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PubMed2006

Method for measuring thickness of dielectric films using microdielectric fringe-effect sensors.

A method for noninvasive thickness measurements of dielectric films using fringe-effect (FE) sensors is developed and experimentally validated. The fringing electrical field, created by electrodes microfabricated at the film substrate, depends on the film thickness and dielectric permittivity of the film under test (FUT). The unknown film thickness is estimated by matching the theoretical prediction of thickness-dependent sensor admittance with the measured value. In the case of FE sensors with spatially periodic, interdigitated electrode (IDE) configuration, the admittance prediction is simplified, which allows for the real-time measurements of changing thickness. The developed method can be used to continuously measure the changing dielectric permittivity of the FUT material, which makes it possible to determine the thickness of films of changing dielectric properties, caused by chemical or other transformations. The application of the developed method is demonstrated experimentally by measuring the thickness of silicon nitride film deposited in several increments on the quartz substrate of the IDE sensor. In the expected range of sensor sensitivity, the results show an excellent agreement with the independent thickness measurements.

Journal Article↗

PubMed2025

Development and validation of a novel risk stratification signature derived from migrasome and tumor microenvironment-related genes for molecular subtyping and improving clinical outcomes in head and neck squamous cell carcinoma.

BACKGROUND: The tumor microenvironment (TME) and migrasomes released by tumor cells significantly influence carcinogenesis and immune evasion. However, our understanding of the prognostic and therapeutic implications of migrasome and tumor microenvironment-related genes (mtmRGs) in head and neck squamous cell carcinoma (HNSCC) remains limited. METHODS: We explored the relationship between mtmRGs and HNSCC prognosis by utilizing The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) databases. Subsequently, we developed an innovative prognostic signature, and assessed its prognostic significance using the Kaplan-Meier method, time-dependent receiver operating characteristic (ROC), and Cox regression analyses. To explore the underlying mechanisms, we conducted gene set variation analysis (GSVA), gene set enrichment analysis (GESA), and immune infiltration analysis. A nomogram was developed to estimate the overall survival (OS) rates for HNSCC patients. Lastly, we chose P4HA1, which was part of the signature, for additional experimental validation in vitro and in vivo. RESULTS: The mtmRGs signature effectively classifies HNSCC patients into two distinct risk subgroups, with the high-risk cohort demonstrating significantly poorer OS. The risk score serves as an independent prognostic factor for HNSCC patients; those with lower risk scores are more likely to exhibit favorable responses to immunotherapy, particularly with CTLA4 inhibitors. Furthermore, a lower risk score is significantly correlated with the sensitivity of HNSCC patients to cyclophosphamide, gemcitabine, and axitinib. CONCLUSION: This study presents an innovative gene signature associated with mtmRGs, which may be utilized both for predicting survival and directing personalized chemotherapy and immunotherapy regiments for patients with HNSCC.

Humans↗

PubMed2004

Divergent anticodon recognition in contrasting glutamyl-tRNA synthetases.

The pathogenic bacterium Helicobacter pylori utilizes two essential glutamyl-tRNA synthetases (GluRS1 and GluRS2). These two enzymes are closely related in evolution and yet they aminoacylate contrasting tRNAs. GluRS1 is a canonical discriminating GluRS (D-GluRS) that biosynthesizes Glu-tRNA(Glu) and cannot make Glu-tRNA(Gln). In contrast, GluRS2 is non-canonical as it is only essential for the production of misacylated Glu-tRNA(Gln). The co-existence and evident divergence of these two enzymes was capitalized upon to directly examine how GluRS2 acquired tRNA(Gln) specificity. One key feature that distinguishes tRNA(Glu) from tRNA(Gln) is the third position in the anticodon of each tRNA (C36 versus G36, respectively). By comparing sequence alignments of different GluRSs, including GluRS1s and GluRS2s, to the crystal structure of the Thermus thermophilus D-GluRS:tRNA(Glu) complex, a divergent pattern of conservation in enzymes that aminoacylate tRNA(Glu)versus those specific for tRNA(Gln) emerged and was experimentally validated. In particular, when an arginine conserved in discriminating GluRSs and GluRS1s was inserted into Hp GluRS2 (Glu334Arg GluRS2), the catalytic efficiency of the mutant enzyme (k(cat)/K(Mapp)) was reduced by approximately one order of magnitude towards tRNA(Gln). However, this mutation did not introduce activity towards tRNA(Glu). In contrast, disruption of a glycine that is conserved in all GluRS2s but not in other GluRSs (Gly417Thr GluRS2) generated a mutant GluRS2 with weak activity towards tRNA(Glu1). Synergy between these two mutations was observed in the double mutant (Glu334Arg/Gly417Thr GluRS2), which specifically and more robustly aminoacylates tRNA(Glu1) instead of tRNA(Gln). As GluRS1 and GluRS2 are related by an apparent gene duplication event, these results demonstrate that we can experimentally map critical evolutionary events in the emergence of new tRNA specificities.

Amino Acid Sequence↗

PubMed2002

Folding pathways of prion and doppel.

The relevance of various residue positions for the stability and the folding characteristics of the prion protein in its normal cellular form are investigated by using molecular dynamics simulations of models exploiting the topology of the native state. These models allow for reproducing the experimentally validated two-state behavior of the normal prion isoform. Highly significant correlations are found between the most topologically relevant sites in our analysis and the single point mutations known to be associated with the arousal of the genetic forms of prion disease. Insight into the conformational change is provided by comparing the folding process of cellular prion and doppel that share a similar native state topology: the folding pathways of the former can be grouped in two main classes according to which tertiary structure contacts are formed first enroute to the native state. For the latter a single class of pathways leads to the native state again through a two-state process. Our results are consistent and supportive of the recent experimental findings that doppel lacks the scrapie isoform and that such remarkably different behavior involves residues in the region containing the two beta-strands and the intervening helix.

Amino Acids↗

PubMed2004

Analysis of local T lymphocyte subsets upon stimulation with intravesical BCG: a model to study tuberculosis immunity.

Cell-mediated immune response can control tuberculosis infection. A significant role for immune cells like CD4, CD8 and gammadelta T lymphocytes have been recognized, but little is known about the kinetics of activation and accumulation of these cells in course of Tuberculosis infection in humans. This is due to both the difficult to access to human lung and the fact that most subjects are examined in different periods of infection which may condition T cell changes. To overcome these problems, we have used intravesical BCG (Bacillus Calmette-Guerin) treatment for preventing the recurrences of bladder cancer as an in vivo experimental model of human tuberculosis infection. 20 male caucasian patients with proven bladder superficial transitional cell carcinoma treated with transurethral resection followed by six weekly intravesical instillations of BCG (T0-T6) were enrolled. Changes in T lymphocyte subsets were assessed by flow cytometry in the bladder wash recovered after each BCG instillation. Our study shows that the action of BCG appears to be T cell dependent. Lymphocytes increase at any new instillation and tend towards the reduction with the suspension of the stimulus. BCG induces a massive increase in the proportion of CD4 Th1 subset followed by an increase in gammadelta T cells, while no significant variation for CD8 and NK cells is found. Our results suggest that BCG infection model represents a valid experimental tool to study the immunological events evoked in vivo by Mycobacterium tuberculosis in humans at the site of infection.

BCG Vaccine↗

PubMed2002

Comparison of quantitative perfusion imaging using arterial spin labeling at 1.5 and 4.0 Tesla.

High-field arterial spin labeling (ASL) perfusion MRI is appealing because it provides not only increased signal-to-noise ratio (SNR), but also advantages in terms of labeling due to the increased relaxation time T(1) of labeled blood. In the present study, we provide a theoretical framework for the dependence of the ASL signal on the static field strength, followed by experimental validation in which a multislice pulsed ASL (PASL) technique was carried out at 4T and compared with PASL and continuous ASL (CASL) techniques at 1.5T, both in the resting state and during motor activation. The resting-state data showed an SNR ratio of 2.3:1.4:1 in the gray matter and a contrast-to-noise ratio (CNR) of 2.7:1.1:1 between the gray and white matter for the difference perfusion images acquired using 4T PASL, 1.5T CASL, and 1.5T PASL, respectively. However, the functional data acquired using 4T PASL did not show significantly improved sensitivity to motor cortex activation compared with the 1.5T functional data, with reduced fractional perfusion signal change and increased intersubject variability. Possible reasons for these experimental results, including susceptibility effects and physiological noise, are discussed.

Adult↗

PubMed2006

ModuleFinder and CoReg: alternative tools for linking gene expression modules with promoter sequences motifs to uncover gene regulation mechanisms in plants.

BACKGROUND: Uncovering the key sequence elements in gene promoters that regulate the expression of plant genomes is a huge task that will require a series of complementary methods for prediction, substantial innovations in experimental validation and a much greater understanding of the role of combinatorial control in the regulation of plant gene expression. RESULTS: To add to this larger process and to provide alternatives to existing prediction methods, we have developed several tools in the statistical package R. ModuleFinder identifies sets of genes and treatments that we have found to form valuable sets for analysis of the mechanisms underlying gene co-expression. CoReg then links the hierarchical clustering of these co-expressed sets with frequency tables of promoter elements. These promoter elements can be drawn from known elements or all possible combinations of nucleotides in an element of various lengths. These sets of promoter elements represent putative cis-acting regulatory elements common to sets of co-expressed genes and can be prioritised for experimental testing. We have used these new tools to analyze the response of transcripts for nuclear genes encoding mitochondrial proteins in Arabidopsis to a range of chemical stresses. ModuleFinder provided a subset of co-expressed gene modules that are more logically related to biological functions than did subsets derived from traditional hierarchical clustering techniques. Importantly ModuleFinder linked responses in transcripts for electron transport chain components, carbon metabolism enzymes and solute transporter proteins. CoReg identified several promoter motifs that helped to explain the patterns of expression observed. CONCLUSION: ModuleFinder identifies sets of genes and treatments that form useful sets for analysis of the mechanisms behind co-expression. CoReg links the clustering tree of expression-based relationships in these sets with frequency tables of promoter elements. These sets of promoter elements represent putative cis-acting regulatory elements for sets of genes, and can then be tested experimentally. We consider these tools, both built on an open source software product to provide valuable, alternative tools for the prioritisation of promoter elements for experimental analysis.

Journal Article↗

PubMed2001

Modularity and homology: modelling of the titin type I modules and their interfaces.

Titin is a giant muscle protein with a highly modular architecture consisting of multiple repeats of two sequence motifs, named type I and type II. Type I motifs are homologous to members of the fibronectin type 3 (Fn3) superfamily, one of the motifs most widespread in modular proteins. Fn3 domains are thought to mediate protein-protein interactions and to act as spacers. In titin, Fn3 modules are present in two different super-repeated patterns, likely to be involved in sarcomere assembly through interactions with A-band proteins. Here, we discuss results from homology modelling the whole family of Fn3 domains in titin. Homology modelling is a powerful tool that will play an increasingly important role in the post-genomic era. It is particularly useful for extending experimental structure determinations of parts of multidomain proteins that contain multiple copies of the same motif. The 3D structures of a representative titin type I domain and of other extracellular Fn3 modules were used as a template to model the structures of the 132 copies in titin. The resulting models suggest residues that contribute to the fold stability and allow us to distinguish these from residues likely to have functional importance. In particular, analysis of the models and mapping of the consensus sequence onto the 3D structure suggest putative surfaces of interaction with other proteins. From the structures of isolated modules and the pattern of conservation in the multiple alignment of the whole titin Ig and Fn3 families, it is possible to address the question of how tandem modules are assembled. Our predictions can be validated experimentally.

Amino Acid Motifs↗

PubMed2005

Deconvolution methods for mitigation of transverse blurring in optical coherence tomography.

Imaging resolution in optical coherence tomography (OCT) is a key determinant for acquiring clinically useful optical biopsies of tissues. In contrast to light or confocal microscopy, the axial and transverse resolutions in OCT are independent and each can be analyzed individually. A method for mitigating transverse blurring and the apparent loss of transverse resolution in OCT by means of Gaussian beam deconvolution is presented. Such a method provides better representation of a specimen by using known physical parameters of a lens. To implement this method, deconvolution algorithms based on a focal-dependent kernel are investigated. First, the direct inverse problem is investigated using two types of regularization, truncated singular value decomposition, and Tikhonov. Second, an iterative expectation maximization algorithm, the Richardson-Lucy algorithm, with a beam-width-dependent iteration scheme is developed. A dynamically iterative Richardson-Lucy algorithm can reduce transverse blurring by providing an improvement in the transverse point-spread-function for sparse scattering samples in regions up to two times larger than the confocal region of the lens. These deblurring improvements inside and outside of the confocal region, which are validated experimentally, are possible without introducing new optical imaging hardware or acquiring multiple images of the same specimen. Implementation of this method in sparse scattering specimens, such as engineered tissues, has the potential to improve cellular detection and categorization.

Algorithms↗

PubMed2026

Computational prediction of a multi-epitope Human Metapneumovirus vaccine candidate through integrated reverse vaccinology and pan-genomic approaches.

Human metapneumovirus (HMPV) is a primary cause of global respiratory infections yet no approved vaccine currently exists. This study computationally predicts a multi-epitope vaccine candidate using a diverse dataset of 65 HMPV sequences spanning five continents. Following the screening of lead proteins for antigenicity and virulence, fifteen highly conserved MHC-I, MHC-II and B-cell epitopes were prioritized. These were integrated with a putative L7/L12 adjuvant using optimized AAY, GPGPG, and KK linkers to design three constructs (HMPV_V1-V3). Structural validation identified HMPV-V2 as the lead candidate that exhibits a Z-score of-5.24 and 87.7% of residues in favored Ramachandran regions indicating excellent stereochemical quality and structural stability. In silico docking indicated a strong predicted binding affinity between HMPV-V2 and the TLR4 receptor (energy: -969.2). Immune simulations predicted a robust adaptive response characterized by high IgG1 titers, memory B-cell maturation, and a Th1-dominant cytokine profile. Furthermore, molecular dynamics simulations suggested exceptional structural integrity for HMPV-V2, maintaining a low RMSD of 8.213 and RMSF of 0.737 throughout the simulation. Optimized in silico cloning into the pET28a (+) vector indicated a high potential for protein expression in E. coli systems. While these findings provide a theoretically grounded blueprint for vaccine development, this study is entirely computational and lacks experimental validation. Further in vitro and in vivo testing is required to confirm the actual safety and immunogenicity of the proposed candidate.

Metapneumovirus↗

PubMed2026

Elucidating the Mechanism of Xiaoqinglong Decoction in Chronic Urticaria Treatment: An Integrated Approach of Network Pharmacology, Bioinformatics Analysis, Molecular Docking, and Molecular Dynamics Simulations.

INTRODUCTION: Xiaoqinglong Decoction (XQLD) is a traditional Chinese medicinal formula commonly used to treat chronic urticaria (CU). However, its underlying therapeutic mechanisms remain incompletely characterized. This study employed an integrated approach combining network pharmacology, bioinformatics, molecular docking, and molecular dynamics simulations to identify the active components, potential targets, and related signaling pathways involved in XQLD's therapeutic action against CU, thereby providing a mechanistic foundation for its clinical application. METHODS: The active components of XQLD and their corresponding targets were identified using the Traditional Chinese Medicine Systems Pharmacology (TCMSP) database. CU-related targets were retrieved from the OMIM and GeneCards databases. Subsequently, core components and targets were determined via protein-protein interaction (PPI) network analysis and component-target-pathway network construction. Topological analyses were performed using Cytoscape software to prioritize core nodes within these networks. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were conducted via the DAVID database to identify enriched biological processes and signaling pathways. Molecular docking was performed to evaluate binding interactions between key components and core targets, while molecular dynamics (MD) simulations were employed to assess the stability of the component-target complexes with the lowest binding energy. Finally, CU-related targets of XQLD were validated using datasets from the Gene Expression Omnibus (GEO) database. RESULTS: A total of 135 active components and 249 potential targets of XQLD were identified, alongside 1,711 CU-related targets. Core components, such as quercetin, kaempferol, beta-sitosterol, naringenin, stigmasterol, and luteolin, exhibited high degree values in the constructed networks. The core targets identified included AKT1, TNF, IL6, TP53, PTGS2, CASP3, BCL2, ESR1, PPARG, and MAPK3. GO and KEGG pathway enrichment analyses revealed the PI3K-Akt signaling pathway as a central regulatory mechanism. Molecular docking studies demonstrated strong binding affinities between active components and core targets, with the stigmasterol-AKT1 complex exhibiting the lowest binding energy (-11.4 kcal/mol) and high stability in MD simulations. Validation using GEO datasets identified 12 core genes shared between CU-related targets and XQLD-associated targets, including PTGS2 and IL6, which were also prioritized as core targets in the network pharmacology analyses. DISCUSSION: This study comprehensively integrates multidisciplinary approaches to clarify the potential molecular mechanisms of XQLD in treating CU, highlighting its multitarget and multipathway synergistic effects. Molecular docking and dynamics simulations confirm the stable interaction between stigmasterol and the core target AKT1. Additionally, GEO dataset analysis verifies the pathogenic relevance of targets such as PTGS2 and IL6, significantly enhancing the credibility of our findings. These results provide a modern scientific basis for the traditional therapeutic effects of XQLD on CU and have important implications for developing multitarget treatments for this condition. However, this study mainly relies on database mining and computational simulations. Further in vitro and in vivo experimental validations are needed to confirm the predicted component-target-pathway interactions. CONCLUSION: This study identifies the active components, potential targets, and pathways through which XQLD exerts therapeutic effects on CU. These findings provide a theoretical foundation for further mechanistic studies and support their clinical application in the treatment of CU.

Molecular Docking Simulation↗

PubMed2005

Validation of IC-VIEW fluorescence videography in a rabbit model of mesenteric ischaemia and reperfusion.

BACKGROUND/AIMS: Mortality in mesenteric ischaemia can be reduced by an optimised extent of resection. Up to now, no technique supplementing a surgeon's experience has achieved clinical acceptance. Besides a qualitative interpretation, the new technique of computer-assisted laser-fluorescence videography affords quantification of staining intensities. The aim of this study was to investigate the scientific value of this technique in mesenteric ischaemia in a rabbit model of controlled mesenteric ischaemia and reperfusion. METHODS: We used an established rabbit model of mesenteric ischaemia (group I, n=6) and reperfusion (group II, n=6). In each animal, three loops (each of 10 cm) of the small intestine were clamped (group I, 40 min; group II, 60 and 20 min reperfusion). For further evaluation, all loops were divided into five segments of 2 x 2 cm (total number of investigated areas, n=180). Measurement of vascular patency was performed by laser-fluorescence videography (pixel intensity per second). As standard, we used radioactive microspheres (impulse per minute per gram). In addition, the extent of ischaemic tissue damage was identified by histological examination. Statistical data were analysed by using regression analysis to define the regression coefficient r. RESULTS/FINDINGS: Laser-fluorescence videography and the microsphere technique demonstrated a close and linear correlation: ischaemic segments, r=0.90+/-0.07; reperfusion segments, r=0.85+/-0.02; overall, r=0.92+/-0.07. There was no reproducible correlation to cellular damage in histology. INTERPRETATION/CONCLUSION: Computer-assisted laser-fluorescence videography is a feasible, reliable, and valid experimental method for the detection of mesenteric blood supply and intestinal microcirculation. Clinical application is conceivable in mesenteric ischaemia and infarction as well as the operative transposition of intestine. As limiting values to identify the irreversible necrosis are not yet defined, further studies have to analyse the clinical impact more precisely.

Animals↗

PubMed2003

Exact rotamer optimization for protein design.

Computational methods play a central role in the rational design of novel proteins. The present work describes a new hybrid exact rotamer optimization (HERO) method that builds on previous dead-end elimination algorithms to yield dramatic performance enhancements. Measured on experimentally validated physical models, these improvements make it possible to perform previously intractable designs of entire protein core, surface, or boundary regions. Computational demonstrations include a full core design of the variable domains of the light and heavy chains of catalytic antibody 48G7 FAB with 74 residues and 10(128) conformations, a full core/boundary design of the beta1 domain of protein G with 25 residues and 10(53) conformations, and a full surface design of the beta1 domain of protein G with 27 residues and 10(60) conformations. In addition, a full sequence design of the beta1 domain of protein G is used to demonstrate the strong dependence of algorithm performance on the exact form of the potential function and the fidelity of the rotamer library. These results emphasize that search algorithm performance for protein design can only be meaningfully evaluated on physical models that have been subjected to experimental scrutiny. The new algorithm greatly facilitates ongoing efforts to engineer increasingly complex protein features.

Algorithms↗

PubMed2025

Bioavailable testosterone reduces the risk of lung squamous cell carcinoma: a comprehensive data study.

BACKGROUND: The association between testosterone and lung cancer remains unclear. This study investigates the relationship between testosterone levels and lung cancer risk, focusing on bioavailable testosterone levels (BTLs), total testosterone levels (TTLs), and sex hormone-binding globulin (SHBG) in relation to lung cancer subtypes. METHODS: We utilized bidirectional and multivariable Mendelian randomization (MR) analyses based on genome-wide association studies (GWAS) to assess causal links. To validate the findings clinically, immunohistochemical (IHC) staining for androgen receptor (AR) expression and survival analyses were conducted on a cohort of 90 patients with lung squamous cell carcinoma (LUSC). RESULTS: MR analysis demonstrated that higher BTLs were significantly associated with a reduced risk of LUSC (OR = 0.365, P = 0.001), while no significant associations were observed for TTLs or SHBG. Reverse MR analysis found no causal effect of lung cancer on testosterone levels. Multivariable MR confirmed BTLs as an independent protective factor. In the clinical cohort, AR expression was significantly associated with better prognosis, showing improved median progression-free survival (12.3 vs. 9.0 months, P = 0.01) and median overall survival (35.3 vs. 29.4 months, P < 0.01). Cox regression identified AR expression as an independent protective factor for patient outcomes. However, study limitations include potential residual confounding, ethnic heterogeneity between European GWAS data and Asian clinical cohorts, and the lack of direct experimental validation. CONCLUSIONS: Our findings suggest that higher BTLs may play a protective role against LUSC. BTLs and AR expression show potential as valuable biomarkers for the diagnosis and prognostic assessment of LUSC.

Humans↗

PubMed1996

Lethal experimental infection of rhesus monkeys with Ebola-Zaire (Mayinga) virus by the oral and conjunctival route of exposure.

OBJECTIVE: The source of infection or mode of transmission of Ebola virus to human index cases of Ebola fever has not been established. Field observations in outbreaks of Ebola fever indicate that secondary transmission of Ebola virus is linked to improper needle hygiene, direct contact with infected tissue or fluid samples, and close contact with infected patients. While it is presumed that the virus infects through either breaks in the skin or contact with mucous membranes, the only two routes of exposure that have been experimentally validated are parenteral inoculation and aerosol inhalation. Epidemiologic evidence suggests that aerosol exposure is not an important means of virus transmission in natural outbreaks of human Ebola fever; this study was designed to verify that Ebola virus could be effectively transmitted by oral or conjunctival exposure in nonhuman primates. MATERIALS AND METHODS: Adult rhesus monkeys (Macaca mulatta) were exposed to Ebola-Zaire (Mayinga) virus orally (N=4), conjunctivally (N=4), or by intramuscular inoculation (N=1, virus-positive control). RESULTS: Four of four monkeys exposed by the conjunctival route, three of four monkeys exposed by the oral route, and the intramuscularly inoculated positive control monkey (one of one) were successfully infected with Ebola-Zaire (Mayinga). Seven monkeys died of Ebola fever between days 7 and 8 postexposure. One monkey was given aggressive supportive therapy and a platelet transfusion; it lived until day 12 postexposure. CONCLUSIONS: Findings in this study experimentally confirm that Ebola virus can be effectively transmitted via the oral or conjunctival route of exposure in nonhuman primates.

Animals↗

PubMed2026

Comparative characterization of six teleost piscidins reveals distinct antimicrobial, antibiofilm and stability profiles.

Piscidins are cationic α-helical antimicrobial peptides (AMPs) that constitute a key component of the innate immune defense of teleost fish, yet the relationship between their genomic organization, structural properties, and functional specialization remains incompletely understood. In this study, six piscidin peptides from Epinephelus akaara, Seriola dumerili, Thunnus maccoyii, Argyrosomus regius, Dicentrarchus labrax, and Epinephelus coioides were characterized through an integrated sequence-to-function approach combining comparative genomics, structural modeling, physicochemical analysis, and in vitro validation, with the aim of identifying candidates with potential for biomedical and biotechnological applications. All genes studied exhibited the conserved four-exon, three-intron architecture characteristic of teleost piscidins. Structural modeling and circular dichroism confirmed α-helical conformations under membrane-mimetic conditions, despite measurable differences in hydrophobicity, charge distribution, and predicted membrane insertion parameters. Antimicrobial assays revealed distinct functional profiles: Sd_FI25 and Epinecidin_1 displayed broad antibacterial activity against Gram-positive and Gram-negative pathogens, whereas Dl_FI22 showed selective activity with reduced temporal persistence associated with lower peptide stability. Ea_FF25 exhibited comparatively weak antibacterial potency. Antibiofilm activity varied among peptides and did not uniformly parallel planktonic MIC values. Computational predictions further suggested antiviral and antitumoral potential for several sequences, extending their prospective relevance beyond classical antibacterial roles. Conserved genomic architecture and α-helical structure coexist with pronounced functional diversification among teleost piscidins. These findings demonstrate that integrating structural prediction with experimental validation is an effective strategy for identifying fish-derived innate immune peptides as candidates for biomedical applications.

Antimicrobial activity↗

PubMed2002

A novel quantitative dual-isotope method for simultaneous ventilation and perfusion lung SPET.

A quantitative dual-isotope single-photon emission tomography (SPET) technique for the assessment of lung ventilation (V) and perfusion (Q) using, respectively, technetium-99m labelled Technegas (140 keV) and indium-113m labelled macro-aggregated albumin (392 keV), is presented, validated and clinically tested in a healthy volunteer. In order to assess V, Q and V/Q distributions in quantitative terms, algorithms which correct for down scattering, photon scattering and attenuation, as well as an organ outline algorithm, were implemented. Scatter and down-scatter correction were made in the spatial domain by pixel-wise image subtraction of projection-dependent global scattering factors obtained from the energy domain. The attenuation correction was based on an iterative projection/back-projection method. All studies were made on a three-headed SPET system (Trionix) with medium-energy parallel-hole collimators. The set of input data for quantification was based on SPET acquisition of emission data in four separate energy windows, the associated cumulative energy spectra and transmission data. The attenuation correction routine as well as the edge detection algorithm utilized data from (99m)Tc transmission tomography. Attenuation data for (113m)In were obtained by linear scaling of the (99m)Tc attenuation maps. The correction algorithms were experimentally validated with a stack phantom system and applied on a healthy volunteer. The mean difference between the corrected SPET data of the dense stack lung phantom and those obtained from the corresponding scatter- and attenuation-"free" version was only 1.9% for (99m)Tc and 0.9% for (113m)In. The estimated fractional V/Q distribution in the 3-D lung phantom volume had its peak at V/Q=1, with a width (FWHM) of 0.31 due to noise, particularly in the (113m)In images, and to partial volume effects. For a healthy volunteer, the corresponding values were 0.9 and 0.35, respectively. This method allows accurate assessment of radionuclide distribution on a regional basis. For basic lung physiology and clinical practice, the method allows assessment of the global frequency functions of the V, Q and V/Q distributions.

Algorithms↗

PubMed2026

Genome-Wide Analysis of the PYL Gene Family and Its Expression Dynamics in Response to Abscisic Acid in Tomato.

The plant hormone abscisic acid (ABA) plays a crucial role throughout the plant life cycle and in adaptive responses to environmental stresses. The pyrabactin resistance 1-like (PYR/PYL/RCAR) proteins act as key regulators in the ABA signal transduction pathway by functioning as direct receptors for ABA. Although PYL genes have been identified in a variety of plant species, their evolutionary and structural characteristics in tomatoes (Solanum lycopersicum) remain elusive. To address this gap, we identified nine SlPYL genes, which were classified into three subfamilies: I (two genes), II (three genes), and III (four genes), and their encoded proteins were predicted to be primarily localized in the cytosol and chloroplast. Structural analysis revealed diverse exon-intron organizations along with five conserved motifs. All identified SlPYLs contained the START domain (PF10604), validating their identity as actual PYL proteins. Prediction of cis-acting regulatory elements in SlPYL's promoter regions was found to be associated with light responsiveness, hormone signaling, stress responses, and plant growth and development. Prediction of post-translational modification sites indicated that SlPYLs are predominantly phosphorylated and acetylated at serine and lysine residues, respectively. Tertiary structure modeling demonstrated conserved three-dimensional architectures among SlPYL proteins, supporting their functional conservation. Expression profiling revealed that specific SlPYL genes exhibit distinct expression patterns across different tissues (root, leaf, and bud) following ABA treatment, indicating functional diversification. Considering the well-established negative correlation between ABA accumulation and bud outgrowth, the ABA-induced differential expression (3~5-fold) of some SlPYL genes (SlPYL3, SlPYL4, SlPYL7, and SlPYL8), particularly in bud tissues after 24 hpt, suggests a potential role in ABA-mediated suppression of bud outgrowth. However, these functional inferences are primarily based on genome-wide computational analyses and expression profiling and therefore require further experimental validation.

Solanum lycopersicum↗