Determining complicated winding patterns for shim coils using stream functions and the target-field method

In a magnetic resonance imaging equipment, gradient and shim coils are needed to produce a spatially varying magnetic field throughout the sample being imaged. Such coils consist of turns of wire wound on the surface of a cylindrical tube. Shim coils in particular, must sometimes be designed to produce complicated magnetic fields to correct for impurities. Streamline patterns for shim coils are much more complicated than those for gradient coils, In this work we present a detailed analysis of streamline methods and their application to shim coil design, A method is presented for determining the winding patterns to generate these complicated fields. (C) 2002 John Wiley & Sons, Inc.

Using biplots to interpret gene expression patterns in plants

Sum: Plant biologists in fields of ecology, evolution, genetics and breeding frequently use multivariate methods. This paper illustrates Principal Component Analysis (PCA) and Gabriel's biplot as applied to microarray expression data from plant pathology experiments. Availability: An example program in the publicly distributed statistical language R is available from the web site (www.tpp.uq.edu.au) and by e-mail from the contact. Contact: scott.chapman@csiro.au.

New status, species, distribution records and phylogeny for Australian mandibulate Chironomidae (Diptera)

All life-history stages of the Australian Podonominae (Chironomidae) genus Archaeochlus Brundin are revised, providing evidence for recognition of a separate clade, named here as Austrochlus Cranston. Based on molecular and morphological evidence, the clade contains two additional species: Austrochlus parabrundini Cranston, Edward and Cook sp. n. is described from Western Australia where its granite outcrop seepage habitat and geographical range is almost identical to that of the type species Austrochlus brundini Cranston, Edward and Colless (n. comb); Austrochlus centralaustralis Cranston, Edward and Cook sp. n. is described from ephemeral seepage/flows in the MacDonnell and James Ranges of central Australia. Molecular studies reported here confirm species distinctions, relationships to African taxa, and basal relationships within the Chironomidae. Modelled distributions provide evidence for range restriction by seasonal rainfall patterns.

Patterns of co-morbidity between alcohol use and other substance use in the Australian population

The present study describes patterns of co-morbidity between alcohol use and other substance use problems in the Australian population using data from the 1997 National Survey of Mental Health and Well-Being. Multiple regression analyses examined whether the observed associations between alcohol and other drug use disorders were explained by other variables, including demographic characteristics and neuroticism. We also assessed whether the presence of co-morbid substance use disorders affected treatment seeking for a mental health problem. Alcohol use was related strongly to the use of other substances. Those who did not report alcohol use within the past 12 months were less likely to report using tobacco, cannabis, sedatives, stimulants or opiates. Higher rates again were observed among those with alcohol use disorders: half (51%) of those who were alcohol-dependent were regular tobacco smokers, one-third had used cannabis (32%); 15% reported other drug use; 15% met criteria for a cannabis use disorder and 7% met criteria for another drug use disorder. These associations were not accounted for by the demographic and other variables considered here. Co-morbid substance use disorders (sedatives, stimulants or opioids) predicted a high likelihood of seeking treatment for a mental health problem among alcohol-dependent people.

Is cell surface calreticulin involved in phagocytosis by insect hemocytes?

The innate immune system of insects consists of humoral and cellular components involved in the recognition of and responses to intruding foreign micro- or macroorganisms. Several molecules have been identified so far that recognize molecular patterns present on microorganisms, such as lipopolysaccharides, peptidoglycans and lipoteichonic acid. These molecules, acting as opsonins, trigger immune responses such as phagocytosis, nodule formation, melanization and encapsulation. Here, we investigated the role of calreticulin (CRT) present on the surface of Pieris rapae hemocytes in phagocytosis. Comparative phagocytosis assays using yeast cells showed that hemocytes from different insects exhibit significant variation in their phagocytosing potential and relative CRT involvement. (C) 2003 Elsevier Science Ltd. All rights reserved.

Patterns of variation within self-incompatibility loci

Diverse self-incompatibility (SI) mechanisms permit flowering plants to inhibit fertilization by pollen that express specificities in common with the pistil. Characteristic of at least two model systems is greatly reduced recombination across large genomic tracts surrounding the S-locus, which regulates SI. In three angiosperm families, including the Solanaceae, the gene that controls the expression of gametophytic SI in the pistil encodes a ribonuclease (S-RNase). The gene that controls pollen SI expression is currently unknown, although several candidates have recently been proposed. Although each candidate shows a high level of polymorphism and complete allelic disequilibrium with the S-RNase gene, such properties may merely reflect tight linkage to the S-locus, irrespective of any functional role in SI. We analyzed the magnitude and nature of nucleotide variation, with the objective of distinguishing likely candidates for regulators of SI from other genes embedded in the S-locus region. We studied the S-RNase gene of the Solanaceae and 48A, a candidate for the pollen gene in this system, and we also conducted a parallel analysis of the regulators of sporophytic SI in Brassica, a system in which both the pistil and pollen genes are known. Although the pattern of variation shown by the pollen gene of the Brassica system is consistent with its role as a determinant of pollen specificity, that of 48A departs from expectation. Our analysis further suggests that recombination between 48A and S-RNase may have occurred during the interval spanned by the gene genealogy, another indication that 48A may not regulate SI expression in pollen.

Polarization vision and its role in biological signaling

Visual pigments, the molecules in photoreceptors that initiate the process of vision, are inherently dichroic, differentially absorbing light according to its axis of polarization. Many animals have taken advantage of this property to build receptor systems capable of analyzing the polarization of incoming light, as polarized light is abundant in natural scenes (commonly being produced by scattering or reflection). Such polarization sensitivity has long been associated with behavioral tasks like orientation or navigation. However, only recently have we become aware that it can be incorporated into a high-level visual perception akin to color vision, permitting segmentation of a viewed scene into regions that differ in their polarization. By analogy to color vision, we call this capacity polarization vision. It is apparently used for tasks like those that color vision specializes in: contrast enhancement, camouflage breaking, object recognition, and signal detection and discrimination. While color is very useful in terrestrial or shallow-water environments, it is an unreliable cue deeper in water due to the spectral modification of light as it travels through water of various depths or of varying optical quality. Here, polarization vision has special utility and consequently has evolved in numerous marine species, as well as at least one terrestrial animal. In this review, we consider recent findings concerning polarization vision and its significance in biological signaling.

CysView: protein classification based on cysteine pairing patterns

CysView is a web-based application tool that identifies and classifies proteins according to their disulfide connectivity patterns. It accepts a dataset of annotated protein sequences in various formats and returns a graphical representation of cysteine pairing patterns. CysView displays cysteine patterns for those records in the data with disulfide annotations. It allows the viewing of records grouped by connectivity patterns. CysView's utility as an analysis tool was demonstrated by the rapid and correct classification of scorpion toxin entries from GenPept on the basis of their disulfide pairing patterns. It has proved useful for rapid detection of irrelevant and partial records, or those with incomplete annotations. CysView can be used to support distant homology between proteins. CysView is publicly available at http://research.i2r.a-star.edu.sg/CysView/.

Sequence analysis, chromosomal distribution and long-range organization show that rapid turnover of new and old pBuM satellite DNA repeats leads to different patterns of variation in seven species of the Drosophila buzzatii cluster

We aimed to study patterns of variation and factors influencing the evolutionary dynamics of a satellite DNA, pBuM, in all seven Drosophila species from the buzzatii cluster (repleta group). We analyzed 117 alpha pBuM-1 (monomer length 190 bp) and 119 composite alpha/beta (370 bp) pBuM-2 repeats and determined the chromosome location and long-range organization on DNA fibers of major sequence variants. Such combined methodologies in the study of satDNAs have been used in very few organisms. In most species, concerted evolution is linked to high copy number of pBuM repeats. Species presenting low-abundance and scattered distributed pBuM repeats did not undergo concerted evolution and maintained part of the ancestral inter-repeat variability. The alpha and alpha/beta repeats colocalized in heterochromatic regions and were distributed on multiple chromosomes, with notable differences between species. High-resolution FISH revealed array sizes of a few kilobases to over 0.7 Mb and mutual arrangements of alpha and alpha/beta repeats along the same DNA fibers, but with considerable changes in the amount of each variant across species. From sequence, chromosomal and phylogenetic data, we could infer that homogenization and amplification events involved both new and ancestral pBuM variants. Altogether, the data on the structure and organization of the pBuM satDNA give insights into genome evolution including mechanisms that contribute to concerted evolution and diversification.

Nestmate recognition in a Neotropical swarm-founding wasp: no effect of seasonality on tolerance of alien conspecifics

Previous study revealed that the swarm-founding wasp Polybia paulista is accurately able to distinguish nestmates from non-nestmates in the summer. However, the risk of accepting alien intruders is considered to be low in winter colonies, and additionally brood production is limited in 30-40% of colonies during the winter in this species. Thus, it is expected that colonies might lower their acceptance threshold and accept some conspecific wasps from alien colonies in winter. We conducted field experiments to examine tolerance of conspecific (nestmate and non-nestmate) females in winter. In contrast to our prediction, our colonies did not accept any individuals from alien colonies. We suggest that P. paulista exhibits the colony-specific acceptance threshold in winter, and colonies that produced brood in their nests may have raised the acceptance threshold even if the risk of accepting alien intruders is low in winter.

Decision rules for egg recognition are related to functional roles and chemical cues in the queenless ant Dinoponera quadriceps

The capacity to distinguish colony members from strangers is a key component in social life. In social insects, this extends to the brood and involves discrimination of queen eggs. Chemical substances communicate colony affiliation for both adults and brood; thus, in theory, all colony members should be able to recognize fellow nestmates. In this study, we investigate the ability of Dinoponera quadriceps workers to discriminate nestmate and non-nestmate eggs based on cuticular hydrocarbon composition. We analyzed whether cuticular hydrocarbons present on the eggs provide cues of discrimination. The results show that egg recognition in D. quadriceps is related to both age and the functional role of workers. Brood care workers were able to distinguish nestmate from non-nestmate eggs, while callow and forager workers were unable to do so.

Recognition of cyclic, acyclic, exocyclic, and spiro Acetals via structurally diagnostic ion/molecule reactions with the (CH3)(2)N-C+=O acylium ion

Reactions of the model acylium ion (CH3)(2)N-C+=O with acyclic, exocyclic, and Spiro acetals of the general formula (RO)-O-1-(CRR4)-R-3-OR2-upole mass spectrometry. Characteristic intrinsic reactivities were observed for each of these classes of acetals. The two most Characteristic intrinsic reactivities were observed for each of these classes of acetals. The two most common reactions observed were hydride and alkoxy anion [(RO-)-O-1 and (RO-)-O-2] abstraction. Other specific reactions were also observed: (a) a secondary polar [4(+) + 2] cycloaddition for acetals bearing alpha,beta-unsaturated R-3 or R-4 substituents and (b) OH- abstraction for exocyclic and spiro acetals. These structurally diagnostic reactions, in conjunction with others observed previously for cyclic acetals, are shown to reveal the class of the acetal molecule and its ring type and substituents and to permit their recognition and distinction from other classes of isomeric molecules.