Search Results (48,413)

Codon optimization is widely used to improve heterologous gene expression in Escherichia coli. However, many existing methods focus primarily on maximizing the codon adaptation index (CAI) and neglect broader aspects of biological context. In this study, we present ColiFormer, a transformer-based codon optimization framework fine-tuned on 3676 high-expression E. coli genes curated from the NCBI database. Built on the CodonTransformer BigBird architecture, ColiFormer employs self-attention mechanisms and a mathematical optimization method (the augmented Lagrangian approach) to balance multiple biological objectives simultaneously, including CAI, GC content, tRNA adaptation index (tAI), RNA stability, and minimization of negative cis-regulatory elements. Based on in silico evaluations on 37,053 native E. coli genes and 80 recombinant protein targets commonly used in industrial studies, ColiFormer demonstrated significant improvements in CAI and tAI values, maintained GC content within biologically optimal ranges, and reduced inhibitory cis-regulatory motifs compared with established codon optimization approaches, while maintaining competitive runtime performance. These results represent computational predictions derived from standard in silico metrics; future experimental work is anticipated to validate these computational predictions in vivo. ColiFormer has been released as an open-source tool alongside the benchmark datasets used in this study. Full article

Microbial biological control agents are a sustainable alternative to synthetic pesticides, yet their widespread application is limited by a lack of environmental resilience of commercial products. To address this, we exploited honey—a stringent ecological niche—as a reservoir for stress-tolerant bacteria. In this study, the bioprospection utilizing five types of commercially available honeys yielded a collection of 53 bacteria and 10 fungi. All bacterial isolates were evaluated for antimicrobial activity against a laboratory-standard bacterium and yeast, and six economically relevant phytopathogenic microorganisms. Initial screening with standard laboratory organisms proved to be an efficient method to detect strains with antimicrobial potential, correlating significantly with further phytopathogen inhibition (Spearman’s r = 0.4512, p = 0.0005). Two promising strains, M2.7 and M3.18, were selected for quantitative dual-culture assays along with molecular identification using 16S rDNA and gyrA gene sequencing, classifying them as Bacillus velezensis. These strains exhibited high inhibitory effects against the pathogens (p > 0.001), often with equivalent efficacy to the commercial biocontrol strain, and also induced significant phytopathogen hyphal deformities, such as increased septation and swelling. These findings support honey as a viable source of robust biocontrol agents, offering a sustainable strategy to substitute or complement current agrochemicals. Full article

Robot-assisted radical prostatectomy (RARP) is the definitive surgical treatment for localized prostate cancer (PCa). Some patients with post-RARP biological recurrence (BCR) eventually develop distant metastases and subsequent PCa-related mortality. The objective of this study was to clarify the predictive factors for the risk of metastatic disease after BCR in patients with PCa who underwent RARP. This multicenter retrospective cohort study was conducted in nine Japanese institutions and enrolled 491 men with BCR, detected between 2011 and 2024. During the median 59-month follow-up period, 44 patients (9.0%) had radiological confirmation of distant metastasis. Patients with developed metastases after BCR exhibited higher biopsy Gleason grade and pathological T stage, increased lymphovascular invasion (LVI) in the surgical specimen, and a shorter interval from RARP to BCR. In univariate analysis, LVI and a time to BCR after RARP of ≤14.9 months were significant predictors of distant metastasis. In the multivariate analysis, LVI constituted a significant independent predictor of distant metastasis (p = 0.011). The 3-year metastasis-free survival (MFS) rates were 85.5% and 94.1% in patients with and without LVI, respectively. The MFS was significantly prolonged in patients with negative LVI compared to those with positive LVI (p = 0.007). In Japanese males with BCR after RARP, LVI was identified as an independent predictor of metastatic progression. Full article

Although neurological disease is common in people with human immunodeficiency virus (HIV) (PWH), the contributing factors and underlying inflammatory mechanisms remain challenging to identify. Extracellular vesicles (EVs) constitute a relatively uncharacterized modality of intercellular communication and bioactive cargo transport in the setting of viral infection and pathogenesis. EVs carry inflammatory mediators to areas of the periphery during antiretroviral therapy (ART) suppression but are understudied in the brain. Using a biologically relevant simian–human immunodeficiency chimeric virus with a clade D HIV envelope (SHIV.D)-infected rhesus macaque (RM) model of HIV persistence in the central nervous system (CNS), we investigate circulating EV populations and the protein cargo of myeloid-derived EVs during SHIV infection. Using EV flow cytometry to quantify specific EV subpopulations, we found a significant increase in TMEM119+ microglial EVs and CD171+ neuronal EVs in RM plasma during viremia and ART suppression. Using primary RM monocyte-derived macrophages (MDMs), we determined that MDMs increased EV production after SHIV infection. Whole proteomic analysis of these EVs demonstrated that myeloid EVs isolated from SHIV.D-infected MDMs carried significantly increased levels of neuropathogenic and inflammatory proteins. Altogether, these studies improve our understanding of the contribution of myeloid EVs to neurological disease during SHIV/HIV infection. Full article

Background and Objectives: Overweight and obesity is defined as a Body Mass Index (BMI) of 25.0–29.9 kg/m² and ≥30.0 kg/m². The prognostic significance of obesity in metastatic prostate cancer is still unclear, especially between the castration-sensitive (CSPC) and castration-resistant (CRPC) disease states. New evidence suggests that obese patients who get androgen receptor–targeted therapies may have an unexpected survival advantage. This study examined the correlation between body mass index (BMI) and survival outcomes in patients administered androgen receptor pathway inhibitors. Materials and Methods: A retrospective analysis was conducted on a cohort of 167 patients with metastatic prostate cancer treated between 2015 and 2024. BMI was analyzed as both a continuous variable and a categorical variable, which was classified as normal weight, overweight or obese. The primary goal of this study is to compare PFS and OS among BMI groups. We employed Kaplan–Meier survival analysis and Cox regression modeling to evaluate prognostic indicators. The CSPC and CRPC groups were evaluated separately. Results: PFSs for normal, overweight and obese CSPC patients were 11.3, 15.1, 19.5 months, respectively; p = 0.03 but the OS did not differ significantly between BMI groups. OS for normal, overweight and obese CRPC patients were 32.8, 47.6 and 43.4 months, respectively; p = 0.01. There was also a trend toward better PFS, but it was not statistically significant. Multivariate analysis found that obesity (BMI ≥ 30) was a separate protective factor for PFS in CSPC, while high-volume disease was a bad prognostic factor for OS in CRPC. A high Gleason score and ECOG-PS 2 were consistently associated with poor outcomes. Conclusions: Obesity has a phase-dependent prognostic influence in metastatic prostate cancer, providing a PFS advantage in CSPC and an OS benefit in CRPC. These results suggest that there may be an obesity paradox in people who are getting androgen receptor–targeted therapy. Further prospective studies are required to gain a better understanding of the biological reasons for this association. Full article

Agrobacterium tumefaciens, a destructive pathogen causing crown gall disease, results in substantial agricultural losses. Traditional chemical and existing biocontrol methods are limited by environmental pollution, pesticide resistance, and low efficacy, while bacteriophages emerge as a promising alternative due to their high host specificity, environmental compatibility, and low resistance risk. In this study, we isolated and characterized a lytic phage (PAT-A) targeting A. tumefaciens, evaluating its biological traits, genomic features, and biocontrol potential. The host strain A. tumefaciens CL-1 was isolated from cherry crown gall tissue and identified by 16S rDNA sequencing. Phage PAT-A was recovered from orchard soil via the double-layer agar method, showing a tadpole-shaped morphology (60 nm head diameter, 30 nm tail length) under transmission electron microscopy (TEM). Nucleic acid analysis confirmed a double-stranded DNA genome, susceptible to DNase I but resistant to RNase A and Mung Bean Nuclease. PAT-A exhibited an optimal MOI of 0.01, tolerated wide pH and temperature ranges, but was sensitive to UV (titer declined after 15 min of irradiation) and chloroform (8% survival at a 5% concentration). Whole-genome sequencing revealed a 44,828 bp genome with a compact structure, and phylogenetic/collinearity analyses placed it in the Atuphduvirus genus (Autographiviridae). Biocontrol experiments on tobacco plants demonstrated that PAT-A significantly reduced crown gall incidence. Specifically, simultaneous inoculation of PAT-A and A. tumefaciens CL-1 resulted in the lowest tumor incidence (12.0%), while pre-inoculation of PAT-A 2 days before pathogen exposure achieved an incidence rate of 33.3%. In conclusion, PAT-A is a novel strictly lytic phage with favorable biological properties and potent biocontrol efficacy against A. tumefaciens, enriching phage resources for crown gall management and supporting phage-based agricultural biocontrol strategies. Full article

Isothiocyanates (ITCs) are well-known electrophilic agents with antioxidant and anticancer properties, largely attributed to their ability to activate the Nrf2/ARE pathway. Building on previous work with C1-ITC glycosyl derivatives, we designed and synthesized a new series of S-glycosyl isothiocyanates in which the ITC group was repositioned to the C6 carbon of the glucose scaffold. This structural rearrangement yielded stable and synthetically accessible derivatives with markedly enhanced biological profiles. Several compounds showed potent Nrf2 activation at non-cytotoxic concentrations, with CD values comparable to or exceeding those of natural ITCs. In parallel, the new C6-ITC derivatives displayed significant antiproliferative activity against leukemia and solid tumor cell lines. Among them, the phenylsulfone derivative 13 emerged as a particularly promising dual-action molecule, combining strong Nrf2 induction with low-micromolar cytotoxicity. Molecular docking was used as a hypothesis-generating approach and suggested a possible interaction with the STAT3 SH2 domain, although further studies are needed to validate this target. Overall, these results support glucose-based ITCs as a versatile platform for the development of multifunctional antioxidants with complementary anticancer properties. Full article

Background: Self-amplifying mRNA (sa-mRNA) represents a promising platform for vaccines and gene therapies, offering sustained protein expression at low doses through self-replication. For vaccines targeting respiratory pathogens, pulmonary delivery of sa-mRNA lipid nanoparticles (LNPs) is particularly advantageous, enabling direct delivery to the infection site and induction of mucosal immunity. Objective: In this study, we evaluated the stability of sa-mRNA–LNPs under refrigerated and frozen conditions and developed a dry powder formulation suitable for inhalation, produced by freeze-drying followed by cryomilling with leucine. Methods: sa-mRNA–LNPs formulated in HEPES buffer with 20% (w/v) sucrose were stored for up to 8 weeks as liquid or freeze-dried samples at various temperatures (−80 °C, −20 °C, 4 °C, and 20 °C). Biological stability was assessed by transfection efficiency in HeLa cells, while physical stability was characterized by encapsulation efficiency, zeta potential, particle size, and polydispersity index. Results: Liquid formulations remained stable for at least 8 weeks at −80 °C and −20 °C but rapidly lost stability at 4 °C and 20 °C. Freeze-drying effectively preserved sa-mRNA–LNP functionality and structural integrity for up to 8 weeks at 4 °C, with only minor structural changes. Subsequent cryomilling in the presence of 4 wt-% leucine produced a respirable dry powder while retaining approximately 60% of the original sa-mRNA–LNP functionality. Although cryomilling induced some structural alterations, the remaining functional fraction remained stable during storage. The resulting powders displayed favorable aerosol performance for deep lung delivery, as demonstrated by cascade impaction (MMAD = 4.13 ± 0.26 µm). Conclusions: In conclusion, freeze-drying effectively preserved sa-mRNA–LNP integrity at 4 °C, whereas cryomilling with leucine produced a respirable dry powder suitable for pulmonary delivery, providing a foundation for globally accessible, needle-free sa-mRNA vaccines against respiratory diseases. Full article

Taganrog Bay is part of the Azov Sea, which has significant environmental value. However, in recent years, anthropogenic activity and climate change have increasingly impacted this coastal system. These factors have led to increased sea salinity. These factors also contribute to abundant blooms of potentially toxic cyanobacteria. One additional method for preventing the abundant growth of cyanobacteria may be the introduction of green algae into the bay. The aim of this study was to conduct a computational experiment on the biological rehabilitation of Taganrog Bay using mathematical modeling methods. For this purpose, the authors developed and analyzed a mathematical model of phytoplankton populations. A software model was developed based on modern mathematical modeling methods. The input data for the software module included grid points for advective transport velocities, salinity, and temperature, as well as phytoplankton population and nutrient concentrations. The software module outputs three-dimensional distributions of green algae and cyanobacteria concentrations. A computational experiment on biological rehabilitation of the Taganrog Bay by introducing a suspension of green algae was conducted. Green algae and cyanobacteria concentrations were obtained over 15 and 30-day time intervals. The concentration and volume of introduced suspension were empirically determined to prevent harmful cyanobacteria growth without leading to eutrophication of the bay by green algae. Full article

Aphis gossypii (Glover) (Hemiptera: Aphididae) is a significant pest in cotton fields, and the use of both chemical insecticides and natural enemies is a crucial strategy for its management. Hippodamia variegata (Goeze) (Coleoptera: Coccinellidae), a predominant predatory natural enemy in cotton fields, plays a vital role in controlling A. gossypii populations. In this study, we investigated the toxicity of four insecticides to both A. gossypii and H. variegata larvae, assessed their field efficacy against A. gossypii, and evaluated their effects on the predatory function of H. variegata larvae. The results revealed that afidopyropen and spirotetramat exhibited relatively high toxicity against A. gossypii, with LC₅₀ values of 13.18 mg/L and 22.17 mg/L, respectively. Flonicamid demonstrated the least toxicity to H. variegata larvae, with an LC₅₀ of 512.66 mg/L. The selectivity toxicity ratios for afidopyropen and flonicamid were 5.05 and 4.73, respectively, indicating strong, favourable selectivity towards H. variegata. The maximum field control efficacy against A. gossypii was 96.76% for afidopyropen and 96.92% for flonicamid. The reduction rates of H. variegata larvae in the afidopyropen treatment plots were relatively low. Among the four treatments, the theoretical predation of third-instar H. variegata larvae against A. gossypii was highest with flonicamid, reaching 215.67. Overall, the four insecticides differed substantially in their combined effects on aphid suppression and predator performance. In particular, afidopyropen and flonicamid provided excellent control of A. gossypii while showing comparatively lower toxicity to H. variegata and causing less impairment of its predatory capacity, indicating a more favourable biological trade-off between pest control and natural enemy conservation. However, laboratory toxicity and functional response assays may not fully capture predator–prey dynamics under complex field conditions; therefore, afidopyropen and flonicamid may be considered suitable candidate insecticides for inclusion in integrated pest management (IPM) programs in cotton systems. Full article

Plant organic cation transporters (OCTs) are involved in a variety of beneficial biological processes, such as cadaverine transfer in plants and soil, and play an active role in the formation of plant stress resistance. In this study, 52 OCT family genes were identified in tomato, and comprehensive bioinformatics analyses of these numbers, such as promoter cis-acting elements, gene mapping and collinearity, protein characterization and phylogenetic analysis. By analyzing the expression of tomato OCT family genes under cold and salt stresses using transcriptome data and qRT-PCR experiments, a key gene regulating cold stress tolerance, SlOCT20, was identified. Subcellular localization experiments indicated that SlOCT20 was mainly localized in the cell membrane. When the SlOCT20 gene was silenced in tomato, the tolerance to cold stress was significantly reduced and oxidative stress was aggravated, indicating that this gene positively regulates the tolerance to cold stress in tomato. Full article

Pancreatic ductal adenocarcinoma (PDAC) is highly lethal, and many patients cannot undergo curative surgery due to frailty. Multimodal prehabilitation: combining exercise, nutrition, and psychological support improves functional readiness, but its biological impact on the PDAC tumor microenvironment (TME) is unclear. In this exploratory pilot study, we profiled resected PDAC tissues from prehabilitation-treated patients and matched controls using NanoString GeoMx Digital Spatial Profiling across immune, tumor, and stromal compartments (n = 4). Transcriptomic signatures were analyzed via differential expression, pathway enrichment, and MCP-counter deconvolution; protein-level validation used multiplex immunofluorescence (n = 8). Ligand–receptor modeling assessed cell–cell communication, and prognostic relevance was evaluated in TCGA-PDAC (n = 178). Prehabilitation was associated with increased NK-cell cytotoxicity, interferon response, and chemokine recruitment, as well as higher neutrophil signatures (p < 0.01) and reduced fibroblast signatures (p < 0.05). Tumor regions showed lower MAPK and PI3K/AKT activity, while stroma exhibited decreased TGF-β and Wnt signaling. Immunofluorescence confirmed neutrophil infiltration and reduced fibroblast density. TCGA analysis linked neutrophil-high/fibroblast-low profiles to longer survival (1044.6 vs. 458.7 days, p = 0.0052). These findings suggest prehabilitation may promote a more immune-active, less fibrotic TME in PDAC, resembling transcriptional states associated with improved survival. Prospective studies integrating biological and clinical endpoints are warranted. Full article

Background/Objectives: Patients with eosinophilic chronic obstructive pulmonary disease (COPD) often remain symptomatic despite optimized triple inhaled therapy. Dupilumab is a fully human monoclonal antibody that blocks the IL-4 receptor alpha subunit, thereby inhibiting IL-4 and IL-13 signaling. Evidence from randomized trials supports dupilumab for add-on treatment of type 2-high COPD, but data referring to short-term effectiveness in clinical practice are quite limited. Methods: We conducted an observational, compassionate-use study enrolling 13 consecutive outpatients with eosinophilic COPD (blood eosinophils ≥ 300 cells/µL) receiving add-on biologic therapy with dupilumab 300 mg every two weeks. Clinical (CAT, mMRC), functional (spirometry and body plethysmography), and inflammatory parameters (blood eosinophils/basophils, fibrinogen, FeNO) were evaluated at baseline and after four weeks of treatment. Safety was monitored after injection in a clinical setting, as well as via weekly phone follow-up. Results: Participants (84.6% male; mean age 67.08 ± 11.42 years) experienced rapid and clinically meaningful improvements at four weeks. CAT score decreased from baseline 21.40 ± 6.22 to 14.00 ± 5.58 (p < 0.001) and mMRC scale from 2.90 ± 0.73 to 1.80 ± 0.63 (p < 0.0001), respectively. Pre-bronchodilator FEV₁ increased from baseline 1.35 ± 0.65 L to 1.59 ± 0.84 L (p < 0.05), and FVC from 2.36 ± 0.92 L to 2.83 ± 1.11 L (p < 0.01). A marked lung deflation was observed: indeed, residual volume declined from baseline 4.17 ± 1.98 L to 3.47 ± 2.07 L (p < 0.05), with a concomitant reduction in specific effective airway resistance (from baseline 3.15 ± 1.77 to 2.43 ± 1.44 kPa·s; p < 0.05) associated with significant increases in mid-expiratory flow (FEF₂₅₋₇₅: from baseline 0.62 ± 0.38 to 0.86 ± 0.71 L/s; p < 0.05) and peak expiratory flow (3.80 ± 1.40 to 4.48 ± 1.79 L/s; p < 0.01). Type 2 inflammatory biomarkers changed as follows: blood eosinophil count fell from baseline 390.0 ± 43.75 to 190.0 ± 65.47 cells/µL (p < 0.001); blood basophil number decreased from baseline 37.50 ± 13.89 to 26.25 ± 13.02 cells/µL (p < 0.001); plasma fibrinogen lowered from baseline 388.4 ± 54.81 to 334.9 ± 72.36 mg/dL (p < 0.01); FeNO levels dropped from baseline 23.95 ± 18.10 to 14.00 ± 2.04 ppb (p < 0.0001). Dupilumab was well tolerated, and no treatment-related serious adverse events or discontinuations were detected. Conclusions: Within an exploratory context of daily medical activity referring to eosinophilic COPD already treated with maximal inhaled therapy, we found relevant therapeutic effects of a four-week add-on treatment with dupilumab. In particular, our patients manifested rapid improvements in symptoms, airflow limitation, and lung hyperinflation, paralleled by significant decrements of type 2 inflammatory signatures. Such encouraging results were associated with a favorable short-term safety profile. However, larger and longer studies are necessary to corroborate these preliminary findings. Full article

The essential oils obtained by steam distillation of leaves of Piper species have found several applications in bioeconomy due to their various biological properties. Nevertheless, the analysis of essential oils does not provide information regarding the ecologically relevant volatile organic compounds (VOCs) emitted by metabolically active leaves under real-world conditions, challenged or not by herbivore damage. In this study, P. arboreum growing in a highly diverse area was observed as the host of two generalist caterpillars—Gonodonta maria (Erebidae) and Dysodia spissicornis (Thyrididae)—and one Piper-specialist from the genus Eois (Geometridae). The effect of the leaf attack caused by the three different caterpillars on VOCs emission indicated significant and herbivore-specific changes in leaf-induced responses. The profiles of undamaged leaves showed that the two generalist herbivores induced a higher number of single VOCs and of total VOCs emissions by P. arboreum when compared to the herbivory of the specialist caterpillar. Many of the VOCs emitted by herbivore-damaged leaves contained terpenoids that have been previously shown to attract parasitoids, such as (E)-β-ocimene, linalool, DMNT and (E)-β-caryophyllene. All three herbivores significantly altered the VOC profile of P. arboreum leaves compared to undamaged controls, but specific composition signatures were observed, highlighting the complexity of chemical communication at multitrophic levels. Full article

Objectives: The study examined tear and serum alterations using the ferning test and quantified the number of branches formed during the controlled drying of these biological fluids (tears and serum), in order to identify a potential diagnostic patterning test in individuals with obesity. Methods: A total of 61 patients aged between 25 and 72 years were enrolled (median age [interquartile range] = 39.0 [26] years). BMI values ranged from 19.1 to 47.5 kg/m², with a median BMI (interquartile range) of 29.3 (12.1) kg/m². Results: The Kruskal–Wallis test showed statistically significant differences among at least two Schirmer classes with respect to the number of branches observed in dried tears at a brightness threshold of 220 (H(2) = 8.485, p = 0.014). According to the Dunn post hoc test, Schirmer Class 1 showed a markedly lower number of branches compared with Classes 2 and 3 (p < 0.031 and p < 0.021), whereas no significant difference was found between Classes 2 and 3. The Kruskal–Wallis test further suggested the presence of statistically significant differences in the number of branches in dried serum, quantified using ImageJ2 at a brightness threshold of 190, across visceral fat classes (H(2) = 9.583, p = 0.008). Dunn’s post hoc tests revealed that the number of branches in serum analyzed at a brightness threshold of 190 was significantly higher in visceral fat class 3 compared to class 1 (p_holm = 0.006), while no statistically significant differences were observed between classes 1 and 2 or between classes 2 and 3 (p_holm > 0.05). Conclusions: In addition to other obesity-specific complications patients with obesity exhibit an increased risk of developing dry eye syndrome. The combined assessment of DPT in both the tear film and serum may represent a new method for analyzing obesity-associated biomarkers. Further studies are required to determine the sensitivity and specificity of these approaches in diagnosing systemic alterations induced by excess adipose tissue. Full article