Showing papers by "Macquarie University published in 1995"

Effective population size/adult population size ratios in wildlife : a review

Abstract: Summary The effective population size is required to predict the rate of inbreeding and loss of genetic variation in wildlife. Since only census population size is normally available, it is critical to know the ratio of effective to actual population size (NJN). Published estimates of NJN (192 from 102 species) were analysed to identify major variables affecting the ratio, and to obtain a comprehensive estimate of the ratio with all relevant variables included. The five most important variables explaining variation among estimates, in order of importance, were fluctuation in population size, variance in family size, form of TV used (adults v. breeders v. total size), taxonomic group and unequal sex-ratio. There were no significant effects on the ratio of high v. low fecundity, demographic r. genetic methods of estimation, or of overlapping v. non-overlapping generations when the same variables were included in estimates. Comprehensive estimates of NJN (that included the effects of fluctuation in population size, variance in family size and unequal sex-ratio) averaged only 0-10—0-11. Wildlife populations have much smaller effective population sizes than previously recognized.

Progress with gene‐product mapping of the Mollicutes: Mycoplasma genitalium

Abstract: A protein map of the smallest known self-replicating organism, Mycoplasma genitalium (Class: Mollicutes), revealed a high proportion of acidic proteins. Amino acid composition was used to putatively identify, or provide unique parameters, for 50 gene products separated by two-dimensional gel electrophoresis. A further 19 proteins were subjected to peptide-mass fingerprinting using matrix-assisted laser desorption ionisation-time of flight (MALDI-TOF) mass spectrometry and 4 were subjected to N-terminal Edman degradation. The majority of M. genitalium proteins remain uncharacterised. However, the combined approach of amino acid analysis and peptide-mass fingerprinting allowed gene products to be linked to homologous genes in a variety of organisms. This has allowed proteins to be identified prior to detection of their respective genes via the M. genitalium sequencing initiative. The principle of ‘hierarchical’ analysis for the mass screening of proteins and the analysis of microbial genomes via their protein complement or ‘proteome’ is detailed. Here, characterisation of gene products depends upon the quickest and most economical technologies being employed initially, so as to determine if a large number of proteins are already present in both homologous and heterologous species databases. Initial screening, which lends itself to automation and robotics, can then be followed by more time and cost intensive procedures, when necessary.

Ytterbium-doped silica fiber lasers: versatile sources for the 1-1.2 /spl mu/m region

Abstract: Ytterbium-doped silica fibers exhibit very broad absorption and emission bands, from /spl sim/800 nm to /spl sim/1064 nm for absorption and /spl sim/970 nm to /spl sim/1200 nm for emission. The simplicity of the level structure provides freedom from unwanted processes such as excited state absorption, multiphonon nonradiative decay, and concentration quenching. These fiber lasers therefore offer a very efficient and convenient means of wavelength conversion from a wide variety of pump lasers, including AlGaAs and InGaAs diodes and Nd:YAG lasers. Efficient operation with narrow linewidth at any wavelength in the emission range can be conveniently achieved using fiber gratings. A wide range of application for these sources can be anticipated. In this paper, the capabilities of this versatile source are reviewed. Analytical procedures and numerical data are presented to enable design choices to be made for the wide range of operating conditions. >

Inbreeding and Extinction: A Threshold Effect

Abstract: A fundamental assumption underlying the application of genetics within conservation biology is that inbreeding increases the risk of extinction. However, there is no information on the shape of the relationship, the available evidence has not distinguished genetic and nongenetic effects, and the issue is controversial. Methods were devised to separate genetic and nongenetic causes of extinction in inbred populations, and they were used to analyze data from Drosophila melanogaster, D. virilis and Mus musculus. Inbreeding markedly increased rates of extinction in all cases. All showed a threshold relationship between incremental extinction and inbreeding with low initial extinction, but they showed notably increased extinction beginning at intermediate levels of inbreeding. There was no difference in extinction levels at similar inbreeding coefficients in populations inbred at different rates (full sibling versus double first cousin). Endangered species may give little warning of impending extinction crises due to inbreeding. Una suposicion fundamental que resalta la aplicacion de la genetica en la conservacion biologica es que la endocria aumenta el riesgo de extincion. Sin embargo, no existe informacion sobre la forma en que la endocria y el riesgo de extinction estan relacionados; la evidencia disponible no ha distinguido entre efectos geneticos y efectos no geneticos y este problema resulta controversial. En el presente estudio se desarrollaron metodos para distinguir entre las causas geneticas y no geneticas de la extincion en poblaciones con endocria y los mismos fueron usados para analizar datos sobre Drosophila melanogaster, D. virilis y Mus musculus. La endocria incremento marcadamente las tasas de extincion en todos los casos. Todos mostraron una relacion umbral entre la extincion progresiva y la endocria con una baja tasa de extincion al principio, pero una tasa de extincion notablemente aumentada al alcanzar niveles de endocria intermedios. No existieron diferencias en los niveles de extincion en poblaciones con niveles de endocria similares pero endocriadas a tasas diferentes (hermano versus doble primo hermano). Las especies en peligro, no darian muchas senales de peligro antes de que las crisis de extincion debidas a la endocria se desencadenen.

Evolutionary implications of allozyme and RAPD variation in diploid populations of dioecious buffalograss Buchloë dactyloides

Abstract: Buffalograss, Buchloe dactyloides, is widely distributed throughout the Great Plains of North America, where it is an important species for rangeland forage and soil conservation. The species consists of two widespread polyploid races, with narrowly endemic diploid populations known from two regions: central Mexico and Gulf Coast Texas. We describe and compare the patterns of allozyme and RAPD variation in the two diploid races, using a set of 48 individuals from Texas and Mexico (four population samples of 12 individuals each). Twelve of 22 allozyme loci were polymorphic, exhibiting 35 alleles, while seven 10-mer RAPD primers revealed 98 polymorphic bands. Strong regional differences were detected in the extent of allozyme polymorphism: Mexican populations exhibited more internal gene diversity (He= 0.20, 0.19) than did the Texan populations (He= 0.08, 0.06), although the number of RAPD bands in Texas (n= 62) was only marginally smaller than in Mexico (n= 68). F-statistics for the allozyme data, averaged over loci, revealed strong regional differentiation (mean FRT=+ 0.30), as well as some differentiation among populations within regions (mean FPR=+ 0.09). In order to describe and compare the partitioning of genetic variation for multiple allozyme and RAPD loci, we performed an Analysis of Molecular Variance (AMOVA). AMOVA for both allozyme and RAPD data revealed similar qualitative patterns: large regional differences and smaller (but significant) population differences within regions. RAPDs revealed greater variation among regions (58.4% of total variance) than allozymes (45.2%), but less variation among individuals within populations (31.9% for RAPDs vs. 45.2% for allozymes); the proportion of genetic variance among populations within regions was similar (9.7% for RAPDs vs. 9.6% for allozymes). Despite this large-scale concordance of allozyme and RAPD variation patterns, multiple correlation Mantel techniques revealed that the correlations were low on an individual by individual basis. Our findings of strong regional differences among the diploid races will facilitate further study of polyploid evolution in buffalograss.

The Project for Intercomparison of Land Surface Parameterization Schemes (PILPS): Phases 2 and 3

Abstract: The World Climate Research Programme Project for Intercomparison of Land Surface Parameterization Schemes (PILPS) is moving into its second and third phases that will exploit observational data and consider the performance of land surface schemes when coupled to their host climate models. The first stage of phase 2 will focus on an attempt to understand the large differences found during phase 1. The first site from which observations will be drawn for phase 2 intercomparisons is Cabauw, the Netherlands (51°58°N, 4°56′E), selected specifically to try to reduce one of the causes of the divergence among the phase 1 results: the initialization of the deep soil moisture. Cabauw's deep soil is saturated throughout the year. It also offers a quality controlled set of meteorological forcing and 160 days of flux measurements. PILPS phase 2 follows the form of the phase 1 intercomparisons: simple off-line integrations and comparisons, but in phase 2 participating schemes’ results will be compared against ...

On misinterpreting the phylogenetic correction

Abstract: The last 10 years have seen important advances in methodology for taking phylogeny into account when analysing a comparative dataset. This commentary is about a class of interpretive procedures associated with these new statistical methods. We will call the interpretive logic 'phylogenetic correction' (PC for short), because this phrase summarizes the approach. Our essential message, however, is that a PC procedure is not in fact a 'correction', an adjustment to remove errors. Rather, it is a conceptual decision to give priority to one interpretation over another. Accordingly, it is an error to believe that PC is a methodology that must routinely be applied in all comparative analyses. The present Forum was proposed by the Editor during the review process for a paper about comparative ecology of seed mass (Leishman et al. 1995; see p. 517). Accordingly, examples will be drawn from the literature on seed mass, but the points made would be true of many species attributes. By 'comparative dataset', we mean a table with present-day species as rows, and attributes as columns. Some columns describe phylogenetic relations among the species, and others describe present-day attributes affecting the ecology of each species. Ecological attributes may include both those recording the behaviour of species in the field, such as capacity to establish in small canopy gaps (Kelly & Purvis 1993), and those that would be manifested even in glasshouse or garden, such as seeds per carpel (Hodgson & Mackey 1986). The analyses we are concerned with examine between-species variation in a focal ecological trait (here, seed mass), by investigating its correlation with other columns in the dataset.

Cultural Practices: Toward an Integration of Culture and Development.

Abstract: This chapter explains why the notion of cultural practices has been appealing to developmental researchers and introduces the conceptual framework for the volume.

Bursting the bubble of ballooning plutons: A return to nested diapirs emplaced by multiple processes

Abstract: A popular model for the emplacement of roughly spherical plutons is that of “ballooning” or in situ inflation of a magma chamber. In a common version of this model magma ascends until loss of heat or buoyancy causes the outermost magma to crystallize and cease ascent, while the hotter “tail” of magma continues to rise and expand the already crystallized outer margin. This expansion forms a concentric, gneissic to mylonitic foliation and flattening-type strain in the outer margin of the pluton by means of subsolidus deformation and pushes aside the surrounding country rock to form a dynamothermal aureole that postdates regional structures. Our reexamination of three supposedly ballooned plutons (Ardara, Ireland; Cannibal Creek, Australia; Papoose Flat, California) and evaluation of published descriptions of many others indicate that this model is largely incorrect. Deflections of country-rock structures, strains, and porphyroblast-matrix relationships indicate that only minor to moderate expansion (usually 30% or less) occurred during emplacement, that other emplacement mechanisms must have occurred, and that regional deformation continued during and after emplacement. Internal structures indicate that when magma chamber expansion did occur, it did so by flow of magma, that magmatic foliations and lineations formed late in the magma chamber evolution, that enclave shapes are neither good strain markers nor indicators of the magnitude of expansion, and that only minor internal subsolidus deformation results from emplacement. This study indicates that many plutons previously interpreted as post-tectonic ballooning plutons are better viewed as syntectonic, nested diapirs emplaced by a variety of country-rock material-transfer processes. This nested diapir model implies that magma ascent may occur by rise of large magma batches (instead of transport in dikes followed by ballooning), that magma chamber dynamics differ from that in the ballooning model, and that normally zoned plutons may form by intrusion of several pulses of magma rather than by in situ crystal fractionation from a single parent melt.

An evaluation of Reading Recovery

Abstract: Les AA. ont evalue l'efficacite de la reeducation en lecture dans dix ecoles primaires de la Nouvelle Galles de Sud. Repartis en deux groupes (reeducation en lecture et situation controle), les eleves en difficulte de lecture ont effectue des tests de competences a plusieurs reprises. L'efficacite de la reeducation en lecture n'est alors plus aussi pertinente

Measuring the impact of sewage effluent on the macroinvertebrate community of an upland stream: The effect of different levels of taxonomic resolution and quantification

Abstract: Benthic macroinvertebrates were sampled from four sites on upland streams in the Wentworth Falls area of the Blue Mountains, NSW. One site received effluent from a sewage treatment plant and the others were reference sites. Five replicate collections were taken from each site on four occasions at intervals of 3 months. Macroinvertebrate community data were analysed using univariate (ANOVA) and multivariate (NMDS) techniques and comparisons were made between analyses at different levels of taxonomic aggregation and using different methods of data transformation. Similar patterns were observed at both species and family levels, and even the order level showed a clear community response to effluent input. Binary (presence/ absence) data provided similar results to quantitative data for the species and family levels. However, when binary data were used at the order level, the distinctions between the reference sites became blurred. We discuss the implications of these findings for environmental monitoring.

Global climate sensitivity to tropical deforestation

Abstract: Regional to global-scale climate sensitivity to tropical deforestation is simulated using a modified version of the NCAR Community Climate Model (CCM1-Oz) which includes a mixed-layer ocean model, a 3-layer sea-ice model and BATS (the Biosphere-Atmosphere Transfer Scheme). A fourteen-year control integration is followed by a six year deforestation experiment in which the tropical moist forest throughout the Amazon Basin, S.E. Asia and tropical Africa is replaced by scrub grassland. The three deforested regions sustain different impacts on their regional climates. The largest disturbances occur in the Amazon Basin where total precipitation decreases by −437 mm yr −1 , evaporation decreases by −231 mm yr −1 and a marked decrease in moisture convergence is clear, although the surface temperature increases by 0.3 K. In S.E. Asia, surface temperature decreases in 11 months with an annual average cooling of −0.7 K; total evaporation decreases all the year by 130 mm yr −1 ; while the sign of the precipitation changes is strongly seasonal. The African region is least affected by deforestation, although surface net radiation decreases year-round and there is a detectable decrease in moisture convergence in the dry season. Regional responses to deforestation differ because regional circulation patterns are affected differently. For example, while ground surface temperatures increase in the Southern Amazon and over this basin as a whole, the northern Amazon, S.E. Asia and Africa all exhibit decreases in ground surface temperatures. The modification of atmospheric circulation patterns over deforested tropical regions prompts climate responses distant from the disturbance. Impacts of tropical deforestation include a disturbance of the Asian monsoon and small but statistically significant changes in climate in the middle and high latitudes.

Culture, economics and sustainability

Abstract: In this paper it is argued that systems analysis can provide a means of bringing economic and cultural systems together in a unified framework. It is then proposed that a link between economics and culture can be established through the concept of “culturally sustainable development”, definable in terms of a set of criteria relating to advancement of material and nonmaterial wellbeing, inter-and intra-generational equity, and recognition of interdependence. The paper suggests that conceptualising the interaction between the cultural and economic systems in these terms might provide a workable model for policy analysis.

Multidrug resistance in Klebsiella pneumoniae: a novel gene, ramA, confers a multidrug resistance phenotype in Escherichia coli

Abstract: Spontaneous multidrug-resistant (Mdr) mutants of Klebsiella pneumoniae strain ECL8 arose at a frequency of 2-2 × 10-8 and showed increased resistance to a range of unrelated antibiotics, including chloramphenicol, tetracycline, nalidixic acid, ampicillin, norfloxacin, trimethoprim and puromycin A chromosomal fragment from one such mutant was cloned, and found to confer an Mdr phenotype on Escherichia coli K12 cells that was essentially identical to that of the K pneumoniae mutant Almost complete loss of the OmpF porin in the E coli transformant, and of the corresponding porin in the K pneumoniae mutant, was observed The presence of the Mdr mutation in K pneumoniae or the cloned K pneumoniae ramA (resistance antibiotic multiple) locus in E coli also resulted in active efflux of tetracycline, and increased active efflux of chloramphenicol After transformation of a ramA plasmid into E coli, expression of chloramphenicol resistance occurred later than expression of resistance to tetracycline, puromycin, trimethoprim and nalidixic acid The ramA gene was localized and sequenced It encodes a putative positive transcriptional activator that is weakly related to the E coli MarA and SoxS proteins A ramA gene was also found to be present in an Enterobacter cloacae fragment that has previously been shown to confer an Mdr phenotype, and it appears that ramA, rather than the romA gene identified in that study, is responsible for multidrug resistance The ramA gene from the wild-type K pneumoniae was identical to that of the mutant strain and also conferred an Mdr phenotype on E coli, indicating that the mutation responsible for Mdr in K pneumoniae had not been cloned

Cross-species identification of proteins separated by two-dimensional gel electrophoresis using matrix-assisted laser desorption ionisation/time-of-flight mass spectrometry and amino acid composition

Abstract: Amino acid analysis and matrix-assisted laser desorption/ionisation time-of-flight (MALDI-TOF) mass spectrometry were used to identify nine of twelve proteins originally separated by two-dimensional electrophoresis and derived from an organism poorly defined at the molecular level (Spiroplasma melliferum). Two of three unidentified proteins appeared to be novel. The percentage amino acid composition and the molecular mass of peptide fragments generated by tryptic digestion were used to search the PIR/SWISS-PROT and MOWSE databases respectively. Lists of candidate proteins were independently generated and ranked from data obtained by both methods. A putative identification was allocated when a single candidate protein appeared in both lists of computer-generated rankings. Results were verified using N-terminal protein microsequencing. The combined use of amino acid composition and MALDI-TOF mass spectrometry allowed a high degree of confidence to be placed in such identifications because they were based upon homologous data sets of at least 20 parameters (16 amino acids and 4-10 tryptic digest fragments). A further two parameters, estimated M(r) and, to a lesser extent, pI, were also used to reinforce this measure of confidence. Ranking of candidate proteins by one method alone could lead to false identification. Both techniques can process large numbers of samples rapidly. In light of the increasing number of entries in both gene and protein databases, this approach is likely to become an essential first step for the characterisation of proteins, particularly across species boundaries.

Further Remarks on Phylogenetic Correction

Abstract: In the following pages we publish responses to the papers in the last issue (83:3) by Westoby et al. and Harvey et al. on the use of 'phylogenetic correction' in comparative ecological studies. It has not been possible for every author to comment upon every contribution; in this issue Westoby et al. reply only to Harvey et al. (83:3), while Harvey et al. have been able to comment on all the opinions expressed. A final contribution from Westoby et al. will conclude this debate in the October issue (83:5).

New mobile gene cassettes containing an aminoglycoside resistance gene, aacA7, and a chloramphenicol resistance gene, catB3, in an integron in pBWH301.

Abstract: The multidrug resistance plasmid pBWH301 was shown to contain a sull-associated integron with five inserted gene cassettes, aacA7-catB3-aadB-oxa2-orfD, all of which can be mobilized by the integron-encoded DNA integrase. The aadB, oxa2, and orfD cassettes are identical to known cassettes. The aacA7 gene encodes a protein that is a member of one of the three known families of aminoglycoside acetyltransferases classified as AAC(6')-I. The chloramphenicol acetyltransferase encoded by the catB3 gene is closely related to members of a recently identified family of chloramphenicol acetyltransferases. The catB3 gene displays a relatively high degree of sequence identity to a chromosomally located open reading frame in Pseudomonas aeruginosa, and this may represent evidence for the acquisition by a cassette of a chromosomal gene.

Self Esteem, Depression, Behaviour and Family Functioning in Sexually Abused Children

Abstract: Eighty-four sexually abused children and their families, were compared with controls to look at short-term effects of sexual abuse. The abuse group had more marital breakdown, unemployment, communication problems within the family and poor maternal mental health. The abused children had more depression, low self-esteem and behaviour disorder, There was no relationship between intrafamilial abuse and depression, self-esteem or behaviour disorder. More severe abuse was related to low self-esteem and children's negative perceptions of their mothers. In planning treatment the child's relationship to the perpetrator may need less emphasis, with more on self-esteem, depression, family functioning and the child's perceptions of the family.

Geochemical characteristics of lava-field basalts from eastern Australia and inferred sources: Connections with the subcontinental lithospheric mantle?

Abstract: A large new database of major, trace elements and Sr-Nd isotopic ratios from 11 lava-field provinces in New South Wales and Queensland, eastern Australia allows detailed interpretation of the origin of these basaltic magmas. Isotopic signatures and trace element patterns identify an OIB-type (oceanic island basalt) source as a dominant component for most of these and some provinces appear to have additional significant components derived from the subcontinental lithospheric mantle (SCLM). The SCLM components have geochemical characteristics that overlap those observed in spinel lherzolite xenoliths (samples of shallow lithospheric mantle) from eastern Australia. These SCLM components show geochemical provinciality that indicates the occurrence of distinct geochemical lithospheric domains reflecting the timing and style of tectonic evolution of different regions. One component reflects modification by subduction-related processes during the late Paleozoic and Mesozoic, one records enrichment by fluids during old metasomatic events and another suggests a metasomatic event involving a distinctive amphibole and apatite-style enrichment. The composition and age distribution of volcanic lava-field provinces older than 10 Ma are consistent with a model involving a regional upwelling (elongated N-S along eastern Australia) of deep hot mantle related to marginal rifting and with OIB-type source geochemical characteristics. Thermal inhomogeneities within this plume swath resulted in small diapirs which may have undergone melt segregation at about 100 km and incorporated varying amounts of SCLM components there or from higher levels of the SCLM during ascent. Subsequent hot-spot generated central volcanoes overprinted this lava-field volcanism, tapped a similar OIB-type source component and truncated the thermal events.

A mobile host protocol supporting route optimization and authentication

Abstract: Host mobility is becoming an important issue due to the recent proliferation of notebook and palmtop computers, the development of wireless network interfaces, and the growth in global internetworking. This paper describes the design and implementation of a mobile host protocol, called the Internet mobile host protocol (IMHP), that is compatible with the TCP/IP protocol suite, and allows a mobile host to move around the Internet without changing its identity, In particular, IMHP provides host mobility over both the local and wide area, while remaining transparent to the user and to other hosts communicating with the mobile host. IMHP features route optimization and integrated authentication of all management packets. Route optimization allows a node to cache the location of a mobile host and to send future packets directly to that mobile host. By authenticating all management packets, IMHP guards against possible attacks on packet routing to mobile hosts, including the interception or redirection of arbitrary packets within the network. A simple new authentication mechanism is introduced that preserves the level of security found in the Internet today, while accommodating the transition to stronger authentication based on public key cryptography or shared keys that may either be manually administered or provided by a future Internet key management protocol. >

Magmatism as an essential driving force for formation of active metamorphic core complexes in eastern Papua New Guinea

Abstract: The D'Entrecasteaux Islands in eastern Papua New Guinea are composed of a number of active metamorphic core complexes which have been intruded by granodiorite plutons during their formation. The plutons do not appear to have been intruded by diapiric processes as previously suggested. Late, relatively undeformed plutons form flat-lying bodies which crosscut structural boundaries and are strongly discordant to core complex shear zones. Granodiorite magmatism and the development of the metamorphic core complexes have occurred in a linear zone which coincides with a zone of thick crust and rugged topography. It is proposed that plutonism facilitated deformation in ductile extensional shear zones which resulted in tectonic exhumation of deep crustal rocks and formation of the metamorphic core complexes. The source of the plutons is thought to be related to a linear zone of mantle upwelling beneath the islands related to the propagation of the Woodlark seafloor spreading center into continental crust. It is suggested that a localized heat source of this type, which can provide heat and magmatic material to the crust, is essential for the development of metamorphic core complexes.

Bell's inequality for an entanglement of nonorthogonal states

Abstract: Given an entanglement of two systems involving nonorthogonal states, we find the Schmidt decomposition for the state. The relation between the Schmidt representation and an ideal measurement of the degree of entanglement of the states is discussed, and a Bell inequality is shown to be violated. The maximal violation of the Bell inequality provides a measurement of the degree of entanglement. The entangled coherent states are provided as a concrete example of the Bell inequality for entangled nonorthogonal states.