Preliminary characterisation and extraction of anterior adhesive secretion in monogenean (platyhelminth) parasites

Secreted anterior adhesives, used for temporary attachment to epithelial surfaces of fishes (skin and gills) by some monogenean (platyhelminth) parasites have been partially characterised. Adhesive is composed of protein. Amino acid composition has been determined for seven monopisthocotylean monogeneans. Six of these belong to the Monocotylidae and one species, Entobdella soleae (van Beneden et Hesse, 1864) Johnston, 1929, is a member of the Capsalidae. Histochemistry shows that the adhesive does not contain polysaccharides, including acid mucins, or lipids. The adhesive before secretion and in its secreted form contains no dihydroxyphenylalanine (dopa). Secreted adhesive is highly insoluble, but has a soft consistency and is mechanically removable from glass surfaces. Generally there are high levels of glycine and alanine, low levels of tyrosine and methionine, and histidine is often absent. However, amino acid content varies between species, the biggest differences evident when the monocotylid monogeneans were compared with E. soleae. Monogenean adhesive shows similarity in amino acid profile with adhesives from starfish, limpets and barnacles. However, there are some differences in individual amino acids in the temporary adhesive secretions of, on the one hand, the monogeneans and, on the other hand, the starfish and limpets. These differences may reflect the fact that monogeneans, unlike starfish and barnacles, attach to living tissue (tissue adhesion). A method of extracting unsecreted adhesive was investigated for use in further characterisation studies on monogenean glues.

Rapid quantification of hepatitis B virus DNA by real-time PCR using efficient TaqMan probe and extraction of virus DNA

Aim: To rapidly quantify hepatitis B virus (HBV) DNA by real-time PCR using efficient TaqMan probe and extraction methods of virus DNA. Methods: Three standards were prepared by cloning PCR products which targeted S, C and X region of HBV genome into pGEM-T vector respectively. A pair of primers and matched TaqMan probe were selected by comparing the copy number and the Ct values of HBV serum samples derived from the three different standard curves using certain serum DNA. Then the efficiency of six HBV DNA extraction methods including guanidinium isothiocyanate, proteinase K, NaI, NaOH lysis, alkaline lysis and simple boiling was analyzed in sample A, B and C by real-time PCR. Meanwhile, 8 clinical HBV serum samples were quantified. Results: The copy number of the same HBV serum sample originated from the standard curve of S, C and X regions was 5.7 × 104/ mL, 6.3 × 102/mL and 1.6 × 103/mL respectively. The relative Ct value was 26.6, 31.8 and 29.5 respectively. Therefore, primers and matched probe from S region were chosen for further optimization of six extraction methods. The copy number of HBV serum samples A, B and C was 3.49 × 109/mL, 2.08 × 106/mL and 4.40 × 107/mL respectively, the relative Ct value was 19.9, 30 and 26.2 in the method of NaOH lysis, which was the efficientest among six methods. Simple boiling showed a slightly lower efficiency than NaOH lysis. Guanidinium isothiocyanate, proteinase K and NaI displayed that the copy number of HBV serum sample A, B and C was around 105/ mL, meanwhile the Ct value was about 30. Alkaline failed to quantify the copy number of three HBV serum samples, Standard deviation (SD) and coefficient variation (CV) were very low in all 8 clinical HBV serum samples, showing that quantification of HBV DNA in triplicate was reliable and accurate. Conclusion: Real-time PCR based on optimized primers and TaqMan probe from S region in combination with NaOH lysis is a simple, rapid and accurate method for quantification of HBV serum DNA. © 2006 The WJG Press. All rights reserved.

Critical review of acid in situ leach uranium mining: 1. USA and Australia

The technique of in situ leach (ISL) uranium mining is well established in the USA, as well as being used extensively in Eastern Europe and the former Soviet Union. The method is being proposed and tested on uranium deposits in Australia, with sulfuric acid chemistry and no restoration of groundwater following mining. Test sites in the USA were required to restore groundwater to ascertain the extent of impacts and compare costs to alkaline ISL mines. The problems encountered include expensive and difficult restoration, gypsum precipitation, higher salinity and some heavy metals and radionuclides after restoration. One of the most critical issues is whether natural attenuation is capable of restoring groundwater quality and geochemical conditions in an acid leached aquifer zone. The history of acid ISL sites in the USA and Australia are presented in this study, with a particular focus on the demonstration of restoration of groundwater impacts.

Critical review of acid in situ leach uranium mining: 2. Soviet Block and Asia

The technique of in situ leach (ISL) uranium mining is well established in the USA, as well as being used extensively in Eastern Europe and the former Soviet Union. The method is being proposed and tested on uranium deposits in Australia, with sulphuric acid chemistry and no restoration of groundwater following mining. ISL mines in the former Soviet Union generally used acid reagents and were operated without due consideration given to environmental protection. At many former mine sites, the extent of groundwater contamination is significant because of high salinity, heavy metal and radionuclide concentrations compared with pre-mining and changes in the hydrogeological regime caused by mining. After the political collapse of the Soviet Union by the early 1990s, most uranium mines were shut down or ordered to be phased out by government policy. Programmes of restoration are now being undertaken but are proving technically difficult and hampered by a lack of adequate financial resources. The history and problems of acid ISL sites in countries of the former Soviet Union and Asia are presented in this study.

Begging and food distribution in crimson rosella (Platycercus elegans) broods: why don't hungry chicks beg more?

Altricial nestlings solicit food by begging and engaging in scramble competition. Solicitation displays can thus signal both hunger and competitive ability. I examined nestling solicitation and parental responses in crimson rosellas (Platycercus elegans), a species in which parents engage in complex patterns of food allocation and appear to control the distribution of food. By manipulating the hunger of individual chicks and entire broods, I assessed how chick behaviours and parental food allocation varied with hatching rank, level of hunger, and intensity of nestling competition. Last-hatched chicks begged more than first-hatched chicks irrespective of individual hunger levels. The two parents combined fed individually hungry chicks more, but mothers and fathers varied in their responses to begging chicks: fathers fed last-hatched chicks in proportion to their begging intensity, whereas mothers fed chicks equally. Since fathers generally allocate more food to first-hatched chicks, fathers appear to use begging rates to adjust food allocation to non-preferred chicks within the brood. When I manipulated brood hunger levels, begging rates increased for first- and last-hatched chicks suggesting that chick begging rates are sensitive to the level of competition. This study shows that begging by rosella chicks does not correlate with hunger in a straightforward way and that the primary patterns of food allocation by parents art: not influenced by chick begging. Thus the benefits of increased begging may be limited for nestlings in this species.

Quantifying stresses and support requirements in the undercut and production level drifts of block and panel caving mines

A numerical modelling strategy has been developed in order to quantify the magnitude of induced stresses at the boundaries of production level and undercut level drifts for various in situ stress environments and undercut scenarios. The results of the stress modelling were in line with qualitative experiential guidelines and a limited number of induced stress measurements documented from caving sites. A number of stress charts were developed which quantify the maximum boundary stresses in drift roofs for varying in situ stress regimes, depths and undercut scenarios. This enabled many of the experiential guidelines to be quantified and bounded. A limited number of case histories of support and support performance in cave mine drifts were compared to support recommendations using the NGI classification system, The stress charts were used to estimate the Stress Reduction Factor for this system. The back-analyses suggested that the NGI classification system might be able to give preliminary estimates of support requirements in caving mines with modifications relating to rock bolt length and the support of production level intersections. (C) 2002 Elsevier Science Ltd. All rights reserved.

Predicting cave initiation and propagation

The most widely used method for predicting the onset of continuous caving is Laubscher's caving chart. A detailed examination of this method was undertaken which concluded that it had limitations which may impact on results, particularly when dealing with stronger rock masses that are outside current experience. These limitations relate to inadequate guidelines for adjustment factors to rock mass rating (RMR), concerns about the position on the chart of critical case history data, undocumented changes to the method and an inadequate number of data points to be confident of stability boundaries. A review was undertaken on the application and reliability of a numerical method of assessing cavability. The review highlighted a number of issues, which at this stage, make numerical continuum methods problematic for predicting cavability. This is in particular reference to sensitivity to input parameters that are difficult to determine accurately and mesh dependency. An extended version of the Mathews method for open stope design was developed as an alternative method of predicting the onset of continuous caving. A number of caving case histories were collected and analyzed and a caving boundary delineated statistically on the Mathews stability graph. The definition of the caving boundary was aided by the existence of a large and wide-ranging stability database from non-caving mines. A caving rate model was extrapolated from the extended Mathews stability graph but could only be partially validated due to a lack of reliable data.

Rock fracture mean trace length estimation and confidence interval calculation using maximum likelihood methods

There has been a resurgence of interest in the mean trace length estimator of Pahl for window sampling of traces. The estimator has been dealt with by Mauldon and Zhang and Einstein in recent publications. The estimator is a very useful one in that it is non-parametric. However, despite some discussion regarding the statistical distribution of the estimator, none of the recent works or the original work by Pahl provide a rigorous basis for the determination a confidence interval for the estimator or a confidence region for the estimator and the corresponding estimator of trace spatial intensity in the sampling window. This paper shows, by consideration of a simplified version of the problem but without loss of generality, that the estimator is in fact the maximum likelihood estimator (MLE) and that it can be considered essentially unbiased. As the MLE, it possesses the least variance of all estimators and confidence intervals or regions should therefore be available through application of classical ML theory. It is shown that valid confidence intervals can in fact be determined. The results of the work and the calculations of the confidence intervals are illustrated by example. (C) 2003 Elsevier Science Ltd. All rights reserved.

Stereological and other methods applied to rock joint size estimation - Does Crofton's theorem apply?

A number of authors concerned with the analysis of rock jointing have used the idea that the joint areal or diametral distribution can be linked to the trace length distribution through a theorem attributed to Crofton. This brief paper seeks to demonstrate why Crofton's theorem need not be used to link moments of the trace length distribution captured by scan line or areal mapping to the moments of the diametral distribution of joints represented as disks and that it is incorrect to do so. The valid relationships for areal or scan line mapping between all the moments of the trace length distribution and those of the joint size distribution for joints modeled as disks are recalled and compared with those that might be applied were Crofton's theorem assumed to apply. For areal mapping, the relationship is fortuitously correct but incorrect for scan line mapping.