A Pan-Cancer Analysis of Enhancer Expression in Nearly 9000 Patient Samples.

The role of enhancers, a key class of non-coding regulatory DNA elements, in cancer development has increasingly been appreciated. Here, we present the detection and characterization of a large number of expressed enhancers in a genome-wide analysis of 8928 tumor samples across 33 cancer types using TCGA RNA-seq data. Compared with matched normal tissues, global enhancer activation was observed in most cancers. Across cancer types, global enhancer activity was positively associated with aneuploidy, but not mutation load, suggesting a hypothesis centered on "chromatin-state" to explain their interplay. Integrating eQTL, mRNA co-expression, and Hi-C data analysis, we developed a computational method to infer causal enhancer-gene interactions, revealing enhancers of clinically actionable genes. Having identified an enhancer ∼140 kb downstream of PD-L1, a major immunotherapy target, we validated it experimentally. This study provides a systematic view of enhancer activity in diverse tumor contexts and suggests the clinical implications of enhancers.

Free-space dissemination of time and frequency with 10-19 instability over 113 km.

Networks of optical clocks find applications in precise navigation1,2, in efforts to redefine the fundamental unit of the 'second'3-6 and in gravitational tests7. As the frequency instability for state-of-the-art optical clocks has reached the 10-19 level8,9, the vision of a global-scale optical network that achieves comparable performances requires the dissemination of time and frequency over a long-distance free-space link with a similar instability of 10-19. However, previous attempts at free-space dissemination of time and frequency at high precision did not extend beyond dozens of kilometres10,11. Here we report time-frequency dissemination with an offset of 6.3 × 10-20 ± 3.4 × 10-19 and an instability of less than 4 × 10-19 at 10,000 s through a free-space link of 113 km. Key technologies essential to this achievement include the deployment of high-power frequency combs, high-stability and high-efficiency optical transceiver systems and efficient linear optical sampling. We observe that the stability we have reached is retained for channel losses up to 89 dB. The technique we report can not only be directly used in ground-based applications, but could also lay the groundwork for future satellite time-frequency dissemination.

RNA editing increases the nucleotide diversity of SARS-CoV-2 in human host cells.

SARS-CoV-2 is a positive-sense, single-stranded RNA virus responsible for the COVID-19 pandemic. It remains unclear whether and to what extent the virus in human host cells undergoes RNA editing, a major RNA modification mechanism. Here we perform a robust bioinformatic analysis of metatranscriptomic data from multiple bronchoalveolar lavage fluid samples of COVID-19 patients, revealing an appreciable number of A-to-I RNA editing candidate sites in SARS-CoV-2. We confirm the enrichment of A-to-I RNA editing signals at these candidate sites through evaluating four characteristics specific to RNA editing: the inferred RNA editing sites exhibit (i) stronger ADAR1 binding affinity predicted by a deep-learning model built from ADAR1 CLIP-seq data, (ii) decreased editing levels in ADAR1-inhibited human lung cells, (iii) local clustering patterns, and (iv) higher RNA secondary structure propensity. Our results have critical implications in understanding the evolution of SARS-CoV-2 as well as in COVID-19 research, such as phylogenetic analysis and vaccine development.

A Platinum-Aluminum Bimetallic Salen Complex for Pro-senescence Cancer Therapy.

Cell senescence is defined as irreversible cell cycle arrest, which can be triggered by telomere shortening or by various types of genotoxic stress. Induction of senescence is emerging as a new strategy for the treatment of cancer, especially when sequentially combined with a second senolytic drug capable of killing the resulting senescent cells, however severely suffering from the undesired off-target side effects from the senolytic drugs. Here, we prepare a bimetalic platinum-aluminum salen complex (Alumiplatin) for cancer therapy-a combination of pro-senesence chemotherapy with in situ senotherapy to avoid the side effects. The aluminum salen moiety, as a G-quadruplex stabilizer, enhances the salen's ability to induce cancer cell senescence and this phenotype is in turn sensitive to the cytotoxic activity of the monofunctional platinum moiety. It exhibits an excellent capability for inducing senescence, a potent cytotoxic activity against cancer cells both in vitro and in vivo, and an improved safety profile compared to cisplatin. Therefore, Alumiplatin may be a good candidate to be further developed into safe and effective anticancer agents. This novel combination of cell senescence inducers with genotoxic drugs revolutionizes the therapy options of designing multi-targeting anticancer agents to improve the efficacy of anticancer therapies.

RBP-TSTL is a two-stage transfer learning framework for genome-scale prediction of RNA-binding proteins.

RNA binding proteins (RBPs) are critical for the post-transcriptional control of RNAs and play vital roles in a myriad of biological processes, such as RNA localization and gene regulation. Therefore, computational methods that are capable of accurately identifying RBPs are highly desirable and have important implications for biomedical and biotechnological applications. Here, we propose a two-stage deep transfer learning-based framework, termed RBP-TSTL, for accurate prediction of RBPs. In the first stage, the knowledge from the self-supervised pre-trained model was extracted as feature embeddings and used to represent the protein sequences, while in the second stage, a customized deep learning model was initialized based on an annotated pre-training RBPs dataset before being fine-tuned on each corresponding target species dataset. This two-stage transfer learning framework can enable the RBP-TSTL model to be effectively trained to learn and improve the prediction performance. Extensive performance benchmarking of the RBP-TSTL models trained using the features generated by the self-supervised pre-trained model and other models trained using hand-crafting encoding features demonstrated the effectiveness of the proposed two-stage knowledge transfer strategy based on the self-supervised pre-trained models. Using the best-performing RBP-TSTL models, we further conducted genome-scale RBP predictions for Homo sapiens, Arabidopsis thaliana, Escherichia coli, and Salmonella and established a computational compendium containing all the predicted putative RBPs candidates. We anticipate that the proposed RBP-TSTL approach will be explored as a useful tool for the characterization of RNA-binding proteins and exploration of their sequence-structure-function relationships.

Intestinal mucosal microbiota mediate amino acid metabolism involved in the gastrointestinal adaptability to cold and humid environmental stress in mice.

Growing evidence has demonstrated that cold and humid environmental stress triggers gastrointestinal (GI) disorders. In this study, we explored the effects of intestinal microbiota homeostasis on the intestinal mucus barrier and GI disorders by cold and humid environmental stress. Moreover, the inner link between the intestinal mucosal microbiota and metabolites in mice with cold and humid environmental stress was interpreted by integrative analysis of PacBio HiFi sequencing microbial genomics and targeted metabolomics. In the current study, we found (1) after the cold and wet cold and humid environmental stress intervened in the intestinal microbiota disorder and homeostasis mice respectively, the bacterial culturing and fluorescein diacetate (FDA) microbial activity detection of intestinal microbiota including feces, intestinal contents, and intestinal mucosa suggested that the cold and humid environmental stress decreased the colony of culturable bacteria and microbial activity, in which intestinal microbiota disorder aggravated the injury of the intestinal mucus barrier and the GI symptoms related to cold and humid environmental stress; (2) the serum amino acid transferases such as glutamate pyruvic transa (GPT), and glutamic oxaloacetic transaminase (GOT) in cold and humid environmental stressed mice increased significantly, indicating that the intestinal microbiota adapted to cold and humid environmental stress by regulating the host's amino acid metabolism; (3) the integrative analysis of multi-omics illustrated a prediction model based on the microbiota Lactobacillus reuteri abundance and host amino acid level that can predict intestinal mucoprotein Muc2 with an adjusted R2 of 75.0%. In conclusion, the cold and humid environmental stress regulates the neurotransmitter amino acids metabolic function both in intestinal mucosal microbiota and host serum by adjusting the composition of the dominant bacterial population Lactobacillus reuteri, which contributes to the intestinal mucus barrier injury and GI disorders caused by cold and humid environmental stress.

Targeting the Gut-Kidney Axis in Diarrhea with Kidney-Yang Deficiency Syndrome: The Role of Sishen Pills in Regulating TMAO-Mediated Inflammatory Response.

BACKGROUND Sishen Pills (SSPs) are commonly used to treat diarrhea with kidney-yang deficiency syndrome. Trimethylamine-N-oxide (TMAO) is produced through the metabolism of gut microbiota and can participate in diarrhea in kidney-yang deficiency syndrome by mediating the "gut-kidney axis" to transmit inflammatory factors. This study combined network pharmacology with animal experiments to explore whether SSPs can treat diarrhea with kidney-yang deficiency syndrome by affecting the interaction between TMAO and gut microbiota. MATERIAL AND METHODS A mouse model of diarrhea with kidney-yang deficiency syndrome was constructed by using adenine and Folium sennae decoction, and SSP decoction was used for treatment. This study utilized network pharmacology to predict the potential mechanisms of SSPs in treating diarrhea with kidney-yang deficiency syndrome. 16S rRNA high-throughput sequencing was used to analyze gut mucosal microbial characteristics. ELISA was used to measure TMAO, NOD-like receptor thermal protein domain associated protein 3 (NLRP3), interleukin-1ß (IL-1ß), and transforming growth factor-ß1 (TGF-ß1) levels. We performed Masson and immunohistochemical (Occludin, ZO-1) staining of kidney and small intestinal tissues. The fluorescein diacetate (FDA) hydrolysis spectrophotometric method was used to assess the microbial activity in contents of the small intestine. RESULTS Network pharmacology analysis revealed that SSPs can modulate 108 target points involved in the development of diarrhea, including IL-1ß and TNF. The experimental results demonstrated that SSP decoction significantly improved the general behavioral profiles of the mice, and also reduced TMAO, NLRP3, IL-1ß, and TGF-ß1 levels (P<0.05). Correlation analysis revealed significant positive correlations between TMAO concentrations and NLRP3, IL-1ß and TGF-ß1 levels (P<0.05). Pathological analysis revealed improvements in renal fibrosis and increased expression of the Occludin and ZO-1 proteins in intestinal tissue. In the SSP group, there was a significant increase in microbial activity (P<0.001). According to the sequencing results, the characteristic bacteria of the SSP and NR groups included Succinatimonas hippei, uncultured Solirubrobacter sp., and Clostridium tyrobutyricum. Furthermore, TMAO, NLRP3, IL-1ß, and TGF-ß1 were significantly positively correlated (P<0.05) with Succinatimonas hippei and Clostridium tyrobutyricum. By modulating Firmicutes, Succinatimonas hippei, and Clostridium tyrobutyricum, SSP decoction lowers TMAO levels to alleviate diarrhea with kidney-yang deficiency syndrome. CONCLUSIONS TMAO likely plays a significant role in the "gut-kidney axis" of diarrhea with kidney-yang deficiency syndrome. By adjusting gut microbiota to reduce the inflammatory response that is transmitted through the "gut-kidney axis" as a result of elevated TMAO levels, SSP decoction can alleviate diarrhea with kidney-yang deficiency syndrome.

Preparation of (S)-epichlorohydrin using a novel halohydrin dehalogenase by selective conformation adjustment.

Chiral epichlorohydrin (ECH) is an attractive intermediate for chiral pharmaceuticals and chemicals preparation. The asymmetric synthesis of chiral ECH using 1,3-dicholoro-2-propanol (1,3-DCP) catalyzed by a haloalcohol dehalogenase (HHDH) was considered as a feasible approach. However, the reverse ring opening reaction caused low optical purity of chiral ECH, thus severely restricts the industrial application of HHDHs. In the present study, a novel selective conformation adjustment strategy was developed with an engineered HheCPS to regulate the kinetic parameters of the forward and reverse reactions, based on site saturation mutation and molecular simulation analysis. The HheCPS mutant E85P was constructed with a markable change in the conformation of (S)-ECH in the substrate pocket and a slight impact on the interaction between 1,3-DCP and the enzyme, which resulted in the kinetic deceleration of the reverse reactions. Compared with HheCPS, the catalytic efficiency (kcat(S)-ECH/Km(S)-ECH) of the reversed reaction dropped to 0.23-fold (from 0.13 to 0.03 mM-1 s-1), while the catalytic efficiency (kcat(1,3-DCP)/Km(1,3-DCP)) of the forward reaction only reduced from 0.83 to 0.71 mM-1 s-1. With 40 mM 1,3-DCP as substrate, HheCPS E85P catalyzed the synthesis of (S)-ECH with the yield up to 55.35% and the e.e. increased from 92.54 to >99%. Our work provided an effective approach for understanding the stereoselective catalytic mechanism as well as the green manufacturing of chiral epoxides.

Leveraging the attention mechanism to improve the identification of DNA N6-methyladenine sites.

DNA N6-methyladenine is an important type of DNA modification that plays important roles in multiple biological processes. Despite the recent progress in developing DNA 6mA site prediction methods, several challenges remain to be addressed. For example, although the hand-crafted features are interpretable, they contain redundant information that may bias the model training and have a negative impact on the trained model. Furthermore, although deep learning (DL)-based models can perform feature extraction and classification automatically, they lack the interpretability of the crucial features learned by those models. As such, considerable research efforts have been focused on achieving the trade-off between the interpretability and straightforwardness of DL neural networks. In this study, we develop two new DL-based models for improving the prediction of N6-methyladenine sites, termed LA6mA and AL6mA, which use bidirectional long short-term memory to respectively capture the long-range information and self-attention mechanism to extract the key position information from DNA sequences. The performance of the two proposed methods is benchmarked and evaluated on the two model organisms Arabidopsis thaliana and Drosophila melanogaster. On the two benchmark datasets, LA6mA achieves an area under the receiver operating characteristic curve (AUROC) value of 0.962 and 0.966, whereas AL6mA achieves an AUROC value of 0.945 and 0.941, respectively. Moreover, an in-depth analysis of the attention matrix is conducted to interpret the important information, which is hidden in the sequence and relevant for 6mA site prediction. The two novel pipelines developed for DNA 6mA site prediction in this work will facilitate a better understanding of the underlying principle of DL-based DNA methylation site prediction and its future applications.

Biofilter-constructed wetland-trophic pond system: A new strategy for effective sewage treatment and agricultural irrigation in rural area.

Artificial ecosystems with high biological complexity are generally considered to be efficient in metabolizing substances and resistant to temperature shock. In this study, a novel near-natural system (BCT system), which consisted of simple biofilter, constructed wetland and trophic biology pond, was conducted to treat rural sewage in situ for irrigation into farmland. Water quality related to carbon and nutrients and microbial community were analyzed along the system to reveal the effect of each unit. The annual average removals of BCT system for TN, NH4+-N, TP and COD could reach 46.53%, 52.18%, 41.48%, and 53.21%, respectively. There was no significant decrease for removal efficiencies from high temperature period (HTP, ≥15 °C) to low temperature period (LTP, <15 °C). In LTP, the trophic pond (TRP) removed 34.85% of TN, 33.93% of NH4+-N, 13.71% of TP and 18.77% of COD, while the removal efficiencies of constructed wetland fluctuated greatly. The TRP facilitated the BCT system to maintain the removal capability during low temperature period. The relative abundance of denitrification functional genes in TRP increased nearly tenfold from HTP to LTP. The effluent quality from the system can meet the agricultural irrigation standards, demonstrating the effect of BCT system on sewage treatment and agricultural irrigation in rural area.

Gallium Triggers Ferroptosis through a Synergistic Mechanism.

The gallium ion (Ga3+ ) has long been believed to disrupt ferric homeostasis in the body by competing with iron cofactors in metalloproteins, ultimately leading to cell death. This study revealed that through an indirect pathway, gallium can trigger ferroptosis, a type of non-apoptotic cell death regulated by iron. This is exemplified by the gallium complex of the salen ligand (Ga-1); we found that Ga-1 acts as an effective anion transporter that can affect the pH gradient and change membrane permeability, leading to mitochondrial dysfunction and the release of ferrous iron from the electron transfer chain (ETC). In addition, Ga-1 also targeted protein disulfide isomerases (PDIs) located in the endoplasmic reticulum (ER) membrane, preventing the repair of the antioxidant glutathione (GSH) system and thus enforcing ferroptosis. Finally, a combination treatment of Ga-1 and dietary polyunsaturated fatty acids (PUFAs), which enhances lipid peroxidation during ferroptosis, showed a synergistic therapeutic effect both in vitro and in vivo. This study provided us with a strategy to synergistically induce Ferroptosis in tumor cells, thereby enhancing the anti-neoplastic effect.

Sub-1 nm MoC Quantum Dots Decorating N-Doped Graphene as Advanced Electrocatalysts of Flexible Hybrid Alkali-Acid Zn-Quinone Battery.

The development of flexible energy devices is envisaged to revolutionize the next generation of the wearable electronics industry, the practical application yet faces critical issues of low power density, poor cycling stability, and low energy density. Herein, the authors report a newly flexible hybrid Zn-quinone battery (h-ZnQB) with acidic gel in the cathode and alkaline gel in the anode, in which proton (H+ ) and hydroxide ions (OH- ) are served as the ion charge carriers for acidic quinone cathode and alkaline Zn anode. To this end, the nanohybrids of sub-1 nm MoC quantum dots decorating nitrogen-doped ultrathin graphene (MoC QDs/NG) are developed as the advanced cathode electrocatalysts toward redox conversion between quinone and hydroquinone (H2 Q/Q). Comprehensive characterization studies and density functional theory (DFT) calculations reveal that high valent Mo species originating from the size-effects serve as the active sites for the conversion of H2 Q/Q, contributing to the impressive catalytic performance. The as-developed flexible h-ZnQB displays a high open-circuit voltage of 1.74 V with a specific capacity of 223.3 mAh g-1 and an energy density of 350 Wh kg-1 at 0.2 A g-1 , thanks to the fast kinetics of charge carriers (H+ and OH- ), the high activity of the catalyst, and the elaborate design of alkali-acid gel electrolytes.

Bioinspired Design of seco-Chlorin Photosensitizers to Overcome Phototoxic Effects in Photodynamic Therapy.

Photodynamic therapy (PDT) is a non-invasive treatment modality against a range of cancers and nonmalignant diseases, however one must be aware of the risk of causing phototoxic reactions after treatment. We herein report a bioinspired design of next-generation photosensitizers (PSs) that not only effectively produce ROS but undergo fast metabolism after treatment to overcome undesirable side effects. We constructed a series of ß-pyrrolic ring-opening seco-chlorins, termed beidaphyrin (BP), beidapholactone (BPL), and their zinc(II) derivatives (ZnBP and ZnBPL), featuring intense near-infrared absorption and effective O2 photosensitization. Irradiation of ZnBPL led to a non-cytotoxic, metabolizable beidaphodiacetamide (ZnBPD) via in situ generated O2.- but not 1 O2 , as revealed by mechanistic studies including time-resolved absorption, kinetics, and isotope labeling. Furthermore, water-soluble ZnBPL showed an effective therapeutic outcome, fast metabolism, and negligible phototoxic reactions.

Dominant Contribution of a Lake's Internal Pollution to Eutrophication During Rapid Urbanization.

Artificial lakes that form during rapid urbanization often fail to achieve their desired functions, and gradually become eutrophic. Whether the external discharge or internal release of nutrients dominates the eutrophication of urban lakes has rarely been reported. In this study, a lake that had been formed during ten years of urbanization had become hyper-eutrophic. TP mainly contributed to the eutrophication and algal bloom in the lake. While the release potential of TP fluctuated, TN, particularly NH3-N, was constantly released from the sediment. Concentrations of anthropogenic metals (Pb, Cu and Cr) increased with the increasing depth of the sediment. Even for a lake that had formed rapidly in a short period, the internal phosphorus released from sediment was 1.9-times higher than that of the external discharge. The dominating contribution of internal pollution from sediment requires more attention to restore and manage these urban waters.

Scalable Synthesis of Tungsten Disulfide Nanosheets for Alkali-Acid Electrocatalytic Sulfion Recycling and H2 Generation.

WS2 nanosheets hold great promise for a variety of applications yet faces a grand challenge in terms of large-scale synthesis. We report a reliable, scalable, and high-yield (>93 %) synthetic strategy to fabricate WS2 nanosheets, which exhibit highly desirable electrocatalytic properties toward both the alkaline sulfion (S2- ) oxidation reaction (SOR) and the acidic hydrogen evolution reaction (HER). The findings prompted us to develop a hybrid alkali-acid electrochemical cell with the WS2 nanosheets as bifunctional electrode catalysts of alkaline anodic SOR and acidic cathodic HER. The proof-of-concept device holds promise for self-power or low-electricity electrolytic H2 generation and environmentally friendly recycling of sulfion with enhanced electron utilization efficiency.

Multivalence-Actuated DNA Nanomachines Enable Bicolor Exosomal Phenotyping and PD-L1-Guided Therapy Monitoring.

Exosome-associated liquid biopsies are hampered by challenges in the exosomal quantification and phenotyping. Here, we present a bioinspired exosome-activated DNA molecular machine (ExoADM) with multivalent cyclic amplification that enables highly sensitive detection and phenotyping of circulating exosomes. ExoADM harbors two (an exposed and a hidden) DNA toehold domains that actuate sequential branch migration and multivalent recycling in response to exosomal surface markers. Importantly, this self-powered ExoADM achieves a high sensitivity (33 particles/µL) and is compatible with another DNA nanomachine targeting different exosomal surface markers for dual-color phenotyping. Using this strategy, we can simultaneously track the dynamic changes of ExoPD-L1 and ExoCD63 expression induced by signaling molecules. Further, we found that their expression levels on circulating exosomes could well differentiate cancer patients from the normal individuals. More importantly, ExoPD-L1 levels could reflect the efficacy of different treatments and guide anti-PD-1 immunotherapy, suggesting the potential of ExoPD-L1 in clinical diagnosis and targeted therapy monitoring.

Antibiotic prophylaxis in perioperative period of percutaneous nephrolithotomy: a systematic review and meta-analysis of comparative studies.

OBJECTIVE: To explore the efficacy of antibiotic prophylaxis in perioperative period of percutaneous nephrolithotomy (PCNL) by conducting a systematic review and meta-analysis. MATERIALS AND METHODS: A systematic literature search using Pubmed, Embase, and the Chinese SinoMed, CNKI, WanFang and VIP databases was performed to find comparative studies on the efficacy of different antibiotic prophylaxis strategies in PCNL for preventing postoperative sepsis. The last search was conducted on 21 April 2019. All selected articles were reviewed independently by two, and in case of discordance, three reviewers. Summarized unadjusted odds ratios (ORs) or risk ratios (RRs) with 95% confidence intervals (CIs) were calculated to assess the efficacy of different antibiotic prophylaxis strategies. RESULTS: Thirteen independent studies comprising up to 1549 individuals were included. Compared with single dose before anesthesia, preoperative prophylactic antibiotics significantly reduced postoperative sepsis (OR 0.31, 95% CI 0.20-0.50; P < 0.00001) and fever (OR 0.26, 95% CI 0.14-0.48; P < 0.0001). But no remarkable difference in sepsis risk between patients with and without postoperative prophylactic antibiotics was detected (RR 1.19, 95% CI 0.72-1.97; P = 0.49). And patients receiving postoperative prophylactic antibiotics were at a significantly high risk of fever (OR 1.88, 95% CI 1.01-3.05; P = 0.05). Compared with single dose before anesthesia, preoperative prophylactic antibiotics significantly reduced positive pelvic urine (RR 0.22, 95% CI 0.09-0.54; P = 0.0009) and stone cultures (RR 0.40, 95% CI 0.25-0.64; P = 0.0001). CONCLUSIONS: The conclusion is drawn that preoperative prophylactic antibiotics indeed lowered the risk of postoperative sepsis and fever, whereas its postoperative use seems unnecessary. Besides, preoperative prophylactic antibiotics reduced positive pelvic urine and stone cultures significantly, which are a risk factor for sepsis. In our meta-analysis, the efficacy of different types of antibiotics and different courses of preoperative antibiotics could not be assessed. To verify the correctness of these conclusions, randomized controlled trials with a larger sample size and more rigorous study design are required.

Molten-Salt-Assisted Synthesis of Bismuth Nanosheets for Long-term Continuous Electrocatalytic Conversion of CO2 to Formate.

Two-dimensional (2D) monometallic pnictogens (antimony or Sb, and bismuth or Bi) nanosheets demonstrate potential in a variety of fields, including quantum devices, catalysis, biomedicine and energy, because of their unique physical, chemical, electronic and optical properties. However, the development of general and high-efficiency preparative routes toward high-quality pnictogen nanosheets is challenging. A general method involving a molten-salt-assisted aluminothermic reduction process is reported for the synthesis of Sb and Bi nanosheets in high yields (>90 %). Electrocatalytic CO2 reduction was investigated on the Bi nanosheets, and high catalytic selectively to formate was demonstrated with a considerable current density at a low overpotential and an impressive stability. Bi nanosheets continuously convert CO2 into formate in a flow cell operating for one month, with a yield rate of 787.5 mmol cm-2 h-1 . Theoretical results suggest that the edge sites of Bi are far more active than the terrace sites.

Synergy of Peptide-Nucleic Acid and Spherical Nucleic Acid Enabled Quantitative and Specific Detection of Tumor Exosomal MicroRNA.

Exosomal microRNAs are essential in intercellular communications and disease progression, yet it remains challenging to quantify the expression level due to their small size and low abundance in blood. Here, we report a "sandwich" electrochemical exosomal microRNA sensor (SEEmiR) to detect target microRNA with high sensitivity and specificity. In SEEmiR, neutrally charged peptide nucleic acid (PNA) enables kinetically favorable hybridization with the microRNA target relative to negatively charged DNA, particularly in a short sequence (10 nt). More importantly, this property allows PNA to cooperate with a spherical nucleic acid (SNA) nanoprobe that heavily loads with oligonucleotide-adsorbed electroactive tags to enhance detection sensitivity and specificity. Such a PNA-microRNA-SNA sandwich construct is able to minimize the background noise via PNA, thereby maximizing the SNA-mediated signal amplification in electrostatic adsorption-based SEEmiR. The synergy between PNA and SNA makes the SEEmiR sensor able to achieve a broad dynamic range (from 100 aM to 1 nM) with a detection limit down to 49 aM (2 orders of magnitude lower than that without SNA) and capable of distinguishing a single-base mismatch. This ultrasensitive sensor provides label-free and enzyme-independent microRNA detection in cell lysates, unpurified tumor exosomal lysates, cancer patients' blood, and accurately differentiates the patients with breast cancer from the healthy ones, suggesting its potential as a promising tool in cancer diagnostics.

Intraspecific and Interspecific Variations in the Mitochondrial Genomes of Nilaparvata (Hemiptera: Delphacidae).

Planthoppers in the genus Nilaparvata Distant are serious pests of rice and many other crops in tropical and temperate Asia, and northern Australia. In this study, the mitochondrial genomes of four Nilaparvata planthoppers were sequenced, three in Nilaparvata lugens Stål and one in Nilaparvata muiri China. Mitochondrial genome of Nilaparvata contain the standard set of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and a control region. The nucleotide composition of Nilaparvata mitochondrial sequence is biased toward adenine and thymine, and the amino acid composition is affected to a similar degree by the bias to AT. We compare the four mitochondrial genomes and find intra- and interspecific variation in gene length, base composition, nucleotide and amino acid substitutions, intergenic spacer length, and gene overlap. The intra- and interspecific variations reveal that nucleotide and amino acid substitutions in mitochondrial protein-coding genes make a contribution to the formation of various insect biotypes in one species. Furthermore, the accumulation of nonsynonymous substitutions in the mitochondrial protein-coding genes, as well as differences in start codons, the length of intergenic spacers, and gene overlap regions contribute to differences between the two species investigated here. In addition, cox is the most conserved gene family and nad4-nad4l cluster is variable in Nilaparvata mitochondrial genes for the intra- and interspecific variation.