Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

Quasi-Matrix and Quasi-Inverse-Matrix Projective Synchronization for Delayed and Disturbed Fractional Order Neural Network

This paper is concerned with the quasi-matrix and quasi-inverse-matrix projective synchronization between two nonidentical delayed fractional order neural networks subjected to external disturbances. First, the definitions of quasi-matrix and quasi-inverse-matrix projective synchronization are given, respectively. Then, in order to realize two types of synchronization for delayed and disturbed fractional order neural networks, two sufficient conditions are established and proved by constructing appropriate Lyapunov function in combination with some fractional order differential inequalities. And their estimated synchronization error bound is obtained, which can be reduced to the required standard as small as what we need by selecting appropriate control parameters. Because of the generality of the proposed synchronization, choosing different projective matrix and controllers, the two synchronization types can be reduced to some common synchronization types for delayed fractional order neural networks, like quasi-complete synchronization, quasi-antisynchronization, quasi-projective synchronization, quasi-inverse projective synchronization, quasi-modified projective synchronization, quasi-inverse-modified projective synchronization, and so on. Finally, as applications, two numerical examples with simulations are employed to illustrate the efficiency and feasibility of the new synchronization analysis

Conservation analysis and pathogenicity prediction of mutant genes of ectodysplasin a

Abstract Background Hypohidrotic ectodermal dysplasia (HED) is a common recessive X-linked hereditary disease that affects the development of ectoderm. Gene mutations of ectodysplasin A (EDA) play key roles in process of this disease. In our preliminary study, three unknown mutation sites (c.878 T > G, c.663-697del and c.587-615del) were detected from the pedigrees of HED. Methods Conservation analysis of the related homologous proteins in 3 unknown EDA gene mutation sites was conducted using the University of California Santa Cruz (UCSC) Genome Browser database. SIFT and PolyPhen-2, the online gene function prediction software, were utilized to predict the pathogenicity of point mutation of c.878 T > G. Results All three unknown mutation sites were located in the highly-conserved region of EDA and possessed strong amino acid conservation among different species. In addition, the results of the pathogenicity prediction of point mutation of c.878 T > G by SIFT (P = 0.00) and PolyPhen-2 (S = 0.997) demonstrated that the mutation site had considerable pathogenicity theoretically. Conclusions The EDA mutations of c.878 T > G, c.663-697del and c.587-615del may be responsible for the pathogenesis of HED in their pedigrees

Phenylpropanoid glycoside inhibition of pepsin, trypsin and alpha-chymotrypsin enzyme activity in Kudingcha leaves from Ligustrum purpurascens

Natural Science Funding of Shenzhen University [801-00035911]; Natural Science Funding of Guangdong Province [S2012010008514, S2013010016791]; Shenzhen Funding for Technology Development Project [CXZZ20130320165017541, SW201110010, JCYJ20130326110246234]Phenylpropanoid glycosides (PPGs) are important ingredients in Kudingcha bitter tea from Ligustrum purpurascens, possessing many beneficial properties. Here, we investigated the effect of PPGs on the activity of the digestive enzymes pepsin, trypsin and alpha-chymotrypsin. Furthermore, we explored the interactions between PPGs and digestive enzymes by a multi-spectroscopic method and docking studies. PPGs could inhibit digestive enzyme activities with a non-competitive pattern of inhibition. PPGs may have a binding effect on these digestive enzymes, changing the polarity and the structure of enzymes, which results in decreased enzyme activity. This description of the effects of PPG inactivation of pepsin, trypsin and alpha-chymotrypsin helps reveal the potential anti-nutritional property of PPGs. Crown Copyright (C) 2013 Published by Elsevier Ltd. All rights reserved

Phenylpropanoid glycoside inhibition of pepsin, trypsin and α-chymotrypsin enzyme activity in Kudingcha leaves from Ligustrum purpurascens

Phenylpropanoid glycosides (PPGs) are important ingredients in Kudingcha bitter tea from Ligustrum purpurascens, possessing many beneficial properties. Here, we investigated the effect of PPGs on the activity of the digestive enzymes pepsin, trypsin and α-chymotrypsin. Furthermore, we explored the interactions between PPGs and digestive enzymes by a multi-spectroscopic method and docking studies. PPGs could inhibit digestive enzyme activities with a non-competitive pattern of inhibition. PPGs may have a binding effect on these digestive enzymes, changing the polarity and the structure of enzymes, which results in decreased enzyme activity. This description of the effects of PPG inactivation of pepsin, trypsin and α-chymotrypsin helps reveal the potential anti-nutritional property of PPGs. ? 2013

Use of the systemic inflammation response index (SIRI) as a novel prognostic marker for patients on peritoneal dialysis

Background The systemic inflammatory response index (SIRI), a novel inflammation maker, has proven to be associated with prognostic outcomes in various diseases. However, few studies have been conducted assessing how SIRI may influence outcomes of patients on peritoneal dialysis (PD). Herein, we assessed the predictive value of SIRI on mortality all-cause mortality, including cardiovascular disease (CVD) in PD patients.Methods A total of 646 PD patients were enrolled in this study. PD patients received regular PD treatments at the Zhujiang Hospital from 1 January 2011 to 31 December 2018. SIRI values could be computed as follows: neutrophil count × monocyte count/lymphocyte count. Patients were divided into two groups according to the median level of SIRI. Cox regression analysis and Kaplan–Meier methods were applied to analyze the relationship between SIRI and mortality outcomes in PD patients.Results During the median 31-month follow-up period, 97 (15.0%) PD patients died from all-causes, and 47 (49.0%) died of CVD. Kaplan–Meier analyses revealed that a high SIRI corresponded to the high mortality of all-cause deaths, including CVD (both p < 0.001) in patients on PD. After adjusting for potential confounders, the higher SIRI level was significantly associated with an increased all-cause mortality (HR: 2.007, 95% CI: 1.304–3.088, p = 0.002) and cardiovascular mortality (HR: 2.847, 95% CI: 1.445–5.608, p = 0.002).Conclusions SIRI was a promising predictor of mortality in PD patients, with a higher SIRI corresponding to increased risk of mortality

Evidence for Assimilatory Nitrate Reduction as a Previously Overlooked Pathway of Reactive Nitrogen Transformation in Estuarine Suspended Particulate Matter

Suspended particulate matter (SPM) contributes to the loss of reactive nitrogen (Nr) in estuarine ecosystems. Although denitrification and anaerobic ammonium oxidation in SPM compensate for the current imbalance of global nitrogen (N) inputs and sinks, it is largely unclear whether other pathways for Nr transformation exist in SPM. Here, we combined stable isotope measurements with metagenomics and metatranscriptomics to verify the occurrence of dissimilatory nitrate reduction to ammonium (DNRA) in the SPM of the Pearl River Estuary (PRE). Surprisingly, the conventional functional genes of DNRA (nirBD) were abundant and highly expressed in SPM, which was inconsistent with a low potential rate. Through taxonomic and comparative genomic analyses, we demonstrated that nitrite reductase (NirBD) in conjunction with assimilatory nitrate reductase (NasA) performed assimilatory nitrate reduction (ANR) in SPM, and diverse alpha- and gamma-proteobacterial lineages were identified as key active heterotrophic ANR bacteria. Moreover, ANR was predicted to have a relative higher occurrence than denitrification and DNRA in a survey of Nr transformation pathways in SPM across the PRE spanning 65 km. Collectively, this study characterizes a previously overlooked pathway of Nr transformation mediated by heterotrophic ANR bacteria in SPM and has important implications for our understanding of N cycling in estuaries.</p

Single-Cell Analysis of Human Retina Identifies Evolutionarily Conserved and Species-Specific Mechanisms Controlling Development.

The development of single-cell RNA sequencing (scRNA-seq) has allowed high-resolution analysis of cell-type diversity and transcriptional networks controlling cell-fate specification. To identify the transcriptional networks governing human retinal development, we performed scRNA-seq analysis on 16 time points from developing retina as well as four early stages of retinal organoid differentiation. We identified evolutionarily conserved patterns of gene expression during retinal progenitor maturation and specification of all seven major retinal cell types. Furthermore, we identified gene-expression differences between developing macula and periphery and between distinct populations of horizontal cells. We also identified species-specific patterns of gene expression during human and mouse retinal development. Finally, we identified an unexpected role for ATOH7 expression in regulation of photoreceptor specification during late retinogenesis. These results provide a roadmap to future studies of human retinal development and may help guide the design of cell-based therapies for treating retinal dystrophies