Predicting the membrane permeability of organic fluorescent probes by the deep neural network based lipophilicity descriptor DeepFl-LogP.

Light microscopy has become an indispensable tool for the life sciences, as it enables the rapid acquisition of three-dimensional images from the interior of living cells/tissues. Over the last decades, super-resolution light microscopy techniques have been developed, which allow a resolution up to an order of magnitude higher than that of conventional light microscopy. Those techniques require labelling of cellular structures with fluorescent probes exhibiting specific properties, which are supplied from outside and therefore have to surpass cell membranes. Currently, major efforts are undertaken to develop probes which can surpass cell membranes and exhibit the photophysical properties required for super-resolution imaging. However, the process of probe development is still based on a tedious and time consuming manual screening. An accurate computer based model that enables the prediction of the cell permeability based on their chemical structure would therefore be an invaluable asset for the development of fluorescent probes. Unfortunately, current models, which are based on multiple molecular descriptors, are not well suited for this task as they require high effort in the usage and exhibit moderate accuracy in their prediction. Here, we present a novel fragment based lipophilicity descriptor DeepFL-LogP, which was developed on the basis of a deep neural network. DeepFL-LogP exhibits excellent correlation with the experimental partition coefficient reference data (R2 = 0.892 and MSE = 0.359) of drug-like substances. Further a simple threshold permeability model on the basis of this descriptor allows to categorize the permeability of fluorescent probes with 96% accuracy. This novel descriptor is expected to largely simplify and speed up the development process for novel cell permeable fluorophores.

Integrated geospatial analysis linking metal contamination among three different compartments of Lake Edku ecosystem in Egypt to human health effects.

This study is the first in forming an integrated up-to-date spatial analysis linking heavy metal contamination among three different compartments of Lake Edku ecosystem to human health effects. The study determined the concentrations of iron (Fe), nickel (Ni), lead (Pb), chromium (Cr), and cadmium (Cd) in sediment and water samples collected from 12 stations covering the entire lake, as well as in the liver and muscle tissues of the three commercially edible fish species (African sharptooth catfish (Clarias gariepinus), Blue tilapia (Oreochromis aureus), and Redbelly tilapia (Tilapia zillii)), during winter 2019. Cartographic maps investigating the spatial contamination pattern of each metal in sediment and water samples along the entire lake, as well as correlation analysis between metal pairs, were generated. Moreover, the study examined the affinity of metal transfer among the three compartments and assessed the probability of being exposed to non-carcinogenic health hazards from the consumption of the abovementioned species. Results revealed that Fe and Cd recorded the highest and lowest mean concentrations, respectively, in sediment, water, and fish samples. The mean concentrations of Cd, Pb, and Ni in the water of Lake Edku, as well as the mean concentrations of Cd, Pb, and Cr in muscle tissues of the three examined fish species, exceeded the permissible limits. The northwestern part of the lake exhibited the highest concentrations of Fe, Ni, and Cr in Lake Edku's sediment with strong significant positive correlations recorded between Fe-Ni, Fe-Cr, and Ni-Cr pairs suggesting sharing the same contamination source. Concerning Lake Edku's water, the northwestern area displayed the highest concentrations for all metals. Moreover, Cd, Pb, and Cr exhibited nearly the same spatial contamination pattern with the hotspot located in the western part of the lake. Strong significant positive correlations were found between Cd-Pb, Cd-Cr, and Pb-Cr pairs in surface water, suggesting sharing the same origin of dispersion. The three fish species accumulated heavy metals from water several folds higher than from sediments, indicating that water is the main source of the intensive transfer of heavy metals to the three fish species. Based on the consumption of the three investigated fish species, children recorded the highest estimated daily (EDI) and weekly intakes (EWI) of heavy metals followed by adults. Regardless Pb, EWI values indicated that there are no significant health risks through fish consumption from the examined metals recommending that children should consume less than 85.227 g/day African sharptooth catfish muscle, 108.696 g/day Blue tilapia muscle, and 97.403 g/day Redbelly tilapia muscle to assure their health. Moreover, adults should consume less than 397.727 g/day African sharptooth catfish muscle, 507.24 g/day Blue tilapia muscle, and 454.54 g/day Redbelly tilapia muscle. The estimated hazard quotient (HQ) of all metals was lower than or close to the safe values of one for children and adults in the three investigated fish species indicating the absence of potential non-carcinogenic threats. The hazard index (HI) estimated for the five examined heavy metals in each of the investigated fish species was below one in adults only. Regarding the total hazard index estimated from consuming the three fish species, both children and adults may be subjected to non-carcinogenic risk.

Applying geospatial technology in quantifying spatiotemporal shoreline dynamics along Marina El-Alamein Resort, Egypt.

Human interventions along the northwestern Egyptian Mediterranean coast recently interrupted the stability of Marina El-Alamein shoreline and resulted in spit evolution. Considering Egypt's vision 2030 for developing the northwestern Egyptian coast, continuous up-to-date monitoring programs became essential to ensure sustainability. This study, for the first time, aimed at coupling geospatial technology with Digital Shoreline Analysis System (DSAS) tool in monitoring, analyzing, and quantifying the impacts of anthropogenic activities on the spatiotemporal shoreline dynamics over the last 3 decades (1987-2017) at Marina El-Alamein resort, Egypt. In addition, the study carried out a quantitative geometrical temporal analysis for the newly formed spit from 2015 to 2020. The study used transect- and area-based approaches in estimating the shoreline changes for long- and short-term changes. The former approach computed the change in both the shoreline displacement and the rate of shoreline change, whereas the latter quantified the magnitude of spatial changes in the total land area. Results of the current study revealed that during 1987-2017, Marina El-Alamein shoreline experienced very high accretion, with an average rate of 2.8 ± 4.73 m/year (end-point rate) and 2.52 ± 4.10 m/year (linear regression rate). Quantitatively, Jetties #1 and #3 trapped sand on their western sides for a maximum distance of 706.31 m and 406.5 m, respectively. On the other hand, the eastern side of the resort experienced erosion with a maximum distance of 92.78 m. Regarding changes in the total area, Marina El-Alamein's coast gained 1.130 km2 (0.038 km2/year) land and lost about 0.1115 km2 (0.004 km2/year) of its total area throughout the last 3 decades. During 2015, the continuous progressive accretion along the western side of J#1 resulted in the evolution of sand spit east of the jetty. Results of the temporal analysis showed that the spit's length was about 0.236 km during May 2015 and reached 1.44 km in April 2020 with an increment of 510.5% in length. In addition, the spit's total surface area increased by 33.606 km2 in 5 years (6.7212 km2/year). Both the length and the area of the evolving spit grow annually with 102.11% and 108%, respectively. If this progressive accretion along the evolving spit continued, the lagoon's first inlet would probably suffer sedimentation that could cause its closure and deteriorate the lagoon's water quality. The study recommends carrying out an environmental impact assessment study for the newly formed spit to lessen its negative impact on the opposite tidal inlet and the lagoon's water quality.

Little egret (Egretta garzetta) as a bioindicator of heavy metal contamination from three different localities in Egypt.

This work aimed at using Little Egrets (Egretta garzetta), for the first time in Egypt, as a bioindicator of heavy metal contamination from three different Egyptian land use types (Qillin within Kafr El-Sheikh (S1, agricultural), Toukh within Qalyubia (S2, semi-rural area), and Abu Rawash within Giza (S3, urban)). Concentrations of aluminum (Al), barium (Ba), cobalt (Co), cadmium (Cd), chromium (Cr), copper (Cu), manganese (Mn), iron (Fe), nickel (Ni), lead (Pb), and zinc (Zn) were analyzed in liver and kidney samples of twenty-six adult Little Egrets collected from the three localities during winter 2018. Moreover, the study calculated the Metal Pollution Index (MPI) to highlight the health of the surrounding environment using birds' internal organs as a mirror. Results revealed that, throughout the three sampling sites, the total metal concentrations in liver samples exceeded that of the kidney, indicating that the liver is the target organ of metal accumulation. The Little Egret's liver was found to be the best-recommended organ to use in future biomonitoring of Cu, Zn, Fe, Mn, and Ni, whereas Al, Co, Cr, Ba, Pb, and Cd can be monitored in the kidney. Cu and Pb were higher in the Little Egret's tissues collected from the agricultural site (S1), whereas Ba, Ni, and Fe were higher in the semi-rural site (S2), followed finally by Cd in the urbanized site (S3). The concentrations of trace elements reported in Little Egrets were within the known background level for water birds. However, alarming concentrations were found for Ni levels in liver (from Qillin and Toukh), as well as Pb and Cr levels in kidney samples (from the three localities). MPI of the eleven studied metals in both liver and kidney of the studied species decreased in the order Qillin (24.36) > Abu Rawash (17.98) > Toukh (3.90). In the three investigated localities, the overall calculated MPI values were higher than one, indicating that the ecosystem is polluted. The study suggested using Little Egrets as a bioindicator of metal contamination.

Super-resolution imaging reveals the sub-diffraction phenotype of Zellweger Syndrome ghosts and wild-type peroxisomes.

Peroxisomes are ubiquitous cell organelles involved in many metabolic and signaling functions. Their assembly requires peroxins, encoded by PEX genes. Mutations in PEX genes are the cause of Zellweger Syndrome spectrum (ZSS), a heterogeneous group of peroxisomal biogenesis disorders (PBD). The size and morphological features of peroxisomes are below the diffraction limit of light, which makes them attractive for super-resolution imaging. We applied Stimulated Emission Depletion (STED) microscopy to study the morphology of human peroxisomes and peroxisomal protein localization in human controls and ZSS patients. We defined the peroxisome morphology in healthy skin fibroblasts and the sub-diffraction phenotype of residual peroxisomal structures ('ghosts') in ZSS patients that revealed a relation between mutation severity and clinical phenotype. Further, we investigated the 70 kDa peroxisomal membrane protein (PMP70) abundance in relationship to the ZSS sub-diffraction phenotype. This work improves the morphological definition of peroxisomes. It expands current knowledge about peroxisome biogenesis and ZSS pathoethiology to the sub-diffraction phenotype including key peroxins and the characteristics of ghost peroxisomes.

Pex35 is a regulator of peroxisome abundance.

Peroxisomes are cellular organelles with vital functions in lipid, amino acid and redox metabolism. The cellular formation and dynamics of peroxisomes are governed by PEX genes; however, the regulation of peroxisome abundance is still poorly understood. Here, we use a high-content microscopy screen in Saccharomyces cerevisiae to identify new regulators of peroxisome size and abundance. Our screen led to the identification of a previously uncharacterized gene, which we term PEX35, which affects peroxisome abundance. PEX35 encodes a peroxisomal membrane protein, a remote homolog to several curvature-generating human proteins. We systematically characterized the genetic and physical interactome as well as the metabolome of mutants in PEX35, and we found that Pex35 functionally interacts with the vesicle-budding-inducer Arf1. Our results highlight the functional interaction between peroxisomes and the secretory pathway.

Effects of different combinations of nanocrystallization technologies on avanafil nanoparticles: in vitro, in vivo and stability evaluation.

The study investigated the effects of different combined top-down and bottom-up nanocrystallization technologies on particle size and solid state of avanafil nanoparticles. Combined antisolvent precipitation-ultrasonication (sonoprecipitation) technique was adopted to prepare 18 formulas according to 32.21 factorial design using 3 stabilizers; Tween 80, polyvinyl alcohol (PVA) and Pluronic F68 at different concentrations with different cryoprotectants. Particle size analysis of the lyophilized formulas showed that Tween 80 was an effective nanoparticles stabilizer in contrast to Pluronic F68 and PVA which failed to prevent nanoparticles flocculation when they were used at high concentration. The combined effects of nanonization and amorphism contributed to the improvement in solubility. Further processing of the sonoprecipitated formulas by high pressure homogenization (HPH) (modified NANOEDGE™ technology) resulted in further size reduction of PVA-stabilized particles, while it stimulated flocculation of Tween-stabilized nanoparticles. Nevertheless, all of the homogenized formulas partially retrieved their crystallinity which reduced their solubility. Non-homogenized formula 2E composed of 1:2 (avanafil: Tween) with glucose as cryoprotectant, exhibited 13.68- and 2.59-fold improvement in solubility and in vitro dissolution, respectively. This formula had oral bioavailability of 137.02% relative to Spedra® tablets and it maintained its nanosize, amorphism and dissolution behavior over 6 months of storage under stress conditions.

Effect of different polymers on avanafil-ß-cyclodextrin inclusion complex: in vitro and in vivo evaluation.

In this study, we examined the effect of different polymers on the chemical, physical and pharmacokinetic properties of avanafil-ß-cyclodextrin (ß-CD) inclusion complex. Equimolar mixtures of drug and ß-CD were used to prepare 25 ternary drug-ß-CD-polymer inclusion complexes using five different polymers, polyethylene glycol (PEG 4000), polyvinyl pyrrolidone (PVP K-30), chitosan, hydroxypropylmethyl cellulose, and hydroxyethyl cellulose, each in five different concentrations, 1, 3, 5, 7, and 10% (w/w). The addition of 10% (w/w) PEG 4000 resulted in a significant decrease of drug solubility, where the infrared spectra and differential scanning thermograms revealed an interaction between PEG 4000 and avanafil which hindered drug inclusion. In contrast, addition of 7% (w/w) PVP K-30 facilitated drug inclusion as concluded from differential scanning thermograms, X-ray diffraction patterns and scanning electron micrographs. This resulted in a subsequent improvement in drug solubility and in vitro dissolution. This formula was chemically and physically stable for 6 months under accelerated storage conditions. The formula had a relative bioavailability of 125.56% in rabbits as compared to conventional commercially available avanafil tablets (Spedra(®)).

Formulation of avanafil in a solid self-nanoemulsifying drug delivery system for enhanced oral delivery.

Avanafil was incorporated into solid self-nanoemulsifying systems with the aim of improving its oral bioavailability. Labrafil, Labrafac, and Miglyol 812 N were investigated as oils, Tween 80 and Cremophor EL as surfactants, and Transcutol HP as a co-surfactant. Nine formulations produced clear solutions of 13.89-38.09nm globules after aqueous dilution. Adsorption of preconcentrate onto Aeroperl 300 Pharma at a 2:1 ratio had no effect on nanoemulsion particle size. Differential scanning calorimetry, X-ray diffraction, and scanning electron microscopy indicated that avanafil was molecularly dispersed within the solid nanosystems. A formulation containing 10% Labrafil, 60% Tween 80, and 30% Transcutol HP had the highest drug loading (44.48mg/g) and an acceptable in vitro dissolution profile (96.42% within 30min). This formulation was chemically and physically stable for 6months under accelerated storage conditions and it produced a 3.2-fold increase in bioavailability in rabbits, as compared to conventional commercially available avanafil tablets (Spedra(®)).

CellProfiler: Novel Automated Image Segmentation Procedure for Super-Resolution Microscopy.

BACKGROUND: Super resolution (SR) microscopy enabled cell biologists to visualize subcellular details up to 20 nm in resolution. This breakthrough in spatial resolution made image analysis a challenging procedure. Direct and automated segmentation of SR images remains largely unsolved, especially when it comes to providing meaningful biological interpretations. RESULTS: Here, we introduce a novel automated imaging analysis routine, based on Gaussian, followed by a segmentation procedure using CellProfiler software (www.cellprofiler.org). We tested this method and succeeded to segment individual nuclear pore complexes stained with gp210 and pan-FG proteins and captured by two-color STED microscopy. Test results confirmed accuracy and robustness of the method even in noisy STED images of gp210. CONCLUSIONS: Our pipeline and novel segmentation procedure may benefit end-users of SR microscopy to analyze their images and extract biologically significant quantitative data about them in user-friendly and fully-automated settings.

Peroxisomes are juxtaposed to strategic sites on mitochondria.

Peroxisomes are ubiquitous and dynamic organelles that house many important pathways of cellular metabolism. In recent years it has been demonstrated that mitochondria are tightly connected with peroxisomes and are defective in several peroxisomal diseases. Indeed, these two organelles share metabolic routes as well as resident proteins and, at least in mammals, are connected via a vesicular transport pathway. However the exact extent of cross-talk between peroxisomes and mitochondria remains unclear. Here we used a combination of high throughput genetic manipulations of yeast libraries alongside high content screens to systematically unravel proteins that affect the transport of peroxisomal proteins and peroxisome biogenesis. Follow up work on the effector proteins that were identified revealed that peroxisomes are not randomly distributed in cells but are rather localized to specific mitochondrial subdomains such as mitochondria-ER junctions and sites of acetyl-CoA synthesis. Our approach highlights the intricate geography of the cell and suggests an additional layer of organization as a possible way to enable efficient metabolism. Our findings pave the way for further studying the machinery aligning mitochondria and peroxisomes, the role of the juxtaposition, as well as its regulation during various metabolic conditions. More broadly, the approaches used here can be easily applied to study any organelle of choice, facilitating the discovery of new aspects in cell biology.