Metabolic diversity of progressive kidney disease in 325 patients with type 1 diabetes (the FinnDiane Study)

Type 1 diabetic patients with varying severity of kidney disease were investigated to create multimetabolite models of the disease process. Urinary albumin excretion rate was measured for 3358 patients with type 1 diabetes. Prospective records were available for 1051 patients, of whom 163 showed progression of albuminuria (8.3-year follow-up), and 162 were selected as stable controls. At baseline, serum lipids, lipoprotein subclasses, and low-molecular weight metabolites were quantified by NMR spectroscopy (325 samples). The data were analyzed by the self-organizing map. In cross-sectional analyses, patients with no complications had low serum lipids, less inflammation, and better glycemic control, whereas patients with advanced kidney disease had high serum cystatin-C and sphingomyelin. These phenotype extremes shared low unsaturated fatty acids (UFAs) and phospholipids. Prospectively, progressive albuminuria was associated with high UFAs, phospholipids, and IDL and LDL lipids. Progression at longer duration was associated with high HDL lipids, whereas earlier progression was associated with poor glycemic control, increased saturated fatty acids (SFAs), and inflammation. Diabetic kidney disease consists of diverse metabolic phenotypes: UFAs, phospholipids, IDL, and LDL may be important in the subclinical phase, high SFAs and low HDL suggest accelerated progression, and the sphingolipid pathway in advanced kidney injury deserves further research.     

Indicator groups and congruence of assemblage similarity, species richness and environmental relationships in littoral macroinvertebrates

The rapid decrease of biodiversity and limited resources for surveying it have forced researchers to devise short-cuts for biodiversity surveys and conservation planning. These short-cuts include environmental surrogates, higher taxon surrogates, indicator species and indicator groups. We considered indicator groups as surrogates for wholesale biodiversity and cross-taxon congruence in biodiversity patterns in littoral macroinvertebrates of boreal lakes. Despite the fact that we considered indicator groups amongst a wide variety of taxa, such as two-winged flies, mayflies, caddisflies, beetles, bugs and molluscs, none of the proposed groups possessed all of the qualities of a good indicator taxon for biodiversity surveys and conservation planning. We found generally weak, yet typically significant, relationships between the proposed indicator groups and remaining taxa in both species richness and assemblage similarity. Low congruence was paralleled by somewhat differing relationships of the taxonomic groups to various environmental features of lakes. Furthermore, the relationships of most indicator groups to the environmental features of lakes were not particularly strong. The present findings are unfortunate, because indicator groups did not perform well in predicting the wholesale biodiversity of littoral macroinvertebrates. Thus, there appears to be no short-cut for considering all groups of macroinvertebrates in biodiversity surveys, conservation planning and characterisation of environmental relationships of lake littoral assemblages.     

1H NMR metabonomics approach to the disease continuum of diabetic complications and premature death

Subtle metabolic changes precede and accompany chronic vascular complications, which are the primary causes of premature death in diabetes. To obtain a multimetabolite characterization of these high‐risk individuals, we measured proton nuclear magnetic resonance (¹H NMR) data from the serum of 613 patients with type I diabetes and a diverse spread of complications. We developed a new metabonomics framework to visualize and interpret the data and to link the metabolic profiles to the underlying diagnostic and biochemical variables. Our results indicate complex interactions between diabetic kidney disease, insulin resistance and the metabolic syndrome. We illustrate how a single ¹H NMR protocol is able to identify the polydiagnostic metabolite manifold of type I diabetes and how its alterations translate to clinical phenotypes, clustering of micro‐ and macrovascular complications, and mortality during several years of follow‐up. This work demonstrates the diffuse nature of complex vascular diseases and the limitations of single diagnostic biomarkers. However, it also promises cost‐effective solutions through high‐throughput analytics and advanced computational methods, as applied here in a case that is representative of the real clinical situation.     

Latitudinal variation in sexual dimorphism in life‐history traits of a freshwater fish

Sexual dimorphism is common across the animal kingdom, but the contribution of environmental factors shaping differences between the sexes remains controversial. In ectotherms, life‐history traits are known to correlate with latitude, but sex‐specific responses are not well understood. We analyzed life‐history trait variation between the sexes of European perch (Perca fluviatilis L.), a common freshwater fish displaying larger female size, by employing a wide latitudinal gradient. We expected to find sex‐dependent latitudinal variation in life‐history variables: length at age, length increment, and size at maturity, with females showing consistently higher values than males at all latitudes. We further anticipated that this gender difference would progressively decrease with the increasingly harsh environmental conditions toward higher latitude. We hypothesized that growth and length increment would decrease and size/age at maturity would increase at higher latitudes. Our results confirmed female‐biased sexual size dimorphism at all latitudes and the magnitude of sexual dimorphism diminished with increase in latitude. Growth of both sexes decreased with increase in latitude, and the female latitudinal clines were steeper than those of males. Hence, we challenge two predominant ecological rules (Rensch's and Bergmann's rules) that describe common large‐scale patterns of body size variation. Our data demonstrate that these two rules are not universally applicable in ectotherms or female‐biased species. Our study highlights the importance of sex‐specific differences in life‐history traits along a latitudinal gradient, with evident implications for a wide range of studies from individual to ecosystems level.     

Alignment of chain-like molecules

The steric obstruction model, that describes the enhanced alignment of folded proteins by anisotropic medium, is extended to account for the residual dipolar couplings of chain-like polypeptides. The average alignment of each chain segment is calculated from an ensemble of conformations represented by a spatial probability distribution. The segmental alignment depends on chain length, flexibility and segment's position in the chain. Residual dipolar couplings in turn depend on internuclear vector directions within each fragment. The results of calculations and simulations explain salient features of the experimental data. With this insight residual dipolar couplings can be interpreted to assess the degree of denaturation, local structures and spatial organization of weakly structured proteins.     

Nucleolin expressed at the cell surface is a marker of endothelial cells in angiogenic blood vessels

A tumor-homing peptide, F3, selectively binds to endothelial cells in tumor blood vessels and to tumor cells. Here, we show that the cell surface molecule recognized by F3 is nucleolin. Nucleolin specifically bound to an F3 peptide affinity matrix from extracts of cultured breast carcinoma cells. Antibodies and cell surface biotin labeling revealed nucleolin at the surface of actively growing cells, and these cells bound and internalized fluorescein-conjugated F3 peptide, transporting it into the nucleus. In contrast, nucleolin was exclusively nuclear in serum-starved cells, and F3 did not bind to these cells. The binding and subsequent internalization of F3 were blocked by an antinucleolin antibody. Like the F3 peptide, intravenously injected antinucleolin antibodies selectively accumulated in tumor vessels and in angiogenic vessels of implanted "matrigel" plugs. These results show that cell surface nucleolin is a specific marker of angiogenic endothelial cells within the vasculature. It may be a useful target molecule for diagnostic tests and drug delivery applications.     

MLN64 is involved in actin-mediated dynamics of late endocytic organelles

MLN64 is a late endosomal cholesterol-binding membrane protein of an unknown function. Here, we show that MLN64 depletion results in the dispersion of late endocytic organelles to the cell periphery similarly as upon pharmacological actin disruption. The dispersed organelles in MLN64 knockdown cells exhibited decreased association with actin and the Arp2/3 complex subunit p34-Arc. MLN64 depletion was accompanied by impaired fusion of late endocytic organelles and delayed cargo degradation. MLN64 overexpression increased the number of actin and p34-Arc-positive patches on late endosomes, enhanced the fusion of late endocytic organelles in an actin-dependent manner, and stimulated the deposition of sterol in late endosomes harboring the protein. Overexpression of wild-type MLN64 was capable of rescuing the endosome dispersion in MLN64-depleted cells, whereas mutants of MLN64 defective in cholesterol binding were not, suggesting a functional connection between MLN64-mediated sterol transfer and actin-dependent late endosome dynamics. We propose that local sterol enrichment by MLN64 in the late endosomal membranes facilitates their association with actin, thereby governing actin-dependent fusion and degradative activity of late endocytic organelles.     

How does nitrous oxide reductase interact with its electron donors?—A docking study

Electron transfer reactions are crucial for respiration and denitrification. In this article, we analyze the interaction of nitrous oxide reductase with its electron donors cytochrome c550 and pseudoazurin. Our docking protocol comprises generation of candidate complexes followed by a selection step based on the distance of the donor and acceptor groups in each partner protein. Finally, the structures of the candidate complexes were optimized using a force field calculation, together with a second distance filtering step. The prediction power of this protocol was studied using the crystal structure of the cytochrome c2/photosynthetic reaction center of Rhodobacter sphaeroides as a reference. The results suggest that both cytochrome c550 and pseudoazurin bind at the same hydrophobic surface patch residing near the CuA center of nitrous oxide reductase. The central, well-conserved interaction surface of the donors is hydrophobic, but it is surrounded by numerous lysine side-chains, which interact electrostatically with analogously positioned side-chain carboxylates of the acceptor. The prediction output is an ensemble of energetically similar structures that are rotationally related to each other. While such an ensemble may reflect incomplete prediction power of the docking protocol, it may also manifest a biological situation where there are multiple ways of forming a productive electron transfer complex. Analyses of the predicted structures and the conservation pattern of the amino acid residues suggest the existence of specific electron transfer pathways to and from the CuA center of nitrous oxide reductase.