The aspartic proteinase family of three Phytophthora species

Background - Phytophthora species are oomycete plant pathogens with such major social and economic impact that genome sequences have been determined for Phytophthora infestans, P. sojae and P. ramorum. Pepsin-like aspartic proteinases (APs) are produced in a wide variety of species (from bacteria to humans) and contain conserved motifs and landmark residues. APs fulfil critical roles in infectious organisms and their host cells. Annotation of Phytophthora APs would provide invaluable information for studies into their roles in the physiology of Phytophthora species and interactions with their hosts. Results - Genomes of Phytophthora infestans, P. sojae and P. ramorum contain 11-12 genes encoding APs. Nine of the original gene models in the P. infestans database and several in P. sojae and P. ramorum (three and four, respectively) were erroneous. Gene models were corrected on the basis of EST data, consistent positioning of introns between orthologues and conservation of hallmark motifs. Phylogenetic analysis resolved the Phytophthora APs into 5 clades. Of the 12 sub-families, several contained an unconventional architecture, as they either lacked a signal peptide or a propart region. Remarkably, almost all APs are predicted to be membrane-bound. Conclusions - One of the twelve Phytophthora APs is an unprecedented fusion protein with a putative G-protein coupled receptor as the C-terminal partner. The others appear to be related to well-documented enzymes from other species, including a vacuolar enzyme that is encoded in every fungal genome sequenced to date. Unexpectedly, however, the oomycetes were found to have both active and probably-inactive forms of an AP similar to vertebrate BACE, the enzyme responsible for initiating the processing cascade that generates the Aß peptide central to Alzheimer's Disease. The oomycetes also encode enzymes similar to plasmepsin V, a membrane-bound AP that cleaves effector proteins of the malaria parasite Plasmodium falciparum during their translocation into the host red blood cell. Since the translocation of Phytophthora effector proteins is currently a topic of intense research activity, the identification in Phytophthora of potential functional homologues of plasmepsin V would appear worthy of investigation. Indeed, elucidation of the physiological roles of the APs identified here offers areas for future study. The significant revision of gene models and detailed annotation presented here should significantly facilitate experimental design

Vroegtijdig vuur detecteren kan bollentelers uit de brand helpen: identificatie en detectie van Botrytis-soorten in bloembolgewassen

In bloembolgewassen kan de schimmel Botrytis veel schade veroorzaken. Botrytis kan snel toeslaan. Snelle en gevoelige toetsen kunnen dan bijdragen tot het op tijd nemen van maatregelen om ‘vuur’ te beheersen. Er komen verschillende Botrytis-soorten voor, die moleculair- genetisch gedetecteerd en geïdentificeerd kunnen worden. Serologische toetsen bleken niet te werken. PCR-methodieken, gebaseerd op enkele kleine verschillen in DNA-sequenties wel. Mogelijk kunnen via monitoring van luchtmonsters waarschuwingssystemen voor vuur verder worden verbeterd

The thermal equation of state of FeTiO_3 ilmenite based on in situ X-ray diffraction at high pressures and temperatures

We present in situ measurements of the unit-cell volume of a natural terrestrial ilmenite (Jagersfontein mine, South Africa) and a synthetic reduced ilmenite (FeTiO_3) at simultaneous high pressure and high temperature up to 16 GPa and 1273 K. Unit-cell volumes were determined using energy-dispersive synchrotron X-ray diffraction in a multi-anvil press. Mössbauer analyses show that the synthetic sample contained insignificant amounts of Fe^(3+) both before and after the experiment. Results were fit to Birch-Murnaghan thermal equations of state, which reproduce the experimental data to within 0.5 and 0.7 GPa for the synthetic and natural samples, respectively. At ambient conditions, the unit-cell volume of the natural sample [V_0 = 314.75 ± 0.23 (1 ) Å^3] is significantly smaller than that of the synthetic sample [V_0 = 319.12 ± 0.26 Å^3]. The difference can be attributed to the presence of impurities and Fe^(3+) in the natural sample. The 1 bar isothermal bulk moduli K_(T0) for the reduced ilmenite is slightly larger than for the natural ilmenite (181 ± 7 and 165 ± 6 GPa, respectively), with pressure derivatives K_0' = 3 ± 1. Our results, combined with literature data, suggest that the unit-cell volume of reduced ilmenite is significantly larger than that of oxidized ilmenite, whereas their thermoelastic parameters are similar. Our data provide more appropriate input parameters for thermo-chemical models of lunar interior evolution, in which reduced ilmenite plays a critical role

Absence of evidence is not evidence of absence:On the limited use of regression discontinuity analysis in higher education

When higher education students are assessed multiple times, teachers need to consider how these assessments can be combined into a single pass or fail decision. A common question that arises is whether students should be allowed to take a resit. Previous research has found little to no clear learning benefits of resits and therefore suggested they might not be advantangeous as they are costly for both students and institutions. However, we conducted a simulation study that shows such a conclusion to be presumptuous. Absence of evidence is not evidence of absence; our results illustrate that if a resit effect were to exist, the analysis used in these studies (i.e. regression discontinuity analysis; RDA) lacked the power to detect such an effect. Power of RDA was only sufficient under extremely implausible conditions (i.e. large sample, large effect size, high correlation between examinations). To adequately compare the effect of assessment policies, researchers are recommended to use other methods than RDA

Effects of electrostatic screening on the conformation of single DNA molecules confined in a nanochannel

Single T4-DNA molecules were confined in rectangular-shaped channels with a depth of 300 nm and a width in the range 150-300 nm casted in a poly(dimethylsiloxane) nanofluidic chip. The extensions of the DNA molecules were measured with fluorescence microscopy as a function of the ionic strength and composition of the buffer as well as the DNA intercalation level by the YOYO-1 dye. The data were interpreted with scaling theory for a wormlike polymer in good solvent, including the effects of confinement, charge, and self-avoidance. It was found that the elongation of the DNA molecules with decreasing ionic strength can be interpreted in terms of an increase of the persistence length. Self-avoidance effects on the extension are moderate, due to the small correlation length imposed by the channel cross-sectional diameter. Intercalation of the dye results in an increase of the DNA contour length and a partial neutralization of the DNA charge, but besides effects of electrostatic origin it has no significant effect on the bare bending rigidity. In the presence of divalent cations, the DNA molecules were observed to contract, but they do not collapse into a condensed structure. It is proposed that this contraction results from a divalent counterion mediated attractive force between the segments of the DNA molecule.Comment: 38 pages, 10 figures, accepted for publication in The Journal of Chemical Physic

Translation, cross-cultural adaptation, and validation of a Dutch version of the actions and feelings questionnaire in autistic and neurotypical adult

The actions and feelings questionnaire (AFQ) provides a short, self-report measure of how well someone uses and understands visual communicative signals such as gestures. The objective of this study was to translate and cross-culturally adapt the AFQ into Dutch (AFQ-NL) and validate this new version in neurotypical and autistic populations. Translation and adaptation of the AFQ consisted of forward translation, synthesis, back translation, and expert review. In order to validate the AFQ-NL, we assessed convergent and divergent validity. We additionally assessed internal consistency using Cronbach’s alpha. Validation and reliability outcomes were all satisfactory. The AFQ-NL is a valid adaptation that can be used for both autistic and neurotypical populations in the Netherlands