AdenPredictor: accurate prediction of the adenylation domain specificity of nonribosomal peptide biosynthetic gene clusters in microbial genomes.

Microbial natural products represent a major source of bioactive compounds for drug discovery. Among these molecules, nonribosomal peptides (NRPs) represent a diverse class that include antibiotics, immunosuppressants, anticancer agents, toxins, siderophores, pigments, and cytostatics. The discovery of novel NRPs remains a laborious process because many NRPs consist of nonstandard amino acids that are assembled by nonribosomal peptide synthetases (NRPSs). Adenylation domains (A-domains) in NRPSs are responsible for selection and activation of monomers appearing in NRPs. During the past decade, several support vector machine-based algorithms have been developed for predicting the specificity of the monomers present in NRPs. These algorithms utilize physiochemical features of the amino acids present in the A-domains of NRPSs. In this article, we benchmarked the performance of various machine learning algorithms and features for predicting specificities of NRPSs and we showed that the extra trees model paired with one-hot encoding features outperforms the existing approaches. Moreover, we show that unsupervised clustering of 453 560 A-domains reveals many clusters that correspond to potentially novel amino acids. While it is challenging to predict the chemical structure of these amino acids, we developed novel techniques to predict their various properties, including polarity, hydrophobicity, charge, and presence of aromatic rings, carboxyl, and hydroxyl groups.

A new NCDs@ZIF-90-based sensor: fluorescent "turn-on" detection of Al3+ ions with high selectivity and sensitivity.

A new NCDs@ZIF-90 composite as fluorescence sensor was designed and prepared by encapsulation of N-doped carbon dots (NCDs) in metal-organic framework (MOF) ZIF-90 in one-pot synthesis. NCDs@ZIF-90 retained the crystal structure and high thermal stability of ZIF-90; meanwhile, it also displayed the good chemical stability. NCDs@ZIF-90 dispersion in ethanol exhibited selective "turn-on" fluorescence response towards Al3+. The other coexisting competing metal ions had no obvious influence on the sensing performance of NCDs@ZIF-90 for Al3+. The fluorescence intensity at 447 nm of NCDs@ZIF-90 dispersion in ethanol had good linear relation with the concentrations of Al3+ with a low detection limit of 3.196 µM. The fluorescence enhancement after the addition of Al3+ was attributed to the release of NCDs from the inside of ZIF-90 to ethanol solution. In addition, NCDs@ZIF-90 displayed good recovery in detection of Al3+ in water samples indicating its practical application capability. The high selectivity and sensitivity indicate that NCDs@ZIF-90 is a good candidate as a "turn-on" fluorescence chemosensor to identify and detect Al3+.

Discovery and validation of extracellular vesicle-associated miRNAs as noninvasive detection biomarkers for early-stage non-small-cell lung cancer.

miRNAs in circulating extracellular vesicles (EVs) are promising biomarkers for cancer. However, their diagnostic ability for early-stage non-small-cell lung cancer (NSCLC) is not well known. In this study, the circulating EV miRNAs profiling was initially performed in 36 untreated NSCLC patients and 36 healthy controls by TaqMan Low Density Array (TLDA). Subsequently, we performed quantitative reverse-transcription PCR assay (RT-qPCR) validation in several independent cohorts that included 159 NSCLC patients, 120 age/sex-matched healthy controls and 31 benign nodule patients enrolled from three different clinical centres. In addition, 38 cases of NSCLC were analysed before and after surgery. We demonstrated that miR-520c-3p and miR-1274b were significantly and steadily increased in NSCLC patients in comparison with healthy controls and benign nodule patients (P < 0.001) and decreased markedly after tumour resection (P < 0.001). The areas under the curve (AUCs) of the ROC curve of the two-miRNA panel were 0.857 (95% CI, 0813-0.901; P < 0.0001) and 0.845 (95% CI, 0.793-0.896; P < 0.0001) for NSCLC and NSCLC stage I, respectively. Furthermore, the panel was able to differentiate NSCLC from benign nodules with an AUC of 0.823 (95% CI, 0.730-0.915; P < 0.0001). Furthermore, logistic regression analysis revealed the two-miRNA panel as an independent risk factor for NSCLC (OR = 16.128, P < 0.0001). In conclusion, miR-520c-3p and miR-1274b have biomarker potential for early diagnosis of NSCLC in multiple centres.

[The miR-184 level in the seminal plasma exosome of male infertility patients and its clinical significance].

OBJECTIVE: To study the miR-184 level in the seminal plasma exosome of male infertility patients and its clinical significance. METHODS: Between 2015 and 2019, we collected 285 seminal plasma samples from 97 azoospermia (AS) and 96 asthenospermia (AZS) patients and 92 age-matched normal fertile controls in Jiangsu Provincial Hospital of Traditional Chinese Medicine, General Hospital of Eastern Theater Command and the First Hospital Affiliated to Wenzhou Medical University, identified the isolated seminal plasma exosomes by nanoparticle tracking analysis (NTA), transmission electron microscopy (TEM) and Western blot, and detected the miR-184 level in the seminal plasma exosomes by quantitative real-time PCR (qRT-PCR). We determined the clinical value of the miR-184 level and its correlation with semen parameters by multiple statistics, predicted the target genes and involved pathways of miR-184 by bioinformatic algorithms, and analyzed their relationship with male infertility. RESULTS: NTA, TEM and Western blot exhibited plenty of exosomes in the seminal plasma of the patients. The results of qRT-PCR showed that the miR-184 level in the seminal plasma exosome was dramatically decreased in the AS patients compared with that in the normal fertile controls (0.227 ［0.092, 0.790］ vs 0.650 ［0.408, 1.061］, P < 0.01), but increased in AZS males in comparison with that in the control group (1.176 ［0.661, 1.946］ vs 0.650 ［0.408, 1.061］, P < 0.01). The areas under the ROC curve (AUC) for differentiating the AS and AZS patients from the controls were 0.866 (95% CI: 0.815－0.916) and 0.724 (95% CI: 0.653－0.795), respectively, and that for differentiating the AS from the AZS group was 0.964 (95% CI: 0.943－0.985). The miR-184 level in the seminal plasma exosome of the AZS patients was correlated positively with the sperm count (r = 0.243, P = 0.017) but negatively with the percentage of progressively motile sperm (r = －0.407, P = 0.006). Bioinformatics analysis indicated that the downstream target genes of miR-184 were significantly enriched in the protein regulatory pathways closely related to male reproduction and spermatogenesis. CONCLUSIONS: The miR-184 level in the seminal plasma exosome of infertility patients is significantly different from that of normal fertile males, which may serve as a potential auxiliary marker for the diagnosis of and participate in the development and progression of male infertility.

Different expression pattern of human cytomegalovirus-encoded microRNAs in circulation from virus latency to reactivation.

BACKGROUND: Human cytomegalovirus (HCMV) is a beta-hersvirinae that has a high latent infection rate worldwide and can cause serious consequences in immunocompromised patients when reactivation; however, the mechanism of how HCMV convert from latent to reactivation has rarely been investigated. In the present study, we aimed to perform a comprehensive analysis of the HCMV-encoded microRNA (miRNA) profile in serum of patients upon HCMV reactivation from latency and to further evaluate its clinical significance for the disease monitoring and preventing usefulness. METHODS: Serum samples from 59 viremia patients and 60 age-gender matched controls were enrolled in this study for screening and validation of different expression of HCMV miRNAs. Serum concentrations of 22 known HCMV miRNAs were determined by a hydrolysis probe-based stem-loop quantitative reverse transcription polymerase chain reaction (RT-qPCR) assay. HCMV DNA was measured by quantitative real-time PCR (qPCR) with the whole blood sample. Serum HCMV IgG and IgM were assessed using enzyme linked immunosorbent assay (ELISA). Another 47 samples from 5 patients at different time points were collected to evaluate the monitoring effectiveness and disease prediction ability of differential expression HCMV-miRNAs during the antiviral treatment. RESULTS: The RT-qPCR analysis revealed that the serum levels of 16 of the 22 examined HCMV miRNAs were elevated in HCMV viremia patients compared with controls, and a profile of 8 HCMV miRNAs including hcmv-miR-US25-2-3p, hcmv-miR-US4-5p, hcmv-miR-US25-2-5p, hcmv-miR-US25-1-3p, hcmv-miR-US25-1, hcmv-miR-UL36, hcmv-miR-UL148D, hcmv-miR-US29-3p were markedly elevated (fold change > 2, P < 0.01). Receiver operating characteristic curve (ROC) analysis were performed on the selected HCMV-miRNAs in all of the patients and controls that enrolled in this study, and which ranged from 0.72 to 0.80 in the autoimmune patients. In addition, hcmv-miR-US25-1-3p levels were significantly correlated with HCMV DNA load (r = 0.349, P = 0.007), and were obviously higher in the reactivation set than the latency set in the autoimmune patients, which could be a predictor for the monitoring of the antiviral treatment. CONCLUSIONS: HCMV miRNAs profile showed markedly shift-switch from latency to reactivation in circulation from HCMV infected patients and hcmv-miR-US25-1-3p may be served as a predictor for the switch upon reactivation from latency in patients suffered with autoimmune diseases.

Comprehensive analysis of differentially expressed serum microRNAs in humans responding to Brucella infection.

BACKGROUND: MicroRNAs (miRNAs), a subset of small non-coding RNA molecules, play crucial roles in various pathophysiological processes. Studies increasingly indicate that dysregulated miRNAs are associated with bacterial infection. Nevertheless, little is known about miRNAs that respond to Brucella infection and their potential clinical value. Our research aimed to identify the serum miRNAs altered during Brucella infection. METHODS: We enrolled serum samples from 73 patients diagnosed with brucellosis and 65 age- and sex-matched control individuals. Illumina sequencing via synthesis (SBS) technology was performed for an initial screen of miRNAs expression profile in serum samples pooled from 29 patients and 29 controls, respectively. A quantitative real-time polymerase chain reaction (qRT-PCR) assay was conducted in the training and validation sets to confirm the concentrations of differentially expressed miRNAs in individual serum samples from 73 patients and 65 controls. RESULTS: The Illumina SBS technology identified 1,372 known miRNAs and 1,893 novel miRNAs in brucellosis patients. The three markedly upregulated miRNAs (miR-15a-3p, miR-7-2-3p, miR-103b) in brucellosis patients were subsequently validated by qRT-PCR assay, of which miR-103b was confirmed to be significantly and steadily increased in the brucellosis patients compared with the controls (>2-fold, P<0.001). The area under the receiver operating characteristic (ROC) curve (AUC) for miR-103b was 0.714 (95% CI, 0.624-0.804). Bioinformatics analysis predicted that some putative target genes of miR-103b are involved in immune regulation or the processes of apoptosis and autophagy in humans. CONCLUSIONS: The serum miR-103b level markedly increases after Brucella infection and has the potential to serve as an auxiliary diagnostic indicator for Brucella infection that deserves further investigation.

[Relationship of small non-coding RNA in the seminal plasma with male infertility: An update].

The incidence of male infertility is increasing year by year, but there is a lack of non-invasive accurate diagnostic indicators for this disease, and the pathogenesis of idiopathic infertility is not yet fully clarified. Recent studies have found that there are various small non-coding RNAs (sncRNA) in the human seminal plasma and spermatic exosomes, which can be used as a novel non-invasive biomarker of male infertility. This review outlines the latest research updates on the relationship between sncRNAs in the seminal plasma and male infertility, aiming to provide some new ideas for the screening of the molecular markers of male infertility and study of its underlying molecular mechanisms.