A sampling technique for two-spotted mite in papaya

Two-spotted mite, Tetranychus urticae Koch, was until recently regarded as a minor and infrequent pest of papaya in Queensland through the dry late winter/early summer months. The situation has changed over the past 4-5 years, so that now some growers consider spider mites significant pests all year round. This altered pest status corresponded with a substantial increase in the use of fungicides to control black spot (Asperisporium caricae). A project was initiated in 1998 to examine the potential reasons for escalating mite problems in commercially-grown papaya, which included regular sampling over a 2 year period for mites, mite damage and beneficial arthropods on a number of farms on the wet tropical coast and drier Atherton Tableland. Differences in soil type, papaya variety, chemical use and some agronomic practices were included in this assessment. Monthly visits were made to each site where 20 randomly-selected plants from each of 2 papaya lines (yellow and red types) were surveyed. Three leaves were selected from each plant, one from each of the bottom, middle and top strata of leaves. The numbers of mobile predators were recorded, along with visual estimates of the percentage and age of mite damage on each leaf. Leaves were then sprayed with hairspray to fix the mites and immature predators to the leaf surface. Four leaf disks, 25 mm in diameter, were then punched from each leaf into a 50 ml storage container with a purpose-built disk-cutting tool. Disks from each leaf position were separated by tissue paper, within the container. On return to the laboratory, each leaf disk was scrutinised under a binocular microscope to determine the numbers of two-spotted mites and eggs, predatory mites and eggs, and the immature stages of predatory insects (mainly Stethorus, Halmus and lacewings). A total of 2160 leaf disks have been examined each month. All data have been entered into an Access database to facilitate comparisons between sites.

Catalysis and mechanism of malonyl transferase activity in type II fatty acid biosynthesis acyl carrier proteins

One of the unexplored, yet important aspects of the biology of acyl carrier proteins (ACPs) is the self-acylation and malonyl transferase activities dedicated to ACPs in polyketide synthesis. Our studies demonstrate the existence of malonyl transferase activity in ACPs involved in type II fatty acid biosynthesis from Plasmodium falciparum and Escherichia coli. We also show that the catalytic malonyl transferase activity is intrinsic to an individual ACP. Mutational analysis implicates an arginine/lysine in loop II and an arginine/glutamine in helix III as the catalytic residues for transferase function. The hydrogen bonding properties of these residues appears to be indispensable for the transferase reaction. Complementation of fabD(Ts) E. coli highlights the putative physiological role of this process. Our studies thus shed light on a key aspect of ACP biology and provide insights into the mechanism involved therein.

Structural Basis of Drug Resistance by Genetic Variants of HIV Type 1 Clade C Protease from India

Using computer modeling of three-dimensional structures and structural information available on the crystal structures of HIV-1 protease, we investigated the structural effects of mutations, in treatment-naive and treatment-exposed individuals from India and postulated mechanisms of resistance in clade C variants. A large number of models (14) have been generated by computational mutation of the available crystal structures of drug bound proteases. Localized energy minimization was carried out in and around the sites of mutation in order to optimize the geometry of interactions present. Most of the mutations result in structural differences at the flap that favors the semiopen state of the enzyme. Some of the mutations were also found to confer resistance by affecting the geometry of the active site. The E35D mutation affects the flap structure in clade B strains and E35N and E35K mutation, seen in our modeled strains, have a more profound effect. Common polymorphisms at positions 36 and 63 in clade C also affected flap structure. Apart from a few other residues Gln-58, Asn-83, Asn-88, and Gln-92 and their interactions are important for the transition from the closed to the open state. Development of protease inhibitors by structure-based design requires investigation of mechanisms operative for clade C to improve the efficacy of therapy.

New Perspectives on the Roman Coinage on the Eastern Limes in the Late Republican and Roman Imperial Period

The Ph.D. thesis discusses the monetary development in Roman Syria and Judaea in the Late Republican and the Early Imperial Period, from a numismatic, archaeological and historical point of view. In effect, the work focuses on the 1st century B.C. to the 1st century A.D., that is, the assumed time of introduction of Roman denarii to the region. The work benefits from the silver coin hoards of Khirbet Qumran recently published by the author. Though discovered as early as 1955 at Qumran, where the famous Dead Sea Scrolls had been found prior to that in 1947, most hoards remained unpublished until 2007. A second important source utilized is the so-called Tax Law from Palmyra in Syria. Its significance lies in the fact that Palmyra used to be one of the most important cities on the Silk Road, along which luxury goods were transported into the Roman Empire and Rome itself. During the research conducted, studies of the provincial coinage of Judaea (A.D. 6-66) shed new light on the authority of the Roman governors in economic and monetary matters in eastern Mediterranean regions. Furthermore, a new suggestion as to the length of the mandate period of Pontius Pilate is made. The extent of Emperor Augustus monetary reforms as well as the military history of Judaea are discussed in the light of new analytical studies, which show that the production of Roman base metal coins appears to have been a highly controlled process, contrary to popular opinion. Statistical calculations related to the coin alloy revealed striking similarities with Roman and other local metalwork found in Israel; a fact previously unknown. Results indicate that both Roman and local metalwork consisted of outstandingly systematized practises and may have exploited the same metal sources. Information: Kenneth Lönnqvist (*25.7.1962) has studied at the University of Helsinki since 1981. Furthermore, Lönnqvist has lived in the Mediterranean countries and the Near East, and made research there at various scientific institutions and universities for ca. 7 years. Contact and sales of thesis: kenneth.lonnqvist@helsinki.fi

Family type and depression in pregnancy: Factors mediating risk in a community sample

The rate of severe depression among women in single-parent and biological families and in a variety of stepfamilies was examined in a large community sample of 13,088 pregnant women in the United Kingdom. Compared with women in biological families and published population rates, women in single-parent families and step-families reported significantly elevated rates of depression. Family-type differences in several risk factors were examined, including cohabiting (vs. married) status, relationship history, and socioeconomic and psychosocial risks, such as crowding, social support, and stressful life events. Family-type differences in depression were mediated partly by differences in social support, stressful life events, and crowding, but a main effect of family type in predicting depression remained after statistically controlling for these risks.

Death, Destruction and Commemoration : Tracing ritual activities in Finnish Late Iron Age cemeteries (AD 550-1150)

The thesis is connected with death, memory and ancestor commemoration during the Merovingian Period, the Viking Age and the beginning of the Crusade Period (AD 550-1150) in Finland. During this time, cremation was the dominant burial rite. It was not until the end of the Viking Age that inhumation became more common but both cremations and inhumations are performed even at the same sites throughout the time. Three different burial types 1) cremation cemeteries below level ground, 2) inhumation burials and 3) water burials are discussed in five articles. I consider these burial forms from three different viewpoints; collectivity-individuality, visibility-invisibility and cremation-inhumation. The thesis also discusses the topics of memory, memorialisation and monument re-use, which have been neglected subjects in Finnish archaeology until now. Both cremation cemeteries below level ground and inhumation burials have been re-used during their time of usage, and on most occasions are situated in a landscape that is overlaid by other monuments as well. The main questions of the thesis are: What kinds of ritual behaviour can we detect in the burials during the period (AD 550-1150)? How did people perceive the moraine hills that functioned as burial places? What kind of re-use can be detected in the Iron Age cemeteries? Why have ancient sites and artefacts been re-used? This thesis shows that it is possible to claim that both artefact and site re-use is a much more widespread phenomenon than has previously been thought in Finnish archaeology. It is also a conscious and deliberate behaviour that can be related to an ancestor cult and commemoration of the dead. The funerary rituals during this time period show great variation and complex, both regionally and nationally. Not only have the dead been buried using elaborate rituals, they have also been mourned and commemorated in intricate ways that proves that death was not an end product, but the start of something new.

Approaching Sacred Pregnancy : The Cult of the Visitation and Narrative Altarpieces in Late Fifteenth-Century Florence

The study focuses on the Visitation as a narrative subject of altarpieces in late fifteenth-century Florence. Although the Visitation was a well-known story in both verbal and visual representations since the early medieval period, it became a popular subject of altarpieces only towards the end of the fifteenth century. In this study, the first part provides an overview of the complex religious and historical background to an emerging cult of the Visitation. Devotional practices focusing on the Visitation belong in a context of late medieval Marian devotion and in 1389 a new feast of the Visitation was introduced into the liturgical calendar of the Catholic Church. Because of the ongoing schism within the Catholic Church, the feast was not unanimously accepted across Western Europe until the later part of the fifteenth century. Contrary to a widely disseminated view, the feast of the Visitation cannot be associated with Franciscan spirituality, but was rather a clearly defined Dominican project that primarily emphasised the importance of peace and unity within the Christian Church. Simultaneously with the gradual acceptance of the new feast, visual representations of the Visitation began to appear at the centre of altarpieces. The Visitation exemplifies an increasing preference for narrative subjects within the genre of the altarpiece. The second part of the study presents an analysis of the concept of the narrative altarpiece and highlights the complexities involved in combining a narrative content with the traditional devotional function of the altarpiece. In detailed case studies some prominent art works produced in Florence between 1490 and 1503 are discussed within a framework of contextual analysis, narrative theory and iconography. Altarpieces by Domenico Ghirlandaio, Piero di Cosimo and Mariotto Albertinelli represent visual manifestations of a cult of the Visitation with roots in late medieval devotional practices. At the same time, the altarpieces highlight the multiple functions of altarpieces in a culture where art works responded to a variety of social and religious needs. Building on earlier studies, each case study presents new insights and evidence not considered in previous art historical research.

Assessing the relationship between patch type and soil mites: A molecular approach

An urgent need exists for indicators of soil health and patch functionality in extensive rangelands that can be measured efficiently and at low cost. Soil mites are candidate indicators, but their identification and handling is so specialised and time-consuming that their inclusion in routine monitoring is unlikely. The aim of this study was to measure the relationship between patch type and mite assemblages using a conventional approach. An additional aim was to determine if a molecular approach traditionally used for soil microbes could be adapted for soil mites to overcome some of the bottlenecks associated with soil fauna diversity assessment. Soil mite species abundance and diversity were measured using conventional ecological methods in soil from patches with perennial grass and litter cover (PGL), and compared to soil from bare patches with annual grasses and/or litter cover (BAL). Soil mite assemblages were also assessed using a molecular method called terminal-restriction fragment length polymorphism (T-RFLP) analysis. The conventional data showed a relationship between patch type and mite assemblage. The Prostigmata and Oribatida were well represented in the PGL sites, particularly the Aphelacaridae (Oribatida). For T-RFLP analysis, the mite community was represented by a series of DNA fragment lengths that reflected mite sequence diversity. The T-RFLP data showed a distinct difference in the mite assemblage between the patch types. Where possible, T-RFLP peaks were matched to mite families using a reference 18S rDNA database, and the Aphelacaridae prevalent in the conventional samples at PGL sites were identified, as were prostigmatids and oribatids. We identified limits to the T-RFLP approach and this included an inability to distinguish some species whose DNA sequences were similar. Despite these limitations, the data still showed a clear difference between sites, and the molecular taxonomic inferences also compared well with the conventional ecological data. The results from this study indicated that the T-RFLP approach was effective in measuring mite assemblages in this system. The power of this technique lies in the fact that species diversity and abundance data can be obtained quickly because of the time taken to process hundreds of samples, from soil DNA extraction to data output on the gene analyser, can be as little as 4 days.

Detection of equine herpesvirus type 1 using a real-time polymerase chain reaction.

Equid herpesvirus 1 (EHV1) is a major disease of equids worldwide causing considerable losses to the horse industry. A variety of techniques, including PCR have been used to diagnose EHV1. Some of these PCRs were used in combination with other techniques such as restriction enzyme analysis (REA) or hybridisation, making them cumbersome for routine diagnostic testing and increasing the chances of cross-contamination. Furthermore, they involve the use of suspected carcinogens such as ethidium bromide and ultraviolet light. In this paper, we describe a real-time PCR, which uses minor groove-binding probe (MGB) technology for the diagnosis of EHV1. This technique does not require post-PCR manipulations thereby reducing the risk of cross-contamination. Most importantly, the technique is specific; it was able to differentiate EHV1 from the closely related member of the Alphaherpesvirinae, equid herpesvirus 4 (EHV4). It was not reactive with common opportunistic pathogens such as Escherichia coli, Klebsiella oxytoca, Pseudomonas aeruginosa and Enterobacter agglomerans often involved in abortion. Similarly, it did not react with equine pathogens such as Streptococcus equi, Streptococcus equisimilis, Streptococcus zooepidemicus, Taylorella equigenitalis and Rhodococcus equi, which also cause abortion. The results obtained with this technique agreed with results from published PCR methods. The assay was sensitive enough to detect EHV1 sequences in paraffin-embedded tissues and clinical samples. When compared to virus isolation, the test was more sensitive. This test will be useful for the routine diagnosis of EHV1 based on its specificity, sensitivity, ease of performance and rapidity.

Completion of the genome sequence of Lettuce necrotic yellows virus, type species of the genus Cytorhabdovirus

We completed the genome sequence of Lettuce necrotic yellows virus (LNYV) by determining the nucleotide sequences of the 4a (putative phosphoprotein), 4b, M (matrix protein), G (glycoprotein) and L (polymerase) genes. The genome consists of 12,807 nucleotides and encodes six genes in the order 3′ leader-N-4a(P)-4b-M-G-L-5′ trailer. Sequences were derived from clones of a cDNA library from LNYV genomic RNA and from fragments amplified using reverse transcription-polymerase chain reaction. The 4a protein has a low isoelectric point characteristic for rhabdovirus phosphoproteins. The 4b protein has significant sequence similarities with the movement proteins of capillo- and trichoviruses and may be involved in cell-to-cell movement. The putative G protein sequence contains a predicted 25 amino acids signal peptide and endopeptidase cleavage site, three predicted glycosylation sites and a putative transmembrane domain. The deduced L protein sequence shows similarities with the L proteins of other plant rhabdoviruses and contains polymerase module motifs characteristic for RNA-dependent RNA polymerases of negative-strand RNA viruses. Phylogenetic analysis of this motif among rhabdoviruses placed LNYV in a group with other sequenced cytorhabdoviruses, most closely related to Strawberry crinkle virus.

Notes on the type, synonyms, and other specimens of the balansioid fungus, Nigrocornus scleroticus

The type, and other specimens of the balansioid fungus, Nigrocornus scleroticus, its synonyms, and similar fungi studied during extensive research on the taxonomy and biology of the fungus, are described. Two hypocrealean fungi found parasitising the ascostromata of N. scleroticus are also discussed.

Characterization of disease resistance gene candidates of the nucleotide binding site (NBS) type from banana and correlation of a transcriptional polymorphism with resistance to Fusarium oxysporum f.sp. cubense race 4

Most plant disease resistance (R) genes encode proteins with a nucleotide binding site and leucine-rich repeat structure (NBS-LRR). In this study, degenerate primers were used to amplify genomic NBS-type sequences from wild banana (Musa acuminata ssp. malaccensis) plants resistant to the fungal pathogen Fusarium oxysporum formae specialis (f. sp.) cubense (FOC) race 4. Five different classes of NBS-type sequences were identified and designated as resistance gene candidates (RGCs). The deduced amino acid sequences of the RGCs revealed the presence of motifs characteristic of the majority of known plant NBS-LRR resistance genes. Structural and phylogenetic analyses grouped the banana RGCs within the non-TIR (homology to Toll/interleukin-1 receptors) subclass of NBS sequences. Southern hybridization showed that each banana RGC is present in low copy number. The expression of the RGCs was assessed by RT-PCR in leaf and root tissues of plants resistant or susceptible to FOC race 4. RGC1, 3 and 5 showed a constitutive expression profile in both resistant and susceptible plants whereas no expression was detected for RGC4. Interestingly, RGC2 expression was found to be associated only to FOC race 4 resistant lines. This finding could assist in the identification of a FOC race 4 resistance gene.

HNbWO6 and HTaWO6: Novel oxides related to ReO3 formed by ion exchange of rutile-type LiNbWO6 and LiTaWO6

Both LiNbWO6 and LiTaWO6 undergo ion exchange in hot aqueous H2SO4 yielding the hydrates HMWO6 · H2O (M = Nb or Ta). The reaction is accompanied by a structural transformation from the rutile to the ReO3 structure. The cell constants are a = 3.783(3)Å for HNbWO6 · H2O and a = 3.785(5)Å for HTaWO6 · H2O. The ReO3 structure is retained by the dehydration products HMWO6 and MWO5.5 as well. HMWO6 phases yield H1+xMWO6 hydrogen bronzes on exposure to hydrogen in the presence of platinum catalyst.

Identification of two distinct bovine parainfluenza virus type 3 genotypes

The partial gene sequencing of the matrix (M) protein from seven clinical isolates of bovine parainfluenza virus type 3 (BPIV-3), and the complete sequencing of a representative isolate (Q5592) was completed in this study. Nucleotide sequence analysis was initiated because of the failure of in-house BPIV-3 RT-PCR methods to yield expected products for four of the isolates. Phylogenetic reconstructions based on the nucleotide sequences for the M-protein and the entire genome, using all of the available BPIV-3 nucleotide sequences, demonstrated that there were two distinct BPIV-3 genotypes (BPIV-3a and BPIV-3b). These newly identified genotypes have implications for the development of BPIV-3 molecular detection methods and may also impact on BPIV-3 vaccine formulations.