Targeted transcriptomic and metabolic profiling reveals temporal bottlenecks in the maize carotenoid pathway that may be addressed by multigene engineering

Carotenoids are a diverse group of tetraterpenoid pigments found in plants, fungi, bacteria and some animals. They play vital roles in plants and provide important health benefits to mammals, including humans. We previously reported the creation of a diverse population of transgenic maize plants expressing various carotenogenic gene combinations and exhibiting distinct metabolic phenotypes. Here we performed an in‐depth targeted mRNA and metabolomic analysis of the pathway to characterize the specific impact of five carotenogenic transgenes and their interactions with 12 endogenous genes in four transgenic lines representing distinct genotypes and phenotypes. We reconstructed the temporal profile of the carotenoid pathway during endosperm development at the mRNA and metabolic levels (for total and individual carotenoids), and investigated the impact of transgene expression on the endogenous pathway. These studies enabled us to investigate the extent of any interactions between the introduced transgenic and native partial carotenoid pathways during maize endosperm development. Importantly, we developed a theoretical model that explains these interactions, and our results suggest genetic intervention points that may allow the maize endosperm carotenoid pathway to be engineered in a more effective and predictable manner.     

Identification of a novel arylpiperazine scaffold for fatty acid amide hydrolase inhibition with improved drug disposition properties

We herein describe the systematic approach used to develop new analogues of compound 2, recently identified as a potent and selective fatty acid amide hydrolase (FAAH) inhibitor. Aiming at identifying new scaffolds endowed with improved drug disposition properties with respect to the phenylpyrrole-based lead, we subjected it to two different structural modification strategies. This process allowed the identification of derivatives 4b and 5c as potent, reversible and non-competitive FAAH inhibitors.     

Quinazolinecarboline alkaloid evodiamine as scaffold for targeting topoisomerase I and sirtuins

This paper reports the synthesis of a series of evodiamine derivatives. We assayed the ability to inhibit cell growth on three human tumour cell lines (H460, MCF-7 and HepG2) and we evaluated the capacity to interfere with the catalytic activity of topoisomerase I both by the relaxation assay and the occurrence of the cleavable complex. Moreover, whose effect on sirtuins 1, 2 and 3 was investigated. Finally, molecular docking analyses were performed in an attempt to rationalize the biological results.     

Strategies for the design and operation of enzymatic reactors for the degradation of highly and poorly soluble recalcitrant compounds

The presence of recalcitrant compounds in both wastewaters and soils is an important environmental problem. Oxidative enzymes from white-rot fungi have been successfully utilised for the in vitro degradation of xenobiotics, such as the azo dye Orange II and the polycyclic aromatic hydrocarbon anthracene (compounds with high and low solubilities, respectively). Two different reactor configurations are proposed: (i) an enzymatic membrane reactor for the treatment of soluble compounds, consisting of a continuous stirred tank reactor coupled to an ultrafiltration membrane to facilitate the retention and recycling of enzyme; and (ii) a two-phase enzymatic reactor for the degradation of poorly soluble compounds, consisting of an immiscible solvent, which contains the contaminant at high concentrations, and the aqueous phase containing the enzyme and cofactors involved in the catalytic cycle. In this paper, factors affecting the design and operation of both systems are discussed, and experimental results concerning the efficiency and stability of the processes are presented.     

Functional genomics tools to decipher the pathogenicity mechanisms of the necrotrophic fungus Plectosphaerella cucumerina in Arabidopsis thaliana

The analysis of the interaction between Arabidopsis thaliana and adapted (PcBMM) and nonadapted (Pc2127) isolates of the necrotrophic fungus Plectosphaerella cucumerina has contributed to the identification of molecular mechanisms controlling plant resistance to necrotrophs. To characterize the pathogenicity bases of the virulence of necrotrophic fungi in Arabidopsis, we developed P. cucumerina functional genomics tools using Agrobacterium tumefaciens‐mediated transformation. We generated PcBMM‐GFP and Pc2127‐GFP transformants constitutively expressing the green fluorescence protein (GFP), and a collection of random T‐DNA insertional PcBMM transformants. Confocal microscopy analyses of the initial stages of PcBMM‐GFP infection revealed that this pathogen, like other necrotrophic fungi, does not form an appressorium or penetrate into plant cells, but causes successive degradation of leaf cell layers. By comparing the colonization of Arabidopsis wild‐type plants and hypersusceptible (agb1‐1 and cyp79B2cyp79B3) and resistant (irx1‐6) mutants by PcBMM‐GFP or Pc2127‐GFP, we found that the plant immune response was already mounted at 12–18 h post‐inoculation, and that Arabidopsis resistance to these fungi correlated with the time course of spore germination and hyphal growth on the leaf surface. The virulence of a subset of the PcBMM T‐DNA insertional transformants was determined in Arabidopsis wild‐type plants and agb1‐1 mutant, and several transformants were identified that showed altered virulence in these genotypes in comparison with that of untransformed PcBMM. The T‐DNA flanking regions in these fungal mutants were successfully sequenced, further supporting the utility of these functional genomics tools in the molecular characterization of the pathogenicity of necrotrophic fungi.     

The molecular basis for antimicrobial activity of pore-forming cyclic peptides

The mechanism of action of antimicrobial peptides is, to our knowledge, still poorly understood. To probe the biophysical characteristics that confer activity, we present here a molecular-dynamics and biophysical study of a cyclic antimicrobial peptide and its inactive linear analog. In the simulations, the cyclic peptide caused large perturbations in the bilayer and cooperatively opened a disordered toroidal pore, 1–2 nm in diameter. Electrophysiology measurements confirm discrete poration events of comparable size. We also show that lysine residues aligning parallel to each other in the cyclic but not linear peptide are crucial for function. By employing dual-color fluorescence burst analysis, we show that both peptides are able to fuse/aggregate liposomes but only the cyclic peptide is able to porate them. The results provide detailed insight on the molecular basis of activity of cyclic antimicrobial peptides.     

Determination of enzymatic activities and metabolites in microliter sample size

A new generation of spectrophotometers able to measure a wide range of absorbance in microliter aliquots is currently used for the determination of DNA, RNA, and proteins. The object of this article is to show that these instruments could be easily adapted for routine evaluation of enzymes and metabolites in 1–2-μl volumes of biological samples.     

Retrospective application of transposon-directed insertion site sequencing to a library of signature-tagged mini-Tn5Km2 mutants of Escherichia coli O157:H7 screened in cattle

Massively parallel sequencing of transposon-flanking regions assigned the genotype and fitness score to 91% of Escherichia coli O157:H7 mutants previously screened in cattle by signature-tagged mutagenesis (STM). The method obviates the limitations of STM and markedly extended the functional annotation of the prototype E. coli O157:H7 genome without further animal use.     

Spatial and temporal effects of soil temperature and moisture and the relation to fine root density on root and soil respiration in a mature apple orchard

We identified the role of various soil parameters and root density as drivers of soil respiration (R_s) in an apple orchard, measured during different periods of the year and at a range of distances from trees, in plots with a different history of nutrient supply. R_s was measured in April, May, August and December and studied in relation to soil temperature and moisture, total soil C and N, as well as to fine root density and medium-, and large-sized root density and root N concentration. The study also aimed to partition R_s by applying the root regression technique. R_s ranged from 0.06 in December to 1.49 g CO₂ m^?2 h^?1 in August. Average soil temperature alone explained up to 71% of the annual variability of R_s, while soil water content was negatively correlated to R_s. Fertilization, soil C and N concentration and root N had negligible effects on R_s. Fine root density, but not medium- and large-sized root density, contributed to explaining part of the yearly variability of R_s and proved to be a good predictor in December, when the statistical significance of the regression made it possible to estimate the autotrophic component of R_s as being about 35% of total soil respiration.     

Alternative markers for the long-term detection of oral testosterone misuse

The screening of testosterone misuse in the doping control field is normally performed by the measurement of the ratio between the concentrations of testosterone and epitestosterone excreted as glucuronides (T/E). Despite the satisfactory results obtained with this approach, the measurement of T/E presents some limitations like the long-term detection of oral testosterone administration. Recently, several testosterone metabolites released after basic treatment of the urine have been reported (androsta-1,4-dien-3,17-dione, androsta-4,6-dien-3,17-dione, 17β-hydroxy-androsta-4,6-dien-3-one and 15-androsten-3,17-dione). In the present work, the usefulness of these metabolites for the detection of oral testosterone misuse has been evaluated and compared with the conventional T/E measurement. For this purpose, 173 urine samples collected from healthy volunteers were analysed in order to obtain reference concentrations for the four metabolites released after alkaline treatment. On the other hand, urine samples collected from five volunteers before and after testosterone undecanoate administration were also analysed. Concentrations of androsta-4,6-dien-3,17-dione and 17β-hydroxy-androsta-4,6-dien-3-one showed a similar behaviour as the T/E, allowing the detection of the misuse for several hours after administration. More promising results were obtained by quantifying androsta-1,4-dien-3,17-dione and 15-androsten-3,17-dione. The time in which the concentrations of these analytes could be differentiated from the basal level was between 3 and 6 times longer than the obtained with T/E, as a result, an improvement in the detection of testosterone abuse can be achieved. Moreover, several ratios between these compounds were evaluated. Some of them improved the detection of testosterone misuse when comparing with T/E. The best results were obtained with those ratios involving androsta-1,4-dien-3,17-dione.