On some structural and evolutionary aspects of rDNA amplification in oogenesis of Trachemys scripta turtles.

The features of rDNA amplification have been studied in oocytes of the red-eared slider Trachemys scripta using a number of specific histochemical and cytomolecular methods. A single nucleolus in early diplotene oocytes is associated with the nucleolus organizer region (NOR). With oocyte growth, the number of nucleoli increases dramatically and reaches hundreds by the lampbrush chromosome stage (pre-vitellogenesis). RNA-polymerase I, fibrillarin, and PCNA immunodetection in the amplified nucleoli and FISH of the 5'ETS probe to the oocyte nuclear content suggest pre-rRNA and rDNA synthesis in the nucleoli at all stages studied. This implies a continuous reproduction of the nucleoli during oocyte development from early diplotene up to vitellogenesis. The data obtained offer a different way for rDNA amplification and formation of extrachromosomal nucleoli in turtle oocytes compared with the amplified nucleoli formation in amphibian and fish oocytes. In the Sauropsida clade of Archelosauria, which includes turtles, crocodiles, and birds, rDNA function is known to be suppressed in avian oogenesis during the lampbrush stage (Gaginskaya et al. in Cytogenet Genome Res 124:251-267, 2009).

Magnetically Controlled Carbonate Nanocomposite with Ciprofloxacin for Biofilm Eradication.

Biofilms are the reason for a vast majority of chronic inflammation cases and most acute inflammation. The treatment of biofilms still is a complicated task due to the low efficiency of drug delivery and high resistivity of the involved bacteria to harmful factors. Here we describe a magnetically controlled nanocomposite with a stimuli-responsive release profile based on calcium carbonate and magnetite with an encapsulated antibiotic (ciprofloxacin) that can be used to solve this problem. The material magnetic properties allowed targeted delivery, accumulation, and penetration of the composite in the biofilm, as well as the rapid triggered release of the entrapped antibiotic. Under the influence of an RF magnetic field with a frequency of 210 kHz, the composite underwent a phase transition from vaterite into calcite and promoted the release of ciprofloxacin. The effectiveness of the composite was tested against formed biofilms of E. coli and S. aureus and showed a 71% reduction in E. coli biofilm biomass and an 85% reduction in S. aureus biofilms. The efficiency of the composite with entrapped ciprofloxacin was higher than for the free antibiotic in the same concentration, up to 72%. The developed composite is a promising material for the treatment of biofilm-associated inflammations.

Microbiota and cancer: host cellular mechanisms activated by gut microbial metabolites.

In recent years, more and more data indicate the effect of human microbiota on carcinogenesis. Despite the numerous studies on the relationship between gut microbiota and carcinogenesis, the exact mechanisms of this interaction are not well studied. It becomes apparent that this relationship can be mediated by microbial metabolites. Mechanisms of some well-known bacterial genotoxins and oncogenes, such as colibactin, CagA, IpgD, VirA, P37, have been studied in detail. At the same time, a role in carcinogenesis of a large group of gut microbial metabolites, including short-chain fatty acids, polyamines, and products of polyphenol and tryptophan catabolism, is less well understood. However, more and more evidence data show the effect of bacterial metabolites on cancer development and progression. In this review, we summarize relevant data regarding the possible mechanisms that can account for the effects of gut microbial metabolites mentioned above in carcinogenesis.

New high copy tandem repeat in the content of the chicken W chromosome.

The content of repetitive DNA in avian genomes is considerably less than in other investigated vertebrates. The first descriptions of tandem repeats were based on the results of routine biochemical and molecular biological experiments. Both satellite DNA and interspersed repetitive elements were annotated using library-based approach and de novo repeat identification in assembled genome. The development of deep-sequencing methods provides datasets of high quality without preassembly allowing one to annotate repetitive elements from unassembled part of genomes. In this work, we search the chicken assembly and annotate high copy number tandem repeats from unassembled short raw reads. Tandem repeat (GGAAA)n has been identified and found to be the second after telomeric repeat (TTAGGG)n most abundant in the chicken genome. Furthermore, (GGAAA)n repeat forms expanded arrays on the both arms of the chicken W chromosome. Our results highlight the complexity of repetitive sequences and update data about organization of sex W chromosome in chicken.

Nanostructured Layer-by-Layer Polyelectrolyte Containers to Switch Biofilm Fluorescence.

The development of stimuli-responsive nanocontainers is an issue of utmost importance for many applications such as targeted drug delivery, regulation of the cell and tissue behavior, making bacteria have useful functions and here converting light. The present work shows a new contribution to the design of polyelectrolyte (PE) containers based on surface modified mesoporous titania particles with deposited Ag nanoparticles to achieve chemical light upconversion via biofilms. The PE shell allows slowing down the kinetics of a release of loaded l-arabinose and switching the bacteria luminescence in a certain time. The hybrid TiO2/Ag/PE containers activated at 980 nm (IR) illumination demonstrate 10 times faster release of l-arabinose as opposed to non-activated containers. Fast IR-released l-arabinose switch bacteria fluorescence which we monitor at 510 nm. The approach described herein can be used in many applications where the target and delayed switching and light upconversion are required.

Chicken Microchromosomes in the Lampbrush Phase: A Cytogenetic Description.

Lampbrush chromosomes are giant, transcriptionally active, meiotic chromosomes found in oocytes of all vertebrates with the exception of mammals. Lampbrush chromosomes offer a convenient tool for cytogenetic mapping and, in particular, have been instrumental in mapping genes and linkage groups on chicken (GGA) chromosomes. Whereas cytogenetic maps of macrochromosome GGA1-10 and microchromosome GGA11-16 lampbrush bivalents have been established, identification and description of smaller microchromosome bivalents are still missing. In this work, we used specific FISH probes for the identification of 12 chicken lampbrush chromosomes formed by GGA17-28. Our observations on chromomere and lateral loop arrangement and chiasma position allowed us to construct the respective cytogenetic maps for these microchromosomes. For the 10 smallest chicken microchromosomes, GGA29-38, no individual molecular tags are available, yet they can be collectively marked using the PO41 repeat. The reported results contribute to building of working cytogenetic maps of the chicken karyotype.

Coordination to Imidazole Ring Switches on Phosphorescence of Platinum Cyclometalated Complexes: The Route to Selective Labeling of Peptides and Proteins via Histidine Residues.

In this study, we have shown that substitution of chloride ligand for imidazole (Im) ring in the cyclometalated platinum complex Pt(phpy)(PPh3)Cl (1; phpy, 2-phenylpyridine; PPh3, triphenylphosphine), which is nonemissive in solution, switches on phosphorescence of the resulting compound. Crystallographic and nuclear magnetic resonance (NMR) spectroscopic studies of the substitution product showed that the luminescence ignition is a result of Im coordination to give the [Pt(phpy)(Im)(PPh3)]Cl complex. The other imidazole-containing biomolecules, such as histidine and histidine-containing peptides and proteins, also trigger luminescence of the substitution products. The complex 1 proved to be highly selective toward the imidazole ring coordination that allows site-specific labeling of peptides and proteins with 1 using the route, which is orthogonal to the common bioconjugation schemes via lysine, aspartic and glutamic acids, or cysteine and does not require any preliminary modification of a biomolecule. The utility of this approach was demonstrated on (i) site-specific modification of the ubiquitin, a small protein that contains only one His residue in its sequence, and (ii) preparation of nonaggregated HSA-based Pt phosphorescent probe. The latter particles easily internalize into the live HeLa cells and display a high potential for live-cell phosphorescence lifetime imaging (PLIM) as well as for advanced correlation PLIM and FLIM experiments.

Evolution of ribosomal internal transcribed spacers in Deuterostomia.

Sequences of ribosomal internal transcribed spacers (ITSs) are of great importance to molecular phylogenetics and DNA barcoding, but remain unstudied in some large taxa of Deuterostomia. We have analyzed complete ITS1 and ITS2 sequences in 62 species from 16 Deuterostomia classes, with ITS sequences in 24 species from 11 classes initially obtained using unannotated contigs and raw read sequences. A general tendency for both ITS length and GC-content increase from interior to superior Deuterostomia taxa, a uniform GC-content in both ITSs within the same species, thymine content decrease in sense DNA sequences of both ITSs are shown. A possible role of GC-based gene conversion in Deuterostomia ITS evolutionary changes is hypothesized. The first example of non-LTR retrotransposon insertion into ITS sequence in Deuterostomia is described in turtle Geochelone nigra. The roles of mobile genetic element insertions in the evolution of ITS sequences in some Sauropsida taxa are discussed as well.

Ribosomal RNA gene functioning in avian oogenesis.

Despite long-term exploration into ribosomal RNA gene functioning during the oogenesis of various organisms, many intriguing problems remain unsolved. In this review, we describe nucleolus organizer region (NOR) activity in avian oocytes. Whereas oocytes from an adult avian ovary never reveal the formation of the nucleolus in the germinal vesicle (GV), an ovary from juvenile birds possesses both nucleolus-containing and non-nucleolus-containing oocytes. The evolutionary diversity of oocyte NOR functioning and the potential non-rRNA-related functions of the nucleolus in oocytes are also discussed.

Dual-Function Hydrogel Dressings with a Dynamic Exchange of Iron Ions and an Antibiotic Drug for Treatment of Infected Wounds.

Bacterial infection is a major problem with diabetic wounds that may result in nonhealing chronic ulcers. Here, we report an approach to antibacterial hydrogel dressings for enhanced treatment of infected skin wounds. A fibrous hydrogel was derived from cellulose nanocrystals that were modified with dopamine and cross-linked with gelatin. The hydrogel was loaded with gentamicin, an antibiotic drug. Enhanced antibacterial hydrogel performance resulted from (i) a highly specific sequestration of Fe3+ ions (much needed by bacteria) from the wound exudate and (ii) a dynamic exchange between gentamicin released from the hydrogel and Fe3+ ions withdrawn from the wound exudate. Such exchange was possible due to the high value of the binding constant of Fe3+ ions to dopamine. The hydrogel did not affect the metabolic activity of skin-related cells and showed enhanced antibacterial performance against common wound pathogens such as S. aureus and P. aeruginosa. Furthermore, it promoted healing of infected diabetic wounds due to a synergistic antibacterial effect providing the dynamic exchange between Fe3+ ions and gentamicin. This work provides a strategy for the design of dual-function wound dressings, with both starving and killing bacteria and enhanced wound healing performance.

Detection of Multiplex NASBA RNA Products Using Colorimetric Split G Quadruplex Probes.

Structural RNA is a challenging target for recognition by hybridization probes. This chapter addresses the recognition problem of RNA amplicons in samples obtained by multiplex nucleic acid sequence-based amplification (NASBA). The method describes the design of G-quadruplex binary (split) DNA peroxidase sensors that produces colorimetric signal upon recognition of NASBA amplicons.

Bio-Inspired Surface Modification of Magnetite Nanoparticles with Dopamine Conjugates.

Organically-coated nanomaterials are intensively studied and find numerous applications in a wide range of areas from optics to biomedicine. One of the recent trends in material science is the application of bio-mimetic polydopamine coatings that can be produced on a variety of substrates in a cost-efficient way under mild conditions. Such coatings not only modify the biocompatibility of the material but also add functional amino groups to the surface that can be further modified by classic conjugation techniques. Here we show an alternative strategy for substrates modification using dopamine conjugates instead of native dopamine. Compared to the classic scheme, the proposed strategy allows separation of the "organic" and "colloidal" stages, and simplified identification and purification steps. Modification with pre-modified dopamine made it possible to achieve high loading capacities with active components up to 10.5% wt. A series of organo-inorganic hybrids were synthesized and their bioactivity was analyzed.

Characteristics of the Skin Microbiome in Selected Dermatological Conditions: A Narrative Review.

The skin is the largest and outermost organ of the human body. The microbial diversity of the skin can be influenced by several variable factors such as physiological state, lifestyle, and geographical locations. Recent years have seen increased interest in research aiming at an improved understanding of the relationship between the human microbiota and several diseases. Albeit understudied, interesting correlations between the skin microbiota and several dermatological conditions have been observed. Studies have shown that a decrease or increase in the abundance of certain microbial communities can be implicated in several dermatological pathologies. This narrative review (i) examines the role of the skin microbiota in the maintenance of skin homeostasis and health, (ii) provides examples on how some common skin diseases (acne inversa, candidiasis, psoriasis) are associated with the dysbiosis of microbial communities, and (iii) describes how recent research approaches used in skin microbiome studies may lead to improved, more sensitive diagnostics and individual therapeutics in the foreseeable future.

Fluorescent Hybrid Material Based on Natural Spider Silk and Carbon Dots for Bioapplication.

Since the outcome of an operation largely depends on the quality of wound healing, it is one of the most challenging stages in surgery. Today, wound closure is mostly undertaken by means of a surgical suture. Good surgical sutures are biocompatible and biodegradable and possess excellent mechanical properties. Preferably, these sutures demonstrate optical activity for bacteria detection as there is a risk of surgical site infections. In this study, a solution, which fulfills all the requirements for manufacturing a multifunctional hybrid material, is proposed. In this work, a method for the in situ modification of spider silk with fluorescent carbon dots has been developed. The basic concept is the use of silk fibers as both the main framework for tissue regeneration and a carbon source during carbon dot synthesis. The resulting hybrid material exhibits strong photoluminescence in the red region of the spectrum (590 nm) when irradiated with blue light (480 nm). The proposed approach potentially allows for simultaneous wound closure and pathogen detection.

Heparin-coated iron oxide nanoparticles: application as a liver contrast agent, toxicity and pharmacokinetics.

The prepared heparin-coated iron oxide nanoparticles (Hep-IONPs) contrasted cholangioma tumors in the liver in T2 MRI. The NPs were not toxic to rats and rabbits after 14 days of consecutive IV injections as observed from the monitoring of the body weight and biochemical and hematological parameters. No embryotoxic or immunotoxic side effects of the material were detected. However, we observed mutagenicity of iron oxide NPs in the Ames test and micronucleus assay. The pharmacokinetic studies showed that Hep-IONPs circulated in the blood for 14 days after IV injection. The liver iron level reached its maximum after 6 hours and slowly decreased within 30 days. Altogether, these results suggest that the synthesized Hep-IONPs are promising for use as the MRI contrast agent to identify liver malignancies.

ClO2-Loaded Aerogels with Biocide Effect.

In this work, the mechanism of chlorine dioxide's (ClO2) interaction with aerogel surfaces is described for the first time. To determine the mechanism, three types of aerogels (namely, silica, titania, and zirconia composites) were synthesized and characterized using N2 sorption isotherm analysis, X-ray diffraction analysis, scanning electron microscopy, and X-ray photoelectron spectroscopy. The kinetics of the ClO2 interaction mechanism was investigated via ClO2-controlled sorption and desorption at different temperatures. The process was studied through the theoretical calculation of ClO2 interaction with the aerogel surface. The biocide efficiency of the as-synthesized ClO2-loaded aerogels on different bacteria strains was investigated, and efficient microorganism extermination was demonstrated. This system is a disinfectant that can find potential applications in various fields.

Metal Oxide Nanoparticles Against Bacterial Biofilms: Perspectives and Limitations.

At present, there is an urgent need in medicine and industry to develop new approaches to eliminate bacterial biofilms. Considering the low efficiency of classical approaches to biofilm eradication and the growing problem of antibiotic resistance, the introduction of nanomaterials may be a promising solution. Outstanding antimicrobial properties have been demonstrated by nanoparticles (NPs) of metal oxides and their nanocomposites. The review presents a comparative analysis of antibiofilm properties of various metal oxide NPs (primarily, CuO, Fe3O4, TiO2, ZnO, MgO, and Al2O3 NPs) and nanocomposites, as well as mechanisms of their effect on plankton bacteria cells and biofilms. The potential mutagenicity of metal oxide NPs and safety problems of their wide application are also discussed.

One-pot synthesis of template-free hollow anisotropic CaCO3 structures: towards inorganic shape-mimicking drug delivery systems.

A major obstacle in the introduction of nanoformulated drugs has been the fact that the shape of the drug delivery systems (DDSs) - the most important parameter driven by the nature of viruses and bacteria - remains almost out-of-scope in artificial systems. Here we propose a potential solution for this problem by developing a template-free approach for the formulation of hollow bacteria-like CaCO3-based pH-sensitive DDSs with controllable anisotropy and click-release behavior.

Positive and Negative Effects of Metal Oxide Nanoparticles on Antibiotic Resistance Genes Transfer.

Rapid development of antibiotic resistance in bacteria is a critical public health problem in the world. One of the main routes of resistance development is the transfer of genes containing antibiotic resistance cassettes. Gene transfer can be done through horizontal transfer of genes: transduction, conjugation, and transformation. Many factors in the environment influence these processes, and one of them is the action of metal oxide nanoparticles (MONPs), which can appear in the milieu through both biological synthesis and the release of engineered nanomaterial. In this study, the effect of AlOOH, CuO, Fe3O4, TiO2, and ZnO MONPs on the transformation (heat shock transformation) of bacteria Escherichia coli K12, and the conjugation between E. coli cc118 and E. coli Nova Blue were studied. The MONPs were synthesized by one method and fully characterized. ZnO nanoparticles (NPs) have significantly increased the efficiency of transformation (more than 9-fold), while the other NPs have reduced it to 31 times (TiO2 NPs). AlOOH NPs increased the number of transconjugants more than 1.5-fold, while CuO and Fe3O4 NPs did not have a significant effect on transformation and conjugation. Thus, the data shows that different types of MONPs can enhance or inhibit different gene transfer mechanisms, affecting the spread of antibiotic resistance genes.

Oscillating of physicochemical and biological properties of metal particles on their sonochemical treatment.

Different metal particles are increasingly used to target bacteria as an alternative to antibiotics. Despite numerous data about treating bacterial infections, the utilization of metal particles in antibacterial coatings for implantable devices and medicinal materials promoting wound healing. The antibacterial mechanisms of nanoscale and microscale particles are poorly understood, but the currently accepted mechanisms include oxidative stress induction, metal ion release, and non-oxidative mechanisms. Thus, investigation of the antibacterial mechanisms of nanostructured metal particles is very important for the development of more effective antimicrobial materials. However, it is very difficult to develop a proper model for revealing the antibacterial mechanisms due to difficulty to choose a method that allows obtaining materials of various properties under approximately the same conditions. In this paper, we propose a green and feasible technique to create critical conditions for modification of zinc particles at highly non-equilibrium states. We demonstrate that the sonication process can be useful for fabrication the materials with oscillating physical, chemical and antibacterial properties. We believe this method besides medical applications can be also used in natural science basic research as an experimental tool for modelling the physical and chemical processes. After the sonication, the zinc particles exhibit a different surface morphology and amount of leached Zn2+ ions compared to initial ones. It has been revealed that oscillations of the Zn2+ ions concentration lead to oscillation the antibacterial properties. Thus, the properties of the materials can be easily altered by adjusting the ultrasound energy dissipated via varying the sonication.