Compensation for a defective interaction of the hsp70 ssq1 with the mitochondrial Fe-S cluster scaffold isu

Ssq1, a specialized yeast mitochondrial Hsp70, plays a critical role in the biogenesis of proteins containing Fe-S clusters through its interaction with Isu, the scaffold on which clusters are built. Two substitutions within the Ssq1 substrate binding cleft, both of which severely reduced affinity for Isu, had very different effects in vivo. Cells expressing Ssq1(F462S), which had no detectable affinity for Isu, are indistinguishable from Deltassq1 cells, underscoring the importance of the Ssq1-Isu1 interaction in vivo. In contrast, cells expressing Ssq1(V472F), whose affinity for Isu is at least 10-fold lower than that of wild-type Ssq1, had only moderately reduced Fe-S enzyme activities and increased iron levels and grew similarly to wild-type cells. Consistent with the reduced affinity for Isu, the ATPase activity of Ssq1(V472F) was stimulated less well than that of Ssq1 upon addition of Isu and Jac1, the J-protein partner of Ssq1. However, higher concentrations of Jac1 or Isu1, which form a stable complex, could compensate for this defect in stimulation of Ssq1(V472F). Expression of Isu1 was up-regulated 10-fold in ssq1(V472F) compared with wild-type cells, suggesting that formation of a Jac1-Isu1 complex can overcome a lowered affinity of Ssq1 for Isu in vivo as well as in vitro.     

Diversification of Neoaves: integration of molecular sequence data and fossils

Patterns of diversification and timing of evolution within Neoaves, which includes almost 95% of all bird species, are virtually unknown. On the other hand, molecular data consistently indicate a Cretaceous origin of many neoavian lineages and the fossil record seems to support an Early Tertiary diversification. Here, we present the first well-resolved molecular phylogeny for Neoaves, together with divergence time estimates calibrated with a large number of stratigraphically and phylogenetically well-documented fossils. Our study defines several well-supported clades within Neoaves. The calibration results suggest that Neoaves, after an initial split from Galloanseres in Mid-Cretaceous, diversified around or soon after the K/T boundary. Our results thus do not contradict palaeontological data and show that there is no solid molecular evidence for an extensive pre-Tertiary radiation of Neoaves.     

Nuclear DNA from old collections of avian study skins reveals the evolutionary history of the Old World suboscines (Aves, Passeriformes)

Museum study skins represent an invaluable source of DNA for phylogenetics, phylogeography and population genetics. This becomes evident by comparing the number of study skins of birds housed in museums worldwide ( c . 10 million) with the corresponding number of tissue samples (probably fewer than 500 000). While the laboratory techniques used hitherto have primarily allowed PCR-based studies of mitochondrial genes from museum skins, we present here the first avian phylogeny based on a large number of nuclear sequences. The targeted fragment sizes and the properties of the primers used are important contributory factors to obtain good amplification results. In this study we routinely amplified fragments of c. 350 bp nuclear DNA. This advance in methodology opens up a new avenue for the use of avian museum skins, as nuclear DNA is especially useful when studying ancient patterns of diversification. The phylogenetic hypothesis of the Old World suboscines (Eurylaimides) presented herein strongly supports a monophyletic origin of the pittas (Pittidae). The phylogeny further suggests that pittas could be divided into three major groups, in agreement with the external morphological variation found in this group. The broadbills (Eurylaimidae) as currently defined are, on the other hand, found to be a paraphyletic family, as both Sapayoa aenigma and the asities (Philepittidae) are nested among them. Based on the phylogenetic results we suggest a revised classification of the Old World suboscines (Eurylaimides).     

A label-free continuous total-internal-reflection-fluorescence-based immunosensor

In this study, we continuously monitored, second-by-second, concentration changes of two different carbohydrates (maltose and panose) by using monoclonal antibodies in an optical immunosensor based on total internal reflection fluorescence. Earlier studies have demonstrated that these antibodies increase their intrinsic tryptophan fluorescence upon binding of carbohydrate antigens. Using the four immobilized monoclonal antibodies with low affinities (K(d)>10(-6)M), fast kinetics (k(off)>1s(-1)), and high reversibility gave opportunities for developing a continuous immunosensor without any need for regeneration. Since intrinsic fluorescence was used, no extrinsic labeling was necessary. Sensitivity was in the range of 1-5 microM for panose, and 10-15 microM for maltose and the loss of intensity was as low as 3.5% per hour during measurements. Calculations of DeltaH degrees and DeltaS degrees from the temperature dependence of K(d) indicated an enthalpic driven antigen-antibody binding event that is diminished upon antibody immobilization. We feel certain that weakly interacting antibodies can be used in future applications for continuous monitoring where there is a need to achieve instantaneous information on the concentration of an analyte.     

Improved alignment quality by combining evolutionary information, predicted secondary structure and self-organizing maps

Background  

Protein sequence alignment is one of the basic tools in bioinformatics. Correct alignments are required for a range of tasks including the derivation of phylogenetic trees and protein structure prediction. Numerous studies have shown that the incorporation of predicted secondary structure information into alignment algorithms improves their performance. Secondary structure predictors have to be trained on a set of somewhat arbitrarily defined states (e.g. helix, strand, coil), and it has been shown that the choice of these states has some effect on alignment quality. However, it is not unlikely that prediction of other structural features also could provide an improvement. In this study we use an unsupervised clustering method, the self-organizing map, to assign sequence profile windows to "structural states" and assess their use in sequence alignment.     

Mineral diversity in wild plants: benefits and bane for moose

We studied the mineral nutrition ecology of moose, Alces alces , by a comprehensive examination of concentration levels of 18 elements in browsing plants, and in rumen and distal colon contents, respectively. The plants, in total 14 species, included deciduous and evergreen trees, shrubs, herbs, grasses and aquatic macrophytes. Our study was done in four sites in southern Norway and the plants were sampled in spring, summer, autumn and winter to document seasonal trends. The plants were generally characterized by low concentrations of major elements, very low phosphorus: calcium ratios, and the willow Salix aurita – a preferred browse – had high cadmium concentrations, up to 9 ppm (dry mass). Sodium concentrations in terrestrial plants were significantly under the dietary requirement, while levels were sufficient in aquatic plants, which, however, had high concentrations of toxic heavy metals. We suggest that the moose experience a nutritional dilemma as a strong physiological need for sodium results in an overintake of heavy metals. A selective intake of plants rich in heavy metals was corroborated by high heavy metal concentrations in rumen and distal colon. Over all, the plants were characterized by a marked mineral diversity due to element concentration levels that were highly variable between species and sites. Thus, there is a strong link between plant species diversity and mineral diversity, which has a pivotal role for herbivores. It is concluded that a diversity of plant species is a prerequisite for the mineral diversity that the moose needs to obtain essential minerals, not only in sufficient amounts, but also in physiologically balanced proportions.     

Detection and characterization of weak affinity antibody antigen recognition with biomolecular interaction analysis

In biological systems, weak-affinity interactions (association constant, K_a, of less than approximately 10⁴ M ⁻¹) between biomolecules are common and essential to the integrity of such units. However, studies of weak biological interactions are difficult due to the scarcity of analytical methods available for the bioscientist. In this communication, we report on the use of biosensors based on surface plasmon resonance to detect and characterize weak affinity antibody–antigen interactions. Monoclonal antibodies towards carbohydrate antigens were immobilized on sensor surfaces and were used to detect weak binding of the carbohydrate tetraglucose of dissociation constant, K_d, in the millimolar range. Sensorgrams were received in the form of square pulses where the kinetic rate constants were difficult to assess due to the rapid association and dissociation of the antigen to/from the immobilized antibody. © 1997 John Wiley & Sons, Ltd.     

Epizoochorous seed dispersal in relation to seed availability – an experiment with a red fox dummy

Questions: Is the red fox a potential vector for epizoochorous seed dispersal? Can seed attachment and retention be predicted from plant and seed traits? Location: Grasslands in southern Norway. Methods: Epizoochorous seed attachment on the red fox was studied by walking a dummy fox through the vegetation and comparing seeds found on the dummy with the estimated seed availability in the vegetation. Seed retention, i.e. the ability of different seeds to stay on the fox, was estimated in a separate experiment. Seed attachment and retention were related to plant and seed traits using statistical models that account for heteroscedasticity and zero‐inflated data. Results: The majority of seeds attached to the fox originated from a few species, but also species without specific seed traits that are supposed to enhance epizoochory attached at least some seeds to the fox. The probability of seed attachment was positively related to plant height, bristle and hooked seed appendages, and negatively related to winged appendages, seed mass, and seed sphericity. Seed retention was positively related to the seed traits bristles, hooks and pappus. For several species, the results indicate a high potential for dispersal over long distances. Conclusions: In modern agricultural landscapes, large herbivores are often restricted in their mobility or are found at low densities, and other animal vectors may therefore be important for seed dispersal. In our study, a range of plant species were able to disperse by attaching seeds to, and having their seeds retained in, the fox fur some distance. We suggest that the red fox may be an important vector for epizoochorous seed dispersal in the agricultural landscape.