Comparison of normalisation methods for surface-enhanced laser desorption and ionisation (SELDI) time-of-flight (TOF) mass spectrometry data

Background  

Mass spectrometry for biological data analysis is an active field of research, providing an efficient way of high-throughput proteome screening. A popular variant of mass spectrometry is SELDI, which is often used to measure sample populations with the goal of developing (clinical) classifiers. Unfortunately, not only is the data resulting from such measurements quite noisy, variance between replicate measurements of the same sample can be high as well. Normalisation of spectra can greatly reduce the effect of this technical variance and further improve the quality and interpretability of the data. However, it is unclear which normalisation method yields the most informative result.     

Antarctic patterns of shallow subtidal habitat and inhabitants in Wilke’s Land

Studies of east Antarctic marine assemblages on hard substrata are rare. In relation to sea-ice breakout, we assessed benthic patterns of habitat and inhabitants between islands and bays at each of two depths (6 and 12 m) across the Windmill Islands coast. Island sites experience sea-ice breakout in the austral spring, while bay sites typically retain sea-ice cover into the summer and in some places the cover is virtually permanent. Composition of assemblages differed between sheltered bays and exposed islands. Islands were dominated by macroalgae, which also varied with depth. Immediately below the ice–foot zone at 6 m, substratum space were monopolised by foliose red (Palmaria decipiens) and foliose brown (Desmarestia sp.) algae, whereas at 12 m large canopies of Himantothallus grandifolius was abundant. The understorey consisted of a mixture of turfs and encrusting red algae at 6 m, and coralline algae at 12 m. Sheltered bays had large areas of sediment/algal complex and no canopy-forming macroalgae. We found more sponges and hydroids in bays, and more brittle stars around islands. Experiments testing factors that covary with exposure and depth in Antarctica, such as light, sedimentation and ice scour are necessary to determine processes that maintain these striking patterns.     

The H8 antigen of pathogenic Neisseriae

We cloned and sequenced the H8 gene from N. meningitidis FAM18. The predicted amino acid sequence included a consensus lipoprotein signal sequence processing site, consistent with lipid modification that could account for the unusual electrophoretic and solubilization properties of H8. The amino acid sequence was rich in alanine and proline, especially in an imperfectly periodic region near the amino terminus, which encompassed the epitope recognized by available monoclonal antibodies. In a panel of neisserial strains, the presence of DNA homologous to the H8 gene correlated with the expression of an H8 protein. We cloned a gene from N. meningitidis JB515 that was distinct from the H8 gene but encoded a protein also recognized by an anti-H8 monoclonal antibody. Mice were not protected from meningococcemia by passive immunization with such an antibody.     

A refined panel of 42 microsatellite loci to universally genotype catarrhine primates

1. Microsatellite genotyping is an important genetic method for a number of research questions in biology. Given that the traditional fragment length analysis using polyacrylamide gel or capillary electrophoresis has several drawbacks, microsatellite genotyping‐by‐sequencing (GBS) has arisen as a promising alternative. Although GBS mitigates many of the problems of fragment length analysis, issues with allelic dropout and null alleles often remain due to mismatches in primer binding sites and unnecessarily long PCR products. This is also true for GBS in catarrhine primates where cross‐species amplification of loci (often human derived) is common.
2. We therefore redesigned primers for 45 microsatellite loci based on 17 available catarrhine reference genomes. Next, we tested them in singleplex and different multiplex settings in a panel of species representing all major lineages of Catarrhini and further validated them in wild Guinea baboons (Papio papio) using fecal samples.
3. The final panel of 42 microsatellite loci can efficiently be amplified with primers distributed into three amplification pools.
4. With our microsatellite panel, we provide a tool to universally genotype catarrhine primates via GBS from different sample sources in a cost‐ and time‐efficient way, with higher resolution, and comparability among laboratories and species.

     

Biogeography of Banksia in southwestern Australia

Comprehensive new data bases on the taxonomy, distribution, ecology and climate of Banksia (Proteaceae) were used to study the biogeography of the sixty endemic species in southwestern Australia. They occur at the wettest coastal tip, with up to 1.5 m rainfall p.a., 1500 km along the north coast, 1000 km along the south coast and up to 450 km inland to the desert margin, with as low as 0.2 m rainfall p.a. The largest areas (sum of 30´ lat.×30´ long. grid cells) containing banksias were under much more arid climates than those with highest species density. Species density was usually lowest at the climatic extremes. Two nodes of species richness and ten floristic groups, each with a characteristic climate, landscape, vegetation and soil types and suite of indicator and endemic species, were recognized. A case is made for resurrecting the Lesueur (northern node) and Stirling (west portion of the southern node) phytogeographic districts, together with separating the West (east portion of the southern node) from the East Eyre district. These species-rich areas coincide with nutrient impoverished sands and laterite associated with dissected uplands having low, highly sclerophyllous vegetation. The distribution of strongly serotinous species and those with persistent florets is consistent with greater reliance on fire for creating suitable recruitment conditions with increasing aridity. The distribution of needle-leaved species is only partly explained by their superior drought tolerance. A preliminary transplant trial with two Banksia species showed that their distribution was only partly restricted by their current climatic profile.