Gires Usup

• National University of Malaysia

Fiddler crab burrows alter sediment conditions and create favourable niches for the colonization of several benthic species. Previous studies examined the effect of crab burrows on benthic communities without considering changes in sediment properties. This study aimed to reveal the relationship between the abundance of benthic fauna and altered en...

Dinoflagellate Alexandrium minutum Halim is commonly associated with harmful algal blooms (HABs) in tropical marine waters due to its saxitoxin production. However, limited information is available regarding the cellular and metabolic changes of A. minutum in nutrient-deficient environments. To fill this gap, our study aimed to investigate the tran...

Serinicoccus kebangsaanensis sp. nov strain P2D13-UKM is a new species of Gram-positive bacteria isolated from a toxic diatom, Nitzschia navis-varingica. It is a halophilic aerobic, oxidase-negative, catalase-positive, circular, and colonies with white colour. Based on the 16S rRNA gene, the closest species were Serinicoccus profundi MCCC 1A05965 s...

This study investigates bacterial diversity and potential pathogens in the international ships' ballast water at Tanjung Pelepas Port, Malaysia, using 16S rRNA amplicon sequencing. Thirty-four bacterial phylum, 305 families, 577 genera, and 941 species were detected in eight ballast water samples of different origins. The similarity of the bacteria...

Simple Summary Alexandrium minutum is one of the causing organisms for the occurrence of harmful algae bloom (HABs) in marine ecosystems. This species produces saxitoxin, one of the deadliest neurotoxins which can cause human mortality. However, molecular information such as genes and proteins catalog on this species is still lacking. Therefore, th...

Current occurrence of Nitzschia Hassall from marine and freshwater environment in Malaysia is compiled from current and previously published materials. Phytoplankton was collected using a 20 µm plankton net from waterfronts of Peninsular Malaysia and Borneo. Some Nitzschia cells were successfully isolated and established into clonal cultures. For m...

This study was conducted to purify and characterize an anti- C. albicans bacteriocin produced by Bacillus sp. Sh10 isolated from marine carpet clam, Paphia textile. Extracellularly produced bacteriocin was purified by 80 % ammonium sulfate precipitation and size exclusive gel chromatography using superdex-200 column chromatographyThe purification s...

Background & Objectives Actinomycetes are commonly known as exceptionally prolific source of secondary metabolites with diverse biological activities. The aim of this study was to identify some Actinomycete isolates from Malaysia marine environment and evaluate for type-I polyketide synthase (PKS-I) and nonribosomal peptide synthetase (NRPS) genes...

Background and objectives: Biofilm formed by Proteus mirabilis strains is one of the most important medical problems especially in the case of device-related urinary tract infections. This study was conducted to evaluate the bacteriocin produced by a marine isolate of Bacillus sp. Sh10, for it's in vitro inhibitory activity against pre-formed biof...

Saxitoxin is an alkaloid neurotoxin originally isolated from the clam Saxidomus giganteus in 1957. This group of neurotoxins is produced by several species of freshwater cyanobacteria and marine dinoflagellates. The saxitoxin biosynthesis pathway was described for the first time in the 1980s and, since then, it was studied in more than seven cyanob...

Information on benthic dinoflagellates in Indonesia is rare since it often neglected in many microalgae researches. Thus, not much information is available about the ecology of benthic dinoflagellates in Indonesia, especially for three important genus, Gambierdiscus, Prorocentrum and Ostreopsis. Sampling were carried three times: in August, October...

Quorum-sensing regulates bacterial biofilm formation and virulence factors, thereby making it an interesting target for attenuating pathogens. In this study, we investigated anti-biofilm and anti-quorum-sensing compounds from secondary metabolites of halophiles marine streptomyces against uri-nary catheter biofilm forming Proteus mirabilis without...

Microbiologically influenced corrosion (MIC) that responsible for corrosion problems, especially in oil and gas industry. The microorganism capable of iron reduction (IRB) that involving in MIC mechanisms, was contributing as a main problem for localized corrosion. Shewanella species are considered to be major iron-reducing bacteria (IRB) of crude...

Catheter-associated urinary tract infection is caused primarily by the multidrug-resistant biofilm forming bacteria of uropathogens. The prevention and successful treatment of infections is difficult when catheters are colonized by bacterial biofilm growth. There have been several efforts utilizing biocides in catheterizations, in attempts to inhib...

ABSTRACT The aim of this study was to determine the potential of secondary metabolites of Streptomyces as bacterial anti-biofilm and anti-quorum sensing agents against biofilm forming uropathogens. From a total of 100 isolates isolated from urinary catheters, six isolates were selected as target pathogens based on multi-drug resistance and strong...

Previous studies have suggested that a specific community of bacteria coexists within the phycosphere of marine dinoflagellates. In order to better understand the dinoflagellate-bacteria relationships, a fosmid clone library was constructed from the metagenome DNA and analyzed. Some of the fosmid clones were end-sequenced. A total of 1501 fosmid cl...

The marine dinoflagellate Alexandrium minutum is known to produce saxitoxins that cause paralytic shellfish poisoning in human worldwide through consumption of the contaminated shellfish mollusks. Despite numerous studies on the growth physiology and saxitoxin production of this species, the knowledge on the molecular basis of nutrient uptakes in r...

ABSTRACT: The need for passive and periodic surveillance on the presence of potential pathogenic bacteria in water bodies, sediments and tissues of fish in Malaysian water bodies is imperative. This study aimed at determining the presence of potential pathogenic bacteria in water bodies, sediment and tissues of sea bass, snapper, grouper and tilapi...

Buku Ikan Kekek di Semenanjung Malaysia ini mengandungi pelbagai maklumat khas, khususnya kepelbagaian spesies, keunikan anatomi sistem organ pendarcahaya, biologi dan ekologi ikan kekek. Selain itu, kekunci bergambar pengecaman spesies ikan kekek juga diperincikan oleh penulis supaya memudahkan pembaca mengenal pasti jenis ikan kekek semasa di pas...

Sub-minimum inhibitory concentration levels of Pseudoalteromonas ruthenica KLPp3 extract showed antibiofilm activity against Vibrio alginolyticus and Serratia marcescens. The KLPp3 crude extract was fractionated by thin layer chromatography, flash chromatography, solid phase extraction and semi-preparative high performance liquid chromatography. Th...

GlobalHAB, “Global Harmful Algal Blooms,” is a new scientific programme on harmful algal blooms (HABs) cosponsored by the Intergovernmental Oceanographic Commission (IOC) of UNESCO and the Scientific Committee on Oceanic Research (SCOR) that will operate for 10 years from 2016 to 2025. GlobalHAB builds on the solid foundation established by the for...

A total of 90 isolates of bacteria were isolated, from sediment (10) samples, water (10) samples and fish (12) samples (Sea bass, Snapper, Grouper and Tilapia). These include 22 isolates of bacteria from sediment, 28 isolates from water and 40 isolates from fish. All the isolates were tested for sensitivity to 13 antibiotics using disc diffusion me...

The growth of microbes in biofilms are associated with repeated and chronic human infections and are extremely resistant to antimicrobial agents. The purpose of this study was to determine the diversity of bacteria from necrotic roots canals of teeth and to detect their biofilm formation ability. A total of 42 bacterial isolates were isolated and i...

Over the past ten years, marine natural product researchers have expanded the scope of their studies from macroorganisms such as algae to marine microorganisms. The marine environment is believed to be able to provide novel lead against pathogenic microbes that are evolving and developing resistance to existing pharmaceutical agents. In this study,...

In this study, length-weight and length-length relationships of common carp (Cyprinus carpio L.) in the middle and southern Iraq provinces were determined. Fish specimens were procured from seven provinces from July to December, 2015. A negative and positive allometric growth pattern was obtained, where the total length (TL) ranged from 25.60 cm to...

Dinoflagellates are essential components in marine ecosystems, and they possess two dissimilar flagella to facilitate movement. Dinoflagellates are major components of marine food webs and of extreme importance in balancing the ecosystem energy flux in oceans. They have been reported to be the primary cause of harmful algae bloom (HABs) events arou...

Harmful Algal Bloom (HAB) is a natural phenomenon that has been reported all over the world including in Malaysia. The impact of this event to the human health, economy and tourism industry can be devastated depending on the scale. In Malaysia, HAB cases have been reported since the past decade. Since then, more and more cases were reported coverin...

Dinoflagellates are the large group of marine phytoplankton with primary studies interest regarding their symbiosis with coral reef and the abilities to form harmful algae blooms (HABs). Toxin produced by dinoflagellates during events of HABs cause severe negative impact both in the economy and health sector. However, attempts to understand the din...

ABSTRACT: This study was aimed to investigate the presence of virulence genes, antibiotic resistance genes and molecular diversity of V. vulnificus isolated from several coastal areas in Malaysia. Fifty five isolates were first tested for the presence of seven virulence genes including Hemolysin (vvhA), Extracellular Capsule Polysaccharide (CPS) (...

In 2015, a remarkably high density bloom of Alexandrium minutum occurred in Sungai Geting, a semi-enclosed lagoon situated in the northeast of Peninsular Malaysia, causing severe discoloration and contaminated the benthic clams (Polymesoda). Plankton and water samples were collected to investigate the mechanisms of bloom development of this toxic s...

p>Amnesic Shellfish Poisoning (ASP) is a type of intoxication caused by the neurotoxin domoic acid (DA). The diatom genus Nitzschia is capable of producing this toxin. Screening for the presence of toxic Nitzschia spp. was carried out at various estuaries in Malaysia. Nitzschia -like cells were isolated and established into clonal cultures. Late st...

In the last few years, Actinomycetes have been extensively studied in several underexplored environments, niche, and extreme habitats in various regions across the globe. Yet, there is no report regarding isolation of actinomycetes from the coastal waters of Malaysia. Given that marine environmental conditions are extremely different from the terre...

Mortality of hundreds of marine and freshwater fishes was reported in Malacca River, Malaysia on 22 April 2014. Water samples were collected from water surface (<10 m) using 20 m mesh plankton net. Observation under light microscope revealed relatively high abundance of zooplankton dominated by the red-tide forming ciliate Mesodinium rubrum (syn:...

Shallow, well-illuminated coastal waters from tropical to temperate latitudes are attractive environments for humans. Beaches and coral reefs have provided lodging and food to coastal communities for centuries. Unfortunately, tropical regions traditionally have been threatened by outbreaks of the toxic benthic dinoflagellate Gambierdiscus, which is...

The need for passive and periodic surveillance on the presence of potential pathogenic bacteria in water bodies, sediments and tissues of fish in Malaysian water bodies is imperative. This study aimed at determining the presence of potential pathogenic bacteria in water bodies, sediment and tissues of sea bass, snapper, grouper and tilapia which ma...

Background Toxic dinoflagellate in recent years, have become a significant problem in coastal regions worldwide because of their production of toxin. To manage and control the adverse impact of harmful algal blooms, many strategies including chemical, physical and biological methods have been developed Objective The aim of this study was to determi...

Background: Association between bacteria and marine dinoflagellates is one of the important factors in harmful algae bloom formation and toxin production by dinoflagellates. The diversity of the bacteria associated with clonal cultures of both toxic and non-toxic dinoflagellates, Alexandrium tamiyavanichii and Alexandrium leei were assessed by usin...

Background Toxic dinoflagellate in recent years, have become a significant problem in coastal regions worldwide because of their production of toxin. To manage and control the adverse impact of harmful algal blooms, many strategies including chemical, physical and biological methods have been developed Objective The aim of this study was to determi...

Abstract. Biogenic souring and microbial-influenced corrosion is a common scenario in petroleum reservoir .The serious threat normally comes from sulfate-reducing bacteria (SRB). Alcaligenes faecalis was tested in this study for the ability to inhibit the growth of SRB. Ethyl acetate extraction of A. faecalis grown in marine broth was carried out t...

Marine actinomycetes are now in demand as they are capable of producing unique and novel compounds with wide biological activities. Marine Streptomyces sp. UKMCC_PT15 previously isolated from seawater collected in Pulau Tinggi, Johor was used in this study. Molecular identification showed high similarity of Streptomyces sp. UKMCC_PT15 with Streptom...

This study was aimed to evaluate the algicidal activity of Loktanella sp. Gb-03 bacterial extracts against toxic dinoflagellate, using various polar and non-polar solvents. For this purpose, six different solvent extracts were prepared (i.e. methanol, ethyl acetate, hexane, chloroform, acetonitrile and water). Ratio of 1:100 (v:v) (extract to dinof...

Vibrio parahaemolyticus is widely recognized pathogenic Vibrio species due to numerous outbreaks and its’ wide occurrence in the marine environment. A total of 50 Vibrio parahaemolyticus isolates were isolated from seawater and sediments in Malaysia were tested for sensitivity to 19 antibiotics using disc diffusion method. It was found that all iso...

Bacillus sp. strain UMTAT18 was isolated from the harmful dinoflagellate Alexandrium tamiyavanichii. Its genome consists of 5,479,367 bp with 5,546 open reading frames, 102 tRNAs, and 29 rRNAs. Gene clusters for biosynthesis of nonribosomal peptides, bacteriocin, and lantipeptide were identified. It also contains siderophore and genes related to st...

Mameliella alba strain UMTAT08 was isolated from clonal culture of paralytic shellfish toxin producing dinoflagel-late, Alexandrium tamiyavanichii. Genome of the strain UMTAT08 was sequenced in order to gain insights into the dinoflagellate-bacteria interactions. The draft genome sequence of strain UMTAT08 contains 5.84Mbp with an estimated G + C c...

A study was carried out to determine the pathogenicity (hemolytic activity) on corals (Turbinaria sp.) and sea bass (Lates calcarifer) of Aeromonas hydrophila from water, sediment, and coral. Samples were collected from coastal water and coral reef areas. One hundred and sixty-two isolates were successfully isolated. Out of 162, 95 were from seawat...

Microbiologically influenced corrosion (MIC) that responsible for corrosion problems, especially in oil and gas industry. The microorganism capable of iron reduction (IRB) that involving in MIC mechanisms, was contributing as a main problem for locali corrosion. Shewanella species are considered to be major iron whether any of the Shewanella sp.are...

This study aimed to resolve the taxonomic status of a morphologically undetermined sea cucumber species of order Apodida from Malaysia (GenBank accession no.: FJ223867) using partial 16S mitochondrial rRNA gene sequences and subsequently to determine the validity of morphological taxonomy of Holothuria species into its current subgenera. The undete...

This study aimed to generate the genetic profile of Holothuria (Mertensiothuria) leucospilota (Brandt 1835) from Intan Besar Island, Langkawi, Kedah Darul Aman, Malaysia and then to determine the phylogenetic relationship between H. leucospilota and other members of genus Holothuria available in the GenBank using partial sequences of cytochrome c o...

Microbiologically influenced corrosion (MIC) that responsible for corrosion problems, especially in oil and gas industry. The microorganism capable of iron reduction (IRB) that involving in MIC mechanisms, was contributing as a main problem for locali corrosion. Shewanella species are considered to be major iron whether any of the Shewanella sp.are...

Indoor air pollution is an important risk factor for the generation of lung diseases in developing countries. The indigenous population is particularly susceptible to be exposed to the mixture of pollutants from the biomass burning, among them, polycyclic aromatic hydrocarbons (PAHs). The objective of this study was to assess respiratory health and...

Aims: Several harmful dinoflagellate species are widely found in Malaysian marine waters. These microalgae are capable of producing a variety of toxins that can intoxicate humans through consumption of contaminated seafood. Therefore, the present work aimed to investigate the potential of a marine bacterium sdPS-7 isolate as a biological control ag...

Aims: Pseudoalteromonas ruthenica KLPp3 is the marine Gram-negative strain isolated from the surface of mud crab at Pulau Perhentian Malaysia. In this work, the anti-biofilm activity of P. ruthenica supernatant was examined on Serratia marcescen and Vibrio alginolyticus. Methodology and results: The crude extract of P. ruthenica KLPp3 was obtained...

Aim: Bacteria associated with harmful algal blooms can play a crucial role in regulating algal blooms in the environment. This study aimed at isolating and identifying algicidal bacteria in Dinoflagellate culture and to determine the optimum growth requirement of the algicidal bacteria, Loktanella sp. Gb-03. Materials and methods: The Dinoflagel...

In mangrove ecosystems, litter fall accumulates as refractory organic carbon on the sediment surface and creates anoxic sediment layers. Fiddler crabs, through their burrowing activity, translocate oxygen into the anoxic layers and promote aerobic respiration, iron reduction and nitrification. In this study, the effects of four species of fiddler c...

Fiddler crabs burrow creates oxic-anoxic interfaces on the burrow walls. Accordingly burrow walls represent the transitions site between oxic and anoxic condition where the sediment properties varied significantly across it. In this study the burrows of three species of fiddler crabs including Uca rosea, Uca forcipata and Uca pardussumieri were sam...

Diversity of bacteria associated with toxic dinoflagellates Alexandrium minutum, Alexandrium tamiyavanichii and Pyrodinium bahamense var compressum were assessed using culture-dependent and -independent approaches. Total DNA from the dinoflagellate cultures as well as those of culturable bacteria was extracted and used as templates for PCR amplific...

Harmful algal blooms have caused huge damage to the marine ecosystem and the coastal economy all over the world. To identify a capable bio-agent of controlling dinoflagellate blooms, a bacterial strain Gb03 was isolated, which showed strong algicidal activity against toxic dinoflagellate Cooliamalayensis. The aim of this study is to extract and ide...

A test of implicit solvent models on the folding simulation of the GB1 peptide Abstract. This study was aimed to evaluate the algicidal activity of Loktanella sp. Gb-03 bacterial extracts against toxic dinoflagellate, using various polar and non-polar solvents. For this purpose, six different solvent extracts were prepared (i.e. methanol, ethyl ace...

A test of implicit solvent models on the folding simulation of the GB1 peptide Abstract. This study was aimed to evaluate the algicidal activity of Loktanella sp. Gb-03 bacterial extracts against toxic dinoflagellate, using various polar and non-polar solvents. For this purpose, six different solvent extracts were prepared (i.e. methanol, ethyl ace...

A test of implicit solvent models on the folding simulation of the GB1 peptide Abstract. This study was aimed to evaluate the algicidal activity of Loktanella sp. Gb-03 bacterial extracts against toxic dinoflagellate, using various polar and non-polar solvents. For this purpose, six different solvent extracts were prepared (i.e. methanol, ethyl ace...

A test of implicit solvent models on the folding simulation of the GB1 peptide Abstract. This study was aimed to evaluate the algicidal activity of Loktanella sp. Gb-03 bacterial extracts against toxic dinoflagellate, using various polar and non-polar solvents. For this purpose, six different solvent extracts were prepared (i.e. methanol, ethyl ace...

Abstract. Biogenic souring and microbial-influenced corrosion is a common scenario in petroleum reservoir .The serious threat normally comes from sulfate-reducing bacteria (SRB). Alcaligenes faecalis was tested in this study for the ability to inhibit the growth of SRB. Ethyl acetate extraction of A. faecalis grown in marine broth was carried out t...

Screening of the occurrence of potentially toxic diatoms was carried out at two sites of cage cultures in Tebrau Straits, Johor. Phytoplankton samples from Sungai Pendas and Teluk Sengat were collected using a 20 μm mesh plankton net and salinity was recorded in-situ. Nitzschia and Pseudo-nitzschia cells were isolated and established into clonal cu...

This study aimed to examine the anti-biofilm activity of Pseudoalteromonas flavipulchra SktPp1 crude extract against the biofilm producer, Serratia marcescens. The crude extract of P. flavipulchra SktPp1 was extracted with ethyl acetate. The sub-minimum inhibitory concentration (MIC), 0.1 mg/ml, has been used in this study. The anti-biofilm activit...

Marine sponges were known to produce novel bioactive compounds that have anti-bacterial, anti-viral, anti-cancer and anti-fungal activities. Most of the bioactive compounds were secreted from the bacteria that lives on the sponges. The bacterial communities also produced biofilm, toxin or biosurfactant that protect the sponges from disease or in-co...

This study is aimed to isolate, detect biofilm formation ability and antibiotic susceptibility of urinary catheter adherent microorganisms from elderly hospitalized patient at the Universiti Kebangsaan Malaysia Medical Center. Microorganisms were isolated from three samples of urinary catheters (UC) surface; one of the acute vascular rejection pati...

The bacteriocin-producing strain Bacillus sp., Sh10, isolated from the marine environment, exhibited a broad spectrum of antimicrobial activity against different food spoilage and human pathogens, with a maximum inhibitory activity against Candida albicans. The inhibitory compound was sensitive to trypsin but resistant to proteinase K, lysozyme, li...

Dinoflagellates are microscopic unicellular microalgae found in aquatic environments worldwide. Several marine dinoflagellate species are producers of a wide variety of toxins that can cause seafood poisoning, including fatalities in humans. In this study a combination of ultrastructure studies using transmission electron microscopy (TEM), and mole...

Harmful algae bloom or red tide seems to be considered as threat to ecosystem, especially to human consumption because of the production of neurotoxin by dinoflagellates species such as Alexandrium minutum which can lead to paralytic shellfish poisoning. The aim of this study is to determine the most suitable method for protein extraction of A. min...

The dinoflagellate Alexandrium minutum is typically known for the production of potent neurotoxins such as saxitoxin, affecting the health of human seafood consumers via paralytic shellfish poisoning (PSP). These phenomena is related to the harmful algal blooms (HABs) that is believed to be influenced by environmental and nutritional factors. Previ...

Vibrio campbellii strain UMTGB204 was isolated from a green barrel tunicate. The genome of this strain comprises 5,652,224 bp with 5,014 open reading frames, 9 rRNAs, and 116 tRNAs. It contains genes related to virulence and environmental tolerance. Gene clusters for the biosynthesis of nonribosomal peptides and bacteriocin were also identified.

This study aimed at documenting species richness and distribution of sea cucumbers (Phylum Echinodermata: Class Holothuroidea) in Malaysia. Sea cucumber collections were conducted from August 2004 until November 2011 from several study sites in Peninsular Malaysia and Sabah. A total of fifty two morphospecies of sea cucumbers from four orders compr...

In tropical regions, different species of fiddler crabs coexist on the mangrove floor, which sometimes makes it difficult to define species-specific habitat by visual inspection. The aim of this study is to find key environmental parameters which affect the distribution of fiddler crabs and to determine the habitats in which each species was most a...

Dinoflagellates are microscopic unicellular microalgae found in aquatic environments worldwide. Several marine dinoflagellate species are producers of a wide variety of toxins that can cause seafood poisoning, including fatalities in humans. One common feature of dinoflagellates is the presence of two unequal flagella: one that extends toward the p...

There is currently no bacteriological beach quality monitoring (BQM) program in place in Malaysia. To initiate cost-effective, sustainable bacteriological BQM schemes for the ultimate goal of protecting public health, policy decision makers need to be provided robust, indigenous empirical findings that validate appropriate water quality parameters...

Nitratireductor basaltis strain UMTGB225 is a Gram-negative bacterium isolated from a marine tunicate found in Bidong Island, Terengganu, Malaysia. In this study, the genome of Nitratireductor basaltis UMTGB225 was sequenced to gain insight into the role of this bacterium and its association with tunicate hosts in a coral reef habitat.

A study was conducted to optimize gradient gel electrophoresis (DGGE) protocols for determination of marine eukaryotic phytoplankton genetic diversity. The target genetic marker was a 330-bp fragment of the 18S subunit of the ribosomal RNA gene. PCR products incorporating a 40 base pair (bp) GC-clamp were successfully obtained from clonal cultures...

Serratia marcescens biofilms are formed when they are bound to surfaces in aqueous environments. S. marcescens utilizes N-acylhomoserine lactone (AHL) as its quorum sensing signal molecule. The accumulation of AHL indicates the bacteria to produce matrices to form biofilms. Prodigiosin (2-methyl-3-pentyl-6-methoxyprodigiosin), which causes red pig...

This research was conducted to investigate and compare the various metabolite, produced from the metabolism of two different SRB strain, that were involved in the biocorrosion process. Stainless steel coupons were immersed in two strains of sulfatereducing bacteria, A1H1 and EB3 (designated as SRB1 and SRB2 repectively) were isolated from Port Dick...

Antibacterial peptides have emerged as an alternative therapeutic to protect food and other products from deterioration and spoilage. In this study, bacteria were isolated from marine clams and screened for bacteriocin production using cross-streaking and spot-on-lawn methods. One of the isolates, identified as Bacillus species Sh10, produced prote...