Displaying publications 1 - 20 of 49 in total

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  1. Fulltext Integrated genomic view of SARS-CoV-2 in India
    Kumar P, Pandey R, Sharma P, Dhar MS, A V, Uppili B, et al.
    Wellcome Open Res, 2020;5:184.
    PMID: 32995557 DOI: 10.12688/wellcomeopenres.16119.1
    Background: India first detected SARS-CoV-2, causal agent of COVID-19 in late January 2020, imported from Wuhan, China. From March 2020 onwards, the importation of cases from countries in the rest of the world followed by seeding of local transmission triggered further outbreaks in India. Methods: We used ARTIC protocol-based tiling amplicon sequencing of SARS-CoV-2 (n=104) from different states of India using a combination of MinION and MinIT sequencing from Oxford Nanopore Technology to understand how introduction and local transmission occurred. Results: The analyses revealed multiple introductions of SARS-CoV-2 genomes, including the A2a cluster from Europe and the USA, A3 cluster from Middle East and A4 cluster (haplotype redefined) from Southeast Asia (Indonesia, Thailand and Malaysia) and Central Asia (Kyrgyzstan). The local transmission and persistence of genomes A4, A2a and A3 was also observed in the studied locations. The most prevalent genomes with patterns of variance (confined in a cluster) remain unclassified, and are here proposed as A4-clade based on its divergence within the A cluster. Conclusions: The viral haplotypes may link their persistence to geo-climatic conditions and host response. Multipronged strategies including molecular surveillance based on real-time viral genomic data is of paramount importance for a timely management of the pandemic.
  2. Fulltext Ophthalmic problems among the elderly in Malaysia
    Singh P
    Med J Malaysia, 1997 Sep;52(3):213-6.
    PMID: 10968087
  3. Fulltext Low attendance of preschool children in government clinics in a rural community
    Singh PJ
    Med J Malaysia, 1980 Mar;34(3):199-204.
    PMID: 7412659
  4. Fulltext Malignant melanomas of the vulva: two case reports
    Singh P, Chong PY
    Med J Malaysia, 1987 Sep;42(3):209-11.
    PMID: 3506648
  5. Fulltext The effect of piroxicam in preventing surgically induced miosis
    Au MK, Singh P
    Med J Malaysia, 1991 Dec;46(4):329-32.
    PMID: 1840440
    The effect of an antiprostaglandin, piroxicam, in preventing surgically induced miosis is studied. Patients undergoing extracapsular cataract surgery were randomly divided into the piroxicam and placebo groups. Intra-operative measurements of the pupillary diameters were performed. The stages of procedure at which they were measured were at the beginning of operation (Stage 1), after anterior capsulotomy (Stage 2), after lens nucleus delivery (Stage 3) and at the end of irrigation and aspiration (Stage 4). It is noted in this Study that the pupillary diameters were larger at stages 2,3 and 4 in the piroxicam group. The increase in the mean pupillary areas of the piroxicam group were statistically significant for Stages 3 and 4.
  6. Fulltext Preradiation peplomycin for advanced squamous cell carcinomas
    Azhar T, Singh P
    Med J Malaysia, 1988 Mar;43(1):40-3.
    PMID: 2468988
  7. Amniocentesis for antenatal diagnosis of chromosomal abnormalities and neural tube defects
    Singh P
    Med J Malaysia, 1979 Jun;33(4):311-6.
    PMID: 93235
  8. The diabetic: his ocular complications and his visual prognosis
    SINGH P
    Med J Malaya, 1955 Sep;10(1):83-6.
    PMID: 13287497
  9. Long-term phenothiazine administration and the eye in 100 Malaysians
    Ngen CC, Singh P
    Br J Psychiatry, 1988 Feb;152:278-80.
    PMID: 3167349
    Seventy-three out of a hundred Malaysians on phenothiazines for more than 24 months had ocular pigmentation. Seventy-one had conjunctiva pigmentation. No pigmentary retinopathy or visual impairment was detected. Frequency of pigmentation increased with age and with higher total dosage prescribed, but there was no critical level below which pigmentation was not detected.
  10. Amyloid precursor protein in Alzheimer's disease
    Maurya R, Bhattacharjee G, Khambhati K, Gohil N, Singh P, Mani I, et al.
    Prog Mol Biol Transl Sci, 2023;196:261-270.
    PMID: 36813361 DOI: 10.1016/bs.pmbts.2022.09.006
    Amyloid precursor protein (APP) is a membrane protein expressed in several tissues. The occurrence of APP is predominant in synapses of nerve cells. It acts as a cell surface receptor and plays a vital role as a regulator of synapse formation, iron export and neural plasticity. It is encoded by the APP gene that is regulated by substrate presentation. APP is a precursor protein activated by proteolytic cleavage and thereby generating amyloid beta (Aβ) peptides which eventually form amyloid plaques that accumulate in Alzheimer's disease patients' brains. In this chapter, we highlight basic mechanism, structure, expression patterns and cleavage of amyloid plaques, and its diagnosis and potential treatment for Alzheimer's disease.
  11. Fulltext Serological response to influenza vaccination among children vaccinated for multiple influenza seasons
    Rafiq S, Russell ML, Webby R, Fonseca K, Smieja M, Singh P, et al.
    PLoS One, 2012;7(12):e51498.
    PMID: 23240030 DOI: 10.1371/journal.pone.0051498
    BACKGROUND: To evaluate if, among children aged 3 to 15 years, influenza vaccination for multiple seasons affects the proportion sero-protected.

    METHODOLOGY/PRINCIPAL FINDINGS: Participants were 131 healthy children aged 3-15 years. Participants were vaccinated with trivalent inactivated seasonal influenza vaccine (TIV) over the 2005-06, 2006-07 and 2007-8 seasons. Number of seasons vaccinated were categorized as one (2007-08); two (2007-08 and 2006-07 or 2007-08 and 2005-06) or three (2005-06, 2006-07, and 2007-08). Pre- and post-vaccination sera were collected four weeks apart. Antibody titres were determined by hemagglutination inhibition (HAI) assay using antigens to A/Solomon Islands/03/06 (H1N1), A/Wisconsin/67/05 (H3N2) and B/Malaysia/2506/04. The proportions sero-protected were compared by number of seasons vaccinated using cut-points for seroprotection of 1:40 vs. 1:320. The proportions of children sero-protected against H1N1 and H3N2 was high (>85%) regardless of number of seasons vaccinated and regardless of cut-point for seroprotection. For B Malaysia there was no change in proportions sero-protected by number of seasons vaccinated; however the proportions protected were lower than for H1N1 and H3N2, and there was a lower proportion sero-protected when the higher, compared to lower, cut-point was used for sero-protection.

    CONCLUSION/SIGNIFICANCE: The proportion of children sero-protected is not affected by number of seasons vaccinated.

  12. Sheath blight of rice: a review and identification of priorities for future research
    Singh P, Mazumdar P, Harikrishna JA, Babu S
    Planta, 2019 Nov;250(5):1387-1407.
    PMID: 31346804 DOI: 10.1007/s00425-019-03246-8
    MAIN CONCLUSION: Rice sheath blight research should prioritise optimising biological control approaches, identification of resistance gene mechanisms and application in genetic improvement and smart farming for early disease detection. Rice sheath blight, caused by Rhizoctonia solani AG1-1A, is one of the most devasting diseases of the crop. To move forward with effective crop protection against sheath blight, it is important to review the published information related to pathogenicity and disease management and to determine areas of research that require deeper study. While progress has been made in the identification of pathogenesis-related genes both in rice and in the pathogen, the mechanisms remain unclear. Research related to disease management practices has addressed the use of agronomic practices, chemical control, biological control and genetic improvement: Optimising nitrogen fertiliser use in conjunction with plant spacing can reduce spread of infection while smart agriculture technologies such as crop monitoring with Unmanned Aerial Systems assist in early detection and management of sheath blight disease. Replacing older fungicides with natural fungicides and use of biological agents can provide effective sheath blight control, also minimising environmental impact. Genetic approaches that show promise for the control of sheath blight include treatment with exogenous dsRNA to silence pathogen gene expression, genome editing to develop rice lines with lower susceptibility to sheath blight and development of transgenic rice lines overexpressing or silencing pathogenesis related genes. The main challenges that were identified for effective crop protection against sheath blight are the adaptive flexibility of the pathogen, lack of resistant rice varieties, abscence of single resistance genes for use in breeding and low access of farmers to awareness programmes for optimal management practices.
  13. Late blight in tomato: insights into the pathogenesis of the aggressive pathogen Phytophthora infestans and future research priorities
    Mazumdar P, Singh P, Kethiravan D, Ramathani I, Ramakrishnan N
    Planta, 2021 May 08;253(6):119.
    PMID: 33963935 DOI: 10.1007/s00425-021-03636-x
    MAIN CONCLUSION: This review provides insights into the molecular interactions between Phytophthora infestans and tomato and highlights research gaps that need further attention. Late blight in tomato is caused by the oomycota hemibiotroph Phytophthora infestans, and this disease represents a global threat to tomato farming. The pathogen is cumbersome to control because of its fast-evolving nature, ability to overcome host resistance and inefficient natural resistance obtained from the available tomato germplasm. To achieve successful control over this pathogen, the molecular pathogenicity of P. infestans and key points of vulnerability in the host plant immune system must be understood. This review primarily focuses on efforts to better understand the molecular interaction between host pathogens from both perspectives, as well as the resistance genes, metabolomic changes, quantitative trait loci with potential for improvement in disease resistance and host genome manipulation via transgenic approaches, and it further identifies research gaps and provides suggestions for future research priorities.
  14. Fulltext Impact of sea-salt on morpho-physiological and biochemical responses in banana (Musa acuminata cv. Berangan)
    Mazumdar P, Lau SE, Singh P, Takhtgahi HM, Harikrishna JA
    Physiol Mol Biol Plants, 2019 May;25(3):713-726.
    PMID: 31168234 DOI: 10.1007/s12298-019-00659-3
    Banana is often grown in coastal-regions, and while known for its sensitivity towards seawater, little is documented on the effect of sea-salt on the growth, physiology and metal homeostasis. Here we report that banana plantlets exposed to sea-salt at extreme (average seawater concentration; 52.7 dS m-1), severe (28.5 dS m-1) or moderate (10.2 dS m-1) salinity levels had reduced root length (2.0-6.0-fold), plant height (1.2-1.6-fold), leaf number (2.0-2.3-fold) and leaf area (3.3-4.0-fold) compared to control plantlets. Degradation of pigments (total chlorophyll: 1.3-12.3-fold, chlorophyll a: 1.3-9.2-fold; chlorophyll b: 1.3-6.9-fold lower and carotenoids: 1.4-3.7-fold lower) reflected vulnerability of photosystems to salt stress. Relative water content showed a maximum decrease of 1.5-fold in salt stress. MDA analysis showed sea-salt exposure triggers 2.3-3.5-fold higher lipid peroxidation. Metal content analysis showed a 73-fold higher Na value from roots exposed to extreme salinity compared to control plantlets. While phenotype was clearly affected, moderate salinity showed no significant alteration of macro (N, P, K and Ca) and micro (Fe, Mn and Cu) metal content. The antioxidant enzymes: SOD (3.2-fold), CAT (1.7-fold) and GR (6-fold) showed higher activity at moderate salinity level compared to control plantlets but lower activity at severe (SOD: 1.3-fold; CAT: 1.5-fold; GR: 2-fold lower) and extreme seawater salinity (SOD: 1.5; CAT: 1.9; GR: 1.3-fold lower). Mild changes in growth and physiology at sea-salt levels equivalent to moderate seawater flooding, indicate that banana will survive such flooding, while extreme seawater inundation will be lethal. This data provides a reference for future salinity-mediated work in banana.
  15. Fulltext Expression and DNA methylation of SERK, BBM, LEC2 and WUS genes in in vitro cultures of Boesenbergia rotunda (L.) Mansf
    Karim R, Tan YS, Singh P, Khalid N, Harikrishna JA
    Physiol Mol Biol Plants, 2018 Sep;24(5):741-751.
    PMID: 30150851 DOI: 10.1007/s12298-018-0566-8
    The process of somatic embryogenesis and plant regeneration involve changes in gene expression and have been associated with changes in DNA methylation. Here, we report the expression and DNA methylation patterns of SOMATIC EMBRYOGENESIS RECEPTOR-LIKE KINASE (SERK), BABY BOOM (BBM), LEAFY COTYLEDON 2 (LEC2) and WUSCHEL (WUS) in meristematic block of newly emerged shoots from rhizome, embryogenic and non-embryogenic calli, prolonged cell suspension culture, ex vitro leaf, and in vitro leaf of regenerated plants of Boesenbergia rotunda. Among all seven samples, based on qRT-PCR, the highest level of expression of SERK, BBM and LEC2 was in embryogenic callus, while WUS was most highly expressed in meristematic block tissue followed by embryogenic callus. Relatively lower expression was observed in cell suspension culture and watery callus for SERK, LEC2 and WUS and in in vitro leaf for BBM. For gene specific methylation determined by bisulfite sequencing data, embryogenic callus samples had the lowest levels of DNA methylation at CG, CHG and CHH contexts of SERK, LEC2 and WUS. We observed negative correlation between DNA methylation at the CG and CHG contexts and the expression levels of SERK, BBM, LEC2 and WUS. Based on our results, we suggest that relatively higher expression and lower level of DNA methylation of SERK, BBM, LEC2 and WUS are associated with somatic embryogenesis and plant regeneration in B. rotunda.
  16. Fulltext Graphery: interactive tutorials for biological network algorithms
    Zeng H, Zhang J, Preising GA, Rubel T, Singh P, Ritz A
    Nucleic Acids Res, 2021 07 02;49(W1):W257-W262.
    PMID: 34037782 DOI: 10.1093/nar/gkab420
    Networks have been an excellent framework for modeling complex biological information, but the methodological details of network-based tools are often described for a technical audience. We have developed Graphery, an interactive tutorial webserver that illustrates foundational graph concepts frequently used in network-based methods. Each tutorial describes a graph concept along with executable Python code that can be interactively run on a graph. Users navigate each tutorial using their choice of real-world biological networks that highlight the diverse applications of network algorithms. Graphery also allows users to modify the code within each tutorial or write new programs, which all can be executed without requiring an account. Graphery accepts ideas for new tutorials and datasets that will be shaped by both computational and biological researchers, growing into a community-contributed learning platform. Graphery is available at https://graphery.reedcompbio.org/.
  17. The global burden of coeliac disease: opportunities and challenges
    Makharia GK, Singh P, Catassi C, Sanders DS, Leffler D, Ali RAR, et al.
    Nat Rev Gastroenterol Hepatol, 2022 Jan 03.
    PMID: 34980921 DOI: 10.1038/s41575-021-00552-z
    Coeliac disease is a systemic disorder characterized by immune-mediated enteropathy, which is caused by gluten ingestion in genetically susceptible individuals. The clinical presentation of coeliac disease is highly variable and ranges from malabsorption through solely extra-intestinal manifestations to asymptomatic. As a result, the majority of patients with coeliac disease remain undiagnosed, misdiagnosed or experience a substantial delay in diagnosis. Coeliac disease is diagnosed by a combination of serological findings of disease-related antibodies and histological evidence of villous abnormalities in duodenal biopsy samples. However, variability in histological grading and in the diagnostic performance of some commercially available serological tests remains unacceptably high and confirmatory assays are not readily available in many parts of the world. Currently, the only effective treatment for coeliac disease is a lifelong, strict, gluten-free diet. However, many barriers impede patients' adherence to this diet, including lack of widespread availability, high cost, cross-contamination and its overall restrictive nature. Routine follow-up is necessary to ensure adherence to a gluten-free diet but considerable variation is evident in follow-up protocols and the optimal disease management strategy is not clear. However, these challenges in the diagnosis and management of coeliac disease suggest opportunities for future research.
  18. Correction: Recent trends in carbon nanotube (CNT)-based biosensors for the fast and sensitive detection of human viruses: a critical review
    Meskher H, Mustansar HC, Thakur AK, Sathyamurthy R, Lynch I, Singh P, et al.
    Nanoscale Adv, 2023 Oct 24;5(21):5983.
    PMID: 37881720 DOI: 10.1039/d3na90097e
    [This corrects the article DOI: 10.1039/D2NA00236A.].
  19. Fulltext Recent trends in carbon nanotube (CNT)-based biosensors for the fast and sensitive detection of human viruses: a critical review
    Meskher H, Mustansar HC, Thakur AK, Sathyamurthy R, Lynch I, Singh P, et al.
    Nanoscale Adv, 2023 Feb 14;5(4):992-1010.
    PMID: 36798507 DOI: 10.1039/d2na00236a
    The current COVID-19 pandemic, with its numerous variants including Omicron which is 50-70% more transmissible than the previously dominant Delta variant, demands a fast, robust, cheap, and easily deployed identification strategy to reduce the chain of transmission, for which biosensors have been shown as a feasible solution at the laboratory scale. The use of nanomaterials has significantly enhanced the performance of biosensors, and the addition of CNTs has increased detection capabilities to an unrivaled level. Among the various CNT-based detection systems, CNT-based field-effect transistors possess ultra-sensitivity and low-noise detection capacity, allowing for immediate analyte determination even in the presence of limited analyte concentrations, which would be typical of early infection stages. Recently, CNT field-effect transistor-type biosensors have been successfully used in the fast diagnosis of COVID-19, which has increased research and commercial interest in exploiting current developments of CNT field-effect transistors. Recent progress in the design and deployment of CNT-based biosensors for viral monitoring are covered in this paper, as are the remaining obstacles and prospects. This work also highlights the enormous potential for synergistic effects of CNTs used in combination with other nanomaterials for viral detection.
  20. Biotransformation of Raw Mango Seed Waste into Bacterial Hydrolytic Enzymes Enhancement Via Solid State Fermentation Strategy
    Khan PA, Mohammad A, Bansal SL, Lal B, Singh P, Singh R, et al.
    Mol Biotechnol, 2024 Jan 09.
    PMID: 38195817 DOI: 10.1007/s12033-023-01022-4
    Solid waste generation is a huge contributor to environmental pollution issues, and food wastes are prominent in this category due to their large generation on a day-to-day basis. Thus, the settlement of daily food waste is one of the major constraints and needs innovative manufacturing sheme to valorize solid waste in sustainable manner. Moreover, these food wastes are rich in organic content, which has promising scope for their value-added products. In the present study, raw mango seed waste has been biotransformed to produce bacterial hydrolytic enzymes as feedstock. On investigating the impact of substrate, the highest bacterial cellulase production was recorded to be 18 IU/gds FP (filter paper) in 24 h of microbial incubation at 5 g of substrate in solid-state fermentation (SSF). Furthermore, at 40 °C and pH 6.0, 23 IU/gds FP enzyme could be produced in 24 h of SSF. Beside this, on comparing the influence of inorganic and organic nitrogen sources, urea has been found to provide better cellulase production, which yielded 28 IU/gds FP in 24 h of incubation, along with 77 IU/gds BG (β-glucosidase) and 89 IU/gds EG (endoglucanase). On the other hand, Tween-40 and Tween-80, two different surfactants, were employed at a 1.0% concentration for 24 h of incubation. It was noticed that Tween-80 showed complete enzyme activity at 24 h, which was found to be relatively superior to that of Tween-40. This study may have potential utility in enzyme production using mango seed as a food waste for various industrial applications.
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