Arbuscular mycorrhizal fungi in a wetland constructed for benzene‐, methyl tert‐butyl ether‐ and ammonia‐contaminated groundwater bioremediation

Arbuscular mycorrhizal fungi (AMF), which are present in most natural environments, have demonstrated capacity to promote biodegradation of organic pollutants in the greenhouse. However, it is not certain whether AMF can spontaneously establish in phytoremediation systems constructed to decontaminate groundwater, because of the unusual conditions during the construction and operation of such systems. To assess this possibility, root samples from a wetland constructed for the phytoremediation of groundwater contaminated with benzene, methyl tert‐butyl ether and ammonia were analysed. Substantial AMF colonization was observed in plant roots sampled close to the inlet of a basin filled with fine gravel and planted with Phragmites australis. In addition, analysis of a fragment of the nuclear large ribosomal subunit, amplified by nested PCR, revealed the presence of AMF molecular operational taxonomic units closely related to Funneliformis mosseae and Rhizophagus irregularis in the samples. These findings demonstrate the capacity of generalist AMF strains to establish spontaneously, rapidly and extensively in groundwater bioremediation technical installations.     

Quantitation and characterization of process impurities and extractables in protein‐containing solutions using proton NMR as a general tool

The ability to detect and quantitate a variety of components in solution has become increasingly important in carrying out efficient and rigorous validation studies for biopharmaceutical manufacturing processes. Here, we demonstrate the general applicability of NMR spectroscopy for the identification and quantitation of leachables and other impurities in protein‐based drugs, at low levels previously unattainable in protein‐containing solutions. With improved NMR technology (i.e., CryoProbes) and the application of a Carr‐Purcell‐Meiboom‐Gill pulse sequence (CPMG) to attenuate protein signals, we have been able to use NMR to quantify impurities in a protein‐based biopharmaceutical product at ～1 μg mL^?1. The data indicate that NMR spectra can be used to quantitate a range of impurities, from small molecule components to higher molecular weight leachables, without removing protein from solution. Furthermore, quantitation of impurities by NMR is reliable and accurate enough for biopharmaceutical process validation, even for high molecular weight extractables whose structures are not precisely known. © 2012 American Institute of Chemical Engineers Biotechnol. Prog., 2012     

Home‐range size in large‐bodied carnivores as a model for predicting neandertal territory size

Adult human foragers expend roughly 30–60 kcal per km in unburdened walking at optimal speeds.^1,2 In the context of foraging rounds and residential moves, they may routinely travel distances of 50–70 km per week, often while carrying loads.³ Movement on the landscape, then, is arguably the single most expensive item in the activity budgets of hunter‐gatherers. Mobility costs may have been greater still for Neandertals. They had stocky, short‐limbed physiques that were energetically costly to move⁴ and lived in relatively unproductive Pleistocene environments⁵ that may have required greater movement to deal with problems of biodepletion and resource patchiness.⁶ But just how mobile were the Neandertals?     

Alkane‐degrading properties of Dietzia sp. H0B,a key player in the Prestige oil spill biodegradation (NW Spain)

Aims: Investigation of the alkane‐degrading properties of Dietzia sp. H0B, one of the isolated Corynebacterineae strains that became dominant after the Prestige oil spill. Methods and Results: Using molecular and chemical analyses, the alkane‐degrading properties of strain Dietzia sp. H0B were analysed. This Grampositive isolate was able to grow on n‐alkanes ranging from C₁₂ to C₃₈ and branched alkanes (pristane and phytane). 8‐Hexadecene was detected as an intermediate of hexadecane degradation by Dietzia H0B, suggesting a novel alkane‐degrading pathway in this strain. Three putative alkane hydroxylase genes (one alkB homologue and two CYP153 gene homologues of cytochrome P450 family) were PCR‐amplified from Dietzia H0B and differed from previously known hydroxylase genes, which might be related to the novel degrading activity observed on Dietzia H0B. The alkane degradation activity and the alkB and CYP153 gene expression were observed constitutively regardless of the presence of the substrate, suggesting additional, novel pathways for alkane degradation. Conclusions: The results from this study suggest novel alkane‐degrading pathways in Dietzia H0B and a genetic background coding for two different putative oil‐degrading enzymes, which is mostly unexplored and worth to be subject of further functional analysis. Significance and Impact of the Study: This study increases the scarce information available about the genetic background of alkane degradation in genus Dietzia and suggests new pathways and novel expression mechanisms of alkane degradation.     

Co‐recruitment analysis of the CBL and CBLB signalosomes in primary T cells identifies CD5 as a key regulator of TCR‐induced ubiquitylation

T‐cell receptor (TCR) signaling is essential for the function of T cells and negatively regulated by the E3 ubiquitin–protein ligases CBL and CBLB. Here, we combined mouse genetics and affinity purification coupled to quantitative mass spectrometry to monitor the dynamics of the CBL and CBLB signaling complexes that assemble in normal T cells over 600 seconds of TCR stimulation. We identify most previously known CBL and CBLB interacting partners, as well as a majority of proteins that have not yet been implicated in those signaling complexes. We exploit correlations in protein association with CBL and CBLB as a function of time of TCR stimulation for predicting the occurrence of direct physical association between them. By combining co‐recruitment analysis with biochemical analysis, we demonstrated that the CD5 transmembrane receptor constitutes a key scaffold for CBL‐ and CBLB‐mediated ubiquitylation following TCR engagement. Our results offer an integrated view of the CBL and CBLB signaling complexes induced by TCR stimulation and provide a molecular basis for their negative regulatory function in normal T cells.     

Monooxygenation of an aromatic ring by F43W/H64D/V68I myoglobin mutant and hydrogen peroxide. Myoglobin mutants as a model for P450 hydroxylation chemistry

Myoglobin (Mb) is used as a model system for other heme proteins and the reactions they catalyze. The latest novel function to be proposed for myoglobin is a P450 type hydroxylation activity of aromatic carbons (Watanabe, Y., and Ueno, T. (2003) Bull. Chem. Soc. Jpn. 76, 1309-1322). Because Mb does not contain a specific substrate binding site for aromatic compounds near the heme, an engineered tryptophan in the heme pocket was used to model P450 hydroxylation of aromatic compounds. The monooxygenation product was not previously isolated because of rapid subsequent oxidation steps (Hara, I., Ueno, T., Ozaki, S., Itoh, S., Lee, K., Ueyama, N., and Watanabe, Y. (2001) J. Biol. Chem. 276, 36067-36070). In this work, a Mb variant (F43W/H64D/V68I) is used to characterize the monooxygenated intermediate. A modified (+16 Da) species forms upon the addition of 1 eq of H2O2. This product was digested with chymotrypsin, and the modified peptide fragments were isolated and characterized as 6-hydroxytryptophan using matrix-assisted laser desorption ionization time-of-flight tandem mass spectroscopy and 1H NMR. This engineered Mb variant represents the first enzyme to preferentially hydroxylate the indole side chain of Trp at the C6 position. Finally, heme extraction was used to demonstrate that both the formation of the 6-hydroxytryptophan intermediate (+16 Da) and subsequent oxidation to form the +30 Da final product are catalyzed by the heme cofactor, most probably via the compound I intermediate. These results provide insight into the mechanism of hydroxylation of aromatic carbons by heme proteins, demonstrating that non-thiolate-ligated heme enzymes can perform this function. This establishes Mb compound I as a model for P450 type aromatic hydroxylation chemistry.     

Nitrogen cycling and dynamics in a macrophyte‐rich stream as determined by a release

1. A tracer release study was conducted in a macrophyte‐rich stream, the River Lilleaa in Denmark. The objectives of the study were to compare uptake rates per unit area of by primary producers and consumers in macrophyte and non‐macrophyte habitats, estimate whole‐stream uptake rates of and compare this to other stream types, and identify the pathways and estimate the rate at which enters the food web in macrophyte and non‐macrophyte habitats. 2. Macrophyte habitats had four times higher primary uptake rates and an equal uptake rate by primary consumers per unit habitat area as compared to non‐macrophyte habitats. These rates represent the lower limit of potential macrophyte effects because the rates will be highly dependent on macrophyte bed height and mean bed height in the River Lilleaa was low compared to typical bed heights in many lowland streams. Epiphytes accounted for 30% of primary uptake in macrophyte habitats, illustrating a strong indirect effect of macrophytes as habitat for epiphytes. N flux per unit habitat area from primary uptake compartments to primary consumers was four times lower in macrophyte habitats compared to non‐macrophyte habitats, reflecting much greater biomass accrual in macrophyte habitats. Thus, we did not find higher N flux from macrophyte habitats to primary consumers compared to non‐macrophyte habitats. 3. Whole‐stream uptake rate was 447 mgN m^?2 day^?1. On a habitat‐weighted basis, fine benthic organic matter (FBOM) accounted for 72% of the whole‐stream uptake rate, and macrophytes and epiphytes accounted for 19 and 8%, respectively. 4. We had expected a priori relatively high whole‐stream N uptake in our study stream compared to other stream types mainly due to generally high biomass and the macrophyte’s role as habitat for autotrophic and heterotrophic organisms, but our results did not confirm this. In comparison with other release study streams, we conclude that nutrient concentration is the overall controlling factor for N uptake rates across streams, mostly as a result of high biomass of primary uptake compartments in streams with high nutrient concentrations in general and not in macrophyte streams in particular. 5. Our results indicate that macrophytes play an important role in the longer‐term retention of N and thus a decrease in net downstream transport during the growing season compared to streams without macrophytes, through direct and indirect effects on the stream reach. Direct effects are high uptake efficiency, low turnover rate (partly due to no direct feeding on macrophytes) and high longevity. An indirect effect is increased sedimentation of FBOM in macrophytes compared to non‐macrophyte habitats and streams which possibly also increase denitrification. Increased retention with macrophyte presence would decrease downstream transport during the growing season and thus the N loading on downstream ecosystems.     

Trait‐mediated indirect interactions in a marine intertidal system as quantified by functional responses

Studies of trait‐mediated indirect interactions (TMIIs) typically focus on effects higher predators have on per capita consumption by intermediate consumers of a third, basal prey resource. TMIIs are usually evidenced by changes in feeding rates of intermediate consumers and/or differences in densities of this third species. However, understanding and predicting effects of TMIIs on population stability of such basal species requires examination of the type and magnitude of the functional responses exhibited towards them. Here, in a marine intertidal system consisting of a higher‐order fish predator, the shanny Lipophrys pholis, an intermediate predator, the amphipod Echinogammarus marinus, and a basal prey resource, the isopod Jaera nordmanni, we detected TMIIs, demonstrating the importance of habitat complexity in such interactions, by deriving functional responses and exploring consequences for prey population stability. Echinogammarus marinus reacted to fish predator diet cues by reducing activity, a typical anti‐predator response, but did not alter habitat use. Basal prey, Jaera nordmanni, did not respond to fish diet cues with respect to activity, distribution or aggregation behaviour. Echinogammarus marinus exhibited type II functional responses towards J. nordmanni in simple habitat, but type III functional responses in complex habitat. However, while predator cue decreased the magnitude of the type II functional response in simple habitat, it increased the magnitude of the type III functional response in complex habitat. These findings indicate that, in simple habitats, TMIIs may drive down consumption rates within type II responses, however, this interaction may remain de‐stabilising for prey populations. Conversely, in complex habitats, TMIIs may strengthen regulatory influences of intermediate consumers on prey populations, whilst potentially maintaining prey population stability. We thus highlight that TMIIs can have unexpected and complex ramifications throughout communities, but can be unravelled by considering effects on intermediate predator functional response types and magnitudes. Synthesis Higher‐order predators and habitat complexity can influence behaviour of intermediate species, affecting their consumption of prey through trait‐mediated indirect interactions (TMIIs). However, it is not clear how these factors interact to determine prey population stability. Using functional responses (FRs), relating predator consumption to prey density, we detected TMIIs in a marine system. In simple habitats, TMIIs reduced consumption rates, but FRs remained de‐stabilising for prey populations. In complex habitats, TMIIs strengthened prey regulation with population stabilizing FRs. We thus demonstrate that FRs can assess interactions of environmental and biological cues that result in complex and unexpected outcomes for prey populations.     

Temporal dynamics of soil organic carbon after land‐use change in the temperate zone – carbon response functions as a model approach

Land‐use change (LUC) is a major driving factor for the balance of soil organic carbon (SOC) stocks and the global carbon cycle. The temporal dynamic of SOC after LUC is especially important in temperate systems with a long reaction time. On the basis of 95 compiled studies covering 322 sites in the temperate zone, carbon response functions (CRFs) were derived to model the temporal dynamic of SOC after five different LUC types (mean soil depth of 30±6 cm). Grassland establishment caused a long lasting carbon sink with a relative stock change of 128±23% and afforestation on former cropland a sink of 116±54%, 100 years after LUC (mean±95% confidence interval). No new equilibrium was reached within 120 years. In contrast, there was no SOC sink following afforestation of grasslands and 75% of all observations showed SOC losses, even after 100 years. Only in the forest floor, there was carbon accumulation of 0.38±0.04 Mg ha^?1 yr^?1 in afforestations adding up to 38±4 Mg ha^?1 labile carbon after 100 years. Carbon loss after deforestation (?32±20%) and grassland conversion to cropland (?36±5%), was rapid with a new SOC equilibrium being reached after 23 and 17 years, respectively. The change rate of SOC increased with temperature and precipitation but decreased with soil depth and clay content. Subsoil SOC changes followed the trend of the topsoil SOC changes but were smaller (25±5% of the total SOC changes) and with a high uncertainty due to a limited number of datasets. As a simple and robust model approach, the developed CRFs provide an easily applicable tool to estimate SOC stock changes after LUC to improve greenhouse gas reporting in the framework of UNFCCC.     

Belly up: Reduced crevice accessibility as a cost of reproduction caused by increased girth in a rock‐using lizard

Costs of reproduction are any aspect of current reproduction that has the potential to reduce survivorship or reproductive output, and may include physiological costs or increased risks. Females of many species experience increased body mass, and increased girth, when gravid. Increased body mass reduces running speed and increases the cost of locomotion during pregnancy, but few studies have examined the cost of increased girth. If increased girth of gravid females reduces access to shelter from predators or the elements, increased girth could constitute a cost of reproduction. In the laboratory, we experimentally tested whether access to crevices was limited in viviparous, saxicolous female lizards (Eulamprus brachysoma), which use crevices for shelter, by measuring access to artificial crevices of known widths, and body height during and after pregnancy. Gravid E. brachysoma had significantly greater body height (11.2% on average), and as a result were forced to use significantly wider crevices (18.4% wider on average) than post‐parturition. Females with larger clutch sizes had wider mid‐bodies and required larger crevices. Control females, which were not gravid at either time of testing, showed no significant change in the size of crevice they could enter over time. If access to narrow crevices provides advantages such as protection from predators, or is important for thermoregulation, then gravid females may suffer a cost of reproduction because their access to narrower crevices is limited.     

<Emphasis Type="Italic">In vitro</Emphasis> study of HAX1 gene therapy by retro viral transduction as a therapeutic target in severe congenital neutropenia

Severe congenital neutropenia (SCN) is a primary immunodeficiency disease in which a number of underlying gene defects are responsible for abnormalities in neutrophil development. The HCLS1-associated protein X1 (HAX1) mutation is associated with an autosomal-recessive form of SCN. Considering the potential of gene therapy approaches for the treatment of monogenic disorders, in this study we aimed to develop retroviral vectors expressing coding sequences (CDS) to be used for the removal of the genetic blockade in deficient hematopoietic cells. Following amplification of CDS with primers containing appropriate restriction sites, HAX1 CDS was cloned into an intermediate vector using TA-cloning. The sequence was transferred into a retroviral vector, followed by retroviral packaging in Plat-A cells. To show HAX1 protein expression, HEK293T cells were exposed to 10 multiplicity of infection (MOI) of retroviral particles and HAX1 expression was confirmed in these cells, using indirect intracellular flow cytometry. This vector was applied for in vitro transduction of hematopoietic stem cell with HAX1 mutation; after 11 days, cultured cells were analyzed for CD66acde and CD177 (neutrophil surface markers) expression. Increased neutrophil production in HAX1 viral vector-expressing hematopoietic cells was observed as compared to control vector transduced cells. Hence, according to the results, this type of therapy could be considered a potential treatment protocol for the disease.     

<Emphasis Type="Italic">In vitro</Emphasis> regenerating plantlets in <Emphasis Type="Italic">Pandanus amaryllifolius</Emphasis> Roxb. as a model system to study the development of lower epidermal papillae

Pandanus amaryllifolius Roxb. has been identified as a rich source of principal basmati aroma compound 2 acetyl-1-pyrroline (2AP). An easy and efficient protocol for clonal propagation of P. amaryllifolius Roxb. using lateral buds as an explant has been developed and the in vitro-raised seedlings were used to study the lower epidermal papillae development. The principal aroma compound 2AP along with other aroma compounds are stored in the lower epidermis papillae of leaf. The developmental pattern of these papillae was traced out using scanning electron microscopy. It was observed that stomata act as the site of initiation for development of the papillae followed by their lateral spread across the epidermal cells. During development, the first papillae bulged out as a protrusion of the lower epidermis that further metamorphosed into well-grown papillae. These developments are well-correlated with 2AP contents, in which the in vitro-raised seedlings had less 2AP contents (66.99 ppb) than the mother plant (96.88 ppb).     

Retraction: Circular RNA‐0007874 (circMTO1) reverses chemoresistance to temozolomide by acting as a sponge of microRNA‐630 in glioblastoma by Jiang Rao,Xinxin Cheng,Huimin Zhu,Lifeng Wang,Li Liu

The above article, published online on 11 December 2018 in Wiley Online Library ( https://doi.org/10.1002/cbin.11080 ), has been withdrawn by agreement with the journal Editor, Sergio Schenkman, and John Wiley & Sons Ltd. The withdrawal has been agreed because the authors have not provided a signed Copyright Transfer Agreement.     

Consecutive oral administration of Bifidobacterium longum MM‐2 improves the defense system against influenza virus infection by enhancing natural killer cell activity in a murine model

Bifidobacterium, one of the major components of intestinal microflora, shows anti‐influenza virus (IFV) potential as a probiotic, partly through enhancement of innate immunity by modulation of the intestinal immune system. Bifidobacterium longum MM‐2 (MM‐2), a very safe bacterium in humans, was isolated from healthy humans and its protective effect against IFV infection in a murine model shown. In mice that were intranasally inoculated with IFV, oral administration of MM‐2 for 17 consecutive days improved clinical symptoms, reduced mortality, suppressed inflammation in the lower respiratory tract, and decreased virus titers, cell death, and pro‐inflammatory cytokines such as IL‐6 and TNF‐α in bronchoalveolar lavage fluid. The anti‐IFV mechanism of MM‐2 involves innate immunity through significant increases in NK cell activities in the lungs and spleen and a significant increase in pulmonary gene expression of NK cell activators such as IFN‐γ, IL‐2, IL‐12 and IL‐18. Even in non‐infected mice, MM‐2 administration also induced significant enhancement of both IFN‐γ production by Peyer's patch cells (PPs) and splenetic NK cell activity. Oral administration of MM‐2 for 17 days activates systemic immunoreactivity in PPs, which contributes to innate immunity, including NK cell activation, resulting in an anti‐IFV effect. MM‐2 as a probiotic may function as a prophylactic agent in the management of an IFV epidemic.