Influence of different sample preparation techniques on imaging viruses and virus-like particles by scanning electron and scanning transmission electron microscopes

Scanning electron microscopy (SEM) and scanning transmission electron microscopy (STEM) were applied in many laboratories to visualize and image viruses and virus-like particles (VLPs). Two bacteriophages, P1 and Φ6, were chosen as model microorganisms known for their distinct structure, and viruses obtained from biofilms associated with modern travertines (Terme di Saturnia, Italy; Karahayıt "Kızılsu" and Pamukkale, Turkey) were also investigated. Three protocols, (1) full, (2) simplified, and (3) all at once were developed and tested for sample preparation and imaging. The full procedure enabled the observation of P1 bacteriophages, whereas the simplified protocol, successful in visualizing Φ6, did not yield satisfactory results for P1. The preservation state of the latter appeared to be compromised and led to less informative images in SEM and STEM. Viruses in biofilms exhibited various levels of mineralization and aggregation, complicating their characterization. In the all at once procedure, although effective in preserving bacteriophage tails, excessive coating and thickening of samples with heavy chemical reagents led to a reduction in overall image quality. Despite a final washing step, some residues of chemical reagents (OsO4 and uranyl acetate) remained, impacting the clarity of the images. Finally, the results obtained emphasize the critical role of sample preparation and imaging techniques in effectively visualizing and characterizing viruses and VLPs. The choice of analytical procedure significantly influences the resolution and preservation state of the observed bacteriophages and VLPs. It is suggested that the appropriate imaging technique is carefully selected based on the specific objectives of the project and the nature of the samples being investigated to obtain the best images of the viruses.

Mechanisms of temperature acclimatisation in the psychrotolerant green alga Coccomyxa subellipsoidea C-169 (Trebouxiophyceae)

Despite the interest in different temperature acclimatisations of higher plants, few studies have considered the mechanisms that allow psychrotolerant microalgae to live in a cold environment. Although the analysis of the genomes of some algae revealed the presence of specific genes that encode enzymes that can be involved in the response to stress, this area has not been explored deeply. This work aims to clarify the acclimatisation mechanisms that enable the psychrotolerant green alga Coccomyxa subellipsoidea C-169 to grow in a broad temperature spectrum. The contents of various biochemical compounds in cells, the lipid composition of the biological membranes of entire cells, and the thylakoid fraction as well as the electron transport rate and PSII efficiency were investigated. The results demonstrate an acclimatisation mechanism that is specific for C. subellipsoidea and that allows the maintenance of appropriate membrane fluidity, for example, in thylakoid membranes. It is achieved almost exclusively by changes within the unsaturated fatty acid pool, like changes from C18:2 into C18:3 and C16:2 into C16:3 or vice versa. This ensures, for example, an effective transport rate through PSII and in consequence a maximum quantum yield of it in cells growing at different temperatures. Furthermore, reactions characteristic for both psychrotolerant and mesophilic microalgae, involving the accumulation of lipids and soluble sugars in cells at temperatures other than optimal, were observed. These findings add substantially to our understanding of the acclimatisation of psychrotolerant organisms to a wide range of temperatures and prove that this process could be accomplished in a species-specific manner.

Viruses participate in the organomineralization of travertines

Travertines, which precipitate from high temperature water saturated with calcium carbonate, are generally considered to be dominated by physico-chemical and microbial precipitates. Here, as an additional influence on organomineral formation, metagenomic data and microscopic analyses clearly demonstrate that highly diverse viral, bacterial and archaeal communities occur in the biofilms associated with several modern classic travertine sites in Europe and Asia, along with virus-like particles. Metagenomic analysis reveals that bacteriophages (bacterial viruses) containing icosahedral capsids and belonging to the Siphoviridae, Myoviridae and Podoviridae families are the most abundant of all viral strains, although the bacteriophage distribution does vary across the sampling sites. Icosahedral shapes of capsids are also the most frequently observed under the microscope, occurring as non-mineralized through to mineralized viruses and virus-like particles. Viruses are initially mineralized by Ca-Si amorphous precipitates with subordinate Mg and Al contents; these then alter to nanospheroids composed of Ca carbonate with minor silicate 80-300 nm in diameter. Understanding the roles of bacteriophages in modern carbonate-saturated settings and related organomineralization processes is critical for their broader inclusion in the geological record and ecosystem models.

Surface modification of magnetic nanoparticles by bacteriophages and ionic liquids precursors

Magnetic nanoparticles (MNPs) have recently been a point of interest for many researchers due to their properties. However, the studies on the influence of bacteriophages on the synthesis of MNPs seem to be lacking. Furthermore, bacteriophage-modified MNPs have not been combined with n-alkyl quaternary ammonium ionic liquid precursors (QAS). In this study, the aim was to assess the influence of two distinctly different bacteriophages (Escherichia phage P1 and Pseudomonas phage Φ6) on MNPs synthesis in the presence or absence of QAS. Synthesized MNPs have been characterized with X-ray diffraction (XRD) and Mössbauer spectroscopy in terms of changes in the crystallographic structure; scanning electron microscopy (SEM) for changes in the morphology; and ζ-potential. Moreover, the sorption parameters and the loss of viability of bacteria that interacted with MNPs have been determined. The sorption of bacteria differs significantly among the tested samples. Furthermore, the viability of the bacteria adsorbed on MNPs varies in the presence of QAS, depending on the length of the n-alkyl chain. The study has revealed that MNPs can be bound with bacteriophages. Mössbauer spectroscopy has also revealed the probable influence of bacteriophages on the formation of crystals. However, these phenomena require further studies.

A Non-Invasive Method of Estimating Populations of Tomicus Piniperda on Scots Pine (Pinus Sylvestris L.)

The fully non-invasive method presented here can be used to evaluate Tomicus piniperda L. population sizes in areas subject to strict protection. Data were collected in 2021−2022 in forests containing P. sylvestris, with different stand structures, in the Suchedniowsko-Oblęgorski Landscape Park, Poland. Entomological analyses were carried out on natural traps made from live uncolonised trees. Stepwise regression was used to describe the size of T. piniperda populations. From a set of features representing stem colonisation parameters, stem traits and habitat, the following had a significant effect (p < 0.05) on the total number of galleries of T. piniperda on stems: (1) the number of T. piniperda maternal tunnels in the sixth stem section covering 2.5% of the total length, (2) the length of the stem section with bark thickness greater than 7 mm, and (3) stand structure (homogeneous Scots pine stands). The model can explain 93% (Radj2=0.9333) of the variability in the total number of T. piniperda galleries on trap trees. The mean relative error of estimation is 20.1%. The proposed method is particularly valuable in a climate context. The data obtained enable the prediction of the direct effects of climate change on the population dynamics of T. piniperda in natural forests.

The Effect of Brilliant Blue-Based Plaque-Staining Agents on Aesthetic Orthodontic Appliances

Orthodontic appliances discolour over treatment time, and a yellowish plaque builds up on the contact area of the brackets, adhesive and teeth. Brilliant Blue-based plaque-staining agents (BBPSAs), which increase tooth brushing efficiency, have the potential to support the maintenance of proper oral hygiene during orthodontic treatment. However, they exhibit strong colouring properties, and their impact on the aesthetics of braces remains unclear. Therefore, the aim of this study was to investigate the influence of commercially available BBPSAs on the colour of aesthetic orthodontic materials. A light-cured, colour-changing orthodontic adhesive and new-generation, monocrystalline, sapphire brackets were chosen for the experiments. The effect of the staining agent on the tested materials was investigated in terms of the reaction temperature and time, as well as the presence of black tea-induced impurities on the materials. The CIELAB (Commission Internationale de L'éclairage L* a* b*) colour system parameters were measured, and the colour differences (ΔE*ab and ΔE00-the Commission Internationale de L'éclairage 2000 colour-difference) were determined for the materials under several experimental conditions. The braces' green-red colour expression was positively affected by the BBPSA. Under in vitro conditions, the regular use of the BBPSA for 90 days visibly improved the unfavourable colour change caused by the black tea.

Using Deep Learning for Whole Slide Image Prostate Cancer Diagnosis and Grading in South Florida Veteran Population

Introduction/Objective

Prostate cancer is the most common non-cutaneous malignancy in veterans, with approximately 11,000 new prostate cancer cases diagnosed in the Veteran’s Affairs system each year. Prostate cancer diagnosis and grading can be challenging even for experienced pathologists. Although large VA medical centers have pathologists that specialize in urologic pathology, the vast majority have not. We hypothesized that the AI-augmented diagnosis and grading may provide the solution for such situations.

Methods/Case Report

Dataset consisted of 10,000 prostate biopsy whole slide images (WSI) from the Kaggle PANDA challenge, and 6,000 WSI from the James A. Haley Veterans’ Hospital. Two Classification models were trained on the combined Kaggle and VA datasets using whole slide labels, and not annotated slides that resemble semi-supervised training.

Two-Class Classification to predict Benign: ISUP [0] / Cancerous: ISUP [1,2,3,4,5] Three-Class Classification to predict Benign: ISUP [0] / Low-grade: ISUP [1,2] / High-grade: ISUP [3,4,5] WSI split into “tiles” were used for training the models to reduce whitespace around samples, manage large images, and normalize dimensions/orientations.

Results (if a Case Study enter NA)

Models trained purely as binary and 3-class classifiers performed very well. Two-Class Model:

Accuracy = 0.937

Precision = 0.965

F1 = 0.94

AUC = 0.979

Three-Class Model:

Accuracy 0.89

o Benign:

Precision=0.897

f1=0.928

o Low-grade:

Precision=0.866

f1=0.841

o High-grade:

Precision=0.91

f1=0.878

We plan to develop multi-stage prediction models using these 2-Class and 3-Class classifiers as the first stage and a cancer grade predictor in the second stage.

Conclusion

We successfully showed that AI can augment pathologist’s diagnosis and grading of prostate cancer.

Interactions of Fe-N-S Co-Doped Porous Carbons with Bacteria: Sorption Effect and Enzyme-Like Properties

Carbon-based (nano)materials doped with transition metals, nitrogen and other heteroatoms are considered active heterogeneous catalysts in a wide range of chemical processes. Recently they have been scrutinized as artificial enzymes since they can catalyze proton-coupled electron transfer reactions vital for living organisms. Herein, interactions between Gram-positive and Gram-negative bacteria and either metal-free N and/or S doped or metal containing Fe-N-S co-doped porous carbons are studied. The Fe- and N-co-doped porous carbons (Fe-N-C) exhibit enhanced affinity toward bacteria as they show the highest adsorption capacity. Fe-N-C materials also show the strongest influence on the bacteria viability with visible toxic effect. Both types of bacteria studied reacted to the presence of Fe-doped carbons in a similar manner, showing a decrease in dehydrogenases activity in comparison to controls. The N-coordinated iron-doped carbons (Fe-N-C) may exhibit oxidase/peroxidase-like activity and activate O2 dissolved in the solution and/or oxygen-containing species released by the bacteria (e.g., H2O2) to yield highly bactericidal reactive oxygen species. As Fe/N/ and/or S-doped carbon materials efficiently adsorb bacteria exhibiting simultaneously antibacterial properties, they can be applied, inter alia, as microbiological filters with enhanced biofouling resistance.

Herbicidal Ionic Liquids Containing the Acetylcholine Cation

This study presents a new group of herbicidal ionic liquids (HILs) based on a cation occurs commonly in nature-acetylcholine. The HILs were obtained with a high yield through ion exchange between acetylcholine chloride and potassium or sodium salts of selected acids with herbicidal activity. The results of the herbicidal activity measurement against common oilseed rape (Brassica napus L.) exceeded those of the commercial products. Spray solutions of the synthesized HILs revealed high surface activity and wetting properties which further manifested as higher herbicidal activity. The reduction of surface tension and low contact angles together with the specific action of acetylcholine allowed for better penetration of synthesized HILs into plant tissues. In addition, OECD 301F tests confirmed high mineralization of the HILs. The simple transformation of commercial herbicides into acetylcholine HILs proved to be a very effective method of increasing their activity, and constitutes an interesting solution to the problem of weed infestation with the use of a substance commonly found in nature.

Transformation of herbicides into dual function quaternary tropinium salts

Quaternary tropinium salts as novel, efficient herbicides and plant-growth promoting agents in case of crops.

Hybrid electrochemical and biological treatment of herbicidal ionic liquids comprising the MCPA anion

The present study was focused on the application of an electrochemical oxidation process combined with biodegradation for the removal of novel Herbicidal Ionic Liquids (HILs) -promising protection plant products which incorporate herbicidal anions and ammonium cations. The influence of carbon chain length (n = 8, 10, 12, 14, 16, 18) in the dialkyldimethylammonium cations on electrochemical oxidation kinetics, degradation efficiency and biodegradation by activated sludge was investigated. It was established that the applied cation influenced the heterogeneous rate constant and diffusion coefficient of electrochemical oxidation. The oxidation efficiency ranged from 17% in case of HILs with C8 alkyl chain to approx. 60% in case of HILs comprising C14 and C16 alkyl chains after 3 h of electrochemical treatment. Subsequent biodegradation studies revealed that electrochemical oxidation improved the mineralization efficiency of the studied HILs. The mineralization efficiency of electrochemically-treated HILs ranged from 28% in case of HILs comprising the C8 alkyl chain to 57% in case of HILs with C14 and C16 alkyl chains after 28 days. In case of untreated HILs, the corresponding mineralization efficiency ranged from 0 to 8%, respectively. This confirms the feasibility of a hybrid electrochemical-biological approach for treatment of herbicidal ionic liquids based on MCPA.

A benzimidazole-based ruthenium(IV) complex inhibits Pseudomonas aeruginosa biofilm formation by interacting with siderophores and the cell envelope, and inducing oxidative stress

Pseudomonas aeruginosa biofilm-associated infections are a serious medical problem, and new compounds and therapies acting through novel mechanisms are much needed. Herein, the authors report a ruthenium(IV) complex that reduces P. aeruginosa PAO1 biofilm formation by 84%, and alters biofilm morphology and the living-to-dead cell ratio at 1 mM concentration. Including the compound in the culture medium altered the pigments secreted by PAO1, and fluorescence spectra revealed a decrease in pyoverdine. Scanning electron microscopy showed that the ruthenium complex did not penetrate the bacterial cell wall, but accumulated on external cell structures. Fluorescence quenching experiments indicated strong binding of the ruthenium complex to both plasmid DNA and bovine serum albumin. Formamidopyrimidine DNA N-glycosylase (Fpg) protein digestion of plasmid DNA isolated after ruthenium(IV) complex treatment revealed the generation of oxidative stress, which was further proved by the observed upregulation of catalase and superoxide dismutase gene expression.

Ionic liquids strongly affect the interaction of bacteria with magnesium oxide and silica nanoparticles

The antibacterial properties of nanoparticles can be strongly affected by interactions with ionic liquids.

Adaptation of bacteria Escherichia coli in presence of quaternary ammonium ionic liquids

This paper presents the adaptation of Escherichia coli Gram-negative bacteria to increased concentrations of ionic liquids. Theophylline-based quaternary ammonium salts were used as an example of an ionic liquid that on the one hand includes an anion of natural origin and on the other hand is characterized by amphiphilic properties due to aliphatic chains in its structure. Theophylline-based ionic liquids can be synthesized relatively cheaply and easily and can exhibit strong antibacterial properties depending on the alkyl chain length. These compounds can also strongly affect bacterial membrane properties, including changes in electrokinetic potential as well as net surface charge. The experiments performed in this study succeeded in obtaining bacterial cultures growing at a tetradecyltrimethylammonium theophyllinate concentration three times higher than the minimum inhibition and bactericidal concentration. The adapted bacteria were characterized by intriguing changes in morphology and grew in the form of almost one-millimeter spheres in a liquid medium. It was shown that cultivation of adapted bacteria with tetradecyltrimethylammonium theophyllinate resulted in changes in the lipid membrane composition and protein patterns of the bacterial lysates, depending on the ionic liquid concentration. This study also revealed that such bacterial adaptation can increase sensitivity to antibiotics by affecting membrane properties like ionophores. These results can be potentially important with regard to synergistic or antagonistic action with other bactericidal compounds like antibiotics and nanoparticles.

The effect of dietary level of two inulin types differing in chain length on biogenic amine concentration, oxidant-antioxidant balance and DNA repair in the colon of piglets

The effect of dietary level of two types of inulin on amine concentration, redox status and DNA glycosylase activity in the colon of piglets was investigated. Seven groups of piglets were fed diets without inulin addition (control) or with 1%, 2% or 3% inulin with an average degree of polymerisation of 10 (IN10) or 23 (IN23) for 40 days. The 2% and 3% IN10 diets increased tryptamine concentration in the proximal colon, while methylamine concentration in the distal colon was increased by the 1% and 3% IN10 diets. The 1% and 2% IN23 diets increased phenylethylamine and methylamine concentration in the proximal colon, respectively, while 1,7-diaminoheptane content was increased by both diets. Its concentration in the middle and distal colon was increased by the 1% and 2% IN23 diet, respectively. There was no improvement in the oxidant-antioxidant balance in colonic digesta of piglets fed IN10 and IN23 diets. Piglets fed IN10 diets had lower 1,N⁶-etheno-2’-deoxyadenosine excision activity in each colon segment, as compared with the control group. It was also reduced by the 2% and 3% IN23 diets in the proximal colon, while in the middle and distal colon by all IN23 diets. Feeding all IN10 and IN23 diets reduced 3,N⁴-etheno-2’-deoxycytidine and 8-oxo-deoxyguanosine excision activities in each colon segment. Feeding IN10 and IN23 diets neither decreased amine concentrations nor improved the oxidant-antioxidant balance in colonic digesta of piglets. However, both types of inulin efficiently reduced the activity of DNA repair enzymes.

Esterquat herbicidal ionic liquids (HILs) with two different herbicides: evaluation of activity and phytotoxicity

Novel weed control agents in the form of herbicidal ionic liquids comprising two different herbicides as a cation and an anion.

Bacterial Communities from the Arsenic Mine in Złoty Stok, Sudety Mountains, Poland

Investigations of bacterial communities and characterization of mineralogy of the environment in the Złoty Stok As-Au deposit were carried out. PXRD analysis revealed the presence of picropharmacolite as the most common secondary arsenic mineral in the mine. Total DNA was extracted from slime streams or slime biofilms samples to investigate the bacterial communities. PCR amplification of 16S rDNA was performed followed by subcloning of its products. Over 170 clones were analyzed by means of RFLP method. Eight group of clones representing different restriction patterns were identified. The nucleotide sequences of their inserts suggest that bacteria present in the mine environment belong to: Flavobacteria, Sphingobacteriia, Bacteroides, Proteobacteria, Mollicutes and Firmicutes. The metagenomic approach allows to demonstrate a higher diversity of microbiota than classical microbiological studies of cultivable isolates.

A Direct Georeferencing Method for Terrestrial Laser Scanning Using GNSS Data and the Vertical Deflection from Global Earth Gravity Models

Terrestrial laser scanning is an efficient technique in providing highly accurate point clouds for various geoscience applications. The point clouds have to be transformed to a well-defined reference frame, such as the global Geodetic Reference System 1980. The transformation to the geocentric coordinate frame is based on estimating seven Helmert parameters using several GNSS (Global Navigation Satellite System) referencing points. This paper proposes a method for direct point cloud georeferencing that provides coordinates in the geocentric frame. The proposed method employs the vertical deflection from an external global Earth gravity model and thus demands a minimum number of GNSS measurements. The proposed method can be helpful when the number of georeferencing GNSS points is limited, for instance in city corridors. It needs only two georeferencing points. The validation of the method in a field test reveals that the differences between the classical georefencing and the proposed method amount at maximum to 7 mm with the standard deviation of 8 mm for all of three coordinate components. The proposed method may serve as an alternative for the laser scanning data georeferencing, especially when the number of GNSS points is insufficient for classical methods.

Evolution in the approach to overlooked ureteral injuries after gynecological surgery

OBJECTIVES

To analyzed the therapeutic results for patients with overlooked iatrogenic ureteral injuries after gynecological surgery, treated at the department since 1990. Before the era of endourology, ureteral injuries were operated on immediately after making a diagnosis. This approach was changed after the popularization of percutaneous nephrostomy (PN) and ureteral stenting using a JJ stent.

MATERIAL AND METHODS

27 patients who were diagnosed with a ureteral injury between the first and sixty-fourth day after injury were included. Only PN was performed in 21 patients (group A). In 6 patients, a JJ stent was introduced either immediately after making a diagnosis or after PN (group B).

RESULTS

In group A, a good therapeutic result was obtained in only 6 patients (28.6%). Of the 12 patients subjected to PN up to two weeks after injury, 5 had a good result without a need for repair surgery. Of the 9 patients with an injury diagnosed after 3 weeks, only one had a good therapeutic outcome. In Group B, a good result was achieved in 5 out of 6 patients. In 2 patients, a JJ stent was introduced immediately after making the diagnosis, and, in 3 patients, after PN. A successful attempt to "tunnelize" a complete and long obstruction in the sixth patient failed.

CONCLUSIONS

Attempting to introduce a JJ stent should be the treatment of choice in patients with an overlooked iatrogenic ureteral injury. If an attempt to introduce the JJ stent fails, PN should be performed as a first step to manage the injury.

Influence of oligomeric herbicidal ionic liquids with MCPA and Dicamba anions on the community structure of autochthonic bacteria present in agricultural soil

The aim of this study was to evaluate the impact of selected herbicidal ionic liquids (HILs), which exhibit high efficacy in terms of weed control and low toxicity, but may be persistent due to limited biodegradability, on the community structure of autochthonic bacteria present in agricultural soil. Four different oligomeric HILs (with two types of cations and different ratio of herbicidal anions) were synthesized and characterized by employing (1)H and (13)C NMR. The results of biodegradation assay indicated that none of the tested HILs could be classified as readily biodegradable (biodegradation rate ranged from 0 to 7%). The conducted field studies confirmed that the herbicidal efficacy of the HILs was higher compared to the reference herbicide mixture by 10 to 30%, depending on the dose and weed species. After termination of field studies, the soil treated with the tested HILs was subjected to next generation sequencing in order to investigate the potential changes in the bacterial community structure. Proteobacteria was the dominant phylum in all studied samples. Treatment with the studied HILs resulted in an increase of Actinobacteria compared to the reference herbicidal mixture. Differenced among the studied HILs were generally associated with a significantly higher abundance of Bacteroidetes in case of 1-HIL-Dicamba 1/3 and Firmicutes in case of 2-HIL-Dicamba 1/3.

Different antibacterial activity of novel theophylline-based ionic liquids - Growth kinetic and cytotoxicity studies

The aim of this study was to investigate novel theophylline-based ionic liquids and their cytotoxic effects towards model Gram-positive and Gram-negative bacteria (Bacillus cereus and Escherichia coli, respectively). Growth kinetics, respiratory rates and dehydrogenase activities were studied in the presence of ionic liquids at concentrations ranging from 10 to 1000mg/L. Additionally, the influence of ionic liquids on bacterial cells associated with specific interactions based on the structure of cell wall was evaluated. This effect was assessed by viability tests and scanning electron microscope observations. The obtained results confirmed that ionic liquids exhibit different levels of toxicity in relation to Gram-positive and Gram-negative bacteria. Those effects are associated with the chemical structure of the cationic species of the ionic liquids and their critical micelle concentration value. It was established that the presence of an alkyl or allyl group increased the toxicity, whereas the presence of an aryl group in the cation decreased the toxic effect of ILs. Results presented in this study also revealed unexpected effects of self-aggregation of E. coli cells. Overall, it was established that the studied ILs exhibited higher toxicity towards Gram-positive bacteria due to different interactions between the ILs and the cell membranes. These findings may be of importance for the design of ILs with targeted antimicrobial properties.

UAV-BASED AUTOMATIC TREE GROWTH MEASUREMENT FOR BIOMASS ESTIMATION

Manual in-situ measurements of geometric tree parameters for the biomass volume estimation are time-consuming and economically non-effective. Photogrammetric techniques can be deployed in order to automate the measurement procedure. The purpose of the presented work is an automatic tree growth estimation based on Unmanned Aircraft Vehicle (UAV) imagery. The experiment was conducted in an agriculture test field with scots pine canopies. The data was collected using a Leica Aibotix X6V2 platform equipped with a Nikon D800 camera. Reference geometric parameters of selected sample plants were measured manually each week. In situ measurements were correlated with the UAV data acquisition. The correlation aimed at the investigation of optimal conditions for a flight and parameter settings for image acquisition. The collected images are processed in a state of the art tool resulting in a generation of dense 3D point clouds. The algorithm is developed in order to estimate geometric tree parameters from 3D points. Stem positions and tree tops are identified automatically in a cross section, followed by the calculation of tree heights. The automatically derived height values are compared to the reference measurements performed manually. The comparison allows for the evaluation of automatic growth estimation process. The accuracy achieved using UAV photogrammetry for tree heights estimation is about 5cm.

Interaction of Gram-Positive and Gram-Negative Bacteria with Ceramic Nanomaterials Obtained by Combustion Synthesis - Adsorption and Cytotoxicity Studies

This paper presents the interactions of Gram-positive (Staphylococcus aureus) and Gram-negative (Pseudomonas putida) bacteria with ceramic materials obtained by combustion synthesis. These studies were conducted based on an analysis of the adsorption of bacteria onto aggregates of ceramic materials in an aqueous suspension. The materials used in the studies were of a nanostructured nature and consisted mainly of carbides: silicon carbide (SiC) in the form of nanofibers (NFs) and nanorods (NRs), titanium carbide, and graphite, which can also be formed by combustion synthesis. Micrometric SiC was used as a reference material. Gram-positive bacteria adsorbed more strongly to these materials. It seems that both the point of zero charge value and the texture of the ceramic material affected the bacterial adsorption process. Additionally, the viability of bacteria adsorbed onto aggregates of the materials decreased. Generally, P. putida cells were more sensitive to the nanomaterials than S. aureus cells. The maximum loss of viability was noted in the case of bacteria adsorbed onto NRSiC and NFSiC aggregates.

Interaction of Gram-Positive and Gram-Negative Bacteria with Ceramic Nanomaterials Obtained by Combustion Synthesis – Adsorption and Cytotoxicity Studies

This paper presents the interactions of Gram-positive (Staphylococcus aureus) and Gram-negative (Pseudomonas putida) bacteria with ceramic materials obtained by combustion synthesis. These studies were conducted based on an analysis of the adsorption of bacteria onto aggregates of ceramic materials in an aqueous suspension. The materials used in the studies were of a nanostructured nature and consisted mainly of carbides: silicon carbide (SiC) in the form of nanofibers (NFs) and nanorods (NRs), titanium carbide, and graphite, which can also be formed by combustion synthesis. Micrometric SiC was used as a reference material. Gram-positive bacteria adsorbed more strongly to these materials. It seems that both the point of zero charge value and the texture of the ceramic material affected the bacterial adsorption process. Additionally, the viability of bacteria adsorbed onto aggregates of the materials decreased. Generally, P. putida cells were more sensitive to the nanomaterials than S. aureus cells. The maximum loss of viability was noted in the case of bacteria adsorbed onto NRSiC and NFSiC aggregates.

Evaluation and management of male lower urinary tract symptoms: treatment patterns and guidelines in a correlation study among Polish urology consultants

INTRODUCTION

In March 2013, the European Association of Urology (EAU) released a new edition of the guidelines on management of male lower urinary tract symptoms (LUTS), including benign prostatic obstruction. The objective of this study was to evaluate how well the EAU guidelines have been implemented in day-to-day practice by Polish urologists.

MATERIAL AND METHODS

A structured questionnaire, which explored how urologists diagnose and manage male lower urinary tract symptoms, was emailed to all certified, actively practicing urologists from a list provided by the Polish Urological Association.

RESULTS

The questionnaire return rate was 33.7% (135/400). Overall, the median (quartile 1; quartile 3) frequency of correct answers was 65.0% (58.0%; 69.0%). Analysis of the association of availability and acceptance of the EAU guidelines with question answers showed no pattern. A multivariate regression model showed a positive correlation with regards to correct answers given in the survey and doctors' participation in international congresses (p = 0.018, r = 0.181). Basket analysis showed the strongest association for those who failed to correctly answer the questions regarding diagnosis of LUTS and overactive bladder (OAB) (support = 27.41%, confidence = 86.05%).

CONCLUSIONS

Although there is a significant degree of adherence to the 2013 EAU guidelines, some discrepancies between urologists' practice and the recommendations regarding diagnosis and treatment of male LUTS do exist. The data obtained provide valuable benchmarks and also identify possible interventions that may improve the standard of care in this population of patients.

Oxidative stress in bacteria (Pseudomonas putida) exposed to nanostructures of silicon carbide

Silicon carbide (SiC) nanostructures produced by combustion synthesis can cause oxidative stress in the bacterium Pseudomonas putida. The results of this study showed that SiC nanostructures damaged the cell membrane, which can lead to oxidative stress in living cells and to the loss of cell viability. As a reference, micrometric SiC was also used, which did not exhibit toxicity toward cells. Oxidative stress was studied by analyzing the activity of peroxidases, and the expression of the glucose-6-phosphate dehydrogenase gene (zwf1) using real-time PCR and northern blot techniques. Damage to nucleic acid was studied by isolating and hydrolyzing plasmids with the formamidopyrimidine [fapy]-DNA glycosylase (also known as 8-oxoguanine DNA glycosylase) (Fpg), which is able to detect damaged DNA. The level of viable microbial cells was investigated by propidium iodide and acridine orange staining.

Adsorption studies of the gram-negative bacteria onto nanostructured silicon carbide

In this study, we demonstrated a significant adsorption of Pseudomonas putida bacteria onto aggregates of nanofibers (NFSiC) and nanorods (NRSiC) of silicon carbide (SiC) in aqueous suspensions. Langmuir and Freundlich isotherms were used to quantify adsorption affinities. It was found that adsorption of the bacteria strongly depended on the structure of the silicon carbide and the pH of the aqueous solution, which affected the isoelectric point of both the silicon carbide and the bacterial cells. The strongest affinity of bacteria was noted in the case of NRSiC aggregates. Affinity was inversely proportional to pH. Similarly, the adsorption of bacteria to the surface of the aggregates increased with decreasing pH. For NFSiC, the affinity of the bacteria for the surface of the aggregates was also inversely proportional to pH. However, adsorption increased at higher pH values. This discrepancy was explained by microscopic analysis, which showed that the bacterial cells were both adsorbed onto and trapped by NFSiC. The adsorption of bacteria onto a micrometric silicon carbide reference material was significantly smaller than adsorption onto nanostructured SiC.

Ammonium ionic liquids with anions of natural origin

Ammonium ionic liquids with anions of natural origin are biodegradable agents with antifeedant and anti-microbial activity.

Biologically-Induced Precipitation of Minerals in a Medium with Zinc Under Sulfate-Reducing Conditions

Sulfate-reducing microbial communities were enriched from soils collected in areas with crude-oil exploitation. Cultures were grown in modified Postgate C medium and minimal medium, with ethanol or lactate as an electron donor. The batch cultures were grown with addition of zinc in concentrations of 100-700 mg/l. A lack of increased protein concentration in the solutions compared with the control batch, was noted in cultures containing over 200 mg Zn2+/l. The 16S rRNA method was applied to determine the specific composition of the selected microorganism communities. The analysis indicated the presence of Desulfovibrio spp., Desulfobulbus spp. and Desulfotomaculum spp. in the communities. Diffractometric analysis indicated the presence of biogenic sphalerite in cultures with 100 and 200 mg Zn2+/l and elemental sulfur in cultures with 200 mg Zn2+/l. Other post culture sediments (300-700 mg Zn2+/l) contained only hopeite [Zn3(PO4)2·4H2O] formed abiotically during the experiment, which was confirmed by studies of the activity of sulfate-reducing microbial communities.

Toxicity assessment of SiC nanofibers and nanorods against bacteria

In the present study, evidence of the antibacterial effects of silicon carbide (SiC) nanofibers (NFSiC) and nanorods (NRSiC) obtained by combustion synthesis has been presented. It has been shown that the examined bacteria, Pseudomonas putida, could bind to the surface of the investigated SiC nanostructures. The results of respiration measurements, dehydrogenase activity measurements, and evaluation of viable bacteria after incubation with NFSiC and NRSiC demonstrated that the nanostructures of SiC affect the growth and activity of the bacteria examined. The direct count of bacteria stained with propidium iodide after incubation with SiC nanostructures revealed that the loss of cell membrane integrity could be one of the main effects leading to the death of the bacteria.

The presence of prostate cancer at biopsy is predicted by a number of genetic variants

Several single nucleotide polymorphisms (SNPs) have been associated with an elevated risk of prostate cancer risk. It is not established if they are useful in predicting the presence of prostate cancer at biopsy or if they can be used to define a low-risk group of men. In this study, 4,548 men underwent a prostate biopsy because of an elevated prostate specific antigen (PSA; ≥4 ng/mL) or an abnormal digital rectal examination (DRE). All men were genotyped for 11 selected SNPs. The effect of each SNP, alone and in combination, on prostate cancer prevalence was studied. Of 4,548 men: 1,834 (40.3%) were found to have cancer. A positive association with prostate cancer was seen for 5 of 11 SNPs studied (rs1800629, rs1859962, rs1447295, rs4430796, rs11228565). The cancer detection rate rose with the number of SNP risk alleles from 29% for men with no variant to 63% for men who carried seven or more risk alleles (OR = 4.2; p = 0.002). The SNP data did not improve the predictive power of clinical factors (age, PSA and DRE) for detecting prostate cancer (AUC: 0.726 vs. 0.735; p = 0.4). We were unable to define a group of men with a sufficiently low prevalence of prostate cancer that a biopsy might have been avoided. In conclusion, our data do not support the routine use of SNP polymorphisms as an adjunct test to be used on the context of prostate biopsy for Polish men with an abnormal screening test.

The G84E mutation in the HOXB13 gene is associated with an increased risk of prostate cancer in Poland

BACKGROUND

The G84E mutation in the HOXB13 gene has been associated with a high lifetime risk of prostate cancer in North America (about 20-fold). The geographical and ethnic extent of this recurrent allele has not yet been determined.

METHODS

We assayed for the presence of the G84E mutation in 3,515 prostate cancer patients and 2,604 controls from Poland and estimated the odds ratio for prostate cancer associated with the allele.

RESULTS

The G84E mutation was detected in 3 of 2,604 (0.1%) individuals from the general population in Poland and in 20 of 3,515 (0.6%) men with prostate cancer (Odds ratio [OR] = 5.0; 95% CI: 1.5-16.7; P = 0.008). The allele was present in 4 of 416 (1.0%) men with familial prostate cancer (OR = 8.4, 95% CI: 1.9-37.7; P = 0.005).

CONCLUSIONS

The G84E mutation predisposes to prostate cancer in Poland, but accounts for only a small proportion of cases. We expect that the G84E founder mutation might be present in other Slavic populations.

Adsorption studies of azotetrazolate and 3,6-dihydrazinotetrazine on peat

The objective of our studies was the evaluation of the adsorption process of two high-nitrogen compounds-dihydrazinotetrazine (DHTz) and azotetrazolate ion (AZ)-on a chosen peat. The experiments were performed using a static method at three different temperatures (283, 298, and 333 K). The adsorption process of DHTz and AZ on peat was characterized by isotherms according to the Freundlich and Langmuir models. The obtained correlations between adsorption and equilibrium concentration were in good accordance with the Freundlich and Langmuir models, as confirmed by high values of the correlation coefficients (0.97-0.99). Adsorption of AZ on peat was less efficient than that of DHTz, and this inference was experimentally proven. The maximum surface coverages of peat particles with adsorbate according to the Langmuir model were calculated as 0.02 and 0.17 mol kg(-1) (at 298 K) for AZ and DHTz, respectively. The determined adsorption equilibrium constants confirmed greater adsorption of DHTz on the investigated peat. It can be concluded that adsorption of AZ occurred to a much lesser extent compared to that of DHTz, pointing to a potentially greater threat of migration of soluble azotetrazolates in soil. Standard enthalpies of adsorption estimated for AZ and DHTz were -11.1 and -23.7 kJ mol(-1), respectively. Based on these adsorption enthalpy values, it can be stated that both investigated compounds are adsorbed on peat by a physisorption process.

An inherited NBN mutation is associated with poor prognosis prostate cancer

BACKGROUND

To establish the contribution of eight founder alleles in three DNA damage repair genes (BRCA1, CHEK2 and NBS1) to prostate cancer in Poland, and to measure the impact of these variants on survival among patients.

METHODS

Three thousand seven hundred fifty men with prostate cancer and 3956 cancer-free controls were genotyped for three founder alleles in BRCA1 (5382insC, 4153delA, C61G), four alleles in CHEK2 (1100delC, IVS2+1G>A, del5395, I157T), and one allele in NBS1 (657del5).

RESULTS

The NBS1 mutation was detected in 53 of 3750 unselected cases compared with 23 of 3956 (0.6%) controls (odds ratio (OR)=2.5; P=0.0003). A CHEK2 mutation was seen in 383 (10.2%) unselected cases and in 228 (5.8%) controls (OR=1.9; P<0.0001). Mutation of BRCA1 (three mutations combined) was not associated with the risk of prostate cancer (OR=0.9; P=0.8). In a subgroup analysis, the 4153delA mutation was associated with early-onset (age ≤ 60 years) prostate cancer (OR=20.3, P=0.004). The mean follow-up was 54 months. Mortality was significantly worse for carriers of a NBS1 mutation than for non-carriers (HR=1.85; P=0.008). The 5-year survival for men with an NBS1 mutation was 49%, compared with 72% for mutation-negative cases.

CONCLUSION

A mutation in NBS1 predisposes to aggressive prostate cancer. These data are relevant to the prospect of adapting personalised medicine to prostate cancer prevention and treatment.

A prospective, randomised EORTC intergroup phase 3 study comparing the oncologic outcome of elective nephron-sparing surgery and radical nephrectomy for low-stage renal cell carcinoma

BACKGROUND

Nephron-sparing surgery (NSS) can safely be performed with slightly higher complication rates than radical nephrectomy (RN), but proof of oncologic effectiveness is lacking.

OBJECTIVE

To compare overall survival (OS) and time to progression.

DESIGN, SETTING, AND PARTICIPANTS

From March 1992 to January 2003, when the study was prematurely closed because of poor accrual, 541 patients with small (≤5 cm), solitary, T1-T2 N0 M0 (Union Internationale Contre le Cancer [UICC] 1978) tumours suspicious for renal cell carcinoma (RCC) and a normal contralateral kidney were randomised to NSS or RN in European Organisation for Research and Treatment of Cancer Genito-Urinary Group (EORTC-GU) noninferiority phase 3 trial 30904.

INTERVENTION

Patients were randomised to NSS (n=268) or RN (n=273) together with limited lymph node dissection (LND).

MEASUREMENTS

Time to event end points was compared with log-rank test results.

RESULTS AND LIMITATIONS

Median follow-up was 9.3 yr. The intention-to-treat (ITT) analysis showed 10-yr OS rates of 81.1% for RN and 75.7% for NSS. With a hazard ratio (HR) of 1.50 (95% confidence interval [CI], 1.03-2.16), the test for noninferiority is not significant (p=0.77), and test for superiority is significant (p=0.03). In RCC patients and clinically and pathologically eligible patients, the difference is less pronounced (HR=1.43 and HR=1.34, respectively), and the superiority test is no longer significant (p=0.07 and p=0.17, respectively). Only 12 of 117 deaths were the result of renal cancer (four RN and eight NSS). Twenty-one patients progressed (9 after RN and 12 after NSS). Quality of life and renal function outcomes have not been addressed.

CONCLUSIONS

Both methods provide excellent oncologic results. In the ITT population, NSS seems to be significantly less effective than RN in terms of OS. However, in the targeted population of RCC patients, the trend in favour of RN is no longer significant. The small number of progressions and deaths from renal cancer cannot explain any possible OS differences between treatment types.

Regional and age-specific patterns of pandemic H1N1 influenza virus seroprevalence inferred from vaccine clinical trials, August-October 2009

The extent of the H1N1 pandemic has been estimated from case counts and deaths but the proportion of exposed populations with inapparent infections has not been described in detail. We analysed haemagglutination-inhibition (HI) antibody titres of pre-vaccination sera from pandemic vaccine trials conducted in six countries on four continents to provide an indication of A/CA/07/2009(H1N1)-like influenza seroprevalence in those populations. Among 7,962 subjects, ranging in age from 12 months to over 60 years, the proportions with HI antibody titres > or =40 to the H1N1pnd virus in the period from August to October 2009 were, by country: Costa Rica 26.4%, United States (US) 22.5%, Switzerland 16.9%, Germany 12.6%, Belgium 10.1%, and Japan 5.9%. Age-specific seropositivity rates in the samples were higher in children and adolescents in Costa Rica and in the US than in Europe and in Japan. The low proportion of seropositive children in Europe and Japan suggests that little local viral transmission had occurred in those regions even as late as September and October 2009, while in the US and Costa Rica, the greater proportion of previously infected children and young adults suggested that a significant number of asymptomatic infections had occurred during the first pandemic wave. Nevertheless, in all locations, the majority of the population remained susceptible to the pandemic virus at the beginning of the influenza season in the northern hemisphere, justifying the implementation of public health interventions.

Regional and age-specific patterns of pandemic H1N1 influenza virus seroprevalence inferred from vaccine clinical trials, August-October 2009

The extent of the H1N1 pandemic has been estimated from case counts and deaths but the proportion of exposed populations with inapparent infections has not been described in detail. We analysed haemagglutination-inhibition (HI) antibody titres of pre-vaccination sera from pandemic vaccine trials conducted in six countries on four continents to provide an indication of A/CA/07/2009(H1N1)-like influenza seroprevalence in those populations. Among 7,962 subjects, ranging in age from 12 months to over 60 years, the proportions with HI antibody titres ≥40 to the H1N1pnd virus in the period from August to October 2009 were, by country: Costa Rica 26.4%, United States (US) 22.5%, Switzerland 16.9%, Germany 12.6%, Belgium 10.1%, and Japan 5.9%. Age-specific seropositivity rates in the samples were higher in children and adolescents in Costa Rica and in the US than in Europe and in Japan. The low proportion of seropositive children in Europe and Japan suggests that little local viral transmission had occurred in those regions even as late as September and October 2009, while in the US and Costa Rica, the greater proportion of previously infected children and young adults suggested that a significant number of asymptomatic infections had occurred during the first pandemic wave. Nevertheless, in all locations, the majority of the population remained susceptible to the pandemic virus at the beginning of the influenza season in the northern hemisphere, justifying the implementation of public health interventions.

MF59-adjuvanted influenza vaccine (FLUAD) in children: safety and immunogenicity following a second year seasonal vaccination

After priming with two intramuscular doses of MF59-adjuvanted (Sub/MF59) or split influenza vaccines during the 2006/07 season, 89 healthy children received a third booster dose of the respective vaccine (2007/08 Northern Hemisphere formulation) approximately 1 year later, and were followed up for 6 months post-third injection. Immunogenicity was evaluated on 81 of them by a hemagglutination inhibition (HI) assay before and 3 weeks after vaccination. The Sub/MF59 influenza vaccine was safe and well tolerated following the booster vaccination. Pre-booster HI antibody titers were consistently higher in the Sub/MF59 group than in the comparator group, confirming significantly longer persistence of antibodies after priming with Sub/MF59 vaccine. Post-booster immune responses were significantly higher in the Sub/MF59 group compared with the split group, especially vs. the influenza B strain, which is epidemiologically relevant in the pediatric population. Altogether, these data further support the potential use of MF59-adjuvanted influenza vaccine as a safe and highly immunogenic influenza vaccine for young children.

Multiple sclerosis produces significant changes in urinary bladder innervation which are partially reflected in the lower urinary tract functional status-sensory nerve fibers role in detrusor overactivity

BACKGROUND

Detrusor overactivity is often observed in patients with multiple sclerosis (MS), and neurotoxins are emerging as second-line therapies albeit with different degrees of success per patient basis.

OBJECTIVE

To investigate lower urinary tract (LUT) functional status and bladder innervation (calcitonin gene related peptide [CGRP] and substance P [SP] positive nerve fibers) in patients with MS.

METHOD

Eighteen MS patients with LUT symptoms underwent urodynamic investigations, and six non-MS patients undergoing cystoscopy due to microscopic hematuria served as controls. Cold cut bladder biopsies were taken from the bladder trigone region. Neurotransmitter expression was determined by individual immunohistochemical staining.

RESULTS

Two distinct groups could be distinguished: group 1 with pronounced neurogenic detrusor overactivity and mild outflow obstruction; group 2 with some degree of neurogenic detrusor overactivity, detrusor hypocontractility during voiding, and high degree of an outflow obstruction. The presence of SP and CGRP immunoreactive + fiber density was observed in greater numbers in group 1.

CONCLUSION

Density of CGRP and SP positive nerve fibers within the urinary bladder of patients with MS may be suggestive of functional status of the lower urinary tract, namely denser innervation is observed in patients with mild outflow obstruction and strong detrusor overactivity. This observation could be useful when planning second-line treatment (neurotoxins) in these patients. Patients with denser innervation probably will respond better to such a therapy.

Application of aerobic microorganisms in bioremediation in situ of soil contaminated by petroleum products

Aerobic microorganisms able to biodegrade benzene, toluene, ethylbenzene, xylene (BTEX) have been isolated from an area contaminated by petroleum products. The activity of the isolated communities was tested under both laboratory and field conditions. Benzene, toluene, ethylbenzene and xylene were added to the cultures as the sole carbon source, at a concentration of 500 mg/L. In batch cultures under laboratory conditions, an 84% reduction of benzene, 86% of toluene and 82% of xylene were achieved. In cultures with ethylbenzene as the sole carbon source, the reduction was around 80%. Slightly lower values were observed under field conditions: 95% reduction of benzene and toluene, 81% of ethylbenzene and 80% of xylene. A high biodegradation activity of benzene (914 microM/L/24h), toluene (771 microM/L/24h), xylene (673 microM/L/24h) and ethylbenzene (644 microM/L/24h) was observed in the isolated communities.

Re-innervation pattern of the 'neovagina' created from the bladder flap in patients with Mayer-Rokitanski-Kistner-Hauser syndrome: an immunochemical study

BACKGROUND

Cystovaginoplasty (CVP) is a method of vaginal reconstruction in women with Mayer-Rokitansky-Kistner-Hauser Syndrome (MRKHS). The neo-vagina allows normal sexual intercourses, but after CVP, the sexual life of patients with MRKHS does not differ significantly from normal females. Therefore, we decided to elucidate the pattern of sensory re-innervation of the bladder flap used for the surgery.

METHODS

Biopsies were taken from vaginal vestibule and urinary bladder during the CVP and 1 year later in four patients with MRKHS. The following neurotransmitters were studied calcitonin gene-related peptide (CGRP), galanin (GAL), vasoactive intestinal polypeptide (VIP) and pituitary adenylate cyclase-activating peptide (PACAP).

RESULTS

CGRP and PACAP nerve fibres were sparse under the urothelium and in submucosal layer of the neovagina, they were more numerous around blood vessels and in the vicinity of smooth muscles. This was similar to the pattern observed in the urinary bladder. VIP- and GAL-positive nerve fibres were most numerous in the submucosa around blood vessels and in smooth muscle bundles of neovagina. They were distinctly less numerous beneath the epithelium. This innervation pattern mimicked that seen in normal vagina and in vaginal vestibule of patients with MRKHS.

CONCLUSIONS

Our findings demonstrate considerable nervous system plasticity in the bladder flap. Distribution of presumably sensory CGRP and PACAP immunoreactive nerve fibers was similar to the pattern observed within the intact bladder wall, and VIP or GAL immunoreactive nerve fibers (vasomotor functions) were distributed in a manner similar to that observed in the intact vaginal wall.