Urinary Metabolic Markers of Bladder Cancer: A Reflection of the Tumor or the Response of the Body?

This work will review the metabolic information that various studies have obtained in recent years on bladder cancer, with particular attention to discovering biomarkers in urine for the diagnosis and prognosis of this disease. In principle, they would be capable of complementing cystoscopy, an invasive but nowadays irreplaceable technique or, in the best case, of replacing it. We will evaluate the degree of reproducibility that the different experiments have shown in the indication of biomarkers, and a synthesis will be attempted to obtain a consensus list that is more likely to become a guideline for clinical practice. In further analysis, we will inquire into the origin of these dysregulated metabolites in patients with bladder cancer. For this purpose, it will be helpful to compare the imbalances measured in urine with those known inside tumor cells or tissues. Although the urine analysis is sometimes considered a liquid biopsy because of its direct contact with the tumor in the bladder wall, it contains metabolites from all organs and tissues of the body, and the tumor is separated from urine by the most impermeable barrier found in mammals. The distinction between the specific and systemic responses can help understand the disease and its consequences in more depth.

DpaA Detaches Braun’s Lipoprotein from Peptidoglycan

ABSTRACT Gram-negative bacteria have a unique cell envelope with a lipopolysaccharide-containing outer membrane that is tightly connected to a thin layer of peptidoglycan. The tight connection between the outer membrane and peptidoglycan is needed to maintain the outer membrane as an impermeable barrier for many toxic molecules and antibiotics. Enterobacteriaceae such as Escherichia coli covalently attach the abundant outer membrane-anchored lipoprotein Lpp (Braun’s lipoprotein) to tripeptides in peptidoglycan, mediated by the transpeptidases LdtA, LdtB, and LdtC. LdtD and LdtE are members of the same family of ld-transpeptidases but they catalyze a different reaction, the formation of 3-3 cross-links in the peptidoglycan. The function of the sixth homologue in E. coli, LdtF, remains unclear, although it has been shown to become essential in cells with inhibited lipopolysaccharide export to the outer membrane. We now show that LdtF hydrolyzes the Lpp-peptidoglycan linkage, detaching Lpp from peptidoglycan, and have renamed LdtF to peptidoglycan meso-diaminopimelic acid protein amidase A (DpaA). We show that the detachment of Lpp from peptidoglycan is beneficial for the cell under certain stress conditions and that the deletion of dpaA allows frequent transposon inactivation in the lapB (yciM) gene, whose product downregulates lipopolysaccharide biosynthesis. DpaA-like proteins have characteristic sequence motifs and are present in many Gram-negative bacteria, of which some have no Lpp, raising the possibility that DpaA has other substrates in these species. Overall, our data show that the Lpp-peptidoglycan linkage in E. coli is more dynamic than previously appreciated. IMPORTANCE Gram-negative bacteria have a complex cell envelope with two membranes and a periplasm containing the peptidoglycan layer. The outer membrane is firmly connected to the peptidoglycan by highly abundant proteins. The outer membrane-anchored Braun’s lipoprotein (Lpp) is the most abundant protein in E. coli, and about one-third of the Lpp molecules become covalently attached to tripeptides in peptidoglycan. The attachment of Lpp to peptidoglycan stabilizes the cell envelope and is crucial for the outer membrane to function as a permeability barrier for a range of toxic molecules and antibiotics. So far, the attachment of Lpp to peptidoglycan has been considered to be irreversible. We have now identified an amidase, DpaA, which is capable of detaching Lpp from peptidoglycan, and we show that the detachment of Lpp is important under certain stress conditions. DpaA-like proteins are present in many Gram-negative bacteria and may have different substrates in these species.

DpaA detaches Braun’s lipoprotein from peptidoglycan

ABSTRACTGram-negative bacteria have a unique cell envelope with a lipopolysaccharide-containing outer membrane that is tightly connected to a thin layer of peptidoglycan. The tight connection between the outer membrane and peptidoglycan is needed to maintain the outer membrane as an impermeable barrier for many toxic molecules and antibiotics. Enterobacteriaceae such as Escherichia coli covalently attach the abundant outer membrane-anchored lipoprotein Lpp (Braun’s lipoprotein) to tripeptides in peptidoglycan, mediated by the transpeptidases LdtA, LdtB and LdtC. LdtD and LdtE are members of the same family of LD-transpeptidases but they catalyse a different reaction, the formation of 3-3 cross-links in the peptidoglycan. The function of the sixth homologue in E. coli, LdtF remains unclear, although it has been shown to become essential in cells with inhibited LPS export to the outer membrane. We now show that LdtF hydrolyses the Lpp-peptidoglycan linkage, detaching Lpp from peptidoglycan, and have renamed LdtF to peptidoglycan meso-diaminopimelic acid protein amidase A (DpaA). We show that the detachment of Lpp from peptidoglycan is beneficial for the cell under certain stress conditions and that the deletion of dpaA allows frequent transposon inactivation in the lapB (yciM) gene, whose product down-regulates lipopolysaccharide biosynthesis. DpaA-like proteins have characteristic sequence motifs and are present in many Gram-negative bacteria of which some have no Lpp, raising the possibility that DpaA has other substrates in these species. Overall, our data show that the Lpp-peptidoglycan linkage in E. coli is more dynamic than previously appreciated.IMPORTANCEGram-negative bacteria have a complex cell envelope with two membranes and a periplasm containing the peptidoglycan layer. The outer membrane is firmly connected to the peptidoglycan by highly abundant proteins. The outer membrane-anchored Braun’s lipoprotein (Lpp) is the most abundant protein in E. coli and about one third of the Lpp molecules become covalently attached to tripeptides in peptidoglycan. The attachment of Lpp to peptidoglycan stabilizes the cell envelope and is crucial for the outer membrane to function as a permeability barrier for a range of toxic molecules and antibiotics. So far the attachment of Lpp to peptidoglycan has been considered to be irreversible. We have now identified an amidase, DpaA, which is capable of detaching Lpp from PG and we show that the detachment of Lpp is important under certain stress conditions. DpaA-like proteins are present in many Gram-negative bacteria and may have different substrates in these species.

Collapse of n Point Vortices, Formation of the Vortex Sheets and Transport of Passive Markers

In this paper, the motion of the n-vortex system as it collapses to a point in finite time is studied. The motion of vortices is described by the set of ordinary differential equations that we are able to solve analytically. The explicit formula for the solution demands the initial location of collapsing vortices. To find the collapsing locations of vortices, the algebraic, nonlinear system of equations was built. The solution of that algebraic system was obtained using Newton’s procedure. A good initial iterate needs to be provided to succeed in the application of Newton’s procedure. An unconstrained Leverber–Marquart optimization procedure was used to find such a good initial iterate. The numerical studies were conducted, and numerical evidence was presented that if in a collapsing system n=50 point vortices include a few vortices with much greater intensities than the others in the set, the vortices with weaker intensities organize themselves onto the vortex sheet. The collapsing locations depend on the value of the Hamiltonian. By changing the Hamiltonian values in a specific interval, the collapsing curves can be obtained. All points on the collapse curves with the same Hamiltonian value represent one collapsing system of vortices. To show the properties of vortex sheets created by vortices, the passive tracers were used. Advection of tracers by the velocity induced by vortices was calculated by solving the proper differential equations. The vortex sheets are an impermeable barrier to inward and outward fluxes of tracers. Arising vortex structures are able to transport the passive tracers. In this paper, several examples showing the diversity of collapsing structures with the vortex sheet are presented. The collapsing phenomenon of many vortices, their ability to self organize and the transportation of the passive tracers are novelties in the context of point vortex dynamics.

The Role of Red Blood Cells in Hemostasis

New emerging evidence is now prompting researchers to devote greater focus on the roles played by red blood cells (RBCs) in hemostasis. This short narrative review aims to outline the available research, past and current, that has revealed the role of RBCs in hemostasis, particularly blood clotting. Although early researchers suggested that RBCs were involved in blood clotting, they had insufficient evidence to support such claims. As a result, this area of research received little attention from other scientists. Early researchers primarily used quantitative measures of RBCs, namely hematocrit or RBC count, as higher numbers of RBCs modulate blood rheology by increasing viscosity. Recent research has instead shed light on the different measures of RBC function, such as expression of phosphatidylserine and adhesive proteins, aggregation, hemolysis, release of extracellular microvesicles, and erythrocyte volume. RBCs play a role in the contraction of clots by platelets, and the resulting densely packed array of polyhedral erythrocytes forms an almost impermeable barrier that is essential for hemostasis and wound healing. Renewed interest in RBCs is primarily due to the clinically and experimentally established relationships between erythrocytes and hemostasis, which have suggested that erythrocytes are potential targets for the treatment of hemostatic disturbances.

The eastern boundary of the geographic range of the Pallas’ spadefoot Pelobates vespertinus (Anura, Amphibia) is limited by overwintering temperatures

We studied the relationship between the geographic distribution of the Pallas’ spadefoot (Pelobates vespertinus) and the soil temperature regime at the eastern boundary of this species’ range (south-western West Siberia and northwest Kazakhstan). This species overwinters underground, burrowing down to 1.5 m or deeper and has poor frost tolerance – it is unable to withstand temperatures below 0 °C, therefore, the temperature at its overwintering depth has to be above zero. A cartographic approach to identifying the distribution of zero isotherms was used. Winter soil temperatures at depths of 80 cm, 120 cm, 160 cm and 240 cm were plotted, based on deep soil thermometer data and the outline of the spadefoot’s range was compared with close-to-zero isotherms in deep soil. Within the range of this species, the depth of the position of zero isotherms increases eastwards: from 80 cm in European Russia, to more than 160 cm in the south-west of Western Siberia. The eastern boundary of the species’ range lies in the forest-steppe, steppe and semi-desert zones in the Tobol-Ishim interfluve and further south, on the left bank area of the Turgai River. This boundary clearly coincides with the zero isotherm, which lies here at a depth of 160 cm, forming an impermeable barrier to the spadefoot’s distribution.

Shelf-edge delta and reef development on a mixed siliciclastic–carbonate margin, central Great Barrier Reef

ABSTRACT The Great Barrier Reef (GBR) is the world's largest extant mixed silicilastic–carbonate margin. Previous research on the Great Barrier Reef has suggested that the extensive barrier reef system may act as an impermeable barrier and limit the development of delta systems during lowstands, but sufficient geophysical data to support this hypothesis are lacking. We use dense sparker seismic and sub-bottom profiler data to better understand the structure of a large lobe-shaped feature (∼ 10 km × 10 km) on the shelf edge of the central GBR and the interactions between siliciclastic and carbonate sedimentary systems. Interpreted sparker seismic contains prograding clinoforms and suggest that the lobe-shaped feature was a river-dominated shelf-edge delta. A delta on the shelf edge implies that the presence of an exposed barrier reef was not a major impediment to deposition and that other adjacent lobe-shaped features are also deltaic deposits. The shelf-edge deltas were deposited onto a broad upper-slope terrace that allowed continued progradation and limited incision when sea level fell below the shelf edge. Delta foresets are commonly colonized by coral reefs, but the spatial and temporal relationship between reefs and some deltaic units remains unclear. The presence of multiple shelf-edge deltas that link to previously mapped Burdekin River paleo-channels indicates a complex history of sedimentation, with the Burdekin River delta migrating up to 100 km along the GBR margin during the late Quaternary. Regional bathymetric data suggest that large modern or recent shelf-edge deltas are rare on the GBR and that there was a broad range of sedimentary processes operating along the margin of the GBR during periods of low sea level.

Potential Sealing Effects of Permanent Casing Deformation

Permanent plugging and abandonment (P&A) of oil- and gas wells requires proper sealing between the formation and the casing as well as proper sealing inside the casing. The cement sheath in the annulus is intended to function as an “impermeable” barrier. Typically, shrinkage of cement sheath takes place when the cement sets and a microannulus (MA) may be formed. In addition, cyclic pressure and temperature variations may result in cracks and debonding of the cement sheath. This paper investigates the possibility of improved cement sealing imposed by permanent deformation of the casing, thus providing a mechanical compression force to the cement and thus closing the MA when performing P&A. Two experimental setups were designed in this context. The first setup termed casing/cement plug test, where the casing is contracted by an external pressure and simultaneous measurement of the flow rate through the setup. The second setup is termed casing/cement annular test where the casing is internally pressurized while the gas flow rate is measured. Nonlinear finite element analyses were carried out to simulate the two test setups. The numerical results showed an acceptable agreement with the observations in the lab. The second setup was not tested in the lab, but simulated using the FEM code. The numerical analyses indicated that the same concept of casing permanent deformation is also relevant for the annular test. It is shown that the micro-annulus formed due to cycles of pressurization/depressurization as a result of inelastic deformations in the cement can be repaired by inducing permanent deformation in the casing to some extent. Finally, we concluded that permanent casing deformation could play a positive role in favour of closing the micro-annuli in P&A operations.

Addressing differentiation in live human keratinocytes by assessment of membrane packing order

Differentiation of keratinocytes is critical for epidermal stratification and formation of a protective stratum corneum. It involves a series of complex processes leading through gradual changes in characteristics and functions of keratinocytes up to their programmed cell death via cornification. The stratum corneum is an impermeable barrier, comprised of dead cell remnants (corneocytes) embedded within lipid matrix. Corneocyte membranes are comprised of specialized lipids linked to late differentiation proteins, contributing to the formation of a highly stiff and mechanically strengthen layer. To date, the assessment of the progression of keratinocyte differentiation is only possible by determination of specific differentiation markers, e.g. by using proteomics-based approaches. Unfortunately, this requires fixation or cell lysis, and currently there is no robust methodology available to study differentiation in living cells, neither at a single cell, nor in high throughput. Here, we explore a new live-cell based approaches for screening differentiation advancement in keratinocytes, in a “calcium switch” model. We employ a polarity-sensitive dye, Laurdan, and Laurdan general polarization function (GP) as a reporter of the degree of membrane lateral packing order or condensation, as an adequate marker of differentiation. We show that the assay is straightforward and can be conducted either on a single cell level using confocal spectral imaging or on the ensemble level using a fluorescence plate reader. Such systematic quantification may become useful for understanding mechanisms of keratinocyte differentiation, such as the role of membrane inhomogeneities in stiffness, and for future therapeutic development.

Embedded Corrosion Sensing with ZnO-PVDF Sensor Textiles

Corrosion in underground and submerged steel pipes is a global problem. Coatings serve as an impermeable barrier or a sacrificial element to the transport of corrosive fluids. When this barrier fails, corrosion in the metal initiates. There is a critical need for sensors at the metal/coating interface as an early alert system. Current options utilize metal sensors, leading to accelerating corrosion. In this paper, a non-conductive sensor textile as a viable solution was investigated. For this purpose, non-woven Zinc (II) Oxide-Polyvinylidene Fluoride (ZnO-PVDF) nanocomposite fiber textiles were prepared in a range of weight fractions (1%, 3%, and 5% ZnO) and placed at the coating/steel interface. The properties of ZnO-PVDF nanocomposite meshes were characterized using scanning electron microscopy (SEM), X-ray diffraction (XRD), Fourier transform infrared (FTIR) and d33 meter. Electrochemical impedance spectroscopy (EIS) testing was performed during the immersion of the coated samples to validate the effectiveness of the sensor textile. The results offer a new option for sub-surface corrosion sensing using low cost, easily fabricated sensor textiles.