Diurnal patterns of growth and transient reserves of sink and source tissues are affected by cold nights in barley

Barley is described to mostly use sucrose for night carbon requirements. To understand how the transient carbon is accumulated and utilized in response to cold, barley plants were grown in a combination of cold days and/or nights. Both daytime and night cold reduced growth. Sucrose was the main carbohydrate supplying growth at night, representing 50–60% of the carbon consumed. Under warm days and nights, starch was the second contributor with 26% and malate the third with 15%. Under cold nights, the contribution of starch was severely reduced, due to an inhibition of its synthesis, including under warm days, and malate was the second contributor to C requirements with 24–28% of the total amount of carbon consumed. We propose that malate plays a critical role as an alternative carbon source to sucrose and starch in barley. Hexoses, malate, and sucrose mobilization and starch accumulation were affected in barley elf3 clock mutants, suggesting a clock regulation of their metabolism, without affecting growth and photosynthesis however. Altogether, our data suggest that the mobilization of sucrose and malate and/or barley growth machinery are sensitive to cold.     

Isolation of Arsenic Resistant and Arsenopyrite Oxidizing Acidithiobacillus Species from pH Neutral Colombian Mine Effluents

Abstract

Inactive mines provide a great source of bacterial diversity for studying acidophilic communities and their biotechnological applications, but prospecting of these anthropogenic environments in Colombia has been limited. Conventional microbiological methods were used to isolate acidophilic bacterial strains from effluents emanating from the Colombian gold mine ‘El Zancudo’ (Titiribí, Antioquia). Despite the drainage waters having circumneutral pH, all of the isolated strains were phylogenetically related to the extreme acidophile Acidithiobacillus genus. However, based upon 16S rRNA gene sequences the mesophilic sulfur-oxidizing indigenous strains could not be assigned to a species. Pure cultures were selected by screening in medium with soluble inorganic arsenic (III) and their mineral-oxidative activity was evaluated at 30?°C in Erlenmeyer flasks with arsenopyrite ore under rotary shaking conditions. The indigenous strains were able to catalyze arsenopyrite oxidation in a mixed culture with a pulp density of 10%, maintaining their growth in the presence of >80?mM leached arsenic. This research provides information regarding the isolation of arsenic resistant bacterial communities from neutral effluents from El Zancudo mine and the possibility of the isolated strains to be useful in the biooxidation pretreatment of refractory gold-bearing arsenopyrite ores and concentrates.     

Exposure to nectar-realistic sugar concentrations negatively impacts the ability of the trypanosome parasite (Crithidia bombi) to infect its bumblebee host

1. The ideal conditions for a parasite are typically found with its preferred host. However, prior to transmission to a naïve host and successful infection, a parasite may have to withstand extrinsic environmental conditions. Some parasites have adapted to time away from hosts, for example, by co-opting vectors or by having drought-resistant growth stages. However, other parasites may have no obvious adaptations to persist during prolonged transmission cycles. Consequently, the environment may detrimentally impact parasite fitness and ultimately epidemiology. 2. Here, we investigate the impact of nectar-realistic sugar concentrations on the ability of the trypanosome parasite Crithidia bombi, which may be transmitted between conspecifics at flowers, to infect its bumblebee host Bombus terrestris and to reproduce during the infection (parasitaemia). Our results show, following 30 min exposure to our experimental nectars that as sugar concentration increases, infection prevalence and parasitaemia decrease. This is likely due to the increased osmotic stress C. bombi experiences in high sugar, aqueous environments. 3. Consequently, if C. bombi transmission is facilitated by nectar or a high-sugar environment, it may have a negative impact on parasite fitness.     

Divergence and support among slightly suboptimal likelihood gene trees

Contemporary phylogenomic studies frequently incorporate two-step coalescent analyses wherein the first step is to infer individual-gene trees, generally using maximum-likelihood implemented in the popular programs PhyML or RAxML . Four concerns with this approach are that these programs only present a single fully resolved gene tree to the user despite potential for ambiguous support, insufficient phylogenetic signal to fully resolve each gene tree, inexact computer arithmetic affecting the reported likelihood of gene trees, and an exclusive focus on the most likely tree while ignoring trees that are only slightly suboptimal or within the error tolerance. Taken together, these four concerns are sufficient for RAxML and Phy ML users to be suspicious of the resulting (perhaps over-resolved) gene-tree topologies and (perhaps unjustifiably high) bootstrap support for individual clades. In this study, we sought to determine how frequently these concerns apply in practice to contemporary phylogenomic studies that use RAxML for gene-tree inference. We did so by re-analyzing 100 genes from each of ten studies that, taken together, are representative of many empirical phylogenomic studies. Our seven findings are as follows. First, the few search replicates that are frequently applied in phylogenomic studies are generally insufficient to find the optimal gene-tree topology. Second, there is often more topological variation among slightly suboptimal gene trees relative to the best-reported tree than can be safely ignored. Third, the Shimodaira–Hasegawa-like approximate likelihood ratio test is highly effective at identifying dubiously supported clades and outperforms the alternative approaches of relying on bootstrap support or collapsing minimum-length branches. Fourth, the bootstrap can, but rarely does, indicate high support for clades that are not supported amongst slightly suboptimal trees. Fifth, increasing the accuracy by which RA xML optimizes model-parameter values generally has a nominal effect on selection of optimal trees. Sixth, tree searches using the GTRCAT model were generally less effective at finding optimal known trees than those using the GTRGAMMA model. Seventh, choice of gene-tree sampling strategy can affect inferred coalescent branch lengths, species-tree topology and branch support.     

Immunodiagnostic Assays for the Investigation of Fungal Outbreaks

Mycopathologia - Fungal pathogens can affect humans, animals, and plants, and they can be found in the environment or as part of the host microbiome. Fungal diseases present a broad clinical...     

The incidence of turnip yellows virus in oilseed rape crops (Brassica napus L.) in three different regions of England over three consecutive growing seasons and the relationship with the abundance of flying Myzus persicae

Turnip yellows virus (TuYV) is the most important virus infecting oilseed rape in the United Kingdom. The incidence and spatial distribution of TuYV in winter oilseed rape (WOSR) crops in three regions of England were determined over three growing seasons. Leaf samples were collected from three fields in each region, in autumn (November–December) and spring (April) of the three crop seasons and tested for virus presence by enzyme-linked immunosorbent assay. Infection was detected in all fields except one. Higher TuYV incidences were recorded in 2007–2008 (≤89%) and 2009–2010 (≤100%) crop seasons than in 2008–2009 (≤24%). Highest incidences were recorded in Lincolnshire (≤100%), followed by Warwickshire (≤88%), with lowest incidences in Yorkshire (1–74%). There was a significant increase in incidence detected between autumn and spring sampling in eight fields, a significant decrease in one field and no significant change in 18 fields. Rothamsted Insect Survey suction trap data for the aphid Myzus persicae in Lincolnshire, Warwickshire and Yorkshire revealed two peaks of flight activity in most years (2007–2009). The second peak (September–November) coincided with emergence of WOSR. The highest cumulative (August–November) trap catches in the three regions during the three crop seasons occurred in Lincolnshire and the lowest in Yorkshire; catches in autumn 2009 were highest and lowest in autumn 2008. Regression analysis revealed a highly significant association between the cumulative numbers of M. persicae caught in the suction traps closest to the crops between August and November each year and the incidence of TuYV detected in the WOSR crops in the autumn of each year. Results are discussed in the light of factors affecting the spread of TuYV and future possibilities for control.     

One-step targeted maximum likelihood estimation for time-to-event outcomes

Researchers in observational survival analysis are interested in not only estimating survival curve nonparametrically but also having statistical inference for the parameter. We consider right-censored failure time data where we observe n independent and identically distributed observations of a vector random variable consisting of baseline covariates, a binary treatment at baseline, a survival time subject to right censoring, and the censoring indicator. We assume the baseline covariates are allowed to affect the treatment and censoring so that an estimator that ignores covariate information would be inconsistent. The goal is to use these data to estimate the counterfactual average survival curve of the population if all subjects are assigned the same treatment at baseline. Existing observational survival analysis methods do not result in monotone survival curve estimators, which is undesirable and may lose efficiency by not constraining the shape of the estimator using the prior knowledge of the estimand. In this paper, we present a one-step Targeted Maximum Likelihood Estimator (TMLE) for estimating the counterfactual average survival curve. We show that this new TMLE can be executed via recursion in small local updates. We demonstrate the finite sample performance of this one-step TMLE in simulations and an application to a monoclonal gammopathy data.     

Improved protein A resin for antibody capture in a continuous countercurrent tangential chromatography system

Continuous countercurrent tangential chromatography (CCTC) enables steady-state continuous bioprocessing with low-pressure operation and high productivity. CCTC has been applied to initial capture of monoclonal antibodies (mAb) from clarified cell culture harvest and postcapture polishing of mAb; however, these studies were performed with commercial chromatography resins designed for conventional column chromatography. In this study, a small particle size prototype agarose resin (20–25 µm) with lower cross-linking was co-developed with industrial partner Purolite and tested with CCTC. Due to increased binding capacity and faster kinetics, the resulting CCTC process showed more than a 2X increase in productivity, and a 2X reduction in buffer consumption over commercial protein A resins used in previous CCTC studies, as well as more than a 10X productivity increase versus conventional column operation. Single-pass tangential flow filtration was integrated with the CCTC system, enabling simple control of eluate concentration. A scale-up exercise was conducted to provide a quantitative comparison of CCTC and batch column chromatography. These results clearly demonstrate opportunities for using otherwise unpackable soft small particle size resins with CCTC as the core of a continuous bioprocessing platform.     

Heterogeneous diffusion in aerobic granular sludge

Aerobic granular sludge (AGS) technology allows simultaneous nitrogen, phosphorus, and carbon removal in compact wastewater treatment processes. To operate, design, and model AGS reactors, it is essential to properly understand the diffusive transport within the granules. In this study, diffusive mass transfer within full-scale and lab-scale AGS was characterized with nuclear magnetic resonance (NMR) methods. Self-diffusion coefficients of water inside the granules were determined with pulsed-field gradient NMR, while the granule structure was visualized with NMR imaging. A reaction-diffusion granule-scale model was set up to evaluate the impact of heterogeneous diffusion on granule performance. The self-diffusion coefficient of water in AGS was ∼70% of the self-diffusion coefficient of free water. There was no significant difference between self-diffusion in AGS from full-scale treatment plants and from lab-scale reactors. The results of the model showed that diffusional heterogeneity did not lead to a major change of flux into the granule (<1%). This study shows that differences between granular sludges and heterogeneity within granules have little impact on the kinetic properties of AGS. Thus, a relatively simple approach is sufficient to describe mass transport by diffusion into the granules.