Biology subjects
Publications and source records attributed to Hu, I..
Phaeodactylum tricornutum is an unusual member of the clade of diatoms, eukaryotic marine brown algae that possess a distinct cell wall made of silica. Phaeodactylum is a rare exception in diatom biology in that it does not require silica throughout its whole life cycle. Here, we demonstrate that Phaeodactylum has a calcifying activity, which is highly unusual in unicellular eukaryotes.
Chlorella sorokiniana is an industrially important microalga, but its genetic manipulation remains limited by poor transformation efficiency. Although several barriers have been proposed, the role of intracellular nuclease activity has received little attention. Here, we compared the degradation of exogenous double-stranded DNA in whole-cell lysates from transformation-recalcitrant (Chlorella sorokiniana and Tetradesmus obliquus) and transformation-proficient (Phaeodactylum tricornutum, Microchloropsis gaditana, and Nannochloropsis oceanica) microalgae. C. sorokiniana rapidly degraded both linear and plasmid DNA, while T. obliquus exhibited intermediate activity. In contrast, no detectable degradation was observed in the transformation-proficient species. DNA degradation in C. sorokiniana occurred within minutes, and nuclease activity in both recalcitrant species was inhibited by EDTA and Zn2+, consistent with a metal ion-dependent endonuclease. These findings suggest that intracellular nuclease activity may represent an underexplored barrier to exogenous DNA stability during transformation and provide a potential target for improving genetic transformation of recalcitrant microalgae.
ObjectiveWe introduce ggrecipes, an R package that provides a collection of ggplot2-based functions for data exploration and analysis. Each function encapsulates data preprocessing and visualization construction, and returns a ggplot2 object that can be further customized using standard ggplot2 syntax. The package includes both general-purpose and domain-specific visualizations. ggrecipes is implemented in R under an open-source MIT license, with source code and documentation available at https://github.com/Ignophi/ggrecipes and https://ignophi.github.io/ggrecipes/.
Abstract: Circadian clocks regulate daily rhythms in all eukaryotes through [~]24-hour transcriptional-translational feedback loops driven by clock proteins. However, the molecular mechanisms that set the 24-hour period remain poorly defined. Here, using single-molecule imaging and nascent RNA sequencing, we uncover an unexpected RNA-based molecular timer: a single intron in the Drosophila timeless (tim) gene that regulates circadian period length by controlling mRNA localization. Strikingly, we find that [~]50% of tim mRNAs are localized to the nucleus due to inefficient post-transcriptional splicing of a single intron (which we named intron P), in contrast to other core clock transcripts that localize predominantly to the cytoplasm. CRISPR-mediated removal of intron P abolishes nuclear retention of tim transcripts, leading to accelerated TIM protein accumulation and a shortened [~]22-hour period with reduced rhythmic robustness. Remarkably, insertion of intron P alone into heterologous reporters is sufficient to promote nuclear retention in both Drosophila and human cells, acting as a conserved checkpoint that withholds transcripts in the nucleus until splicing is complete. Finally, we identify three RNA-binding proteins, two repressors (Hrb27C and Squid) and one activator (Qkr58E-2, a Sam68 homolog), that modulate intron P splicing in a rheostat-like manner. Together, these findings establish tim intron P as the first intron-based molecular timer in circadian clocks and reveal splicing kinetics as a critical regulatory layer in temporal gene expression programs, with broad implications for other processes such as development and immunity.
ObjectiveThis article examines the structural implications of composite variables developed in the field of "ageing". First, using data from the Balti-more Longitudinal Study of Aging (BLSA), we illustrate how the property of feature convergence arises in practice. Second, we show how this constrains both cross-sectional stratification and longitudinal monitoring. Third, we extend the analysis to molecular implementations and demonstrate that similar structural issues persist. Fourth, we examine how these properties impact common objectives - intervention evaluation, prediction, and investigation - and show that the limitations are not confined to linear models. Finally, we consider additional properties that may help explain the widespread appeal and persistence of these models, despite clear conflicts with their stated objectives.
The commercialisation of miniprep kits supplanted the original alkaline lysis method for plasmid DNA preparation, and had remained relatively unchanged for almost two decades. The Miraprep substantially improved the yields of miniprep kits. However, the method still relies on commercial kits, which can be a burden financially to certain projects. Additionally, Pronobis et al. also identified loss of RNAse activities in miniprep kits over time. The present novel plasmid DNA isolation protocol addresses the two issues mentioned above utilising alkaline lysis and alkaline hydrolysis principles. With a largely identical workflow and operation time, the Macerprep will significantly reduce costs of establishing new laboratories as well as maintenance of running molecular biology laboratories.