Predicting protein function with hierarchical phylogenetic profiles: The Gene3D phylo-tuner method applied to eukaryotic Genomes

"Phylogenetic profiling'' is based on the hypothesis that during evolution functionally or physically interacting genes are likely to be inherited or eliminated in a codependent manner. Creating presence-absence profiles of orthologous genes is now a common and powerful way of identifying functionally associated genes. In this approach, correctly determining orthology, as a means of identifying functional equivalence between two genes, is a critical and nontrivial step and largely explains why previous work in this area has mainly focused on using presence-absence profiles in prokaryotic species. Here, we demonstrate that eukaryotic genomes have a high proportion of multigene families whose phylogenetic profile distributions are poor in presence-absence information content. This feature makes them prone to orthology mis-assignment and unsuited to standard profile-based prediction methods. Using CATH structural domain assignments from the Gene3D database for 13 complete eukaryotic genomes, we have developed a novel modification of the phylogenetic profiling method that uses genome copy number of each domain superfamily to predict functional relationships. In our approach, superfamilies are subclustered at ten levels of sequence identity from 30% to 100% - and phylogenetic profiles built at each level. All the profiles are compared using normalised Euclidean distances to identify those with correlated changes in their domain copy number. We demonstrate that two protein families will "auto-tune'' with strong co-evolutionary signals when their profiles are compared at the similarity levels that capture their functional relationship. Our method finds functional relationships that are not detectable by the conventional presence - absence profile comparisons, and it does not require a priori any fixed criteria to define orthologous genes

Influence of 4-vinylbenzylation on the rheological and swelling properties of photo activated collagen hydrogels

Covalent functionalisation of collagen has been shown to be a promising strategy to adjust the mechanical properties of highly swollen collagen hydrogels. At the same time, secondary interactions between for example, amino acidic terminations or introduced functional groups also play an important role and are often challenging to predict and control. To explore this challenge, 4-vinylbenzyl chloride (4VBC) and methacrylic anhydride (MA) were reacted with type I collagen, and the swelling and rheological properties of resulting photo-activated hydrogel systems investigated. 4VBC-based hydrogels showed significantly increased swelling ratio, in light of the lower degree of collagen functionalisation, with respect to methacrylated collagen networks, whilst rheological storage moduli were found to be comparable between the two systems. To explore the role of benzyl groups in the mechanical properties of the 4VBC-based collagen system, model chemical force microscopy (CFM) was carried out in aqueous environment with an aromatised probe against an aromatised gold-coated glass slide. A marked increase in adhesion force (F: 0.11±0.01 nN) was measured between aromatised samples, compared to the adhesion force observed between the non-modified probe and a glass substrate (F: 2.64±1.82 nN). These results suggest the formation of additional and reversible π-π stacking interactions in aromatic 4VBC-based networks and explain the remarkable rheological properties of this system in comparison to MA-based hydrogels

Describing whisker morphology of the Carnivora

One of the largest ecological transitions in carnivoran evolution was the shift from terrestrial to aquatic lifestyles, which has driven morphological diversity in skulls and other skeletal structures. In this paper, we investigate the association between those lifestyles and whisker morphology. However, comparing whisker morphology over a range of species is challenging since the number of whiskers and their positions on the mystacial pads vary between species. Also, each whisker will be at a different stage of growth and may have incurred damage due to wear and tear. Identifying a way to easily capture whisker morphology in a small number of whisker samples would be beneficial. Here, we describe individual and species variation in whisker morphology from two-dimensional scans in red fox, European otter and grey seal. A comparison of long, caudal whiskers shows inter-species differences most clearly. We go on to describe global whisker shape in 24 species of carnivorans, using linear approximations of curvature and taper, as well as traditional morphometric methods. We also qualitatively examine surface texture, or the presence of scales, using scanning electron micrographs. We show that gross whisker shape is highly conserved, with whisker curvature and taper obeying simple linear relationships with length. However, measures of whisker base radius, length, and maybe even curvature, can vary between species and substrate preferences. Specifically, the aquatic species in our sample have thicker, shorter whiskers that are smoother, with less scales present than those of terrestrial species. We suggest that these thicker whiskers may be stiffer and able to maintain their shape and position during underwater sensing, but being stiffer may also increase wear

Instability of 8E5 calibration standard revealed by digital PCR risks inaccurate quantification of HIV DNA in clinical samples by qPCR

Establishing a cure for HIV is hindered by the persistence of latently infected cells which constitute the viral reservoir. Real-time qPCR, used for quantification of this reservoir by measuring HIV DNA, requires external calibration; a common choice of calibrator is the 8E5 cell line, which is assumed to be stable and to contain one HIV provirus per cell. In contrast, digital PCR requires no external calibration and potentially provides ‘absolute’ quantification. We compared the performance of qPCR and dPCR in quantifying HIV DNA in 18 patient samples. HIV DNA was detected in 18 by qPCR and in 15 by dPCR, the difference being due to the smaller sample volume analysed by dPCR. There was good quantitative correlation (R2 = 0.86) between the techniques but on average dPCR values were only 60% of qPCR values. Surprisingly, investigation revealed that this discrepancy was due to loss of HIV DNA from the 8E5 cell calibrant. 8E5 extracts from two other sources were also shown to have significantly less than one HIV DNA copy per cell and progressive loss of HIV from 8E5 cells during culture was demonstrated. We therefore suggest that the copy number of HIV in 8E5 extracts be established by dPCR prior to use as calibrator

A dynamic network approach for the study of human phenotypes

The use of networks to integrate different genetic, proteomic, and metabolic datasets has been proposed as a viable path toward elucidating the origins of specific diseases. Here we introduce a new phenotypic database summarizing correlations obtained from the disease history of more than 30 million patients in a Phenotypic Disease Network (PDN). We present evidence that the structure of the PDN is relevant to the understanding of illness progression by showing that (1) patients develop diseases close in the network to those they already have; (2) the progression of disease along the links of the network is different for patients of different genders and ethnicities; (3) patients diagnosed with diseases which are more highly connected in the PDN tend to die sooner than those affected by less connected diseases; and (4) diseases that tend to be preceded by others in the PDN tend to be more connected than diseases that precede other illnesses, and are associated with higher degrees of mortality. Our findings show that disease progression can be represented and studied using network methods, offering the potential to enhance our understanding of the origin and evolution of human diseases. The dataset introduced here, released concurrently with this publication, represents the largest relational phenotypic resource publicly available to the research community.Comment: 28 pages (double space), 6 figure

Using read codes to identify patients with irritable bowel syndrome in general practice: a database study

BACKGROUND: Estimates of the prevalence of irritable bowel syndrome (IBS) vary widely, and a large proportion of patients report having consulted their general practitioner (GP). In patients with new onset gastrointestinal symptoms in primary care it might be possible to predict those at risk of persistent symptoms. However, one of the difficulties is identifying patients within primary care. GPs use a variety of Read Codes to describe patients presenting with IBS. Furthermore, in a qualitative study, exploring GPs' attitudes and approaches to defining patients with IBS, GPs appeared reluctant to add the IBS Read Code to the patient record until more serious conditions were ruled out. Consequently, symptom codes such as 'abdominal pain', 'diarrhoea' or 'constipation' are used. The aim of the current study was to investigate the prevalence of recorded consultations for IBS and to explore the symptom profile of patients with IBS using data from the Salford Integrated Record (SIR). METHODS: This was a database study using the SIR, a local patient sharing record system integrating primary, community and secondary care information. Records were obtained for a cohort of patients with gastrointestinal disorders from January 2002 to December 2011. Prevalence rates, symptom recording, medication prescribing and referral patterns were compared for three patient groups (IBS, abdominal pain (AP) and Inflammatory Bowel Disease (IBD)). RESULTS: The prevalence of IBS (age standardised rate: 616 per year per 100,000 population) was much lower than expected compared with that reported in the literature. The majority of patients (69%) had no gastrointestinal symptoms recorded in the year prior to their IBS. However a proportion of these (22%) were likely to have been prescribed NICE guideline recommended medications for IBS in that year. The findings for AP and IBD were similar. CONCLUSIONS: Using Read Codes to identify patients with IBS may lead to a large underestimate of the community prevalence. The IBS diagnostic Read Code was rarely applied in practice. There are similarities with many other medically unexplained symptoms which are typically difficult to diagnose in clinical practice

3-D Ultrastructure of O. tauri: Electron Cryotomography of an Entire Eukaryotic Cell

The hallmark of eukaryotic cells is their segregation of key biological functions into discrete, membrane-bound organelles. Creating accurate models of their ultrastructural complexity has been difficult in part because of the limited resolution of light microscopy and the artifact-prone nature of conventional electron microscopy. Here we explored the potential of the emerging technology electron cryotomography to produce three-dimensional images of an entire eukaryotic cell in a near-native state. Ostreococcus tauri was chosen as the specimen because as a unicellular picoplankton with just one copy of each organelle, it is the smallest known eukaryote and was therefore likely to yield the highest resolution images. Whole cells were imaged at various stages of the cell cycle, yielding 3-D reconstructions of complete chloroplasts, mitochondria, endoplasmic reticula, Golgi bodies, peroxisomes, microtubules, and putative ribosome distributions in-situ. Surprisingly, the nucleus was seen to open long before mitosis, and while one microtubule (or two in some predivisional cells) was consistently present, no mitotic spindle was ever observed, prompting speculation that a single microtubule might be sufficient to segregate multiple chromosomes

Who bullies whom at a garden feeder? Interspecific agonistic interactions of small passerines during a cold winter

Interspecific agonistic interactions are important selective factors for maintaining ecological niches of different species, but their outcome is difficult to predict a priori. Here, we examined the direction and intensity of interspecific interactions in an assemblage of small passerines at a garden feeder, focussing on three finch species of various body sizes. We found that large and mediumsized birds usually initiated and won agonistic interactions with smaller species. Also, the frequency of fights increased with decreasing differences in body size between the participants. Finally, the probability of engaging in a fight increased with the number of birds at the feeder