Integrative analysis for finding genes and networks involved in diabetes and other complex diseases

We have developed an integrative analysis method combining genetic interactions, identified using type 1 diabetes genome scan data, and a high-confidence human protein interaction network. Resulting networks were ranked by the significance of the enrichment of proteins from interacting regions. We identified a number of new protein network modules and novel candidate genes/proteins for type 1 diabetes. We propose this type of integrative analysis as a general method for the elucidation of genes and networks involved in diabetes and other complex diseases.     

Photografted poly(ethylene glycol) matrix for affinity interaction studies

A poly(ethylene glycol) (PEG)-based matrix for studies of affinity interactions is developed and demonstrated. The PEG matrix, less than 0.1 microm thick, is graft copolymerized onto a cycloolefin polymer from a mixture of PEG methacrylates using a free radical reaction initiated by UV light at 254 nm. The grafting process is monitored in real time, and characteristics such as thickness, homogeneity, relative composition, photostability, and performance in terms of protein resistance in complex biofluids and sensor qualities are investigated with null ellipsometry, infrared spectroscopy, and surface plasmon resonance. The matrix is subsequently modified to contain carboxyl groups, thereby making it possible to immobilize ligands in a controlled and functional manner. Human serum albumin and fibrinogen are immobilized and successfully detected by antibody recognition using surface plasmon resonance. The results are encouraging and suggest that the PEG matrix is suitable for biochip and biosensor applications in demanding biofluids.     

Recommendations for photo‐identification methods used in capture‐recapture models with cetaceans

Capture‐recapture methods are frequently employed to estimate abundance of cetaceans using photographic techniques and a variety of statistical models. However, there are many unresolved issues regarding the selection and manipulation of images that can potentially impose bias on resulting estimates. To examine the potential impact of these issues we circulated a test data set of dorsal fin images from bottlenose dolphins to several independent research groups. Photo‐identification methods were generally similar, but the selection, scoring, and matching of images varied greatly amongst groups. Based on these results we make the following recommendations. Researchers should: (1) determine the degree of marking, or level of distinctiveness, and use images of sufficient quality to recognize animals of that level of distinctiveness; (2) ensure that markings are sufficiently distinct to eliminate the potential for “twins” to occur; (3) stratify data sets by distinctiveness and generate a series of abundance estimates to investigate the influence of including animals of varying degrees of markings; and (4) strive to examine and incorporate variability among analysts into capture‐recapture estimation. In this paper we summarize these potential sources of bias and provide recommendations for best practices for using natural markings in a capture‐recapture framework.     

Phylogenetic placement and population structure of Indo‐Pacific bottlenose dolphins (Tursiops aduncus) off Zanzibar,Tanzania, based on mtDNA sequences

Phylogenetic placement of bottlenose dolphins from Zanzibar, East Africa and putative population differentiation between animals found off southern and northern Zanzibar were examined using variation in mtDNA control region sequences. Samples (n= 45) from animals bycaught in fishing gear and skin biopsies collected during boat surveys were compared to published sequences (n= 173) of Indo‐Pacific bottlenose dolphin, Tursiops aduncus, from southeast Australian waters, Chinese/Indonesian waters, and South African waters (which recently was proposed as a new species) and to published sequences of common bottlenose dolphin, Tursiops truncatus. Bayesian and maximum parsimony analyses indicated a close relationship between Zanzibar and South African haplotypes, which are differentiated from both Chinese/Indonesian and Australian T. aduncus haplotypes. Our results suggest that the dolphins found off Zanzibar should be classified as T. aduncus alongside the South African animals. Further, analyses of genetic differentiation showed significant separation between the T. aduncus found off northern and southern Zanzibar despite the relatively short distance (approximately 80 km) between these areas. Much less differentiation was found between southern Zanzibar and South Africa, suggesting a more recent common evolutionary history for these populations than for the northern and southern Zanzibar populations.     

Limited gene flow may enhance adaptation to local optima in isolated populations of the Roesel's bush cricket (Metrioptera roeselii)

Variation in morphological traits along latitudinal gradients often manifests as size clines. In insects, both positive and negative correlations are seen, and the mechanism behind the response is unclear. We studied variation in seven morphological traits of Roesel's bush cricket, Metrioptera roeselii, sampled from seven latitude-matched-pair populations that were either geographically isolated from or connected to the species continuous distribution range. The aim was to examine whether morphological traits differed between isolated and continuous populations, and whether latitudinal variation was apparent. The data were used to indicate whether variation in trait means originates from plastic responses to the environment or genetic adaptation to local conditions. To evaluate the influence of gene flow on trait means, we analysed the genetic variation in seven microsatellites. Data showed that individuals from isolated populations display a positive relationship between latitude and body size, whereas individuals from continuous populations show little or no such relationship. The combined morphological and genetic data suggest that the isolated populations have adapted to local optima, while gene flow between continuous populations appears to counteract this process.     

Nucleotide modifications and tRNA anticodon-mRNA codon interactions on the ribosome

We have carried out molecular dynamics simulations of the tRNA anticodon and mRNA codon, inside the ribosome, to study the effect of the common tRNA modifications cmo(5)U34 and m(6)A37. In tRNA(Val), these modifications allow all four nucleotides to be successfully read at the wobble position in a codon. Previous data suggest that entropic effects are mainly responsible for the extended reading capabilities, but detailed mechanisms have remained unknown. We have performed a wide range of simulations to elucidate the details of these mechanisms at the atomic level and quantify their effects: extensive free energy perturbation coupled with umbrella sampling, entropy calculations of tRNA (free and bound to the ribosome), and thorough structural analysis of the ribosomal decoding center. No prestructuring effect on the tRNA anticodon stem-loop from the two modifications could be observed, but we identified two mechanisms that may contribute to the expanded decoding capability by the modifications: The further reach of the cmo(5)U34 allows an alternative outer conformation to be formed for the noncognate base pairs, and the modification results in increased contacts between tRNA, mRNA, and the ribosome.     

Temperature and resource availability may interactively affect over-wintering success of juvenile fish in a changing climate

The predicted global warming may affect freshwater systems at several organizational levels, from organism to ecosystem. Specifically, in temperate regions, the projected increase of winter temperatures may have important effects on the over-winter biology of a range of organisms and especially for fish and other ectothermic animals. However, temperature effects on organisms may be directed strongly by resource availability. Here, we investigated whether over-winter loss of biomass and lipid content of juvenile roach (Rutilus rutilus) was affected by the physiologically relatively small (2-5 °C) changes of winter temperatures predicted by the Intergovernmental Panel on Climate Change (IPCC), under both natural and experimental conditions. This was investigated in combination with the effects of food availability. Finally, we explored the potential for a correlation between lake temperature and resource levels for planktivorous fish, i.e., zooplankton biomass, during five consecutive winters in a south Swedish lake. We show that small increases in temperature (+2 °C) affected fish biomass loss in both presence and absence of food, but negatively and positively respectively. Temperature alone explained only a minor part of the variation when food availability was not taken into account. In contrast to other studies, lipid analyses of experimental fish suggest that critical somatic condition rather than critical lipid content determined starvation induced mortality. Our results illustrate the importance of considering not only changes in temperature when predicting organism response to climate change but also food-web interactions, such as resource availability and predation. However, as exemplified by our finding that zooplankton over-winter biomass in the lake was not related to over-winter temperature, this may not be a straightforward task.     

A new species of Otostegia (Lamiaceae) from Somalia

A new species from gypsum plains in northern Somalia, Otostegia ericoidea Ryding is described and illustrated.     

Fluorescent detection of beta-lactamase activity in living Escherichia coli cells via esterase supplementation

The TEM-1 beta-lactamase protein fragment complementation assay was investigated for its applicability in affinity protein-based interaction studies in Escherichia coli, using an affibody-based model system. Results from co-transformation experiments showed that an ampicillin resistant phenotype was specifically associated with cognate affibody-target pairings. Attempts to monitor beta-lactamase complementation in vitro with the fluorescent beta-lactamase substrates CCF2/AM and CCF2 showed that E. coli lacks an esterase activity necessary for activation of the esterified and membrane-permeable CCF2/AM form of the substrate. Interestingly, supplementation of the assay reaction with a purified fungal lipase (cutinase) resulted in efficient activation of CCF2/AM in vitro. Further, periplasmic expression of cutinase allowed for fluorescent discrimination between beta-lactamase positive and negative living E. coli cells using the CCF2/AM substrate, which should open the way for novel applications for this prokaryotic host in protein interaction studies.