Biological, Chemical, and Mathematical Sciences

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    Open Access
    The molecular investigation of Blood cockles (Anadara granosa) associated bacterial communities using 16S rRNA sequencing
    (2/12/2018) Zarkasi, Kamarul Zaman; Mardani Abdul Halim; Teh Faridah Nazari; Feizal Daud
    This article contains data on the bacterial communities and its diversity associated with Anadara granosa. The A. granosa samples were obtained from two major estuaries in Penang, Malaysia using a culture dependent and 16S rRNA Illumina sequencing approaches. A. granosa, a commercial blood cockles and popular seafoods, is fragile to the surrounding environments. Thus, our research focused to better understand the bacterial communities and it diversity in the A. granosa, as well as on the generation of a metagenomic library from A. granosa to further understanding on it diversity. The bacteria Vibrionaceae (34.1%) was predominant in the A. granosa from both environments followed by Enterobacteriaceae (33.3%) and Bacillaceae (16.75%). Vibrio sp., Klebsiella sp., and Bacillus subtilis were the most abundant species present. The data generated in this research is the first metagenomic examination of A. granosa and will provide as a baseline to understand the bacterial communities associated with A. granosa and its surrounding natural environments.
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    Open Access
    Data on antibiogram and resistance genes harboured by Salmonella strains and their Pulsed-field gel electrophoresis clusters
    (Elsevier, 2018-02-03) Li-Oon Chuah; Ahamed-Kamal Shamila Syuhada; Ismail Mohamad Suhaimi; Tajudin Farah Hanim; Gulam Rusul
    This article describes the Pulsed-field gel electrophoresis clustering of the predominant Salmonella strains (Salmonella ser. Albany, Salmonella ser. Brancaster, and Salmonella ser. Corvallis) isolated from poultry and processing environment in wet market and small-scale processing plant in Penang and Perlis, the northern states of Malaysia. Agar disk diffusion assay was performed to determine the phenotypic antibiotic resistance of these Salmonella strains. The most common antibiograms among the three predominant Salmonella serovars were reported. The presence of integrase genes and antibiotic resistance genes conferring to resistance against β-lactams, aminoglycosides, tetracyclines, quinolones, sulphonamides and chloramphenicol, was detected via PCR amplification.
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    Metagenomic 16S rDNA amplicon data of microbial diversity of guts of fully fed tropical bed bugs, Cimex hemipterus (F.) (Hemiptera: Cimicidae)
    (Elsevier, 2020-04-18) Li Lim; Abdul Hafiz Ab Majid
    The metagenomic datasets of the microbial DNA from tropical bed bugs (Cimex hemipterus) after feeding on human blood were presented. Next-generation sequencing of the community DNA was carried out on an Illumina Miseq platform and the raw fastq files were analyzed using QIIME (version 1.9.1). The metagenome of three samples comprised of 108,198 sequences representing 44,646,263 bps with a mean length of 412.63 bps. The sequence data is accessible at the NCBI SRA under the bioproject number PRJNA600667. Community analysis showed Proteobacteria was the most abundance (more than 99%) microbial community that present in the guts of fully fed tropical bed bugs.
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    Draft genome dataset of Tapinoma indicum (Forel) (Hymenoptera: Formicidae) in Penang Island, Malaysia
    (Elsevier, 2020-06-21) Li Yang Lim; Abdul Hafiz Ab Majid
    Tapinoma indicum is a household pest that is widely distributed in Asian countries. It is known as nuisance pest that causes annoyance and disturbance by constructing nests and foraging in building for food and water. This article documents the draft genome dataset of T. indicum collected in Penang Island, Malaysia using the next-generation sequencing known as the Illumina platform. This article presents the pair-end 150 bp genome dataset and the quality of the sequencing result. This dataset provides the information for further understanding of T. indicum in the molecular aspect and the opportunity to develop a novel method for pest control and regulation. The dataset is available under Sequence Read Archive (SRA) databases with the accession number SRR10848807.
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    Dataset of complete genome assembly and analysis of mycobacterium tuberculosis strain SIT745/EAI1-MYS
    (Elsevier, 2020-06-30) Mohammad Abdullah; Siti Suraiya; Suharni Mohamad; Azian Harun
    In this dataset, we report the genome assembly and data analysis of Mycobacterium tuberculosis strain SIT745/EAI1-MYS. Previously, this strain was isolated from a Malaysian patient with extra-pulmonary tuberculosis, and identification of this strain is done by spoligotype patterns with fifteen known Shared International Type (SITs). Further analysis showed that this strain has a remarkable phylogeographical specificity for Malaysia. Based on the National Center for Biotechnology Information (NCBI) nucleotide database information, the complete genome consists of 150 contigs with various sequence lengths and was not assembled. In this assembly, the aforementioned contigs along with reference sequence from Mycobacterium tuberculosis strain H37Rv and Mycobacterium bovis strain AF2122/97 was used for gap closures, were assembled into a single circular chromosome length of approximately 4.42 Mega bases (Mb) with an average GC content of 65.6%. The single circular chromosome was shown to contain 4,009 protein-coding sequences, 3 ribosomal RNAs, 45 transfer RNAs, and 12 superclasses distributed with 277 subsystems which constitute nearly 1900 genes, respectively. The genome information will provide fundamental knowledge of this organism as well as insight for understanding genomic and proteomic profiling, phylogenetic relationship.
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    16S rRNA metagenomic data of microbial diversity of Pheidole decarinata Santschi (Hymenoptera: Formicidae) workers
    (Elsevier, 2020-07-17) Mohammed Ahmed Ashigar; Abdul Hafiz Ab Majid
    Metagenomic datasets of the microbial DNA of workers of a Pheidole decarinata Santschi (Hymenoptera: Formicidae) around houses with three replicates were presented. Next-generation sequencing of the microbial DNA was performed on an Illumina Miseq platform. QIIME (version 1.9.1) was used to analyze the raw fastq files. Metagenome of the three (3) samples consist of 333,708 sequences representing 137,359,149 bps with an average length of 413.67 bps. The sequence data is available at the NCBI SRA with the bioproject number PRJNA632430. Community analysis revealed Proteobacteria was the predominant (84.77%) microbial community present in the microbial DNA of workers of the P. decarinata.
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    Transcriptome dataset from bark and latex tissues of three Hevea brasiliensis clones
    (Elsevier, 2020-08-17) Mohd Fahmi Abu Bakar; Urwashi Kamerkar; Siti Nurfazilah Abdul Rahman; Muhd Khairul Luqman Muhd Sakaff; Ahmad Sofiman Othman
    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.
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    Data analysis of molecular dynamics simulation trajectories of β-sitosterol, sonidegib and cholesterol in smoothened protein with the CHARMM36 force field
    (Elsevier, 2020-09-29) Mohammad Tasyriq Che Omar
    Inactivation of smoothened protein (SMO) by the antagonists in SHH-driven cancer types is essential for inhibition of cancer progression. This article presents molecular dynamics (MD) trajectories of water solution of three protein-ligand complexes smoothened-β-sitosterol (SMO-BST), smoothened-sonidegib (SMO-SNG) and smoothened-cholesterol (SMO-CLR) using CHARMM36 and SPC/E water model combination. Additionally, the work presents the topologies and trajectories of GROMACS files that were employed to analyse the protein-ligand interaction types (PyContact) and binding energy calculation (g_mmpbsa). The data demonstrated that equilibrated models of SMO-SNG and SMO-CLR complexes showed crucial residues that almost similar for interaction and contribution energy as previously reported in laboratory setup (in vitro). Initial simulations confirmed the role of ARG451 and TRP535 in the dynamic regulation of SMO. These data then were used as a reference for understanding the molecular dynamics of SMO-BST complex and thus predicted its mechanism of action.
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    Data on RNA-seq analysis of Drosophila melanogaster during ageing
    (Elsevier, 2021-09-22) Morteza Bajgiran; Azali Azlan; Shaharum Shamsuddin; Ghows Azzam; Mardani Abdul Halim
    Ageing is defined as gradual decline of physiological, cellular and molecular state of an organism with time. The age-associated cell dysfunctions usually cause chronic diseases such as diabetes, cancers and other age-related diseases. Many of the genes and pathways involved in ageing are conserved in different species. These genes and pathways have been categorised into nine cellular and molecular hallmarks, namely, genomic instability, telomere attrition, loss of proteostasis, mitochondrial dysfunction, epigenetic alterations, deregulated nutrient sensing, stem cell exhaustion, cellular senescence and altered intercellular communication. Despite countless studies on ageing, the molecular mechanism of ageing is poorly understood. Here, we performed genome wide transcriptome mapping of ageing process in D. melanogaster. In which, transcriptomic analysis conducted on the 1 day and 60 days flies. Illumina Hiseq platform were used to generate raw data. Afterwards, further analysis including differential expression analysis, GO classification and KEGG pathway enrichment analysis were performed. The raw data were uploaded to SRA database and the BioProject ID is PRJNA718442. These data provide the basis for future research in order to discover the genes and pathways involved in ageing.
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    Phosphorylation of human interferon regulatory factor 9
    (University of California, San Diego, 2022-01-01) Siew Kit Ng
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    Protein profiles Insecticide resistant Ae. aegypti
    (University of California, San Diego, 2022-01-01) Nurulhasanah Othman
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    Complete chloroplast genome data for Cryptocoryne elliptica (Araceae) from Peninsular Malaysia
    (Elsevier, 2022-03-23) Nurul Shakina Mohd Talkah; Suwidji Wongso; Ahmad Sofiman Othman
    The aquatic plant genus Cryptocoryne, a popular plant genus in the aquarium industry, is made up of more than 50 described species and some 15 naturally occurring named and unnamed interspecific hybrids. Cryptocoryne elliptica has a restricted distribution in the north part of Peninsular Malaysia. Destruction of its natural habitats for various human activities has led to a decline in numbers. Here, we report the complete chloroplast genome of C. elliptica and establish a molecular dataset for a maternally inherited genome. Here, we utilized an Illumina NovaSeq 6000 protocol to sequence the partial genome of C. elliptica and used bioinformatic tools to reconstruct the chloroplast genome in de novo mode. The assembled chloroplast genome is a circular DNA molecule 159,968 bp in length. The chloroplast genome has a quadripartite structure composed of a large single-copy region of 96,273 bp and a small single-copy (SSC) region of 15,205 bp, separated by a pair of inverted repeats (IRa and IRb), each of which is 24,245 bp. The chloroplast genome of C. elliptica encodes a total of 108 genes, comprising 74 protein-coding genes, 30 tRNA genes and 4 rRNA genes. In total, 204 SSR loci were identified, most of which were located within intergenic regions.
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    Transcriptome data for Hevea brasiliensis associated with powdery Mildew infection
    (Elsevier, 2022-05-11) Urwashi Kamerkar; Ahmad Sofiman Othman
    The Hevea brasiliensis or rubber tree belongs to the Euphorbiaceae family and is the only economically viable natural rubber source worldwide. The development of enhanced rubber tree clones with agronomically important traits is critical due to the growing demand for natural rubber around the world. Throughout the years, numerous disease-causing pathogens of H. brasiliensis have been identified and studied. One of the more prominent diseases affecting H. brasiliensis is powdery mildew caused by Oidium heveae. Oidium heveae primarily infects the newly formed leaves and buds of H. brasiliensis. Severe Oidium heveae infections cause extensive defoliation and yield loss. We performed RNA sequencing (RNA-Seq) for healthy and O. heveae-infected leaf tissues from RRIM 2025 and RRIM 929 rubber tree clones using the Illumina HiSeq 2000 platform. RNA-Seq generated 92007684 (12.9 GB) and 96070286 (13.5 GB) paired raw reads for healthy H. brasiliensis clones RRIM 2025 and RRIM 929 respectively. Similarly, RNA-Seq generated 93747858 (13.2 GB) and 93324564 (13.1 GB) paired raw reads for disease-infected H. brasiliensis clones RRIM 2025 and RRIM 929 respectively. The raw data were deposited in the NCBI under bio-project accession number PRJNA723431. The raw reads were quality trimmed and the reference-based transcriptome assembly was generated using the H. brasiliensis genome (ASM165405v1). The data were used to identify between the significantly differentially expressed genes of the healthy and diseased samples.
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    Genome sequence data of Bacillus sp. CCB-MMP212 isolated from Malaysian mangrove: A potential strain in arsenic resistance with ArsI, C•As lyase
    (Elsevier, 2022-09-13) Azami, Nor Azura; Lau, Nyok-Sean; Furusawa, Go
    Bacillus sp. CCB-MMP212 is a Gram-positive bacterium isolated from mangrove sediment in Matang Perak, Malaysia (4.85496°E, 100.73495°N). Genome sequencing was performed using the Oxford Nanopore and Illumina platforms. The assembled genome was annotated using the rapid annotation subsystem technology server (RAST) (rast.nmpdr.org). The genome size of the Bacillus sp. CCB-MMP212 was 6,151,644 base pairs (bp) with a G+C content of 34.75%. The genome includes 6,311 coding sequences and 58 RNAs. The sequence has been deposited at Genbank with the accession number of JALDQE000000000. Interestingly, an arsenic resistance (ars) operon consisted of arsenic resistance operon repressor (arsR), ACR3 family arsenite efflux transporter (arsB), and arsenate reductase (arsC) genes were found in the genome. In addition, the arsenic inducible gene (arsI), which encoded a dioxygenase with C•As lyase activity, was also found in the ars operon. The enzyme is crucial for the methylation of methylarsonous acid [MAs(III)] and trivalent roxarsone [Rox(III)]. This dataset reveals the genetic ability of this strain in arsenic resistance. To the best of our knowledge, the arsI encoding C•As lyase is rarely reported within the genus Bacillus. Therefore, the dataset presented in this manuscript provides further insight into the arsenic resistance mechanisms of the genus Bacillus.
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    A UK-based ground truth data set of GCMS analysed ignitable liquid samples — a template for making chromatographic data accessible as an open source data set
    (Elsevier, 2022-10-12) Miller, Jonathan; Puch-Solis, Roberto; Mat Desa, Wan Nur Syuhaila; Nic Daeid, Niamh
    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.
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    A transcriptomic (RNA-seq) analysis of Drosophila melanogaster adult testes overexpressing microRNA-2b-1
    (Elsevier, 2022-11-13) Sharvin Manickam; Shallinie Thangadurai; Azali Azlan; Zarina Amin; Ghows Azzam; Mardani Abdul Halim
    MicroRNAs (miRNAs) are short non-coding single-stranded RNAs with approximately 22 nucleotides in length that negatively regulate the mRNA translation of a target gene. MiR-2b-1 belongs to the largest miR-2 family in Drosophila melanogaster with 8 members and this miRNA family is conserved in invertebrates. miRNAs play key roles in gene regulation, cell proliferation, cell death, cell differentiation and cell developmental homeostasis in multicellular organisms. Its role in various human diseases is continuously being studied. miRNAs also found out to be crucial in maintaining stem cell niche in D. melanogaster gonads. We have identified that ectopic overexpression of miR-2b-1 of D. melanogaster causes testicular bulging (a tumour like phenotype) in 3-5 days old adult flies. Hence, we have performed a transcriptomic (RNA-seq) analysis to understand the role of miR-2b-1 in the development, maintenance, and differentiation of D. melanogaster adult testis stem cells. Data are available from GEO (accession number GSE211399).
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    Dataset for modified heated molecular dynamics for anti-human CXCR2 fragment variable vH-vL interface simulation
    (Mendeley, 2022-12-10) Muhamad Alif Che Nordin; Mohammad Tasyriq Che Omar
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    Metagenomic 16S rRNA amplicon data of gut microbial diversity in three species of subterranean termites (Coptotermes gestroi, Globitermes sulphureus and Macrotermes gilvus)
    (Elsevier, 2023-02-06) Qurratu'Aini Syasya Shamsuri; Abdul Hafiz Ab Majid
    In this paper, we present the metagenomic dataset of gut microbial DNA of the lower group of subterranean termites, i.e. Coptotermes gestroi, and the higher groups, i.e. Globitermes sulphureus and Macrotermes gilvus, in Penang, Malaysia. Two replicates of each species were sequenced using Next-Generation Sequencing (Illumina MiSeq) and analysed via QIIME2. The results returned with 210,248 sequences in C. gestroi, 224,972 in G. sulphureus, and 249,549 in M. gilvus. The sequence data were deposited in the NCBI Sequence Read Archive (SRA) under BioProject number of PRJNA896747. The community analysis showed that Bacteroidota is the most abundant phylum in C. gestroi and M. gilvus, while Spirochaetota is prevalent in G. sulphureus.