In vivo DNA double-strand breaks enhance gene targeting in cultured silkworm cells

Astaxanthin Isomers: A Comprehensive Review of Isomerization Methods and Analytic Techniques

The presence of multiple conjugated double bonds and chiral carbon atoms endows astaxanthin with geometric and optical isomers, and these isomers widely exist in biological sources, food processing, and in vivo absorption. However, there remains no systematic summary of astaxanthin isomers regarding isomerization methods and analytic techniques. To address this need, this Review focuses on a comprehensive analysis of Z-isomerization methods of astaxanthin, including solvent system, catalyst, and heat treatment. Comparatively, high-efficiency and health-friendly methods are more conducive to put into practical use, such as food-grade solvents and food-component catalysts. In addition, we outline the recent advances in analysis techniques of astaxanthin isomers, as well as the structural characteristics reflected by various methods (e.g., HPLC, NMR, FTIR, and RS). Furthermore, we summarized the related research on the safety evaluation of astaxanthin isomers. Finally, future trends and barriers in Z-transformation and analysis of astaxanthin isomers are also discussed.

Integration of intestinal microbiota and metabonomics to elucidate different alleviation impacts of non-saponification and saponification astaxanthin pre-treatment on paracetamol-induced oxidative stress in rats

Intestinal microbiota and metabonomics were integrated to investigate the efficiency of non-saponification or saponification astaxanthin (N-Asta or S-Asta) derived from Penaeus sinensis by-products on alleviating paracetamol (PCM)-induced oxidative stress. Pre-treatment with N-Asta or S-Asta for 14 days restored the cellular morphology of the intestine and increased glutathione (GSH) levels under PCM overdose in rats. However, S-Asta displayed higher adsorption than that of N-Asta. PCM overdose reduced the richness and diversity of intestinal microbiota in the model group. Comparably, N-Asta or S-Asta pre-treatment increased the Actinobacteria abundance. Increased phyla Bacteroidetes and Verrucomicrobia were only found in the S-Asta-pre-treated group. At the genus level, N-Asta pre-treatment increased Lactobacillus and Parasutterella abundance, whereas S-Asta pre-treatment elevated Bacteroidales_S24-7_group_norank and Ruminococcaceae_uncultured. Compared to the control and model groups, remarkable increases of fecal short-chain fatty acids were detected in both N-Asta and S-Asta pre-treatment groups, suggesting the contribution of N-Asta and S-Asta adsorption to SCFA-producing bacteria enrichment. Furthermore, the genera of Ruminococcaceae_uncultured, Ruminiclostridium_9, Ruminococcaceae_unclassified and Ruminococcus_1 showed high correlations with propionic acid, isobutyric acid, butyric acid, isovaleric acid and valeric acid increases in the S-Asta pre-treated group. Seventeen plasma biomarker metabolites in more than 10 metabolic pathways were responsible for the difference between the N-Asta and S-Asta pre-treated groups. Metabolites GSH, retinol, all-trans-Retinoic acid and taurine related to antioxidant activities were significantly accumulated in the S-Asta pre-treated group, while increasing taurocholic acid levels associated with the anti-inflammatory activity was found in the N-Asta-pre-treated group. Therefore, N-Asta and S-Asta could have potential applications in counterbalancing intestinal flora and metabolite disturbances by overdose chemical induction.

Structure of supramolecular astaxanthin aggregates revealed by molecular dynamics and electronic circular dichroism spectroscopy

Biomolecular aggregation is omnipresent in nature and important for metabolic processes or in medical treatment; however, the phenomenon is rather difficult to predict or understand on the basis of computational models. Recently, we found that electronic circular dichroism (ECD) spectroscopy and closely related resonance Raman optical activity (RROA) are extremely sensitive to the aggregation mechanism and structure of the astaxanthin dye. In the present study, molecular dynamics (MD) and quantum chemical (QC) computations (ZIndo/S, TDDFT) are used to link the aggregate structure with ECD spectral shapes. Realistic absorption and ECD intensities were obtained and the simulations reproduced many trends observed experimentally, such as the prevalent sign pattern and dependence of the aggregate structure on the solvent type. The computationally cheaper ZIndo/S method provided results very similar to those obtained by TDDFT. In the future, the accuracy of the combined MD/QC methodology of spectra interpretation should be improved to provide more detailed information on astaxanthin aggregates and similar macromolecular systems.

The genome of the Hi5 germ cell line from Trichoplusia ni, an agricultural pest and novel model for small RNA biology

We report a draft assembly of the genome of Hi5 cells from the lepidopteran insect pest, Trichoplusia ni, assigning 90.6% of bases to one of 28 chromosomes and predicting 14,037 protein-coding genes. Chemoreception and detoxification gene families reveal T. ni-specific gene expansions that may explain its widespread distribution and rapid adaptation to insecticides. Transcriptome and small RNA data from thorax, ovary, testis, and the germline-derived Hi5 cell line show distinct expression profiles for 295 microRNA- and >393 piRNA-producing loci, as well as 39 genes encoding small RNA pathway proteins. Nearly all of the W chromosome is devoted to piRNA production, and T. ni siRNAs are not 2´-O-methylated. To enable use of Hi5 cells as a model system, we have established genome editing and single-cell cloning protocols. The T. ni genome provides insights into pest control and allows Hi5 cells to become a new tool for studying small RNAs ex vivo.

A common moth called the cabbage looper is becoming increasingly relevant to the scientific community. Its caterpillars are a serious threat to cabbage, broccoli and cauliflower crops, and they have started to resist the pesticides normally used to control them. Moreover, the insect’s germline cells – the ones that will produce sperm and eggs – are used in laboratories as ‘factories’ to artificially produce proteins of interest.

The germline cells also host a group of genetic mechanisms called RNA silencing. One of these processes is known as piRNA, and it protects the genome against ‘jumping genes’. These genetic elements can cause mutations by moving from place to place in the DNA: in germline cells, piRNA suppresses them before the genetic information is transmitted to the next generation. Not all germline cells grow equally well under experimental conditions, or are easy to use to examine piRNA mechanisms in a laboratory. The germline cells from the cabbage looper, on the other hand, have certain characteristics that would make them ideal to study piRNA in insects.

However, the genome of the moth had not yet been fully resolved. This hinders research on new ways of controlling the pest, on how to use the germline cells to produce more useful proteins, or on piRNA.

Decoding a genome requires several steps. First, the entire genetic information is broken in short sections that can then be deciphered. Next, these segments need to be ‘assembled’ – put together, and in the right order, to reconstitute the entire genome. Certain portions of the genome, which are formed of repeats of the same sections, can be difficult to assemble. Finally, the genome must be annotated: the different regions – such as the genes – need to be identified and labeled.

Here, Fu et al. assembled and annotated the genome of the cabbage looper, and in the process developed strategies that could be used for other species with a lot of repeated sequences in their genomes. Having access to the looper’s full genetic information makes it possible to use their germline cells to produce new types of proteins, for example for pharmaceutical purposes. Fu et al. went on to make working with these cells even easier by refining protocols so that modern research techniques, such as the gene-editing technology CRISPR-Cas9, can be used on the looper germline cells.

The mapping of the genome also revealed that the genes involved in removing toxins from the insects’ bodies are rapidly evolving, which may explain why the moths readily become resistant to insecticides. This knowledge could help finding new ways of controlling the pest.

Finally, the genes involved in RNA silencing were labeled: results show that an entire chromosome is the source of piRNAs. Combined with the new protocols developed by Fu et al., this could make cabbage looper germline cells the default option for any research into the piRNA mechanism. How piRNA works in the moth could inform work on human piRNA, as these processes are highly similar across the animal kingdom.

CRISPR/Cas9-mediated knockout of factors in non-homologous end joining pathway enhances gene targeting in silkworm cells

Gene targeting can be achieved by precise genetic modifications through homology-directed repair (HDR) after DNA breaks introduced by genome editing tools such as CRISPR/Cas9 system. The most common form of HDR is homologous recombination (HR). Binding to the DNA breaks by HR factors is thought to compete with non-homologous end joining (NHEJ), an alternative DNA repair pathway. Here, we knocked out the factors in NHEJ by CRISPR/Cas9 system in silkworm cells, so that increased the activities of HR up to 7-fold. Also efficient HR-mediated genome editing events occurred between the chromosomal BmTUDOR-SN gene and donor DNA sequences with an EGFP gene in the middle of two homologous arms for the target gene. Utilizing the NHEJ-deficient silkworm cells, we found that homologous arms as short as 100 bp in donor DNA could be designed to perform precise genome editing. These studies should greatly accelerate investigations into genome editing of silkworm.

CRISPR/Cas9 mediated multiplex genome editing and heritable mutagenesis of BmKu70 in Bombyx mori

CRISPR/Cas9, a bacterial adaptive immune system derived genome-editing technique, has become to be one of the most compelling topics in biotechnology. Bombyx mori is an economically important insect and a model organism for studying lepidopteran and arthropod biology. Here we reported highly efficient and multiplex genome editing in B. mori cell line and heritable site-directed mutagenesis of Bmku70, which is required for NHEJ pathway and also related to antigen diversity, telomere length maintenance and subtelomeric gene silencing, using CRISPR/Cas9 system. We established a simple and practicable method and obtained several Bmku70 knockout B. mori lines, and showed that the frequency of HR was increased in embryos of the Bmku70 knockout B. mori. The mutant lines obtained in this study could be a candidate genetic resource for efficient knock-in and fundamental research of DNA repair in B. mori. We also provided a strategy and procedure to perform heritable genome editing of target genes with no significant phenotype effect.

Milks pigmentation with astaxanthin and determination of colour stability during short period cold storage

Astaxanthin has been used as a colorant and antioxidant with excellent results, its application and stability in food matrices to human consumption has been little studied. The aim of this work was the incorporation of astaxanthin oleoresin to milks with different fat content, simulating the red-orange color that can impart apricot fruit. For astaxanthin determination by HPLC, a methodology was implemented for its extraction from the food matrix, followed by saponification with KOH. Milk samples were stored (5 ± 2 °C) and stability of color and astaxanthin content were determined by colorimetry and high performance liquid chromatography each 24 h for a week. Pigment degradation followed first-order kinetic with a constant degradation of 0.259 day(-1) and 0.104 day(-1), in whole and semi-skimmed milk, respectively. Chromaticity coordinates L*, a*, b* for different types of milk showed a low dispersion of their values during the storage time, indicating high stability of astaxanthin within the matrix.

Soaking RNAi-mediated modification of Sf9 cells for baculovirus expression system by ectopic expression of Caenorhabditis elegans SID-1

RNA interference (RNAi) is a biological phenomenon that silences the expression of genes of interest. Passive double-stranded RNA (dsRNA) uptake has been uniquely observed in Caenorhabditis elegans due to the expression of systemic RNAi defective-1 (SID-1). We report that ectopic expression of CeSID-1 endows the Sf9 cells with a capacity for soaking RNAi. Soaking the Sf9-SID1 with dsRNA corresponding to either exogenous or endogenous target genes induced a significant decrease in the amount of mRNA or protein. These results enabled us to modify the target proteins of baculovirus expression vector system in both quantities and posttranslational modifications. The current low-cost and high-efficiency RNAi system is useful for high-throughput gene function analysis and mass production of recombinant protein.

Soaking RNAi in Bombyx mori BmN4-SID1 cells arrests cell cycle progression

RNA interference (RNAi) is an evolutionarily conserved mechanism for sequence-specific gene silencing. Previously, the BmN4-SID1 cell expressing Caenorhabditis ele gans SID-1 was established, in which soaking RNAi could induce effective gene silencing. To establish its utility, 6 cell cycle progression related cDNAs, CDK1, MYC, MYB, RNRS, CDT1, and GEMININ, were isolated from the silkworm, Bombyx mori L. (Lepidoptera: Bombycidae), and their expressions were further silenced by soaking RNAi in the BmN4-SID1 cells. The cell cycle progression analysis using flow cytometer demonstrated that the small amount of double stranded RNA was enough to arrest cell cycle progression at the specific cell phases. These data suggest that RNAi in the BmN4-SID1 cells can be used as a powerful tool for loss-of-function analysis of B. mori genes.

Monoubiquitination-dependent chromatin loading of FancD2 in silkworms, a species lacking the FA core complex

The Fanconi anemia (FA) pathway is required for activation and operation of the DNA interstrand cross-link (ICL) repair pathway, although the precise mechanism of the FA pathway remains largely unknown. A critical step in the FA pathway is the monoubiquitination of FANCD2 catalyzed by a FA core complex. This modification appears to allow FANCD2 to coordinate ICL repair with other DNA repair proteins on chromatin. Silkworm, Bombyx mori, lacks apparent homologues of the FA core complex. However, BmFancD2 and BmFancI, the putative substrates of the complex, and BmFancL, the putative catalytic E3 ubiquitin ligase, are conserved. Here, we report that the silkworm FancD2 is monoubiquitinated depending on FancI and FancL, and stabilized on chromatin, following MMC treatment. A substitution of BmFancD2 at lysine 519 to arginine abolishes the monoubiquitination, but not the interaction between the FancD2 and FancI. In addition, we demonstrated that depletion of BmFancD2, BmFancI or BmFancL had effects on cell proliferation in the presence of MMC. These results suggest that the FA pathway in B. mori works in the same manner as that in vertebrates.

Effective RNA interference in cultured silkworm cells mediated by overexpression of Caenorhabditis elegans SID-1

RNA interference (RNAi) is a conserved mechanism that catalyzes sequence-specific gene silencing and has been used for loss-of-function genetic screens in many organisms. Here, we demonstrated that the expression of Caenorhabditis elegans SID-1 (CeSID-1) could trigger effective gene silencing in the cultured silkworm cell line, BmN4 (BmN4-SID1). Soaking the BmN4-SID1 in dsRNA corresponding to endogenous target genes induced a significant decrease of the amount of mRNA or protein. A small amount of dsRNA was enough to silence the target gene in a few days. Overexpression of CeSID-1 did not affect the cell viability. Our results suggest that BmN4-SID1 can be used in many applications in silkworm cells and will become a valuable resource for gene analysis.

Double-strand breaks repair by gene conversion in silkworm holocentric chromosomes

Maintenance of genome stability relies on the accurate repair of DNA double-strand breaks (DSBs) that arise during DNA replication or introduced by DNA-damaging agents. Failure to repair such breaks can lead to the introduction of mutations and chromosomal translocations. Several pathways, homologous recombination, single-strand annealing and nonhomologous end-joining, are known to repair DSBs. So far in the silkworm Bombyx mori, these repair pathways have been analyzed using extrachromosomal plasmids in vitro or in cultured cells. To elucidate the precise nature of the chromosomal DSB repair pathways in cultured silkworm cells, we developed a luciferase-based assay system for measuring the frequency of chromosomal homologous recombination and SSA. An I-SceI-induced DSB, within a nonfunctional luciferase gene, could be efficiently repaired by HR. Additionally, the continuous expression of the I-SceI endonuclease in the HR reporter cell allowed us to investigate the interrelationship between HR, SSA and NHEJ. In this study, we demonstrated that chromosome DSBs were mainly repaired by NHEJ and HR, whereas SSA was unlikely to be a dominant repair pathway in cultured silkworm cell. These results indicate that the assay system presented here will be useful to analyze the mechanisms of DSB repair in insect cells.

Role of the silkworm argonaute2 homolog gene in double-strand break repair of extrachromosomal DNA

The argonaute protein family provides central components for RNA interference (RNAi) and related phenomena in a wide variety of organisms. Here, we isolated, from a Bombyx mori cell, a cDNA clone named BmAGO2, which is homologous to Drosophila ARGONAUTE2, the gene encoding a repressive factor for the recombination repair of extrachromosomal double-strand breaks (DSBs). RNAi-mediated silencing of the BmAGO2 sequence markedly increased homologous recombination (HR) repair of DSBs in episomal DNA, but had no effect on that in chromosomes. Moreover, we found that RNAi for BmAGO2 enhanced the integration of linearized DNA into a silkworm chromosome via HR. These results suggested that BmAgo2 protein plays an indispensable role in the repression of extrachromosomal DSB repair.