Polymerase chain reaction: A molecular diagnostic tool in periodontology

Molecular methods in cancer diagnostics: a short review

BACKGROUND

One of the ailments with the greatest fatality rates in the 21st century is cancer. Globally, molecular methods are widely employed to treat cancer-related disorders, and the body of research on this subject is growing yearly. A thorough and critical summary of the data supporting molecular methods for illnesses linked to cancer is required.

OBJECTIVE

In order to guide clinical practice and future research, it is important to examine and summarize the systematic reviews (SRs) that evaluate the efficacy and safety of molecular methods for disorders associated to cancer.

METHODS

We developed a comprehensive search strategy to find relevant articles from electronic databases like PubMed, Google Scholar, Web of Science (WoS), or Scopus. We looked through the literature and determined which diagnostic methods in cancer genetics were particularly reliable. We used phrases like 'cancer genetics', genetic susceptibility, Hereditary cancer, cancer risk assessment, 'cancer diagnostic tools', cancer screening', biomarkers, and molecular diagnostics, reviews and meta-analyses evaluating the efficacy and safety of molecular therapies for cancer-related disorders. Research that only consider treatment modalities that don't necessitate genetic or molecular diagnostics fall under the exclusion criteria.

RESULTS

The results of this comprehensive review clearly demonstrate the transformative impact of molecular methods in the realm of cancer genetics.This review underscores how these technologies have empowered researchers and clinicians to identify and understand key genetic alterations that drive malignancy, ranging from point mutations to structural variations. Such insights are instrumental in pinpointing critical oncogenic drivers and potential therapeutic targets, thus opening the door for methods in precision medicine that can significantly improve patient outcomes.

LIMITATION

The search does not specify a timeframe for publication inclusion, it may have missed recent advancements or changes in the field's landscape of molecular methods for cancer. As a result, it may not have included the most recent developments in the field.

CONCLUSION

After conducting an in-depth study on the molecular methods in cancer genetics, it is evident that these cutting-edge technologies have revolutionized the field of oncology, providing researchers and clinicians with powerful tools to unravel the complexities of cancer at the genetic level. The integration of molecular methods techniques has not only enhanced our understanding of cancer etiology, progression, and treatment response but has also opened new avenues for personalized medicine and targeted therapies, leading to improved patient outcomes.

Molecular diagnosis of human toxoplasmosis: the state of the art

Toxoplasma gondii (T. gondii) is an obligate intracellular apicomplexan protozoan that causes toxoplasmosis. Approximately one-third of the world's population is currently T. gondii-seropositive. Although most infections are symptomless, a few can produce retinal lesions and, in immunocompromised persons or when congenitally contracted, can progress to life-threatening central nervous system disseminated infections. Therefore, quick, and precise diagnosis is a must. Molecular techniques nowadays play a crucial role in toxoplasmosis diagnosis, particularly in immunocompromised patients or congenital toxoplasmosis. This review aimed to detail recent advancements in molecular diagnostics of T. gondii infections. The terms "Toxoplasmosis," "Molecular diagnostics," "PCR," "qPCR," "B1," and "rep529" were used to search the English-language literature. In developed nations, conventional PCR (PCR) and nested PCR have been supplanted by quantitative PCR (qPCR), although they are still widely employed in poor nations. The diagnosis of toxoplasmosis has been revolutionized by the emergence of molecular diagnostics. Unfortunately, there is still substantial interlaboratory variability. There is an immediate need for standardization to increase the comparability of results between laboratories and clinical trials.

Graphical abstract

A graphical abstract highlighting the summary of Toxoplasma molecular diagnostics, created using Biorender.com.

Rapid and Routine Molecular Typing Using Multiplex Polymerase Chain Reaction and MinION Sequencer

Molecular typing is an essential tool that has been extensively applied in laboratories as well as in clinical settings. Next-generation sequencing technologies promise high-throughput and cost-effective molecular applications; however, the accessibility of these technologies is limited due to the high capital cost. Oxford Nanopore Technologies (ONT) offers a MinION device with the advantages of real-time data analysis, rapid library preparation, and low cost per test. However, the advantages of the MinION device are often overshadowed by its lower raw accuracy. Herein, we present a concise multilocus sequence typing protocol of Staphylococcus aureus using multiplex polymerase chain reaction and Rapid Barcoding Kit for barcoding and MinION device for sequencing. Moreover, to clarify the effects of carryover DNA on tasks that require high sequence accuracy, we used the MinION flow cell in successive runs of washing and reusing. Our results revealed that the MinION flow cell could achieve accurate typing of a total of 467 samples with 3,269 kilobase-long genes within a total of 5 runs. This thus demonstrates the effectiveness of a portable nanopore MinION sequencer in providing accurate, rapid, and routine molecular typing.

A View on Polymerase Chain Reaction as an Outstanding Molecular Diagnostic Technique in Periodontology

Objectives

This study presents a discussion on the fundamentals of polymerase chain reaction (PCR) and its use as a diagnostic tool in periodontology.

Materials and Methods

A computer-aided as well as hand-made search in PubMed and Scopus indexed journals (relevant to the topic) was done by keywords of molecular technique in periodontology, PCR, applications of PCR, and PCR in periodontics. Only the papers in the English language and outlining PCR and its association with periodontology were collected and utilized to provide a succinct review. There was no limitation for publication time.

Results

The results of our search showed that PCR has turned into a standard in diagnosis in the field of periodontology. A variety of researches has demonstrated that its sensitive, and specific characteristics make it a quick and effective technique of recognition, identification, and quantification of microorganisms. Identification of various immunoinflammatory markers at the mRNA expression level as well as ascertaining gene-related polymorphisms can also be performed.

Conclusions

The mechanisms of periodontal disease can further become clarified using PCR. Clinical Relevance. PCR as a diagnostic method can play a main part in the validation of the clinical diagnosis of periodontal disease indicating the reason, pathogenesis, clinical steps, progress, and prognosis of the disease.

Traditional System Versus DNA Barcoding in Identification of Bamboo Species: A Systematic Review

Bamboo, a gramineous plant belonging to the family Poaceae, comprises of 1575 species from 116 genera across the globe. It has the ability to grow and evolve on degraded land and hence, can be utilized in the various applications as an alternative for plastic and wood. DNA barcoding, a long genomic sequence, identifies barcode region which shows species-specific nucleotide differences. This technology is considered as advanced molecular technique utilized for characterization and classification of the various species by applying distinctive molecular markers. Recent investigations revealed the potential application of various barcode regions such as matK, rbcL, rpoB, rpoC1, psbA-trnH, and ITS2, in identification of many bamboo species from different genus. In this review we comprehensively discussed the relevance of DNA barcoding as a tool in classification/identification of various bamboo species. We highlighted the methodology, how this advance technology overcomes the challenges associated with traditional methods along with prospects for future research.

Genotypic diversity of Streptococcus mutans in children with and without early childhood caries- A systematic review

OBJECTIVE

Genotypic diversity and polymorphism of Streptococcus mutans remain as a topic of interest, as this provides a satisfactory explanation for the contrasting caries status in people harboring Sterptococcus mutans. This systematic review aimed to analyze and appraise Genomic diversity of Streptococcus mutans and its relationship in Early Childhood Caries.

METHODS

A literature search was conducted until August 2020 using PubMed, Cochrane central, SIGLE using search keywords and MeSH headings include "Early Childhood caries", "Streptococcus mutans" and "Genotypic diversity". Apart from the aforementioned electric search, manual search was also done. The retrieved papers were assessed by three review authors and the disagreements were discussed and the final decision was made by consensus. Qualities of the included studies were assessed and data were extracted for analysis.

RESULTS

A total of 4081 papers were retrieved for screening after the removal of duplicate articles. Among the retrieved studies, 4074 papers did not satisfy the study inclusion criteria. Finally, those 7 papers which fulfilled all the inclusion criteria were selected and reviewed systematically.

CONCLUSION

Genetic polymorphism and genetic mutation exist in S.mutans strain and the missense mutation varies between children with and without Early Childhood caries. The number of genotypes of S.mutans varies between caries active and caries-free children. Due to the lack of adequate studies on gene mutations for direct comparison, further studies are needed to evaluate these gene mutation and its diversities to draw a definitive conclusion.

Comparison of Bacterial Load Parameters in Subgingival Plaque during Peri-implantitis and Periodontitis Using the RT-PCR Method

Objective

To estimate the actual parameters of bacterial load in subgingival plaque during periodontitis and peri-implantitis pathologies using the RT-PCR (real-time polymerase chain reaction) method and evaluate their associations with clinical periodontal indicators.

Materials and Methods

Five different groups of subjects were selected according to a formulated design of the study: with mild/moderate periodontitis, with severe periodontitis, with peri-implantitis, healthy periodontal group and healthy peri-implant group. Subgingival plaque samples were formed with paper points inserted in the pocket/sulcus area for 30 seconds. A standardized test the “ParodontoScreen” was provided for identification of target opportunistic pathogens (A. actinomycetemcomitans, P. gingivalis, T. forsythia, P. intermedia, T. denticola) by the RT-PCR.

Results

Bacterial load parameters demonstrated a significant tendency towards an increase within periodontitis progression and during the presence of peri-implantitis pathology. Each targeted mean bacterial load level was statistically associated with periodontitis or peri-implantitis pathology (p < 0, 05) according to the provided univariate analyses and upon condition that bacterial load parameters of healthy sites were used as reference for equiparation. The highest correlation values were found between periodontal probing depth and bacterial load parameters of A. actinomycetemcomitans (r=0, 37; p < 0, 05) and P. gingivalis (r=0, 28; p < 0, 05); and also between clinical attachment loss and bacterial load values of A. actinomycetemcomitans (r=0, 38; p < 0, 05) and P. gingivalis (r=0, 24; p < 0, 05).

Conclusions

Periodontitis and peri-implantitis are associated with the same microbial pathogens even though the distribution pattern of their bacterial load and detection frequency parameters registered with RT-PCR could be distinct and linked to the individual patient-related conditions and the severity stage of pathology.

Rapid Multiplex Real-Time PCR Method for the Detection and Quantification of Selected Cariogenic and Periodontal Bacteria

Dental caries and periodontal diseases are associated with a shift from symbiotic microbiota to dysbiosis. The aim of our study was to develop a rapid, sensitive, and economical method for the identification and quantification of selected cariogenic and periodontal oral bacteria. Original protocols were designed for three real-time multiplex PCR assays to detect and quantify the ratio of 10 bacterial species associated with dental caries (“cariogenic” complex) or periodontal diseases (red complex, orange complex, and Aggregatibacter actinomycetemcomitans). A total number of 60 samples from 30 children aged 2–6 years with severe early childhood caries and gingivitis were tested. In multiplex assays, the quantification of total bacterial (TB) content for cariogenic bacteria and red complex to eliminate differences in quantities caused by specimen collection was included. The mean counts for the TB load and that of ten evaluated specimens corresponded to previously published results. We found a significant difference between the microbial compositions obtained from the area of control and the affected teeth (p < 0.05). Based on this comprehensive microbiological examination, the risk of dental caries or periodontal inflammation may be determined. The test could also be used as a tool for behavioral intervention and thus prevention of the above-mentioned diseases.