Interactions between glycosaminoglycans and blood coagulation factors: 1. Affinity chromatography of glycosaminoglycans on thrombin-substituted agarose

Various glycosaminoglycans have been subjected to affinity chromatography on immobilized bovine thrombin. Chondroitin sulphate, dermatan sulphate and heparan sulphate variants with a sulphate-to-hexosamine molar ratio of ～ 1 exhibited weak affinities. Heparan sulphate/heparin fractions of higher sulphate content could be separated into material with high and low affinity for thrombin. Removal of N-sulphate followed by N-acetylation did not affect binding, whereas oxidation and cleavage of non-sulphated hexuronate abolished the interaction. Heparan-related molecules of high thrombin-affinity comprised sequences where large blocks of sulphated iduronate-containing repeats were joined via a few repeats carrying non-sulphated iduronate or glucuronate to form continuous segments that were larger than decasaccharide.     

Variation of colony types in the antFormica cinerea

Summary Formica cinerea is a rare ant species in northern Europe where it occurs in few isolated populations. Estimates of genetic relatedness among worker nestmates revealed very different colonial structures. Relatedness was g = 0.81 in one population, and g = –0.03 and = 0.01 in two others. These results indicate that some populations of the species have mainly monogynous colonies (perhaps with monandrous queens), whereas others consist of polygynous and possibly polydomous colonies. Genetic differentiation of closely located populations suggests restricted dispersal.     

Allele imputation for the killer cell immunoglobulin-like receptor KIR3DL1/S1

Highly polymorphic interaction of KIR3DL1 and KIR3DS1 with HLA class I ligands modulates the effector functions of natural killer (NK) cells and some T cells. This genetically determined diversity affects severity of infections, immune-mediated diseases, and some cancers, and impacts the course of immunotherapies, including transplantation. KIR3DL1 is an inhibitory receptor, and KIR3DS1 is an activating receptor encoded by the KIR3DL1/S1 gene that has more than 200 diverse and divergent alleles. Determination of KIR3DL1/S1 genotypes for medical application is hampered by complex sequence and structural variation, requiring targeted approaches to generate and analyze high-resolution allele data. To overcome these obstacles, we developed and optimized a model for imputing KIR3DL1/S1 alleles at high-resolution from whole-genome SNP data. We designed the model to represent a substantial component of human genetic diversity. Our Global imputation model is effective at genotyping KIR3DL1/S1 alleles with an accuracy ranging from 88% in Africans to 97% in East Asians, with mean specificity of 99% and sensitivity of 95% for alleles >1% frequency. We used the established algorithm of the HIBAG program, in a modification named Pulling Out Natural killer cell Genomics (PONG). Because HIBAG was designed to impute HLA alleles also from whole-genome SNP data, PONG allows combinatorial diversity of KIR3DL1/S1 with HLA-A and -B to be analyzed using complementary techniques on a single data source. The use of PONG thus negates the need for targeted sequencing data in very large-scale association studies where such methods might not be tractable.     

The relationship between emergence from spawning gravel and growth in farmed rainbow trout Oncorhynchus mykiss

The relationship between the timing of emergence from spawning gravel and growth after emergence was investigated in farmed Oncorhynchus mykiss. A relationship between the time of emergence and growth became evident after 6 months of rearing, where individuals with an intermediate emergence time had grown larger compared with early and late emerging individuals.     

Functional and Molecular Effects of Arginine Butyrate and Prednisone on Muscle and Heart in the mdx Mouse Model of Duchenne Muscular Dystrophy

Background

The number of promising therapeutic interventions for Duchenne Muscular Dystrophy (DMD) is increasing rapidly. One of the proposed strategies is to use drugs that are known to act by multiple different mechanisms including inducing of homologous fetal form of adult genes, for example utrophin in place of dystrophin.

Methodology/Principal Findings

In this study, we have treated mdx mice with arginine butyrate, prednisone, or a combination of arginine butyrate and prednisone for 6 months, beginning at 3 months of age, and have comprehensively evaluated the functional, biochemical, histological, and molecular effects of the treatments in this DMD model. Arginine butyrate treatment improved grip strength and decreased fibrosis in the gastrocnemius muscle, but did not produce significant improvement in muscle and cardiac histology, heart function, behavioral measurements, or serum creatine kinase levels. In contrast, 6 months of chronic continuous prednisone treatment resulted in deterioration in functional, histological, and biochemical measures. Arginine butyrate-treated mice gene expression profiling experiments revealed that several genes that control cell proliferation, growth and differentiation are differentially expressed consistent with its histone deacetylase inhibitory activity when compared to control (saline-treated) mdx mice. Prednisone and combination treated groups showed alterations in the expression of genes that control fibrosis, inflammation, myogenesis and atrophy.

Conclusions/Significance

These data indicate that 6 months treatment with arginine butyrate can produce modest beneficial effects on dystrophic pathology in mdx mice by reducing fibrosis and promoting muscle function while chronic continuous treatment with prednisone showed deleterious effects to skeletal and cardiac muscle. Our results clearly indicate the usefulness of multiple assays systems to monitor both beneficial and toxic effects of drugs with broad range of in vivo activity.     

Fine root dynamics in a Norway spruce forest (Picea abies (L.) Karst) in eastern Sweden

The annual dynamics of live and dead fine roots for trees and the field layer species and live/dead ratios were investigated at a coniferous fern forest (Picea abies L. Karts) in Sweden. Our methods of estimating the average amount of fine roots involved the periodic sampling of fine roots in sequential cores on four sampling occasions. The highest live/dead ratio was found in the upper part of the humus layer for both tree and field-layer species and decreased with depth. Most tree fine roots on the four sampling occasions were found in the mineral soil horizon, where 86, 81, 85 and 89% of <1 mm and 89, 88, 89 and 92% of <2 mm diameter of the total amounts of live fine roots in the soil profile were found. The mean amounts of live fine roots of tree species for the total soil profile on the four sampling occasions was 317, 150, 139 and 248 g m^?2 for <1 mm and 410, 225, 224 and 351 g m^?2 for <2 mm diameter fine roots. The related amount of dead fine roots was 226, 321, 176 and 299 g m^?2 and 294, 424, 282 and 381 g m^?2, respectively. Average amounts of live and dead fine-roots and live/dead ratios from other Picea abies forest ecosystems were within the range of our estimates. The production of fine roots, <1 and <2 mm in diameter, estimated from the annual increments in live fine roots, was 207 and 303 g m^?2. The related accumulation of dead fine roots was 257 and 345 g m^?2, The turnover rate of tree fine roots <1 mm in diameter in the total soil profile amounted to 0.7 yr^?1 for live and 0.8 yr^?1 for dead fine roots. The related turnover rates for tree fine roots <2 mm were 0.4 yr^?1 and 0.7 yr^?1. Our data, although based on minimum estimates of the annual fluxes of live and dead fine roots, suggests a carbon flow to the forest soil from dead fine-roots even more substantial than from the needle litter fall. Fine-root data from several Picea abies forest ecosystems, suggest high turnover rates of both live and dead tree fine-roots.     

Temporal change in inbreeding depression in life‐history traits in captive populations of guppy (Poecilia reticulata): evidence for purging?

Inbreeding depression, which generally affects the fitness of small populations, may be diminished by purging recessive deleterious alleles when inbreeding persists over several generations. Evidence of purging remains rare, especially because of the difficulties of separating the effects of various factors affecting fitness in small populations. We compared the expression of life-history traits in inbred populations of guppy (Poecilia reticulata) with contemporary control populations over 10 generations in captivity. We estimated inbreeding depression as the difference between the two types of populations at each generation. After 10 generations, the inbreeding coefficient reached a maximum value of 0.56 and 0.16 in the inbred and control populations, respectively. Analysing changes in the life-history traits across generations showed that inbreeding depression in clutch size and offspring survival increased during the first four to six generations in the populations from the inbred treatment and subsequently decreased as expected if purging occurred. Inbreeding depression in two other traits was weaker but showed similar changes across generations. The loss of six populations in the inbred treatment indicates that removal of deleterious alleles also occurred by extinction of populations that presumably harboured high genetic load.     

Insulin analog with additional disulfide bond has increased stability and preserved activity

Insulin is a key hormone controlling glucose homeostasis. All known vertebrate insulin analogs have a classical structure with three 100% conserved disulfide bonds that are essential for structural stability and thus the function of insulin. It might be hypothesized that an additional disulfide bond may enhance insulin structural stability which would be highly desirable in a pharmaceutical use. To address this hypothesis, we designed insulin with an additional interchain disulfide bond in positions A10/B4 based on Cα‐Cα distances, solvent exposure, and side‐chain orientation in human insulin (HI) structure. This insulin analog had increased affinity for the insulin receptor and apparently augmented glucodynamic potency in a normal rat model compared with HI. Addition of the disulfide bond also resulted in a 34.6°C increase in melting temperature and prevented insulin fibril formation under high physical stress even though the C‐terminus of the B‐chain thought to be directly involved in fibril formation was not modified. Importantly, this analog was capable of forming hexamer upon Zn addition as typical for wild‐type insulin and its crystal structure showed only minor deviations from the classical insulin structure. Furthermore, the additional disulfide bond prevented this insulin analog from adopting the R‐state conformation and thus showing that the R‐state conformation is not a prerequisite for binding to insulin receptor as previously suggested. In summary, this is the first example of an insulin analog featuring a fourth disulfide bond with increased structural stability and retained function.