Spatiotemporal heterogeneity of plankton communities in Lake Donghu, China, as revealed by PCR-denaturing gradient gel electrophoresis and its relation to biotic and abiotic factors

The 16S and 18S rRNA genes of planktonic organisms derived from five stations with nutrient gradients in Lake Donghu, China, were studied by PCR-denaturing gradient gel electrophoresis (DGGE) fingerprinting, and the relationships between the genetic diversity of the plankton community and biotic/abiotic factors are discussed. The concentrations of total nitrogen (TN), total phosphorus (TP), NH4-N and As were found to be significantly related (P < 0.05) to morphological composition of the plankton community. Both chemical and morphological analyses suggested that temporal heterogeneity was comparatively higher than spatial heterogeneity in Lake Donghu. Although the morphological composition was not identical to the DGGE fingerprints in characterizing habitat similarity, the two strongest eutrophic stations (I and II) were always initially grouped into one cluster. Canonical correspondence analysis suggested that the factors strongly correlated with the first two ordination axes were seasonally different. The concentrations of TN and TP and the densities of rotifers and crustaceans were generally the main factors related to the DGGE patterns of the plankton communities. The study suggested that genetic diversity as depicted by metagenomic techniques (such as PCR-DGGE fingerprinting) is a promising tool for ecological study of plankton communities and that such techniques are likely to play an increasingly important role in assessing the environmental conditions of aquatic habitats.

On-line hyphenation of capillary isoelectric focusing and capillary gel electrophoresis by a dialysis interface

An on-line two-dimensional (2D) capillary electrophoresis (CE) system consisting of capillary isoelectric focusing (CIEF) and capillary gel electrophoresis (CGE) was introduced. To validate this 2D system, a dialysis interface was developed by mounting a hollow fiber on a methacrylate resin plate to hyphenate the two CE modes. The two dimensions of capillary shared a cathode fixated into a reservoir in the methacrylate plate; thus, with three electrodes and only one high-voltage source, a 2D CE framework was successfully established. A practical 2D CIEF-CGE experiment was carried out to deal with a target protein, hemoglobin (Hb). After the Hb variants with different isoelectric points (pIs) were focused in various bands in the first-dimension capillary, they were chemically mobilized one after another and fed to the second-dimension capillary for further separation in polyacrylamide gel. During this procedure, a single CIEF band was separated into several peaks due to different molecular weights. The resulting electrophoregrarn is quite different from that of either CIEF or CGE; therefore, more information about the studied Hb sample can be obtained.

Profiling of Complex Microbial Populations by Denaturing Gradient Gel Electrophoresis Analysis of Polymerase Chain Reaction-Amplified Genes Coding for 16S rRNA

We describe a new molecular approach to analyzing the genetic diversity of complex microbial populations. This technique is based on the separation of polymerase chain reaction-amplified fragments of genes coding for 16S rRNA, all the same length, by denaturing gradient gel electrophoresis (DGGE). DGGE analysis of different microbial communities demonstrated the presence of up to 10 distinguishable bands in the separation pattern, which were most likely derived from as many different species constituting these populations, and thereby generated a DGGE profile of the populations. We showed that it is possible to identify constituents which represent only 1% of the total population. With an oligonucleotide probe specific for the V3 region of 16S rRNA of sulfate-reducing bacteria, particular DNA fragments from some of the microbial populations could be identified by hybridization analysis. Analysis of the genomic DNA from a bacterial biofilm grown under aerobic conditions suggests that sulfate-reducing bacteria, despite their anaerobicity, were present in this environment. The results we obtained demonstrate that this technique will contribute to our understanding of the genetic diversity of uncharacterized microbial populations.

Soil microbial community analysis using denaturing gradient gel electrophoresis

The most biological diversity on this planet is probably harbored in soils. Understanding the diversity and function of the microbiological component of soil poses great challenges that are being overcome by the application of molecular biological approaches. This review covers one of many approaches being used: separation of polymerase chain reaction (PCR) amplicons using denaturing gradient gel electrophoresis (DGGE). Extraction of nucleic acids directly from soils allows the examination of a community without the limitation posed by cultivation. Polymerase chain reaction provides a means to increase the numbers of a target for its detection on gels. Using the rRNA genes as a target for PCR provides phylogenetic information on populations comprising communities. Fingerprints produced by this method have allowed spatial and temporal comparisons of soil communities within and between locations or among treatments. Numerous samples can be compared because of the rapid high throughput nature of this method. Scientists now have the means to begin addressing complex ecological questions about the spatial, temporal, and nutritional interactions faced by microbes in the soil environment.

Application of matrix-assisted laser desorption/ionization-time of flight-mass spectrometry and sodium dodecyl sulfate-polyacrylamide gel electrophoresis in determining arginine esterase from snake venom

Using matrix-assisted laser desorption/ionization-time of flight-mass spectrometry (MALDI-TOF-MS). The homogeneities and molecular weights of three arginine esterases from snake venom, which possessing therapeutic use in myocardial infarction, were determined and compared, MALDI-TOF-MS is possessed of high accuracy, high sensitivity and rapidity. MALDI-TOF-MS and sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) can provide complementary and confirmatory results information. MALDI-TOF-MS can be directly used as an important method for the purification of snake venom complexes successfully.

Toxicity of microcystins in the isolated hepatocytes of common carp (Cyprinus carpio L.)

The toxicity of hepatotoxic microcystins produced mainly by Microcystis aeruginosa in mammals and fishes was well studied in recent years. However, there were scarcely reports in toxic effects of microcystins on isolated hepatocytes of fishes, especially investigation of microcystin-induced apoptosis and/or necrosis in carp hepatocytes. In the present study, the isolated hepatocytes of common carp were exposed to various concentrations of microcystins (0.01, 0.1, 1, 10, 100, 1000 mu g L-1) for 2, 4, 8, 16 and 24 h, respectively, and cytotoxicity of microcystins in the toxin-treated cells was determined. Results of this study showed that cytotoxicity of microcystins on carp hepatocytes was time and dose-dependent, and the approximate LC50 of microcystins in carp hepatocytes was 169.2 mu g L-1. The morphological changes typical of apoptosis, such as blebbing of cell membrane, condensation and fragmentation of cell nucleus were observed in the hepatocytes exposed to microcystins (1, 10 and 100 mu g L-1) using fluorescence and differential interference contrast microscopy. Agarose gel electrophoresis of DNA demonstrated a typical apoptotic "ladder pattern" in microcystin-treated hepatocytes after 16 h of exposure. Results of the present study indicated that the form of cell death in microcystin-treated hepatocytes depend on the exposure dose of toxin. When lower concentration of microcystins (10 and 100 mu g L-1) was used for exposure, carp hepatocytes died in apoptosis while, when higher one used (1000 mu g L-1), they died in the form of necrosis. (C) 2006 Elsevier Inc. All rights reserved.

Induction of oxidative stress and apoptosis by PFOS and PFOA in primary cultured hepatocytes of freshwater tilapia (Oreochromis niloticus)

Perfluorinated organic compounds (PFOCs) are emerging persistent organic pollutants (POPs) widely present in the environment, wildlife and human. We studied the cellular toxicology of perfluorooctane sulfonate (PFOS) and perfluorooctanoic acid (PFOA) on oxidative stress and induction of apoptosis in primary cultured hepatocytes of freshwater tilapia (Oreochromis niloticus). Cultured hepatocytes were exposed to PFOS or PFOA (0, 1, 5, 15 and 30 mg L-1) for 24 h, and a dose-dependent decrease in cell viability was determined using trypan blue exclusion method. Significant induction of reactive oxygen species (ROS) accompanied by increases in activities of superoxide dismutase (SOD), catalase (CAT) and glutathione reductase (GR) were found, while activities of glutathione peroxidase (GPx) and glutathione-S-transferase (GST) were decreased. Glutathione (GSH) content was reduced following treatment of PFOA and PFOS. A dose-dependent increase in the lipid peroxidation (LPO) level (measured as maleic dialdehyde, MDA) was observed only in the PFOA exposure groups, whereas LPO remained unchanged in the PFOS exposure groups. Furthermore, a significant activation of caspase-3, -8, -9 activities was evident in both PFOS and PFOA exposure groups. Typical DNA fragmentation (DNA laddering) was further characterized by agarose gel electrophoresis. The overall results demonstrated that PFOS and PFOA are able to produce oxidative stress and induce apoptosis with involvement of caspases in primary cultured tilapia hepatocytes. (c) 2007 Elsevier B.V. All rights reserved.

Induction of apoptosis in a carp leucocyte cell line infected with turbot (Scophthalmus maximus L.) rhabdovirus

A rhabdovirus was observed from the diseased turbot (Scophthalmus maximus L.) with lethal syndrome. In this study, a carp leucocyte (CLC) cell line was used to investigate the infection process and cell death mechanism occurring during the virus infection. Strong cytopathogenic effect (CPE) and the morphological changes, such as extreme chromatin condensation, nucleus fragmentation, and apoptotic body formation, were observed under fluorescence microscopy after DAPI staining in the infected CLC cells. Transmission electron microscopy analysis showed cell shrinkage, plasma membrane blebbing, cytoplasm vacuolization, chromatin condensation, nuclear breakdown and formation of discrete apoptotic bodies. The bullet-shaped nucleocapsids were measured and ranged in size from 110 to 150 nm in length and 40 to 60 nm in diameter. And therefore the virus is called Scophthalmus maximus rhabdovirus (SMRV). Agarose gel electrophoresis analysis of the DNA extracted from infected cells showed typical DNA ladder in the course of SMRV infection. Flow cytometry analysis of SMRV infected CLC cells detected apoptotic peak in the virus infected CLC cells. Virus titre analysis and electron microscopic observation revealed that the virus replication fastigium was earlier than that of the apoptosis occurrence. No apoptosis was observed in the CLC infected with UV-inactivated SMRV. All these supported that SMRV infected CLC cells undergo apoptosis and the virus replication is necessary for apoptosis induction of CLC cells. (C) 2004 Published by Elsevier B.V.

A detection method for grass carp hemorrhagic virus (GCHV) based on a reverse transcription polymerase chain reaction

A rapid, sensitive and highly specific detection method for grass carp hemorrhagic virus (GCHV) based on a reverse transcription-polymerase chain reaction (RT-PCR) has been developed. Two pairs of PCR primers were synthesized according to the cloned cDNA sequences of the GCHV-861 strain. For each primer combination, only one specific major product was obtained when amplification was performed by using the genomic dsRNA of GCHV-861 strain. The lengths of their expected products were 320 and 223 bp, respectively. No products were obtained when nucleic acids other than GCHV-861 genomic RNA were used as RT-PCR templates. To assess the sensitivity of the method, dilutions of purified GCHV-861 dsRNA total genome (0.01 pg up to 1000 pg) were amplified and quantities of as little as 0.1 pg of purified dsRNA were detectable when the amplification product was analyzed by 1.5% agarose gel electrophoresis. This technique could detect GCHV-861 not only in infected cell culture fluids, but also in infected grass carp Ctenopharyngodon idellus and rare minnow Gobiocypris rarus with or without hemorrhagic symptoms. The results show that the RT-PCR amplification method is useful for the direct detection of GCHV.

不同小麦品种（系）中主要矿质元素的含量比较及与品质的关系

采用微波消解、电感耦合高频等离子体原子发射光谱（ICP-AES）的方法,对62份不同小麦品种（系）中锌、铁、铜、钙、钠和钾的含量进行了测定。同时利用红外线品质测定仪对主要品质指标粗蛋白、湿面筋、沉降值进行了测定。结果表明，不同小麦品种（系）中各种矿质元素的含量存在差异，2006年小麦品种中铁含量变幅为18.55-58.19 ug/g，平均为30.83ug/g ，最高与最低的相差39.64ug/g；锌含量变幅为5.70-25.80 ug/g，平均为15.13ug/g ，最高与最低相差20.10ug/g。2008年小麦品种（系）中铁含量变幅为16.68-52.25 ug/g，平均为30.10ug/g，最高与最低相差35.58ug/g；锌含量变幅为12.29-33.47 ug/g，平均为21.11ug/g，最高与最低相差21.18ug/g；钙含量变幅为167.53-348.80ug/g，平均为248.59ug/g，最高与最低相差192.59ug/g；铜含量变幅为2.32-5.83 ug/g，平均为2.98ug/g，最高与最低的相差3.61ug/g；钾含量变幅为1822.71-4414.91 ug/g，平均为2617.87ug/g，最高与最低的相差2634.72ug/g；钠含量变幅为10.25-39.82 ug/g，平均为23.05ug/g，最高与最低的相差29.57ug/g。 两年不同小麦品种（系）中矿质元素的含量分析结果表明：铁、铜、钙、钠和钾含量年际变化不明显,说明小麦对铁、铜、钙、钠和钾的吸收较稳定；锌含量变化较大，可能受环境的影响比较大。分析各矿质元素含量与粗蛋白、湿面筋、沉降值及元素之间的相关关系，结果表明，锌含量与粗蛋白含量呈极显著正相关关系，相关系数为0.317，与湿面筋含量之间呈显著正相关，相关系数达到0.246；铁含量与粗蛋白含量呈显著的正相关关系，相关系数是0.262；铜、钙、钠和钾含量与粗蛋白含量、湿面筋和沉降值之间存在正相关，但不显著，其中钠与沉降值之间为负相关。表明施锌或铁对提高小麦粗蛋白和湿面筋有显著效应，其余矿质元素有促进作用但不明显。 利用RAPD分子标记技术对川育23、41058、川育20及其父母本进行分析，力图从分子水平找到小麦矿质元素含量之间的差异性，琼脂糖电泳结果表明不同的小麦品种（系）间扩增出了差异条带。 以上研究结果，将对筛选“微量营养强化型”小麦新材料，选育“微量营养强化型”小麦新品种奠定基础。 62 different wheat cultivars was digested with HNO3 in a tightly closed vessel heated under micro-wave,then contents of zinc，iron,copper，calcium，sodium and potassium were determined by inductively coupled plasma-atomic emission spectroscopy(ICP-AES)．The main indexes of wheat quality such as total protein、wet glu and sedimentation volume were detected by Infratec 1255 Food & Feed Analyzer at the same time.The obtained results showed that variation for all of the mineral elements concentrations among different cultivars were observed .In 2006, the amplitude variation of the iron content was 18.55-58.19 ug/g,the average value was 30.83ug/g,and 39.64ug/g between the highest-content cultivar and the lowest one; the amplitude variation of the zinc content was 5.70-25.8 ug/g,the average value was 15.13ug/g,and 20.10ug/g between the highest-content cultivar and the lowest one.In 2008, the amplitude variation of the iron content was 16.68-52.25 ug/g,the average value was 30.10ug/g,and 35.58ug/g between the highest-content cultivar and the lowest one; the amplitude variation of the zinc content was 12.29-33.47 ug/g,the average value was 21.11ug/g,and 21.18ug/g between the highest-content cultivar and the lowest one; the amplitude variation of the calcium content was 167.53-348.80ug/g,the average value was 248.59ug/g,and 192.59ug/g between the highest-content cultivar and the lowest one; the amplitude variation of the copper content was 2.32-5.83 ug/g,the average value was 2.98ug/g,and 3.61ug/g between the highest-content cultivar and the lowest one; the amplitude variation of the potassium content was 1822.71-4414.91 ug/g,the average value was 2617.87ug/g,and 2634.72ug/g between the highest-content cultivar and the lowest one; the amplitude variation of the sodium content was 10.25-39.82 ug/g,the average value was 23.05ug/g,and 29.57ug/g between the highest-content cultivar and the lowest one. Analysis was made on the annual variation of mineral elements content in different Wheat cultivars ,the result shows:there is no obvious difference of iron ,copper ,sodium、calcium and potassium concentrations in wheat cultivars, suggesting the absorption of the iron, copper, sodium、calcium and potassium by wheat are relatively steady ,but zinc concentrations change obviously ,maybe influenced heavily by environment . The correlation between mineral elements 、mineral elements and total protein、mineral elements and sedimentation volume as well as mineral elements and wet glut were analysed in this paper, the result showed that there was significant positive correlation between zinc content and total protein (the correlation coefficient is 0.317), positive correlation between zinc content and wet glu (the correlation coefficient is 0.246), positive correlation between iron content and total protein (the correlation coefficient is 0.262). there was positive but not obvious correlation between the contents of copper, calcium, sodium or potassium and total protein, wet glut or sedimentation volume,among which was negative correlation between sodium and sedimentation volume.It was indicated zinc or iron fertilization has prominent effects in improving the total protein in wheat, the rest mineral elements have Non- obvious facilitation. The study then forecasted the genetic difference of different wheat by the molecular marker of RAPD in order to find differences in molecular level. Chuanyu23、41058、chuanyu20 as well as their male and female parents were analysed by RAPD markers,Agarose gel electrophoresis of DNA revealed the appearance of differential bands . The above-mentioned results of this study establish the foundation to screening the new materials of wheat of " strengthening type of micro- nutrition ", and to breeding the new wheat cultivars of" strengthening type of micro- nutrition ".

Determination of SARS-coronavirus by a microfluidic chip system

We have developed a new experimental system based on a microfluidic chip to determine severe acute respiratory syndrome coronavirus (SARS-Cov). The system includes a laser-induced fluorescence microfluidic chip analyzer, a glass microchip for both polymerase chain reaction (PCR) and capillary electrophoresis, a chip thermal cycler based on dual Peltier thermoelectric elements, a reverse transcription-polymerase chain reaction (RT-PCR) SARS diagnostic kit, and a DNA electrophoretic sizing kit. The system allows efficient cDNA amplification of SARS-CoV followed by electrophoretic sizing and detection on the same chip. To enhance the reliability of RT-PCR on SARS-CoV detection, duplex PCR was developed on the microchip. The assay was carried out on a home-made microfluidic chip system. The positive and the negative control were cDNA fragments of SARS-CoV and parainfluenza virus, respectively. The test results showed that 17 positive samples were obtained among 18 samples of nasopharyngeal swabs from clinically diagnosed SARS patients. However, 12 positive results from the same 18 samples were obtained by the conventional RT-PCR with agarose gel electrophoresis detection. The SARS virus species can be analyzed with high positive rate and rapidity on the microfluidic chip system.