Search Results (171)

Pseudomonas fluorescens is the main spoilage bacterium in milk, and its proliferation is one of the factors leading to the deterioration of the quality of raw milk. In this study, a rapid detection system for P. fluorescens was developed based on recombinase-aided amplification combined with a test strip (RAA-TS), which contained a double test line (DTL) targeting the virulence gene aprX of P. fluorescens and the housekeeping gene gyrB of Pseudomonas. Visual observation could detect gyrB (50 CFU/mL) and aprX (250 CFU/mL) within 90 min, including sample pretreatment and RAA reaction and detection steps. No cross-reactions were observed with Pseudomonas or other bacteria (n = 19). The quantitative detection limits (LOD) of gyrB and aprX for P. fluorescens in milk were 37 CFU/mL and 233 CFU/mL, respectively. Compared with polymerase chain reaction-agarose gel electrophoresis (PCR-AGE), the sensitivity of the developed RAA-TS-DTL system was increased by approximately four times. Furthermore, it could detect live P. fluorescens in milk when combined with optimized sample pretreatment by propidium monoazide (PMAxx). Its consistency with the traditional culture method in the detection of P. fluorescens spiked in milk samples (n = 25) was 100%. The developed RAA-TS-DTL had the advantages of high accuracy and short time consumption. Thus, it provides a new way or tool for the rapid screening or detection of P. fluorescens in milk. Full article

Background/Objectives: To design the pDNA delivery carrier for delivery into skeletal muscle, a total of twelve terminal-alkylated PEGs (Cx-I-PEGy) with four alkyl groups of different carbon numbers (Cx: x = 4, 8, 12, 16) modified via an imine spacer at the ends of three methoxy PEGs of different molecular weights (PEGy: y = 500, 2k, 5k) have been synthesized. Methods: Among them, four Cx-I-PEG5k formed an imine-mediated complex formation with pDNA, as assessed by agarose gel electrophoresis, defined as an iminium mono-ion complex (I-MIC) without multivalent electrostatic interaction by minimizing potential toxic cations. Results: Most resulting I-MICs maintained the flexible structure of pDNA and promoted the binding to pDNA. The expression of pDNA by intramuscular injection with the resulting I-MICs was the highest by using I-MICs with C4-I-PEG5k and was observed extensively by the in vivo imaging system (IVIS). Conclusions: These results suggest that the I-MICs with C4-I-PEG5k are promising for pDNA transfection into skeletal muscle, offering the alkyl iminium for the pDNA binding group to demonstrate the factor of pDNA’s flexible structure as one of the key parameters for in vivo local pDNA transfection. Full article

Background: This study is the first to investigate the association between colorectal cancer (CRC) risk and the hMLH1 −93G>A and hMSH2 1032G>A polymorphisms of mismatch repair (MMR) genes in the Azerbaijani population. Methods: Peripheral blood samples containing EDTA were collected from the study subjects (134 patients and 137 controls), and genomic DNA was extracted using the non-enzymatic salting-out method. Genotypes were determined by polymerase chain reaction–restriction fragment length polymorphism (PCR-RFLP), and the results were visualized through agarose gel electrophoresis. Results: Overall, no statistically significant correlation was observed between CRC risk and the hMLH1 −93G>A polymorphism in the heterozygous GA (OR = 0.760; 95% CI = 0.374–1.542; p = 0.446), the mutant AA (OR = 1.474; 95% CI = 0.738–2.945; p = 0.270), or the A allele (OR = 1.400; 95% CI = 0.984–1.995; p = 0.062). However, in contrast to the dominant model, a statistically significant association was found between the recessive model and an increased CRC risk, with an odds ratio of 1.788 (95% CI = 1.102–2.900; p = 0.018). The hMLH1 −93G>A polymorphism was identified at a significantly higher frequency across the TNM stages, with the distribution showing statistical significance (p < 0.05). Additionally, no statistically significant association was observed between the hMSH2 1032G>A polymorphism and CRC risk. Conclusions: Although no overall association was observed for hMLH1 −93G>A, our findings suggest a potential link with increased colorectal cancer risk under the recessive model in the Azerbaijani population. Further studies are warranted to confirm this model-specific association and investigate the underlying biological mechanisms. Full article

The synthesis of novel biodegradable polymers as non-viral vectors remains one of the challenging tasks in the field of gene delivery. In this study, the synthesis of the polysaccharide-g-polypeptide copolymers, namely, hyaluronic acid-g-polylysine (HA-g-PLys), using a copper-free strain-promoted azide-alkyne cycloaddition reaction was proposed. For this purpose, hyaluronic acid was modified with dibenzocyclooctyne moieties, and poly-L-lysine with a terminal azido group was obtained using ring-opening polymerization of N-carboxyanhydride of the corresponding protected amino acid, initiated with the amino group azido-PEG₃-amine. Two HA-g-PLys samples with different degrees of grafting were synthesized, and the structures of all modified and synthesized polymers were confirmed using ¹H NMR and FTIR spectroscopy. The HA-g-PLys samples obtained were able to form nanoparticles in aqueous media due to self-assembly driven by electrostatic interactions. The binding of DNA and model siRNA by copolymers to form polyplexes was analyzed using ethidium bromide, agarose gel electrophoresis, and SybrGreen I assays. The hydrodynamic diameter of polyplexes was ˂300 nm (polydispersity index, PDI ˂ 0.3). The release of a model fluorescently-labeled oligonucleotide in the complex biological medium was significantly higher in the case of HA-g-PLys as compared to that in the case of PLys-based polyplexes. In addition, the cytotoxicity in normal and cancer cells, as well as the ability of HA-g-PLys to facilitate intracellular delivery of anti-GFP siRNA to NIH-3T3/GFP+ cells, were evaluated. Full article

Thyroid eye disease (TED) is characterized by autoimmune inflammation and structural remodelling of orbital tissues, which is a consequence of the activation of orbital fibroblasts (OFs). As a result of this activation, the production of hyaluronan (HA) and the proliferation and adipocyte differentiation of OFs are enhanced. Adipogenesis leads to additional accumulation of HA. The aim of this study was to elucidate the molecular weight distribution of HA produced by OFs under basic conditions and after adipogenic stimuli. The concentration and the molecular weight distribution of HA were examined using ELISA and agarose gel electrophoresis, respectively, in TED (n = 3) and non-TED (n = 3) OF cultures. Under adipogenic stimuli, HA production is increased in OFs. In TED OF cultures, which, unlike non-TED OFs, can differentiate into adipocytes, the enhanced proportion of high-molecular-weight (HMW) HA of more than 2000 kDa is responsible for the increased HA concentration in the culture media. In non-TED OF cultures, which contain a negligible number of differentiating cells after adipogenic stimulation, the medium-molecular-weight (MMW) HA fragments from 50 to 1000 kDa also contribute to the enhanced HA content. Increased production of HMW-HA during adipocyte differentiation of TED OFs is responsible for the elevated HA content in the culture media, which may be an important contributor to both connective tissue matrix expansion and edema in the pathogenesis of TED. Full article

Bovine anaplasmosis, caused by Anaplasma marginale, is a major tick-borne disease in tropical and subtropical regions of the world, leading to significant production losses. Prolonged convalescence periods are common and surviving animals often become subclinical carriers. This study aimed to detect and characterise A. marginale in bovines in smallholder dairy farms across diverse climatic zones of Pakistan using molecular methods. In total, 321 blood DNA samples from apparently healthy cattle (n = 174) and buffaloes (n = 147) from six districts in Pakistan were tested for A. marginale using a nested PCR assay, targeting part of the major surface protein B gene (msp1β) as a genetic marker, followed by agarose gel electrophoresis and selective sequencing of amplicons from test-positive samples. Of the 321 DNA samples tested, 135 (42.1%) were test-positive for A. marginale. Prevalence was significantly higher in cattle (64.4%; 112/174) than in buffaloes (15.6%; 23/147), and female bovines (43.5%; 108/248) were more frequently infected than males (37%; 27/73). Phylogenetic analysis of the msp1β sequence data (n = 42) revealed that A. marginale from Pakistan clustered with those from Brazil, Thailand, South Africa, and the USA. This study represents the first comprehensive investigation of A. marginale from bovines from diverse agroecological zones of Pakistan and will further stimulate population genetic studies of A. marginale and investigations into the economic impact of subclinical infections in bovines in smallholder farming systems. Full article

Rice (Oryza sativa L.) is essential for global food security and sustains billions worldwide, emphasizing the need to improve production and quality. One key challenge in rice breeding is the inheritance and environmental sensitivity of amylose content, a starch component that influences the texture, water absorption, and firmness after cooking, which are crucial for market acceptance. While international markets prefer low-amylose varieties for their softness, intermediate- and high-amylose varieties are favored in Latin America for their firmness. The objective of this study was to develop a molecular quality assessment methodology that, combined with morphological and culinary evaluations, helps in the selection of rice varieties during the breeding process. First, ten Ecuadorian rice materials were evaluated for milling and culinary quality characteristics, revealing significant grain size, sterility, milling yield, cooking time, and texture variations. Amylose content (AC) is genetically regulated by the waxy gene and its allelic variants, affecting granule-bound starch synthase (GBSS) enzyme expression. Secondly, to classify rice varieties molecularly based on AC, the testing ten genotypes plus nine control varieties were analyzed using microsatellite (SSR) markers. The waxy molecular marker, combined with metaphor agarose gel electrophoresis (MAGE), proved effective for early-stage AC analysis, reducing variety selection costs and improving breeding efficiency. Additionally, a restriction enzyme protocol assay facilitated variety differentiation by selectively cleaving the waxy gene sequence at a specific single-nucleotide polymorphism (SNP) site, allowing for precise AC genetic classification. By integrating molecular techniques with traditional assessments, this study reveals that using marker-assisted selection in breeding programs, as well as supporting the identification and development of high-quality local rice varieties to meet market demands, improves production efficiency and optimizes the assessment of developing varieties under diverse environmental conditions. Full article

The increasing prevalence of antimicrobial-resistant (AMR) bacteria in humans, animals, and the environment underscores the necessity for a rapid, sensitive, and specific method to identify resistance genes. Objectives: This study aims to develop a reliable detection tool for identifying the tetracycline-resistant gene tet(M) in Enterococcus species using a real-time loop-mediated isothermal amplification (RT-LAMP) assay. Real-time visualization through a turbidimeter enabled precise estimation of time-to-positivity for gene detection. Methodology: Six primers were designed using PrimerExplorer v.5, and the assay was optimized across different temperatures and incubation times. Validation was conducted by testing 52 tet(M)-positive clinical enterococci isolates and spiking urine samples from a healthy volunteer and a cow with tet(M)-positive Enterococcus species. Results: The tet(M) gene was detected as early as 33 min, with optimal amplification occurring within 60 min at 60 °C. The assay demonstrated 100% specificity with the established primers. The sigmoidal graphs were corroborated with visual confirmation methods, including a green color change (visible to the naked eye), green fluorescence (under UV light), and a 200 bp PCR product observed via agarose gel electrophoresis. Notably, the tet(M) RT-LAMP assay exhibited a detection limit of 0.001 pg/μL, significantly surpassing conventional PCR, which had a detection limit of 0.1 pg/μL. Conclusions: This rapid, cost-effective, highly sensitive, and specific tet(M) RT-LAMP assay holds significant promise as a surveillance tool for antimicrobial resistance monitoring within a One Health framework, particularly in low-resource countries. Full article

Background/Objectives: PURE (Protein synthesis Using Recombinant Elements), an ideal system for ribosome display, has been successfully used for nanobody selection. However, its limitations in nanobody selection, especially for synthetic nanobody libraries, have not been clearly elucidated, thereby restricting its utilization. Methods: The PURE ribosome display selection process was closely monitored using RNA agarose gel electrophoresis to assess the presence of mRNA molecules in each fraction, including the flow-through, washing, and elution fractions. Additionally, a real-time validation method for monitoring each biopanning round was implemented, ensuring the successful enrichment of target protein-specific binders. The selection process was further optimized by introducing a target protein elution step prior to the EDTA-mediated disassembly, as well as by altering the immobilization surfaces. Finally, the efficiency of PURE ribosome display was enhanced by replacing the spacer gene. Results: The efficiency of PURE ribosome display was merely 4% with an unfavourable spacer gene. Using this spacer gene, EGFP- and human fatty acid-binding protein 4-specific nanobodies from a synthetic nanobody library were we successfully identified through optimizing the selection process. Choosing a spacer gene less prone to secondary structure formation increased significantly its efficiency in displaying synthetic nanobody libraries. Conclusions: Implementing a target protein elution step prior to EDTA-mediated disassembly and modifying the immobilization surfaces effectively increase selection efficiency. For PURE ribosome display, efficiency was further improved using a suitable spacer gene, enabling the display of large libraries. Full article

This study presents an innovative approach to the sustainable valorization of industrial sweet cherry (Prunus avium L.) waste from the Vignola Region, Italy, transforming what is typically discarded into a high-value bioactive resource. Unlike conventional extractions, our hydroethanolic extract (VCE) was obtained from the entire cherry waste, including the pericarp, pulp, and stone, as generated by industrial processing. This full-fruit extraction strategy represents a novel and efficient use of agricultural by-products, aligning with circular bioeconomy principles. Sweet cherries are known for their phenolic richness, and spectrophotometric assays (TPC, TFC, reducing power, DPPH, and ABTS) confirmed the extract’s antioxidant capacity. In vitro studies using RAW 264.7 macrophages revealed no cytotoxic effects (MTT assay), along with significant anti-inflammatory activity, evidenced by reduced ROS and NO production and downregulation of iNOS and COX-2. Western blotting showed inhibition of NF-κB nuclear translocation and MAPK pathway signaling. Additionally, agarose gel electrophoresis showed protection against oxidative DNA damage. UPLC-MS/MS analysis identified sakuranetin, aequinetin, and dihydrowogonin as the most representative compounds in VCE. Molecular docking simulations revealed strong and specific binding affinities of these compounds to NF-κB p65 and key MAPK targets. These findings highlight whole sweet cherry waste—including the pit—as a potent and sustainable source of bioactive compounds with promising nutraceutical and pharmaceutical applications. Full article

Hellenic Open University has developed Onlabs, a virtual biology laboratory designed to safely and effectively prepare its students for hands-on work in the university’s on-site labs. This platform simulates key experimental processes, such as 10X TBE solution preparation, agarose gel preparation and electrophoresis, which involve liquid transfers between bottles. However, accurately depicting liquid volumes and their flow within complex-shaped laboratory vessels, such as Erlenmeyer flasks and burettes, remains a challenge. This paper addresses this limitation by introducing a unified parametric framework for modeling circular cross-section pipes, including straight pipes with a constant diameter, curved pipes with a constant diameter and straight conical pipes. Analytical expressions are developed to define the position and orientation of points along a pipe’s central axis, as well as the surface geometry of composite pipes formed by combining these elements in planar configurations. Moreover, the process of surface discretization with finite triangular elements is analyzed with the aim of optimizing their representation during the algorithmic implementation. The functions of the current length with respect to the volume of each considered container shape are developed. Finally, the methodology for handling and combining the analytical expressions during the filling of a composite pipe is explained, the filling of certain characteristic bottles is implemented and the results of the implementations are presented. The primary goal is to enable the precise algorithmic generation of 3D graphics representing the surfaces of liquids within various laboratory vessels and, subsequently, the simulation of their flow. By leveraging these parametric models, liquid volumes can be accurately visualized, reflecting the vessels’ geometries and improving the realism of simulations and the filling of various vessels can be realistically simulated. Full article

A conventional PCR (cPCR) remains an effective molecular technique for the diagnosis of canine monocytic ehrlichiosis. However, agarose gel electrophoresis requires additional time after thermal cycling. In the present study, we developed a PCR-based lateral flow biosensor (PCR-LFB) to detect Ehrlichia canis (E. canis). Lateral flow strips allow for the simple and rapid detection of PCR products and provide an alternative to gel electrophoresis. The sensitivity, specificity, and detection limit of PCR-LFB were compared to those of TaqMan probe-based real-time PCRs (qPCRs). The PCR-LFB was performed with 5′ 6-FITC and biotin-labeled primers specific to E. canis, targeting the dsb gene. The detection limit of the PCR-LFB assay was 10⁻⁶ for the target DNA sequence in a 10-fold dilution of the recombinant plasmid, which is 10 times lower than that of qPCR. Among the confirmed qPCR results in the 30 dog samples, false-positive results were not detected by the PCR-LFB. Compared to qPCR, the sensitivity and specificity of PCR-LFB were 63.6% (95% CI; 42.9–80.2%) and 100% (95% CI; 67.5–100%), respectively. The Kappa value of the PCR-LFB is in moderate agreement with the qPCR (κ = 0.483). Perfect agreement (κ = 1) was observed between cPCR and PCR-LFB. Lower cost and shorter time consumption were demonstrated using PCR-LFB. Full article

Chinese cabbage (Brassica rapa L. ssp. pekinensis), an important traditional vegetable indigenous to China, is a typical cross-pollinated Brassica crop exhibiting pronounced heterosis. However, its small flower organs make artificial pollination for hybrid seed production highly challenging. The use of male-sterile lines has emerged as a crucial approach in hybrid seed production. Therefore, understanding the genetic and molecular mechanisms underlying male sterility in Chinese cabbage holds profound theoretical and economic importance and is pivotal for advancing Chinese cabbage crossbreeding. Here, cytological comparative analysis of anthers from sterile line 366-2S and fertile line 366-2F revealed abnormalities in 366-2S during the late tetrad stage, including delayed tapetum degradation and the aggregation of tetrad microspores without separation, which prevented pollen production and caused male sterility. Construction of the F₂ segregating population, with 366-2S as the female parent and genetically diverse fertile material Y636-9 as the male parent, indicated that male sterility in 366-2S is controlled by a single recessive gene. Using bulked segregant analysis sequencing and kompetitive allele-specific polymerase chain reaction (KASP) technology, the sterile gene was mapped to 65 kb between the PA11 and PA13 markers, with 11 genes in the candidate region. Functional annotation, expression, and sequence variation analyses identified BraA09g012710.3C, encoding acyl-CoA synthetase 5, as a candidate gene for 366-2S male sterility. Quantitative real-time polymerase chain reaction analysis revealed minimal expression of BraA09g012710.3C in 366-2S but high expression in the flower buds of 366-2F. Further analysis of candidate gene DNA sequences identified a large deletion encompassing BraA09g012710.3C, BraA09g012720.3C, BraA09g012730.3C, and BraA09g012740.3C in sterile line 366-2S (A09: 7452347–7479709). Cloning and verification of the other three deleted genes in the F₂ population via agarose gel electrophoresis confirmed their presence in F₂ sterile individuals, indicating that their deletion was not associated with male sterility, underscoring BraA09g012710.3C as the key gene driving male sterility in 366-2S. Full article

Although a variety of protocols to isolate high-molecular-weight genomic DNA exist, the isolation and preservation of ultra-high-molecular-weight genomic DNA of sufficient quality and length for error-free third-generation sequencing remains challenging. Inspired by the isolation of high-molecular-weight DNA in agarose plugs suitable to be separated by pulsed-field gel electrophoresis, we report the construction of an incubation chamber for DNA isolation. The chamber is flanked by semi-permeable polycarbonate membranes of variable pore size for the selective diffusion of compounds and components, which allows efficient cell lysis and the subsequent isolation of ultra-high-molecular-weight genomic DNA without shearing. The designed experimental approach is simple, but effective in isolating high-quality ultra-long genomic DNA that is suitable for third-generation sequencing by Oxford Nanopore Technology from challenging bacterial samples. We envisage that genomic DNA isolation using the incubation chamber, or variations thereof, will facilitate the regular sequencing of megabasepair-long DNA fragments, with a multitude of applications in microbiology, immunology, oncology, paleontology and forensic science. Full article

Chestnut trees are an essential source of both food and timber. However, the severe threats from invasive pests and diseases compromise their existence and productivity. In Europe, chestnut hybridization programs have been initiated to produce resilient rootstocks in response to ink disease. However, the gap in the identification of these hybrid plants is typically based on field observations and morphological features and remains a challenge. Our study presents a marker set for distinguishing between chestnut hybrid CA90 (Castanea sativa × Castanea crenata), a hybrid with demonstrated resistance to Phytophthora cinnamomi, and other varieties using microsatellite (SSR) markers and bioinformatics tools. We used 35 chestnut samples, including three CA90 controls, hybrids sampled within Portugal, with an aim to define the profiles of the chestnut hybrids and varieties in this study based on band patterns and SSR motifs. We selected and modified nine distinct SSR primers with null allelic features from 43 already developed simple sequence repeat (SSR) markers. PCR amplification and agarose gel electrophoresis were used to amplify and visualize the DNA bands. To confirm genetic variations, 27 amplified bands were sequenced by Sanger sequencing. This analysis identified 31 SSRs across 22 SSR-containing sequences, with trinucleotide (67.74%) repeats being the most common, followed by repeats of dinucleotide (22.58%), mononucleotide (6.45%), and hexanucleotide (3.23%). A total of 18 alleles were observed for the nine loci. The alleles ranged from one to three per locus for the 35 samples. The novel locus CP4 could only be found in CA90 hybrids. This tool can aid in identifying and selecting disease-resistant hybrids, thereby contributing to chestnut production and management strategies. Full article