Next Generation Sequencing Reveals the Hidden Diversity of Zooplankton Assemblages

Zooplankton play an important role in our oceans, in biogeochemical cycling and providing a food source for commercially important fish larvae. However, difficulties in correctly identifying zooplankton hinder our understanding of their roles in marine ecosystem functioning, and can prevent detection of long term changes in their community structure. The advent of massively parallel next generation sequencing technology allows DNA sequence data to be recovered directly from whole community samples. Here we assess the ability of such sequencing to quantify richness and diversity of a mixed zooplankton assemblage from a productive time series site in the Western English Channel. Methodology/Principle Findings Plankton net hauls (200 µm) were taken at the Western Channel Observatory station L4 in September 2010 and January 2011. These samples were analysed by microscopy and metagenetic analysis of the 18S nuclear small subunit ribosomal RNA gene using the 454 pyrosequencing platform. Following quality control a total of 419,041 sequences were obtained for all samples. The sequences clustered into 205 operational taxonomic units using a 97% similarity cut-off. Allocation of taxonomy by comparison with the National Centre for Biotechnology Information database identified 135 OTUs to species level, 11 to genus level and 1 to order, <2.5% of sequences were classified as unknowns. By comparison a skilled microscopic analyst was able to routinely enumerate only 58 taxonomic groups. Conclusions Metagenetics reveals a previously hidden taxonomic richness, especially for Copepoda and hard-to-identify meroplankton such as Bivalvia, Gastropoda and Polychaeta. It also reveals rare species and parasites. We conclude that Next Generation Sequencing of 18S amplicons is a powerful tool for elucidating the true diversity and species richness of zooplankton communities. While this approach allows for broad diversity assessments of plankton it may become increasingly attractive in future if sequence reference libraries of accurately identified individuals are better populated.

Packet classification by multi-level cutting of the classification space: An algorithmic-architectural solution for IP packet classification in next generation networks

Traditionally, the Internet provides only a “best-effort” service, treating all packets going to the same destination equally. However, providing differentiated services for different users based on their quality requirements is increasingly becoming a demanding issue. For this, routers need to have the capability to distinguish and isolate traffic belonging to different flows. This ability to determine the flow each packet belongs to is called packet classification. Technology vendors are reluctant to support algorithmic solutions for classification due to their non-deterministic performance. Although CAMs are favoured by technology vendors due to their deterministic high lookup rates, they suffer from the problems of high power dissipation and high silicon cost. This paper provides a new algorithmic-architectural solution for packet classification that mixes CAMs with algorithms based on multi-level cutting the classification space into smaller spaces. The provided solution utilizes the geometrical distribution of rules in the classification space. It provides the deterministic performance of CAMs, support for dynamic updates, and added flexibility for system designers.

Taking the Next Step? Achieving another Bill of Rights

The aim of this article is to explore the recent Bill of Rights debate in the UK. This is deliberately located in the UK’s complex ‘national question’ because of the obsessive focus on achieving a proper grounding for human rights. A new form of national human rights protectionism appears to be emerging and merits careful consideration. The article suggests that it is better to acknowledge and accept the existence of a plurality of nationalisms in the UK in these discussions and understand how an essentially ‘British nationalist’ discourse sounds and works in that overall context. The concern is that the Bill of Rights debate is becoming an inadequate surrogate for the more challenging constitutional conversations that are required, and human rights discourse thus invested with expectations of national renewal that it can never meet and does not have the internal resources to resolve. If the process does go forward it may be better to prepare the ground for a deeper and wider constitutional dialogue across these islands than stumble clumsily and divisively into this territory simply via ‘another’ UK Bill of Rights.

Electrical energy storage and Smart Grid technologies to integrate the next generation of Renewable Power Systems

The growth of renewable power sources, distributed generation and the potential for alternative fuelled modes of transport such as electric vehicles has led to concerns over the ability of existing grid systems to facilitate such diverse portfolio mixes in already congested power systems. Internationally the growth in renewable energy sources is driven by government policy targets associated with the uncertainties of fossil fuel supplies, environmental issues and a move towards energy independence. Power grids were traditionally designed as vertically integrated centrally managed entities with fully dispatchable generating plant. Renewable power sources, distributed generation and alternative fuelled vehicles will place these power systems under additional stresses and strains due to their different operational characteristics. Energy storage and smart grid technologies are widely proposed as the tools to integrate these future diverse portfolio mixes within the more conventional power systems. The choice in these technologies is determined not only by their location on the grid system, but by the diversification in the power portfolio mix, the electricity market and the operational demands. This paper presents a high level technical and economic overview of the role and relevance of electrical energy storage and smart grid technologies in the next generation of renewable power systems.

Implementation of a network flow lookup circuit for next-generation packet classifiers

This paper presents a lookup circuit with advanced memory techniques and algorithms that examines network packet headers at high throughput rates. Hardware solutions and test scenarios are introduced to evaluate the proposed approach. The experimental results show that the proposed lookup circuit is able to achieve at least 39 million packet header lookups per second, which facilitates the application of next-generation stateful packet classifications at beyond 20Gbps internet traffic throughput rates.

Validated ligand binding sites in CCK receptors. Next step: Computer aided design of novel CCK ligands

Computer-aided drug design becomes an important part of G-protein coupled receptors (GPCR) drug discovery process that is applied for improving the efficiency of derivation and optimization of novel ligands. It represents the combination of methods that-use-structural information of a receptor binding site of known ligands to design new ligands. In this report, we give a brief description of ligand binding sites in cholecystokinin and gastrin receptors (CK1R and CCK2R) which were delineated using experimental and computational methods, and then, we show how the validated ligand binding sites can be used to design and improve novel ligands. The translation of the knowledge of ligand-binding sites of different GPCRs to computer-aided design of novel ligands is summarized.