Identification of insects, spiders and mites in vegetable crops. Workshop Manual, 2nd edition

Accurate and confident identification of the insects, spiders and mites in vegetable crops is the first step towards successful management of pests and natural enemies. It is an essential prerequisite for crop monitoring, which is the backbone of an effective pest management program. This workshop manual and trainer's handbook were compiled as part of an insect, spider and mite identification program for Australian vegetable growers. The workshop training is designed to help growers to: • know how to collect and preserve insects for identification • be able to classify most common insects (particularly those of horticultural significance) into broad groups • appreciate the importance of these groups in pest, predator and parasite identification and management • collect and classify some insect pests, predators and parasites of horticultural importance.

Identification of amino acid residues essential for enzyme activity of sheep liver 5,10-methylenetetrahydrofolate reductase

Sheep liver 5,10-methylenetetrahydrofolate reductase was subjected to specific chemical modification with phenylglyoxal, diethyl pyrocarbonate and N-bromosuccinimide. The second-order rate constants for inactivation were calculated to be 54 M-1 X min-1, 103 M-1 X min-1 and 154 M-1 X min-1 respectively. This inactivation could be prevented by incubation with substrates or products, suggesting that the residues modified, namely arginine, histidine and tryptophan, are essential for enzyme activity.

Identification of insects, spiders and mites in vegetable crops: Trainer's handbook

The trainers manual provides workshop plans and sample slides for trainers wishing to conduct the 'Identification of insects, spiders and mites in vegetable crops' workshop.

Bivalves for the remediation of prawn farm effluent: identification of some potentially useful species in Southern Queensland

Several species of oysters, clams and mussels are currently being used around the world to create extra profits and help remediate waste-waters from mariculture operations. To identify opportunities and potentially suitable species of bivalves for remediation of prawn farm effluent in Australia, recent literature dealing with bivalve filtration is reviewed, and species occurring naturally in a banana prawn, Penaeus (Fenneropenaeus) merguiensis, grow-out pond and effluent streams at the Bribie Island Aquaculture Research Centre (BIARC) were collected, identified and assessed in terms of their tolerance of high silt loadings over 3 months. Three bivalve species predominated in the BIARC case study. These were the mud ark, Anadara trapezia, the rock oyster, Dendostrea folium, and the pearl shell, Pinctada maculata. The mud ark demonstrated the highest tolerance of silt loading (99% survival), followed by pearl shells and rock oysters (88 and 63% survival respectively).

Microarrays in molecular profiling of cancer - focus on head and neck squamous cell carcinoma

Microarrays have a wide range of applications in the biomedical field. From the beginning, arrays have mostly been utilized in cancer research, including classification of tumors into different subgroups and identification of clinical associations. In the microarray format, a collection of small features, such as different oligonucleotides, is attached to a solid support. The advantage of microarray technology is the ability to simultaneously measure changes in the levels of multiple biomolecules. Because many diseases, including cancer, are complex, involving an interplay between various genes and environmental factors, the detection of only a single marker molecule is usually insufficient for determining disease status. Thus, a technique that simultaneously collects information on multiple molecules allows better insights into a complex disease. Since microarrays can be custom-manufactured or obtained from a number of commercial providers, understanding data quality and comparability between different platforms is important to enable the use of the technology to areas beyond basic research. When standardized, integrated array data could ultimately help to offer a complete profile of the disease, illuminating mechanisms and genes behind disorders as well as facilitating disease diagnostics. In the first part of this work, we aimed to elucidate the comparability of gene expression measurements from different oligonucleotide and cDNA microarray platforms. We compared three different gene expression microarrays; one was a commercial oligonucleotide microarray and the others commercial and custom-made cDNA microarrays. The filtered gene expression data from the commercial platforms correlated better across experiments (r=0.78-0.86) than the expression data between the custom-made and either of the two commercial platforms (r=0.62-0.76). Although the results from different platforms correlated reasonably well, combining and comparing the measurements were not straightforward. The clone errors on the custom-made array and annotation and technical differences between the platforms introduced variability in the data. In conclusion, the different gene expression microarray platforms provided results sufficiently concordant for the research setting, but the variability represents a challenge for developing diagnostic applications for the microarrays. In the second part of the work, we performed an integrated high-resolution microarray analysis of gene copy number and expression in 38 laryngeal and oral tongue squamous cell carcinoma cell lines and primary tumors. Our aim was to pinpoint genes for which expression was impacted by changes in copy number. The data revealed that especially amplifications had a clear impact on gene expression. Across the genome, 14-32% of genes in the highly amplified regions (copy number ratio >2.5) had associated overexpression. The impact of decreased copy number on gene underexpression was less clear. Using statistical analysis across the samples, we systematically identified hundreds of genes for which an increased copy number was associated with increased expression. For example, our data implied that FADD and PPFIA1 were frequently overexpressed at the 11q13 amplicon in HNSCC. The 11q13 amplicon, including known oncogenes such as CCND1 and CTTN, is well-characterized in different type of cancers, but the roles of FADD and PPFIA1 remain obscure. Taken together, the integrated microarray analysis revealed a number of known as well as novel target genes in altered regions in HNSCC. The identified genes provide a basis for functional validation and may eventually lead to the identification of novel candidates for targeted therapy in HNSCC.

Oral Actinomyces Species in Health and Disease: Identification, Occurence and Importance of Early Colonization

The genus Actinomyces consists of a heterogeneous group of gram-positive, mainly facultatively anaerobic or microaerobic rods showing various degrees of branching. In the oral cavity, streptococci and Actinomyces form a fundamental component of the indigenous microbiota, being among initial colonizers in polymicrobial biofilms. The significance of the genus Actinomyces is based on the capability of species to adhere to surfaces such as on teeth and to co-aggregate with other bacteria. Identification of Actinomyces species has mainly been based on only a few biochemical characteristics, such as pigmentation and catalase production, or on the use of a single commercial kit. The limited identification of oral Actinomyces isolates to species level has hampered knowledge of their role both in health and disease. In recent years, Actinomyces and related organisms have attracted the attention of clinical microbiologists because of a growing awareness of their presence in clinical specimens and their association with disease. This series of studies aimed to amplify the identification methods for Actinomyces species. With the newly developed identification scheme, the age-related occurrence of Actinomyces in healthy mouths of infants and their distribution in failed dental implants was investigated. Adhesion of Actinomyces species to titanium surfaces processed in various ways was studied in vitro. The results of phenotypic identification methods indicated a relatively low applicability of commercially available test kits for reliable identification within the genus Actinomyces. However, in the study of conventional phenotypic methods, it was possible to develop an identification scheme that resulted in accurate differentiation of Actinomyces and closely related species, using various different test methods. Genotypic methods based on 16S rRNA sequence analysis of Actinomyces proved to be a useful method for genus level identification and further clarified the species level identification with phenotypic methods. The results of the study of infants showed that the isolation frequency of salivary Actinomyces species increased according to age: thirty-one percent of the infants at 2 months but 97% at 2 years of age were positive for Actinomyces. A. odontolyticus was the most prominent Actinomyces colonizer during the study period followed in frequency by A. naeslundii and A. viscosus. In the study of explanted dental implants, Actinomyces was the most prevalent bacterial genus, colonizing 94% of the fixtures. Also in the implants A. odontolyticus was revealed as the most common Actinomyces species. It was present in 84% of Actinomyces -positive fixtures followed in frequency by A. naeslundii, A. viscosus and A. israelii. In an in vitro study of titanium surfaces, different Actinomyces species showed variation regarding their adhesion to titanium. Surface roughness as well as albumin coating of titanium had significant effects on adhesion. The use of improved phenotypic and molecular diagnostic methods increased the accuracy of the identification of the Actinomyces to species level. This facilitated an investigation of their occurrence and distribution in oral specimens in both health and disease.

Soft Functional Materials Induced by Fibrillar Networks of Small Molecular Photochromic Gelators

Low-molecular-mass organogelators (LMOGs) based on photochromic molecules aggregate in selected solvents to form gels through various spatio-temporal interactions. The factors that control the mode of aggregation of the chromophoric core in the LMOGs during gelation, gelation-induced changes in fluorescence, the formation of stacked superstructures of extended pi-conjugated systems, and so forth are discussed with selected examples. Possible ways of generating various light-harvesting assemblies are proposed, and some unresolved questions, future challenges, and their possible solutions on this topic are presented.

Choice of the End Functional Groups in Tri(p-phenylenevinylene) Derivatives Controls Its Physical Gelation Abilities

New supramolecular organogels based on all-trans-tri(p-phenylenevinylene) (TPV) systems possessing different terminal groups, e.g., oxime, hydrazone, phenylhydrazone, and semicarbazone have been synthesized. The self-assembly properties of the compounds that gelate in specific organic solvents and the aggregation motifs of these molecules in the organogels were investigated using UV−vis, fluorescence, FT-IR, and 1H NMR spectroscopy, electron microscopy, differential scanning calorimetry (DSC), and rheology. The temperature variable UV−vis and fluorescence spectroscopy in different solvents clearly show the aggregation pattern of the self-assemblies promoted by hydrogen bonding, aromatic π-stacking, and van der Waals interactions among the individual TPV units. Gelation could be controlled by variation in the number of hydrogen-bonding donors and acceptors in the terminal functional groups of this class of gelators. Also wherever gelation is observed, the individual fibers in gels change to other types of networks in their aggregates depending on the number of hydrogen-bonding sites in the terminal functions. Comparison of the thermal stability of the gels obtained from DSC data of different gelators demonstrates higher phase transition temperature and enthalpy for the hydrazone-based gelator. Rheological studies indicate that the presence of more hydrogen-bonding donors in the periphery of the gelator molecules makes the gel more viscoelastic solidlike. However, in the presence of more numbers of hydrogen-bonding donor/acceptors at the periphery of TPVs such as with semicarbazone a precipitation as opposed to gelation was observed. Clearly, the choice of the end functional groups and the number of hydrogen-bonding groups in the TPV backbone holds the key and modulates the effective length of the chromophore, resulting in interesting optical properties.

Photo identification portrait of Walter Reiss Portraits Men

Walter Reiss, 1908-1937

Functional evaluation of genetic variants associated with endometriosis near GREB1

STUDY QUESTION: Do DNA variants in the growth regulation by estrogen in breast cancer 1 (GREB1) region regulate endometrial GREB1 expression and increase the risk of developing endometriosis in women? SUMMARY ANSWER: We identified new single nucleotide polymorphisms (SNPs) with strong association with endometriosis at the GREB1 locus although we did not detect altered GREB1 expression in endometriosis patients with defined genotypes. WHAT IS ALREADY KNOWN: Genome-wide association studies have identified the GREB1 region on chromosome 2p25.1 for increasing endometriosis risk. The differential expression of GREB1 has also been reported by others in association with endometriosis disease phenotype. STUDY DESIGN, SIZE, DURATION: Fine mapping studies comprehensively evaluated SNPs within the GREB1 region in a large-scale data set (>2500 cases and >4000 controls). Publicly available bioinformatics tools were employed to functionally annotate SNPs showing the strongest association signal with endometriosis risk. Endometrial GREB1 mRNA and protein expression was studied with respect to phases of the menstrual cycle (n = 2-45 per cycle stage) and expression quantitative trait loci (eQTL) analysis for significant SNPs were undertaken for GREB1 [mRNA (n = 94) and protein (n = 44) in endometrium]. PARTICIPANTS/MATERIALS, SETTING, METHODS: Participants in this study are females who provided blood and/or endometrial tissue samples in a hospital setting. The key SNPs were genotyped using Sequenom MassARRAY. The functional roles and regulatory annotations for identified SNPs are predicted by various publicly available bioinformatics tools. Endometrial GREB1 expression work employed qRT-PCR, western blotting and immunohistochemistry studies. MAIN RESULTS AND THE ROLE OF CHANCE: Fine mapping results identified a number of SNPs showing stronger association (0.004 < P < 0.032) with endometriosis risk than the original GWAS SNP (rs13394619) (P = 0.034). Some of these SNPs were predicted to have functional roles, for example, interaction with transcription factor motifs. The haplotype (a combination of alleles) formed by the risk alleles from two common SNPs showed significant association (P = 0.026) with endometriosis and epistasis analysis showed no evidence for interaction between the two SNPs, suggesting an additive effect of SNPs on endometriosis risk. In normal human endometrium, GREB1 protein expression was altered depending on the cycle stage (significantly different in late proliferative versus late secretory, P < 0.05) and cell type (glandular epithelium, not stromal cells). However, GREB1 expression in endometriosis cases versus controls and eQTL analyses did not reveal any significant changes. LIMITATIONS, REASONS FOR CAUTION: In silico prediction tools are generally based on cell lines different to our tissue and disease of interest. Functional annotations drawn from these analyses should be considered with this limitation in mind. We identified cell-specific and hormone-specific changes in GREB1 protein expression. The lack of a significant difference observed following our GREB1 expression studies may be the result of moderate power on mixed cell populations in the endometrial tissue samples. WIDER IMPLICATIONS OF THE FINDINGS: This study further implicates the GREB1 region on chromosome 2p25.1 and the GREB1 gene with involvement in endometriosis risk. More detailed functional studies are required to determine the role of the novel GREB1 transcripts in endometriosis pathophysiology. STUDY FUNDING/COMPETING INTERESTS: Funding for this work was provided by NHMRC Project Grants APP1012245, APP1026033, APP1049472 and APP1046880. There are no competing interests.

Biochemical and structural characterization of residue 96 mutants of Plasmodium falciparum triosephosphate isomerase: active-site loop conformation, hydration and identification of a dimer-interface ligand-binding site

Plasmodium falciparum TIM (PfTIM) is unique in possessing a Phe residue at position 96 in place of the conserved Ser that is found in TIMs from the majority of other organisms. In order to probe the role of residue 96, three PfTIM mutants, F96S, F96H and F96W, have been biochemically and structurally characterized. The three mutants exhibited reduced catalytic efficiency and a decrease in substrate-binding affinity, with the most pronounced effects being observed for F96S and F96H. The k(cat) values and K-m values are (2.54 +/- 0.19) x 10(5) min(-1) and 0.39 +/- 0.049 mM, respectively, for the wild type; (3.72 +/- 0.28) x 10(3) min(-1) and 2.18 +/- 0.028 mM, respectively, for the F96S mutant;(1.11 +/- 0.03) x 10(4) min(-1) and 2.62 +/- 0.042 mM, respectively, for the F96H mutant; and (1.48 +/- 0.05) x 10(5) min(-1) and 1.20 +/- 0.056 mM, respectively, for the F96W mutant. Unliganded and 3-phosphoglycerate (3PG) complexed structures are reported for the wild-type enzyme and the mutants. The ligand binds to the active sites of the wild-type enzyme (wtPfTIM) and the F96W mutant, with a loop-open state in the former and both open and closed states in the latter. In contrast, no density for the ligand could be detected at the active sites of the F96S and F96H mutants under identical conditions. The decrease in ligand affinity could be a consequence of differences in the water network connecting residue 96 to Ser73 in the vicinity of the active site. Soaking of crystals of wtPfTIM and the F96S and F96H mutants resulted in the binding of 3PG at a dimer-interface site. In addition, loop closure at the liganded active site was observed for wtPfTIM. The dimer-interface site in PfTIM shows strong electrostatic anchoring of the phosphate group involving the Arg98 and Lys112 residues of PfTIM.

Virus identification and development of long-term management strategies for the rhubarb industry

The purpose of this report is to present the final results of all activities conducted under HAL Project VG05053 ‘Virus identification and development of long-term management strategies for the rhubarb industry’. The report provides a summary of project findings, a description of technology transfer activities, and recommendations arising from the outcomes of the project. The overall objective of this project was to devise a strategy for the control of rhubarb decline disease through 1) knowledge of the viruses present and their epidemiology, 2) production of virus-free planting material via tissue culture, and 3) formation of a national grower group to represent industry.

DAQ339A Pest and disease identification and management in herbs

The major objective is to produce an educational tool for growers and research/extension personnel to allow accurate identification of a range of pests and diseases encountered in herbs. To a lessor extent develop both a mechanism to manage beneficial insects in field crops pre-harvest and to identify some common seed borne diseases in herbs.