Can antimicrobial peptides scavenge around a cell in less than a second?

Antimicrobial peptides, which play multiple host-defense roles, have garnered increased experimental focus because of their potential applications in the pharmaceutical and food production industries. While their mechanisms of action are richly debated, models that have been advanced share modes of peptide-lipid interactions that require peptide dynamics. Before the highly cooperative and specific events suggested in these models take place, peptides must undergo an important process of migration along the membrane surface and delivery from their site of binding on the membrane to the actual site of functional performance. This phenomenon, which contributes significantly to antimicrobial function, is poorly understood, largely due to a lack of experimental and computational tools needed to assess it. Here, we use ¹⁵N solid-state nuclear magnetic resonance to obtain molecular level data on the motions of piscidin's amphipathic helices on the surface of phospholipid bilayers. The studies presented here may help contribute to a better understanding of the speed at which the events that lead to antimicrobial response take place. Specifically, from the perspective of the kinetics of cellular processes, we discuss the possibility that piscidins and perhaps many other amphipathic antimicrobial peptides active on the membrane surface may represent a class of fast scavengers rather than static polypeptides attached to the water-lipid interface.     

Site-directed mutagenesis of the Saccharomyces cerevisiae CDC25 gene: effects on mitotic growth and cAMP signalling

Summary A potential membrane-interacting site within the essential growth-controlling carboxy-terminal region of the CDC25 protein was interrupted by a lethal mutation (1461 TyrAsp and 1462 LeuArg). The elimination of two potential phosphorylation sites found in the same region (1489 ThrPro and 1584 SerPro) does not affect growth but completely prevents glucose-induced cAMP signalling in the double mutant, whereas the single mutants produce normal or slightly retarded cAMP signals. A cluster of five potential targets for cAMP-dependent phosphorylation at the amino-terminal region could be deleted without affecting phenotypic properties. It is concluded that the carboxy-terminal 137 residues of the CDC25 protein are involved in three different functions: control of mitotic growth, glucose-induced hyperactivation of adenylate cyclase, and feedback inhibition of cAMP synthesis.     

A systematic search for protein signature sequences.

Signature sequences are contiguous patterns of amino acids 10-50 residues long that are associated with a particular structure or function in proteins. These may be of three types (by our nomenclature): superfamily signatures, remnant homologies, and motifs. We have performed a systematic search through a database of protein sequences to automatically and preferentially find remnant homologies and motifs. This was accomplished in three steps: 1. We generated a nonredundant sequence database. 2. We used BLAST3 (Altschul and Lipman, Proc. Natl. Acad. Sci. U.S.A. 87:5509-5513, 1990) to generate local pairwise and triplet sequence alignments for every protein in the database vs. every other. 3. We selected "interesting" alignments and grouped them into clusters. We find that most of the clusters contain segments from proteins which share a common structure or function. Many of them correspond to signatures previously noted in the literature. We discuss three previously recognized motifs in detail (FAD/NAD-binding, ATP/GTP-binding, and cytochrome b5-like domains) to demonstrate how the alignments generated by our procedure are consistent with previous work and make structural and functional sense. We also discuss two signatures (for N-acetyltransferases and glycerol-phosphate binding) which to our knowledge have not been previously recognized.     

A Functional Group Database: A Charge Density – DARC Approach

The principle of the DARC approach of hierarchical organization is applied to a molecular electron density representation of functional groups, designed to represent some of the large-scale features of biomolecules, especially macromolecules important in biotechnology and bioinformatics. The proposed representation of the hierarchical structure of the interrelations among functional groups and other, chemically identifiable molecular moieties within a molecule, and a weighting scheme assigned to these local molecular components are justified by the internal structures of the actual fuzzy electron density distributions associated with these molecular moieties. These hierarchical relations serve as a basis for the organization of a functional group database, providing a tool for synthesis design and molecular engineering.     

Phylogenetic information improves homology detection.

We present a database search method that is based on phylogenetic trees (treesearch). The method is used to search a protein sequence database for homologs to a protein family. In preparation for the search, a phylogenetic tree is constructed from a given multiple alignment of the family. During the search, each database sequence is temporarily inserted into the tree, thus adding a new edge to the tree. Homology between family and sequence is then judged from the length of this edge. In a comparison of our method to profiles (ISREC pfsearch), two implementations of hidden Markov models (HMMER hmmsearch and SAM hmmscore), and to the family pairwise search (FPS) method on 43 families from the SCOP database based on minimum false-positive counts (min-FPCs), we found a considerable gain in sensitivity. In 69% of the test cases, treesearch showed a min-FPC of at most 50, whereas the two second best methods (hmmsearch and FPS) showed this performance only in 53% cases. A similar impression holds for a large range of min-FPC thresholds. The results demonstrate that phylogenetic information can significantly improve the detection of distant homologies and justify our method as a useful alternative to existing methods.     

活植物信息数据库中的植物编码系统

本文概述了南京中山植物园活植物信息数据库中的植物编码系统,重点介绍了植物编码的生成方法。该系统通过将关系数据库ORACLE与Microsoft C所提供的完备的计算模型与关系查询语言的强功能管理手段结合起来,弥补了现行商用数据库的不足,获得了较高的时空效率。     

Creating,curating and evaluating a mitogenomic reference database to improve regional species identification using environmental DNA

Species detection using eDNA is revolutionizing global capacity to monitor biodiversity. However, the lack of regional, vouchered, genomic sequence information—especially sequence information that includes intraspecific variation—creates a bottleneck for management agencies wanting to harness the complete power of eDNA to monitor taxa and implement eDNA analyses. eDNA studies depend upon regional databases of mitogenomic sequence information to evaluate the effectiveness of such data to detect and identify taxa. We created the Oregon Biodiversity Genome Project to create a database of complete, nearly error-free mitogenomic sequences for all of Oregon's fishes. We have successfully assembled the complete mitogenomes of 313 specimens of freshwater, anadromous and estuarine fishes representing 24 families, 55 genera and 129 species and lineages. Comparative analyses of these sequences illustrate that many regions of the mitogenome are taxonomically informative, that the short (~150 bp) mitochondrial ‘barcode’ regions typically used for eDNA assays do not consistently diagnose for species and that complete single or multiple genes of the mitogenome are preferable for identifying Oregon's fishes. This project provides a blueprint for other researchers to follow as they build regional databases, illustrates the taxonomic value and limits of complete mitogenomic sequences and offers clues as to how current eDNA assays and environmental genomics methods of the future can best leverage this information.     

The Nordic Vegetation Survey - concepts and perspectives

Abstract. The background of the Nordic Vegetation Survey is outlined and the concepts for this international collaboration project are reviewed. The project includes, so far, institutions in Denmark, Faeroes, Finland, Norway and Sweden. We are setting up a common basis for a vegetation database, with a Nordic species list, exchange of data and joint revisions of important Nordic vegetation types. Progress in the Nordic Vegetation Survey is described and the future perspectives indicated.     

The CAMP effect of Actinobacillus pleuropneumoniae is caused by Apx toxins

Abstract Actinobacillus pleuropneumoniae shows synergistic haemolysis when cocultured with Staphylococcus aureus on blood agar plates. This CAMP effect has been attributed to a discrete CAMP factor, but also to the A. pleuropneumoniae -RTX-toxins I, II, and III. We examined the CAMP effect of recombinant Escherichia coli strains that secreted each of these toxins, and of A. pleuropneumoniae mutant strains that were devoid of one or more these toxins. We found that the E. coli strains were CAMP positive, whereas the A. pleuropneumoniae strain devoid of functional toxin genes was CAMP negative. This demonstrated that the CAMP effect of A. pleuropneumoniae is caused by the toxins and that no CAMP factor per se exists.