Amalia Mohd Hashim

Universiti Putra Malaysia

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Shuhaimi Mustafa

Universiti Putra Malaysia

Nur Fadhilah Khairil Mokhtar

Universiti Putra Malaysia

Mohd Nasir Mohd Desa

Universiti Putra Malaysia

Mohd Termizi Yusof

Universiti Putra Malaysia

Mohd Hafis Yuswan

Universiti Putra Malaysia

Noor Baity Saidi

Universiti Putra Malaysia

Raja Kamil

Kolej Poly-Tech MARA

Yanty Noorzianna Abdul Manaf

Universiti of Malaysia Sabah

Muhamad Shirwan Abdullah Sani

International Islamic University Malaysia

Helmi Wasoh

Universiti Putra Malaysia

Cooperative Institutions

Universiti Putra Malaysia

148

Serdang Hospital

Universiti Teknologi Petronas

National University of Malaysia

Malaysian Agricultural Research and Development Institute

Universiti Teknologi MARA

National Institutes of Biotechnology Malaysia

Jabatan Perkhidmatan Awam Malaysia

Petronas (Malaysia)

University of Malaya

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Submerged modular breakwaters for coastal protection

WIT transactions on engineering sciences (2014)

Hee Min Teh Amalia Mohd Hashim

Submerged breakwaters are widely used for establishment and protection of coastal wetlands; nevertheless, construction of breakwaters in the sea domain has always been a challenge to engineers.This research introduces a number of submerged breakwaters that are made of a plurality of rectangular/triangular concrete modules.The wave transmission characteristics of the breakwaters are evaluated using small-scale physical modelling.A series of experiments are conducted in a wave flume to study the performance of the breakwaters in regular waves.Wave suppression ability of the breakwaters is quantified by the wave transmission coefficient.The effects of breakwater width, face type and configuration on wave transmission of the breakwaters are addressed in this paper.

Breakwater

10.2495/afm140111

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Citations (1)

Diversity, Relative Abundance, and Functional Genes of Intestinal Microbiota of Tiger Grouper (Epinephelus fuscoguttatus) and Asian Seabass (Lates calcarifer) Reared in A Semi-Closed Hatchery in Dry and Wet Seasons

Pertanika journal of tropical agricultural science (2021)

Jumria Sutra Hamidu Saadu Amalia Mohd Hashim Mohd Zamri Saad Md Yasin Ina‐Salwany

Grouper and Asian seabass are among the economically important cultured marine fish in Malaysia. However, fry productions in large scale tend to introduce stress that changes the fish microbiota and increases susceptibility to diseases. Currently, high-throughput sequencing is used to study fish microbiota and their respective gene functions. In this study, we investigate the diversity, abundance and functional genes of intestinal microbiota of tiger grouper and Asian seabass that were reared in a semi-closed hatchery during dry and wet seasons. Intestinal samples were collected from tiger grouper and Asian seabass of different sizes before proceeded to DNA extraction. The extracted DNA were then subjected to 16S rRNA gene amplicon sequencing using the Illumina Miseq platform targeting V3 and V4 regions for determination of the bacterial diversity, abundance and functional genes in both seasons. The results revealed that intestinal microbiota of Asian seabass were dominated by the phylum Proteobacteria and order Vibrionales in both seasons. Meanwhile, intestinal microbiome of tiger groupers were shifted from domination of phylum Firmicutes and order Clostridiales in dry season to Proteobacteria and order Lactobacillales in wet season. PICRUSt analysis revealed that the functional genes that were dominantly present were the genes encoded for metabolism, genetic information processing, environmental information processing, cellular process and human diseases. Remarkably, SIMPER analysis showed several potential metagenomics biomarker genes in dry and wet seasons. This study revealed the importance of utilizing amplicon metagenomics approaches in microbiome studies for better identification of the microbial profiling in aquaculture systems.

Sea bass

10.47836/pjtas.44.2.06

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Analysis of bacterial communities in rhizosphere soil of symptomless and basal stem rot (BSR)-infected oil palm using terminal restriction fragment length polymorphism (T-RFLP)

Norazreena Zainudin Amalia Mohd Hashim Nurulfiza Mat Isa Idris Abu Seman

Basal Stem Rot (BSR) disease caused by pathogenic fungi known as Ganoderma boninense has been identified as a major threat in oil palm plantation. Previously used methods to control this disease have been ineffective while method using chemical treatment is not environmentally friendly. An inadequate knowledge on the core microbiome of oil palm rhizosphere and the relationship between BSR disease incidences hinders effective controls against this pathogenic disease. Hence, the objectives of this project are to determine the bacterial communities of symptomless and BSR-infected oil palm using T-RFLP analysis, to perform cluster analysis of the samples based on the T-RFLP data and to analyze the relationship between soil bacterial communities and soil pH. The rhizosphere samples of symptomless and BSR-infected oil palm were collected at different microsites (bulk soil from harvesting path and rhizosphere soil from weeded circle and frond pile) and at different depths (10 cm and 30 cm from upper soil surface) from Oil Palm Plantation, Seberang Perak. In T-RFLP analysis, 16s rRNA region of the bacterial DNA were amplified by using 8F forward primer labelled with 6-FAM fluorescent dye and unlabelled 1492R reverse primer. The PCR products were then digested either with restriction enzyme AluI or HhaI or double digestion using AluI and HhaI. The raw fragments data were aligned and analyzed in T-REX (T-RFLP Analysis Expedited Software). The ordination analysis of Additive Main Effects and Multiplicative Interaction Model (AMMI) analysis from T-REX software revealed higher percentages of signal compared to noise interaction effects for frond pile at depth 30 cm with interaction difference of 21.28% (analysis based on relative abundance). The higher difference between signal and noise indicates that there are larger differences in microbial community between symptomless and BSR-infected oil palm. Meanwhile, cluster analysis showed that the sample obtained from harvesting path (bulk soil) at 10 cm and 30 cm depth clustered closely together indicating that there are small differences in microbial community at these microsites. Clustering analysis based on relative abundance shows that there is larger difference in microbial abundance between symptomless and BSR-infected sample at Frond Pile (30 cm depth). These results will provide preliminary knowledge in selecting representative samples of symptomless and BSR-infected oil palm for further microbial interaction analysis using Next Generation Sequencing.

Stem rot

Phylotype

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Bacterial community structure, predicted metabolic activities, and formation of volatile compounds attributed to Malaysian fish sauce flavour

Food Chemistry (2023)

Shanti Dwita Lestari Anis Shobirin Meor Hussin Shuhaimi Mustafa Yun Shin Sew Han Ming Gan

Catabolism

Phenylacetaldehyde

Flavour

Fermented fish

Halomonas

10.1016/j.foodchem.2023.136568

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Inhibition mechanisms of secretome proteins from Paenibacillus polymyxa Kp10 and Lactococcus lactis Gh1 against methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococcus

Asian Pacific Journal of Tropical Biomedicine (2022)

Nurul Hana Zainal Baharin Nur Fadhilah Khairil Mokhtar Mohd Nasir Mohd Desa Nurul Diana Dzaraly AbdulRahman Muthanna

Objective: To determine the inhibition mechanisms of secretome protein extracted from Paenibacillus polymyxa Kp10 (Kp10) and Lactococcus lactis Gh1 (Gh1) against methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus (VRE). Methods: The sensitivity and viability of MRSA and VRE treated with secretome proteins of Kp10 and Gh1 were determined using minimal inhibitory concentration, minimum bactericidal concentration, and time-to-kill assays. The morphological changes were observed using scanning electron microscopy and transmission electron microscopy. To elucidate the antimicrobial mechanism of secretome protein of Kp10 and Gh1 against MRSA and VRE, 2D gel proteomic analysis using liquid chromatography-mass spectrometry was run by comparing upregulated and downregulated proteins, and the proton motive force study including the efflux of ATP, pH gradient, and the membrane potential study were conducted. Results: MRSA and VRE were sensitive to Kp10 and Gh1 secretome protein extracts and displayed apparent morphological and internal composition changes. Several proteins associated with cellular component functions were either downregulated or upregulated in treated MRSA and VRE by changing the membrane potential gradient. Conclusions: Kp10 and Gh1 secretome proteins reduce the growth of VRE and MRSA by damaging the cell membrane. Cell division, cell wall biosynthesis, and protein synthesis are involved in the inhibition mechanism.

Paenibacillus polymyxa

Lysostaphin

Efflux

10.4103/2221-1691.360564

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Citations (2)

Performance evaluation of innovative concrete armor unit for coastal protection structure

Amalia Mohd Hashim Nur Diyana Md Noor

Various local innovative armor units for coastal protection structure have been developed to mitigate and control serious coastal erosion problems. The armor units designed by researchers from several institutions in Malaysia include SAUH, SINE SLAB, L-Block and Labuan Block armor. These armor units were implemented to prevent critical erosion problems along various stretches of Malaysia's coastline. This paper discusses the site assessment that was conducted covering selected coastal protection projects along West Coast of Peninsular Malaysia to evaluate the' performance level and identify concerns regarding these armor units. Initial condition of the armor units and the site location were identified and documented as the base condition for the performance evaluation. Comparisons were later made with current observation and findings. The breakage, displacement and settlement of the armor units were noted and any sign of accretion and erosion were also taken into consideration. Most of the armor units remain intact in their initial position especially SAUH and SINESLAB armor units. Corrosion of reinforcement steel bars was observed in most of the armor units as evidenced from the presence of brownish color substance at the concrete surface. This was caused by intrusion of salt water in the concrete through minor fractures and gaps. No major failure on the armor unit was observed during the site assessment indicating good structural stability as expected in their design life. Overall, the impIemented schemes were observed to be performing successfully with occurrence of accretion at most of the sites. The findings and result from this site assessment are important as guidance for future research and other initiative to improve the current innovations. The up-to-date assessment are also critical to estimate further maintenance works to prevent major failure due to prolong exposure to damage that may lead to potentially high maintenance costs to local authorities and nearby residences.

Armour

Breakwater

Slab

Settlement (finance)

10.1109/beiac.2013.6560215

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Citations (5)

Dynamic Responses of Float-over Barge Subjected to Random Waves

The Twenty-second International Offshore and Polar Engineering Conference (2012)

V.J. Kurian Nurul Husna Baharuddin Amalia Mohd Hashim A.R. Magee

BARGE

Float (project management)

Source

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Profiling bacterial communities and foodborne pathogens on food-associated surface following contact with raw beef, chicken and pork using 16S amplicon metagenomics

Food Control (2023)

Mohsen Emamjomeh Amalia Mohd Hashim Noor Azira Abdul-Mutalib Nur Fadhilah Khairil Mokhtar Nurul Asyifah Mustapha

Pathogenic bacteria

Meat spoilage

Isolation

Food microbiology

10.1016/j.foodcont.2023.109698

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Citations (13)

Next Generation Sequencing-based DNA metabarcoding for animal species profiling in fish feed

Food Additives & Contaminants Part A (2022)

Nur Fadhilah Khairil Mokhtar Siti Zaharah Imran Ming Gan Han Mun Chun Leong Mohd Nasir Mohd Desa

The expansion of worldwide aquaculture has been accompanied by extensive growth in the fish feed industry. However, improper labelling of many commercially available fish feeds has raised security and safety concerns over the species' origin of the ingredients. The inclusion of ruminants-derived ingredients in fish feed is prohibited according to EU legislation while porcine inclusion in fish feed has been a great concern among Muslim farmers. In contrast to the limited species that could be simultaneously determined using multiplex PCR, this study utilised Next Generation Sequencing-based DNA metabarcoding assay to determine the compositional profiles of animal species in fish feed samples in a more holistic manner. In relation to the religious issue associated with porcine-derived ingredients in fish feed, this study firstly aimed to determine the sensitivity of the methods in profiling fish feed adulterated with porcine blood and muscle tissues. Next, 10 commercially available fish feed samples were analysed. As a result, a detection limit of as low as 3% (w/w) porcine muscle and blood in the laboratory-prepared fish feed was obtained. The analysis of 10 commercial fish feeds shows surprising findings: 50% of the feeds contain Sus scrofa and 80% contain Bos taurus, a ruminant. Only one commercial fish feed was found to be solely composed of marine species. This study shows that commercial fish feeds sold in Malaysia contain undesirable animal species, and emphasises the need for accurate and legally enforced labelling of mammalian species in fish feed products.

Commercial fish feed

Fish products

Diversity of fish

Animal Feed

10.1080/19440049.2022.2077458

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Citations (2)

Characterization of the Synergistic Effect of Fungal Isolates in Suppressing Ganoderma boninense and Enhancing Oil Palm Growth

Journal of Basic Microbiology (2024)

Muhammad Salahudin Kheirel Anuar Amalia Mohd Hashim Shamala Sundram Siti Rahmah Abdul Rahman Chai Ling Ho

ABSTRACT The globally vital oil palm, a major oil producer, confronts productivity challenges due to Ganoderma boninense (Gb), causing output decline. Chemical control efforts have proven ineffective, prompting exploration of microbial‐based biocontrol. While single fungal biocontrol research exists, the impact of employing multiple biocontrols concurrently to combat Ganoderma and enhance oil palm growth remains uncharted. This study examined four soil‐derived fungal isolates for their ability to antagonize Gb PER71 in vitro. Molecular identification categorized them as Talaromyces spp. and Penicillium sp. Moreover, all isolates were revealed to have at least three plant growth‐promoting (PGP) traits and were shown to have phosphoric hydrolase, ester hydrolase, peptide hydrolase, and glycosidase activities which are essential for plant growth. Furthermore, the synergistic evaluation of fungal isolates was tested against Gb PER71. One out of six combinations of fungal isolates showed a synergistic effect in vitro , and two showed a synergistic effect in planta . The application of single and combined fungal isolates tested in planta also suppressed Gb PER71 and enhanced oil palm growth compared to control groups. The findings indicate the promising potential of these isolates as biocontrol agents (BCAs) and bioformulations against Gb in oil palm cultivation.

Stem rot

Fungal growth

10.1002/jobm.202400312

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