Displaying publications 1 - 20 of 64 in total

  1. Nordin F, Hamid ZA, Chan L, Farzaneh F, Hamid MK
    Methods Mol Biol, 2016;1448:159-73.
    PMID: 27317180 DOI: 10.1007/978-1-4939-3753-0_12
    Non-integrating lentiviral vectors or also known as integrase-defective lentiviral (IDLV) hold a great promise for gene therapy application. They retain high transduction efficiency for efficient gene transfer in various cell types both in vitro and in vivo. IDLV is produced via a combined mutations introduced on the HIV-based lentiviral to disable their integration potency. Therefore, IDLV is considered safer than the wild-type integrase-proficient lentiviral vector as they could avoid the potential insertional mutagenesis associated with the nonspecific integration of transgene into target cell genome afforded by the wild-type vectors.Here we describe the system of IDLV which is produced through mutation in the integrase enzymes at the position of D64 located within the catalytic core domain. The efficiency of the IDLV in expressing the enhanced green fluorescent protein (GFP) reporter gene in transduced human monocyte (U937) cell lines was investigated. Expression of the transgene was driven by the spleen focus-forming virus (SFFV) LTRs. Transduction efficiency was studied using both the IDLV (ID-SFFV-GFP) and their wild-type counterparts (integrase-proficient SFFV-GFP). GFP expression was analyzed by fluorescence microscope and FACS analysis.Based on the results, the number of the GFP-positive cells in ID-SFFV-GFP-transduced U937 cells decreased rapidly over time. The percentage of GFP-positive cells decreased from ~50 % to almost 0, up to 10 days post-transduction. In wild-type SFFV-GFP-transduced cells, GFP expression is remained consistently at about 100 %. These data confirmed that the transgene expression in the ID-SFFV-GFP-transduced cells is transient in dividing cells. The lack of an origin of replication due to mutation of integrase enzymes in the ID-SFFV-GFP virus vector has caused the progressive loss of the GFP expression in dividing cells.Integrase-defective lentivirus will be a suitable choice for safer clinical applications. It preserves the advantages of the wild-type lentiviral vectors but with the benefit of transgene expression without stable integration into host genome, therefore reducing the potential risk of insertional mutagenesis.
  2. Bashir M, Hassan NH
    Methods Mol Biol, 2016;1420:135-42.
    PMID: 27259737 DOI: 10.1007/978-1-4939-3597-0_11
    Insertion/deletion polymorphisms (INDELs) are a relatively new class of a DNA marker to be used in forensic casework; used most commonly as a supplementary method to STR-based typing. INDELs, like SNPs, are particularly useful for the analysis of highly degraded DNA as the amplicon sizes are typically below 160 bp; they can also be valuable as an additional tool to help resolve kinship cases, with the advantage over STRs that they do not have high mutation rates. INDELs have an advantage over SNPs in that they are length polymorphisms and so can be analyzed by simply measuring the length of the allele(s). The Qiagen Investigator(®) DIPplex Kit is currently only one of two commercially available kits for the amplification of INDEL polymorphisms; it amplifies 30 biallelic INDEL loci and the amelogenin locus. The primers used are fluorescence labeled with 6-FAM, BTG, BTY, and BTR. This technique is robust, relatively simple, and the results are analyzed using the same capillary electrophoresis equipment and software as used for STR typing.
  3. Mehrbod P, Harun MS, Shuid AN, Omar AR
    Methods Mol Biol, 2015;1282:241-50.
    PMID: 25720485 DOI: 10.1007/978-1-4939-2438-7_20
    Feline infectious peritonitis (FIP) is a lethal systemic disease caused by FIP virus (FIPV). There are no effective vaccines or treatment available, and the virus virulence determinants and pathogenesis are not fully understood. Here, we describe the sequencing of RNA extracted from Crandell Rees Feline Kidney (CRFK) cells infected with FIPV using the Illumina next-generation sequencing approach. Bioinformatics analysis, based on Felis catus 2X annotated shotgun reference genome, using CLC bio Genome Workbench is used to map both control and infected cells. Kal's Z test statistical analysis is used to analyze the differentially expressed genes from the infected CRFK cells. In addition, RT-qPCR analysis is used for further transcriptional profiling of selected genes in infected CRFK cells and Peripheral Blood Mononuclear Cells (PBMCs) from healthy and FIP-diagnosed cats.
  4. Chen Q, Narayanan K
    Methods Mol Biol, 2015;1227:27-54.
    PMID: 25239740 DOI: 10.1007/978-1-4939-1652-8_2
    Recombineering is a powerful genetic engineering technique based on homologous recombination that can be used to accurately modify DNA independent of its sequence or size. One novel application of recombineering is the assembly of linear BACs in E. coli that can replicate autonomously as linear plasmids. A circular BAC is inserted with a short telomeric sequence from phage N15, which is subsequently cut and rejoined by the phage protelomerase enzyme to generate a linear BAC with terminal hairpin telomeres. Telomere-capped linear BACs are protected against exonuclease attack both in vitro and in vivo in E. coli cells and can replicate stably. Here we describe step-by-step protocols to linearize any BAC clone by recombineering, including inserting and screening for presence of the N15 telomeric sequence, linearizing BACs in vivo in E. coli, extracting linear BACs, and verifying the presence of hairpin telomere structures. Linear BACs may be useful for functional expression of genomic loci in cells, maintenance of linear viral genomes in their natural conformation, and for constructing innovative artificial chromosome structures for applications in mammalian and plant cells.
  5. Dharshanan S, Hung CS
    Methods Mol Biol, 2014;1131:105-12.
    PMID: 24515462 DOI: 10.1007/978-1-62703-992-5_7
    Generation of high-producing clones is a perquisite for achieving recombinant protein yields suitable for biopharmaceutical production. However, in many industrially important cell lines used to produce recombinant proteins such as Chinese hamster ovary, mouse myeloma line (NS0), and hybridomas, only a minority of clones show significantly above-average productivity. Thus, in order to have a reasonable probability of finding rare high-producing clones, a large number of clones need to be screened. Limiting dilution cloning is the most commonly used method, owing to its relative simplicity and low cost. However the use of liquid media in this method makes the selection of monoclonal hybridoma and transfectoma colonies to be labor intensive and time consuming, thus significantly limiting the number of clones that can be feasibly screened. Hence, we describe the use of semisolid media to immobilize clones and a high-throughput, automated colony picker (ClonePix FL) to efficiently isolate monoclonal high-producing clones secreting monoclonal antibodies.
  6. AL Azzam KM, Aboul-Enein HY
    Methods Mol Biol, 2013;919:67-78.
    PMID: 22976091 DOI: 10.1007/978-1-62703-029-8_7
    Capillary electrophoresis coupled with a capacitively coupled contactless conductivity detector (CE-C(4)D) has been employed for the determination of the β-blocker drugs (atenolol and amiloride) in pharmaceutical formulations. 150 mM acetic acid was used as background electrolyte. The influence of several factors (detector excitation voltage and frequency, buffer concentration, applied voltage, capillary temperature, and injection time) was studied. Non-UV absorbing L-valine was used as an internal standard; the analytes were all separated in less than 7 min. The separation was carried out in normal polarity mode at 28 °C, 25 kV, and using hydrodynamic injection (25 s). The separation was effected in a bare fused-silica capillary 75 μm × 52 cm. The CE-C(4)D method was validated with respect to linearity, limit of detection and quantification, accuracy, precision, and selectivity. Calibration curves were linear over the range 5-250 μg mL(-1) for the studied analytes. The relative standard deviations of intra- and inter-day precisions of migration times and corrected peak areas were less than 6.0%. The method showed good precision and accuracy and was successfully applied to the simultaneous determination of the β-blocker drugs in different pharmaceutical tablets.
  7. 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.
  8. Izawati AM, Parveez GK, Masani MY
    Methods Mol Biol, 2012;847:177-88.
    PMID: 22351008 DOI: 10.1007/978-1-61779-558-9_15
    Transgenic oil palm (Elaeis guineensis Jacq.) plantlets are regenerated after Agrobacterium tumefaciens-mediated transformation of embryogenic calli derived from young leaves of oil palm. The calli are transformed with an Agrobacterium strain, LBA4404, harboring the plasmid pUBA, which carries a selectable marker gene (bar) for resistance to the herbicide Basta and is driven by a maize ubiquitin promoter. Modifications of the transformation method, treatment of the target tissues using acetosyringone, exposure to a plasmolysis medium, and physical injury via biolistics are applied. The main reasons for such modifications are to activate the bacterial virulence system and, subsequently, to increase the transformation efficiency. Transgenic oil palm cells are selected and regenerated on a medium containing herbicide Basta. Molecular analyses revealed the presence and integration of the introduced bar gene into the genome of the transformants.
  9. Parveez GK, Bahariah B
    Methods Mol Biol, 2012;847:163-75.
    PMID: 22351007 DOI: 10.1007/978-1-61779-558-9_14
    The effectiveness of mannose (using phosphomannose isomerase [pmi] gene) as a positive selection agent to preferably allow the growth of transformed oil palm embryogenic calli was successfully evaluated. Using the above selection agent in combination with the previously optimized physical and biological parameters and the best constitutive promoter, oil palm embryogenic calli were transformed with pmi gene for producing transgenic plants. Bombarded embryogenic calli were exposed to embryogenic calli medium containing 30:0 g/L mannose to sucrose 3 weeks postbombardment. Selectively, proliferating embryogenic calli started to emerge around 6 months on the above selection medium. The proliferated embryogenic calli were individually isolated once they reached a specific size and regenerated to produce complete plantlets. The complete regenerated plantlets were evaluated for the presence of transgenes by PCR and Southern analyses.
  10. Poh CL, Tan EL
    Methods Mol Biol, 2011;665:65-77.
    PMID: 21116796 DOI: 10.1007/978-1-60761-817-1_5
    Enteroviruses are positive stranded RNA viruses belonging to the genus Enterovirus of the Picornaviridae family. Human enteroviruses are transmitted through the fecal-oral route and have been shown to cause mild to life-threatening diseases. Various diagnostic methods have been developed to detect enteroviruses from clinical specimens but many were impeded by requirements for special reagents, lengthy procedures, low sensitivity or cross-reactivity. This chapter describes rapid and highly sensitive methods of enteroviral detection directly from clinical specimens based on a conventional one-step Reverse Transcription polymerase chain reaction (RT-PCR) and a one-step real-time RT-PCR.
  11. Maziah M, Rosli N
    Methods Mol Biol, 2009;547:359-69.
    PMID: 19521859 DOI: 10.1007/978-1-60327-287-2_29
    Plant cell culture technology is potentially useful in producing high-valued secondary metabolites. Eurycoma longifolia root extracts are consumed as a health tonic but more popularly used as an aphrodisiac. Studies on the aphrodisiac properties and the possible compounds involved have been widely studied. There are many potentially useful compounds reported from the root extracts of E. longifolia. However, studies on the in vitro production of useful compounds from this plant have not been reported. This chapter will describe methods of callus induction and extraction of 9-methoxycanthin-6-one from E. longifolia Jack explants with emphasis on the tap and fibrous roots. This compound, known to have anti-tumour activity, is present in intact plant parts and in callus tissues of different explants.
  12. Kadir Ahmad Parveez G
    Methods Mol Biol, 2008;477:301-20.
    PMID: 19082956 DOI: 10.1007/978-1-60327-517-0_23
    Physical and biological parameters affecting DNA delivery into oil palm embryogenic calli using the biolistic device are optimized. Five different promoters are also evaluated to identify the most suitable promoter for use in oil palm transformation. Finally, the effectiveness of kanamycin, geneticin (G418), neomycin, hygromycin, and herbicide Basta as selection agents to inhibit growth of oil palm embryogenic calli is evaluated. Combination of optimized parameters, best promoter and selection agent is later used to transform oil palm embryogenic calli for producing transgenic oil palm plants. Bombarded embryogenic calli are exposed to 50 mg/l of Basta after 3 weeks. Basta-resistant embryogenic calli started to emerge five to six months in medium containing Basta. The Basta-resistant embryogenic calli are proliferated until they reach a specific size, and the Basta-resistant calli are later individually isolated and regenerated to produce complete plantlets. The complete regenerated plantlets are evaluated for the presence of transgenes by PCR, Southern and thin layer chromatography analyses.
  13. Yip CH
    Methods Mol Biol, 2009;471:51-64.
    PMID: 19109774 DOI: 10.1007/978-1-59745-416-2_3
    Breast cancer is the commonest cancer in most countries in Asia. The incidence rates remain low, although increasing at a more rapid rate than in western countries, due to changes in the lifestyle and diet. There are many differences between breast cancer in Asia compared with western countries. The mean age at onset is younger than in the west, and unlike the west, the age-specific incidence decreases after the age of 50 years. Because there is no population-based breast cancer screening program in the majority of Asian countries, the majority of patients present with advanced disease. There is a higher proportion of hormone receptor-negative patients, and some evidence that the cancers in Asia are of a higher grade. Most of the Asian countries are low- and middle-income countries, where access to effective care is limited. Because of the late detection and inadequate access to care, survival of women with breast cancer in Asia is lower than in western countries. Improving breast health in most of the Asian countries remains a challenge that may be overcome with collaboration from multiple sectors, both public and private.
  14. Ibrahim WA, Hermawan D, Sanagi MM
    Methods Mol Biol, 2013;970:349-61.
    PMID: 23283789 DOI: 10.1007/978-1-62703-263-6_22
    The separation of enantiomers is one of the important fields of modern analytical chemistry, especially for agrochemical and pharmaceutical products because the stereochemistry has a significant influence on the biological activities of compounds. Cyclodextrin-modified micellar electrokinetic chromatography (CD-MEKC) has become an important capillary electrophoresis mode for enantioseparations. Here, we describe an example of a CD-MEKC method using hydroxypropyl-γ-cyclodextrin as chiral selector and sodium dodecyl sulfate as micellar solution for enantioseparation of triazole fungicides and the drug econazole.
  15. Syahir A, Tomizaki KY, Kajikawa K, Mihara H
    Methods Mol Biol, 2016;1352:97-110.
    PMID: 26490470 DOI: 10.1007/978-1-4939-3037-1_8
    The importance of protein detection system for protein functions analyses in recent post-genomic era is rising with the emergence of label-free protein detection methods. We are focusing on a simple and practical label-free optical-detection method called anomalous reflection (AR) of gold. When a molecular layer forms on the gold surface, significant reduction in reflectivity can be observed at wavelengths of 400-500 nm. This allows the detection of molecular interactions by monitoring changes in reflectivity. In this chapter, we describe the AR method with three different application platforms: (1) gold, (2) gold containing alloy/composite (AuAg2O), and (3) metal-insulator-metal (MIM) thin layers. The AuAg2O composite and MIM are implemented as important concepts for signal enhancement process for the AR technique. Moreover, the observed molecular adsorption and activity is aided by a three-dimensional surface geometry, performed using poly(amidoamine) or PAMAM dendrimer modification. The described system is suitable to be used as a platform for high-throughput detection system in a chip format.
  16. Poh CL, Kirk K, Chua HN, Grollo L
    Methods Mol Biol, 2015;1348:341-50.
    PMID: 26424285 DOI: 10.1007/978-1-4939-2999-3_29
    Enterovirus 71 (EV-71) is the main causative agent of hand, foot, and mouth disease (HFMD) which is generally regarded as a mild childhood disease. In recent years, EV71 has emerged as a significant pathogen capable of causing high mortalities and severe neurological complications in large outbreaks in Asia. A formalin-inactivated EV71 whole virus vaccine has completed phase III trial in China but is currently unavailable clinically. The high cost of manufacturing and supply problems may limit practical implementations in developing countries. Synthetic peptides representing the native primary structure of the viral immunogen which is able to elicit neutralizing antibodies can be made readily and is cost effective. However, it is necessary to conjugate short synthetic peptides to carrier proteins to enhance their immunogenicity. This review describes the production of cross-neutralizing anti-peptide antibodies in response to immunization with synthetic peptides selected from in silico analysis, generation of B-cell epitopes of EV71 conjugated to a promiscuous T-cell epitope from Poliovirus, and evaluation of the neutralizing activities of the anti-peptide antibodies. Besides neutralizing EV71 in vitro, the neutralizing antibodies were cross-reactive against several Enteroviruses including CVA16, CVB4, CVB6, and ECHO13.
  17. Kardia E, Halim NSSA, Yahaya BH
    Methods Mol Biol, 2016;1516:243-255.
    PMID: 27062596 DOI: 10.1007/7651_2016_327
    Aerosol-based cell delivery technique via intratracheal is an effective route for delivering transplant cells directly into the lungs. An aerosol device known as the MicroSprayer(®) Aerosolizer is invented to transform liquid into an aerosol form, which then can be applied via intratracheal administration for drug delivery. The device produces a uniform and concentrated distribution of aerosolized liquid. Using the capability of MicroSprayer(®) Aerosolizer to transform liquid into aerosol form, our group has designed a novel method of cell delivery using an aerosol-based technique. We have successfully delivered skin-derived fibroblast cells and airway epithelial cells into the airway of a rabbit with minimum risk of cell loss and have uniformly distributed the cells into the airway. This chapter illustrates the application of aerosol device to deliver any type of cells for future treatment of lung diseases.
  18. Halim NHA, Zakaria N, Satar NA, Yahaya BH
    Methods Mol Biol, 2016;1516:371-388.
    PMID: 27032945 DOI: 10.1007/7651_2016_326
    Cancer is a major health problem worldwide. The failure of current treatments to completely eradicate cancer cells often leads to cancer recurrence and dissemination. Studies have suggested that tumor growth and spread are driven by a minority of cancer cells that exhibit characteristics similar to those of normal stem cells, thus these cells are called cancer stem cells (CSCs). CSCs are believed to play an important role in initiating and promoting cancer. CSCs are resistant to currently available cancer therapies, and understanding the mechanisms that control the growth of CSCs might have great implications for cancer therapy. Cancer cells are consist of heterogeneous population of cells, thus methods of identification, isolation, and characterisation of CSCs are fundamental to obtain a pure CSC populations. Therefore, this chapter describes in detail a method for isolating and characterizing a pure population of CSCs from heterogeneous population of cancer cells and CSCs based on specific cell surface markers.
  19. Thayan R, Yusof MA, Saat Z, Sekaran SD, Wang SM
    Methods Mol Biol, 2016;1426:11-9.
    PMID: 27233257 DOI: 10.1007/978-1-4939-3618-2_2
    Molecular surveillance of Chikungunya virus (CHIKV) is important as it provides data on the circulating CHIKV genotypes in endemic countries and enabling activation of measures to be taken in the event of a pending outbreak. Molecular surveillance is carried out by first detecting CHIKV in susceptible humans or among field-caught mosquitoes. This is followed by sequencing a selected region of the virus which will provide evidence on the source of the virus and possible association of the virus to increased cases of Chikungunya infections.
  20. Wong HV, Chan YF, Sam IC, Sulaiman WY, Vythilingam I
    Methods Mol Biol, 2016;1426:119-28.
    PMID: 27233266 DOI: 10.1007/978-1-4939-3618-2_11
    In vivo infection of mosquitoes is an important method to study and characterize arthropod-borne viruses. Chikungunya virus (CHIKV) is a mosquito-borne alphavirus that is transmitted primarily by Aedes mosquitoes. In this chapter, we describe a protocol for infection of CHIKV in two species of Aedes mosquitoes, Aedes aegypti and Aedes albopictus, together with the isolation of CHIKV in different parts of the infected mosquito such as midgut, legs, wings, salivary gland, head, and saliva. This allows the study of viral infection, replication and dissemination within the mosquito vector.
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