Biology subjects

Mohammedi, R.

Publications and source records attributed to Mohammedi, R..

3 recordsLinked to original sources

bioRxiv2026

Highly sensitive enzyme- and amplification-free, quantitative DNA detection using YVO4:Eu luminescent nanoparticle probes

The sensitive detection of nucleic acids is crucial for the accurate diagnosis of infections. In this context, amplification-based methods, such as the quantitative Polymerase Chain Reaction (qPCR) are the gold standard for ultrasensitive DNA or RNA detection and quantification. However, despite its widespread use in developed countries during the COVID-19 pandemic, qPCR remains a costly tool, difficult to implement into low-infrastructure locations. Efforts for the development of alternative tools have yielded high sensitivity approaches but sensitivity is typically reached at the expense of complexity. We here report the development of a simple, sensitive, amplification-, and enzyme-free nucleic acid detection technique using YVO4:Eu luminescent nanoparticles. We established an optimized interaction scheme to efficiently reveal target DNA fragments with nanoparticles. By exploiting the extremely strong absorption of the vanadate matrix in the UV to excite the nanoparticles inducing the characteristic Eu3+ emission at 617 nm via energy transfer, we achieved a highly sensitive (down to 500 particles/mm2; 17,000 particles/well) read-out in standard microplates using a home-made optical reader with light-emitting diode (LED), 275-nm excitation. We reached a 50-aM (30,000 copies/mL) sensitivity for the detection of the 72-base DNA fragment of the SARS-CoV-2 n1 gene. Our new quantitative analytical method detects nucleic acids without amplification with performances close to standard PCR (10,000 copies/mL)1, and could be the basis for a transportable alternative for the diagnosis of infectious diseases.

bioengineering↗

bioRxiv2025

Ultrasensitive quantitative protein detection using Eu-ion doped vanadate nanoparticles

Disease prevention, diagnosis, and treatment monitoring often require ultrasensitive (sub-)femtomolar biomarker detection and quantification. While standard ELISA assays yield picomolar sensitivity, existing ultrasensitive approaches reach fM, aM or even zM sensitivity. This, however, is obtained at the expense of increased complexity and cost which hampers their biomedical applications. We propose a novel approach, NLISA, combining ultrasensitive, fM/sub-fM, quantitative detection with simplicity and ease of use based on 38-nm YVO4:Eu (20%) crystalline nanoparticles used as detection probes. These particles possess an extremely strong absorption in the UV leading to bright Eu3+-ion emission. We developed a transportable, multi-well plate reader providing LED excitation and detection with a photomultiplier enabling detection down to 16,000 nanoparticle probes/well. We obtained sensitivity gain factors with respect to ELISA ranging from 65 to 35,000 for insulin, IFN-{gamma}, and HIV-GAG-p24 while maintaining the same antibodies. We demonstrated femtomolar LOD and a dynamic range of 4-5 orders of magnitude and NLISA efficiency for HIV-positive patient diagnosis. This approach for straightforward, ultrasensitive polypeptide/protein detection is easily generalizable paving the way for a new generation of diagnostic tests.

bioengineering↗

bioRxiv2022

Microaerobic conditions and the complex regulation of natural competence in Staphylococcus aureus

To perform genetic transformation, one of the three main Horizontal Gene Transfer mechanisms leading to virulence and antibiotic resistance genes acquisition, bacteria need to enter a physiological differentiated state called natural competence. Diverse environmental and cellular cues have been shown to trigger complex regulatory pathways ultimately activating central competence regulators controlling the expression of the genetic transformation genes. Interestingly, new bacteria displaying such aptitude are often discovered, and one of the latest is the human pathogen Staphylococcus aureus. However, a clear understanding of the environmental signals, regulatory pathways and central regulators involved in the development of competence in S. aureus is not yet available. Here, using an original optimized protocol to naturally induce competence in planktonic cells, leading to improved transformation efficiencies (up to 5.10-6), we showed that the three putative central competence regulators identified in S. aureus are all essential for a complete development of competence. We also found that genes involved in genetic transformation can be divided in several classes depending on the regulators controlling their expression. In addition, we showed that oxygen availability is an important signal leading to competence development through the induction of one of the three central regulators. Our results demonstrate the complexity of competence development in S. aureus, in comparison to other historical model organisms. We anticipate our findings to be a starting point for proving the importance of natural competence and genetic transformation for S. aureus genomic plasticity. Furthermore, we also believe that our data will allow us to elucidate the environmental conditions leading to antibiotic resistance acquisitions in vivo, in this important human pathogen. Introductory paragraphStaphylococcus aureus has become over the years an important public health concern, due to a large range of infections and the emergence of outbreaks associated to antibiotic multi-resistant strains. S. aureus remarkable adaptive powers have been acquired through the acquisition of new genetic sequences, thanks to Horizontal Gene Transfer (HGT). The recent demonstration of the capacity of S. aureus to induce natural competence for genetic transformation prompted scientists to investigate this important mode of HGT in this new model organism in the field. Few key reports have already established that the development of competence in S. aureus might be complex, involving several potential master regulators, activated in response to multiple environmental signals and regulatory pathways. In this study, we deciphered, thanks to the design of an optimized protocol, the complexity of the regulatory pathways leading to the development of competence as well as its true potential for S. aureuss genomic plasticity in vivo. In addition, we clearly demonstrated that natural competence develops in response to oxygen limitation, a key environmental signal for a facultative anaerobe organism such as S. aureus.

microbiology↗