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Fulltext Risk factors of gestational diabetes mellitus in the refugee population in Gaza Strip: a case-control study

AlKasseh AS, Zaki NM, Aljeesh YI, Soon LK

East Mediterr Health J, 2014 Jan 09;19 Suppl 3:S12-8.
PMID: 24995734

To determine the risk factors of gestational diabetes mellitus in refugee populations in the Gaza Strip, a retrospective case-control study was performed between March and June 2011 in the United Nations Relief and Works Agency (UNRWA) primary health care clinics. Data were collected on maternal sociodemographics and the prevalence of diagnosed GDM according to World Health Organization criteria from clinics where postnatal Palestinian refugee women had been diagnosed with GDM during previous pregnancies, and non-GDM women were used as controls. Sociodemographic characteristics, pre-pregnancy body-mass index (BMI), obstetrics history and family history of diabetes were used as study variables. In total, 189 incident cases of GDM were identified. The most significant risk factors for GDM were: history of miscarriage more than once; overweight before pregnancy; history of stillbirth; history of caesarean birth; and positive family history of diabetes mellitus.
Fulltext Elaeis oleifera genomic-SSR markers: exploitation in oil palm germplasm diversity and cross-amplification in arecaceae

Zaki NM, Singh R, Rosli R, Ismail I

Int J Mol Sci, 2012;13(4):4069-88.
PMID: 22605966 DOI: 10.3390/ijms13044069

Species-specific simple sequence repeat (SSR) markers are favored for genetic studies and marker-assisted selection (MAS) breeding for oil palm genetic improvement. This report characterizes 20 SSR markers from an Elaeis oleifera genomic library (gSSR). Characterization of the repeat type in 2000 sequences revealed a high percentage of di-nucleotides (63.6%), followed by tri-nucleotides (24.2%). Primer pairs were successfully designed for 394 of the E. oleifera gSSRs. Subsequent analysis showed the ability of the 20 selected E. oleifera gSSR markers to reveal genetic diversity in the genus Elaeis. The average Polymorphism Information Content (PIC) value for the SSRs was 0.402, with the tri-repeats showing the highest average PIC (0.626). Low values of observed heterozygosity (H(o)) (0.164) and highly positive fixation indices (F(is)) in the E. oleifera germplasm collection, compared to the E. guineensis, indicated an excess of homozygosity in E. oleifera. The transferability of the markers to closely related palms, Elaeis guineensis, Cocos nucifera and ornamental palms is also reported. Sequencing the amplicons of three selected E. oleifera gSSRs across both species and palm taxa revealed variations in the repeat-units. The study showed the potential of E. oleifera gSSR markers to reveal genetic diversity in the genus Elaeis. The markers are also a valuable genetic resource for studying E. oleifera and other genus in the Arecaceae family.
Estimating the five-year survival of cervical cancer patients treated in hospital universiti sains malaysia

Razak NA, Mn K, Zubairi YZ, Naing NN, Zaki NM

Asian Pac J Cancer Prev, 2013;14(2):825-8.
PMID: 23621246

OBJECTIVE: The objective of this study was to determine the five-year survival among patients with cervical cancer treated in Hospital Universiti Sains Malaysia.
METHODS: One hundred and twenty cervical cancer patients diagnosed between 1st July 1995 and 30th June 2007 were identified. Data were obtained from medical records. The survival probability was determined using the Kaplan-Meier method and the log-rank test was applied to compare the survival distribution between groups.
RESULTS: The overall five-year survival was 39.7% [95%CI (Confidence Interval): 30.7, 51.3] with a median survival time of 40.8 (95%CI: 34.0, 62.0) months. The log-rank test showed that there were survival differences between the groups for the following variables: stage at diagnosis (p=0.005); and primary treatment (p=0.0242). Patients who were diagnosed at the latest stage (III-IV) were found to have the lowest survival, 18.4% (95%CI: 6.75, 50.1), compared to stage I and II where the five-year survival was 54.7% (95%CI: 38.7, 77.2) and 40.8% (95%CI: 27.7, 60.3), respectively. The five-year survival was higher in patients who received surgery [52.6% (95%CI: 37.5, 73.6)] as a primary treatment compared to the non-surgical group [33.3% (95%CI: 22.9, 48.4)].
CONCLUSION: The five-year survival of cervical cancer patients in this study was low. The survival of those diagnosed at an advanced stage was low compared to early stages. In addition, those who underwent surgery had higher survival than those who had no surgery for primary treatment.
Arterial stiffness, inflammatory and pro-atherogenic markers in gestational diabetes mellitus

Salmi AA, Zaki NM, Zakaria R, Nor Aliza AG, Rasool AH

VASA, 2012 Mar;41(2):96-104.
PMID: 22403127 DOI: 10.1024/0301-1526/a000171

This study aims to determine whether gestational diabetes mellitus (GDM) is associated with increased arterial stiffness, inflammatory and pro-atherogenic markers compared to age matched controls.
Short-term estrogen replacement therapy reduces platelet marker levels in Malaysian postmenopausal women

Sheikh SA, Roshan TM, Khattak MN, Baig AA, Noor SJ, Hassan R, et al.

Menopause Int, 2011 Mar;17(1):6-10.
PMID: 21427417 DOI: 10.1258/mi.2011.011001

In healthy postmenopausal women (PMW) increased platelet activation has been associated with adverse cardiovascular events. There is much debate about the relationship between platelet function and serum estradiol level in PMW. This study assessed the effect of short-term oral estrogen replacement therapy (ERT) on platelet activation markers (CD62P and PAC-1) and its correlation with age and body mass index (BMI) among healthy PMW.
Fulltext Older Age Group in Pregnancy is Associated with Increased Arterial Stiffness

Salmi AA, Nor Aliza AG, Nik Zaki NM, Wong AR, Aida HR

Med J Malaysia, 2010 Jun;65(2):115-8.
PMID: 23756794 MyJurnal

Arterial stiffness is an index of vascular health; normal pregnancy is associated with reduced arterial stiffness. This cross sectional study compared arterial stiffness in older (≥35 years) and the younger (≤34 years) age groups of pregnant women. Arterial stiffness was assessed noninvasively in 66 pregnant women between 23 - 32 weeks gestation (41 women ≤ 34 years, 25 women ≥ 35 years) using the parameters pulse wave analysis and pulse wave velocity. Blood pressure (BP), body mass index (BMI), serum total cholesterol (TC) and fasting blood glucose (FBS) were also recorded. Mean ages of the younger and older age groups were 27.6±0.62 and 39.3±0.58 years; no significant difference was seen between the groups in their BMI, TC, FBS, SBP, DBP and gestational age. The older age group of women have increased arterial stiffness (augmentation index 19.4±1.9% vs 13.2±1.6%, p=0.015) and aortic stiffness (pulse wave velocity 8.7±0.3 vs 7.7±0.2 m/s, p=0.004) compared to the younger women. Linear regression analysis showed a positive significant correlation between age and augmentation index (R=0.278, p=0.026), and pulse wave velocity (R=0.350, p=0.004). We conclude that older pregnant women has increased arterial stiffness compared to a younger age group of pregnant women suggesting that vascular changes due to ageing occurs in pregnancy despite cardiovascular adaptations occurring in pregnancy.
SSR mining in oil palm EST database: application in oil palm germplasm diversity studies

Ting NC, Zaki NM, Rosli R, Low ET, Ithnin M, Cheah SC, et al.

J Genet, 2010 Aug;89(2):135-45.
PMID: 20861564

This study reports on the detection of additional expressed sequence tags (EST) derived simple sequence repeat (SSR) markers for the oil palm. A large collection of 19243 Elaeis guineensis ESTs were assembled to give 10258 unique sequences, of which 629 ESTs were found to contain 722 SSRs with a variety of motifs. Dinucleotide repeats formed the largest group (45.6%) consisting of 66.9% AG/CT, 21.9% AT/AT, 10.9% AC/GT and 0.3% CG/CG motifs. This was followed by trinucleotide repeats, which is the second most abundant repeat types (34.5%) consisting of AAG/CTT (23.3%), AGG/CCT (13.7%), CCG/CGG (11.2%), AAT/ATT (10.8%), AGC/GCT (10.0%), ACT/AGT (8.8%), ACG/CGT (7.6%), ACC/GGT (7.2%), AAC/GTT (3.6%) and AGT/ACT (3.6%) motifs. Primer pairs were designed for 405 unique EST-SSRs and 15 of these were used to genotype 105 E. guineensis and 30 E. oleifera accessions. Fourteen SSRs were polymorphic in at least one germplasm revealing a total of 101 alleles. The high percentage (78.0%) of alleles found to be specific for either E. guineensis or E. oleifera has increased the power for discriminating the two species. The estimates of genetic differentiation detected by EST-SSRs were compared to those reported previously. The transferability across palm taxa to two Cocos nucifera and six exotic palms is also presented. The polymerase chain reaction (PCR) products of three primer-pairs detected in E. guineensis, E. oleifera, C. nucifera and Jessinia bataua were cloned and sequenced. Sequence alignments showed mutations within the SSR site and the flanking regions. Phenetic analysis based on the sequence data revealed that C. nucifera is closer to oil palm compared to J. bataua; consistent with the taxanomic classification.
Chromosome identification in oil palm (Elaeis guineensis) using in situ hybridization with massive pools of single copy oligonucleotides and transferability across Arecaceae species

Zaki NM, Schwarzacher T, Singh R, Madon M, Wischmeyer C, Hanim Mohd Nor N, et al.

Chromosome Res, 2021 12;29(3-4):373-390.
PMID: 34657216 DOI: 10.1007/s10577-021-09675-0

Chromosome identification is essential for linking sequence and chromosomal maps, verifying sequence assemblies, showing structural variations and tracking inheritance or recombination of chromosomes and chromosomal segments during evolution and breeding programs. Unfortunately, identification of individual chromosomes and chromosome arms has been a major challenge for some economically important crop species with a near-continuous chromosome size range and similar morphology. Here, we developed oligonucleotide-based chromosome-specific probes that enabled us to establish a reference chromosome identification system for oil palm (Elaeis guineensis Jacq., 2n = 32). Massive oligonucleotide sequence pools were anchored to individual chromosome arms using dual and triple fluorescent in situ hybridization (EgOligoFISH). Three fluorescently tagged probe libraries were developed to contain, in total 52,506 gene-rich single-copy 47-mer oligonucleotides spanning each 0.2-0.5 Mb across strategically placed chromosome regions. They generated 19 distinct FISH signals and together with rDNA probes enabled identification of all 32 E. guineensis chromosome arms. The probes were able to identify individual homoeologous chromosome regions in the related Arecaceae palm species: American oil palm (Elaeis oleifera), date palm (Phoenix dactylifera) and coconut (Cocos nucifera) showing the comparative organization and concerted evolution of genomes in the Arecaceae. The oligonucleotide probes developed here provide a valuable approach to chromosome arm identification and allow tracking chromosome transfer in hybridization and breeding programs in oil palm, as well as comparative studies within Arecaceae.
Detection of ploidy and chromosomal aberrations in commercial oil palm using high-throughput SNP markers

Ngoot-Chin T, Zulkifli MA, van de Weg E, Zaki NM, Serdari NM, Mustaffa S, et al.

Planta, 2021 Feb 05;253(2):63.
PMID: 33544231 DOI: 10.1007/s00425-021-03567-7

MAIN CONCLUSION: Karyotyping using high-density genome-wide SNP markers identified various chromosomal aberrations in oil palm (Elaeis guineensis Jacq.) with supporting evidence from the 2C DNA content measurements (determined using FCM) and chromosome counts. Oil palm produces a quarter of the world's total vegetable oil. In line with its global importance, an initiative to sequence the oil palm genome was carried out successfully, producing huge amounts of sequence information, allowing SNP discovery. High-capacity SNP genotyping platforms have been widely used for marker-trait association studies in oil palm. Besides genotyping, a SNP array is also an attractive tool for understanding aberrations in chromosome inheritance. Exploiting this, the present study utilized chromosome-wide SNP allelic distributions to determine the ploidy composition of over 1,000 oil palms from a commercial F1 family, including 197 derived from twin-embryo seeds. Our method consisted of an inspection of the allelic intensity ratio using SNP markers. For palms with a shifted or abnormal distribution ratio, the SNP allelic frequencies were plotted along the pseudo-chromosomes. This method proved to be efficient in identifying whole genome duplication (triploids) and aneuploidy. We also detected several loss of heterozygosity regions which may indicate small chromosomal deletions and/or inheritance of identical by descent regions from both parents. The SNP analysis was validated by flow cytometry and chromosome counts. The triploids were all derived from twin-embryo seeds. This is the first report on the efficiency and reliability of SNP array data for karyotyping oil palm chromosomes, as an alternative to the conventional cytogenetic technique. Information on the ploidy composition and chromosomal structural variation can help to better understand the genetic makeup of samples and lead to a more robust interpretation of the genomic data in marker-trait association analyses.