Nucleic Acid Content Research Articles

Macromolecular crowding potently stimulates DNA supercoiling activity of Mycobacterium tuberculosis DNA gyrase

Macromolecular crowding, manifested by high concentrations of proteins and nucleic acids in living cells, significantly influences biological processes such as enzymatic reactions. Studying these reactions in vitro, using agents such as polyethylene glycols (PEGs) and polyvinyl alcohols (PVAs) to mimic intracellular crowding conditions, is essential due to the notable differences from enzyme behaviors observed in diluted aqueous solutions. In this article, we studied Mycobacterium tuberculosis (Mtb) DNA gyrase under macromolecular crowding conditions by incorporating PEGs and PVAs into the DNA supercoiling reactions. We discovered that high concentrations of potassium glutamate, glycine betaine, PEGs, and PVA substantially stimulated the DNA supercoiling activity of Mtb DNA gyrase. Steady-state kinetic studies showed that glycine betaine and PEG400 significantly reduced the KM of Mtb DNA gyrase, and simultaneously increased the Vmax or kcat of Mtb DNA gyrase for ATP and the plasmid DNA molecule. Molecular dynamics simulation studies demonstrated that PEG molecules kept the ATP lid of GyrB in a closed or semi-closed conformation, which prevented ATP molecules from leaving the ATP-binding pocket of GyrB. The stimulation of the DNA supercoiling activity of Mtb DNA gyrase by these molecular crowding agents likely results from a decrease in water activity and an increase in excluded volume.

PSV-26 Use of Garlic Drench in the Modulation of Galectin Gene Expression in St Croix Sheep

Abstract St. Croix sheep are parasite resistant and can live in a wide variety of climates. Dietary supplements can influence innate immunity. Garlic (Allium sativum) is used as an immune modulator and an alternative antibiotic. Lectins in garlic could interfere with animal lectins such as Galectins (Gals). Galectins bind β-galactosides and modulate pathological processes and immunity. The effect of garlic drench on Gal (1,3,9) gene expression in sheep blood was evaluated. All protocols were approved by the IACUC. Clinically healthy, adult St. Croix sheep were divided into two groups. The treatment group (n = 6) was drenched with 5 mL garlic barrier at a rate of 10 mL diluted in sterile distilled water 1:1. The control group (n = 6) was drenched with 10 mL sterile distilled water for four weeks. Cells and plasma were separated by centrifugation of whole blood. The concentration of total plasma protein was determined using the BCA assay kit (Pierce). Secretion of Galectins 1,3,9 was evaluated using Sheep-specific ELISA(My-BioSource). Data were analyzed using SAS Statistical analysis software 9.4 (SAS Institute). Nucleic acid purity and concentrations were assessed using the Nanodrop spectrophotometer. Galectin gene transcription was evaluated using sheep Gal 1,3 and 9 specific primers commercially sequenced (Eurofins Genomics). The house keeping genes, Ribosomal Protein Lateral Stalk Subunit P0 and Ubiquitin C-Terminal Hydrolase L5, were used as internal controls. Samples were amplified in duplicate using the CFX Connect real-time PCR system. The Livak Method was used to calculate the fold change in gene expression. Galectin 1, 3, and 9 were transcribed and translated. Transcription and translation were differentially affected by garlic. Galectin 1 transcription increased; secretion decreased. Galectin 3 transcription and secretion increased at P < 0.05. There was no change in the transcription of galectin 9, however, secretion was increased. Thus, garlic drench deferentially impacted transcription and secretion of structurally distinct Gal in sheep blood. Further studies are needed to determine the effect of Garlic on Gal-mediated functions important to sheep health and production.

PCR standard curve quantification in an extensive wastewater surveillance program: results from the Dutch SARS-CoV-2 wastewater surveillance.

Since the start of the COVID-19 pandemic in 2020, wastewater surveillance programs were established, or upscaled, in many countries around the world and have proven to be a cost-effective way of monitoring infectious disease pathogens. Many of these programs use RT-qPCR, and quantify the viral concentrations in samples based on standard curves, by including preparations of a reference material with known nucleic acid or virus concentrations in the RT-qPCR analyses. In high-throughput monitoring programs it is possible to combine data from multiple previous runs, circumventing the need for duplication and resulting in decreased costs and prolonged periods during which the reference material is obtained from the same batch. However, over time, systematic shifts in standard curves are likely to occur. This would affect the reliability and usefulness of wastewater surveillance as a whole. We aim to find an optimal combination of standard curve data to compensate for run-to-run measurement variance while ensuring enough flexibility to capture systematic longitudinal shifts. Based on more than 4000 observations obtained with the CDC N1 and N2 assays, taken as a part of the National Sewage Surveillance program at the Dutch National Institute for Public Health and the Environment, we show that seasonal and long-term shifts in RT-qPCR efficiency and sensitivity occur. We find that in our setting, using five days of standard-curve data to quantify, results in the least error prone curve or best approximation. This results in differences up to 100% in quantified viral loads when averaged out over a nationwide program of >300 treatment plants. Results show that combining standard curves from a limited set of runs can be a valid approach to quantification without obscuring the trends in the viral load of interest.

Rapid genotype recognition of human adenovirus based on surface-enhanced Raman scattering combined with machine learning

Currently, more than 100 genotypes of human adenovirus (HAdV) are classified into seven species (A–G). The tissue tropism and virulence of HAdV are closely related to the genotypes, different genotypes of HAdV infection lead to different types and severity of the disease. Although traditional genotype identification techniques are widely used, they are time-consuming, complex and low sensitivity. Therefore, a rapid and accurate genotype recognition method for HAdV is necessary. In this study, silver nanoparticles incubated with iodine ions and aggregated with calcium ions were used as the enhanced substrate to form a good "hot spot" suitable for viral nucleic acid. The method could rapidly identify the seven common genotypes of respiratory HAdV characteristic fingerprints, combined with machine learning technology could classify and identify HAdV (500 copies/mL) within 5 min, with an accuracy rate of over 98%. In addition, the concentration dependence curve assessing the relationship between the intensity of the characteristic peak and the nucleic acid concentration showed a good linear relationship, the method can be used to quantitatively detect HAdV nucleic acid. This technique can enhance diagnosis and genotype identification of HAdV infection, thus providing a feasible method for the efficient response to respiratory human adenovirus outbreaks.

Efficiency of DNA Extractions Methods from Pigeons and Cockatiels Feathers

This study aimed to compare different DNA extraction methods to achieve higher amounts and purity levels from molted feathers of pigeons (Columba livia f. domestica) and cockatiels (Nymphicus hollandicus). We evaluated 226 animals consisting of 202 pigeons and 24 cockatiels for these purposes. We performed three commercially available DNA extraction kits to isolate DNA from the feather samples. These kits were compared regarding DNA yield and quality depending on the different applications made during the isolation. DNA concentration (ng/mL) and absorbance ratio (260/280) were measured using a Nanodrop spectrophotometer. Kruskal-Wallis test with the Dunn’s post hoc comparison was performed for the statistical comparisons. The mean DNA concentration was the highest in isolation with the kit C. Among three commercial kits, statistically significant differences were observed concerning nucleic acid concentration (ng/µL) (P

Comprehensive biosafety assessment of Ag-ZnO/talc nanomaterials: Implications for antibacterial applications

Given the global proliferation of pathogenic microorganisms, there exists a pressing imperative to cultivate efficacious nanomaterials possessing antimicrobial attributes, thereby impeding the transmission of infectious diseases. Clay-based nanoparticles, due to their inherent properties, serve as optimal candidates for the creation of innovative antimicrobial agents, particularly for coating materials. In this study, ZnO nanoparticles were synthesized on talc surfaces and doped with Ag+, yielding an effective antimicrobial composite (Ag-ZnO/talc). The primary aim was to comprehensively evaluate the antimicrobial effectiveness, material compatibility, and biosafety of Ag-ZnO/talc, as well as its potential applications in antibacterial coatings. The finding underscored the remarkable antibacterial properties of Ag-ZnO/talc composites, chiefly through the generation of reactive oxygen species, leading to impairment of the bacterial membrane and leakage of nucleic acid content. A biosafety evaluation indicated minimal cytotoxicity, a low hemolysis rate, and negligible skin tissue reactions, thereby suggesting its suitability for human application. Furthermore, the incorporation of the antimicrobial agent Ag-ZnO/talc did not significantly alter the physicochemical characteristics of the coating, while maintaining an enduring antimicrobial effect for a duration of two months. These findings establish the potential of clay-based antimicrobials for effective and safe application in coatings, facilitating the development of antimicrobial coatings in diverse industrial and public health environments.

Comparison of adsorption-extraction (AE) workflows for improved measurements of viral and bacterial nucleic acid in untreated wastewater

The lack of standardized methods and large differences in virus concentration and extraction workflows have hampered Severe Acute Respiratory Syndrome (SARS-CoV-2) wastewater surveillance and data reporting practices. Numerous studies have shown that adsorption-extraction (AE) method holds promise, yet several uncertainties remain regarding the optimal AE workflow. Several procedural components may influence the recovered concentrations of target nucleic acid, including membrane types, homogenization instruments, speed and duration, and lysis buffer. In this study, 42 different AE workflows that varied these components were compared to determine the optimal workflow by quantifying endogenous SARS-CoV-2, human adenovirus 40/41 (HAdV 40/41), and a bacterial marker gene of fecal contamination (Bacteroides HF183). Our findings suggest that the workflow chosen had a significant impact on SARS-CoV-2 concentrations, whereas it had minimal impact on HF183 and no effect on HAdV 40/41 concentrations. When comparing individual components in a workflow, such as membrane type (MF-Millipore™ 0.45 μm MCE vs. Isopore™ 0.40 μm), we found that they had no impact on SARS-CoV-2, HAdV 40/41, and HF183 concentrations. This suggests that at least some consumables and equipment are interchangeable. Buffer PM1 + TRIzol-based workflows yielded higher concentrations of SARS-CoV-2 than other workflows. HF183 concentrations were higher in workflows without chloroform. Similarly, higher homogenization speeds (5000–10,000 rpm) led to increased concentrations of SARS-CoV-2 and HF183 but had no effect on HAdV 40/41. Our findings indicate that minor enhancements to the AE workflow can improve the recovery of viruses and bacteria from the wastewater, leading to improved outcomes from wastewater surveillance efforts.

Latest Update on Outer Membrane Vesicles and Their Role in Horizontal Gene Transfer: A Mini-Review.

Outer membrane vesicles (OMVs) are spherical, lipid-based nano-structures, which are released by Gram-negative bacteria in both in vitro and in vivo conditions. The size and composition of OMVs depend on not only the producer bacterial species but also cells belonging to the same strain. The mechanism of vesicles' biogenesis has a key role in determining their cargo and the pattern of macromolecules exposed on their surface. Thus, the content of proteins, lipids, nucleic acids, and other biomolecules defines the properties of OMVs and their beneficial or harmful effects on human health. Many studies have provided evidence that OMVs can be involved in a plethora of biological processes, including cell-to-cell communication and bacteria-host interactions. Moreover, there is a growing body of literature supporting their role in horizontal gene transfer (HGT). During this process, OMVs can facilitate the spreading of genes involved in metabolic pathways, virulence, and antibiotic resistance, guaranteeing bacterial proliferation and survival. For this reason, a deeper understanding of this new mechanism of genetic transfer could improve the development of more efficient strategies to counteract infections sustained by Gram-negative bacteria. In line with this, the main aim of this mini-review is to summarize the latest evidence concerning the involvement of OMVs in HGT.

Single virus fingerprinting by widefield interferometric defocus-enhanced mid-infrared photothermal microscopy

Clinical identification and fundamental study of viruses rely on the detection of viral proteins or viral nucleic acids. Yet, amplification-based and antigen-based methods are not able to provide precise compositional information of individual virions due to small particle size and low-abundance chemical contents (e.g., ~ 5000 proteins in a vesicular stomatitis virus). Here, we report a widefield interferometric defocus-enhanced mid-infrared photothermal (WIDE-MIP) microscope for high-throughput fingerprinting of single viruses. With the identification of feature absorption peaks, WIDE-MIP reveals the contents of viral proteins and nucleic acids in single DNA vaccinia viruses and RNA vesicular stomatitis viruses. Different nucleic acid signatures of thymine and uracil residue vibrations are obtained to differentiate DNA and RNA viruses. WIDE-MIP imaging further reveals an enriched β sheet components in DNA varicella-zoster virus proteins. Together, these advances open a new avenue for compositional analysis of viral vectors and elucidating protein function in an assembled virion.

Surface Hybridization Chain Reaction of Binary Mixture DNA-PEG Corona Nanostructures Produced by Low-Volume RAFT-Mediated Photopolymerization-Induced Self-Assembly.

DNA-polymer hybrids have been attracting interest as adaptable functional materials by combining the stability of polymers with DNA nanotechnology. Both research fields have in common the capacity to be precise, versatile, and tunable, a prerequisite for creating powerful tools which can be easily tailored and adapted for bio-related applications. However, the conjugation of hydrophilic DNA with hydrophobic polymers remains challenging. In recent years, polymerization-induced self-assembly (PISA) has attracted significant attention for constructing nano-objects of various morphologies owing to the one-step nature of the process, creating a beneficial method for the creation of amphiphilic DNA-polymer nanostructures. This process not only allows pure DNA-polymer-based systems to be produced but also enables the mixture of other polymeric species with DNA conjugates. Here, we present the first report of a DNA-PEG corona nano-object's synthesis without the addition of an external photoinitiator or photocatalyst via photo-PISA. Furthermore, this work shows the use of DNA-macroCTA, which was first synthesized using a solid-support method resulting in high yields, easy upscaling, and no need for HPLC purification. In addition, to the formation of DNA-polymer structures, increasing the nucleic acid loading of assemblies is of great importance. One of the most intriguing phenomena of DNA is the hybridization of single-stranded DNA with a second strand, increasing the nucleic acid content. However, hybridization of DNA in a particle corona may destabilize the nanomaterial due to the electrostatic repulsive force on the DNA corona. Here, we have investigated how changing the DNA volume fraction in hybrid DNA-polymer self-assembled material affects the morphology. Moreover, the effect of the corona composition on the stability of the system during the hybridization was studied. Additionally, the hybridization chain reaction was successfully applied as a new method to increase the amount of DNA on a DNA-based nano-object without disturbing the morphology achieving a fluorescence signal amplification.

Raman Spectroscopy as a Potential Adjunct of Thyroid Nodule Evaluation: A Systematic Review.

The incidence of thyroid nodules (TNs) is estimated at 36.5% and 23% in females and males, respectively. A single thyroid nodule is usually detected during ultrasound assessment in patients with symptoms of thyroid dysfunction or neck mass. TNs are classified as benign tumours (non-malignant hyperplasia), benign neoplasms (e.g., adenoma, a non-invasive follicular tumour with papillary nuclear features) or malignant carcinomas (follicular cell-derived or C-cell derived). The differential diagnosis is based on fine-needle aspiration biopsies and cytological assessment (which is burdened with the bias of subjectivity). Raman spectroscopy (RS) is a laser-based, semiquantitative technique which shows for oscillations of many chemical groups in one label-free measurement. RS, through the assessment of chemical content, gives insight into tissue state which, in turn, allows for the differentiation of disease on the basis of spectral characteristics. The purpose of this study was to report if RS could be useful in the differential diagnosis of TN. The Web of Science, PubMed, and Scopus were searched from the beginning of the databases up to the end of June 2023. Two investigators independently screened key data using the terms "Raman spectroscopy" and "thyroid". From the 4046 records found initially, we identified 19 studies addressing the differential diagnosis of TNs applying the RS technique. The lasers used included 532, 633, 785, 830, and 1064 nm lines. The thyroid RS investigations were performed at the cellular and/or tissue level, as well as in serum samples. The accuracy of papillary thyroid carcinoma detection is approx. 90%. Furthermore, medullary, and follicular thyroid carcinoma can be detected with up to 100% accuracy. These results might be biased with low numbers of cases in some research and overfitting of models as well as the reference method. The main biochemical changes one can observe in malignancies are as follows: increase of protein, amino acids (like phenylalanine, tyrosine, and tryptophan), and nucleic acid content in comparison with non-malignant TNs. Herein, we present a review of the literature on the application of RS in the differential diagnosis of TNs. This technique seems to have powerful application potential in thyroid tumour diagnosis.

Bioactive molecular family construction: Design, optimization and antifungal mechanism study of novel 2-phenylglycine derivatives

With the widespread use of fungicides, some problems have also gradually emerged, such as resistance, toxicity and residues. Therefore, to develop novel antifungal pesticides with unique structures, safety and high efficiency, a series of 2-phenylglycine derivatives were designed and synthesized. The bioactivity results revealed good antifungal activity of compound III11 and boscalid against Nigrospora oryzae, and they both effectively inhibited spore germination with EC50 values of 17.3 and 3.1 μg/mL, respectively. An antifungal mechanism study showed that both III11 and boscalid significantly increased the content of nucleic acids, proteins and MDA, which indicated that they could destroy the integrity of the mycelial cell membrane, thus affecting the normal growth of mycelia. Molecular docking results revealed that III11 bound with some amino acid residues (SER-39, ARG-14 and ARG-43) of succinate dehydrogenase (SDH) through a unique mode involving hydrogen bonds, different from the binding mode of boscalid. Further investigation demonstrated that III11 exhibited moderate inhibitory activity against SDH (IC50 = 54.5 μg/mL), weaker than that of boscalid (IC50 = 10.7 μg/mL). The results provided sufficient support for the optimization and derivatization of 2-phenylglycine derivatives, which could be further developed and designed as potential fungicides.

Promoting Nucleic Acid Synthesis in Saccharomyces cerevisiae through Enhanced Expression of Rrn7p, Rrn11p, IMPDH, and Pho84p.

Saccharomyces cerevisiae has emerged as a preferred source for industrial production of ribonucleic acids (RNAs) and their derivatives, which find wide applications in the food and pharmaceutical sectors. In this study, we employed a modified RNA polymerase I-mediated green fluorescent protein expression system, previously developed by our team, to screen and identify an industrial S. cerevisiae strain with an impressive 18.2% increase in the RNA content. Transcriptome analysis revealed heightened activity of genes and pathways associated with rRNA transcription, purine metabolism, and phosphate transport in the high nucleic acid content mutant strains. Our findings highlighted the crucial role of the transcription factor Sfp1p in enhancing the expression of two key components of the transcription initiation factor complex, Rrn7p and Rrn11p, thereby promoting rRNA synthesis. Moreover, elevated expression of 5'-inosine monophosphate dehydrogenases, regardless of the specific isoform (IMD2, 3, or 4), resulted in increased rRNA synthesis through heightened GTP levels. Additionally, exogenous phosphate application, coupled with overexpression of the phosphate transporter PHO84, led to a 61.4% boost in the RNA yield, reaching 2050.4 mg/L. This comprehensive study provides valuable insights into the mechanism of RNA synthesis and serves as a reference for augmenting RNA production in the food industry.

QPCR-based eDNA workflow for humic-rich lake sediments: Combined use of sedimentary DNA (sedDNA) and Indigenous Knowledge in reconstructing historical fish records

Lake sediment serves as a natural archive of historical biological information. The use of sedimentary DNA (sedDNA), a form of environmental DNA (eDNA) shed by aquatic organisms and preserved in sediment, has been instrumental in reconstructing past faunal composition in aquatic communities. However, the low abundance of fish sedDNA and the often humic-rich nature of lake sediments create methodological challenges for the accurate detection of target sedDNA using quantitative polymerase chain reaction (qPCR)-based approaches. Herein, we present a consolidated qPCR-based eDNA workflow to reconstruct past and current fish fauna in Cowpar Lake located in the Oil Sands region in Alberta (Canada), which were then validated using Indigenous Knowledge from Chipewyan Prairie First Nation community members. The present study highlights the importance of combining column- and precipitation-based PCR inhibitor clean-up, nucleic acid concentration, incorporating endogenous chloroplast DNA as a sample integrity control. Robust qPCR-based eDNA assays were also useful in preventing the false-negative detection of low copies of target fish DNA. The presence of Northern pike (1905 to 2019) and Cisco (1919 to 1942) in Cowpar Lake was confirmed based on detected sedDNA from sediment core. The reconstructed fish records from sedDNA-inferred data aligned with the Indigenous accounts of natural and human-mediated changes in land use around the lake. Overall, the present study addresses common methodological concerns in processing lake sediment samples for fish eDNA detection and demonstrates the great potential of combined eDNA-inferred data and Indigenous Knowledge in reconstructing historical fish records in aquatic communities.

Research on a Magnetic Separation-Based Rapid Nucleic Acid Extraction System and Its Detection Applications.

Nucleic acid extraction represents the "first step" in molecular diagnostic experiments. The quality of this extraction serves as a fundamental prerequisite for ensuring the accuracy of nucleic acid detection. This article presents a comprehensive design scheme for a rapid automated nucleic acid extraction system based on magnetic separation. The design and implementation of the system are analyzed and investigated in-depth, focusing on the core methods, hardware control, and software control of the automated nucleic acid extraction system. Additionally, a study and evaluation were carried out concerning the nucleic acid extraction and detection aspects encompassed by the system. The results demonstrate that the temperature deviation in the lysis and elution fluids is approximately ±1 °C, the positioning accuracy of the system's movement is ±0.005 mm, the average magnetic bead recovery rate is 94.98%, and the average nucleic acid recovery rate is 91.83%. The developed automated system and manual methods are employed for sample extraction, enabling the isolation of highly pure nucleic acids from bacteria, blood, and animal tissues for RT-PCR detection. The instrument employs lysis temperatures ranging from 70-80 °C, elution temperature of 80 °C, and drying time of 5-10 min, with a total extraction time of less than 35 min for different sample types. Overall, the system yields high nucleic acid concentration and purity, exhibits stable instrument operation, good repeatability, high efficiency, and low cost. It meets the requirements of genetic-level research and is worthy of clinical promotion and usage.

Exosomes and their miRNA/protein profile in keratoconus-derived corneal stromal cells

Keratoconus (KC) is a corneal thinning disorder and a leading cause of corneal transplantation worldwide. Exosomes are small, secreted extracellular vesicles (30–150 nm) that mediate cellular communication via their protein, lipid, and nucleic acid content. We aimed to characterize the exosomes secreted by primary corneal fibroblasts from subjects with or without KC. Using human keratoconus stromal fibroblast cells (HKC, n = 4) and healthy stromal fibroblasts (HCF, n = 4), we collected and isolated exosomes using serial ultracentrifugation. Using nanoparticle tracking analysis (NTA) with ZetaView®, we compared the size and concentration of isolated exosomes. Different exosomal markers were identified and quantified using a transmission electron microscope (TEM) (CD81) and Western blot (CD9 and CD63). Exosomal miRNA profiles were determined by qRT-PCR using Exiqon Human panel I miRNA assays of 368 pre-selected miRNAs. Proteomic profiles were determined using a label-free spectral counting method with mass spectrometry. Differential expression analysis for miRNAs and proteins was done using student's t-test with a significance cutoff of p-value ≤0.05. We successfully characterized exosomes isolated from HCFs using several complementary techniques. We found no significant differences in the size, quantity, or morphology between exosomes secreted by HCFs with or without KC. Expression of CD81 was confirmed by immuno-EM, and expression of CD63 and CD9 with western blots in all exosome samples. We detected the expression of 72–144 miRNAs (threshold cycle Ct < 36) in all exosome samples. In HKC-derived exosome samples, miR-328-3p, miR-532-5p, miR-345-5p, and miR-424-5p showed unique expression, while let-7c-5p and miR-665 have increased expression. Protein profiling identified 157 proteins in at least half of the exosome samples, with 38 known exosomal proteins. We identified 12 up- and 2 down-regulated proteins in HKC-derived exosomes. The proteins are involved in membrane-bounded vesicles, cytoskeletal, calcium binding, and nucleotide binding. These proteins are predicted to be regulated by NRF2, miR-205, and TGF-β1, which are involved in KC pathogenesis. We successfully characterized the HKC-derived exosomes and profiled their miRNA and protein contents, suggesting their potential role in KC development. Further studies are necessary to determine if and how these exosomes with differential protein/miRNA profiles contribute to the pathogenesis of KC.

On assessing the viral safety of individual units of the substance "Human plasma for fractionation" by nucleic acid amplification

Scientific relevance. The absence of blood-borne viruses in human plasma-derived medicinal products must be ensured by the control of raw materials and the manufacturing process.Aim. This study aimed to analyse system suitability criteria for analytical procedures to assess the viral safety of individual units of the substance "Human plasma for fractionation" in terms of the content of nucleic acids of blood-borne viruses, considering the requirements of the European Pharmacopoeia.Materials and methods. The authors analysed individual units of the substance "Human plasma for fractionation" (hereinafter, plasma). The study used the International Standards (ISs) for human immunodeficiency virus RNA, hepatitis A virus (HAV) RNA, hepatitis C virus (HCV) RNA, hepatitis B virus (HBV) DNA, and parvovirus B19 DNA, as well as nucleic acid detection kits for these viruses based on polymerase chain reaction (PCR).Results. HCV RNA was not detected in any of the eight plasma samples studied, and parvovirus B19 DNA was detected in one of the samples at a concentration not exceeding 104 IU/mL. Three tests with the corresponding ISs showed that the studied reagent kits detected HCV RNA at a concentration of 102 IU/mL and parvovirus B19 DNA (M1 genotype) at a concentration of 104 IU/mL. In additional tests that were conducted in two samples considering the requirements of the European Pharmacopoeia for the detection of HCV RNA and parvovirus B19 DNA, a new batch of reagent kit I detected the HCV RNA IS at a concentration of 102 IU/mL only in one of three replicates, which did not correspond to the claimed sensitivity of the reagent kit. HCV RNA was not detected in either replicate in one of two plasma samples spiked with the HCV RNA IS at concentrations of 102 and 103 IU/mL, possibly because of plasma inhibitory properties. The sensitivity of the reagent kits to parvovirus B19 DNA corresponded to the label claims; the study did not show any inhibitory properties of the plasma samples.Conclusions. Polymerase chain reaction testing of the viral safety of plasma intended for manufacturing medicinal products should include control samples calibrated in IU/mL. Further research and appropriate pharmacopoeial reference materials are needed to set system suitability criteria for analytical procedures using such control samples.

Saponin-Derived Silver Nanoparticles from Phoenix dactylifera (Ajwa Dates) Exhibit Broad-Spectrum Bioactivities Combating Bacterial Infections.

The emergence of antibiotic resistance poses a serious threat to humankind, emphasizing the need for alternative antimicrobial agents. This study focuses on investigating the antibacterial, antibiofilm, and anti-quorum-sensing (anti-QS) activities of saponin-derived silver nanoparticles (AgNPs-S) obtained from Ajwa dates (Phoenix dactylifera L.). The design and synthesis of these novel nanoparticles were explored in the context of developing alternative strategies to combat bacterial infections. The Ajwa date saponin extract was used as a reducing and stabilizing agent to synthesize AgNPs-S, which was characterized using various analytical techniques, including UV-Vis spectroscopy, Fourier transform infrared (FTIR) spectroscopy, and transmission electron microscopy (TEM). The biosynthesized AgNPs-S exhibited potent antibacterial activity against both Gram-positive and Gram-negative bacteria due to their capability to disrupt bacterial cell membranes and the leakage of nucleic acid and protein contents. The AgNPs-S effectively inhibited biofilm formation and quorum-sensing (QS) activity by interfering with QS signaling molecules, which play a pivotal role in bacterial virulence and pathogenicity. Furthermore, the AgNPs-S demonstrated significant antioxidant activity against 2,2-diphenyl-1-picrylhydrazyl (DPPH) free radicals and cytotoxicity against small lung cancer cells (A549 cells). Overall, the findings of the present study provide valuable insights into the potential use of these nanoparticles as alternative therapeutic agents for the design and development of novel antibiotics. Further investigations are warranted to elucidate the possible mechanism involved and safety concerns when it is used in vivo, paving the way for future therapeutic applications in combating bacterial infections and overcoming antibiotic resistance.

A biospectroscopic approach toward colorectal cancer diagnosis from bodily fluid samples via ATR–MIR spectroscopy combined with multivariate data analysis

In this study, a biospectroscopic approach was reported for the detection of spectral changes and biomarkers for the diagnosis of colorectal cancer (CC) cases from different bodily fluids (blood plasma, blood serum, saliva and colonoscopy disinfection/wash fluids) by using attenuated total reflection–mid infrared (ATR–MIR) spectroscopy. To recognize the molecular level changes in the spectral characteristics of CC and their healthy/control (CH) groups, different multivariate data analyses (HCA, LDA, PCA and SIMCA) were successfully performed over the data of ATR–MIR spectroscopy. Two hundred specimens were characterized in detail over the data of spectral regions (4000–650 cm−1 and regions V–XXII). The findings revealed that significant changes were clearly observed in the concentrations of lipid, protein, nucleic acid and carbohydrate biomolecules for cancer cases based upon their necessity to overcome energy requirements. Supervised multivariate data methodology SIMCA, presented an excellent classification for the studied groups; similarly 100% of the specimens from different bodily fluids were correctly classified by supervised methodology LDA. As a result, the developed ATR–MIR methodology for the classification of CC and their healthy groups highlighted a rapid cancer diagnosis approach from different bodily fluids; therefore, it could be guide to make well decision before histopathological assessment and to screen CC populations existing in society.

A Multicenter Analysis of Nucleic Acid Quantification Using Aqueous Humor Liquid Biopsy in Retinoblastoma: Implications for Clinical Testing.

Retinoblastoma (RB) is most often diagnosed with clinical features and not diagnosed with tumor biopsy. This study describes tumor-derived analyte concentrations from aqueous humor (AH) liquid biopsy and its use in clinical assays. Case series study. Sixty-two RB eyes from 55 children and 14 control eyes from 12 children from 4 medical centers. This study included 128 RB AH samples including: diagnostic (DX) samples, samples from eyes undergoing treatment (TX), samples after completing treatment (END), and during bevacizumab injection for radiation therapy after completing RB treatment (BEV). Fourteen-control AH were analyzed for unprocessed analytes (double-stranded DNA [dsDNA], single-stranded DNA [ssDNA], micro-RNA [miRNA], RNA, and protein) with Qubit fluorescence assays. Double-stranded DNA from 2 RB AH samples underwent low-pass whole-genome sequencing to detect somatic copy number alterations. Logistic regression was used to predict disease burden given analyte concentrations. Unprocessed analyte (dsDNA, ssDNA, miRNA, RNA and protein) concentrations. Results revealed dsDNA, ssDNA, miRNA, and proteins, but not RNA, were quantifiable in most samples (up to 98%) with Qubit fluorescence assays. Median dsDNA concentration was significantly higher in DX (3.08 ng/μl) compared to TX (0.18 ng/μl; P<0.0001) at an order of 17 times greater and 20 times greater than END samples (0.15 ng/μl; P=0.001). Using logistic regression, nucleic acid concentrations were useful in predicting higher versus lower RB disease burden. Retinoblastoma somatic copy number alterations were identified in a TX, but not in a BEV sample, indicating the correlation with RB activity. Aqueous humor liquid biopsy in RB is a high-yield source of dsDNA, ssDNA, miRNA, and protein. Diagnostic samples are most useful for RB 1 gene mutational analyses. Genomic analysis may be more informative of tumor activity status than quantification alone and can be performed even with smaller analyte concentrations obtained from TX samples. Proprietary or commercial disclosure may be found after the references.