Comprehensive evaluation of methods for differential expression analysis of metatranscriptomics data.

Understanding the function of the human microbiome is important but the development of statistical methods specifically for the microbial gene expression (i.e. metatranscriptomics) is in its infancy. Many currently employed differential expression analysis methods have been designed for different data types and have not been evaluated in metatranscriptomics settings. To address this gap, we undertook a comprehensive evaluation and benchmarking of 10 differential analysis methods for metatranscriptomics data. We used a combination of real and simulated data to evaluate performance (i.e. type I error, false discovery rate and sensitivity) of the following methods: log-normal (LN), logistic-beta (LB), MAST, DESeq2, metagenomeSeq, ANCOM-BC, LEfSe, ALDEx2, Kruskal-Wallis and two-part Kruskal-Wallis. The simulation was informed by supragingival biofilm microbiome data from 300 preschool-age children enrolled in a study of childhood dental disease (early childhood caries, ECC), whereas validations were sought in two additional datasets from the ECC study and an inflammatory bowel disease study. The LB test showed the highest sensitivity in both small and large samples and reasonably controlled type I error. Contrarily, MAST was hampered by inflated type I error. Upon application of the LN and LB tests in the ECC study, we found that genes C8PHV7 and C8PEV7, harbored by the lactate-producing Campylobacter gracilis, had the strongest association with childhood dental disease. This comprehensive model evaluation offers practical guidance for selection of appropriate methods for rigorous analyses of differential expression in metatranscriptomics. Selection of an optimal method increases the possibility of detecting true signals while minimizing the chance of claiming false ones.

Nitrogen-Doped Carbon Quantum Dots from Poly(ethyleneimine) for Optical Dual-Mode Determination of Cu2+ and l-Cysteine and Their Logic Gate Operation.

In this work, nitrogen-doped carbon quantum dots from poly(ethyleneimine) (PQDs) were synthesized by a low-cost and facile one-step hydrothermal method without other reagents. A quantum yield (QY) of up to 23.2% with maximum emission at 460 nm under an excitation wavelength of 340 nm was ascribed to the high nitrogen doping (20.59%). The PQDs selectively form a blue complex with Cu2+ accompanied by strong quenching of the fluorescence emission. Meanwhile, the PQD-Cu2+ complex exhibited selective fluorescence recovery and color disappearance on exposure to l-cysteine (Cys). The electron transfer from amino or oxygen groups on the PQDs to Cu2+ leads to fluorescence quenching, and a chromogenic reaction of the cuprammonium complex results in a color change. The strong affinity between Cys and Cu2+ causes the detachment of Cu2+ from the surface of PQDs, so the color of the solution disappears and the fluorescence of PQDs recovers. Under the optimized condition, the proposed sensor was applied to detect Cu2+ in the linear range of 0-280 µM. A detection limit of 4.75 µM is achieved using fluorescence spectroscopy and 4.74 µM by monitoring the absorbance variation at 272 nm. For Cys detection, the linear range of 0-800 µM with detection limits of 28.11 µM (fluorescence determination) and 19.74 µM (peak shift determination at 272 nm) was obtained. Meanwhile, the PQD-Cu2+ system exhibits distinguishable responses to other biothiols such as l-glutathione (GSH) and dl-homocysteine (Hcy). Based on the multimode signals, an "AND" logic gate was constructed successfully. Interestingly, besides Cu2+, Fe3+ can also quench the fluorescence of PQDs and the PQD-Fe3+ system exhibits superior selectivity for Cys detection. Most importantly, the proposed assay is not only simple, cheap, and stable but also suitable for detecting Cu2+ and Cys in some real samples.

Hydrogen peroxide primes heart regeneration with a derepression mechanism.

While the adult human heart has very limited regenerative potential, the adult zebrafish heart can fully regenerate after 20% ventricular resection. Although previous reports suggest that developmental signaling pathways such as FGF and PDGF are reused in adult heart regeneration, the underlying intracellular mechanisms remain largely unknown. Here we show that H2O2 acts as a novel epicardial and myocardial signal to prime the heart for regeneration in adult zebrafish. Live imaging of intact hearts revealed highly localized H2O2 (~30 µM) production in the epicardium and adjacent compact myocardium at the resection site. Decreasing H2O2 formation with the Duox inhibitors diphenyleneiodonium (DPI) or apocynin, or scavenging H2O2 by catalase overexpression markedly impaired cardiac regeneration while exogenous H2O2 rescued the inhibitory effects of DPI on cardiac regeneration, indicating that H2O2 is an essential and sufficient signal in this process. Mechanistically, elevated H2O2 destabilized the redox-sensitive phosphatase Dusp6 and hence increased the phosphorylation of Erk1/2. The Dusp6 inhibitor BCI achieved similar pro-regenerative effects while transgenic overexpression of dusp6 impaired cardiac regeneration. H2O2 plays a dual role in recruiting immune cells and promoting heart regeneration through two relatively independent pathways. We conclude that H2O2 potentially generated from Duox/Nox2 promotes heart regeneration in zebrafish by unleashing MAP kinase signaling through a derepression mechanism involving Dusp6.