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

Molecular characterization of three Rana grylio virus (RGV) isolates and Paralichthys olivaceus lymphocystis disease virus (LCDV-C) in iridoviruses

Three Rana grylio virus (RGV) isolates and lymphocystis disease virus (LCDV-C) were molecularly characterized by antigenicity comparison, Western blot detection of viral polypeptides, restriction fragment length polymorphism analysis of viral genomes, and MCP sequence analysis. Significant antigenicity differences existed among the three RGV isolates and LCDV-C. Western blot detection indicated that the viral polypeptides of three RGV isolates could be recognized by the anti-RGV9807 serum, whereas no bands were observed in the LCDV-C, and significant differences exist among the band patterns of three RGV isolates. Restriction fragment length polymorphism (RFLP) analysis was performed by digesting genomic DNA of the four iridovirus isolates with restriction endonucleases HindIII, KpnI, XbaI and BamHI. On the whole, obvious discrepancies existed between LCDV-C and RGV isolates, and some significant band pattern differences were also revealed between RGV9808 and RGV9506 (or RGV9807) in the profiles of restriction endonucleases Xbal, Kpn I and BamHI. PCR amplification and sequence analysis of MCP gene sequence further revealed their phylogenetic relationship among the three RGV isolates, LCDV-C and other iridoviruses. RGV9506, RGV9807 and RGV9808 are clustered together with other ranaviruses, such as FV3, BIV, TFV and ENHV, although the RGV9808 is more close to EHNV than to other ranaviruses. Additionally, LCDV-C is clustered with LCDV-1, the type species of genus Lymphocystisvirus. The current study provides clear evidence that significant genetic difference exists among the three RGV isolates. Therefore, further work on comparative genomic studies will contribute significantly to understanding of their taxonomic position and pathological mechanism. (C) 2005 Elsevier B.V. All rights reserved.

Transcriptome of embryonic and neonatal mouse cortex by high-throughput RNA sequencing

Brain structure and function experience dramatic changes from embryonic to postnatal development. Microarray analyses have detected differential gene expression at different stages and in disease models, but gene expression information during early brain development is limited. We have generated >27 million reads to identify mRNAs from the mouse cortex for>16,000 genes at either embryonic day 18 (E18) or postnatal day 7 (P7), a period of significant synapto-genesis for neural circuit formation. In addition, we devised strategies to detect alternative splice forms and uncovered more splice variants. We observed differential expression of 3,758 genes between the 2 stages, many with known functions or predicted to be important for neural development. Neurogenesis-related genes, such as those encoding Sox4, Sox11, and zinc-finger proteins, were more highly expressed at E18 than at P7. In contrast, the genes encoding synaptic proteins such as synaptotagmin, complexin 2, and syntaxin were up-regulated from E18 to P7. We also found that several neurological disorder-related genes were highly expressed at E18. Our transcriptome analysis may serve as a blueprint for gene expression pattern and provide functional clues of previously unknown genes and disease-related genes during early brain development.

Seasonal dynamics of the hepatotoxic microcystins in various organs of four freshwater bivalves from the large eutrophic Lake Taihu of subtropical China and the risk to human consumption

So far, little is known on the distribution of hepatotoxic microcystin (MC) in various organs of bivalves, and there is no study on MC accumulation in bivalves from Chinese waters. Distribution pattern and seasonal dynamics of MC-LR, -YR and -RR in various organs (hepatopancreas, intestine, visceral mass, gill, foot, and rest) of four edible freshwater mussels (Anodonta woodiana, Hyriopsis cumingii, Cristaria plicata, and Lamprotula leai) were studied monthly during Oct. 2003-Sep. 2004 in Lake Taihu with toxic cyanobacterial blooms in the summer. Qualitative and quantitative determinations of MCs in the organs were done by LC-MS and HPLC. The major toxins were present in the hepatopancreas (45.5-55.4%), followed by visceral mass with substantial amount of gonad (27.6-35.5%), whereas gill and foot were the least (1.8-5.1%). The maximum MC contents in the hepatopancreas, intestine, visceral mass, gill, foot, and rest were 38.48, 20.65, 1.70, 0.64, 0.58, and 0.61 mu g/g DW, respectively. There were rather good positive correlation in MC contents between intestines and hepatopancreas of the four bivalves (r = 0.75-0.97, p < 0.05). There appeared to be positive correlations between the maximum MC content in the hepatopancreas and the delta(13)C (r = 0.919) or delta(15)N (r = 0.878) of the foot, indicating that the different MC content in the hepatopancreas might be due to different food ingestion. A glutathione (GSH) conjugate of MC-LR was also detected in the foot sample of C. plicata. Among the foot samples analyzed, 54% were above the provisional WHO tolerable daily intake (TDI) level, and the mean daily intakes from the four bivalves were 8-23.5 times the TDI value when the bivalves are eaten as a whole, suggesting the high risk of consuming bivalves in Lake Taihu. (C) 2005 Wiley Periodicals, Inc.

DNA diagnosis by capillary electrophoresis and microfabricated electrophoretic devices

DNA diagnosis is experiencing an impressive progression towards the development of novel technology to identity various clinically relevant categories of genetic changes and to meet the exponential growth of genomics. The introduction of capillary electrophoresis has dramatically accelerated the completion of the first draft of the human DNA sequence in the Human Genome Project, and thus, has become the method of choice for analysis of various genetic variants. The recent development of microfabricated electrophoretic devices has led to the possibility of integrating multiple sample handling with the actual measurement steps required for automation of molecular diagnostics. This review highlights the most recent progress in capillary electrophoresis and electrophoretic microdevices for DNA-based diagnostics, including the important areas of genotyping for point mutation, single nucleotide polymorphisms, short tandem repeats and organism identification. The application of these techniques for infectious and genetic disease diagnosis, as well as forensic identification purpose, are covered. The promising development and the challenges for techinical problems are also discussed.

An ultramicroelectrode study of ferrocene diffusion and heterogeneous electron transfer rate in polyelectrolyte

Steady-state voltammograms at a microdisk electrode are used to measure the diffusion coefficient (D) and standard heterogeneous rate constant (k(s)) of ferrocene in polyelectrolyte PEG.MClO(4). The diffusion coefficient and standard heterogeneous rate constant of ferrocene are both smaller in polymer solvents than in monomeric solvents. The D and k(s) of ferrocene have been estimated in PEG containing different concentrations and cations of supporting electrolytes, and the dependencies of D and k(s) on temperature have been observed. These results show that the D and k(s) of ferrocene increase with increasing temperature in polyelectrolyte, and with increasing cation radius of supporting electrolyte, eg D and k(s) increase in the order Bu(4)NClO(4) > NaClO4 > LiClO4. On the other hand, D and k(s) increase with decreasing concentration of supporting electrolyte. The dependence of the half-wave potential (E(1/2)) on the concentration of the supporting electrolyte is also observed. E(1/2) shifts in the negative direction as the concentration of supporting electrolyte increases. (C) 1997 Elsevier Science Ltd.

Evaluation of a combined wavelet and a combined principal component analysis classification system for BCG diagnostic problem

Heart disease is one of the main factor causing death in the developed countries. Over several decades, variety of electronic and computer technology have been developed to assist clinical practices for cardiac performance monitoring and heart disease diagnosis. Among these methods, Ballistocardiography (BCG) has an interesting feature that no electrodes are needed to be attached to the body during the measurement. Thus, it is provides a potential application to asses the patients heart condition in the home. In this paper, a comparison is made for two neural networks based BCG signal classification models. One system uses a principal component analysis (PCA) method, and the other a discrete wavelet transform, to reduce the input dimensionality. It is indicated that the combined wavelet transform and neural network has a more reliable performance than the combined PCA and neural network system. Moreover, the wavelet transform requires no prior knowledge of the statistical distribution of data samples and the computation complexity and training time are reduced.

Feeding, morphological changes and allometric growth during starvation in miiuy croaker larvae

We investigated the effects of the timing of first feeding (larvae in F0, F1, F2, F3 and S were first fed on day 3, 4, 5, 6 days after hatching (DAH) and unfed, respectively) on feeding, morphological changes, survival and growth in miiuy croaker larvae at 24A degrees C. The fed larvae initiated feeding on 3 DAH and reached point of no return (PNR) on 6 DAH. Larvae in F0 and F1 groups survived apparently better than F2 group at the end of the experiment on 36 DAH. High larval mortality occurred from 3 to 7 DAH in all feeding groups, accounting for 40% (F0, F1 and F2 groups) to 90% (F3 and S groups) of the total mortality. Larvae in F0 and F1 groups grew better than F2 group throughout the experiment. Eye diameter, body height, head height and mouth gape of the first feeding larvae were more sensitive to starvation than other morphometrics and could be used as indicators for evaluating their nutritional status. Results indicated that delayed first feeding over 1 day after yolk exhaustion could lead to poor larval survival and growth. To avoid starvation and obtain good growth in culturing, larvae feeding should be initiated within 1 day after yolk exhaustion at 24A degrees C.

Seasonal and spatial variation in abundance and egg production of Paracalanus parvus (Copepoda: Calanoida) in/out Jiaozhou Bay, China

The spatial distribution of stage-specific abundance and reproduction of the copepod Paracalanus parvus were studied from October 2005 to September 2006 in the Jiaozhou Bay. This copepod occurred continuously in this bay throughout the year. The species reached the lowest abundance in April and peaked in June. From October to December, distribution center mainly occurred in offshore water and at the mouth of the bay. In winter, early copepodites and adults gradually decreased and till February, most of the population was only comprised of CIV-CV stages. Overwintering copepodites matured in March and males tended to mature before female. From May to September, each stage occurred in the population and gradually reached high abundance. Temperature and chlorophyll a (Chl-a) concentration in the three stations can't clearly explain the seasonal variation in stage-specific abundance, so we surmised the important effect of the Yellow Sea. Egg production rate (EPR) reached its lowest in winter and peaked in June at 60.8 eggs female(-1) day(-1) in nearshore water. In the warming period, EPR in nearshore water was statistically higher and EPR > 10 eggs female(-1) day(-1) lasted longer than that in offshore water, showing the importance of nearshore water for recruitment of R parvus. Our study showed that EPR was positively related to temperature and total chlorophyll a in offshore water and mouth of the bay. In nearshore water, the relationships between EPR and temperature and Chl-a in three size fractions were not the same as those in offshore water, suggesting complicated ecosystem in such a eutrophic area in warming period. (C) 2008 Elsevier Ltd. All rights reserved.