Venomics and biological analysis of Scatophagus argus argus (Spotted scat) venom isolated in Persian Gulf, extraction and purification of hemolytic protein

Green scat namely as Scatophagus argus argus is a venomous aquarium fish belonging to Scatophagidae family. It can induce painful wounds in injured hand with partial paralysis to whom that touch the spines. Dorsal and ventral rough spines contain cells that produce venom with toxic activities. According to unpublished data collected from local hospitals in southern coastal region of Iran, S. argus is reported as a venomous fish. Envenomation induces clinical symptoms such as local pain, partial paralysis, erythema and itching. In the present study green scat (spotted scat) was collected from Persian Gulf coastal waters. SDS-PAGE indicated 12 distinct bands in the venom ranged between 10-250 KDa. The crude venom had hemolytic activity on human erythrocytes (1%) with an LC100 (Lytic Concentration) of about 1.7 μg. The crude venom can release 813 μg proteins from 0.5% casein. Phospholipase C activity was recorded at 3.125 μg of total venom. Our findings showed that the edematic activity remained over 48 h after injection. The purification of the venom was done by HPLC and 30 peaks were obtained within 80 min but only one peak in 68 min retention time showed hemolytic activity at 90% acetonitril was isolated. The area percentage of the hemolytic protein showed that this hemolytic protein consist of 32 percent of total proteins and its molecular weight was 72 KDa in SDS_PAGE. The results demonstrated that crude venom extracted from Iranian coastal border has different toxic and enzymatic activities.

Bibliometric analysis of biological invasions research during the period of 1991 to 2007

The objective of this study is to conduct a bibliometric analysis of all biological invasions-related publications in the Science Citation Index (SCI) from 1991 to 2007. The indicator citation per publication (CPP) was used to evaluate the impact of articles, journals, and institutions. In the 3323 articles published in 521 journals, 7261 authors from 1905 institutions of 100 countries participated. As the most productive country of biological invasions research, the US will benefit from more collaboration between institutions, countries, and continents. In addition, analysis of keywords was applied to reveal research trends.

Genetic analysis of all-fish growth hormone gene transferred carp (Cyprinus carpio L.) and its F-1 generation

Recombinant "all-fish" growth hormone gene (GH) was microinjected Into the fertilized eggs of carp. A comparison between the growth traits of transgenics and non-transgenics was carried out, and the transgenic individuals with significant "fast-growing" effect were successfully gained. A comparison on the reproductivities was also given out between the transgenics and their non-transgenic siblings, and showed that the reproductive capacity of transgenics was substantially equivalent to those of the non-transgenics. On the other hand, the genetic separation and the characteristic distribution of the F-1 generation were genetically analyzed, which gave solid evidence for the hypothesis that 2-3 chromosomes are integrated with transgene. In addition, the distinct biological effects for multisite-integrated transgenes were further discussed. The present study opens a door for the breeding of "fast-growing" transgenic fish.

Quantitative traits correlative analysis and growth comparison among different populations of bay scallop, Argopecten irradians

The shell traits and weight traits are measured in cultured populations of bay scallop, Argopecten irradians. The results of regression analysis show that the regression relationships for all the traits are significant (P < 0.01). The correlative coefficients between body weight, as well as tissue weight with shell length, shell height and shell width are significant (P < 0.05). But the correlative coefficients between the anterior and posterior auricle length with body weight as well as tissue weight are not significant (P > 0.05). The multiple regression equation is obtained to estimate live body weight and tissue weight. The above traits except anterior and posterior auricle length are used for the growth and production comparison among three cultured populations, Duncan's new multiple range procedure analysis shows that all the traits in the Lingshuiqiao (LSQ) population are much more significant than those of the other two populations (P < 0.01), and there is no significant difference between the Qipanmo (QPM) and Dalijia (DLJ) populations in all traits (P > 0.05). The results indicate that the LSQ population has a higher growth rate and is expected to be more productive than the other two populations.

Representation, comparison, and interpretation of metabolome fingerprint data for total composition analysis and quality trait investigation in potato cultivars

Manfred Beckmann, David P. Enot, David P. Overy, and John Draper (2007). Representation, comparison, and interpretation of metabolome fingerprint data for total composition analysis and quality trait investigation in potato cultivars. Journal of Agricultural and Food Chemistry, 55 (9) pp.3444-3451 RAE2008

Assessment of LD matrix measures for the analysis of biological pathway association.

Complex diseases will have multiple functional sites, and it will be invaluable to understand the cross-locus interaction in terms of linkage disequilibrium (LD) between those sites (epistasis) in addition to the haplotype-LD effects. We investigated the statistical properties of a class of matrix-based statistics to assess this epistasis. These statistical methods include two LD contrast tests (Zaykin et al., 2006) and partial least squares regression (Wang et al., 2008). To estimate Type 1 error rates and power, we simulated multiple two-variant disease models using the SIMLA software package. SIMLA allows for the joint action of up to two disease genes in the simulated data with all possible multiplicative interaction effects between them. Our goal was to detect an interaction between multiple disease-causing variants by means of their linkage disequilibrium (LD) patterns with other markers. We measured the effects of marginal disease effect size, haplotype LD, disease prevalence and minor allele frequency have on cross-locus interaction (epistasis). In the setting of strong allele effects and strong interaction, the correlation between the two disease genes was weak (r=0.2). In a complex system with multiple correlations (both marginal and interaction), it was difficult to determine the source of a significant result. Despite these complications, the partial least squares and modified LD contrast methods maintained adequate power to detect the epistatic effects; however, for many of the analyses we often could not separate interaction from a strong marginal effect. While we did not exhaust the entire parameter space of possible models, we do provide guidance on the effects that population parameters have on cross-locus interaction.

A Quantitative Analysis of Growth and Size Regulation in Manduca sexta: The Physiological Basis of Variation in Size and Age at Metamorphosis.

Body size and development time are important life history traits because they are often highly correlated with fitness. Although the developmental mechanisms that control growth have been well studied, the mechanisms that control how a species-characteristic body size is achieved remain poorly understood. In insects adult body size is determined by the number of larval molts, the size increment at each molt, and the mechanism that determines during which instar larval growth will stop. Adult insects do not grow, so the size at which a larva stops growing determines adult body size. Here we develop a quantitative understanding of the kinetics of growth throughout larval life of Manduca sexta, under different conditions of nutrition and temperature, and for genetic strains with different adult body sizes. We show that the generally accepted view that the size increment at each molt is constant (Dyar's Rule) is systematically violated: there is actually a progressive increase in the size increment from instar to instar that is independent of temperature. In addition, the mass-specific growth rate declines throughout the growth phase in a temperature-dependent manner. We show that growth within an instar follows a truncated Gompertz trajectory. The critical weight, which determines when in an instar a molt will occur, and the threshold size, which determines which instar is the last, are different in genetic strains with different adult body sizes. Under nutrient and temperature stress Manduca has a variable number of larval instars and we show that this is due to the fact that more molts at smaller increments are taken before threshold size is reached. We test whether the new insight into the kinetics of growth and size determination are sufficient to explain body size and development time through a mathematical model that incorporates our quantitative findings.

Biological and ecological traits of marine species

This paper reviews the utility and availability of biological and ecological traits for marine species so as to prioritise the development of a world database on marine species traits. In addition, the ‘status’ of species for conservation, that is, whether they are introduced or invasive, of fishery or aquaculture interest, harmful, or used as an ecological indicator, were reviewed because these attributes are of particular interest to society. Whereas traits are an enduring characteristic of a species and/or population, a species status may vary geographically and over time. Criteria for selecting traits were that they could be applied to most taxa, were easily available, and their inclusion would result in new research and/or management applications. Numerical traits were favoured over categorical. Habitat was excluded as it can be derived from a selection of these traits. Ten traits were prioritized for inclusion in the most comprehensive open access database on marine species (World Register of Marine Species), namely taxonomic classification, environment, geography, depth, substratum, mobility, skeleton, diet, body size and reproduction. These traits and statuses are being added to the database and new use cases may further subdivide and expand upon them.

Microbial analysis of soil and groundwater from a gasworks site and comparison to a sequenced biological reactive barrier remediation process (SEREBAR)

Aims: To investigate the distribution of a polymicrobial community of biodegradative bacteria in (i) soil and groundwater at a former manufactured gas plant (FMGP) site and (ii) in a novel SEquential REactive BARrier (SEREBAR) bioremediation process designed to bioremediate the contaminated groundwater. Methods and Results: Culture-dependent and culture-independent analyses using denaturing gradient gel electrophoresis (DGGE) and polymerase chain reaction (PCR) for the detection of 16S ribosomal RNA gene and naphthalene dioxygenase (NDO) genes of free-living (planktonic groundwater) and attached (soil biofilm) samples from across the site and from the SEREBAR process was applied. Naphthalene arising from groundwater was effectively degraded early in the process and the microbiological analysis indicated a dominant role for Pseudomonas and Comamonas in its degradation. The microbial communities appeared highly complex and diverse across both the sites and in the SEREBAR process. An increased population of naphthalene degraders was associated with naphthalene removal. Conclusion: The distribution of micro-organisms in general and naphthalene degraders across the site was highly heterogeneous. Comparisons made between areas contaminated with polycyclic aromatic hydrocarbons (PAH) and those not contaminated, revealed differences in the microbial community profile. The likelihood of noncultured bacteria being dominant in mediating naphthalene removal was evident. Significance and Impact of the Study: This work further emphasizes the importance of both traditional and molecular-based tools in determining the microbial ecology of contaminated sites and highlights the role of noncultured bacteria in the process.

A meta-analysis of latitudinal variations in life-history traits of roach, Rutilus rutilus, over its geographical range: linear or non-linear relationships?

1. We collated information from the literature on life history traits of the roach (a generalist freshwater fish), and analysed variation in absolute fecundity, von Bertalanffy parameters, and reproductive lifespan in relation to latitude, using both linear and non-linear regression models. We hypothesized that because most life history traits are dependent on growth rate, and growth rate is non-linearly related with temperature, it was likely that when analysed over the whole distribution range of roach, variation in key life history traits would show non-linear patterns with latitude.