Natural mineral and industrial solid waste-based adsorbent for perfluorooctanoic acid and perfluorooctane sulfonate removal from surface water: Advances and prospects.

PER: and polyfluorinated alkyl substances, especially perfluorooctanoic acid and perfluorooctane sulfonic acid (PFOX), have attracted considerable attention lately because of their widespread occurrence in aquatic environment and potential biological toxicity to animals and human beings. The development of economical, efficient, and engineerable adsorbents for removing PFOX in water has become one of the research focuses. This review summarized the recent progress on natural mineral and industrial solid based adsorbent (NM&ISW-A) and removal mechanisms concerning PFOX onto NM&ISW-A, as well as proposed the current challenges and future perspectives of using NM&ISW-A for PFOX removal in water. Kaolinite and montmorillonite are usually used as model clay minerals for PFOX removal, and have been proved to adsorb PFOX by ligand exchange and electrostatic attraction. Fe-based minerals, such as goethite, magnetite, and hematite, have better PFOX adsorption capacity than clay minerals. The adsorbent prepared from industrial solid waste by high temperature roasting has great potential application prospects. Fabricating nanomaterials, amination modification, surfactant modification, fluorination modification, developing versatile composites, and designing special porous structure are beneficial to improve the adsorption performance of PFOX onto NM&ISW-A by enhancing the specific surface area, positive charge, and hydrophobicity. Electrostatic interaction, hydrophobic interaction, hydrogen bond, ligand and ion exchange, and self-aggregation (formation of micelle or hemimicelle) are the main adsorption mechanisms of PFOX by NM&ISW-A. Among them, electrostatic and hydrophobic interactions play a considerable role in the removal of PFOX by NM&ISW-A. Therefore, NM&ISW-A with electrostatic functionalities and considerable hydrophobic segments enables rapid, efficient, and high-capacity removal of PFOX. The future directions of NM&ISW-A for PFOX removal include the preparation and regeneration of engineerable NM&ISW-A, the development of coupling technology for PFOX removal based on NM&ISW-A, the in-depth research on adsorption mechanism of PFOX by NM&ISW-A, as well as the development of NM&ISW-A for PFOX alternatives removal. This review paper would be helpful the comprehensive understanding of NM&ISW-A potential for PFOX removal and the PFOX removal mechanisms, and identifies the gaps for future research and development.

Intertwined role of mechanism identification by DFT-XAFS and engineering considerations in the evolution of P adsorbents.

Adsorption method exhibits promising potential in effectively removal of phosphate from wastewater, yet it faces tremendous challenges in practical application. Limited comprehension of adsorption mechanisms and the lack of evaluation method for scaling up application are the two main obstacles. To fully realize the practical application of P adsorbents, we reviewed advanced tools, including density functional theory (DFT) and/or X-ray absorption fine structure (XAFS) to elucidate mechanisms, underscored the significance of thermodynamics and kinetics in engineering design, and proposed strategies for regenerating and reusing P adsorbents. Specifically, we delved into the utilization of DFT and XAFS to gain insights into adsorption mechanisms, focusing on active site verification and molecular interaction configurations. Additionally, we explored precise calculation methods for adsorption thermodynamics and adsorption kinetics, encompassing thermodynamic equilibrium constants, reactor selection, and the regeneration, recovery, and disposal of P adsorbents. Our comprehensive review aims to serve as a guiding light in advancing the development of highly efficient P adsorbents for engineering applications.

LncRNAway: a web-based sgRNA design tool for precise and effective suppression of long noncoding RNAs.

Thousands of long noncoding RNAs (lncRNAs) have been annotated via high-throughput RNA sequencing, yet only a small fraction have been functionally investigated. Genomic knockout is the mainstream strategy for studying the biological function of protein-coding genes and lncRNAs, whereas the complexity of the lncRNA locus, especially the natural antisense lncRNAs (NAT-lncRNAs), presents great challenges. Knocking out lncRNAs often results in unintended disruptions of neighboring protein-coding genes and small RNAs, leading to ambiguity in observing phenotypes and interpreting biological function. To address this issue, we launched LncRNAway, a user-friendly web tool based on the BESST (branchpoint to 3' splicing site targeting) method, to design sgRNAs for lncRNA knockout. LncRNAway not only provides specific and effective lncRNA knockout guidelines but also integrates genotyping primers and quantitative PCR primers designing, thereby streamlining experimental procedures of lncRNA function study. LncRNAway is freely available at https://www.lncrnaway.com.

OrthoVenn3: an integrated platform for exploring and visualizing orthologous data across genomes.

Advancements in comparative genomics research have led to a growing interest in studying species evolution and genetic diversity. To facilitate this research, OrthoVenn3 has been developed as a powerful, web-based tool that enables users to efficiently identify and annotate orthologous clusters and infer phylogenetic relationships across a range of species. The latest upgrade of OrthoVenn includes several important new features, including enhanced orthologous cluster identification accuracy, improved visualization capabilities for numerous sets of data, and wrapped phylogenetic analysis. Furthermore, OrthoVenn3 now provides gene family contraction and expansion analysis to support researchers better understanding the evolutionary history of gene families, as well as collinearity analysis to detect conserved and variable genomic structures. With its intuitive user interface and robust functionality, OrthoVenn3 is a valuable resource for comparative genomics research. The tool is freely accessible at https://orthovenn3.bioinfotoolkits.net.

A molecular atlas reveals the tri-sectional spinning mechanism of spider dragline silk.

The process of natural silk production in the spider major ampullate (Ma) gland endows dragline silk with extraordinary mechanical properties and the potential for biomimetic applications. However, the precise genetic roles of the Ma gland during this process remain unknown. Here, we performed a systematic molecular atlas of dragline silk production through a high-quality genome assembly for the golden orb-weaving spider Trichonephila clavata and a multiomics approach to defining the Ma gland tri-sectional architecture: Tail, Sac, and Duct. We uncovered a hierarchical biosynthesis of spidroins, organic acids, lipids, and chitin in the sectionalized Ma gland dedicated to fine silk constitution. The ordered secretion of spidroins was achieved by the synergetic regulation of epigenetic and ceRNA signatures for genomic group-distributed spidroin genes. Single-cellular and spatial RNA profiling identified ten cell types with partitioned functional division determining the tri-sectional organization of the Ma gland. Convergence analysis and genetic manipulation further validated that this tri-sectional architecture of the silk gland was analogous across Arthropoda and inextricably linked with silk formation. Collectively, our study provides multidimensional data that significantly expand the knowledge of spider dragline silk generation and ultimately benefit innovation in spider-inspired fibers.

RetroScan: An Easy-to-Use Pipeline for Retrocopy Annotation and Visualization.

Retrocopies, which are considered "junk genes," are occasionally formed via the insertion of reverse-transcribed mRNAs at new positions in the genome. However, an increasing number of recent studies have shown that some retrocopies exhibit new biological functions and may contribute to genome evolution. Hence, the identification of retrocopies has become very meaningful for studying gene duplication and new gene generation. Current pipelines identify retrocopies through complex operations using alignment programs and filter scripts in a step-by-step manner. Therefore, there is an urgent need for a simple and convenient retrocopy annotation tool. Here, we report the development of RetroScan, a publicly available and easy-to-use tool for scanning, annotating and displaying retrocopies, consisting of two components: an analysis pipeline and a visual interface. The pipeline integrates a series of bioinformatics software programs and scripts for identifying retrocopies in just one line of command. Compared with previous methods, RetroScan increases accuracy and reduces false-positive results. We also provide a Shiny app for visualization. It displays information on retrocopies and their parental genes that can be used for the study of retrocopy structure and evolution. RetroScan is available at https://github.com/Vicky123wzy/RetroScan.