Glass transition of low-density amorphous water and related structures

In this work, the glass transition of water was studied with density functional theory. The transition temperature was determined by measuring the heat capacity Cp of low-density amorphous water during rapid heating. This technique ensures that all measurements were implemented without crystallization occurring, which is difficult to be achieved experimentally. The results showed that the glass transition occurs at 171 K, which is much higher than the reported value of 136 K. In addition, the triply hydrogen-bonded water molecules were found when T > 180 K, demonstrating the existence of the liquid structure at the higher temperature range.

Rapid identification of high particle number emitting on-road vehicles and its application to a large fleet of diesel buses

Pollutant concentrations measured in the exhaust plume of a vehicle may be related to the pollutant emission factor using the CO2 concentration as a measure of the dilution factor. We have used this method for the rapid identification of high particle number (PN) emitting on-road vehicles. The method was validated for PN using a medium-duty vehicle and successfully applied to measurements of PN emissions from a large fleet of on-road diesel buses. The ratio of PN concentration to CO2 concentration, Z, in the exhaust plume was estimated for individual buses. On the average, a bus emitted about 1.5 x 10(9) particles per mg of CO2 emitted. A histogram of the number of buses as a function of Z showed, for the first time, that the PN emissions from diesel buses followed a gamma distribution, with most of the values within a narrow range and a few buses exhibiting relatively large values. It was estimated that roughly 10% and 50% of the PN emissions came from just 2% and 25% of the buses, respectively. A regression analysis showed that there was a positive correlation between Z and age of buses, with the slope of the best line being significantly different from zero. The mean Z value for the pre-Euro buses was significantly greater than each of the values for the Euro I and II buses.

High-resolution measurements of small field beams using polymer gels

Small field sizes are increasingly becoming important in radiotherapy particularly since the introduction of intensity-modulated radiation therapy (IMRT) techniques. It is normally a challenging task to reliably measure the delivered dose and to determine its distribution in a medium for such small fields using conventional-type dosimeters such as gas ionisation chambers. Recently, attempts have been made to use films, but they are not tissue equivalent, they measure the dose only in two dimensions and they are not as responsive to radiations. In the present work, polyacrylamide gel (PAG) dosimeters are employed to measure the dose and its distribution in three dimensions for very small field sizes, such as those typically used in stereotactic radiosurgery. Field sizes of 6 x 6 and 18 x 18 mm in width are investigated. The results show an agreement with radiochromic film and ionisation diode measurements, with some variation in measured doses near the edge of the field, where the gel data decreases more rapidly than the other methods.

Long-term outcome and neuroradiological findings of 31 patients with 6-pyruvoyltetrahydropterin synthase deficiency

Tetrahydrobiopterin (BH(4)) deficiency is an autosomal recessive disorder caused by enzyme defects in the biosynthesis or recycling of BH(4). Patients with BH(4) deficiency present with severe neurological signs and symptoms and require a different treatment from classical phenylketonuria. During the last 12 years, 31 cases of BH(4) deficiency were identified in our department. They were all classified as 6-pyruvoyl-tetrahydropterin synthase (PTPS) deficiency. They were diagnosed at the ages of 2.5-48 months and treated with BH(4), L-dopa and 5-hydroxytryptophan immediately after diagnosis. The average development quotients (DQ) at diagnosis and after treatment for more than 3 years were 53+/- 16, and 78+/- 15, respectively. A significant negative correlation was observed between the level of the DQ and the age at which treatment was commenced (r = -0.751, p = 0.002). Developmental profiles were uneven. Language, adaptability and at later age mathematics were particularly weak areas. Only two patients achieved a good performance in mathematics. Eleven patients who were treated with drugs from ages of 2.9-48 months had neuroradiological scanning. Computed tomography disclosed calcification in lentiform nuclei in one patient and magnetic resonance imaging disclosed delayed myelination and abnormal high intensity signal in cerebral white matter in all of them. Even though most of abnormalities were reversible, small patchy or spotted areas were still present on these regions after treatment for 10-46 months. In summary, our study supports the substantial efficacy of the current therapeutic approach in PTPS deficiency of normalizing amine neurotransmitters with three drugs as early as possible. For the first time, calcifications could be detected in patients with PTPS deficiency. Abnormalities in white matter on magnetic resonance imaging were not related to clinical manifestations and most were reversible.

Particle number emissions and source signatures of an industrial facility

The work presented was conducted within the scope of a larger study investigating impacts of the Stuart Oil Shale project, a facility operating to the north of the industrial city of Gladstone, Australia. The aims of the investigations were threefold: (a) the identification of the plant signatures in terms of particle size distributions in the submicrometer range (13-830 nm) through stack measurements, (b) exploring the applicability of these signatures in tracing the source contributions at locations of interest, at a distance from the plant, and (c) assessing the contribution of the plant to the total particle number concentration at locations of interest. The stack measurements conducted for three different conditions of plant operation showed that the particle size distributions were bimodal with average modal count median diameters (CMDs) of 24 (SD 4) and 52 (SD 9) nm. The average of all the particle size distributions recorded within the plant sector at a site located 4.5 km from the plant, over the sampling period when the plant was operating, also showed a bimodal distribution. The modal CMDs in this case were 27 and 50 nm, similar to those at the stack. This bimodal size distribution is distinct from the size distribution of the most common ambient anthropogenic emission source, which is vehicle emissions, and can be considered as a signature of this source. The average contribution of the plant (for plant sector winds) was estimated to be (10.0 +/- 3.8) x 10(2) particles cm(-3) and constituted approximately a 50% increase overthe local particle ambient concentration for plant sector winds. This increase in particle number concentration compared to the local background concentration, while high compared to the clean environment concentration, is not significant when compared to concentrations generally encountered in the urban environment of Brisbane.

Electronic Structures and Hydrogen Bond Network of High-Density and Very High-Density Amorphous Ices

Electronic structures of hexagonal ice (ice Ih), high-density amorphous ice (HDA), and very high-density amorphous ice (VHDA) are investigated using ab initio density functional theory (DFT) at 77 K under a pressure of 0.1 MPa, focusing on band structure, density of states (DOS), partial density of states (PDOS), and electron density. It is found that the integration intensity of the O-2p bonding band in HDA is 1.53 eV wider than that in the VHDA. Because more 2p electrons in HDA participate the 2p-1s hybridization of O-H. The classical molecular dynamics (MD) method has further been carried out to analyze the hydrogen bond network of HDA and VHDA with larger numbers of water molecules under the same temperature, pressure, and boundary conditions used as those during the DFT calculation. MD results show that there exists some water molecules with five hydrogen bonds in both HDA (4.1 +/- 0.1%) and VHDA (2.8 +/- 0.1%), as compared with the LDA, being consistent with the integration intensity results of PDOS. This result can be used to interpret the physical nature of the similar transition temperature of HDA and VHDA to LDA with different heating rates.

Motifs that mediate dendritic targeting in hippocampal neurons: a comparison with basolateral targeting signals

One model for dendritic protein sorting in neurons is based on parallels with basolateral targeting in Madin-Darby Canine Kidney (MDCK) epithelial cells. The goal of this study was to further evaluate this model by analyzing the neuronal targeting of several proteins that contain well-defined basolateral sorting motifs. When we expressed FcRgammaII-B2 and CD44, two basolateral markers whose sorting depends on dihydrophobic motifs, they were unpolarized in hippocampal neurons. We also assessed the localization of the Epidermal Growth Factor Receptor (EGFR), a basolateral protein whose sorting signal contains a proline-rich motif and two dihydrophobic motifs. EGFR was restricted to the dendrites in neurons and relied on the same sorting signal for proper targeting. These results show that the dendritic sorting machinery in neurons does not recognize dihydrophobic-based basolateral sorting signals. In contrast, the sorting signal present in EGFR directs both basolateral and dendritic targeting and defines a novel dendritic targeting motif.

High-rate stormwater clarification with polymeric flocculant addition

Treatment of urban stormwater by clarification, with flocculant addition, was studied in Toronto, Canada using a pilot-scale clarifier with removable lamellar plates. Almost 90 stormwater runoff events were characterised at the study site and found fairly polluted. The previous research phase indicated good treatability of this stormwater by lamellar clarification with flocculant addition (total suspended solids, TSS, removal of 84%, at a surface load of 15 m/h), but there were concerns about cleaning plates after storm events. With the aid of numerical modelling, hydraulic improvements to the clarifier inlet zone were retrofitted in 2004 and permitted the removal of the lamellar pack without a loss in treatment efficiency. In the modified clarifier, a cationic polymeric flocculant dosage of 4 mg/L with conventional clarification provided a TSS removal of 77%, at surface loads up to 43 m/h. The use of the polymer did not increase the acute toxicity of the treated effluent. The clarifier sludge was severely polluted by several heavy metals and would require special disposal. The treatment process tested could be well applied in projects requiring intensive stormwater treatment at compact sites.

A combined linkage-physical map of the human genome

We have constructed de novo a high-resolution genetic map that includes the largest set, to our knowledge, of polymorphic markers (N=14,759) for which genotype data are publicly available; that combines genotype data from both the Centre d'Etude du Polymorphisme Humain (CEPH) and deCODE pedigrees; that incorporates single-nucleotide polymorphisms; and that also incorporates sequence-based positional information. The position of all markers on our map is corroborated by both genomic sequence and recombination-based data. This specific combination of features maximizes marker inclusion, coverage, and resolution, making this map uniquely suitable as a comprehensive resource for determining genetic map information (order and distances) for any large set of polymorphic markers.

Physical mapping of a rice lesion mimic gene, Spl1 , to a 70-kb segment of rice chromosome 12

The rice lesion mimic mutant spotted leaf 1 ( spl1) was first identified in the rice ( Oryza sativa) cultivar Asahi in 1965. This mutant displayed spontaneous disease-like lesions in the absence of any pathogen, and was found to confer resistance to multiple isolates of rice blast. We employed a map-based cloning strategy to localize the Spl1 gene. A total of ten cleaved amplified polymorphic sequence (CAPS) markers linked to the Spl1 gene were identified and mapped to an 8.5-cM region on chromosome 12. A high-resolution genetic map was developed using these ten CAPS markers and a segregating population consisting of 3202 individuals. A BAC contig containing four BAC clones was constructed, and Spl1 was localized to a 423-kb region. Seven spl1 mutants were obtained from the IR64 deletion mutant collection, and molecular analysis using these mutants delimited the Spl1 gene to a 70-kb interval, covered by two BAC clones. These results provide the basis for cloning this gene, which is involved in cell death and disease resistance in rice.

Aqueous and Micelle-bound Structural Characterization of the Epidermal Growth Factor Receptor Juxtamembrane Domain Containing Basolateral Sorting Motifs

The EGF receptor is the prototype for four highly related receptors constituting the ErbB family. The EGF receptor is normally targeted to the basolateral membrane in polarized epithelial cells, where it relays information from underlying tissues. Two basolateral sorting signals have been mapped to the cytoplasmic juxtamembrane region of the receptor, a dominant signal comprised of a polyproline core (667-PXXP) and a preceding basic residue (Arg662), and a consensus leucine-based signal (658-LL) responsible for residual sorting when the 667-PXXP signal is absent or defective. The goal of this study was to define the structure of these signals, and gain some insights into how these structures might be regulated by cellular microenvironment. Structural information was acquired for two peptides corresponding to EGF receptor residues Arg645 and Ala674 in aqueous solution or in the presence of membrane-mimicking dodecylphosphocholine micelles, using a variety of NMR and CD spectroscopic methods. Chemical shift data indicate that the 667-PXXP signal does not bind to the micelles and is in random coil state in both aqueous solution and a micellar environment, raising the possibility that 667-PXXP switches to an ordered structure during interaction with the basolateral sorting machinery. In contrast, the adjacent region including 658-LL does bind to micelles mediated by a highly positively charged region located between Arg645 and Arg656. The micelle-bound region also includes Thr654, a known substrate for PKC. This suggests a distinct mode of regulation for this signal involving membrane association and/or phosphorylation.

Ionic Pair Complexes with Well-Separated Columnar Stack Structure Based on [Pt(mnt)2]-Ions Showing Unusual Magnetic Transition: Syntheses, Crystal Structures, and Magnetic Properties

Three ion pair complexes, [4-R-benzylpyridinium][bis(maleodinitriledithiolato)platinum(III)] (abbreviated as [RBzPy][Pt(mnt)(2)]; R = Cl (1), Br (2), or NO(2) (3)), have been synthesized. The cations and anions stack into well-separated columns in the solid state, and the Pt(III) ions form a 1-D zigzag chain within a [Pt(mnt)(2)](-) column through Pt...S, S...S, and Pt...S...Pt interactions. The chain is uniform in 1 and 2, while it alternates in 3. Unusual magnetic phase transitions from paramagnetism to diamagnetism were observed in these three complexes at approximately 275 K for 1, approximately 269 K for 2, and approximately 184 K for 3. These phase transitions were also found in DSC measurements for 1 and 2. The overall magnetic behaviors for 1-3 indicate the presence of antiferromagnetic exchange interactions in the high-temperature phase and spin-gapped systems in the low-temperature phase. Below 50 K, 2 exhibits weak ferromagnetism. The spontaneous moments are nearly repressed by a field of 1.0 T. The crystal structure of 2 at 173 K reveals that there are two crystallographically independent [Pt(mnt)(2)](-) entries in an asymmetric unit. These two crystallographically independent [Pt(mnt)(2)](-) entries satisfy the spin-canting condition, and the EPR spectra measured at room temperature exhibit anisotropic character. Therefore, the weak ferromagnetic behavior in the low-temperature region for 2 can be attributed to the spin-canting phenomenon.

Putative SNP discovery in interspecific hybrids of catfish by comparative EST analysis

In this study, we identified putative SNP markers within genes by comparative analysis of expressed sequence tags (ESTs). Comparison of 849 ESTs from blue catfish (Ictalurus furcatus) with >11,000 ESTs from channel catfish (I. punctatus) deposited in GenBank resulted in the identification of 1020 putative SNPs within 161 genes, of which 145 were nuclear genes of known function. The observed frequency of SNPs within ESTs of the two closely related catfish species was 1.32 SNP per 100 bp. The majority of identified SNPs differed between the two species and, therefore, these SNPs are useful for mapping genes in channel catfish x blue catfish interspecific resource families. The SNPs that differed within species were also observed; these can be applied to genome scans in channel catfish resource families.

Isolation and characterization of rice mutants compromised in Xa21-mediated resistance to X. oryzae pv. oryzae

The rice gene, Xa21, confers resistance to diverse races of Xanthomonas oryzae pv. oryzae (Xoo) and encodes a receptor-like kinase with leucine-rich repeats in the extra-cellular domain. To identify genes essential for the function of the Xa21 gene, 4,500 IRBB21 ( Xa21 isogenic line in IR24 background) mutants, induced by diepoxybutane and fast neutrons, were screened against Philippine race six (PR6) Xoo for a change from resistance to susceptibility. From two greenhouse screens, 23 mutants were identified that had changed from resistant to fully (6) or partially (17) susceptible to PR6. All fully susceptible mutants carried rearrangements at the Xa21 locus as detected by PCR and Southern hybridization. For the partially susceptible mutants, no changes were detected at the Xa21 locus based on Southern and PCR analyses. However, two of these mutants were confirmed via genetic analysis to have mutations at the Xa21 locus. Partially susceptible mutants exhibited variation in level of susceptibility to different Xoo strains, suggesting that they may carry different mutations required for the Xa21-mediated resistance. The mutants identified in this study provide useful materials for dissecting the Xa21-mediated resistance pathway in rice.

Generation and flanking sequence analysis of a rice T-DNA tagged population

Insertional mutagenesis provides a rapid way to clone a mutated gene. Transfer DNA (T-DNA) of Agrobacterium tumefaciens has been proven to be a successful tool for gene discovery in Arabidopsis and rice ( Oryza sativa L. ssp. japonica). Here, we report the generation of 5,200 independent T-DNA tagged rice lines. The T-DNA insertion pattern in the rice genome was investigated, and an initial database was constructed based on T-DNA flanking sequences amplified from randomly selected T-DNA tagged rice lines using Thermal Asymmetric Interlaced PCR (TAIL-PCR). Of 361 T-DNA flanking sequences, 92 showed long T-DNA integration (T-DNA together with non-T-DNA). Another 55 sequences showed complex integration of T-DNA into the rice genome. Besides direct integration, filler sequences and microhomology (one to several nucleotides of homology) were observed between the T-DNA right border and other portions of the vector pCAMBIA1301 in transgenic rice. Preferential insertion of T-DNA into protein-coding regions of the rice genome was detected. Insertion sites mapped onto rice chromosomes were scattered in the genome. Some phenotypic mutants were observed in the T1 generation of the T-DNA tagged plants. Our mutant population will be useful for studying T-DNA integration patterns and for analyzing gene function in rice.