Characterization of Sarcocystis species in domestic animals using a PCR-RFLP analysis of variation in the 18S rRNA gene: a cost-effective and simple technique for routine species identification

Thirteen restriction endonucleases were used to investigate nucleotide sequence variation in the 18S rRNA DNA of 88 individuals from ten Sarcocystis taxa collected as cysts from their intermediate hosts, swine, cattle and water buffalo. A DNA sequence of

Slope Stability Analysis Using Anisotropic and Nonlinear Failure Criteria

The shear strength of soils or rocks developed in a landslide usually exhibits anisotropic and nonlinear behavior. The process of sedimentation and subsequent consolidation can cause anisotropy of sedimentary soils or rocks, for instance. Nonlinearity of failure envelope could be attributed to "interlocking" or "dilatancy" of the material, which is generally dependent upon the stress level. An analytical method considering both anisotropy and nonlinearity of the failure envelops of soil and rocks is presented in the paper. The nonlinearfailure envelopes can be determined from routine triaxial tests. A spreadsheet program, which uses the Janbu's Generalized Procedure of Slice and incorporates anisotropic, illustrates the implementation of the approach and nonlinearfailure envelops. In the analysis, an equivalent Mohr-Coulomb linear failure criterion is obtained by drawing a tangent to the nonlinear envelope of an anisotropic soil at an appropriate stress level. An illustrative example is presented to show the feasibility and numerical efficiency of the method.

A numerical investigation on the flow physics of koi carp (Cyprinus carpio koi) burst-and-coast swimming

Abstract—Burst-and-coast is the most common locomotion type in freely routine swimming of koi carps (Cyprinus carpio koi), which consists of a burst phase and a coast phase in each cycle and mostly leads to a straight-line trajectory. Combining with the tracking experiment, the flow physics of koi carp’s burst-andcoast swimming is investigated using a novel integrated CFD method solving the body-fluid interaction problem. The dynamical equations of a deforming body are formulated. Following that, the loose-coupled equations of the body dynamics and the fluid dynamics are numerically solved with the integrated method. The two burst modes, MT (Multiple Tail-beat) and HT (Half Tail-beat), which have been reported by the experiments, are investigated by numerical simulations in this paper. The body kinematics is predicted and the flow physics is visualized, which are in good agreement with the corresponding experiments. Furthermore, the optimization on the energy cost and several critical control mechanisms in burst-and-coast swimming of koi carps are explored, by varying the parameters in its selfpropelled swimming. In this paper, energetics is measured by the two mechanical quantities, total output power CP and Froude efficiency Fr. Results and discussion show that from the standpoint of mechanical energy, burst-and-coast swimming does not actually save energy comparing with steady swimming at the same average speed, in that frequently changing of speed leads to decrease of efficiency.

Median network analysis of defectively sequenced entire mitochondrial genomes from early and contemporary disease studies

Sequence analysis of the mitochondrial genome has become a routine method in the study of mitochondrial diseases. Quite often, the sequencing efforts in the search of pathogenic or disease-associated mutations are affected by technical and interpretive pr

Exaggerated Status of

Given its relative ease, screening the entire mitochondrial DNA (mtDNA) for heteroplasmic or novel homoplasmic mutations has become part of the routine diagnostic workup for the molecular geneticist confronted with a disease case exhibiting clinical and b

Metabolism traits of 'all-fish' growth hormone transgenic common carp (Cyprinus carpio L.)

Transgenic animals with improved qualities have the potential to upset the ecological balance of a natural environment. We investigated metabolic rates of 'all-fish' growth hormone (GH) transgenic common carp under routine conditions and during starvation periods to determine whether energy stores in transgenic fish would deplete faster than controls during natural periods of starvation. Before the oxygen uptake was measured, the mean daily feed intake of transgenic carp was 2.12 times greater than control fish during 4 days of feeding. The average oxygen uptake of GH transgenic fish was 1.32 times greater than control fish within 96 h of starvation, but was not significantly different from controls between 96 and 144 h of starvation. At the same time, GH transgenic fish did not deplete energy reserves at a faster rate than did the controls, as the carcass energy contents of the two groups following a 60-d starvation period were not significantly different. Consequently, we suggest that increased routine oxygen uptake in GH transgenic common carp over that of control fish may be mainly due to the effects of feeding, and not to an increase in basal metabolism. GH transgenic fish are similar to controls in the regulation of metabolism to normally distribute energy reserves during starvation. (c) 2008 Published by Elsevier B.V.

Different tolerances and responses to low temperature and darkness between waterbloom forming cyanobacterium Microcystis and a green alga Scenedesmus

The dynamics of planktonic cyanobacteria in eutrophicated freshwaters play an important role in formation of annual summer blooms, yet overwintering mechanisms of these water bloom forming cyanobacteria remain unknown. The responses to darkness and low temperature of three strains (unicellular Microcystis aeruginosa FACHB-905, colonial M. aeruginosa FACHB-938, and a green alga Scenedesmus quadricauda FACHB-45) were investigated in the present study. After a 30-day incubation under darkness and low temperature, cell morphology, cell numbers, chlorophyll a, photosynthetic activity (ETRmax and I-k), and malodialdehyde (MDA) content exhibited significant changes in Scenedesmus. In contrast, Microcystis aeruginosa cells did not change markedly in morphology, chlorophyll a, photosynthetic activity, and MDA content. The stress caused by low temperature and darkness resulted in an increase of the antioxidative enzyme-catalase (CAT) in all three strains. When the three strains re-grew under routine cultivated condition subjected to darkness and low temperature, specific growth rate of Scenedesmus was lower than that of Microcystis. Flow cytometry (FCM) examination indicated that two distinct types of metabolic response to darkness and low temperature existed in the three strains. The results from the present study reveal that the cyanobacterium Microcystis, especially colonial Microcystis, has greater endurance and adaptation ability to the stress of darkness and low temperature than the green alga Scenedesmus.

The temporal and spatial distribution, composition and abundance of Protozoa in Chaohu Lake, China: Relationship with eutrophication

Systematic investigations into the temporal and spatial distribution, composition and abundance of protozoa in two regions with different trophic levels in Chaohu Lake, a large, shallow and highly eutrophic freshwater lake in China, were conducted during 2002-2003. A total of 114 species of protozoa, including phytomastigophorans, zoomastigophorans, amoebae and ciliates, were identified from 120 polyurethane foam unit (PFU) samples exposed at four stations and from various types of natural substrates. Of the 114 taxa, 36 core species were found on PFU substrates and 23 of these were found on natural ones. Protozoan abundance and chemical physical parameters at nine sampling stations, four in the western lake and five in the eastern part, indicate trophic gradient changes along the lake. Seasonal variations in the species composition of major groups at littoral PFU sampling stations illustrate the effect of a severe algal bloom on the protozoan community structure. Temporal and spatial distributions of individual abundance as functions of water temperature and trophic status were revealed. This study demonstrates again that the PFU artificial substrate method samples protozoan communities more effectively than routine natural substrate methods. (c) 2005 Elsevier GmbH. All rights reserved.

Dioxin-like components in human breast milk collected from Hong Kong and Guangzhou

The H4IIE rat hepatoma cell line was employed as a cell model to screen 7-ethoxyresorufin O-deethylase (EROD)-TCDD equivalents (EROD-TEQ) of human breast milk samples collected from Hong Kong and Guangzhou, China. The screening methods employed a 96-well plate spectrofluorometer-EROD assay. For cell-line validation, our results demonstrated a dose-dependent increase in the Ah receptor-mediated response (i.e., CYP1A1 mRNA and EROD) of the cells upon exposure to a number of known Ah receptor agonists, including 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), 2,3,7,8-tetrachlorodibenzothiophene, benzo[a]pyrene, and beta-naphthaflavone. TCDD induced CYP1A1 mRNA and EROD was in a close positive correlation (r = 0.98). For the screening of dioxin-like compounds, breast milk samples collected during lactation weeks 3-5 were used. One hundred (from Hong Kong) and 48 (from Guangzhou) breast milk samples were assayed, of which 65% and 68% of the samples, respectively, showed detectable dioxin-like activities using the H4IIE cell EROD screening method. For sixty-five samples from Hong Kong the mean EROD-TEQ values ranged from 58.1 to 96.5 pg/g of milk fat for those aged 21-36 years while 32 samples from Guangzhou had mean values of 98.8-202.1 pg/g of milk fat. In comparisons of the EROD-TEQ values for different age groups from both cities, there were no significant differences (P < 0.05). However, the mean and median EROD-TEQ values of the Guangzhou population were in general higher than those of the Hong Kong population. The results of the present study indicate that it is feasible to use the H4IIE cell-line as a model for screening dioxin-like compounds in human breast milk. In addition, the method is rapid and cost-effective, particularly for a routine and high-throughput sample screening analysis, compared to the costly and time-intensive chemical analytical techniques. (C) 2003 Elsevier Inc. All rights reserved.

New development of advanced superconducting electron cyclotron resonance ion source SECRAL (invited)

Superconducting electron cyclotron resonance ion source with advance design in Lanzhou (SECRAL) is an 18-28 GHz fully superconducting electron cyclotron resonance (ECR) ion source dedicated for highly charged heavy ion beam production. SECRAL, with an innovative superconducting magnet structure of solenoid-inside-sextupole and at lower frequency and lower rf power operation, may open a new way for developing compact and reliable high performance superconducting ECR ion source. One of the recent highlights achieved at SECRAL is that some new record beam currents for very high charge states were produced by 18 GHz or 18+14.5 GHz double frequency heating, such as 1 e mu A of Xe-129(43+), 22 e mu A of Bi-209(41+), and 1.5 e mu A of Bi-209(50+). To further enhance the performance of SECRAL, a 24 GHz/7 kW gyrotron microwave generator was installed and SECRAL was tested at 24 GHz. Some promising and exciting results at 24 GHz with new record highly charged ion beam intensities were produced, such as 455 e mu A of Xe-129(27+) and 152 e mu A of Xe-129(30+), although the commissioning time was limited within 3-4 weeks and rf power only 3-4 kW. Bremsstrahlung measurements at 24 GHz show that x-ray is much stronger with higher rf frequency, higher rf power. and higher minimum mirror magnetic field (minimum B). Preliminary emittance measurements indicate that SECRAL emittance at 24 GHz is slightly higher that at 18 GHz. SECRAL has been put into routine operation at 18 GHz for heavy ion research facility in Lanzhou (HIRFL) accelerator complex since May 2007. The total operation beam time from SECRAL for HIRFL accelerator has been more than 2000 h, and Xe-129(27+), Kr-78(19+), Bi-209(31+), and Ni-58(19+) beams were delivered. All of these new developments, the latest results, and long-term operation for the accelerator have again demonstrated that SECRAL is one of the best in the performance of ECR ion source for highly charged heavy ion beam production. Finally the future development of SECRAL will be presented.

The Application of Toolkit of Optimization in Designs of Accelerator Magnets

The traditional design of accelerator magnet usually involves many time consuming iterations of the manual analysis process. A software platform to do these iterations automatically is proposed in this paper. In this platform, we use DAKOTA (a open source software developed by Sandia National Laboratories) as the optimizing routine, which provides a variety of optimization methods and algorithms, and OPERA (software from Vector Fields) is selected as the electromagnetic simulating routine. In this paper, two examples of designs of accelerator magnets are used to illustrate how an optimization algorithm is chosen and the platform works.

Determination of 1-phenyl-3-methyl-5-pyrazolone-labeled carbohydrates by liquid chromatography and micellar electrokinetic chromatography

In this paper, the method for the derivatization of carbohydrates with 1-phenyl-3-methyl-5-pyrazolone (PMP) was simplified. One-third of the derivatization time was saved. Five monosaccharide derivatives have been well separated by MEKC and HPLC under optimized conditions. Good reproducibility could be obtained with relative standard deviation (RSD) values of the migration times within 5.0 and 2.3%, respectively. Furthermore, the developed methods have been successfully applied to the analysis of carbohydrates in Aloe powder and food. These methods are quite useful for routine analysis of monosaccharides and oligosaccharides in real samples. (C) 2003 Elsevier B.V. All rights reserved.

Determination of total calcium in plasma by flow injection analysis with tris(2,2 '-bipyridyl)ruthenium(II) electrochemiluminescent detection

We described here a new method for the determination of total calcium in plasma. The method is based on the precipitation of calcium with excess oxalate and the measurement of residual oxalate by flow injection analysis with Ru(bpy)(3)(2+) electrochemiluminescent detection. It has the advantages of extremely stable reagent, user-friendly instrument, high selectivity, good analytical recovery, wide dynamic range, and nice correlation with atomic absorption spectroscopy. The calibration plot for calcium is linear over a concentration range from 0.5 mmol L-1 to 4.8 mmol L-1, which is wider than those obtained by most other methods. The analytical recoveries for plasma calcium are 98.4-101.2% with coefficients of variation (CVs) of 1.96-2.52%. The within-day CVs range from 0.76% to 0.95%, and between-day CVs were from 1.12% to 1.46%. The time for each injection is one minute. Because the proposed method can be readily carried out on increasingly popular instruments for Ru(bpy)(3)(2+) ECL immunoassays and DNA probe assays, Ru(bpy)32+ ECL method is suitable for routine clinical analysis of calcium.

Miniaturized tris(2,2 '-bipyridyl)ruthenium(II) electrochemiluminescence detection cell for capillary electrophoresis and flow injection analysis

The design and performance of a miniaturized chip-type tris(2,2'-bipyridyl)ruthenium(II) [Ru(bpy)(3)(2+)] electrochemiluminescence (ECL) detection cell suitable for both capillary electrophoresis (CE) and flow injection (FI) analysis are described. The cell was fabricated from two pieces of glass (20 x 15 x 1.7 mm), and the 0.5-mm-diameter platinum disk was used as working electrode held at +1.15 V (vs silver wire quasi-reference), the stainless steel guide tubing as counter electrode, and the silver wire as quasi-reference electrode. The performance traits of the cell in both CE and FI modes were evaluated using tripropylamine, proline, and oxalate and compared favorably to those reported for CE and FI detection cells. The advantages of versatility, sensitivity, and accuracy make the device attractive for the routine analysis of amine-containing species or oxalate by CE and FI with Ru(bPY)(3)(2divided by) ECL detection.

Temperature dependence of the distribution of the first passage time: Results from discontinuous molecular dynamics simulations of an all-atom model of the second beta-hairpin fragment of protein G

More than 22 000 folding kinetic simulations were performed to study the temperature dependence of the distribution of first passage time (FPT) for the folding of an all-atom Go-like model of the second beta-hairpin fragment of protein G. We find that the mean FPT (MFPT) for folding has a U (or V)-shaped dependence on the temperature with a minimum at a characteristic optimal folding temperature T-opt*. The optimal folding temperature T-opt* is located between the thermodynamic folding transition temperature and the solidification temperature based on the Lindemann criterion for the solid. Both the T-opt* and the MFPT decrease when the energy bias gap against nonnative contacts increases. The high-order moments are nearly constant when the temperature is higher than T-opt* and start to diverge when the temperature is lower than T-opt*. The distribution of FPT is close to a log-normal-like distribution at T* greater than or equal to T-opt*. At even lower temperatures, the distribution starts to develop long power-law-like tails, indicating the non-self-averaging intermittent behavior of the folding dynamics. It is demonstrated that the distribution of FPT can also be calculated reliably from the derivative of the fraction not folded (or fraction folded), a measurable quantity by routine ensemble-averaged experimental techniques at dilute protein concentrations.