Assessing the taxonomic status of dingoes Canis familiaris dingo for conservation

1. The conservation status of the dingo Canis familiaris dingo is threatened by hybridization with the domestic dog C. familiaris familiaris. A practical method that can estimate the different levels of hybridization in the field is urgently required so that animals below a specific threshold of dingo ancestry (e.g. 1/4 or 1/2 dingoes) can reliably be identified and removed from dingo populations. 2. Skull morphology has been traditionally used to assess dingo purity, but this method does not discriminate between the different levels of dingo ancestry in hybrids. Furthermore, measurements can only be reliably taken from the skulls of dead animals. 3. Methods based on the analysis of variation in DNA are able to discriminate between the different levels of hybridization, but the validity of this method has been questioned because the materials currently used as a reference for dingoes are from captive animals of unproven genetic purity. The use of pre-European materials would improve the accuracy of this method, but suitable material has not been found in sufficient quantity to develop a reliable reference population. Furthermore, current methods based on DNA are impractical for the field-based discrimination of hybrids because samples require laboratory analysis. 4. Coat colour has also been used to estimate the extent of hybridization and is possibly the most practical method to apply in the field. However, this method may not be as powerful as genetic or morphological analyses because some hybrids (e.g. Australian cattle dog x dingo) are similar to dingoes in coat colour and body form. This problem may be alleviated by using additional visual characteristics such as the presence/absence of ticking and white markings.

Identification and analysis of chromodomain-containing proteins encoded in the mouse transcriptome

The chromodomain is 40-50 amino acids in length and is conserved in a wide range of chromatic and regulatory proteins involved in chromatin remodeling. Chromodomain-containing proteins can be classified into families based on their broader characteristics, in particular the presence of other types of domains, and which correlate with different subclasses of the chromodomains themselves. Hidden Markov model (HMM)-generated profiles of different subclasses of chromodomains were used here to identify sequences encoding chromodomain-containing proteins in the mouse transcriptome and genome. A total of 36 different loci encoding proteins containing chromodomains, including 17 novel loci, were identified. Six of these loci (including three apparent pseudogenes, a novel HP1 ortholog, and two novel Msl-3 transcription factor-like proteins) are not present in the human genome, whereas the human genome contains four loci (two CDY orthologs and two apparent CDY pseuclogenes) that are not present in mouse. A number of these loci exhibit alternative splicing to produce different isoforms, including 43 novel variants, some of which lack the chromodomain. The likely functions of these proteins are discussed in relation to the known functions of other chromodomain-containing proteins within the same family.

An analysis of clinical characteristics in genetically linked migraine-affected pedigrees

Migraine is a common complex disorder characterized by severe recurrent headache and usually accompanied by nausea and vomiting. Previous studies in our laboratory have utilized three large multigenerational Australian pedigrees affected with migraine to indicate that the disease is genetically heterogeneous, with linkage results implicating genomic susceptibility regions on both chromosomes 19p and Xq. The present study explores the possibility of a correlation between genetic and clinical heterogeneity in these affected pedigrees. Specifically, the clinical characteristics of migraine including subtype, age of onset, frequency, duration, and disease symptoms were compared between the migraine pedigrees, and gender differences were also assessed. Our exploratory analyses revealed no significant differences in any of the clinical characteristics tested between the chromosome 19-linked family and the two X-linked families. Also, we did not detect any differences in male vs. female clinical features for these pedigrees. In conclusion, migraine is considered to be a clinically and genetically heterogeneous disorder; however, our study provided no conclusive evidence that variation in genomic susceptibility region is related to heterogeneity at the clinical level in these migraine-affected pedigrees.

Real-time PCR in the microbiology laboratory

Use of PCR in the field of molecular diagnostics has increased to the point where it is now accepted as the standard method for detecting nucleic acids from a number of sample and microbial types. However, conventional PCR was already an essential tool in the research laboratory. Real-time PCR has catalysed wider acceptance of PCR because it is more rapid, sensitive and reproducible, while the risk of carryover contamination is minimised. There is an increasing number of chemistries which are used to detect PCR products as they accumulate within a closed reaction vessel during real-time PCR. These include the non-specific DNA-binding fluorophores and the specific, fluorophore-labelled oligonucleotide probes, some of which will be discussed in detail. It is not only the technology that has changed with the introduction of real-time PCR. Accompanying changes have occurred in the traditional terminology of PCR, and these changes will be highlighted as they occur. Factors that have restricted the development of multiplex real-time PCR, as well as the role of real-time PCR in the quantitation and genotyping of the microbial causes of infectious disease, will also be discussed. Because the amplification hardware and the fluorogenic detection chemistries have evolved rapidly, this review aims to update the scientist on the current state of the art. Additionally, the advantages, limitations and general background of real-time PCR technology will be reviewed in the context of the microbiology laboratory.

Analysis of service stress corrosion cracking in a natural gas transmission pipeline, active or dormant?

Stress corrosion cracks (SCC) had been found in a natural gas transmission pipeline during a dig-up and inspection program. The question was raised as to whether the SCC was active or dormant. This paper describes the resultant investigation to determine if a particular service crack was actively growing. The strategy adopted was to assess the appearance of the fracture surface of the service crack and to compare with expectations from laboratory specimens with active SCC. The conclusions from this study are as follows. To judge whether a crack in the service pipe is active or dormant, it is reasonable to compare the very crack tip of the service crack and a fresh crack in a laboratory sample. If the crack tip of the active laboratory sample is similar to that of the service pipe, it means the crack in the service pipe is likely to be active. From the comparison of the crack tip between the service pipe and the laboratory samples, it appears likely that the cracks in the samples extracted from service were most likely to have been active intergranular stress corrosion cracks. (C) 2003 Elsevier Ltd. All rights reserved.

Wave-generated flow on coral reefs - an analysis for two-dimensional horizontal reef-tops with steep faces

Waves breaking on the seaward rim of a coral reef generate a flow of water from the exposed side of the reef to the sheltered side and/or to either channels through the reef-rim or lower sections of the latter. This wave-generated flow is driven by the water surface gradient resulting from the wave set-up created by the breaking waves. This paper reviews previous approaches to modelling wave-generated flows across coral reefs and discusses the influence of reef morphology and roughness upon these flows. Laboratory measurements upon a two-dimensional horizontal reef platform with a steep reef face provide the basis for extending a previous theoretical analysis for wave set-up on a reef in the absence of a flow [Gourlay, M.R., 1996b. Wave set-up on coral reefs. 2. Set-up on reefs with various profiles. Coastal Engineering 28, 1755] to include the interaction between a unidirectional flow and the wave set-up. The laboratory model results are then used to demonstrate that there are two basic reef-top flow regimes-reef-top control and reef-rim control. Using open channel flow theory, analytical relationships are derived for the reef-top current velocity in terms of the offreef wave conditions, the reef-top water depth and the physical characteristics of the reef-top topography. The wave set-up and wave-generated flow relationships are found to predict experimental values with reasonable accuracy in most cases. The analytical relationships are used to investigate wave-generated flows into a boat harbour channel on Heron Reef in the southern Great Barrier Reef. (c) 2005 Elsevier B.V. All rights reserved.

Demographic category membership and leadership in small groups: A social identity analysis

Developing the social identity theory of leadership (e.g., [Hogg, M. A. (2001). A social identity theory of leadership. Personality and Social Psychology Review, 5, 184-200]), an experiment (N=257) tested the hypothesis that as group members identify more strongly with their group (salience) their evaluations of leadership effectiveness become more strongly influenced by the extent to which their demographic stereotype-based impressions of their leader match the norm of the group (prototypicality). Participants, with more or less traditional gender attitudes (orientation), were members, under high or low group salience conditions (salience), of non-interactive laboratory groups that had instrumental or expressive group norms (norm), and a male or female leader (leader gender). As predicted, these four variables interacted significantly to affect perceptions of leadership effectiveness. Reconfiguration of the eight conditions formed by orientation, norm and leader gender produced a single prototypicality variable. Irrespective of participant gender, prototypical leaders were considered more effective in high then low salience groups, and in high salience groups prototypical leaders were more effective than less prototypical leaders. Alternative explanations based on status characteristics and role incongruity theory do not account well for the findings. Implications of these results for the glass ceiling effect and for a wider social identity analysis of the impact of demographic group membership on leadership in small groups are discussed. (c) 2006 Elsevier Inc. All rights reserved.

Phytotoxicity of surface waters of the Thames and Brisbane River Estuaries: A combined chemical analysis and bioassay approach for the comparison of two systems

The Thames Estuary, UK, and the Brisbane River, Australia, are comparable in size and catchment area. Both are representative of the large and growing number of the world's estuaries associated with major cities. Principle differences between the two systems relate to climate and human population pressures. In order to assess the potential phytotoxic impact of herbicide residues in the estuaries, surface waters were analysed with a PAM fluorometry-based bioassay that employs the photosynthetic efficiency (photosystem II quantum yield) of laboratory cultured microalgae, as an endpoint measure of phytotoxicity. In addition, surface waters were chemically analysed for a limited number of herbicides. Diuron atrazine and simazine were detected in both systems at comparable concentrations. In contrast, bioassay results revealed that whilst detected herbicides accounted for the observed phytotoxicity of Brisbane River extracts with great accuracy, they consistently explained only around 50% of the phytotoxicity induced by Thames Estuary extracts. Unaccounted for phytotoxicity in Thames surface waters is indicative of unidentified phytotoxins. The greatest phytotoxic response was measured at Charing Cross, Thames Estuary, and corresponded to a diuron equivalent concentration of 180 ng L-1. The study employs relative potencies (REP) of PSII impacting herbicides and demonstrates that chemical analysis alone is prone to omission of valuable information. Results of the study provide support for the incorporation of bioassays into routine monitoring programs where bioassay data may be used to predict and verify chemical contamination data, alert to unidentified compounds and provide the user with information regarding cumulative toxicity of complex mixtures. (c) 2005 Elsevier B.V. All rights reserved.

Teaching principles of genetics through SNP analysis

An understanding of inheritance requires comprehension of genetic processes at all levels, from molecules to populations. Frequently genetics courses are separated into molecular and organismal genetics and students may fail to see the relationships between them. This is particularly true with human genetics, because of the difficulties in designing experimental approaches which are consistent with ethical restrictions, student abilities and background knowledge, and available time and materials. During 2005 we used analysis of single nucleotide polymorphisms (SNPs) in two genetic regions to enhance student learning and provide a practical experience in human genetics. Students scanned databases to discover SNPs in a gene of interest, used software to design PCR primers and a restriction enzyme based assay for the alleles, and carried out an analysis of the SNP on anonymous individual and family DNAs. The project occupied eight to ten hours per week for one semester, with some time spent in the laboratory and some spent in database searching, reading and writing the report. In completing their projects, students acquired a knowledge of Mendel’s first law (through looking at inheritance patterns), Mendel’s second law and the exceptions (the concepts of linkage and linkage disequilibrium), DNA structure (primer design and restriction enzyme analysis) and function (SNPs in coding and non-coding regions), population genetics and the statistical analysis of allele frequencies, genomics, bioinformatics and the ethical issues associated with the use of human samples. They also developed skills in presentation of results by publication and conference participation. Deficiencies in their understanding (for example of inheritance patterns, gene structure, statistical approaches and report writing) were detected and guidance given during the project. SNP analysis was found to be a powerful approach to enhance and integrate student understanding of genetic concepts.