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Effects of changes in chemical and structural characteristic of ammonia fibre expansion (AFEX) pretreated oil palm empty fruit bunch fibre on enzymatic saccharification and fermentability for biohydrogen

Abdul PM, Jahim JM, Harun S, Markom M, Lutpi NA, Hassan O, et al.

Bioresour Technol, 2016 Jul;211:200-8.
PMID: 27017130 DOI: 10.1016/j.biortech.2016.02.135

Oil palm empty fruit bunch (OPEFB) fibre is widely available in Southeast Asian countries and found to have 60% (w/w) sugar components. OPEFB was pretreated using the ammonia fibre expansion (AFEX) method and characterised physically by the Fourier transform infrared spectroscopy, X-ray diffraction and scanning electron microscopy. The results show that there were significant structural changes in OPEFB after the pretreatment step, and the sugar yield after enzymatic hydrolysis using a cocktail of Cellic Ctec2® and Cellic Htec2® increased from 0.15gg(-1) of OPEFB in the raw untreated OPEFB sample to 0.53gg(-1) of OPEFB in AFEX-pretreated OPEFB (i.e. almost a fourfold increase in sugar conversion), which enhances the economic value of OPEFB. A biohydrogen fermentability test of this hydrolysate was carried out using a locally isolated bacterium, Enterobacter sp. KBH6958. The biohydrogen yield after 72h of fermentation was 1.68mol H2 per mol sugar. Butyrate, ethanol, and acetate were the major metabolites.
Fulltext Transcriptome profiling of Stevia rebaudiana MS007 revealed genes involved in flower development

Samsulrizal NH, Khadzran KS, Meenakshi Sundram TC, Zainuddin Z, Shaarani SHN, Azmi NSA, et al.

Turk J Biol, 2021;45(3):314-322.
PMID: 34377055 DOI: 10.3906/biy-2103-3

Stevia rebaudiana is a medicinal plant recommended to diabetic or obese patients as an alternative sweetener owing to its low-calorie property. Previous studies have found that the stevioside level is highest at the time of flower bud formation and lowest at the time of preceding and following flower bud formation. Hence, this study aims to identify the genes involved in the flowering of local S. rebaudiana accession MS007 by investigating the transcriptomic data of two stages of growth, before flowering (BF) and after flowering (AF) that were deposited under accession number SRX6362785 and SRX6362784 at the NCBI SRA database. The transcriptomic study managed to annotate 108299 unigenes of S. rebaudiana with 8871 and 9832 genes that were differentially expressed in BF and AF samples, respectively. These genes involved in various metabolic pathways related to flower development, response to stimulus as well as photosynthesis. Pheophorbide A oxygenase ( PAO ), eukaryotic translation initiation factor 3 subunit E ( TIF3E1 ), and jasmonate ZIM domain-containing protein 1 ( JAZ1 ) were found to be involved in the flower development. The outcome of this study will help further research in the manipulation of the flowering process, especially in the breeding programme to develop photo-insensitive Stevia plant.
Current and future effects of global change on a hotspot's freshwater diversity

Gallardo B, Bogan AE, Harun S, Jainih L, Lopes-Lima M, Pizarro M, et al.

Sci Total Environ, 2018 Sep 01;635:750-760.
PMID: 29680765 DOI: 10.1016/j.scitotenv.2018.04.056

Deforestation, climate change and invasive species constitute three global threats to biodiversity that act synergistically. However, drivers and rates of loss of freshwater biodiversity now and in the future are poorly understood. Here we focus on the potential impacts of global change on freshwater mussels (Order Unionida) in Sundaland (SE Asia), a vulnerable group facing global declines and recognized indicators of overall freshwater biodiversity. We used an ensemble of distribution models to identify habitats potentially suitable for freshwater mussels and their change under a range of climate, deforestation and invasion scenarios. Our data and models revealed that, at present, Sundaland features 47 and 32 Mha of habitat that can be considered environmentally suitable for native and invasive freshwater mussels, respectively. We anticipate that by 2050, the area suitable for palm oil cultivation may expand between 8 and 44 Mha, representing an annual increase of 2-11%. This is expected to result in a 20% decrease in suitable habitat for native mussels, a drop that reaches 30% by 2050 when considering concomitant climate change. In contrast, the habitat potentially suitable for invasive mussels may increase by 44-56% under 2050 future scenarios. Consequently, native mussels may compete for habitat, food resources and fish hosts with invasive mussels across approximately 60% of their suitable range. Our projections can be used to guide future expeditions to monitor the conservation status of freshwater biodiversity, and potentially reveal populations of endemic species on the brink of extinction. Future conservation measures-most importantly the designation of nature reserves-should take into account trends in freshwater biodiversity generally, and particularly species such as freshwater mussels, vital to safeguard fundamental ecosystem services.
Fulltext Preparation of kenaf stem hemicellulosic hydrolysate and its fermentability in microbial production of xylitol by Escherichia coli BL21

Shah SSM, Luthfi AAI, Low KO, Harun S, Manaf SFA, Illias RM, et al.

Sci Rep, 2019 03 11;9(1):4080.
PMID: 30858467 DOI: 10.1038/s41598-019-40807-z

Kenaf (Hibiscus cannabinus L.), a potential fibre crop with a desirably high growth rate, could serve as a sustainable feedstock in the production of xylitol. In this work, the extraction of soluble products of kenaf through dilute nitric-acid hydrolysis was elucidated with respect to three parameters, namely temperature, residence time, and acid concentration. The study will assist in evaluating the performance in terms of xylose recovery. The result point out that the maximum xylose yield of 30.7 g per 100 g of dry kenaf was attained from 2% (v/v) HNO3 at 130 °C for 60 min. The detoxified hydrolysate was incorporated as the primary carbon source for subsequent fermentation by recombinant Escherichia coli and the performance of strain on five different semi-synthetic media on xylitol production were evaluated herein. Among these media, batch cultivation in a basal salt medium (BSM) afforded the highest xylitol yield of 0.35 g/g based on xylose consumption, which corresponded to 92.8% substrate utilization after 38 h. Subsequently, fermentation by E. coli in the xylose-based kenaf hydrolysate supplemented with BSM resulting in 6.8 g/L xylitol which corresponding to xylitol yield of 0.38 g/g. These findings suggested that the use of kenaf as the fermentation feedstock could be advantageous for the development of sustainable xylitol production.
Heterologous expression of Arabidopsis laccase2, laccase4 and peroxidase52 driven under developing xylem specific promoter DX15 improves saccharification in populus

Ahlawat YK, Biswal AK, Harun S, Harman-Ware AE, Doeppke C, Sharma N, et al.

Biotechnol Biofuels Bioprod, 2024 Jan 13;17(1):5.
PMID: 38218877 DOI: 10.1186/s13068-023-02452-7

BACKGROUND: Secondary cell wall holds considerable potential as it has gained immense momentum to replace the lignocellulosic feedstock into fuels. Lignin one of the components of secondary cell wall tightly holds the polysaccharides thereby enhancing the recalcitrance and complexity in the biomass. Laccases (LAC) and peroxidases (PRX) are the major phenyl-oxidases playing key functions during the polymerization of monolignols into lignin. Yet, the functions of laccase and peroxidases gene families remained largely unknown. Hence, the objective of this conducted study is to understand the role of specific LAC and PRX in Populus wood formation and to further investigate how the altered Lac and Prx expression affects biomass recalcitrance and plant growth. This study of heterologous expression of Arabidopsis Lac and Prx genes was conducted in poplar to avoid any otherwise occurring co-suppression mechanism during the homologous overexpression of highly expressed native genes. In the pursuit of optimizing lignocellulosic biomass for biofuel production, the present study focuses on harnessing the enzymatic potential of Arabidopsis thaliana Laccase2, Laccase4, and Peroxidase52 through heterologous expression.
RESULTS: We overexpressed selected Arabidopsis laccase2 (AtLac2), laccase4 (AtLac4), and peroxidase52 (AtPrx52) genes, based on their high transcript expression respective to the differentiating xylem tissues in the stem, in hybrid poplar (cv. 717) expressed under the developing xylem tissue-specific promoter, DX15 characterized the transgenic populus for the investigation of growth phenotypes and recalcitrance efficiency. Bioinformatics analyses conducted on AtLac2 and AtLac4 and AtPrx52, revealed the evolutionary relationship between the laccase gene and peroxidase gene homologs, respectively. Transgenic poplar plant lines overexpressing the AtLac2 gene (AtLac2-OE) showed an increase in plant height without a change in biomass yield as compared to the controls; whereas, AtLac4-OE and AtPrx52-OE transgenic lines did not show any such observable growth phenotypes compared to their respective controls. The changes in the levels of lignin content and S/G ratios in the transgenic poplar resulted in a significant increase in the saccharification efficiency as compared to the control plants.
CONCLUSIONS: Overall, saccharification efficiency was increased by 35-50%, 21-42%, and 8-39% in AtLac2-OE, AtLac4-OE, and AtPrx52-OE transgenic poplar lines, respectively, as compared to their controls. Moreover, the bioengineered plants maintained normal growth and development, underscoring the feasibility of this approach for biomass improvement without compromising overall plant fitness. This study also sheds light on the potential of exploiting regulatory elements of DX15 to drive targeted expression of lignin-modifying enzymes, thereby providing a promising avenue for tailoring biomass for improved biofuel production. These findings contribute to the growing body of knowledge in synthetic biology and plant biotechnology, offering a sustainable solution to address the challenges associated with lignocellulosic biomass recalcitrance.
Fulltext A Parametric Time-to-Event Modelling of Recurrent Ischemic Stroke After Index Stroke Among Patients With and Without Diabetes Mellitus: Implementation of Temporal Validation of the Model

Elhefnawy M, Noor Harun S, Leykhim T, Tangiisuran B, Zainal H, Looi I, et al.

Cureus, 2023 Dec;15(12):e50794.
PMID: 38239519 DOI: 10.7759/cureus.50794

Objectives Compared with the first stroke, neurological impairment caused by stroke recurrence is more serious, more difficult to treat, and has a higher mortality rate, especially among ischemic stroke (IS) patients with diabetes mellitus (DM). Although there are established correlations between factors and IS recurrence, there were some issues regarding the naive hazard of IS recurrence with no risk factor influence, and how does the baseline hazard differ among patients with DM and non-DM? To answer all these questions, two time-to-event (TTE) models of recurrent IS after the index IS were developed among IS patients with DM and non-DM. Method A total of 7697 patients with an index IS attack were extracted from the Malaysian Registry of Neurology and stratified according to DM status. Several parametric survival models were evaluated using nonlinear mixed-effect modeling software (NONMEM 7.5). The final model was determined according to the lowest objective function value, graphical evaluation, numerical diagnostics, and clinical plausibility. Additionally, the final model was validated internally and temporally using Kaplan-Meier visual predictive checks (KM-VPCs). Results One hundred ninety-five (5.82%) of 3493 DM patients and 138 (3.28%) of 4204 non-DM patients developed a recurrent IS with a maximum follow-up of 7.37 years. Gompertz's model best fitted the data. With no influence on risk factors, the index IS attack was predicted to contribute to the hazard of recurrent IS by 0.356 and 0.253 within the first six months after the index IS among patients with and without DM, respectively. Even after six months of index IS, the recurrent IS baseline hazard was not equal to zero among both groups (0.0023, 0.0018). Moreover, after incorporating the time and risk factors, the recurrent hazards increased exponentially during the first three years after the index IS followed by an exponential reduction afterward. The recurrent IS predictors among DM patients were ischemic heart disease (IHD) and hyperlipidemia (HPLD). IHD and HPLD increased the hazard of recurrent IS by 2.40 and 1.88 times, respectively, compared to those without IHD and HPLD before index IS (HR, 2.40 (1.79-3.20)), and (HR, 1.88 (1.44-2.45)) respectively. Conclusion The baseline hazard was the highest during the first six months after the index IS. Moreover, receiving medications for secondary prevention failed to demonstrate a significant association with reducing IS recurrence among IS patients with DM, suggesting a need for more intensive patient screening and new strategies for secondary prevention among IS patients with DM.
Fulltext Heatwaves in Peninsular Malaysia: a spatiotemporal analysis

Muhammad MKI, Hamed MM, Harun S, Sa'adi Z, Sammen SS, Al-Ansari N, et al.

Sci Rep, 2024 Feb 21;14(1):4255.
PMID: 38383678 DOI: 10.1038/s41598-024-53960-x

One of the direct and unavoidable consequences of global warming-induced rising temperatures is the more recurrent and severe heatwaves. In recent years, even countries like Malaysia seldom had some mild to severe heatwaves. As the Earth's average temperature continues to rise, heatwaves in Malaysia will undoubtedly worsen in the future. It is crucial to characterize and monitor heat events across time to effectively prepare for and implement preventative actions to lessen heatwave's social and economic effects. This study proposes heatwave-related indices that take into account both daily maximum (Tmax) and daily lowest (Tmin) temperatures to evaluate shifts in heatwave features in Peninsular Malaysia (PM). Daily ERA5 temperature dataset with a geographical resolution of 0.25° for the period 1950-2022 was used to analyze the changes in the frequency and severity of heat waves across PM, while the LandScan gridded population data from 2000 to 2020 was used to calculate the affected population to the heatwaves. This study also utilized Sen's slope for trend analysis of heatwave characteristics, which separates multi-decadal oscillatory fluctuations from secular trends. The findings demonstrated that the geographical pattern of heatwaves in PM could be reconstructed if daily Tmax is more than the 95th percentile for 3 or more days. The data indicated that the southwest was more prone to severe heatwaves. The PM experienced more heatwaves after 2000 than before. Overall, the heatwave-affected area in PM has increased by 8.98 km2/decade and its duration by 1.54 days/decade. The highest population affected was located in the central south region of PM. These findings provide valuable insights into the heatwaves pattern and impact.
Mapping the influence of hydrocarbons mixture on molecular mechanisms, involved in breast and lung neoplasms: in silico toxicogenomic data-mining

Abu-Bakar A, Ismail M, Zulkifli MZI, Zaini NAS, Shukor NIA, Harun S, et al.

Genes Environ, 2024 Jul 09;46(1):15.
PMID: 38982523 DOI: 10.1186/s41021-024-00310-y

BACKGROUND: Exposure to chemical mixtures inherent in air pollution, has been shown to be associated with the risk of breast and lung cancers. However, studies on the molecular mechanisms of exposure to a mixture of these pollutants, such as hydrocarbons, in the development of breast and lung cancers are scarce. We utilized in silico toxicogenomic analysis to elucidate the molecular pathways linked to both cancers that are influenced by exposure to a mixture of selected hydrocarbons. The Comparative Toxicogenomics Database and Cytoscape software were used for data mining and visualization.
RESULTS: Twenty-five hydrocarbons, common in air pollution with carcinogenicity classification of 1 A/B or 2 (known/presumed or suspected human carcinogen), were divided into three groups: alkanes and alkenes, halogenated hydrocarbons, and polyaromatic hydrocarbons. The in silico data-mining revealed 87 and 44 genes commonly interacted with most of the investigated hydrocarbons are linked to breast and lung cancer, respectively. The dominant interactions among the common genes are co-expression, physical interaction, genetic interaction, co-localization, and interaction in shared protein domains. Among these genes, only 16 are common in the development of both cancers. Benzo(a)pyrene and tetrachlorodibenzodioxin interacted with all 16 genes. The molecular pathways potentially affected by the investigated hydrocarbons include aryl hydrocarbon receptor, chemical carcinogenesis, ferroptosis, fluid shear stress and atherosclerosis, interleukin 17 signaling pathway, lipid and atherosclerosis, NRF2 pathway, and oxidative stress response.
CONCLUSIONS: Within the inherent limitations of in silico toxicogenomics tools, we elucidated the molecular pathways associated with breast and lung cancer development potentially affected by hydrocarbons mixture. Our findings indicate adaptive responses to oxidative stress and inflammatory damages are instrumental in the development of both cancers. Additionally, ferroptosis-a non-apoptotic programmed cell death driven by lipid peroxidation and iron homeostasis-was identified as a new player in these responses. Finally, AHR potential involvement in modulating IL-8, a critical gene that mediates breast cancer invasion and metastasis to the lungs, was also highlighted. A deeper understanding of the interplay between genes associated with these pathways, and other survival signaling pathways identified in this study, will provide invaluable knowledge in assessing the risk of inhalation exposure to hydrocarbons mixture. The findings offer insights into future in vivo and in vitro laboratory investigations that focus on inhalation exposure to the hydrocarbons mixture.
Mode-locked ytterbium-doped fiber laser with zinc phthalocyanine thin film saturable absorber

Soboh RSM, Al-Masoodi AHH, Erman FNA, Al-Masoodi AHH, Nizamani B, Arof H, et al.

Front Optoelectron, 2022 Jun 13;15(1):28.
PMID: 36637608 DOI: 10.1007/s12200-022-00027-2

A stable mode-locked laser was demonstrated using a newly developed zinc phthalocyanine (ZnPc) thin film as passive saturable absorber (SA) in ytterbium-doped fiber laser (YDFL). The ZnPc thin film was obtained using a casting method and then inserted between the two fiber ferrules of a YDFL ring cavity to generate mode-locked pulses. The resulting pulsed laser operated at a wavelength of 1034.5 nm having a repetition rate of 3.3 MHz. At pump power of 277 mW, the maximum output power and pulse energy are achieved at 4.92 mW and 1.36 nJ, respectively. ZnPc has a high chemical and photochemical stability, and its significance for use as a potential SA in a mode-locked laser is reported in this work.