A colorimetric strategy based on dynamic chemistry for direct detection of Trypanosomatid species

Base-Filling in Double-Helical Nucleic Acids

Base-filling, i. e., post-synthetic furnishing of an oligonucleotide scaffold with base moieties or their analogues, is an interesting alternative to the conventional approach of sequential coupling of building blocks (modified or otherwise). Reversible attachment of the base moieties is particularly attractive as it allows the use of dynamic combinatorial chemistry and usually leads to higher fidelity. This concept article summarizes the various backbones and coupling reactions used for base-filling over the past fifteen years, discusses the impact of base stacking and pairing on efficiency and fidelity and highlights potential and realized applications.

A comprehensive review of Dynamic Chemical Labelling on Luminex xMAP technology: a journey towards Drug-Induced Liver Injury testing

Drug-Induced Liver Injury (DILI) is a grave global adverse event that can result in fatal consequences, causing drug failures, market withdrawals, and regulatory warnings, leading to substantial financial losses. The early detection of DILI remains a significant challenge in global healthcare. Although circulating microRNAs (miRs) show promise as clinical biomarkers for DILI, the current analytical methods for their measurement are insufficient. There is a pressing need for rapid and reliable miR detection methods that eliminate the need for nucleic acid extraction and PCR-based amplification. This review highlights recent advancements achieved by integrating Dynamic Chemical Labelling (DCL) with Luminex xMAP technology. This powerful combination has resulted in groundbreaking bead-based assays that allow (1) the direct, multiplex detection of miRs, and (2) the simultaneous testing of miR and protein biomarkers. This triple capability enables a comprehensive assessment that significantly enhances the detection and analysis of crucial biomarkers, thus improving the understanding and diagnosis of DILI. In conclusion, this review offers valuable insights into the capabilities and potential applications of these groundbreaking assays in DILI research, as well as their potential use in other diagnostic and research domains that require direct or multiplex analysis of miRs or analysis of miRs in combination with proteins.

SARS-CoV-2 viral RNA detection using the novel CoVradar device associated with the CoVreader smartphone app

The COVID-19 pandemic has highlighted the need for innovative approaches to its diagnosis. Here we present CoVradar, a novel and simple colorimetric method that combines nucleic acid analysis with dynamic chemical labeling (DCL) technology and the Spin-Tube device to detect SARS-CoV-2 RNA in saliva samples. The assay includes a fragmentation step to increase the number of RNA templates for analysis, using abasic peptide nucleic acid probes (DGL probes) immobilized to nylon membranes in a specific dot pattern to capture RNA fragments. Duplexes are formed by labeling complementary RNA fragments with biotinylated SMART bases, which act as templates for DCL. Signals are generated by recognizing biotin with streptavidin alkaline phosphatase and incubating with a chromogenic substrate to produce a blue precipitate. CoVradar results are analysed by CoVreader, a smartphone-based image processing system that can display and interpret the blotch pattern. CoVradar and CoVreader provide a unique molecular assay capable of detecting SARS-CoV-2 viral RNA without the need for extraction, preamplification, or prelabeling steps, offering advantages in terms of time (∼3 h/test), cost (∼€1/test manufacturing cost) and simplicity (does not require large equipment). This solution is also promising for the development of assays for other infectious diseases.

Direct detection of alpha satellite DNA with single-base resolution by using abasic Peptide Nucleic Acids and Fluorescent in situ Hybridization

The detection of repetitive sequences with single-base resolution is becoming increasingly important aiming to understand the biological implications of genomic variation in these sequences. However, there is a lack of techniques to experimentally validate sequencing data from repetitive sequences obtained by Next-Generation Sequencing methods, especially in the case of Single-Nucleotide Variations (SNVs). That is one of the reasons why repetitive sequences have been poorly studied and excluded from most genomic studies. Therefore, in addition to sequencing data, there is an urgent need for efficient validation methods of genomic variation in these sequences. Herein we report the development of chemFISH, an alternative method for the detection of SNVs in repetitive sequences. ChemFISH is an innovative method based on dynamic chemistry labelling and abasic Peptide Nucleic Acid (PNA) probes to detect in situ the α-satellite DNA, organized in tandem repeats, with single-base resolution in a direct and rapid reaction. With this approach, we detected by microscopy the α-satellite DNA in a variety of human cell lines, we quantified the detection showing a low coefficient of variation among samples (13.16%-25.33%) and we detected single-base specificity with high sensitivity (82.41%-88.82%). These results indicate that chemFISH can serve as a rapid method to validate previously detected SNVs in sequencing data, as well as to find novel SNVs in repetitive sequences. Furthermore, the versatile chemistry behind chemFISH can lead to develop novel molecular assays for the in situ detection of nucleic acids.

In Vivo Therapeutic Effect of Some Medicinal Plants' Methanolic Extracts on the Growth and Development of Secondary Hydatid Cyst Infection

PURPOSE

The current study aimed to explore the in vivo therapeutic effects of the methanolic extracts of Citrullus colocynthis, Ruta graveolens, and Peganum harmala against hydatid cyst secondary infection.

METHODS

Aerial parts of P. harmala and R. graveolens, including leaves and stems, and seeds of C. colocynthis were collected and extracted using absolute methanol. Rats that are infected with secondary infection of hydatid cysts were treated orally and intraperitoneally according to the determined lethal doses for 30 days. Histological, hematological, and biochemical investigations were done 8 months after the infection.

RESULTS

Compared to Albendazole drug, C. colocynthis, and P. harmala, the methanol extract of R. graveolens showed higher and significant (P < 0.05) therapeutic effects on the secondary hydatid cysts growth. Those effects were represented by the reduction in the cysts' number, size, and weight; as well as the significant changes (P < 0.05) in values of hematological and biochemical parameters, the elevation of IFN-γ levels, and the decline of IL-10 and IL-4 cytokines, compared to the negative control group in both routes of treatment (oral and IP). Moreover, the histological sections showed that R. graveolens has a clear damaging effect on the hydatid cysts GL in the infected rats represented by the detachment of GL from LL and AL.

CONCLUSION

This study can open an avenue to find new therapeutics for secondary hydatid cyst infections using the studied plant extracts, especially the extract of R. graveolens.

Development of a nanotechnology-based approach for capturing and detecting nucleic acids by using flow cytometry

Nucleic acid-based molecular diagnosis has gained special importance for the detection and early diagnosis of genetic diseases as well as for the control of infectious disease outbreaks. The development of systems that allow for the detection and analysis of nucleic acids in a low-cost and easy-to-use way is of great importance. In this context, we present a combination of a nanotechnology-based approach with the already validated dynamic chemical labeling (DCL) technology, capable of reading nucleic acids with single-base resolution. This system allows for the detection of biotinylated molecular products followed by simple detection using a standard flow cytometer, a widely used platform in clinical and molecular laboratories, and therefore, is easy to implement. This proof-of-concept assay has been developed to detect mutations in KRAS codon 12, as these mutations are highly important in cancer development and cancer treatments.

Inexpensive Graphene Oxide Heaters Lithographed by Laser

In this paper, we present a simple and inexpensive method for the fabrication of high-performance graphene-based heaters on different large-scale substrates through the laser photothermal reduction of graphene oxide (laser-reduced graphene-oxide, LrGO). This method allows an efficient and localized high level of reduction and therefore a good electrical conductivity of the treated films. The performance of the heaters is studied in terms of steady-state temperature, power consumption, and time response for different substrates and sizes. The results show that the LrGO heaters can achieve stable steady-state temperatures higher than 200 °C when a voltage of 15 V is applied, featuring a time constant of around 4 s and a heat transfer coefficient of ~200 °C cm²/W. These characteristics are compared with other technologies in this field, demonstrating that the fabrication approach described in this work is competitive and promising to fabricate large-scale flexible heaters with a very fast response and high steady-state temperatures in a cost-effective way. This technology can be easily combined with other fabrication methods, such as screen printing or spray-deposition, for the manufacturing of complete sensing systems where the temperature control is required to adjust functionalities or to tune sensitivity or selectivity.