Study on Characteristics of Sediment and Sedimentation Rate at Sungai Lembing, Kuantan, Pahang

Ghani, Nadiatul Adilah Ahmad Abdul; Othman, Norhayani; Baharudin, Mohd Khairun Hafiz

doi:10.1016/j.proeng.2013.02.013

Cited by 8 publications

(5 citation statements)

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“…In principle of PCR chemistry, dNTP-Mg 2+ soluble complexes tend to interact with the DNA template backbone thereby activating DNA polymerase function (Figure 1). Soluble complexes are recognized as a substrate for DNA polymerase to act on [21]. However, increased magnesium ion can reduce polymerase specificity, stabilize the duplex strand of DNA template or fidelity of Taq DNA polymerase, stabilize the duplex strand of DNA template and spurious incorrect primer annealing thereby resulting in undesired or non-specific amplicons [22].…”

Section: Resultsmentioning

confidence: 99%

CHEMICAL COMPONENTS OF POLYMERASE CHAIN REACTION IN 18S rRNA FOR DETECTION OF Cryptosporidium FROM RIVER WATER SAMPLES

2019

MJAS

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The gene of 18S ribosomal RNA or 18S rRNA is the universal gene function as a general genetic marker for species identification of microorganisms including parasites. Cryptosporidium has distinct 18S rRNA genes along different species within the same genus. In this study, polymerase chain reaction or PCR was used to study chemical components of PCR setup in amplification of 18S rRNA gene of this parasite. Cryptosporidium was collected from river water samples and its presence was confirmed using specific immunofluorescence detection of this parasite. Isolated water containing Cryptosporidium was then subjected to genomic DNA extraction before PCR step. The chemical components of PCR consisting of MgCI 2 , deoxynucleotide triphosphate (DNTPs), Polymerases, free DNase-water, universal primers and PCR buffer were studied in different volume and concentration. Each chemical component of PCR was optimized differently in yielding the same final volume of 20 µL per each reaction. The value range of chemical components of PCR consisted of MgCI 2 (0.1 µM-0.5 µM), dNTPs (50-250 mM), free DNase water (5-10 µL), polymerases (0.2-0.5 U) and universal primers (2-20 µM). The result indicated that 0.2 µM of MgCI 2 , 100 mM of dNTPs, less than 10 µL of free DNase water, 0.5 U of polymerases and 10 mM of universal primers were the best combination to get better result for molecular identification of 18S rRNA Cryptosporidium. As a conclusion, accurate and proper concentration or volume of each PCR chemical components is essential for molecular identification of 18S rRNA Cryptosporidium gene. In future studies, study on gradient temperature parameters of PCR run can be included to study the chemical nature of amplified genes either in denaturation, annealing or extension steps. AbstrakGen 18S ribosomal RNA adalah gen universal yang berfungsi sebagai penanda genetik umum untuk pengenalpastian spesies mikroorganisma termasuk parasit. Cryptosporidium mempunyai gen 18S rRNA yang berlainan daripada spesies berbeza dalam genus yang sama. Dalam kajian ini, tindak balas berantai polymerase atau PCR digunakan untuk mengkaji komponen kimia susun atur PCR dalam amplifikasi gen 18S rRNA bagi parasit ini. Cryptosporidium telah diambil dari sampel air sungai dan disahkan kehadirannya menggunakan pengesanan immunopendaflour terhadap parasit ini. Sampel air yang diambil mengandungi Cryptosporidium yang kemudiannya diteruskan untuk pengekstrakan genomik DNA sebelum peringkat PCR. Komponen kimia PCR yang terdiri daripada MgCI 2 , deoksinukleotida trifosfat (dNTPs), polimerase, air yang bebas DNase, primer umum dan larutan penimbal PCR telah dikaji dalam isipadu dan kepekatan yang berbeza. Setiap komponen kimia PCR dioptimakan secara ISSN 1394 -2506 Mohd Aiman et al: CHEMICAL COMPONENTS OF POLYMERASE CHAIN REACTION IN 18S rRNA FOR DETECTION OF Cryptosporidium FROM RIVER WATER SAMPLES 402 berbeza dalam menghasilkan isipadu akhir 20 uL bagi setiap tindak balas. Nilai julat komponen kimia PCR terdiri daripada MgCI 2 (0.1 µM-0.5 µM), dNTPs (50-250 mM), ai...

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Section: Resultsmentioning

confidence: 99%

CHEMICAL COMPONENTS OF POLYMERASE CHAIN REACTION IN 18S rRNA FOR DETECTION OF Cryptosporidium FROM RIVER WATER SAMPLES

2019

MJAS

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“…In contrast, only one water sample from the upstream point of Kuantan River was detected to be negative for C. parvum. This could be due to the location of upstream point in Kuantan River (normally shallow), which is due to the sedimentation process resulting in reduction of aquatic life [20]. Furthermore, fast river water flow due to high number rainfall from the higher area at Tapis Mountain in Lembing River, Kuantan also could be one of the contributing factors [21].…”

Section: Discussionmentioning

confidence: 99%

First molecular characterization of Cryptosporidium from three different points of two main rivers in Kuantan, Malaysia using 18S rRNA gene nested PCR

Barudin¹,

Isa²,

Othman³

et al. 2017

APJTD

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“…Grain size is a characteristic of sediments that can be measured in real terms in which to obtain this data; a filter analysis of sediment samples is required using the (Ghani et al, 2012). However, there are several other studies that use the wet sieving method with stratified sediment filters with different diameters.…”

Section: Sample Preparationmentioning

confidence: 99%

Characteristic of Sediment at Lekok Coastal Waters, Pasuruan Regency, East Java

Anggraini¹,

Yanuhar²,

Risjani³

2020

J. Ilmu dan Teknologi Kelautan Tropis

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Sedimentation is one of the dynamics that occur in coastal areas to determine the condition of the coast. Lekok coastal water is one of the open water areas that have very fluctuating dynamics in coastal changes. The structural study of sediment distribution conducted in this location is used to provide information about the process of transportation and sedimentation based on the distribution of sediment grain size. This study aims to determine the horizontal grain sediment size in the Lekok coastal waters. This research was conducted at nine sampling points by sampling in the form of primary sediments randomly using the grab sampler method. Furthermore, further analysis is done by the gravimetric method. Based on the results of the study note that sediments characteristic in Lekok coastal water are generally dominated by three types of sediments, namely: sandy loam, loam, and silt loam. Sorting values are in a well-sorted to the moderately well-sorted condition where the sediment conditions are well sorted. The skewness value is skewed positively, where the value indicates a positive skewed sedimentary condition. The value of kurtosis is in the leptokurtic condition where the sediment from station 1 to station 9 is homogeneous.

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Study on Characteristics of Sediment and Sedimentation Rate at Sungai Lembing, Kuantan, Pahang

Cited by 8 publications

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CHEMICAL COMPONENTS OF POLYMERASE CHAIN REACTION IN 18S rRNA FOR DETECTION OF Cryptosporidium FROM RIVER WATER SAMPLES

CHEMICAL COMPONENTS OF POLYMERASE CHAIN REACTION IN 18S rRNA FOR DETECTION OF Cryptosporidium FROM RIVER WATER SAMPLES

First molecular characterization of Cryptosporidium from three different points of two main rivers in Kuantan, Malaysia using 18S rRNA gene nested PCR

Characteristic of Sediment at Lekok Coastal Waters, Pasuruan Regency, East Java

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