Microbial metabolomics: essential definitions and the importance of cultivation conditions for utilizing Bacillus species as bionematicides

Root-knot nematodes are destructive phytopathogens that damage agricultural crops globally, and there is growing interest in the use of biocontrol based on rhizobacteria such as Bacillus to combat Meloidogyne species. It is hypothesized that nematicidal activity of Bacillus can be attributed to the production of secondary metabolites and hydrolytic enzymes. Yet, few studies have characterized these metabolites and their identities remain unknown. Others are speculative or fail to elaborate on how secondary metabolites were detected or distinguished from primary metabolites. Metabolites can be classified based on their origin as either intracellular or extracellular and based on their function, as either primary or secondary. Although this classification is in general use, the boundaries are not always well defined. An understanding of the secondary metabolite and hydrolytic enzyme classification of Bacillus species will facilitate investigations aimed at bionematicide development. This review summarizes the significance of Bacillus hydrolytic enzymes and secondary metabolites in bionematicide research and provides an overview of known classifications. The importance of appropriate cultivation conditions for optimum metabolite and enzyme production is also discussed. Finally, the use of metabolomics for the detection and identification of nematicidal compounds is considered.     

Insect taxa with similar habitat requirements may differ in response to the environment in heterogeneous patches of traditional fruit orchards

Semi-natural habitats are currently one of the most important environments for many taxa. The main aim of this study was to discover how diurnal butterflies (Lepidoptera) and flower-visiting beetles (Coleoptera) respond to the environment of traditional fruit orchards. In total, 25 orchards were studied in the rural-agricultural landscape in the Czech Republic. Both study taxa were sampled using timed survey walks in 2010. Seven variables in two environmental categories (patch and geography) were evaluated with respect to the species richness of the studied taxa using partial regression, hierarchical partitioning and generalized linear modeling of the best selected variables. Butterflies were highly influenced at a patch level. An increased number of flowering plants, as a reflection of nectar sources for adults, significantly explained a high level of variability, both alone and via interaction with other studied variables. Beetles were influenced by patch and geography to the same degree, although altitude (as a reflection of geographical heterogeneity) significantly negatively explained the highest level of variability. The results indicate that diurnal butterflies and flower-visiting beetles as insect taxa with similar habitat requirements respond differently in heterogeneous environments of traditional fruit orchards. They also indicate the need for multi-taxa studies, even in marginal ecosystems of recent landscapes.     

Circulating Endothelial Progenitor Cells in Castration Resistant Prostate Cancer: A Randomized,Controlled, Biomarker Study

Background

Endothelial progenitor cells (CEPs) and circulating endothelial cells (CECs) are potential biomarkers of response to anti-angiogenic treatment regimens. In the current study, we investigated the effect of docetaxel and sunitinib on CEP/CEC kinetics and clinical response in castration resistant prostate cancer (CRPC) patients.

Patients and methods

Chemonaive patients with CRPC were enrolled in this study to receive either sunitinib (37.5 mg/d), in combination with docetaxel (75 mg/m²) or docetaxel alone. CEP and CEC kinetics were analyzed for every cycle. The primary objective was to compare CEP/CEC pharmacodynamics between both treatment arms. We also investigated if CEC/CEP spikes, induced by MTD docetaxel, are suppressed by sunitinib in patients treated with docetaxel/sunitinib relative to docetaxel monotherapy.

Results

A total of 27 patients were enrolled. We observed a significant increase of CEP/CEC (total/viable) counts over time within each cycle (coefficients 0.29233, 0.22092 and 0.26089, respectively; p<0.001). However, no differences between the treatment groups, in terms of CEP and CEC kinetics, were detected. In the docetaxel monotherapy arm 4 (30%) patients responded to therapy with a 50% PSA decline, while 9 (64%) patients showed a PSA decline in the combination group (n.s.). The median PFS in the docetaxel monotherapy group was 3.1 months (2.6–3.6 months, 95% CI) and 6.2 months (4.9–7.4 months, 95% CI; p = 0.062) in the combination arm. Sunitinib/docetaxel was reasonably well tolerated and toxicity manageable.

Conclusion

In summary, no significant differences in CEC and CEP kinetics between the treatment arms were observed, although a highly significant increase of CEPs/CECs within each cycle over time was detected. These results mirror the challenge we have to face when employing anti-angiogenic strategies in CRPC. Additional preclinical research is needed to elucidate the underlying molecular mechanisms. However, docetaxel/sunitinib therapy resulted in a better response in terms of PSA decline and a trend towards improved PFS.

Trial Registery

clinicaltrialsregister.eu EudraCT 2007-003705-27     

Role of the fourth membrane domain of the NR2B subunit in the assembly of the NMDA receptor

N-methyl-D-aspartate (NMDA) receptors play crucial roles in excitatory synaptic transmission as well as in excitotoxicity. A growing body of evidence suggests that the regulation of both subunit composition and the number of NMDA receptors reaching the surface membrane are tightly regulated. Recently, we have shown that the third membrane domains (M3) of both NR1 and NR2B subunits contain endoplasmic reticulum (ER) retention signals that prevent the unassembled subunits from leaving the ER. Furthermore, these membrane domains together with NR1 M4 are necessary for negating the ER retention signals found in M3 of NR1 and NR2B. In this addendum, we present new electrophysiological data showing that mutation of the HLFY motif, located immediately after M4 of the NR2B subunit, abolishes the surface trafficking of full-length NR1/NR2B complexes (supporting previous immunofluorescent experiments from our lab); however, the deletion of the NR2B C-terminus including the HLFY motif did not affect the formation of functional receptors when two pieces of the NR2B subunit, NR2B truncated before M4 and NR2B M4, were co-expressed together with the NR1 subunit. These observations will help to uncover the processes involved in the assembly of NR1 and NR2 subunits into functional NMDA receptors.     

Restoration of ATP synthesis in urea-treated membranes prepared from pea cotyledon mitochondria

Submitochondrial particles were prepared from pea cotyledon mitochondria by sonication in a medium containing 5 mM MgCl₂. The resulting particles (Mg²⁺-submitochondrial particles) catalyzed oxidative phosphorylation at the rate of 100–200 nmol ATP formed / min per mg protein. Treatment of Mg²⁺-submitochondrial particles with 3.0 M urea resulted in a preparation of highly resolved particles with low ATPase activity and no capacity for oxidative phosphorylation. However, the resulting membranes were not capable of reconstitution of oxidative posphorylation with the purified mitochondrial F₁-ATPase. Urea particles capable of reconstitution of oxidative phosphorylation could be prepared by extracting Mg²⁺-submitochondrial particles with concentrations of urea ranging from 1.7 to 2.0 M. We have used 1.9 M urea for large-scale preparation of urea particles that could be stored in liquid nitrogen without any loss of reconstitution capacity. The residual oxidative phosphorylation rate of these particles was 6–8 nmol ATP / min per mg protein and this rate could increase to 60–70 nmol ATP / min per mg protein on incubation with saturating amounts of purified mitochondrial F₁-ATPase. In contrast to the mitochondrial F₁, purified activated pea chloroplast CF₁ was unable to stimulate ATP synthesis in 1.9 M urea particles.     

Increasing the affinity for tumor antigen enhances bispecific antibody cytotoxicity

We tested the hypothesis that bispecific Abs (Bsab) with increased binding affinity for tumor Ags augment retargeted antitumor cytotoxicity. We report that an increase in the affinity of Bsab for the HER2/neu Ag correlates with an increase in the ability of the Bsab to promote retargeted cytotoxicity against HER2/neu-positive cell lines. A series of anti-HER2/neu extracellular domain-directed single-chain Fv fragments (scFv), ranging in affinity for HER2/neu from 10(-7) to 10(-11) M, were fused to the phage display-derived NM3E2 human scFV: NM3E2 associates with the extracellular domain of human FcgammaRIII (CD16). The resulting series of Bsab promoted cytotoxicity of SKOV3 human ovarian carcinoma cells overexpressing HER2/neu by human PBMC preparations containing CD16-positive NK cells. The affinity for HER2/neu clearly influenced the ability of the Bsab to promote cytotoxicity of (51)Cr-labeled SKOV3 cells. Lysis was 6.5% with an anti-HER2/neu K(D) = 1.7 x 10(-7) M, 14.5% with K(D) = 5.7 x 10(-9) M, and 21.3% with K(D) = 1.7 x 10(-10) M at 50:1 E:T ratios. These scFv-based Bsab did not cross-link receptors and induce leukocyte calcium mobilization in the absence of tumor cell engagement. Thus, these novel Bsab structures should not induce the dose-limiting cytokine release syndromes that have been observed in clinical trials with intact IgG BSAB: Additional manipulations in Bsab structure that improve selective tumor retention or facilitate the ability of Bsab to selectively cross-link tumor and effector cells at tumor sites should further improve the utility of this therapeutic strategy.     

Increasing temperature may compensate for lower amounts of dead wood in driving richness of saproxylic beetles

Global warming and land‐use change are expected to be additive threats to global diversity, to which insects contribute the highest proportion. Insects are strongly influenced by temperature but also require specific habitat resources, and thus interaction between the two factors is likely. We selected saproxylic beetles as a model group because their life cycle depends on dead wood, which is highly threatened by land use. We tested the extent to which higher temperatures compensate for the negative effects of low amounts of dead wood on saproxylic beetle species richness (Temperature–Dead wood compensation hypothesis) on both a macroclimate and a topoclimate scale (north‐ and south‐facing slopes). We analyzed 1404 flight‐interception trap catches across Europe to test for interaction effects of temperature and dead‐wood amount on species richness. To experimentally test our findings from the activity trap data, we additionally reared beetles from 80 bundles of dead wood initially exposed at high and low elevations. At the topoclimate scale, we analyzed trap catches and reared beetles from dead wood exposed in 20 forest stands on south‐facing and north‐facing slopes in one region. On the macroscale, both temperature and dead‐wood amount positively affected total and threatened species richness independently, but their interaction was significantly negative, indicating compensation. On both scales and irrespective of the method, species richness decreased with temperature decline. Our observation that increasing temperature compensates for lower amounts of dead wood has two important implications. First, managers of production forests should adapt their dead‐wood enrichment strategy to site‐specific temperature conditions. Second, an increase in temperature will compensate at least partially for poor habitat conditions in production forests. Such a perspective contrasts the general assumption of reinforcing impacts of global warming and habitat loss on biodiversity, but it is corroborated by recent range expansions of threatened beetle species.     

Monoclonal Antibodies to the [alpha]- and [beta]-Subunits of the Plant Mitochondrial F1-ATPase

We have generated nine monoclonal antibodies against subunits of the maize (Zea mays L.) mitochondrial F1-ATPase. These monoclonal antibodies were generated by immunizing mice against maize mitochondrial fractions and randomly collecting useful hybridomas. To prove that these monoclonal antibodies were directed against ATPase subunits, we tested their cross-reactivity with purified F1-ATPase from pea cotyledon mitochondria. One of the antibodies ([alpha]-ATPaseD) cross-reacted with the pea F1-ATPase [alpha]-subunit and two ([beta]-ATPaseD and [beta]-ATPaseE) cross-reacted with the pea F1-ATPase [beta]-subunit. This established that, of the nine antibodies, four react with the maize [alpha]-ATPase subunit and the other five react with the maize [beta]-ATPase subunit. Most of the monoclonal antibodies cross-react with the F1-ATPase from a wide range of plant species. Each of the four monoclonal antibodies raised against the [alpha]-subunit recognizes a different epitope. Of the five [beta]-subunit antibodies, at least three different epitopes are recognized. Direct incubation of the monoclonal antibodies with the F1-ATPase failed to inhibit the ATPase activity. The monoclonal antibodies [alpha]-ATPaseD and [beta]-ATPaseD were bound to epoxide-glass QuantAffinity beads and incubated with a purified preparation of pea F1-ATPase. The ATPase activity was not inhibited when the antibodies bound the ATPase. The antibodies were used to help map the pea F1-ATPase subunits on a two-dimensional map of whole pea cotyledon mitochondrial protein. In addition, the antibodies have revealed antigenic similarities between various isoforms observed for the [alpha]- and [beta]-subunits of the purified F1-ATPase. The specificity of these monoclonal antibodies, along with their cross-species recognition and their ability to bind the F1-ATPase without inhibiting enzymic function, makes these antibodies useful and invaluable tools for the further purification and characterization of plant mitochondrial F1-ATPases.     

Sites of attachment and intraspecific infestation densities of the brown paralysis tick (Rhipicephalus punctatus) on Angora goats

Significant differences in the distribution of brown paralysis ticks on various age classes of Angora goats were recorded. In kids, most (>98%) of the ticks attached to the head and ears, whereas in older groups, in addition to the ears, a high proportion (>20%) of ticks also attached to the ventral side of the neck. There were significant differences in the mean infestation densities of both male and femaleR. punctatus in kids and older animals. These differences were, however, only significant for the first two sample dates involving kids, and are probably related to behavioural attributes of the kids which enhance tick/host contact. Newly born Angora goat kids are considered a high-risk group with regard to paralysis caused by the brown paralysis tick. Methods of avoiding mortality amongst kids are suggested.