Thrombotic risk assessment in antiphospholipid syndrome: the role of new antibody specificities and thrombin generation assay

Antiphospholipid syndrome (APS) is an autoimmune condition characterized by the presence of antiphospholipid antibodies (aPL) in subjects presenting with thrombosis and/or pregnancy loss. The currently used classification criteria were updated in the international consensus held in Sidney in 2005. Vascular events seem to result of local procoagulative alterations upon triggers influence (the so called “second-hit theory”), while placental thrombosis and complement activation seem to lead to pregnancy morbidity. The laboratory tests suggested by the current classification criteria include lupus anticoagulant, a functional coagulation assay, and anticardiolipin and anti-β2-glycoprotein-I antibodies, generally detected by solid phase enzyme-linked immunosorbent assay. The real challenge for treating physicians is understanding what is the actual weight of aPL in provoking clinical manifestations in each case. As thrombosis has a multi-factorial cause, each patient needs a risk-stratified approach. In this review we discuss the role of thrombotic risk assessment in primary and secondary prevention of venous and arterial thromboembolic disease in patients with APS, focusing on new antibody specificities, available risk scoring models and new coagulation assays.     

Morphological variations of an invasive cyprinid fish (Carassius gibelio) in lentic and lotic environments inferred from the body,otolith, and scale shapes

This study investigated the morphological variation of gibel carp Carassius gibelio collected from various water bodies in Türkiye. The fish samples were obtained from three dams (Karacaören-1, Karakaya, and Keban), two natural lakes (Beyşehir and Suğla), and a river (the Tigris River). The dimorphism in body shape was examined with geometric morphometrics, while elliptic Fourier analysis and shape indices were used to describe the variation in lapilli otoliths (hereafter “otoliths”) and scale shapes. The body of C. gibelio revealed higher variations, particularly in the body depth, snout length, caudal fin, and caudal peduncle, among different stations. Geometric morphometric analysis determined a streamlined body shape of C. gibelio in the Tigris River compared to other stations, while C. gibelio from the natural lakes had a deeper body shape. The body of C. gibelio exhibited a significant homogenous shape between the Beyşehir and Suğla lakes, providing the lowest Procrustes distance. The elliptic Fourier analysis revealed that the otolith shape varied significantly between all stations. However, the scale shape was remarkably similar among nearby areas such as Karacaören dam, Suğla, and Beyşehir lakes. These results evinced high degree of intra-population morphological variation in C. gibelio in response to prevailing environmental conditions that probably facilitate their successful establishment in a novel environment.     

The role of human factor in maritime environment risk assessment: A practical application on Ballast Water Treatment (BWT) system in ship

The role of human factor plays a critical role in the safe and clean operation of maritime industry. Human error prediction can be beneficial to assess risk in maritime industry since shipping activities can pose potential hazards to human life and maritime ecology. The aim of this paper is to propose a risk assessment tool by considering the role of human factor. Hence, the desired safety control level in maritime transportation activities can be ascertained. In the proposed approach, a Success Likelihood Index Method (SLIM) extended with fuzzy logic is used to calculate human error probability (HEP). Severity of consequences are adopted in the proposed approach to assess risk. The quantitative risk assessment approach under fuzzy SLIM methodology will be applied to a very specific case on-board ship: Ballast Water Treatment (BWT) system. In order to improve consistency of research and minimize subjectivity of experts' judgments, the paper adopts the dominance factor which is used to adjust the impact level of experts' judgments in the aggregation stage of the methodology. The paper aims at not only highlighting the importance of human factor in maritime risk assessment but also enhancing safety control level and minimizing potential environmental impacts to marine ecology.     

Biomonitoring of metal(oid)s in mining-affected Borcka Dam Lake coupled with public health outcomes

Due to increased anthropogenic activities, the aquatic environment is exposed to pollutants much more than ever. These pollutants go into the food chain and can pose a health risk to human. Correlatively, Borcka Dam Lake, Turkey has been affected by mining activities since decades. In the present study, therefore, Cu, Pb, As, Zn, Mn, Cd, Cr, and Se concentrations in water, sediment, and different tissues (muscle, gill, liver) of 11 fish species sampled from the lake were analyzed regarding metal(oid)s pollution and potential human health risk through fish consumption. The metal(oid) concentrations in the water were below the limit values recommended by USEPA for aquatic life criteria but sediments were heavily polluted by As, Cu, Pb, and Zn based on Sediment Quality Guideline. The lowest metal(oid) values among tissues for all fish species were determined in muscle (p < 0.05) which was lower than the limits for human consumption declared by European Union Regulation. Target Hazard Quotient and Hazard Index used non-cancer risk estimate which was lower than 1. In the view of these results, the consumption of fish caught from the Borcka Dam Lake may not pose a potential risk to human.     

Characterization of Cell Boundary and Confocal Effects Improves Quantitative FRAP Analysis

Fluorescence recovery after photobleaching (FRAP) is an important tool used by cell biologists to study the diffusion and binding kinetics of vesicles, proteins, and other molecules in the cytoplasm, nucleus, or cell membrane. Although many FRAP models have been developed over the past decades, the influence of the complex boundaries of 3D cellular geometries on the recovery curves, in conjunction with regions of interest and optical effects (imaging, photobleaching, photoswitching, and scanning), has not been well studied. Here, we developed a 3D computational model of the FRAP process that incorporates particle diffusion, cell boundary effects, and the optical properties of the scanning confocal microscope, and validated this model using the tip-growing cells of Physcomitrella patens. We then show how these cell boundary and optical effects confound the interpretation of FRAP recovery curves, including the number of dynamic states of a given fluorophore, in a wide range of cellular geometries—both in two and three dimensions—namely nuclei, filopodia, and lamellipodia of mammalian cells, and in cell types such as the budding yeast, Saccharomyces pombe, and tip-growing plant cells. We explored the performance of existing analytical and algorithmic FRAP models in these various cellular geometries, and determined that the VCell VirtualFRAP tool provides the best accuracy to measure diffusion coefficients. Our computational model is not limited only to these cells types, but can easily be extended to other cellular geometries via the graphical Java-based application we also provide. This particle-based simulation—called the Digital Confocal Microscopy Suite or DCMS—can also perform fluorescence dynamics assays, such as number and brightness, fluorescence correlation spectroscopy, and raster image correlation spectroscopy, and could help shape the way these techniques are interpreted.     

Subcellular localization prediction with new protein encoding schemes

Subcellular localization is one of the key properties in functional annotation of proteins. Support vector machines (SVMs) have been widely used for automated prediction of subcellular localizations. Existing methods differ in the protein encoding schemes used. In this study, we present two methods for protein encoding to be used for SVM-based subcellular localization prediction: n-peptide compositions with reduced amino acid alphabets for larger values of n and pairwise sequence similarity scores based on whole sequence and N-terminal sequence. We tested the methods on a common benchmarking data set that consists of 2,427 eukaryotic proteins with four localization sites. As a result of 5-fold cross-validation tests, the encoding with n-peptide compositions provided the accuracies of 84.5, 88.9, 66.3, and 94.3 percent for cytoplasmic, extracellular, mitochondrial, and nuclear proteins, where the overall accuracy was 87.1 percent. The second method provided 83.6, 87.7, 87.9, and 90.5 percent accuracies for individual locations and 87.8 percent overall accuracy. A hybrid system, which we called PredLOC, makes a final decision based on the results of the two presented methods which achieved an overall accuracy of 91.3 percent, which is better than the achievements of many of the existing methods. The new system also outperformed the recent methods in the experiments conducted on a new-unique SWISSPROT test set     

Protective effects of curcumin on biochemical and molecular changes in sodium arsenite‐induced oxidative damage in embryonic fibroblast cells

The present study was aimed at determining the oxidative damage caused by sodium arsenite in 3T3 fibroblast cells and the possible protective role of curcumin (Cur) against sodium arsenite toxicity. Embryonic fibroblast cells were exposed to sodium arsenite (0.01, 0.1, 1, and 10 μM) in the presence and absence of Cur (2.5 μM) for 24 hours. Cell viability, cytotoxicity, lipid peroxidation, hydroxyl radical, hydrogen peroxide, antioxidant enzymes (superoxide dismutase, catalase, glutathione peroxidase, and glutathione‐S‐transferase) and expression levels of antioxidant genes (superoxide dismutase, catalase, and glutathione peroxidase) were measured in embryonic fibroblast cells. Results demonstrated that sodium arsenite directly affects antioxidant enzymes and genes in 3T3 embryonic fibroblast cells and induces oxidative damage by increasing the amount of hydrogen peroxide, hydroxyl radical, and lipid peroxidation in the cell. Furthermore, the study indicated that Cur might be a potential ameliorative antioxidant to protect the fibroblast cell toxicity induced by sodium arsenite.     

Therapeutic effect of curcumin on acrylamide‐induced apoptosis mediated by MAPK signaling pathway in Leydig cells

The aim of this study was to investigate the possible therapeutic effects of curcumin (CUR), against acrylamide (AA)‐induced toxic effects on Leydig cells. The AA and CUR‐treated cells were evaluated for cell viability, lipid peroxidation, reactive oxygen species (hydroxyl radical and hydrogen peroxide), antioxidant levels (glutathione peroxidase, glutathione‐S‐transferase, and catalase), apoptosis/necrosis rates and phosphorylation status of mitogen‐activated protein kinases (MAPKs). Leydig cells were exposed to four concentrations of AA (1, 10, 100, 1000 µM) in the presence and absence of CUR (2.5 µM) for 24 hours. According to the present result, AA concentration‐dependently, increased the oxidative stress parameters and suppressed the antioxidant enzyme levels, meanwhile induced apoptosis and activated the phosphorylation of extracellular signal‐regulated kinase, p38, and c‐Jun NH ₂‐terminal kinase. Moreover, CUR ameliorated the detrimental effects of AA. Thus, AA‐induced apoptosis through activation of the MAPK signaling pathway and CUR has a protective effect against AA‐induced damage in Leydig cells.     

The Anticonvulsant Effects of Alpha-2 Adrenoceptor Agonist Dexmedetomidine on Pentylenetetrazole-Induced Seizures in Rats

Neurochemical Research - Alpha2-adrenoreceptor (α2-AR) is a noradrenergic receptor that is frequently studied for modulation of seizure activity. However, the precise role of this receptor...     

Human sorting nexin 2 protein interacts with Influenza A virus PA protein and has a negative regulatory effect on the virus replication

Molecular Biology Reports - Replication of the influenza A viruses occurs in the cells through the viral RdRP consisting of PB1, PB2, and PA. Several cellular proteins are involved in these...