Displaying publications 1 - 20 of 48 in total

  1. Ong YH, Chua AS, Lee BP, Ngoh GC, Hashim MA
    Water Environ. Res., 2012 Jan;84(1):3-8.
    PMID: 22368821
    A sequencing batch reactor (SBR) seeded with flocculated sludge and fed with synthetic wastewater was operated for an enhanced biological phosphorus removal (EBPR) process. Eight weeks after reactor startup, sludge granules were observed. The granules had a diameter of 0.5 to 3.0 mm and were brownish in color and spherical or ellipsoidal in shape. No significant change was observed in sludge granule size when operational pH was changed from 7 to 8. The 208-day continuous operation of the SBR showed that sludge granules were stably maintained with a sludge volume index (SVI) between 30 to 55 mL/g while securing a removal efficiency of 83% for carbon and 97% for phosphorus. Fluorescent in situ hybridization (FISH) confirmed the enrichment of polyphosphate accumulating organisms (PAOs) in the SBR. The observations of sludge granulation in this study encourage further studies in the development of granules-based EBPR process.
    Matched MeSH terms: In Situ Hybridization, Fluorescence
  2. Gagliano MC, Ismail SB, Stams AJM, Plugge CM, Temmink H, Van Lier JB
    Water Res., 2017 09 15;121:61-71.
    PMID: 28511041 DOI: 10.1016/j.watres.2017.05.016
    For the anaerobic biological treatment of saline wastewater, Anaerobic Digestion (AD) is currently a possibility, even though elevated salt concentrations can be a major obstacle. Anaerobic consortia and especially methanogenic archaea are very sensitive to fluctuations in salinity. When working with Upflow Sludge Blanket Reactor (UASB) technology, in which the microorganisms are aggregated and retained in the system as a granular biofilm, high sodium concentration negatively affects aggregation and consequently process performances. In this research, we analysed the structure of the biofilm and granules formed during the anaerobic treatment of high salinity (at 10 and 20 g/L of sodium) synthetic wastewater at lab scale. The acclimated inoculum was able to accomplish high rates of organics removal at all the salinity levels tested. 16S rRNA gene clonal analysis and Fluorescence In Situ Hybridization (FISH) analyses identified the acetoclastic Methanosaeta harundinacea as the key player involved acetate degradation and microbial attachment/granulation. When additional calcium (1 g/L) was added to overcome the negative effect of sodium on microbial aggregation, during the biofilm formation process microbial attachment and acetate degradation decreased. The same result was observed on granules formation: while calcium had a positive effect on granules strength when added to UASB reactors, Methanosaeta filaments were not present and the degradation of the partially acidified substrate was negatively influenced. This research demonstrated the possibility to get granulation at high salinity, bringing to the forefront the importance of a selection towards Methanosaeta cells growing in filamentous form to obtain strong and healthy granules.
    Matched MeSH terms: In Situ Hybridization, Fluorescence
  3. Ho CC, Tan WP, Pathmanathan R, Tan WK, Tan HM
    Asian Pac. J. Cancer Prev., 2013;14(7):4057-9.
    PMID: 23991952
    BACKGROUND: Fluorescence in situ hybridization (FISH) testing may be useful to screen for bladder carcinoma or dysplasia by detecting aneuploidy chromosomes 3, 7, 17 and deletion of the chromosome 9p21 locus in urine specimens. This study aimed to assess the sensitivity, specificity, positive and negative predictive value of FISH in a multi-ethnic population in Asia.

    MATERIALS AND METHODS: Patients with haematuria and/or past history of urothelial cancer on follow-up had their voided urine tested with FISH. Patients then underwent cystoscopy/ ureteroscopy and any lesions seen were biopsied. The histopathological reports of the bladder or ureteroscopic mucosal biopsies were then compared with the FISH test results.

    RESULTS: Two hundred sixty patients were recruited. The sensitivity and specificity of the FISH test was 89.2% and 83.4% respectively. The positive (PPV) and negative predictive values (NPV) were 47.1% and 97.9%. By excluding patients who had positive deletion of chromosome 9, the overall results of the screening test improved: sensitivity 84.6%; specificity 96.4%; PPV 75.9% and NPV 97.9%.

    CONCLUSIONS: UroVysion FISH has a high specificity of detecting urothelial cancer or dysplasia when deletion of chromosome 9 is excluded. Negative UroVysion FISH-tests may allow us to conserve health resources and minimize trauma by deferring cystoscopic or ureteroscopic examination.

    Matched MeSH terms: In Situ Hybridization, Fluorescence/methods*
  4. Tan YO, Han S, Lu YS, Yip CH, Sunpaweravong P, Jeong J, et al.
    Cancer, 2010 Dec 1;116(23):5348-57.
    PMID: 20715159 DOI: 10.1002/cncr.25476
    Overexpression of the epidermal growth factor receptor-related gene ErbB2 occurs in 18% to 25% of patients with breast cancer in Western countries and is associated with a poor prognosis. The prevalence of ErbB2-positive tumors in Asia is unclear, partly because data are limited. The objective of this review was to summarize the reported prevalence of ErbB2-positive tumors from a large sample of Asian patients and to examine ErbB2 assessment methods in Asia. From searches of MEDLINE, local language journals, and local and international conference proceedings as well as locoregional breast cancer experts' recommendations, the authors selected up to 5 studies each from India, Korea, Malaysia, the Philippines, Singapore, Taiwan, and Thailand that reported ErbB2 results based on assessment with immunohistochemistry (IHC) and/or fluorescence in situ hybridization (FISH). The reported prevalence of ErbB2-positive tumors in 22 studies on 24,671 patients, of whom 14,398 patients were assessed for ErbB2 status, varied widely (range, 6%-65%) as did the assessment methods used. Most studies (n=21) used IHC to assess ErbB2 status, but definitions for positivity varied. When robust assessment methods were used, the median prevalence was 19% based on strong IHC staining (IHC3+; n=9812 patients) and 25% based on FISH (n=681 patients). Data on the prevalence of ErbB2-positive breast cancer in Asia are limited. The current survey indicated that the prevalence in Asia may be similar to that in Western countries; thus, up to 1 in 4 Asian patients with breast cancer potentially could benefit from ErbB2-targeted treatment. A standard, reliable ErbB2 assessment method available to patients across Asia is urgently required.
    Matched MeSH terms: In Situ Hybridization, Fluorescence
  5. Reena Rahayu Md Zin, Sharifah Noor Akmal, Zubaidah Zakaria, Haut, Clarence Ko Ching, Siti Mariam Yusof, Julia Mohd Idris, et al.
    Medicine & Health, 2008;3(1):22-29.
    Turner syndrome is one of the most common chromosomal abnormalities affecting newborn females. More than half of patients with Turner syndrome have a 45X karyotype The rest of the patients may have structurally abnormal sex chromosomes or are mosaics with normal or abnormal sex chromosomes. Mosaicism with a second X sex chromosome is not usually of clinical significance. However, Turner syndrome patients having a second Y chromosome or Y chromosomal material are at risk of developing gonadoblastoma later in life. The aim of this study is to compare the results of conventional (karyotyping) and molecular cytogenetics (FISH), and discuss the advantages and limitations in the diagnosis of Turner syndrome. We also aim to compare the degree of mosaicism identified using conventional cytogenetics and FISH techniques. Conventional cytogenetics and FISH analyses were performed on eight peripheral blood samples of patients with Turner syndrome collected between 2004 and 2006. From this study, two out of eight patients with Turner syndrome were found to have the sex determining region on the Y chromosome (SRY) gene by FISH analysis. Our results showed that the rate of detection of mosaic cases in Turner syndrome was also increased to 88% after using the FISH technique. We concluded that FISH is more superior to conventional cytogenetics in the detection of the Y chromosomal material. FISH is also a quick and cost effective method in diagnosing Turner syndrome and assessing the degree of mosaicism.
    Matched MeSH terms: In Situ Hybridization, Fluorescence
  6. Chia, W.K., Zubaidah, Z., Reena Rahayu Md Zin, Rohaizak, M., Asmiati, A., Rafie, M.K., et al.
    Medicine & Health, 2012;7(1):47-56.
    Aneusomy is an early genetic event and a characteristic feature of many solid tumors. It is often associated with poor prognosis in cancer patients. The involvement of PAX8-PPARγ rearrangement in tumorigenesis of follicular thyroid lesions has been widely assessed. However, there were few reports on aneusomy of the PPARγ gene at the 3p25 locus in follicular thyroid lesions. It remains undetermined whether these abnormalities can be translated into improved diagnosis, classification, or outcome prediction. Herein, we report three cases of follicular thyroid neoplasms [two follicular thyroid carcinomas (FTCs) and one Hurthle cell adenoma (HCA)] with 3p25 aneusomy detected by fluorescence in situ hybridization (FISH). 3p25 trisomy was observed in one FTC and one HCA while 3p25 tetrasomy was observed in one FTC. Furthermore, all three lesions did not show overexpression of PPARγ protein. Hurthle cell neoplasms (HCN) are distinct clinically and histologically from other follicular thyroid neoplasms (FTN). However, the presence of the aneusomy in HCA and FTC indicates that there could be a biological continuum between the two and chromosomal gains might play an important role in the pathogenesis of these two types of neoplasms. Despite their differences, HCN and FTN may share the same early genetic event in tumour development.
    Matched MeSH terms: In Situ Hybridization, Fluorescence
  7. Wong EH, Subramaniam G, Navaratnam P, Sekaran SD
    Indian J Med Microbiol, 2007 Oct;25(4):391-4.
    PMID: 18087092
    Fluorescent in situ hybridization (FISH) was carried out using two different oligonucleotide probes specific for Pseudomonas spp. and Acinetobacter spp. These probes were tested against different organisms and were found to be highly specific. Sensitivity testing showed that the probes were able to detect as low as 10 3 CFU/mL. In addition, FISH was carried out directly on positive blood culture samples and the detection of microorganisms took less than 2 h. We believe that FISH is a rapid method that can be used as a routine laboratory diagnostic technique for the detection of Acinetobacter spp. and Pseudomonas spp. in clinical samples.
    Matched MeSH terms: In Situ Hybridization, Fluorescence/methods*
  8. Lee YI, Yap JW, Izan S, Leitch IJ, Fay MF, Lee YC, et al.
    BMC Genomics, 2018 Aug 02;19(1):578.
    PMID: 30068293 DOI: 10.1186/s12864-018-4956-7
    BACKGROUND: Satellite DNA is a rapidly diverging, largely repetitive DNA component of many eukaryotic genomes. Here we analyse the evolutionary dynamics of a satellite DNA repeat in the genomes of a group of Asian subtropical lady slipper orchids (Paphiopedilum subgenus Parvisepalum and representative species in the other subgenera/sections across the genus). A new satellite repeat in Paphiopedilum subgenus Parvisepalum, SatA, was identified and characterized using the RepeatExplorer pipeline in HiSeq Illumina reads from P. armeniacum (2n = 26). Reconstructed monomers were used to design a satellite-specific fluorescent in situ hybridization (FISH) probe. The data were also analysed within a phylogenetic framework built using the internal transcribed spacer (ITS) sequences of 45S nuclear ribosomal DNA.

    RESULTS: SatA comprises c. 14.5% of the P. armeniacum genome and is specific to subgenus Parvisepalum. It is composed of four primary monomers that range from 230 to 359 bp and contains multiple inverted repeat regions with hairpin-loop motifs. A new karyotype of P. vietnamense (2n = 28) is presented and shows that the chromosome number in subgenus Parvisepalum is not conserved at 2n = 26, as previously reported. The physical locations of SatA sequences were visualised on the chromosomes of all seven Paphiopedilum species of subgenus Parvisepalum (2n = 26-28), together with the 5S and 45S rDNA loci using FISH. The SatA repeats were predominantly localisedin the centromeric, peri-centromeric and sub-telocentric chromosome regions, but the exact distribution pattern was species-specific.

    CONCLUSIONS: We conclude that the newly discovered, highly abundant and rapidly evolving satellite sequence SatA is specific to Paphiopedilum subgenus Parvisepalum. SatA and rDNA chromosomal distributions are characteristic of species, and comparisons between species reveal that the distribution patterns generate a strong phylogenetic signal. We also conclude that the ancestral chromosome number of subgenus Parvisepalum and indeed of all Paphiopedilum could be either 2n = 26 or 28, if P. vietnamense is sister to all species in the subgenus as suggested by the ITS data.

    Matched MeSH terms: In Situ Hybridization, Fluorescence/methods*
  9. Shuib S, Saaid NN, Zakaria Z, Ismail J, Abdul Latiff Z
    Malays J Pathol, 2017 Apr;39(1):77-81.
    PMID: 28413209 MyJurnal
    Potocki-Lupski syndrome (PTLS), also known as duplication 17p11.2 syndrome, trisomy 17p11.2 or dup(17)(p11.2p11.2) syndrome, is a developmental disorder and a rare contiguous gene syndrome affecting 1 in 20,000 live births. Among the key features of such patients are autism spectrum disorder, learning disabilities, developmental delay, attention-deficit disorder, infantile hypotonia and cardiovascular abnormalities. Previous studies using microarray identified variations in the size and extent of the duplicated region of chromosome 17p11.2. However, there are a few genes which are considered as candidates for PTLS which include RAI1, SREBF1, DRG2, LLGL1, SHMT1 and ZFP179. In this report, we investigated a case of a 3-year-old girl who has developmental delay. Her chromosome analysis showed a normal karyotype (46,XX). Analysis using array CGH (4X44 K, Agilent USA) identified an ~4.2 Mb de novo duplication in chromosome 17p11.2. The result was confirmed by fluorescence in situ hybridization (FISH) using probes in the critical PTLS region. This report demonstrates the importance of microarray and FISH in the diagnosis of PTLS.
    Matched MeSH terms: In Situ Hybridization, Fluorescence*
  10. Sharifah NA, Zakaria Z, Chia WK
    Methods Mol. Biol., 2013;952:187-96.
    PMID: 23100233 DOI: 10.1007/978-1-62703-155-4_13
    Fluorescence in situ hybridization (FISH) is increasingly gaining importance in clinical diagnostics settings. Due to the ability of the technique to detect chromosomal abnormalities in samples with low cellularity or containing a mixed population of cells even at a single-cell level, it has become more popular in cancer research and diagnosis. Here, we describe the FISH technique for detection of PAX8-PPARγ translocation in follicular thyroid neoplasms, and the optimal protocol for the detection of this fusion gene using in archival formalin-fixed paraffin-embedded (FFPE) thyroid tissue sections.
    Matched MeSH terms: In Situ Hybridization, Fluorescence/methods*
  11. Palasubramaniam S, Muniandy S, Navaratnam P
    J. Microbiol. Methods, 2008 Jan;72(1):107-9.
    PMID: 18054098
    Multi-resistant Enterobacteriaceae pose a serious threat of hospital acquired infections and their rapid identification is important for better clinical outcome. This study describes the rapid identification of extended-spectrum beta-lactamase-producing Klebsiella pneumoniae of the sulphydryl variable-type by fluorescent in-situ hybridization. The method which rapidly identifies the target genes within 1 h could be a potentially rapid bacterial diagnostic tool.
    Matched MeSH terms: In Situ Hybridization, Fluorescence/methods*
  12. Masir N, Campbell LJ, Goff LK, Jones M, Marafioti T, Cordell J, et al.
    Br. J. Haematol., 2009 Mar;144(5):716-25.
    PMID: 19120369 DOI: 10.1111/j.1365-2141.2008.07528.x
    The t(14;18)(q32;q21) chromosomal translocation induces BCL2 protein overexpression in most follicular lymphomas. However the expression of BCL2 is not always homogeneous and may demonstrate a variable degree of heterogeneity. This study analysed BCL2 protein expression pattern in 33 cases of t(14;18)-positive follicular lymphomas using antibodies against two different epitopes (i.e. the widely used antibody BCL2/124 and an alternative antibody E17). 16/33 (49%) cases demonstrated strong BCL2 expression. In 10/33 (30%) cases, BCL2 expression was heterogeneous and in some of these, its loss appeared to be correlated with cell proliferation, as indicated by Ki67 expression. Double immunofluorescence labelling confirmed an inverse BCL2/Ki67 relationship, where in 24/28 (86%) cases cellular expression of BCL2 and Ki67 was mutually exclusive. In addition, seven BCL2 'pseudo-negative' cases were identified in which immunostaining was negative with antibody BCL2/124, but positive with antibody E17. Genomic DNA sequencing of these 'pseudo-negative' cases demonstrated eleven mutations in four cases and nine of these were missense mutations. It can be concluded that in follicular lymphomas, despite carrying the t(14;18) translocations, BCL2 protein expression may be heterogeneous and loss of BCL2 could be related to cell proliferation. Secondly, mutations in translocated BCL2 genes appear to be common and may cause BCL2 pseudo-negative immunostaining.
    Matched MeSH terms: In Situ Hybridization, Fluorescence/methods
  13. Tai YC, Kim LH, Peh SC
    Pathology, 2003 Oct;35(5):436-43.
    PMID: 14555389
    The most common recurrent genetic aberration in anaplastic large cell lymphoma (ALCL) is translocation involving the ALK gene that results in ectopic expression of ALK protein in lymphoid tissue. This study aims to investigate the frequency of ALK gene rearrangement in a series of Asian ALCL.
    Matched MeSH terms: In Situ Hybridization, Fluorescence*
  14. Shaminie J, Peh SC, Tan MJ
    Pathology, 2003 Oct;35(5):414-21.
    PMID: 14555386
    PCR has been the primary method used for the detection of t(14;18) translocation in formalin-fixed, paraffin-embedded tissues. This technique mainly targets the well-characterised breakpoint regions in chromosomes 14 and 18. FISH is now applicable on paraffin tissue sections and has been suggested to be capable of detecting essentially 100% of t(14;18) translocated cases. In this study, we described the application of both PCR and FISH for the detection of t(14;18) translocation.
    Matched MeSH terms: In Situ Hybridization, Fluorescence/methods*
  15. Heah KG, Hassan MI, Huat SC
    Asian Pac. J. Cancer Prev., 2011;12(4):1017-22.
    PMID: 21790244
    INTRODUCTION: Oral squamous cell carcinoma (OSCC) has high local recurrence, partly caused by the lack of clear margin identification on surgical removal of cancerous tissues. Direct visualization by immunostaining and fluorescent in situ hybridization (FISH) in tissue sections gives more definite information about genetic damage at margins with appropriately selected biomarkers.

    AIMS: To determine the usefulness of immunohistochemical techniques and FISH of the tumour suppressor TP 53 gene to identify microinvasion in marginal tissue sections and to relate the possible correlation between protein expression and genetic aberrations in OSCC cases in Malaysia.

    METHODS: Immunohistochemistry and FISH of TP 53 genes were applied on 26 OSCC formalin fixed paraffin embed (FFEP) blocks selected from two oral cancer referral centers in Malaysia.

    RESULTS: For p53 protein immunohistochemistry, 96% of the 26 OSCC studied showed positive immunostaining at the excision margins. In FISH assay, 48.9±9.7% of the cancerous cells were monoploid for p53 probe signals, 41.0±9.5 % were diploid, and 10.2±7.8 % were polyploid. A correlation between p53 immunostaining and TP53 gene aberrations was noted (p< 0.05).

    CONCLUSIONS: Immunohistochemical analysis of p53 protein expression and FISH of TP53 gene could be applied as screening tool for microinvasion of OSCC.

    Matched MeSH terms: In Situ Hybridization, Fluorescence/methods
  16. Chiam CW, Sam IC, Chan YF, Wong KT, Ong KC
    Methods Mol. Biol., 2016;1426:235-40.
    PMID: 27233276 DOI: 10.1007/978-1-4939-3618-2_21
    Immunohistochemistry is a histological technique that allows detection of one or more proteins of interest within a cell using specific antibody binding, followed by microscopic visualization of a chromogenic substrate catalyzed by peroxidase and/or alkaline phosphatase. Here, we describe a method to localize Chikungunya virus (CHIKV) antigens in formalin-fixed and paraffin-embedded infected mouse brain.
    Matched MeSH terms: In Situ Hybridization, Fluorescence
  17. Takeuchi Y, Chaffron S, Salcher MM, Shimizu-Inatsugi R, Kobayashi MJ, Diway B, et al.
    Syst. Appl. Microbiol., 2015 Jul;38(5):330-9.
    PMID: 26138047 DOI: 10.1016/j.syapm.2015.05.006
    Pitchers are modified leaves used by carnivorous plants for trapping prey. Their fluids contain digestive enzymes from the plant and they harbor abundant microbes. In this study, the diversity of bacterial communities was assessed in Nepenthes pitcher fluids and the composition of the bacterial community was compared to that in other environments, including the phyllosphere of Arabidopsis, animal guts and another pitcher plant, Sarracenia. Diversity was measured by 454 pyrosequencing of 16S rRNA gene amplicons. A total of 232,823 sequences were obtained after chimera and singleton removal that clustered into 3260 distinct operational taxonomic units (OTUs) (3% dissimilarity), which were taxonomically distributed over 17 phyla, 25 classes, 45 orders, 100 families, and 195 genera. Pyrosequencing and fluorescence in situ hybridization yielded similar estimates of community composition. Most pitchers contained high proportions of unique OTUs, and only 22 OTUs (<0.6%) were shared by ≥14/16 samples, suggesting a unique bacterial assemblage in each pitcher at the OTU level. Diversity analysis at the class level revealed that the bacterial communities of both opened and unopened pitchers were most similar to that of Sarracenia and to that in the phyllosphere. Therefore, the bacterial community in pitchers may be formed by environmental filtering and/or by phyllosphere bacteria.
    Matched MeSH terms: In Situ Hybridization, Fluorescence
  18. Ogawa S, Ramadasan PN, Goschorska M, Anantharajah A, Ng KW, Parhar IS
    J. Comp. Neurol., 2012 Sep 1;520(13):2991-3012.
    PMID: 22430310 DOI: 10.1002/cne.23103
    The tachykinins are a family of neuropeptides, including substance P (SP), neurokinin A (NKA), and neurokinin B (NKB), that are encoded by the tac1 (SP and NKA) or tac2/3 (NKB) genes. Tachykinins are widely distributed in the central nervous system and have roles as neurotransmitters and/or neuromodulators. Recent studies in mammals have demonstrated the coexpression of NKB and kisspeptin and their comodulatory roles over the control of reproduction. We have recently identified two kisspeptin-encoding genes, kiss1 and kiss2, in teleosts. However, such relationship between tachykinins and kisspeptins has not been demonstrated in non-mammalian species. To determine the involvement of tachykinins in the reproduction in teleosts, we identified tac1 and two tac2 (tac2a and tac2b) sequences in the zebrafish genome using in silico data mining. Zebrafish tac1 encodes SP and NKA, whereas the tac2 sequences encode NKB and an additional peptide homologous to NKB (NKB-related peptide). Digoxigenin in situ hybridization in the brain of zebrafish showed tac1 mRNA-containing cells in the olfactory bulb, telencephalon, preoptic region, hypothalamus, mesencephalon, and rhombencephalon. The zebrafish tac2a mRNA-containing cells were observed in the preoptic region, habenula, and hypothalamus, whereas the tac2b mRNA-containing cells were predominantly observed in the dorsal telencephalic area. Furthermore, we examined the coexpression of tachykinins and two kisspeptin genes in the brain of zebrafish. Dual fluorescent in situ hybridization showed no coexpression of tachykinins mRNA with kisspeptins mRNA in hypothalamic nuclei or the habenula. These results suggest the presence of independent pathways for kisspeptins and NKB neurons in the brain of zebrafish.
    Matched MeSH terms: In Situ Hybridization, Fluorescence
  19. Masir N, Ghoddoosi M, Mansor S, Abdul-Rahman F, Florence CS, Mohamed-Ismail NA, et al.
    Histopathology, 2012 Apr;60(5):804-15.
    PMID: 22320393 DOI: 10.1111/j.1365-2559.2011.04127.x
    To investigate RCL2 as a fixative for tissue fixation in routine histopathological examination and to assess tissue suitability for ancillary investigations.
    Matched MeSH terms: In Situ Hybridization, Fluorescence
  20. Mdzin R, Ko C, Abdul Latif Z, Zakaria Z
    Singapore Med J, 2008 Nov;49(11):e336-9.
    PMID: 19037546
    Interstitial deletions of the long arm of chromosome 4 are rare. The deletions may occur at the proximal or the distal portions of the chromosome and different breakpoints may be involved. We report an interstitial deletion of 4q: 46XY der 4 (q28;q35) in a six-year-old boy with dysmorphic features associated with moderate mental retardation. Parental chromosomal analysis showed a balanced paternal translocation.
    Matched MeSH terms: In Situ Hybridization, Fluorescence
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