Selective Cell-Cell Adhesion Regulation via Cyclic Mechanical Deformation Induced by Ultrafast Nanovibrations.

The adoption of dynamic mechanomodulation to regulate cellular behavior is an alternative to the use of chemical drugs, allowing spatiotemporal control. However, cell-selective targeting of mechanical stimuli is challenging due to the lack of strategies with which to convert macroscopic mechanical movements to different cellular responses. Here, we designed a nanoscale vibrating surface that controls cell behavior via selective repetitive cell deformation based on a poroelastic cell model. The vibrating indentations induce repetitive water redistribution in the cells with water redistribution rates faster than the vibrating rate; however, in the opposite case, cells perceive the vibrations as a one-time stimulus. The selective regulation of cell-cell adhesion through adjusting the frequency of nanovibration was demonstrated by suppression of cadherin expression in smooth muscle cells (fast water redistribution rate) with no change in vascular endothelial cells (slow water redistribution rate). This technique may provide a new strategy for cell-type-specific mechanical stimulation.

Biomimetic and bioorthogonal nanozymes for biomedical applications.

Nanozymes mimic the function of enzymes, which drive essential intracellular chemical reactions that govern biological processes. They efficiently generate or degrade specific biomolecules that can initiate or inhibit biological processes, regulating cellular behaviors. Two approaches for utilizing nanozymes in intracellular chemistry have been reported. Biomimetic catalysis replicates the identical reactions of natural enzymes, and bioorthogonal catalysis enables chemistries inaccessible in cells. Various nanozymes based on nanomaterials and catalytic metals are employed to attain intended specific catalysis in cells either to mimic the enzymatic mechanism and kinetics or expand inaccessible chemistries. Each nanozyme approach has its own intrinsic advantages and limitations, making them complementary for diverse and specific applications. This review summarizes the strategies for intracellular catalysis and applications of biomimetic and bioorthogonal nanozymes, including a discussion of their limitations and future research directions.

ZnO/Graphene Oxide on Halloysite Nanotubes as a Superabsorbent Nanocomposite Photocatalyst for the Degradation of Organic Dyes.

Using renewable photocatalysts for pollutant degradation represents a promising approach to addressing environmental water challenges by harnessing solar energy without additional energy consumption. However, for the practical use of photocatalysts, it is necessary to improve catalyst efficiency, considering cost and biocompatibility. In this study, we developed a new superabsorbent photocatalyst for the degradation of organic dyes in water. Our photocatalyst comprises halloysite nanotubes (HNTs) with a large outer diameter and Si-O and Al-O groups on the outer and inner surfaces, respectively; graphene oxide (GO) possessing numerous sp2 bonds and light-conductive properties; and ZnO, which can degrade organic molecules via a photon source. By exploiting the superabsorbent properties of GOs for organic dyes and stabilizing ZnO nanoparticles on HNTs to inhibit aggregation, our photocatalysts demonstrated significantly improved degradability compared to ZnO nanoparticles alone and combinations of ZnO with HNTs or GO. The structural characteristics of the nanocomposites were characterized using SEM, EDX, Raman spectroscopy, and XRD. Their enhanced photocatalytic activity was demonstrated by the degradation of rhodamine b in water, showing 95% photodegradation under UV illumination for 60 min, while the ZnO nanoparticles showed only 56% dye degradation under the same condition. Additionally, the degradation rate was enhanced by four times. Furthermore, the catalysts maintained their initial activity with no significant loss after four uses, showing their potential for practical implementation in the mass purification of wastewater.

Strainer-Separable TiO2 on Halloysite Nanocomposite-Embedded Alginate Capsules with Enhanced Photocatalytic Activity for Degradation of Organic Dyes.

Photocatalysis driven by natural sunlight is an attractive approach to removing pollutants from wastewater. Although TiO2-based photocatalysts using various support nano-materials with high catalytic activity and reusability have been developed for purifying wastewater, the centrifugal separation methods used for the nanocatalysts limit their use for treating large amounts of water. Here, we prepared a TiO2 nano-catalyst supported on a halloysite nanotube (HNT)-encapsulated alginate capsule (TiO2@HNT/Alcap) to recapture the catalysts rapidly without centrifugation. The structure of TiO2@HNT/Alcap was characterized by X-ray diffraction, SEM, and TGA. In our system, the combination of HNTs and alginate capsules (Alcaps) improved the efficiency of adsorption of organic pollutants to TiO2, and their milli = meter scale structure allowed ultra-fast filtering using a strainer. The TiO2@HNT/Alcaps showed ~1.7 times higher adsorption of rhodamine B compared to empty alginate capsules and also showed ~10 and ~6 times higher degradation rate compared to the HNT/Alcaps and TiO2/Alcaps, respectively.

Stimuli-Responsive Adaptive Nanotoxin to Directly Penetrate the Cellular Membrane by Molecular Folding and Unfolding.

Biological nanomachines, including proteins and nucleic acids whose function is activated by conformational changes, are involved in every biological process, in which their dynamic and responsive behaviors are controlled by supramolecular recognition. The development of artificial nanomachines that mimic the biological functions for potential application as therapeutics is emerging; however, it is still limited to the lower hierarchical level of the molecular components. In this work, we report a synthetic machinery nanostructure in which actuatable molecular components are integrated into a hierarchical nanomaterial in response to external stimuli to regulate biological functions. Two nanometers core-sized gold nanoparticles are covered with ligand layers as actuatable components, whose folding/unfolding motional response to the cellular environment enables the direct penetration of the nanoparticles across the cellular membrane to disrupt intracellular organelles. Furthermore, the pH-responsive conformational movements of the molecular components can induce the apoptosis of cancer cells. This strategy based on the mechanical motion of molecular components on a hierarchical nanocluster would be useful to design biomimetic nanotoxins.

Genome Size Estimation of Callipogon relictus Semenov (Coleoptera: Cerambycidae), an Endangered Species and a Korea Natural Monument.

We estimated the genome size of a relict longhorn beetle, Callipogon relictus Semenov (Cerambycidae: Prioninae)-the Korean natural monument no. 218 and a Class I endangered species-using a combination of flow cytometry and k-mer analysis. The two independent methods enabled accurate estimation of the genome size in Cerambycidae for the first time. The genome size of C. relictus was 1.8 ± 0.2 Gb, representing one of the largest cerambycid genomes studied to date. An accurate estimation of genome size of a critically endangered longhorned beetle is a major milestone in our understanding and characterization of the C. relictus genome. Ultimately, the findings provide useful insight into insect genomics and genome size evolution, particularly among beetles.

Population Genomic Analysis Reveals Contrasting Demographic Changes of Two Closely Related Dolphin Species in the Last Glacial.

Population genomic data can be used to infer historical effective population sizes (Ne), which help study the impact of past climate changes on biodiversity. Previous genome sequencing of one individual of the common bottlenose dolphin Tursiops truncatus revealed an unusual, sharp rise in Ne during the last glacial, raising questions about the reliability, generality, underlying cause, and biological implication of this finding. Here we first verify this result by additional sampling of T. truncatus. We then sequence and analyze the genomes of its close relative, the Indo-Pacific bottlenose dolphin T. aduncus. The two species exhibit contrasting demographic changes in the last glacial, likely through actual changes in population size and/or alterations in the level of gene flow among populations. Our findings suggest that even closely related species can have drastically different responses to climatic changes, making predicting the fate of individual species in the ongoing global warming a serious challenge.

Draft genome of the sea cucumber Apostichopus japonicus and genetic polymorphism among color variants.

The Japanese sea cucumber (Apostichopus japonicus Selenka 1867) is an economically important species as a source of seafood and ingredient in traditional medicine. It is mainly found off the coasts of northeast Asia. Recently, substantial exploitation and widespread biotic diseases in A. japonicus have generated increasing conservation concern. However, the genomic knowledge base and resources available for researchers to use in managing this natural resource and to establish genetically based breeding systems for sea cucumber aquaculture are still in a nascent stage. A total of 312 Gb of raw sequences were generated using the Illumina HiSeq 2000 platform and assembled to a final size of 0.66 Gb, which is about 80.5% of the estimated genome size (0.82 Gb). We observed nucleotide-level heterozygosity within the assembled genome to be 0.986%. The resulting draft genome assembly comprising 132 607 scaffolds with an N50 value of 10.5 kb contains a total of 21 771 predicted protein-coding genes. We identified 6.6-14.5 million heterozygous single nucleotide polymorphisms in the assembled genome of the three natural color variants (green, red, and black), resulting in an estimated nucleotide diversity of 0.00146. We report the first draft genome of A. japonicus and provide a general overview of the genetic variation in the three major color variants of A. japonicus. These data will help provide a comprehensive view of the genetic, physiological, and evolutionary relationships among color variants in A. japonicus, and will be invaluable resources for sea cucumber genomic research.

Comparative transcriptome analysis of three color variants of the sea cucumber Apostichopus japonicus.

The sea cucumber Apostichopus japonicus Selenka 1867 represents an important resource in biomedical research, traditional medicine, and the seafood industry. Much of the commercial value of A. japonicus is determined by dorsal/ventral color variation (red, green, and black), yet the taxonomic relationships between these color variants are not clearly understood. We performed the first comparative analysis of de novo assembled transcriptome data from three color variants of A. japonicus. Using the Illumina platform, we sequenced nearly 177,596,774 clean reads representing a total of 18.2Gbp of sea cucumber transcriptome. A comparison of over 0.3 million transcript scaffolds against the Uniprot/Swiss-Prot database yielded 8513, 8602, and 8588 positive matches for green, red, and black body color transcriptomes, respectively. Using the Panther gene classification system, we assessed an extensive and diverse set of expressed genes in three color variants and found that (1) among the three color variants of A. japonicus, genes associated with RNA binding protein, oxidoreductase, nucleic acid binding, transferase, and KRAB box transcription factor were most commonly expressed; and (2) the main protein functional classes are differently regulated in all three color variants (extracellular matrix protein and phosphatase for green color, transporter and potassium channel for red color, and G-protein modulator and enzyme modulator for black color). This work will assist in the discovery and annotation of novel genes that play significant morphological and physiological roles in color variants of A. japonicus, and these sequence data will provide a useful set of resources for the rapidly growing sea cucumber aquaculture industry.