Coexisting presentation of two rare genetic variants of autosomal dominant polycystic kidney disease and Alport syndrome.

Alport syndrome and autosomal dominant polycystic kidney disease are monogenic causes of chronic kidney disease and end-stage kidney failure. We present a case of a man in his 60s with progressive chronic kidney disease, bilateral sensorineural hearing loss and multiple renal cysts. Genetic analysis revealed a heterozygous variant in COL4A3 (linked to Alport syndrome) and in the GANAB gene (associated with a milder form of autosomal dominant polycystic kidney disease). Although each variant confers a mild risk of developing end-stage kidney disease, the patient presented a pronounced and accelerated progression of chronic kidney disease, which goes beyond what would be predicted by adding up their individual effects. This suggests a potential synergic effect of both variants, which warrants further investigation.

Skin pigmentation as landmark for arteriovenous fistula cannulation in hemodialysis.

BACKGROUND: The cannulation of the arteriovenous fistula (AVF) for hemodialysis (HD) has traditionally depended on the nurse's tactile sensation, which has been associated with suboptimal needle placement and detrimental effects on vascular access (VA) longevity. While the introduction of ultrasound (US) has proven beneficial in mapping the AVF outflow vein and assisting in cannulation planning, aneurysmal deformations remain a common occurrence resulting from various factors, including inadequate cannulation techniques. Within this context, the utilization of skin pigmentation as a clinical landmark has emerged as a potential approach to enhance cannulation planning in HD. METHODS: A prospective longitudinal study was undertaken to investigate the correlation between the occurrence of venous morphological deformations and the cannulation technique guided by skin pigmentation after a 2-month period of implementation. RESULTS: Thirty patients were enrolled in the study with 433 cannulations being described within the first 2 months of AVF use. The overall rate of cannulation-related adverse events was 21.9%. Comparative analysis demonstrated a statistically significant relationship (p < 0.001) between aneurysmal deformation and non-compliance with the proposed cannulation technique, resulting in cannulation outside the designated points. Non-compliance was primarily attributed to nurse's decision (57.1%). CONCLUSION: The integration of US mapping of the AVF outflow vein and the utilization of skin pigmentation as a guiding tool have shown promising results in enhancing cannulation planning over time. Consistent adherence to a cannulation technique other than the area technique has been found to reduce the risk of AVF morphological deformation. These findings underscore the potential benefits of incorporating skin pigmentation as a clinical landmark in cannulation practices, highlighting its ability to impact positively cannulation outcomes.

Extracellular Vesicles in Diffuse Large B Cell Lymphoma: Characterization and Diagnostic Potential.

Diffuse large B cell lymphoma (DLBCL) is an aggressive B cell lymphoma characterized by a heterogeneous behavior and in need of more accurate biological characterization monitoring and prognostic tools. Extracellular vesicles are secreted by all cell types and are currently established to some extent as representatives of the cell of origin. The present study characterized and evaluated the diagnostic and prognostic potential of plasma extracellular vesicles (EVs) proteome in DLBCL by using state-of-the-art mass spectrometry. The EV proteome is strongly affected by DLBCL status, with multiple proteins uniquely identified in the plasma of DLBCL. A proof-of-concept classifier resulted in highly accurate classification with a sensitivity and specificity of 1 when tested on the holdout test data set. On the other hand, no proteins were identified to correlate with non-germinal center B-cell like (non-GCB) or GCB subtypes to a significant degree after correction for multiple testing. However, functional analysis suggested that antigen binding is regulated when comparing non-GCB and GCB. Survival analysis based on protein quantitative values and clinical parameters identified multiple EV proteins as significantly correlated to survival. In conclusion, the plasma extracellular vesicle proteome identifies DLBCL cancer patients from healthy donors and contains potential EV protein markers for prediction of survival.

Complete Genome Sequence of Two Deep-Sea Streptomyces Isolates from Madeira Archipelago and Evaluation of Their Biosynthetic Potential.

The deep-sea constitutes a true unexplored frontier and a potential source of innovative drug scaffolds. Here, we present the genome sequence of two novel marine actinobacterial strains, MA3_2.13 and S07_1.15, isolated from deep-sea samples (sediments and sponge) and collected at Madeira archipelago (NE Atlantic Ocean; Portugal). The de novo assembly of both genomes was achieved using a hybrid strategy that combines short-reads (Illumina) and long-reads (PacBio) sequencing data. Phylogenetic analyses showed that strain MA3_2.13 is a new species of the Streptomyces genus, whereas strain S07_1.15 is closely related to the type strain of Streptomyces xinghaiensis. In silico analysis revealed that the total length of predicted biosynthetic gene clusters (BGCs) accounted for a high percentage of the MA3_2.13 genome, with several potential new metabolites identified. Strain S07_1.15 had, with a few exceptions, a predicted metabolic profile similar to S. xinghaiensis. In this work, we implemented a straightforward approach for generating high-quality genomes of new bacterial isolates and analyse in silico their potential to produce novel NPs. The inclusion of these in silico dereplication steps allows to minimize the rediscovery rates of traditional natural products screening methodologies and expedite the drug discovery process.

Proteomic Landscape of Extracellular Vesicles for Diffuse Large B-Cell Lymphoma Subtyping.

The role of extracellular vesicles (EVs) proteome in diffuse large B-cell lymphoma (DLBCL) pathology, subclassification, and patient screening is unexplored. We analyzed by state-of-the-art mass spectrometry the whole cell and secreted extracellular vesicles (EVs) proteomes of different molecular subtypes of DLBCL, germinal center B cell (GCB subtype), and activated B cell (ABC subtype). After quality control assessment, we compared whole-cell and secreted EVs proteomes of the two cell-of-origin (COO) categories, GCB and ABC subtypes, resulting in 288/1115 significantly differential expressed proteins from the whole-cell proteome and 228/608 proteins from EVs (adjust p-value < 0.05/p-value < 0.05). In our preclinical model system, we demonstrated that the EV proteome and the whole-cell proteome possess the capacity to separate cell lines into ABC and GCB subtypes. KEGG functional analysis and GO enrichment analysis for cellular component, molecular function, and biological process of differential expressed proteins (DEP) between ABC and GCB EVs showed a significant enrichment of pathways involved in immune response function. Other enriched functional categories for DEPs constitute cellular signaling and intracellular trafficking such as B-cell receptor (BCR), Fc_gamma R-mediated phagocytosis, ErbB signaling, and endocytosis. Our results suggest EVs can be explored as a tool for patient diagnosis, follow-up, and disease monitoring. Finally, this study proposes novel drug targets based on highly expressed proteins, for which antitumor drugs are available suggesting potential combinatorial therapies for aggressive forms of DLBCL. Data are available via ProteomeXchange with identifier PXD028267.

Characterization of Protein Hydrolysates from Fish Discards and By-Products from the North-West Spain Fishing Fleet as Potential Sources of Bioactive Peptides.

Fish discards and by-products can be transformed into high value-added products such as fish protein hydrolysates (FPH) containing bioactive peptides. Protein hydrolysates were prepared from different parts (whole fish, skin and head) of several discarded species of the North-West Spain fishing fleet using Alcalase. All hydrolysates had moisture and ash contents lower than 10% and 15%, respectively. The fat content of FPH varied between 1.5% and 9.4% and had high protein content (69.8-76.6%). The amino acids profiles of FPH are quite similar and the most abundant amino acids were glutamic and aspartic acids. All FPH exhibited antioxidant activity and those obtained from Atlantic horse mackerel heads presented the highest 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging activity, reducing power and Cu2+ chelating activity. On the other hand, hydrolysates from gurnard heads showed the highest ABTS radical scavenging activity and Fe2+ chelating activity. In what concerns the α-amylase inhibitory activity, the IC50 values recorded for FPH ranged between 5.70 and 84.37 mg/mL for blue whiting heads and whole Atlantic horse mackerel, respectively. α-Glucosidase inhibitory activity of FPH was relatively low but all FPH had high Angiotensin Converting Enzyme (ACE) inhibitory activity. Considering the biological activities, these FPH are potential natural additives for functional foods or nutraceuticals.

Ibuprofen disrupts a WNK1/GSK3ß/SRPK1 protein complex required for expression of tumor-related splicing variant RAC1B in colorectal cells.

A major risk factor promoting tumor development is chronic inflammation and the use of nonsteroidal anti-inflammatory drugs (NSAID), including ibuprofen, can decrease the risk of developing various types of cancer, including colorectal cancer (CRC). Although the molecular mechanism behind the antitumor properties of NSAIDs has been largely attributed to inhibition of cyclooxygenases (COXs), several studies have shown that the chemopreventive properties of ibuprofen also involve multiple COX-independent effects. One example is its ability to inhibit the alternative splicing event generating RAC1B, which is overexpressed in a specific subset of BRAF-mutated colorectal tumors and sustains cell survival. Here we describe the mechanism by which ibuprofen prevents RAC1B alternative splicing in a BRAF mutant CRC cell line: it leads to decreased translocation of SRPK1 and SRSF1 to the nucleus and is regulated by a WNK1/GSK3ß/SRPK1 protein kinase complex. Surprisingly, we demonstrate that ibuprofen does not inhibit the activity of any of the involved kinases but rather promotes disassembly of this regulatory complex, exposing GSK3ß serine 9 to inhibitory phosphorylation, namely by AKT, which results in nuclear exclusion of SRPK1 and SRSF1 hypophosphorylation. The data shed new light on the biochemical mechanisms behind ibuprofen's action on alternative spliced RAC1B and may support its use in personalized approaches to CRC therapy or chemoprevention regimens.

Is the Proteome of Bronchoalveolar Lavage Extracellular Vesicles a Marker of Advanced Lung Cancer?

Acellular bronchoalveolar lavage (BAL) proteomics can partially separate lung cancer from non-lung cancer patients based on principal component analysis and multivariate analysis. Furthermore, the variance in the proteomics data sets is correlated mainly with lung cancer status and, to a lesser extent, smoking status and gender. Despite these advances BAL small and large extracellular vehicles (EVs) proteomes reveal aberrant protein expression in paracrine signaling mechanisms in cancer initiation and progression. We consequently present a case-control study of 24 bronchoalveolar lavage extracellular vesicle samples which were analyzed by state-of-the-art liquid chromatography-mass spectrometry (LC-MS). We obtained evidence that BAL EVs proteome complexity correlated with lung cancer stage 4 and mortality within two years´ follow-up (p value = 0.006). The potential therapeutic target DNMT3B complex is significantly up-regulated in tumor tissue and BAL EVs. The computational analysis of the immune and fibroblast cell markers in EVs suggests that patients who deceased within the follow-up period display higher marker expression indicative of innate immune and fibroblast cells (four out of five cases). This study provides insights into the proteome content of BAL EVs and their correlation to clinical outcomes.

WNK1 phosphorylation sites in TBC1D1 and TBC1D4 modulate cell surface expression of GLUT1.

Glucose uptake by mammalian cells is a key mechanism to maintain cell and tissue homeostasis and relies mostly on plasma membrane-localized glucose transporter proteins (GLUTs). Two main cellular mechanisms regulate GLUT proteins in the cell: first, expression of GLUT genes is under dynamic transcriptional control and is used by cancer cells to increase glucose availability. Second, GLUT proteins are regulated by membrane traffic from storage vesicles to the plasma membrane (PM). This latter process is triggered by signaling mechanisms and well-studied in the case of insulin-responsive cells, which activate protein kinase AKT to phosphorylate TBC1D4, a RAB-GTPase activating protein involved in membrane traffic regulation. Previously, we identified protein kinase WNK1 as another kinase able to phosphorylate TBC1D4 and regulate the surface expression of the constitutive glucose transporter GLUT1. Here we describe that downregulation of WNK1 through RNA interference in HEK293 cells led to a 2-fold decrease in PM GLUT1 expression, concomitant with a 60% decrease in glucose uptake. By mass spectrometry, we identified serine (S) 704 in TBC1D4 as a WNK1-regulated phosphorylation site, and also S565 in the paralogue TBC1D1. Transfection of the respective phosphomimetic or unphosphorylatable TBC1D mutants into cells revealed that both affected the cell surface abundance of GLUT1. The results reinforce a regulatory role for WNK1 in cell metabolism and have potential impact for the understanding of cancer cell metabolism and therapeutic options in type 2 diabetes.

A framework for the development of a global standardised marine taxon reference image database (SMarTaR-ID) to support image-based analyses.

Video and image data are regularly used in the field of benthic ecology to document biodiversity. However, their use is subject to a number of challenges, principally the identification of taxa within the images without associated physical specimens. The challenge of applying traditional taxonomic keys to the identification of fauna from images has led to the development of personal, group, or institution level reference image catalogues of operational taxonomic units (OTUs) or morphospecies. Lack of standardisation among these reference catalogues has led to problems with observer bias and the inability to combine datasets across studies. In addition, lack of a common reference standard is stifling efforts in the application of artificial intelligence to taxon identification. Using the North Atlantic deep sea as a case study, we propose a database structure to facilitate standardisation of morphospecies image catalogues between research groups and support future use in multiple front-end applications. We also propose a framework for coordination of international efforts to develop reference guides for the identification of marine species from images. The proposed structure maps to the Darwin Core standard to allow integration with existing databases. We suggest a management framework where high-level taxonomic groups are curated by a regional team, consisting of both end users and taxonomic experts. We identify a mechanism by which overall quality of data within a common reference guide could be raised over the next decade. Finally, we discuss the role of a common reference standard in advancing marine ecology and supporting sustainable use of this ecosystem.

Development of Fe/Nb-based solar photocatalysts for water treatment: impact of different synthesis routes on materials properties.

Semiconductors based on Fe/Nb oxides can present both solar sensitivity and high catalytic activity. However, there is still a lack regarding the comparison between different routes to produce Fe/Nb-based solar photocatalysts and the evaluation of the impact of the synthesis operating conditions on the material properties. In this work, Fe/Nb2O5 ratio, type of precipitating agent, presence/absence of washing stage, and temperature of calcination were verified to be the most relevant parameters in the synthesis by the co-precipitation method. These factors led to remarkable differences in the properties and performance of the photocatalysts produced by each distinct synthesis route. Composition, iron species present in the materials, crystallinity characteristics, and pH of the catalysts were affected, leading to different photocatalytic activities under UV-Vis light. Due to their characteristics, the synthesized materials are potential photocatalysts for application in solar processes. Graphical abstract ᅟ.

From nano- to micrometer scale: the role of microwave-assisted acid and alkali pretreatments in the sugarcane biomass structure.

BACKGROUND: To date, great strides have been made in elucidating the role of thermochemical pretreatments in the chemical and structural features of plant cell walls; however, there is no clear picture of the plant recalcitrance and its relationship to deconstruction. Previous studies precluded full answers due to the challenge of multiscale features of plant cell wall organization. Complementing the previous efforts, we undertook a systematic, multiscale, and integrated approach to track the effect of microwave-assisted H2SO4 and NaOH treatments on the hierarchical structure of plants, i.e., from a nano- to micrometer scale. We focused on the investigation of the highly recalcitrant sclerenchyma cell walls from sugarcane bagasse. RESULTS: Through atomic force microscopy and X-ray diffraction analyses, remarkable details of the assembly of cellulose microfibrils not previously seen were revealed. Following the H2SO4 treatment, we observed that cellulose microfibrils were almost double the width of the alkali pretreated sample at the temperature of 160 °C. Such enlargement led to a greater contact between cellulose chains, with a subsequent molecule alignment, as indicated by the X-ray diffraction (XRD) results with the conspicuous expansion of the average crystallite size. The delignification process had little effect on the local nanometer-sized arrangement of cellulose molecules. However, the rigidity and parallel alignment of cellulose microfibrils were partially degraded. The XRD analysis also agrees with these findings as evidenced by large momentum transfer vectors (q > 20 nm-1), interpreted as indicators of the long-range order of cell wall components, which were similar for all the studied samples except with application of the NaOH treatment at 160 °C. These changes were followed by the eventual swelling of the fiber cell walls. CONCLUSIONS: Based on an integrated approach, we presented multidimensional architectural models of cell wall deconstruction resulting from microwave-assisted pretreatments. We provided direct evidence supporting the idea that hemicellulose is the main barrier for the swelling of cellulose microfibrils, whereas lignin adds rigidity to cell walls. Our findings shed light on the design of more efficient strategies, not only for the conversion of biomass to fuels but also for the production of nanocellulose, which has great potential for several applications such as composites, rheology modifiers, and pharmaceuticals.

Expression of tumor-related Rac1b antagonizes B-Raf-induced senescence in colorectal cells.

Mutations in the BRAF oncogene have been identified as a tumor-initiating genetic event in mainly melanoma, thyroid and colon cancer, resulting in an initial proliferative stimulus that is followed by a growth arrest period known as oncogene-induced senescence (OIS). It remains unknown what triggers subsequent escape from OIS to allow further tumor progression. A previous analysis revealed that around 80% of colorectal tumors carrying a mutation in BRAF also overexpress splice variant Rac1b. We used normal NCM460 colonocytes as a model to express oncogenic B-Raf-V600E in the presence or absence of co-transfected Rac1b and then analyzed the effect on expression of senescence markers. When oncogenic B-Raf-V600E was expressed we observed the induction of the senescence-associated ß-galactosidase and of the cell-cycle inhibitors p14, p15 and p21 whereas proliferation marker Ki67 was suppressed. Upon co-expression of splice variant Rac1b, but not of Rac1, the B-Raf-induced senescence phenotype was reverted and expression of the cell-cycle inhibitors downregulated in a reactive oxygen-species dependent manner. We thus provide evidence that co-expression of splice variant Rac1b counteracts B-Raf-induced senescence, indicating the selection for increased Rac1b expression as one potential mechanism by which colorectal tumor cells can escape from B-Raf-induced OIS.

Steel wastes as versatile materials for treatment of biorefractory wastewaters.

Recent research on novel cost-effective adsorbent materials suggests potential use of industrial wastes for effluent treatment, with the added benefit of reuse of the wastes. Waste steel materials, including blast oxygen furnace sludge (BOFS), blast furnace sludge (BFS), and blast furnace dust (BFD), were investigated as low-cost adsorbents for removal of an oil emulsion and RR195 dye. The residues were characterized by X-ray diffraction, Brunauer-Emmett-Teller area, volume and distribution of pore diameters, Mössbauer spectroscopy, X-ray fluorescence, granulometry, scanning electron microscopy/energy dispersive spectroscopy, and pHpzc. Adsorption kinetics data were obtained by UV-vis spectrophotometry at the maximum absorption wavelength of the dye solution and crude oil emulsion. The use of waste as an adsorbent was more efficient for treatment of the oil emulsion than the dye solution. BOFS had higher total organic carbon (TOC) removal efficiency than the other waste materials. For the RR195 dye, good color removal was observed for all adsorbents, >90 % within 24 h. TOC removal was poor, <10 % for BFD and BFS and a maximum of 37 % for BOFS. For the oil emulsion, 97 % TOC removal was obtained by adsorption onto BOFS and 87 % onto BFS.

New species of Heteropathes (Anthozoa: Antipatharia) expands genus distribution to the NE Atlantic.

Heteropathes opreski, a new antipatharian species from the northern border of the Oceanographer Fracture Zone is here described and illustrated. An emended diagnosis of the genus and a dichotomous key containing the four Heteropathes species are presented. This species is unique in that it forms smaller colonies compared to the other species in the genus, with some of the lateral pinnules presenting a small ramified subpinnule. Additionally, the polypar spines found on the lateral pinnules are the highest so far recorded in the genus. This record greatly expands the known distribution of this genus, as it was not previously reported to occur in the Northeastern Atlantic.

The effects of whole green tea infusion on mouse urinary bladder chemical carcinogenesis.

OBJECTIVE(S): Green tea (GT) is one of the most popular beverages worldwide whose beneficial effects on health have been demonstrated. Recent studies suggest that GT may contribute to reduction of cancer risk and progression. The aim of this study was to evaluate the effects of whole GT on urinary bladder chemical carcinogenesis in male and female ICR mice. MATERIALS AND METHODS: The GT characterization was performed using spectrophotometric methods. Urinary bladder lesions were induced using N-butyl-N-(4-hydroxybutyl) nitrosamine (BBN) by gavage during 10 weeks and whole GT (0.5%) was provided ad libitum during 20 weeks. RESULTS: Animals from groups BBN+GT and BBN only developed preneoplastic lesions. CONCLUSION: We did not observe any effects by GT infusion administration on urinary bladder cancer development.