Scavenger receptor-mediated uptake of cell-penetrating peptide nanocomplexes with oligonucleotides

Cell-penetrating peptides (CPPs) are short cationic peptides that penetrate cells by interacting with the negatively charged plasma membrane; however, the detailed uptake mechanism is not clear. In contrary to the conventional mode of action of CPPs, we show here that a CPP, PepFect14 (PF14), forms negatively charged nanocomplexes with oligonucleotides and their uptake is mediated by class-A scavenger receptors (SCARAs). Specific inhibitory ligands of SCARAs, such as fucoidin, polyinosinic acid, and dextran sulfate, totally inhibit the activity of PF14-oligonucleotide nanocomplexes in the HeLa pLuc705 splice-correction cell model, while nonspecific, chemically related molecules do not. Furthermore, RNA interference (RNAi) knockdown of SCARA subtypes (SCARA3 and SCARA5) that are expressed in this cell line led to a significant reduction of the activity to <50%. In line with this, immunostaining shows prevalent colocalization of the nanocomplexes with the receptors, and electron microscopy images show no binding or internalization of the nanocomplexes in the presence of the inhibitory ligands. Interestingly, naked oligonucleotides also colocalize with SCARAs when used at high concentrations. These results demonstrate the involvement of SCARA3 and SCARA5 in the uptake of PF14-oligonucleotide nanocomplexes and suggest for the first time that some CPP-based systems function through scavenger receptors, which could yield novel possibilities to understand and improve the transfection by CPPs.     

Different sensitivity of H69 modification enzymes RluD and RlmH to mutations in Escherichia coli 23S rRNA

Nucleoside modifications are introduced into the ribosomal RNA during the assembly of the ribosome. The number and the localization of the modified nucleosides in rRNAs are known for several organisms. In bacteria, rRNA modified nucleosides are synthesized by a set of specific enzymes, the majority of which have been identified in Escherichia coli. Each rRNA modification enzyme recognizes its substrate nucleoside(s) at a specific stage of ribosome assembly. Not much is known about the specificity determinants involved in the substrate recognition of the modification enzymes. In order to shed light on the substrate specificity of RluD and RlmH, the enzymes responsible for the introduction of modifications into the stem-loop 69 (H69), we monitored the formation of H69 pseudouridines (Ψ) and methylated pseudouridine (m3Ψ) in vitro on ribosomes with alterations in 23S rRNA. While the synthesis of Ψs in H69 by RluD is relatively insensitive to the point mutations at neighboring positions, methylation of one of the Ψs by RlmH exhibited a much stronger sensitivity. Apparently, in spite of synthesizing modifications in the same region or even at the same position of rRNA, the two enzymes employ different substrate recognition mechanisms.     

A comparative spectroscopic and kinetic study of photoexcitations in detergent-isolated and membrane-embedded LH2 light-harvesting complexes

Integral membrane proteins constitute more than third of the total number of proteins present in organisms. Solubilization with mild detergents is a common technique to study the structure, dynamics, and catalytic activity of these proteins in purified form. However beneficial the use of detergents may be for protein extraction, the membrane proteins are often denatured by detergent solubilization as a result of native lipid membrane interactions having been modified. Versatile investigations of the properties of membrane-embedded and detergent-isolated proteins are, therefore, required to evaluate the consequences of the solubilization procedure. Herein, the spectroscopic and kinetic fingerprints have been established that distinguish excitons in individual detergent-solubilized LH2 light-harvesting pigment-protein complexes from them in the membrane-embedded complexes of purple photosynthetic bacteria Rhodobacter sphaeroides. A wide arsenal of spectroscopic techniques in visible optical range that include conventional broadband absorption-fluorescence, fluorescence anisotropy excitation, spectrally selective hole burning and fluorescence line-narrowing, and transient absorption-fluorescence have been applied over broad temperature range between physiological and liquid He temperatures. Significant changes in energetics and dynamics of the antenna excitons upon self-assembly of the proteins into intracytoplasmic membranes are observed, analyzed, and discussed. This article is part of a Special Issue entitled: Photosynthesis Research for Sustainability: from Natural to Artificial.     

Reproducibility of anthropometric measurements in children: a longitudinal study

The purpose of this study was to establish the reproducibility of a series of anthropometric measures performed twice during one week during a three year period in boys and girls. The subjects of this investigation were 39 children (21 boys and 18 girls), 9-10 year of age at the beginning of the study. Children were measured three times with one year interval. Children were classified by Tanner stage 1-2 during the first measurements, stage 1-3 during the second measurements and stage 1-4 during the third measurements. Body height and weight were measured and BMI calculated. All anthropometric parameters were measured according to the protocol recommended by the International Society for the Advancement of Kinanthropometry (Norton & Olds 1996). Nine skinfolds, 13 girths, eight lengths and eight breadths/lengths were measured. The reproducibility of body height (r = 0.995-0.999), body weight (r = 0.990-0.999) and BMI (r = 0.969-0.999) was very high in boys and girls. The intraclass correlations (ICC), technical errors (TE) and coefficients of variation (CV) were quite different depending on the measurement site of the skinfold thickness. It was surprising that the ICCs were highest and TEs and CVs were lowest during the second year of the measurement. The computed ICC was high, and TE and CV values were quite similar and relatively low in girth, length and breadth/length measurements. It was concluded that the reproducibility of girths, lengths and breadths/lengths in children is very high and the reproducibility of skinfolds is high. Specifically, the reproducibility is very high immediately before puberty in boys and girls.     

The genetics of bile acid degradation in Pseudomonas spp.: location and cloning of catabolic genes

Four Pseudomonas spp. capable of utilizing bile acids as sole carbon source were examined for the presence of plasmids. One plasmid was found in Pseudomonas sp. RAL8, but no plasmids could be detected in the other three strains. Mitomycin C curing of RAL8 did not affect the ability of the strain to grow on bile acids. This suggested that the genetic information for bile acid catabolism in all four strains was chromosomally located. To isolate bile acid catabolic genes. DNA from RAL8 was partially digested with Sau3A, then the DNA fragments cloned into the broad-host-range cosmid vector pMMB33. The resulting gene bank was screened by plate-mating with two stable RAL8 mutants. Four of the gene bank clones were found to give a positive complementation with one or both mutants. Examination of the plasmids in the four clones revealed that they were unstable, but detailed mapping enabled a 52 kb restriction map to be derived. Further complementation work showed that two of the bile acid catabolic genes are located close together on the map, and may be contiguous.     

Deoxycholic acid degradation by a Pseudomonas sp. Acidic intermediates with A-ring unsaturation.

The microbial catabolism of deoxycholic acid by a Pseudomonas sp. was studied, and six further acidic intermediates were isolated, as their methyl esters. Evidence is presented that the compounds are methyl 12 alpha-hydroxy-3-oxochol-4-en-24-oate, methyl 12 alpha-hydroxy-3-oxo-23,24-dinorchol-4-en-22-oate, methyl 12 alpha-hydroxy-3-oxochola-1,4-dien-24-oate, methyl 12 alpha-hydroxy-3-oxo-23,24-dinorchola-1,4-dien-22-oate, methyl 12 alpha-hydroxy-3-oxochola-1,4,22E-trien-24-oate and methyl 12 alpha-hydroxy-3-oxo-23,24-dinorchola-1,4,17(20)-trien-22-oate. On the basis of these compounds, together with the seven intermediates previously reported, a catabolic pathway is proposed.     

Biochemical and Genetic Studies on Ubiquinone Biosynthesis in Escherichia coli K-12: 4-Hydroxybenzoate Octaprenyltransferase

Three ubiquinone-deficient mutants of Escherichia coli unable to convert 4-hydroxybenzoate into 3-octaprenyl-4-hydroxybenzoate were isolated and examined. The results of genetic analysis suggest that each of the mutants carries a mutation in a gene designated ubiA which can be represented at minute 79 on the E. coli chromosome map. The conversion of 4-hydroxybenzoate into 3-octaprenyl-4-hydroxybenzoate, catalyzed by 4-hydroxybenzoate octaprenyltransferase, was studied with a strain of E. coli that is blocked in the common pathway of aromatic biosynthesis and consequently accumulates the precursor of the side chain of ubiquinone. Both the side-chain precursor and 4-hydroxybenzoate octaprenyltransferase were shown to be membrane-bound. The enzyme required Mg(2+) for optimal activity. The ubiA(-) mutants were found to lack 4-hydroxybenozate octaprenyltransferase activity, which suggested that the ubiA gene is the structural gene coding for this enzyme.     

Oviposition site selection of the Alcon blue butterfly at the northern range margin

Female oviposition decisions in insects may strongly affect offspring growth and survival, and thus determine population performance. In this study, we examined oviposition site selection in the xerophilous ecotype of the endangered myrmecophilous butterfly Phengaris (=Maculinea) alcon (Lepidoptera, Lycaenidae) in Estonia, at the northern distribution margin of both the butterfly and its host plant, Gentiana cruciata L. Egg distribution on individual host plants appeared to be highly uneven: plants carrying high egg loads contrasted to a high proportion of host plants without any or with a few eggs. Host plant use for oviposition was strongly dependent on plant characteristics and environmental context. Host plant height relative to the surrounding vegetation rather than the absolute height of host plants was a key factor determining the use of particular host plant individuals for oviposition. In particular, plants protruding above surrounding vegetation had a higher probability of being used for oviposition, and carried more eggs. Additionally, the number of eggs laid on individual host plants was positively associated with the presence of flowers and the number of shoots. More aggregated host plants received fewer eggs than those with less conspecifics around. Feeding damage by wild herbivores, found in a substantial proportion of the butterfly’s host plants, strongly reduced the number of eggs on individual plants. Our results underline the need to assure that butterfly’s host plants do not become overgrown by surrounding vegetation. Best practices for opening vegetation around host plants may need further studies that explicitly account for butterfly’s host ants—their abundance in relation to vegetation height and their response to opening vegetation.     

Sequence variation and regulatory variation in acetylcholinesterase genes contribute to insecticide resistance in different populations of Leptinotarsa decemlineata

Although insect herbivores are known to evolve resistance to insecticides through multiple genetic mechanisms, resistance in individual species has been assumed to follow the same mechanism. While both mutations in the target site insensitivity and increased amplification are known to contribute to insecticide resistance, little is known about the degree to which geographic populations of the same species differ at the target site in a response to insecticides. We tested structural (e.g., mutation profiles) and regulatory (e.g., the gene expression of Ldace1 and Ldace2, AChE activity) differences between two populations (Vermont, USA and Belchow, Poland) of the Colorado potato beetle, Leptinotarsa decemlineata in their resistance to two commonly used groups of insecticides, organophosphates, and carbamates. We established that Vermont beetles were more resistant to azinphos‐methyl and carbaryl insecticides than Belchow beetles, despite a similar frequency of resistance‐associated alleles (i.e., S291G) in the Ldace2 gene. However, the Vermont population had two additional amino acid replacements (G192S and F402Y) in the Ldace1 gene, which were absent in the Belchow population. Moreover, the Vermont population showed higher expression of Ldace1 and was less sensitive to AChE inhibition by azinphos‐methyl oxon than the Belchow population. Therefore, the two populations have evolved different genetic mechanisms to adapt to organophosphate and carbamate insecticides.     

Prediction of Cell-Penetrating Peptides

Cell-penetrating peptides, CPPs, are used as delivery vectors for pharmacologically interesting substances, such as antisense oligonucleotides, proteins and peptides. We present a general principle for designing cell-penetrating peptides derived from naturally occurring proteins as well as from randomly generated polyamino acid sequences. Thereby, we introduce a novel pharmacological principle for identification of cell-penetrating peptides for which the applications can be numerous, including cellular transduction vectors and mimics of intracellular protein–protein interactions. The methods of identifying a CPP comprises assessing the averaged bulk property values of the defined sequence, and ensuring that they fall within the bulk property value interval obtained from the training set. Despite this simplistic approach, the search criteria proved useful for finding CPP properties in either proteins or random sequences. We have experimentally verified cell-penetrating properties of 10–20-mer peptides derived from naturally occurring proteins as well as from random poly-amino acids. We note that since CPPs can be found in part of the protein sequences that may govern protein interactions, it is possible to produce cell-penetrating protein agonists or antagonists.