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Jasmin MY, Isa NM, Kamarudin MS, Lim KC, Karim M. Evaluating Bacillus flexus as bioremediators for ammonia removal in shrimp culture water and wastewater and characterizing microbial communities in shrimp pond sludge. Braz J Microbiol 2024; 55:529-536. [PMID: 38280093 PMCID: PMC10920598 DOI: 10.1007/s42770-024-01246-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 01/02/2024] [Indexed: 01/29/2024] Open
Abstract
The accumulation of nitrogen compounds in shrimp farming water and effluent presents a major challenge. Ammonia is a form of nitrogen that limits shrimp growth due to its potential toxicity and effects on shrimp health and water quality. This study is aimed at identifying promising bioremediators from shrimp pond sludge to mitigate ammonia levels in both culture water and wastewater and at determining major bacterial communities in sludge using metagenomic analysis. A sludge sample was collected from a shrimp pond in Selangor, Malaysia, to isolate potential ammonia-removing bacteria. Out of 64 isolated strains, Bacillus flexus SS2 showed the highest growth in synthetic basal media (SBM) containing ammonium sulfate at a concentration of 70 mg/L as the sole nitrogen source. The strain was then incubated in SBM with varying pH levels and showed optimal growth at pH 6.5-7. After 24 h of incubation, B. flexus SS2 reduced the ammonia concentration from an initial concentration of 5 to 0.01 mg/L, indicating a 99.61% reduction rate, which was highest in SBM at pH 7. Moreover, the strain showed ammonia removal ability at concentrations ranging from 5 to 70 mg/L. Metagenomic analysis revealed that Proteobacteria was the most abundant phylum in the sludge, followed by Cyanobacteria, Actinobacteria, Chloraflexi, Firmicutes, and Campilobacterota. Bacillus flexus SS2 belongs to the Bacillota phylum and has the potential to serve as a bioremediator for removing ammonia from shrimp culture water and wastewater.
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Kho SS, Lim KC, Muhammad NA, Nasaruddin MZ, Ismail I, Daut UM, Abdul Rahaman JA. Clinical and radiological outcomes of SARS-CoV-2 related organising pneumonia in COVID-19 survivors. THE MEDICAL JOURNAL OF MALAYSIA 2023; 78:131-138. [PMID: 36988520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/19/2023]
Abstract
INTRODUCTION COVID-19 patients frequently demonstrate radiological organising pneumonia (OP) pattern. The longterm outcome and treatment options for this group of patients remain uncertain. We aim to describe the clinical and radiological outcomes of patients with COVID-19-related OP and identify possible clinical factors associated with inferior radiological outcome. MATERIALS AND METHODS Post-COVID-19 clinic attendees, consisting of post-COVID-19 patients discharged from major hospitals in the state of Selangor during the third pandemic wave of COVID-19 in Malaysia, were enrolled in this retrospective study for 6 months. Physician-scored Modified Medical Research Council (mMRC), patient self-reported quality of life (EQ-VAS) score and follow-up CT scan were evaluated. RESULTS Our cohort comprised 131 patients, with a median age of 52 (IQR 39-60) years and median BMI of 29.40 (IQR 25.59-34.72). Majority (72.5%) had co-morbidities, and 97.7% had severe disease requiring supplementary oxygen support during the acute COVID-19 episode. 56.5% required intensive care; among which one-third were invasively ventilated. Median equivalent dose of methylprednisolone prescribed was 2.60 (IQR 1.29-5.18) mg/kg during admission, while the median prednisolone dose upon discharge was 0.64 (IQR 0.51-0.78) mg/kg. It was tapered over a median of 8.0 (IQR 5.8-9.0) weeks. Upon follow-up at 11 (IQR 8-15) weeks, one-third of patients remained symptomatic, with cough, fatigue and dyspnoea being the most reported symptoms. mMRC and EQ-VAS scores improved significantly (p<0.001) during follow-up. Repeat CT scans were done in 59.5% of patients, with 94.8% of them demonstrating improvement. In fact, 51.7% had complete radiological resolution. Intensive care admission and mechanical ventilation are among the factors which were associated with poorer radiological outcomes, p<0.05. CONCLUSION Approximately one-third of patients with SARSCoV- 2-related OP remained symptomatic at 3 months of follow-up. Majority demonstrated favourable radiological outcomes at 5-month reassessment, except those who required intensive care unit admission and mechanical ventilation.
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Kosasih S, Metussin A, Lim KC, Telisinghe PU, Basir N, Chong VH. Gastrointestinal: Cholangiocarcinoma with Strongyloides stercoralis infestation. J Gastroenterol Hepatol 2023; 38:161. [PMID: 35831976 DOI: 10.1111/jgh.15934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 06/28/2022] [Indexed: 12/09/2022]
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Lim KC, Then AY. Environmental DNA approach complements social media reports to detect an endangered freshwater stingray species in the wild. ENDANGER SPECIES RES 2022. [DOI: 10.3354/esr01187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Attili D, Schill DJ, DeLong CJ, Lim KC, Jiang G, Campbell KF, Walker K, Laszczyk A, McInnis MG, O'Shea KS. Astrocyte-Derived Exosomes in an iPSC Model of Bipolar Disorder. ADVANCES IN NEUROBIOLOGY 2020; 25:219-235. [PMID: 32578149 DOI: 10.1007/978-3-030-45493-7_8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Bipolar I Disorder (BP) is a serious, recurrent mood disorder that is characterized by alternating episodes of mania and depression. To begin to identify novel approaches and pathways involved in BP, we have obtained skin samples from BP patients and undiagnosed control (C) individuals, reprogrammed them to form induced pluripotent stem cells (iPSC), and then differentiated the stem cells into astrocytes. RNAs from BP and C astrocytes were extracted and RNAseq analysis carried out. 501 differentially expressed genes were identified, including genes for cytoskeletal elements, extracellular matrix, signaling pathways, neurodegeneration, and notably transcripts that identify exosomes. When we compared highly expressed genes using hierarchial cluster analysis, "Exosome" was the first and most highly significant cluster identified, p < 5 × 10-13, Benjamini correction. Exosomes are membrane-bound vesicles that package and remove toxic proteins from cells and also enable cell to cell communication. They carry genetic material, including DNA, mRNA and microRNAs, proteins, and lipids to target cells throughout the body. Exosomes are released by cortical neurons and astrocytes in culture and are present in BP vs C postmortem brain tissue. Little is known about what transcripts and proteins are targeted to neurons, how they regulate biological functions of the acceptor cell, or how that may be altered in mood disorders. Since astrocyte-derived exosomes have been suggested to promote neuronal plasticity, as well as to remove toxic proteins in the brain, alterations in their function or content may be involved in neurodevelopmental, neuropathological, and neuropsychiatric conditions. To examine exosome cargos and interactions with neural precursor cells, astrocytes were differentiated from four bipolar disorder (BP) and four control (C) iPSC lines. Culture supernatants from these astrocytes were collected, and exosomes isolated by ultra-centrifugation. Western blot analysis demonstrated the presence of the exosome markers CD9, CD81, and Hsp70. Nanosight technology was used to characterize exosomes from each astrocyte cell line, suggesting that exosomes were slightly more concentrated in culture supernatants derived from BP compared with C astrocytes but there was no difference in the mean sizes of the exosomes. Analysis of their function in neuronal differentiation is being carried out by labeling exosomes derived from bipolar patient and control astrocytes and adding them to control neural progenitor cells. Given the current interest in clearing toxic proteins from brains of patients with neurodegenerative disorders, exosomes may present similar opportunities in BP.
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Bashir A, Chauhdary WA, Rubel AR, Soe ZN, Hla Aye MT, Javed N, Mani BI, Lim KC, Chong VH. Pulmonary aspergilloma. QJM 2020; 113:821-822. [PMID: 32077956 DOI: 10.1093/qjmed/hcaa032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Lim KC, Yap LB, Amin AN. Definite stent thrombosis among Malaysian population: predictors and insights of mechanisms from intracoronary imaging. THE MEDICAL JOURNAL OF MALAYSIA 2020; 75:472-478. [PMID: 32918412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
INTRODUCTION Stent thrombosis (ST) is an uncommon, but significant complication following angioplasty. We aimed to examine the predictors, clinical outcomes and mechanism of definite ST cases among patients who underwent percutaneous coronary intervention (PCI). METHODS This was a retrospective observational registry of 14,935 patients from the year 2011 till 2015. Clinical characteristics, clinical outcome and intracoronary imaging data were recorded in all the patients. The SPSS Statistic version 24 was used for statistical analysis. The Cox regression hazard model was used to report calculate the hazard ratio (HR) with a 95% confidence interval (95%CI). Independent predictors of ST were identified by univariate logistic regression analysis. Variables that showed a statistically significant effect in univariate analyses were entered in a multivariate Cox proportional hazards model. A p-value<0.05 was regarded as significant. RESULTS The incidence of definite ST was 0.25% (37 out of 14935 patients). 75% of ST group patients presented with ST elevation myocardial infarction (75% vs. 19.8%, p<0.01). There was higher mortality among patients with ST when compared to the group without ST (Hazard Ratio, HR=10.69, 95%CI: 1.13, 100). Two independent predictors of ST were 1) previous history of acute myocardial infarction (HR=2.36, 95%CI: 1.19, 4.70) and 2) PCI in the context of acute coronary syndrome when compared to elective PCI (HR=37, 95%CI: 15.7, 91.5). Examination of 19 ST cases with intracoronary imaging identified nine cases (47%) of underexpanded stents and five cases (26%) of malopposition of stents. CONCLUSIONS ST is associated with high mortality. PCI in acute coronary syndrome setting and a previous history of acute myocardial infarction were significant predictors for ST. Intracoronary imaging identified stent underexpansion and malopposition as common reasons for ST. In cases where the risk of ST is high, the use of intracoronary imaging guided PCI is recommended.
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Carter DS, Jacobs RT, Freund YR, Berry PW, Akama T, Easom EE, Lunde CS, Rock F, Stefanakis R, McKerrow J, Fischer C, Bulman CA, Lim KC, Suzuki BM, Tricoche N, Sakanari JA, Lustigman S, Plattner JJ. Macrofilaricidal Benzimidazole-Benzoxaborole Hybrids as an Approach to the Treatment of River Blindness: Part 2. Ketone Linked Analogs. ACS Infect Dis 2020; 6:180-185. [PMID: 31876143 PMCID: PMC7026882 DOI: 10.1021/acsinfecdis.9b00397] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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The optimization
of a series of benzimidazole–benzoxaborole hybrid molecules
linked via a ketone that exhibit good activity against Onchocerca
volvulus, a filarial nematode responsible for the disease
onchocerciasis, also known as river blindness, is described. The lead
identified in this series, 21 (AN15470), was found to
have acceptable pharmacokinetic properties to enable an evaluation
following oral dosing in an animal model of onchocerciasis. Compound 21was effective in killing worms implanted in Mongolian gerbils
when dosed orally as a suspension at 100 mg/kg/day for 14 days but
not when dosed orally at 100 mg/kg/day for 7 days.
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Akama T, Freund YR, Berry PW, Carter DS, Easom EE, Jarnagin K, Lunde CS, Plattner JJ, Rock F, Stefanakis R, Fischer C, Bulman CA, Lim KC, Suzuki BM, Tricoche N, Mansour A, DiCosty U, McCall S, Carson B, McCall JW, McKerrow J, Hübner MP, Specht S, Hoerauf A, Lustigman S, Sakanari JA, Jacobs RT. Macrofilaricidal Benzimidazole-Benzoxaborole Hybrids as an Approach to the Treatment of River Blindness: Part 1. Amide Linked Analogs. ACS Infect Dis 2020; 6:173-179. [PMID: 31876154 PMCID: PMC7026885 DOI: 10.1021/acsinfecdis.9b00396] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
A series of benzimidazole–benzoxaborole
hybrid molecules
linked via an amide linker are described that exhibit good in vitro activity against Onchocerca volvulus, a filarial nematode responsible for the disease onchocerciasis,
also known as river blindness. The lead identified in this series, 8a (AN8799), was found to have acceptable pharmacokinetic
properties to enable evaluation in animal models of human filariasis.
Compound 8a was effective in killing Brugia malayi, B. pahangi, and Litomosoides sigmodontis worms present in Mongolian gerbils when dosed subcutaneously as
a suspension at 100 mg/kg/day for 14 days but not when dosed orally
at 100 mg/kg/day for 28 days. The measurement of plasma levels of 8a at the end of the dosing period and at the time of sacrifice
revealed an interesting dependence of activity on the extended exposure
for both 8a and the positive control, flubendazole.
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Lim M, Kheok SW, Lim KC, Venkatanarasimha N, Small JE, Chen RC. Subdural haematoma mimics. Clin Radiol 2019; 74:663-675. [PMID: 31109715 DOI: 10.1016/j.crad.2019.04.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 04/09/2019] [Indexed: 11/30/2022]
Abstract
A subdural haematoma (SDH) is a frequently encountered pathology seen on an emergency room computed tomography (CT) head scan. An extra-axial crescentic density along the convexity of the brain or within the interhemispheric fissure is generally thought to represent a SDH; however, SDH mimics are known to occur in nature, and can be broadly classified under the subcategories of normal anatomy, artefacts, tumour, inflammation, infection, ischaemia, trauma, and iatrogenic. Understanding the typical characteristics of a SDH, knowledge of normal anatomy, close inspection of the morphology of the subdural process, changes to the adjacent structures, and rigorous attention to clinical details may reveal subtle clues that distinguish a true SDH from a mimic. This is crucial in appropriately directing clinical management. This review amalgamates most of the rare subdural processes that have been reported to mimic SDH, and discusses the imaging and clinical features that help to differentiate between them. This topic is highly valuable for radiology trainees, general radiologists, and emergency room physicians, and may serve as a refresher for the practising neuroradiologist.
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Fischer C, Ibiricu Urriza I, Bulman CA, Lim KC, Gut J, Lachau-Durand S, Engelen M, Quirynen L, Tekle F, Baeten B, Beerntsen B, Lustigman S, Sakanari J. Efficacy of subcutaneous doses and a new oral amorphous solid dispersion formulation of flubendazole on male jirds (Meriones unguiculatus) infected with the filarial nematode Brugia pahangi. PLoS Negl Trop Dis 2019; 13:e0006787. [PMID: 30650084 PMCID: PMC6334909 DOI: 10.1371/journal.pntd.0006787] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 08/26/2018] [Indexed: 12/12/2022] Open
Abstract
River blindness and lymphatic filariasis are two filarial diseases that globally affect millions of people mostly in impoverished countries. Current mass drug administration programs rely on drugs that primarily target the microfilariae, which are released from adult female worms. The female worms can live for several years, releasing millions of microfilariae throughout the course of infection. Thus, to stop transmission of infection and shorten the time to elimination of these diseases, a safe and effective drug that kills the adult stage is needed. The benzimidazole anthelmintic flubendazole (FBZ) is 100% efficacious as a macrofilaricide in experimental filarial rodent models but it must be administered subcutaneously (SC) due to its low oral bioavailability. Studies were undertaken to assess the efficacy of a new oral amorphous solid dispersion (ASD) formulation of FBZ on Brugia pahangi infected jirds (Meriones unguiculatus) and compare it to a single or multiple doses of FBZ given subcutaneously. Results showed that worm burden was not significantly decreased in animals given oral doses of ASD FBZ (0.2-15 mg/kg). Regardless, doses as low as 1.5 mg/kg caused extensive ultrastructural damage to developing embryos and microfilariae (mf). SC injections of FBZ in suspension (10 mg/kg) given for 5 days however, eliminated all worms in all animals, and a single SC injection reduced worm burden by 63% compared to the control group. In summary, oral doses of ASD formulated FBZ did not significantly reduce total worm burden but longer treatments, extended takedown times or a second dosing regimen, may decrease female fecundity and the number of mf shed by female worms.
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Chow AT, Quah SY, Bergenholtz G, Lim KC, Yu VSH, Tan KS. Bacterial species associated with persistent apical periodontitis exert differential effects on osteogenic differentiation. Int Endod J 2018; 52:201-210. [PMID: 30099741 DOI: 10.1111/iej.12994] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 08/06/2018] [Indexed: 01/11/2023]
Abstract
AIM To determine if bacteria associated with persistent apical periodontitis induce species-specific pro-inflammatory cytokine responses in macrophages, and the effects of this species-specific microenvironment on osteogenic differentiation. METHODOLOGY Macrophages were exposed to Enterococcus faecalis, Streptococcus oralis, Streptococcus mitis, Fusobacterium nucleatum, Treponema denticola or Tannerella forsythia, and levels of TNF-α and IL-1β elicited were determined by immunoassay. Following treatment of MG-63 pre-osteoblasts with conditioned media from bacteria-exposed macrophages, osteogenic differentiation and viability of osteoblasts were analyzed by Alizarin Red Staining and MTS assay, respectively. Statistical analysis was carried out by one-way anova with the Tukey post-hoc test. Differences were considered to be significant if P < 0.05. RESULTS Macrophages exposed to Gram-positive bacteria did not produce significant amounts of cytokines. F. nucleatum-challenged macrophages produced up to four-fold more TNF-α and IL-1β compared to T. denticola or T. forsythia. Only conditioned media from macrophages treated with Gram-negative bacteria decreased mineralization and viability of osteoblasts. CONCLUSIONS Gram-positive bacteria did not impact osteogenic differentiation and appeared innocuous. Gram-negative bacteria, in particular F. nucleatum elicited an enhanced pro-inflammatory response in macrophages, inhibited osteogenic differentiation and reduced cell viability. The findings suggest that the presence of this organism could potentially increase the severity of persistent apical periodontitis.
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Daud A, Johar S, Lim KC, Chong VH. Gastrointestinal: Atrioesophageal fistula. J Gastroenterol Hepatol 2017; 32:9. [PMID: 27164272 DOI: 10.1111/jgh.13438] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/05/2016] [Indexed: 12/09/2022]
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Marcellino C, Gut J, Lim KC, Singh R, McKerrow J, Sakanari J. WormAssay: a novel computer application for whole-plate motion-based screening of macroscopic parasites. PLoS Negl Trop Dis 2012; 6:e1494. [PMID: 22303493 PMCID: PMC3269415 DOI: 10.1371/journal.pntd.0001494] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Accepted: 12/07/2011] [Indexed: 11/28/2022] Open
Abstract
Lymphatic filariasis is caused by filarial nematode parasites, including Brugia malayi. Adult worms live in the lymphatic system and cause a strong immune reaction that leads to the obstruction of lymph vessels and swelling of the extremities. Chronic disease leads to the painful and disfiguring condition known as elephantiasis. Current drug therapy is effective against the microfilariae (larval stage) of the parasite, but no drugs are effective against the adult worms. One of the major stumbling blocks toward developing effective macrofilaricides to kill the adult worms is the lack of a high throughput screening method for candidate drugs. Current methods utilize systems that measure one well at a time and are time consuming and often expensive. We have developed a low-cost and simple visual imaging system to automate and quantify screening entire plates based on parasite movement. This system can be applied to the study of many macroparasites as well as other macroscopic organisms. The World Health Organization estimates that there are approximately 37 million people who are afflicted by Onchocerca volvulus (the parasitic worm that causes river blindness) and over 120 million people afflicted by the filarial worms Wuchereria and Brugia spp. (causative agents of lymphatic filariasis or elephantiasis). Current mass drug administration includes albendazole and either diethylcarbamazine or ivermectin. These drugs, however, are effective at killing the early larval stage (microfilariae) released from adult female worms but they do not kill the adult worms. Adult worms can live up to 10 or more years, releasing thousands of microfilariae per day. It is essential therefore to treat infected individuals with macrofilaricides in order to prevent the adult parasites from producing microfiliariae for the duration of the infection and to treat the disease. In order to screen candidate drugs for use as macrofilaricides, we have developed an inexpensive system and simple method for quantifying the effectiveness of drugs on parasite movement. The apparatus uses a commodity video camera, a computer and a newly developed free and open source software application to provide automated and quantitative measurements of parasite motility on each plate of worms. This system is not only useful for high throughput screening of macroparasites but can also be applied to the study of other macroscopic organisms as well.
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Lim KC, Chai P, Teo LS. Incidental cardiac abnormalities on non-electrocardiogram-gated multi-detector computed tomography imaging of the thorax and abdomen. Singapore Med J 2011; 52:906-913. [PMID: 22159935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Little attention is usually paid to the heart on non-electrocardiogram (ECG)-gated multi-detector computed tomography (MDCT) imaging of the thorax and abdomen. The current MDCT systems have fast scanning capabilities that render non-ECG-gated images with reduced cardiac motion artefacts due to greater temporal and spatial resolution. This has allowed for better evaluation of the cardiac structures. We present a pictorial review of incidental cardiac abnormalities found on MDCT imaging of the thorax and abdomen performed in our institution. We systematically describe abnormalities involving the pericardium, myocardium, cardiac valves, cardiac chambers, coronary artery and congenital heart disease. Some of these images have echocardiograph and magnetic resonance imaging correlation. The purpose of this pictorial essay is to draw attention to cardiac abnormalities found incidentally on non-ECG-gated MDCT imaging of the thorax and abdomen, which may or may not be related to the patient's symptoms.
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Perna D, Fagà G, Verrecchia A, Gorski MM, Barozzi I, Narang V, Khng J, Lim KC, Sung WK, Sanges R, Stupka E, Oskarsson T, Trumpp A, Wei CL, Müller H, Amati B. Genome-wide mapping of Myc binding and gene regulation in serum-stimulated fibroblasts. Oncogene 2011; 31:1695-709. [PMID: 21860422 PMCID: PMC3324106 DOI: 10.1038/onc.2011.359] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The transition from quiescence to proliferation is a key regulatory step that can be induced by serum stimulation in cultured fibroblasts. The transcription factor Myc is directly induced by serum mitogens and drives a secondary gene expression program that remains largely unknown. Using mRNA profiling, we identify close to 300 Myc-dependent serum response (MDSR) genes, which are induced by serum in a Myc-dependent manner in mouse fibroblasts. Mapping of genomic Myc-binding sites by ChIP-seq technology revealed that most MDSR genes were directly targeted by Myc, but represented a minor fraction (5.5%) of all Myc-bound promoters (which were 22.4% of all promoters). Other target loci were either induced by serum in a Myc-independent manner, were not significantly regulated or were negatively regulated. MDSR gene products were involved in a variety of processes, including nucleotide biosynthesis, ribosome biogenesis, DNA replication and RNA control. Of the 29 MDSR genes targeted by RNA interference, three showed a requirement for cell-cycle entry upon serum stimulation and 11 for long-term proliferation and/or survival. Hence, proper coordination of key regulatory and biosynthetic pathways following mitogenic stimulation relies upon the concerted regulation of multiple Myc-dependent genes.
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Hansell E, Braschi S, Medzihradszky KF, Sajid M, Debnath M, Ingram J, Lim KC, McKerrow JH. Proteomic analysis of skin invasion by blood fluke larvae. PLoS Negl Trop Dis 2008; 2:e262. [PMID: 18629379 PMCID: PMC2467291 DOI: 10.1371/journal.pntd.0000262] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2008] [Accepted: 06/12/2008] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND During invasion of human skin by schistosome blood fluke larvae (cercariae), a multicellular organism breaches the epidermis, basement membrane, and dermal barriers of skin. To better understand the pathobiology of this initial event in schistosome infection, a proteome analysis of human skin was carried out following invasion by cercariae of Schistosoma mansoni. METHODOLOGY AND RESULTS Human skin samples were exposed to cercariae for one-half hour to two hours. Controls were exposed to water used to collect cercariae in an identical manner, and punctured to simulate cercarial tunnels. Fluid from both control and experimental samples was analyzed by LC/MS/MS using a linear ion trap in "triple play" mode. The coexistence of proteins released by cercariae and host skin proteins from epidermis and basement membrane confirmed that cercarial tunnels in skin were sampled. Among the abundant proteins secreted by cercariae was the cercarial protease that has been implicated in degradation of host proteins, secreted proteins proposed to mediate immune invasion by larvae, and proteins implicated in protection of parasites against oxidative stress. Components of the schistosome surface tegument, previously identified with immune serum, were also released. Both lysis and apoptosis of epidermal cells took place during cercarial invasion of the epidermis. Components of lysed epidermal cells, including desmosome proteins which link cells in the stratum granulosum and stratum spinosum, were identified. While macrophage-derived proteins were present, no mast cell or lymphocyte cytokines were identified. There were, however, abundant immunoglobulins, complement factors, and serine protease inhibitors in skin. Control skin samples incubated with water for the same period as experimental samples ensured that invasion-related proteins and host protein fragments were not due to nonspecific degeneration of the skin samples. CONCLUSIONS This analysis identified secreted proteins from invasive larvae that are released during invasion of human skin. Analysis of specific host proteins in skin invaded by cercariae served to highlight both the histolytic events facilitating cercarial invasion, and the host defenses that attempt to arrest or retard invasion. Proteins abundant in psoriatic skin or UV and heat-stressed skin were not abundant in skin invaded by cercariae, suggesting that results did not reflect general stress in the surgically removed skin specimen. Abundant immunoglobulins, complement factors, and serine protease inhibitors in skin form a biochemical barrier that complements the structural barrier of the epidermis, basement membrane, and dermis. The fragmentation of some of these host proteins suggests that breaching of host defenses by cercariae includes specific degradation of immunoglobulins and complement, and either degradation of, or overwhelming the host protease inhibitor repertoire.
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Chong VH, Lim KC, Rajendran N. Prevalence of active Helicobacter pylori infection among patients referred for endoscopy in Brunei Darussalam. Singapore Med J 2008; 49:42-46. [PMID: 18204768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
INTRODUCTION The prevalence of Helicobacter pylori (H. pylori) infection has been reported to vary between and even within countries. We retrospectively assessed the prevalence among patients referred for endoscopy in our local setting. METHODS 4,700 patients, who had endoscopy and H. pylori testing for the first time over a five-year period, were reviewed. RESULTS The mean age was 45.4 +/- 17.1 years (male 51.1 percent), with racial breakdown similar to the national breakdown. The main indications for endoscopy were dyspepsia (59.6 percent), anaemia (12.6 percent), gastrointestinal bleeding (9.4 percent) and gastro-oesophageal reflux (7.6 percent). The overall prevalence of H. pylori was 26.9 percent, highest in the 30-39 years (30.3 percent) age group. This was higher in males compared to females (30.3 percent versus 23.3 percent, p-value is less than 0.001). Among the racial groups, the expatriate (35.3 percent, p-values are less than 0.001) and the indigenous (31.3 percent, p-values are less than 0.001) groups had significantly higher prevalence rates compared to the Malays (25.9 percent) and the Chinese (23.2 percent). Patients with dyspepsia had the highest prevalence (29.8 percent) compared to the other indications. In patients with peptic ulcer disease, the prevalence rate was 46.9 percent. Over the five-year period, there was a decline in prevalence from 32.3 percent to 25.6 percent. This trend was seen in the Malays and the Chinese, but not the indigenous and the expatriate groups. CONCLUSION Similar to reported data from the regions, prevalence of H. pylori infection varies, with the Malays and the Chinese having the lowest prevalence rate. The prevalence among those with peptic ulcer disease was lower than reported. There was also a decline in the overall prevalence.
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Jolly ER, Chin CS, Miller S, Bahgat MM, Lim KC, DeRisi J, McKerrow JH. Gene expression patterns during adaptation of a helminth parasite to different environmental niches. Genome Biol 2007; 8:R65. [PMID: 17456242 PMCID: PMC1896014 DOI: 10.1186/gb-2007-8-4-r65] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2006] [Revised: 01/29/2007] [Accepted: 04/24/2007] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Schistosome bloodflukes are complex trematodes responsible for 200 million cases of schistosomiasis worldwide. Their life cycle is characterized by a series of remarkable morphological and biochemical transitions between an invertebrate host, an aquatic environment, and a mammalian host. We report a global transcriptional analysis of how this parasite alters gene regulation to adapt to three distinct environments. RESULTS Utilizing a genomic microarray made of 12,000 45-50-mer oligonucleotides based on expressed sequence tags, three different developmental stages of the schistosome parasite were analyzed by pair-wise comparisons of transcript hybridization signals. This analysis resulted in the identification of 1,154 developmentally enriched transcripts. CONCLUSION This study expands the repertoire of schistosome genes analyzed for stage-specific expression to over 70% of the predicted genome. Among the new associations identified are the roles of robust protein synthesis and programmed cell death in development of cercariae in the sporocyst stages, the relative paucity of cercarial gene expression outside of energy production, and the remarkable diversity of adult gene expression programs that reflect adaptation to the host bloodstream and an average lifespan that may approach 10 years.
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Phua J, Koay ESC, Zhang D, Tai LK, Boo XL, Lim KC, Lim TK. Soluble triggering receptor expressed on myeloid cells-1 in acute respiratory infections. Eur Respir J 2006; 28:695-702. [PMID: 16837506 DOI: 10.1183/09031936.06.00005606] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Levels of the soluble form of the triggering receptor expressed on myeloid cells (sTREM)-1 are elevated in severe sepsis. However, it is not known whether sTREM-1 measurements can distinguish milder bacterial infections from noninfectious inflammation. The present authors studied whether serum sTREM-1 levels differ in community-acquired pneumonia, exacerbations of chronic obstructive pulmonary disease (COPD), asthma and controls, and whether sTREM-1 may be used as a surrogate marker for the need for antibiotics. Serum sTREM-1 levels in 150 patients with pneumonia, COPD and asthma exacerbations and 62 healthy controls were measured. Serum sTREM-1 levels were significantly elevated in pneumonia (median 295.2 ng x mL(-1)), COPD (280.3 ng x mL(-1)) and asthma exacerbations (184.0 ng x mL(-1)) compared with controls (83.1 ng x mL(-1)). Levels were higher in pneumonia and Anthonisen type 1 COPD exacerbations than in type 2 and 3 COPD and asthma exacerbations. The area under the receiver operating characteristics curve for sTREM-1 as a surrogate marker for the need for antibiotics was 0.77. Serum levels of the soluble form of the triggering receptor expressed on myeloid cells-1 were elevated predominantly in pneumonia and Anthonisen type 1 COPD exacerbations versus type 2 and 3 chronic obstructive pulmonary disease exacerbations, asthma and controls. Serum levels of the soluble form of the triggering receptor expressed on myeloid cells-1 has moderate but insufficient accuracy as a surrogate marker for the need for antibiotics in lower respiratory tract infections.
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Davies SJ, Smith SJ, Lim KC, Zhang H, Purchio AF, McKerrow JH, West DB. In vivo imaging of tissue eosinophilia and eosinopoietic responses to schistosome worms and eggs. Int J Parasitol 2006; 35:851-9. [PMID: 15950229 PMCID: PMC2891237 DOI: 10.1016/j.ijpara.2005.02.017] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2004] [Revised: 01/31/2005] [Accepted: 02/21/2005] [Indexed: 10/25/2022]
Abstract
Using a sensitive transgenic reporter mouse system and in vivo biophotonic imaging techniques, we present a dynamic analysis of eosinophil responses to schistosome infection. Use of this methodology provided previously unattainable detail on the spatial and temporal distribution of tissue eosinophilia and eosinopoietic responses to schistosome worms and eggs. Dramatic hepatic and intestinal eosinophilia in response to the deposition of schistosome eggs, with accompanying eosinopoiesis in the bone marrow, was observed between weeks 8 and 10 p.i., with subsequent downregulation evident by week 11. Contrary to expectations, we also demonstrate that schistosome parasites themselves induce significant intestinal eosinophilia and eosinopoiesis in the bone marrow at very early stages during prepatent infection.
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Abstract
Intracoronal bleaching is a simple, useful procedure for restoring the colour of discoloured root-filled teeth that are not extensively restored. It is important to minimise the extraradicular diffusion of hydrogen peroxide, as excessive levels of hydrogen peroxide in conjunction with existing inflammatory changes in the periodontium predispose the tooth to external root resorption. To keep the levels of extraradicular diffusion of hydrogen peroxide below the safety limit, it is imperative that an effective intermediate base cement of at least 2 mm be placed at the level of the buccal cemento-enamel junction over the root-filling prior to bleaching. The use of 35% carbamide peroxide as the intracoronal bleaching agent seems to combine the safety of sodium perborate together with the efficacy of 35% hydrogen peroxide. As bleaching agents may reduce the composite-tooth bond of some adhesive systems, the post-bleaching composite restoration should be delayed for at least three weeks.
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Davies SJ, Lim KC, Blank RB, Kim JH, Lucas KD, Hernandez DC, Sedgwick JD, McKerrow JH. Involvement of TNF in limiting liver pathology and promoting parasite survival during schistosome infection. Int J Parasitol 2004; 34:27-36. [PMID: 14711587 PMCID: PMC2859728 DOI: 10.1016/j.ijpara.2003.10.010] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
CD4(+) T cell responses and macrophage activation are essential components of schistosome egg-induced granuloma formation. Previous studies implicated tumour necrosis factor (TNF) as a potential mediator of macrophage recruitment and activation during schistosome infection. Here we demonstrate that signalling by TNF and its receptors can influence granuloma formation, but is ultimately dispensable for granuloma formation in this system. However, we identify a previously unrecognised role for TNF in limiting hepatocellular damage in response to schistosome eggs. Further, we show that this activity of TNF is independent of TNF receptors (TNFR1 and TNFR2). Taken together, these data suggest that additional, as yet unrecognised receptors exist for TNF and that these receptors are capable of mediating important pathological effects in the liver. Finally, we provide evidence that TNF plays an unexpected role in maintaining adult schistosome viability in the portal system.
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Quek SL, Tay CK, Tay KH, Toh SL, Lim KC. Pattern of third molar impaction in a Singapore Chinese population: a retrospective radiographic survey. Int J Oral Maxillofac Surg 2003; 32:548-52. [PMID: 14759117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
One thousand orthopantomograms (OPGs) of patients 20-40 years old were examined. Where impacted third molars were present, the angle and depth of impaction were recorded. Results were analysed using the Pearson chi2 test. 68.6% of OPGs showed at least one impacted third molar. The frequency was three-fold higher in the mandible (1024/1079=90%) than in the maxilla (306/1077=28%), with a significantly higher frequency (P<0.05) in females (56%) than males (44%). The mesioangular impaction was the most common, and 80% of all impacted third molars were partially buried in bone. Of the 429 bilateral occurrence of impacted third molars, 423 were in the mandible. It was concluded that the frequency of impacted third molars in the Singapore Chinese population studied was generally two to three times that reported in races of the Caucasian stock. There was also double the frequency of impacted third molars when compared to a previous study in a Chinese population published in 1932 with females being more frequently affected than males.
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Ong CHS, Asaad M, Lim KC, Ngeow YF. Infrequent occurrence of vancomycin-resistant enterococci in poultry from Malaysian wet markets. THE MALAYSIAN JOURNAL OF PATHOLOGY 2002; 24:91-4. [PMID: 12887166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
Fifty samples of chicken, duck and geese faeces were obtained from 13 wet markets in Kuala Lumpur to study the prevalence of vancomycin-resistant enterococci (VRE) among local market poultry. Biotyping of colonies grown on azide agar incubated at 45 degrees C yielded E. pseudoavium, E. faecalis, E. faecium and E. gallinarum from chicken faeces and E. malodoratus, E. faecalis, E. faecium, E. gallinarum, E. hirae/dispar, and E. durans from goose and duck faeces. On agar containing 6 mg/ l of vancomycin, one strain of E. flavescens was identified, giving a VRE detection rate of 2.0%. This isolate had a vancomycin M.I.C. of 8 mg/l as determined by the Etest, and the van C-3 gene that was identified by PCR followed by sequence analysis. The prevalence of VRE among poultry sold in local markets appears to be low, and may reflect the infrequent use of antimicrobials in our poultry farms. Nevertheless, the possibility of human acquisition of microbes via the food chain cautions against the use of antimicrobials in animal husbandry that may encourage the emergence and spread of multi-drug resistant organisms like the VRE among animal microbial flora.
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