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

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

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

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 Aβ 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.Fil: Kay, John. Cardiff University; Reino UnidoFil: Meijer, Harold J. G.. Wageningen University; Reino UnidoFil: Ten Have, Arjen. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Mar del Plata. Instituto de Investigaciones Biológicas; Argentina. Universidad Nacional de Mar del Plata. Facultad de Ciencias Exactas y Naturales; ArgentinaFil: van Kan, Jan A. L.. Wageningen University; Reino Unid

Sensitivity Analysis of List Scheduling Heuristics

When jobs have to be processed on a set of identical parallel machines so as to minimize the makespan of the schedule, list scheduling rules form a popular class of heuristics. The order in which jobs appear on the list is assumed here to be determined by the relative size of their processing times; well known special cases are the LPT rule and the SPT rule, in which the jobs are ordered according to non-increasing and non-decreasing processing time respectively. When one of the job processing times is gradually increased, the schedule produced by a list scheduling rule will be affected in a manner reflecting its sensitivity to data perturbations. We analyze this phenomenon and obtain analytical support for the intuitively plausible notion that the sensitivity of a list scheduling rule increases with the quality of the schedule produced

Extensive expansion of A1 family aspartic proteinases in fungi revealed by evolutionary analyses of 107 complete eukaryotic proteomes

The A1 family of eukaryotic aspartic proteinases (APs) forms one of the 16 AP families. Although one of the best characterized families, the recent increase in genome sequence data has revealed many fungal AP homologs with novel sequence characteristics. This study was performed to explore the fungal AP sequence space and to obtain an in-depth understanding of fungal AP evolution. Using a comprehensive phylogeny of approximately 700 AP sequences from the complete proteomes of 87 fungi and 20 nonfungal eukaryotes, 11 major clades of APs were defined of which clade I largely corresponds to the A1A subfamily of pepsin-archetype APs. Clade II largely corresponds to the A1B subfamily of nepenthesin-archetype APs. Remarkably, the nine other clades contain only fungal APs, thus indicating that fungal APs have undergone a large sequence diversification. The topology of the tree indicates that fungal APs have been subject to both “birth and death” evolution and “functional redundancy and diversification.” This is substantiated by coclustering of certain functional sequence characteristics. A meta-analysis toward the identification of Cluster Determining Positions (CDPs) was performed in order to investigate the structural and biochemical basis for diversification. Seven CDPs contribute to the secondary structure of the enzyme. Three other CDPs are found in the vicinity of the substrate binding cleft. Tree topology, the large sequence variation among fungal APs, and the apparent functional diversification suggest that an amendment to update the current A1 AP classification based on a comprehensive phylogenetic clustering might contribute to refinement of the classification in the MEROPS peptidase database

Force transmissibility and vibration power flow behaviour of inerter-based vibration isolators

This paper investigates the dynamics and performance of inerter-based vibration isolators. Force / displacement transmissibility and vibration power flow are obtained to evaluate the isolation performance. Both force and motion excitations are considered. It is demonstrated that the use of inerters can enhance vibration isolation performance by enlarging the frequency band of effective vibration isolation. It is found that adding inerters can introduce anti-resonances in the frequency-response curves and in the curves of the force and displacement transmissibility such that vibration transmission can be suppressed at interested excitation frequencies. It is found that the introduction of inerters enhances inertial coupling and thus have a large influence on the dynamic behaviour at high frequencies. It is shown that force and displacement transmissibility increases with the excitation frequency and tends to an asymptotic value as the excitation frequency increases. In the high-frequency range, it was shown that adding inerters can result in a lower level of input power. These findings provide a better understanding of the effects of introducing inerters to vibration isolation and demonstrate the performance benefits of inerter-based vibration isolators

Optics-less smart sensors and a possible mechanism of cutaneous vision in nature

Optics-less cutaneous (skin) vision is not rare among living organisms, though its mechanisms and capabilities have not been thoroughly investigated. This paper demonstrates, using methods from statistical parameter estimation theory and numerical simulations, that an array of bare sensors with a natural cosine-law angular sensitivity arranged on a flat or curved surface has the ability to perform imaging tasks without any optics at all. The working principle of this type of optics-less sensor and the model developed here for determining sensor performance may be used to shed light upon possible mechanisms and capabilities of cutaneous vision in nature

Micromachining using focused high energy ion beams

Abstract The combination of deep X-ray lithography with electroforming and micromoulding (i.e., LIGA) has been shown to oer high potential for the production of high aspect-ratio microstructures. The LIGA technique, employing synchrotron light and a suitable X-ray mask, allows production of 3D microstructures in PMMA with aspect ratios around 100. Here we demonstrate that the novel technique of Deep Ion Beam Lithography (DIBL), a direct process utilizing a focused beam of MeV ions scanned in a predetermined pattern over a suitable resist material, can produce three dimensional microstructures with sub-micrometer feature sizes. Microstructures extending up to 100 lm from the substrate with aspect ratios approaching 100 can be produced. Multiple exposures at dierent ion energies allow production of multilayer structures in single resist layers of SU-8, a newly developed, chemically accelerated, negative tone, near UV, photoresist.