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Genetic architecture of Al3+ toxicity tolerance in rice F2:3 populations determined through QTL mapping

Jahan N, Javed MA, Khan A, Manan FA, Tabassum B

Ecotoxicology, 2021 Jul;30(5):794-805.
PMID: 33871748 DOI: 10.1007/s10646-021-02413-6

Aluminum (Al3+) toxicity is one of the factors limiting crop production in acidic soils. Identifying quantitative trait loci (QTLs)/genes for tolerance to Al3+ toxicity at seed germination can aid the development of new tolerant cultivars. The segregating population derived from Pak Basmati (Indica) × Pokkali (Indica) was used for mapping QTLs linked with tolerance to Al3+ toxicity ranging from 0 to 20 mM at pH 4 ± 0.2 at germination. The favorable alleles for all new QTLs were analyzed based on germination traits, i.e., final germination percentage (FG%), germination energy (GE), germination speed (GS), germination index (GI), mean germination time (MGT), germination value (GV), germination velocity (GVe), peak value of germination (GPV), and germination capacity (GC), and growth traits, such as root length (RL), shoot length (SL), total dry biomass (TDB) and germination vigor index (GVI). The phenotypic evolution showed transgressive variations. For genome-wide mapping, 90 polymorphic SSRs with 4 gene-specific markers and Win QTL Cart were used for QTL analysis. In all, 35 QTLs for germination and 11 QTLs for seedling growth were detected in distinct chromosomal regions by composite interval mapping (CIM), and multiple interval mapping (MIM) confirmed the pleiotropy at region RM128 on chromosome 1. Based on our genetic mapping studies, the genes/QTLs underlying tolerance to Al3+ toxicity could differ for both the germination and seedling stages in segregated populations. The QTLs identified in this study could be a source of new alleles for improving tolerance to Al3+ toxicity in rice.
Plant Bioactive Peptides: Current Status and Prospects Towards Use on Human Health

Chai TT, Ee KY, Kumar DT, Manan FA, Wong FC

Protein Pept Lett, 2021;28(6):623-642.
PMID: 33319654 DOI: 10.2174/0929866527999201211195936

Large numbers of bioactive peptides with potential applications in protecting against human diseases have been identified from plant sources. In this review, we summarized recent progress in the research of plant-derived bioactive peptides, encompassing their production, biological effects, and mechanisms. This review focuses on antioxidant, antimicrobial, antidiabetic, and anticancer peptides, giving special attention to evidence derived from cellular and animal models. Studies investigating peptides with known sequences and well-characterized peptidic fractions or protein hydrolysates will be discussed. The use of molecular docking tools to elucidate inter-molecular interactions between bioactive peptides and target proteins is highlighted. In conclusion, the accumulating evidence from in silico, in vitro and in vivo studies to date supports the envisioned applications of plant peptides as natural antioxidants as well as health-promoting agents. Notwithstanding, much work is still required before the envisioned applications of plant peptides can be realized. To this end, future researches for addressing current gaps were proposed.
Fulltext Macular thickness as determined by optical coherence tomography in relation to degree of myopia, axial length and vitreous chamber depth in Malay subjects

Othman SF, Sharanjeet-Kaur, Manan FA, Zulkarnain AI, Mohamad Z, Ariffin AE

Clin Exp Optom, 2012 Sep;95(5):484-91.
PMID: 22716100 DOI: 10.1111/j.1444-0938.2012.00752.x

PURPOSE:This study aimed to determine the relationship between macular thickness and spherical equivalent refraction (SER), axial length (AL) and vitreous chamber depth (VCD) in Malay subjects.
METHODS: Sixty-three subjects (aged 19-24 years) with a mean SER of -1.79 ± 2.24 D, mean axial length of 24.26 ± 1.35 mm and mean vitreous chamber depth of 17.02 ± 1.33 mm were included in this clinical cross-sectional study. Stratus optical coherence tomography (Time Domain optical coherence tomography) was used to determine the thickness of the outer macular (perifovea) and inner macular (parafovea) at four different locations, that is, temporal, superior, nasal and inferior quadrants and also the fovea itself.
RESULTS: Positive correlations were found between the outer macular (perifovea) thickness and SER at the temporal (R = 0.47, p < 0.05), superior (R = 0.36, p < 0.05) and inferior (R = 0.31, p < 0.05) quadrants. Foveal thickness was also positively correlated with AL (R = 0.34, p < 0.05) and VCD (R = 0.32, p < 0.05). Negative correlations were found between outer macular thickness and axial length at the temporal (R = -0.46, p < 0.05), superior (R = -0.27, p < 0.05), nasal (R = -0.25, p < 0.05) and inferior (R = -0.36, p < 0.05) quadrants. Negative correlations were also found between outer macular thickness and VCD at the temporal (R = -0.51, p < 0.05), superior (R = -0.32, p < 0.05), nasal (R = -0.31, p < 0.05) and inferior (R = -0.40, p < 0.05) quadrants.
CONCLUSIONS: This study shows that the degree of myopia and elongation of the globe are associated with thinning of most areas of the perifovea. A trend for foveal thickening in the high myopia group is also inferred, although this does not apply to the low and moderate myopia groups.
Study site: Optometry and ophthalmology clinics, National Institute of Ophthalmic Sciences, Tun Hussein Onn National Eye Hospital (THONEH), Petaling Jaya
Fulltext Characterization of the mechanism of prolonged adaptation to osmotic stress of Jeotgalibacillus malaysiensis via genome and transcriptome sequencing analyses

Yaakop AS, Chan KG, Ee R, Lim YL, Lee SK, Manan FA, et al.

Sci Rep, 2016 09 19;6:33660.
PMID: 27641516 DOI: 10.1038/srep33660

Jeotgalibacillus malaysiensis, a moderate halophilic bacterium isolated from a pelagic area, can endure higher concentrations of sodium chloride (NaCl) than other Jeotgalibacillus type strains. In this study, we therefore chose to sequence and assemble the entire J. malaysiensis genome. This is the first report to provide a detailed analysis of the genomic features of J. malaysiensis, and to perform genetic comparisons between this microorganism and other halophiles. J. malaysiensis encodes a native megaplasmid (pJeoMA), which is greater than 600 kilobases in size, that is absent from other sequenced species of Jeotgalibacillus. Subsequently, RNA-Seq-based transcriptome analysis was utilised to examine adaptations of J. malaysiensis to osmotic stress. Specifically, the eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) and KEGG (Kyoto Encyclopaedia of Genes and Genomes) databases were used to elucidate the overall effects of osmotic stress on the organism. Generally, saline stress significantly affected carbohydrate, energy, and amino acid metabolism, as well as fatty acid biosynthesis. Our findings also indicate that J. malaysiensis adopted a combination of approaches, including the uptake or synthesis of osmoprotectants, for surviving salt stress. Among these, proline synthesis appeared to be the preferred method for withstanding prolonged osmotic stress in J. malaysiensis.
Fulltext Characterization of a glucose-tolerant β-glucosidase from Anoxybacillus sp. DT3-1

Chan CS, Sin LL, Chan KG, Shamsir MS, Manan FA, Sani RK, et al.

Biotechnol Biofuels, 2016;9(1):174.
PMID: 27555880 DOI: 10.1186/s13068-016-0587-x

In general, biofuel production involves biomass pretreatment and enzymatic saccharification, followed by the subsequent sugar conversion to biofuel via fermentation. The crucial step in the production of biofuel from biomass is the enzymatic saccharification. Many of the commercial cellulase enzyme cocktails, such as Spezyme(®) CP (Genencor), Acellerase™ 1000 (Genencor), and Celluclast(®) 1.5L (Novozymes), are ineffectively to release free glucose from the pretreated biomass without additional β-glucosidase.
Visual efficiency among teenaged athletes and non-athletes

Omar R, Kuan YM, Zuhairi NA, Manan FA, Knight VF

Int J Ophthalmol, 2017;10(9):1460-1464.
PMID: 28944208 DOI: 10.18240/ijo.2017.09.20

AIM: To compare visual efficiency, specifically accom-modation, vergence, and oculomotor functions among athletes and non-athletes.
METHODS: A cross-sectional study on sports vision screening was used to evaluate the visual skills of 214 elementary students (107 athletes, 107 non-athletes), aged between 13 and 16y. The visual screening assessed visual parameters such as ocular motor alignment, accommodation, and vergence functions.
RESULTS: Mean visual parameters were compared between age-group matched athletes (mean age 14.82±0.98y) and non-athletes (mean age 15.00±1.04y). The refractive errors of all participants were corrected to maximal attainable best corrected visual acuity of logMAR 0.0. Accommodation function assessment evaluated amplitude of accommodation and accommodation facility. Vergence functions measured the near point of convergence, vergence facility, and distance fusional vergence at break and recovery point. Ocular motor alignment was not statistically significant between both groups. Athletes had a statistically significant amplitude of accommodation for both the right eye (t=2.30, P=0.02) and the left eye (t=1.99, P=0.05). Conversely, non-athletes had better accommodation facility (t=-2.54, P=0.01) and near point of convergence (t=4.39, P<0.001) when compared to athletes. Vergence facility was found to be better among athletes (t=2.47, P=0.01). Nevertheless, non-athletes were significantly better for both distance negative and positive fusional vergence.
CONCLUSION: Although the findings are still inconclusive as to whether athletes had superior visual skills as compared to non-athletes, it remains important to identify and elucidate the key visual skills needed by athletes in order for them to achieve higher performance in their sports.