Metal nanoparticle assisted polymerase chain reaction for strain typing of Salmonella Typhi

Current Advances in Nanotechnology for the Next Generation of Sequencing (NGS)

This communication aims at discussing strategies based on developments from nanotechnology focused on the next generation of sequencing (NGS). In this regard, it should be noted that even in the advanced current situation of many techniques and methods accompanied with developments of technology, there are still existing challenges and needs focused on real samples and low concentrations of genomic materials. The approaches discussed/described adopt spectroscopical techniques and new optical setups. PCR bases are introduced to understand the role of non-covalent interactions by discussing about Nobel prizes related to genomic material detection. The review also discusses colorimetric methods, polymeric transducers, fluorescence detection methods, enhanced plasmonic techniques such as metal-enhanced fluorescence (MEF), semiconductors, and developments in metamaterials. In addition, nano-optics, challenges linked to signal transductions, and how the limitations reported in each technique could be overcome are considered in real samples. Accordingly, this study shows developments where optical active nanoplatforms generate signal detection and transduction with enhanced performances and, in many cases, enhanced signaling from single double-stranded deoxyribonucleic acid (DNA) interactions. Future perspectives on miniaturized instrumentation, chips, and devices aimed at detecting genomic material are analyzed. However, the main concept in this report derives from gained insights into nanochemistry and nano-optics. Such concepts could be incorporated into other higher-sized substrates and experimental and optical setups.

Application of Nanomaterials to Enhance Polymerase Chain Reaction

Polymerase Chain Reaction (PCR) is one of the most common technologies used to produce millions of copies of targeted nucleic acid in vitro and has become an indispensable technique in molecular biology. However, it suffers from low efficiency and specificity problems, false positive results, and so on. Although many conditions can be optimized to increase PCR yield, such as the magnesium ion concentration, the DNA polymerases, the number of cycles, and so on, they are not all-purpose and the optimization can be case dependent. Nano-sized materials offer a possible solution to improve both the quality and productivity of PCR. In the last two decades, nanoparticles (NPs) have attracted significant attention and gradually penetrated the field of life sciences because of their unique chemical and physical properties, such as their large surface area and small size effect, which have greatly promoted developments in life science and technology. Additionally, PCR technology assisted by NPs (NanoPCR) such as gold NPs (Au NPs), quantum dots (QDs), and carbon nanotubes (CNTs), etc., have been developed to significantly improve the specificity, efficiency, and sensitivity of PCR and to accelerate the PCR reaction process. This review discusses the roles of different types of NPs used to enhance PCR and summarizes their possible mechanisms.

Biosurfactants in the sustainable eradication of SARS COV-2 from the environmental surfaces

The COVID-19 outbreak has brought the world, at least, to one consensus that cleanliness is unavoidable under all circumstances. Hands are the main body part to interact with the environment and thus are prone to receive, initiate and propagate the chain of infection. Hand hygiene has, therefore, been most emphasized by experts to interrupt the spread of infection. Various harsh chemicals like synthetic surfactants and alcoholic preparations have been in practice to eradicate and disinfect the germs. This choice may be unsafe and cause a subsequent chain of adversities. Thereby, biosurfactants have been proposed as sustainable, non-toxic and safe surface cleaners cum disinfectants under a wide range of physiological and environmental conditions. The amphiphilic micellar behavior of biosurfactants makes them promising candidates as hygienic surface cleaners and therapeutic carriers. We overview the possibilities of using biosurfactants in different ways against microbial pathogens, in general, and the SARS COV-2, in specific.

Development and Preliminary Evaluation of a Nanoparticle-Assisted PCR Assay for the Detection of Cryptosporidium parvum in Calves

C. parvum is an important diarrheal pathogen in humans and animals, especially in young hosts. To accurately and rapidly detect C. parvum infection in calves, we established a nano-PCR assay targeting the cgd3_330 gene for the specific detection of C. parvum. This nano-PCR assay was ten times more sensitive than that of the normal PCR assay by applying the same primers and did not cross-react with C. andersoni, C. bovis, C. ryanae, Balantidium coli, Enterocytozoon bieneusi, Giardia lamblia, and Blastocystis sp. To further test the nano-PCR in clinical settings, a total of 20 faecal samples from calves were examined by using the nano-PCR, the normal PCR, and the nested PCR assays. The positive rates were 30% (6/20), 30% (6/20), and 25% (5/20) for the nano-PCR, the normal PCR, and the nested PCR assays, respectively, indicating that the nano-PCR and the normal PCR assays had the same positive rate (30%). Taken together, the present study could provide a candidate method for the specific detection of C. parvum infection in calves in clinical settings.

Establishment and preliminary application of nanoparticle-assisted PCR assay for detection of Cryptosporidium spp

Cryptosporidium is an important intestinal protozoan parasite that causes diarrhoea in humans and animals. To rapidly and specifically detect Cryptosporidium spp., we designed a pair of primers based on the small subunit ribosomal RNA (SSU rRNA) gene of Cryptosporidium spp. to be used in a new nanoparticle-assisted PCR (nano-PCR) assay. The minimum detectable concentration (1.02 pg) of this nano-PCR was 10 times more sensitive than conventional PCR using the same primer pair. The DNA samples of C. parvum, C. baileyi, C. xiaoi, C. ryanae, and C. andersoni were successfully detected by the nano-PCR. No amplifications were evident with DNA samples of some common intestinal pathogens, including Eimeria tenella, Blastocystis sp., Giardia lamblia, Enterocytozoon bieneusi, and Balantidium coli. To validate the clinical usefulness of the novel nano-PCR, a total of 40 faecal samples from goats, camels, calves, and chickens were examined. The positive rate of Cryptosporidium spp. was 27.5% (11/40), which was consistent with that of an established nested PCR. These results indicate that the novel nano-PCR assay enables the rapid, specific, and accurate detection of Cryptosporidium infection in animals. The findings provide a technical basis for the clinical diagnosis, prevention, and control of cryptosporidiosis.

Simultaneous Detection of Bovine Rotavirus, Bovine Parvovirus, and Bovine Viral Diarrhea Virus Using a Gold Nanoparticle-Assisted PCR Assay With a Dual-Priming Oligonucleotide System

Bovine rotavirus (BRV), bovine parvovirus (BPV), and bovine viral diarrhea virus (BVDV) are the pathogens that cause diarrhea primarily in newborn calves. A mixed infection of BRV, BPV, and BVDV makes clinical diagnosis difficult. In this study, we designed dual-priming oligonucleotide (DPO) primers the VP6 gene of BRV, VP2 gene of BPV, and 5′UTR gene of BVDV and synthesized gold nanoparticles (GNPs) with an average diameter of 10 nm. We combined the DPOs with the GNPs to develop a DPO-nanoPCR assay for detecting BRV, BPV, and BVDV. The annealing temperature, primer concentration, and GNP concentration were optimized for this assay. Compared to a conventional PCR assay, the DPO-nanoPCR assay allowed the use of a wider range of annealing temperatures (41–65°C) to effectively amplify target genes. PCR amplification was the most efficient at 56.2°C using conventional primers. The optimal volume of all the primers (10 μM) was 1.0 μL. The optimal volume of GNPs (10 nM) for all the reactions was 0.5 μL. The detection limits of DPO-nanoPCR for pMD19-T-VP6, pMD19-T-VP2, and pMD19-T-5′UTR were 9.40 × 10² copies/μL, 5.14 × 10³ copies/μL, and 4.09 × 10¹ copies/μL, respectively; and those using conventional PCR were 9.40 × 10⁴ copies/μL, 5.14 × 10⁵ copies/μL, and 4.09 × 10⁴ copies/μL, respectively. The sensitivity of DPO-nanoPCR was at least 100-fold higher than that of conventional PCR. The specificity detection showed that the DPO-nanoPCR was able to specifically detect BRV, BPV, and BVDV. Use of clinical samples indicated that target viruses can be detected accurately. Thus, DPO-nanoPCR is a new powerful, simple, specific, and sensitive tool for detecting mixed infections of BRV, BPV, and BVDV.

Quantum dots for a high-throughput Pfu polymerase based multi-round polymerase chain reaction (PCR)

We developed a Pfu polymerase based multi-round PCR technique assisted by quantum dots (QDs).

The effect of gold nanoparticles on the diagnostic polymerase chain reaction technique for equine herpes virus 1 (EHV-1)

We experimented the effect of 15 nm unmodified citrate coated GNPs on the key PCR reactants to see if these would enhance the overall outcomes of the reaction. Thus, the optimized GNPs-assisted PCR could be used for more efficient diagnosis of EHV-1.