Pleistocene isolation, secondary introgression and restricted contemporary gene flow in the pig-eye shark, Carcharhinus amboinensis across northern Australia

We examine the structure and phylogeography of the pig-eye shark (Carcharhinus amboinensis) common in shallow coastal environments in northern Australia using two types of genetic markers, two mitochondrial (control region and NADH hydrogenase 4) and two nuclear (microsatellite and Rag 1) DNA. Two populations were defined within northern Australia on the basis of mitochondrial DNA evidence, but this result was not supported by nuclear microsatellite or Rag 1 markers. One possibility for this structure might be sex-specific behaviours such as female philopatry, although we argue it is doubtful that sufficient time has elapsed for any potential signatures from this behaviour to be expressed in nuclear markers. It is more likely that the observed pattern represents ancient populations repeatedly isolated and connected during episodic sea level changes during the Pleistocene epoch, until current day with restricted contemporary gene flow maintaining population genetic structure. Our results show the need for an understanding of both the history and ecology of a species in order to interpret patterns in genetic structure.

Teacher quality in upper secondary science education in Australia

Science education has been the subject of increasing public interest over the last few years. While a good part of this attention has been due to the fundamental reshaping of school curricula and teacher professional standards currently underway, there has been a heightened level of critical media commentary about the state of science education in schools and science teacher education in universities. In some cases, the commentary has been informed by sound evidence and balanced perspectives. More recently, however, a greater degree of ignorance and misrepresentation has crept into the discourse. This chapter provides background on the history and status of science teacher education in Australia, along with insights into recent developments and challenges.

Dimethyl sulfide and other biogenic volatile organic compound emissions from branching coral and reef seawater: Potential sources of secondary aerosol over the Great Barrier Reef

Volatile organic compounds (VOCs) in the headspace of bubble chambers containing branches of live coral in filtered reef seawater were analysed using gas chromatography with mass spectrometry (GC-MS). When the coral released mucus it was a source of dimethyl sulfide (DMS) and isoprene; however, these VOCs were not emitted to the chamber headspace from mucus-free coral. This finding, which suggests that coral is an intermittent source of DMS and isoprene, was supported by the observation of occasional large pulses of atmospheric DMS (DMSa) over Heron Island reef on the southern Great Barrier Reef (GBR), Australia, in the austral winter. The highest DMSa pulse (320 ppt) was three orders of magnitude less than the DMS mixing ratio (460 ppb) measured in the headspace of a dynamically purged bubble chamber containing a mucus-coated branch of Acropora aspera indicating that coral reefs can be strong point sources of DMSa. Static headspace GC-MS analysis of coral fragments identified mainly DMS and seven other minor reduced sulfur compounds including dimethyl disulfide, methyl mercaptan, and carbon disulfide, while coral reef seawater was an indicated source of methylene chloride, acetone, and methyl ethyl ketone. The VOCs emitted by coral and reef seawater are capable of producing new atmospheric particles < 15 nm diameter as observed at Heron Island reef. DMS and isoprene are known to play a role in low-level cloud formation, so aerosol precursors such as these could influence regional climate through a sea surface temperature regulation mechanism hypothesized to operate over the GBR.

Why Don't Students Talk? Causes of Foreign Language Communication Apprehension in English Classes: A Comparison of High Apprehensive and Low Apprehensive Upper Secondary Students.

OBJECTIVES. Oral foreign language skills are an integral part of one's social, academic and professional competence. This can be problematic for those suffering from foreign language communication apprehension (CA), or a fear of speaking a foreign language. CA manifests itself, for example, through feelings of anxiety and tension, physical arousal and avoidance of foreign language communication situations. According to scholars, foreign language CA may impede the language learning process significantly and have detrimental effects on one's language learning, academic achievement and career prospects. Drawing on upper secondary students' subjective experiences of communication situations in English as a foreign language, this study seeks, first, to describe, analyze and interpret why upper secondary students experience English language communication apprehension in English as a foreign language (EFL) classes. Second, this study seeks to analyse what the most anxiety-arousing oral production tasks in EFL classes are, and which features of different oral production tasks arouse English language communication apprehension and why. The ultimate objectives of the present study are to raise teachers' awareness of foreign language CA and its features, manifestations and impacts in foreign language classes as well as to suggest possible ways to minimize the anxiety-arousing features in foreign language classes. METHODS. The data was collected in two phases by means of six-part Likert-type questionnaires and theme interviews, and analysed using both quantitative and qualitative methods. The questionnaire data was collected in spring 2008. The respondents were 122 first-year upper secondary students, 68 % of whom were girls and 31 % of whom were boys. The data was analysed by statistical methods using SPSS software. The theme interviews were conducted in spring 2009. The interviewees were 11 second-year upper secondary students aged 17 to 19, who were chosen by purposeful selection on the basis of their English language CA level measured in the questionnaires. Six interviewees were classified as high apprehensives and five as low apprehensives according to their score in the foreign language CA scale in the questionnaires. The interview data was coded and thematized using the technique of content analysis. The analysis and interpretation of the data drew on a comparison of the self-reports of the highly apprehensive and low apprehensive upper secondary students. RESULTS. The causes of English language CA in EFL classes as reported by the students were both internal and external in nature. The most notable causes were a low self-assessed English proficiency, a concern over errors, a concern over evaluation, and a concern over the impression made on others. Other causes related to a high English language CA were a lack of authentic oral practise in EFL classes, discouraging teachers and negative experiences of learning English, unrealistic internal demands for oral English performance, high external demands and expectations for oral English performance, the conversation partner's higher English proficiency, and the audience's large size and unfamiliarity. The most anxiety-arousing oral production tasks in EFL classes were presentations or speeches with or without notes in front of the class, acting in front of the class, pair debates with the class as audience, expressing thoughts and ideas to the class, presentations or speeches without notes while seated, group debates with the class as audience, and answering to the teacher's questions involuntarily. The main features affecting the anxiety-arousing potential of an oral production task were a high degree of attention, a large audience, a high degree of evaluation, little time for preparation, little linguistic support, and a long duration.

Analysis of Hydrogen Bonding and Stability of Protein Secondary Structures in Molecular Dynamics Simulation

Molecular Dynamics (MD) simulations provide an atomic level account of the molecular motions and have proven to be immensely useful in the investigation of the dynamical structure of proteins. Once an MD trajectory is obtained, specific interactions at the molecular level can be directly studied by setting up appropriate combinations of distance and angle monitors. However, if a study of the dynamical behavior of secondary structures in proteins becomes important, this approach can become unwieldy. We present herein a method to study the dynamical stability of secondary structures in proteins, based on a relatively simple analysis of backbone hydrogen bonds. The method was developed for studying the thermal unfolding of beta-lactamases, but can be extended to other systems and adapted to study relevant properties.

High precision Mg isotope measurements of meteoritic samples by secondary ion mass spectrometry

The possibility of establishing an accurate relative chronology of the early solar system events based on the decay of short-lived Al-26 to Mg-26 (half-life of 0.72 Myr) depends on the level of homogeneity (or heterogeneity) of Al-26 and Mg isotopes. However, this level is difficult. to constrain precisely because of the very high precision needed for the determination of isotopic ratios, typically of +/- 5 ppm. In this study, we report for the first time a detailed analytical protocol developed for high precision in situ Mg isotopic measurements ((25)mg/(24)mg and (26)mg/Mg-24 ratios, as well as Mg-26 excess) by MC-SIMS. As the data reduction process is critical for both accuracy and precision of the final isotopic results, factors such as the Faraday cup (FC) background drift and matrix effects on instrumental fractionation have been investigated. Indeed these instrumental effects impacting the measured Mg-isotope ratios can be as large or larger than the variations we are looking for to constrain the initial distribution of Al-26 and Mg isotopes in the early solar system. Our results show that they definitely are limiting factors regarding the precision of Mg isotopic compositions, and that an under- or over-correction of both FC background instabilities and instrumental isotopic fractionation leads to important bias on delta Mg-25, delta(26)mg and Delta Mg-26 values (for example, olivines not corrected for FC background drifts display Delta Mg-26 values that can differ by as much as 10 ppm from the truly corrected value). The new data reduction process described here can then be applied to meteoritic samples (components of chondritic meteorites for instance) to accurately establish their relative chronology of formation.

Throughput analysis of primary and secondary networks in a shared IEEE 802.11 system

In this paper, we analyze the coexistence of a primary and a secondary (cognitive) network when both networks use the IEEE 802.11 based distributed coordination function for medium access control. Specifically, we consider the problem of channel capture by a secondary network that uses spectrum sensing to determine the availability of the channel, and its impact on the primary throughput. We integrate the notion of transmission slots in Bianchi's Markov model with the physical time slots, to derive the transmission probability of the secondary network as a function of its scan duration. This is used to obtain analytical expressions for the throughput achievable by the primary and secondary networks. Our analysis considers both saturated and unsaturated networks. By performing a numerical search, the secondary network parameters are selected to maximize its throughput for a given level of protection of the primary network throughput. The theoretical expressions are validated using extensive simulations carried out in the Network Simulator 2. Our results provide critical insights into the performance and robustness of different schemes for medium access by the secondary network. In particular, we find that the channel captures by the secondary network does not significantly impact the primary throughput, and that simply increasing the secondary contention window size is only marginally inferior to silent-period based methods in terms of its throughput performance.

A landscape-level assessment of Asian elephant habitat, its population and elephant-human conflict in the Anamalai hill ranges of southern Western Ghats, India

Spatial information at the landscape scale is extremely important for conservation planning, especially in the case of long-ranging vertebrates. The biodiversity-rich Anamalai hill ranges in the Western Ghats of southern India hold a viable population for the long-term conservation of the Asian elephant. Through rapid but extensive field surveys we mapped elephant habitat, corridors, vegetation and land-use patterns, estimated the elephant population density and structure, and assessed elephant-human conflict across this landscape. GIS and remote sensing analyses indicate that elephants are distributed among three blocks over a total area of about 4600 km(2). Approximately 92% remains contiguous because of four corridors; however, under 4000 km2 of this area may be effectively used by elephants. Nine landscape elements were identified, including five natural vegetation types, of which tropical moist deciduous forest is dominant. Population density assessed through the dung count method using line transects covering 275 km of walk across the effective elephant habitat of the landscape yielded a mean density of 1.1 (95% Cl = 0.99-1.2) elephant/km(2). Population structure from direct sighting of elephants showed that adult male elephants constitute just 2.9% and adult females 42.3% of the population with the rest being subadults (27.4%), juveniles (16%) and calves (11.4%). Sex ratios show an increasing skew toward females from juvenile (1:1.8) to sub-adult (1:2.4) and adult (1:14.7) indicating higher mortality of sub-adult and adult males that is most likely due to historical poaching for ivory. A rapid questionnaire survey and secondary data on elephant-human conflict from forest department records reveals that villages in and around the forest divisions on the eastern side of landscape experience higher levels of elephant-human conflict than those on the western side; this seems to relate to a greater degree of habitat fragmentation and percentage farmers cultivating annual crops in the east. We provide several recommendations that could help maintain population viability and reduce elephant-human conflict of the Anamalai elephant landscape. (C) 2013 Deutsche Gesellschaft far Saugetierkunde. Published by Elsevier GmbH. All rights reserved.

Nucleated polymerization with secondary pathways. I. Time evolution of the principal moments.

Self-assembly processes resulting in linear structures are often observed in molecular biology, and include the formation of functional filaments such as actin and tubulin, as well as generally dysfunctional ones such as amyloid aggregates. Although the basic kinetic equations describing these phenomena are well-established, it has proved to be challenging, due to their non-linear nature, to derive solutions to these equations except for special cases. The availability of general analytical solutions provides a route for determining the rates of molecular level processes from the analysis of macroscopic experimental measurements of the growth kinetics, in addition to the phenomenological parameters, such as lag times and maximal growth rates that are already obtainable from standard fitting procedures. We describe here an analytical approach based on fixed-point analysis, which provides self-consistent solutions for the growth of filamentous structures that can, in addition to elongation, undergo internal fracturing and monomer-dependent nucleation as mechanisms for generating new free ends acting as growth sites. Our results generalise the analytical expression for sigmoidal growth kinetics from the Oosawa theory for nucleated polymerisation to the case of fragmenting filaments. We determine the corresponding growth laws in closed form and derive from first principles a number of relationships which have been empirically established for the kinetics of the self-assembly of amyloid fibrils.

System requirement report for Level 2 – national management institutions, for the Bureau of Fisheries and Aquatic Resources in the Philippines

This report presents the findings from a thorough literature review, workshops, and group and individual interviews conducted by STREAM in the Philippines in November and December 2003. The ambitious scope of the report combined with the limited time frame and funding available to compile it necessitated the extensive use of secondary data, including both published and unpublished material written by staff of the agencies / organisations involved, with very limited editing of material used. All possible efforts were made to generate information in participation with the government institutions responsible for managing the fisheries, and all contributors (as well as many other stakeholders) were provided with multiple opportunities to comment on the report content. The contributors are listed on the front page of the report. (Pdf contains 56 pages).

Influence of the Azores high on sea level pressure and wind, and on precipitation, in the Eastern Tropical Pacific Ocean

ENGLISH: Intensification of the Azores high pressure cell in mid-year, with concomitant air flow from the Caribbean into the Pacific, is shown to be responsible for a secondary minimum of precipitation observed along the tropical Pacific coast of the Americas, and to have a measurable effect on wind and precipitation several hundred kilometers offshore. SPANISH: La intensificación de la célula de alta presión de las Azores a mediados del año, y la corriente de aire concomitante que entra al Pacífico procedente del Caribe, se demuestra que es la causante de un mínimo secundario de precipitación observado a lo largo de la costa tropical de las Américas en el Pacífico y que tiene un efecto mensurable sobre el viento y la precipitación varios cientos de kilómetros mar afuera. (PDF contains 23 pages.)

Chemistry of secondary organic aerosol

The photooxidation of volatile organic compounds (VOCs) in the atmosphere can lead to the formation of secondary organic aerosol (SOA), a major component of fine particulate matter. Improvements to air quality require insight into the many reactive intermediates that lead to SOA formation, of which only a small fraction have been measured at the molecular level. This thesis describes the chemistry of secondary organic aerosol (SOA) formation from several atmospherically relevant hydrocarbon precursors. Photooxidation experiments of methoxyphenol and phenolic compounds and C₁₂ alkanes were conducted in the Caltech Environmental Chamber. These experiments include the first photooxidation studies of these precursors run under sufficiently low NO_x levels, such that RO₂ + HO₂ chemistry dominates, an important chemical regime in the atmosphere. Using online Chemical Ionization Mass Spectrometery (CIMS), key gas-phase intermediates that lead to SOA formation in these systems were identified. With complementary particle-phase analyses, chemical mechanisms elucidating the SOA formation from these compounds are proposed.

Three methoxyphenol species (phenol, guaiacol, and syringol) were studied to model potential photooxidation schemes of biomass burning intermediates. SOA yields (ratio of mass of SOA formed to mass of primary organic reacted) exceeding 25% are observed. Aerosol growth is rapid and linear with the organic conversion, consistent with the formation of essentially non-volatile products. Gas and aerosol-phase oxidation products from the guaiacol system show that the chemical mechanism consists of highly oxidized aromatic species in the particle phase. Syringol SOA yields are lower than that of phenol and guaiacol, likely due to unique chemistry dependent on methoxy group position.

The photooxidation of several C₁₂ alkanes of varying structure n-dodecane, 2-methylundecane, cyclododecane, and hexylcyclohexane) were run under extended OH exposure to investigate the effect of molecular structure on SOA yields and photochemical aging. Peroxyhemiacetal formation from the reactions of several multifunctional hydroperoxides and aldehyde intermediates was found to be central to organic growth in all systems, and SOA yields increased with cyclic character of the starting hydrocarbon. All of these studies provide direction for future experiments and modeling in order to lessen outstanding discrepancies between predicted and measured SOA.

Phylogenetic analyses of Fringillidae (Aves : Passeriformes) using mitochondrial tRNA gene sequences and secondary structure

Fringillidae is a large and diverse family of Passeriformes. So far, however, Fringillidae relationships deduced from morphological features and by a number of molecular approaches have remained unproven. Recently, much attention has been attracted to mitochondrial tRNA genes, whose sequence and secondary structural characteristics have shown to be useful for Acrodont Lizards and deep-branch phylogenetic studies. In order to identify useful phylogenetic markers and test Fringillidae relationships, we have sequenced three major clusters of mitochondrial tRNA genes from 15 Fringillidae, taxa. A coincident tree, with coturnix as outgroup, was obtained through Maximum-likelihood method using combined dataset of 11 mitochondrial tRNA gene sequences. The result was similar to that through Neighbor-joining but different from Maximum-parsimony methods. Phylogenetic trees constructed with stem-region sequences of 11 genes had many different topologies and lower confidence than with total sequences. On the other hand, some secondary structural characteristics may provide phylogenetic information on relatively short internal branches at under-genus level. In summary, our data indicate that mitochondrial tRNA genes can achieve high confidence on Fringillidae phylogeny at subfamily level, and stem-region sequences may be suitable only at above-family level. Secondary structural characteristics may also be useful to resolve phylogenetic relationship between different genera of Fringillidae with good performance.

Diversity, abundance distribution and secondary production of intertidal and subtidal benthic macrofauna of Bushehr Province with emphasis on annelida groups

The present investigation was undertaken to establish a reference situation for future use, to identify temporal and spatial composition of macrofauna and estimate some ecological indices in the sub tidal waters along the Bushehr coastal waters in Persian Gulf. Six transects were selected including Genaveh, Farakeh, Shif, Bandargah, Rostami and Asalouyeh, at each transect 3 station were sampled in depths of zero, 5 and 10 metres. Sampling was seasonally carried out by a VAN VEEN grab 0.0225 m2, during summer 2008 until spring 2009. Samples were wet sieved immediately using 0.5 mm mesh size sieves and sediment retained in the sieve was preserved in 4% buffered formalin solution. Macrofauna specimen were separated from the sediments using decantation and elutriation methods, enumerated and identified up to the Genus level. Environmental factors such as temperature. pH, and salinity were recorded in field using sensitive probs and refractometer (for salinity) and also sediment samples were taken for TOM and grain size analysis in all the stations. 5611 specimens belonging to 66 genera were collected during the present study. Polychaetes were dominant both in terms of genus number (31) and relative abundance (74 % of total macrofaunal abundance). The other dominant groups were Artheropoda, (16.1%), Molusca (2.8%), Echinodermata (1.29%) and others including Nematoda, Nemertina, Echiura and Turbellaria (5.8%). Thirty one Genera belong of 27 families of polychaeta, one genus and family of Subphylum Chlicerata,19 genera belong to 14 families of Crustacea, 8 genera belong to 6 families of Molusca, were indentified in the studied region. 1 family (Polygordidae) and 3 genera (Flabeligera, Pilargis and Polygordius) of Polychaeta, 1 family (Nymphonidae) and genus (Nymphon) of Chelicerata, 1 Family (Nematoplanidae) and genus (Nematoplana) of Turbellaria, were identified for the first time in Persian Gulf area. The result indicated that macrofauna organism have strong relationship with the grain size characteristics of the sediments they inhabit. The most surface deposit feeder specimens such as Prionospio and Cossura were found in zero meters depth of Genaveh, Farakeh, Bandargah, Rostami and Asalouyeh stations with sandy substratum, however the most burrowing deposit feeder and scavenger specimens such as Capitella and Petaloproctus were collected in 5 and 10 meter depths of stations with silty–clay substratum. The annual mean abundance, Shanon- weiner diversity and evenness of macrofauna were estimated1152.73 N/ m² , 2.72 and 0.792 respectively .The annual average biomass and secondary production were computed 1.797 gDW m² and 3.594 gDW m² y-1 .The average of water temperature, salinity, pH and oxygen concentration were recorded between 16.37-36.05 °C, 38-42 g/l, 7.89-8.76 and 4.23-8.23 mg/l, respectively during this study in 6 studied region. Among of investigated stations Asalouyeh adjacent of effluent canal of Gas and petrochemical industry sewage and Farakeh regions adjacent the Helleh estuary had the lowets and the highest community indices. The average of diversity and density in 5 meters depth stations with moderate of sand, silt and clay were slightly more than 2 other depths stations, it seems that 5 meters stations are made a transition habitats between 2 sandy and clay habitats, that can be used by 2 groups of surface and borrowing deposit feeders. Based on the data provided in this survey, the temperature variation, sediment texture, TOM, type habitat and manmade factors of Gas and petrochemical industries have had the most effect on the macrofauna community structure in the studied region during sampling periods.

Is there a genetic relationship between mRNA and the encoded protein at three-dimensional level?

A comparative study on the structures of some mRNAs and their encoded proteins shows an intriguing correlation between the two foldings. Non-random distribution of codons in the secondary structures of mRNAs is also shown, which appears to be in accordance with the conformational properties of amino acids in protein structures to some extent. These results seem to suggest that there may be a kind of genetic relationship between mRNA and protein at three-dimensional level.