Frequency of Fimbrial Gene Types I, Ib, and II in Clinical Strains of Porphyromonas gingivalis Characterized From Periodontitis Patients.

Objective Porphyromonas gingivalis (P. gingivalis) is considered the predominant pathogen in association with different stages of periodontitis, and fim genes play a vital role in adherence and colonization. This study is thus aimed to detect the prevalence of P. gingivalis and the frequency of fim gene types among the clinical strains isolated from periodontitis patients. Methods Plaque samples (N = 45) were collected from patients with three different stages of periodontitis (n = 15 in each group). All the samples were inoculated onto sterile anaerobic blood agar and were processed anaerobically using a GasPak system at 37°C for five to seven days. Standard microbiological techniques were used to identify P. gingivalis. Genomic DNA was extracted, and polymerase chain reaction (PCR) was carried out to detect the frequency of three fim gene types, using specific primers. Results P. gingivalis was more prevalent in Group III (93.3%), followed by 26.7% in Group II, and 13.3% in Group I. Maximum isolates were seen in the age group of 40-50, with no significance within the genders. fim type I was frequent in Group III (78.5% (n = 11)), followed by 0.25% (n = 1) under Group II, with no other fim types in the other groups.  Conclusion Prevalence of P. gingivalis and frequency of fim genes, in association with its virulence, were observed. Periodical monitoring of such virulence genes would aid in the theranostic approach to combat the complications caused by P. gingivalis in periodontitis cases.

Targeting compensatory proliferation signals in oral cancer.

Apoptosis is an orchestrated phenomenon that regulates cell populations in physiological and pathological conditions. Carcinogenesis involves a state of disequilibrium between cell proliferation and cell death. The resistance to conventional therapeutic modalities of cancer, including surgery, radiotherapy, and chemotherapy, can be explained by the compensatory repair and regeneration that occurs in the tumor microenvironment following apoptosis through the apoptotic compensatory proliferation signaling microvesicles (ACPSVs) or apoptotic extracellular microvesicles (ApoEVs). These microvesicles provide proliferative signals and act as mutagens, triggering cell proliferation, angiogenesis, immune evasion, metastasis, and invasion. This review discusses the phenomenon of apoptosis-induced proliferation and the role of ApoEVs in establishing an oncoregenerative niche, resulting in therapeutic resistance and recurrence of malignancies.

Detection of the early putative biofilm marker pgaB among the MDR strains of A.baumannii.

Background: pgaB associated biofilm formation in Acinetobacter baumannii enhances the virulence in concert with the high propensity of drug resistance. This research is thus aimed to characterize the pgaB gene molecularly and to examine its co-occurrence with MDR. Methodology: MDR strains of A. baumannii (N = 73) were selected to detect the formation of biofilms. Genomic DNA was extracted further and screened for pgaB followed by amplicon sequencing from the representative strains. Frequency of its distribution in different groups of drug resistant strains at a significant p-value of <0.05 was further checked. Results: The biofilm assay showed high, low and negative biofilm formers in 58.9%, 31.5% and 0.9% of the strains respectively. The pgaB gene was detected in 14 strains of MDR A. baumannii (19.17%). Co-occurrence of pgaB gene was seen in all the strains that showed resistance to ß-lactam inhibitors, cephems, carbapenems, fluoroquinolones and folates followed by 96% for the aminoglycosides and 25% in the efflux pump groups. Conclusion: The study findings showed the occurrence of biofilms associated with pgaB in MDR A. baumannii strains. The results also suggest to track its role in varying the pattern of drug resistance with further experimentation.

Comparative Evaluation of Bacterial Reduction by Laser-Activated Irrigation Technique (LAI) With Conventional Needle Irrigation (CNI) in Single-Rooted Teeth With Pulpal Necrosis: A Single-Blinded Randomized Controlled Trial.

Aim  To compare the bacterial reduction in single-rooted teeth with pulpal necrosis after laser-activated irrigation technique (LAI) and conventional needle irrigation (CNI). Methodology In this clinical trial (CTRI/2021/09/047767), 32 patients with pulpal necrosis were enrolled. Under complete aseptic conditions, access cavity preparation was done and the baseline sample S1 was collected from the root canal using paper points. After chemo-mechanical preparation they were allocated into two groups, following block randomization; Group A - CNI with 27 gauge side-vented needle, Group B - LAI with pulsed Er,Cr:YSGG (erbium, chromium:yttrium-scandium-gallium-garnet) (2780 nm) laser. After irrigant activation, canals were dried and a second sample S2 was taken using paper points. Microbial analysis using quantitative polymerase chain reaction (qPCR) was done to quantify the bacterial reduction among the two groups. Inter-group and intra-group analysis was done using the independent student t-test and Bonferroni test, respectively. The data was represented in terms of quantification cycle (Cq) values, which are inversely proportional to the microbial count.  Results There was no significant difference in S1 between the two groups (mean difference=0.0205; p=0.912). There was a significant difference in S2 between the two groups for the organisms (mean difference=0.8042; p=0.000). The mean percentage of bacterial reduction in CNI was 10.82% and in LAI it was 25.92%.  There was a significant difference in S1 through S2 within the two groups for the organisms (p=0.000). The mean difference of Cq value is high for LAI compared to CNI (1.3494).  The fold change was calculated by taking the ΔCq value and ΔΔCq value after the logarithmic transformation of the Cq value. LAI showed lower levels of DNA at S2 similar to CNI. There is no significant difference in mean fold change between CNI and LAI (p=0.564).  Conclusion This clinical trial concluded that both LAI and CNI were effective in bacterial reduction. There was greater bacterial reduction with LAI (25.92%) than with the CNI (10.82%) in single-rooted teeth with pulpal necrosis using qPCR analysis.

Delineating the potential targets of thymoquinone in ESKAPE pathogens using a computational approach.

The present study was designed to identify and analyze the targets of thymoquinone on drug resistant pathogens employing in silico tools. The target identification was performed using STITCH tool, followed by the functional analysis of protein targets by VICMPred. Further, VirulentPred was used to determine the nature of virulence of target proteins. The putative epitopes present on the virulent proteins were identified using BepiPred tool. The subcellular location of the virulent proteins was assessed using PSORTb. The results showed multiple targets of the pathogens being targeted. The nitric-oxide synthase-like protein of Staphylococcus aureus and acetyltransferase family protein, histone acetyltransferase HPA2, GNAT family acetyltransferase of Acinetobacter baumannii was found to be the virulent proteins interacting with thymoquinone. Molinspiration assessments showed zero violations suggesting the druggability of TQ. The study unveils the molecular mechanisms underlying the antimicrobial effect of thymoquinone as demonstrated by in silico procedures.

Molecular characterization and epitope-based vaccine predictions for ompA gene associated with biofilm formation in multidrug-resistant strains of A.baumannii.

The present study was conducted to molecularly characterize the biofilm associated ompA gene from the drug resistant strains of A. baumannii and its immuno-dominant vaccine epitope predictions through immuno-informatic approach. ompA was amplified by PCR from the genomic DNA and was sequenced. Using the ORF, ompA protein sequence was retrieved and was subjected for IEDB T cell and B cell epitope analysis for the selection of the epitope peptides. Selected peptides were evaluated using appropriate servers and tools to assess the propensity for its antigenicity, solubility, physico-chemical property, toxigenicity and class-I immunogenicity. MHC class I and II restriction of HLA alleles was also performed. 48% (n = 24) of the strains possessed ompA gene. Protein structure was successfully retrieved with the selection of two epitopes viz., E1- FDGVNRGTRGTSEEGTLGNA and E2-KLSEYPNATARIEGHTDNTGPRKL. Final docking with TLR-2, showed E2 as the best epitope candidate predicted with the highest number of hydrogen bonds.

An in silico approach towards identification of virulence factors in red complex pathogens targeted by reserpine.

Oral cavity hosts an exhaustive collection of microorganisms which are known to be associated with disease such as dental caries, periodontal and deep-seated infections. Elimination of these pathogens from the site of infection remains a perplexing task, which demands the use of antibiotics. The emergence of drug resistant forms has spurred interest into identifying novel therapeutic targets against these pathogens. In this context, the present study has been designed to analyse and identify potential drug targets of the phytocompound reserpine in red complex pathogens. Computational tools were used to identify the targets, assess its functional role and virulence property. Further, the peptide epitopes present in the virulence factors were identified using BepiPred tool. The subcellular location of the virulence proteins were also elucidated using PSORTb. Reserpine was found to target vital protein transporters such as ABC transporter and efflux pumps which are known to play a crucial role in the survival of bacterial cells. Hence the present in silico study provides substantial evidence on the anti-bacterial activity of reserpine against red complex pathogens. However, in vitro studies using the compound is warranted to further confirm the efficacy of the compound.

Genetic alterations in Wnt family of genes and their putative association with head and neck squamous cell carcinoma

Head and neck squamous cell carcinoma (HNSCC) is the most frequent type of head and neck cancer that usually arises from the mucosal surfaces of several organs including nasal cavity, paranasal sinuses, oral cavity, tongue, pharynx, and larynx. The Wnt signaling pathway is a crucial mechanism for cellular maintenance and development. It regulates cell cycle progression, apoptosis, proliferation, migration, and differentiation. Dysregulation of this pathway correlates with oncogenesis in various tissues including breast, colon, pancreatic as well as head and neck cancers. The present study aims to assess the gene alterations in the Wnt family of genes so as to derive an association with HNSCC. Computational approaches have been utilized for the identification of gene alterations in the Wnt family of genes. Several databases such as cBioportal, STRING, and UALCAN were used for the purpose. The frequency of alteration was high in case of Wnt family member 11 (5%). Gene amplification, deep deletions, missense and truncating mutations were observed in HNSCC patients. There was a marked difference in the gene expression profile of WNT11 between grades as well as normal samples. The survival probability measured using the Kaplan-Meier curve also presented with a significant difference among male and female subjects experiencing a low/medium level expression. The female patients showed less survival probability when compared to the male subjects. This provides the prognostic significance of the WNT11 gene in HNSCC. Taken together, the present study provides clues on the possible association of WNT11 gene alterations with HNSCC, which has to be further validated using experimental approaches.

Systematic review on the genetic factors associated with skeletal Class II malocclusion.

AIM: The aim of this study is to review studies evaluating the role of genetics in skeletal class II malocclusion. OBJECTIVE: To assess the scientific evidence associating the role of genes in skeletal class II malocclusion. Materials and Methods: A complete search across the electronic database through PubMed, Cochrane, LILACS, BMC and manual hand search of orthodontic journals were done till May 2019. The keywords for the search included: "Genetics", "class II malocclusion", "maxillary prognathism", "mandibular retrognathism". DATA COLLECTION AND ANALYSIS: Studies were selected based on PRISMA guidelines. RESULTS: Articles were selected based on the inclusion and exclusion criteria. A total of 11 cross-sectional studies satisfied the inclusion criteria and were analyzed for the role of genes in skeletal class II malocclusion. Almost all the studies except for one revealed a positive correlation of genes with skeletal class II malocclusion. CONCLUSIONS: Out of the 11 studies included, a positive correlation of the genes with the skeletal II malocclusion was found in 10 studies. Genes FGFR2, MSX1, MATN1, MYOH1, ACTN3, GHR, KAT6B, HDAC4, AJUBA were found to be positively linked to skeletal class II malocclusion.

Decoding The Genetic Alterations In Cytochrome P450 Family 3 Genes And Its Association With HNSCC.

INTRODUCTION: Cytochrome P450 (CYPs) are enzymes belonging to the family of heme-containing proteins, most commonly found in the endoplasmic reticulum and mitochondria. These enzymes catalyze a variety of functions including metabolism of steroids, fatty acids, natural compounds, drugs and carcinogenic chemicals. The inherent association of CYPs with disease conditions have turned the focus into the genetic alterations or variations associated with phenotypes such as drug responsiveness, chemical toxicity and bioconversion of procarcinogens to active carcinogens. RESULTS: A total of 8 genes of the CYP3 family were analyzed, among which 4 genes were found to harbour gross abnormalities and variations. The genes CYP3A4, CYP3A5, CYP3A7, CYP3A43 showed a common pattern of gene amplification in a group of patients. Truncating and missense variants were also identified of which rs199908125 of CYP3A4 and rs768530577 of CYP3A5 were reported in different populations. MATERIALS AND METHODS: The present observation study utilizes several computational tools to identify and predict the possible outcomes of gene alterations in CYP3 family of genes with head and neck squamous cell carcinoma (HNSCC). cBioportal hosts an exhaustive collection of datasets of various cancers which was the primary source of analysis. Oncoprint data obtained was further analysed using tools such as PROVEAN, I-Mutant and gnomAD. DISCUSSION: The gnomAD analysis revealed a few polymorphic rare variants with minor allele frequency less than 0.01, which could have a putative association with HNSCC. Five out of eight variants identified were found to be deleterious exhibiting decreased protein stability. CONCLUSION: Further screening of the genetic abnormalities through experimental validation in different populations are warranted to derive an association between the gene identifiers and disease phenotype.

Genetic alterations in Wnt family of genes and their putative association with head and neck squamous cell carcinoma

Head and neck squamous cell carcinoma (HNSCC) is the most frequent type of head and neck cancer that usually arises from the mucosal surfaces of several organs including nasal cavity, paranasal sinuses, oral cavity, tongue, pharynx, and larynx. The Wnt signaling pathway is a crucial mechanism for cellular maintenance and development. It regulates cell cycle progression, apoptosis, proliferation, migration, and differentiation. Dysregulation of this pathway correlates with oncogenesis in various tissues including breast, colon, pancreatic as well as head and neck cancers. The present study aims to assess the gene alterations in the Wnt family of genes so as to derive an association with HNSCC. Computational approaches have been utilized for the identification of gene alterations in the Wnt family of genes. Several databases such as cBioportal, STRING, and UALCAN were used for the purpose. The frequency of alteration was high in case of Wnt family member 11 (5%). Gene amplification, deep deletions, missense and truncating mutations were observed in HNSCC patients. There was a marked difference in the gene expression profile of WNT11 between grades as well as normal samples. The survival probability measured using the Kaplan-Meier curve also presented with a significant difference among male and female subjects experiencing a low/medium level expression. The female patients showed less survival probability when compared to the male subjects. This provides the prognostic significance of the WNT11 gene in HNSCC. Taken together, the present study provides clues on the possible association of WNT11 gene alterations with HNSCC, which has to be further validated using experimental approaches.

Prevalence of Acb and non-Acb complex in elderly population with urinary tract infection (UTI).

Background: To assess the prevalence of Acinetobacter calcoaceticus-baumannii complex [Acb complex] and non-Acb strains from the urine samples of elderly population with urinary tract infection (UTI) by both phenotypic and genotypic (PCR) characterisation methods from India.Methods: A longitudinal cohort study on 1000 elderly population with UTI was performed for a period of 1 year. Using standard microbiological guidelines, the urine samples were cultured and the Acb and non-Acb complex were identified by standard biochemical characterisation tests. DNA was extracted from all the phenons of the complex for further confirmation by PCR. The amplicons were sequenced for the phylogenetic analysis and clonal identification by comparative genomic assessments.Results and conclusions: Study population yielded 8.5% of Acb and non-Acb-complex with other gram-negative pathogens ranging from 1 to 49.3%. Males were highly affected with the complex under the age group of 70-90. Statistics of the demographic data within the groups showed significant results of the prevalence of Acb and non-Acb complex towards the age group selected and with other associated co-morbidities recorded (at p < 0.05). Chi2 statistics for the goodness of fit was significance for genotypic confirmation of the complex.Conclusions: The present investigation documents the prevalence of the Acb and non-Acb complex among the elderly population and suggests the implementation of phenotypic and molecular strategies to assess the correct prevalence rate of the same for surveillance which will also aid in the effective clinical management of UTI by Acb and non-Acb-complex in elderly population.

Decoding the Genetic Alterations in Genes of DNMT Family (DNA Methyl-Transferase) and their Association with Head and Neck Squamous Cell Carcinoma.

OBJECTIVE: Epigenetic modifications are gaining focus due to their indirect association with tumorigenesis. DNA methylation plays a prime role in regulation of gene expression. Any aberrations in this gene family may lead to chromosomal instability and increased magnitude of tumour progression. In line with the above fact, the present study has been designed to identify genetic alterations in the genes of the DNMT (DNA methyl-transferase) family among head and neck squamous cell carcinoma patients (HNSCC). METHODS: The present study follows an observational design employing computational tools for analysis. The TCGA-Firehose Legacy data was assessed using the cBioportal database. The dataset comprised of 530 samples from HNSCC patients which were assessed for genetic alterations in the DNMT family. Furthermore, the protein stability analysis and pathogenicity of the mutations were assessed using I-Mutant Suite and PROVEAN tools. RESULTS: Almost all genes of the DNMT family harboured gene amplification. The TRDMT1 and DNMT3L genes showed deep deletions. Apart from these several non-synonymous, truncating and splice-site mutations were also documented. Protein stability and pathogenicity analysis revealed that majority of the mutations were found to decrease the stability and impose pathogenicity. Upon probing for reported mutations using gnomAD database, around six reference single nucleotide polymorphisms were identified which were found to exhibit a minor allele frequency less than 0.01. CONCLUSIONS: Screening of an exhaustive collection of patient's samples could provide immense knowledge about the disease pathogenesis and identification of therapeutic leads. The variants identified in the present study could be used as diagnostic markers. However, further experimental analysis through genotyping assay is warranted to validate the present findings.
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Protein targets in the red complex organisms binding with an herbal compound silymarin.

Periodontitis is attributed to the dental biofilm formation caused by various microbial changes that occurs in the biofilm. Red complex organisms are a group of organisms linked with periodontal diseases. Therefore, it is of interest to identify potential targets from the red complex organisms to bind with the herbal compound silymarin. We report a list of potential proteins having optimal drug like binding features with the herbal agent silymarin for further consideration. We used the STITCH v.5 pipeline using VICMPred and VirulentPred tools to identify such targets as potential virulent factors in the red complex organisms. We considered the strains of Porphyromonas gingivalis ATCC 33277, Treponema denticola ATCC 35405 and Tannerella forsythia ATCC 43037 in the red complex pathogens for this analysis. Protein targets in the red complex organisms with optimal binding features with the herbal compound silymarin were thus identified and reported for further consideration.

CLSI based antibiogram profile and the detection of MDR and XDR strains of Acinetobacter baumannii isolated from urine samples.

Background: Acinetobacter baumannii is an emerging nosocomial pathogen causing serious complications due to the propensity of its multi-drug resistant property. Due to the indiscriminate and wide-spread use of antibiotics, A. baumannii strains emerge as MDR-Ab, XDR-Ab and in recent years pan-DR-Ab strains. Routine therapy incorporates the application of fewer antibiotics and antibiotic surveillance data is not monitored frequently. This study is thus an attempt to screen for the frequency of antibiotic resistance profile against different classes of antibiotics as per CLSI guidelines. Methods: Phenotypically and genotypically characterized 73 A. baumannii strains were utilized for the antibiogram profile using Group A, B, and U antibiotics as per CLSI recommendations using standard Kirby Bauer disc diffusion method. Interpretations of susceptible, intermediate and resistance were recorded by measuring zone diameter criteria. Results: Group A antibiogram profile showed highest non-susceptibility (n=73) (100%) to ampicillin-sulbactam, ceftazidime and imipenem followed by 82.19%, 79.45%, 67.12%, 56.16% and 49.31% non-susceptible isolates against ciprofloxacin, gentamicin, meropenem, tobramycin, and levofloxacin respectively. Group B antibiogram profile showed 100% non-susceptibility piperacillin-tazobactam and to amikacin, 91.78% (n=67) resistance against ceftriaxone. Among the cyclines, 19.71% and 6.84% of isolates were resistant to doxycycline and minocycline respectively. Under Group U, 76.71% showed resistance against tetracycline. The frequency of MDR (71.23%) and XDR (39.72%) A. baumannii isolates were detected. Conclusion: Periodical antibiotic surveillance is essential to curb the menace of the emergence of MDR and XDR A. baumannii in the hospital environment thus improving the patient care by the administration of alternate drug of choice or by combination therapy.