Improved detection sensitivity using an optimal eDNA preservation and extraction workflow and its application to threatened sawfishes

1. Pressures on coastal ecosystems are increasing and aquatic species that are restricted to these habitats are facing the threat of extinction. However, the true extent of many threatened and rare aquatic species, especially elasmobranchs, remains unclear due to high levels of data deficiency and poor efficacy of traditional survey methods. Sawfishes (Pristidae), a family of shark-like rays, are among the most threatened and rare elasmobranch species and are difficult to detect in turbid, coastal habitats. Reliable cost-effective tools to detect these species are urgently needed to increase their conservation potential.
2. Characterization of environmental DNA (eDNA) extracted from water samples has garnered significant appeal for detection of rare and threatened species. To assist conservation and monitoring efforts for sawfishes using eDNA, species-specific TaqMan quantitative polymerase chain reaction assays were developed and validated to detect 1.25–5 copies of a 12S rRNA gene fragment. Filter samples were collected in Northern Territory, Australia to assess the utility of the developed eDNA assays and compare the efficacy of preservation and extraction workflows for detecting rare species.
3. Dwarf sawfish (Pristis clavata) were detected in three of 20 sites, and there was a significant effect of preservation and extraction workflow on total eDNA yield and subsequent detection success. Longmire's preserved samples extracted using glycogen-aided precipitation yielded a significantly higher concentration of total eDNA (n = 60; β = 1.27, t(95) = 8.172, P < 0.0001) and yielded positive P. clavata eDNA detections compared to ethanol preserved samples extracted using QIAGEN DNeasy kit, which did not yield any positive detections.
4. The optimized eDNA assays were developed to support monitoring efforts for endangered sawfishes. Importantly, this study demonstrates that choice of preservation and extraction workflow requires careful consideration, especially when detection of rare or threatened species can have important management and conservation outcomes.

     

The protein composition of sheep foetal fluids

Amniotic fluid contains several proteins including alpha-foetoprotein derived from the foetal plasma, but lacks the higher molecular weight alpha2- and gamma-globulins. The protein composition of the fluid, like that of the serum, remains unchanged after the first month of gestation, and is buffered from the influence of the allantoic fluid by the amnion. Allantoic fluid contains a significantly higher concentration and a greater variety of proteins; it is not a simple transudate of either foetal or maternal plasma, and though containing proteins derived from both sources, it is deficient in albumin but relatively abundant in gamma-globulins. The latter comprises gamma-foetoprotein and mature type IgG. It is believed that maternal IgG may reach the allantoic sac in appreciable amount, but its transmission to the amniotic sac and thence to the foetus may be prevented by the impermeability of the amnion.     

Just Add Water and Salt: the Optimisation of Petrogenic Hydrocarbon Biodegradation in Soils from Semi-arid Barrow Island, Western Australia

We investigated the potential of soil moisture and nutrient amendments to enhance the biodegradation of oil in the soils from an ecologically unique semi-arid island. This was achieved using a series of controlled laboratory incubations where moisture or nutrient levels were experimentally manipulated. Respired CO₂ increased sharply with moisture amendment reflecting the severe moisture limitation of these porous and semi-arid soils. The greatest levels of CO₂ respiration were generally obtained with a soil pore water saturation of 50?C70%. Biodegradation in these nutrient poor soils was also promoted by the moderate addition of a nitrogen fertiliser. Increased biodegradation was greater at the lowest amendment rate (100 mg N kg^?1 soil) than the higher levels (500 or 1,000 mg N kg^?1 soil), suggesting the higher application rates may introduce N toxicity. Addition of phosphorous alone had little effect, but a combined 500 mg N and 200 mg P kg^?1 soil amendment led to a synergistic increase in CO₂ respiration (3.0×), suggesting P can limit the biodegradation of hydrocarbons following exogenous N amendment.     

Gallium arsenide transistors: realization through a molecularly designed insulator

A GaAs-based transistor, analogous to commercial silicon devices, has been fabricated with vapor-deposited cubic GaS as the insulator material. The n-channel, depletion mode, GaAs field-effect transistor shows, in addition to classical transistor characteristics, a channel mobility of 4665.6 square centimeters per volt per second, an interfacial trap density of 10(11) per electron volt per square centimeter, and a transconductance of 7 millisiemens for a 5-micrometer gate length at a gate voltage of 8 volts. Furthermore, the GaAs transistor shows an on-to-off resistance ratio comparable to that of commercial devices.     

An ice-free cretaceous? Results from climate model simulations

We have quantitatively investigated the mechanisms that could explain the warm, equable climate that is believed to have been typical of the mid-Cretaceous (100 million years ago). By performing simulations with a climate model based on zonal energy balance, we demonstrate that past changes in geography were important in bringing about climatic change. However, the meridional distribution of Cretaceous temperatures cannot be successfully simulated unless additional physical "feedback mechanisms" are included in the model. These mechanisms may involve cloud and meridional heat transport changes. We also conclude that paleoclimatologists should reexamine carefully both existing data and their interpretations with regard to reconstruction of Cretaceous tropical and polar surface temperatures.     

Linking the biology and ecology of key herbivorous unicornfish to fisheries management in the Pacific

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Conservation farming strategies in East and Southern Africa: Yields and rain water productivity from on-farm action research

Improved agricultural productivity using conservation farming (CF) systems based on non-inversion tillage methods, have predominantly originated from farming systems in sub-humid to humid regions where water is not a key limiting factor for crop growth. This paper presents evidence of increased yields and improved water productivity using conservation farming in semi-arid and dry sub-humid locations in Ethiopia, Kenya, Tanzania and Zambia. Results are based on on-farm farmer and research managed experiments during the period 1999–2003. Grain yield of maize (Zea mays L.) and tef (Eragrostis Tef (Zucc)) from conventional (inversion) tillage are compared with CF with and without fertilizer. Rain water productivity (WP_rain) is assessed for the locations, treatments and seasons. Results indicate significantly higher yields (p < 0.05) for CF+ fertilizer treatments over conventional treatments in most locations, increasing from 1.2 to 2 t ha^?1 with 20–120% for maize. For tef in Ethiopian locations, the yield gains nearly doubled from 0.5–0.7 to 1.1 t ha^?1 for “best bet” CF+ fertilizer. WP_rain improved for CF+ fertilizer treatments with WP gains of 4500–6500 m³ rainwater per t maize grain yield in the lower yield range from 0 to 2.5 t ha^?1. This is explained by the large current unproductive water losses in the on-farm water balance. There was a tendency of improved WP_rain in drier locations, which can be explained by the water harvesting effect obtained in the CF treatments. The experiences from East and Southern Africa presented in this paper indicate that for smallholder farmers in savannah agro-ecosystems, conservation farming first and foremost constitutes a water harvesting strategy. It is thus a non-inversion tillage strategy for in situ moisture conservation, rather than solely aimed at minimum tillage with mulch cover. Challenges for the future adoption of CF in sub-Saharan Africa include how to improve farmer awareness of CF benefits, and how to efficiently incorporate green manure/cover crops and manage weeds.     

Biochemical markers: Efficient tools for the assessment of wheat grain tissue proportions in milling fractions

To produce safe and healthy whole wheat food products, various grain or bran dry fractionation processes have been developed recently. In order to control the quality of the products and to adapt these processes, it is important to be able to monitor the grain tissue proportions in the different milling fractions produced. Accordingly, a quantitative method based on biochemical markers has been developed for the assessment of grain tissue proportions in grain fractions. Grain tissues that were quantified were the outer pericarp, an intermediate layer (including the outer pericarp, the testa and the hyaline layer), the aleurone cell walls, the aleurone cell contents, the endosperm and the germ, for two grain cultivars (Tiger and Crousty). Grain tissues were dissected by hand and analysed. Biochemical markers chosen were ferulic acid trimer, alkylresorcinols, para-coumaric acid, phytic acid, starch and wheat germ agglutinin, for outer pericarp, intermediate layer, aleurone cell walls, aleurone cell contents, endosperm and germ respectively. The results of tissue quantification by hand dissection and by calculation were compared and the sensitivity of the method was regarded as good (mean relative errors of 4% and 8% for Crousty and Tiger outer layers respectively). The impact of the analytical variability (maximum 13% relative error on coarse bran) was also regarded as acceptable. Wheat germ agglutinin seems to be a promising marker of wheat germ: even if the quantification method was not able to quantify the germ proportions in milling fractions, it was able to classify these fractions according to their germ content. The efficiency of this method was tested, by assessing the grain tissue proportions of fractions exhibiting very different compositions such as flour, bran and aleurone-rich fractions obtained from three different grain or bran dry fractionation processes (conventional milling, debranning process, production of aleurone-rich fractions from coarse bran). By calculation of the composition of the different products generated, it was possible to study the distribution of the different tissues among fractions resulting from the different fractionation processes. This quantitative method is thus a useful tool for the monitoring and improvement of processes, and allows the effects of these processes to be understood and their adaption to reach the objectives.