Interactions of amidated acids with heparin

Raman and NMR studies are performed to characterize the solution structures of complexes between heparin and a group of amidated acids, which act as delivery agents that facilitate the gastrointestinal absorption of orally administered heparin. At concentrations typically employed for the oral drug delivery of heparin, the contact points between heparin complexed with the delivery agents include points near the OH groups of heparin. The results suggest that heparin interacts rather nonspecifically with the amidated acids as monomers and with self-associated complexes of the delivery agents. It is also found that the carboxyl groups of at least one of the bioactive delivery agents easily protonates when it forms complexes with itself or heparin. This attribute may be one reason why this class of compounds is effective in the oral delivery of heparin.     

Characterization of a novel mutation causing hepatic lipase deficiency among French Canadians

Individuals with hepatic lipase (HL) deficiency are often characterized by elevated levels of triglycerides (TGs) and cholesterol. The aim of the present study was to characterize the molecular defect leading to severe HL deficiency in a Québec-based kindred. In the proband and two of her brothers, the very low to undetectable HL activity resulted from compound heterozygosity for two rare HL gene mutations, a previously unknown missense mutation in exon 5 designated A174T and the previously reported T383M mutation in exon 8 of the HL gene. The mutation at codon 174 resulted in the substitution of alanine for threonine, a polar amino acid, in a highly conserved nonpolar region of the protein involved in the catalytic activity of the enzyme. The severe HL deficiency among the three related compound heterozygotes was associated with a marked TG enrichment of LDL and HDL particles. The two men with severe HL deficiency also presented with abdominal obesity, which appeared to amplify the impact of HL deficiency on plasma TG-rich lipoprotein levels. Our results demonstrated that HL deficiency in this Québec kindred is associated with an abnormal lipoprotein-lipid profile, which may vary considerably in the presence of secondary factors such as abdominal obesity.     

Ligninolytic characteristics of Pleurotus ostreatus strain F6 and its monokaryotic protoplast derivative P19

A stable isolate of Pleurotus ostreatus P19 differing in some morphological and physiological characteristics from its parental wild-type strain F6 was obtained via protoplast isolation during the preparation of strains with altered ligninolytic abilities. The isolate is monokaryotic, does not form clamp-connections, and produces much higher activities of enzymes involved in lignin modification (laccase, manganese peroxidase). Cellulase activity was comparable to that of wild-type strain F6, but the xylanase activity was slightly higher in isolate P19. However, this monokaryotic derivative degrades lignin at a slightly lower rate than its parental strain F6. Electron microscopy observations of wood degradation as a function of mycelium growth were performed on three zones of birch wafers delimited according to the distance from the point of inoculation. The different stages of fungal mycelium growth showed differences in the ultrastructural patterns of the decay not only between the strains P19 and F6, but also depending on the distance from the point of inoculation. This suggests a spatio-temporally controlled secretion of enzymes along the hyphae. The enhanced ability of P19 to degrade the condensed forms of lignin in middle lamellae is correlated to its higher laccase activity.     

The potential role of rodents in the enzootic cycle of Rift Valley fever virus in Senegal

Wild rodents (214) of fourteen species were trapped at seven sites in Senegal. Arvicanthis niloticus and Mastomys erythroleucus were among the most frequently collected species (77.2% of total capture). All rodents were examined for the presence of anti-Rift Valley fever virus (RVFV) antibody; the prevalence over all sampled species was 3.8%, varying widely with respect to species and location. Four of 14 species of rodents were found to have anti-RVFV antibodies: Rattus rattus (one positive of two tested) Mastomys huberti (13.5%), A. niloticus (4.3%), and M. erthroleucus (2.4%). The highest prevalence of anti-RVFV antibody was recorded within the enzootic area of the Senegal River delta, at Richard Toll (9.6%). A. niloticus and M. erythroleucus and a strain of laboratory-bred mice were experimentally inoculated with two strains of RVFV and examined for viremia, illness, seroconversion and mortality. A. niloticus and M. erythroleucus demonstrated a limited resistance to infection, thus potentially allowing for the replication of virus in these animals and making these species possible candidates as hosts in the maintenance cycle of RVFV in nature.     

Identification of an ABCA1-dependent phospholipid-rich plasma membrane apolipoprotein A-I binding site for nascent HDL formation: implications for current models of HDL biogenesis

It is well accepted that both apolipoprotein A-I (apoA-I) and ABCA1 play crucial roles in HDL biogenesis and in the human atheroprotective system. However, the nature and specifics of apoA-I/ABCA1 interactions remain poorly understood. Here, we present evidence for a new cellular apoA-I binding site having a 9-fold higher capacity to bind apoA-I compared with the ABCA1 site in fibroblasts stimulated with 22-(R)-hydroxycholesterol/9-cis-retinoic acid. This new cellular apoA-I binding site was designated "high-capacity binding site" (HCBS). Glyburide drastically reduced (125)I-apoA-I binding to the HCBS, whereas (125)I-apoA-I showed no significant binding to the HCBS in ABCA1 mutant (Q597R) fibroblasts. Furthermore, reconstituted HDL exhibited reduced affinity for the HCBS. Deletion of the C-terminal region of apoA-I (Delta187-243) drastically reduced the binding of apoA-I to the HCBS. Interestingly, overexpressing various levels of ABCA1 in BHK cells promoted the formation of the HCBS. The majority of the HCBS was localized to the plasma membrane (PM) and was not associated with membrane raft domains. Importantly, treatment of cells with phosphatidylcholine-specific phospholipase C, but not sphingomyelinase, concomitantly reduced the binding of (125)I-apoA-I to the HCBS, apoA-I-mediated cholesterol efflux, and the formation of nascent apoA-I-containing particles. Together, these data suggest that a functional ABCA1 leads to the formation of a major lipid-containing site for the binding and the lipidation of apoA-I at the PM. Our results provide a biochemical basis for the HDL biogenesis pathway that involves both ABCA1 and the HCBS, supporting a two binding site model for ABCA1-mediated nascent HDL genesis.     

GBSX: a toolkit for experimental design and demultiplexing genotyping by sequencing experiments

Background

Massive parallel sequencing is a powerful tool for variant discovery and genotyping. To reduce costs, sequencing of restriction enzyme based reduced representation libraries can be utilized. This technology is generally referred to as Genotyping By Sequencing (GBS). To deal with GBS experimental design and initial processing specific bioinformatic tools are needed.

Results

GBSX is a package that assists in selecting the appropriate enzyme and the design of compatible in-line barcodes. Post sequencing, it performs optimized demultiplexing using these barcodes to create fastq files per barcode which can easily be plugged into existing variant analysis pipelines. Here we demonstrate the usability of the GBSX toolkit and demonstrate improved in-line barcode demultiplexing and trimming performance compared to existing tools.

Conclusions

GBSX provides an easy to use suite of tools for designing and demultiplexing of GBS experiments.     

Ecohydrological gradients and their restoration on the periphery of extracted peatlands

The moss layer transfer technique is effective at restoring extracted peatland surfaces. However, remnant peatlands persist on the periphery of extracted surfaces. These remnant peatlands drop steeply to extracted surfaces, producing artificial ecotones that are more challenging to restore. We asked to what degree natural ecotones at undisturbed reference fens can act as models for the restoration of artificial ecotones around an extracted peatland, and whether management actions can ameliorate conditions in artificial ecotones. We compared changes in elevation, water table, peat, and multiple vegetation characteristics between natural ecotones and unmanaged artificial ecotones. We then clear‐cut peripheral strips, completely filled perimeter canals, and smoothed peripheral slopes around sections of the extracted surfaces to assess whether hydrological conditions improved. Without management, artificial ecotones are not good models of natural ecotones. The elevation gradient is steep, and water tables drop steeply within 8 m of blocked perimeter canals, with possible effects at 25 m. The consequent vegetation had denser tree saplings, faster tree growth, almost no moss cover, and low moss species richness. After these management actions, water tables increased to within approximately 5 cm of those along natural ecotones. Future study is required to assess the extent of vegetation recovery, but these results hold promise for a more holistic rehabilitation of ecotones on the periphery of extracted peatland surfaces. We present recommendations to optimize the management actions on the periphery of extracted peatlands.     

Effects of cell volume regulating osmolytes on glycerol 3-phosphate binding to triosephosphate isomerase

During cell volume regulation, intracellular concentration changes occur in both inorganic and organic osmolytes in order to balance the extracellular osmotic stress and maintain cell volume homeostasis. Generally, salt and urea increase the Km's of enzymes and trimethylamine N-oxide (TMAO) counteracts these effects by decreasing Km's. The hypothesis to account for these effects is that urea and salt shift the native state ensemble of the enzyme toward conformers that are substrate-binding incompetent (BI), while TMAO shifts the ensemble toward binding competent (BC) species. Km's are often complex assemblies of rate constants involving several elementary steps in catalysis, so to better understand osmolyte effects we have focused on a single elementary event, substrate binding. We test the conformational shift hypothesis by evaluating the effects of salt, urea, and TMAO on the mechanism of binding glycerol 3-phosphate, a substrate analogue, to yeast triosephosphate isomerase. Temperature-jump kinetic measurements promote a mechanism consistent with osmolyte-induced shifts in the [BI]/[BC] ratio of enzyme conformers. Importantly, salt significantly affects the binding constant through its effect on the activity coefficients of substrate, enzyme, and enzyme-substrate complex, and it is likely that TMAO and urea affect activity coefficients as well. Results indicate that the conformational shift hypothesis alone does not account for the effects of osmolytes on Km's.