Integrating batch marks and radio tags to estimate the size of a closed population with a movement model

Movement models require individually identifiable marks to estimate the movement rates among strata. But they are relatively expensive to apply and monitor. Batch marks can be readily applied, but individual animal movements cannot be identified. We describe a method to estimate population size in a stratified population when movement takes place among strata and animals are marked with a combination of batch and individually identifiable tags. A hierarchical model with Bayesian inference is developed that pools information across segments on the detection efficiency based on radio‐tagged fish and also uses the movement of the radio‐tagged fish to impute the movement of the batch‐marked fish to provide estimates of the population size on a segment and river level. The batch marks provide important information to help estimate the movement rates, but contribute little to the overall estimate of the population size. In this case, the approximate equal catchability among strata in either sample obviates the need for stratification.     

Growth and toxin production in batch cultures of a marine dinoflagellate Alexandrium tamarense HK9301 isolated from the South China Sea

Nutritional and environmental conditions were characterized for a batch culture of the marine dinoflagellate Alexandrium tamarense HK9301 isolated from the South China Sea for its growth (cells ml⁻¹), cellular toxin content (Qt in fmol cell⁻¹) and toxin composition (mol%). Under a nutrient replete condition, Qt increased with cell growth and peaked at the late stationary phase. Toxin content increased with the nitrate concentration in the culture while it reached a maximum at 5 μM phosphate. When nitrate was replaced with ammonia, Qt decreased by 4.5-fold. Salinity and light intensity were important factors affecting Qt. The latter increased two-fold over the range of salinity from 15 to 30‰, while decreased 38% as light intensity increased from 80 to 220 μE m⁻² s⁻¹. Toxin composition varied with growth phase and culture conditions. In nutrient replete cultures, toxin composition varied greatly in the early growth phase (first 3 days) and then C1/C2, C3/C4 and GTX1 remained relatively constant while GTX4 increased from 32 to 46% and GTX5 decreased from 28 to 15%. In general, the composition of GTXs was affected in a much greater extent than C toxins by changes in nutrient conditions, salinity and light intensity. This is especially true with GTX4 and GTX5. These data indicate that the cellular toxin content and toxin composition of A. tamarense HK9301 are not constant, but that they vary with growth phase and culture conditions. Use of toxin composition to identify a toxigenic marine dinoflagellate is not always valid. The data also reveal that high salinity and low light intensity, together with high nitrate and low phosphate concentrations, would favor toxin production by this species.     

Comparative proteome analysis of robust <Emphasis Type="Italic">Saccharomyces cerevisiae</Emphasis> insights into industrial continuous and batch fermentation

A robust Saccharomyces cerevisiae strain has been widely applied in continuous and batch/fed-batch industrial fermentation. However, little is known about the molecular basis of fermentative behavior of this strain in the two realistic fermentation processes. In this paper, we presented comparative proteomic profiling of the industrial yeast in the industrial fermentation processes. The expression levels of most identified protein were closely interrelated with the different stages of fermentation processes. Our results indicate that, among the 47 identified protein spots, 17 of them belonging to 12 enzymes were involved in pentose phosphate, glycolysis, and gluconeogenesis pathways and glycerol biosynthetic process, indicating that a number of pathways will need to be inactivated to improve ethanol production. The differential expressions of eight oxidative response and heat-shock proteins were also identified, suggesting that it is necessary to keep the correct cellular redox or osmotic state in the two industrial fermentation processes. Moreover, there are significant differences in changes of protein levels between the two industrial fermentation processes, especially these proteins associated with the glycolysis and gluconeogenesis pathways. These findings provide a molecular understanding of physiological adaptation of industrial strain for optimizing the performance of industrial bioethanol fermentation. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Targeted deletion of the <Emphasis Type="Italic">uvrBA</Emphasis> operon and biological containment in the industrially important <Emphasis Type="Italic">Bacillus licheniformis</Emphasis>

From a Bacillus licheniformis wild type as well as a defined asporogenous derivative, stable UV hypersensitive mutants were generated by targeted deletion of the uvrBA operon, encoding highly conserved key components of the nucleotide excision repair. Comparative studies, which included the respective parental strains, revealed no negative side effects of the deletion, neither on enzyme secretion nor on vegetative propagation. Thus, the uvrBA locus proved to be a useful deletion target for achieving biological containment in this industrially exploited bacterium. In contrast to recA mutants, which also display UV hypersensitivity, further strain development via homologous recombination techniques will be still possible in such uvr mutants.     

Decolorization of Acid Red 27 and Reactive Red 2 by <Emphasis Type="Italic">Enterococcus faecalis</Emphasis> under a batch system

The objectives of this study were to investigate: (1) the capacity of Enterococcus faecalis on the decolorization of the azo dyes Acid Red 27 and Reactive Red 2; and (2) the growth characteristics of E. faecalis on those dyes. E. faecalis was able to decolorize Acid Red 27 and Reactive Red 2 effectively. High decolorization efficiency (95–100%) was achieved within 3 h of incubation for Acid Red 27, and 12 h for Reactive Red 2, at room temperature, neutral pH, static and non-aerated condition. Growth characteristics of E. faecalis on azo dyes, which were indicated by cell growth rate, biomass production, and growth yield, was worse than the control. E. faecalis grew better on Acid Red 27 rather than Reactive Red 2.     

Influence of N/P ratio on competitive abilities for nitrogen and phosphorus by <Emphasis Type="Italic">Microcystis aeruginosa</Emphasis> and <Emphasis Type="Italic">Aulacoseira distans</Emphasis>

Microcystis aeruginosa and Aulacoseira distans strains were grown in batch cultures to investigate the consequences of N/P ratio on the growth of these species and on their abilities to take up nitrogen and phosphorus. N/P ratio did not influence the growth rates, which were similar under all the experimental conditions. However, exponential growth lasted longer in Microcystis than in Aulacoseira, especially under low N/P ratio conditions. Distinct patterns of nutrient uptake for Aulacoseira and Microcystis were observed. N-uptake was higher in Microcystis, but not influenced by N/P ratio. However, the amount absorbed was proportional to the concentration in the culture medium for both strains studied. Although Microcystis showed lower uptake of N per biomass unit, a greater yield of Microcystis growth relative to the diatom was observed. This could have resulted from its ability to produce biomass using less nitrogen per unit of biomass. A variation of N/P ratio in the culture medium during the growth of both species was observed. This owed to the uptake of nutrients, with Microcystis showing greater potential than Aulacoseira to influence the N/P ratio. Thus, in contrast to what has been stated in the literature, our results indicated that a low N/P ratio could be a consequence of the capacities and rates of cyanobacterial uptake of nitrogen and phosphorus.     

单细胞转录组数据批次效应评测的研究进展

单细胞转录组测序(Single cell RNA sequencing,ScRNA seq)是一种变革性的生物技术,以前所未有的高分辨率来解析组织复杂性,解决了普通转录组测序(Bulk RNA sequencing)无法回答的问题。但单细胞数据的高通量及复杂性给分析带来极大难度,批次效应(Batch effects,BEs)的处理便是主要挑战之一。批次效应是高通量生物数据分析中的技术性偏倚,其来源及处理具有高复杂性和研究依赖性。根据组织类型、测序技术及实验设计的不同,测序数据需采用不同的评估、分析、测量及处置流程来实现有效的批次效应处理。评测批次效应在单细胞数据分析中极易被忽略,但却有助于判断批次效应的来源、对数据变异的解释度、对数据分析结果的影响度及处理方法,是有效处理批次效应的基础。因此,本篇综述聚焦单细胞转录组数据的批次效应,分别论述批次效应的概念、与普通转录组批次效应的区别、评测方法及面临的挑战,并对未来发展做出展望。     

Degradation of ferrous(II) cyanide complex ions by Pseudomonas fluorescens

Degradation of ferrous(II) cyanide complex (ferrocyanide) ions by free cells of P. fluorescens in the presence of glucose and dissolved oxygen was investigated as a function of initial pH, initial ferrocyanide and glucose concentrations and aeration rate in a batch fermenter. The microorganism used the ferrocyanide ions as the sole source of nitrogen. The ferrocyanide biodegradation rate was 30.7 mg g⁻¹ h⁻¹ under the conditions of initial pH: 5, stirring rate: 150 rpm, aeration rate: 0.15 vvm, initial ferrous(II) cyanide complex ion and glucose concentrations: 100 mg l⁻¹ and 0.465 g l⁻¹, respectively. The culture utilized glucose as the main substrate following the non-competitive toxic component inhibition model in the presence of 100 mg l⁻¹ initial ferrous(II) cyanide complex ion concentration. The inhibition of ferrous(II) cyanide complex ions as a secondary substrate began at very low concentrations. A mathematical model, based on non-competitive substrate inhibition was used to describe the inhibitory effect of ferrous(II) cyanide complex ions on the growth of microorganism and the best fitted model parameters were determined by non-linear regression techniques.