Mass spectrometric characterization of the oxidation of the fluorescent lipid peroxidation reporter molecule C11-BODIPY(581/591)

C11-BODIPY^581/591 is a fluorescent lipid peroxidation reporter molecule that shifts its fluorescence from red to green when challenged with oxidizing agents, i.e., reactive oxygen species (ROS) or reactive nitrogen species (RNS). To understand the molecular mechanism responsible for this shift, we studied the molecular rearrangements leading to the shift in fluorescence in C11-BODIPY^581/591. Furthermore, we aimed to determine if these rearrangements were dependent on the nature of the applied ROS, in homogenous solution, bilayer vesicles, and living cells. C11-BODIPY^581/591 was challenged with various ROS- or RNS-generating systems, including peroxynitrite, NO₂^√, peroxides, and hydroxyl, alkoxyl, tyrosyl, and peroxyl radicals. The reaction products were subsequently analyzed by means of mass spectrometry. Our results show that the initial target for free radical-mediated oxidation is the conjugated diene interconnection between the BODIPY core and the terminal phenyl moiety, which already explains the shift in fluorescence properties of the probe. After oxidative challenge, three different stable products were identified, one of which was specific for oxidation by peroxynitrite. The two other stable end products had lost the entire phenyl moiety, irrespective of the type of radical generating system used. These products were also recovered from Rat-1 fibroblasts stressed either by GSH depletion/serum starvation or by exposure to peroxynitrite, and were the only C11-BODIPY^581/591 oxidation products detectable in these cells.     

Agrocin-producing pathogenic and nonpathogenic biotype-3 strains ofAgrobacterium tumefaciens active against biotype-3 pathogens

Agrocin-producing pathogenic and nonpathogenic biotype-3 strains ofAgrobacterium tumefaciens were isolated from grapevine gall tissue. In vitro activity of the nonpathogenic agrocin producers was restricted to biotype-3 pathogens used. Pathogenic agrocin producers were active in vitro against biotype-3 agrocin-producing nonpathogens, non-agrocin-producing pathogens, and biotype-1 strains when cultivated on a modified Stonier's medium; on a medium designated AB, two strains stested showed no activity against agrocin-producing nonpathogens, but agrocin of one of these strains was active against other agrocin-producing pathogens. In a greenhouse experiment a marked tendency toward decreased gall formation by biotype-3 pathogens on grapevines was obtained when biotype-3 pathogens and nonpathogenic biotype-3 agrocin producers were applied to wounds simultaneously. In this experiment, agrocin-producting pathogens tended to be more virulent than non-agrocin-producing pathogens.     

Appropriate Body Mass Index Cut-Offs to Determine Thinness,Overweight and Obesity in South Asian Children in The Netherlands

Background

Asian populations have an increased risk of developing cardiometabolic disorders at a lower body mass index (BMI) than other ethnic groups. Therefore, lower adult BMI cut-offs to determine overweight and obesity are recommended to assess the associated health risks for Asian (23 and 27.5 kg/m² respectively) and Asian Indian (23, 25 kg/m²) populations. The objective of this study was to develop BMI cut-offs for thinness, overweight, and obesity for South Asian children in the Netherlands, and to compare the BMI cut-offs and distribution with an Asian Indian reference, the WHO Child Growth Reference, and universal BMI cut-offs.

Methods

A reference cohort of 546 Surinamese South Asian boys and 521 girls, born between 1974–1976 (during the pre-obesity era) with 3408 and 3267 BMI measurements respectively, was retrospectively analysed. BMI-for-age charts were created with the LMS method. BMI centile curves passing through the cut-off points of 15 (thinness), 23 (overweight), 25 and 27.5 kg/m² (obesity) at 18y were drawn as cut-off levels.

Results

The BMI of Surinamese South Asian children had a similar distribution to the Asian Indian reference, apart from a lower mean and less variation. The BMI distribution differed considerably from the WHO reference and universal BMI criteria. The calculated BMI cut-offs corresponding to a BMI of 15, 23, 25, and 27.5 kg/m² at 18y were at the 7.1, 81.1, 89.8, and 95.5 percentile respectively in boys, and at the 2.7, 79.5, 89.2, and 95.2 percentile in girls.

Conclusions

This is the first study proposing BMI cut-offs for South Asian children based on measurements from a prosperous population unaffected by the obesity epidemic. We recommend the use of these cut-offs in South Asian children in the Netherlands as these better reflect the health risks associated with thinness, overweight and obesity, and therefore may prevent the development of cardiometabolic disorders.     

Text-derived concept profiles support assessment of DNA microarray data for acute myeloid leukemia and for androgen receptor stimulation

Background  

High-throughput experiments, such as with DNA microarrays, typically result in hundreds of genes potentially relevant to the process under study, rendering the interpretation of these experiments problematic. Here, we propose and evaluate an approach to find functional associations between large numbers of genes and other biomedical concepts from free-text literature. For each gene, a profile of related concepts is constructed that summarizes the context in which the gene is mentioned in literature. We assign a weight to each concept in the profile based on a likelihood ratio measure. Gene concept profiles can then be clustered to find related genes and other concepts.     

Tissue-type plasminogen activator is a multiligand cross-beta structure receptor

Tissue-type plasminogen activator (tPA) regulates fibrin clot lysis by stimulating the conversion of plasminogen into the active protease plasmin. Fibrin is required for efficient tPA-mediated plasmin generation and thereby stimulates its own proteolysis. Several fibrin regions can bind to tPA, but the structural basis for this interaction is unknown. Amyloid beta (Abeta) is a peptide aggregate that is associated with neurotoxicity in brains afflicted with Alzheimer's disease. Like fibrin, it stimulates tPA-mediated plasmin formation. Intermolecular stacking of peptide backbones in beta sheet conformation underlies cross-beta structure in amyloid peptides. We show here that fibrin-derived peptides adopt cross-beta structure and form amyloid fibers. This correlates with tPA binding and stimulation of tPA-mediated plasminogen activation. Prototype amyloid peptides, including Abeta and islet amyloid polypeptide (IAPP) (associated with pancreatic beta cell toxicity in type II diabetes), have no sequence similarity to the fibrin peptides but also bind to tPA and can substitute for fibrin in plasminogen activation by tPA. Moreover, the induction of cross-beta structure in an otherwise globular protein (endostatin) endows it with tPA-activating potential. Our results classify tPA as a multiligand receptor and show that cross-beta structure is the common denominator in tPA binding ligands.     

Latent class evaluation of the performance of serological tests for exposure to Brucella spp. in cattle,sheep, and goats in Tanzania

BackgroundBrucellosis is a neglected zoonosis endemic in many countries, including regions of sub-Saharan Africa. Evaluated diagnostic tools for the detection of exposure to Brucella spp. are important for disease surveillance and guiding prevention and control activities.Methods and findingsBayesian latent class analysis was used to evaluate performance of the Rose Bengal plate test (RBT) and a competitive ELISA (cELISA) in detecting Brucella spp. exposure at the individual animal-level for cattle, sheep, and goats in Tanzania. Median posterior estimates of RBT sensitivity were: 0.779 (95% Bayesian credibility interval (BCI): 0.570–0.894), 0.893 (0.636–0.989), and 0.807 (0.575–0.966), and for cELISA were: 0.623 (0.443–0.790), 0.409 (0.241–0.644), and 0.561 (0.376–0.713), for cattle, sheep, and goats, respectively. Sensitivity BCIs were wide, with the widest for cELISA in sheep. RBT and cELISA median posterior estimates of specificity were high across species models: RBT ranged between 0.989 (0.980–0.998) and 0.995 (0.985–0.999), and cELISA between 0.984 (0.974–0.995) and 0.996 (0.988–1). Each species model generated seroprevalence estimates for two livestock subpopulations, pastoralist and non-pastoralist. Pastoralist seroprevalence estimates were: 0.063 (0.045–0.090), 0.033 (0.018–0.049), and 0.051 (0.034–0.076), for cattle, sheep, and goats, respectively. Non-pastoralist seroprevalence estimates were below 0.01 for all species models. Series and parallel diagnostic approaches were evaluated. Parallel outperformed a series approach. Median posterior estimates for parallel testing were ≥0.920 (0.760–0.986) for sensitivity and ≥0.973 (0.955–0.992) for specificity, for all species models.ConclusionsOur findings indicate that Brucella spp. surveillance in Tanzania using RBT and cELISA in parallel at the animal-level would give high test performance. There is a need to evaluate strategies for implementing parallel testing at the herd- and flock-level. Our findings can assist in generating robust Brucella spp. exposure estimates for livestock in Tanzania and wider sub-Saharan Africa. The adoption of locally evaluated robust diagnostic tests in setting-specific surveillance is an important step towards brucellosis prevention and control.     

Linking the experiential,affective and cognitive domains in biology education: a case study – microscopy

A greater emphasis in school curricula on the technology of science would encourage teachers to engage their students more in practical work. This in turn might be expected to improve students’ attitudes towards science and enhance cognitive outcomes. The paper presents findings from a study on first-year university students’ school experience of, attitudes towards, and knowledge of, microscopy. The findings reinforce the general expectations alluded to above. They also draw attention to the importance of the lower secondary science experience – often a suboptimal one owing to a poor resource base – to the formation of student attitudes and cognitive development with respect to science.     

Qbeta-phage resistance by deletion of the coiled-coil motif in elongation factor Ts

Elongation factor Ts (EF-Ts) is the guanine-nucleotide exchange factor of elongation factor Tu (EF-Tu), which promotes the binding of aminoacyl-tRNA to the mRNA-programmed ribosome in prokaryotes. The EF-Tu.EF-Ts complex, one of the EF-Tu complexes during protein synthesis, is also a component of RNA-dependent RNA polymerases like the polymerase from coliphage Qbeta. The present study shows that the Escherichia coli mutant GRd.tsf lacking the coiled-coil motif of EF-Ts is completely resistant to phage Qbeta and that Qbeta-polymerase complex formation is not observed. GRd.tsf is the first E. coli mutant ever described that is unable to form a Qbeta-polymerase complex while still maintaining an almost normal growth behavior. The phage resistance correlates with an observed instability of the mutant EF-Tu.EF-Ts complex in the presence of guanine nucleotides. Thus, the mutant EF-Tu.EF-Ts is the first EF-Tu.EF-Ts complex ever described that is completely inactive in the Qbeta-polymerase complex despite its almost full activity in protein synthesis. We propose that the role of EF-Ts in the Qbeta-polymerase complex is to control and trap EF-Tu in a stable conformation with affinity for RNA templates while unable to bind aminoacyl-tRNA.     

The Papaver self-incompatibility pollen S-determinant, PrpS, functions in Arabidopsis thaliana

Many angiosperms use specific interactions between pollen and pistil proteins as "self" recognition and/or rejection mechanisms to prevent self-fertilization. Self-incompatibility (SI) is encoded by a multiallelic S locus, comprising pollen and pistil S-determinants. In Papaver rhoeas, cognate pistil and pollen S-determinants, PrpS, a pollen-expressed transmembrane protein, and PrsS, a pistil-expressed secreted protein, interact to trigger a Ca(2+)-dependent signaling network, resulting in inhibition of pollen tube growth, cytoskeletal alterations, and programmed cell death (PCD) in incompatible pollen. We introduced the PrpS gene into Arabidopsis thaliana, a self-compatible model plant. Exposing transgenic A. thaliana pollen to recombinant Papaver PrsS protein triggered remarkably similar responses to those observed in incompatible Papaver pollen: S-specific inhibition and hallmark features of Papaver SI. Our findings demonstrate that Papaver PrpS is functional in a species with no SI system that diverged ~140 million years ago. This suggests that the Papaver SI system uses cellular targets that are, perhaps, common to all eudicots and that endogenous signaling components can be recruited to elicit a response that most likely never operated in this species. This will be of interest to biologists interested in the evolution of signaling networks in higher plants.     

Effects of increased and deregulated expression of cell division genes on the morphology and on antibiotic production of streptomycetes

This paper describes the effects of increased expression of the cell division genes ftsZ, ftsQ, and ssgA on the development of both solid- and liquid-grown mycelium of Streptomyces coelicolor and Streptomyces lividans. Over-expression of ftsZ in S. coelicolor M145 inhibited aerial mycelium formation and blocked sporulation. Such deficient sporulation was also observed for the ftsZ mutant. Over-expression of ftsZ also inhibited morphological differentiation in S. lividans 1326, although aerial mycelium formation was less reduced. Furthermore, antibiotic production was increased in both strains, and in particular the otherwise dormant actinorhodin biosynthesis cluster of S. lividans was activated in liquid- and solid-grown cultures. No significant alterations were observed when the gene dosage of ftsQ was increased. Analysis by transmission electron microscopy of an S. coelicolor strain over-expressing ssgA showed that septum formation had strongly increased in comparison to wild-type S. coelicolor, showing that SsgA clearly influences Streptomyces cell division. The morphology of the hyphae was affected such that irregular septa were produced with a significantly wider diameter, thereby forming spore-like compartments. This suggests that ssgA can induce a process similar to submerged sporulation in Streptomyces strains that otherwise fail to do so. A working model is proposed for the regulation of septum formation and of submerged sporulation.