Displaying publications 21 - 40 of 70 in total

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  1. Analysis and functional annotation of expressed sequence tags (ESTs) from multiple tissues of oil palm (Elaeis guineensis Jacq.)
    Ho CL, Kwan YY, Choi MC, Tee SS, Ng WH, Lim KA, et al.
    BMC Genomics, 2007;8:381.
    PMID: 17953740
    Oil palm is the second largest source of edible oil which contributes to approximately 20% of the world's production of oils and fats. In order to understand the molecular biology involved in in vitro propagation, flowering, efficient utilization of nitrogen sources and root diseases, we have initiated an expressed sequence tag (EST) analysis on oil palm.
    Matched MeSH terms: Gene Library
  2. Fulltext Identification and analysis of expressed sequence tags present in xylem tissues of kelampayan (Neolamarckia cadamba (Roxb.) Bosser)
    Ho WS, Pang SL, Abdullah J
    Physiol Mol Biol Plants, 2014 Jul;20(3):393-7.
    PMID: 25049467 DOI: 10.1007/s12298-014-0230-x
    The large-scale genomic resource for kelampayan was generated from a developing xylem cDNA library. A total of 6,622 high quality expressed sequence tags (ESTs) were generated through high-throughput 5' EST sequencing of cDNA clones. The ESTs were analyzed and assembled to generate 4,728 xylogenesis unigenes distributed in 2,100 contigs and 2,628 singletons. About 59.3 % of the ESTs were assigned with putative identifications whereas 40.7 % of the sequences showed no significant similarity to any sequences in GenBank. Interestingly, most genes involved in lignin biosynthesis and several other cell wall biosynthesis genes were identified in the kelampayan EST database. The identified genes in this study will be candidates for functional genomics and association genetic studies in kelampayan aiming at the production of high value forests.
    Matched MeSH terms: Gene Library
  3. Identification of chromosome 21 materials using the whole chromosome 21 specific library
    Isa MN, Boyd E, Turner TL, Tolmie J, Connor JM
    Southeast Asian J. Trop. Med. Public Health, 1995;26 Suppl 1:92-5.
    PMID: 8629150
    The chromosome in situ suppression hybridization or chromosome painting technic was applied to confirm and eliminate the markers involving chromosome 21 segments using a chromosome 21 DNA library. The library ATCCLL21SNO2 was amplified, directly biotinylated using the polymerase chain reaction. The results demonstrated a translocation of chromosome 21 material on chromosome 2 and X and eliminate the origin of the marker. Thus, the technique provides an important tool to complement the conventional G-banding technic.
    Matched MeSH terms: Gene Library
  4. Structural and functional changes with depth in microbial communities in a tropical Malaysian peat swamp forest
    Jackson CR, Liew KC, Yule CM
    Microb Ecol, 2009 Apr;57(3):402-12.
    PMID: 18548182 DOI: 10.1007/s00248-008-9409-4
    Tropical peat swamp forests are important and endangered ecosystems, although little is known of their microbial diversity and ecology. We used molecular and enzymatic techniques to examine patterns in prokaryotic community structure and overall microbial activity at 0-, 10-, 20-, and 50-cm depths in sediments in a peat swamp forest in Malaysia. Denaturing gradient gel electrophoresis profiles of amplified 16S ribosomal ribonucleic acid (rRNA) gene fragments showed that different depths harbored different bacterial assemblages and that Archaea appeared to be limited to the deeper samples. Cloning and sequencing of longer 16S rRNA gene fragments suggested reduced microbial diversity in the deeper samples compared to the surface. Bacterial clone libraries were largely dominated by ribotypes affiliated with the Acidobacteria, which accounted for at least 27-54% of the sequences obtained. All of the sequenced representatives from the archaeal clone libraries were Crenarchaeota. Activities of microbial extracellular enzymes involved in carbon, nitrogen, and phosphorus cycling declined appreciably with depth, the only exception being peroxidase. These results show that tropical peat swamp forests are unusual systems with microbial assemblages dominated by members of the Acidobacteria and Crenarchaeota. Microbial communities show clear changes with depth, and most microbial activity is likely confined to populations in the upper few centimeters, the site of new leaf litter fall, rather than the deeper, older, peat layers.
    Matched MeSH terms: Gene Library
  5. Fulltext The best method for isolated total RNA from durian tissues
    Ky, H., Yeap, S. K., Napis, S. B.
    International Food Research Journal, 2012;19(3):1181-1183.
    MyJurnal
    Plant tissues, especially durian tissues contain high content of polysaccharides, polyphenols and other secondary metabolites which can co-precipitate with RNA causing problem in further transcriptomic study. In this experiment, three basic chaotic agents, CTAB, SDS and guanidine are used in three basic protocols for RNA isolation. The effectiveness of each method was determined by spectrophotometer, denaturing agarose gels analysis and northern blot hybridization. CTAB combining with additional sodium acetate precipitation step showed highest yield and best quality of isolated RNA which was free from contaminations of polysaccharides, polyphenols and other secondary metabolites. Furthermore, the total RNA from 4-month old durian flesh of clone D24 was successfully used to construct a cDNA library. In conclusion, CTAB method is effective to isolate total RNA on various types of durian tissues for further gene expression analysis.
    Matched MeSH terms: Gene Library
  6. Construction of Naïve and Immune Human Fab Phage Display Library
    Lai JY, Lim TS
    Methods Mol Biol, 2023;2702:39-58.
    PMID: 37679614 DOI: 10.1007/978-1-0716-3381-6_3
    Phage display has been applied successfully for the rapid isolation of monoclonal antibodies against various targets including infectious diseases, autoantigens, cancer markers, and even small molecules. The main component in any phage display experiment is the availability of an antibody library to carry out the selection process of target-specific antibodies through an iterative process termed as biopanning. To generate human antibody libraries, the antibody repertoire can be obtained from human peripheral blood mononuclear cell (PBMC) or directly from cell-sorted B-cell populations. The choice of antibody isotype is dictated by the nature of the library. Naïve libraries would utilize IgM repertoires, whereas the IgG repertoire is commonly used for immune libraries. Antibody genes are amplified through polymerase chain reaction (PCR) and paired in a combinatorial fashion to expand the diversity of the cloned library repertoire. The protocol here describes the use of a two-step cloning method that can be applied for the construction of either a naïve or immune human antibody library in Fab format followed by the subsequent panning.
    Matched MeSH terms: Gene Library
  7. Field calibration of blowfly-derived DNA against traditional methods for assessing mammal diversity in tropical forests
    Lee PS, Gan HM, Clements GR, Wilson JJ
    Genome, 2016 May 11.
    PMID: 27696907
    Mammal diversity assessments based on DNA derived from invertebrates have been suggested as alternatives to assessments based on traditional methods; however, no study has field-tested both approaches simultaneously. In Peninsular Malaysia, we calibrated the performance of mammal DNA derived from blowflies (Diptera: Calliphoridae) against traditional methods used to detect species. We first compared five methods (cage trapping, mist netting, hair trapping, scat collection, and blowfly-derived DNA) in a forest reserve with no recent reports of megafauna. Blowfly-derived DNA and mist netting detected the joint highest number of species (n = 6). Only one species was detected by multiple methods. Compared to the other methods, blowfly-derived DNA detected both volant and non-volant species. In another forest reserve, rich in megafauna, we calibrated blowfly-derived DNA against camera traps. Blowfly-derived DNA detected more species (n = 11) than camera traps (n = 9), with only one species detected by both methods. The rarefaction curve indicated that blowfly-derived DNA would continue to detect more species with greater sampling effort. With further calibration, blowfly-derived DNA may join the list of traditional field methods. Areas for further investigation include blowfly feeding and dispersal biology, primer biases, and the assembly of a comprehensive and taxonomically-consistent DNA barcode reference library.
    Matched MeSH terms: Gene Library
  8. Fulltext Directed evolution of nucleotide-based libraries using lambda exonuclease
    Lim BN, Choong YS, Ismail A, Glökler J, Konthur Z, Lim TS
    Biotechniques, 2012 Dec;53(6):357-64.
    PMID: 23227986 DOI: 10.2144/000113964
    Directed evolution of nucleotide libraries using recombination or mutagenesis is an important technique for customizing catalytic or biophysical traits of proteins. Conventional directed evolution methods, however, suffer from cumbersome digestion and ligation steps. Here, we describe a simple method to increase nucleotide diversity using single-stranded DNA (ssDNA) as a starting template. An initial PCR amplification using phosphorylated primers with overlapping regions followed by treatment with lambda exonuclease generates ssDNA templates that can then be annealed via the overlap regions. Double-stranded DNA (dsDNA) is then generated through extension with Klenow fragment. To demonstrate the applicability of this methodology for directed evolution of nucleotide libraries, we generated both gene shuffled and regional mutagenesis synthetic antibody libraries with titers of 2×108 and 6×107, respectively. We conclude that our method is an efficient and convenient approach to generate diversity in nucleic acid based libraries, especially recombinant antibody libraries.
    Matched MeSH terms: Gene Library*
  9. Fulltext A checklist of the bats of Peninsular Malaysia and progress towards a DNA barcode reference library
    Lim VC, Ramli R, Bhassu S, Wilson JJ
    PLoS One, 2017;12(7):e0179555.
    PMID: 28742835 DOI: 10.1371/journal.pone.0179555
    Several published checklists of bat species have covered Peninsular Malaysia as part of a broader region and/or in combination with other mammal groups. Other researchers have produced comprehensive checklists for specific localities within the peninsula. To our knowledge, a comprehensive checklist of bats specifically for the entire geopolitical region of Peninsular Malaysia has never been published, yet knowing which species are present in Peninsular Malaysia and their distributions across the region are crucial in developing suitable conservation plans. Our literature search revealed that 110 bat species have been documented in Peninsular Malaysia; 105 species have precise locality records while five species lack recent and/or precise locality records. We retrieved 18 species from records dated before the year 2000 and seven species have only ever been recorded once. Our search of Barcode of Life Datasystems (BOLD) found that 86 (of the 110) species have public records of which 48 species have public DNA barcodes available from bats sampled in Peninsular Malaysia. Based on Neighbour-Joining tree analyses and the allocation of DNA barcodes to Barcode Index Number system (BINs) by BOLD, several DNA barcodes recorded under the same species name are likely to represent distinct taxa. We discuss these cases in detail and highlight the importance of further surveys to determine the occurences and resolve the taxonomy of particular bat species in Peninsular Malaysia, with implications for conservation priorities.
    Matched MeSH terms: Gene Library
  10. Fulltext Transcriptome analysis of the Cryptocaryon irritans tomont stage identifies potential genes for the detection and control of cryptocaryonosis
    Lokanathan Y, Mohd-Adnan A, Wan KL, Nathan S
    BMC Genomics, 2010;11:76.
    PMID: 20113487 DOI: 10.1186/1471-2164-11-76
    Cryptocaryon irritans is a parasitic ciliate that causes cryptocaryonosis (white spot disease) in marine fish. Diagnosis of cryptocaryonosis often depends on the appearance of white spots on the surface of the fish, which are usually visible only during later stages of the disease. Identifying suitable biomarkers of this parasite would aid the development of diagnostic tools and control strategies for C. irritans. The C. irritans genome is virtually unexplored; therefore, we generated and analyzed expressed sequence tags (ESTs) of the parasite to identify genes that encode for surface proteins, excretory/secretory proteins and repeat-containing proteins.
    Matched MeSH terms: Gene Library
  11. Fulltext Oil palm (Elaeis guineensis Jacq.) tissue culture ESTs: identifying genes associated with callogenesis and embryogenesis
    Low ET, Alias H, Boon SH, Shariff EM, Tan CY, Ooi LC, et al.
    BMC Plant Biol, 2008 May 29;8:62.
    PMID: 18507865 DOI: 10.1186/1471-2229-8-62
    BACKGROUND: Oil palm (Elaeis guineensis Jacq.) is one of the most important oil bearing crops in the world. However, genetic improvement of oil palm through conventional breeding is extremely slow and costly, as the breeding cycle can take up to 10 years. This has brought about interest in vegetative propagation of oil palm. Since the introduction of oil palm tissue culture in the 1970s, clonal propagation has proven to be useful, not only in producing uniform planting materials, but also in the development of the genetic engineering programme. Despite considerable progress in improving the tissue culture techniques, the callusing and embryogenesis rates from proliferating callus cultures remain very low. Thus, understanding the gene diversity and expression profiles in oil palm tissue culture is critical in increasing the efficiency of these processes.

    RESULTS: A total of 12 standard cDNA libraries, representing three main developmental stages in oil palm tissue culture, were generated in this study. Random sequencing of clones from these cDNA libraries generated 17,599 expressed sequence tags (ESTs). The ESTs were analysed, annotated and assembled to generate 9,584 putative unigenes distributed in 3,268 consensi and 6,316 singletons. These unigenes were assigned putative functions based on similarity and gene ontology annotations. Cluster analysis, which surveyed the relatedness of each library based on the abundance of ESTs in each consensus, revealed that lipid transfer proteins were highly expressed in embryogenic tissues. A glutathione S-transferase was found to be highly expressed in non-embryogenic callus. Further analysis of the unigenes identified 648 non-redundant simple sequence repeats and 211 putative full-length open reading frames.

    CONCLUSION: This study has provided an overview of genes expressed during oil palm tissue culture. Candidate genes with expression that are modulated during tissue culture were identified. However, in order to confirm whether these genes are suitable as early markers for embryogenesis, the genes need to be tested on earlier stages of tissue culture and a wider range of genotypes. This collection of ESTs is an important resource for genetic and genome analyses of the oil palm, particularly during tissue culture development.

    Matched MeSH terms: Gene Library
  12. Fulltext Isolation and characterization of novel microsatellite markers in commercial selected golden Malaysian arowana fish, Scleropages formosus (Osteoglossidae)
    Manoharan B, Sulaimen Z, Omar F, Othman RY, Mohamed SZ, Bhassu S
    Genet. Mol. Res., 2011;10(2):712-6.
    PMID: 21523650 DOI: 10.4238/vol10-2gmr944
    Malaysian arowana (dragonfish; Scleropages formosus) is an ancient osteoglossid fish from southeast Asia. Due to the high demand of the ornamental fish trade and because of habitat loss, the species is close to extinction. We isolated and characterized 10 polymorphic microsatellites of this species, using 5'-anchored PCR. The number of alleles at the 10 microsatellite loci ranged from 2 to 28, with a mean of 7.8/locus. The observed heterozygosity ranged from 0.03 to 0.93 (mean: 0.39), whereas the expected heterozygosity ranged from 0.03 to 0.94 (mean: 0.46). Seven microsatellites deviated from Hardy-Weinberg equilibrium, and three conformed to Hardy-Weinberg equilibrium and were in linkage equilibrium. These 10 novel microsatellites should facilitate studies of genetic diversity and population structure of arowana to help plan actions for the conservation of the indigenous Malaysian arowana.
    Matched MeSH terms: Gene Library
  13. Source Determination of Red Gel Pen Inks using Raman Spectroscopy and Attenuated Total Reflectance Fourier Transform Infrared Spectroscopy combined with Pearson's Product Moment Correlation Coefficients and Principal Component Analysis
    Mohamad Asri MN, Mat Desa WNS, Ismail D
    J Forensic Sci, 2018 Jan;63(1):285-291.
    PMID: 28480527 DOI: 10.1111/1556-4029.13522
    The potential combination of two nondestructive techniques, that is, Raman spectroscopy (RS) and attenuated total reflectance-fourier transform infrared (ATR-FTIR) spectroscopy with Pearson's product moment correlation (PPMC) coefficient (r) and principal component analysis (PCA) to determine the actual source of red gel pen ink used to write a simulated threatening note, was examined. Eighteen (18) red gel pens purchased from Japan and Malaysia from November to December 2014 where one of the pens was used to write a simulated threatening note were analyzed using RS and ATR-FTIR spectroscopy, respectively. The spectra of all the red gel pen inks including the ink deposited on the simulated threatening note gathered from the RS and ATR-FTIR analyses were subjected to PPMC coefficient (r) calculation and principal component analysis (PCA). The coefficients r = 0.9985 and r = 0.9912 for pairwise combination of RS and ATR-FTIR spectra respectively and similarities in terms of PC1 and PC2 scores of one of the inks to the ink deposited on the simulated threatening note substantiated the feasibility of combining RS and ATR-FTIR spectroscopy with PPMC coefficient (r) and PCA for successful source determination of red gel pen inks. The development of pigment spectral library had allowed the ink deposited on the threatening note to be identified as XSL Poppy Red (CI Pigment Red 112).
    Matched MeSH terms: Gene Library
  14. Production of 3-Oxo-2-(2'-pentenyl)-cyclopentane-1-octanoic Acid in the Fungus Aspergillus oryzae: A Step Towards Heterologous Production of Pyrethrins in Fungi
    Mohamed ME, Pahirulzaman KA, Lazarus CM
    Mol Biotechnol, 2016 Mar;58(3):172-8.
    PMID: 26718544 DOI: 10.1007/s12033-015-9911-0
    Pyrethrins are natural insecticides, which accumulate to high concentrations in pyrethrum (Chrysanthemum cinerariaefolium) flowers. Synthetic pyrethroids are more stable, more efficacious and cheaper, but contemporary requirements for safe and environmentally friendly pesticides encourage a return to the use of natural pyrethrins, and this would be favoured by development of an efficient route to their production by microbial fermentation. The biosynthesis of pyrethrins involves ester linkage between an acid moiety (chrysanthemoyl or pyrethroyl, synthesised via the mevalonic acid pathway from glucose), and an alcohol (pyrethrolone). Pyrethrolone is generated from 3-oxo-2-(2'-pentenyl)-cyclopentane-1-octanoic acid, which originates from α-linolenic acid via the jasmonic acid biosynthetic cascade. The first four genes in this cascade, encoding lipoxygenase 2, allene-oxide synthase, allene-oxide cyclase 2 and 12-oxophytodienoic acid reductase 3, were amplified from an Arabidopsis thaliana cDNA library, cloned in a purpose-built fungal multigene expression vector and expressed in Aspergillus oryzae. HPLC-MS analysis of the transgenic fungus homogenate gave good evidence for the presence of 3-oxo-2-(2'-pentenyl)-cyclopentane-1-octanoic acid.
    Matched MeSH terms: Gene Library
  15. Fulltext A new insight to biomarkers related to resistance in survived-white spot syndrome virus challenged giant tiger shrimp, Penaeus monodon
    Mohd Ghani F, Bhassu S
    PeerJ, 2019;7:e8107.
    PMID: 31875142 DOI: 10.7717/peerj.8107
    The emergence of diseases such as white spot disease has become a threat to Penaeus monodon cultivation. Although there have been a few studies utilizing RNA-Seq, the cellular processes of host-virus interaction in this species remain mostly anonymous. In the present study, P. monodon was challenged with WSSV by intramuscular injection and survived for 12 days. The effect of the host gene expression by WSSV infection in the haemocytes, hepatopancreas and muscle of P. monodon was studied using Illumina HiSeq 2000. The RNA-Seq of cDNA libraries was developed from surviving WSSV-challenged shrimp as well as from normal healthy shrimp as control. A comparison of the transcriptome data of the two groups showed 2,644 host genes to be significantly up-regulated and 2,194 genes significantly down-regulated as a result of the infection with WSSV. Among the differentially expressed genes, our study discovered HMGB, TNFSF and c-Jun in P. monodon as new potential candidate genes for further investigation for the development of potential disease resistance markers. Our study also provided significant data on the differential expression of genes in the survived WSSV infected P. monodon that will help to improve understanding of host-virus interactions in this species.
    Matched MeSH terms: Gene Library
  16. Fulltext RNA-seq and ChIP-seq as Complementary Approaches for Comprehension of Plant Transcriptional Regulatory Mechanism
    Muhammad II, Kong SL, Akmar Abdullah SN, Munusamy U
    Int J Mol Sci, 2019 Dec 25;21(1).
    PMID: 31881735 DOI: 10.3390/ijms21010167
    The availability of data produced from various sequencing platforms offer the possibility to answer complex questions in plant research. However, drawbacks can arise when there are gaps in the information generated, and complementary platforms are essential to obtain more comprehensive data sets relating to specific biological process, such as responses to environmental perturbations in plant systems. The investigation of transcriptional regulation raises different challenges, particularly in associating differentially expressed transcription factors with their downstream responsive genes. In this paper, we discuss the integration of transcriptional factor studies through RNA sequencing (RNA-seq) and Chromatin Immunoprecipitation sequencing (ChIP-seq). We show how the data from ChIP-seq can strengthen information generated from RNA-seq in elucidating gene regulatory mechanisms. In particular, we discuss how integration of ChIP-seq and RNA-seq data can help to unravel transcriptional regulatory networks. This review discusses recent advances in methods for studying transcriptional regulation using these two methods. It also provides guidelines for making choices in selecting specific protocols in RNA-seq pipelines for genome-wide analysis to achieve more detailed characterization of specific transcription regulatory pathways via ChIP-seq.
    Matched MeSH terms: Gene Library
  17. Fulltext Prevalence of falls and its characteristics among malaysian older adults: a review
    Muhammad Iqbal, S., Bahman, J., Aslinda, C.M.
    Medicine & Health, 2020;15(1):18-33.
    MyJurnal
    Kejatuhan adalah isu kesihatan yang sering dikaitkan dengan warga emas di seluruh dunia. Kejatuhan boleh menyebabkan kesan negatif pada individu dan juga menyebabkan kematian dalam kes tertentu. Kajian semasa kejatuhan adalah amat terhad di Malaysia. Tujuan kajian ini adalah untuk merumuskan kajian semasa yang dijalankan di Malaysia yang mengenai prevalens dan ciri-cirinya. Artikel telah dikenalpasti melalui menggunakan pangkalan data elektronik berikut: EBSCOhost, ClinicalKey, ScienceDirect, Wiley Online Library, SpringerLink dan Google Scholar. Pemilihan artikel adalah terhad kepada artikel bahasa Inggeris yang diterbitkan antara tahun 2013 hingga 2019. Kajian ini menilai golongan warga emas yang berumur 60 tahun ke atas; sama ada di kediaman, komuniti atau institut perubatan. Sembilan artikel yang berkaitan telah dikenalpasti dan disiasat. Hasil kajian menunjukkan variasi yang ketara dengan julat 4-74 % dalam prevalens kejatuhan di kalangan warga emas di Malaysia. Salah satu kajian yang dijalankan dalam komuniti menunjukkan prevalens kejatuhan yang lebih rendah. Majoriti peristiwa kejatuhan berlaku pada waktu pagi seperti yang dilaporkan oleh tiga kajian iaitu sebanyak 49%-64.7%. Kejatuhan dalam kawasan bangunan adalah jumlah tertinggi lokasi jatuh dengan 50-87% manakala di luar bangunan adalah 13-49.3%. Lokasi di bilik mandi / tandas mempunyai peratusan kejatuhan tertinggi dalam bangunan. Kejatuhan yang menyebabkan kecederaan adalah antara 47% -82%. Perubahan pada prevalens kejatuhan dalam warga emas ditentukan oleh faktor-faktor seperti lokasi dan keadaan kesihatan. Maklumat yang dikumpulkan dalam kajian ini menunjukkan terdapat kekurangan alat ukur piawai bagi mengkaji ciri-ciri kejatuhan di Malaysia. Kajian prospektif diperlukan untuk menubuhkan prevalens dan hubungan faktor-kesan kejatuhan di Malaysia.
    Matched MeSH terms: Gene Library
  18. Optimization of illumina truseq targeted RNA Expression (TREx) library quality
    Nadiah Abu, Noraini Nordin, Noorjahan Banu Alitheen, Nadiah Abu, Sheau Wei Tan, Swee Keong Yeap, et al.
    Sains Malaysiana, 2018;47:303-308.
    RNA-seq has become an essential tool in molecular research. Nevertheless, application of RNA-seq was limited by cost and technical difficulties. Illumina has introduced the cost effective and ease to handle Truseq Targeted RNA Sequencing. In this study, we present the requirements and the optimization procedure for this Truseq Targeted RNA sequencing on cell line. Total RNA was recommended as starting materials but it required optimization including additional purification step and adjusting the AMPure beads ratio to eliminate unwanted contaminants. This can be resolved by using PolyA-enriched mRNA as starting material. TREx is a useful assay to evaluate gene expression. Quality library of TREx can be prepared by adding multiple washing steps or changing input sample to mRNA.
    Matched MeSH terms: Gene Library
  19. Fulltext Phosphoinositide-dependent Kinase-1 (PDPK1) regulates serum/glucocorticoid-regulated Kinase 3 (SGK3) for prostate cancer cell survival
    Nalairndran G, Hassan Abdul Razack A, Mai CW, Fei-Lei Chung F, Chan KK, Hii LW, et al.
    J Cell Mol Med, 2020 Oct;24(20):12188-12198.
    PMID: 32926495 DOI: 10.1111/jcmm.15876
    Prostate cancer (PCa) is the most common malignancy and is the second leading cause of cancer among men globally. Using a kinome-wide lentiviral small-hairpin RNA (shRNA) library screen, we identified phosphoinositide-dependent kinase-1 (PDPK1) as a potential mediator of cell survival in PCa cells. We showed that knock-down of endogenous human PDPK1 induced significant tumour-specific cell death in PCa cells (DU145 and PC3) but not in the normal prostate epithelial cells (RWPE-1). Further analyses revealed that PDPK1 mediates cancer cell survival predominantly via activation of serum/glucocorticoid-regulated kinase 3 (SGK3). Knock-down of endogenous PDPK1 in DU145 and PC3 cells significantly reduced SGK3 phosphorylation while ectopic expression of a constitutively active SGK3 completely abrogated the apoptosis induced by PDPK1. In contrast, no such effect was observed in SGK1 and AKT phosphorylation following PDPK1 knock-down. Importantly, PDPK1 inhibitors (GSK2334470 and BX-795) significantly reduced tumour-specific cell growth and synergized docetaxel sensitivity in PCa cells. In summary, our results demonstrated that PDPK1 mediates PCa cells' survival through SGK3 signalling and suggest that inactivation of this PDPK1-SGK3 axis may potentially serve as a novel therapeutic intervention for future treatment of PCa.
    Matched MeSH terms: Gene Library
  20. Fulltext Identification of floral genes for sex determination in Calamus palustris Griff. by using suppression subtractive hybridization
    Ng CY, Wickneswari R, Choong CY
    Genet. Mol. Res., 2014;13(3):6037-49.
    PMID: 25117361 DOI: 10.4238/2014.August.7.18
    Calamus palustris Griff. is an economically important dioecious rattan species in Southeast Asia. However, dioecy and onset of flowering at 3-4 years old render uncertainties in desired female:male seedling ratios to establish a productive seed orchard for this rattan species. We constructed a subtractive library for male floral tissue to understand the genetic mechanism for gender determination in C. palustris. The subtractive library produced 1536 clones with 1419 clones of high quality. Reverse Northern screening showed 313 clones with differential expression, and sequence analyses clustered them into 205 unigenes, including 32 contigs and 173 singletons. The subtractive library was further validated with reverse transcription-quantitative polymerase chain reaction analysis. Homology identification classified the unigenes into 12 putative functional proteins with 83% unigenes showing significant match to proteins in databases. Functional annotations of these unigenes revealed genes involved in male flower development, including MADS-box genes, pollen-related genes, phytohormones for flower development, and male flower organ development. Our results showed that the male floral genes may play a vital role in sex determination in C. palustris. The identified genes can be exploited to understand the molecular basis of sex determination in C. palustris.
    Matched MeSH terms: Gene Library
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