their applications in non-healthy subjects, particularly patients with irritable bowel syndrome, inflammatory bowel disease, and colorectal cancer, but these data suggest the DESS wipe method can be used for stable, room temperature collection and transport of human stool specimens.

microbiology↗

Assessing the potential for assisted gene flow using past introduction of Norway spruce in Southern Sweden: Local adaptation and genetic basis of quantitative traits in trees.

Norway spruce (Picea abies) is a dominant conifer species of major economic importance in Northern Europe. Extensive breeding programs were established to improve phenotypic traits of interest. In southern Sweden seeds used to create progeny tests were collected on about 3000 trees of outstanding phenotype (\"plus\" trees) across the region. Some were of local origin but many were recent introductions from the rest of the natural range. The mixed origin of the trees together with partial sequencing of the exome of >1,500 of these trees and phenotypic data retrieved from the Swedish breeding program offered us a unique opportunity to dissect the genetic basis of local adaptation of three quantitative traits (height, diameter and budburst). Through a combination of multivariate analyses and genome-wide association studies, we showed that there was a very strong effect of geographical origin on growth (height and diameter) and phenology (budburst) with trees from southern origins outperforming local provenances. Association studies also indicated that growth traits were highly polygenic and budburst somewhat less. Hence, our results suggest that assisted gene flow and genomic selection approaches could help alleviating the effect of climate change on P. abies breeding programs in Sweden.

evolutionary biology↗