Sequence Features of Drosha and Dicer Cleavage Sites Affect the Complexity of IsomiRs

The deep-sequencing of small RNAs has revealed that different numbers and proportions of miRNA variants called isomiRs are formed from single miRNA genes and that this effect is attributable mainly to imprecise cleavage by Drosha and Dicer. Factors that influence the degree of cleavage precision of Drosha and Dicer are under investigation, and their identification may improve our understanding of the mechanisms by which cells modulate the regulatory potential of miRNAs. In this study, we focused on the sequences and structural determinants of Drosha and Dicer cleavage sites, which may explain the generation of homogeneous miRNAs (in which a single isomiR strongly predominates) as well as the generation of heterogeneous miRNAs. Using deep-sequencing data for small RNAs, we demonstrate that the generation of homogeneous miRNAs requires more sequence constraints at the cleavage sites than the formation of heterogeneous miRNAs. Additionally, our results indicate that specific Drosha cleavage sites have more sequence determinants in miRNA precursors than specific cleavage sites for Dicer and that secondary structural motifs in the miRNA precursors influence the precision of Dicer cleavage. Together, we present the sequence and structural features of Drosha and Dicer cleavage sites that influence the heterogeneity of the released miRNAs.     

An effect of suint on sheep wool impedance and heat resistance values

ABSTRACT

The phenomenon of impedance finds an application in many areas of science; however, no studies relate to wool. Thus, the aim of the study was an examination of an effect of from the presence of suint layer on sheep wool fibers on impedance and heat resistance values. Electrical characteristics (impedance [Ω]) and heat resistance were compared in terms of wool washing effect. The impedance of wool samples was tested in the frequency range of 10 Hz to 1 MHz. In order to measure electrical characteristics and heat resistance values, five samples of greasy wool were collected from different sheep breeds, standardized by weight. After the analyses, the samples were washed and reexamined. The results showed significant differences in the impedance between the greasy and washed wool samples in each of the tested breed (p > 0.05). The suint layer reduces the impedance level, which was also confirmed by a heat resistance test results demonstrating that absence of suint layer on wool fibers significantly reduced this feature value (p > 0.05). This was also reflected in the weight differences between the examined wool samples before and after their washing.     

The Involvement of Xanthone and (E)-Cinnamoyl Chromophores for the Design and Synthesis of Novel Sunscreening Agents

Excessive UV exposure contributes to several pathological conditions like skin burns, erythema, premature skin aging, photodermatoses, immunosuppression, and skin carcinogenesis. Effective protection from UV radiation may be achieved with the use of sunscreens containing UV filters. Currently used UV filters are characterized by some limitations including systemic absorption, endocrine disruption, skin allergy induction, and cytotoxicity. In the research centers all over the world new molecules are developed to improve the safety, photostability, solubility, and absorption profile of new derivatives. In our study, we designed and synthesized seventeen novel molecules by combining in the structures two chromophores: xanthone and (E)-cinnamoyl moiety. The ultraviolet spectroscopic properties of the tested compounds were confirmed in chloroform solutions. They acted as UVB or UVA/UVB absorbers. The most promising compound 9 (6-methoxy-9-oxo-9H-xanthen-2-yl)methyl (E)-3-(2,4-dimethoxyphenyl)acrylate) absorbed UV radiation in the range 290–369 nm. Its photoprotective activity and functional photostability were further evaluated after wet milling and incorporation in the cream base. This tested formulation with compound 9 possessed very beneficial UV protection parameters (SPF_{in vitro} of 19.69 ± 0.46 and UVA PF of 12.64 ± 0.32) which were similar as broad-spectrum UV filter tris-biphenyl triazine. Additionally, compound 9 was characterized by high values of critical wavelength (381 nm) and UVA/UVB ratio (0.830) thus it was a good candidate for broad-spectrum UV filter and it might protect skin against UVA-induced photoaging. Compound 9 were also shown to be photostable, non-cytotoxic at concentrations up to 50 µM when tested on five cell lines, and non-mutagenic in Ames test. It also possessed no estrogenic activity, according to the results of MCF-7 breast cancer model. Additionally, its favorable lipophilicity (miLogP = 5.62) does not predispose it to penetrate across the skin after topical application.     

Alterations in the Genomic Distribution of 5hmC in In Vivo Aged Human Skin Fibroblasts

5-Hydroxymethylcytosine (5hmC) is a functionally active epigenetic modification. We analyzed whether changes in DNA 5-hydroxymethylation are an element of age-related epigenetic drift. We tested primary fibroblast cultures originating from individuals aged 22–35 years and 74–94 years. Global quantities of methylation-related DNA modifications were estimated by the dot blot and colorimetric methods. Regions of the genome differentially hydroxymethylated with age (DHMRs) were identified by hMeDIP-seq and the MEDIPS and DiffBind algorithms. Global levels of DNA modifications were not associated with age. We identified numerous DHMRs that were enriched within introns and intergenic regions and most commonly associated with the H3K4me1 histone mark, promoter-flanking regions, and CCCTC-binding factor (CTCF) binding sites. However, only seven DHMRs were identified by both algorithms and all of their settings. Among them, hypo-hydroxymethylated DHMR in the intron of Rab Escort Protein 1 (CHM) coexisted with increased expression in old cells, while increased 5-hydroxymethylation in the bodies of Arginine and Serine Rich Protein 1 (RSRP1) and Mitochondrial Poly(A) Polymerase (MTPAP) did not change their expression. These age-related differences were not associated with changes in the expression of any of the ten-eleven translocation (TET) enzymes or their activity. In conclusion, the distribution of 5hmC in DNA of in vivo aged human fibroblasts underwent age-associated modifications. The identified DHMRs are, likely, marker changes.     

Vanadium promoted Ni(Mg,Al)O hydrotalcite-derived catalysts for CO2 methanation

A series of V-promoted hydrotalcite-derived nickel catalysts (1.0, 2.0, and 4.0 wt%) were tested in CO₂ methanation. Ni–I–V2.0 with 2.0 wt% vanadium loading showed the highest catalytic activity, achieving 74.7% of CO₂ conversion and 100% of CH₄ selectivity at 300 °C. XRD and XANES analyses showed that the smallest Ni⁰ particles in Ni–I–V2.0 were consistent with the improved textural features observed for this catalyst. Moreover, CO₂-TPD revealed the highest sum of weak and medium basic sites in Ni–I–V2.0 that can positively influence catalytic behavior. For the studied catalysts, a clear correlation was demonstrated between the catalytic activity and specific surface area, as well as the basic properties.     

The influence of the carrier addition and spray drying temperatures on physicochemical properties of microencapsulated carrot juice powder

The objective of this study was to determinate the influence of carrier addition and spray drying temperatures (160 or 200°C) on physicochemical properties of spray-dried carrot juice powder. As carriers, maltodextrin and gum Arabic in different proportions were used. In powders were determined the following: moisture content, water activity, apparent density, size of particles, colour and carotenoids content. The content of carotenoids in powders prepared from solutions with juice to carrier ratio 2:3 was 324.3–406.6 mg/kg d.m., while in powders with a J:C = 3:2 values ranged from 576.7 to 637.7 mg/kg d.m. The highest content of carotenoids and the most yellow colour were observed in powders with 1:3 gum Arabic to maltodextrin ratio. Powders with the highest amount of gum Arabic have the highest diameter and the lowest water activity. High inlet temperature caused brighter colour of powders, higher dry matter content, lower water activity and apparent density of powders.     

Antitumor Effects of Vitamin D Analogs on Hamster and Mouse Melanoma Cell Lines in Relation to Melanin Pigmentation

Deregulated melanogenesis is involved in melanomagenesis and melanoma progression and resistance to therapy. Vitamin D analogs have anti-melanoma activity. While the hypercalcaemic effect of the active form of Vitamin D (1,25(OH)₂D₃) limits its therapeutic use, novel Vitamin D analogs with a modified side chain demonstrate low calcaemic activity. We therefore examined the effect of secosteroidal analogs, both classic (1,25(OH)₂D₃ and 25(OH)D₃), and novel relatively non-calcemic ones (20(OH)D₃, calcipotriol, 21(OH)pD, pD and 20(OH)pL), on proliferation, colony formation in monolayer and soft-agar, and mRNA and protein expression by melanoma cells. Murine B16-F10 and hamster Bomirski Ab cell lines were shown to be effective models to study how melanogenesis affects anti-melanoma treatment. Novel Vitamin D analogs with a short side-chain and lumisterol-like 20(OH)pL efficiently inhibited rodent melanoma growth. Moderate pigmentation sensitized rodent melanoma cells towards Vitamin D analogs, and altered expression of key genes involved in Vitamin D signaling, which was opposite to the effect on heavily pigmented cells. Interestingly, melanogenesis inhibited ligand-induced Vitamin D receptor translocation and ligand-induced expression of VDR and CYP24A1 genes. These findings indicate that melanogenesis can affect the anti-melanoma activity of Vitamin D analogs in a complex manner.     

On nanotube carbon deposition at equilibrium in catalytic partial oxidation of selected hydrocarbon fuels

Computations of thermodynamic equilibrium conditions for depositing carbon in various crystallographic forms are carried out for C-H-O reformates from methane and LPG. Selected examples of reactions accompanying oxidation or thermal decomposition of C₁ to C₄ hydrocarbons are presented, followed by theoretical fundamentals for chemical equilibrium. Table values of the standard chemical potential of the reactants are cited along with respective reaction equilibrium constants. Thermodynamic critical conditions for deposition of several carbon allotropes from gaseous reformates originated from partial oxidation with either air or pure oxygen are also quantified. Computation results are presented graphically in terms of the oxygen-to-carbon ratio, O/C, against temperature for varied pressure and oxidant. Zones of either carbon deposition or carbon-free are specified for graphite or one of the two carbon nanotubes, CNTs. The maximum effect of increase in the critical O/C for a CNT against pure graphite is estimated at 85%.     

Interaction of Cationic Carbosilane Dendrimers and Their siRNA Complexes with MCF-7 Cells

The application of siRNA in gene therapy is mainly limited because of the problems with its transport into cells. Utilization of cationic dendrimers as siRNA carriers seems to be a promising solution in overcoming these issues, due to their positive charge and ability to penetrate cell membranes. The following two types of carbosilane dendrimers were examined: CBD-1 and CBD-2. Dendrimers were complexed with pro-apoptotic siRNA (Mcl-1 and Bcl-2) and the complexes were characterized by measuring their zeta potential, circular dichroism and fluorescence of ethidium bromide associated with dendrimers. CBD-2/siRNA complexes were also examined by agarose gel electrophoresis. Both dendrimers form complexes with siRNA. Moreover, the cellular uptake and influence on the cell viability of the dendrimers and dendriplexes were evaluated using microscopic methods and XTT assay on MCF-7 cells. Microscopy showed that both dendrimers can transport siRNA into cells; however, a cytotoxicity assay showed differences in the toxicity of these dendrimers.     

Lipidation of Temporin-1CEb Derivatives as a Tool for Activity Improvement,Pros and Cons of the Approach

The alarming raise of multi-drug resistance among human microbial pathogens makes the development of novel therapeutics a priority task. In contrast to conventional antibiotics, antimicrobial peptides (AMPs), besides evoking a broad spectrum of activity against microorganisms, could offer additional benefits, such as the ability to neutralize toxins, modulate inflammatory response, eradicate bacterial and fungal biofilms or prevent their development. The latter properties are of special interest, as most antibiotics available on the market have limited ability to diffuse through rigid structures of biofilms. Lipidation of AMPs is considered as an effective approach for enhancement of their antimicrobial potential and in vivo stability; however, it could also have undesired impact on selectivity, solubility or the aggregation state of the modified peptides. In the present work, we describe the results of structural modifications of compounds designed based on cationic antimicrobial peptides DK5 and CAR-PEG-DK5, derivatized at their N-terminal part with fatty acids with different lengths of carbon chain. The proposed modifications substantially improved antimicrobial properties of the final compounds and their effectiveness in inhibition of biofilm development as well as eradication of pre-formed 24 h old biofilms of Candida albicans and Staphylococcus aureus. The most active compounds (C5-DK5, C12-DK5 and C12-CAR-PEG-DK5) were also potent against multi-drug resistant Staphylococcus aureus USA300 strain and clinical isolates of Pseudomonas aeruginosa. Both experimental and in silico methods revealed strong correlation between the length of fatty acid attached to the peptides and their final membranolytic properties, tendency to self-assemble and cytotoxicity.