Biology subjects

Lu, S.-Y.

Publications and source records attributed to Lu, S.-Y..

3 recordsLinked to original sources

bioRxiv2025

Laboratory evolution can improve algal cell yield and lipid production under mildly cold conditions

One challenge to large-scale microalgae cultivation, e.g., for biodiesel production, is the seasonal low-temperature conditions. We argue that seasonally varying selection in natural environments has prevented algae from better adapting to cold temperatures, and that laboratory evolution offers a promising approach for obtaining cold-adapted algal materials. We conducted a population-level artificial selection experiment with the unicellular green microalgae Chlorella sorokiniana at both a benign temperature (25) and a mildly cold temperature (15). Four artificial selection regimes were established: random selection, selection for high biomass (i.e., cell yield), selection for high lipid production, and rotation between high-biomass and high-lipid selection. We did not observe significant differences among the four selection regimes in evolutionary changes of algal cell yield or lipid yield, suggesting that natural selection at the individual level had dominated the evolutionary changes in our experiment. Compared with the ancestral strain, selection lines that had evolved at 15 typically exhibited increased cell yield and reduced lipid content per cell, indicating a trade-off relationship. However, substantial increases in cell yield may compensate for the reduction in lipid content per cell. Notably, three out of 16 selection lines showed > 1-fold increase in cell yield, and one exhibited > 1-fold increase in population-level lipid yield. Selection lines that had evolved at 25 displayed even greater increases in both cell and lipid yields, with a positive relationship between cell yield and lipid content per cell. Our results demonstrated the potential for laboratory evolution to obtain algal materials suitable for biofuel production under seasonal low-temperature conditions. HighlightsO_LIAlgae from natural environments not well-adapted to seasonal cold conditions. C_LIO_LILaboratory evolution under constant conditions with Chlorella sorokiniana. C_LIO_LIBoth cell yield and lipid production at a low temperature increased. C_LI

ecology↗

bioRxiv2025

Analysis of crosslinking sites suggests C. elegnas PIWI Argonaute exhibits flexible conformations for target recognition

Small RNAs play critical roles in gene regulation in diverse processes across organisms. Crosslinking, ligation, and analyses of sequence hybrid (CLASH) experiments have shown PIWI and Argonaute proteins bind to diverse mRNA targets, raising questions about their functional relevance and the degree of flexibility in target recognition. As crosslinking-induced mutations (CIMs) provides nucleotide-resolution of RNA binding sites, we developed MUTACLASH to systematically analyze CIMs in piRNA and miRNA CLASH data in C. elegans. We found CIMs are enriched at the nucleotide positions of mRNA corresponding to the center of targeting piRNAs and miRNAs. Notably, CIMs are also enriched at nucleotides with local pairing mismatches to piRNA. In addition, distinct patterns of CIMs are observed between canonical and non-canonical base pairing interactions, suggesting that the worm PIWI Argonaute PRG-1 adopts distinct conformations for canonical vs. non-canonical interactions. Critically, non-canonical miRNA or piRNA binding sites with CIMs exhibit more regulatory effects than those without CIMs, demonstrating CIM analysis as a valuable approach in assessing functional significance of small RNA targeting sites in CLASH data. Together, our analyses reveal the landscapes of Argonaute crosslinking sites on mRNAs and highlight MUTACLASH as an advanced tool in analyzing CLASH data.

molecular biology↗

bioRxiv2018

cis-Regulatory Chromatin Contacts in Neural Cells Reveal Contributions of Genetic Variants to Complex Neurological Disorders

Mutations in gene regulatory elements have been associated with a wide range of complex neurological disorders. However, due to their inherent cell type-specificity and difficulties in characterizing their regulatory targets, our ability to identify causal genetic variants has remained limited. To address these constraints, we perform integrative analysis of chromatin interactions using promoter capture Hi-C (pcHi-C), open chromatin regions using ATAC-seq, and transcriptomes using RNA-seq in four functionally distinct neural cell types: iPSC-induced excitatory neurons and lower motor neurons, iPSC-derived hippocampal dentate gyrus (DG)-like neurons, and primary astrocytes. We identify hundreds of thousands of long-range cis interactions between promoters and distal promoter-interacting regions (PIRs), enabling us to link regulatory elements to their target genes and reveal putative pathways that are dysregulated in disease. We validate several novel PIRs using CRISPR techniques in human excitatory neurons, demonstrating that CDK5RAP3, STRAP, and DRD2 are transcriptionally regulated by physically linked enhancers. Finally, we show that physical chromatin interactions mediate genetic interactions in autism spectrum disorder (ASD). Our study illustrates how characterizing the 3D epigenome elucidates novel regulatory relationships in the central nervous system (CNS), shedding light on previously unknown functions for noncoding variants in complex neurological disorders.

genomics↗