Complete genomic sequence of the Australian south-west genotype of Sindbis virus: Comparisons with other Sindbis strains and identification of a unique deletion in the 3 '-untranslated region

Our previous studies have shown that two distinct genotypes of Sindbis (SIN) virus occur in Australia. One of these, the Oriental/Australian type, circulates throughout most of the Australian continent, whereas the recently identified south-west (SW) genetic type appears to be restricted to a distinct geographic region located in the temperate south-west of Australia. We have now determined the complete nucleotide and translated amino acid sequences of a SW isolate of SIN virus (SW6562) and performed comparative analyses with other SIN viruses at the genomic level. The genome of SW6562 is 11,569 nucleotides in length, excluding the cap nucleotide and poly (A) tail. Overall this virus differs from the prototype SIN virus (strain AR339) by 23% in nucleotide sequence and 12.5% in amino acid sequence. Partial sequences of four regions of the genome of four SW isolates were determined and compared with the corresponding sequences from a number of SIN isolates from different regions of the World. These regions are the non-structural protein (nsP3), the E2 gene, the capsid gene, and the repeated sequence elements (RSE) of the 3'UTR. These comparisons revealed that the SW SIN viruses were more closely related to South African and European strains than to other Australian isolates of SIN virus. Thus the SW genotype of SIN virus may have been introduced into this region of Australia by viremic humans or migratory birds and subsequently evolved independently in the region. The sequence data also revealed that the SW genotype contains a unique deletion in the RSE of the 3'UTR region of the genome. Previous studies have shown that deletions in this region of the SIN genome can have significant effects on virus replication in mosquito and avian cells, which may explain the restricted distribution of this genotype of SIN virus.

The value of idiosyncratic markers and changes to conserved tRNA sequences from the mitochondrial genome of hard ticks (Acari: Ixodida: Ixodidae) for phylogenetic inference

Idiosyncratic markers are features of genes and genomes that are so unusual that it is unlikely that they evolved more than once in a lineage of organisms. Here we explore further the potential of idiosyncratic markers and changes to typically conserved tRNA sequences for phylogenetic inference. Hard ticks were chosen as the model group because their phylogeny has been studied extensively. Fifty-eight candidate markers from hard ticks ( family Ixodidae) and 22 markers from the subfamily Rhipicephalinae sensu lato were mapped onto phylogenies of these groups. Two of the most interesting markers, features of the secondary structure of two different tRNAs, gave strong support to the hypothesis that species of the Prostriata ( Ixodes spp.) are monophyletic. Previous analyses of genes and morphology did not strongly support this relationship, instead suggesting that the Prostriata is paraphyletic with respect to the Metastriata ( the rest of the hard ticks). Parallel or convergent evolution was not found in the arrangements of mitochondrial genes in ticks nor were there any reversals to the ancestral arthropod character state. Many of the markers identified were phylogenetically informative, whereas others should be informative with study of additional taxa. Idiosyncratic markers and changes to typically conserved nucleotides in tRNAs that are phylogenetically informative were common in this data set, and thus these types of markers might be found in other organisms.

Towards the on-farm conservation of the assassin bug Pristhesancus plagipennis (Walker) (Hemiptera : Reduviidae) during winter using crop plants as refuges

Habitat instability associated with seasonal crop succession in broad-acre farming systems presents a problem for the conservation and utilisation of beneficial insects in annual field crops. The present paper describes two experiments used to measure the potential of seven plant species to be utilised as winter refuges to support and conserve the predatory bug Pristhesancus plagipennis (Walker). In the first experiment, replicated plots of canola (Brassica napus ), red salvia (Salvia coccinea ), niger (Guizotia abyssinica ), linseed (Linum usitatissimum ), lupins (Lupinus angustifolius ), and lucerne (Medicago falcata ) were planted in a randomized experiment during Autumn 1998. Upon crop establishment, adults and nymphs of P. plagipennis were released into treatment plots and their numbers were assessed, along with those of their potential prey, throughout the ensuing winter months. Post-release sampling suggested that canola and niger retained a proportion of adult P. plagipennis , while niger, lucerne and canola retained some nymphs. The other plant species failed to support P. plagipennis nymphs and adults postrelease. In the second experiment, niger was compared with two lines of sunflower (Helianthus annus ). Both sunflower lines harboured significantly higher (P < 0.05) densities of P. plagipennis nymphs than did niger. The more successful refuge treatments (sunflower, niger and canola) had an abundance of yellow flowers that were attractive to pollinating insects, which served as supplementary prey on which P. plagipennis were observed to feed. Sunflower and niger also supported high densities of the prey insect Creontiades dilutus (Stal) and provided protective leafy canopies which supplied shelter during the winter months. The potential and limitations for using each plant species as a winter refuge to retain P. plagipennis during winter are discussed.

Stereological and other methods applied to rock joint size estimation - Does Crofton's theorem apply?

A number of authors concerned with the analysis of rock jointing have used the idea that the joint areal or diametral distribution can be linked to the trace length distribution through a theorem attributed to Crofton. This brief paper seeks to demonstrate why Crofton's theorem need not be used to link moments of the trace length distribution captured by scan line or areal mapping to the moments of the diametral distribution of joints represented as disks and that it is incorrect to do so. The valid relationships for areal or scan line mapping between all the moments of the trace length distribution and those of the joint size distribution for joints modeled as disks are recalled and compared with those that might be applied were Crofton's theorem assumed to apply. For areal mapping, the relationship is fortuitously correct but incorrect for scan line mapping.

Measurement of muscle contraction with ultrasound imaging

To investigate the ability of ultrasonography to estimate musactivity, we measured architectural parameters (pennation angles, fascicle lengths, and muscle thickness) of several human muscles (tibialis anterior, biceps brachii, brachialis, transversus abdominis, obliquus internus abdominis, and obliquus externus abdominis) during isometric contractions of from 0 to 100% maximal voluntary contraction (MVC). Concurrently, electromyographic (EMG) activity was measured with surface (tibialis anterior only) or fine-wire electrodes. Most architectural parameters changed markedly with contractions up to 30% MVC but changed little at higher levels of contraction. Thus, ultrasound imaging can be used to detect low levels of muscle activity but cannot discriminate between moderate and strong contractions. Ultrasound measures could reliably detect changes in EMG of as little as 4% MVC (biceps muscle thickness), 5% MVC (brachialis muscle thickness), or 9% MVC (tibialis anterior pennation angle). They were generally less sensitive to changes in abdominal muscle activity, but it was possible to reliably detect contractions of 12% MVC in transversus abdominis (muscle length) and 22% MVC in obliquus internus (muscle thickness). Obliquus externus abdominis thickness did not change consistently with muscle contraction, so ultrasound measures of thickness cannot be used to detect activity of this muscle. Ultrasound imaging can thus provide a non-invasive method of detecting isometric muscle contractions of certain individual muscles.

Sustained swimming performance in crocodiles (Crocodylus porosus): Effects of body size and temperature

We examined effects of body size and temperature on swimming performance in juvenile estuarine crocodiles, Crocodylus porosus, over the size range of 30-110 cm total body length. Swimming performance, expressed as maximum sustainable swimming speed, was measured in a temperature- and flow-controlled swimming flume. Absolute sustainable swimming speed increased with body length, but length-specific swimming performance decreased as body length increased. Sustained swimming speed increased with temperature between 15degreesC and 23degreesC, remained constant between 23degrees and 33degreesC, and decreased as temperature rose above 33degreesC. Q(10)-values of swimming speed were 2.60 (+/- 0.091 SE) between 18degreesC and 23degreesC, and there were no differences in Q(10) between crocodiles of different sizes. The broad plateau of thermal independence in swimming speed observed in C. porosus may be of adaptive significance by allowing dispersal of juvenile animals at suboptimal body temperatures.

The ultrastructure and function of the silk-producing basitarsus in the Hilarini (Diptera : Ernpididae)

The tribe Hilarini (Diptera: Empididae), commonly known as dance flies, can be recognised by their swollen silk-producing prothoracic basitarsus, a male secondary sexual characteristic. The ultrastructure and function of the silk-producing basitarsus from one undescribed morphospecies of Hilarini, 'Hilarempis 20', is presented. Male H. 20 collect small parcels of diatomaceous algae from the surface of freshwater creeks that they bind with silk produced by the gland in the basitarsus. The gift is then presented to females in a nearby swarm, composed predominately of females. The basitarsus houses approximately 12 pairs of class III dermal glandular units that congregate on the ventral side of the cavity. Each gland cell has a large extracellular lumen where secretion accumulates. The lumen drains to the outside via a conducting canal encompassed by a canal cell and a duct extending through the shaft of a specialised secretory spine. The secretory spines lie in pairs in a ventral groove that runs the length of the basitarsus. A comparison of the basitarsal secretory spines with sensilla on the basitarsi of non gland-bearing legs of males, and with non gland-bearing prothoracic. basitarsi of females, suggests that the glandular units are derived from contact chemosensory sensilla. (C) 2003 Elsevier Ltd. All rights reserved.

Epitope map for a growth hormone receptor agonist monoclonal antibody, MAb 263

Monoclonal antibody (MAb) 263 is a widely used monoclonal antibody that recognizes the extracellular domain (ECD) of the GH receptor. It has been shown to act as a GH agonist both in vitro and in vivo, and we report here that it must be divalent to exert its effect on the full-length receptor. To understand the mechanism of its agonist action, we have determined the precise epitope for this antibody using a novel random PCR mutagenesis approach together with expression screening in yeast. A library of 5200 clones of rabbit GH receptor ECD mutants were screened both with MAb 263 and with an anticarboxy-tag antibody to verify complete ECD expression. Sequencing for clones that expressed complete ECD but were not MAb 263 positive identified 20 epitope residues distributed in a discontinuous manner throughout the ECD. The major part of the epitope, as revealed after mapping onto the crystal structure model of the ECD molecule, was located on the side and upper portion of domain 1, particularly within the D - E strand disulfide loop 79 - 96. Molecular dynamics docking of an antibody of the same isotype as MAb 263 was used to dock the bivalent antibody to the 1528-Angstrom(2) epitope and to visualize the likely consequences of MAb binding. The minimized model enables the antibody to grasp two receptors in a pincer-like movement from opposite sides, facilitating alignment of the receptor dimerization domains in a manner similar to, but not identical with, GH.

Winding patterns for actively shielded shim coils with asymmetric target-fields

A method is presented for calculating the currents and winding patterns required to design independent zonal and tesseral shim coils for magnetic resonance imaging. Both actively shielded and unshielded configurations are considered, and the region of interest can be located asymmetrically with respect to the coil's length. Streamline, target-field and Fourier-series methods are utilized. The desired target-field is specified at two cylindrical radii, on and inside a circular conducting cylinder of length 2L and radius a. The specification is over some asymmetric portion pL < z < qL of the coil's length (-1 < p < q < 1). Arbitrary functions are used in the outer sections, -L < z < pL and qL < z < L, to ensure continuity of the magnetic field across the entire length of the coil. The entire field is then periodically extended as a half-range cosine Fourier series about either end of the coil. The resultant Fourier coefficients are then substituted into the Fourier-series expressions for the internal and external magnetic fields, and current densities and stream functions on both the primary coil and shield. A contour plot of the stream function directly gives the required coil winding patterns. Spherical harmonic analysis and shielding analysis on field calculations from a ZX shim coil indicate that example designs and theory are well matched.

Multilayer transverse gradient coil design

In small, cylindrical gradient coils consisting of a single layer of wires, the limiting factor in achieving large magnetic field gradients is the rapid increase in coil resistance with efficiency. This behavior results from the decrease in the maximum usable wire diameter as the number of turns is increased. By adopting a multilayer design in which the coil wires are allowed to spread out into multiple layers wound at increasing radii, a more favorable scaling of resistance with efficiency is achieved, thus allowing the design of more powerful gradient coils with acceptable resistance values. By extending the theory used to design standard cylindrical gradient coils, mathematical expressions have been developed that allow the design of multilayer coils. These expressions have previously been applied to the design of a four-layer z-gradient coil. As a further development, the equations have now been modified to allow the design of multilayer transverse gradient coils. The variation in coil performance with the number of layers employed has been investigated for coils of a size suitable for use in NMR microscopy, and the effect of constructing the coil using wires or cuts in a continuous conducting surface has also been assessed. We find that at fixed resistance a small wire-wound two-layer coil offers an increase in efficiency of a factor of about 1.5 compared with a single-layer coil. In addition, a two-layer coil of 10-mm inner diameter has been designed and built. This coil had an efficiency of 0.41 Tm-1 A(-1), a resistance of 0.96 +/- 0.01 Omega, and an inductance of 22.3 +/- 0.2 muH. The coil produces a gradient that deviates from linearity by less than 5% over a central cylindrical region of interest of height and length 6.2 mm. (C) 2003 Wiley Periodicals, Inc.

A novel target-field method for magnetic resonance shim coils: III. Shielded zonal and tesseral coils

This paper continues the development of a new approach for the design of shim and gradient coils, used in magnetic resonance imaging (MRI) applications. A cylindrical primary coil of radius a and length 2L is placed inside a co-axial shield cylinder of radius b. An active shielding strategy is used to create a desired target field at an arbitrarily specified (cylindrical) location within the primary coil, and to annul the field at a certain radius outside the shield. The form of the interior target field may be chosen arbitrarily by the designer, although zonal and tesseral harmonics are typically used in MRI applications. The method presented here designs coil windings on both the primary and shielding cylinders, to produce fields that conform to the specified interior target field and the annulled field exterior to the shield. An additional feature of the method presented here is that the target field inside the primary coil is matched at two different radii, to improve overall accuracy. The method is illustrated by designing several shielded shim coils, for creating higher order tesseral fields located asymmetrically within the coil. The simpler case of pure zonal fields is discussed separately and applied to the design of some higher order shielded coils.

GRIP domain-mediated targeting of two new coiled-coil proteins, GCC88 and GCC185, to subcompartments of the trans-Golgi network

The GRIP domain is a targeting sequence found in a family of coiled-coil peripheral Golgi proteins. Previously we demonstrated that the GRIP domain of p230/golgin245 is specifically recruited to tubulovesicular structures of the traps-Golgi network (TGN). Here we have characterized two novel Golgi proteins with functional GRIP domains, designated GCC88 and GCC185. GCC88 cDNA encodes a protein of 88 kDa, and GCC185 cDNA encodes a protein of 185 kDa. Both molecules are brefeldin A-sensitive peripheral membrane proteins and are predicted to have extensive coiled-coil regions with the GRIP domain at the C terminus. By immunofluorescence and immunoelectron microscopy GCC88 and GCC185, and the GRIP protein golgin97, are all localized to the TGN of Hela cells. Overexpression of full-length GCC88 leads to the formation of large electron dense structures that extend from the traps-Golgi. These de novo structures contain GCC88 and co-stain for the TGN markers syntaxin 6 and TGN38 but not for alpha2,6-sialyltransferase, beta-COP, or cis-Golgi GM130. The formation of these abnormal structures requires the N-terminal domain of GCC88. TGN38, which recycles between the TGN and plasma membrane, was transported into and out of the GCC88 decorated structures. These data introduce two new GRIP domain proteins and implicate a role for GCC88 in the organization of a specific TGN subcompartment involved with membrane transport.

Contextual binding of p120ctn to E-cadherin at the basolateral plasma membrane in polarized epithelia

E-cadherin-catenin complexes mediate cell-cell adhesion on the basolateral membrane of epithelial cells. The cytoplasmic tail of E-cadherin supports multiple protein interactions, including binding of beta-catenin at the C terminus and of p120(ctn) to the juxtamembrane domain. The temporal assembly and polarized trafficking of the complex or its individual components to the basolateral membrane are not fully understood. In Madin-Darby canine kidney cells at steady state and after treatment with cycloheximide or temperature blocks, E-cadherin and beta-catenin localized to the Golgi complex, but p120ctn was found only at the basolateral plasma membrane. We previously identified a dileucine sorting motif (Leu(586)-Leu(587), termed S1) in the juxtamembrane domain of E-cadherin and now show that it is required to target full-length E-cadherin to the basolateral membrane. Removal of S1 resulted in missorting of E-cadherin mutants (EcadDeltaS1) to the apical membrane; beta-catenin was simultaneously missorted and appeared at the apical membrane. p120(ctn) was not mistargeted with EcadDeltaS1, but could be recruited to the E-cadherin-catenin complex only at the basolateral membrane. These findings help define the temporal assembly and sorting of the E-cadherin-catenin complex and show that membrane recruitment of p120(ctn) in polarized cells is contextual and confined to the basolateral membrane.

Does participation in a pain course based on the international association for the study of pain's curricula guidelines change student knowledge about pain?

The People in Pain course was set up as a joint initiative of the Departments of Occupational Therapy and Physiotherapy within the School of Health and Rehabilitation Sciences at The University of Queensland. It was instigated in response to the publication of Pain Curricula for Occupational Therapy and Physiotherapy by the International Association for the Study of Pain (IASP) in 1994 (1). The first year it was offered, the "People in Pain" course comprised 14 h of lecture content. It was then expanded to encompass 28 h of lectures and seminar involvement. OBJECTIVES: To evaluate the impact of participation in a university pain course that meets the IASP pain curricula guidelines to increase health professional students' knowledge about pain. METHODS: Students who participated in the People in Pain course over the first three years were invited to complete the Revised Pain Knowledge and Attitudes Questionnaire (R-PKAQ) pre- and postcourse. Data obtained from 22 students in the short course formed a pilot project, and data from 22 students in the longer version of the course were used in the present study. RESULTS: Examination of the correlation matrix indicated substantial correlations between all R-PKAQ subscales except physiological basis of pain and pharmacological management of pain. In both the pilot project during the first year of the course and the expanded course in the following two years, significant improvement was found in the students' knowledge on five of the six subscales of the R-PKAQ: physiological basis of pain, psychological factors of pain perception, assessment and measurement of pain, cognitive-behavioural methods of pain relief, and pharmacological management of pain. Improvements in the developmental aspects of pain perception subscale failed to reach significance. CONCLUSIONS: An integrated pain course developed according to the pain curriculum guidelines developed by the IASP resulted in increased student knowledge regardless of the length of the program attended.

Theoretical and experimental studies of unbraced tubular trusses allowing for torsional stiffness

This paper describes the buckling phenomenon of a tubular truss with unsupported length through a full-scale test and presents a practical computational method for the design of the trusses allowing for the contribution of torsional stiffness against buckling, of which the effect has never been considered previously by others. The current practice for the design of a planar truss has largely been based on the linear elastic approach which cannot allow for the contribution of torsional stiffness and tension members in a structural system against buckling. The over-simplified analytical technique is unable to provide a realistic and an economical design to a structure. In this paper the stability theory is applied to the second-order analysis and design of the structural form, with detailed allowance for the instability and second-order effects in compliance with design code requirements. Finally, the paper demonstrates the application of the proposed method to the stability design of a commonly adopted truss system used in support of glass panels in which lateral bracing members are highly undesirable for economical and aesthetic reasons.