Building Block and Building Rule: Dual Descriptor Method for Biological Sequence Analysis

The emergence of “Systems Biology” in recent years highlights the systematic viewpoint of bio-system modeling. Building on such a background, Dual Descriptor Method, a generic methodology for biological sequence analysis is proposed. From a systematic perspective, Dual Descriptor is defined as a two element set of Composition Weight Map and Position Weight Function which aim at reflecting the composition and permutation information of a sequence. An alternate training algorithm is provided to get an optimum description of the building patterns of the sequences. In this paper, dual descriptor method has been applied to the analysis of two typical problems of molecular biology: gene identification and the prediction of protein function. Satisfactory and insightful results are achieved. Owing to the generality of this methodology, dual descriptor method has wide application perspective for many problems of pattern recognition, especially those involved in “Systems Biology”

FDserver: A web service for protein folding research

*Summary:* To facilitate the study of protein folding, we have developed a web service for protein folding rate and folding type prediction as well as for the calculation of a variety of topological parameters of protein structure, which is freely available to the community.
*Availability:* http://sdbi.sdut.edu.cn/FDserve

Investigating the topological structure of quenched lattice QCD with overlap fermions by using multi-probing approximation

The topological charge density and topological susceptibility are determined by multi-probing approximation using overlap fermions in quenched SU(3) gauge theory. Then we investigate the topological structure of the quenched QCD vacuum, and compare it with results from the all-scale topological density, the results are consistent. Random permuted topological charge density is used to check whether these structures represent underlying ordered properties. Pseudoscalar glueball mass is extracted from the two-point correlation function of the topological charge density. We study $3$ ensembles of different lattice spacing $a$ with the same lattice volume $16^{3}\times32$, the results are compatible with the results of all-scale topological charge density, and the topological structures revealed by multi-probing are much closer to all-scale topological charge density than that by eigenmode expansion.Comment: 12 pages,34 figure

Protective efficacy of a broadly cross-reactive swine influenza DNA vaccine encoding M2e, cytotoxic T lymphocyte epitope and consensus H3 hemagglutinin

BACKGROUND: Pigs have been implicated as mixing reservoir for the generation of new pandemic influenza strains, control of swine influenza has both veterinary and public health significance. Unlike human influenza vaccines, strains used for commercially available swine influenza vaccines are not regularly replaced, making the vaccines provide limited protection against antigenically diverse viruses. It is therefore necessary to develop broadly protective swine influenza vaccines that are efficacious to both homologous and heterologous virus infections. In this study, two forms of DNA vaccines were constructed, one was made by fusing M2e to consensus H3HA (MHa), which represents the majority of the HA sequences of H3N2 swine influenza viruses. Another was made by fusing M2e and a conserved CTL epitope (NP147-155) to consensus H3HA (MNHa). Their protective efficacies against homologous and heterologous challenges were tested. RESULTS: BALB/c mice were immunized twice by particle-mediated epidermal delivery (gene gun) with the two DNA vaccines. It was shown that the two vaccines elicited substantial antibody responses, and MNHa induced more significant T cell-mediated immune response than MHa did. Then two H3N2 strains representative of different evolutional and antigenic clusters were used to challenge the vaccine-immunized mice (homosubtypic challenge). Results indicated that both of the DNA vaccines prevented homosubtypic virus infections completely. The vaccines’ heterologous protective efficacies were further tested by challenging with a H1N1 swine influenza virus and a reassortant 2009 pandemic strain. It was found that MNHa reduced the lung viral titers significantly in both challenge groups, histopathological observation showed obvious reduction of lung pathogenesis as compared to MHa and control groups. CONCLUSIONS: The combined utility of the consensus HA and the conserved M2e and CTL epitope can confer complete and partial protection against homologous and heterologous challenges, respectively, in mouse model. This may provide a basis for the development of universal swine influenza vaccines

Facile in situ solution synthesis of SnSe/rGO nanocomposites with enhanced thermoelectric performance

Constructing nanostructured composite architectures has been considered as an effective strategy to reduce the lattice thermal conductivity (κL) and enhance the dimensionless figure of merit (ZT) of thermoelectric materials. Herein, a series of SnSe/reduced graphene oxide (rGO)-x (x = 0.1, 0.3, 0.5, 0.7 wt%) nanocomposites are controllably synthesised in situ via a facile single-step bottom-up solution method, where rGO nanosheets are incorporated intimately into the SnSe matrix. Nanocompositing performs two key functions: (i) significantly reducing the lattice thermal conductivity of the material, which can be attributed to enhanced phonon scattering from high-density SnSe/rGO interfaces, and (ii) improving the electrical conductivity over the low temperature range, as result of an increased carrier concentration. The subsequent thermoelectric performance of SnSe/rGO sintered pellets has been optimised by tuning the rGO mass fraction, with SnSe/rGO-0.3 achieving κL = 0.36 W m−1 K−1 at 773 K (cutting the κL of SnSe by 33%) to yield a maximum ZT of 0.91 at 823 K (representing a ∼47% increase compared to SnSe). This study provides a new pathway to improve the thermoelectric performance of polycrystalline SnSe by way of engineering metal chalcogenide/rGO composite architectures at the nanoscale