Search Results (431)

Evaluating cancer gene mutations is critical for effective therapeutic selection. Although massive parallel sequencing can efficiently detect gene mutations, most are variants of uncertain significance (VUS). Saturation genome editing (SGE) can facilitate VUS analysis by leveraging CRISPR-Cas9 and homology-directed repair to simultaneously introduce abundant gene mutations. Chronic myelogenous leukemia-derived HAP1 cells are widely used in SGE because of their clear genotype–phenotype relationship; however, the sole use of haploid cells limits SGE applicability in cancer research. Therefore, we developed an SGE-based system for evaluating KRAS mutations in diploid HCT 116 colon carcinoma cells. Single-nucleotide variants (SNVs) in KRAS codons A11–V14 were generated using Cas9-based SGE. Massive parallel sequencing revealed increased abundance of KRAS ^G12 and KRAS ^G13 SNVs and decreased abundance of the KRAS ^G12C SNV after KRAS ^G12C inhibitor treatment in SGE pooled cells. These results indicate that SGE is applicable to diploid HCT 116 cells and useful for evaluating SNV population changes and drug sensitivity. Thus, although haploid HAP1 cells are the primary models for SGE, the successful application of SGE to diploid HCT 116 colon carcinoma cells provides a practical framework for implementing SGE in KRAS-dependent carcinoma cells. Full article

Forward osmosis (FO) membranes face challenges in balancing high water permeability, low reverse salt flux (RSF), and mechanical durability. Although nanopores in graphene have great theoretical potential, the existing methods make it difficult to independently optimize the nanopores of the graphene layer and the microstructure of the substrate without damaging each other. Here, we propose a defect engineering strategy based on oxygen plasma etching to address this collaborative optimization challenge. Monolayer porous graphene (PG) was integrated with polysulfone (Psf) substrates, followed by oxygen plasma etching to introduce nanopores and oxygen-containing functional groups (e.g., carboxyl, hydroxyl). By controlling the etching time to 10 s, the resulting membrane (S-PG10) exhibited a water flux of 0.24 LMH in 0.5 M NaCl, representing an order-of-magnitude increase compared to the pristine graphene membrane (S-G). Remarkably, S-PG10 maintained a high salt rejection (>96%) and a low J_s/J_w (<0.35 g·L⁻¹). Substrate modification via short-term plasma etching (5 min) further doubled the water flux of S*5-PG10 (0.47 LMH in 0.5 M NaCl) by increasing porosity (81.8%→85.6%) and hydrophilicity. However, prolonged etching (>15 min) degraded mechanical strength and increased RSF due to pore structure disruption. To enhance robustness, Poly(D,L-lactic acid) (PDLLA)-doped substrates (S^#-PG) were engineered, with 0.1 wt.% PDLLA optimizing mechanical properties while maintaining low RSF and high flux. Excessive PDLLA (10 wt.%) induced hydrophobicity and crystalline structures, reducing permeability. The study demonstrates that synergistic optimization of plasma etching duration on the graphene selective layer (5~10 s) and substrates (5 min) as well as PDLLA doping (0.1 wt.%) balances pore architecture, surface chemistry, and substrate integrity, achieving FO membranes with superior water-salt selectivity and mechanical stability. These findings provide critical insights into designing high-performance graphene-based membranes for sustainable desalination and water purification. Full article

In (colloquial) Italian, the fixed expression mi sa functions as an evidential/epistemic marker, requiring the dative 1SG clitic experiencer and the 3SG default form of the verb sapere. Mi sa diachronically develops from the verb for taste/smell, sapere, which is still productive in contemporary Italian, and the structure that it projects. This comprises an obligatory PP introduced by di encoding the type/quality of taste/smell (often metaphorically extended); a subject expressing the perceived entity; and an optional dative experiencer. We systematically analyzed data from the KIParla corpus, comparing the distribution of mi sa to the distribution of one of the most frequent Italian epistemic verb forms, namely, credo ‘I believe’. This study aimed to establish how the original perceptual meaning of mi sa influences its epistemic meaning. The results suggest that the persistence of the original object-oriented perception verb makes mi sa more likely to appear in particular contexts, i.e., events/situations that are known by the speaker through an inferential-like process. Furthermore, mi sa can only rarely be uttered out of the blue and seems to need a situative context (a stage), often containing an explicit QUD. Full article

Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a positive-sense RNA virus, and its genome includes a highly conserved 5′ untranslated region (5′UTR). This region contains the so-called ‘leader sequence’, a crucial genomic region responsible for the viral replication and the synthesis of all subgenomic RNAs (sgRNAs). It has been demonstrated that targeting highly conserved genomic regions is essential for developing broad-spectrum antiviral therapies that resist viral mutation and evasion. Hypothesis: Given the high level of nucleotide homology between SARS-CoV and SARS-CoV-2, particularly in essential regions like the 5′UTR, the identification of a perfect sequence alignment across SARS-CoV-2 variants within this conserved region would provide a robust, mutation-resistant target for novel RNA-based drugs, such as small interfering RNAs (siRNAs) or microRNAs (miRNAs). Materials and Methods: Sequence alignment was performed across the different SARS-CoV-2 strains (i.e., the different variants that have appeared so far) to identify conserved genomic areas, leading to the selection of potential target sites for antiviral molecules. Specifically, computational analyses were utilized to map available binding sites for human miRNAs within the SARS-CoV-2 5′UTR. Results: Comparative alignments revealed that the leader sequence/5′UTR region is highly stable and conserved in all the considered SARS-CoV-2 sequences, representing a common therapeutic target across different variants and strains. Discussion: The perfect alignment observed in the 5′UTR confirms that this region is a highly critical target, less prone to mutations in all the considered variants. This property makes the region ideal for therapeutic intervention using non-coding RNAs. If endogenous miRNAs were found to bind this region (e.g., miR-638, miR-3150b-3p, etc.) and promote viral replication similarly to mechanisms observed in viruses like hepatitis C virus (HCV), their activity could be inhibited using chemically modified antisense analogs, such as locked nucleic acid (LNA) oligonucleotides. Full article

4D millimeter-wave radar provides a promising solution for robust perception in adverse weather. Existing detectors still struggle with sparse and noisy point clouds, and maintaining real-time inference while achieving competitive accuracy remains challenging. We propose SGE-Flow, a streamlined PointPillars-based 4D radar 3D detector that embeds lightweight spatiotemporal geometric enhancements into the voxelization front-end. Velocity Displacement Compensation (VDC) leverages compensated radial velocity to align accumulated points in physical space and improve geometric consistency. Distribution-Aware Density (DAD) enables fast density feature extraction by estimating per-pillar density from simple statistical moments, which also restores vertical distribution cues lost during pillarization. To compensate for the absence of tangential velocity measurements, a Transformer-based Inter-frame Flow (IFF) module infers latent motion from frame-to-frame pillar occupancy changes. Evaluations on the View-of-Delft (VoD) dataset show that SGE-Flow achieves 53.23% 3D mean Average Precision (mAP) while running at 72 frames per second (FPS) on an NVIDIA RTX 3090. The proposed modules are plug-and-play and can also improve strong baselines such as MAFF-Net. Full article

The speckle-type BTB/POZ protein (SPOP) is an E3 ubiquitin ligase adaptor typically considered a tumor suppressor, yet its role in head and neck squamous cell carcinoma (HNSCC) remains unclear. This study investigated SPOP expression, arecoline regulation, and its potential as a HNSCC biomarker. SPOP mRNA and its protein were quantified in HNSCC (FaDu, GMN, HSC-3, SAS, and A253) and normal oral epithelial (SG) cell lines via RT-qPCR and Western blot; arecoline’s effect on SG, SAS, and A253 cells was evaluated. SPOP mRNA was analyzed using The Cancer Genome Atlas (TCGA) HNSCC cohort, and protein localization was assessed via immunohistochemistry (IHC) on tissue microarrays. SPOP mRNA was higher in some HNSCC lines; arecoline induced SPOP in SG cells, but not in HNSCC cell lines. TCGA confirmed SPOP mRNA upregulation in tumors correlating with grade. IHC showed SPOP upregulation in HNSCC, particularly in palate and pharynx/hypopharynx sites. The nuclear SPOP-positive ratio shifted from 12.14 ± 9.82% in normal tissues to 61.26 ± 33.03% in tumors (p < 0.0001), differentiating grades and sites better than total expression. SPOP is upregulated in HNSCC and inducible by arecoline. Enhanced nuclear SPOP localization indicates malignancy and progression, identifying it as a potential HNSCC diagnostic and progression biomarker. Full article

Extracellular vesicles, which carry bioactive cargos such as proteins, RNAs, and lipids, represent promising drug delivery vehicles owing to their biocompatibility, low immunogenicity, and inherent tissue-targeting capabilities. To address the current limitations in controlled cargo loading, we developed an abscisic acid (ABA)-inducible proximity system that directs proteins into exosomes during biogenesis. We engineered exosomal scaffolds by fusing the ABA receptor PYL1 to EV-enriched proteins—including BASP1, CD9, PTGFRN, and a truncated form PTGFRNΔ687—thereby creating docking sites within the exosomal lumen, while the target cargo (e.g., EGFP, firefly luciferase, or Cas9) was tagged with the ABI1 phosphatase domain. We demonstrate that ABA administration in producer cells induces PYL1–ABI1 complex formation, which recruits ABI1-fused cargo for selective encapsulation into EVs. Among the scaffolds tested, BASP1–PYL1 proved the most effective, enabling robust, ABA-dependent enrichment of cargo proteins. Purified EVs maintained canonical morphology, size, and marker expression (CD63, syntenin-1, CD9), confirming preserved biogenesis. Critically, these loaded exosomes efficiently delivered functional cargo to recipient cells, enabling Cas9/sgRNA-mediated genome editing. Together, our findings establish an ABA-triggered molecular switch for controllable EV protein loading, providing a versatile platform for next-generation therapeutic delivery. Full article

Background/Objectives: Iron deficiency affects 2% of infants under six months of age and 4–18% of infants aged 6–12 months and may lead to anemia. Given the consequences of iron deficiency in infancy and the importance of adequate nutrition, this study aimed to assess indicators of iron metabolism in infants whose parents participated in nutritional education. Methods: The study included 104 infants, divided into a study group (SG, n = 52) receiving a nutritional education intervention and a control group (CG, n = 52). Peripheral blood morphology parameters and biochemical markers, e.g., iron status (serum iron, transferrin, ferritin, and hepcidin), were evaluated at 3 and 12 months of age. Additionally, at study end, parents completed a three-day dietary diary to assess their infant’s iron intake. Results: After nearly one year of intervention, no cases of anemia based on hemoglobin concentration were identified in either group. However, infants in the SG were less likely to present iron and ferritin concentrations below reference ranges compared to the CG. In the CG, low ferritin levels occurred more frequently at 12 months than at baseline. This finding may be related to higher dietary iron intake in the SG, as insufficient iron intake was more common among the CG. Heatmap analysis revealed strong positive correlations among erythrocyte indices, confirming their internal consistency. No single parameter emerged as a superior marker of iron deficiency, emphasizing the need for a combined assessment of iron status. Conclusions: Parental nutritional education may improve iron status and reduce the risk of iron metabolism disorders in infants. Full article

A simple mechanical polishing treatment of commercial solid-gold electrodes (SGEs) can renew the active gold surface, reduce manufacturing-related grooves, and markedly improve the repeatability of geometric-area estimation and the analytical performance in stripping voltammetry. The work focuses on the accurate determination of the geometric area of a SGE by two voltammetric techniques. Cyclic voltammetry (CV) at different scan rates, referred to as the Randles–Ševčik equation, and voltage scans at different electrode rotation rates, based on the Levich equation, were performed. The geometric area of the SGE was also evaluated by scanning electron microscopy (SEM). Commercial SGEs show grooves on their surface, derived from the fabrication processes. The effects of these grooves on the voltammetric response were investigated. The measurements were carried out on the SGE both as received from the manufacturer and after a reduction in the grooves height by a drastic mechanical treatment. After the treatment, the estimated area values were lower and more precise (3.05 ± 0.02 mm²). Moreover, the reduction in the grooves’ height affected the area estimations in contrast with the meaning of the geometric area, as intended by the Randles–Ševčik and Levich equations. Furthermore, the gold exposed surface was measured by CV in sulphuric acid. Finally, the SGE was tested for the detection of Hg in a NaCl solution by anodic stripping voltammetry: the repeatability of the response improved after the mechanical treatment, confirming the usefulness of this step before electrode usage. Full article

African swine fever virus (ASFV) is a highly contagious and lethal double-stranded DNA virus that relies on host cellular translation machinery for replication and immune evasion. The multigene family 110 (MGF110) contains several members with incompletely defined functions. Here, the role of MGF110-7L in host translation regulation was investigated in HEK-293T and PK15 cells. Ribopuromycylation assays demonstrated that MGF110-7L expression resulted in potent, dose- and time-dependent inhibition of nascent polypeptide synthesis. Western blotting revealed a selective reduction in eIF4G1 protein abundance, with no significant changes in eIF4G2, eIF4E, and eIF4A, while eIF4G1 mRNA levels remained unaffected, indicating post-transcriptional regulation. Overexpression of eIF4G1 partially rescued translation suppression. MGF110-7L also decreased eIF4B phosphorylation and activated the PERK/eIF2α pathway, consistent with the induction of endoplasmic reticulum (ER) stress. ER stress promoted stress granule (SG) formation and enhanced eIF4G1 association with the SG marker G3BP1. The inhibitor assays demonstrated that the suppression of eIF2α phosphorylation by ISRIB restored the abundance of eIF4G1 protein. In addition, the downregulation of eIF4G1 was reversed by the inhibition of autophagy using bafilomycin A1, indicating an SG-linked autophagy–lysosome degradation pathway. Co-immunoprecipitation assays confirmed increased eIF4G1-G3BP1 interaction, but no direct binding between MGF110-7L and eIF4G1. This work provides the first experimental evidence that an ASFV protein, MGF110-7L, suppresses cap-dependent translation through SG-mediated autophagic degradation of eIF4G1, thereby revealing a previously unrecognized mechanism of ASFV translational control. These findings not only extend current understanding of ASFV–host interactions but also suggest potential molecular targets for antiviral strategies and rational vaccine design. Full article

Steel defects, stemming from issues like raw material imperfections and processing inconsistencies, present substantial challenges for the material’s effective use and subsequent manufacturing. Consequently, the real-time, accurate, and rapid detection of these defects is paramount in production, playing a vital role in cost reduction, efficiency enhancement, and resource conservation. To address these needs, this paper proposes a deep deep-learning-based image recognition method for defect detection using YOLOv7 (You Only Look Once), designated YOLOv7-SGS. This approach introduces a novel architecture, the YOLOv7-SGS network, which builds upon the standard YOLOv7. The enhancements include integrating a Shape-IoU model into the core backbone, innovatively incorporating an SGE attention mechanism, and refining the convolution algorithm with GSConv to boost model performance. The resulting YOLOv7-SGS model achieves an absolute 6% improvement in mAP@0.5 compared to the baseline model. Moreover, it attains a detection speed of 32 FPS, showcasing significant advantages and offering valuable insights for future research and practical applications. Full article

The post-genomic era, defined by large-scale sequencing initiatives, has generated an unprecedented catalogue of human genetic variation. Yet, the vast majority of genetic variants remain classified as variants of uncertain significance or are located within poorly characterized non-coding regions, thereby hindering the effective translation of genomic data into meaningful biological understanding and clinical application. Bridging this genotype-to-phenotype gap requires precise, high-throughput functional genomics. Early CRISPR–Cas9 knockout and CRISPR interference/activation (CRISPRi/a) screens mapped gene-level functions but could not assess single nucleotide variants (SNVs). Bridging this genotype-to-phenotype gap demands precise, high-throughput functional genomics. Multiplexed assays of variant effect (MAVEs), like saturation genome editing, systematically test all possible mutations using CRISPR–Cas9 and donor libraries. Base editors allow targeted single-base changes without double-strand breaks but are limited in scope, while prime editing can introduce any small substitution, insertion, or deletion without double-strand breaks (DSBs) or donor templates. This review traces the evolution of functional screens from gene-level knockouts to saturation genomic editing (SGE), and highlights how prime editing is driving a new paradigm for the systematic functional characterization of thousands of variants across disease-relevant genes. We also detail the architecture, mechanism, and progressive optimization of PE systems and their delivery methods. Collectively, prime editing stands as a transformative platform poised to accelerate precision functional genomics and advance the diagnosis and treatment of genetic diseases. Full article

This study presents an integrated chemical and anatomical characterization of leaves from seven Asparagaceae species (Agave convallis Trel., A. salmiana Otto ex Salm.-Dyck, A. striata Zucc., Dasylirion acrotrichum Zucc., Nolina excelsa García-Mend. & E. Solano, Yucca filifera Chabaud, and Y. periculosa Baker). Leaf biomass was subjected to successive Soxhlet extractions to quantify extractives, followed by isolation of lignocellulosic fractions. Lignin and cellulose were analyzed by Fourier-transform infrared (FTIR) spectroscopy to determine the syringyl/guaiacyl (S/G) ratio and total crystallinity index. Leaf anatomy was examined using fluorescence microscopy. Total extractives ranged from 13.4 to 24.0%, with A. salmiana and D. acrotrichum showing the highest values. Lignin content varied markedly among genera, reaching up to 45.1% in Yucca species, whereas cellulose content ranged from 31.3 to 42.2%. Crystalline cellulose accounted for 42.1–56.9% of total cellulose, with the highest crystallinity observed in A. convallis. FTIR analysis revealed a predominance of guaiacyl-type lignin in all species except Y. periculosa (S/G = 1.2). Multivariate analyses discriminated between genera primarily based on lignin, hemicellulose, and cellulose contents. These findings highlight genus-level differences in leaf lignocellulosic composition and support the potential use of Asparagaceae leaves as feedstocks for bioenergy and biomaterial applications. Full article

Objective: This study evaluated the effects of a 12-week High-Intensity Functional Training (HIFT) program combined with thylakoid supplementation on plasma adipo-myokine levels (Decorin, Myostatin, Follistatin, Activin A, and TGF-β1) in men with obesity. Secondary outcomes included anthropometric indices, lipid profiles, and insulin resistance markers. Methods: Sixty men with obesity (age: 27.6 ± 8.4 years; BMI: 32.6 ± 2.6 kg/m²) were randomly assigned to four groups (n = 15 per group): Placebo (PG), Supplement (SG), HIFT + placebo (TPG), and HIFT + supplement (TSG). To ensure robustness against the 27% attrition rate, statistical analyses included both per-protocol and intention-to-treat (ITT) models. HIFT was performed for 3 sessions/week (Borg scale: 15–17). Results: Following Bonferroni correction for multiple endpoints, repeated-measures ANOVA showed significant Time × Group interactions for most adipo-myokines and metabolic markers. Both training groups (TPG and TSG) demonstrated improvements in body composition and insulin sensitivity compared to PG (p < 0.05). While no significant differences were observed between TPG and TSG for systemic metabolic markers, preliminary data suggested that thylakoid supplementation might provide modest complementary modulations in specific myokines (e.g., decorin and follistatin). However, these observed trends did not reach clinical superiority over exercise alone in the broader metabolic profile. Conclusions: Twelve weeks of HIFT is an effective primary driver for modulating the adipo-myokine network in obese men. Although thylakoid supplementation showed potential for selective complementary effects on certain myokines, these findings are exploratory given the small sample size. The clinical significance and long-term complementary value of thylakoid-exercise interactions require further validation in larger, more diverse cohorts. Full article

CRISPR-Cas9 technology has opened new perspectives in genome editing of clonally, asexually propagated and polyploid plants by enabling multiple allelic gene edits. Traditional Agrobacterium- and particle bombardment-mediated transformations, which rely on integration of gene-editing transgene cassettes, have been efficiently applied to several plants; however, concerns about the acceptability of resultant edited transgenic genotypes make these methods less attractive for vegetatively propagated crops. We leveraged and optimized the CRISPR-Cas9/sgRNA-RNPs system for delivery into protoplasts of the hexaploid sweetpotato cultivar PI-318846, targeting eukaryotic translation initiation factor isoform 4E genes to enhance resistance to SPFMV potyviruses. To evaluate the efficiency of pre-assembled Cas9/sgRNA-RNP in sweetpotato transfection, single guide RNAs were designed to target putative host susceptibility genes: IbeIF4E, IbeIF(iso)4E, and IbCBP. Freshly isolated leaf protoplasts were subjected to CRISPR-CAS9-RNP PEG-mediated transfection under different parameters. Sweetpotato regenerants screened using PCR-RE-T7 assay, sequencing, and Inference CRISPR Edit analyses of target-site amplicons revealed the most efficient editing conditions utilizing 25% PEG with a 3:1 (15 µg:45 µg) ratio of Cas9/sgRNA-RNP for 25 min and 48 h incubation period. Different allelic InDels were obtained with editing efficiencies of 10–20% in regenerated plantlets, demonstrating that PEG-mediated CRISPR-RNP transfection system is key for advancing DNA-free editing tools in polyploid and vegetatively propagated crops. Full article