Environmental biotechnology and the involving biological process using graphene-based biocompatible material

Biotechnology is a promising approach to environmental remediation but requires improvement in efficiency and convenience. The improvement of biotechnology has been illustrated with the help of biocompatible materials as biocarrier for environmental remediations. Recently, graphene-based materials (GBMs) have become promising materials in environmental biotechnology. To better illustrate the principle and mechanisms of GBM application in biotechnology, the comprehension of the biological response of microorganisms and enzymes when facing the GBMs is needed. The review illustrated distinct GBM-microbe/enzyme composites by providing the GBM-microbe/enzyme interaction and the determining factors. There are diverse GBM modifications for distinct biotechnology applications. Each of these methods and applications depends on the physicochemical properties of GBMs. The applications of these composites were mainly categorized as pollutant adsorption, anaerobic digestion, microbial fuel cells, and organics degradation. Where information was available, the strategies and mechanisms of GBMs in improving application efficacies were also demonstrated. In addition, the biological response, from microbial community changes, extracellular polymeric substances changes to biological pathway alteration, may become important in the application of these composites. Furthermore, we also discuss challenges facing the environmental application of GBMs, considering their fate and toxicity in the ecosystem, and offer potential solutions. This research significantly enhances our comprehension of the fundamental principles, underlying mechanisms, and biological pathways for the in-situ utilization of GBMs.

Ultrafast Real-Time PCR in Photothermal Microparticles

As the turnaround time of diagnosis becomes important, there is an increasing demand for rapid, point-of-care testing (POCT) based on polymerase chain reaction (PCR), the most reliable diagnostic tool. Although optical components in real-time PCR (qPCR) have quickly become compact and economical, conventional PCR instruments still require bulky thermal systems, making it difficult to meet emerging needs. Photonic PCR, which utilizes photothermal nanomaterials as heating elements, is a promising platform for POCT as it reduces power consumption and process time. Here, we develop a photonic qPCR platform using hydrogel microparticles. Microparticles consisting of hydrogel matrixes containing photothermal nanomaterials and primers are dubbed photothermal primer-immobilized networks (pPINs). Reduced graphene oxide is selected as the most suitable photothermal nanomaterial to generate heat in pPIN due to its superior light-to-heat conversion efficiency. The photothermal reaction volume of 100 nL (predefined by the pPIN dimensions) provides fast heating and cooling rates of 22.0 ± 3.0 and 23.5 ± 2.6 °C s^-1, respectively, enabling ultrafast qPCR within 5 min only with optical components. The microparticle-based photonic qPCR facilitates multiplex assays by loading multiple encoded pPIN microparticles in a single reaction. As a proof of concept, four-plex pPIN qPCR for bacterial discrimination are successfully demonstrated.

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.

Graphene oxide-based qRT-PCR assay enables the sensitive and specific detection of miRNAs for the screening of ovarian cancer

Circulating microRNAs (miRNAs) have the potential to become reliable and noninvasive biomarkers for ovarian cancer (OC) diagnosis; however, the conventional miRNAs detection techniques exhibit enduring limitations of low sensitivity and specificity. Graphene oxide (GO), a novel nanomaterial, is at the forefront of material design for extensive biomedical applications. Owing to the excellent water affinity and single-stranded DNA (ssDNA) adsorption characteristics of GO, we designed and developed a GO-based qRT-PCR assay for the detection of miRNAs associated with OC. In the GO-based qRT-PCR system, GO could significantly improve the sensitivity and specificity of the qRT-PCR assay by noncovalently interacting with primers and ssDNA and reducing the occurrence of non-specific amplification. Moreover, the detection of miRNAs associated with OC confirmed that GO-based qRT-PCR assay could differentiate benign ovarian tumors from OC (sensitivity, 0.91; specificity, 1.00). Collectively, these findings provide robust evidence that GO-based qRT-PCR assay can be effectively used as a promising method to detect miRNAs for the screening of OC patients.

Effects of graphene oxide on PCR amplification for microbial community survey

BACKGROUND

Graphene oxide (GO) has been suggested as an efficient assistant additive to eliminate non-specific amplification of the polymerase chain reaction (PCR). Although many studies have focused on exploring its molecular mechanism, the practice of GO on the quantitation of microbial community has not been implemented yet. In this study, GO was added in PCR system to explore the changes on removing typical amplification errors, such as chimera and mismatches on two kinds of mock communities (an evenly mixed and a staggered mock communities) and environmental samples.

RESULTS

High-throughput sequencing of bacterial and fungal communities, based on 16S rRNA genes and internal transcribed spacers (ITS) respectively, showed that GO could significantly increase large segmental error (chimeric sequence) in PCR procedure while had no specific effect on point error (mismatched sequence). Besides, GO reduced the α-diversity of community, and changed the composition of fungal community more obviously than bacterial community.

CONCLUSIONS

Our study provides the first quantitative data on microbial community level to prove the negative effect of GO, and also indicates that there may be a more complex interaction between GO and comprehensive DNA fragments in PCR process.

Graphene Quantum Dots Downregulate Multiple Multidrug-Resistant Genes via Interacting with Their C-Rich Promoters

Multidrug resistance (MDR) is the major factor in the failure of many forms of chemotherapy, mostly due to the increased efflux of anticancer drugs that mediated by ATP-binding cassette (ABC) transporters. Therefore, inhibiting ABC transporters is one of effective methods of overcoming MDR. However, high enrichment of ABC transporters in cells and their broad substrate spectra made to circumvent MDR are almost insurmountable by a single specific ABC transporter inhibitor. Here, this study demonstrates that graphene quantum dots (GQDs) could downregulate the expressions of P-glycoprotein, multidrug resistance protein MRP1, and breast cancer resistance protein genes via interacting with C-rich regions of their promoters. This is the first example that a single reagent could suppress multiple MDR genes, suggesting that it will be possible to target multiple ABC transporters simultaneously with a single reagent. The inhibitory ability of the GQDs to these drug-resistant genes is validated further by reversing the doxorubicin resistance of MCF-7/ADR cells. Notably, GQDs have superb chemical and physical properties, unique structure, low toxicity, and high biocompatibility; hence, their capability of inhibiting multiple drug-resistant genes holds great potential in cancer therapy.

Facilitation of Polymerase Chain Reaction with Poly(ethylene glycol)-Engrafted Graphene Oxide Analogous to a Single-Stranded-DNA Binding Protein

Polymerase chain reaction (PCR), a versatile DNA amplification method, is a fundamental technology in modern life sciences and molecular diagnostics. After multiple rounds of PCR, however, nonspecific DNA fragments are often produced and the amplification efficiency and fidelity decrease. Here, we demonstrated that poly(ethylene glycol)-engrafted nanosized graphene oxide (PEG-nGO) can significantly improve the PCR specificity and efficiency. PEG-nGO allows the specificity to be maintained even after multiple rounds of PCR, allowing reliable amplification at low annealing temperatures. PEG-nGO decreases the nonspecific annealing of single-stranded DNA (ssDNA), such as primer dimerization and false priming, by adsorbing excess primers. Moreover, PEG-nGO interrupts the reannealing of denatured template DNA by preferentially binding to ssDNA. Thus, PEG-nGO enhances the PCR specificity by preferentially binding to ssDNA without inhibiting DNA polymerase, which is analogous to the role of ssDNA binding proteins.