Displaying publications 1 - 20 of 65 in total

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  1. Al Nakshabandi A, Daher AM
    Ear Nose Throat J, 2023 Jan;102(1):20-23.
    PMID: 33320015 DOI: 10.1177/0145561320982164
    Alveolar soft part sarcoma (ASPS) is an aggressive soft-tissue malignancy, notorious for its metastasis to other tissues. A considerable number of cases in the head and neck have been reported but not in the hypopharynx. We describe a 31-year-old man with an incidental finding of a hypopharyngeal mass. Flexible laryngoscopy revealed a fleshy mass 2 × 2 cm2 originating from the left hypopharynx and overlying the epiglottis. Computed tomography scan demonstrated a soft tissue mass in the left wall of the oropharynx measuring about 2.2 × 1.8 cm2, projecting into the hypopharyngeal air space. Magnetic resonance imaging showed a significant thickening of the left hypopharyngeal wall forming a mass lesion occupying the left pyriform sinus and abutting the left aryepiglottic fold. Histopathology indicated that tumor cells were polygonal and epithelioid, with abundant eosinophilic to clear flocculent cytoplasm, eccentric nuclei, and prominent nucleoli. The tumor was positive for smooth muscle actin with rare cells staining for Human Melanoma Black (HMB45). Fluorescence in situ hybridization for transcription factor E3 was also performed and supported the above diagnosis. Our study reports the first case of ASPS in the hypopharynx.
    Matched MeSH terms: In Situ Hybridization, Fluorescence
  2. Zaki NM, Schwarzacher T, Singh R, Madon M, Wischmeyer C, Hanim Mohd Nor N, et al.
    Chromosome Res, 2021 12;29(3-4):373-390.
    PMID: 34657216 DOI: 10.1007/s10577-021-09675-0
    Chromosome identification is essential for linking sequence and chromosomal maps, verifying sequence assemblies, showing structural variations and tracking inheritance or recombination of chromosomes and chromosomal segments during evolution and breeding programs. Unfortunately, identification of individual chromosomes and chromosome arms has been a major challenge for some economically important crop species with a near-continuous chromosome size range and similar morphology. Here, we developed oligonucleotide-based chromosome-specific probes that enabled us to establish a reference chromosome identification system for oil palm (Elaeis guineensis Jacq., 2n = 32). Massive oligonucleotide sequence pools were anchored to individual chromosome arms using dual and triple fluorescent in situ hybridization (EgOligoFISH). Three fluorescently tagged probe libraries were developed to contain, in total 52,506 gene-rich single-copy 47-mer oligonucleotides spanning each 0.2-0.5 Mb across strategically placed chromosome regions. They generated 19 distinct FISH signals and together with rDNA probes enabled identification of all 32 E. guineensis chromosome arms. The probes were able to identify individual homoeologous chromosome regions in the related Arecaceae palm species: American oil palm (Elaeis oleifera), date palm (Phoenix dactylifera) and coconut (Cocos nucifera) showing the comparative organization and concerted evolution of genomes in the Arecaceae. The oligonucleotide probes developed here provide a valuable approach to chromosome arm identification and allow tracking chromosome transfer in hybridization and breeding programs in oil palm, as well as comparative studies within Arecaceae.
    Matched MeSH terms: In Situ Hybridization, Fluorescence
  3. 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
  4. 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
  5. Setiawan AB, Teo CH, Kikuchi S, Sassa H, Kato K, Koba T
    PLoS One, 2020;15(1):e0227578.
    PMID: 31945109 DOI: 10.1371/journal.pone.0227578
    Centromeres are prerequisite for accurate segregation and are landmarks of primary constrictions of metaphase chromosomes in eukaryotes. In melon, high-copy-number satellite DNAs (SatDNAs) were found at various chromosomal locations such as centromeric, pericentromeric, and subtelomeric regions. In the present study, utilizing the published draft genome sequence of melon, two new SatDNAs (CmSat162 and CmSat189) of melon were identified and their chromosomal distributions were confirmed using fluorescence in situ hybridization. DNA probes prepared from these SatDNAs were successfully hybridized to melon somatic and meiotic chromosomes. CmSat162 was located on 12 pairs of melon chromosomes and co-localized with the centromeric repeat, Cmcent, at the centromeric regions. In contrast, CmSat189 was found to be located not only on centromeric regions but also on specific regions of the chromosomes, allowing the characterization of individual chromosomes of melon. It was also shown that these SatDNAs were transcribed in melon. These results suggest that CmSat162 and CmSat189 might have some functions at the centromeric regions.
    Matched MeSH terms: In Situ Hybridization, Fluorescence
  6. Taheri S, Teo CH, Heslop-Harrison JS, Schwarzacher T, Tan YS, Wee WY, et al.
    Int J Mol Sci, 2022 Jun 30;23(13).
    PMID: 35806276 DOI: 10.3390/ijms23137269
    Boesenbergia rotunda (Zingiberaceae), is a high-value culinary and ethno-medicinal plant of Southeast Asia. The rhizomes of this herb have a high flavanone and chalcone content. Here we report the genome analysis of B. rotunda together with a complete genome sequence as a hybrid assembly. B. rotunda has an estimated genome size of 2.4 Gb which is assembled as 27,491 contigs with an N50 size of 12.386 Mb. The highly heterozygous genome encodes 71,072 protein-coding genes and has a 72% repeat content, with class I TEs occupying ~67% of the assembled genome. Fluorescence in situ hybridization of the 18 chromosome pairs at the metaphase showed six sites of 45S rDNA and two sites of 5S rDNA. An SSR analysis identified 238,441 gSSRs and 4604 EST-SSRs with 49 SSR markers common among related species. Genome-wide methylation percentages ranged from 73% CpG, 36% CHG and 34% CHH in the leaf to 53% CpG, 18% CHG and 25% CHH in the embryogenic callus. Panduratin A biosynthetic unigenes were most highly expressed in the watery callus. B rotunda has a relatively large genome with a high heterozygosity and TE content. This assembly and data (PRJNA71294) comprise a source for further research on the functional genomics of B. rotunda, the evolution of the ginger plant family and the potential genetic selection or improvement of gingers.
    Matched MeSH terms: In Situ Hybridization, Fluorescence
  7. 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*
  8. Liu S, Punthambaker S, Iyer EPR, Ferrante T, Goodwin D, Fürth D, et al.
    Nucleic Acids Res, 2021 06 04;49(10):e58.
    PMID: 33693773 DOI: 10.1093/nar/gkab120
    We present barcoded oligonucleotides ligated on RNA amplified for multiplexed and parallel insitu analyses (BOLORAMIS), a reverse transcription-free method for spatially-resolved, targeted, in situ RNA identification of single or multiple targets. BOLORAMIS was demonstrated on a range of cell types and human cerebral organoids. Singleplex experiments to detect coding and non-coding RNAs in human iPSCs showed a stem-cell signature pattern. Specificity of BOLORAMIS was found to be 92% as illustrated by a clear distinction between human and mouse housekeeping genes in a co-culture system, as well as by recapitulation of subcellular localization of lncRNA MALAT1. Sensitivity of BOLORAMIS was quantified by comparing with single molecule FISH experiments and found to be 11%, 12% and 35% for GAPDH, TFRC and POLR2A, respectively. To demonstrate BOLORAMIS for multiplexed gene analysis, we targeted 96 mRNAs within a co-culture of iNGN neurons and HMC3 human microglial cells. We used fluorescence in situ sequencing to detect error-robust 8-base barcodes associated with each of these genes. We then used this data to uncover the spatial relationship among cells and transcripts by performing single-cell clustering and gene-gene proximity analyses. We anticipate the BOLORAMIS technology for in situ RNA detection to find applications in basic and translational research.
    Matched MeSH terms: In Situ Hybridization, Fluorescence/methods*
  9. Kong PL, Cheah PL, Mun KS, Chiew SF, Lau TP, Koh CC, et al.
    Malays J Pathol, 2020 Dec;42(3):369-376.
    PMID: 33361717
    Together with isocitrate dehydrogenase (IDH) mutation, co-deletion of 1p19q (1p19q codel) is a prerequisite for diagnosis of oligodendroglioma, making it imperative that histopathology laboratories introduce testing for 1p19q codel. To date there is still no consensus reference range and cut-offs that confirm deletion of 1p or 19q. We embarked on determining our reference range in 11 formalinfixed, paraffin-embedded non-neoplastic brain tissue using fluorescence in situ hybridisation (FISH) with the Vysis 1p36/1q25 and 19q13/19p13 FISH Probe Kit (Abbott Molecular Inc., USA). At same time we attempted to validate our methodology in 13 histologically-confirmed IDH-mutant oligodendrogliomas. For 1p, percentage cells with deletion (range=8-23%; mean±SD = 15.73±5.50%) and target: control (1p36:1q25) ratio (range = 0.89-0.96; mean±SD = 0.92±0.03) in non-neoplastic brain, differed significantly (p<0.000) from oligodendroglioma (percentage cells with deletion: range = 49-100%; mean±SD = 82.46±15.21%; target:control ratio range:0.50-0.76; mean±SD = 0.59±0.08). For 19q, percentage cells with deletion (range = 7-20%; mean±SD = 12.00±3.49%) and target:control (19q13/19p13) ratio (range:0.90-0.97; mean±SD = 0.94±0.02) in non-neoplastic brain also differed significantly from oligodendroglioma (percentage cells with deletion: range = 45-100%; mean±SD = 82.62±18.13%; target:control ratio range:0.50-0.78; mean±SD = 0.59±0.09). Using recommended calculation method, for diagnosis of 1p deletion, percentage of cells showing deletion should be >32-33% and/or target:control ratio <0.83. For 19q, percentage of cells showing deletion should be >22% and target:control ratio <0.88. Using these cut-offs all 13 oligodendroglioma demonstrated 1p19q codel.
    Matched MeSH terms: In Situ Hybridization, Fluorescence*
  10. 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
  11. Ling KH, Brautigan PJ, Moore S, Fraser R, Leong MP, Leong JW, et al.
    Data Brief, 2016 Jun;7:282-90.
    PMID: 26958646 DOI: 10.1016/j.dib.2016.01.045
    SRY (Sex Determining Region Y)-Box 4 or Sox4 is an important regulator of the pan-neuronal gene expression during post-mitotic cell differentiation within the mammalian brain. Sox4 gene locus has been previously characterized with multiple sense and overlapping natural antisense transcripts [1], [2]. Here we provide accompanying data on various analyses performed and described in Ling et al. [2]. The data include a detail description of various features found at Sox4 gene locus, additional experimental data derived from RNA-Fluorescence in situ Hybridization (RNA-FISH), Western blotting, strand-specific reverse-transcription quantitative polymerase chain reaction (RT-qPCR), gain-of-function and in situ hybridization (ISH) experiments. All the additional data provided here support the existence of an endogenous small interfering- or PIWI interacting-like small RNA known as Sox4_sir3, which origin was found within the overlapping region consisting of a sense and a natural antisense transcript known as Sox4ot1.
    Matched MeSH terms: In Situ Hybridization, Fluorescence
  12. Goh TC, Bajuri MY, Yusof MF, Mohd Apandi H, Sarifulnizam FA
    Cureus, 2021 Mar 03;13(3):e13664.
    PMID: 33824815 DOI: 10.7759/cureus.13664
    We report the case of a 14-year-old girl who presented with a one-month history of back pain and bilateral lower limb weakness preceded by constitutional symptoms. She neither had a family history of malignancy nor a previous history of trauma. A series of imaging procedures revealed an aggressive lesion of the T12 vertebra with a large soft-tissue component and intraspinal extension leading to spinal cord compression causing cord edema. She underwent urgent posterior instrumentation and fixation of T9 to T12 vertebrae due to worsening neurological deficits. Adjuvant and neoadjuvant chemotherapy with palliative spinal stabilisation were also performed. Features of the lesion were highly consistent with ES on immunohistochemical study and fluorescence in situ hybridization (FISH) analysis for the EWSR1 gene. Postoperatively, both of her lower limbs improved in power and she benefited from regular physiotherapy.
    Matched MeSH terms: In Situ Hybridization, Fluorescence
  13. 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.
    MyJurnal
    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
  14. 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.
    MyJurnal
    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
  15. Amri MF, Abdullah A, Azmi MI, Mohd Zaki F, Md Pauzi SH
    Malays J Pathol, 2021 Aug;43(2):319-325.
    PMID: 34448796
    BACKGROUND: Ewing sarcoma (ES) is an aggressive tumour which is typically skeletal in origin. ES involving the head and neck region is uncommon and can be easily confused with other small round blue cell tumours. We herein present a rare case of ES involving the sinonasal area.

    CASE PRESENTATION: A 5-year-old Somalian boy with no known medical illness presented with progressive nasal blockage associated with clear nasal discharge and intermittent spontaneous epistaxis for three months. CT paranasal sinus and neck region revealed poorly enhancing expansile mass in the right maxillary sinus with areas of necrosis within. Initial radiological differential diagnoses were lymphoma and rhabdomyosarcoma. The mass was biopsied and histologically showed diffuse sheets of small round blue cells that was positive to CD99, NSE and vimentin. The muscle and lymphoid markers were negative. Fluorescence in-situ hybridisation (FISH) study revealed the presence of EWSR1 gene rearrangement thus diagnosis of ES was rendered.

    CONCLUSIONS: ES of sinonasal tract is a rare entity and its pathological features significantly overlap with others small round blue cells tumour. Demonstration of EWSR1 gene translocation is recommended for the diagnosis of ES particularly at uncommon sites.

    Matched MeSH terms: In Situ Hybridization, Fluorescence
  16. 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*
  17. 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*
  18. 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*
  19. 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*
  20. 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
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