Inclusive sharing of mass spectrometry imaging data requires a converter for all

With continued efforts towards a single MSI data format, data conversion routines must be made universally available. The benefits of a common imaging format, imzML, are slowly becoming more widely appreciated but the format remains to be used by only a small proportion of imaging groups. Increased awareness amongst researchers and continued support from major MS vendors in providing tools for converting proprietary formats into imzML are likely to result in a rapidly increasing uptake of the format. It is important that this does not lead to the exclusion of researchers using older or unsupported instruments. We describe an open source converter, imzMLConverter, to ensure against this. We propose that proprietary formats should first be converted to mzML using one of the widely available converters, such as msconvert and then use imzMLConverter to convert mzML to imzML. This will allow a wider audience to benefit from the imzML format immediately.     

Recovery from the most profound mass extinction of all time

The end-Permian mass extinction, 251 million years (Myr) ago, was the most devastating ecological event of all time, and it was exacerbated by two earlier events at the beginning and end of the Guadalupian, 270 and 260 Myr ago. Ecosystems were destroyed worldwide, communities were restructured and organisms were left struggling to recover. Disaster taxa, such as Lystrosaurus, insinuated themselves into almost every corner of the sparsely populated landscape in the earliest Triassic, and a quick taxonomic recovery apparently occurred on a global scale. However, close study of ecosystem evolution shows that true ecological recovery was slower. After the end-Guadalupian event, faunas began rebuilding complex trophic structures and refilling guilds, but were hit again by the end-Permian event. Taxonomic diversity at the alpha (community) level did not recover to pre-extinction levels; it reached only a low plateau after each pulse and continued low into the Late Triassic. Our data showed that though there was an initial rise in cosmopolitanism after the extinction pulses, large drops subsequently occurred and, counter-intuitively, a surprisingly low level of cosmopolitanism was sustained through the Early and Middle Triassic.     

Body mass estimation in xenarthra: A predictive equation suitable for all quadrupedal terrestrial placentals?

The Magnorder Xenarthra includes strange extinct groups, like glyptodonts, similar to large armadillos, and ground sloths, terrestrial relatives of the extant tree sloths. They have created considerable paleobiological interest in the last decades; however, the ecology of most of these species is still controversial or unknown. The body mass estimation of extinct species has great importance for paleobiological reconstructions. The commonest way to estimate body mass from fossils is through linear regression. However, if the studied species does not have similar extant relatives, the allometric pattern described by the regression could differ from those shown by the extinct group. That is the case for glyptodonts and ground sloths. Thus, stepwise multiple regression were developed including extant xenarthrans (their taxonomic relatives) and ungulates (their size and ecological relatives). Cases were weighted to maximize the taxonomic evenness. Twenty‐eight equations were obtained. The distribution of the percent of prediction error (%PE) was analyzed between taxonomic groups (Perissodactyla, Artiodactyla, and Xenarthra) and size groups (0–20 kg, 20–300 kg, and more than 300 kg). To assess the predictive power of the functions, equations were applied to species not included in the regression development [test set cross validation, (TSCV)]. Only five equations had a homogeneous %PE between the aforementioned groups. These were applied to five extinct species. A mean body mass of 80 kg was estimated for Propalaehoplophorus australis (Cingulata: Glyptodontidae), 594 kg for Scelidotherium leptocephalum (Phyllophaga: Mylodontidae), and 3,550.7 kg for Lestodon armatus (Phyllophaga: Mylodontidae). The high scatter of the body mass estimations obtained for Catonyx tarijensis (Phyllophaga: Mylodontidae) and Thalassocnus natans (Phyllophaga: Megatheriidae), probably due to different specializations, prevented us from predicting its body mass. Surprisingly, although obtained from ungulates and xenarthrans, these five selected equations were also able to predict the body mass of species from groups as different as rodents, carnivores, hyracoideans, or tubulidentates. This result suggests the presence of a complex common allometric pattern for all quadrupedal placentals. J. Morphol., 2008. © 2008 Wiley‐Liss, Inc.     

Networks for all

A report on the Cold Spring Harbor Laboratory/Wellcome Trust conference on Network Biology, Hinxton, UK, 27-31 August 2008.     

Functional annotation prediction: all for one and one for all

In an era of rapid genome sequencing and high-throughput technology, automatic function prediction for a novel sequence is of utter importance in bioinformatics. While automatic annotation methods based on local alignment searches can be simple and straightforward, they suffer from several drawbacks, including relatively low sensitivity and assignment of incorrect annotations that are not associated with the region of similarity. ProtoNet is a hierarchical organization of the protein sequences in the UniProt database. Although the hierarchy is constructed in an unsupervised automatic manner, it has been shown to be coherent with several biological data sources. We extend the ProtoNet system in order to assign functional annotations automatically. By leveraging on the scaffold of the hierarchical classification, the method is able to overcome some frequent annotation pitfalls.     

Use of information dependent acquisition mass spectra and sequential window acquisition of all theoretical fragment-ion mass spectra for fruit juices metabolomics and authentication

Metabolomics - The metabolic alterations reflecting the influence of prostate cancer cells can be captured through metabolomic profiling. To characterize the plasma metabolomic profile in prostatic...     

Examining troughs in the mass distribution of all theoretically possible tryptic peptides

This work describes the mass distribution of all theoretically possibly tryptic peptides made of 20 amino acids, up to the mass of 3 kDa, with resolution of 0.001 Da. We characterize regions between the peaks of the distribution, including gaps (forbidden zones) and low-populated areas (quiet zones). We show how the gaps shrink over the mass range and when they completely disappear. We demonstrate that peptide compositions in quiet zones are less diverse than those in the peaks of the distribution and that by eliminating certain types of unrealistic compositions the gaps in the distribution may be increased. The mass distribution is generated using a parallel implementation of a recursive procedure that enumerates all amino acid compositions. It allows us to enumerate all compositions of tryptic peptides below 3 kDa in 48 min using a computer cluster with 12 Intel Xeon X5650 CPUs (72 cores). The results of this work can be used to facilitate protein identification and mass defect labeling in mass spectrometry-based proteomics experiments.     

Annotations for all by all - the BioSapiens network

The BioSapiens network has developed a distributed infrastructure for genome and proteome annotation by laboratories anywhere in the world.     

Mimicry for all modalities

Mimicry is a canonical example of adaptive signal design. In principle, what constitutes mimicry is independent of the taxonomic identity of the mimic, the ecological context in which it operates, and the sensory modality through which it is expressed. However, in practice the study of mimicry is inconsistent across research fields, with theoretical and empirical advances often failing to cross taxonomic and sensory divides. We propose a novel conceptual framework whereby mimicry evolves if a receiver perceives the similarity between a mimic and a model and as a result confers a selective benefit onto the mimic. Here, misidentification and/or deception are no longer formal requirements, and mimicry can evolve irrespective of the underlying proximate mechanisms. The centrality of receiver perception in this framework enables us to formally distinguish mimicry from perceptual exploitation and integrate mimicry and multicomponent signalling theory for the first time. In addition, it resolves inconsistencies in our understanding of the role of learning in mimicry evolution, and shows that imperfect mimicry is expected to be the norm. Mimicry remains a key model for understanding signal evolution and cognition, and we recommend the adoption of a unified approach to stimulate future interdisciplinary developments in this fascinating area of research.     

Cryonics for all?

In fascinating recent work, some philosophers have argued that it would be morally permissible and prudentially rational to sign up for cryonics—if you can afford the price tag of the procedure. In this paper I ask: why not share the elixir of extended life with everyone? Should governments financially support, positively encourage, or even require people to undergo cryonics? From a general principle of beneficence, I construct a formal argument for cryonics promotion policies. I consider the objection that a subset of these policies would violate autonomy, but I argue that—to the contrary—considerations of autonomy weigh in their favour. I then consider objections based on cost and population, but argue that neither is fatal. Finally, I raise the objection that I believe poses the most serious challenge: that those who revive the cryonically preserved might inflict suffering upon them.     

The chromosomal passenger complex: one for all and all for one

The chromosomal passenger complex-composed of Aurora B kinase and its regulatory subunits INCENP, Survivin, and Borealin-modulates multiple events during mitosis. In this issue, Jeyaprakash et al. (2007) report the crystal structure of the regulatory subunit complex and reveal how interactions between these proteins promote the targeting and function of the chromosomal passenger complex during mitosis.