Displaying publications 1 - 20 of 33 in total

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  1. Chong LC, Khan AM
    BMC Genomics, 2019 Dec 24;20(Suppl 9):921.
    PMID: 31874646 DOI: 10.1186/s12864-019-6311-z
    BACKGROUND: The sequence diversity of dengue virus (DENV) is one of the challenges in developing an effective vaccine against the virus. Highly conserved, serotype-specific (HCSS), immune-relevant DENV sequences are attractive candidates for vaccine design, and represent an alternative to the approach of selecting pan-DENV conserved sequences. The former aims to limit the number of possible cross-reactive epitope variants in the population, while the latter aims to limit the cross-reactivity between the serotypes to favour a serotype-specific response. Herein, we performed a large-scale systematic study to map and characterise HCSS sequences in the DENV proteome.

    METHODS: All reported DENV protein sequence data for each serotype was retrieved from the NCBI Entrez Protein (nr) Database (txid: 12637). The downloaded sequences were then separated according to the individual serotype proteins by use of BLASTp search, and subsequently removed for duplicates and co-aligned across the serotypes. Shannon's entropy and mutual information (MI) analyses, by use of AVANA, were performed to measure the diversity within and between the serotype proteins to identify HCSS nonamers. The sequences were evaluated for the presence of promiscuous T-cell epitopes by use of NetCTLpan 1.1 and NetMHCIIpan 3.2 server for human leukocyte antigen (HLA) class I and class II supertypes, respectively. The predicted epitopes were matched to reported epitopes in the Immune Epitope Database.

    RESULTS: A total of 2321 nonamers met the HCSS selection criteria of entropy  0.8. Concatenating these resulted in a total of 337 HCSS sequences. DENV4 had the most number of HCSS nonamers; NS5, NS3 and E proteins had among the highest, with none in the C and only one in prM. The HCSS sequences were immune-relevant; 87 HCSS sequences were both reported T-cell epitopes/ligands in human and predicted epitopes, supporting the accuracy of the predictions. A number of the HCSS clustered as immunological hotspots and exhibited putative promiscuity beyond a single HLA supertype. The HCSS sequences represented, on average, ~ 40% of the proteome length for each serotype; more than double of pan-DENV sequences (conserved across the four serotypes), and thus offer a larger choice of sequences for vaccine target selection. HCSS sequences of a given serotype showed significant amino acid difference to all the variants of the other serotypes, supporting the notion of serotype-specificity.

    CONCLUSION: This work provides a catalogue of HCSS sequences in the DENV proteome, as candidates for vaccine target selection. The methodology described herein provides a framework for similar application to other pathogens.

  2. Lim WC, Khan AM
    BMC Genomics, 2018 01 19;19(Suppl 1):42.
    PMID: 29363421 DOI: 10.1186/s12864-017-4328-8
    BACKGROUND: Ebolavirus (EBOV) is responsible for one of the most fatal diseases encountered by mankind. Cellular T-cell responses have been implicated to be important in providing protection against the virus. Antigenic variation can result in viral escape from immune recognition. Mapping targets of immune responses among the sequence of viral proteins is, thus, an important first step towards understanding the immune responses to viral variants and can aid in the identification of vaccine targets. Herein, we performed a large-scale, proteome-wide mapping and diversity analyses of putative HLA supertype-restricted T-cell epitopes of Zaire ebolavirus (ZEBOV), the most pathogenic species among the EBOV family.

    METHODS: All publicly available ZEBOV sequences (14,098) for each of the nine viral proteins were retrieved, removed of irrelevant and duplicate sequences, and aligned. The overall proteome diversity of the non-redundant sequences was studied by use of Shannon's entropy. The sequences were predicted, by use of the NetCTLpan server, for HLA-A2, -A3, and -B7 supertype-restricted epitopes, which are relevant to African and other ethnicities and provide for large (~86%) population coverage. The predicted epitopes were mapped to the alignment of each protein for analyses of antigenic sequence diversity and relevance to structure and function. The putative epitopes were validated by comparison with experimentally confirmed epitopes.

    RESULTS & DISCUSSION: ZEBOV proteome was generally conserved, with an average entropy of 0.16. The 185 HLA supertype-restricted T-cell epitopes predicted (82 (A2), 37 (A3) and 66 (B7)) mapped to 125 alignment positions and covered ~24% of the proteome length. Many of the epitopes showed a propensity to co-localize at select positions of the alignment. Thirty (30) of the mapped positions were completely conserved and may be attractive for vaccine design. The remaining (95) positions had one or more epitopes, with or without non-epitope variants. A significant number (24) of the putative epitopes matched reported experimentally validated HLA ligands/T-cell epitopes of A2, A3 and/or B7 supertype representative allele restrictions. The epitopes generally corresponded to functional motifs/domains and there was no correlation to localization on the protein 3D structure. These data and the epitope map provide important insights into the interaction between EBOV and the host immune system.

  3. Mahmud MR, Khan AM, Nadol JB
    Ann Otol Rhinol Laryngol, 2003 Nov;112(11):979-86.
    PMID: 14653368
    Although hearing loss is the most common presenting symptom in patients with acoustic neuroma, the pathophysiology of hearing loss associated with acoustic neuroma is unknown. Although primary dysfunction of the auditory nerve is intuitively logical, available histopathologic and clinical data suggest that although neural degeneration is common, it alone does not adequately account for hearing loss in many cases. The purpose of this study was to evaluate 11 cases of unoperated unilateral acoustic neuromas. Temporal bones were identified by means of a search mechanism provided by the National Temporal Bone, Hearing, and Balance Pathology Resource Registry and were prepared for light microscopy by standard techniques. Quantification of spiral ganglion cells, hair cells, stria vascularis, and spiral ligament was accomplished for each specimen. In addition, the maximum diameter and volume of each tumor were calculated from histopathologic sections. Increasing tumor size did predict a reduced spiral ganglion count. However, although there was a tendency for decreasing spiral ganglion cell count and for increasing tumor size to predict a higher pure tone average and lower speech discrimination score, these correlations did not reach statistical significance. In tumor ears in which the speech discrimination score was 50% or less, there was always significant degeneration of other structures of the inner ear in addition to neurons, including hair cells, the stria vascularis, and the spiral ligament. Endolymphatic hydrops and eosinophilic precipitate in the perilymphatic spaces were found in 2 of 3 such cases. It is concluded that acoustic neuromas appear to cause hearing loss, not only by causing degeneration of the auditory nerve, but also by inducing degenerative changes in the inner ear. It is hypothesized that the proteinaceous material seen histologically may represent the products of up-regulated genes in acoustic neuroma, some of which may interfere with normal cochlear function.
  4. Patro CP, Khan AM, Tan TW, Fu XY
    PLoS One, 2014;9(8):e104597.
    PMID: 25157689 DOI: 10.1371/journal.pone.0104597
    Signal transducers and activators of transcription (STAT) proteins are key signalling molecules in metazoans, implicated in various cellular processes. Increased research in the field has resulted in the accumulation of STAT sequence and structure data, which are scattered across various public databases, missing extensive functional annotations, and prone to effort redundancy because of the dearth of community sharing. Therefore, there is a need to integrate the existing sequence, structure and functional data into a central repository, one that is enriched with annotations and provides a platform for community contributions. Herein, we present STATdb (publicly available at http://statdb.bic.nus.edu.sg/), the first integrated resource for STAT sequences comprising 1540 records representing the known STATome, enriched with existing structural and functional information from various databases and literature and including manual annotations. STATdb provides advanced features for data visualization, analysis and prediction, and community contributions. A key feature is a meta-predictor to characterise STAT sequences based on a novel classification that integrates STAT domain architecture, lineage and function. A curation policy workflow has been devised for regulated and structured community contributions, with an update policy for the seamless integration of new data and annotations.
  5. James SA, Ong HS, Hari R, Khan AM
    BMC Genomics, 2021 Sep 28;22(Suppl 3):700.
    PMID: 34583643 DOI: 10.1186/s12864-021-07657-4
    BACKGROUND: Biology has entered the era of big data with the advent of high-throughput omics technologies. Biological databases provide public access to petabytes of data and information facilitating knowledge discovery. Over the years, sequence data of pathogens has seen a large increase in the number of records, given the relatively small genome size and their important role as infectious and symbiotic agents. Humans are host to numerous pathogenic diseases, such as that by viruses, many of which are responsible for high mortality and morbidity. The interaction between pathogens and humans over the evolutionary history has resulted in sharing of sequences, with important biological and evolutionary implications.

    RESULTS: This study describes a large-scale, systematic bioinformatics approach for identification and characterization of shared sequences between the host and pathogen. An application of the approach is demonstrated through identification and characterization of the Flaviviridae-human share-ome. A total of 2430 nonamers represented the Flaviviridae-human share-ome with 100% identity. Although the share-ome represented a small fraction of the repertoire of Flaviviridae (~ 0.12%) and human (~ 0.013%) non-redundant nonamers, the 2430 shared nonamers mapped to 16,946 Flaviviridae and 7506 human non-redundant protein sequences. The shared nonamer sequences mapped to 125 species of Flaviviridae, including several with unclassified genus. The majority (~ 68%) of the shared sequences mapped to Hepacivirus C species; West Nile, dengue and Zika viruses of the Flavivirus genus accounted for ~ 11%, ~ 7%, and ~ 3%, respectively, of the Flaviviridae protein sequences (16,946) mapped by the share-ome. Further characterization of the share-ome provided important structural-functional insights to Flaviviridae-human interactions.

    CONCLUSION: Mapping of the host-pathogen share-ome has important implications for the design of vaccines and drugs, diagnostics, disease surveillance and the discovery of unknown, potential host-pathogen interactions. The generic workflow presented herein is potentially applicable to a variety of pathogens, such as of viral, bacterial or parasitic origin.

  6. Abd Raman HS, Tan S, August JT, Khan AM
    PeerJ, 2020;7:e7954.
    PMID: 32518710 DOI: 10.7717/peerj.7954
    Background: Influenza A (H5N1) virus is a global concern with potential as a pandemic threat. High sequence variability of influenza A viruses is a major challenge for effective vaccine design. A continuing goal towards this is a greater understanding of influenza A (H5N1) proteome sequence diversity in the context of the immune system (antigenic diversity), the dynamics of mutation, and effective strategies to overcome the diversity for vaccine design.

    Methods: Herein, we report a comprehensive study of the dynamics of H5N1 mutations by analysis of the aligned overlapping nonamer positions (1-9, 2-10, etc.) of more than 13,000 protein sequences of avian and human influenza A (H5N1) viruses, reported over at least 50 years. Entropy calculations were performed on 9,408 overlapping nonamer position of the proteome to study the diversity in the context of immune system. The nonamers represent the predominant length of the binding cores for peptides recognized by the cellular immune system. To further dissect the sequence diversity, each overlapping nonamer position was quantitatively analyzed for four patterns of sequence diversity motifs: index, major, minor and unique.

    Results: Almost all of the aligned overlapping nonamer positions of each viral proteome exhibited variants (major, minor, and unique) to the predominant index sequence. Each variant motif displayed a characteristic pattern of incidence change in relation to increased total variants. The major variant exhibited a restrictive pyramidal incidence pattern, with peak incidence at 50% total variants. Post this peak incidence, the minor variants became the predominant motif for majority of the positions. Unique variants, each sequence observed only once, were present at nearly all of the nonamer positions. The diversity motifs (index and variants) demonstrated complex inter-relationships, with motif switching being a common phenomenon. Additionally, 25 highly conserved sequences were identified to be shared across viruses of both hosts, with half conserved to several other influenza A subtypes.

    Discussion: The presence of distinct sequences (nonatypes) at nearly all nonamer positions represents a large repertoire of reported viral variants in the proteome, which influence the variability dynamics of the viral population. This work elucidated and provided important insights on the components that make up the viral diversity, delineating inherent patterns in the organization of sequence changes that function in the viral fitness-selection. Additionally, it provides a catalogue of all the mutational changes involved in the dynamics of H5N1 viral diversity for both avian and human host populations. This work provides data relevant for the design of prophylactics and therapeutics that overcome the diversity of the virus, and can aid in the surveillance of existing and future strains of influenza viruses.

  7. Khan AM, Bakar NKA, Bakar AFA, Ashraf MA
    Environ Sci Pollut Res Int, 2017 Oct;24(29):22764-22789.
    PMID: 27722986 DOI: 10.1007/s11356-016-7427-1
    Rare earths (RE), chemically uniform group of elements due to similar physicochemical behavior, are termed as lanthanides. Natural occurrence depends on the geological circumstances and has been of long interest for geologist as tools for further scientific research into the region of ores, rocks, and oceanic water. The review paper mainly focuses to provide scientific literature about rare earth elements (REEs) with potential environmental and health effects in understanding the research. This is the initial review of RE speciation and bioavailability with current initiative toward development needs and research perceptive. In this paper, we have also discussed mineralogy, extraction, geochemistry, analytical methods of rare earth elements. In this study, REEs with their transformation and vertical distribution in different environments such as fresh and seawater, sediments, soil, weathering, transport, and solubility have been reported with most recent literature along key methods of findings. Speciation and bioavailability have been discussed in detail with special emphasis on soil, plant, and aquatic ecosystems and their impacts on the environment. This review shows that REE gained more importance in last few years due to their detrimental effects on living organisms, so their speciation, bioavailability, and composition are much more important to evaluate their health risks and are discussed thoroughly as well.
  8. Ashraf MA, Khan AM, Ahmad M, Sarfraz M
    Front Chem, 2015;3:42.
    PMID: 26322304 DOI: 10.3389/fchem.2015.00042
    Microencapsulation has become a hot topic in chemical research. Technology mainly used for control release and protection purposes. The sol-gel micro encapsulation approach for fragrance and aroma in porous silica-based materials leads to sustainable odorant and flavored materials with novel and unique beneficial properties. Sol-gel encapsulation of silica based micro particles considered economically cheap as capital investment in manufacturing is very low and environmentally friendly. Amorphous sol-gel SiO2 is non-toxic and safe, whereas the sol-gel entrapment of delicate chemicals in its inner pores results in pronounced chemical and physical stabilization of the entrapped active agents, thereby broadening the practical utilization of chemically unstable essential oils (EOs). Reviewing progress in the fabrication of diverse odorant and flavored sol-gels, shows us how different synthetic strategies are appropriate for practical application with important health and environmental benefits.
  9. Ashraf MA, Khan AM, Ahmad M, Akib S, Balkhair KS, Bakar NK
    Environ Geochem Health, 2014 12;36(6):1165-90.
    PMID: 24804829 DOI: 10.1007/s10653-014-9620-9
    Radionuclide contamination in terrestrial ecosystems has reached a dangerous level. The major artificial radionuclide present in the environment is (137)Cs, which is released as a result of weapon production related to atomic projects, accidental explosions of nuclear power plants and other sources, such as reactors, evaporation ponds, liquid storage tanks, and burial grounds. The release of potentially hazardous radionuclides (radiocesium) in recent years has provided the opportunity to conduct multidisciplinary studies on their fate and transport. Radiocesium's high fission yield and ease of detection made it a prime candidate for early radio-ecological investigations. The facility setting provides a diverse background for the improved understanding of various factors that contribute toward the fate and transfer of radionuclides in the terrestrial ecosystem. In this review, we summarize the significant environmental radiocesium transfer factors to determine the damaging effects of radiocesium on terrestrial ecosystem. It has been found that (137)Cs can trace the transport of other radionuclides that have a high affinity for binding to soil particles (silts and clays). Possible remedial methods are also discussed for contaminated terrestrial systems. This review will serve as a guideline for future studies of the fate and transport of (137)Cs in terrestrial environments in the wake of the Fukushima Nuclear Power Plant disaster in 2011.
  10. Hu Y, Tan PT, Tan TW, August JT, Khan AM
    PLoS One, 2013;8(4):e59994.
    PMID: 23593157 DOI: 10.1371/journal.pone.0059994
    The rapid mutation of human immunodeficiency virus-type 1 (HIV-1) and the limited characterization of the composition and incidence of the variant population are major obstacles to the development of an effective HIV-1 vaccine. This issue was addressed by a comprehensive analysis of over 58,000 clade B HIV-1 protein sequences reported over at least 26 years. The sequences were aligned and the 2,874 overlapping nonamer amino acid positions of the viral proteome, each a possible core binding domain for human leukocyte antigen molecules and T-cell receptors, were quantitatively analyzed for four patterns of sequence motifs: (1) "index", the most prevalent sequence; (2) "major" variant, the most common variant sequence; (3) "minor" variants, multiple different sequences, each with an incidence less than that of the major variant; and (4) "unique" variants, each observed only once in the alignment. The collective incidence of the major, minor, and unique variants at each nonamer position represented the total variant population for the position. Positions with more than 50% total variants contained correspondingly reduced incidences of index and major variant sequences and increased minor and unique variants. Highly diverse positions, with 80 to 98% variant nonamer sequences, were present in each protein, including 5% of Gag, and 27% of Env and Nef, each. The multitude of different variant nonamer sequences (i.e. nonatypes; up to 68%) at the highly diverse positions, represented by the major, multiple minor, and multiple unique variants likely supported variants function both in immune escape and as altered peptide ligands with deleterious T-cell responses. The patterns of mutational change were consistent with the sequences of individual HXB2 and C1P viruses and can be considered applicable to all HIV-1 viruses. This characterization of HIV-1 protein mutation provides a foundation for the design of peptide-based vaccines and therapeutics.
  11. Wani AA, Khan AM, Manea YK, Salem MAS, Shahadat M
    J Hazard Mater, 2021 08 15;416:125754.
    PMID: 33813294 DOI: 10.1016/j.jhazmat.2021.125754
    Neodymium-doped polyaniline supported Zn-Al layered double hydroxide (PANI@Nd-LDH) nanocomposite has been prepared via an ex-situ oxidative polymerization process. The as-prepared nanocomposite shows selective fluorescence detection and adsorption of hexavalent chromium Cr(VI) within a short period. The fluorescence intensity of PANI@Nd-LDH decreases linearly with Cr(VI) concentrations ranging from 200 ppb to 1000 ppb with a limit of detection (LOD) of 1.5 nM and a limit of quantification (LOQ) of 96 nM. The sensing mechanism can be ascribed by the inner filter effect of Cr(VI), the intercalation of Cr(VI) within the intergallery region of LDH, and the synergistic affinity of metal ions along with the polymer chain for Cr(VI). The adsorption performance of PANI@Nd-LDH nanocomposite is evaluated for Cr(VI) from wastewaters, which displayed high removal capacity towards Cr(VI) (219 mg/g) as compared on bare Nd-LDH (123 mg/g) and LDH (88 mg/g) respectively. The adsorption of Cr(VI) on PANI@Nd-LDH depends on the pH of the aqueous solution. The adsorption isotherm and kinetics are supported by the Langmuir model and pseudo-second-order model, respectively. Owing to the highly sensitive detection and adsorption of Cr(VI) from aqueous water samples demonstrated the potential application of PANI@Nd-LDH as an excellent environmental probe can be exploited.
  12. Chaudhary FA, Ahmad B, Javed MQ, Yakub SS, Arjumand B, Khan AM, et al.
    Pain Res Manag, 2021;2021:5512755.
    PMID: 34055118 DOI: 10.1155/2021/5512755
    This study aims to examine the association of orofacial pain and oral health status and oral health behaviours in facial burn patients. The participants in this cross-sectional study were randomly recruited from the Burn Care Center, Institute of Medical Sciences, Islamabad, Pakistan. An intraoral evaluation was carried out to record the DMFT and OHI-S. A self-administered questionnaire was used to collect information on sociodemographic status, brushing frequency, and dental visits. Orofacial pain during mandibular movement was assessed using the Visual Analogue Scale (VAS). Psychological status was assessed using the Generalized Anxiety Disorder Scale and Impact of Events Scale. ANOVA and simple and multiple linear regression tests were used to analyse the data. From the 90 facial burn patients included, the majority were below 34 years of age, female, single or divorced, and unemployed. The mean DMFT was 10.7, and 71% had poor oral hygiene. 56% of the participants had moderate-to-severe anxiety, and 68% had posttraumatic stress disorder. 53% of the participants had moderate-to-severe pain during mouth opening or moving the mandible with a mean score of 41.5. Analyses showed that orofacial pain was associated with less frequent brushing, irregular dental visits, greater DMFT score, and more plaque accumulation (OHI-S). It was also associated with employment status, the severity of a burn, anxiety, and stress. The treatment and management of dental and oral conditions in burn patients need judicious balance in controlling and accurate assessment of the pain and improving psychological problems in burn patients.
  13. Khan AM, Behkami S, Yusoff I, Md Zain SB, Bakar NKA, Bakar AFA, et al.
    Chemosphere, 2017 Oct;184:673-678.
    PMID: 28628904 DOI: 10.1016/j.chemosphere.2017.06.032
    Rare earth elements (REEs) are becoming significant due to their huge applications in many industries, large-scale mining and refining activities. Increasing usage of such metals pose negative environmental impacts. In this research ICP-MS has been used to analyze soil samples collected from former ex-mining areas in the depths of 0-20 cm, 21-40 cm, and 41-60 cm of residential, mining, natural, and industrial areas of Perak. Principal component analysis (PCA) revealed that soil samples taken from different mining, industrial, residential, and natural areas are separated into four clusters. It was observed that REEs were abundant in most of the samples from mining areas. Concentration of the rare elements decrease in general as we move from surface soil to deeper soils.
  14. Suwinski P, Ong C, Ling MHT, Poh YM, Khan AM, Ong HS
    Front Genet, 2019;10:49.
    PMID: 30809243 DOI: 10.3389/fgene.2019.00049
    There is a growing attention toward personalized medicine. This is led by a fundamental shift from the 'one size fits all' paradigm for treatment of patients with conditions or predisposition to diseases, to one that embraces novel approaches, such as tailored target therapies, to achieve the best possible outcomes. Driven by these, several national and international genome projects have been initiated to reap the benefits of personalized medicine. Exome and targeted sequencing provide a balance between cost and benefit, in contrast to whole genome sequencing (WGS). Whole exome sequencing (WES) targets approximately 3% of the whole genome, which is the basis for protein-coding genes. Nonetheless, it has the characteristics of big data in large deployment. Herein, the application of WES and its relevance in advancing personalized medicine is reviewed. WES is mapped to Big Data "10 Vs" and the resulting challenges discussed. Application of existing biological databases and bioinformatics tools to address the bottleneck in data processing and analysis are presented, including the need for new generation big data analytics for the multi-omics challenges of personalized medicine. This includes the incorporation of artificial intelligence (AI) in the clinical utility landscape of genomic information, and future consideration to create a new frontier toward advancing the field of personalized medicine.
  15. Soe HJ, Khan AM, Manikam R, Samudi Raju C, Vanhoutte P, Sekaran SD
    J Gen Virol, 2017 Dec;98(12):2993-3007.
    PMID: 29182510 DOI: 10.1099/jgv.0.000981
    Plasma leakage is the main pathophysiological feature in severe dengue, resulting from altered vascular barrier function associated with an inappropriate immune response triggered upon infection. The present study investigated functional changes using an electric cell-substrate impedance sensing system in four (brain, dermal, pulmonary and retinal) human microvascular endothelial cell (MEC) lines infected with purified dengue virus, followed by assessment of cytokine profiles and the expression of inter-endothelial junctional proteins. Modelling of changes in electrical impedance suggests that vascular leakage in dengue-infected MECs is mostly due to the modulation of cell-to-cell interactions, while this loss of vascular barrier function observed in the infected MECs varied between cell lines and DENV serotypes. High levels of inflammatory cytokines (IL-6 and TNF-α), chemokines (CXCL1, CXCL5, CXCL11, CX3CL1, CCL2 and CCL20) and adhesion molecules (VCAM-1) were differentially produced in the four infected MECs. Further, the tight junctional protein, ZO-1, was down-regulated in both the DENV-1-infected brain and pulmonary MECs, while claudin-1, PECAM-1 and VE-cadherin were differentially expressed in these two MECs after infection. Non-purified virus stock was also studied to investigate the impact of virus stock purity on dengue-specific immune responses, and the results suggest that virus stock propagated through cell culture may include factors that mask or alter the DENV-specific immune responses of the MECs. The findings of the present study show that high DENV load differentially modulates human microvascular endothelial barrier function and disrupts the function of inter-endothelial junctional proteins during early infection with organ-specific cytokine production.
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