MyMedR

A mesocarp-and species-specific cDNA clone from oil palm encodes for sesquiterpene synthase

Shah FH, Cha TS

Plant Sci, 2000 May 29;154(2):153-160.

The differential display method was used to isolate cDNAs corresponding to transcripts that accumulate during the period of lipid synthesis, 12-20 weeks after anthesis (WAA) in the mesocarp of two oil palms, Elaeis oleifera and Elaeis guineensis, Tenera. DNA-free total RNA from mesocarp and kernel of E. guineensis, Tenera and E. oleifera (15 WAA) were used to obtain differential gene expression patterns between these tissues from the two species. In this report, we describe the isolation and characterization of a specific cDNA clone, MO1 (434 bp) which was shown to be mesocarp-specific as well as species-specific for E. oleifera Sequencing of this fragment showed homology to the enzyme sesquiterpene synthase. Its longer cDNA clone, pMO1 (1072 bp), isolated from a 15-week E. oleifera mesocarp cDNA library confirmed that it encodes for sesquiterpene synthase. The complete sequence of 1976 bp was obtained using 5'RACE method. Northern hybridization showed that MO1 and pMO1 mRNA transcripts are highly expressed only in the mesocarp of E. oleifera from 5 to 20 WAA. No expression was detected in the kernel (12-17 WAA) and vegetative tissues of both species nor in the mesocarp of E. guineensis. This is the first communication to document on the isolation and characterisation of a mesocarp-and species-specific cDNA clone from oil palm.

Levels of plasma immunoglobulins in Malaysians

Shah FH, Yadav M

Southeast Asian J. Trop. Med. Public Health, 1973 Dec;4(4):468-73.

PMID: 4207078

Normal plasma-immunoglobulin levels in Malaysians

Yadav M, Shah FH

Lancet, 1973 Aug 25;2(7826):450-1.

PMID: 4124938

Variation in serum immunoglobulin G, A and M levels in Malaysian blood donors

Yadav M, Shah FH

Med J Malaysia, 1978 Sep;33(1):57-71.

PMID: 750898

Normal serum immunoglobulin G, A and M levels in full term Malaysian newborns

Yadav M, Shah FH

Med J Malaysia, 1979 Mar;33(3):247-51.

PMID: 522730

Serum immunoglobin A. G and M levels in blood donors of four racial groups in Malaysia

Yadav M, Shah FH

Trop Geogr Med, 1977 Sep;29(3):245-50.

PMID: 595130

Serum levels were determined in urban Chinese, Malays and Indians and in the forest-residing Orang Asli of age group 11 to 50. There was no difference in the IgM levels in the Chinese, Indians and Malays, but the serum IgG was elevated (p less than 0.05) in the Malays and the serum IgA level (p less than 0.01) in the Indians, when compared to the other two races. In contrast to the three other races there was a significant elevation of all three immunoglobulins in the Orang Asli. The mean immunoglobulin levels of the urban Malaysians are comparable to those reported for Caucasians residing in temperate countries. However, in the Orang Asli, the immunoglobulin levels were higher than observed for populations of the temperate regions but are comparable to the levels reported for several other populations of the tropical regions. Females had higher IgM levels than males in the Chinese, Indian and Malays but in the Orang Asli there was no sex difference in the immunoglobulin levels.

Fulltext Maternal and cord serum immunoglobulins in four Malaysian races

Shah FH, Yadav M

Singapore Med J, 1977 Dec;18(4):246-57.

PMID: 614701

Immunoglobulin G, A and M levels were determined in paired maternal and cord sera of premature, full term and postmature newborns of urban dwelling Chinese, Indian, Malay and full term newborn of the forest dwelling Orang Asli (Malaysian aborigines). The mean serum IgC level in the full term Orang Asli newborns (1254±441 mg per 100 mil is comparable to that of the Indians (1211±282 mg per 100 ml) and Malays (1169±286 mg per 100 ml) but these levels are higher than those of the Chinese
newborns (1092±270 mg per 100 ml). Statistical analysis indicates a significant dependence of cord serum IgG level on maternal serum IgG level in the . Chinese, Indians and Malays. In addition, in Indians the cord serum IgG was significantly dependent at 5% level on the gestation age. The fetomaternal serum IgG level ratios at term were equal to or just less than one. The cord serum IgM levels of the Chinese, Indian, Malay and Orang Asli newborns at term were 11.6.±. 6.5, 12.5.±. 7.3, 10.9.±. 5.8 and
16.7±6.9 mg per 100 ml respectively. Statistical analysis showed absence of correlation between cord serum IgM level and birthweight, gestation age or maternal serum IgM level in Chinese and Malays. In Indians the cord sera IgM level showed a dependence on the birthweight. Immunoglobulin A was present in 34.6%, 40.5%, 31.6% and 62.5% of full term Chinese, Indian, Malay and Orang Asli newborns respectively. These observations are discussed in relation to the immunoglobulin levels observed in populations residing in temperate and other tropical regions.

Differential gene expression and characterization of tissue-specific cDNA clones in oil palm using mRNA differential display

San CT, Shah FH

Mol Biol Rep, 2005 Dec;32(4):227-35.

PMID: 16328884

The mRNA differential display method was utilized to study the differential expression and regulation of genes in two species of oil palm, the commercially grown variety Elaeis guineensis, var. tenera and the South American species, Elaeis oleifera. We demonstrated the differential expression of genes in the mesocarp and kernel at the week of active oil synthesis (15 week after anthesis) during fruit development as compare to the roots and leaves and the isolation of tissue-specific and species-specific cDNA clones. A total of eight specific cDNA clones were isolated and their specificities were confirmed by Northern hybridization and classified into three groups. Group one contains four clones (KT3, KT4, KT5 and KT6) that are kernel-specific for E. guineensis, tenera and E. oleifera. The second group represents clone FST1, which is mesocarp and kernel-specific for E. guineensis, tenera and E. oleifera. The third group represents clones MLT1, MLT2 and MLO1 that are mesocarp and leaf-specific. Northern analysis showed that their expressions were developmentally regulated. Nucleotide sequencing and homology search in GenBank data revealed that clones KT3 and KT4 encode for the same maturation protein PM3. While clones MLT1 and MLT2 encode for S-ribonuclease binding protein and fibrillin, respectively. The other clones (KT5, KT6, FST1 and MLO1) did not display any significant homology to any known protein.

The utility of RAPD markers for the determination of genetic variation in oil palm (Elaeis guineensis)

Shah FH, Rashid O, Simons AJ, Dunsdon A

Theor Appl Genet, 1994 Nov;89(6):713-8.

PMID: 24178016 DOI: 10.1007/BF00223710

The genetic variation among different accessions of oil-palm germplasm collected from Africa was estimated using random primers and the polymerase chain reaction. The present study revealed high levels of genetic variation in these accessions. Electrophoresis of the amplification products indicated that nine out of 20 primers were able to generate polymorphic products ranging in length from 0.2 kb to 2.3 kb. No individual palm or population-specific products were observed. Greatest diversity was seen in Zaire population 5 and the least in Zaire population 2.

Serum immunoglobulin levels in the Malaysian Orang Asli

Yadav M, Shah FH, Dhaliwal SS

Southeast Asian J. Trop. Med. Public Health, 1978 Dec;9(4):501-9.

PMID: 751216

Serum immunoglobulin G, A, M, D and E levels were determined in the forest-dwelling Orang Asli of age group 8 to 64 years. The levels are higher than observed for urban Malaysians and comparable to levels reported for populations residing in the tropics. There was no significant difference in serum levels of all the immunoglobulins studied in both sexes. The elevated serum immunoglobulins levels are discussed in terms of the nature of the immune defence developed in the Orang Asli to contend with the many parasites prevalent in their environment.

Micropropagation of Elaeis guineensis Jacq. 'Dura': Comparison of three basal media for efficient regeneration

Muniran F, Bhore SJ, Shah FH

Indian J Exp Biol, 2008 Jan;46(1):79-82.

PMID: 18697576

Three basal plant tissue culture media, namely, N6, MS, and modified Y3, were compared to optimize micropropagation protocol for E. guineensis. Full strength media were used separately to regenerate plantlets directly using immature zygotic embryos (IZEs), and through somatic embryogenesis of calli obtained from IZEs. The plantlets regenerated by direct regeneration on three media were examined for shoot length and rooting percentage. For the induction of callus, somatic embryogenesis, and rooting modified Y3 medium was the most effective. In conclusion, the results indicate that modified Y3 medium is the most suitable for direct regeneration, callus induction and somatic embryogenesis in E. guineensis.

Insights from the GC content analysis of 76genome survey sequences (GSS) from Elaeisoleifera

Bhore SJ, Kassim A, Shah FH

Bioinformation, 2010 Sep 20;5(4):141-5.

PMID: 21364775

South American oil-palm (Elaeis oleifera) is not cultivated in tropical countries like Malaysia on large scale due to low yield of palm oil derived from its fruit mesocarp. However, its fruit mesocarp oil contains about 68.6 % oleic acid (C(18:1)) which is more than double in comparison to commercially cultivated oilpalm, E. guineensis Jacq Tenera (hybrid of Dura (♀) x Pisifera (♂)). It is also known that E. oleifera is a good source of tocotrienols and carotenoids. Therefore, it is of interest to know the genome sequence of E. oleifera. The objective of this study is to generate genome survey sequences (GSS) to get GC content insight in the E. oleifera genome. The nuclear genomic DNA isolated from young leaf-tissues was digested with EcoRI and NdeI/DraI restriction enzymes; and three genomic DNA libraries were constructed using Lambda ZAP-II, pGEM®-T Easy, and pDONR 222™ as cloning vectors. Generated 76 GSSs were analyzed by using Bioinformatics tools. The analysis result indicates that the adenine, cytosine, guanine and thymine content in generated GSSs are 30%, 20%, 20%, and 30% respectively. In conclusion, based on the precise GC content analysis of the randomly isolated 76 GSSs by using Bioinformatics tools we hypothesize that GC content in E. oleifera genome is 40%. The hypothesized 40% GC content in E. oleifera genome is expected to remain close to the GC content based on the whole genome analysis.(ψ)The nucleotide sequence data reported in this paper have been submitted to dbGSS division of the international DNA database (GenBank/DDBJ/EMBL) under accession numbers: DX575945- DX575972 and EI798032-EI798079.

ABBREVIATIONS: gDNA - Nuclear genomic DNA, GSSs - Genome survey sequences K12, SAOP - South American oil-palm Db1.

Fulltext Insights from computational analysis of full-length β-ketoacyl-[ACP] synthase-II cDNA isolated from American and African oil palms

Bhore SJ, Cha TS, Amelia K, Shah FH

J Nat Sci Biol Med, 2014 Jan;5(1):73-81.

PMID: 24678202 DOI: 10.4103/0976-9668.127292

Palm oil derived from fruits (mesocarp) of African oil palm (Elaeis guineensis Jacq. Tenera) and American oil palm (E. oleifera) is important for food industry. Due to high yield, Elaeis guineensis (Tenera) is cultivated on commercial scale, though its oil contains high (~54%) level of saturated fatty acids. The rate-limiting activity of beta-ketoacyl-[ACP] synthase-II (KAS-II) is considered mainly responsible for the high (44%) level of palmitic acid (C16:0) in the oil obtained from E. guineensis.

Fulltext Computational analysis of common bean (Phaseolus vulgaris L., genotype BAT93) lycopene β-cyclase and β-carotene hydroxylase gene's cDNA

Bhore SJ, Amelia K, Wang E, Priyadharsini S, Shah FH

Bioinformation, 2013;9(4):197-206.

PMID: 23519320 DOI: 10.6026/97320630009197

The identification of genes and understanding of genes' expression and regulation in common bean (Phaseolus vulgaris L.) is necessary in order to strategize its improvement using genetic engineering techniques. Generation of expressed sequence tags (ESTs) is useful in rapid isolation, identification and characterization of the genes. To study the gene expression in P. vulgaris pods tissue, ESTs generation work was initiated. Early stage and late stage bean-pod-tissues cDNA libraries were constructed using CloneMiner cDNA library construction kit. In total, 5972 EST clones were isolated using random method of gene isolation. While processing ESTs, we found lycopene β-cyclase (PvLCY-β) and β-carotene hydroxylase (PvCHY-β) gene's cDNA. In carotenoid biosynthesis pathway, PvLCY-β catalyzes the production of carotene; and PvCHY-β is known to function as a catalyst in the production of lutein and zeaxanthin. To understand more about PvLCY-β and PvCHY-β, both strands of both cDNA clones were sequenced using M13 forward and reverse primers. Nucleotide and deduced protein sequences were analyzed and annotated using online bioinformatics tools. Results showed that PvLCY-β and PvCHY-β cDNAs are 1639 and 1107 bp in length, respectively. Analysis results showed that PvLCY-β and PvCHY-β gene's cDNA contains an open reading frame (ORF) that encodes for 502 and 305 amino acid residues, respectively. The deduced protein sequence analysis results also showed the presence of conserved domains needed for PvLCY-β and PvCHY-β functions. The phylogenetic analysis of both PvLCY-β and PvCHY-β proteins showed it's closeness with the LCY-β and CHY-β proteins from Glycine max, respectively. The nucleotide sequence of PvLCY-β and PvCHY-β gene's cDNA and it's annotation is reported in this paper.

Fulltext Analysis of common bean (Phaseolus vulgaris L., genotype BAT93) calmodulin cDNA using computational tools

Amelia K, Singh J, Shah FH, Bhore SJ

Pharmacognosy Res, 2015 Apr-Jun;7(2):209-12.

PMID: 25829797 DOI: 10.4103/0974-8490.150536

Common bean (Phaseolus vulgaris L.) is an important part of the human diet and serves as a source of natural products. Identification and understanding of genes in P. vulgaris is important for its improvement. Characterization of expressed sequence tags (ESTs) is one of the approaches in understanding the expressed genes. For the understanding of genes expression in P. vulgaris pod-tissue, research work of ESTs generation was initiated by constructing cDNA libraries using 5-day and 20-day old bean-pod-tissues. Altogether, 5972 cDNA clones were isolated to have ESTs. While processing ESTs, we found a transcript for calmodulin (CaM) gene. It is an important gene that encodes for a calcium-binding protein and known to express in all eukaryotic cells. Hence, this study was undertaken to analyse and annotate it.

Fulltext Nucleotide sequence of Phaseolus vulgaris L. alcohol dehydrogenase encoding cDNA and three-dimensional structure prediction of the deduced protein

Amelia K, Khor CY, Shah FH, Bhore SJ

Pharmacognosy Res, 2015 Apr-Jun;7(2):203-8.

PMID: 25829796 DOI: 10.4103/0974-8490.150532

Common beans (Phaseolus vulgaris L.) are widely consumed as a source of proteins and natural products. However, its yield needs to be increased. In line with the agenda of Phaseomics (an international consortium), work of expressed sequence tags (ESTs) generation from bean pods was initiated. Altogether, 5972 ESTs have been isolated. Alcohol dehydrogenase (AD) encoding gene cDNA was a noticeable transcript among the generated ESTs. This AD is an important enzyme; therefore, to understand more about it this study was undertaken.

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