The glycine arginine‐rich domain of the RNA‐binding protein nucleolin regulates its subcellular localization

Nucleolin is a multifunctional RNA Binding Protein (RBP) with diverse subcellular localizations, including the nucleolus in all eukaryotic cells, the plasma membrane in tumor cells, and the axon in neurons. Here we show that the glycine arginine rich (GAR) domain of nucleolin drives subcellular localization via protein‐protein interactions with a kinesin light chain. In addition, GAR sequences mediate plasma membrane interactions of nucleolin. Both these modalities are in addition to the already reported involvement of the GAR domain in liquid‐liquid phase separation in the nucleolus. Nucleolin transport to axons requires the GAR domain, and heterozygous GAR deletion mice reveal reduced axonal localization of nucleolin cargo mRNAs and enhanced sensory neuron growth. Thus, the GAR domain governs axonal transport of a growth controlling RNA‐RBP complex in neurons, and is a versatile localization determinant for different subcellular compartments. Localization determination by GAR domains may explain why GAR mutants in diverse RBPs are associated with neurodegenerative disease.     

Natural Occurrence of Enantiomers of Organic Compounds Versus Phytoremediations: Should Research on Phytoremediations Be Revisited? A Mini‐review

Decontamination of polluted soils using plants is based on the ability of plant species (including transgenic plants) to enhance bioavailability of pollutants in the rhizosphere and support growth of pollutant‐degrading microorganisms via root exudation and plant species‐specific composition of the exudates. In this work, we review current knowledge of enantiomers of low‐molecular‐weight (LMW) organic compounds with emphasis on their use in phytoremediation. Many research studies have been performed to search for plants suitable for decontamination of polluted soils. Nevertheless, the natural occurrence of L‐ versus D‐enantiomers of dominant compounds of plant root exudates which play different roles in the complexation of heavy metals, chemoattraction, and support of pollutant‐degrading microorganisms were not included in these studies. D‐enantiomers of aliphatic organic acids and amino acids or L‐enantiomers of carbohydrates occur in high concentrations in root exudates of some plant species, especially under stress, and are less stimulatory for plants to extract heavy metals or for rhizosphere microflora to degrade pollutants compared with L‐enantiomers (organic acids and amino acids) or D‐carbohydrates. Determining the ratio of L‐ versus D‐enantiomers of organic compounds as a criterion of plant suitability for decontamination of polluted soils and development of other types of bioremediation technologies need to be subjects of future research. Chirality 26:1–20, 2013. © 2013 Wiley Periodicals, Inc.     

Removal of Al, Fe and Mn by Pistia stratiotes L. and its stress response

The influence of different chelates applied in the soil primary on Al and secondary on Fe and Mn mobilization and their removal from solution was investigated. The work compared the efficiency of 10 mM tartaric acid and 3 mM EDTA in soil washing process and accumulation potential of Pistia stratiotes in rhizofiltration process. The plant response on the toxic element Al and other elements Fe and Mn was determined through the nitrogen and free amino acids content in plants. The efficiency of chelates decreased in order 10 mM tartaric acid > deionized water > 3 mM EDTA for all studied elements. P. stratiotes was able to remove up to 90% of elements during the 15 days period. Higher content of toxic element Al and potential toxic elements Fe and Mn were observed in the roots than in the leaves with the increased time. The trend of Al accumulation correlated with Fe accumulation (R²=0.89). Toxicity impact of high level of Al was observed by increased free amino acids (AA) level. Proline, histidine, glutamic acid and glycine were the most synthesised free AA in leaves. Total AA content in leaves was significantly higher under chelates addition compared to control.     

Synthesis of spiroannulated oligopyrrole macrocycles derived from lithocholic acid

Two new steroidal spiroannulated calix[4]pyrroles 5 and 10, derived from bile acids (lithocholate), were prepared by the acid catalyzed condensation of methyl-3,3-bis(pyrrol-2-yl)-5β-cholan-24-oate 3 with carbonyl compounds and with 2,2′-propane-2,2-diylbis(1H-pyrrole), respectively. The new compounds were fully characterized by physicochemical methods.     

Benthic macroinvertebrates along the Czech part of the Labe and lower section of the Vltava rivers from 1996–2005, with a particular focus on rare and alien species

In the Czech part of the Labe River and the lower part of the Vltava River, we examined if the benthic macroinvertebrate composition changed from 1996 to 2005 due to expected improvements in water quality resulting from socioeconomic changes in the Czech Republic since the 1990s. Special attention was given to rare and alien species. The four biological metrics used (Number of taxa, BMWP, Number of sensitive taxa, and Number of EPT taxa) demonstrated that there was indeed an improvement in water quality as well as a slight improvement of the Labe microhabitats during the investigated period. An increasing Number of taxa over time was observed at most sites. Two main concurrent ecological processes are recently in progress in the Labe: a recovery of native species and an expansion of alien species, some of which are considered invasive. The caddisfly Setodes punctatus and the beetle Pomatinus substriatus, considered as regionally extinct in the Czech Republic until 2005, were rediscovered during our investigations. Findings of the crustacean Hemimysis anomala (invasive) and the chironomids Stenochironomus sp. and Lipiniella sp. were the first records of these taxa in the Czech Republic.     

Tangential Flow Ultrafiltration: A “Green” Method for the Size Selection and Concentration of Colloidal Silver Nanoparticles

Nowadays, AgNPs are extensively used in the manufacture of consumer products,¹ water disinfectants,² therapeutics,^{1, 3} and biomedical devices⁴ due to their powerful antimicrobial properties.^3-6 These nanoparticle applications are strongly influenced by the AgNP size and aggregation state. Many challenges exist in the controlled fabrication⁷ and size-based isolation^4,8 of unfunctionalized, homogenous AgNPs that are free from chemically aggressive capping/stabilizing agents or organic solvents.^7-13 Limitations emerge from the toxicity of reagents, high costs or reduced efficiency of the AgNP synthesis or isolation methods (e.g., centrifugation, size-dependent solubility, size-exclusion chromatography, etc.).^10,14-18 To overcome this, we recently showed that TFU permits greater control over the size, concentration and aggregation state of Creighton AgNPs (300 ml of 15.3 μg ml^-1 down to 10 ml of 198.7 μg ml^-1) than conventional methods of isolation such as ultracentrifugation.¹⁹TFU is a recirculation method commonly used for the weight-based isolation of proteins, viruses and cells.^20,21 Briefly, the liquid sample is passed through a series of hollow fiber membranes with pore size ranging from 1,000 kD to 10 kD. Smaller suspended or dissolved constituents in the sample will pass through the porous barrier together with the solvent (filtrate), while the larger constituents are retained (retentate). TFU may be considered a "green" method as it neither damages the sample nor requires additional solvent to eliminate toxic excess reagents and byproducts. Furthermore, TFU may be applied to a large variety of nanoparticles as both hydrophobic and hydrophilic filters are available.The two main objectives of this study were: 1) to illustrate the experimental aspects of the TFU approach through an invited video experience and 2) to demonstrate the feasibility of the TFU method for larger volumes of colloidal nanoparticles and smaller volumes of retentate. First, unfuctionalized AgNPs (4 L, 15.2 μg ml^-1) were synthesized using the well-established Creighton method^22,23 by the reduction of AgNO₃ with NaBH₄. AgNP polydispersity was then minimized via a 3-step TFU using a 50-nm filter (460 cm²) to remove AgNPs and AgNP-aggregates larger than 50 nm, followed by two 100-kD (200 cm² and 20 cm²) filters to concentrate the AgNPs. Representative samples were characterized using transmission electron microscopy, UV-Vis absorption spectrophotometry, Raman spectroscopy, and inductively coupled plasma optical emission spectroscopy. The final retentate consisted of highly concentrated (4 ml, 8,539.9 μg ml^-1) yet lowly aggregated and homogeneous AgNPs of 1-20 nm in diameter. This corresponds to a silver concentration yield of about 62%.     

Association between polymorphism in the FTO gene and growth and carcass traits in pig crosses

Background

Independent studies have shown that several single nucleotide polymorphisms (SNP) in the human FTO (fat mass and obesity associated) gene are associated with obesity. SNP have also been identified in the pig FTO gene, among which some are associated with selected fat-deposition traits in F₂ crosses and commercial populations. In this study, using both commercial pig populations and an experimental Meishan × Pietrain F₂ population, we have investigated the association between one FTO SNP and several growth and carcass traits. Association analyses were performed with the FTO polymorphism either alone or in combination with polymorphisms in flanking loci.

Methods

SNP ({"type":"entrez-nucleotide","attrs":{"text":"FM244720","term_id":"209570741","term_text":"FM244720"}}FM244720:g.400C>G) in exon 3 of porcine FTO was genotyped by PCR-RFLP and tested for associations with some growth, carcass and fat-related traits. Proportions of genetic variance of four pig chromosome 6 genes (FTO, RYR1, LIPE and TGFB1) on selected traits were evaluated using single- and multi-locus models.

Results

Linkage analysis placed FTO on the p arm of pig chromosome 6, approximately 22 cM from RYR1. In the commercial populations, allele C of the FTO SNP was significantly associated with back fat depth and allele G with muscling traits. In the Meishan × Pietrain F₂ pigs, heterozygotes with allele C from the Pietrain sows and allele G from the Meishan boar were more significantly associated with fat-related traits compared to homozygotes with allele G from the Pietrain and allele G from the Meishan breed. In single- and multi-locus models, genes RYR1, TGFB1 and FTO showed high associations. The contribution in genetic variance from the polymorphism in the FTO gene was highest for back fat depth, meat area on the musculus longissimus lumborum et thoracis tissues and metabolite glucose-6-phosphate dehydrogenase.

Conclusions

Our results show that in pig, FTO influences back fat depth in the commercial populations, while in the Meishan × Pietrain F₂ pigs with a CG genotype, heterosis occurs for several fat-related traits.     

Remarkable coexistence of multiple cytotypes of the Gymnadenia conopsea aggregate (the fragrant orchid): evidence from flow cytometry

Background and Aims

One of the prerequisites for polyploid research in natural systems is knowledge of the geographical distribution of cytotypes. Here inter- and intrapopulational ploidy diversity was examined in the Gymnadenia conopsea aggregate in central Europe and potential explanations and evolutionary consequences of the observed spatial patterns investigated.

Methods

DAPI flow cytometry supplemented by confirmatory chromosome counts was used to determine ploidy in 3581 samples of the G. conopsea aggregate from 43 populations. The fine-scale spatial pattern of cytotype distribution (intra- and interploidy associations) was analysed with univariate and bivariate K-functions.

Key Results

Gymnadenia tissues undergo a progressively partial endoreplication, which accounts for about 60 % and 75 % of the total genome in G. conopsea and G. densiflora, respectively. Flow cytometric profiles are therefore species-specific and can be used as a marker for rapid and reliable species recognition. Two majority (4x, 8x) and three minority (6x, 10x, 12x) cytotypes were found, often in mixed-ploidy populations (harbouring up to all five different ploidy levels). The scarcity of the minority cytotypes (about 2·7 %) suggests the existence of strong pre- or postzygotic mating barriers. Spatial structure was observed in plots of populations with the highest cytotype variation, including clumping of individuals of the same ploidy and negative association between tetra- and octoploids.

Conclusions

The remarkable ploidy coexistence in the G. conopsea aggregate has reshaped our perception of intrapopulational ploidy diversity under natural conditions. This system offers unique opportunities for studying processes governing the formation and establishment of polyploids and assessing the evolutionary significance of the various pre- and postzygotic mating barriers that maintain this ploidy mixture.     

Modulation of Bleomycin-Induced Lung Fibrosis by Pegylated Hyaluronidase and Dopamine Receptor Antagonist in Mice

Hyaluronidases are groups of enzymes that degrade hyaluronic acid (HA). To stop enzymatic hydrolysis we modified testicular hyaluronidase (HYAL) by activated polyethylene oxide with the help of electron-beam synthesis. As a result we received pegylated hyaluronidase (pegHYAL). Spiperone is a selective D₂ dopamine receptor antagonist. It was demonstrated on the model of a single bleomycin damage of alveolar epithelium that during the inflammatory phase monotherapy by pegHYAL or spiperone reduced the populations of hematopoietic stem /progenitor cells in the lung parenchyma. PegHYAL also reduced the levels of transforming growth factor (TGF)-β, interleukin (IL)-1β, tumor necrosis factor (TNF)-α in the serum and lungs, while spiperone reduced the level of the serum IL-1β. Polytherapy by spiperone and pegHYAL caused the increase of the quantity of hematopoietic stem/ progenitor cells in the lungs. Such an influx of blood cell precursors was observed on the background of considerable fall level of TGF-β and the increase level of TNF-α in the serum and lungs. These results show pegHYAL reduced the bleomycin-induced fibrosis reaction (production and accumulation of collagen) in the lung parenchyma. This effect was observed at a single and repetitive bleomycin damage of alveolar epithelium, the antifibrotic activity of pegHYAL surpassing the activity of testicular HYAL. The antifibrotic effect of pegHYAL is enhanced by an additional instillation of spiperone. Therapy by pegHYAL causes the flow of CD31^‒CD34^‒CD45^‒CD44⁺CD73⁺CD90⁺CD106⁺-cells into the fibrous lungs. These cells are incapable of differentiating into fibroblast cells. Spiperone instillation separately or together with pegHYAL reduced the MSC-like cells considerably. These data enable us to assume, that pegHYAL is a new and promising instrument both for preventive and therapy of toxic pneumofibrosis. The blockage of D₂ dopamine receptors with the following change of hyaluronan matrix can be considered as a new strategy in treatment of pneumofibrosis.     

Stretching the rules: monocentric chromosomes with multiple centromere domains

The centromere is a functional chromosome domain that is essential for faithful chromosome segregation during cell division and that can be reliably identified by the presence of the centromere-specific histone H3 variant CenH3. In monocentric chromosomes, the centromere is characterized by a single CenH3-containing region within a morphologically distinct primary constriction. This region usually spans up to a few Mbp composed mainly of centromere-specific satellite DNA common to all chromosomes of a given species. In holocentric chromosomes, there is no primary constriction; the centromere is composed of many CenH3 loci distributed along the entire length of a chromosome. Using correlative fluorescence light microscopy and high-resolution electron microscopy, we show that pea (Pisum sativum) chromosomes exhibit remarkably long primary constrictions that contain 3-5 explicit CenH3-containing regions, a novelty in centromere organization. In addition, we estimate that the size of the chromosome segment delimited by two outermost domains varies between 69 Mbp and 107 Mbp, several factors larger than any known centromere length. These domains are almost entirely composed of repetitive DNA sequences belonging to 13 distinct families of satellite DNA and one family of centromeric retrotransposons, all of which are unevenly distributed among pea chromosomes. We present the centromeres of Pisum as novel "meta-polycentric" functional domains. Our results demonstrate that the organization and DNA composition of functional centromere domains can be far more complex than previously thought, do not require single repetitive elements, and do not require single centromere domains in order to segregate properly. Based on these findings, we propose Pisum as a useful model for investigation of centromere architecture and the still poorly understood role of repetitive DNA in centromere evolution, determination, and function.