Structure–activity relationships in 1,4-benzodioxan-related compounds. 10. Novel α1-adrenoreceptor antagonists related to openphendioxan: Synthesis,biological evaluation,and α1d computational study

A series of novel openphendioxan analogues were synthesized and tested at α₁-adrenoreceptor (AR) subtypes by binding and functional assays. The α_1d-AR binding profile was also examined by means of 2D, 3D-QSAR together with docking studies. Multiple regression analysis suggested the relevance of adequate number of heteroatoms in the whole molecule and of passive membrane diffusion to enhance α_1d-AR affinity. Docking simulations against a computational structural model of the biological target further proved this evidence and furnished support for chemiometric analysis, where polar, electrostatic, hydrophobic and shape effects of the ortho substituents in the phenoxy terminal, most likely governing ligand binding, helped the depiction of pharmacophore hypothesis for the examined ligands data set.     

Single cell oils of the cold-adapted oleaginous yeast <Emphasis Type="Italic">Rhodotorula glacialis</Emphasis> DBVPG 4785

Background  

The production of microbial lipids has attracted considerable interest during the past decade since they can be successfully used to produce biodiesel by catalyzed transesterification with short chain alcohols. Certain yeast species, including several psychrophilic isolates, are oleaginous and accumulate lipids from 20 to 70% of biomass under appropriate cultivation conditions. Among them, Rhodotorula glacialis is a psychrophilic basidiomycetous species capable to accumulate intracellular lipids.     

Pantothenate Kinase 1 Is Required to Support the Metabolic Transition from the Fed to the Fasted State

Coenzyme A (CoA) biosynthesis is regulated by the pantothenate kinases (PanK), of which there are four active isoforms. The PanK1 isoform is selectively expressed in liver and accounted for 40% of the total PanK activity in this organ. CoA synthesis was limited using a Pank1 ^−/− knockout mouse model to determine whether the regulation of CoA levels was critical to liver function. The elimination of PanK1 reduced hepatic CoA levels, and fasting triggered a substantial increase in total hepatic CoA in both Pank1 ^−/− and wild-type mice. The increase in hepatic CoA during fasting was blunted in the Pank1 ^−/− mouse, and resulted in reduced fatty acid oxidation as evidenced by abnormally high accumulation of long-chain acyl-CoAs, acyl-carnitines, and triglycerides in the form of lipid droplets. The Pank1 ^−/− mice became hypoglycemic during a fast due to impaired gluconeogenesis, although ketogenesis was normal. These data illustrate the importance of PanK1 and elevated liver CoA levels during fasting to support the metabolic transition from glucose utilization and fatty acid synthesis to gluconeogenesis and fatty acid oxidation. The findings also suggest that PanK1 may be a suitable target for therapeutic intervention in metabolic disorders that feature hyperglycemia and hypertriglyceridemia.     

MIDAS: software for analysis and visualisation of interallelic disequilibrium between multiallelic markers

Background  

Various software tools are available for the display of pairwise linkage disequilibrium across multiple single nucleotide polymorphisms. The HapMap project also presents these graphics within their website. However, these approaches are limited in their use of data from multiallelic markers and provide limited information in a graphical form.     

A generalization of the PST algorithm: modeling the sparse nature of protein sequences

MOTIVATION: A central problem in genomics is to determine the function of a protein using the information contained in its amino acid sequence. Variable length Markov chains (VLMC) are a promising class of models that can effectively classify proteins into families and they can be estimated in linear time and space. RESULTS: We introduce a new algorithm, called Sparse Probabilistic Suffix Trees (SPST), that identifies equivalence between the contexts of a VLMC. We show that, in many cases, the identification of these equivalence can improve the classification rate of the classical Probabilistic Suffix Trees (PST) algorithm. We also show that better classification can be achieved by identifying representative fingerprints in the amino acid chains, and this variation in the SPST algorithm is called F-SPST.     

NESCA: A new NEMO/IKKgamma and TRAF6 interacting protein

NEMO/IKKγ is the essential regulatory subunit of the IkB Kinase (IKK) complex, required for the activation of Nuclear Factor kB (NF‐kB) in many physiological processes such as inflammation, immunity, apoptosis, or development. NEMO works at a converging point of the NF‐kB pathway as it interacts with upstream signaling molecules to orchestrate its activation. Here we report on the identification of a novel NEMO‐interacting protein, NESCA, an adapter molecule previously shown to be involved in the NGF‐pathway via the TrkA receptor. We demonstrated that NESCA and NEMO interact by their N‐terminal region. Beside to NEMO, we revealed that NESCA directly associates to the E3 ubiquitin ligase TRAF6, which in turn catalyzes NESCA polyubiquitination. Finally, we demonstrated that NESCA overexpression strongly inhibits TRAF6‐mediated polyubiquitination of NEMO. In summary, our results highlight that NESCA represents a novel missing link in the NEMO‐mediated NF‐kB activation pathway. J. Cell. Physiol. 220: 410–417, 2009. © 2009 Wiley‐Liss, Inc.     

Stabilized ferrous gluconate as iron source for food fortification: bioavailability and toxicity studies in rats

The iron bioavailability and acute oral toxicity in rats of a ferrous gluconate compound stabilized with glycine (SFG), designed for food fortification, was studied in this work by means of the prophylactic method and the Wilcoxon method, respectively. For the former studies, SFG was homogeneously added to a basal diet of low iron content, reaching a final iron concentration of 20.1 +/- 2.4 mg Fe/kg diet. A reference standard diet using ferrous sulfate as an iron-fortifying source (19.0 +/- 2.1 mg Fe/kg diet) and a control diet without iron additions (9.3 +/- 1.4 mg Fe/kg diet) were prepared in the laboratory in a similar way. These diets were administered to three different groups of weaning rats during 23 d as the only type of solid nourishment. The iron bioavailability of SFG was calculated as the relationship between the mass of iron incorporated into hemoglobin during the treatment and the total iron intake per animal. This parameter resulted in 36.6 +/- 6.2% for SFG, whereas a value of 35.4 +/- 8.0% was obtained for ferrous sulfate. The acute toxicological studies were performed in two groups of 70 female and 70 male Sprague-Dawley rats that were administered increasing doses of iron from SFG. The LD50 values of 1775 and 1831 mg SFG/kg body wt were obtained for female and male rats, respectively, evidencing that SFG can be considered as a safe compound from a toxicological point of view.     

Association of the adaptor TANK with the I kappa B kinase (IKK) regulator NEMO connects IKK complexes with IKK epsilon and TBK1 kinases

Canonical activation of NF-kappa B is mediated via phosphorylation of the inhibitory I kappa B proteins by the I kappa B kinase complex (IKK). IKK is composed of a heterodimer of the catalytic IKK alpha and IKK beta subunits and a presumed regulatory protein termed NEMO (NF-kappa B essential modulator) or IKK gamma. NEMO/IKK gamma is indispensable for activation of the IKKs in response to many signals, but its mechanism of action remains unclear. Here we identify TANK (TRAF family member-associated NF-kappa B activator) as a NEMO/IKK gamma-interacting protein via yeast two-hybrid analyses. This interaction is confirmed in mammalian cells, and the domains required are mapped. TANK was previously shown to assist NF-kappa B activation in a complex with TANK-binding kinase 1 (TBK1) or IKK epsilon, two kinases distantly related to IKK alpha/beta, but the underlying mechanisms remained unknown. Here we show that TBK1 and IKK epsilon synergize with TANK to promote interaction with the IKKs. The TANK binding domain within NEMO/IKK gamma is required for proper functioning of this IKK subunit. These results indicate that TANK can synergize with IKK epsilon or TBK1 to link them to IKK complexes, where the two kinases may modulate aspects of NF-kappa B activation.     

TUCAN/CARDINAL and DRAL participate in a common pathway for modulation of NF-kappaB activation

Prior to genome sequencing, information on base composition (GC level) and its variation in mammalian genomes could be obtained using density gradient ultracentrifugation. Analyses using this approach led to the conclusion that mammalian genomes are organized into mosaics of fairly homogeneous regions, called isochores. We present an initial compositional overview of the chromosomes of the recently available draft human genome sequence, in the form of color-coded moving window plots and corresponding GC level histograms. Results obtained from the draft human genome sequence agree well with those obtained or deduced earlier from CsCl experiments. The draft sequence now permits the visualization of the mosaic organization of the human genome at the DNA sequence level.     

FINE STRUCTURE OF DWARF MALES IN OEDOGONIUM PLUVIALE (CHLOROPHYCEAE)

Oedogonium pluviale Nordstedt is nannandrous, described as possessing single-celled dwarf males. In some studies the dwarf males appear to have a reduced, lens-shaped pedicular portion whose nature and structure remain unclear. The present study aims to: 1) establish whether dwarf males of O. pluviale are single- or two-celled, 2) describe the different developmental stages of dwarf males, and 3) understand the nature of the pedicular portion. Mitotic division of the dwarf male was observed, but neither upwards phycoplast migration nor synthesis of a gametangial cell wall occurred. Instead, the phycoplast and cell plate migrated downwards, producing a small pedicular portion whose content then degenerated. The antheridium occupied most of the dwarf male wall. Gametogenesis thus took place inside the wall of the young dwarf male (internal gametangium). Because the pedicular cell degenerated, we define this type of dwarf male as pseudo-single-celled to differentiate it from a true single-celled dwarf male. The antheridial nucleus underwent one mitotic division to give rise to two gametes. Instead of a true wall between gametes, mucilage condensed and was observed as a discrete layer that disappeared during gamete release.