Experimental investigation of a filter with natural sorbent charge for runoff cleaning from heavy metals and petroleum products

An experimental investigation on the removal of heavy metals (HM) and petroleum products (PP) from a solution by natural sorbents zeolite and vermiculite was carried out in a laboratory pilot‐scaled test bench. For this purpose a model of a runoff filter which was invented by the authors was used. 25 kg of natural zeolite and 2 kg of vermiculite were used for the filter charge. An experimental solution of 20 l contained 1 g/l of HM Cu, Pb, Zn, Ni and Mn nitrates and 200 ml of PP gasoline and diesel. The solution was poured into the filter through a funnel and passed over natural zeolite and vermiculite media. The first sample was taken through a sample mixer tap immediately after the contact of the experimental solution with the charge media, the second sample was taken after 5 min, then after 10, 20, 30, 60, 120, 240, 360 and 720 min. TOG/TPH analyser was used for measuring concentration of filtrate samples. The highest efficiency of 99,7 % was reached for PP removal from water. Filtro su natūralių sobentų įkrova, skirto sunkiesiems metalams ir naftos produktams iš lietaus nuotekų valyti, eksperimentiniai tyrimai Santrauka Atlikti eksperimentiniai sunkiųjų metalų ir naftos produktų šalinimo iš tirpalų kaip sorbentus naudojant gamtinius ceolitą ir vermikulitą tyrimai. Šiam tikslui naudotas sukurto lietaus nuotekų valymo įrenginio maketas. Filtro įkrova – 25 kg gamtinio ceolito ir 2 kg vermikulito. Eksperimentiniam tirpalui paruošti sunaudota 20 l distiliuoto vadens bei 1 g/l sunkiųjų metalų Cu, Pb, Zn, Ni ir Mn bei po 200 ml benzino ir dyzelino. Eksperimentinis tirpalas įpiltas į filtrą per piltuvėlį, tekėjo pro ceolito ir vermikulito sluoksnius. Pirmasis mėginys paimtas iš čiaupo iškarto po tirpalo sąlyčio su filtro įkrova – po 1 min., antrasis – po 5 min., o kiti – po 10, 20, 30, 60, 120, 240, 360 ir 720 min. Filtrato mėginiai analizuoti TOG/TPH analizatoriumi, kuris nustato naftos produktų koncnetraciją tirpale. Didžiausias filtro efektyvumas – 99,7 % pasiektas šalinant naftos produktus. Sunkieji metalai taip pat pašalinti efektyviai (pvz., Pb – 98,6 %). Firstd Published Online: 14 Oct 2010 Reikšminiai žodžiai: naftos produktai, sunkieji metalai, vandens teršimas, natūralusis sorbentas, ceolitas, vermikulitas

Direct structural analysis of modified RNA by fluorescent in-line probing

Chemical probing is a common method for the structural characterization of RNA. Typically, RNA is radioactively end-labelled, subjected to probing conditions, and the cleavage fragment pattern is analysed by gel electrophoresis. In recent years, many chemical modifications, like fluorophores, were introduced into RNA, but methods are lacking that detect the influence of the modification on the RNA structure with single-nucleotide resolution. Here, we first demonstrate that a 5′-terminal 32P label can be replaced by a dye label for in-line probing of riboswitch RNAs. Next, we show that small, highly structured FRET-labelled Diels–Alderase ribozymes can be directly probed, using the internal or terminal FRET dyes as reporters. The probing patterns indeed reveal whether or not the attachment of the dyes influences the structure. The existence of two dye labels in typical FRET constructs is found to be beneficial, as ‘duplexing’ allows observation of the complete RNA on a single gel. Structural information can be derived from the probing gels by deconvolution of the superimposed band patterns. Finally, we use fluorescent in-line probing to experimentally validate the structural consequences of photocaging, unambiguously demonstrating the intentional destruction of selected elements of secondary or tertiary structure

Importance of RNA-protein interactions in bacterial ribonuclease P structure and catalysis

Ribonuclease P (RNase P) is a ribonucleoprotein (RNP) complex that catalyzes the metal-dependent maturation of the 5′ end of precursor tRNAs (pre-tRNAs) in all organisms. RNase P is comprised of a catalytic RNA (P RNA), and at least one essential protein (P protein). Although P RNA is the catalytic subunit of the enzyme and is active in the absence of P protein under high salt concentrations in vitro, the protein is still required for enzyme activity in vivo. Therefore, the function of the P protein and how it interacts with both P RNA and pre-tRNA have been the focus of much ongoing research. RNA-protein interactions in RNase P serve a number of critical roles in the RNP including stabilizing the structure, and enhancing the affinity for substrates and metal ions. This review examines the role of RNA-protein interactions in bacterial RNase P from both structural and mechanistic perspectives. © 2007 Wiley Periodicals, Inc. Biopolymers 87: 329–338, 2007. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at [email protected] Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/57327/1/20846_ftp.pd

Investigation of catalysis by bacterial RNase P via LNA and other modifications at the scissile phosphodiester

We analyzed cleavage of precursor tRNAs with an LNA, 2′-OCH3, 2′-H or 2′-F modification at the canonical (c0) site by bacterial RNase P. We infer that the major function of the 2′-substituent at nt −1 during substrate ground state binding is to accept an H-bond. Cleavage of the LNA substrate at the c0 site by Escherichia coli RNase P RNA demonstrated that the transition state for cleavage can in principle be achieved with a locked C3′ -endo ribose and without the H-bond donor function of the 2′-substituent. LNA and 2′-OCH3 suppressed processing at the major aberrant m−1 site; instead, the m+1 (nt +1/+2) site was utilized. For the LNA variant, parallel pathways leading to cleavage at the c0 and m+1 sites had different pH profiles, with a higher Mg2+ requirement for c0 versus m+1 cleavage. The strong catalytic defect for LNA and 2′-OCH3 supports a model where the extra methylene (LNA) or methyl group (2′-OCH3) causes a steric interference with a nearby bound catalytic Mg2+ during its recoordination on the way to the transition state for cleavage. The presence of the protein cofactor suppressed the ground state binding defects, but not the catalytic defects

Thick collagen-based 3D matrices including growth factors to induce neurite outgrowth

Designing synthetic microenvironments for cellular investigations is a very active area of research at the crossroads of cell biology and materials science. The present work describes the design and functionalization of a three-dimensional (3D) culture support dedicated to the study of neurite outgrowth from neural cells. It is based on a dense self-assembled collagen matrix stabilized by 100-nm wide interconnected native fibrils without chemical crosslinking. The matrices were made suitable for cell manipulation and direct observation in confocal microscopy by anchoring them to traditional glass supports with a calibrated thickness of ∼50 μm. The matrix composition can be readily adapted to specific neural cell types, notably by incorporating appropriate neurotrophic growth factors. Both PC-12 and SH-SY5Y lines respond to growth factors (nerve growth factor and brain-derived neurotrophic factor, respectively) impregnated and slowly released from the support. Significant neurite outgrowth is reported for a large proportion of cells, up to 66% for PC12 and 49% for SH-SY5Y. It is also shown that both growth factors can be chemically conjugated (EDC/NHS) throughout the matrix and yield similar proportions of cells with longer neurites (61% and 52%, respectively). Finally, neurite outgrowth was observed over several tens of microns within the 3D matrix, with both diffusing and immobilized growth factors

Association of Variants at UMOD with Chronic Kidney Disease and Kidney Stones—Role of Age and Comorbid Diseases

Chronic kidney disease (CKD) is a worldwide public health problem that is associated with substantial morbidity and mortality. To search for sequence variants that associate with CKD, we conducted a genome-wide association study (GWAS) that included a total of 3,203 Icelandic cases and 38,782 controls. We observed an association between CKD and a variant with 80% population frequency, rs4293393-T, positioned next to the UMOD gene (GeneID: 7369) on chromosome 16p12 (OR = 1.25, P = 4.1×10−10). This gene encodes uromodulin (Tamm-Horsfall protein), the most abundant protein in mammalian urine. The variant also associates significantly with serum creatinine concentration (SCr) in Icelandic subjects (N = 24,635, P = 1.3×10−23) but not in a smaller set of healthy Dutch controls (N = 1,819, P = 0.39). Our findings validate the association between the UMOD variant and both CKD and SCr recently discovered in a large GWAS. In the Icelandic dataset, we demonstrate that the effect on SCr increases substantially with both age (P = 3.0×10−17) and number of comorbid diseases (P = 0.008). The association with CKD is also stronger in the older age groups. These results suggest that the UMOD variant may influence the adaptation of the kidney to age-related risk factors of kidney disease such as hypertension and diabetes. The variant also associates with serum urea (P = 1.0×10−6), uric acid (P = 0.0064), and suggestively with gout. In contrast to CKD, the UMOD variant confers protection against kidney stones when studied in 3,617 Icelandic and Dutch kidney stone cases and 43,201 controls (OR = 0.88, P = 5.7×10−5)

2D versus 3D human induced pluripotent stem cell-derived cultures for neurodegenerative disease modelling

Neurodegenerative diseases, such as Alzheimer's disease (AD), Parkinson's disease (PD), Huntington's disease (HD) and amyotrophic lateral sclerosis (ALS), affect millions of people every year and so far, there are no therapeutic cures available. Even though animal and histological models have been of great aid in understanding disease mechanisms and identifying possible therapeutic strategies, in order to find disease-modifying solutions there is still a critical need for systems that can provide more predictive and physiologically relevant results. One possible avenue is the development of patient-derived models, e.g. by reprogramming patient somatic cells into human induced pluripotent stem cells (hiPSCs), which can then be differentiated into any cell type for modelling. These systems contain key genetic information from the donors, and therefore have enormous potential as tools in the investigation of pathological mechanisms underlying disease phenotype, and progression, as well as in drug testing platforms. hiPSCs have been widely cultured in 2D systems, but in order to mimic human brain complexity, 3D models have been proposed as a more advanced alternative. This review will focus on the use of patient-derived hiPSCs to model AD, PD, HD and ALS. In brief, we will cover the available stem cells, types of 2D and 3D culture systems, existing models for neurodegenerative diseases, obstacles to model these diseases in vitro, and current perspectives in the field

An experimental study on the use of natural zeolite for Cu, Pb and Zn immobilization in soil

An experiment of the immobilization of heavy metals Cu, Pb and Zn in soil by means of natural zeolite was performed in the laboratory. The natural zeolite employed was from a deposit near the village of Sokyrnytsia in the Ukrainian Transcarpathian region. Sandy soil was contaminated by Cu 2+ , Pb 2+ and Zn 2+ nitrates at three contamination levels, 50, 100 and 500 mg/kg of each metal. Sandy soil samples contaminated with three different concentrations of three metal solutions were mixed with 5%, 10% and 20% of zeolite. 200 ml of distilled water was added to each plastic container with soil and zeolite mixtures and left for 1 month. After one month sandy soil samples of 0.5 g from each plastic container were analysed by ICP-OES. Zeolite immobilised metals in the order: Pb 2+ > Zn 2+ > Cu 2+