Unveiling Endophytic Bacterial Community Structures of Different Rice Cultivars Grown in a Cadmium-Contaminated Paddy Field.

Endophytic bacteria play potentially important roles in the processes of plant adaptation to the environment. Understanding the composition and dynamics of endophytic bacterial communities under heavy metal (HM) stress can reveal their impacts on host development and stress tolerance. In this study, we investigated root endophytic bacterial communities of different rice cultivars grown in a cadmium (Cd)-contaminated paddy field. These rice cultivars are classified into low (RBQ, 728B, and NX1B) and high (BB and S95B) levels of Cd-accumulating capacity. Our metagenomic analysis targeting 16S rRNA gene sequence data reveals that Proteobacteria, Firmicutes, Actinobacteria, Acidobacteria, Bacteroidetes, and Spirochaetes are predominant root endophytic bacterial phyla of the five rice cultivars that we studied. Principal coordinate analysis shows that the developmental stage of rice governs a larger source of variation in the bacterial communities compared to that of any specific rice cultivar or of the root Cd content. Endophytic bacterial communities during the reproductive stage of rice form a more highly interconnected network and exhibit higher operational taxonomic unit numbers, diversities, and abundance than those during the vegetative stage. Forty-five genera are significantly correlated with Cd content in rice root, notably including positive-correlating Geobacter and Haliangium; and negative-correlating Pseudomonas and Streptacidiphilus. Furthermore, Phylogenetic Investigation of Communities by Reconstruction of Unobserved States analysis shows that functional pathways, such as biosynthesis of siderophore and type II polyketide products, are significantly enhanced during the reproductive stage compared to those during the vegetative stage under Cd stress. The isolated endophytic bacteria from the Cd-contaminated rice roots display high Cd resistance and multiple traits that may promote plant growth, suggesting their potential application in alleviating HM stress on plants. This study describes in detail for the first time the assemblage of the bacterial endophytomes of rice roots under Cd stress and may provide insights into the interactions among endophytes, plants, and HM contamination.

Breaking Through Bead-Supported Assay: Integration of Optical Tweezers Assisted Fluorescence Imaging and Luminescence Confined Upconversion Nanoparticles Triggered Luminescent Resonance Energy Transfer (LRET).

Herein, a conceptual approach for significantly enhancing a bead-supported assay is proposed. For the fluorescence imaging technology, optical tweezers are introduced to overcome the fluid viscosity interference and immobilize a single tested bead at the laser focus to guarantee a fairly precise imaging condition. For the selection of fluorescent materials and the signal acquisition means, a type of innovative luminescence confined upconversion nanoparticle with a unique sandwich structure is specially designed to act as an efficient energy donor to trigger the luminescent resonance energy transfer (LRET) process. By further combining the double breakthrough with a molecular beacon model, the newly developed detection strategy allows for achieving a pretty high LRET ratio (≈ 88%) to FAM molecules and offering sound assay performance toward miRNA analysis with a detection limit as low as the sub-fM level, and is capable of well identifying single-base mismatching. Besides, this approach not only is able to accurately qualify the low-abundance targets from as few as 30 cancer cells but also can be employed as a valid cancer early warning tool for performing liquid biopsy.

Combining Holographic Optical Tweezers with Upconversion Luminescence Encoding: Imaging-Based Stable Suspension Array for Sensitive Responding of Dual Cancer Biomarkers.

Establishment of a stable analytical methodology with high-quality results is an urgent need for screening cancer biomarkers in early diagnosis of cancer. In this study, we incorporate holographic optical tweezers with upconversion luminescence encoding to design an imageable suspension array and apply it to conduct the detection of two liver cancer related biomarkers, carcinoembryonic antigen and alpha fetal protein. This bead-based assay is actualized by forming a bead array with holographic optical tweezers and synchronously exciting the upconversion luminescence of corresponding trapped complex beads fabricated with a simple one-step sandwich immunological recognition. Owing to the fact that these flowing beads are stably trapped in the focal plane of the objective lens which tightly converges the array of the laser beams by splitting a 980 nm beam using a diffraction optical element, a fairly stable excitation condition is achieved to provide reliable assay results. By further taking advantage of the eminent encoding capability of upconversion nanoparticles and the extremely low background signals of anti-Stokes luminescence, the two targets are well-identified and simultaneously detected with quite sound sensitivity and specificity. Moreover, the potential on-demand clinical application is presented by employing this approach to respond the targets toward complex matrices such as serum and tissue samples, offering a new alternative for cancer diagnosis technology.

Dual Amplification Fluorescence Assay for Alpha Fetal Protein Utilizing Immunohybridization Chain Reaction and Metal-Enhanced Fluorescence of Carbon Nanodots.

As an emerging fascinating fluorescent nanomaterial, carbon nanodots (CDs) have attracted much attention owing of their unique properties such as small size, antiphotobleaching, and biocompatibility. However, its use in biomedical analysis is limited because of its low quantum yield. Herein, we constructed a dual amplification fluorescence sensor by incorporating immunohybridization chain reaction (immuno-HCR) and metal-enhanced fluorescence (MEF) of CDs for the detection of alpha fetal protein (AFP). The immunoplasmonic slide and detection antibodies-conjugated oligonucleotide initiator are served to capture and probe AFP molecules, respectively. Then, CD-tagged hairpin nucleic acids were introduced to trigger the HCR, in which the hairpin nucleic acid and oligonucleotide initiator are complementary. The interaction between CDs and the gold nanoisland film greatly improves the radiative decay rate, increases the quantum yield, and enhances the fluorescence emission of the CDs. Furthermore, the HCR provides secondary amplification of fluorescence intensity. Therefore, the MEF-capable immunohybridization reactions provide obvious advantages and result in exceptional sensitivity. In addition, the sandwich immunoassay method offers high specificity. The results show a wide linearity between the fluorescence intensity and AFP concentration over 5 orders of magnitude (0.0005-5 ng/mL), and the detection limit reaches as low as 94.3 fg/mL. This method offers advantages of high sensitivity and reliability, wide detection range, and versatile plasmonic chips, thus presenting an alternative for the technologies in biomedical analysis and clinical applications.

Integrating optical tweezers with up-converting luminescence: a non-amplification analytical platform for quantitative detection of microRNA-21 sequences.

We report a single-microsphere based imaging assay method by integrating up-converting luminescence with optical tweezers for detecting microRNA-21 sequences. This method achieves a competitive detection limit of 12 fM with good selectivity and no dedicated signal amplification designs.