Noor Azmi Shaharuddin

Universiti Putra Malaysia | UPM · Department of Biochemistry

The protoplast system is robust and versatile for plant genetic engineering works. There are various ways to deliver nucleic acid materials into the protoplasts, but polyethylene glycol (PEG)-mediated method offers minimal damage compared to others. Therefore, an established PEG-mediated transformation protocol with optimised parameters is needed t...

The CRISPR/Cas9 system is a precise and versatile genetic tool used to induce site-specific manipulation in the targeted gene. This study elaborates on the strategy to select the gRNAs targeting the oil palm phytoene desaturase (EgPDS) gene, which complements CRISPR-GE and sequence analysis. Sixty-one gRNAs were selected from 167 gRNA candidates ge...

Agricultural sorbents have received attention for their effectiveness in oil removal. In Malaysia, oil palm’s empty fruit bunch (EFB) spikelets are an abundant agricultural waste that provides a non-toxic, renewable resource of cellulosic materials. In this study, the effectiveness of EFB spikelets to remove oil spills from seawater pollution in a...

Pesticide treatment dramatically reduces crop loss and enhances agricultural productivity, promoting global food security and economic growth. However, owing to high accrual and persistent tendency, pesticides could create significant ecological consequences when used often. Lately, the perspective has transitioned to implementing biological materi...

Oil pollution such as diesel poses a significant threat to the environment. Due to this, there is increasing interest in using natural materials mainly from agricultural waste as organic oil spill sorbents. Oil palm’s empty fruit bunch (EFB), a cost-effective material, non-toxic, renewable resource, and abundantly available in Malaysia, contains ce...

The absence of a cell wall on the protoplast contributes to its versatility. Its flexibility for DNA manipulation and the possibility of rapid cell-based assay is desirable in the plant biotechnology field. This study was carried out to improve protoplast isolation from oil palm in vitro leaf and mesocarp tissues. The factors affecting protoplast i...

One of the most severe environmental issues affecting the sustainable growth of human society is water pollution. Phenolic compounds are toxic, hazardous and carcinogenic to humans and animals even at low concentrations. Thus, it is compulsory to remove the compounds from polluted wastewater before being discharged into the ecosystem. Biotechnology...

Since the heroic age of Antarctic exploration, the continent has been pressurized by multiple anthropogenic activities, today including research and tourism, which have led to the emergence of phenol pollution. Natural attenuation rates are very slow in this region due to the harsh environmental conditions; hence, biodegradation of phenol using nat...

Rice straw, an agricultural waste product generated in huge quantities worldwide, is utilized to remediate diesel pollution as it possesses excellent characteristics as a natural sorbent. This study aimed to optimize factors that significantly influence the sorption capacity and the efficiency of oil absorption from diesel-polluted seawater by rice...

Oil spill incidents are hazardous and have prolonged damage to the marine environment. Management and spill clean-up procedures are practical and rapid, with several shortcomings. Coco peat (CP) and coco fibre (CF) are refined from coconut waste, and their abundance makes them desirable for diesel spillage treatment. Using a filter-based system, th...

Imperata cylindrica, often known as cogon grass, is a low-cost and useful sorbent for absorbing oil and optimising processes. The effects of temperature, time, packing density and oil concentration on oil absorption efficiency were investigated and optimised utilising one-factor-at-a-time (OFAT) and response surface methodology (RSM) approaches. Te...

Phycobiliproteins are gaining popularity as long-term, high-value natural products which can be alternatives to synthetic products. This study analyzed research trends of phycobiliproteins from 1909 to 2020 using a bibliometric approach based on the Scopus database. The current findings showed that phycobiliprotein is a burgeoning field in terms of...

Fucoxanthin is a major carotenoid in brown macroalgae and diatoms that possesses a broad spectrum of health benefits. This review evaluated the research trends of the fucoxanthin field from 1928 to June 2021 using the bibliometric method. The present findings unraveled that the fucoxanthin field has grown quickly in recent years with a total of 208...

Basal stem rot (BSR) disease caused by pathogenic fungus Ganoderma boninense is a significant concern in the oil palm industry. G. boninense infection in oil palm induces defense-related genes. To understand oil palm defense mechanisms in response to fungal invasion, we analyzed differentially expressed genes (DEGs) derived from RNA-sequencing (RNA...

Identification of novel genes that are specifically expressed in root is essential for isolation and characterisation of root-specific promoters. Mining the transcriptome of various oil palm tissue-specific data generated from ribonucleic acid-sequencing (RNA-Seq) technology has enabled the discovery of root-specific genes. A total of seven candida...

The versatility of a rare metal, molybdenum (Mo) in many industrial applications is one of the reasons why Mo is currently one of the growing environmental pollutants worldwide. Traces of inorganic contaminants, including Mo, have been discovered in Antarctica and are compromising the ecosystem. Bioremediation utilising bacteria to transform pollut...

Antarctica is a relatively pristine continent that attracts scientists and tourists alike. However, the risk of environmental pollution in Antarctica is increasing with the increase in the number of visitors. Recently, there has been a surge in interest regarding diesel, heavy metals and microplastics pollution. Contamination from these pollutants...

Microalgal biomass is one of the crucial criteria in microalgal studies. Many reported methods, even the well-established protocol on microalgal dry weight (DW) determination, vary greatly, and reliable comparative assessment amongst published results could be problematic. This study aimed to determine the best condition of critical parameters in m...

Despite the continuous enforcement of Antarctic Treaty System, ATS (1961), today Antarctica is constantly plagued by hydrocarbon pollution from both legacy and present-day wastes, especially near where anthropogenic activities are the most intense. The advances of science have led to multiple breakthroughs to bolster bioremediation techniques and r...

Hydrocarbon pollution is widespread around the globe and, even in the remoteness of Antarctica, the impacts of hydrocarbons from anthropogenic sources are still apparent. Antarctica’s chronically cold temperatures and other extreme environmental conditions reduce the rates of biological processes, including the biodegradation of pollutants. However...

Introduction: The protoplast represents a truly single-cell system which is useful and beneficial for in vivo gene functional study. The different source of protoplasts according to the gene of interest, together with robust isolation and cultivation procedure are beneficial for genetic improvement of the perennial crop, such as oil palm. Methods:...

The production of alkaloids in the intact plant is usually low, and some of them are tissue-specific and growth stage–specific. In this study, the total alkaloid content (TAC) in Polyalthia bullata was determined using different extraction solvents, and the extracts were subjected to LC-MS analysis. The manipulation of alkaloid production in P. bul...

Nanotechnology is a promising tool that has opened the doors of improvement to the quality of human’s lives through its potential in numerous technological aspects. Green chemistry of nanoscale materials (1–100 nm) is as an effective and sustainable strategy to manufacture homogeneous nanoparticles (NPs) with unique properties, thus making the synt...

Inorganic phosphate (Pi) starvation is an important abiotic constraint that affects plant cellular homeostasis, especially in tropical regions with high acidic soil and less solubilizable Pi. In the current work, oil palm seedlings were hydroponically maintained under optimal Pi-supply and no Pi-supply conditions for 14 days, and metabolites were m...

A genetic transformation protocol for rubber (Hevea brasiliensis) was established in zygotic embryo derived callus tissue through gfp (green fluorescence protein) detection. Different parameters for transformation efficiency were identified and optimized. Agrobacterium strain LBA 4404 harboring pCAMBIA 1304 for 3 days co-cultivation produced optimu...

Bioremediation of hydrocarbons has received much attention in recent decades, particularly relating to fuel and other oils. While of great relevance globally, there has recently been increasing interest in hydrocarbon bioremediation in the marine environments of Antarctica. To provide an objective assessment of the research interest in this field w...

Endoplasmic reticulum (ER) is an important organelle responsible as protein synthesis regulator in plant. High salinity can also lead to the activation of ER stress, caused by the accumulation of misfolded protein. This could lead to a stress response mechanism, unfolded protein response (UPR). Failure of UPR to reverse the effect of protein misfol...

The globe is presently reliant on natural resources, fossil fuels, and crude oil to support the world’s energy requirements. Human exploration for oil resources is always associated with irreversible effects. Primary sources of hydrocarbon pollution are instigated through oil exploration, extraction, and transportation in the Arctic region. To addr...

Diesel acts as a main energy source to complement human activities in Antarctica. However, the increased expedition in Antarctica has threatened the environment as well as its living organisms. While more efforts on the use of renewable energy are being done, most activities in Antarctica still depend heavily on the use of diesel. Diesel contaminan...

Diesel is a fuel commonly used in Antarctica to supply vessels and domestic applications on site. The increasing human activities in the continent consequently have generated high fuel demand, which in turn has increased the occurrence of oil pollution due to accidental events during refueling. A related study received growing interest as more detr...

Background Hemibiotrophic pathogen such as the fungal pathogen Ganoderma boninense that is destructive to oil palm, manipulates host defense mechanism by strategically switching from biotrophic to necrotrophic phase. Our previous study revealed two distinguishable expression profiles of oil palm genes that formed the basis in deducing biotrophic ph...

Polyalthia bullata is an endangered medicinal plant species. Hence, establishment of P. bullata callus culture is hoped to assist in mass production of secondary metabolites. Leaf and midrib were explants for callus induction. Both of them were cultured on Murashige and Skoog (MS) and Woody Plant Medium (WPM) containing different types and concentr...

Study of the potential of Antarctic microorganisms for use in bioremediation is of increasing interest due to their adaptations to harsh environmental conditions and their metabolic potential in removing a wide variety of organic pollutants at low temperature. In this study, the psychrotolerant bacterium Rhodococcus sp. strain AQ5-07, originally is...

Micropropagation is a reliable technique in biotechnology and genetic engineering domain, which has been widely applied for rapid mass propagation of plants in vitro condition. Through micropropagation techniques, reproduction of plants can be attained from different explants using organogenesis and somatic embryogenesis. Over the decades, micropro...

Aim: Effective bioremediation requires optimisation of conditions under which the process takes place. In this study, an Antarctic soil bacterium, Arthrobacter sp. strain AQ5-15, was evaluated for phenol biodegradation under statistically optimised conditions. Methodology: The composition of degradation media and the culture conditions for this stu...

Arsenic is considered to be a toxic and heavy metal that exists in drinking water and can lead to acute biotoxicity. Water mimosa (Neptunia oleracea) has been widely identified as a feasible phytoremediator to clean up aquatic systems. In the current study, the phytoremediation potential of water mimosa exposed to different concentrations of sodium...

Polyalthia bullata is a woody medicinal plant that contains antioxidant compounds. Finding a suitable solvent is important to obtain a high yield of antioxidants in the phenolic, flavonoid, and terpenoid families. In this study, from different solvent extracts, the leaf methanolic extract exhibited the highest total phenolic content (TPC), total fl...

Mycosporine-like amino acids (MAAs) are a group of more than 40 metabolites originated from 4-deoxygadusol featuring antioxidant, growth stimulation, and UV protective properties in many microorganisms. In D. radiodurans R1, 3-dehydroquinate synthase (DHQS) gene annotated in chromosome 1 encodes the precursor for all MAAs. In this study, a signific...

This study focused on the ability of the Antarctic bacterium Rhodococcus sp. strain AQ5-14 to survive exposure to and to degrade high concentrations of phenol at 0.5 g l ⁻¹ . After initial evaluation of phenol-degrading performance, the effects of salinity, pH and temperature on the rate of phenol degradation were examined. The optimum conditions f...

Background Hemibiotrophic pathogen such as the fungal pathogen Ganoderma boninense that is destructive to oil palm, manipulates host defense mechanism by strategically switching from biotrophic to necrotrophic phase. Our previous study revealed two distinguishable expression profiles of oil palm genes that formed the basis in deducing biotrophic ph...

To cite this paper: Juri, N.M., N.A. Bakar, R.A.Z. Abidin, M. Mahmood, N.B. Saidi, Y. Awang and N.A. Shaharuddin, 2019. RNA-Seq and validation analysis on the important genes involved in early responses to salinity stress of Malaysian rice seedlings (Oryza sativa ssp. Abstract Salinization of rice cultivation land has progressively enlarged, thus n...

Though Antarctica has once been considered as the most pristine land on earth, however, recently many literatures concluded that it is not a zone free from anthropogenic pollutants, which have been mostly associated with long-range atmospheric transport and deposition in the area. Numerous organic pollutants including phenol have been classified as...

To cite this paper: Juri NM, AF Samsuddin, AMA Murad, AA Tamizi, NA Shaharuddin, NA Bakar (2020). Discovery of pathogenesis related and effector genes of Erwinia mallotivora in Carica papaya (Eksotika I) seedlings via transcriptomic analysis. Intl J Agric Abstract A comparative transcriptome of Erwinia mallotivora library across early infection tim...

Any forms of valorization of microorganisms would require accurate identity recognition to ensure repeatability, reproducibility and quality assurance. This study aimed to evaluate the effectiveness of different primers for identifying cultured eukaryotic microalgae using a simple 18S rDNA approach. A total of 34 isolated microalgae and one culture...

Production of Phosphate Starvation Response-2 (PHR2) transcription factor protein from Oil palm in E.coli DE3 (BL21_DE3). This protein could functionally be used to study phosphate starvation stress in oil palm.

Genetic modification of oil palm is being carried out to explore new avenues for improving and expanding the potential of oil palm. Multiple bottlenecks in delivering the DNA into oil palm cells and generating the transgenic oil palm required us to look into an alternative marker which could help us assess the efficiency of the transformation syste...

Hyperhydricity is one of the major problems experienced by in vitro plants including orchids when they are grown on unfavourable nutrient media. The hyperhydric plants have reported to show physiological disorder, excessive hydration and low lignification. In this study, medicinal orchid, the Dendrobium crumenatum or known as pigeon orchid was used...

Turmeric (Curcuma longa) has long been known in Southeast Asia as a medicinal plant and been used as folk remedies to treat minor illnesses like diarrhea or skin diseases. Recent studies on turmeric have shown numerous pharmacological properties such as anti-oxidant, anti-inflammatory, anti-pathogenic including anti-viral protease activities. All t...

Exposing the skin to solar UV radiation induces cascades of signaling pathways and biological alterations such as redox imbalance, suppression of antioxidant genes and programmed cell death. Therefore, the aim of this study was to use RNA-Seq to unravel the effects of UV radiation on Normal Human Adult Fibroblast cells (NHDF). Cells were exposed to...

Curcuma longa L. is a rhizome plant often used as traditional medicinal preparations in Southeast Asia. The dried powder is commonly known as cure-all herbal medicine with a wider spectrum of pharmaceutical activities. In spite of the widely reported therapeutic applications of C. longa, research on its safety and teratogenic effects on zebrafish e...

Proteomic analysis was conducted to identify the rice root proteins induced by exogenous proline and their involvement in root growth. Proteins were extracted from the root tissues grown under two conditions, T1 (control) and T2 (10 mM proline), and profiled by two-dimensional polyacrylamide gel electrophoresis. Seventeen of 30 differentially expre...

Curcuma longa L. is a rhizome plant often used as traditional medicinal preparations in Southeast Asia. The dried powder is commonly known as cure-all herbal medicine with a wider spectrum of pharmaceutical activities. In spite of the widely reported therapeutic applications of C. longa, research on its safety and teratogenic effects on zebrafish e...

Drought is one of the abiotic stresses on plants, causing significant detrimental impacts, especially to lowland rice (Oryza sativa L.) ecosystems. In order to obtain new insights on osmotic stress in rice, a comparative study using a Next-Generation Sequencing platform was conducted to elucidate osmotic-responsive genes from two local Malaysian ri...

Erwinia mallotivora has been identified as the causal pathogen of papaya dieback disease in Malaysia, and has become one of the major threats to the papaya industry. Pathogenesis-related (PR) proteins are considered as plant defense proteins, where they are capable to prevent or reduce the effect of pathogen and insect attacks. Accumulation of PR p...