Displaying publications 1 - 20 of 23 in total

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  1. Adaptive Strategies of Bacillus thuringiensis Isolated from Acid Mine Drainage Site in Sabah, Malaysia
    Yik LY, Chin GJWL, Budiman C, Joseph CG, Musta B, Rodrigues KF
    Indian J Microbiol, 2018 Jun;58(2):165-173.
    PMID: 29651175 DOI: 10.1007/s12088-017-0701-1
    The adaptive process in bacteria is driven by specific genetic elements which regulate phenotypic characteristics such as tolerance to high metal ion concentrations and the secretion of protective biofilms. Extreme environments such as those associated with heavy metal pollution and extremes of acidity offer opportunities to study the adaptive mechanisms of microorganisms. This study focused on the genome analysis of Bacillus thuringiensis (Bt MCMY1), a gram positive rod shaped bacterium isolated from an acid mine drainage site in Sabah, Malaysia by using a combination of Single Molecule Real Time DNA Sequencing, Scanning Electron Microscopy (SEM) and Fourier Transform Infrared Spectroscopy (FTIR). The genome size of Bt MCMY1 was determined to be 5,458,152 bases which was encoded on a single chromosome. Analysis of the genome revealed genes associated with resistance to Copper, Mercury, Arsenic, Cobalt, Zinc, Cadmium and Aluminum. Evidence from SEM and FTIR indicated that the bacterial colonies form distinct films which bear the signature of polyhydroxyalkanoates (PHA) and this finding was supported by the genome data indicating the presence of a genetic pathway associated with the biosynthesis of PHAs. This is the first report of a Bacillus sp. isolated from an acid mine drainage site in Sabah, Malaysia and the genome sequence will provide insights into the manner in which B. thuringiensis adapts to acid mine drainage.
  2. Recombinant LipL32 Protein Developed Using a Synthetic Gene Detects Leptospira-specific Antibodies in Human Serum Samples
    Yaakob Y, Rodrigues KF, Opook F, William T, John DV
    Malays J Med Sci, 2017 Oct;24(5):44-51.
    PMID: 29386971 DOI: 10.21315/mjms2017.24.5.5
    Background: Synthetic biology is emerging as a viable alternative for the production of recombinant antigens for diagnostic applications. It offers a safe alternative for the synthesis of antigenic principles derived from organisms that pose a high biological risk.

    Methods: Here, we describe an enzyme-linked immunosorbent assay (ELISA) using the synthetic recombinant LipL32 (rLipL32) protein expressed in Escherichia coli for the detection of Leptospira-specific antibodies in human serum samples. The rLipL32-based ELISA was compared with a microscopic agglutination test (MAT), which is currently used as the gold standard for the diagnosis of leptospirosis.

    Results: Our results showed that all the MAT-positive serum samples were positive for Leptospira-specific IgG in an ELISA, while 65% (n = 13) of these samples were also positive for Leptospira-specific IgM. In the MAT-negative serum samples, 80% and 55% of the samples were detected as negative by an ELISA for Leptospira-specific IgM and IgG, respectively.

    Conclusion: An ELISA using the synthetic rLipL32 antigen was able to distinguish Leptospira-specific IgM (sensitivity 65% and specificity 80%) and IgG (sensitivity 100% and specificity 55%) in human serum samples and has the potential to serve as a rapid diagnostic test for leptospirosis.

  3. Fulltext Draft Genome Sequence of a Phytopathogenic Ganoderma sp. Strain That Causes Basal Stem Rot Disease on Oil Palm in Sabah, Malaysia
    Voo CLY, Yeo DET, Chong KP, Rodrigues KF
    Microbiol Resour Announc, 2020 Jan 02;9(1).
    PMID: 31896636 DOI: 10.1128/MRA.01240-19
    Basal stem rot (BSR) disease on Elaeis guineens is known to be caused by members of the pathogenic fungal genus Ganoderma, especially the species Ganoderma boninense This species affects oil palm plantation in Sabah, Malaysia. The genome sequence (52.28 Mbp) will add to the representation of this genus, especially in regard to BSR disease.
  4. Fulltext Comparative Transcriptome Profiling of Kappaphycus alvarezii (Rhodophyta, Solieriaceae) in Response to Light of Different Wavelengths and Carbon Dioxide Enrichment
    Thien VY, Rodrigues KF, Voo CLY, Wong CMVL, Yong WTL
    Plants (Basel), 2021 Jun 17;10(6).
    PMID: 34204578 DOI: 10.3390/plants10061236
    Rhodophyta (red algae) comprises over 6000 species, however, there have only been a few comparative transcriptomic studies due to their under-representation in genomic databases. Kappaphycus alvarezii, a Gigartinales algae, is a valuable source of carrageenan and is extensively cultivated in many countries. The majority of seaweed farming in Southeast Asia is done in intertidal zones under varying light (i.e., spectra and irradiance) and carbon dioxide (CO2) conditions, which affects the rate of photosynthesis. This study conducted transcriptome profiling to investigate the photosynthetic mechanisms in K. alvarezii exposed to different wavelengths of light (i.e., blue, green, and red light, in comparison to white light) and CO2 availability. We analyzed the responses of photosynthetic protein complexes to light and observed that light of different wavelengths regulates a similar set of photosynthetic apparatuses. Under CO2 enrichment, genes encoding C3 and C4 enzymes were found to be actively transcribed, suggesting the likely shift in the carbon metabolism pathway or the involvement of these genes in adaptive physiological processes. This study contributes to the understanding of the regulatory mechanisms of photosynthetic carbon metabolism in red algae and has implications for the culture and commercial production of these economically valuable macroalgae.
  5. Fulltext Cloning, Expression and Functional Characterization of a Novel α-Humulene Synthase, Responsible for the Formation of Sesquiterpene in Agarwood Originating from Aquilaria malaccensis
    Sundaraj Y, Abdullah H, Nezhad NG, Rodrigues KF, Sabri S, Baharum SN
    Curr Issues Mol Biol, 2023 Nov 10;45(11):8989-9002.
    PMID: 37998741 DOI: 10.3390/cimb45110564
    This study describes the cloning, expression and functional characterization of α-humulene synthase, responsible for the formation of the key aromatic compound α-humulene in agarwood originating from Aquilaria malaccensis. The partial sesquiterpene synthase gene from the transcriptome data of A. malaccensis was utilized for full-length gene isolation via a 3' RACE PCR. The complete gene, denoted as AmDG2, has an open reading frame (ORF) of 1671 bp and encodes for a polypeptide of 556 amino acids. In silico analysis of the protein highlighted several conserved motifs typically found in terpene synthases such as Asp-rich substrate binding (DDxxD), metal-binding residues (NSE/DTE), and cytoplasmic ER retention (RxR) motifs at their respective sites. The AmDG2 was successfully expressed in the E. coli:pET-28a(+) expression vector whereby an expected band of about 64 kDa in size was detected in the SDS-PAGE gel. In vitro enzyme assay using substrate farnesyl pyrophosphate (FPP) revealed that AmDG2 gave rise to two sesquiterpenes: α-humulene (major) and β-caryophyllene (minor), affirming its identity as α-humulene synthase. On the other hand, protein modeling performed using AlphaFold2 suggested that AmDG2 consists entirely of α-helices with short connecting loops and turns. Meanwhile, molecular docking via AutoDock Vina (Version 1.5.7) predicted that Asp307 and Asp311 act as catalytic residues in the α-humulene synthase. To our knowledge, this is the first comprehensive report on the cloning, expression and functional characterization of α-humulene synthase from agarwood originating from A. malaccensis species. These findings reveal a deeper understanding of the structure and functional properties of the α-humulene synthase and could be utilized for metabolic engineering work in the future.
  6. Fulltext A mini-review on the impact of COVID 19 on vital organs
    Shah MD, Sumeh AS, Sheraz M, Kavitha MS, Venmathi Maran BA, Rodrigues KF
    Biomed Pharmacother, 2021 Nov;143:112158.
    PMID: 34507116 DOI: 10.1016/j.biopha.2021.112158
    COVID-19 (Corona Virus Disease-2019) is an infectious disease caused by a novel coronavirus, known as the acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This is a highly contagious disease that has already affected more than 220 countries globally, infecting more than 212 million people and resulting in the death of over 4.4 million people. This review aims to highlight the pertinent documentary evidence upon the adverse effects of the SARS-CoV-2 infection on several vital human organs. SARS-CoV-2 primarily targets the lung tissue by causing diffuse alveolar damage and may result in Acute Respiratory Distress Syndrome (ARDS). SARS-CoV-2 infects the cell via cell surface receptor, angiotensin-converting enzyme 2 (ACE2). Besides lungs, SARS-CoV-2 critically damage tissues in other vital human organs such as the heart, kidney, liver, brain, and gastrointestinal tract. The effect on the heart includes muscle dysfunction (acute or protracted heart failure), myocarditis, and cell necrosis. Within hepatic tissue, it alters serum aminotransferase, total bilirubin, and gamma-glutamyl transferase levels. It contributes to acute kidney injury (AKI). Localized infection of the brain can lead to loss or attenuation of olfaction, muscular pain, headaches, encephalopathy, dizziness, dysgeusia, psychomotor disorders, and stroke; while the gastrointestinal symptoms include the disruption of the normal intestinal mucosa, leading to diarrhea and abdominal pain. This review encompassed a topical streak of systemic malfunctions caused by the SARS-CoV-2 infection. As the pandemic is still in progress, more studies will enrich our understanding and analysis of this disease.
  7. Fulltext Metagenomic data of bacterial community from different land uses at the river basin, Kelantan
    Rupert R, Lie GJCW, John DV, Annammala KV, Jani J, Rodrigues KF
    Data Brief, 2020 Dec;33:106351.
    PMID: 33072827 DOI: 10.1016/j.dib.2020.106351
    The data provided in the article includes the sequence of bacterial 16S rRNA gene from a high conservation value forest, logged forest, rubber plantation and oil palm plantation collected at Kelantan river basin. The logged forest area was previously notified as a flooding region. The total gDNA of bacterial community was amplified via polymerase chain reaction at V3-V4 regions using a pair of specific universal primer. Amplicons were sequenced on Illumina HiSeq paired-end platform to generate 250 bp paired-end raw reads. Several bioinformatics tools such as FLASH, QIIME and UPARSE were used to process the reads generated for OTU analysis. Meanwhile, R&D software was used to construct the taxonomy tree for all samples. Raw data files are available at the Sequence Read Archive (SRA), NCBI and data information can be found at the BioProject and BioSample, NCBI. The data shows the comparison of bacterial community between the natural forest and different land uses.
  8. Dataset of 16S ribosomal DNA sequences of bacteria isolated from marine red algae Kappaphycus alvarezii
    Rupert R, Rodrigues KF, Chong HLH, Yong WTL
    Data Brief, 2022 Feb;40:107784.
    PMID: 35028352 DOI: 10.1016/j.dib.2021.107784
    The data provided in the article contains bacterial community profiles present on the surface of red algae (Kappaphycus alvarezii) isolated directly after collection and after 30 days of cultivation in a closed circulation system. The explants of Kappaphycus alvarezii were cultivated in a laboratory setting under controlled growth conditions for 30 days in order to determine bacteria that could adapt to controlled culture conditions. Amplification and sequencing of bacterial 16S rDNA amplicon were performed on bacterial isolates associated with the seedlings. The 16S rDNA gene sequences were analyzed, trimmed, and assembled into contigs using DNA Baser Sequence Assembler (V5) software. Taxonomic identification for the assembled sequences was achieved using the online BLAST (blastn) algorithm, and the construction of a phylogenetic tree was performed using the MEGA7 software. The data reveals a distinct set of microbial variations between day one and day 30. The phylogenetic tree depicts four major clusters, Vibrio, Pseudoalteromonas, Alteromonas, and Bacterioplanes resident on the surface of the K. alvarezii. Comparison between these two bacterial groups provides evidence of the persistent marine bacteria that adapt to the long-term culture in closed circulation systems. Raw data files are available at the GenBank, NCBI database under the accession number of MZ570560 to MZ570580.
  9. Extensive sharing of mitochondrial COI and CYB haplotypes among reef-building staghorn corals (Acropora spp.) in Sabah, North Borneo
    Robert R, Rodrigues KF, Waheed Z, Kumar SV
    Mitochondrial DNA A DNA Mapp Seq Anal, 2019 01;30(1):16-23.
    PMID: 29521145 DOI: 10.1080/24701394.2018.1448080
    This study is aimed at establishing a baseline on the genetic diversity of the Acropora corals of Sabah, North Borneo based on variations in the partial COI and CYB nucleotide sequences. Comparison across 50 shallow-water Acropora morphospecies indicated that the low substitution rates in the two genes were due to negative selection and that rate heterogeneity between them was asymmetric. CYB appeared to have evolved faster than COI in the Acropora as indicated by differences in the rate of pairwise genetic distance, degrees of transition bias (Ts/Tv), synonymous-to-nonsynonymous rate ratio (dN/dS), and substitution patterns at the three codon positions. Despite the relatively high haplotype diversity (Hd), nucleotide diversity (π) of the haplotype datasets was low due to stringent purifying selection operating on the genes. Subsequently, we identified individual COI and CYB haplotypes that were each extensively shared across sympatrically and allopatrically distributed Indo-Pacific Acropora. These reciprocally common mtDNA types were suspected to be ancestral forms of the genes whereas other haplotypes have mostly evolved from autoapomorphic mutations which have not been fixed within the species even though they are selectively neutral. To our knowledge, this is the first report on DNA barcodes of Acropora species in North Borneo and this understanding will play an important role in the management and conservation of these important reef-building corals.
  10. Consolidated Checklist of Hard Corals of the Genus Acropora Oken, 1815 (Scleractinia: Acroporidae) in North Borneo, East Malaysia
    Robert R, Lee DJ, Rodrigues KF, Hussein MA, Waheed Z, Kumar SV
    Zootaxa, 2016 Nov 29;4200(2):zootaxa.4200.2.2.
    PMID: 27988618 DOI: 10.11646/zootaxa.4200.2.2
    Acropora is the most biologically diverse group of reef-building coral, and its richness peaks at the Indo-Malay-Philippine Archipelago, the centre of global coral reef biodiversity. In this paper, we describe the species richness of Acropora fauna of North Borneo, East Malaysia, based on review of literature and as corroborated by voucher specimens. Eighty-three species of Acropora are reported here; four species are literature based and 79 are supported by voucher specimens that were subsequently photographed. New records for North Borneo were recorded for 12 species, including Acropora suharsonoi Wallace 1994 that was previously thought to be confined to a few islands along Lombok Strait, Indonesia. The diversity of Acropora in North Borneo is comparable to that of Indonesia and the Philippines, despite the area's smaller reef areas. This further reinforces its inclusion as part the global hotspot of coral biodiversity.
  11. Fulltext Whole genome sequencing of Mycobacterium tuberculosis SB24 isolated from Sabah, Malaysia
    Philip N, Rodrigues KF, William T, John DV
    Genom Data, 2016 Sep;9:137-9.
    PMID: 27556011 DOI: 10.1016/j.gdata.2016.08.007
    Mycobacterium tuberculosis (M. tuberculosis) is the causative agent of tuberculosis (TB) that causes millions of death every year. We have sequenced the genome of M. tuberculosis isolated from cerebrospinal fluid (CSF) of a patient diagnosed with tuberculous meningitis (TBM). The isolated strain was referred as M. tuberculosis SB24. Genomic DNA of the M. tuberculosis SB24 was extracted and subjected to whole genome sequencing using PacBio platform. The draft genome size of M. tuberculosis SB24 was determined to be 4,452,489 bp with a G + C content of 65.6%. The whole genome shotgun project has been deposited in NCBI SRA under the accession number SRP076503.
  12. Fulltext Homogeneous Nature of Malaysian Marine Fish Epinephelus fuscoguttatus (Perciformes; Serranidae): Evidence Based on Molecular Markers, Morphology and Fourier Transform Infrared Analysis
    Nurdalila AA, Bunawan H, Kumar SV, Rodrigues KF, Baharum SN
    Int J Mol Sci, 2015 Jul 02;16(7):14884-900.
    PMID: 26147421 DOI: 10.3390/ijms160714884
    Taxonomic confusion exists within the genus Epinephelus due to the lack of morphological specializations and the overwhelming number of species reported in several studies. The homogenous nature of the morphology has created confusion in the Malaysian Marine fish species Epinephelus fuscoguttatus and Epinephelus hexagonatus. In this study, the partial DNA sequence of the 16S gene and mitochondrial nucleotide sequences of two gene regions, Cytochrome Oxidase Subunit I and III were used to investigate the phylogenetic relationship between them. In the phylogenetic trees, E. fuscoguttatus was monophyletic with E. hexagonatus species and morphology examination shows that no significant differences were found in the morphometric features between these two taxa. This suggests that E. fuscoguttatus is not distinguishable from E. hexagonatus species, and that E. fuscoguttatus have been identified to be E. hexagonatus species is likely attributed to differences in environment and ability to camouflage themselves under certain conditions. Interestingly, this finding was also supported by Principal Component Analysis on Attenuated Total Reflectance-Fourier-transform Infrared (ATR-FTIR) data analysis. Molecular, morphological and meristic characteristics were combined with ATR-FTIR analysis used in this study offer new perspectives in fish species identification. To our knowledge, this is the first report of an extensive genetic population study of E. fuscoguttatus in Malaysia and this understanding will play an important role in informing genetic stock-specific strategies for the management and conservation of this highly valued fish.
  13. Fulltext A Concise Review of Dendrocalamus asper and Related Bamboos: Germplasm Conservation, Propagation and Molecular Biology
    Mustafa AA, Derise MR, Yong WTL, Rodrigues KF
    Plants (Basel), 2021 Sep 14;10(9).
    PMID: 34579429 DOI: 10.3390/plants10091897
    Bamboos represent an emerging forest resource of economic significance and provide an avenue for sustainable development of forest resources. The development of the commercial bamboo industry is founded upon efficient molecular and technical approaches for the selection and rapid multiplication of elite germplasm for its subsequent propagation via commercial agro-forestry business enterprises. This review will delve into the micropropagation of Dendrocalamus asper, one of the most widely cultivated commercial varieties of bamboo, and will encompass the selection of germplasm, establishment of explants in vitro and micropropagation techniques. The currently available information pertaining to molecular biology, DNA barcoding and breeding, has been included, and potential areas for future research in the area of genetic engineering and gene regulation have been highlighted. This information will be of relevance to both commercial breeders and molecular biologists who have an interest in establishing bamboo as a crop of the future.
  14. Fulltext Yeasts in sustainable bioethanol production: A review
    Mohd Azhar SH, Abdulla R, Jambo SA, Marbawi H, Gansau JA, Mohd Faik AA, et al.
    Biochem Biophys Rep, 2017 Jul;10:52-61.
    PMID: 29114570 DOI: 10.1016/j.bbrep.2017.03.003
    Bioethanol has been identified as the mostly used biofuel worldwide since it significantly contributes to the reduction of crude oil consumption and environmental pollution. It can be produced from various types of feedstocks such as sucrose, starch, lignocellulosic and algal biomass through fermentation process by microorganisms. Compared to other types of microoganisms, yeasts especially Saccharomyces cerevisiae is the common microbes employed in ethanol production due to its high ethanol productivity, high ethanol tolerance and ability of fermenting wide range of sugars. However, there are some challenges in yeast fermentation which inhibit ethanol production such as high temperature, high ethanol concentration and the ability to ferment pentose sugars. Various types of yeast strains have been used in fermentation for ethanol production including hybrid, recombinant and wild-type yeasts. Yeasts can directly ferment simple sugars into ethanol while other type of feedstocks must be converted to fermentable sugars before it can be fermented to ethanol. The common processes involves in ethanol production are pretreatment, hydrolysis and fermentation. Production of bioethanol during fermentation depends on several factors such as temperature, sugar concentration, pH, fermentation time, agitation rate, and inoculum size. The efficiency and productivity of ethanol can be enhanced by immobilizing the yeast cells. This review highlights the different types of yeast strains, fermentation process, factors affecting bioethanol production and immobilization of yeasts for better bioethanol production.
  15. Fulltext Complete mitochondrial genome of six Cheilinus undulatus (Napoleon Wrasse): an endangered marine fish species from Sabah, Malaysia
    Matthew P, Manjaji-Matsumoto BM, Rodrigues KF
    Mitochondrial DNA B Resour, 2018 Oct 12;3(2):943-944.
    PMID: 33474374 DOI: 10.1080/23802359.2018.1473725
    We report here the complete mitochondrial (mt) genomes of six individuals of Cheilinus undulatus (Napoleon Wrasse), an endangered marine fish species. The six mt DNA sequences had an average size of 17,000 kb and encoded 22 tRNA, two sRNA, 13 highly conserved protein coding genes and a control region. The polymorphic variation (control region) in these six individuals suggests their potential use as a specific marker for phylogeographic conservation. Moreover, the sequence polymorphism within the control region (D-loop) suggests that this locus can be applied for phylogenetic studies.
  16. Fulltext Complete genome sequence data of an Antarctic bacterium Arthrobacter sp. EM1 from the freshwater lake of the King George Island
    Mahadi WSW, Wong CMVL, Rodrigues KF, Teoh CP, Lindang HU, Budiman C
    Data Brief, 2024 Feb;52:109841.
    PMID: 38146304 DOI: 10.1016/j.dib.2023.109841
    Arthrobacter sp. EM1 is a cold-adapted bacterium isolated from the Antarctic region, which was known to exhibit mannan-degrading activity. Accordingly, this strain not only promises a cell factory for mannan-degrading enzymes, widely used in industry but also serves as a model organism to decipher its cold adaptation mechanism. Accordingly, whole genome sequencing of the EM1 strain was performed via Single Molecule Real Time sequencing under the PacBio platform, followed by genome HGAP de novo assembly and genome annotation through Rapid Annotation System Technology (RAST) server. The chromosome of this strain is 3,885,750 bp in size with a GC content of 65.8. The annotation predicted a total of 3607 protein-coding genes and 65 RNA genes, which were classified under 398 subsystems. The subsystem with the highest number of genes is carbohydrate metabolism (397 genes), which includes two genes encoding mannan-degrading enzymes (endoglucanase and α-mannosidase). This confirmed that the EM1 strain is able to produce cold-adapted mannan degrading enzymes. The complete genome sequence data have been submitted to the National Center for Biotechnology Information (NCBI) and have been deposited at GenBank (Bioproject ID Accession Number: PRJNA963062; Biosample ID Accession Number: SAMN34434776; GenBank: CP124836.1; https://www.ncbi.nlm.nih.gov/nuccore/CP124836).
  17. Fulltext Genomic data of two Bacillus and two Pseudomonas strains isolated from the acid mine drainage site at Mamut Copper Mine, Ranau, Malaysia
    Low YY, Chin GJWL, Joseph CG, Musta B, Rodrigues KF
    Data Brief, 2020 Dec;33:106486.
    PMID: 33225029 DOI: 10.1016/j.dib.2020.106486
    The genomic data of four bacteria strains isolated from the abandoned Mamut Copper Mine, an Acid Mine Drainage (AMD) site is presented in this report. Two of these strains belong to the genus Bacillus, while the other two belong to the genus Pseudomonas. The draft genome size of Pseudomonas sp. strain MCMY3 was 6,396,595 bp (GC: 63.3%), Bacillus sp. strain MCMY6 was 6,815,573 bp (GC: 35.2%), Bacillus sp. strain MCMY13 was 5,559,059 bp (GC: 35.5%) and Pseudomonas sp. strain MCMY15 was 7,381,777 bp (GC: 64.8%). These four genomes contained 493, 495, 495 and 579 annotated subsystems, respectively. The sequence data are available at GenBank sequence read archive with accessions numbers SRX7859406, SRX7859404, SRX7859405 and SRX7293032 for strains MCMY3, MCMY6, MCMY13 and MCMY15, respectively.
  18. Small RNA datasets of drug-susceptible Mycobacterium tuberculosis strains from Sabah, Malaysia
    Jumat MI, Jani J, Mustapha ZA, Rodrigues KF, Azizan N, Acosta A, et al.
    Data Brief, 2023 Feb;46:108795.
    PMID: 36483477 DOI: 10.1016/j.dib.2022.108795
    These datasets present a list of small RNAs from three drug-susceptible Mycobacterium tuberculosis strains isolated from Sabah, Malaysia. Sputum samples were obtained from three tuberculosis patients belonging to different districts. The bacteria were detected using GeneXpert MTB/RIF, isolated and cultured in BACTECTM MGITTM 320, and tested for their drug susceptibility. Total RNAs were extracted, sequenced, and analyzed using bioinformatic tools to filter out small RNA present in the Mycobacterium tuberculosis strains. Small RNA sequencing generated total raw reads of 63,252,209, 63,636,812, and 61,148,224 and total trimmed reads (15-30 nucleotides) of 51,533,188, 53,520,197, and 51,363,772 for Mycobacterium tuberculosis strain SBH49, SBH149, and SBH372, respectively. The raw data were submitted to the Sequence Read Archive (SRA) database of the National Center for Biotechnology Information (NCBI) under the accession numbers of SRX16744291 (SBH49), SRX16744292 (SBH149), and SRX16744293 (SBH372). Small RNAs play important roles in cellular processes such as cell differentiation, cell signaling, development of resistance to antibiotics and immune response, and metabolism regulation. The small RNAs determined here could provide further insights into various cellular processes crucial for Mycobacterium tuberculosis survivability and a better understanding of their gene regulation which ultimately opens a new pathway for combating tuberculosis infection.
  19. Fulltext Draft genome sequence data of two Salmonella bacteria from serogroup C type
    Jiksing C, Voo CLY, Rodrigues KF
    Data Brief, 2020 Aug;31:105920.
    PMID: 32637513 DOI: 10.1016/j.dib.2020.105920
    Salmonella is a gram-negative rod-shape bacterium from the family of Enterobacteriaceae that can cause a wide range of human disease such as enteric fever, gastroenteritis and bacteremia. Here we sequenced two genomes of Salmonella bacteria isolated from the Gallus gallus domesticus host. Genomic DNA of the two Salmonella isolates were extracted and subjected to whole genome sequencing using Illumina platform. The draft genome size of the two Salmonella isolates was determined to be 4,902,295 bp (S18) and 4,847,310 bp (S20) respectively. The percentage of GC content for both draft genomes is the same which is 52.1%. Both the whole genome shotgun project (S18 and S20) has been deposited in National Center for Biotechnology Information Sequence Read Archive under the accession number of SRR7503041 (S18) and SRR7503040 (S20). The sequenced genome (S18 and S20) were aligned with the reference genome and three other Salmonella genomes from serogroup B, D and E. The data obtained show the presence of unique DNA sequences in S18 and S20 genomes. This unique DNA sequences are from the fimbrial gene group.
  20. Fulltext Whole genome sequence data of a marine bacterium, Marinobacter adhaerens PBVC038, associated with toxic harmful algal bloom
    Chin GJWL, Jani J, Law SV, Rodrigues KF
    Data Brief, 2023 Feb;46:108768.
    PMID: 36569539 DOI: 10.1016/j.dib.2022.108768
    Marinobacter adhaerens (PBVC038) was isolated from a harmful algal bloom event caused by the toxic dinoflagellate Pyrodinium bahamense var. compressum (P. bahamense) in Sepanggar Bay, Sabah, Malaysia, in December 2012. Blooms of P. bahamense are frequently linked to paralytic shellfish poisoning, resulting in morbidity and mortality. Prior experimental evidence has implicated the role of symbiotic bacteria in bloom dynamics and the synthesis of biotoxins. The draft genome sequence data of a harmful algal bloom-associated bacterium, Marinobacter adhaerens PBVC038 is presented here. The genome is made up of 21 contigs with an estimated 4,246,508 bases in genome size and a GC content of 57.19%. The raw data files can be retrieved from the National Center for Biotechnology Information (NCBI) under the Bioproject number PRJNA320140. The assessment of bacterial communities associated with harmful algal bloom should be studied more extensively as more data is needed to ascertain the functions of these associated bacteria during a bloom event.
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