Burkholderia sp. IMCC1007 is a gram-negative, aerobic bacterium affiliated with class Betaproteobacteria, which was successfully isolated from maize rhizospheric soil sample in UTM research plot, Pagoh, Malaysia by using enrichment method. Strain IMCC1007 utilized 50 mgL-1 fusaric acid as its carbon source and degraded it completely within 14 h. Genome sequencing was performed using Illumina NovaSeq platform. The assembled genome was annotated using RAST (Rapid Annotation Subsystem Technology) server. The genome size was approximately 8,568,405 base pairs (bp) in 147 contigs with a G+C content of 66.04%. The genome includes 8,733 coding sequences and 68 RNAs. The genome sequence has been deposited at GenBank with the accession number of JAPVQY000000000. In the pairwise genome-to-genome comparisons, the strain IMCC1007 had an average nucleotide identity (ANI) of 91.9% and digital DNA-DNA hybridization (dDDH) value of 55.2% with Burkholderia anthina DSM 16086T respectively. Interestingly, fusaric acid resistance gene (fusC) and nicABCDFXT gene clusters (hydroxylation of pyridine compound) were found in the genome. Additionally, preliminary genome annotation analysis of strain IMCC1007 identified tryptophan halogenase (prnA) gene responsible for antifungal pyrrolnitrin biosynthesis. This dataset herein provides further insights into the fusaric acid degradation mechanism of the genus Burkholderia.
Hevea brasiliensis is exploited for its latex production, and it is the only viable source of natural rubber worldwide. The demand for natural rubber remains high due its high-quality properties, which synthetic rubber cannot compete with. In this paper, we present transcriptomic data and analysis of three H. brasiliensis clones using tissue from latex and bark tissues collected from 10-year-old plant. The combined, assembled transcripts were mapped onto an H. brasiliensis draft genome. Gene ontology analysis showed that the most abundant transcripts related to molecular functions, followed by biological processes and cellular components. Simple sequence repeats (SSR) and single nucleotide polymorphisms (SNP) were also identified, and these can be useful for selection of parental and new clones in a breeding program. Data generated by RNA sequencing were deposited in the NCBI public repository under accession number PRJNA629890.
Proteome data was obtained from the fruit mesocarps of the two oil palm species, namely, the African Elaeis guineensis (commercial tenera or commonly known as D x P and MPOB-Nigerian tenera) and the South American Elaeis oleifera. Total proteins were extracted from randomly selected fruitlets and subjected to proteomics characterisation by means of liquid chromatography mass spectrometry. Number of proteins identified, the grouping of the biological replicates from five developmental weeks after anthesis, and the localisation of gene corresponded to the detected proteins on the oil palm chromosomes, were presented. A total of 4,116, 4,210 and 4,081 proteins were found in commercial tenera and MPOB Nigerian tenera for Elaeis guineensis; and Elaeis oleifera, respectively. Principal component analysis showed two distinct clusters that corresponded to Elaeis guineensis and Elaeis oleifera. Collectively, genes that corresponded to the identified proteins were found to be located in all 16 oil palm chromosomes. A total of 59 proteins from Elaeis guineensis and Elaeis oleifera were down-regulated for >5-fold change during the peak of lipid biosynthesis compared to the onset. The same comparative analysis revealed that 66 proteins were up-regulated for >5-fold change. About 60.0% of the observed proteins were involved in catalytic activity while 28.5% were associated with redox reaction. Based on same datasets, the tricarboxylic acid cycle and 5-hydroxytryptamine degradation pathways were found to be enriched the most (>36-fold change). These data can be used to support the oil palm gene model validation and lipid metabolism research, particularly in the areas of oil yield and quality. The tabulated protein lists of identified proteins and their expression changes from these varieties were provided as supplementary files. Raw MSF and mzid files for all the oil palm species were deposited in the ProteomeXchange (PXD017436).
Heavy metal pollution in an aquatic environment has become of the main concern to the world due to their non-biodegradable properties, toxicity, persistence, and their ability to adsorb into food chains. With rapid industrialization and development nowadays, heavy metals are introduced continuously into the estuaries and coastal region through rivers, runoff, and land-based point sources. These heavy metals may degrade the aquatic environment and harm the living organisms and toward human indirection through secondary contact. The dataset provided is to give an overview of the spatial and temporal distribution of the heavy metals concentration in Merang River surficial sediment collected from September 2017 to July 2018, subsequently every two months dataset. Sediment samples were collected in 44 stations along the river and 20 stations in the coastal area, which total up to 64 stations. Teflon Bomb closed digestion method with mixed acid was used to digest the sediments. The concentration of heavy metals in the sediment were analysed by using Inductively Coupled Plasma Mass Spectrometer (ICP-MS). The spatial distribution of heavy metals shows the effect of monsoon and wet and dry seasons in the sampling area. Thus, this dataset reveals six months of information on natural and anthropogenic sources intrusion at the Merang River and may also help in monitoring the pollution in the area.
The data presented here is the liquid chromatography and mass spectrometry (LC-MS) profile of phytochemical compounds in the aqueous extract of Syzygium polyanthum (Wight) Walp. leaves. This plant is consumed raw and sometimes added to local dishes of people in Southeast Asia countries. Most importantly, it has ethnomedicinal values mainly in treating diabetes and hypertension, and at the same time, this plant has anti-microbial, anti-oxidant, anti-cancer, and anti-tumor properties [1]. There are chemical composition variations reported between the same species of different geographical locations, which eventually affect the plant's therapeutic potential [2], [3]. This dataset represents the identified compounds for S. polyanthum (Wight) Walp. leaves, a variant collected from Kuantan, a city located in the Pahang state on the East Coast of Peninsular Malaysia. The leaves were then dried in an open-air at room temperature for three weeks, ground, and then macerated in water inside a bath-sonicator, freeze-dried, and then run using LCMS. The LCMS was run using the ultra-performance liquid chromatography equipped with an electrospray time-of-flight mass spectrometer detector, operated in a negative-ion mode. The mass spectral features from samples raw data were matched with Traditional Medicine (en) and Waters Screening libraries in the Waters UNIFI™ Scientific Information System software version 1.7 (Waters, USA) for compounds identification.
A diesel engine has been a desirable machine due to its better fuel efficiency, reliability, and higher power output. It is widely used in transportations, locomotives, power generation, and industrial applications. The combustion of diesel fuel emits harmful emissions such as unburned hydrocarbons (HC), particulate matter (PM), nitrogen oxides (NOx), and carbon monoxides (CO). This article presents data on the efficiency, combustion, and emission of a 4-stroke diesel engine. The engine is a 6.8 L turbocharged 6-cylinder Tier II diesel engine fitted with a common rail injection system. The test was carried out at the Powerhouse Energy Campus, Colorado State University Engines and Energy Conversion facility. The ISO Standard 8178:4 Cycle D2 cycle was adopted for this study consists of five test runs at 1800 rpm. During the testing, CO, carbon dioxide (CO2), oxygen (O2), NOx, PM, unburned HC as a total HC (THC), methane (CH4), formaldehyde (CH2O), and volatile organic compound (VOC) emissions were measured. At the same time, the data acquisition system recorded the combustion data. The engine's performance is characterized by the brake specific fuel combustion (BSFC) and thermal efficiency. A dataset of correlations among the parameters was also presented in this article.
The Labroides dimidiatus is known as the "doctor fish" because of its role in removing parasites and infectious pathogens from the body of other fishes. This important role played both in wild and captive conditions could represent a novel form of parasitic transmission process mediated by the cleaning activity of the fish. Yet, there is a paucity of data on the microflora associated with this fish which is important for tracking disease infection and generally monitoring the health status of the fish. This article, therefore, represents the first dataset for the microbiota composition of wild and captive L. dimidiatus. Wild fish samples and carriage water were gotten in Terengganu Malaysia around the corals of the Karah Island. The captive sample, however, was obtained from well-known ornamental fish suppliers in Terengganu Malaysia. Thereafter, bacteria present on the skin, in the stomach and the aquarium water were enumerated using culture-independent approaches and Next Generation Sequencing (NGS) technology. Data obtained from the three metagenomic libraries using NGS analysis gave 1,426,740 amplicon sequence reads which are composed of 508 operational taxonomic units (OTUs) for wild samples and 3,238,564 valid reads and 828 OTUs for captive samples. All sequence reads were deposited in the GeneBank (Accession numbers SAMN14260247, SAMN14260248, SAMN14260249, SAMN14260250, SAMN14260251, and SAMN14260252). The dataset presented is associated with the research article "16S rDNA-Based Metagenomic Analysis of Microbial Communities Associated with Wild Labroides dimidiatus From Karah Island, Terengganu, Malaysia" [1]. The microbiota data presented in this article can be used to monitor the health and wellbeing of the ornamental fish, especially under captivity, hence preventing possible cross-infection.
Perceived Benefits and Risks: A survey data set towards Wolbachia-infected Aedes Mosquitoes in the Klang Valley, Malaysia. Introduction: The paper presents data collected using measures of perceived benefits, perceived risks, trust in key players, attitude towards nature versus material, attitude towards technology, religiosity, and attitude towards the Wolbachia-infected Aedes mosquitoes (WiAM) technique. The validated questionnaires were used to randomly survey targeted stakeholders in the Klang Valley, Malaysia, who had been asked to voluntarily participate in face-to-face interviews. Completed questionnaires were received from 399 respondents (adults above 18 years old) and comprised two stakeholder groups: scientists (n = 202), and the public (n = 197). The detailed findings serve numerous opportunities to examine the social acceptance of Wolbachia-infected Aedes mosquitoes, to ensure the development of policy and action plans, and to encourage further study by other researchers interested in the measures and data presented.
Research on Agarwood Essential Oils (AEO) has undergone dynamic evolution, propelled by its diverse applications in industries such as perfumery, pharmaceuticals, and alternative medicine. The aromatic richness and therapeutic potential of these essential oils have sparked a surge in research interest. Despite extensive exploration, there is a need for a comprehensive analysis of trends, patterns, and the impact of AEO research to provide insights for future studies and applications.This work presents a meticulously curated dataset encompassing the last five years of Agarwood Essential Oil (AEO) research trends. Sourced from two reputable scholarly databases, namely Web of Science and Scopus, following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) protocol, analyzing the data using Biblioshiny, and spanning the period from 2019 to 2023, the dataset is designed to facilitate a comprehensive understanding of the evolving landscape of AEO studies. It covers a wide array of parameters, including authorship, subject areas, citations, source titles, wordcloud, and keywords. This dataset is made available to researchers, institutions, and decision-makers to provide insights into the academic debates on agarwood oil studies, allowing for a nuanced understanding of the progression of scholarly endeavors within the field. The dataset aims to serve as a valuable resource for researchers, policymakers, and industry stakeholders interested in the multifaceted applications of essential oils. The structured and comprehensive nature of the dataset makes it a valuable asset for exploring historical trends, identifying key contributors, and fostering collaborative initiatives within the AEO research domain.
The growth performance and survival rates of juvenile striped catfish, Pangasianodon hypophthalmus, reared at various levels of pH and temperature were described in this article. Two rearing trials were conducted separately for pH and temperature where both trials lasted for 35 days. One hundred and twenty juveniles (1.5 ± 0.23 g) were randomly stocked into 12 rectangle glass aquariums (n = 10 fish/tank; three replicates per treatment) with 100 L of water for each trial. The treatment consisted of four different pH level (7.5, 8.0, 8.5 and 9.0) and four different temperature level (26 °C, 28 °C, 30 °C and 32 °C). The survival of fish was counted at the end of experiments, and the weight of the juvenile was measured once a week. The quantification of feed intake was determined through the measurement of the residual weight of the feeds after the feeding process. Upon the conclusion of the experiment, the data pertaining to weight and feed intake were utilized to calculate the specific growth rate (SGR) and food conversion ratio (FCR) as indicators of growth performance. Additionally, the number of live fish was employed to ascertain the survival rate. The data obtained from the calculation of SGR, FCR and survival rate were next subjected to a normality test, one-way analysis of variance (ANOVA), and a Tukey post-hoc test. The information in this article will help in the business, experimental, and personal usage for P. hypophthalmus juveniles rearing process.
In this dataset, we distinguish 15 accessions of Garcinia mangostana from Peninsular Malaysia using Fourier transform-infrared spectroscopy coupled with chemometric analysis. We found that the position and intensity of characteristic peaks at 3600-3100 cm(-) (1) in IR spectra allowed discrimination of G. mangostana from different locations. Further principal component analysis (PCA) of all the accessions suggests the two main clusters were formed: samples from Johor, Melaka, and Negeri Sembilan (South) were clustered together in one group while samples from Perak, Kedah, Penang, Selangor, Kelantan, and Terengganu (North and East Coast) were in another clustered group.
Metabolic regulation is important during seed germination for the establishment of seedling. The germination strategy of mangosteen (Garcinia mangostana L.) seed is thought to be unique due to its recalcitrant characteristic (sensitive to coldness and drying). To investigate the metabolic changes during seed germination, we performed metabolomics analysis on germinating mangosteen seed sown after zero, one, three, five, seven and nine days. Sampled mangosteen seeds were subjected to methanol extraction prior analysis using Liquid Chromatography-Time of Flight-Mass Spectrometry (LC-TOF-MS). MS data were further analyzed using ProfileAnalysis (version 2.1). This is one of the earliest reports in metabolite identification and profiling of mangosteen seed at different germination stages. This data article refers to the article entitled "Metabolite profiling of mangosteen seed germination highlights metabolic changes related to carbon utilization and seed protection" (Mazlan et al., 2019) [1].
In this dataset, we present 15 Simple Sequence Repeat (SSR) markers with the motifs (AC)n, (GA)n, and (AC)n(AG)n using a ISSR-Suppression-PCR technique in order to discriminate Garcinia mangostana from diverse geographical origins in Peninsular Malaysia. A few loci showed differences between 3 and 6 bp in allele size, indicating that there are some polymorphisms between individuals correlating to the number of SSR repeats that may be useful for differentiate of genotypes. Collectively, these data show that the ISSR-Suppression-PCR is a valuable method to illustrate genetic variation of selected G. mangostana in Malaysia.
The carnivorous plants of genus Nepenthes produce unique pitchers containing secretory glands, which secrete proteins into the digestive fluid. We investigated protein profile in the pitcher fluid during the first three days of opening to understand carnivory trait of Nepenthes × ventrata. The proteome analysis of pitcher fluid from N. × ventrata was performed by label-free quantitative liquid chromatography mass spectrometry (nLC-MS/MSALL). Raw MS data have been deposited to the ProteomeXchange with identifier PXD007251. This dataset allows the identification and quantification of proteins from pitcher fluids to elucidate proteins involved in carnivory physiology of Nepenthes species.
In this dataset, we differentiate four different tissues of Cosmos caudatus Kunth (leaves, flowers, stem and root) obtained from UKM Bangi plot, based on Fourier transform-infrared spectroscopy. Different tissues of C. caudatus demonstrated the position and intensity of characteristic peaks at 4000-450 cm-1. Principal component analysis (PCA) shows three main groups were formed. The samples from leaves and flowers were found to be clustered together in one group, while the samples from stems and roots were clustered into two separate groups, respectively. This data provides an insight into the fingerprint identification and distribution of metabolites in the different organs of this species.
Garcinia mangostana L. (mangosteen) seed is recalcitrant, prone to low temperature and drying which limit its long-term storage. Therefore, it is imperative to understand the metabolic changes throughout its development, to shed some light into the recalcitrant nature of this seed. We performed metabolomics analysis on mangosteen seed at different stages of development; six, eight, ten, twelve and fourteen weeks after anthesis. Seed samples were subjected to methanol extraction prior analysis using liquid chromatography - mass spectrometry (LC-MS). The MS data acquired were analyzed using ProfileAnalysis (version 2.1). This data article refers to the article entitled "Metabolomics analysis of developing Garcinia mangostana seed reveals modulated levels of sugars, organic acids and phenylpropanoid compounds" (Mazlan et al., 2018) [1].
Proteomics is often hindered by the lack of protein sequence database particularly for non-model species such as Persicaria minor herbs. An integrative approach called proteomics informed by transcriptomics is possible [1], in which translated transcriptome sequence database is used as the protein sequence database. In this current study, the proteome profile were profiled using SWATH-MS technology complemented with documented transcriptome profiling [2], the first such report in this tropical herb. The plant was also elicited using a phytohormone, methyl jasmonate (MeJA) and protein changes were elucidated using label-free quantification of SWATH-MS to understand the role of such signal molecule in this herbal species. The mass spectrometry proteomics data was deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD005749. This data article refers to the article entitled "Proteomics (SWATH-MS)-informed by transcriptomics approach of Persicaria minor leaves upon methyl jasmonate elicitation" [3].
In light of the increasing importance digital economy, the significance of computational thinking has grown exponentially, becoming imperative in both workplace and academic settings such as universities. This article addresses the critical need to comprehend the factors influencing the acceptance of computational thinking. The dataset introduces an extensive questionnaire comprising five constructs and 25 items, rooted in the extended Technology Acceptance Model. Notably, the model incorporates facilitating conditions and subjective norm, providing a comprehensive framework for understanding acceptance. Data collection involved 132 undergraduate university students sampled through purposive sampling, specifically targeting courses with a focus on computational thinking. The resulting dataset serves as a valuable resource for future research, offering detailed insights into the factors determining the acceptance of technology in educational contexts beyond mere thinking skills. Given the scarcity of research on technology acceptance in developing nations, this dataset holds particular significance, serving as a foundation for potential cross-cultural comparisons. The dataset contributes to the field by presenting a robust acceptance model, explaining 74.2 per cent of the variance in behavioural intention, 60.2 per cent in perceived usefulness, and 56.1 per cent in perceived ease of use. This high explanatory power positions the dataset as a superior resource for replication, benchmarking, and broader applicability in diverse contexts, thereby enhancing the understanding of computational thinking acceptance across different populations and settings. This dataset stands among the pioneering efforts to assess the novel covariance-based structural equation model algorithm within SmartPLS 4, presenting a valuable resource for future research employing the same mechanism.
The data presented in this article were generated through the gas chromatography (GC) with a flame ionization detector (FID). The flaxseed oil was converted into fatty acid methyl ester (FAME) then used in the GC with FID and observe the retention time of different fatty acid present in the flaxseed oil. The observed retention time was compared with the standard fatty acid to confirm the specific fatty acid presence in the flaxseed oil. The part of the data is used in the article "Optimization of the process variable for biodiesel production by transesterification of flaxseed oil and produced biodiesel characterizations" Renewable Energy journal (Ahmad et al., 2019).
Fire debris is often recovered as part of a fire scene investigation to determine whether an ignitable liquid might be present which may be evidence of a deliberate fire. The analysis of fire debris produces chromatograms that a forensic chemist uses to determine whether or not an ignitable liquid may be present. Currently there are very few publicly available data sets that can be used for training and statistical modelling in this area. The data set in this paper has been prepared with these two applications in mind and covers a wide range of ignitable liquids available in the UK. We created a data set of 35 ignitable liquids including petrol (gasoline), light, medium and heavy petroleum distillates (i.e diesel) from several retailers. Each ignitable liquid was systematically evaporated to produce six additional samples. Each sample was repetitively analysed to provide an overall data set of 751 analytical outputs (including chromatograms). Each data sample is expressed in multiple formats and the metadata containing any data used in the production of the samples is included. The folder and file names are designed to avoid misplacements and to manipulate folders and files systematically using computer code.