iBarcode.org: web-based molecular biodiversity analysis

<p>Abstract</p> <p>Background</p> <p>DNA sequences have become a primary source of information in biodiversity analysis. For example, short standardized species-specific genomic regions, DNA barcodes, are being used as a global standard for species identification and biodiversity studies. Most DNA barcodes are being generated by laboratories that have an expertise in DNA sequencing but not in bioinformatics data analysis. Therefore, we have developed a web-based suite of tools to help the DNA barcode researchers analyze their vast datasets.</p> <p>Results</p> <p>Our web-based tools, available at <url>http://www.ibarcode.org</url>, allow the user to manage their barcode datasets, cull out non-unique sequences, identify haplotypes within a species, and examine the within- to between-species divergences. In addition, we provide a number of phylogenetics tools that will allow the user to manipulate phylogenetic trees generated by other popular programs.</p> <p>Conclusion</p> <p>The use of a web-based portal for barcode analysis is convenient, especially since the WWW is inherently platform-neutral. Indeed, we have even taken care to ensure that our website is usable from handheld devices such as PDAs and smartphones. Although the current set of tools available at iBarcode.org were developed to meet our own analytic needs, we hope that feedback from users will spark the development of future tools. We also welcome user-built modules that can be incorporated into the iBarcode framework.</p

Googling DNA sequences on the World Wide Web

Background: New web-based technologies provide an excellent opportunity for sharing and accessing information and using web as a platform for interaction and collaboration. Although several specialized tools are available for analyzing DNA sequence information, conventional webbased tools have not been utilized for bioinformatics applications. We have developed a novel algorithm and implemented it for searching species-specific genomic sequences, DNA barcodes, by using popular web-based methods such as Google. Results: We developed an alignment independent character based algorithm based on dividing a sequence library (DNA barcodes) and query sequence to words. The actual search is conducted by conventional search tools such as freely available Google Desktop Search. We implemented our algorithm in two exemplar packages. We developed pre and post-processing software to provide customized input and output services, respectively. Our analysis of all publicly available DNA barcode sequences shows a high accuracy as well as rapid results. Conclusion: Our method makes use of conventional web-based technologies for specialized genetic data. It provides a robust and efficient solution for sequence search on the web. The integration of our search method for large-scale sequence libraries such as DNA barcodes provides an excellent web-based tool for accessing this information and linking it to other available categories of information on the web

Pyrosequencing for Mini-Barcoding of Fresh and Old Museum Specimens

DNA barcoding is an effective approach for species identification and for discovery of new and/or cryptic species. Sanger sequencing technology is the method of choice for obtaining standard 650 bp cytochrome c oxidase subunit I (COI) barcodes. However, DNA degradation/fragmentation makes it difficult to obtain a full-length barcode from old specimens. Mini-barcodes of 130 bp from the standard barcode region have been shown to be effective for accurate identification in many animal groups and may be readily obtained from museum samples. Here we demonstrate the application of an alternative sequencing technology, the four-enzymes single-specimen pyrosequencing, in rapid, cost-effective mini-barcode analysis. We were able to generate sequences of up to 100 bp from mini-barcode fragments of COI in 135 fresh and 50 old Lepidoptera specimens (ranging from 53–97 year-old). The sequences obtained using pyrosequencing were of high quality and we were able to robustly match all the tested pyro-sequenced samples to their respective Sanger-sequenced standard barcode sequences, where available. Simplicity of the protocol and instrumentation coupled with higher speed and lower cost per sequence than Sanger sequencing makes this approach potentially useful in efforts to link standard barcode sequences from unidentified specimens to known museum specimens with only short DNA fragments

Optimal rehabilitation planning for aged water distribution mains considering cascading failures of interdependent infrastructure systems

This is the final version. Available on open access from IWA Publishing via the DOI in this recordData availability statement: All relevant data are included in the paper or its Supplementary Information.Water distribution networks (WDNs) with other infrastructures constitute a complex and interdependent multi-utility system. Considering interdependencies between WDNs and other urban infrastructures, this work proposes WDN intervention planning using a dynamic multi-utility approach to tackle the challenges of pressure deficits and cascading failures by the decoupling of different infrastructure systems. For this purpose, the study develops reliability indices representing the hydraulic and decoupled statuses of WDNs with neighbor infrastructures; the hydraulic reliability represents the robustness of the network against the water pressure deficit, and decoupling reliability represents the extent to which WDN elements are decoupled from other assets elements. A multi-objective optimization algorithm is employed to develop rehabilitation strategies by introducing three approaches for WDN upgrade following a phased design and construction method. Evaluating intervention plans based on construction cost, reliability and cascade effects shows that, under budget limitation conditions, decoupling a WDN could significantly save the cascade cost such that 1% improvement in the decoupling reliability brings about 157.42 billion Rials cascade cost saving to asset managers. On the other hand, the decoupled network is weak against hydraulic reliability, which could make it by far less resilient network than the coupled network with around 75% hydraulic reliability difference.University of InnsbruckAustrian Academy of Sciences (ÖAW)Austrian Organization Funding for Basic ResearchDOC FellowshipAustrian Science Fund (FWF)European Union Horizon 202

Pareto-optimal design of water distribution networks: an improved graph theory-based approach

This is the final version. Available on open access from IWA Publishing via the DOI in this recordData availability statement: All relevant data are included in the paper or its Supplementary Information.One of the main drawbacks of using evolutionary algorithms for the multi-objective design of water distribution networks (WDNs) is their computational inefficiency, particularly for large-scale problems. Recently, graph theory-based approaches (GTAs) have gained attention as they can help with the optimal WDN design (i.e., determining optimal diameters). This study aims to extend a GTA to further improve the quality of design solutions. The GTA design is based on a customized metric called ‘demand edge betweenness centrality’, which spatially distributes nodal demands through the weighted edges of a WDN graph and provides an estimation of water flows. Assigned edge weights can be constant (i.e., static) or modified iteratively (i.e., dynamic) during the design process, leading to different flow estimations and alternative design options. Three hydraulic-inspired dynamic weights are developed in this study to better reproduce hydraulic behavior and, consequently, find better solutions. Additionally, this work proposes a framework for the optimal design of multi-source WDNs and provides guidelines for obtaining near-optimal solutions in such networks. A comparative study between GTAs and evolutionary optimizations confirms the efficiency of the improved GTA in providing optimal/near-optimal solutions, especially for large WDNs, with a runtime reduction of up to seven orders of magnitude.Austrian Science Fund (FWF

Comparing eDNA metabarcoding and conventional pelagic netting to inform biodiversity monitoring in deep ocean environments

The performance of environmental DNA (eDNA) metabarcoding has rarely been evaluated against conventional sampling methods in deep ocean mesopelagic environments. We assessed the biodiversity patterns generated with eDNA and two co-located conventional methods, oblique midwater trawls and vertical multinets, to compare regional and sample-level diversity. We then assessed the concordance of ecological patterns across water column habitats and evaluated how DNA markers and the level of sampling effort influenced the inferred community. We found eDNA metabarcoding characterized regional diversity well, detecting more taxa while identifying similar ecological patterns as conventional samples. Within sampling locations, eDNA metabarcoding rarely detected taxa across more than one replicate. While more taxa were found in eDNA than oblique midwater trawls within sample stations, fewer were found compared to vertical multinets. Our simulations show greater eDNA sampling effort would improve concordance with conventional methods. We also observed that using taxonomic data from multiple markers generated ecological patterns most similar to those observed with conventional methods. Patterns observed with Exact Sequence Variants were more stable across markers suggesting they are more powerful for detecting change. eDNA metabarcoding is a valuable tool for identifying and monitoring biological hotspots but some methodological adjustments are recommended for deep ocean environments

Egg yolk fatty acid profile of avian species - influence on human nutrition

Lipids are an important nutritional component of the avian egg. A review of the literature was completed to determine the fatty acid compositions in egg yolk from some avian species. Additionally, the nutritional influence of lipid and lipoprotein content on the plasma of male participants during 30-day feeding was discussed. The ostrich eggs had the highest unsaturated fatty acid and the lowest cholesterol content in relation to other avian species. Ostrich had a higher proportion of 18:3n-3 (p < 0.01) compared with other species. Chicken yolk numerically contained much higher levels of 22:6n-3 than those found in turkeys, quails and geese, but the amount of 22:6n-3 in ostrich egg was lower by comparison with other species (p < 0.01). After the storage of eggs at the room temperature, there was a notable loss of vitamin E (vitE) in the yolks of all species and this decrease was marginal (p < 0.01) in ostrich compared with other species. There were significant (p < 0.05) increases in plasma low-density lipoprotein (LDL) level in all male subjects. Plasma high-density lipoprotein (HDL) level decreased (p < 0.05) only in men who were fed chicken or ostrich eggs daily. Consumption of different species’ eggs had no influence on the total male plasma cholesterol and triglyceride levels. LDL-C:HDL-C ratio increased (p < 0.05) after goose and turkey egg consumption. Consumption of one egg/month by healthy human subjects had no effect on serum total cholesterol and triglyceride. The LDL-C:HDL-C ratio (which is a strong predictor of coronary heart disease risk) increased, although non-significantly, by consuming chicken, quail and ostrich eggs.http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1439-0396hb201

DNA Barcoding Reveals Cryptic Diversity in Lumbricus terrestris L., 1758 (Clitellata): Resurrection of L. herculeus (Savigny, 1826)

The widely studied and invasive earthworm, Lumbricus terrestris L., 1758 has been the subject of nomenclatural debate for many years. However these disputes were not based on suspicions of heterogeneity, but rather on the descriptions and nomenclatural acts associated with the species name. Large numbers of DNA barcode sequences of the cytochrome oxidase I obtained for nominal L. terrestris and six congeneric species reveal that there are two distinct lineages within nominal L. terrestris. One of those lineages contains the Swedish population from which the name-bearing specimen of L. terrestris was obtained. The other contains the population from which the syntype series of Enterion herculeum Savigny, 1826 was collected. In both cases modern and old representatives yielded barcode sequences allowing us to clearly establish that these are two distinct species, as different from one another as any other pair of congeners in our data set. The two are morphologically indistinguishable, except by overlapping size-related characters. We have designated a new neotype for L. terrestris. The newly designated neotype and a syntype of L. herculeus yielded DNA adequate for sequencing part of the cytochrome oxidase I gene (COI). The sequence data make possible the objective determination of the identities of earthworms morphologically identical to L. terrestris and L. herculeus, regardless of body size and segment number. Past work on nominal L. terrestris could have been on either or both species, although L. herculeus has yet to be found outside of Europe

Oligonucleotide Frequencies of Barcoding Loci Can Discriminate Species across Kingdoms

Background: DNA barcoding refers to the use of short DNA sequences for rapid identification of species. Genetic distance or character attributes of a particular barcode locus discriminate the species. We report an efficient approach to analyze short sequence data for discrimination between species. Methodology and Principal Findings: A new approach, Oligonucleotide Frequency Range (OFR) of barcode loci for species discrimination is proposed. OFR of the loci that discriminates between species was characteristic of a species, i.e., the maxima and minima within a species did not overlap with that of other species. We compared the species resolution ability of different barcode loci using p-distance, Euclidean distance of oligonucleotide frequencies, nucleotide-character based approach and OFR method. The species resolution by OFR was either higher or comparable to the other methods. A short fragment of 126 bp of internal transcribed spacer region in ribosomal RNA gene was sufficient to discriminate a majority of the species using OFR. Conclusions/Significance: Oligonucleotide frequency range of a barcode locus can discriminate between species. Ability to discriminate species using very short DNA fragments may have wider applications in forensic and conservation studies