Biology subjects

Zakaria, R.

Publications and source records attributed to Zakaria, R..

5 recordsLinked to original sources

bioRxiv2026

Validated LC-MS/MS quantification of kynurenine pathway metabolites and pathway-balance ratios in brain tissue and microglial culture supernatant: application to neonatal stroke

Kynurenine pathway (KP) metabolite imbalance is implicated in perinatal brain injury, and KP metabolites are measured in human plasma and cerebrospinal fluid as markers of neuroinflammation. Methods validated in neonatal brain tissue or glial culture supernatant to the same standard are scarce, limiting comparisons across preclinical and clinical measurements. We optimised LC-MS/MS detection of tryptophan (TRYP), kynurenine (KYN), kynurenic acid (KYNA), 3-hydroxykynurenine (3-HK), 3-hydroxyanthranilic acid (3-HAA), quinolinic acid (QA), anthranilic acid and picolinic acid after protein precipitation and Enhanced Matrix Removal-Lipid clean-up, validated it against Clinical and Laboratory Standards Institute (CLSI) acceptance criteria in brain tissue homogenate and cell culture supernatant, and applied it to a rat model of neonatal stroke and immune-activated BV2 microglia, reporting KYN/TRYP, KYNA/KYN, 3-HK/3-HAA and QA/KYNA ratios. The lower limit of quantification was 6.53-34.17 nM; imprecision was 0.57-11.47%, accuracy was 84.9-108.3%, recovery was 83.2-112.3%, and matrix effect was 87.8-108.8%, with linear calibration (R2 > 0.99) over 6.5-2000 nM. KYN/TRYP and QA/KYNA ratios were higher in the stroke hemisphere than in control brain at 1, 7 and 14 days (p<0.001), and KYNA/KYN was lower; lipopolysaccharide- and cytokine-stimulated BV2 microglia showed the same change in all four ratios (p<0.01). The assay quantifies eight KP metabolites and four pathway-balance ratios in brain tissue and microglial supernatant within clinical acceptance limits, allowing direct comparison with KP ratios reported in human plasma and cerebrospinal fluid. Changes in these ratios after neonatal stroke identify KYN/TRYP and QA/KYNA as candidate targets for neonatal biofluid studies.

biochemistry↗

bioRxiv2022

Impact of genus (Geotrigona, Melipona, Scaptotrigona) in the 1H-NMR organic profile and authenticity test of honey processed in cerumen pots by stingless bees in Ecuador

The biodiversity of Ecuadorian stingless bees is almost 200 species. Traditional pot-honey harvest in Ecuador is mostly done from nests of the three genera selected here Geotrigona Moure, 1942, Melipona, Illiger, 1806 and Scaptotrigona, Moure 1943. The 20 pot-honey samples collected from cerumen pots and three ethnic honeys "abeja de tierra", "bermejo", and "cushillomishki" were analyzed for qualitative and quantitative 1H-NMR honey profiling and for the Honey Authenticity Test by Interphase Emulsion (HATIE). Extensive data of targeted organic compounds (41 parameters) was identified, quantified and described. The three honey types were compared by ANOVA. Amino acids, ethanol, hydroxymethylfurfural, aliphatic organic acids, sugars, and markers of botanical or entomological origin. The number of phases observed with the HATIE was one in Scaptotrigona and three in Geotrigona and Melipona honeys. Acetic acid (19.60 {+/-} 1.45 g/kg) and lactic acid (24.30 {+/-} 1.65 g/kg) were particularly high in Geotrigona honey (in contrast to 1.3 g/kg acetic acid and 1.6 g/kg lactic acid in Melipona and Scaptotrigona), with the lowest fructose + glucose (18.39 {+/-} 1.68) g/100g honey compared to Melipona (52.87 {+/-} 1.75) and Scaptotrigona (52.17 {+/-} 0.60). Three local honeys were tested using PCA (Principal Component Analysis), two were assigned with a correct declared bee origin, but "bermejo" was not a Melipona and grouped with the Scaptotrigona cluster. However, after HCA (Hierarchical Cluster Analysis), the three kinds of honey were positioned in the Melipona-Scaptotrigona cluster. This research supports the targeted NMR-based profiling in pot-honey metabolomics approach for multi-parameter visualization of organic compounds, descriptive and pertained multivariate statistics (Hierarchical Cluster Analysis HCA, and Principal Component Analysis PCA) to discriminate the stingless bee genus in a set of Geotrigona, Melipona and Scaptotrigona honey types. The NMR characterization of Ecuadorian honey produced by stingless bees is a contribution to the needed regulatory norms. A final note on searching stingless bee markers in pot-honey metabolites that may become nutritional trait candidates for phylogeny. Scaptotrigona honey revealed biosurfactant activity in the HATIE, originating a fingerprint Honey Biosurfactant Test (HBT) for the genus in this set of pot-honeys.

biochemistry↗

bioRxiv2019

Cryopreservation of Rosa hybrida cv. Helmut Schmidt by PVS2 vitrification method using in vitro fragmented explants (IFEs)

This is the first report on cryopreservation via PVS2 vitrification method on roses using in vitro fragmented explants (IFEs) as the starting material. The aim of this study is to optimize the efficient plant recovery and regeneration system for cryopreservation of Rosa hybrida cv. Helmut Schmidt using IFEs. Some important parameters have been optimized in this study are the effect of ascorbic acid (0.3 mM) examined separately and in combination at all steps in cryopreservation procedure (preculture, loading, unloading and growth recovery), loading type, loading duration, and PVS2 duration. The highest growth recovery of 43.33% was obtained when 3-4 mm size IFEs precultured on 0.25 M sucrose media supplemented with full-strength MS for one (1) day, followed by loading treatment supplemented with 1.5 M glycerol + 0.4 M sucrose + 5% DMSO + 0.3 mM ascorbic acid for 20 minutes, dehydration with PVS2 solution for 30 minutes and then treated with unloading solution supplemented with 1.2 M sucrose + 0.3 mM ascorbic acid for 20 minutes. This finding implies that long-term storage of Rosa Hybrida cv. Helmut Schmidt by PVS2 vitrification method was successful with essential biomolecules.

plant biology↗

bioRxiv2018

Measuring Orangutan nest structure using Unmanned Aerial Vehicle (UAV) and ImageJ

The nest is one of the crucial elements in orangutan daily activities. Previously, most of the nest structure studies were done manually by estimating measurement directly from visual observation. However, using the latest unmanned aerial vehicle (UAV) technology, we can reduce the workforce, time and energy while simultaneously ensuring the safety of the researcher conducting nest structure analysis. We recorded 49 pictures of orangutan nests at Sepilok Orangutan Rehabilitation Centre (SORC) using UAV (DJI Phantom 3 Quadcopter). The nest structure (length, depth, and width) was digitally measured by using ImageJ. Most of the nests were built at a strong, stable, and comfortable position at the top of the tree. Most orangutans chose Eusideroxylon zwageri to build nest compared to other tree species because of the strong and durable wood characteristic which would create a sturdy, strong and comfortable nest. We propose the use of drone with digital image analysis could provide a more accurate, less time consuming and safe method for studying orangutan nest structure.

zoology↗

bioRxiv2017

An integrated genomic analysis of anaplastic meningioma identifies prognostic molecular signatures

Anaplastic meningioma is a rare and aggressive brain tumor characterised by intractable recurrences and dismal outcomes. Here, we present an integrated analysis of the whole genome, transcriptome and methylation profiles of primary and recurrent anaplastic meningioma. A key finding was the delineation of two distinct molecular subgroups that were associated with diametrically opposed survival outcomes. Relative to lower grade meningiomas, anaplastic tumors harbored frequent driver mutations in SWI/SNF complex genes, which were confined to the poor prognosis subgroup. Our analyses discern two biologically distinct variants of anaplastic meningioma with potential prognostic and therapeutic significance.

genomics↗