Papers by Dr. Ali Al-Homaidan
Journal of King Saud University - Science
Abstract: This investigation was aimed to compare the inference of antelope phylogenies resulting... more Abstract: This investigation was aimed to compare the inference of antelope phylogenies resulting from the 16S rRNA, cytochrome-b (cyt-b) and d-loop segments of mitochondrial DNA using three different computational models including Bayesian (BA), maximum parsimony (MP) and unweighted pair group method with arithmetic mean (UPGMA). The respective nucleotide sequences of three Oryx species (Oryx leucoryx, Oryx dammah and Oryx gazella) and an out-group (Addax nasomaculatus) were aligned and subjected to BA, MP and UPGMA models for comparing the topologies of respective phylogenetic trees. The 16S rRNA region possessed the highest frequency of conserved sequences (97.65%) followed by cyt-b (94.22%) and d-loop (87.29%). There were few transitions (2.35%) and none transversions in 16S rRNA as compared to cyt-b (5.61 % transitions and 0.17 % transversions) and d-loop (11.57 % transitions and 1.14 % transversions) while comparing the four taxa. All the three mitochondrial segments clearly d...
International Journal of Molecular Sciences, May 10, 2010
Massive loss of valuable plant species in the past centuries and its adverse impact on environmen... more Massive loss of valuable plant species in the past centuries and its adverse impact on environmental and socioeconomic values has triggered the conservation of plant resources. Appropriate identification and characterization of plant materials is essential for the successful conservation of plant resources and to ensure their sustainable use. Molecular tools developed in the past few years provide easy, less laborious means for assigning known and unknown plant taxa. These techniques answer many new evolutionary and taxonomic questions, which were not previously possible with only phenotypic methods. Molecular techniques such as DNA barcoding, random amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP), microsatellites and single nucleotide polymorphisms (SNP) have recently been used for plant diversity studies. Each technique has its own advantages and limitations. These techniques differ in their resolving power to detect genetic differences, type of data they generate and their applicability to particular taxonomic levels. This review presents a basic description of different molecular techniques that can be utilized for DNA fingerprinting and molecular diversity analysis of plant species.
Genetics and Molecular Research, 2012
DNA barcoding is currently gaining popularity due to its simplicity and high accuracy as compared... more DNA barcoding is currently gaining popularity due to its simplicity and high accuracy as compared to the complexity and subjective biases associated with morphology-based identification of taxa. The standard chloroplast DNA barcode for land plants recommended by the Consortium for the Barcode of Life (CBOL) plant working group needs to be evaluated for a wide range of plant species. We therefore tested the potential of the rbcL marker for the identification of wild plants belonging to diverse families of arid regions. Maximum likelihood tree analysis was performed to evaluate the discriminatory power of the rbcL gene. Our findings showed that using rbcL gene sequences enabled identification of the majority of the samples (92%) to genus level and only 17% to species level.
Genetics and Molecular Research, 2012
DNA barcoding is currently gaining popularity due to its simplicity and high accuracy as compared... more DNA barcoding is currently gaining popularity due to its simplicity and high accuracy as compared to the complexity and subjective biases associated with morphology-based identification of taxa. The standard chloroplast DNA barcode for land plants recommended by the Consortium for the Barcode of Life (CBOL) plant working group needs to be evaluated for a wide range of plant species. We therefore tested the potential of the rbcL marker for the identification of wild plants belonging to diverse families of arid regions. Maximum likelihood tree analysis was performed to evaluate the discriminatory power of the rbcL gene. Our findings showed that using rbcL gene sequences enabled identification of the majority of the samples (92%) to genus level and only 17% to species level.
Brown macroalgae as bio-indicators for heavy metals pollution of Al-Jubail coastal area of Saudi ... more Brown macroalgae as bio-indicators for heavy metals pollution of Al-Jubail coastal area of Saudi Arabia
PLOS ONE
Multifunctional drugs have shown great promise in biomedicine. Organisms with antimicrobial and a... more Multifunctional drugs have shown great promise in biomedicine. Organisms with antimicrobial and anticancer activity in combination with antioxidant activity need further research. The Red Sea and the Arabian Gulf coasts were randomly sampled to find fungi with multifunctional activity. One hundred strains (98 fungi and 2 lichenized forms) were isolated from 15 locations. One-third of the isolates inhibited clinical bacterial (Staphylococcus aureus, Bacillus subtilis, Vibrio cholerae, Salmonella typhi, S. paratyphi) and fungal pathogens (Talaromycets marneffei, Malassezia globose, Cryptococcus neoformans, Candida albicans, Aspergillus fumigatus) and four cancer cell lines (Hep G2 liver, A-549 lung, A-431skin, MCF 7 breast cancer). Bacterial and cancer inhibition was often accompanied by a high antioxidant activity, as indicated by the principal component analysis (PCA). PCA also indicated that fungal and bacterial pathogens appeared to be inhibited mostly by different marine fungal i...
Environmental Monitoring and Assessment
Marine Pollution Bulletin, 2021
The transporting of oil via the Arabian Gulf for centuries has resulted in the pollution of the c... more The transporting of oil via the Arabian Gulf for centuries has resulted in the pollution of the coasts by heavy metals, and therefore, remediation actions are needed. In this review, we first evaluated heavy metal pollution on the coasts by assembling the research on published metal concentrations in sediments and water bodies surrounding the Arabian Peninsula. Research revealed uneven pollution of heavy metals, meaning that before remediation, the most polluted sites should be found. This could be done most conveniently using biomonitoring. The Arabian Peninsula is a unique ecoregion due to the extremely high temperature in summer, and therefore, it needs its specific standardization procedure for biomonitoring. To get an overview of the current information on biomonitoring, we gathered a dataset of 306 published macroalgal observations from the Arabian Gulf and the Gulf of Aden. The heavy metal concentration dataset of macroalgae was analyzed with a multivariate principal component analysis. As a result of the published works elsewhere and our data analysis, we recommend that green Ulva and brown Padina species are used in the biomonitoring of heavy metal pollution on the Arabian Peninsula's eastern and southern coasts. However, more species might be needed if these species do not occur at the site. The species incidence should first be monitored systematically in each area, and common species should be used. The species used should be chosen locally and sampled at the same depth at low tide in spring or early summer, from February to May, before the hottest season. The composite samples of different apical sections of the thallus should be collected. The standardization of the monitoring processes benefits future remediation actions.
Applied Nanoscience, 2021
This study is to implement an easy and greener method for the preparation of silver nanoparticles... more This study is to implement an easy and greener method for the preparation of silver nanoparticles (AgNPs) using fungal extract and investigate their antioxidant (DPPH), antifungal (Aspergillus niger) and cytotoxic effect against human breast cancer cell line MCF-7. The synthesized AgNPs were characterized by several analytical techniques, such as UV–Vis spectrophotometer (UV–Vis), Fourier transform infrared spectroscopy (FTIR), X-ray diffraction (XRD), scanning electron microscope (SEM) and transmission electron microscope (TEM). The results of analyses using spectroscopy (UV and FTIR) and diffraction (XRD) were compared and discussed with available literature. Electron microscopic techniques, such as SEM and TEM, illustrated spherical AgNPs. The inhibition of free radical DPPH by AgNPs was significant. The cytotoxicity of AgNPs was dose-dependent, and therefore, an increase in cell death was obtained with increasing concentrations of AgNPs. The IC50 values were found to be 34.27 µL/mL for the AgNPs and 17.69 µL/mL for the standard drug, Cisplatin. According to the knowledge of the authors and published literature, this is the first-ever report on the synthesis of AgNPs using the fungus Cladosporium halotolerans and evaluation of their biological activities.
DNA barcoding is the use of short DNA sequences (~650 bp) of the standard segment of the genome f... more DNA barcoding is the use of short DNA sequences (~650 bp) of the standard segment of the genome for large scale species identification. The Consortium for the Barcode of Life (CBOL) plant-working group recommended the 2-locus combination of rbcL and matK as the standard plant barcode. These two regions of chloroplast DNA were chosen due to efficient recovery of quality sequences and high levels of species discrimination. We evaluated the success rates of universal primers for amplification of matK and rbcL loci in 26 different plant species (covering 14 families) from Saudi Arabia. Success rate in PCR was higher for rbcL (88%) compared with matK (69%). The universal primers of both matK and rbcL failed to amplify the DNA form 3 plant species belonging to the family Asteraceae (Anthemis deserti, Pulicaria undulate, and Sonchus oleraceus). Two plant species Malva parviflora (Malvaceae) and Salsola imbricate (Chenopodiaceae) indicated different primer binding site (matK) as the amplifi...
Anthropogenic activities around the main stream of Wadi Hanifah may lead to a considerable increa... more Anthropogenic activities around the main stream of Wadi Hanifah may lead to a considerable increase in the heavy metal loading of the stream. The two filamentous green algae Enteromorpha intestinalis (Linnaeus) Nees and Cladophora glomerata (Linnaeus) Kutzing were collected from three sites along the valley and used to determine the heavy metal concentrations in the main stream. The dried algal samples were digested using appropriate acids and the concentrations of manganese (Mn), copper (Cu), Zinc (Zn), Arsenic (As), cadmium (Cd) and lead (Pb) were measured in the aliquot samples using Inductively Coupled plasma-Optical Emission spectrometer (ICP-OES). High burden of manganese, copper and arsenic were detected at all sites indicating a high degree of pollution by these elements. The levels of zinc, cadmium and lead were within the expected limits for uncontaminated areas. E. intestinalis could be used as an excellent indicator for manganese, zinc and arsenic pollution, whereas C. g...
Environmental pollution, 2021
Wastewater containg proteinaceous ossein effluents are problematic to be treated. We studied the ... more Wastewater containg proteinaceous ossein effluents are problematic to be treated. We studied the possibility to treat ossein effluents with the marine cyanobacterium strain Cylindrospermum stagnale. After optimizing the culture conditions of the bacterium, three different types of ossein effluents were tested: dicalcium phosphate (DCP), high total dissolved solids (HTDS) and low total dissolved (LTDS). The effluents were diluted with sea water at the following ratios 1:1, 2:1 and 3:2. The optimum operating conditions were at 3000 lux light intensity and 37 °C temperature. The highest degradation of ossein effluens by C. stagnale was attained for a dilution ratio of 1:1. However, less diluted ossein effluents reduced the growth of C. stagnale drastically. The degradation was shown by measuring the chlorophyll a content and the dry weight of bacterial cells during a seven-day incubation period degradation. Fourier Transform Infrared Spectroscopy (FT-IR) analysis verified the degradati...
Polish Journal of Environmental Studies, 2011
We have determined the levels of five heavy metals (Cu, Hg, Mn, Pb, Zn) in outer tissue washings,... more We have determined the levels of five heavy metals (Cu, Hg, Mn, Pb, Zn) in outer tissue washings, outer tissues, and inner tissues of different vegetable samples (beans, cabbage, capsicum, carrot, cauliflower, cucumber, eggplant, green pepper, pea, and tomato) from the Qassim region of Saudi Arabia. Instead of using the customary dried tissue power, we conducted all the analysis directly in the wet tissues following microwave digestion; the levels of heavy metals being reported in wet as well as dry tissue using the watercontent factor. Pb was absent in the washings but present in most of the vegetables in the range of 0.0130.251 μg/g wet tissue (0.201-5.055 μg/g dry tissue). Although traces of Hg (5.994-6.520 ng/g wet tissue) were present in the washing, this metal was not detected in the vegetable tissues. Cu was observed in the range of 0.079-1.785 μg/g wet tissue (1.104-22.919 μg/g dry tissue), whereas the range of Mn was found to be 0.2393.263 μg/g wet tissue (4.626-47.036 μg/g...
Anthropogenic activities may lead to the release of several heavy metals to the surrounding envir... more Anthropogenic activities may lead to the release of several heavy metals to the surrounding environment. Cadmium is one of the most toxic substances in our environment and it causes many health problems for humans. Removal of heavy metals is a challenging matter. Several species of micro-and macro-algae are used for the adsorption of heavy metals. In this investigation, three species of brown algae (Cystoseira myrica, Sargassum filipendula and Padina boryana) were collected from the Saudi coast of the Arabian Gulf on several occasions during 2013. They were transferred to the laboratory, cleaned, dried, and the dry biomass were used for the removal of cadmium ions from aqueous solutions. The experiments were carried out in triplicate in 250 ml conical flasks using an orbital incubator at 150 oscillation/minute.The biosorption characteristics were investigated as a function of pH (2, 3, 4, 5, 6,7), contact time (30, 60, 90, 120 minutes), initial concentration of cadmium (5, 10, 20, 30, 40, 50 mg/l) and initial concentration of algal dry biomass (0.5, 1, 2, 4, 8 g/l). Concentrations of the metal were measured using Atomic Absorption Spectrophotometer. The removal was solution pH dependent. At low pH (2) there was a competition between hydrogen ions (H +) and cadmium ions (Cd 2+) on binding sites. As the pH increased the number of H + decreased and the number of available binding sites increased which leads to the increase of biosorption until we reached equilibrium at pH 5. Contact time was also important and the biosorption increased with time and the maximum removal was obtained after 90 minutes of incubation. The biosorption was affected also by the initial concentration of the metal. The highest level of removal was achieved at 10 mg/l. After that, the removal was decreased and the lowest removal level was at 50 mg/l. The dry biomass concentration was very important. Low biomass levels (≤ 2g/l) ensured metal removal up to 97%. At higher concentrations the removal was not greatly affected and this is probably attributed to the occupation of binding sites by metal ions. Very high levels of cadmium removal were obtained by the three species of algae. The highest level (97.16%) was achieved by using S. filipendula. The adsorption levels by C. myrica and P. boryana were also very high and they were 96.09% and 94.64%, respectively. The ideal conditions for cadmium removal were: pH 5, 90 minutes of contact time, 10 mg/l of cadmium initial concentration and 2 g/l of dry biomass. The results of this study indicated that brown algae are good candidate for cadmium removal from polluted waters; they are very effective, cheap and eco-friendly.
International journal of food, agriculture and environment, 2008
Nickel contamination may have an adverse impact on the fragile coastal and marine ecosystems of t... more Nickel contamination may have an adverse impact on the fragile coastal and marine ecosystems of the Arabian Gulf. Oil pollution is a major source of this heavy metal. The nickel concentrations were measured in seawater and in 12 species of green, brown and red algae which were collected from Dammam area on the Saudi coast of the Arabian Gulf. The algal samples were cleaned, air dried and digested with concentrated nitric acid. The Ni concentrations were measured in seawater and in the aliquot samples of algae using atomic absorption spectrophotometer. High levels of Ni were found in seawater (1.26-6.73 µg L -1 ) and in algal samples (7.3-57.4 µg g -1 dry weight). The highest levels of Ni were found in the red algae Acanthophora spicifera, Hypnea cornuta and Digenia simplex, the green alga Chaetromorpha aerea and the brown alga Sargassum latifolium and these species may be used as biomonitors of Ni contamination in the Arabian Gulf region. The alerting high levels of Ni in the Gulf r...
Plant Omics, 2011
DNA barcoding is the use of short DNA sequences ( 650 bp) of the standard segment of the genome f... more DNA barcoding is the use of short DNA sequences ( 650 bp) of the standard segment of the genome for large scale species identification. The Consortium for the Barcode of Life (CBOL) plant-working group recommended the 2-locus combination of rbcL and matK as the standard plant barcode. These two regions of chloroplast DNA were chosen due to efficient recovery of quality sequences and high levels of species discrimination. We evaluated the success rates of universal primers for amplification of matK and rbcL loci in 26 different plant species (covering 14 families) from Saudi Arabia. Success rate in PCR was higher for rbcL (88%) compared with matK (69%). The universal primers of both matK and rbcL failed to amplify the DNA form 3 plant species belonging to the family Asteraceae (Anthemis deserti, Pulicaria undulate, and Sonchus oleraceus). Two plant species Malva parviflora (Malvaceae) and Salsola imbricate (Chenopodiaceae) indicated different primer binding site (matK) as the amplifi...
This study focuses on lead detoxification using roots, stems, leaves and whole plants of Plantago... more This study focuses on lead detoxification using roots, stems, leaves and whole plants of Plantago major L. and Phaseolus vulgaris L. (decoration kidney bean) as a ball hanging hydroponically in deionized water supplemented with concentrations of lead ion under different duration times and temperatures regimes. Roots of studied plants showed that the highest removal of lead than other parts, while using a mixture of whole plants were more efficient than using each one alone. The largest amounts of lead 85, 77 and 71 % were accumulated in roots of P. major + P. vulgaris, P. major alone and P. vulgaris alone, respectively. The highest rate of Pb ions uptake from the medium took place during the first 2-days of incubation and after 5-days of incubation, lead content in the medium decreased by half. This study suggested that roots of P. major + P. vulgaris could be used removal of pollutants from water contaminated with lead.
The molecular phylogeny using mitochondrial DNA sequences provides valuable insights for wildlife... more The molecular phylogeny using mitochondrial DNA sequences provides valuable insights for wildlife conservation. However, the inference of phylogenies may be affected by the marker type as well as by the statistical model applied for data analysis. This study reports a comparative evaluation of neighbor-joining (NJ) and maximum-parsimony (MP) methods for phylogenetic inference among three Oryx species (Oryx leucoryx, Oryx dammah and Oryx gazella) as well as two closely related (same subfamily but different genera) outgroups including Addax and Roan, using 12S rRNA and 16S rRNA genes. We observed that the 12S rRNA based phylogenetic inference is unable to differentiate between the genus Oryx and Addax, regardless of the method used. However, the 16S rRNA gene segment accurately grouped all the five taxa using MP but not the NJ suggesting the possible superiority of the former method for phylogenetic analysis using similar data structure. This report also describes a stepwise protocol ...
Four species of brown algae (Phaeophyta) were collected from Al-Khafji and Al-Dammam areas on the... more Four species of brown algae (Phaeophyta) were collected from Al-Khafji and Al-Dammam areas on the Saudi coast of the Arabian Gulf. The algal samples were dry digested. The concentrations of Cd, Cu, Fe, Pb and Zn were measured in the aliquot samples of the algae using Atomic Absorption Spectrophotometer. Normal levels were found for Cd, Cu and Zn. The average concentration of these metals ranged between 0.62 and 1.95 µg g -1 for Cd, 3.95 and 11.23 µg g -1 for Cu and 15.70 and 75.25 µg g -1 for Zn. High burden of Fe (161-1,466 µg g -1 ) and Pb (8.84-18.60 µg g -1 ) were found in the four algae at both sites. The highest levels of Cd and Cu were found at Al-Khafji area, whereas elevated concentrations of Fe and Zn were obtained from Al-Dammam area. Lead levels were high at both sites. There is evidence of heavy metal contamination, especially with Fe and Pb, at both areas. Among the studied algae, the highest levels of Cd, Cu, Fe and Pb were detected in Padina gymnospora and this speci...
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Papers by Dr. Ali Al-Homaidan