Publications by authors named "Vineet Sharma"

95 Publications

Longitudinal study of the scalp microbiome suggests coconut oil to enrich healthy scalp commensals.

Sci Rep 2021 Mar 31;11(1):7220. Epub 2021 Mar 31.

Metagenomics and Systems Biology Laboratory, Academic Building 3, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhauri, Bhopal, 462066, India.

Dandruff is a recurrent chronic scalp disorder, affecting majority of the population worldwide. Recently a metagenomic study of the Indian scalp microbiome described an imperative role of bacterial commensals in providing essential vitamins and amino acids to the scalp. Coconut oil and its formulations are commonly applied on the scalp in several parts of the world to maintain scalp health. Thus, in this study we examined the effect of topical application of coconut oil on the scalp microbiome (bacterial and fungal) at the taxonomic and functional levels and their correlation with scalp physiological parameters. A 16-weeks-long time-course study was performed including 12-weeks of treatment and 4-weeks of relapse phase on a cohort of 140 (70 healthy and 70 dandruff) Indian women, resulting in ~ 900 metagenomic samples. After the treatment phase, an increase in the abundance of Cutibacterium acnes and Malassezia globosa in dandruff scalp was observed, which were negatively correlated to dandruff parameters. At the functional level, an enrichment of healthy scalp-related bacterial pathways, such as biotin metabolism and decrease in the fungal pathogenesis pathways was observed. The study provides novel insights on the effect of coconut oil in maintaining a healthy scalp and in modulating the scalp microbiome.
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http://dx.doi.org/10.1038/s41598-021-86454-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8012655PMC
March 2021

Correlation driven topological nodal ring ferromagnetic spin gapless semimetal: CsMnF.

J Phys Condens Matter 2021 Mar 18. Epub 2021 Mar 18.

Department of Physics, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Hyderabad, Telangana, 502285, INDIA.

The observation of in-plane ferromagnetism in layered magnetic materials in conjunction with the topological nodal-ring dispersion in a spin gapless semimetal (SGS) with 100 % spin polarization has a fertile ground for novel physics, rich scientific significance and for the next-generation advanced spintronic and topological devices. Topological nodal ring spin gapless semimetals (TNRSGSM) with large band gap in the other spin channel prevents the spin leakage and are excellent spintronic materials. On the basis of density functional theory (DFT), we have studied the layered magnetic perovskite, CsMnFwhich is predicted to be a ferromagnetic insulator though the fellow compounds like AMnF(A = Na, K, Rb) are anti-ferromagnetic in nature. DFT+U calculations reveal that this layered system undergoes an insulating to half-semimetallic nature with decreasing on-site Hubbard Coulomb interaction, U. For U = 2.5 eV, we observe the topological nature in the system with the emergence of four Mexican hat like dispersions associated with band-flipping. Also, we calculated the magneto-crystalline anisotropic energy (MAE) with inclusion of spin-orbit coupling (SOC) and found that the system consists of in-plane ferromagnetism. Transport properties infer huge anisotropy of one order of magnitude between 'a' and 'c' axes. Interestingly, the estimated Fermi velocities are 2.66×10and 2.24× 10m/s for Z(=0) and Z(=0.5) plane respectively and are comparable to that of graphene, which might fetch high speed spin electronic devices. The topological phase observed is robust to spin-orbit coupling and the band-crossings associated with nodal rings could be preserved by additional symmetry as the time-reversal symmetry breaks in magnetic systems. The nearly charge compensation observed from Fermi surfaces might fetch memory device applications.
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http://dx.doi.org/10.1088/1361-648X/abeffaDOI Listing
March 2021

The genome sequence of reveals adaptive evolution of drought tolerance mechanisms.

iScience 2021 Feb 21;24(2):102079. Epub 2021 Jan 21.

MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, Madhya Pradesh, India.

is a species from Asphodelaceae family having characteristics like drought resistance and numerous medicinal properties. However, the genetic basis of these phenotypes is yet unknown primarily due to unavailability of its genome sequence. Thus, we report the first genome sequence comprising of 12.93 Gbp and harboring 86,177 protein-coding genes. It is the first genome from Asphodelaceae family and the largest angiosperm genome sequenced and assembled till date. We also report the first genome-wide phylogeny of monocots including to resolve its phylogenetic position. The comprehensive comparative analysis of with other available high-quality monocot genomes revealed adaptive evolution in several genes of drought stress response, CAM pathway, and circadian rhythm and positive selection in DNA damage response genes in . This study provides clues on the genetic basis of evolution of drought stress tolerance capabilities of .
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http://dx.doi.org/10.1016/j.isci.2021.102079DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7889978PMC
February 2021

spp.: A Review on Its Immune-Stimulatory and Other Biological Potentials.

Front Pharmacol 2020 8;11:602364. Epub 2021 Feb 8.

Research Institute of Biotechnology and Medical Converged Science, Dongguk University-Seoul, Goyangsi, South Korea.

In recent decades, interest in the genus has amplified due to its immunostimulatory potential. species, its extracts, and bioactive constituents have been related with cytokine production such as interleukin (IL)-1β, IL-2, IL-6, IL-8, IL-10, IL-12, and tumor necrosis factor (TNF)-α, phagocytosis stimulation of immune cells, nitric oxide production by increasing inducible nitric oxide synthase activity, and stimulation of inflammatory response via mitogen-activated protein kinase pathway. Other pharmacological activities like antioxidant, anti-cancer, antihyperlipidemic, anti-diabetic, anti-fatigue, anti-aging, hypocholesterolemic, hypotensive, vasorelaxation, anti-depressant, aphrodisiac, and kidney protection, has been reported in pre-clinical studies. These biological activities are correlated with the bioactive compounds present in including nucleosides, sterols, flavonoids, cyclic peptides, phenolic, bioxanthracenes, polyketides, and alkaloids, being the cyclic peptides compounds the most studied. An organized review of the existing literature was executed by surveying several databanks like PubMed, Scopus, etc. using keywords like , cordycepin, immune system, immunostimulation, immunomodulatory, pharmacology, anti-cancer, anti-viral, clinical trials, ethnomedicine, pharmacology, phytochemical analysis, and different species names. This review collects and analyzes state-of-the-art about the properties of species along with ethnopharmacological properties, application in food, chemical compounds, extraction of bioactive compounds, and various pharmacological properties with a special focus on the stimulatory properties of immunity.
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http://dx.doi.org/10.3389/fphar.2020.602364DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7898063PMC
February 2021

Pressure-Induced Enhancement of Thermoelectric Figure of Merit and Structural Phase Transition in TiNiSn.

J Phys Chem Lett 2021 Jan 20;12(3):1046-1051. Epub 2021 Jan 20.

Department of Physics, University of Nevada Las Vegas, 4505 Maryland Parkway, Las Vegas, Nevada 89054, United States.

Half-Heusler thermoelectric materials are potential candidates for high thermoelectric efficiency. We report high-pressure thermoelectric and structural property measurements, density functional theory calculations on the half-Heusler material TiNiSn, and an increase of 15% in the relative dimensionless figure of merit, ZT, around 3 GPa. Thermal and electrical properties were measured utilizing a specialized sample cell assembly designed for the Paris-Edinburgh large-volume press to a maximum pressure of 3.5 GPa. High-pressure structural measurements performed up to 50 GPa in a diamond-anvil cell indicated the emergence of a new high-pressure phase around 20 GPa. A first-principles structure search performed using an ab initio random structure search approach identified the high-pressure phase as an orthorhombic type, in good agreement with the experimental results.
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http://dx.doi.org/10.1021/acs.jpclett.0c03609DOI Listing
January 2021

SkinBug: an artificial intelligence approach to predict human skin microbiome-mediated metabolism of biotics and xenobiotics.

iScience 2021 Jan 10;24(1):101925. Epub 2020 Dec 10.

MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, Madhya Pradesh 462066, India.

In addition to being pivotal for the host health, the skin microbiome possesses a large reservoir of metabolic enzymes, which can metabolize molecules (cosmetics, medicines, pollutants, etc.) that form a major part of the skin exposome. Therefore, to predict the complete metabolism of any molecule by skin microbiome, a curated database of metabolic enzymes (1,094,153), reactions, and substrates from ∼900 bacterial species from 19 different skin sites were used to develop "SkinBug." It integrates machine learning, neural networks, and chemoinformatics methods, and displays a multiclass multilabel accuracy of up to 82.4% and binary accuracy of up to 90.0%. SkinBug predicts all possible metabolic reactions and associated enzymes, reaction centers, skin microbiome species harboring the enzyme, and the respective skin sites. Thus, SkinBug will be an indispensable tool to predict xenobiotic/biotic metabolism by skin microbiome and will find applications in exposome and microbiome studies, dermatology, and skin cancer research.
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http://dx.doi.org/10.1016/j.isci.2020.101925DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7772573PMC
January 2021

Emergency Department Well-being Initiatives During the COVID-19 Pandemic: An After-action Review.

AEM Educ Train 2020 Oct 1;4(4):411-414. Epub 2020 Jul 1.

Department of Emergency Medicine New York Presbyterian-Columbia University Vagelos College of Physicians and Surgeons New York NY USA.

The COVID-19 pandemic has significantly impacted the well-being of our health care professionals, particularly frontline providers in the emergency department (ED). Our ED, located in New York City, was severely affected, exposing the staff to a combination of unique stressors. Our ED Wellness Committee responded by implementing various initiatives focusing on the physical, mental, and social needs of our providers to support them through this difficult time. The initiatives we describe offer a framework that may help other departments understand the importance of provider well-being during a pandemic.
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http://dx.doi.org/10.1002/aet2.10490DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7592823PMC
October 2020

The Gene Catalog and Comparative Analysis of Gut Microbiome of Big Cats Provide New Insights on Species.

Front Microbiol 2020 4;11:1012. Epub 2020 Jun 4.

Metagenomics and Systems Biology Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India.

Majority of metagenomic studies in the last decade have focused on revealing the gut microbiomes of humans, rodents, and ruminants; however, the gut microbiome and genic information (gene catalog) of large felids such as species are largely unknown to date. In this study, the gut bacterial, fungal, and viral metagenomic composition was assessed from three species (lion, leopard, and tiger) of Indian origin, which were consuming the same diet and belonged to the same geographical location. A non-redundant bacterial gene catalog of the gut consisting of 1,507,035 putative genes was constructed from 27 individuals, which revealed a higher abundance of purine metabolism genes correlating with their purine-rich dietary intake. Analysis with Carbohydrate Active enZyme (CAZy) and MEROPS databases identified enrichment of glycoside hydrolases (GHs), glycoside-transferases, and collagenases in the gut, which are important for nutrient acquisition from animal biomass. The bacterial, fungal, and viral community analysis provided the first comprehensive insights into the -specific microbial community. The gene catalog and the largest comparative study of the gut bacterial composition of 68 individuals of Carnivora species from different geographical locations and diet underscore the role of diet and geography in shaping the gut microbiome, which is significant for the health and conservation management of these highly endangered species.
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http://dx.doi.org/10.3389/fmicb.2020.01012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7287027PMC
June 2020

Role of Vacha ( Linn.) in Neurological and Metabolic Disorders: Evidence from Ethnopharmacology, Phytochemistry, Pharmacology and Clinical Study.

J Clin Med 2020 Apr 19;9(4). Epub 2020 Apr 19.

Faculty of Medicine, University of Porto, Alameda Prof. Hernani Monteiro, 4200-319 Porto, Portugal.

Vacha ( Linn. (Acoraceae)) is a traditional Indian medicinal herb, which is practiced to treat a wide range of health ailments, including neurological, gastrointestinal, respiratory, metabolic, kidney, and liver disorders. The purpose of this paper is to provide a comprehensive up-to-date report on its ethnomedicinal use, phytochemistry, and pharmacotherapeutic potential, while identifying potential areas for further research. To date, 145 constituents have been isolated from this herb and identified, including phenylpropanoids, sesquiterpenoids, and monoterpenes. Compelling evidence is suggestive of the biopotential of its various extracts and active constituents in several metabolic and neurological disorders, such as anticonvulsant, antidepressant, antihypertensive, anti-inflammatory, immunomodulatory, neuroprotective, cardioprotective, and anti-obesity effects. The present extensive literature survey is expected to provide insights into the involvement of several signaling pathways and oxidative mechanisms that can mitigate oxidative stress, and other indirect mechanisms modulated by active biomolecules of to improve neurological and metabolic disorders.
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http://dx.doi.org/10.3390/jcm9041176DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7230970PMC
April 2020

Molib: A machine learning based classification tool for the prediction of biofilm inhibitory molecules.

Genomics 2020 07 27;112(4):2823-2832. Epub 2020 Mar 27.

Metagenomics and Systems Biology Laboratory, Indian Institute of Science Education and Research, Bhopal, Madhya Pradesh, India. Electronic address:

Identification of biofilm inhibitory small molecules appears promising for therapeutic intervention against biofilm-forming bacteria. However, the experimental identification of such molecules is a time-consuming task, and thus, the computational approaches emerge as promising alternatives. We developed the 'Molib' tool to predict the biofilm inhibitory activity of small molecules. We curated a training dataset of biofilm inhibitory molecules, and the structural and chemical features were used for feature selection, followed by algorithms optimization and building of machine learning-based classification models. On five-fold cross validation, Random Forest-based descriptor, fingerprint and hybrid classification models showed accuracies of 0.93, 0.88 and 0.90, respectively. The performances of all models were evaluated on two different validation datasets including biofilm inhibitory and non-inhibitory molecules, attesting to its accuracy (≥ 0.90). The Molib web server would serve as a highly useful and reliable tool for the prediction of biofilm inhibitory activity of small molecules.
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http://dx.doi.org/10.1016/j.ygeno.2020.03.020DOI Listing
July 2020

Comparative analysis of corrected tiger genome provides clues to its neuronal evolution.

Sci Rep 2019 12 5;9(1):18459. Epub 2019 Dec 5.

Metaomics and Systems Biology Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India.

The availability of completed and draft genome assemblies of tiger, leopard, and other felids provides an opportunity to gain comparative insights on their unique evolutionary adaptations. However, genome-wide comparative analyses are susceptible to errors in genome sequences and thus require accurate genome assemblies for reliable evolutionary insights. In this study, while analyzing the tiger genome, we found almost one million erroneous substitutions in the coding and non-coding region of the genome affecting 4,472 genes, hence, biasing the current understanding of tiger evolution. Moreover, these errors produced several misleading observations in previous studies. Thus, to gain insights into the tiger evolution, we corrected the erroneous bases in the genome assembly and gene set of tiger using 'SeqBug' approach developed in this study. We sequenced the first Bengal tiger genome and transcriptome from India to validate these corrections. A comprehensive evolutionary analysis was performed using 10,920 orthologs from nine mammalian species including the corrected gene sets of tiger and leopard and using five different methods at three hierarchical levels, i.e. felids, Panthera, and tiger. The unique genetic changes in tiger revealed that the genes showing signatures of adaptation in tiger were enriched in development and neuronal functioning. Specifically, the genes belonging to the Notch signalling pathway, which is among the most conserved pathways involved in embryonic and neuronal development, were found to have significantly diverged in tiger in comparison to the other mammals. Our findings suggest the role of adaptive evolution in neuronal functions and development processes, which correlates well with the presence of exceptional traits such as sensory perception, strong neuro-muscular coordination, and hypercarnivorous behaviour in tiger.
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http://dx.doi.org/10.1038/s41598-019-54838-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6895189PMC
December 2019

Comparative evaluation of torque prescription of commercially available 018Roth and 022MBT PEA brands in maxillary anterior teeth.

Med J Armed Forces India 2019 Oct 11;75(4):415-423. Epub 2018 Oct 11.

Commandant & Command Dental Adviser, CMDC (NC), India.

Background: Torque is an important component of preadjusted edgewise prescriptions to achieve ideal/optimum tooth position and more so in aesthetics sensitive maxillary anterior teeth. Thus, the need to audit available commercial brands of 018Roth and 022MBT was felt and in vitro analysis of eight brands namely 3M Unitek, Dentaurum, d-tech, IMD Medical, Libral Leone, Modern Orthodontics, Ormco and Ortho Organizer, was carried out.

Methods: The method involved perfect superimposition of two standardized images: one delineating facial axis of the tooth with stainless steel straight wire and other with full dimension arch wire engagement in bracket. The two images were superimposed and opacity of one of the images altered using Adobe Photoshop software to reveal the position of two wires. The angle obtained between two wires gave a direct read-out of torque expression. The comparison was statistically done with one-way ANOVA and Tukey's HSD test.

Results: In 018Roth group, IMD Medical did not show any significant difference from the standard while comparison independent of standard showed that IMD, Modern Orthodontics and Ormco were not significantly different from each other. In 022MBT group, IMD Medical, d-tech, 3M Unitek and Modern Orthodontics did not have statistically significant difference from and independent of standard.

Conclusion: Significant variations from the standard values of both 018 Roth and 022 MBT exist in the market products and thus selection of product must be based on proper guidance in addition to clinical acumen/experience. Also the methodology provides easy to use, inexpensive set-up in the clinical settings.
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http://dx.doi.org/10.1016/j.mjafi.2018.03.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6838513PMC
October 2019

Association of Flavonifractor plautii, a Flavonoid-Degrading Bacterium, with the Gut Microbiome of Colorectal Cancer Patients in India.

mSystems 2019 Nov 12;4(6). Epub 2019 Nov 12.

Metagenomics and Systems Biology Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India

Recently, dysbiosis in the human gut microbiome and shifts in the relative abundances of several bacterial species have been recognized as important factors in colorectal cancer (CRC). However, these studies have been carried out mainly in developed countries where CRC has a high incidence, and it is unclear whether the host-microbiome relationships deduced from these studies can be generalized to the global population. To test if the documented associations between the microbiome and CRC are conserved in a distinct context, we performed metagenomic and metabolomic association studies on fecal samples from 30 CRC patients and 30 healthy controls from two different locations in India, followed by a comparison of CRC data available from other populations. We confirmed the association of and other bacterial taxa with CRC that have been previously reported in other studies. However, the association of CRC with in Indian patients emerged as a novel finding. The plausible role of appears to be linked with the degradation of beneficial anticarcinogenic flavonoids, which was also found to be significantly correlated with the enzymes and modules involved in flavonoid degradation within Indian CRC samples. Thus, we hypothesize that the degradation of beneficial flavonoids might be playing a role in cancer progression within this Indian cohort. We also identified 20 potential microbial taxonomic markers and 33 potential microbial gene markers that discriminate the Indian CRC from healthy microbiomes with high accuracy based on machine learning approaches. This study provides novel insights on the CRC-associated microbiome of a unique cohort in India, reveals the potential role of a new bacterium in CRC, and identifies cohort-specific biomarkers, which can potentially be used in noninvasive diagnosis of CRC. The study gains additional significance, as India is among the countries with a very low incidence of CRC, and the diet and lifestyle in India have been associated with a distinct gut microbiome in healthy Indians compared to other global populations. Thus, in this study, we hypothesize a unique relationship between CRC and the gut microbiome in an Indian population.
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http://dx.doi.org/10.1128/mSystems.00438-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7407896PMC
November 2019

Rust score-An adequate rehabilitation guide for diaphyseal femur fractures managed by TENS.

J Clin Orthop Trauma 2019 Sep-Oct;10(5):922-927. Epub 2018 Jun 28.

Department of Orthopaedics, KGMU, Lucknow, 226018, U.P., India.

Introduction: The optimal mode of treatment among the wide variety of surgical and nonsurgical treatment options for children between 5 and 15 years of age continues to be controversial. Elastic stable intramedullary nailing of long bone fractures in the skeletally immature has gained widespread popularity because of its clinical effectiveness and low risk of complications.

Methods And Methodology: From Jan 2015 to August 2016, 35 patients including 37 limbs with diaphyseal fractures of the femur in the age group 5-15 years were managed by Titanium Elastic nailing and their clinico-radiological and functional outcome was assessed at 1 year post operatively as per the Flynn's criteria. RUST score was used as a guide for post-operative rehabilitation.

Results: 37 patients were managed by TENS nailing including 28 males and 9 females. The outcome in proximal, middle or distal fractures of the shaft were found to be similar and the difference was statistically insignificant. Similarly, the difference in the outcomes as per fracture patterns was also found to be statistically insignificant. Partial weight bearing was allowed after a score of 6 was achieved and full weight bearing after a score of 8.

Conclusion: As per the Flynn's criteria, 75% of the patients (28 out of 37) were found to have an excellent outcome while 7 had a satisfactory outcome and two had a poor outcome. RUST score can be used as an effective guide for post op rehabilitation.
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http://dx.doi.org/10.1016/j.jcot.2018.06.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6738353PMC
June 2018

Development and characterization of non-coding RNA based simple sequence repeat markers in Capsicum species.

Genomics 2020 03 7;112(2):1554-1564. Epub 2019 Sep 7.

Translational and Evolutionary Genomics Lab, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India; Department of Biotechnology, Delhi Technological University, Delhi 110042, India. Electronic address:

Plant growth and development are largely regulated by non-coding RNAs (ncRNA); thus ncRNA based markers would be rewarding in molecular breeding. In the present study, for the first time we developed total 623 ncRNA based SSRs including 119 microRNASSRs (miRNASSRs) and 504 long non-coding RNASSRs (lncRNASSRs) distributed across 12 Capsicum chromosomes. Out of 623 ncRNASSRs, 120 (including 60 each miRNASSRs and lncRNASSRs) were used for genotyping of 96 Capsicum accessions belonging to C. annuum, C. chinense and C. frutescens; and 75% SSRs were polymorphic. Model-based and distance-based cluster analyses identified three species specific clusters, i.e. cluster-I (C. annuum), cluster-II (C. frutescens) and cluster-III (C. chinense); therefore, these SSRs may have a potential role to play in interspecific Capsicum breeding. Tissue specific expression of SSR containing ncRNAs and versatile functions of their targets suggested the usefulness of SSRs for mapping of genes/QTLs and breeding of wide range of traits in Capsicum.
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http://dx.doi.org/10.1016/j.ygeno.2019.09.005DOI Listing
March 2020

Oto-acoustic emissions and brainstem evoked response audiometry in patients of tinnitus with normal hearing.

Int Tinnitus J 2019 01 1;23(1):17-25. Epub 2019 Jan 1.

Department of Otorhinolaryngology, Head & Neck Surgery, Shri Ram Murti Institute of Medical Sciences, Bareilly, UP, India.

Introduction: Tinnitus is defined as the perception of sound that results completely from activity within the nervous system without any corresponding mechanical, vibratory activity within the cochlea, and not related to external stimulation of any kind. It disrupts the daily life of 1 out of every 200 adults. The source of tinnitus generation is not limited to the peripheral auditory system. However, there are abnormalities seen in BERA in tinnitus patients depicting auditory pathway involvement. Oto-acoustic emissions are mechanical vibrations generated in the cochlea, which are evaluated by TEOAE and DPOAE whereas BERA evaluates both cochlea and brainstem auditory pathway for any conduction abnormalities. The aim of the study is to analyze the changes in OAE and BERA in patients suffering from tinnitus with normal hearing, which may help us to understand the patho-physiology of tinnitus.

Methods: This is a prospective study conducted in a tertiary care hospital in Northern India between 1 December 2015 to 31 July 2017. All patients of tinnitus with normal hearing were included in the study group, whereas Individuals with normal hearing with no other ear complaints were included in control group. Total 160 Ears were evaluated with 80 ears in both study and control group each. Patients with PTA >25dB, age >55 years or any chronic medical illness were excluded from the study.

Results: 80 individuals (46 Males and 34 Females) were divided into study and control Group (80 Ears each). Tinnitus was bilateral in 28 subjects (53.84%) and unilateral in 24 subjects (46.16%). Both control and study group showed significant difference in TEOAE and DPOAE study. In TEOAE, 8 (10%) ears in control group and 30 ears (37.5%) in study group showed test result as REFER whereas in DPOAE 10 (12.5%) ears in control group and 35 (43.8%) ears showed test result as REFER. All these result were statistically significant. In BERA the latency of wave I was significantly prolonged in study group as compared to control group, while difference between all other parameters between the two groups was insignificant.

Conclusions: There were various significant abnormalities seen in parameters of Oto-Acoustic Emissions (OAE) and Brainstem Evoked Response Audiometry (BERA). So these tests should be included in the test battery for the screening of patients complaining of tinnitus even with normal hearing.
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http://dx.doi.org/10.5935/0946-5448.20190004DOI Listing
January 2019

Genome-scale metabolic reconstruction and metabolic versatility of an obligate methanotroph str. Bath.

PeerJ 2019 14;7:e6685. Epub 2019 Jun 14.

Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India.

The increase in greenhouse gases with high global warming potential such as methane is a matter of concern and requires multifaceted efforts to reduce its emission and increase its mitigation from the environment. Microbes such as methanotrophs can assist in methane mitigation. To understand the metabolic capabilities of methanotrophs, a complete genome-scale metabolic model (GSMM) of an obligate methanotroph, str. Bath was reconstructed. The model contains 535 genes, 899 reactions and 865 metabolites and is named MC535. The predictive potential of the model was validated using previously-reported experimental data. The model predicted the Entner-Duodoroff pathway to be essential for the growth of this bacterium, whereas the Embden-Meyerhof-Parnas pathway was found non-essential. The performance of the model was simulated on various carbon and nitrogen sources and found that can grow on amino acids. The analysis of network topology of the model identified that six amino acids were in the top-ranked metabolic hubs. Using flux balance analysis, 29% of the metabolic genes were predicted to be essential, and 76 double knockout combinations involving 92 unique genes were predicted to be lethal. In conclusion, we have reconstructed a GSMM of a methanotroph str. Bath. This is the first high quality GSMM of a Methylococcus strain which can serve as an important resource for further strain-specific models of the Methylococcus genus, as well as identifying the biotechnological potential of Bath.
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http://dx.doi.org/10.7717/peerj.6685DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6613435PMC
June 2019

Mechanistic elucidation of amphetamine metabolism by tyramine oxidase from human gut microbiota using molecular dynamics simulations.

J Cell Biochem 2019 Jan 30. Epub 2019 Jan 30.

Department of Biological Sciences, Metagenomics and Systems Biology Laboratory, Indian Institute of Science Education and Research Bhopal, Bhopal, India.

The human gut harbors diverse bacterial species in the gut, which play an important role in the metabolism of food and host health. Recent studies have also revealed their role in altering the pharmacological properties and efficacy of oral drugs through promiscuous metabolism. However, the atomistic details of the enzyme-drug interactions of gut bacterial enzymes which can potentially carry out the metabolism of drug molecules are still scarce. A well-known example is the FDA drug amphetamine (a central nervous system stimulant), which has been predicted to undergo promiscuous metabolism by gut bacteria. Therefore, to understand the atomistic details and energy landscape of the gut microbial enzyme-mediated metabolism of this drug, molecular dynamics studies were performed. It was observed that amphetamine binds to tyramine oxidase from the Escherichia coli strain present in the human gut microbiota at the binding site harboring polar and nonpolar amino acids. The stability analysis of amphetamine at the binding site showed that the binding is stable and the free energy for the binding of amphetamine was found to be ~ -51.71 kJ/mol. The insights provided by this study on promiscuous metabolism of amphetamine by a gut enzyme will be very useful to improve the efficacy of the drug.
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http://dx.doi.org/10.1002/jcb.28396DOI Listing
January 2019

Perturbation in cellular redox homeostasis: Decisive regulator of T cell mediated immune responses.

Int Immunopharmacol 2019 Feb 27;67:449-457. Epub 2018 Dec 27.

Department of Biotechnology, Thapar University, Patiala, Punjab, India.

Cellular redox homeostasis plays a pivotal role in generation and maintenance of physiological responses. Perturbation in cellular redox status causes modulation in redox sensitive signaling pathways determining the cell fate. Depending on the extent of generation and spatio-temporal regulation of reactive oxygen species (ROS) generating oxidative stress, it can act as death stimulus or as secondary messenger. Multiple exogenous oxidants or thiol reactive compounds, endogenous oxidants such as NADPH oxidase, superoxide dismutase regulate T cell mediated immune responses. Thus, a meticulous understanding of the coordinated functioning of T cell mediated immune responses in oxidative niche is essential. The present review aims to delineate the effect of cellular redox status on T cell activation and subsequent regulation of redox sensitive immunoregulatory transcription factors such as NF-κB, NFAT and AP-1, which manifests the onset of inflammation associated disorders.
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http://dx.doi.org/10.1016/j.intimp.2018.12.049DOI Listing
February 2019

Comparison of Healthy and Dandruff Scalp Microbiome Reveals the Role of Commensals in Scalp Health.

Front Cell Infect Microbiol 2018 4;8:346. Epub 2018 Oct 4.

Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India.

Several scalp microbiome studies from different populations have revealed the association of dandruff with bacterial and fungal dysbiosis. However, the functional role of scalp microbiota in scalp disorders and health remains scarcely explored. Here, we examined the bacterial and fungal diversity of the scalp microbiome and their potential functional role in the healthy and dandruff scalp of 140 Indian women. and emerged as the core bacterial species, where the former was associated with a healthy scalp and the latter with dandruff scalp. Along with the commonly occurring species ( and ) on the scalp, a strikingly high association of dandruff with yet uncharacterized species was observed in the core mycobiome. Functional analysis showed that the fungal microbiome was enriched in pathways majorly implicated in cell-host adhesion in the dandruff scalp, while the bacterial microbiome showed a conspicuous enrichment of pathways related to the synthesis and metabolism of amino acids, biotin, and other B-vitamins, which are reported as essential nutrients for hair growth. A systematic measurement of scalp clinical and physiological parameters was also carried out, which showed significant correlations with the microbiome and their associated functional pathways. The results point toward a new potential role of bacterial commensals in maintaining the scalp nutrient homoeostasis and highlights an important and yet unknown role of the scalp microbiome, similar to the gut microbiome. This study, therefore, provides new perspectives on the better understanding of the pathophysiology of dandruff.
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http://dx.doi.org/10.3389/fcimb.2018.00346DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6180232PMC
September 2019

Genome Sequence of Peacock Reveals the Peculiar Case of a Glittering Bird.

Front Genet 2018 19;9:392. Epub 2018 Sep 19.

Metagenomics and Systems Biology Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India.

The unique ornamental features and extreme sexual traits of Peacock have always intrigued scientists and naturalists for centuries. However, the genomic basis of these phenotypes are yet unknown. Here, we report the first genome sequence and comparative analysis of peacock with the high quality genomes of chicken, turkey, duck, flycatcher and zebra finch. Genes involved in early developmental pathways including TGF-β, BMP, and Wnt signaling, which have been shown to be involved in feather patterning, bone morphogenesis, and skeletal muscle development, revealed signs of adaptive evolution and provided useful clues on the phenotypes of peacock. Innate and adaptive immune genes involved in complement system and T-cell response also showed signs of adaptive evolution in peacock suggesting their possible role in building a robust immune system which is consistent with the predictions of the Hamilton-Zuk hypothesis. This study provides novel genomic and evolutionary insights into the molecular understanding toward the phenotypic evolution of Indian peacock.
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http://dx.doi.org/10.3389/fgene.2018.00392DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6156156PMC
September 2018

Legends of Indian Orthopedics: Prof. B. N. Sinha.

Indian J Orthop 2018 Jul-Aug;52(4):443-444

Department of Orthopedics, All India Institute of Medical Sciences, New Delhi, India.

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http://dx.doi.org/10.4103/ortho.IJOrtho_333_18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6055462PMC
August 2018

Gut Microbial Dysbiosis in Indian Children with Autism Spectrum Disorders.

Microb Ecol 2018 Nov 21;76(4):1102-1114. Epub 2018 Mar 21.

Metagenomics and Systems Biology Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India.

Autism spectrum disorder (ASD) is a term associated with a group of neurodevelopmental disorders. The etiology of ASD is not yet completely understood; however, a disorder in the gut-brain axis is emerging as a prominent factor leading to autism. To identify the taxonomic composition and markers associated with ASD, we compared the fecal microbiota of 30 ASD children diagnosed using Childhood Autism Rating Scale (CARS) score, DSM-5 approved AIIMS-modified INCLEN Diagnostic Tool for Autism Spectrum Disorder (INDT-ASD), and Indian Scale for Assessment of Autism (ISAA) tool, with family-matched 24 healthy children from Indian population using next-generation sequencing (NGS) of 16S rRNA gene amplicon. Our study showed prominent dysbiosis in the gut microbiome of ASD children, with higher relative abundances of families Lactobacillaceae, Bifidobacteraceae, and Veillonellaceae, whereas the gut microbiome of healthy children was dominated by the family Prevotellaceae. Comparative meta-analysis with a publicly available dataset from the US population consisting of 20 ASD and 20 healthy control samples from children of similar age, revealed a significantly high abundance of genus Lactobacillus in ASD children from both the populations. The results reveal the microbial dysbiosis and an association of selected Lactobacillus species with the gut microbiome of ASD children.
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http://dx.doi.org/10.1007/s00248-018-1176-2DOI Listing
November 2018

Gut microbiome contributes to impairment of immunity in pulmonary tuberculosis patients by alteration of butyrate and propionate producers.

Environ Microbiol 2018 01 21;20(1):402-419. Epub 2017 Dec 21.

Department of Microbial Pathogenesis, CSIR-Institute of Genomics & Integrative Biology (IGIB), Mall Road, Delhi, India.

Tuberculosis (TB) is primarily associated with decline in immune health status. As gut microbiome (GM) is implicated in the regulation of host immunity and metabolism, here we investigate GM alteration in TB patients by 16S rRNA gene and whole-genome shotgun sequencing. The study group constituted of patients with pulmonary TB and their healthy household contacts as controls (HCs). Significant alteration of microbial taxonomic and functional capacity was observed in patients with active TB as compared to the HCs. We observed that Prevotella and Bifidobacterium abundance were associated with HCs, whereas butyrate and propionate-producing bacteria like Faecalibacterium, Roseburia, Eubacterium and Phascolarctobacterium were significantly enriched in TB patients. Functional analysis showed reduced biosynthesis of vitamins and amino acids in favour of enriched metabolism of butyrate and propionate in TB subjects. The TB subjects were also investigated during the course of treatment, to analyse the variation of GM. Although perturbation in microbial composition was still evident after a month's administration of anti-TB drugs, significant changes were observed in metagenome gene pool that pointed towards recovery in functional capacity. Therefore, the findings from this pilot study suggest that microbial dysbiosis may contribute to pathophysiology of TB by enhancing the anti-inflammatory milieu in the host.
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http://dx.doi.org/10.1111/1462-2920.14015DOI Listing
January 2018

Mechanistic and structural insight into promiscuity based metabolism of cardiac drug digoxin by gut microbial enzyme.

J Cell Biochem 2018 07 6;119(7):5287-5296. Epub 2018 Apr 6.

Metagenomics and Systems Biology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India.

The recent advances in microbiome studies have revealed the role of gut microbiota in altering the pharmacological properties of oral drugs, which contributes to patient-response variation and undesired effect of the drug molecule. These studies are essential to guide us for achieving the desired efficacy and pharmacological activity of the existing drug molecule or for discovering novel and more effective therapeutics. However, one of the main limitations is the lack of atomistic details on the binding and metabolism of these drug molecules by gut-microbial enzymes. Therefore, in this study, for a well-known and important FDA-approved cardiac glycoside drug, digoxin, we report the atomistic details and energy economics for its binding and metabolism by the Cgr2 protein of Eggerthella lenta DSM 2243. It was observed that the binding pocket of digoxin to Cgr2 primarily involved the negatively charged polar amino acids and a few non-polar hydrophobic residues. The drug digoxin was found to bind Cgr2 at the same binding site as that of fumarate, which is the proposed natural substrate. However, digoxin showed a much lower binding energy (17.75 ± 2 Kcal mol ) than the binding energy (42.17 ± 2 Kcal mol ) of fumarate. This study provides mechanistic insights into the structural and promiscuity-based metabolism of widely used cardiac drug digoxin and presents a methodology, which could be useful to confirm the promiscuity-based metabolism of other orally administrated drugs by gut microbial enzymes and also help in designing strategies for improving the efficacy of the drugs.
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http://dx.doi.org/10.1002/jcb.26638DOI Listing
July 2018

ToxiM: A Toxicity Prediction Tool for Small Molecules Developed Using Machine Learning and Chemoinformatics Approaches.

Front Pharmacol 2017 30;8:880. Epub 2017 Nov 30.

Metagenomics and Systems Biology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, India.

The experimental methods for the prediction of molecular toxicity are tedious and time-consuming tasks. Thus, the computational approaches could be used to develop alternative methods for toxicity prediction. We have developed a tool for the prediction of molecular toxicity along with the aqueous solubility and permeability of any molecule/metabolite. Using a comprehensive and curated set of toxin molecules as a training set, the different chemical and structural based features such as descriptors and fingerprints were exploited for feature selection, optimization and development of machine learning based classification and regression models. The compositional differences in the distribution of atoms were apparent between toxins and non-toxins, and hence, the molecular features were used for the classification and regression. On 10-fold cross-validation, the descriptor-based, fingerprint-based and hybrid-based classification models showed similar accuracy (93%) and Matthews's correlation coefficient (0.84). The performances of all the three models were comparable (Matthews's correlation coefficient = 0.84-0.87) on the blind dataset. In addition, the regression-based models using descriptors as input features were also compared and evaluated on the blind dataset. Random forest based regression model for the prediction of solubility performed better ( = 0.84) than the multi-linear regression (MLR) and partial least square regression (PLSR) models, whereas, the partial least squares based regression model for the prediction of permeability (caco-2) performed better ( = 0.68) in comparison to the random forest and MLR based regression models. The performance of final classification and regression models was evaluated using the two validation datasets including the known toxins and commonly used constituents of health products, which attests to its accuracy. The ToxiM web server would be a highly useful and reliable tool for the prediction of toxicity, solubility, and permeability of small molecules.
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http://dx.doi.org/10.3389/fphar.2017.00880DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5714866PMC
November 2017

IL17eScan: A Tool for the Identification of Peptides Inducing IL-17 Response.

Front Immunol 2017 31;8:1430. Epub 2017 Oct 31.

Metagenomics and Systems Biology Laboratory, Indian Institute of Science Education and Research, Bhopal, Madhya Pradesh, India.

IL-17 cytokines are pro-inflammatory cytokines and are crucial in host defense against various microbes. Induction of these cytokines by microbial antigens has been investigated in the case of ischemic brain injury, gingivitis, candidiasis, autoimmune myocarditis, etc. In this study, we have investigated the ability of amino acid sequence of antigens to induce IL-17 response using machine-learning approaches. A total of 338 IL-17-inducing and 984 IL-17 non-inducing peptides were retrieved from Immune Epitope Database. 80% of the data were randomly selected as training dataset and rest 20% as validation dataset. To predict the IL-17-inducing ability of peptides/protein antigens, different sequence-based machine-learning models were developed. The performance of support vector machine (SVM) and random forest (RF) was compared with different parameters to predict IL-17-inducing epitopes (IIEs). The dipeptide composition-based SVM-model displayed an accuracy of 82.4% with Matthews correlation coefficient = 0.62 at polynomial ( = 1) kernel on 10-fold cross-validation and outperformed RF. Amino acid residues Leu, Ser, Arg, Asn, and Phe and dipeptides LL, SL, LK, IL, LI, NL, LR, FK, SF, and LE are abundant in IIEs. The present tool helps in the identification of IIEs using machine-learning approaches. The induction of IL-17 plays an important role in several inflammatory diseases, and identification of such epitopes would be of great help to the immunologists. It is freely available at http://metagenomics.iiserb.ac.in/IL17eScan/ and http://metabiosys.iiserb.ac.in/IL17eScan/.
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http://dx.doi.org/10.3389/fimmu.2017.01430DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5671494PMC
October 2017

Impact of tetracycline on the toxic effects of titanium dioxide (TiO) nanoparticles towards the freshwater algal species, Scenedesmus obliquus.

Aquat Toxicol 2017 Dec 26;193:168-177. Epub 2017 Oct 26.

Centre for Nanobiotechnology, VIT University, Vellore, 632014, India. Electronic address:

Titanium dioxide nanoparticles (TiO NPs) are the most risk assessed nanoparticles in the aquatic environment due to their increased usage in the various sectors from electronics to consumer products. The natural aquatic system also comprises of numerous toxicants like antibiotics, whose impact on the toxicity of nanoparticles are less assessed. Hence, it is essential to determine the effect of other toxicants on the TiO NP toxicity. In the current study, the impact of antibiotic (tetracycline, TC) on the toxic effect of TiO NPs was studied on a freshwater alga, Scenedesmus obliquus. The median effective concentrations (EC) of TiO NPs and TC were noted to be 136.88±2.30μM and 0.63±0.02μM, respectively. Based on the EC obtained, three different concentrations of TC, such as 0.34, 0.68, and 1.36μM have been selected to evaluate their effect on the toxicity of 18.75, 37.5, and 75μM of TiO NPs. Existence of TC provoked the growth inhibition of TiO NPs at their lower concentrations. In contrast, a reduction in the growth inhibition was noted as the concentrations of TC and TiO NPs were increased. Abbott modeling confirmed the additive and antagonistic effects noted. The stability profile of TiO NPs elucidated the aggregation of NPs with an increase in time. Even though a similar trend has been followed for TiO NPs+TC, a significant difference in the aggregation has not been observed in most cases when compared with TiO NPs alone. The presence of TC lowered the Ti uptake by the algal cells, which portrayed the dominance of TC in the toxic effect of TiO NPs to be either additive or antagonistic. The SEM images of the algal cells upon exposure to TiO NPs, TC, and their mixture elucidated the aggregation of algal cells, cellular deformations like compromised cell membrane, and vacuole formation, etc. In addition, the release of algal exudates was also noticed as a protective layer over the cells to counteract the stress. EPS secretion in response to TiO NPs along with TC is found to be in corroboration with the toxicity patterns observed.
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http://dx.doi.org/10.1016/j.aquatox.2017.10.023DOI Listing
December 2017

Efficacy of Task Oriented Exercise Program Based on Ergonomics on Cobb's Angle and Pulmonary Function Improvement in Adolescent Idiopathic Scoliosis- A Randomized Control Trial.

J Clin Diagn Res 2017 Aug 1;11(8):YC01-YC04. Epub 2017 Aug 1.

Assistant Professor, Department of Physical Medicine and Rehabilitation, King George's Medical University, Lucknow, Uttar Pradesh, India.

Introduction: Scoliosis is lateral curvature of the spine greater than 100 accompanied by vertebral rotation. The prime risk factors for curve progression are a large curve magnitude, skeletal immaturity and female gender. The curve progression can be recorded by measuring the curve magnitude using the Cobb's method on radiographs.

Aim: To assess the effect of task oriented exercises based on ergonomics on Cobb's angle and pulmonary functions on one year outcome of Adolescent Idiopathic Scoliosis(AIS) (defined as curves < 150 for thoracolumbar region and < 200 for thoracic region).

Materials And Methods: A total of 36 patients were enrolled in the study and 18 patients in each group (experimental and control group) were allocated randomly. The subjects in control group underwent spinal strengthening exercises, active self-correction and breathing exercises, whereas subjects in the experimental group followed task oriented exercises based on ergonomics in addition to exercises for conventional group for one year. Chi square test was used to compare the categorical/ dichotomous variables between the groups. Unpaired t-test was used to compare continuous variables between the groups at pre and post intervention. Paired t-test was used to compare the changes in continuous variables from pre to post intervention within the group.

Results: Forced Vital Capacity (FVC) was found to be significantly (p=0.001) higher in experimental group (2.68±0.37) than control group (2.20±0.41) at post-intervention. Force Expritatory Volume 1 (FEV1) (p=0.01) and Vital Capacity (VC) (p=0.002) were also found to be significantly higher in experimental group compared to control group at postintervention. Also, there was significant (p=0.001) mean reduction in Cobb's angle from pre to post intervention in both the groups being higher in Experimental group than control group.

Conclusion: The task oriented exercise protocol benefited patients with AIS which had a significant improvement of their pulmonary functions and Cobb's angle.
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http://dx.doi.org/10.7860/JCDR/2017/27497.10335DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5620903PMC
August 2017

BioFuelDB: a database and prediction server of enzymes involved in biofuels production.

PeerJ 2017 28;5:e3497. Epub 2017 Aug 28.

Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, Madhya Pradesh, India.

Background: In light of the rapid decrease in fossils fuel reserves and an increasing demand for energy, novel methods are required to explore alternative biofuel production processes to alleviate these pressures. A wide variety of molecules which can either be used as biofuels or as biofuel precursors are produced using microbial enzymes. However, the common challenges in the industrial implementation of enzyme catalysis for biofuel production are the unavailability of a comprehensive biofuel enzyme resource, low efficiency of known enzymes, and limited availability of enzymes which can function under extreme conditions in the industrial processes.

Methods: We have developed a comprehensive database of known enzymes with proven or potential applications in biofuel production through text mining of PubMed abstracts and other publicly available information. A total of 131 enzymes with a role in biofuel production were identified and classified into six enzyme classes and four broad application categories namely 'Alcohol production', 'Biodiesel production', 'Fuel Cell' and 'Alternate biofuels'. A prediction tool 'Benz' was developed to identify and classify novel homologues of the known biofuel enzyme sequences from sequenced genomes and metagenomes. 'Benz' employs a hybrid approach incorporating HMMER 3.0 and RAPSearch2 programs to provide high accuracy and high speed for prediction.

Results: Using the Benz tool, 153,754 novel homologues of biofuel enzymes were identified from 23 diverse metagenomic sources. The comprehensive data of curated biofuel enzymes, their novel homologs identified from diverse metagenomes, and the hybrid prediction tool Benz are presented as a web server which can be used for the prediction of biofuel enzymes from genomic and metagenomic datasets. The database and the Benz tool is publicly available at http://metabiosys.iiserb.ac.in/biofueldb& http://metagenomics.iiserb.ac.in/biofueldb.
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http://dx.doi.org/10.7717/peerj.3497DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5578369PMC
August 2017