Publications by authors named "Mehul Jani"

10 Publications

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Specificity of SARS-CoV-2 Real-Time PCR Improved by Deep Learning Analysis.

J Clin Microbiol 2021 05 19;59(6). Epub 2021 May 19.

Department of Pathology, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA

Real-time PCR (RT-PCR) is widely used to diagnose human pathogens. RT-PCR data are traditionally analyzed by estimating the threshold cycle ( ) at which the fluorescence signal produced by emission of a probe crosses a baseline level. Current models used to estimate the value are based on approximations that do not adequately account for the stochastic variations of the fluorescence signal that is detected during RT-PCR. Less common deviations become more apparent as the sample size increases, as is the case in the current SARS-CoV-2 pandemic. In this work, we employ a method independent of value to interpret RT-PCR data. In this novel approach, we built and trained a deep learning model, qPCRdeepNet, to analyze the fluorescent readings obtained during RT-PCR. We describe how this model can be deployed as a quality assurance tool to monitor result interpretation in real time. The model's performance with the TaqPath COVID19 Combo Kit assay, widely used for SARS-CoV-2 detection, is described. This model can be applied broadly for the primary interpretation of RT-PCR assays and potentially replace the interpretive paradigm.
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http://dx.doi.org/10.1128/JCM.02959-20DOI Listing
May 2021

Discovery of mosaic genomic islands in Pseudomonas spp.

Arch Microbiol 2021 Jul 1;203(5):2735-2742. Epub 2021 Mar 1.

Department of Biological Sciences and BioDiscovery Institute, University of North Texas, Denton, TX, USA.

Genomic islands, defined as large clusters of genes mobilized through horizontal gene transfer, have a profound impact on evolution of prokaryotes. Recently, we developed a new program, IslandCafe, for identifying such large localized structures in bacterial genomes. A unique attribute of IslandCafe is its ability to decipher mosaic structures within genomic islands. Mosaic genomic islands have generated immense interest due to novel traits that have been attributed to such islands. To provide the Pseudomonas research community a catalogue of mosaic islands in Pseudomonas spp., we applied IslandCafe to decipher genomic islands in 224 completely sequenced genomes of Pseudomonas spp. We also performed comparative genomic analysis using BLAST to infer potential sources of distinct segments within genomic islands. Of the total 4271 genomic islands identified in Pseudomonas spp., 1036 were found to be mosaic. We also identified drug-resistant and pathogenic genomic islands and their potential donors. Our analysis provides a useful resource for Pseudomonas research community to further examine and interrogate mosaic islands in the genomes of interest and understand their role in the emergence and evolution of novel traits.
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http://dx.doi.org/10.1007/s00203-021-02253-2DOI Listing
July 2021

IslandCafe: Compositional Anomaly and Feature Enrichment Assessment for Delineation of Genomic Islands.

G3 (Bethesda) 2019 10 7;9(10):3273-3285. Epub 2019 Oct 7.

Department of Biological Sciences and BioDiscovery Institute and

One of the evolutionary forces driving bacterial genome evolution is the acquisition of clusters of genes through horizontal gene transfer (HGT). These genomic islands may confer adaptive advantages to the recipient bacteria, such as, the ability to thwart antibiotics, become virulent or hypervirulent, or acquire novel metabolic traits. Methods for detecting genomic islands either search for markers or features typical of islands or examine anomaly in oligonucleotide composition against the genome background. The former tends to underestimate, missing islands that have the markers either lost or degraded, while the latter tends to overestimate, due to their inability to discriminate compositional atypicality arising because of HGT from those that are a consequence of other biological factors. We propose here a framework that exploits the strengths of both these approaches while bypassing the pitfalls of either. Genomic islands lacking markers are identified by their association with genomic islands with markers. This was made possible by performing marker enrichment and phyletic pattern analyses within an integrated framework of recursive segmentation and clustering. The proposed method, IslandCafe, compared favorably with frequently used methods for genomic island detection on synthetic test datasets and on a test-set of known islands from 15 well-characterized bacterial species. Furthermore, IslandCafe identified novel islands with imprints of likely horizontal acquisition.
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http://dx.doi.org/10.1534/g3.119.400562DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6778810PMC
October 2019

Helicobacter pylori Mutations Detected by Next-Generation Sequencing in Formalin-Fixed, Paraffin-Embedded Gastric Biopsy Specimens Are Associated with Treatment Failure.

J Clin Microbiol 2019 07 25;57(7). Epub 2019 Jun 25.

Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA

antibiotic resistance is widespread and increasing worldwide. Routine detection of mutations that invoke antimicrobial resistance may be a useful approach to guide antimicrobial therapy and possibly avert treatment failure. In this study, formalin-fixed, paraffin-embedded (FFPE) gastric biopsy specimens from a cohort of individuals from northern Ohio in the United States were examined using a next-generation sequencing (NGS) assay to detect mutations that are known to confer resistance to clarithromycin, levofloxacin, and tetracycline. From January 2016 to January 2017, 133 -infected gastric biopsy specimens were identified histologically and subsequently analyzed by NGS to detect mutations in , 23S rRNA, and 16S rRNA genes. The method successfully detected in 126 of 133 cases (95% sensitivity). Mutations conferring resistance were present in 92 cases (73%), including 63 cases with one mutation (50%) and 29 cases with mutations in multiple genes (23%). Treatment outcomes were available in 58 cases. Sixteen of the 58 cases failed therapy (28%). Therapy failure correlated with the number of mutated genes: no failure in cases with no mutations (0/15), 19% (5/27) failure in cases with one gene mutation, and 69% (11/16) failure in cases with more than one mutated gene. Common 23S rRNA mutations (A2142G or A2413G) were present in 88% (14/16) of failed cases as opposed to in only 10% (4/42) of eradicated cases ( < 0.001). This NGS assay can be used on remnant specimens collected during standard-of-care testing to detect mutations that correlate with increased risk of treatment failure. A prospective study is needed to determine if the risk of treatment failure can be decreased by using this assay to guide antibiotic therapy.
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http://dx.doi.org/10.1128/JCM.01834-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6595463PMC
July 2019

The mechanistic role of oxidative stress in cigarette smoke-induced cardiac stem cell dysfunction and prevention by ascorbic acid.

Cell Biol Toxicol 2019 04 13;35(2):111-127. Epub 2018 Jul 13.

Department of Pharmaceutical Sciences, Sullivan University College of Pharmacy, 2100 Gardiner Lane, Louisville, KY, 40205, USA.

Cigarette smoking causes a vast array of diseases including cardiovascular diseases. Our laboratory focuses on investigating cigarette smoke (CS)-induced cardiovascular malfunction and the responsible mechanisms utilizing the model, c-kit-positive cardiac stem cells (CSCs). The main objective of our study is to investigate whether CS extracts (CSEs) cause impairment of CSC functions via oxidative damage. We hypothesized that CSE, via oxidative modifications of CSC proteins and antioxidant enzymes, can modulate CSC functions and these modifications can be attenuated by ascorbate treatment. Our specific aims are (1) to investigate CSE-induced oxidative modification of CSC proteins via carbonylation, and prevention by ascorbic acid; (2) to investigate CSE-induced oxidative modification of antioxidant enzymes and ascorbic acid-mediated modulations; and (3) to investigate CSE-induced changes in CSC functions and protection by ascorbic acid. CSCs were cultured, and the aqueous extracts of CSE were prepared. CSE-induced modulations of CSC viability, oxidative modification of proteins, and antioxidant enzyme activities were detected using standard assays including Apostain, bromodeoxyuridine, and Oxiblot. CSE caused oxidative modification of CSC proteins, changed antioxidant enzyme levels, attenuated CSC proliferation, and accelerated CSC apoptosis. Ascorbic acid prevented CSE-induced CSC malfunctions, and ascorbic acid therapy might be useful in smoker CSC recipients and to condition CSCs prior to the transplant in the future. Cardiac stem cell therapy is currently undergoing in clinical trials.
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http://dx.doi.org/10.1007/s10565-018-9437-xDOI Listing
April 2019

Deciphering pathogenicity and antibiotic resistance islands in methicillin-resistant genomes.

Open Biol 2017 12;7(12)

Department of Biological Sciences, University of North Texas, Denton, TX 76203, USA

is a versatile pathogen that is capable of causing infections in both humans and animals. It can cause furuncles, septicaemia, pneumonia and endocarditis. Adaptation of to the modern hospital environment has been facilitated, in part, by the horizontal acquisition of drug resistance genes, such as gene that imparts resistance to methicillin. Horizontal acquisitions of islands of genes harbouring virulence and antibiotic resistance genes have made resistant to commonly used antibiotics. To decipher genomic islands (GIs) in 22 hospital- and 9 community-associated methicillin-resistant strains and classify a subset of GIs carrying virulence and resistance genes as pathogenicity and resistance islands respectively, we applied a host of methods for localizing genomic islands in prokaryotic genomes. Surprisingly, of the frequently used GI prediction methods could perform well in delineating the resistance islands in the genomes. Rather, a gene clustering procedure exploiting biases in codon usage for identifying horizontally transferred genes outperformed the current methods for GI detection, in particular in identifying the known islands in including the SCC island that harbours the resistance gene. The gene clustering approach also identified novel, as yet unreported islands, with many of these found to harbour virulence and/or resistance genes. These as yet unexplored islands may provide valuable information on the evolution of drug resistance in .
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http://dx.doi.org/10.1098/rsob.170094DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5746543PMC
December 2017

Identification of Novel Genomic Islands in Liverpool Epidemic Strain of Pseudomonas aeruginosa Using Segmentation and Clustering.

Front Microbiol 2016 3;7:1210. Epub 2016 Aug 3.

Department of Biological Sciences, University of North TexasDenton, TX, USA; Department of Mathematics, University of North TexasDenton, TX, USA.

Pseudomonas aeruginosa is an opportunistic pathogen implicated in a myriad of infections and a leading pathogen responsible for mortality in patients with cystic fibrosis (CF). Horizontal transfers of genes among the microorganisms living within CF patients have led to highly virulent and multi-drug resistant strains such as the Liverpool epidemic strain of P. aeruginosa, namely the LESB58 strain that has the propensity to acquire virulence and antibiotic resistance genes. Often these genes are acquired in large clusters, referred to as "genomic islands (GIs)." To decipher GIs and understand their contributions to the evolution of virulence and antibiotic resistance in P. aeruginosa LESB58, we utilized a recursive segmentation and clustering procedure, presented here as a genome-mining tool, "GEMINI." GEMINI was validated on experimentally verified islands in the LESB58 strain before examining its potential to decipher novel islands. Of the 6062 genes in P. aeruginosa LESB58, 596 genes were identified to be resident on 20 GIs of which 12 have not been previously reported. Comparative genomics provided evidence in support of our novel predictions. Furthermore, GEMINI unraveled the mosaic structure of islands that are composed of segments of likely different evolutionary origins, and demonstrated its ability to identify potential strain biomarkers. These newly found islands likely have contributed to the hyper-virulence and multidrug resistance of the Liverpool epidemic strain of P. aeruginosa.
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http://dx.doi.org/10.3389/fmicb.2016.01210DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4971588PMC
August 2016

Rapid identification of causative insertions underlying Medicago truncatula Tnt1 mutants defective in symbiotic nitrogen fixation from a forward genetic screen by whole genome sequencing.

BMC Genomics 2016 Feb 27;17:141. Epub 2016 Feb 27.

Department of Biological Sciences, University of North Texas, 1155 Union Circle #305220, Denton, TX, 76203, USA.

Background: In the model legume Medicago truncatula, the near saturation genome-wide Tnt1 insertion mutant population in ecotype R108 is a valuable tool in functional genomics studies. Forward genetic screens have identified many Tnt1 mutants defective in nodule development and symbiotic nitrogen fixation (SNF). However, progress toward identifying the causative mutations of these symbiotic mutants has been slow because of the high copy number of Tnt1 insertions in some mutant plants and inefficient recovery of flanking sequence tags (FSTs) by thermal asymmetric interlaced PCR (TAIL-PCR) and other techniques.

Results: Two Tnt1 symbiotic mutants, NF11217 and NF10547, with defects in nodulation and SNF were isolated during a forward genetic screen. Both TAIL-PCR and whole genome sequencing (WGS) approaches were used in attempts to find the relevant mutant genes in NF11217 and NF10547. Illumina paired-end WGS generated ~16 Gb of sequence data from a 500 bp insert library for each mutant, yielding ~40X genome coverage. Bioinformatics analysis of the sequence data identified 97 and 65 high confidence independent Tnt1 insertion loci in NF11217 and NF10547, respectively. In comparison to TAIL-PCR, WGS recovered more Tnt1 insertions. From the WGS data, we found Tnt1 insertions in the exons of the previously described PHOSPHOLIPASE C (PLC)-like and NODULE INCEPTION (NIN) genes in NF11217 and NF10547 mutants, respectively. Co-segregation analyses confirmed that the symbiotic phenotypes of NF11217 and NF10547 are tightly linked to the Tnt1 insertions in PLC-like and NIN genes, respectively.

Conclusions: In this work, we demonstrate that WGS is an efficient approach for identification of causative genes underlying SNF defective phenotypes in M. truncatula Tnt1 insertion mutants obtained via forward genetic screens.
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http://dx.doi.org/10.1186/s12864-016-2452-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4769575PMC
February 2016

An Evaluation of the Effect of Therapeutic Ultrasound on Healing of Mandibular Fracture.

Craniomaxillofac Trauma Reconstr 2015 Dec 5;8(4):299-306. Epub 2015 Feb 5.

Department of Oral and Maxillofacial Surgery, College of Dental Sciences and Research Centre, Ahmedabad, Gujarat, India.

The mandible is the most frequently fractured bone in maxillofacial trauma, the treatment of which consists of reduction and fixation of dislocated fragments by open or closed approach. Innovative techniques toward reducing the period of the postoperative intermaxillary fixation (IMF) are being researched. A relatively unknown treatment that may have an effect on fracture healing is ultrasound. Recent clinical trials have shown that low-intensity pulsed ultrasound (LIPUS) has a positive effect on bone healing. The aim of this study was to evaluate the effect of LIPUS on healing by its application in fresh, minimally displaced or undisplaced mandibular fracture in young and healthy individuals. A total of 28 healthy patients were selected randomly from the outpatient department needing treatment of mandibular fractures. They were then randomly allocated to either of the following two groups-experimental group and study group. After IMF, patients in experimental group received pulsed ultrasound signals with frequency of 1 MHz, with temporal and spatial intensity of 1.5 W/cm(2), pulsed wave for 5 minutes on every alternate day for 24 days, whereas patients in control group received no therapy except IMF. Radiographic density at the fracture zone was assessed from the radiograph by Emago (Emago, Amsterdam, Netherlands) Image Analysis software before IMF then at 1st to 5th weeks post-IMF. The amount of clinical mobility between fracture fragments was assessed by digital manipulation of fractured fragment with the help of periodontal pocket depth measuring probe in millimeters at pre-IMF and after 3 weeks. Pain was objectively measured using a visual analogue scale at weekly interval. The data collected were subjected to unpaired "t" test. The experimental group showed significant improvement in radiographic density compared with control group at 3- and 5-week interval; pain perception was significantly reduced in experimental group compared with study group in the subsequent weeks. No significant difference was found in clinical mobility between fracture fragments at 3-week interval. The present study provides a basis for application of therapeutic controlled ultrasound as an effective treatment modality to accelerate healing of fresh, minimally displaced mandibular fracture.
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http://dx.doi.org/10.1055/s-0034-1544104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4812795PMC
December 2015

Comparing gray and white mineral trioxide aggregate as a repair material for furcation perforation: an in vitro dye extraction study.

J Clin Diagn Res 2014 Oct 20;8(10):ZC70-3. Epub 2014 Oct 20.

Post-Graduate Student, Department of Oral & Maxillofacial Surgery, College of Dental Sciences , Manipur, Ahmedabad, India .

Introduction: Furcation perforation can have a negative impact on the prognosis of the affected tooth by compromising the attached apparatus. Hence these perforations require immediate repair. A variety of materials have been suggested for repair, of that MTA is the most promising material. The purpose of this study was to compare the ability of Gray and White MTA to seal furcation perforations using a dye extraction method under spectrophotometer.

Materials And Methods: A total of 60 permanent mandibular molars were randomly divided into four experimental groups of 15 samples each as follows: Group A: Perforation repaired with White MTA. Group B: Perforation repaired with Gray MTA. Group C: Perforation left unsealed (positive). Group D: without perforation (negative). Dye extraction was performed using full concentration nitric acid. Dye absorbance was measured at 550 nm using spectrophotometer. The data analyzed using one-way-Anova Ratio and Unpaired t-test showing statistically significance difference among the groups.

Result: It was seen that Group D samples without perforation showed least absorbance followed by Group A (perforation repaired with White MTA) and Group B (perforation repaired with Gray MTA). Group C (perforation left unsealed) showed highest absorbance.

Conclusion: The White and Gray Mineral Trioxide Aggregate performed similarly as a furcation perforation repair material. There was no significant difference between the Gray MTA and White MTA.
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http://dx.doi.org/10.7860/JCDR/2014/9517.5046DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4253270PMC
October 2014
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