Nanomechanical properties of human prion protein amyloid as probed by force spectroscopy

Amyloids are associated with a number of protein misfolding disorders, including prion diseases. In this study, we used single-molecule force spectroscopy to characterize the nanomechanical properties and molecular structure of amyloid fibrils formed by human prion protein PrP90-231. Force-extension curves obtained by specific attachment of a gold-covered atomic force microscope tip to engineered Cys residues could be described by the worm-like chain model for entropic elasticity of a polymer chain, with the size of the N-terminal segment that could be stretched entropically depending on the tip attachment site. The data presented here provide direct information about the forces required to extract an individual monomer from the core of the PrP90-231 amyloid, and indicate that the β-sheet core of this amyloid starts at residue ∼164-169. The latter finding has important implications for the ongoing debate regarding the structure of PrP amyloid.     

Multiple substrates for paraoxonase-1 during oxidation of phosphatidylcholine by peroxynitrite.

Paraoxonase (PON-1) is a high-density lipoprotein (HDL)-bound enzyme with activity toward multiple substrates. It hydrolyzes organic phosphate and aromatic carboxylic acid esters. It also inhibits accumulation of oxidized phospholipids in plasma lipoproteins by a mechanism yet to be determined. Therefore, we subjected apolipoprotein A-I proteoliposomes containing either 1-palmitoyl-2-linoleoyl-sn-glycero-3-phosphocholine or 1-palmitoyl-2-arachidonoyl-sn-glycero-3-phosphocholine to oxidation by a peroxynitrite generator, SIN-1, in the presence and absence of purified PON-1. PON-1 modified the proportion of oxidation products without affecting the overall extent of PC oxidation. However, in the presence of PON-1, phosphatidylcholine isoprostanes were hydrolyzed to lysophosphatidylcholine. In addition, PON-1 hydrolyzed the phosphatidylcholine core aldehydes 1-palmitoyl-2-(9-oxo)nonanoyl-sn-glycero-3-phosphocholine and 1-palmitoyl-2-(5-oxo)valeroyl-sn-glycero-3-phosphocholine to lysophosphatidylcholine. This hydrolysis was not affected by pefabloc, a serine esterase inhibitor. There was no detectable release of linoleate, arachidonate, or their hydroperoxy or hydroxy derivatives in the presence of PON-1. We conclude that PON-1 minimizes the accumulation of phosphatidylcholine oxidation products by the hydrolysis of phosphatidylcholine isoprostanes and core aldehydes to lysophosphatidylcholine with a serine esterase-independent mechanism.     

Heparin can improve the viability of transfected cystic fibrosis cell lines in vitro

Cationic liposomes are widely used as gene transfer agents in in vitro and in vivo studies of cystic fibrosis. In this study we report comparative results of cationic mediated transfection in several cell lines. We have tested epithelial cell lines expressing the wild-type cystic fibrosis transmembrane protein CFTR (bronchial epithelium-16HBE14o-, submucosal gland-Calu3) and their cystic fibrosis counterparts (CFBE41o-, CFSMEo-), as well as baby hamster kidney fibroblast cell lines (BHK) heterologously expressing human CFTR. The cells were transfected with a green fluorescent protein plasmid complexed with commercial cationic liposome (Geneporter2, GP) and 25 kDa polyethylenimine (PEI). At the end of the incubation (2 hours), low molecular weight heparin was added in order to reduce the toxicity of the lipoplexes. Transfection efficiency and cell viability were measured by flow cytometry. Determination of fatty acid composition of cellular phospholipids was performed by capillary gas chromatography. The short incubation time was sufficient to obtain satisfactory transfection in all cell lines studied. Cells treated with PEI-complexes had lower transfection efficiency and viability compared to GP in all tested cell lines. DeltaF508 CFTR carrying airway epithelial cells were easier to transfect but had lower viability compared to their healthy counterparts. This was, however not the case for the BHK cells. The fatty acid analysis showed characteristic polyunsaturated fatty acid patterns, which correlated with the viability of the transfected cells. Low molecular mass heparin added at the end of the lipoplex incubation time could help to maintain the viability of the cells, without interfering with the transfection efficiency.     

Global analysis of RNA secondary structure in two metazoans

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Highlights? RNA folding in miRNA target sites is distinct between animals ? There is a negative correlation between miRNA target-site structure and miRISC binding ? Conserved secondary structure features demarcate protein-coding regions of animal mRNAs ? There are conserved features of RNA secondary structure in animals     

Distribution and characterization of Aegilops and Triticum species from the Bulgarian Black Sea coast

A total of 158 Aegilops-Triticum samples representing six Aegilops species (one diploid, four tetraploid and one hexaploid) and one diploid Triticum were collected along the Bulgarian Black Sea coast, and their distribution on the 350 km long coastal line was reported. The region south of Kamchia river, accepted as the middle point of the coast, was characterized by the greatest diversity of these wild relatives of wheat. The most widely distributed species in this area was Ae. geniculata. Ae. cylindrica was distributed only in north (Durankulak), while Ae. biuncialis and Ae. triuncialis were collected both north and south of Kamchia river. All samples of Ae. neglecta were hexaploid. Natural hybrids of goatgrass and wheat were found in Ae. cylindrica populations. Triticum monococcum ssp. aegilopoides had limited distribution in the south region. Aegilops uniaristata was recorded as a new species for the Bulgarian flora. Most of the samples expressed resistance to powdery mildew in seedling and adult stage, but all of them were polymorphic regarding the resistance to leaf rust (cultures 73760 and 43763). The study revealed additional data for the distribution of Aegilops and Triticum species in Bulgaria and their potential value as genetic resources in wheat improvement.     

A Genome-Scale DNA Repair RNAi Screen Identifies SPG48 as a Novel Gene Associated with Hereditary Spastic Paraplegia

DNA repair is essential to maintain genome integrity, and genes with roles in DNA repair are frequently mutated in a variety of human diseases. Repair via homologous recombination typically restores the original DNA sequence without introducing mutations, and a number of genes that are required for homologous recombination DNA double-strand break repair (HR-DSBR) have been identified. However, a systematic analysis of this important DNA repair pathway in mammalian cells has not been reported. Here, we describe a genome-scale endoribonuclease-prepared short interfering RNA (esiRNA) screen for genes involved in DNA double strand break repair. We report 61 genes that influenced the frequency of HR-DSBR and characterize in detail one of the genes that decreased the frequency of HR-DSBR. We show that the gene KIAA0415 encodes a putative helicase that interacts with SPG11 and SPG15, two proteins mutated in hereditary spastic paraplegia (HSP). We identify mutations in HSP patients, discovering KIAA0415/SPG48 as a novel HSP-associated gene, and show that a KIAA0415/SPG48 mutant cell line is more sensitive to DNA damaging drugs. We present the first genome-scale survey of HR-DSBR in mammalian cells providing a dataset that should accelerate the discovery of novel genes with roles in DNA repair and associated medical conditions. The discovery that proteins forming a novel protein complex are required for efficient HR-DSBR and are mutated in patients suffering from HSP suggests a link between HSP and DNA repair.     

Cyclodextrin glucanotransferase production by cell biocatalysts of alkaliphilic bacilli

Cells of obligated alkaliphiles Bacillus pseudalcaliphilus 20RF and Bacillus pseudalcaliphilus 8SB isolated from Bulgarian habitats, producers of cyclodextrin glucanotransferase (CGTase, EC 2.4.1.19), were immobilized by three different techniques: on two types of polysulphone membranes; entrapped in agar-gel beads containing magnetite and by nano-particles of silanized magnetite covalently bound on the cell surface. The biocatalysts obtained demonstrated the opportunity for a significantly enhanced CGTase production compared to free cells for a long period of time (10 days semicontinuous cultivation) without impact on their mechanical stability. The cell membrane-biocatalysts exhibited the highest enzyme activity after 240 h repeated batch cultivation and retained 1.3–2.3-fold increase of the CGTase yield compared to free cells at the end of the process. Membrane biocatalysts were applied for a direct cyclodextrin (CD) production. The results obtained demonstrated the possibility of starch conversion into cyclodextrins by immobilized cells without using of crude or purified enzyme. The membrane biocatalysts of both obligated alkaliphiles formed mainly β- and γ-CDs after 6 h enzyme reaction at pH 9.0 of the reaction mixture. Under these conditions, the quantity of γ-CDs was a relative high, to 35–37% of the total CD amount.     

Modifications of ouabain inhibition of xenon accumulation in red blood cells. Implications regarding cell water structuring

Ouabain is known to depress uptake of xenon by red blood cells, but it is now found that the depressive effects of phenolsulfonphthalein (PSP) or heavy water are even more marked. Ouabain partly reverses those effects in a manner suggesting it exerts a constant action on xenon exchange regardless of the presence or absence of PSP or D2O. Processes analogous to exchange diffusion between certain anesthetic substances and xenon were also observed. The theoretical consequences of the findings are discussed.