Carbon dots-based fluorescence resonance energy transfer for the prostate specific antigen (PSA) with high sensitivity.

The accurate and sensitive detection of biomarkers has great clinical value for the early diagnosis and treatment of cancer. Due to the excellent optical properties of carbon dots (CDs), CDs-based fluorescent detection methods have attracted increasing attention in bioanalytics. Signal reporters using CDs labeled hairpin DNA, based on Föster resonance energy transfer (FRET), have shown promise for the sensitive detection of biomarkers. In this work, a new method for sensitive biomarker detection using an enzyme-free amplified fluorescence strategy was developed. The strategy was based on FRET between CDs and graphene oxide (GO) combined with catalytic hairpin assembly (CHA). In the absence of the target, the CD-labeled hairpin DNA adsorb onto GO via hydrophobic and π-π stacking interactions, resulting in a FRET quenching of the CDs fluorescence. The introduction of the target could trigger the CHA circuits to form Y-shaped double-stranded DNA (dsDNA), resulting in a recovery of the CD's fluorescence signal. This novel strategy was successfully applied for the selective detection of prostate specific antigen (PSA) with a limit of detection (LOD) of 0.22 ng mL-1 (3σ/k). Additionally, the method could be used to detect carcinoembryonic antigen (CEA) and adenosine triphosphate (ATP) with LOD of 0.56 ng mL-1 (3σ/k) and 80 nM (3σ/k), respectively. Therefore, this work demonstrates a promising way to construct a sensitive and versatile detection platform.

Förster Resonance Energy Transfer-Based Soft Nanoballs for Specific and Amplified Detection of MicroRNAs.

Förster resonance energy transfer (FRET) by using fluorescent carbon dots (CDs) as energy donors shows potential for biosensing and bioimaging. However, it remains underused and underestimated for CDs as a building block for FRET owing to the low efficiency and complex operation originating from the surface modification of CDs. To overcome these limitations, herein we develop a novel FRET soft nanoball (fretSNB) in which thousands of green CDs and black hole quencher 2 (BHQ-2) dyes are loaded, and FRET occurs from CDs to BHQ-2 dyes with the consequence of effective fluorescence quenching. These fretSNBs can be ruptured in the presence of phospholipase A2 (PLA2) released in a process of duplex-specific nuclease (DSN)-assisted target recycling amplification (TRA), making the fluorescence of CDs recovered. Thus, a dual amplification strategy is successfully developed for amplified detection of microribonucleic acids (miRNAs) in the concentration range 0.025-10 nM with a limit of detection (3σ) reaching 16.5 pM which is about 515 times lower than without fretSNBs. In addition, the developed strategy exhibits high selectivity for discrimination of a single nucleotide difference and capability to detect miRNAs extracted from cells, suggesting excellent potential in biomedical analysis and clinical diagnosis.

A single gold nanoprobe for colorimetric detection of silver(i) ions with dark-field microscopy.

Highly sensitive colorimetric detection of silver(i) ions (Ag+) at the single-particle level was developed based on the color of a gold nanoparticle (AuNP) assembly captured by dark-field microscopy (DFM) imaging. Formation of C-Ag+-C bonding between cytosines was utilized to induce interparticle coupling of AuNPs modified with single-strand DNA, resulting in a color change as the signal transduction to quantify Ag+ under DFM imaging. This method allowed visual quantitation of Ag+ in the range of 0.05 nM-250.00 nM and a detection limit of 28.8 pM was achieved. Furthermore, we demonstrated its applicability for the colorimetric detection of Ag+ in a small quantity of real samples, showing the good potential of this developed method for environmental monitoring and drug quality control.

Functional preserving carbon dots-based fluorescent probe for mercury (II) ions sensing in herbal medicines via coordination and electron transfer.

Mercury ions (Hg2+) are one of the compulsory items in the quality control of herbal medicines for its serious toxicity to human health. Highly selective and sensitive Hg2+ detection, especially in complex real samples, is still challenging. In this work, Fluorescent (FL) carbon dots (CDs) with a core-shell structures composed of the crystalline core of stacked sp2-hybridized carbon layers and the shell of functional groups on the periphery of carbon layers are facilely prepared through a one-step hydrothermal synthetic route. They can specifically interact with Hg2+ in aqueous medium to form aggregates, during which coordination of carboxyl functional groups on the surface of CDs with Hg2+ occurred, which facilitated electron transfer from the CDs to Hg2+. As a result, fluorescence of the CDs was quenched with a high efficiency, making the detection of Hg2+ highly sensitive with the limit of determination (LOD) of 2.2 nM (3σ). With that, detection of Hg2+ in the complex compound herbal medicines samples with highly reproducible results has been successfully realized by using the as-prepared CDs, showing that fluorescent CDs-based probe may have great potential in the quality controls of heavy metals for pharmaceutical analysis.

Genome-wide identification, evolution of chromobox family genes and their expression in Nile tilapia.

Chromobox (Cbx) family proteins are transcriptional repressors that involved in epigenetic and developmental processes. In this study, comprehensive analyses of Cbxs were performed using available genome databases from representative animal species. The Cbx family were originated from one Polycomb (Pc) gene like the yeast Pc, which duplicated into two and gave rise to the Pc and the Heterochromatin protein 1 (Hp1) identified in invertebrates from protozoon to lancelet. Rapid expansion of Cbx family members was observed in vertebrates as ~8 (5 Pc and 3 Hp1) were identified in spotted gar, coelacanth and tetrapods. Further expansion of the members to ~14 (9 Pc and 5 Hp1) was observed in teleosts due to the third round genome duplication (3R). Based on transcriptome data from eight adult tilapia tissues, most of the Cbxs were found to be dominantly expressed in the brain, testis, ovary and heart. Analyses of the gonadal transcriptome data from four developmental stages revealed that all Cbxs were expressed in both ovary and testis except Cbx7b, with significant increase of the total and average RPKM from 5 to 90dah (days after hatching). By in situ hybridization, the three most highly and sexual dimorphically expressed Cbx genes in gonads, Cbx1b, Cbx3a and Cbx5, were found to be expressed in phase I and II oocytes of the ovary, and in secondary spermatocytes (Cbx1b and Cbx3a) and spermatids (Cbx5) of the testis. Our results revealed the evolution of Cbx genes and indicated a potential role of Cbxs in epigenetic regulation of gametogenesis.

Genome-wide identification, evolution and expression analysis of nuclear receptor superfamily in Nile tilapia, Oreochromis niloticus.

The nuclear receptor (NR) superfamily, which is divided into 7 subfamilies, constitutes one of the largest classes of transcription factors. In this study, through comprehensive database search, we identified all NRs (including 4 novel members) from the tilapia (75), common carp (137), zebrafish (73), fugu (73), tetraodon (72), stickleback (70), medaka (69), coelacanth (55), spotted gar (51) and elephant shark (50). For 21 NRs, two duplicates were found in teleosts, while only one in tetrapods. These duplicates, except those of DAX1, SHP and GCNF found in the elephant shark, were derived from 3R (third round of genome duplication). The linkage duplication of 5 syntenic blocks (comprising 14 duplicated NR couples) in teleosts further supported their 3R origin. Based on transcriptome data from adult tilapia, 53 NRs were found to be expressed in more than one tissue (brain, head kidney, heart, liver, kidney, muscle, ovary and testis), and 4 were tissue-specific, indicating their essential roles in the corresponding tissue. Based on the XX and XY gonadal transcriptome data from four developmental stages, 65 NRs were detected in gonads, with 21, 31, 11 and 29 expressed sexual dimorphically at 5, 30, 90 and 180days after hatching, respectively. The expression of four selected genes was examined by in situ hybridization (ISH) and quantitative PCR (qPCR) to validate the spatial and temporal expression profiles of NRs. Comparative analyses of the expression profiles of duplicated NRs revealed divergence in gene expression as well as gene function. Our results demonstrated that NRs may play important roles in sex determination and gonadal development in teleosts.