Designing mRNA- and Peptide-Based Vaccine Construct against Emerging Multidrug-Resistant Citrobacter freundii: A Computational-Based Subtractive Proteomics Approach.

Background and Objectives: Citrobacter freundii (C. freundii) is an emerging and opportunistic Gram-negative bacteria of the human gastrointestinal tract associated with nosocomial and severe respiratory tract infections. It has also been associated with pneumonia, bloodstream, and urinary tract infections. Intrinsic and adaptive virulence characteristics of C. freundii have become a significant source of diarrheal infections and food poisoning among immune-compromised patients and newborns. Impulsive usage of antibiotics and these adaptive virulence characteristics has modulated the C. freundii into multidrug-resistant (MDR) bacteria. Conventional approaches are futile against MDR C. freundii. Materials and Methods: The current study exploits the modern computational-based vaccine design approach to treat infections related to MDR C. freundii. A whole proteome of C. freundii (strain: CWH001) was retrieved to screen pathogenic and nonhomologous proteins. Six proteins were shortlisted for the selection of putative epitopes for vaccine construct. Highly antigenic, nonallergen, and nontoxic eleven B-cell, HTL, and TCL epitopes were selected for mRNA- and peptide-based multi-epitope vaccine construct. Secondary and tertiary structures of the multi-epitope vaccine (MEVC) were designed, refined, and validated. Results: Evaluation of population coverage of MHC-I and MHC-II alleles were 72% and 90%, respectively. Docking MEVC with TLR-3 receptor with the binding affinity of 21.46 (kcal/mol) occurred through the mmGBSA process. Further validations include codon optimization with an enhanced CAI value of 0.95 and GC content of about 51%. Immune stimulation and molecular dynamic simulation ensure the antibody production upon antigen interaction with the host and stability of the MEVC construct, respectively. Conclusions: These interpretations propose a new strategy to combat MDR C. freundii. Further, in vivo and in vitro trials of this vaccine will be valuable in combating MDR pathogens.

Isolated electron spins in silicon carbide with millisecond coherence times.

The elimination of defects from SiC has facilitated its move to the forefront of the optoelectronics and power-electronics industries. Nonetheless, because certain SiC defects have electronic states with sharp optical and spin transitions, they are increasingly recognized as a platform for quantum information and nanoscale sensing. Here, we show that individual electron spins in high-purity monocrystalline 4H-SiC can be isolated and coherently controlled. Bound to neutral divacancy defects, these states exhibit exceptionally long ensemble Hahn-echo spin coherence times, exceeding 1 ms. Coherent control of single spins in a material amenable to advanced growth and microfabrication techniques is an exciting route towards wafer-scale quantum technologies.

Identification of Bacterial Strains and Development of anmRNA-Based Vaccine to Combat Antibiotic Resistance in Staphylococcus aureus via In Vitro and In Silico Approaches.

The emergence of antibiotic-resistant microorganisms is a significant concern in global health. Antibiotic resistance is attributed to various virulent factors and genetic elements. This study investigated the virulence factors of Staphylococcus aureus to create an mRNA-based vaccine that could help prevent antibiotic resistance. Distinct strains of the bacteria were selected for molecular identification of virulence genes, such as spa, fmhA, lukD, and hla-D, which were performed utilizing PCR techniques. DNA extraction from samples of Staphylococcus aureus was conducted using the Cetyl Trimethyl Ammonium Bromide (CTAB) method, which was confirmed and visualized using a gel doc; 16S rRNA was utilized to identify the bacterial strains, and primers of spa, lukD, fmhA, and hla-D genes were employed to identify the specific genes. Sequencing was carried out at Applied Bioscience International (ABI) in Malaysia. Phylogenetic analysis and alignment of the strains were subsequently constructed. We also performed an in silico analysis of the spa, fmhA, lukD, and hla-D genes to generate an antigen-specific vaccine. The virulence genes were translated into proteins, and a chimera was created using various linkers. The mRNA vaccine candidate was produced utilizing 18 epitopes, linkers, and an adjuvant, known as RpfE, to target the immune system. Testing determined that this design covered 90% of the population conservancy. An in silico immunological vaccine simulation was conducted to verify the hypothesis, including validating and predicting secondary and tertiary structures and molecular dynamics simulations to evaluate the vaccine's long-term viability. This vaccine design may be further evaluated through in vivo and in vitro testing to assess its efficacy.

Molecular Insights into the Role of Pathogenic nsSNPs in GRIN2B Gene Provoking Neurodevelopmental Disorders.

The GluN2B subunit of N-methyl-D-aspartate receptors plays an important role in the physiology of different neurodevelopmental diseases. Genetic variations in the GluN2B coding gene (GRIN2B) have consistently been linked to West syndrome, intellectual impairment with focal epilepsy, developmental delay, macrocephaly, corticogenesis, brain plasticity, as well as infantile spasms and Lennox-Gastaut syndrome. It is unknown, however, how GRIN2B genetic variation impacts protein function. We determined the cumulative pathogenic impact of GRIN2B variations on healthy participants using a computational approach. We looked at all of the known mutations and calculated the impact of single nucleotide polymorphisms on GRIN2B, which encodes the GluN2B protein. The pathogenic effect, functional impact, conservation analysis, post-translation alterations, their driving residues, and dynamic behaviors of deleterious nsSNPs on protein models were then examined. Four polymorphisms were identified as phylogenetically conserved PTM drivers and were related to structural and functional impact: rs869312669 (p.Thr685Pro), rs387906636 (p.Arg682Cys), rs672601377 (p.Asn615Ile), and rs1131691702 (p.Ser526Pro). The combined impact of protein function is accounted for by the calculated stability, compactness, and total globularity score. GluN2B hydrogen occupancy was positively associated with protein stability, and solvent-accessible surface area was positively related to globularity. Furthermore, there was a link between GluN2B protein folding, movement, and function, indicating that both putative high and low local movements were linked to protein function. Multiple GRIN2B genetic variations are linked to gene expression, phylogenetic conservation, PTMs, and protein instability behavior in neurodevelopmental diseases. These findings suggest the relevance of GRIN2B genetic variations in neurodevelopmental problems.

Coherent electrical readout of defect spins in silicon carbide by photo-ionization at ambient conditions.

Quantum technology relies on proper hardware, enabling coherent quantum state control as well as efficient quantum state readout. In this regard, wide-bandgap semiconductors are an emerging material platform with scalable wafer fabrication methods, hosting several promising spin-active point defects. Conventional readout protocols for defect spins rely on fluorescence detection and are limited by a low photon collection efficiency. Here, we demonstrate a photo-electrical detection technique for electron spins of silicon vacancy ensembles in the 4H polytype of silicon carbide (SiC). Further, we show coherent spin state control, proving that this electrical readout technique enables detection of coherent spin motion. Our readout works at ambient conditions, while other electrical readout approaches are often limited to low temperatures or high magnetic fields. Considering the excellent maturity of SiC electronics with the outstanding coherence properties of SiC defects, the approach presented here holds promises for scalability of future SiC quantum devices.

High-fidelity spin and optical control of single silicon-vacancy centres in silicon carbide.

Scalable quantum networking requires quantum systems with quantum processing capabilities. Solid state spin systems with reliable spin-optical interfaces are a leading hardware in this regard. However, available systems suffer from large electron-phonon interaction or fast spin dephasing. Here, we demonstrate that the negatively charged silicon-vacancy centre in silicon carbide is immune to both drawbacks. Thanks to its 4A2 symmetry in ground and excited states, optical resonances are stable with near-Fourier-transform-limited linewidths, allowing exploitation of the spin selectivity of the optical transitions. In combination with millisecond-long spin coherence times originating from the high-purity crystal, we demonstrate high-fidelity optical initialization and coherent spin control, which we exploit to show coherent coupling to single nuclear spins with ∼1 kHz resolution. The summary of our findings makes this defect a prime candidate for realising memory-assisted quantum network applications using semiconductor-based spin-to-photon interfaces and coherently coupled nuclear spins.