A review of the biology and ecology of key fishes targeted by coastal fisheries in south-east Australia: identifying critical knowledge gaps required to improve spatial management

Knowledge of the population biology, life-history ecology and scales of pre and post-settlement movement of marine species are needed to inform effective conservation management strategies, particularly when spatial information is required for management purposes such as zoning in Marine Protected Areas. This review provides the most current summary from primary and grey literature on the biology and ecology of several coastal fishes of economic and ecological significance in south-east Australia; identifies key knowledge gaps which may impede the development of effective spatial management; and recommends future research directions and methods. Reviewed species are luderick (Girella tricuspidata), eastern rock blackfish (Girella elevata), yellowfin bream (Acanthopagrus australis), tarwhine (Rhabdosargus sarba), snapper (Pagrus auratus), red morwong (Cheilodactylus fuscus) and eastern blue grouper (Achoerodus viridis). The species have a diverse range of life-histories and population traits, and selected parameters were well studied in several species, such as growth (blue groper, luderick, yellowfin bream, tarwhine, snapper), post-settlement movement (red morwong), and larval ecology (yellowfin bream). However, empirical data on levels of pre- and post-settlement connectivity and real-time movements are not available for most species, and this represents a significant gap for improved spatial management. A multidisciplinary approach incorporating a range of methods including acoustic tracking and telemetry, otolith chemistry, intergenerational markers, and biophysical modelling will provide a more comprehensive understanding of life history parameters, movement and connectivity at scales relevant to MPA planning and monitoring.     

Genome Sequence of the Corynebacterium pseudotuberculosis Cp316 Strain,Isolated from the Abscess of a Californian Horse

The bacterium Corynebacterium pseudotuberculosis is of major veterinary importance because it affects livestock, particularly sheep, goats, and horses, in several countries, including Australia, Brazil, the United States, and Canada, resulting in significant economic losses. In the present study, we describe the complete genome of the Corynebacterium pseudotuberculosis Cp316 strain, biovar equi, isolated from the abscess of a North American horse.     

Effects of bacillamide and newly synthesized derivatives on the growth of cyanobacteria and microalgae cultures

The antialgal activity of newly synthesized bacillamides against several cyanobacteria and microalgae isolates was screened using a rapid 96-well microplate bioassay. Cultures were exposed to serial dilutions of each bacillamide derivative (0–160 μg mL⁻¹) in the microplate wells and daily optical measurements were used to estimate growth over a 216 h period. Inhibition values (%) were calculated from the estimated growth curves and inhibitory concentrations (IC₅₀-216 h) were obtained from the sigmoidal inhibition curves fitted by regression analysis. The effects of bacillamides on cell morphology and ultrastructure were also analysed by light and transmission electron microscopy. In general, the toxic cyanobacteria Microcystis aeruginosa, Aphanizomenon gracile, Anabaena circinalis and Anabaenopsis circularis were much more sensitive to bacillamides then the chlorophytes Ankistrodesmus falcatus and Scenedesmus obliquus. However, clear signs of morphological and ultrastructural changes induced by bacillamide were observed on both cyanobacteria and chlorophytes. Other cyanobacteria, namely the nostocalean Nodularia spumigena and the oscillatorialeans Leptolyngbya sp. and Planktothrix rubescens, exhibit higher tolerances to bacillamides, similar to that shown by different eukaryotic microalgae. Diatoms, on the other hand, proved to be quite as sensitive to most bacillamides as the most affected cyanobacteria. The properties of 5-iodo-Bacillamide (algicide or algistatic) were further investigated. This compound acted as an algistactic agent against eukaryotic algae and, depending on its concentration, acted as either an algicide or algistactic agent against most of the cyanobacteria tested. Although bacillamides cannot be considered as broad spectrum cyanobacterial algicides, different bacillamides might be of use in selectively controlling the growth of particular species of cyanobacteria.     

High‐resolution photo‐mosaic time‐series imagery for monitoring human use of an artificial reef

Successful marine management relies on understanding patterns of human use. However, obtaining data can be difficult and expensive given the widespread and variable nature of activities conducted. Remote camera systems are increasingly used to overcome cost limitations of conventional labour‐intensive methods. Still, most systems face trade‐offs between the spatial extent and resolution over which data are obtained, limiting their application. We trialed a novel methodology, CSIRO Ruggedized Autonomous Gigapixel System (CRAGS), for time series of high‐resolution photo‐mosaic (HRPM) imagery to estimate fine‐scale metrics of human activity at an artificial reef located 1.3 km from shore. We compared estimates obtained using the novel system to those produced with a web camera that concurrently monitored the site. We evaluated the effect of day type (weekday/weekend) and time of day on each of the systems and compared to estimates obtained from binocular observations. In general, both systems delivered similar estimates for the number of boats observed and to those obtained by binocular counts; these results were also unaffected by the type of day (weekend vs. weekday). CRAGS was able to determine additional information about the user type and party size that was not possible with the lower resolution webcam system. However, there was an effect of time of day as CRAGS suffered from poor image quality in early morning conditions as a result of fixed camera settings. Our field study provides proof of concept of use of this new cost‐effective monitoring tool for the remote collection of high‐resolution large‐extent data on patterns of human use at high temporal frequency.     

Which Type of Planets do We Expect to Observe in the Habitable Zone?

We used a sample of super-Earth-like planets detected by the Doppler spectroscopy and transit techniques to explore the dependence of orbital parameters of the planets on the metallicity of their host stars. We confirm the previous results (although still based on small samples of planets) that super-Earths orbiting around metal-rich stars are not observed to be as distant from their host stars as we observe their metal-poor counterparts to be. The orbits of these super-Earths with metal-rich hosts usually do not reach into the Habitable Zone (HZ), keeping them very hot and inhabitable. We found that most of the known planets in the HZ are orbiting their GK-type hosts which are metal-poor. The metal-poor nature of planets in the HZ suggests a high Mg abundance relative to Si and high Si abundance relative to Fe. These results lead us to speculate that HZ planets might be more frequent in the ancient Galaxy and had compositions different from that of our Earth.     

Effect of Acute Inspiratory Muscle Exercise on Blood Flow of Resting and Exercising Limbs and Glucose Levels in Type 2 Diabetes

To evaluate the effects of inspiratory loading on blood flow of resting and exercising limbs in patients with diabetic autonomic neuropathy. Ten diabetic patients without cardiovascular autonomic neuropathy (DM), 10 patients with cardiovascular autonomic neuropathy (DM-CAN) and 10 healthy controls (C) were randomly assigned to inspiratory muscle load of 60% or 2% of maximal inspiratory pressure (PImax) for approximately 5 min, while resting calf blood flow (CBF) and exercising forearm blood flow (FBF) were measured. Reactive hyperemia was also evaluated. From the 20 diabetic patients initially allocated, 6 wore a continuous glucose monitoring system to evaluate the glucose levels during these two sessions (2%, placebo or 60%, inspiratory muscle metaboreflex). Mean age was 58 ± 8 years, and mean HbA1c, 7.8% (62 mmol/mol) (DM and DM-CAN). A PImax of 60% caused reduction of CBF in DM-CAN and DM (P<0.001), but not in C, whereas calf vascular resistance (CVR) increased in DM-CAN and DM (P<0.001), but not in C. The increase in FBF during forearm exercise was blunted during 60% of PImax in DM-CAN and DM, and augmented in C (P<0.001). Glucose levels decreased by 40 ± 18.8% (P<0.001) at 60%, but not at 2%, of PImax. A negative correlation was observed between reactive hyperemia and changes in CVR (Beta coefficient = -0.44, P = 0.034). Inspiratory muscle loading caused an exacerbation of the inspiratory muscle metaboreflex in patients with diabetes, regardless of the presence of neuropathy, but influenced by endothelial dysfunction. High-intensity exercise that recruits the diaphragm can abruptly reduce glucose levels.     

Evaluating <Emphasis Type="Italic">Theobroma grandiflorum</Emphasis> for comparative genomic studies with <Emphasis Type="Italic">Theobroma cacao</Emphasis>

The seeds of Theobroma cacao (cacao) are the source of cocoa, the raw material for the multi-billion dollar chocolate industry. Cacao’s two most important traits are its unique seed storage triglyceride (cocoa butter) and the flavor of its fermented beans (chocolate). The genome of T. cacao is being sequenced, and to expand the utility of the genome sequence to the improvement of cacao, we are evaluating Theobroma grandiflorum, the closest economically important species of Theobroma for its potential use in a comparative genomic study. T. grandiflorum differs from cacao in important agronomic traits such as flavor of the fermented beans, disease resistance to witches’ broom and abscission of mature fruits. By comparing genomic sequences and analyzing viable inter-specific hybrids, we hope to identify the key genes that regulate cacao’s most important traits. We have investigated the utility in T. grandiflorum of three types of markers (microsatellite markers, single-strand conformational polymorphism markers and single nucleotide polymorphism (SNP) markers) developed in cacao. Through sequencing of amplicons of 12 diverse individuals of both cacao and T. grandiflorum, we have identified new intra- and inter-specific SNPs. Two markers which had no overlap of alleles between the species were used to genotype putative inter-specific hybrid seedlings. Sequence conservation was significant and species-specific differences numerous enough to suggest that comparative genomics of T. grandiflorum and T. cacao will be useful in elucidating the genetic differences that lead to a variety of important agronomic trait differences.     

Computational annotation of genes differentially expressed along olive fruit development

Background  

Olea europaea L. is a traditional tree crop of the Mediterranean basin with a worldwide economical high impact. Differently from other fruit tree species, little is known about the physiological and molecular basis of the olive fruit development and a few sequences of genes and gene products are available for olive in public databases. This study deals with the identification of large sets of differentially expressed genes in developing olive fruits and the subsequent computational annotation by means of different software.     

Development of an integrated genetic map of a sugarcane (Saccharum spp.) commercial cross, based on a maximum-likelihood approach for estimation of linkage and linkage phases

Sugarcane (Saccharum spp.) is a clonally propagated outcrossing polyploid crop of great importance in tropical agriculture. Up to now, all sugarcane genetic maps had been developed using either full-sib progenies derived from interspecific crosses or from selfing, both approaches not directly adopted in conventional breeding. We have developed a single integrated genetic map using a population derived from a cross between two pre-commercial cultivars (‘SP80-180’ × ‘SP80-4966’) using a novel approach based on the simultaneous maximum-likelihood estimation of linkage and linkage phases method specially designed for outcrossing species. From a total of 1,118 single-dose markers (RFLP, SSR and AFLP) identified, 39% derived from a testcross configuration between the parents segregating in a 1:1 fashion, while 61% segregated 3:1, representing heterozygous markers in both parents with the same genotypes. The markers segregating 3:1 were used to establish linkage between the testcross markers. The final map comprised of 357 linked markers, including 57 RFLPs, 64 SSRs and 236 AFLPs that were assigned to 131 co-segregation groups, considering a LOD score of 5, and a recombination fraction of 37.5 cM with map distances estimated by Kosambi function. The co-segregation groups represented a total map length of 2,602.4 cM, with a marker density of 7.3 cM. When the same data were analyzed using JoinMap software, only 217 linked markers were assigned to 98 co-segregation groups, spanning 1,340 cM, with a marker density of 6.2 cM. The maximum-likelihood approach reduced the number of unlinked markers to 761 (68.0%), compared to 901 (80.5%) using JoinMap. All the co-segregation groups obtained using JoinMap were present in the map constructed based on the maximum-likelihood method. Differences on the marker order within the co-segregation groups were observed between the two maps. Based on RFLP and SSR markers, 42 of the 131 co-segregation groups were assembled into 12 putative homology groups. Overall, the simultaneous maximum-likelihood estimation of linkage and linkage phases was more efficient than the method used by JoinMap to generate an integrated genetic map of sugarcane. E.A. Kido, A.N. Meza and H.M.B. Souza contributed equally to this work.