177,817 research outputs found
Construction of an adult barnacle (Balanus amphitrite) cDNA library and selection of reference genes for quantitative RT-PCR studies
No full textDe Gregoris TB, Borra M, Biffali E, et al. Construction of an adult barnacle (Balanus amphitrite) cDNA library and selection of reference genes for quantitative RT-PCR studies. BMC Molecular Biology. 2009;10(1):62.BACKGROUND:
Balanus amphitrite is a barnacle commonly used in biofouling research. Although many aspects of its biology have been elucidated, the lack of genetic information is impeding a molecular understanding of its life cycle. As part of a wider multidisciplinary approach to reveal the biogenic cues influencing barnacle settlement and metamorphosis, we have sequenced and annotated the first cDNA library for B. amphitrite. We also present a systematic validation of potential reference genes for normalization of quantitative real-time PCR (qRT-PCR) data obtained from different developmental stages of this animal.
RESULTS:
We generated a cDNA library containing expressed sequence tags (ESTs) from adult B. amphitrite. A total of 609 unique sequences (comprising 79 assembled clusters and 530 singlets) were derived from 905 reliable unidirectionally sequenced ESTs. Bioinformatics tools such as BLAST, HMMer and InterPro were employed to allow functional annotation of the ESTs. Based on these analyses, we selected 11 genes to study their ability to normalize qRT-PCR data. Total RNA extracted from 7 developmental stages was reverse transcribed and the expression stability of the selected genes was compared using geNorm, BestKeeper and NormFinder. These software programs produced highly comparable results, with the most stable gene being mt-cyb, while tuba, tubb and cp1 were clearly unsuitable for data normalization.
CONCLUSION:
The collection of B. amphitrite ESTs and their annotation has been made publically available representing an important resource for both basic and applied research on this species. We developed a qRT-PCR assay to determine the most reliable reference genes. Transcripts encoding cytochrome b and NADH dehydrogenase subunit 1 were expressed most stably, although other genes also performed well and could prove useful to normalize gene expression studies
Assessment and implications of the supply of Semibalanus balanoides (L.) larvae to shores in Fife, East Scotland
No full textInvestigations into the supply, settlement and recruitment of the barnacle Semibalanus balanoides (L.) to shores in Fife, East Scotland were undertaken over three consecutive years (2004 – 2006). Several designs of a passive larval trap, based on earlier published designs, were employed to quantify the delivery (supply) of cyprids to the substratum. Pump samples from the water column were collected to provide a measure of intertidal cyprid concentration. Cyprid concentration was found to exhibit both spatial and temporal variation, but was also found to be significantly correlated with cyprid supply, as quantified by the traps. In some years, pump and trap samples suggested that cyprid abundance in the intertidal was mediated by wind-driven processes.
An artificial substratum was used to quantify cyprid settlement, allowing investigations into the supply-settlement relationship. Supply and settlement were found to be two very distinct biological phases. Supply describes the flux of larvae to the substratum. Settlement provides a measure of the amount of larvae that decide to settle on the substratum, as initial attachment for barnacle larvae is not permanent. Whilst supply saturation is unfeasible, daily saturation of the substratum by settlers was observed at many sites along the Fife coast.
Levels of settlement saturation were found to vary both temporally, between years, and spatially, over scales of km. Varying levels of the desperation of larvae to settle, mediated by dwindling energy reserves, was thought to explain some of this variation. The supply data also provided some evidence of the possible movement of cyprids along the Fife coast from Fife Ness to Tentsmuir. However, wind-induced transport may also play a dominant role on the Fife coast. A comparison of supply and recruitment of larvae into adult populations revealed that both pre- and post-settlement events may influence recruitment. The relative importance of these factors was shown to be density-dependent. Negative intraspecific interactions were only seen in denser aggregations of adults. In less crowded aggregations, recruitment reflected initial patterns of larval supply
Barnacle recruitment.
No full text<p>Adjusted R<sup>2</sup> coefficients for functional forms (exponential, logistic and hyperbolic) in models with and without barnacle traits characterising body size (basal or operculum surface area). All models were significant (<i>P</i><10<sup>−3</sup>).</p
Molecular Dynamics Simulation of Barnacle Cement
No full textBarnacle cement is an underwater adhesive that is used for permanent settlement. Its main components are insoluble protein complexes that have not been fully studied. In present article, we chose two proteins of barnacle cement for study, 36-KD protein and Mrcp-100K protein. In order to investigate the characteristic of above two proteins, we introduced the method of molecular modeling. And the simulation package GROMACS was used to simulate the behavior of these proteins. In this article, before the simulations, we introduce some theories to predict the time scale for polymer relaxation. During the simulation, we mainly focus on two properties of these two proteins: structural stability and adhesive force to substrate. First, we simulate the structural stability of two proteins in water, and then the stability of 36-KD protein in seawater environment is investigated.We find that the stability varies in the different environments. Next, to study adhesive ability of two proteins, we simulate the process of peeling the two proteins from the substrate (graphite). Then, we analyze the main reasons of these results. We find that hydrogen bonds in proteins play an important role in the protein stability. In the process of the peeling, we use Lennard–Jones 12-6 potential to calculate the van der Waals interactions between proteins and substrate
Three Men Examining a Barnacle 2 (B8F011_021)
No full textThree men examining a barnacle. Pictured are geneticist Roger Keller, unidentified, and pollution biologist Walt Macior (L-R). The map in the middle is drawing liquid from the barnacle
Three Men Examining a Barnacle (B8F001_017)
No full textThree men examining a barnacle. Pictured are geneticist Roger Keller, unidentified, and pollution biologist Walt Macior (L-R). The map in the middle is drawing liquid from the barnacle
A phototaxis inhibition assay using barnacle larvae
No full textThe effects of sublethal concentrations of phenol and cadmium on the phototactic responses of the stage II nauplii of the barnacle Balanus amphitrite were investigated. Increased toxicant concentrations caused a reduction in phototactic responses. Balanus amphitrite nauplii exposed to nominal phenol concentrations of 100 ppm and higher for 1-12 h failed to exhibit phototactic responses, while longer exposure times of 24 and 48 h reduced the lowest observable effect concentration (LOECs) to 80 and 60 ppm, respectively. For cadmium, the LOECs, based on nominal concentrations, for B. amphitrite following 1, 6, 12, 24, and 48 h exposures were 20, 4.5, 4.0, 1, and 0.75 ppm, respectively. The LOECs can be significantly reduced by increasing the duration of exposure to the toxicants. A good relationship exists between the phototactic response and toxicant concentration as well as exposure time. Results of this study indicate that the toxicant-induced reduction in phototactic responses of barnacle larvae can be used in a sensitive, rapid screening test for ecotoxicological assessments.link_to_subscribed_fulltex
The bromotyrosine derivative Ianthelline isolated from the Arctic marine sponge Stryphnus fortis inhibits marine micro- and macrobiofouling
No full textInternational audienceThe inhibition of marine biofouling by the bromotyrosine derivative ianthelline, isolated from the Arctic marine sponge Stryphnus fortis, is described. All major stages of the fouling process are investigated. The effect of ianthelline on adhesion and growth of marine bacteria and microalgae is tested to investigate its influence on the initial microfouling process comparing with the known marine antifoulant barettin as a reference. Macrofouling is studied via barnacle (Balanus improvisus) settlement assays and blue mussel (Mytilus edulis) phenoloxidase inhibition. Ianthelline is shown to inhibit both marine micro-and macrofoulers with a pronounced effect on marine bacteria (minimum inhibitory concentration (MIC) values 0.1-10 mu g/mL) and barnacle larval settlement (IC50= 3.0 mu g/mL). Moderate effects are recorded on M. edulis (IC50= 45.2 mu g/mL) and microalgae, where growth is more affected than surface adhesion. The effect of ianthelline is also investigated against human pathogenic bacteria. Ianthelline displayed low micromolar MIC values against several bacterial strains, both Gram positive and Gram negative, down to 2.5 mu g/mL. In summary, the effect of ianthelline on 20 different representative marine antifouling organisms and seven human pathogenic bacterial strains is presented
Appropriate Similarity Measures for Author Cocitation Analysis
No full textWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
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