Raha Rahim | Universiti Putra Malaysia (original) (raw)

Papers by Raha Rahim

Fifty signal peptides of Pediococcus pentosaceus were characterized by in silico analysis and, ba... more Fifty signal peptides of Pediococcus pentosaceus were characterized by in silico analysis and, based on the physicochemical analysis, (two potential signal peptides Spk1 and Spk3 were identified). The coding sequences of SP were amplified and fused to the gene coding for green fluorescent protein (GFP) and cloned into Lactococcus lactis pNZ8048 and pMG36e vectors, respectively. Western blot analysis indicated that the GFP proteins were secreted using both heterologous SPs. ELISA showed that the secretion efficiency of GFP using Spk1 (0.64 lg/ml) was similar to using Usp45 (0.62 lg/ml) and Spk3 (0.58 lg/ml).

Microbial cell factories, 2015

Bacterial biofilms are a preferred mode of growth for many types of microorganisms in their natur... more Bacterial biofilms are a preferred mode of growth for many types of microorganisms in their natural environments. The ability of pathogens to integrate within a biofilm is pivotal to their survival. The possibility of biofilm formation in Lactobacillus communities is also important in various industrial and medical settings. Lactobacilli can eliminate the colonization of different pathogenic microorganisms. Alternatively, new opportunities are now arising with the rapidly expanding potential of lactic acid bacteria biofilms as bio-control agents against food-borne pathogens. A new isolate Lactobacillus plantarum PA21 could form a strong biofilm in pure culture and in combination with several pathogenic and food-spoilage bacteria such as Salmonella enterica, Bacillus cereus, Pseudomonas fluorescens, and Aeromonas hydrophila. Exposure to Lb. plantarum PA21 significantly reduced the number of P. fluorescens, A. hydrophila and B. cereus cells in the biofilm over 2-, 4- and 6-day time pe...

Molecules (Basel, Switzerland), 2015

Dominant strains of lactic acid bacteria (LAB) isolated from honey bees were evaluated for their ... more Dominant strains of lactic acid bacteria (LAB) isolated from honey bees were evaluated for their γ-aminobutyric acid (GABA)-producing ability. Out of 24 strains, strain Taj-Apis362 showed the highest GABA-producing ability (1.76 mM) in MRS broth containing 50 mM initial glutamic acid cultured for 60 h. Effects of fermentation parameters, including initial glutamic acid level, culture temperature, initial pH and incubation time on GABA production were investigated via a single parameter optimization strategy. The optimal fermentation condition for GABA production was modeled using response surface methodology (RSM). The results showed that the culture temperature was the most significant factor for GABA production. The optimum conditions for maximum GABA production by Lactobacillus plantarum Taj-Apis362 were an initial glutamic acid concentration of 497.97 mM, culture temperature of 36 °C, initial pH of 5.31 and incubation time of 60 h, which produced 7.15 mM of GABA. The value is co...

Health Benefits of Fermented Foods and Beverages, 2015

Microbial Biotechnology, 2015

isms through decarboxylation of glutamate by glutamate decarboxylase (GAD). In this study, a full... more isms through decarboxylation of glutamate by glutamate decarboxylase (GAD). In this study, a fulllength GAD gene was obtained by cloning the template deoxyribonucleic acid to pTZ57R/T vector. The open reading frame of the GAD gene showed the cloned gene was composed of 1410 nucleotides and encoded a 469 amino acids protein. To improve the GABA-production, the GAD gene was cloned into pMG36e-LbGAD, and then expressed in Lactobacillus plantarum Taj-Apis362 cells. The overexpression was confirmed by SDS-PAGE and GAD activity, showing a 53 KDa protein with the enzyme activity increased by sevenfold compared with the original GAD activity. The optimal fermentation conditions for GABA production established using response surface methodology were at glutamic acid concentration of 497.973 mM, temperature 36°C, pH 5.31 and time 60 h. Under the conditions, maximum GABA concentration obtained (11.09 mM) was comparable with the predicted value by the model at 11.23 mM. To our knowledge, this is the first report of successful cloning (clone-back) and overexpression of the LbGAD gene from L. plantarum to L. plantarum cells. The recombinant Lactobacillus could be used as a starter culture for direct incorporation into a food system during fermentation for production of GABA-rich products.

Microbiological and Functional Aspects, Fourth Edition, 2011

Tree Genetics & Genomes, 2006

Salinity is a major abiotic stress that greatly affects plant growth and crop production. Sodium ... more Salinity is a major abiotic stress that greatly affects plant growth and crop production. Sodium ions in saline soil are toxic to plants because of their adverse effects on potassium nutrition, cytosolic enzyme activities, photosynthesis, and metabolism. It is important to identify genes involved in salinity tolerance from mangrove plants that survive under saline conditions. In this study, a total

Food and Bioprocess Technology, 2009

The effectiveness of formulations using different protective agents to maintain viability of Lact... more The effectiveness of formulations using different protective agents to maintain viability of Lactobacillus salivarius I 24 during freeze drying for production of live cell in powdered form was investigated. The influence of prefreezing and cultivation conditions on viability of cells after freeze drying was also studied. Surface methodology was used to determine the most suitable combination of the protective agents. Concentrations of skim milk, sucrose, glycerol, and calcium carbonate were selected as operating variables, and survivals of cultures after freeze drying were used as results. Skim milk and sucrose were better protective agents than glycerol and calcium carbonate when used individually for preserving L. salivarius I 24 during freeze drying. Their protective abilities could be enhanced significantly when using them as a mixture (9.85% w/v skim milk and 10.65% w/v sucrose). Prefreezing of the cells at −80°C for 5 h prior to freeze drying and cultivation with regulated pH and temperature gave the highest cell viability.

... This micropropagation has introduced the potential of continuous supply of ... Adverse effect... more ... This micropropagation has introduced the potential of continuous supply of ... Adverse effects brought about by the commercially available therapeutic agents for treating diabetes such as insulin has gain an interest for the search of more effective therapeutic options from ...

International Journal of Hydrogen Energy, 2009

A hydrogen producer was successfully isolated from anaerobic digested palm oil mill effluent (POM... more A hydrogen producer was successfully isolated from anaerobic digested palm oil mill effluent (POME) sludge. The strain, designated as Clostridium butyricum EB6, efficiently produced hydrogen concurrently with cell growth. A controlled study was done on a synthetic medium at an initial pH value of 6.0 with 10g/L glucose with the maximum hydrogen production at 948mLH2/L-medium and the volumetric hydrogen production

The Scientific World Journal, 2014

Lactococcus lactis is the most studied mesophilic fermentative lactic acid bacterium. It is used ... more Lactococcus lactis is the most studied mesophilic fermentative lactic acid bacterium. It is used extensively in the food industry and plays a pivotal role as a cell factory and also as vaccine delivery platforms. The proteome of the Malaysian isolated L. lactis M4 dairy strain, obtained from the milk of locally bred cows, was studied to elucidate the physiological changes occurring between the growth phases of this bacterium. In this study, ultraperformance liquid chromatography nanoflow electrospray ionization tandem mass spectrometry (UPLC-nano-ESI-MS ) approach was used for qualitative proteomic analysis. A total of 100 and 121 proteins were identified from the midexponential and early stationary growth phases, respectively, of the L. lactis strain M4. During the exponential phase, the most important reaction was the generation of sufficient energy, whereas, in the early stationary phase, the metabolic energy pathways decreased and the biosynthesis of proteins became more important. Thus, the metabolism of the cells shifted from energy production in the exponential phase to the synthesis of macromolecules in the stationary phase. The resultant proteomes are essential in providing an improved view of the cellular machinery of L. lactis during the transition of growth phases and hence provide insight into various biotechnological applications.

Two plasmids, pFLAG-ATS and pET 26b(+), were studied for the periplasmic expression of recombinan... more Two plasmids, pFLAG-ATS and pET 26b(+), were studied for the periplasmic expression of recombinant human interferon-α2b (IFN-α2b) in Escherichia coli. The pFLAG-ATS contains ompA signal sequence and tac promoter while pET 26b(+) contains pelB signal sequence and T7lac promoter. It was observed that periplasmic expression of IFN-α2b from pET 26b(+) was around 3000 times higher than pFLAG-ATS. Difference in the expression level was attributed to the difference in the promoters and the signal sequences. In silico analysis of mRNA secondary structures were analyzed using Vienna RNA package and MFOLD. The results suggested that the increase of expression would mainly due to the difference in the translation initiation associated with secondary structure of mRNA transcribed by both plasmids.

Trees, 2007

... Functional screening for key genes essential for salinity tolerance mechanisms using E. coli ... more ... Functional screening for key genes essential for salinity tolerance mechanisms using E. coli as the host organism, has been used to isolate two mangrove genes, &amp;#x27;mangrin&amp;#x27; and cytosolic chaperonin-containing TCP-1a ... effectiveness of this method in isolating salinity tolerant ...

Tree Genetics & Genomes, 2008

In this study, we report the sequence, Southern analyses and spatial distribution of four cDNA se... more In this study, we report the sequence, Southern analyses and spatial distribution of four cDNA sequences related to reactive oxygen species (ROS) scavenging systems from a mangrove plant, Acanthus ebracteatus. These four complementary DNA (cDNA) sequences encode cytosolic ascorbate peroxidase (AeAPX), monodehydroascorbate reductase (AeMDHR), glutathione-S-transferase (AeGST), and mitochondrial manganese superoxide dismutase (AeMnSOD), respectively. Experimental results indicated that AeAPX and AeGST belong to multigene families, whereas AeMDHAR and AeMnSOD exhibited substantial differences from other members of the same families. Transcript analyses indicated that all these genes were expressed in flowers. However, only AeAPX, AeMDHAR, and AeMnSOD were expressed in all tissues examined. Although both AeMDHAR and AeMnSOD were highly expressed in flowers, the highest expression of AeMnSOD was in the leaf tissue. The expression of AeMDHAR and AeMnSOD in stem was slightly higher than in the root.

The Open Biotechnology Journal, 2010

The effectiveness of various physical and chemical methods for the removal of contaminants from t... more The effectiveness of various physical and chemical methods for the removal of contaminants from the microalgae, Tetraselmis suecica, culture was investigated. The information obtained was used as the basis for the development of improved protocol for the preparation of axenic culture to be adapted to heterotrophic cultivation. Repeated centrifugation and rinsing effectively removed the free bacterial contaminants from the microalgae culture while sonication helped to loosen up the tightly attached bacterial contaminants on the microalgae cells. Removal of bacterial spores was accomplished using a mixture of two antibiotics, 5 mg/mL vancomycine and 10 mg/mL neomycine. Walne medium formulation with natural seawater was preferred for the enhancement of growth of T. suecica. Adaptation of growth from photoautotrophic to heterotrophic conditions was achieved by the repeated cultivation of photoautotrophic culture with sequential reduction in illumination time, and finally the culture was inoculated into the medium containing 10 g/L glucose, incubated in total darkness to obtain heterotrophic cells. Changes in the morphology and composition of T. suecica cells during the adaptation from photoautotrophic to heterotrophic condition, as examined under Transmission Electron Microscope, were also reported.

Process Biochemistry, 2010

Methane derived from anaerobic treatment of organic wastes has a great potential to be an alterna... more Methane derived from anaerobic treatment of organic wastes has a great potential to be an alternative fuel. Abundant biomass from various industries could be a source for biomethane production where combination of waste treatment and energy production would be an advantage. This article summarizes the importance of the microbial population, with a focus on the methanogenic archaea, on the anaerobic fermentative biomethane production from biomass. Types of major wastewaters that could be the source for biomethane generation such as brewery wastewater, palm oil mill effluent, dairy wastes, cheese whey and dairy wastewater, pulp and paper wastewaters and olive oil mill wastewaters in relevance to their dominant methanogenic population are fully discussed in this article.

Plasmid, 2014

Plasmid DNAs isolated from lactic acid bacteria (LAB) such as Lactococcus lactis (L. lactis) has ... more Plasmid DNAs isolated from lactic acid bacteria (LAB) such as Lactococcus lactis (L. lactis) has been gaining more interests for its positive prospects in genetic engineering-related applications. In this study, the lactococcal plasmid, pNZ8048 was modified so as to be able to express multiple genes in the eukaryotic system. Therefore, a cassette containing an internal ribosome entry site (IRES) was cloned between VP2 gene of a very virulent infectious bursal disease (vvIBDV) UPM 04190 of Malaysian local isolates and the reporter gene, green fluorescent protein (GFP) into pNZ:CA, a newly constructed derivative of pNZ8048 harboring the cytomegalovirus promoter (P cmv ) and polyadenylation signal. The new bicistronic vector, denoted as pNZ:vig was subjected to in vitro transcription/translation system followed by SDS-PAGE and Western blot analysis to rapidly verify its functionality. Immunoblotting profiles showed the presence of 49 and 29 kDa bands that corresponds to the sizes of the VP2 and GFP proteins respectively. This preliminary result shows that the newly constructed lactococcal bicistronic vector can co-express multiple genes in a eukaryotic system via the IRES element thus suggesting its feasibility to be used for transfection of in vitro cell cultures and vaccine delivery.

Nanotechnology, 2009

The delivery of a full plasmid, encoding the green fluorescent protein gene into African monkey k... more The delivery of a full plasmid, encoding the green fluorescent protein gene into African monkey kidney (Vero3) cells, was successfully achieved using nanobiocomposites based on layered double hydroxides. This demonstrated the potential of using the system as an alternative DNA delivery vector. Intercalation of the circular plasmid DNA, pEGFP-N2, into Mg/Al-NO − 3 layered double hydroxides (LDH) was accomplished through anion exchange routes to form the nanobiocomposite material. The host was previously synthesized at the Mg 2+ to Al 3+ molar ratio R i = 2 and subsequently intercalated with plasmid DNA. Size expansion of the interlamellae host from 8.8Å in LDH to 42Å was observed in the resulting nanobiocomposite, indicating stable hybridization of the plasmid DNA. The powder x-ray diffraction (PXRD) results, supplemented with Fourier-transform infrared (FTIR) spectroscopy, compositional and electrophoresis studies confirmed the encapsulation episode of the biomaterial. In order to elucidate the use of this resulting nanobiocomposite as a delivery vector, an MTT assay was performed to determine any cytotoxic effects of the host towards cells. The intercalated pEGFP-N2 anion was later successfully recovered through acidification with HNO 3 after treatment with DNA-degrading enzymes, thus also showing the ability of the LDH host to protect the intercalated biomaterial from degradation. Cell transfection studies on Vero3 cells were then performed, where cells transfected with the nanobiocomposite exhibited fluorescence as early as 12 h post-treatment compared to naked delivery of the plasmid itself.

Marine Biotechnology, 2009

Light regulates photosynthesis, growth and reproduction, yield and properties of phycocolloids, a... more Light regulates photosynthesis, growth and reproduction, yield and properties of phycocolloids, and starch contents in seaweeds. Despite its importance as an environmental cue that regulates many developmental, physiological, and biochemical processes, the network of genes involved during light deprivation are obscure. In this study, we profiled the transcriptome of Gracilaria changii at two different irradiance levels using a cDNA microarray containing more than 3,000 cDNA probes. Microarray analysis revealed that 93 and 105 genes were up- and down-regulated more than 3-fold under light deprivation, respectively. However, only 50% of the transcripts have significant matches to the nonredundant peptide sequences in the database. The transcripts that accumulated under light deprivation include vanadium chloroperoxidase, thioredoxin, ferredoxin component, and reduced nicotinamide adenine dinucleotide dehydrogenase. Among the genes that were down-regulated under light deprivation were genes encoding light harvesting protein, light harvesting complex I, phycobilisome 7.8 kDa linker polypeptide, low molecular weight early light-inducible protein, and vanadium bromoperoxidase. Our findings also provided important clues to the functions of many unknown sequences that could not be annotated using sequence comparison.