Etiologic Diagnosis of Lower Respiratory Tract Bacterial Infections Using Sputum Samples and Quantitative Loop-Mediated Isothermal Amplification

Etiologic diagnoses of lower respiratory tract infections (LRTI) have been relying primarily on bacterial cultures that often fail to return useful results in time. Although DNA-based assays are more sensitive than bacterial cultures in detecting pathogens, the molecular results are often inconsistent and challenged by doubts on false positives, such as those due to system- and environment-derived contaminations. Here we report a nationwide cohort study on 2986 suspected LRTI patients across P. R. China. We compared the performance of a DNA-based assay qLAMP (quantitative Loop-mediated isothermal AMPlification) with that of standard bacterial cultures in detecting a panel of eight common respiratory bacterial pathogens from sputum samples. Our qLAMP assay detects the panel of pathogens in 1047(69.28%) patients from 1533 qualified patients at the end. We found that the bacterial titer quantified based on qLAMP is a predictor of probability that the bacterium in the sample can be detected in culture assay. The relatedness of the two assays fits a logistic regression curve. We used a piecewise linear function to define breakpoints where latent pathogen abruptly change its competitive relationship with others in the panel. These breakpoints, where pathogens start to propagate abnormally, are used as cutoffs to eliminate the influence of contaminations from normal flora. With help of the cutoffs derived from statistical analysis, we are able to identify causative pathogens in 750 (48.92%) patients from qualified patients. In conclusion, qLAMP is a reliable method in quantifying bacterial titer. Despite the fact that there are always latent bacteria contaminated in sputum samples, we can identify causative pathogens based on cutoffs derived from statistical analysis of competitive relationship

Automatic Measurement System of Hydrated Sodium Silicate Composition Analysis

Sodium silicate is one of the most successful inorganic binder. Along with the broad application of sodium silicate for domestic and industrial purposes, the composition analysis, include modulus (m), ratio of SiO2:Na2O, Na2O%, SiO2%, and solid-containing content, is important for the products strength and service life. However, it is perplexing to operate, inefficient and low precision for traditional standard testing method of these parameters. In this study, an automatic measurement system of sodium silicate composition analysis, with the potential electrode for potentiometer titration, micro-controller, PCB, heater, stirrer, printer and micro peristaltic pump, was developed according to the determine method principle. The end-points of pH value in the two titrating steps, first was 4.3 and second was 6.0, were set in the micro-controller to control the reaction in the processing of the sodium silicate composition analysis. And all the potential signals of the pH electrode were transited in the special PCB for the micro-controller

Increased Incidence of Mitochondrial Cytochrome C Oxidase 1 Gene Mutations in Patients with Primary Ovarian Insufficiency

Primary ovarian insufficiency (POI), also known as premature ovarian failure (POF), is defined as more than six months of cessation of menses before the age of 40 years, with two serum follicle stimulating hormone (FSH) levels (at least 1 month apart) falling in the menopause range. The cause of POI remains undetermined in the majority of cases, although some studies have reported increased levels of reactive oxygen species (ROS) in idiopathic POF. The role of mitochondrial DNA in the pathogenesis of POI has not been studied extensively. This aim of this study was to uncover underlying mitochondrial genetic defects in patients with POI. The entire region of the mitochondrial genome was amplified in subjects with idiopathic POI (n=63) and age-matched healthy female controls (n=63) using nine pair sets of primers, followed by screening of the mitochondrial genome using an Illumina MiSeq. We identified a total of 96 non-synonymous mitochondrial variations in POI patients and 93 non-synonymous variations in control subjects. Of these, 21 (9 in POI and 12 in control) non-synonymous variations had not been reported previously. Eight mitochondrial cytochrome coxidase 1 (MT-CO1) missense variants were identified in POI patients, whereas only four missense mutations were observed in controls. A high incidence of MT-CO1 missense variants were identified in POI patients compared with controls, and the difference between the groups was statistically significant (13/63 vs. 5/63, p=0.042). Our results show that patients with primary ovarian insufficiency exhibit an increased incidence of mitochondrial cytochrome c oxidase 1 gene mutations, suggesting that MT-CO1 gene mutation may be causal in POI

A novel 1.38-kb deletion combined with a single nucleotide variant in KIAA0586 as a cause of Joubert syndrome

Abstract Background KIAA0586, also known as Talpid3, plays critical roles in primary cilia formation and hedgehog signaling in humans. Variants in KIAA0586 could cause some different ciliopathies, including Joubert syndrome (JBTS), which is a clinically and genetically heterogeneous group of autosomal recessive neurological disorders. Methods and Results A 9-month-old girl was diagnosed as JBTS by the “molar tooth sign” of the mid-brain and global developmental delay. By whole-exome sequencing, we identified a single nucleotide variant c.3303G > A and a 1.38-kb deletion in KIAA0586 in the proband. These two variants of KIAA0586 were consistent with the mode of autosomal recessive inheritance in the family, which was verified using Sanger sequencing. Conclusions This finding of a compound heterozygote with a 1.38-kb deletion and c.3303G > A gave a precise genetic diagnosis for the patient, and the novel 1.38-kb deletion also expanded the pathogenic variation spectrum of JBTS caused by KIAA0586

Characteristics of women with POI and age-matched healthy women.

<p>* <i>p</i> = 0.000,</p><p>** <i>p</i> = 0.002,</p><p>***<i>p</i> = 0.0098</p><p>^#ovarian volume was the average of volume of each ovaries. Ovarian volume was calculated using the formula for a prolate ellipsoid: longitudinal diameter × anterioposterior diameter × transverse diameter × 0.5233.</p><p>Characteristics of women with POI and age-matched healthy women.</p

<i>MT-CO1</i> missense mutations in control subjects.

<p><i>MT-CO1</i> missense mutations in control subjects.</p

Nonsynonymous variations in different mitochondrial genes.

<p>The X axis was the mitochondrial gene name. The Y axis was the sample numbers which have nonsynonymous variations.</p

<i>MT-CO1</i> missense mutations in POI patients.

<p><i>MT-CO1</i> missense mutations in POI patients.</p

Genome-wide analysis of the first sequenced mycoplasma <em>capricolum</em> subsp<em> capripneumoniae</em> Strain M1601

International audienceMycoplasma capricolum subsp. capripneumoniae (Mccp) is a common pathogen of goats that causes contagious caprine pleuropneumonia. We closed the gap and corrected rRNA operons in the draft genome of Mccp M1601: a strain isolated from an infected goat in a farm in Gansu, China. The genome size of M1601 is 1,016,707 bp with a GC content of 23.67%. We identified 915 genes (occupying 90.27% of the genome), of which 713 are protein-coding genes (excluding 163 pseudogenes). No genomic islands and complete insertion sequences were found in the genome. Putative determinants associated with the organism's virulence were analyzed, and 26 genes (including one adhesion protein gene, two capsule synthesis gene clusters, two lipoproteins, hemolysin A, ClpB, and proteins involved in pyruvate metabolism and cation transport) were potential virulence factors. In addition, two transporter systems (ATP-binding cassette [ABC] transporters and phosphotransferase) and two secretion systems (Sec and signal recognition particle [SRP] pathways) were observed in the Mccp genome. Genome synteny analysis reveals a good collinear relationship between M1601 and Mccp type strain F38. Phylogenetic analysis based on 11 single-copy core genes of 31 Mycoplasma strains revealed good collinearity between M1601 and Mycoplasma capricolum subsp. capricolum (Mcc) and close relationship among Mycoplasma mycoides cluster strains. Our genome-wide analysis of Mccp M1601 provides helpful information on the pathogenic mechanisms and genetics of Mccp

Induction chemotherapy plus concurrent chemoradiotherapy versus induction chemotherapy plus volumetric modulated arc therapy alone in the treatment of stage II-IVB nasopharyngeal carcinoma patients: a retrospective controlled study

Abstract Background In the era of intensity-modulated radiotherapy (IMRT), the role of additional concurrent chemotherapy (CC) to radiotherapy (RT) after induction chemotherapy (IC) compared to IC followed by RT alone remains unclear for stage II-IVB nasopharyngeal carcinoma (NPC) patients. The aim of this study was to evaluate the efficacy and toxicities of IC/RT and IC/CCRT in the treatment of NPC with volumetric modulated arc therapy (VMAT). Methods From January 2012 to March 2016, a total of 217 NPC patients were retrospectively assessed. Of the 217 patients, 139 patients received IC followed by VMAT alone and 78 patients received IC plus CCRT. Overall survival (OS), progression-free survival (PFS) and toxicities were assessed. Results The 5-year OS, PFS rates were 57.5%, 41.8% and 47.8%, 38.4% for the IC/RT and IC/CCRT arms, respectively, without significant difference in survival between the two groups (both p > 0.05). Multivariate analysis indicated that treatment modality (IC/RT vs. IC/CCRT) was not an independent prognostic factor for OS or PFS. Grade 3–4 leukopenia/neutropenia (3.60% vs. 20.51%, p < 0.001), gastrointestinal disorder (nausea/vomiting/diarrhea, 2.16% vs. 41.03%, p < 0.001), mucositis (29.50% vs. 47.44%, p = 0.01) and xerostomia (34.53% vs. 48.72%, p = 0.04) were more frequent in the IC/ CCRT arm than in the IC/RT arm during VMAT. Conclusions No significant difference in OS and PFS was observed between IC plus VMAT alone and IC/CCRT in the treatment of stage II-IVB NPC patients, however, more side effects were observed in the IC/CCRT arm