Echolocation calls, wing shape, diet and phylogenetic diagnosis of the endemic Chinese bat Myotis pequinius

We describe the echolocation calls, flight morphology and diet of the endemic Chinese bat Myotis pequinius Thomas, 1908. Orientation calls are broadband, and reach low terminal frequencies. Diet comprised 80% beetles by volume. Wing shape and call design suggest that the bats fly in cluttered habitats, and the possession of moderately long ears and the dietary composition imply they forage at least sometimes by gleaning. Myotis pequinius resembles a larger Oriental version of the western Palaearctic species M. nattereri. Phylogenetic analysis based on sequences of the cytochrome b gene of mitochondrial DNA (1,140 base pairs) from a range of Palaearctic Myotis species confirmed that M. pequinius is close to the nattereri group, and is a sister-species to the eastern Palaearctic M. bombinus. One bat sequenced from China could not be identified from available species descriptions. It was smaller than M. pequinius, and also differed from it in sequence divergence by 6.7%, suggesting the existence of additional, cryptic taxonomic diversity in this group. Our phylogenetic analysis also supports the recognition of M. schaubi as a species distinct from M. nattereri in Transcaucasia and south-western Asia. Myotis nattereri tschuliensis is more closely related to M. schaubi than to M. nattereri, and is best considered either as a subspecies of M. schaubi, or possibly as a distinct species.

Molecular data extend Australian Cricotopus midge (Chironomidae) species diversity, and provide a phylogenetic hypothesis for biogeography and freshwater monitoring

Resolving species relationships and confirming diagnostic morphological characters for insect clades that are highly plastic, and/or include morphologically cryptic species, is crucial for both academic and applied reasons. Within the true fly (Diptera) family Chironomidae, a most ubiquitous freshwater insect group, the genera CricotopusWulp, 1874 and ParatrichocladiusSantos-Abreu, 1918 have long been taxonomically confusing. Indeed, until recently the Australian fauna had been examined in just two unpublished theses: most species were known by informal manuscript names only, with no concept of relationships. Understanding species limits, and the associated ecology and evolution, is essential to address taxonomic sufficiency in biomonitoring surveys. Immature stages are collected routinely, but tolerance is generalized at the genus level, despite marked variation among species. Here, we explored this issue using a multilocus molecular phylogenetic approach, including the standard mitochondrial barcode region, and tested explicitly for phylogenetic signal in ecological tolerance of species. Additionally, we addressed biogeographical patterns by conducting Bayesian divergence time estimation. We sampled all but one of the now recognized Australian Cricotopus species and tested monophyly using representatives from other austral and Asian locations. Cricotopus is revealed as paraphyletic by the inclusion of a nested monophyletic Paratrichocladius, with in-group diversification beginning in the Eocene. Previous morphological species concepts are largely corroborated, but some additional cryptic diversity is revealed. No significant relationship was observed between the phylogenetic position of a species and its ecology, implying either that tolerance to deleterious environmental impacts is a convergent trait among many Cricotopus species or that sensitive and restricted taxa have diversified into more narrow niches from a widely tolerant ancestor.

Dissimilarities in alignment-free methods for phylogenetic analysis based on genomes

Whole genome sequences are generally accepted as excellent tools for studying evolutionary relationships. Due to the problems caused by the uncertainty in alignment, existing tools for phylogenetic analysis based on multiple alignments could not be directly applied to the whole-genome comparison and phylogenomic studies. There has been a growing interest in alignment-free methods for phylogenetic analysis using complete genome data. The “distances” used in these alignment-free methods are not proper distance metrics in the strict mathematical sense. In this study, we first review them in a more general frame — dissimilarity. Then we propose some new dissimilarities for phylogenetic analysis. Last three genome datasets are employed to evaluate these dissimilarities from a biological point of view.

Phylogenetic lineage and pilus protein Spb1/SAN1518 affect opsonin-independent phagocytosis and intracellular survival of Group B Streptococcus

Opsonin-independent phagocytosis of Group B Streptococcus (GBS) is important in defense against neonatal GBS infections. A recent study indicated a role for GBS pilus in macrophage phagocytosis (Maisey et al Faseb J 22 2008 1715-24). We studied 163 isolates from different phylogenetic backgrounds and those possessing or lacking the gene encoding the pilus backbone protein, Spb1 (SAN1518, PI-2b) and spb1-deficient mutants of wild-type (WT) serotype III-3 GBS 874391 in non-opsonic phagocytosis assays using J774A.1 macrophages. Numbers of GBS phagocytosed differed up to 23-fold depending on phylogenetic background; isolates possessing spb1 were phagocytosed more than isolates lacking spb1. Comparing WT GBS and isogenic spb1-deficient mutants showed WT was phagocytosed better compared to mutants; Spb1 also enhanced intracellular survival as mutants were killed more efficiently. Complementation of mutants restored phagocytosis and resistance to killing in J774A.1 macrophages. Spb1 antiserum revealed surface expression in WT GBS and spatial distribution relative to capsular polysaccharide. spb1 did not affect macrophage nitric oxide and TNF-alpha responses; differences in phagocytosis did not correlate with N-acetyl d-glucosamine (from GBS cell-wall) according to enzyme-linked lectin-sorbent assay. Together, these findings support a role for phylogenetic lineage and Spb1 in opsonin-independent phagocytosis and intracellular survival of GBS in J774A.1 macrophages.

Phylogenetic analysis of human Chlamydia pneumoniae strains reveals a distinct Australian indigenous clade that predates European exploration of the continent

Background The obligate intracellular bacterium Chlamydia pneumoniae is a common respiratory pathogen, which has been found in a range of hosts including humans, marsupials and amphibians. Whole genome comparisons of human C. pneumoniae have previously highlighted a highly conserved nucleotide sequence, with minor but key polymorphisms and additional coding capacity when human and animal strains are compared. Results In this study, we sequenced three Australian human C. pneumoniae strains, two of which were isolated from patients in remote indigenous communities, and compared them to all available C. pneumoniae genomes. Our study demonstrated a phylogenetically distinct human C. pneumoniae clade containing the two indigenous Australian strains, with estimates that the most recent common ancestor of these strains predates the arrival of European settlers to Australia. We describe several polymorphisms characteristic to these strains, some of which are similar in sequence to animal C. pneumoniae strains, as well as evidence to suggest that several recombination events have shaped these distinct strains. Conclusions Our study reveals a greater sequence diversity amongst both human and animal C. pneumoniae strains, and suggests that a wider range of strains may be circulating in the human population than current sampling indicates.

A comparative structural bioinformatics analysis of the insulin receptor family ectodomain based on phylogenetic information

The insulin receptor (IR), the insulin-like growth factor 1 receptor (IGF1R) and the insulin receptor-related receptor (IRR) are covalently-linked homodimers made up of several structural domains. The molecular mechanism of ligand binding to the ectodomain of these receptors and the resulting activation of their tyrosine kinase domain is still not well understood. We have carried out an amino acid residue conservation analysis in order to reconstruct the phylogeny of the IR Family. We have confirmed the location of ligand binding site 1 of the IGF1R and IR. Importantly, we have also predicted the likely location of the insulin binding site 2 on the surface of the fibronectin type III domains of the IR. An evolutionary conserved surface on the second leucine-rich domain that may interact with the ligand could not be detected. We suggest a possible mechanical trigger of the activation of the IR that involves a slight ‘twist’ rotation of the last two fibronectin type III domains in order to face the likely location of insulin. Finally, a strong selective pressure was found amongst the IRR orthologous sequences, suggesting that this orphan receptor has a yet unknown physiological role which may be conserved from amphibians to mammals.

Error, Bias, and Long-Branch Attraction in Data for Two Chloroplast Photosystem Genes in Seed Plants

Sequences of two chloroplast photosystem genes, psaA and psbB, together comprising about 3,500 bp, were obtained for all five major groups of extant seed plants and several outgroups among other vascular plants. Strongly supported, but significantly conflicting, phylogenetic signals were obtained in parsimony analyses from partitions of the data into first and second codon positions versus third positions. In the former, both genes agreed on a monophyletic gymnosperms, with Gnetales closely related to certain conifers. In the latter, Gnetales are inferred to be the sister group of all other seed plants, with gymnosperms paraphyletic. None of the data supported the modern ‘‘anthophyte hypothesis,’’ which places Gnetales as the sister group of flowering plants. A series of simulation studies were undertaken to examine the error rate for parsimony inference. Three kinds of errors were examined: random error, systematic bias (both properties of finite data sets), and statistical inconsistency owing to long-branch attraction (an asymptotic property). Parsimony reconstructions were extremely biased for third-position data for psbB. Regardless of the true underlying tree, a tree in which Gnetales are sister to all other seed plants was likely to be reconstructed for these data. None of the combinations of genes or partitions permits the anthophyte tree to be reconstructed with high probability. Simulations of progressively larger data sets indicate the existence of long-branch attraction (statistical inconsistency) for third-position psbB data if either the anthophyte tree or the gymnosperm tree is correct. This is also true for the anthophyte tree using either psaA third positions or psbB first and second positions. A factor contributing to bias and inconsistency is extremely short branches at the base of the seed plant radiation, coupled with extremely high rates in Gnetales and nonseed plant outgroups. M. J. Sanderson,* M. F. Wojciechowski,*† J.-M. Hu,* T. Sher Khan,* and S. G. Brady

The reliability of information on work-related injuries available from hospitalisation data in Australia

Objective: To examine the reliability of work-related activity coding for injury-related hospitalisations in Australia. Method: A random sample of 4373 injury-related hospital separations from 1 July 2002 to 30 June 2004 were obtained from a stratified random sample of 50 hospitals across 4 states in Australia. From this sample, cases were identified as work-related if they contained an ICD-10-AM work-related activity code (U73) allocated by either: (i) the original coder; (ii) an independent auditor, blinded to the original code; or (iii) a research assistant, blinded to both the original and auditor codes, who reviewed narrative text extracted from the medical record. The concordance of activity coding and number of cases identified as work-related using each method were compared. Results: Of the 4373 cases sampled, 318 cases were identified as being work-related using any of the three methods for identification. The original coder identified 217 and the auditor identified 266 work-related cases (68.2% and 83.6% of the total cases identified, respectively). Around 10% of cases were only identified through the text description review. The original coder and auditor agreed on the assignment of work-relatedness for 68.9% of cases. Conclusions and Implications: The current best estimates of the frequency of hospital admissions for occupational injury underestimate the burden by around 32%. This is a substantial underestimate that has major implications for public policy, and highlights the need for further work on improving the quality and completeness of routine, administrative data sources for a more complete identification of work-related injuries.

A phenomenological explication of dream interpretation among rural and urban Nguni people

Psychologists investigating dreams in non-Western cultures have generally not considered the meanings of dreams within the unique meaning-structure of the person in his or her societal context. The majority of dream studies in African societies are no exception. Researchers approaching dreams within rural Xhosa and Zulu speaking societies have either adopted an anthropological or a psychodynamic orientation. The latter approach particularly imposes a Western perspective in the interpretation of dream material. There have been no comparable studies of dream interpretation among urban blacks participating in the African Independent Church Movement. The present study focuses on the rural Xhosa speaking people and the urban black population who speak one of the Nguni languages and identify with the African Independent Church Movement. The study is concerned with understanding the meanings of dreams within the cultural context in which they occur. The specific aims of the study are: 1. To explicate the indigenous system of dream interpretation as revealed by acknowledged dream experts. 2. To examine the commonalities and the differences between the interpretation of dreams in two groups, drawn from a rural and urban setting respectively. 3. To elaborate upon the life-world of the participants by the interpretations gained from the above investigation. One hundred dreams and interpretations are collected from two categories of participants referred to as the Rural Group and the Urban Group. The Rural Group is made up of amagqira [traditional healers] and their clients, while the Urban Group consists of prophets and members of the African Independent Churches. Each group includes acknowledged dream experts. A phenomenological methodology is adopted in explicating the data. The methodological precedure involves a number of rigorous stages of expl ication whereby the original data is reduced to Constituent Profiles leading to the construction of a Thematic Index File. By searching and reflect ing upon the data, interpretative themes are identified. These themes are explicated to provide a rigorous description of the interpretative-reality of each group. Themes explicated w i thin the Rural Group are: the physiognomy of the dreamer's life-world as revealed by ithongo, the interpretation of ithongo as revealed through action, the dream relationship as an anticipatory mode-of-existence, iphupha as disclosing a vulnerable mode-of-being, human bodiliness as revealed in dream interpretations and the legitimation of the interpretative-reality within the life-world. Themes explicated within the Urban Group are: the phys iognomy of the dreamer's life-world revealed in their dream-existence, the interpretative-reality revealed through the enaction of dreams, tension between the newer Christian-based cosomology and the traditional cultural-based cosmology, a moral imperative, prophetic perception and human bodiliness, as revealed in dream interpretations and the legitimation of the interpretative-reality within the life-world. The essence of the interpretative-reality of both groups is very similar and is expressed in the notion of relatedness to a cosmic mode-of-being. The cosmic mode-of-being includes a numinous dimension which is expressed through divine presence in the form of ancestors, Holy Spirit or God. These notions cannot be apprehended by theoretical constructs alone but may be grasped and given form in meaning-disclosing intuitions which are expressed in the lifeworld in terms of bodiliness, revelatory knowledge, action and healing. Some differences b e tween the two groups are evident and reveal some conflict between the monotheistic Christian cosmology and the traditional cosmology. Unique aspects of the interpetative-reality of the Urban Group are expressed in terms of difficulties in the urban social environment and the notion of a moral imperative. It is observed that cul tural self-expression based upon traditional ideas continues to play a significant role in the urban environment. The apparent conflict revealed between the respective cosmologies underlies an integration of the aditional meanings with Christian concepts. This finding is consistent with the literature suggesting that the African Independent Church is a syncretic movement. The life-world is based upon the immediate and vivid experience of the numinous as revealed in the dream phenomenon. The participants' approach to dreams is not based upon an explicit theory, but upon an immediate and pathic understanding of the dream phenomenon. The understanding is based upon the interpreter's concrete understanding of the life-world, which includes the possibility of cosmic integration and continuity between the personal and transpersonal realms of being. The approach is characterized as an expression of man's primordial attunement with the cosmos. The approach of the participants to dreams may not b e consistent with a Western rational orientation, but neverthele ss, it is a valid approach . The validity is based upon the immediate life-world of experience which is intelligible, coherent, and above all, it is meaning-giving in revealing life-possibility within the context of human existence.

Integrated versus non-integrated management and care for clients with co-occurring mental health and substance use disorders : a qualitative systematic review of randomised controlled trials

The purpose of this paper is to conduct a qualitative review of randomised controlled trials in relation to the treatment of adults with co-occurring mental health and substance use disorder (MH/SUD). In particular, integrated approaches are compared with non-integrated approaches to treatment. Ten articles were identified for inclusion in the review. The findings are equivocal with regard to the superior efficacy of integrated approaches to treatment, although the many limitations of the studies need to be considered in our understanding of this finding. Clearly, this is an extremely challenging client group to engage and maintain in intervention research, and the complexity and variability of the problems render control particularly difficult. The lack of available evidence to support the superiority of integration is discussed in relation to these challenges. Much remains to be investigated with regard to integrated management and care for people with co-occurring and MH/SUD, particularly for specific combinations of dual diagnosis and giving consideration to the level of inter-relatedness between the disorders.

Evidence that human chlamydia pneumoniae was zoonotically acquired

Zoonotic infections are a growing threat to global health. Chlamydia pneumoniae is a major human pathogen that is widespread in human populations, causing acute respiratory disease, and has been associated with chronic disease. C. pneumoniae was first identified solely in human populations; however, its host range now includes other mammals, marsupials, amphibians, and reptiles. Australian koalas (Phascolarctos cinereus) are widely infected with two species of Chlamydia, C. pecorum and C. pneumoniae. Transmission of C. pneumoniae between animals and humans has not been reported; however, two other chlamydial species, C. psittaci and C. abortus, are known zoonotic pathogens. We have sequenced the 1,241,024-bp chromosome and a 7.5-kb cryptic chlamydial plasmid of the koala strain of C. pneumoniae (LPCoLN) using the whole-genome shotgun method. Comparative genomic analysis, including pseudogene and single-nucleotide polymorphism (SNP) distribution, and phylogenetic analysis of conserved genes and SNPs against the human isolates of C. pneumoniae show that the LPCoLN isolate is basal to human isolates. Thus, we propose based on compelling genomic and phylogenetic evidence that humans were originally infected zoonotically by an animal isolate(s) of C. pneumoniae which adapted to humans primarily through the processes of gene decay and plasmid loss, to the point where the animal reservoir is no longer required for transmission.

Attractiveness of venture ideas : a conjoint study

Principal Topic : According to Shane & Venkataraman (2000) entrepreneurship consists of the recognition and exploitation of venture ideas - or opportunities as they often called - to create future goods and services. This definition puts venture ideas is at the heart of entrepreneurship research. Substantial research has been done on venture ideas in order to enhance our understanding of this phenomenon (e.g. Choi & Shepherd, 2004; Shane, 2000; Shepherd & DeTienne, 2005). However, we are yet to learn what factors drive entrepreneurs' perceptions of the relative attractiveness of venture ideas, and how important different idea characteristics are for such assessments. Ruef (2002) recognized that there is an uneven distribution of venture ideas undertaken by entrepreneurs in the USA. A majority introduce either a new product/service or access a new market or market segment. A smaller percentage of entrepreneurs introduce a new method of production, organizing, or distribution. This implies that some forms of venture ideas are perceived by entrepreneurs as more important or valuable than others. However, Ruef does not provide any information regarding why some forms of venture ideas are more common than others among entrepreneurs. Therefore, this study empirically investigates what factors affect the attractiveness of venture ideas as well as their relative importance. Based on two key characteristics of venture ideas, namely venture idea newness and relatedness, our study investigates how different types and degrees of newness and relatedness of venture ideas affect their attractiveness as perceived by expert entrepreneurs. Methodology/Key : Propositions According to Schumpeter (1934) entrepreneurs introduce different types of venture ideas such as new products/services, new method of production, enter into new markets/customer and new method of promotion. Further, according to Schumpeter (1934) and Kirzner (1973) venture ideas introduced to the market range along a continuum of innovative to imitative ideas. The distinction between these two extremes of venture idea highlights an important property of venture idea, namely their newness. Entrepreneurs, in order to gain competitive advantage or above average returns introduce their venture ideas which may be either new to the world, new to the market that they seek to enter, substantially improved from current offerings and an imitative form of existing offerings. Expert entrepreneurs may be more attracted to venture ideas that exhibit high degree of newness because of the higher newness is coupled with increased market potential (Drucker, 1985) Moreover, certain individual characteristics also affect the attractiveness of venture idea. According to Shane (2000), individual's prior knowledge is closely associated with the recognition of venture ideas. Sarasvathy's (2001) Effectuation theory proposes a high degree of relatedness between venture ideas and the resource position of the individual. Thus, entrepreneurs may be more attracted to venture ideas that are closely aligned with the knowledge and/or resources they already possess. On the other hand, the potential financial gain (Shepherd & DeTienne, 2005) may be larger for ideas that are not close to the entrepreneurs' home turf. Therefore, potential financial gain is a stimulus that has to be considered separately. We aim to examine how entrepreneurs weigh considerations of different forms of newness and relatedness as well as potential financial gain in assessing the attractiveness of venture ideas. We use conjoint analysis to determine how expert entrepreneurs develop preferences for venture ideas which involved with different degrees of newness, relatedness and potential gain. This analytical method paves way to measure the trade-offs they make when choosing a particular venture idea. The conjoint analysis estimates respondents' preferences in terms of utilities (or part-worth) for each level of newness, relatedness and potential gain of venture ideas. A sample of 50 expert entrepreneurs who were awarded young entrepreneurship awards in Sri Lanka in 2007 is used for interviews. Each respondent is interviewed providing with 32 scenarios which explicate different combinations of possible profiles open them into consideration. Conjoint software (SPSS) is used to analyse data. Results and Implications : The data collection of this study is still underway. However, results of this study will provide information regarding the attractiveness of each level of newness, relatedness and potential gain of venture idea and their relative importance in a business model. Additionally, these results provide important implications for entrepreneurs, consultants and other stakeholders as regards the importance of different of attributes of venture idea coupled with different levels. Entrepreneurs, consultants and other stakeholders could make decisions accordingly.

The development of a serological-based diagnostic test for Dasheen mosaic potyvirus (DsMV)

Dasheen mosaic potyvirus (DsMV) is an important virus affecting taro. The virus has been found wherever taro is grown and infects both the edible and ornamental aroids, causing yield losses of up to 60%. The presence of DsMV, and other viruses,prevents the international movement of taro germplasm between countries. This has a significant negative impact on taro production in many countries due to the inability to access improved taro lines produced in breeding programs. To overcome this problem, sensitive and reliable virus diagnostic tests need to be developed to enable the indexing of taro germplasm. The aim of this study was to generate an antiserum against a recombinant DsMV coat protein (CP) and to develop a serological-based diagnostic test that would detect Pacific Island isolates of the virus. The CP-coding region of 16 DsMV isolates from Papua New Guinea, Samoa, Solomon Islands, French Polynesia, New Caledonia and Vietnam were amplified,cloned and sequenced. The size of the CP-coding region ranged from 939 to 1038 nucleotides and encoded putative proteins ranged from 313 to 346 amino acids, with the molecular mass ranging from 34 to 38 kDa. Analysis ofthe amino acid sequences revealed the presence of several amino acid motifs typically found in potyviruses,including DAG, WCIE/DN, RQ and AFDF. When the amino acid sequences were compared with each other and the DsMV sequences on the database, the maximum variability was21.9%. When the core region ofthe CP was analysed, the maximum variability dropped to 6% indicating most variability was present in the N terminus. Within seven PNG isolates ofDsMV, the maximum variability was 16.9% and 3.9% over the entire CP-coding region and core region, respectively. The sequence ofPNG isolate P1 was most similar to all other sequences. Phylogenetic analysis indicated that almost all isolates grouped according to their provenance. Further, the seven PNG isolates were grouped according to the region within PNG from which they were obtained. Due to the extensive variability over the entire CP-coding region, the core region ofthe CP ofPNG isolate Pl was cloned into a protein expression vector and expressed as a recombinant protein. The protein was purified by chromatography and SDS-PAGE and used as an antigen to generate antiserum in a rabbit. In western blots, the antiserum reacted with bands of approximately 45-47 kDa in extracts from purified DsMV and from known DsMV -infected plants from PNG; no bands were observed using healthy plant extracts. The antiserum was subsequently incorporated into an indirect ELISA. This procedure was found to be very sensitive and detected DsMV in sap diluted at least 1:1,000. Using both western blot and ELISA formats,the antiserum was able to detect a wide range ofDsMV isolates including those from Australia, New Zealand, Fiji, French Polynesia, New Caledonia, Papua New Guinea, Samoa, Solomon Islands and Vanuatu. These plants were verified to be infected with DsMV by RT-PCR. In specificity tests, the antiserum was also found to react with sap from plants infected with SCMV, PRSV-P, PRSV-W, but not with PVY or CMV -infected plants.