The identification and characterisation of alleles of sucrose phosphate synthase gene family III in sugarcane

Little is known about the extent of allelic diversity of genes in the complex polyploid, sugarcane. Using sucrose phosphate synthase (SPS) Gene (SPS) Family III as an example, we have amplified and sequenced a 400 nt region from this gene from two sugarcane lines that are parents of a mapping population. Ten single nucleotide polymorphisms (SNPs) were identified within the 400 nt region of which seven were present in both lines. In the elite commercial cultivar Q165(A), 10 sequence haplotypes were identified, with four haplotypes recovered at 9% or greater frequency. Based on SNP presence, two clusters of haplotypes were observed. In IJ76-514, a Saccharum officinarum accession, 8 haplotypes were identified with 4 haplotypes recovered at 13% or greater frequency. Again, two clusters of haplotypes were observed. The results suggest that there may be two SPS Gene Family III genes per genome in sugarcane, each with different numbers of different alleles. This suggestion is supported by sequencing results in an elite parental sorghum line, 403463-2-1, in which 4 haplotypes, corresponding to two broad types, were also identified. Primers were designed to the sugarcane SNPs and screened over bulked DNA from high and low Sucrose-containing progeny from a cross between Q165(A) and IJ76-514. The SNP frequency did not vary in the two bulked DNA samples, suggesting that these SNPs from this SPS gene family are not associated with variation in sucrose content. Using an ecotilling approach, two of the SPS Gene Family III haplotypes were mapped to two different linkage groups in homology group 1 in Q165(A). Both haplotypes mapped near QTLs for increased sucrose content but were not themselves associated with any sugar-related trait.

Spectral pattern, grouping, and the pitches of complex tones and their components

Harmonically related components are typically heard as a unified entity with a rich timbre and a pitch corresponding to the fundamental frequency. Mistuning a component generally has four consequences: (i) the global pitch of the complex shifts in the same direction as the mistuning; (ii) the component makes a reduced contribution to global pitch; (iii) the component is heard out as a separate sound with a pure timbre; (iv) its pitch differs from that of a pure tone of equal frequency in a small but systematic way. Local interactions between neighbouring components cannot explain these effects; instead they are usually explained in terms of the global operation of a single harmonic-template mechanism. However, several observations indicate that separate mechanisms govern the selection of spectral components for perceptual fusion and for the computation of global pitch. First, an increase in mistuning causes a harmonic to be heard out before it begins to be excluded from the computation of global pitch. Second, a single even harmonic added to an odd-harmonic complex is typically more salient than its odd neighbours. Third, the mistuning of a component in frequency-shifted stimuli, or stimuli with a moderate spectral stretch, results in changes in salience and component pitch like those seen for harmonic stimuli. Fourth, the global pitch of frequency-shifted stimuli is predicted well by the weighted fit of a harmonic template, but, with the exception of the lowest component, the fusion of individual partials for shifted stimuli is best predicted by the common pattern of spectral spacing. Fifth, our sensitivity to spectral pattern is surprisingly resistant to random variations in component spacing induced by applying mistunings to several harmonics at once. These findings are evaluated in the context of an autocorrelogram model of the proposed pitch/grouping dissociation. © S. Hirzel Verlag · EAA.

A systems and cybernetic perspective on complex problem solving

This thesis is concerned with Organisational Problem Solving. The work reflects the complexities of organisational problem situations and the eclectic approach that has been necessary to gain an understanding of the processes involved. The thesis is structured into three main parts. Part I describes the author's understanding of problems and suitable approaches. Chapter 2 identifies the Transcendental Realist (TR) view of science (Harre 1970, Bhaskar 1975) as the best general framework for identifying suitable approaches to complex organisational problems. Chapter 3 discusses the relationship between Checkland's methodology (1972) and TR. The need to generate iconic (explanatory) models of the problem situation is identified and the ability of viable system modelling to supplement the modelling stage of the methodology is explored in Chapter 4. Chapter 5 builds further on the methodology to produce an original iconic model of the methodological process. The model characterises the mechanisms of organisational problem situations as well as desirable procedural steps. The Weltanschauungen (W's) or "world views" of key actors is recognised as central to the mechanisms involved. Part II describes the experience which prompted the theoretical investigation. Chapter 6 describes the first year of the project. The success of this stage is attributed to the predominance of a single W. Chapter 7 describes the changes in the organisation which made the remaining phase of the project difficult. These difficulties are attributed to a failure to recognise the importance of differing W's. Part III revisits the theoretical and organisational issues. Chapter 8 identifies a range of techniques embodying W's which are compatible with .the framework of Part I and which might usefully supplement it. Chapter 9 characterises possible W's in the sponsoring organisation. Throughout the work, an attempt 1s made to reflect the process as well as the product of the author's leaving.

Discriminating antigen and non-antigen using proteome dissimilarity III:tumour and parasite antigens

Computational genome analysis enables systematic identification of potential immunogenic proteins within a pathogen. Immunogenicity is a system property that arises through the interaction of host and pathogen as mediated through the medium of a immunogenic protein. The overt dissimilarity of pathogenic proteins when compared to the host proteome is conjectured by some to be the determining principal of immunogenicity. Previously, we explored this idea in the context of Bacterial, Viral, and Fungal antigen. In this paper, we broaden and extend our analysis to include complex antigens of eukaryotic origin, arising from tumours and from parasite pathogens. For both types of antigen, known antigenic and non-antigenic protein sequences were compared to human and mouse proteomes. In contrast to our previous results, both visual inspection and statistical evaluation indicate a much wider range of homologues and a significant level of discrimination; but, as before, we could not determine a viable threshold capable of properly separating non-antigen from antigen. In concert with our previous work, we conclude that global proteome dissimilarity is not a useful metric for immunogenicity for presently available antigens arising from Bacteria, viruses, fungi, parasites, and tumours. While we see some signal for certain antigen types, using dissimilarity is not a useful approach to identifying antigenic molecules within pathogen genomes.

Covalent attachment of chiral manganese(III) salen complexes onto functionalised hexagonal mesoporous silica and application to the asymmetric epoxidation of alkenes

Two modified Jacobsen-type catalysts were anchored onto an amine functionalised hexagonal mesoporous silica (HMS) using two distinct anchoring procedures: (i) one was anchored directly through the carboxylic acid functionalised diimine bridge fragment of the complex (CAT1) and (ii) the other through the hydroxyl group on the aldehyde fragment of the complex (CAT2), mediated by cyanuric chloride. The new heterogeneous catalyst, as well as the precedent materials, were characterised by elemental analyses, DRIFT, UV-vis, porosimetry and XPS which showed that the complexes were successfully anchored onto the hexagonal mesoporous silica. These materials acted as active heterogeneous catalysts in the epoxidation of styrene, using m-CPBA as oxidant, and α-methylstyrene, using NaOCl as oxidant. Under the latter conditions they acted also as enantioselective heterogeneous catalysts. Furthermore, when compared to the reaction run in homogeneous phase under similar experimental conditions, an increase in asymmetric induction was observed for the heterogenised CAT1, while the opposite effect was observed for the heterogenised CAT2, despite of CAT2 being more enantioselective than CAT1 in homogeneous phase. These results indicate that the covalent attachment of the Jacobsen catalyst through the diimine bridge leads to improved enantiomeric excess (%ee), whereas covalent attachment through one of the aldehyde fragments results in a negative effect in the %ee. Using α-methylstyrene and NaOCl as oxidant, heterogeneous catalyst reuse led to no significant loss of catalytic activity and enantioselectivity. © 2005 Elsevier Inc. All rights reserved.

Labeled EF-Tus for rapid kinetic studies of pretranslocation complex formation

The universally conserved translation elongation factor EF-Tu delivers aminoacyl(aa)-tRNA in the form of an aa-tRNA·EF-Tu·GTP ternary complex (TC) to the ribosome where it binds to the cognate mRNA codon within the ribosomal A-site, leading to formation of a pretranslocation (PRE) complex. Here we describe preparation of QSY9 and Cy5 derivatives of the variant E348C-EF-Tu that are functional in translation elongation. Together with fluorophore derivatives of aa-tRNA and of ribosomal protein L11, located within the GTPase associated center (GAC), these labeled EF-Tus allow development of two new FRET assays that permit the dynamics of distance changes between EF-Tu and both L11 (Tu-L11 assay) and aa-tRNA (Tu-tRNA assay) to be determined during the decoding process. We use these assays to examine: (i) the relative rates of EF-Tu movement away from the GAC and from aa-tRNA during decoding, (ii) the effects of the misreading-inducing antibiotics streptomycin and paromomycin on tRNA selection at the A-site, and (iii) how strengthening the binding of aa-tRNA to EF-Tu affects the rate of EF-Tu movement away from L11 on the ribosome. These FRET assays have the potential to be adapted for high throughput screening of ribosomal antibiotics.

Deconvolution of magnetic acoustic change complex (mACC)

Objective: The aim of this study was to design a novel experimental approach to investigate the morphological characteristics of auditory cortical responses elicited by rapidly changing synthesized speech sounds. Methods: Six sound-evoked magnetoencephalographic (MEG) responses were measured to a synthesized train of speech sounds using the vowels /e/ and /u/ in 17 normal hearing young adults. Responses were measured to: (i) the onset of the speech train, (ii) an F0 increment; (iii) an F0 decrement; (iv) an F2 decrement; (v) an F2 increment; and (vi) the offset of the speech train using short (jittered around 135. ms) and long (1500. ms) stimulus onset asynchronies (SOAs). The least squares (LS) deconvolution technique was used to disentangle the overlapping MEG responses in the short SOA condition only. Results: Comparison between the morphology of the recovered cortical responses in the short and long SOAs conditions showed high similarity, suggesting that the LS deconvolution technique was successful in disentangling the MEG waveforms. Waveform latencies and amplitudes were different for the two SOAs conditions and were influenced by the spectro-temporal properties of the sound sequence. The magnetic acoustic change complex (mACC) for the short SOA condition showed significantly lower amplitudes and shorter latencies compared to the long SOA condition. The F0 transition showed a larger reduction in amplitude from long to short SOA compared to the F2 transition. Lateralization of the cortical responses were observed under some stimulus conditions and appeared to be associated with the spectro-temporal properties of the acoustic stimulus. Conclusions: The LS deconvolution technique provides a new tool to study the properties of the auditory cortical response to rapidly changing sound stimuli. The presence of the cortical auditory evoked responses for rapid transition of synthesized speech stimuli suggests that the temporal code is preserved at the level of the auditory cortex. Further, the reduced amplitudes and shorter latencies might reflect intrinsic properties of the cortical neurons to rapidly presented sounds. Significance: This is the first demonstration of the separation of overlapping cortical responses to rapidly changing speech sounds and offers a potential new biomarker of discrimination of rapid transition of sound.

Performance on WAIS-III relates to the Ability to Derive Relations

Experimental evidence suggests that derived relational responding (DRR) may provide a behavioral model of complex language phenomena. This study assigned 72 students to groups based upon their performance on a complex relational task. It was found that performance on DRR relates to scores on the WAIS-III.

Chemical composition of igneous rocks and origin of the sill and pillow-basalt complex at DSDP Site 61-462

The sill and pillow complex cored on Deep Sea Drilling Project Leg 61 (Site 462) is divided into two groups, A and B types, on the basis of chemical composition and volcanostratigraphy. The A-type basalt is characterized by a higher FeO*/MgO ratio and abundant TiO2, whereas the B-type basalt is characterized by a lower FeO*/MgO ratio and scarcity of TiO2. The A type is composed of sills interbedded with hyaloclastic sediments, and the B type consists of basalt sills and pillow basalt with minor amounts of sediment. However, the structure of pillow basalts in the B type is atypical; they might be eruptive. From paleontological study of the interbedded sediments and radiometric age determination of the basalt, the volcanic event of A type is assumed to be Cenomanian to Aptian, and that of B type somewhat older. The oceanic crust in the Nauru Basin was assumed to be Oxfordian, based on the Mesozoic magnetic anomaly. Consequently, two events of intraplate volcanism are recognized. It is thus assumed that the sill-pillow complex did not come from a normal oceanic ridge, and that normal oceanic basement could therefore underlie the complex. The Site 462 basalts are quartz-normative, and strongly hypersthene-normative, and have a higher FeO*/MgO ratio and lower TiO2 content. Olivine from the Nauru Basin basalts has a lower Mg/(Mg + Fe**2+) ratio (0.83-0.84) and coexists with spinel of lower Mg/(Mg + Fe**2+) ratio when compared to olivine-spinel pairs from mid-ocean ridge (MAR) basalt. The glass of spinel-bearing basalts has a higher FeO*/(FeO* + MgO) ratio (0.58-0.60) than that of MAR (<0.575). Therefore, the Nauru Basin basalts are chemically and mineralogically distinct from ocean-ridge tholeiite. That the Nauru Basin basalts are quartz-normative and strongly hypersthene-normative and have a lower TiO2 content suggests that the basaltic liquids of Site 462 were generated at shallower depths (<5 kbar) than ocean-ridge tholeiite: Site 462 basalts are similar to basalts from the Manihiki Plateau and the Ontong-Java Plateau, but different from Hawaiian tholeiite of hot-spot type, with lower K2O and TiO2 content. We propose a new type of basalt, ocean-plateau tholeiite, a product of intraplate volcanism.

Geochemistry of sheeted dike complex minerals of ODP Hole 140-504B

Diabases were recovered during Legs 137 and 140 at Hole 504B from depths between 1621.5 and 2000.4 meters below seafloor in the lower sheeted dike complex. The samples contain multiple generations of millimetric to centimetric veins. The orientation of the measured veins suggests that two main vein sets exist: one characterized by shallow dipping and the other by random trend. Thermal contraction during rock cooling is considered the main mechanism responsible for fracture formation. Vein infill is related to the circulation of hydrothermal fluids near the spreading axis. Some veins are surrounded by millimeter-sized alteration halos due to fluid percolation from the fractures through the host rock. Vein-filling minerals are essentially amphibole, chlorite, and zeolites. Amphibole composition is controlled by the microstructural site of the rock. Actinolite is the main amphibole occurring in the veins and also in the groundmass away from the halos. In the alteration halos, amphibole shows composition of actinolitic hornblende and Mg-hornblende. Late-stage tension gashes and interstitial spaces in some amphibole-bearing veins are filled with zeolites, suggesting that the veins likely suffered multiple opening stages that record the cooling history of the circulating fluids. Evidence of deformation recorded by the recovered samples seems to be restricted to veins that clearly represent elements of weakness of the rock. On the basis of vein geometry and microstructure we infer structural interpretations for the formation mechanism and for deformation of veins.

The silent statue theme: complex imitation and Neo-Latin poetry

This paper analyses how the topic of the silent statue is dealt with in Neo-Latin literature. The subject matter comes from the epigrams about Pythagoras of the Palatine Anthology. There are numerous Neo-Latin imitations of this topic that are complex as various sources are used at the same time. The authors focus on an active reading of the epigrams of their predecessors, applying the traditional motive to new subjects and adapting it to the religious theme.

Laparoscopic versus open total mesorectal excision for stage I-III mid and low rectal cancer: a retrospective 5 years analysis

Introduction. Total mesorectal excision (TME) is the cornerstone of a correct surgical therapy for extraperitoneal rectal cancer. Aim of the study is to evaluate our 5 years experience confronting retrospectively laparoscopic (lap) TME in respect to its laparotomic (open) counterpart. Patients and Methods. 30 patients were treated laparoscopically for stage I-III extraperitoneal rectal cancer and retrospectively compared to a homogeneous group, stratified for sex, age, comorbidities and stage of disease. Results. 30 days mortality was zero for both groups, while morbidity was 20% for the lap group and 36.6% for the open group. Mean lymph nodes harvested was 24 ± 12 for the lap group, 26 ± 14 for the open group (p > 0.05). Five years overall and disease free survival was respectively 82.2% and 81.4% in the lap group, 79.9% and 79.6% in the open group, without statistical significance (p>0.05). Discussion. Minimally invasive TME resulted a safe, effective and oncologically adequate procedure when retrospectively compared to its laparotomic counterpart, with 5 years overall survival and disease free survival reaching no statistical significance compared to the open approach, but with all the advantages of the laparoscopy such as less pain and blood loss, faster recovery, less morbidity and better cosmetics. Conclusions. Our study has retrospectively demonstrated that laparoscopic TME is feasible and oncologically effective, even if it remains a complex minimally invasive procedure, requiring adequate skill. More prospective, randomized studies are necessary to define such a procedure as the new gold standard in treatment of stage I-III extraperitoneal rectal cancer.

Growth and application of planar III-V semiconductor nanowires grown with MOCVD

The semiconductor nanowire has been widely studied over the past decade and identified as a promising nanotechnology building block with application in photonics and electronics. The flexible bottom-up approach to nanowire growth allows for straightforward fabrication of complex 1D nanostructures with interesting optical, electrical, and mechanical properties. III-V nanowires in particular are useful because of their direct bandgap, high carrier mobility, and ability to form heterojunctions and have been used to make devices such as light-emitting diodes, lasers, and field-effect transistors. However, crystal defects are widely reported for III-V nanowires when grown in the common out-of-plane <111>B direction. Furthermore, commercialization of nanowires has been limited by the difficulty of assembling nanowires with predetermined position and alignment on a wafer-scale. In this thesis, planar III-V nanowires are introduced as a low-defect and integratable nanotechnology building block grown with metalorganic chemical vapor deposition. Planar GaAs nanowires grown with gold seed particles self-align along the <110> direction on the (001) GaAs substrate. Transmission electron microscopy reveals that planar GaAs nanowires are nearly free of crystal defects and grow laterally and epitaxially on the substrate surface. The nanowire morphology is shown to be primarily controlled through growth temperature and an ideal growth window of 470 +\- 10 °C is identified for planar GaAs nanowires. Extension of the planar growth mode to other materials is demonstrated through growth of planar InAs nanowires. Using a sacrificial layer, the transfer of planar GaAs nanowires onto silicon substrates with control over the alignment and position is presented. A metal-semiconductor field-effect transistor fabricated with a planar GaAs nanowire shows bulk-like low-field electron transport characteristics with high mobility. The aligned planar geometry and excellent material quality of planar III-V nanowires may lead to highly integrated III-V nanophotonics and nanoelectronics.

Exploring complex chemical systems: insights from mass spectrometry, electrochemistry and continuous cell culture

The work presented herein covers a broad range of research topics and so, in the interest of clarity, has been presented in a portfolio format. Accordingly, each chapter consists of its own introductory material prior to presentation of the key results garnered, this is then proceeded by a short discussion on their significance. In the first chapter, a methodology to facilitate the resolution and qualitative assessment of very large inorganic polyoxometalates was designed and implemented employing ion-mobility mass spectrometry. Furthermore, the potential of this technique for ‘mapping’ the conformational space occupied by this class of materials was demonstrated. These claims are then substantiated by the development of a tuneable, polyoxometalate-based calibration protocol that provided the necessary platform for quantitative assessments of similarly large, but unknown, polyoxometalate species. In addition, whilst addressing a major limitation of travelling wave ion mobility, this result also highlighted the potential of this technique for solution-phase cluster discovery. The second chapter reports on the application of a biophotovoltaic electrochemical cell for characterising the electrogenic activity inherent to a number of mutant Synechocystis strains. The intention was to determine the key components in the photosynthetic electron transport chain responsible for extracellular electron transfer. This would help to address the significant lack of mechanistic understanding in this field. Finally, in the third chapter, the design and fabrication of a low-cost, highly modular, continuous cell culture system is presented. To demonstrate the advantages and suitability of this platform for experimental evolution investigations, an exploration into the photophysiological response to gradual iron limitation, in both the ancestral wild type and a randomly generated mutant library population, was undertaken. Furthermore, coupling random mutagenesis to continuous culture in this way is shown to constitute a novel source of genetic variation that is open to further investigation.

Mutation in NDUFA13/GRIM19 leads to early onset hypotonia, dyskinesia and sensorial deficiencies, and mitochondrial complex I instability

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