PrepMS: TOF MS data graphical preprocessing tool

We introduce a simple-to-use graphical tool that enables researchers to easily prepare time-of-flight mass spectrometry data for analysis. For ease of use, the graphical executable provides default parameter settings, experimentally determined to work well in most situations. These values, if desired, can be changed by the user. PrepMS is a stand-alone application made freely available (open source), and is under the General Public License (GPL). Its graphical user interface, default parameter settings, and display plots allow PrepMS to be used effectively for data preprocessing, peak detection and visual data quality assessment. AVAILABILITY: Stand-alone executable files and Matlab toolbox are available for download at: http://sourceforge.net/projects/prepms     

OmicBrowse: a browser of multidimensional omics annotations

OmicBrowse is a browser to explore multiple datasets coordinated in the multidimensional omic space integrating omics knowledge ranging from genomes to phenomes and connecting evolutional correspondences among multiple species. OmicBrowse integrates multiple data servers into a single omic space through secure peer-to-peer server communications, so that a user can easily obtain an integrated view of distributed data servers, e.g. an integrated view of numerous whole-genome tiling-array data retrieved from a user's in-house private-data server, along with various genomic annotations from public internet servers. OmicBrowse is especially appropriate for positional-cloning purposes. It displays both genetic maps and genomic annotations within wide chromosomal intervals and assists a user to select candidate genes by filtering their annotations or associated documents against user-specified keywords or ontology terms. We also show that an omic-space chart effectively represents schemes for integrating multiple datasets of multiple species. Availability: OmicBrowse is developed by the Genome-Phenome Superbrain Project and is released as free open-source software under the GNU General Public License at http://omicspace.riken.jp.     

CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes

MOTIVATION: The numbers of finished and ongoing genome projects are increasing at a rapid rate, and providing the catalog of genes for these new genomes is a key challenge. Obtaining a set of well-characterized genes is a basic requirement in the initial steps of any genome annotation process. An accurate set of genes is needed in order to learn about species-specific properties, to train gene-finding programs, and to validate automatic predictions. Unfortunately, many new genome projects lack comprehensive experimental data to derive a reliable initial set of genes. RESULTS: In this study, we report a computational method, CEGMA (Core Eukaryotic Genes Mapping Approach), for building a highly reliable set of gene annotations in the absence of experimental data. We define a set of conserved protein families that occur in a wide range of eukaryotes, and present a mapping procedure that accurately identifies their exon-intron structures in a novel genomic sequence. CEGMA includes the use of profile-hidden Markov models to ensure the reliability of the gene structures. Our procedure allows one to build an initial set of reliable gene annotations in potentially any eukaryotic genome, even those in draft stages. AVAILABILITY: Software and data sets are available online at http://korflab.ucdavis.edu/Datasets.     

Enhanced cadmium-induced testicular necrosis and renal proximal tubule damage caused by gene-dose increase in a Slc39a8-transgenic mouse line

Resistance to cadmium (Cd)-induced testicular necrosis is an autosomal recessive trait defined as the Cdm locus. Using positional cloning, we previously identified the Slc39a8 (encoding an apical-surface ZIP8 transporter protein) as the gene most likely responsible for the phenotype. In situ hybridization revealed that endothelial cells of the testis vasculature express high ZIP8 levels in two sensitive inbred mouse strains and negligible amounts in two resistant strains. In the present study, we isolated a 168.7-kb bacterial artificial chromosome (BAC), carrying only the Slc39a8 gene, from a Cd-sensitive 129/SvJ BAC library and generated BAC-transgenic mice. The BTZIP8-3 line, having three copies of the 129/SvJ Slc39a8 gene inserted into the Cd-resistant C57BL/6J genome (having its normal two copies of the Slc39a8 gene), showed tissue-specific ZIP8 mRNA expression similar to wild-type mice, mainly in lung, testis, and kidney. The 2.5-fold greater expression paralleled the fact that the BTZIP8-3 line has five copies, whereas wild-type mice have two copies, of the Slc39a8 gene. The ZIP8 mRNA and protein localized especially to endothelial cells of the testis vasculature in BTZIP8-3 mice. Cd treatment reversed Cd resistance (seen in nontransgenic littermates) to Cd sensitivity in BTZIP8-3 mice; reversal of the testicular necrosis phenotype confirms that Slc39a8 is unequivocally the Cdm locus. ZIP8 also localized specifically to the apical surface of proximal tubule cells in the BTZIP8-3 kidney. Cd treatment caused acute renal failure and signs of proximal tubular damage in the BTZIP8-3 but not nontransgenic littermates. BTZIP8-3 mice should be a useful model for studying Cd-induced disease in kidney. kidney; testis; ZIP8; bacterial artificial chromosome     

Species Differences in the Selective Inhibition of Monoamine Oxidase (1-methyl-2-phenylethyl)hydrazine and its Potentiation by Cyanide

The potentiating effects of cyanide on the inhibition of rat liver mitochondrial monoamine oxidase-A & B and of ox liver mitochondrial MAO-B by pheniprazine [(1-methyl-2-phenylethyl)hydrazine] has been studied. Pheniprazine was shown to behave as a mechanism-based MAO inhibitor. For rat liver MAO-B, the initial non-covalent step was characterized by dissociation constant (K _i) of 2450 nM and the first-order rate constant (k ₊₂) for the covalent adduct formation was 0.16 min⁻¹. As a reversible inhibitor it was selective towards rat liver MAO-A (K _i = 420 nM) but the rate of irreversible inhibition of that enzyme was considerably slower (k ₊₂ = 0.06 min⁻¹). MAO-B from ox liver more closely resembled MAO-A from the rat in sensitivity to reversible inhibition by pheniprazine (K _i = 450 nm) but it was closer to rat liver MAO-B in rate of irreversible inhibition (k ₊₂ = 0.29 min⁻¹). The K _i values were significantly decreased in the presence of KCN but there was little effect on the k ₊₂ values. However, sensitivities of the different enzymes to KCN varied widely and considerably higher concentrations of KCN were required for this effect to be apparent with the rat liver mitochondrial MAO-A than with MAO-B from rat and ox liver. The kinetic behaviour of cyanide activation was consistent with partial (non-essential) competitive activation in all cases. Special issue dedicated to Dr. Moussa Youdim.     

Profiling plasma steroid hormones: a non-lethal approach for the study of skate reproductive biology and its potential use in conservation management

Information regarding sexual maturity and reproductive cycles in skates has largely been based on gross morphological changes within the reproductive tract. While this information has proved valuable in obtaining life history information, it also necessitates sacrificing the skates to obtain this data. In contrast, few studies have used circulating steroid hormones to establish when these batoids become reproductively capable or for the determination of reproductive cyclicity. This study summarizes our current knowledge of hormonal analyses in determining skate reproductive status and offers information that suggests analysis of circulating steroid hormone concentrations provide a means to determine size at sexual maturity and asses reproductive cycles without the need to sacrifice the skate.     

Eel community structure,fluvial recruitment of <Emphasis Type="Italic">Anguilla marmorata</Emphasis> and indication for a weak local production of spawners from rivers of Réunion and Mauritius islands

Anguillid eels were sampled from permanent rivers in the Réunion and Mauritius islands, western Indian Ocean, with a standardized electrofishing method. A. marmorata was very dominant, corresponding to 91.7 and 90.7% of all the eels collected in Réunion and Mauritius, respectively. Three other species (A. mossambica, A. bicolor bicolor and A. nebulosa labiata) were also present in both islands. A. marmorata showed a strong altitudinal gradient of densities from the lower to upper zones, especially in the younger stages (TL <250 mm), while A. mossambica was only found in the upper zones and A. bicolor bicolor occurred only in the lower zones (A. nebulosa labiata was rare). The eel species composition in freshwaters of both islands is very similar because these two adjoining islands are located in the same trail of drifting marine larvae. Mean estimated eel biomasses were noticeably low (11.1 and 22.2 kg ha⁻¹ in Réunion and Mauritius islands, respectively), especially when compared to those of other tropical insular systems without any eel fishery (Comoros or Polynesia, more than 100 kg ha⁻¹). Nevertheless, the fluvial recruitment of A. marmorata seemed to be regular during the surveyed period, staggering from October to April. The obvious lack of large eels in Mauritius but more significantly in Réunion suggests a high pressure from traditional fishery, and the local reproductive turnover is uncertain. Because sexual maturation seems to occur at a large body size for A. marmorata, as for temperate species, the Réunion and Mauritius rivers may only have a weak contribution to the regional production of spawners. However, the giant mottled eel population in the western Indian Ocean is believed to be panmictic at the regional scale, and may not rely exclusively on these islands’ contribution. A comparison is made with those of freshwater systems in other tropical islands.     

Endocrinological investigation into the reproductive cycles of two sympatric skate species, Malacoraja senta and Amblyraja radiata, in the western Gulf of Maine

The smooth skate, Malacoraja senta, and thorny skate, Amblyraja radiata, are two commercially exploited batoids found within the Gulf of Maine. During the past five years, we conducted a large study to accurately describe important biological life history parameters previously lacking for these species. As part of that project, the current study reports our findings on the hormonal profiles associated with the reproductive cycles of M. senta and A. radiata. Blood samples were obtained from mature M. senta and A. radiata of both sexes from all months of the year, and plasma testosterone (T), estradiol (E₂) and progesterone (P₄) concentrations were determined using radioimmunoassay (RIA). In female M. senta and A. radiata, monthly T concentrations ranged from 4,522 pg ml⁻¹ to 1,373 pg ml⁻¹ and 31,940 pg ml⁻¹ to 14,428 pg ml⁻¹, E₂ concentrations from 831 pg ml⁻¹ to 60 pg ml⁻¹ and 8,515 pg ml⁻¹ to 2,902 pg ml⁻¹, and P₄ concentrations from 3,027 pg ml⁻¹ to 20 pg ml⁻¹ and 3,264 pg ml⁻¹ to 331 pg ml⁻¹, respectively. No statistical differences were detected between any months for any hormone. Estradiol concentrations were not correlated with ovary weight, shell gland weight, or diameter of the largest follicles in either species. Monthly T concentrations in male M. senta and A. radiata ranged from 23,146 to 12,660 pg ml⁻¹ and from 57,500pg ml⁻¹ to 24,737 pg ml⁻¹, while E₂ concentrations ranged from 7.5 pg ml⁻¹ to undetectable and 103 to 30 pg ml⁻¹, respectively. No statistical differences were observed between months for either steroid. Testosterone concentrations were weakly correlated with testes weight and percent of stage VI spermatocysts in A. radiata, however, no correlation was detected between T and stage VI spermatocysts in M. senta. Collectively, these data support the previous conclusion that M. senta and A. radiata of both sexes are capable of reproducing year round in the western Gulf of Maine.     

Actin deficiency induces cofilin phosphorylation: proteome analysis of HeLa cells after beta-actin gene silencing

Actin-binding proteins regulate the dynamic structure and function of actin filaments in the cell. Much is known about how manipulation of the actin-binding proteins affects the structure and function of actin filaments; however, little is known about how manipulation of actin in the cell affects actin-binding proteins. We addressed this question by utilizing two technologies: RNA interference and 2-dimensional gel electrophoresis. We knocked down beta-actin expression in HeLa cells using short interfering RNA and applied 2-DGE to examine alterations in the HeLa cell proteome. We revealed a 2-5 fold increases of four protein spots on 2-D gels and identified these proteins by mass spectrometry. Three of the four proteins were actin-binding proteins, including cofilin, which promotes both disassembly and assembly of actin filaments but becomes inactivated when phosphorylated. Further examination revealed that the cofilin total protein level barely increased, but the phosphorylated cofilin level increased dramatically in HeLa cells after beta-actin siRNA treatment. These results suggest that in response to siRNA-induced beta-actin deficiency HeLa cells inactivate cofilin by phosphorylation rather than down-regulate its protein expression level. This study also demonstrates that the combination of RNA interference and 2-dimensional gel electrophoresis technologies provides a valuable method to study protein interactions in a specific cellular pathway.