Displaying publications 1 - 20 of 78 in total

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  1. Yusop MF, Tahir NM, Azim SMSS, Kamaruzaman AA, Hata NRM, Kugaan A, et al.
    Asian J Transfus Sci, 2023;17(2):251-255.
    PMID: 38274975 DOI: 10.4103/ajts.ajts_38_21
    BACKGROUND: Liver transplantation (LT) is a complicated surgical procedure with high risk for massive intraoperative blood loss due to pre-existing coagulopathy, portosystemic shunts with collateral circulations, and splenomegaly. The transfusion service will direct most of their resources toward LT programs with great impact on cost. The purpose of this study was to evaluate single center transfusion strategies and to identify the risk factors associated with the intraoperative blood loss and blood transfusion.

    METHODS: The study includes 18 patients who underwent LT at Hospital Selayang between January 2020 and December 2020. Retrospective analysis of data included preoperative assessment of coagulopathy, intraoperative blood loss, and blood component transfusion.

    RESULTS: The mean age in the study group was 36.4 ± 12.68 years. The mean intraoperative blood loss was 4450 ± 1646 ml requiring 4.17 ± 3.3 packed red blood cell (PRBC) units, 7.56 ± 5.5 platelet units, and 9.50 ± 6.0 fresh-frozen plasma units. The independent risk factor for high blood loss (HBL) group was lower preoperative platelet count and it is statistically significant (P = 0.024). The HBL group is associated with higher usage of PRBC (P = 0.024) and platelet units (P = 0.031) and it is statistically significant. The length of stay (LOS) in intensive care unit (ICU) averaging 8.6 ± 4.95 days, and there is no significant differences comparing the HBL and LBL group (P = 0.552). The mortality <90 days for all recipients was 22.2%.

    CONCLUSION: The preoperative platelet count for is the most important factor associated with HBL in LT procedure. The usage of PRBC and platelet units was statistically higher in the HBL group. Comparing HBL and LBL patients, there is no difference in terms of the LOS in ICU postoperatively. A larger sample size would be needed in view of relatively small sample size.

  2. Yap CK, Ismail A, Omar H, Tan SG
    Environ Int, 2004 Feb;29(8):1097-104.
    PMID: 14680893
    Studies on toxicities and tolerances of cadmium (Cd), copper (Cu), lead (Pb) and zinc (Zn) in the brown alga Isochrysis galbana and in the green-lipped mussel Perna viridis were conducted by short-term bioassays using endpoints growth production and mortality, respectively. The 5-day EC(50) and 24-h LC(50) of these heavy metals were determined in the brown alga and mussel, respectively. The EC(50) values calculated for the alga were 0.74 mg/l for Cd, 0.91 mg/l for Cu, 1.40 mg/l for Pb and 0.60 mg/l for Zn. The LC(50) values for the mussels were 1.53 mg/l for Cd, 0.25 mg/l for Cu, 4.12 mg/l for Pb and 3.20 mg/l for Zn. These LC(50) values were within the concentration ranges as reported by other authors who used P. viridis as the test organism. Based on these EC(50) and LC(50) values, the alga was most sensitive to Zn, followed by Cd, Cu and Pb while the mussel was most sensitive to Cu, followed by Cd, Zn and Pb. Differences in the trophic levels, metal handling strategies, biology and ecology of the primary producer (brown alga) and the primary consumer (mussel) are believed to be the plausible causes for the different toxicities and tolerances of the metals studied.
  3. Yap CK, Tan SG, Ismail A, Omar H
    Environ Int, 2004 Mar;30(1):39-46.
    PMID: 14664863
    It has been widely reported that heavy metal contamination in coastal waters can modify the allozyme profiles of marine organisms. Previous studies have recorded elevated metal concentrations in sediments and mussel tissues off Peninsular Malaysia. In the present study, horizontal starch gel electrophoresis was carried out to estimate the levels of allelic variation of the green-lipped mussel, Perna viridis, collected from one contaminated and three relatively uncontaminated sites off Peninsular Malaysia. Fourteen polymorphic loci were observed. In addition, the concentrations of cadmium, copper, lead, mercury and zinc were determined in the sediments and in the soft tissues of the mussels. Mussels from contaminated site, evidenced by high metal pollution indices (MPI) of the sediment and the mussel tissues, showed the highest percentage of polymorphic loci (78.6%), while those collected from the uncontaminated sites had lower MPI of the sediment and mussel tissue, and exhibited lower percentages of polymorphic loci (35.7-57.1%). The population from the contaminated site showed the highest excess of heterozygosity (0.289) when compared to that of the populations from the three uncontaminated sites (0.108-0.149). Allozyme frequencies at the phosphoglucomutase (PGM; E.C. 2.7.5.1) locus also differed between the contaminated and uncontaminated populations. Previous studies have shown that exposure to heavy metals can select or counter-select for particular alleles at this locus. The present results suggest that allozyme polymorphism in P. viridis is a potential biomonitoring tool for heavy metal contamination but further validation is required.
  4. Yap CK, Ismail A, Tan SG, Omar H
    Environ Int, 2002 Dec;28(6):467-79.
    PMID: 12503912
    Malaysia is now a developing country and on her way towards being an industrialised one by the year 2020. Most of her industries and urban areas are located on the west coast of Peninsular Malaysia. In addition, the offshore area of the west coast is now one of the busiest shipping lanes in the world. These two phenomena make the intertidal and offshore areas of the west coast of Peninsular Malaysia interesting for scientific studies. Therefore, this study focused on both the offshore and intertidal sediments of the west coast of Peninsular Malaysia. Sampling for sediment samples were done from the northern to the southern ends of the peninsula and these sediment samples were analysed for Cu and Pb. It was found that total Cu concentrations ranged from 0.25 to 13.8 and 0.40 to 315 microg/g dry weight (dw) for offshore and intertidal sediments, respectively. For Pb, it ranged from 3.59 to 25.4 and 0.96 to 69.8 microg/g dw for the offshore and intertidal sediments, respectively. The ranges of Cu and Pb found from the west coast of Peninsular Malaysia were low in comparison to regional data. However, some intertidal areas were identified as receiving anthropogenic Cu and Pb. Geochemical studies revealed that the 'nonresistant' fraction for Pb contributed about 70.0% to 75.0% and 54.0% of the total Pb concentration in the offshore and intertidal sediments, respectively. As for Cu, the 'nonresistant' fraction contributed about 46.2% to 60.4% and 46.3% of the total Cu concentration in the offshore and intertidal sediments, respectively. The 'nonresistant' fraction contained mostly of anthropogenic metals besides natural origins. These 'nonresistant' percentages indicated that both the offshore and intertidal areas could have received anthropogenic-derived metals, which could be influenced by physico-chemical properties of the sediments. Although the present data indicated that contamination due to Cu and Pb in the west coast of Peninsular Malaysia especially in the offshore areas were not serious, regular biomonitoring studies along the west coast of Peninsular Malaysia are recommended.
  5. Yap CK, Ismail A, Tan SG, Omar H
    Environ Int, 2002 Apr;28(1-2):117-26.
    PMID: 12046948
    Total concentrations and speciation of cadmium (Cd), copper (Cu), lead (Pb) and zinc (Zn) in surface sediment samples were correlated with the respective metal measured in the total soft tissue of the green-lipped mussel Perna viridis, collected from water off the west coast of Peninsular Malaysia. The aim of this study is to relate the possible differences in the accumulation patterns of the heavy metals in P. viridis to those in the surface sediment. The sequential extraction technique was employed to fractionate the sediment into 'freely leachable and exchangeable' (EFLE), 'acid-reducible,' 'oxidisable-organic' and 'resistant' fractions. The results showed that significant (P .05) was found between Zn in P viridis and all the sediment geochemical fractions of Zn and total Zn in the sediment. This indicated that Zn was possibly regulated from the soft tissue of P. viridis. The present results supported the use of P viridis as a suitable biomonitoring agent for Cd, Cu and Pb.
  6. Wong KW, Yap CK, Yaacob A, Nulit R, Omar H, Aris AZ, et al.
    PMID: 33751349 DOI: 10.1007/s11356-021-13361-3
    Along with the growing utilization of zinc (Zn) and Zn-containing nanoparticles in various industries, Zn ecotoxicological evaluation on human food supply is necessary even though Zn is generally considered safe and rarely concentrated ecotoxicologically. This study aimed to investigate the bioaccumulation of Zn in 18 species of vegetables (seven leafy, nine fruity vegetables and one species each of tuber and legume) collected from two farming sites in the west coast of Peninsular Malaysia. A human health risk assessment (HHRA) was also conducted. In addition to HHRA based on the general population, HHRA based on each major ethnic group of the Malaysian society was also determined considering that the food consumption pattern would definitely be varied across ethnicities and age groups (children and adults). The study results showed that Zn concentrations were significantly higher (p < 0.05) in leafy vegetables than in other types of vegetables. However, the target hazard quotient (THQ) values were all found to be < 1.0. Therefore, based on the Malaysian ethnicities and age groups with their respective vegetable consumption patterns, the results indicated insignificant noncarcinogenic human health risk of Zn via oral consumption of vegetables by the Malaysian population. As a metric of measurement of HHRA, a comparison of THQ values could yield previously unreported insights into HHRA differences among the compared populations. A comparison of THQ values among the consumer groups indicated higher HHR for Chinese Malaysians and children due to their higher vegetable consumption and lower body weight, respectively. A comparison the Zn intakes of all the consumer groups with the recommended nutrient intakes indicated that the oral consumption of the vegetable species collected in this study would not result in Zn-related hazards and would not be able to fulfil the Zn dietary need of the individual consumer.
  7. Urabe M, Nor Hashim NE, Uni S, Iwaki T, Abdullah Halim MR, Marzuki ME, et al.
    Parasitol Int, 2020 Jun;76:102074.
    PMID: 32057926 DOI: 10.1016/j.parint.2020.102074
    We describe Morishitium polonicum malayense n. subsp. from Asian glossy starlings (Aplonis panayensis strigata) (Horsfield, 1821) (Passeriformis: Sturnidae) caught in Malaysia. The trematodes had parasitized the air sacs and the thoracic and body cavities of 40 out of 67 (59.7%) birds examined. The specimens each had an oral sucker, a postpharyngeal genital pore, and tandem testes, but lacked a ventral sucker. The morphological characteristics of our specimens were similar to those of M. polonicum polonicum (Machalska, 1980) from Poland. However, the anterior extremity of vitelline follicles of the present specimens sometimes extended to the level of pharynx. The oral sucker width, oral sucker width/pharynx width ratio, and intertesticular space metrics differed from those of M. p. polonicum. The maximum-likelihood trees based on the cytochrome c oxidase subunit I (COI) and the internal transcribed spacer 2 (ITS2) sequences indicated that the species from the present study formed a sister group with M. p. polonicum from the Czech Republic. The p-distances of COI and ITS2 sequences between the present specimens and M. p. polonicum from the Czech Republic were 6.9-7.5% and 0.6%, respectively. These genetic divergences indicate the border for intra- or interspecific variation of digeneans. The definitive host species and geographical distribution of the current specimens were distinct from those of M. p. polonicum from Europe. We thus concluded that the present specimens are ranked as a new subspecies of M. polonicum, namely M. polonicum malayense n. subsp.
  8. Uni S, Fukuda M, Agatsuma T, Bain O, Otsuka Y, Nakatani J, et al.
    Parasitol Int, 2015 Dec;64(6):493-502.
    PMID: 26165205 DOI: 10.1016/j.parint.2015.07.001
    Human zoonotic onchocercosis is caused by Onchocerca dewittei japonica, parasitic in wild boars (Sus scrofa leucomystax) in Japan. Previously, microfilariae longer than those of Onchocerca dewittei japonica were observed in skin snips from wild boars during the study of O. dewittei japonica. Moreover, the third-stage larvae (L3) of these longer microfilariae were obtained from the blackfly Simulium bidentatum after experimental injections. Based on morphometric and molecular studies, similar L3 were found in blackflies during fieldwork in Oita, Japan. However, except for O. dewittei japonica, adult worms of Onchocerca have not been found in wild boars. In this study, we discovered adult females of a novel Onchocerca species in the skin of a wild boar in Oita, and named it Onchocerca takaokai n. sp. Females of this new species had longer microfilariae and differed from O. dewittei japonica in terms of their morphological characteristics and parasitic location. The molecular characteristics of the cytochrome c oxidase subunit 1 and 12S rRNA genes of the new species were identical to those of the longer microfilariae and L3 previously detected, but they differed from those of O. dewittei japonica at the species level. However, both species indicated a close affinity among their congeners and Onchocerca ramachandrini, parasitic in the warthog in Africa, was basal in the Suidae cluster of the 12S rRNA tree.
  9. Uni S, Mat Udin AS, Agatsuma T, Saijuntha W, Junker K, Ramli R, et al.
    Parasit Vectors, 2017 Apr 20;10(1):194.
    PMID: 28427478 DOI: 10.1186/s13071-017-2105-9
    BACKGROUND: The filarial nematodes Wuchereria bancrofti (Cobbold, 1877), Brugia malayi (Brug, 1927) and B. timori Partono, Purnomo, Dennis, Atmosoedjono, Oemijati & Cross, 1977 cause lymphatic diseases in humans in the tropics, while B. pahangi (Buckley & Edeson, 1956) infects carnivores and causes zoonotic diseases in humans in Malaysia. Wuchereria bancrofti, W. kalimantani Palmieri, Pulnomo, Dennis & Marwoto, 1980 and six out of ten Brugia spp. have been described from Australia, Southeast Asia, Sri Lanka and India. However, the origin and evolution of the species in the Wuchereria-Brugia clade remain unclear. While investigating the diversity of filarial parasites in Malaysia, we discovered an undescribed species in the common treeshrew Tupaia glis Diard & Duvaucel (Mammalia: Scandentia).

    METHODS: We examined 81 common treeshrews from 14 areas in nine states and the Federal Territory of Peninsular Malaysia for filarial parasites. Once any filariae that were found had been isolated, we examined their morphological characteristics and determined the partial sequences of their mitochondrial cytochrome c oxidase subunit 1 (cox1) and 12S rRNA genes. Polymerase chain reaction (PCR) products of the internal transcribed spacer 1 (ITS1) region were then cloned into the pGEM-T vector, and the recombinant plasmids were used as templates for sequencing.

    RESULTS: Malayfilaria sofiani Uni, Mat Udin & Takaoka, n. g., n. sp. is described based on the morphological characteristics of adults and microfilariae found in common treeshrews from Jeram Pasu, Kelantan, Malaysia. The Kimura 2-parameter distance between the cox1 gene sequences of the new species and W. bancrofti was 11.8%. Based on the three gene sequences, the new species forms a monophyletic clade with W. bancrofti and Brugia spp. The adult parasites were found in tissues surrounding the lymph nodes of the neck of common treeshrews.

    CONCLUSIONS: The newly described species appears most closely related to Wuchereria spp. and Brugia spp., but differs from these in several morphological characteristics. Molecular analyses based on the cox1 and 12S rRNA genes and the ITS1 region indicated that this species differs from both W. bancrofti and Brugia spp. at the genus level. We thus propose a new genus, Malayfilaria, along with the new species M. sofiani.

  10. Uni S, Fukuda M, Ogawa K, Lim YA, Agatsuma T, Bunchom N, et al.
    Parasitol Int, 2017 Oct;66(5):593-595.
    PMID: 28648713 DOI: 10.1016/j.parint.2017.06.006
    An 11-year-old boy living in Otsu City, Shiga Prefecture, Kansai Region, Western Honshu, Japan had zoonotic onchocercosis. The patient developed a painful swelling on the little finger of his left hand. The worm detected in the excised mass had external transverse ridges but did not have inner striae in the cuticle. On the basis of the parasite's histopathological characteristics, the causative agent was identified as a female Onchocerca dewittei japonica (Spirurida: Onchocercidae). The species of the filarial parasite was confirmed by sequencing the cox1 gene of the parasite. The Japanese wild boar Sus scrofa leucomystax is a definitive host for O. dewittei japonica, which is then transmitted by blackflies as the vector to humans. The current case described occurred in the Kansai Region, Western Honshu, where such infections were previously not reported.
  11. Uni S, Mat Udin AS, Agatsuma T, Junker K, Saijuntha W, Bunchom N, et al.
    Parasit Vectors, 2020 Feb 06;13(1):50.
    PMID: 32028994 DOI: 10.1186/s13071-020-3907-8
    BACKGROUND: The genus Onchocerca Diesing, 1841 includes species of medical importance, such as O. volvulus (Leuckart, 1893), which causes river blindness in the tropics. Recently, zoonotic onchocercosis has been reported in humans worldwide. In Japan, O. dewittei japonica Uni, Bain & Takaoka, 2001 from wild boars is a causative agent for this zoonosis. Many filarioid nematodes are infected with Wolbachia endosymbionts which exhibit various evolutionary relationships with their hosts. While investigating the filarial fauna of Borneo, we discovered an undescribed Onchocerca species in the bearded pig Sus barbatus Müller (Cetartiodactyla: Suidae).

    METHODS: We isolated Onchocerca specimens from bearded pigs and examined their morphology. For comparative material, we collected fresh specimens of O. d. dewittei Bain, Ramachandran, Petter & Mak, 1977 from banded pigs (S. scrofa vittatus Boie) in Peninsular Malaysia. Partial sequences of three different genes (two mitochondrial genes, cox1 and 12S rRNA, and one nuclear ITS region) of these filarioids were analysed. By multi-locus sequence analyses based on six genes (16S rDNA, ftsZ, dnaA, coxA, fbpA and gatB) of Wolbachia, we determined the supergroups in the specimens from bearded pigs and those of O. d. dewittei.

    RESULTS: Onchocerca borneensis Uni, Mat Udin & Takaoka n. sp. is described on the basis of morphological characteristics and its genetic divergence from congeners. Molecular characteristics of the new species revealed its close evolutionary relationship with O. d. dewittei. Calculated p-distance for the cox1 gene sequences between O. borneensis n. sp. and O. d. dewittei was 5.9%, while that between O. d. dewittei and O. d. japonica was 7.6%. No intraspecific genetic variation was found for the new species. Wolbachia strains identified in the new species and O. d. dewittei belonged to supergroup C and are closely related.

    CONCLUSIONS: Our molecular analyses of filarioids from Asian suids indicate that the new species is sister to O. d. dewittei. On the basis of its morphological and molecular characteristics, we propose to elevate O. d. japonica to species level as O. japonica Uni, Bain & Takaoka, 2001. Coevolutionary relationships exist between the Wolbachia strains and their filarial hosts in Borneo and Peninsular Malaysia.

  12. Uni S, Mat Udin AS, Tan PE, Rodrigues J, Martin C, Junker K, et al.
    PMID: 36589876 DOI: 10.1016/j.crpvbd.2022.100078
    Species of the genus Pelecitus Railliet & Henry, 1910 the most widely distributed avian filariae in Africa and South America. Zoonotic cases in humans were reported in South America. While investigating the filarial fauna of wild animals in Malaysia, we discovered an undescribed filaria from the swollen footpad of the left leg of Copsychus malabaricus (Scopoli) in Pahang, Peninsular Malaysia. Adults of both sexes have a corkscrew-shaped body. Based on comparison of their morphological characteristics (i.e. pre-oesophageal cuticular ring distinct, oesophagus divided, vulva protuberant and situated at the level of anterior half of oesophagus, spicules strongly sclerotized and left spicule with broad blade) with other Pelecitus species, they are here described as Pelecitus copsychi Uni, Mat Udin & Martin n. sp. Multi-locus sequence analyses based on seven genes (12S rDNA, cox1, 18S rDNA, 28S rDNA, MyoHC, rbp1 and hsp70) were performed to determine the phylogenetic position of the new species. The calculated p-distance between the cox1 gene sequences for P. copsychi n. sp. and Pelecitus fulicaeatrae (Diesing, 1861) was 14.1%. Intraspecific genetic variation between two individuals of the new species was 0.4%. In both the Bayesian inference and maximum-likelihood trees, P. copsychi n. sp. was positioned in the second clade of ONC5, containing three genera of the subfamily Dirofilariinae (Foleyella Seurat, 1917, Pelecitus and Loa Stiles, 1905). Immunostaining and molecular analyses remained negative for the presence of Wolbachia endosymbionts. Our findings corroborate the division of the subfamily Dirofilariinae into ONC3 with Dirofilaria Railliet & Henry, 1911 and ONC5 with Pelecitus.
  13. Udechukwu BE, Ismail A, Zulkifli SZ, Omar H
    Environ Sci Pollut Res Int, 2015 Mar;22(6):4242-55.
    PMID: 25292304 DOI: 10.1007/s11356-014-3663-4
    Sungai Puloh mangrove estuary supports a large diversity of macrobenthic organisms and provides social benefits to the local community. Recently, it became a major recipient of heavy metals originating from industries in the hinterland as a result of industrialization and urbanization. This study was conducted to evaluate mobility and pollution status of heavy metals (Cd, Cu, Ni, Pb, Zn, and Fe) in intertidal surface sediments of this area. Surface sediment samples were collected based on four different anthropogenic sources. Metals concentrations were analyzed using an atomic absorption spectrophotometer (AAS). Results revealed that the mean concentrations were Zn (1023.68 ± 762.93 μg/g), Pb (78.8 ± 49.61 μg/g), Cu (46.89 ± 43.79 μg/g), Ni (35.54 ± 10.75 μg/g), Cd (0.94 ± 0.29 μg/g), and Fe (7.14 ± 0.94%). Most of the mean values of analyzed metals were below both the interim sediment quality guidelines (ISQG-low and ISQG-high), except for Pb concentration (above ISQG-low) and Zn concentration (above ISQG-high), thus suggesting that Pb and Zn may pose some environmental concern. Cadmium, Pb, and Zn concentrations were above the threshold effect level (TEL), indicating seldom adverse effect of these metals on macrobenthic organisms. Pollution load index (PLI) indicated deterioration and other indices revealed the intertidal surface sediment is moderately polluted with Cd, Pb, and Zn. Therefore, this mangrove area requires urgent attention to mitigate further contamination. Finally, this study will contribute to data sources for Malaysia in establishing her own ISQG since it is a baseline study with detailed contamination assessment indices for surface sediment of intertidal mangrove area.
  14. Thanh T, Chi VT, Abdullah MP, Omar H, Noroozi M, Ky H, et al.
    Mol Biol Rep, 2011 Jan;38(1):177-82.
    PMID: 20354903 DOI: 10.1007/s11033-010-0092-4
    Green microalga Ankistrodesmus convolutus Corda is a fast growing alga which produces appreciable amount of carotenoids and polyunsaturated fatty acids. To our knowledge, this is the first report on the construction of cDNA library and preliminary analysis of ESTs for this species. The titers of the primary and amplified cDNA libraries were 1.1×10(6) and 6.0×10(9) pfu/ml respectively. The percentage of recombinants was 97% in the primary library and a total of 337 out of 415 original cDNA clones selected randomly contained inserts ranging from 600 to 1,500 bps. A total of 201 individual ESTs with sizes ranging from 390 to 1,038 bps were then analyzed and the BLASTX score revealed that 35.8% of the sequences were classified as strong match, 38.3% as nominal and 25.9% as weak match. Among the ESTs with known putative function, 21.4% of them were found to be related to gene expression, 14.4% ESTs to photosynthesis, 10.9% ESTs to metabolism, 5.5% ESTs to miscellaneous, 2.0% to stress response, and the remaining 45.8% were classified as novel genes. Analysis of ESTs described in this paper can be an effective approach to isolate and characterize new genes from A. convolutus and thus the sequences obtained represented a significant contribution to the extensive database of sequences from green microalgae.
  15. Thanh T, Chi VT, Abdullah MP, Omar H, Noroozi M, Napis S
    Mol Biol Rep, 2011 Nov;38(8):5297-305.
    PMID: 21287365 DOI: 10.1007/s11033-011-0679-4
    An initial study on gene cloning and characterization of unicellular green microalga Ankistrodesmus convolutus was carried out to isolate and characterize the full-length cDNA of ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit (RbcS) as a first step towards elucidating the structure of A. convolutus RbcS gene. The full-length of A. convolutus RbcS cDNA (AcRbcS) contained 28 bp of 5' untranslated region (UTR), 225 bp of 3' non-coding region, and an open reading frame of 165 amino acids consisting of a chloroplast transit peptide with 24 amino acids and a mature protein of 141 amino acids. The amino acid sequence has high identity to those of other green algae RbcS genes. The AcRbcS contained a few conserved domains including protein kinase C phosphorylation site, tyrosine kinase phosphorylation site and N-myristoylation sites. The AcRbcS was successfully expressed in Escherichia coli and a ~21 kDa of anticipated protein band was observed on SDS-PAGE. From the phylogenetic analysis of RbcS protein sequences, it was found that the RbcS of A. convolutus has closer genetic relationship with green microalgae species compared to those of green seaweed and green macroalgae species. Southern hybridization analysis revealed that the AcRbcS is a member of a small multigene family comprising of two to six members in A. convolutus genome. Under different illumination conditions, RT-PCR analysis showed that AcRbcS transcription was reduced in the dark, and drastically recovered in the light condition. Results presented in this paper established a good foundation for further study on the photosynthetic process of A. convolutus and other green algae species where little information is known on Rubisco small subunit.
  16. Thanh T, Omar H, Abdullah MP, Chi VT, Noroozi M, Ky H, et al.
    Mol Biotechnol, 2009 Oct;43(2):148-53.
    PMID: 19507070 DOI: 10.1007/s12033-009-9182-8
    The rapid and effective method for the isolation of RNA from green microalga Ankistrodesmus convolutus based on homogenization in a simple CTAB buffer and selective precipitation of RNA with lithium chloride is developed. This procedure avoids the use of toxic chaotropic agents and phenol while high concentration of dithiothreitol is used to inhibit RNase activity and prevent oxidative cross-linking of nucleic acids by phenolics. The extraction procedure was able to produce high quality and intact RNA from A. convolutus. The yield of total RNA was 0.69-0.73 mg/g of fresh weight, with A(260)/A(280) ratio of 1.79-1.86. The obtained RNA was of sufficient quality and suitable for downstream application such as RT-PCR and cDNA library construction. The procedure may also have wider applicability for total RNA isolation from other green microalgae species.
  17. Thanh T, Chi VT, Abdullah MP, Omar H, Napis S
    Mol Biol (Mosk), 2012 Jan-Feb;46(1):64-70.
    PMID: 22642102
    Isolation of promoter sequences from known gene sequences is a tedious task in genome-related research. An efficient method of obtaining the promoter sequences is necessary in order to successfully use targeted promoters for genetic manipulations. Here, efficiency and usefulness of two PCR-based methods, namely: ligation-mediated PCR and thermal asymmetric interlaced (TAIL) PCR, for isolation of promoter sequences of the ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit (RbcS) gene from green microalgae Ankistrodesmus convolutus (A. convolutus) were evaluated. The results showed that the amplification efficiency of TAIL-PCR was higher than that of the ligation-mediated PCR method, i.e. the amplified promoter fragments of 1.2 and 0.8 kb in length or promoter sequences of 813 and 606 bp (after eliminating the unreadable sequences). The use of TAIL-PCR described here presents a low cost and efficient strategy for the isolation of promoter sequences of known genes, especially in GC-rich regions, and species with little or no available genome information such as A. convolutus.
  18. Thanh T, Chi VTQ, Omar H, Abdullah MP, Napis S
    Int J Mol Sci, 2012;13(3):2676-2691.
    PMID: 22489117 DOI: 10.3390/ijms13032676
    The availability of highly active homologous promoters is critical in the development of a transformation system and improvement of the transformation efficiency. To facilitate transformation of green microalga Ankistrodesmus convolutus which is considered as a potential candidate for many biotechnological applications, a highly-expressed native promoter sequence of ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit (AcRbcS) has been used to drive the expression of β-glucuronidase (gusA) gene in this microalga. Besides the determination of the transcription start site by 5'-RACE, sequence analysis revealed that AcRbcS promoter contained consensus TATA-box and several putative cis-acting elements, including some representative light-regulatory elements (e.g., G-box, Sp1 motif and SORLIP2), which confer light responsiveness in plants, and several potential conserved motifs (e.g., CAGAC-motif, YCCYTGG-motifs and CACCACA-motif), which may be involved in light responsiveness of RbcS gene in green microalgae. Using AcRbcS promoter::gusA translational fusion, it was demonstrated that this promoter could function as a light-regulated promoter in transgenic A. convolutus, which suggested that the isolated AcRbcS promoter was a full and active promoter sequence that contained all cis-elements required for developmental and light-mediated control of gene expression, and this promoter can be used to drive the expression of heterologous genes in A. convolutus. This achievement therefore advances the development of A. convolutus as an alternative expression system for the production of recombinant proteins. This is the first report on development of gene manipulation system for unicellular green alga A. convolutus.
  19. Tan HY, Goh ZY, Loh KH, Then AY, Omar H, Chang SW
    PeerJ, 2021;9:e11825.
    PMID: 34434645 DOI: 10.7717/peerj.11825
    Background: Despite the high commercial fisheries value and ecological importance as prey item for higher marine predators, very limited taxonomic work has been done on cephalopods in Malaysia. Due to the soft-bodied nature of cephalopods, the identification of cephalopod species based on the beak hard parts can be more reliable and useful than conventional body morphology. Since the traditional method for species classification was time-consuming, this study aimed to develop an automated identification model that can identify cephalopod species based on beak images.

    Methods: A total of 174 samples of seven cephalopod species were collected from the west coast of Peninsular Malaysia. Both upper and lower beaks were extracted from the samples and the left lateral views of upper and lower beak images were acquired. Three types of traditional morphometric features were extracted namely grey histogram of oriented gradient (HOG), colour HOG, and morphological shape descriptor (MSD). In addition, deep features were extracted by using three pre-trained convolutional neural networks (CNN) models which are VGG19, InceptionV3, and Resnet50. Eight machine learning approaches were used in the classification step and compared for model performance.

    Results: The results showed that the Artificial Neural Network (ANN) model achieved the best testing accuracy of 91.14%, using the deep features extracted from the VGG19 model from lower beak images. The results indicated that the deep features were more accurate than the traditional features in highlighting morphometric differences from the beak images of cephalopod species. In addition, the use of lower beaks of cephalopod species provided better results compared to the upper beaks, suggesting that the lower beaks possess more significant morphological differences between the studied cephalopod species. Future works should include more cephalopod species and sample size to enhance the identification accuracy and comprehensiveness of the developed model.

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