Single-cell mRNA quantification and differential analysis with Census

Single-cell gene expression studies promise to unveil rare cell types and cryptic states in development and disease through a stunningly high-resolution view of gene regulation. However, measurements from single-cell RNA-Seq are highly variable, frustrating efforts to assay how expression differs between cells. We introduce Census, an algorithm available through our single-cell analysis toolkit Monocle 2, which converts relative RNA-Seq expression levels into relative transcript counts without the need for experimental spike-in controls. We show that analyzing changes in relative transcript counts leads to dramatic improvements in accuracy compared to normalized read counts and enables new statistical tests for identifying developmentally regulated genes. We explore the power of Census through reanalysis of single-cell studies in several developmental and disease contexts. Census counts can be analyzed with widely used regression techniques to reveal changes in cell fate-dependent gene expression, splicing patterns, and allelic imbalances, demonstrating that Census enables robust single-cell analysis at multiple layers of gene regulation.

[The preliminary analysis of chronic rhinosinusitis: clinical phenotypes and inflammation features]

Objective:To explore the clinical phenotypes and inflammatory features of chronic rhinosinusitis in the liminary study.Method:Twenty-five patients suffered with chronic rhinosinusitis and nasal polyps (CRSwNP) and 23 patients suffered with chronic rhinosinusitis without nasal polyps (CRSsNP) were enrolled in our study. Analysis was made in clinical features of the two types, including symptoms with VAS score, nasal endoscopy with Lanza-Kennedy score,and nasal sinus CT with Lund-Mackay score. Eosinophil and neutrophil distribution of lesions in the two groups were compared, inflammatory markers expression of interleukin (IL-5), interleukin-17(IL-17) and interferon gamma (IFN-γ) were assessed.Result:The VAS score of nasal obstruction, nasal endoscopic score and CT score were significantly higher in patients with CRSwNP than that in patients with CRSsNP (P< 0.05). HE staining showed that the lesions in patients with type two were infiltrated by mixed inflammatory cells. 41% (10 cases) out of patients with CRSwNP were mainly with eosinophils infiltration and 59% (15 cases) with neutrophil infiltration. 78%(18 cases) out of patients with CRSsNP were with eosinophilic infiltration and 22% (5 cases) with neutrophil infiltration. The expression of inflammatory factors IL-5, IL-17 and IFN in patients with CRSwNP was significantly increased compared with that in patients with CRSsNP (P< 0.05).Conclusion:The clinical manifestation and the degree of inflammation of patients with CRSwNP are more severe than that of patients with CRSsNP. Lesions in both groups are infiltrated by mixed inflammatory cells.

Socioeconomic status and lifestyle behaviours in cancer survivors: smoking and physical activity

PURPOSE

Smoking cessation and increased physical activity (pa) have been linked to better outcomes in cancer survivors. We assessed whether socioeconomic factors influence changes in those behaviours after a cancer diagnosis.

METHODS

As part of a cross-sectional study, a diverse group of cancer survivors at the Princess Margaret Cancer Centre (Toronto, ON), completed a questionnaire about past and current lifestyle behaviours and perceptions about the importance of those behaviours with respect to their health. The influence of socioeconomic indicators on smoking status and physical inactivity at 1 year before and after diagnosis were assessed using multivariable logistic regression with adjustment for clinico-demographic factors.

RESULTS

Of 1222 participants, 1192 completed the smoking component. Of those respondents, 15% smoked before diagnosis, and 43% of those smokers continued to smoke after. The proportion of survivors who continued to smoke increased with lower education level (p = 0.03). Of the 1106 participants answering pa questions, 39% reported being physically inactive before diagnosis, of whom 82% remained inactive afterward. Survivors with a lower education level were most likely to remain inactive after diagnosis (p = 0.003). Lower education level, household income, and occupation were associated with the perception that pa had no effect or could worsen fatigue and quality of life (p ≤ 0.0001).

CONCLUSIONS

In cancer survivors, education level was a major modifier of smoking and pa behaviours. Lower socioeconomic status was associated with incorrect perceptions about pa. Targeting at-risk survivors by education level should be evaluated as a strategy in cancer survivorship programs.

Limits on Active to Sterile Neutrino Oscillations from Disappearance Searches in the MINOS, Daya Bay, and Bugey-3 Experiments

Searches for a light sterile neutrino have been performed independently by the MINOS and the Daya Bay experiments using the muon (anti)neutrino and electron antineutrino disappearance channels, respectively. In this Letter, results from both experiments are combined with those from the Bugey-3 reactor neutrino experiment to constrain oscillations into light sterile neutrinos. The three experiments are sensitive to complementary regions of parameter space, enabling the combined analysis to probe regions allowed by the Liquid Scintillator Neutrino Detector (LSND) and MiniBooNE experiments in a minimally extended four-neutrino flavor framework. Stringent limits on sin^{2}2θ_{μe} are set over 6 orders of magnitude in the sterile mass-squared splitting Δm_{41}^{2}. The sterile-neutrino mixing phase space allowed by the LSND and MiniBooNE experiments is excluded for Δm_{41}^{2}<0.8  eV^{2} at 95%  CL_{s}.

Search for Sterile Neutrinos Mixing with Muon Neutrinos in MINOS

We report results of a search for oscillations involving a light sterile neutrino over distances of 1.04 and 735 km in a ν_{μ}-dominated beam with a peak energy of 3 GeV. The data, from an exposure of 10.56×10^{20} protons on target, are analyzed using a phenomenological model with one sterile neutrino. We constrain the mixing parameters θ_{24} and Δm_{41}^{2} and set limits on parameters of the four-dimensional Pontecorvo-Maki-Nakagawa-Sakata matrix, |U_{μ4}|^{2} and |U_{τ4}|^{2}, under the assumption that mixing between ν_{e} and ν_{s} is negligible (|U_{e4}|^{2}=0). No evidence for ν_{μ}→ν_{s} transitions is found and we set a world-leading limit on θ_{24} for values of Δm_{41}^{2}≲1  eV^{2}.

Kinetic analysis of RNA editing of Newcastle disease virus P gene in the early period of infection

As a paramyxovirus, Newcastle disease virus (NDV) has the ability to edit its P (phosphoprotein) gene to synthesize three kinds of viral protein (P, V and W). It is technically very difficult to differentiate P, V and W mRNAs, and little was known about NDV regulation of RNA-editing frequency. To investigate the rules of NDV RNA editing, the ratio of the P gene-derived transcripts (P, V and W) was determined by sequencing at different time points post-infection. The results showed unstable ratio of V and W mRNA at different time points, and the frequency of NDV editing was significantly increased at the early period of infection (P 

KEYWORDS

Newcastle disease virus; phosphoprotein; RNA editing; G insertion.

Differential gene expression of two extreme honey bee (Apis mellifera) colonies showing varroa tolerance and susceptibility

Varroa destructor, an ectoparasitic mite of honey bees (Apis mellifera), is the most serious pest threatening the apiculture industry. In our honey bee breeding programme, two honey bee colonies showing extreme phenotypes for varroa tolerance/resistance (S88) and susceptibility (G4) were identified by natural selection from a large gene pool over a 6-year period. To investigate potential defence mechanisms for honey bee tolerance to varroa infestation, we employed DNA microarray and real time quantitative (PCR) analyses to identify differentially expressed genes in the tolerant and susceptible colonies at pupa and adult stages. Our results showed that more differentially expressed genes were identified in the tolerant bees than in bees from the susceptible colony, indicating that the tolerant colony showed an increased genetic capacity to respond to varroa mite infestation. In both colonies, there were more differentially expressed genes identified at the pupa stage than at the adult stage, indicating that pupa bees are more responsive to varroa infestation than adult bees. Genes showing differential expression in the colony phenotypes were categorized into several groups based on their molecular functions, such as olfactory signalling, detoxification processes, exoskeleton formation, protein degradation and long-chain fatty acid metabolism, suggesting that these biological processes play roles in conferring varroa tolerance to naturally selected colonies. Identification of differentially expressed genes between the two colony phenotypes provides potential molecular markers for selecting and breeding varroa-tolerant honey bees.

[Comparison study of subcutaneous immunotherapy and sublingual immunotherapy in patients with allergic rhinitis]

Objective: To observe the compliance, efficacy and safety of subcutaneous immunotherapy(SLIT) and sublingual immunotherapy(SCIT) in patients with allergic rhinitis(AR).Method:One hundred and fifteen patients sensitized to house dust mites were recruited in this study. The standardized extract of house dust mites was used for SLIT in 64 cases, and the standardized extract of dual house dust mites was used for SCIT in the other 51 cases. The compliance, nasal symptom scores, the medication scores, the quality of life and the adverse reaction were evaluated before and 2 years after immunotherapy. SPSS 19.0 was used for data analysis. Result:Forty patients out of 64 completed the 2 years-SLIT, and the compliance rate was 62.50%. Forty three patients out of 51 completed the 2 years-SCIT and the compliance rate was 84.31%.The compliance rate of SLIT was significantly lower than that of SCIT(P <0.05). The nasal symptom scores, the anti-allergic medication, the scores in quality of life decreased significantly after receiving SLIT or SCIT for 2 years（P <0.05）. However, the changed values of scores between the two groups had no significant differences（P >0.05）. There was no moderate or severe adverse reactions occurred in SLIT group but a total of 6 moderate or severe adverse reactions occurred in SCIT group.Conclusion:SLIT has same effect compared with SCIT with a lower compliance rate but a significantly higher safety.

First Measurement of Electron Neutrino Appearance in NOvA

We report results from the first search for ν_{μ}→ν_{e} transitions by the NOvA experiment. In an exposure equivalent to 2.74×10^{20} protons on target in the upgraded NuMI beam at Fermilab, we observe 6 events in the Far Detector, compared to a background expectation of 0.99±0.11(syst) events based on the Near Detector measurement. A secondary analysis observes 11 events with a background of 1.07±0.14(syst). The 3.3σ excess of events observed in the primary analysis disfavors 0.1π<δ_{CP}<0.5π in the inverted mass hierarchy at the 90% C.L.

A single fas gene mutation changes lupus onset, severity, location, and molecular abnormalities in mice

Although genetic predisposition plays a major role in the progression of systemic lupus erythematosus (SLE) and its variation in symptoms, the precise relationships between genetic changes and disease status are not well understood. Here, to demonstrate the effect of a single gene mutation on disease etiology, we examined two mouse models of SLE with the same genetic background but different Fas genes. Mice with the Fas(lpr) gene developed severe SLE with renal dysfunction and inflammatory responses in the lung and kidney. By contrast, mice with the Fas(+) gene showed disease-related abnormalities in the liver and joints. Patterns of inflammatory disease markers differed across organs between the two lines of mice. Fas(lpr) mice showed greater MMP signals in the kidney and IL-11 signals in the lung than Fas(+) mice. Fas(+) mice had higher IL-11 signal intensity in the knee region and higher CXCR4 signal intensity in the liver than Fas(lpr) mice. Our results exemplify the complexity of disease and suggest the need for individualized target-specific treatment regimens. Strengths and Limitations of this Study: Fas gene is a well characterized gene in this disease. The molecular components in human disease need more clinical data.

Quercetin is an effective inhibitor of quorum sensing, biofilm formation and virulence factors in Pseudomonas aeruginosa

AIMS

The study aimed to perform a systematic investigation of the effects of quercetin on biofilm formation and virulence factors in Pseudomonas aeruginosa.

METHODS AND RESULTS

The Ps. aeruginosa strain PAO1 was selected as the test strain. The results indicated that quercetin did not impact the growth of PAO1 as determined by MIC and growth curve analysis. However, this compound significantly inhibited (P < 0·05) biofilm formation and production of virulence factors including pyocyanin, protease and elastase at a lower concentration than those for most previously reported plant extracts and substances. Considering the central role of quorum sensing (QS) in the regulation of biofilm and virulence factor, we further detected the transcriptional changes associated with QS and found that the expression levels of lasI, lasR, rhlI and rhlR were significantly reduced (P < 0·05) by 34, 68, 57 and 50%, respectively, in response to 16 μg ml(-1) quercetin.

CONCLUSIONS

This study indicated that quercetin is an effective inhibitor of biofilm formation and virulence factors in Ps. aeruginosa.

SIGNIFICANCE AND IMPACT OF THE STUDY

This is the first study to demonstrate that quercetin is an effective inhibitor of QS, biofilm formation and virulence factors in Ps. aeruginosa. Furthermore, quercetin might have potential in fighting biofilm-related infections.

Asymmetric block copolymer membranes with ultrahigh porosity and hierarchical pore structure by plain solvent evaporation

Membranes with a hierarchical porous structure and an isoporous skin could be manufactured from a block copolymer blend by pure solvent evaporation (drying induced phase separation).

Direct conjugation of antibodies to the ZnS shell of quantum dots for FRET immunoassays with low picomolar detection limits

Direct conjugation of IgG, F(ab′)₂, and Fab antibodies to the ZnS shells of penicillamine-coated quantum dots for high-sensitivity FRET biosensing.

In situ precision electrospinning as an effective delivery technique for cyanoacrylate medical glue with high efficiency and low toxicity

The side effects or toxicity of cyanoacrylate used in vivo have been argued since its first application in wound closure. We propose an airflow-assisted in situ precision electrospinning apparatus as an applicator and make a detailed comparison with traditional spraying via in vitro and in vivo experiments. This novel method can not only improve operational performance and safety by precisely depositing cyanoacrylate fibers onto a wound, but significantly reduce the dosage of cyanoacrylate by almost 80%. A white blood cell count, liver function test and histological analysis prove that the in situ precision electrospinning applicator produces a better postoperative outcome, e.g., minor hepatocyte injury, moderate inflammation and the significant ability for liver regeneration. This in situ precision electrospinning method may thus dramatically broaden both civilian and military applications of cyanoacrylates.

Effects of dietary quercetin on performance and cytochrome P450 expression of the cotton bollworm, Helicoverpa armigera

Quercetin is ubiquitous in terrestrial plants. The cotton bollworm Helicoverpa armigera as a highly polyphagous insect has caused severe crop losses. Until now, interactions between this pest and quercetin are poorly understood at the biochemical and molecular levels. In this study, we investigated the in vivo effects of quercetin on performance of cotton bollworm and on cytochrome P450 (P450) expression. Deleterious effects of quercetin on the performance of the cotton bollworm, including growth, survival, pupation and adult emergence were observed after oral administration of 3 and 10 mg g(-1) quercetin to larvae since the third instar, whereas no significant toxic effect was found at 0.1 mg g(-1) quercetin treatment. Piperonyl butoxide treatment enhanced the toxicity of quercetin. In vitro metabolism studies showed that quercetin was rapidly transformed by gut enzymes of fifth instar larvae of the cotton bollworm. qRT-PCR results revealed that the effect of quercetin on P450 expression was tissue- and dose-specific. Quercetin regulated P450 expression in a mild manner, and it could serve as P450 inducer (CYP337B1, CYP6B6) or repressor (CYP337B1, CYP6B7, CYP6B27, CYP9A14, CYP6AE11, and CYP4M7). These findings are important for advancing our understanding of the biochemical and molecular response of insects to plant toxins and have implications for a smart pest control.

Single-cell transcriptomics reveals receptor transformations during olfactory neurogenesis

The sense of smell allows chemicals to be perceived as diverse scents. We used single-neuron RNA sequencing to explore the developmental mechanisms that shape this ability as nasal olfactory neurons mature in mice. Most mature neurons expressed only one of the ~1000 odorant receptor genes (Olfrs) available, and at a high level. However, many immature neurons expressed low levels of multiple Olfrs. Coexpressed Olfrs localized to overlapping zones of the nasal epithelium, suggesting regional biases, but not to single genomic loci. A single immature neuron could express Olfrs from up to seven different chromosomes. The mature state in which expression of Olfr genes is restricted to one per neuron emerges over a developmental progression that appears to be independent of neuronal activity involving sensory transduction molecules.