Phage display in the study of infectious diseases

Microbial infections are dependent on the panoply of interactions between pathogen and host and identifying the molecular basis of such interactions is necessary to understand and control infection. Phage display is a simple functional genomic methodology for screening and identifying protein-ligand interactions and is widely used in epitope mapping, antibody engineering and screening for receptor agonists or antagonists. Phage display is also used widely in various forms, including the use of fragment libraries of whole microbial genomes, to identify peptide-ligand and protein-ligand interactions that are of importance in infection. In particular, this technique has proved successful in identifying microbial adhesins that are vital for colonization.     

2-Aryl indole NK1 receptor antagonists: optimisation of the 2-aryl ring and the indole nitrogen substituent

Novel 2-aryl indole hNK1 receptor ligands were prepared utilising palladium cross-coupling chemistry of a late intermediate as a key step. Compounds with high hNK1 receptor binding affinity and good brain penetration (e.g., 9d) were synthesised.     

The conduction of protons in different stereoisomers of dioxolane-linked gramicidin A channels

Two different stereoisomers of the dioxolane-linked gramicidin A (gA) channels were individually synthesized (the SS and RR dimers;. Science. 244:813-817). The structural differences between these dimers arise from different chiralities within the dioxolane linker. The SS dimer mimics the helicity and the inter- and intramolecular hydrogen bonding of the monomer-monomer association of gA's. In contrast, there is a significant disruption of the helicity and hydrogen bonding pattern of the ion channel in the RR dimer. Single ion channels formed by the SS and RR dimers in planar lipid bilayers have different proton transport properties. The lipid environment in which the different dimers are reconstituted also has significant effects on single-channel proton conductance (g(H)). g(H) in the SS dimer is about 2-4 times as large as in the RR. In phospholipid bilayers with 1 M [H(+)](bulk), the current-voltage (I-V) relationship of the SS dimer is sublinear. Under identical experimental conditions, the I-V plot of the RR dimer is supralinear (S-shaped). In glycerylmonooleate bilayers with 1 M [H(+)](bulk), both the SS and RR dimers have a supralinear I-V plot. Consistent with results previously published (. Biophys. J. 73:2489-2502), the SS dimer is stable in lipid bilayers and has fast closures. In contrast, the open state of the RR channel has closed states that can last a few seconds, and the channel eventually inactivates into a closed state in either phospholipid or glycerylmonooleate bilayers. It is concluded that the water dynamics inside the pore as related to proton wire transfer is significantly different in the RR and SS dimers. Different physical mechanisms that could account for this hypothesis are discussed. The gating of the synthetic gA dimers seems to depend on the conformation of the dioxolane link between gA's. The experimental results provide an important framework for a detailed investigation at the atomic level of proton conduction in different and relatively simple ion channel structures.     

The effects of Arcanobacterium pyogenes on endometrial function in vitro, and on uterine and ovarian function in vivo

Uterine bacterial infection after parturition causes endometritis, perturbs ovarian function and leads to infertility in cattle. Although endometritis is caused by mixed infections, endometrial pathology is associated with the presence of Arcanobacterium pyogenes. The aims of the present study were to determine the effects of A. pyogenes on endometrial function in vitro, and on uterine and ovarian function in vivo. Heat-killed A. pyogenes did not affect the production of prostaglandin F2alpha (PGF) or prostaglandin E(2) (PGE) from endometrial explants, or purified populations of endometrial epithelial or stromal cells. However, the explants produced more PGF and PGE than controls when treated with a bacteria-free filtrate (BFF) cultured from A. pyogenes. Similarly, BFF stimulated PGF and PGE production by epithelial and stromal cells, respectively. So, BFF or control PBS was infused into the uterus of heifers (n=7 per group) for 8 days, starting the day after estrus. Emergence of the follicle wave, dominant follicle or corpus luteum diameter, and peripheral plasma FSH, LH, estradiol, progesterone, PGFM, or acute phase protein concentrations were unaffected by the BFF infusion. In the live animal it is likely that the intact uterine mucosa limits the exposure of the endometrial cells to the exotoxin of A. pyogenes, whereas the cells are readily exposed to the toxin in vitro.     

Scratchpads 2.0: a Virtual Research Environment supporting scholarly collaboration, communication and data publication in biodiversity science

The Scratchpad Virtual Research Environment (http://scratchpads.eu/) is a flexible system for people to create their own research networks supporting natural history science. Here we describe Version 2 of the system characterised by the move to Drupal 7 as the Scratchpad core development framework and timed to coincide with the fifth year of the project's operation in late January 2012. The development of Scratchpad 2 reflects a combination of technical enhancements that make the project more sustainable, combined with new features intended to make the system more functional and easier to use. A roadmap outlining strategic plans for development of the Scratchpad project over the next two years concludes this article.     

Phylogenetic biogeography of the leafy liverwort Herbertus (Jungermanniales, Herbertaceae) based on nuclear and chloroplast DNA sequence data: correlation between genetic variation and geographical distribution

Aim The cosmopolitan genus Herbertus is notorious for having a difficult taxonomy and for the fact that there is limited knowledge of species ranges and relationships. Topologies generated from variable molecular markers are used to discuss biogeographical patterns in Herbertus and to compare them with the geological history of continents and outcomes reported for other land plants. Location Africa, Asia, Azores, Europe, southern South America, northern South America, North America, New Zealand. Methods Phylogenetic analyses of nuclear ribosomal internal transcribed spacer and chloroplast (cp) trnL–trnF sequences of 66 accessions of Herbertus and the outgroup species Triandrophyllum subtrifidum and Mastigophora diclados were used to investigate biogeographical patterns in Herbertus. Areas of putative endemism were defined based on the distribution of species included in the analyses. Maximum parsimony analyses were undertaken to reconstruct ancestral areas and intraspecies migration routes. Results The analyses reveal species‐level cladograms with a correlation between genetic variation and the geographical distribution of the related accessions. The southern South American Herbertus runcinatus is sister to the remainder of the genus, which is split into two main clades. One contains the Neotropical–African Herbertus juniperoideus and the New Zealand/Tasmanian Herbertus oldfieldianus. An African accession of H. juniperoideus is nested within Neotropical accessions. The second main clade includes species that inhabit Asia, the Holarctic, Africa, and northern South America. Maximum parsimony analyses indicate that this clade arose in Asia. Herbertus sendtneri originated in Asia and subsequently colonized the Holarctic and northern South America. An Asian origin and colonization into Africa is indicated for H. dicranus. Main conclusions The current distribution of Herbertus cannot be explained by Gondwanan vicariance. A more feasible explanation of the range is a combination of short‐distance dispersal, rare long‐distance dispersal events (especially into regions that faced floral displacements as a result of climatic changes) extinction, recolonization, and diversification. The African Herbertus flora is a mixture of Asian and Neotropical elements. Southern South America harbours an isolated species. The molecular data indicate partial decoupling of molecular and morphological variation in Herbertus. Biogeographical patterns in Herbertus are not dissimilar to those of other groups of bryophytes, but elucidation of the geographical ranges requires a molecular approach. Some patterns could be the result of maintenance of Herbertus in the inner Tropics during glacial maxima, and dispersal into temperate regions in warm phases.     

Plagiochila virginica A.Evans rather than P. dubia Lindenb. & Gottsche occurs in Macaronesia; placement in sect. Contiguae Carl is supported by ITS sequences of nuclear ribosomal DNA

 Plagiochila dubia Lindenb. & Gottsche is reduced to a synonym of the Neotropical P. patula (Sw.) Lindenb. Specimens from the Canary Islands and Madeira proved to belong to the eastern North American P. virginica A.Evans, new to Europe. Phylogenetic analyses of the internal transcribed spacer regions (ITS1-5.8S-ITS2) of nuclear ribosomal DNA of ten Plagiochila species produced four independent lineages that are well supported by all bootstrap analyses (maximum likelihood, maximum parsimony, and distance). These lineages correspond with the Plagiochila sections Arrectae, Contiguae, Cucullatae and Glaucescentes. Spruce's “Ramiflorae” and “Cauliflorae” may no longer be regarded as monophyletic units of Plagiochila. Received August 19, 2001 Accepted October 11, 2001