Variation and Interaction of Distinct Subgenomes Contribute to Growth Diversity in Intergeneric Hybrid Fish.

Intergeneric hybridization greatly reshapes regulatory interactions among allelic and non-allelic genes. However, their effects on growth diversity remain poorly understood in animals. In this study, we conducted whole-genome sequencing and RNA sequencing (RNA-seq) analyses in diverse hybrid varieties resulting from the intergeneric hybridization of goldfish (Carassius auratus red var.) and common carp (Cyprinus carpio). These hybrid individuals were characterized by distinct mitochondrial genomes and copy number variations. Through a weighted gene correlation network analysis, we identified 3693 genes as candidate growth-regulated genes. Among them, the expression of 3672 genes in subgenome R (originating from goldfish) displayed negative correlations with growth rate, whereas 20 genes in subgenome C (originating from common carp) exhibited positive correlations. Notably, we observed intriguing patterns in the expression of slc2a12 in subgenome C, showing opposite correlations with body weight that changed with water temperatures, suggesting differential interactions between feeding activity and weight gain in response to seasonal changes for hybrid animals. In 40.31% of alleles, we observed dominant trans-regulatory effects in the regulatory interaction between distinct alleles from subgenomes R and C. Integrating analyses of allelic-specific expression and DNA methylation data revealed that the influence of DNA methylation on both subgenomes shapes the relative contribution of allelic expression to the growth rate. These findings provide novel insights into the interaction of distinct subgenomes that underlie heterosis in growth traits and contribute to a better understanding of multiple allele traits in animals.

Symmetric subgenomes and balanced homoeolog expression stabilize the establishment of allopolyploidy in cyprinid fish.

BACKGROUND: Interspecific postzygotic reproduction isolation results from large genetic divergence between the subgenomes of established hybrids. Polyploidization immediately after hybridization may reset patterns of homologous chromosome pairing and ameliorate deleterious genomic incompatibility between the subgenomes of distinct parental species in plants and animals. However, the observation that polyploidy is less common in vertebrates raises the question of which factors restrict its emergence. Here, we perform analyses of the genome, epigenome, and gene expression in the nascent allotetraploid lineage (2.95 Gb) derived from the intergeneric hybridization of female goldfish (Carassius auratus, 1.49 Gb) and male common carp (Cyprinus carpio, 1.42 Gb), to shed light on the changes leading to the stabilization of hybrids. RESULTS: We firstly identify the two subgenomes derived from the parental lineages of goldfish and common carp. We find variable unequal homoeologous recombination in somatic and germ cells of the intergeneric F1 and allotetraploid (F22 and F24) populations, reflecting high plasticity between the subgenomes, and rapidly varying copy numbers between the homoeolog genes. We also find dynamic changes in transposable elements accompanied by genome merger and duplication in the allotetraploid lineage. Finally, we observe the gradual decreases in cis-regulatory effects and increases in trans-regulatory effects along with the allotetraploidization, which contribute to increases in the symmetrical homoeologous expression in different tissues and developmental stages, especially in early embryogenesis. CONCLUSIONS: Our results reveal a series of changes in transposable elements, unequal homoeologous recombination, cis- and trans-regulations (e.g. DNA methylation), and homoeologous expression, suggesting their potential roles in mediating adaptive stabilization of regulatory systems of the nascent allotetraploid lineage. The symmetrical subgenomes and homoeologous expression provide a novel way of balancing genetic incompatibilities, providing a new insight into the early stages of allopolyploidization in vertebrate evolution.

Patterned Ag/PI RFID Tag Integrated with Humidity Sensing by In Situ Metallization.

This article presents a cost-efficient flexible chipless radio frequency identification (RFID) tag with wireless humidity sensing, which is fabricated by in situ metallization and inkjet printing techniques. The inkjet printing technique is applied to print the mask for RFID antenna, which is designed with frequency-encoding simulation by a high-frequency structure simulator (HFSS). A high-quality patterned Ag antenna is realized by the in situ metallization of a polyimide (PI) film, leading to strong adhesion between the Ag antenna and PI substrate. The patterned Ag antenna of the chipless RFID tag consists three parallel dipole resonators, one of which is sensitive to humidity, while the other two are utilized to encode and store data. As a result, a 2-bit chipless RFID with high humidity sensitivity based on a Ag/PI film is developed, which displays excellent flexibility and good mechanical stability. The performance of the fabricated tag shows good agreement with the simulation results. Moreover, the tag is applied to detect the water source, where the resonance frequency shows good linearity versus the distance to the water source. These results demonstrate that the proposed chipless RFID tag with humidity sensing has a 2-bit storage capacity, high humidity sensitivity, excellent mechanical properties, and long-term stability, confirming a cost-efficient preparation process for flexible electronics.

Correlations of expression of nuclear and mitochondrial genes in triploid fish.

The expression of nuclear and mitochondrial genes, as well as their coordinated control, regulates cell proliferation, individual development, and disease in animals. However, the potential coregulation between nuclear and mitochondrial genes is unclear in triploid fishes. The two triploids (R2C and RC2) with distinct mitochondrial genomes but similar nuclear genomes exhibit different embryonic development times and growth rates. They are an excellent model for studying how nuclear and mitochondrial genes coordinate. Here, we performed the mRNA-seq of four stages of embryonic development (blastula, gastrula, segmentation, and hatching periods) in the two triploids (R2C and RC2) and their diploid inbred parents (red crucian carp and common carp). After establishing the four patterns of mitochondrial and nuclear gene expression, 270 nuclear genes regulated by mitochondrial genes were predicted. The expression levels of APC16 and Trim33 were higher in RC2 than in R2C, suggesting their potential effects on regulating embryonic development time. In addition, 308 differentially expressed genes filtered from the list of nuclear-encoded mitochondrial genes described by Mercer et al. in 2011 were considered potential genes for which nuclear genes regulate mitochondrial function. The findings might aid in our understanding of the correlation between mitochondrial and nuclear genomes as well as their synergistic effects on embryonic development.

Design and application of DNA nanostructures for organelle-targeted delivery of anticancer drugs.

INTRODUCTION: DNA nanostructures targeting organelles are of great significance for the early diagnosis and precise therapy of human cancers. This review is expected to promote the development of DNA nanostructure-based cancer treatment with organelle-level precision in the future. AREAS COVERED: In this review, we introduce the different principles for targeting organelles, summarize the progresses in the development of organelle-targeting DNA nanostructures, highlight their advantages and applications in disease treatment, and discuss current challenges and future prospects. EXPERT OPINION: Accurate targeting is a basic problem for effective cancer treatment. However, current DNA nanostructures cannot meet the actual needs. Targeting specific organelles is expected to further improve the therapeutic effect and overcome tumor cell resistance, thereby holding great practical significance for tumor treatment in the clinic. With the deepening of the research on the molecular mechanism of disease development, especially on tumorigenesis and tumor progression, and increasing understanding of the behavior of biological materials in living cells, more versatile DNA nanostructures will be constructed to target subcellular organelles for drug delivery, essentially promoting the early diagnosis of cancers, classification, precise therapy and the estimation of prognosis in the future.

Heterosis of growth trait regulated by DNA methylation and miRNA in allotriploid fish.

BACKGROUND: Heterosis of growth traits in allotriploid fish has benefited the production of aquaculture for many years, yet its genetic and molecular basis has remained obscure. Now, an allotriploid complex, including two triploids and their diploid inbred parents, has provided an excellent model for investigating the potential regulatory mechanisms of heterosis. RESULTS: Here, we performed a series of analyses on DNA methylation modification and miRNA expression in combination with gene expression in the allotriploid complex. We first established a model of cis- and trans-regulation related to DNA methylation and miRNA in allotriploids. Then, comparative analyses showed that DNA methylation contributed to the emergence of a dosage compensation effect, which reduced gene expression levels in the triploid to the diploid state. We detected 31 genes regulated by DNA methylation in the subgenomes of the allotriploids. Finally, the patterns of coevolution between small RNAs and their homoeologous targets were classified and used to predict the regulation of miRNA expression in the allotriploids. CONCLUSIONS: Our results uncovered the regulatory network between DNA methylation and miRNAs in allotriploids, which not only helps us understand the regulatory mechanisms of heterosis of growth traits but also benefits the study and application of epigenetics in aquaculture.

Surface Engineering on Polyimide-Silver Films in Low-Cost, Flexible Humidity Sensors.

In this work, surface engineering is applied to polyimide (PI) films to fabricate low-cost Ag/PI wireless humidity sensors with a resonant frequency of 2.45 GHz. The sensors were obtained by in situ metallization technique coupled with inkjet printing, where PI plays triple roles as a flexible substrate, ion-exchange surface, and sensing material to moisture. Moreover, the humidity sensitivity can be enhanced by the improvement of hydrophilicity via loading with different ions on the PI surface, which has been demonstrated by Fourier transform infrared (FTIR), X-ray photoelectron spectroscopy (XPS), and contact angle measurements. The wireless humidity sensor loaded with K+ ions has the maximum sensitivity of 97.7 kHz/% RH at a low relative humidity range of 20-65% and 359.7 kHz/% RH at a high relative humidity of 65-90%, respectively. Accordingly, a sensing mechanism of the fabricated humidity sensor has been discussed in detail. On the other hand, the characteristics of the humidity sensor such as response and recovery speed and stability are analyzed. The mechanical performance tests show that the humidity sensor displays excellent flexibility and good mechanical stability. A strong adhesion between the Ag antenna and PI substrate can be found as well. The passive wireless humidity sensor described in this work has the advantages of having a simple structure, low cost, high sensitivity, long-term stability, and good mechanical properties, which has potential applications in automated industry and healthcare with real-time humidity monitoring.

In Situ Growth of Silver Film on Polyimide with Tuned Morphologies for Flexible Electronics.

In this work, the silver films with tuned morphologies have been fabricated on flexible polyimide substrate by in situ direct-ion-exchange technique. The morphology of Ag films with loose nanoparticles, dense polyhedrons, aggregated nanoparticle clouds, and dendrite structure can be obtained by a controlled reduced process as illustrated by scanning electron microscopy (SEM) and optical microscopy, respectively. All of the Ag films show good crystalline and high conductivity, which is confirmed by X-ray diffraction (XRD) and four-point probe resistance measurements. Infrared (IR) spectra demonstrate the occurrence of the polyimide surface metallization, which favors good adhesion between the Ag films and the flexible substrate. The adhesion test proves the strong adhesion of these Ag films, especially for the Ag films with the dendritic structure. Moreover, the mechanical properties of these Ag/PI films have been investigated as well. It can be found that all of the Ag/PI films exhibit low sensitivity to the bending test. However, the strain sensitivity strongly depends on the morphology of the Ag films, which can be applied for diverse flexible electronics.

Stimuli-Responsive Autonomous-Motion Molecular Machine for Sensitive Simultaneous Fluorescence Imaging of Intracellular MicroRNAs.

DNAzymes with enzymatic activity identified from random DNA pools by in vitro selection have recently attracted considerable attention. In this work, a DNAzyme-based autonomous-motion (AM) molecular machine is demonstrated for sensitive simultaneous imaging of different intracellular microRNAs (miRNAs). The AM molecular machine consists of two basic elements, one of which is a target-analogue-embedded double-stem hairpin substrate (TDHS) and the other is a locking-strand-silenced DNAzyme (LSDz). LSDz can be activated by target miRNA and catalytically cleave TDHS, generating Clv-TDHS and releasing free target analogue capable of triggering the next round of cleavage reaction. As such, the molecular machine can exert sustainable autonomous operation, producing an enhanced signal. Because the active target analogue comes from the machine itself and offers cyclical stimulation in a feedback manner, this target-induced autonomous cleavage circuit is termed a self-feedback circuit (SFC). The SFC-based molecular machine can be used to quantify miRNA-21 down to 10 pM without interference from nontarget miRNAs, indicating a substantial improvement in assay performance compared with its counterpart system without an SFC effect. Moreover, due to the enzyme-free process, the AM molecular machine is suitable for miRNA imaging in living cells, and the quantitative results are consistent with the gold standard PCR assay. More interestingly, the AM molecular machine can be used for the simultaneous fluorescence imaging of several intracellular miRNAs, enabling the accurate discrimination of cancerous cells (e.g., HeLa and MCF-7) from healthy cells. The SFC-based autonomous-motion machine is expected to be a promising tool for the research of molecular biology and early diagnosis of human diseases.

Programmably tiling rigidified DNA brick on gold nanoparticle as multi-functional shell for cancer-targeted delivery of siRNAs.

Small interfering RNA (siRNA) is an effective therapeutic to regulate the expression of target genes in vitro and in vivo. Constructing a siRNA delivery system with high serum stability, especially responsive to endogenous stimuli, remains technically challenging. Herein we develop anti-degradation Y-shaped backbone-rigidified triangular DNA bricks with sticky ends (sticky-YTDBs) and tile them onto a siRNA-packaged gold nanoparticle in a programmed fashion, forming a multi-functional three-dimensional (3D) DNA shell. After aptamers are arranged on the exterior surface, a biocompatible siRNA-encapsulated core/shell nanoparticle, siRNA/Ap-CS, is achieved. SiRNAs are internally encapsulated in a 3D DNA shell and are thus protected from enzymatic degradation by the outermost layer of YTDB. The siRNAs can be released by endogenous miRNA and execute gene silencing within tumor cells, causing cell apoptosis higher than Lipo3000/siRNA formulation. In vivo treatment shows that tumor growth is completely (100%) inhibited, demonstrating unique opportunities for next-generation anticancer-drug carriers for targeted cancer therapies.

Electroacupuncture for the treatment of functional dyspepsia: A systematic review and meta-analysis.

BACKGROUND: Functional dyspepsia (FD) is a common functional gastrointestinal disease. Acupuncture, including electroacupuncture (EA) is widely used as a complementary and alternative treatment for patients with FD. This study aimed to explore the effectiveness of EA for the treatment of FD. METHODS: We searched Embase, PubMed, and the Cochrane Central Register of Controlled Trials (Cochrane Library) for randomized controlled trials of FD treated by EA from inception to February 3, 2020. Two reviewers will independently screen studies for data extraction and assess the quality and risk of bias. The Cochrane Collaboration's risk of bias tool, RevMan 5.3 software were used for meta-analysis. Data were pooled to calculate relative risk and 95% confidence intervals (CIs) of substantial improvement after treatment for dichotomous data and mean differences (SMDs) and 95% CIs for continuous data. RESULTS: Seven randomized clinical trials included 853 patients. This meta-analysis investigated the effectiveness of EA alone in the treatment of FD relative to sham-EA or pharmacologic medication (PM). The results showed that EA could significantly improve clinical symptoms. Compared with sham-EA, EA was more effective in reducing symptom scores (SMD -3.44, 95% CI -4.21 to -2.67) and increasing normal slow waves of electrogastrogram (SMD 0.93, 95% CI -0.30 to1.55). When EA was combined with PM, there was no significant difference in reducing symptom scores (SMD -0.18, 95% CI -0.51 to 0.16), increasing the effective rate of clinical symptoms (risk ratio 1.04, 95% CI 0.96 to 1.13), enhancing the level of plasma motilin (SMD 0.93, 95% CI -0.30 to1.55), and reducing gastric half-emptying time (SMD 0.02, 95% CI -0.16 to 0.20). The results also showed that there were very few adverse events reported. CONCLUSION: This meta-analysis suggests that EA is better than the placebo (sham-EA) in treating FD, and the therapeutic effect of EA on FD is equivalent to that of PM on FD. Compared with PM, EA for FD is safer and has fewer adverse reactions. Despite limitations due to the quality and number of the included studies, EA might be used as an effective and safe treatment for FD.

Biocomputing label-free security system based on homogenous ligation chain reaction-induced dramatic change in melting temperature for screening single nucleotide polymorphisms.

The development of smart platform with accurate, inexpensive and reliable detection of single-nucleotide polymorphisms (SNPs) has long been concerned in the fields of medical diagnosis and basic research. Here, we present a ligation chain reaction (LCR)-based sensing system for the cost-effective screening of SNPs by simply conducting DNA melting analysis. No chemical modification is required and the signaling operation is accomplished in homogeneous solution, circumventing the complex modification process and possibly compromised enzymatic activity associated with heterogeneous materials, such as quantum dot (QD) and gold nanoparticle (GNP). Due to the enzymatic catalysis and high fidelity of ligase, the system is capable of executing signal amplification, providing a high sensitivity and selectivity. KRAS gene is easily recognized and the site-specific mutation of guanine (G) to adenine (A), thymine (T) or cytosine (C) is accurately screened. Moreover, the excellent reliability was demonstrated by blind test and recovery test. LCR-based signaling mechanism was further used to develop the biocomputing security system, and two logic gates consisting of four single-stranded DNAs (ssDNAs) offer a double insurance to protect the information against illegal invasion, guaranteeing the reliability of output information. Once in the absence of one essential factor, the security system was always locked regardless of target key, serving as a novel strategy to ensure the safety of output information at molecular level. As a proof-of-concept scheme, this contribution introduces new insight into the development of DNA security systems and the exploitation of powerful signal transduction strategy suitable for rapid and convenient disease diagnosis.

Rigidified DNA Triangle-Protected Molecular Beacon from Endogenous Nuclease Digestion for Monitoring microRNA Expression in Living Cells.

Utilizing the nucleic acid-based self-assembly technology, Y-shaped backbone-rigidified DNA triangles with substantially enhanced nuclease resistance are built by designing a Y-shaped backbone in the center of a planar DNA triangle. Along this line, we developed aptamer-targeted DNA triangle-based molecular beacon (Apt-Tri-MB) probes for monitoring the microRNA expression in living cells with high sensitivity and specificity. For the Apt-Tri-MB probe, the MB is protected by the DNA triangle from unwanted enzymatic digestion, and a targeting ligand aptamer is introduced to endow the MB with active tumor cell-targeting capability. Thus, the digestion-induced false-positive signal is avoided, and the background fluorescence, which originates from the passive cell uptake (e.g., transfection) of reporting probes, is substantially suppressed. The imaging capability of the Apt-Tri-MB is superior to the commercial transfection agent-based counterpart and exhibits good universality suitable for imaging different miRNAs by changing the recognition fragment of the MB. Meanwhile, the disadvantages are efficiently circumvented, including the susceptibility of nucleic acids to nuclease-mediated degradation, inability of MB probes to enter cells, lipofectamine-determined cellular cytotoxicity, and nontargeting cell uptake. Inspired by the Y-shaped backbone-rigidified Apt-Tri-MB, we also constructed X-shaped backbone-rigidified quadrangle-based probes (Apt-Qua-MB). The experimental results show that cell imaging and antidegradation capability of Apt-Qua-MB are comparable with Apt-Tri-MB. As a proof-of-concept study, the Apt-Tri-MB is expected to open an exciting avenue for the further application of nucleic acid probes in the cellular level research and clinical disease diagnosis.

Oriented Tetrahedron-Mediated Protection of Catalytic DNA Molecular-Scale Detector against in Vivo Degradation for Intracellular miRNA Detection.

We report a tetrahedron-based DNAzyme probe (Tetra-ES) for intracellular miRNA detection. Two DNA tetrahedra (Tetra) were arranged at the different positions of the enzyme (E)/substrate (S) complex in a unique direction. A Na+-dependent DNAzme was designed to be initially locked to inhibit the activity of the DNAzyme. Fluorescence imaging and gel electrophoresis analyses demonstrated that the silenced DNAzyme could be specifically initiated by intracellular target miRNA. The activated DNAzyme repeatedly cleaved the substrates, allowing a controllable signal transduction and amplification effect. The combination of spatially controlled arrangement of DNA tetrahedra with the stimuli-responsive behavior of the locked DNAzyme improved cell permeability and desirable nuclease resistance. The Tetra-ES detector exhibited at least 10 times higher detection sensitivity (LOD of 16 pM) than that of the nonamplification molecular beacon counterpart and was capable of discriminating the miRNA target from the corresponding family members. The expression levels of target miRNA inside the cells of interest as well as different miRNAs inside the same type of cell lines were reliably screened utilizing the Tetra-ES detector. As an intracellular probe, Tetra-ES may provide valuable insight into developing a homogeneous DNA nanostructure-based controllable signal transduction strategy suitable for detection of miRNA and potential application to cancer diagnosis, prognosis, and therapeutics.