Next-generation sequencing technology for the diagnosis of microbial infections in hard-to-heal wounds.

A hard-to-heal wound does not usually progress through the normal wound repair process and remains in an inflammatory state. The aetiology of a hard-to-heal wound may be varied but they are generally recurrent in patients predisposed to certain conditions, including diabetes. Hard-to-heal wounds associated with diabetic foot ulcers are a significant cause of morbidity and mortality. Microbial infections further delay the healing process, contributing to its chronicity and influence the pathogenicity of infection-causing bacteria. Traditionally, culture-based methods have been employed to study microbial communities within the hard-to-heal wound. This method underestimates or excludes most of the dominant species and is oversensitive towards others. These limitations in the culture-based methods can be overcome by advanced molecular technologies, such as next-generation sequencing (NGS), which has significantly broadened our view of the wound-associated microbiome. Sequencing of genes coding for small subunit ribosomal RNA and internal transcribed spacer locus for identification of bacteria and fungi, respectively, has provided more quantitative data in a faster, more cost-effective manner and has resulted in better microbial characterisation of wounds. In this review, we have examined in detail the NGS-based molecular characterisation of wound-associated microbes and its impact on modalities for effective treatment of hard-to-heal wound ulcers. The aim of the review was to highlight the advantages and disadvantages associated with traditional and advanced molecular technologies, such as NGS, to study the wound-associated microbiome. A full understanding of the complete diversity of the wound microbiome will help in devising effective treatment regimens for hard-to-heal wounds.

Signaling pathways promoting epithelial mesenchymal transition in oral submucous fibrosis and oral squamous cell carcinoma.

Epithelial-mesenchymal transition (EMT) is a critical process that occurs during the embryonic development, wound healing, organ fibrosis and the onset of malignancy. Emerging evidence suggests that the EMT is involved in the invasion and metastasis of cancers. The inflammatory reaction antecedent to fibrosis in the onset of oral submucous fibrosis (OSF) and the role of EMT in its malignant transformation indicates a hitherto unexplored involvement of EMT. This review focuses on the role of EMT markers which are regulators of the EMT mediated complex network of molecular mechanisms involved in the pathogenesis of OSF and OSCC. Further the gene enrichment analysis and pathway analysis supports the association of the upregulated and downregulated genes in various EMT regulating pathways.

Correction to: Simultaneous detection of periodontal pathogens in subgingival plaque and placenta of women with hypertension in pregnancy.

The original version of this article unfortunately contained a mistake. Ambika Devi K was not listed among the authors. The corrected authorship is given below.

Genetic association of KCNJ10 rs1130183 with seizure susceptibility and computational analysis of deleterious non-synonymous SNPs of KCNJ10 gene.

Establishing genetic basis of Idiopathic generalized epilepsies (IGE) is challenging because of their complex inheritance pattern and genetic heterogeneity. Kir4.1 inwardly rectifying channel (KCNJ10) is one of the independent genes reported to be associated with seizure susceptibility. In the current study we have performed a comprehensive in silico analysis of genetic variants in KCNJ10 gene at functional and structural level along with a case-control analysis for the association of rs1130183 (R271C) polymorphism in Indian patients with IGE. Age and sex matched 108 epileptic patients and normal healthy controls were examined. Genotyping of KCNJ10rs1130183 variation was performed using PCR-RFLP method. The risk association was determined by using odds ratio and 95% confidence interval. Functional effects of non-synonymous SNPs (nsSNPs) in KCNJ10 gene were analyzed using SIFT PolyPhen-2, I-Mutant 2.0, PANTHER and FASTSNP. Subsequently, homology modeling of protein three dimensional (3D) structures was performed using Modeller tool (9.10v) and compared the native protein with mutant for assessment of structure and stability. SIFT, PolyPhen-2, I-Mutant 2.0 and PANTHER collectively showed rs1130183, rs1130182 and rs137853073 SNPs inKCNJ10 gene affect protein structure and function. There was a considerable variation in the Root Mean Square Deviation (RMSD) value between the native and mutant structure (1.17Ǻ). Association analysis indicate KCNJ10rs1130183 did not contribute to risk of seizure susceptibility in Indian patients with IGE (OR- 0.38; 95%CI, 0.07-2.05) and T allele frequency (0.02%) was in concordance with dbSNP reports. This study identifies potential SNPs that may contribute to seizure susceptibility and further studies with the selected SNPs in larger number of samples and their functional analysis is required for understanding the variants of KCNJ10 with seizure susceptibility.

DNA double-strand break analysis by γ-H2AX foci: a useful method for determining the overreactors to radiation-induced acute reactions among head-and-neck cancer patients.

PURPOSE: Interindividual variability in normal tissue toxicity during radiation therapy is a limiting factor for successful treatment. Predicting the risk of developing acute reactions before initiation of radiation therapy may have the benefit of opting for altered radiation therapy regimens to achieve minimal adverse effects with improved tumor cure. METHODS AND MATERIALS: DNA double-strand break (DSB) induction and its repair kinetics in lymphocytes of head-and-neck cancer patients undergoing chemoradiation therapy was analyzed by counting γ-H2AX foci, neutral comet assay, and a modified version of neutral filter elution assay. Acute normal tissue reactions were assessed by Radiation Therapy Oncology Group criteria. RESULTS: The correlation between residual DSBs and the severity of acute reactions demonstrated that residual γ-H2AX foci in head-and-neck cancer patients increased with the severity of oral mucositis and skin reaction. CONCLUSIONS: Our results suggest that γ-H2AX analysis may have predictive implications for identifying the overreactors to mucositis and skin reactions among head-and-neck cancer patients prior to initiation of radiation therapy.

Simultaneous detection of periodontal pathogens in subgingival plaque and placenta of women with hypertension in pregnancy.

BACKGROUND: There are many studies documenting increased prevalence of periodontal infection in women with preeclampsia. But, very few studies have attempted to establish causal relationship between the two. OBJECTIVE: To find out causal circumstantial evidence by isolating specific periodontal pathogens in oral and placental samples. MATERIALS AND METHODS: Antenatal periodontal screening and subgingival plaque collection was carried out in ten women with hypertension in pregnancy and ten normotensive controls on their hospital admission at term for cesarean delivery. Placental biopsy was obtained after aseptic placental collection at the time of elective cesarean delivery. Subgingival plaque and placental biopsy were studied for Porphyromonas gingivalis, Fusobacterium nucleatum, Treponema denticola, Prevotella intermedia and Aggregatibacter actinomycetemcomitans using quantitative polymerase chain reaction technique. Periodontist and laboratory personnel were unaware of case or control status. Periodontal status was not informed to the obstetrician recruiting the cases and laboratory. Microbiology report was not revealed till end of the study. RESULTS: Periodontal pathogens were found to be high in the group with hypertension than the controls. P gingivalis was found in all the samples from subgingival plaque and placenta, irrespective of the periodontal disease status. CONCLUSION: In cases with hypertension, periodontal pathogens are present in higher proportion in subgingival plaque and placenta.