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Article: Identification of Prominent Genes between 3D Glioblastoma Models and Clinical Samples via GEO/TCGA/CGGA Data Analysis.

Phon, Brandon Wee Siang / Bhuvanendran, Saatheeyavaane / Ayub, Qasim / Radhakrishnan, Ammu Kutty / Kamarudin, Muhamad Noor Alfarizal

Biology

2023 Volume 12, Issue 5

Abstract: A paradigm shift in preclinical evaluations of new anticancer GBM drugs should occur in favour of 3D cultures. This study leveraged the vast genomic data banks to investigate the suitability of 3D cultures as cell-based models for GBM. We hypothesised ... ...

Abstract	A paradigm shift in preclinical evaluations of new anticancer GBM drugs should occur in favour of 3D cultures. This study leveraged the vast genomic data banks to investigate the suitability of 3D cultures as cell-based models for GBM. We hypothesised that correlating genes that are highly upregulated in 3D GBM models will have an impact in GBM patients, which will support 3D cultures as more reliable preclinical models for GBM. Using clinical samples of brain tissue from healthy individuals and GBM patients from The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO), Chinese Glioma Genome Atlas (CGGA), and Genotype-Tissue Expression (GTEx) databases, several genes related to pathways such as epithelial-to-mesenchymal transition (EMT)-related genes (
Language	English
Publishing date	2023-04-25
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2661517-4
ISSN	2079-7737
ISSN	2079-7737
DOI	10.3390/biology12050648
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Article ; Online: Identification of Prominent Genes between 3D Glioblastoma Models and Clinical Samples via GEO/TCGA/CGGA Data Analysis

Phon, Brandon Wee Siang / Bhuvanendran, Saatheeyavaane / Ayub, Qasim / Radhakrishnan, Ammu Kutty / Kamarudin, Muhamad Noor Alfarizal

Biology (Basel). 2023 Apr. 25, v. 12, no. 5

2023

Abstract	A paradigm shift in preclinical evaluations of new anticancer GBM drugs should occur in favour of 3D cultures. This study leveraged the vast genomic data banks to investigate the suitability of 3D cultures as cell-based models for GBM. We hypothesised that correlating genes that are highly upregulated in 3D GBM models will have an impact in GBM patients, which will support 3D cultures as more reliable preclinical models for GBM. Using clinical samples of brain tissue from healthy individuals and GBM patients from The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO), Chinese Glioma Genome Atlas (CGGA), and Genotype-Tissue Expression (GTEx) databases, several genes related to pathways such as epithelial-to-mesenchymal transition (EMT)-related genes (CD44, TWIST1, SNAI1, CDH2, FN1, VIM), angiogenesis/migration-related genes (MMP1, MMP2, MMP9, VEGFA), hypoxia-related genes (HIF1A, PLAT), stemness-related genes (SOX2, PROM1, NES, FOS), and genes involved in the Wnt signalling pathway (DKK1, FZD7) were found to be upregulated in brain samples from GBM patients, and the expression of these genes were also enhanced in 3D GBM cells. Additionally, EMT-related genes were upregulated in GBM archetypes (wild-type IDH1ᴿ¹³²) that historically have poorer treatment responses, with said genes being significant predictors of poorer survival in the TCGA cohort. These findings reinforced the hypothesis that 3D GBM cultures can be used as reliable models to study increased epithelial-to-mesenchymal transitions in clinical GBM samples.
Keywords	brain ; gene expression ; genome ; genomics ; glioblastoma
Language	English
Dates of publication	2023-0425
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article ; Online
ZDB-ID	2661517-4
ISSN	2079-7737
ISSN	2079-7737
DOI	10.3390/biology12050648
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Article ; Online: Male lineages in the Himalayan foothills: a commentary on Y-chromosome haplogroup diversity in the sub-Himalayan Terai and Duars populations of East India.

Ayub, Qasim

Journal of human genetics

2011 Volume 56, Issue 12, Page(s) 813–814

MeSH term(s)	Chromosomes, Human, Y ; Genetic Variation ; Haplotypes ; Humans
Language	English
Publishing date	2011-12
Publishing country	England
Document type	Comment ; Journal Article
ZDB-ID	1425192-9
ISSN	1435-232X ; 1434-5161
ISSN (online)	1435-232X
ISSN	1434-5161
DOI	10.1038/jhg.2011.114
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Article: Discovering naturally-occurring microbiota in disease suppressive soil: Potential role of biological elements in suppressing Ganoderma boninense

Goh, Yit Kheng / Zoqratt, Muhammad Zarul Hanifah Md / Goh, You Keng / Ayub, Qasim / Ting, Adeline Su Yien

Biological control. 2022 Feb., v. 165

2022

Abstract: Blenheim soil (Typic Quartzipsamment) and Bernam soil (Typic Endoaquept) with low and high Ganoderma basal stem rot (BSR) incidence, respectively, were studied to determine the role of naturally-occurring microbiota in suppressing basal stem rot (BSR) ... ...

Abstract	Blenheim soil (Typic Quartzipsamment) and Bernam soil (Typic Endoaquept) with low and high Ganoderma basal stem rot (BSR) incidence, respectively, were studied to determine the role of naturally-occurring microbiota in suppressing basal stem rot (BSR) disease in oil palm. These coastal soils were also compared against a typical soil for nursery use, the inland Bungor soil (Typic Kandiudults). For each soil type, half of the soils were sterilized by autoclaving, and the other half were non-sterilized. These soils were then used for the microbiome analysis, evaluation of disease incidences, and effect on plant growth. Soil microbial communities were profiled using 16S and 18S ribosomal RNA gene amplicon sequencing on the Illumina MiSeq. Polybag trials were conducted over a period of 20 weeks. Results showed that by eliminating or inactivating the indigenous microbial communities from BSR-suppressive Blenheim soil through sterilization, this increased BSR incidences (from 50 to 92%) and severity (from 28 to 78%), and affected plant growth (reduction of 35% leaf area, 11% height, and 19% bole’s girth). Soil microbiome analysis revealed that Acidobacteriota, Nitrospirota, Latesbaciterota, Nanoarchaeota, Entotheonellaeta, Zixibacteria, Candidatus Yanofskybacteria (Patescibacteria), MB-A2-108 (Actinobacteriota), Cnidaria and Acaulospora (Mucoromycota) were less prevalent in sterilized Blenheim soil compared to non-sterilized Blenheim soil. Relative abundance of the genus Ganoderma was also lower in BSR-suppressive Blenheim soil compared to sterilized Blenheim soil. In contrast, disease development and plant growth remained unaffected by sterilization of BSR-conducive Bernam and Bungor soils, suggesting that naturally-occurring microbiota in these two soils played minimal roles in contributing to conducive conditions for disease development. Relative abundance of Ganoderma was higher in BSR-conducive Bernam and Bungor soils as well, compared to BSR-suppressive Blenheim. Results from this study provides the first insights into the soil microbiota in BSR suppressive soils and their role in BSR disease progression and growth of oil palms.
Keywords	Acaulospora ; Cnidaria ; Elaeis guineensis ; Endoaquepts ; Ganoderma boninense ; Kandiudults ; Quartzipsamments ; autoclaving ; biological control ; disease progression ; genes ; leaf area ; microbiome ; oils ; plant growth ; ribosomal RNA ; soil microorganisms ; stem rot ; suppressive soils ; tree trunk
Language	English
Dates of publication	2022-02
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	1149971-0
ISSN	1049-9644
ISSN	1049-9644
DOI	10.1016/j.biocontrol.2021.104787
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Article: The genetic drivers for the successful invasive potential of a generalist bird, the House crow

Iqbal, Farheena / Krzeminska-Ahmadzai, Urszula / Ayub, Qasim / Wilson, Robyn / Song, Beng Kah / Fahim, Muhammad / Rahman, Sadequr

Biological invasions. 2022 Mar., v. 24, no. 3

2022

Abstract: What kind of genetic structure helps the rapid range expansion of the invasive species is fundamental to understand spread of invasion. The House crow (Corvus splendens), an ecological generalist, having a large native and introduced distribution range, ... ...

Abstract	What kind of genetic structure helps the rapid range expansion of the invasive species is fundamental to understand spread of invasion. The House crow (Corvus splendens), an ecological generalist, having a large native and introduced distribution range, is a good study model to investigate the genetic structure and adaptations underpinning the evolutionary potential for successful biological invasion. Thirteen mainland and one island native population from the Indian subcontinent were studied using four nuclear introns and mitochondrial genome to determine the phylogeographic structure and demographic history. A large, panmictic long-term expanding native population dating from the last glacial period (~ 30,000 ya) was inferred leading to great genetic diversity across the whole native range. The thirteen mitochondrial encoded proteins, directly involved in the energy supplying pathway, could underlie metabolic adaptations during range expansion under diverse climate conditions. Therefore, to investigate the molecular selection on these genes in native and introduced ranges, five previously studied introduced populations from Southeast Asia and Africa were included. The native populations originating from hot arid and humid tropical areas exhibited the signatures of positive selection on four codons located in three genes (ND5, Cytb and COX2), suggesting these may have evolved under environmental stresses in those regions. Our findings demonstrated the native range population as the reservoir of the species’ genetic diversity, mitogenomic patterns of the introduced populations related to native range of species and no varaints could be associated with climate in introduced range. Thus,inferred that the pre-adapted standing genetic variations evolved during dispersion over the native range are the predominant source of the high evolutionary potential and contribute to the successful invasion history. These findings will help to predict the future introduced range of the House crow.
Keywords	Corvus splendens ; birds ; codons ; ecological invasion ; energy ; genetic variation ; introns ; invasive species ; mitochondria ; mitochondrial genome ; models ; phylogeography ; Africa ; India ; South East Asia
Language	English
Dates of publication	2022-03
Size	p. 861-878.
Publishing place	Springer International Publishing
Document type	Article
ZDB-ID	1438729-3
ISSN	1573-1464 ; 1387-3547
ISSN (online)	1573-1464
ISSN	1387-3547
DOI	10.1007/s10530-021-02684-4
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Article ; Online: Biomonitoring of heavy metals in the feathers of House crow (Corvus splendens) from some metropolitans of Asia and Africa

Iqbal, Farheena / Wilson, Robyn / Ayub, Qasim / Song, Beng Kah / Krzeminska-Ahmedzai, Urszula / Talei, Amin / Hermawan, Andreas Aditya / Rahman, Sadequr

Environ Sci Pollut Res. 2023 Mar., v. 30, no. 13 p.35715-35726

2023

Abstract: Urban-dwelling birds can be useful biomonitors to assess the impact of the urbanisation on both public and wildlife health. Widely distributed urban bird species, the House crow, was studied for heavy metal accumulation levels from nine cities of South ... ...

Abstract	Urban-dwelling birds can be useful biomonitors to assess the impact of the urbanisation on both public and wildlife health. Widely distributed urban bird species, the House crow, was studied for heavy metal accumulation levels from nine cities of South Asia, Southeast Asia and Africa that border the Indian Ocean. Feathers were spectroscopically investigated for the deposition of ten heavy metals, i.e. As, Zn, Pb, Cd, Ni, iron Fe, Mn, Cr, Cu and Li. Fe and Zn were found to be the most prevalent metals in all sites. Measured concentrations of Pb (4.38–14.77 mg kg⁻¹) overall, and Fe (935.66 mg kg⁻¹) and Cu (67.17 mg kg⁻¹) at some studied sites were above the toxicity levels reported lethal in avian toxicological studies. Multivariate analysis and linear models supported geographical location as a significant predictor for the level of most of the metals. Zn and Cu, generally and Pb, Cd, Mn, Cr at some sites exhibited potential bioaccumulation from surrounding environments. Inter-species comparisons strengthen the inference that the House crow is a reliable bioindicator species for the qualitative assessment of local urban environmental pollution and could be a useful tool for inter-regional monitoring programs.
Keywords	Corvus splendens ; bioaccumulation ; birds ; environmental monitoring ; heavy metals ; indicator species ; multivariate analysis ; pollution ; toxicity ; toxicology ; urbanization ; wildlife ; Africa ; Indian Ocean ; South Asia ; South East Asia
Language	English
Dates of publication	2023-03
Size	p. 35715-35726.
Publishing place	Springer Berlin Heidelberg
Document type	Article ; Online
ZDB-ID	1178791-0
ISSN	1614-7499 ; 0944-1344
ISSN (online)	1614-7499
ISSN	0944-1344
DOI	10.1007/s11356-022-24712-z
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Article ; Online: Characterization of multidrug-resistant Acinetobacter baumannii strain ATCC BAA1605 using whole-genome sequencing.

Ten, Kah Ern / Md Zoqratt, Muhammad Zarul Hanifah / Ayub, Qasim / Tan, Hock Siew

BMC research notes

2021 Volume 14, Issue 1, Page(s) 83

Abstract: Objective: The nosocomial pathogen, Acinetobacter baumannii, has acquired clinical significance due to its ability to persist in hospital settings and survive antibiotic treatment, which eventually resulted in the rapid spread of this bacterium with ... ...

Abstract	Objective: The nosocomial pathogen, Acinetobacter baumannii, has acquired clinical significance due to its ability to persist in hospital settings and survive antibiotic treatment, which eventually resulted in the rapid spread of this bacterium with antimicrobial resistance (AMR) phenotypes. This study used a multidrug-resistant A. baumannii (strain ATCC BAA1605) as a model to study the genomic features of this pathogen. Results: One circular chromosome and one circular plasmid were discovered in the complete genome of A. baumannii ATCC BAA1605 using whole-genome sequencing. The chromosome is 4,039,171 bp long with a GC content of 39.24%. Many AMR genes, which confer resistance to major classes of antibiotics (beta-lactams, aminoglycosides, tetracycline, sulphonamides), were found on the chromosome. Two genomic islands were predicted on the chromosome, one of which (Genomic Island 1) contains a cluster of AMR genes and mobile elements, suggesting the possibility of horizontal gene transfer. A subtype I-F CRISPR-Cas system was also identified on the chromosome of A. baumannii ATCC BAA1605. This study provides valuable genome data that can be used as a reference for future studies on A. baumannii. The genome of A. baumannii ATCC BAA1605 has been deposited at GenBank under accession no. CP058625 and CP058626.
MeSH term(s)	Acinetobacter baumannii/genetics ; Anti-Bacterial Agents/pharmacology ; Genome, Bacterial/genetics ; Plasmids/genetics ; Whole Genome Sequencing
Chemical Substances	Anti-Bacterial Agents
Language	English
Publishing date	2021-03-04
Publishing country	England
Document type	Journal Article
ZDB-ID	2413336-X
ISSN	1756-0500 ; 1756-0500
ISSN (online)	1756-0500
ISSN	1756-0500
DOI	10.1186/s13104-021-05493-z
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Article ; Online: Geographical separation and ethnic origin influence the human gut microbial composition: a meta-analysis from a Malaysian perspective.

Dwiyanto, Jacky / Ayub, Qasim / Lee, Sui Mae / Foo, Su Chern / Chong, Chun Wie / Rahman, Sadequr

Microbial genomics

2021 Volume 7, Issue 8

Abstract: Ethnicity is consistently reported as a strong determinant of human gut microbiota. However, the bulk of these studies are from Western countries, where microbiota variations are mainly driven by relatively recent migration events. Malaysia is a ... ...

Abstract	Ethnicity is consistently reported as a strong determinant of human gut microbiota. However, the bulk of these studies are from Western countries, where microbiota variations are mainly driven by relatively recent migration events. Malaysia is a multicultural society, but differences in gut microbiota persist across ethnicities. We hypothesized that migrant ethnic groups continue to share fundamental gut traits with the population in the country of origin due to shared cultural practices despite subsequent geographical separation. To test this hypothesis, the 16S rRNA gene amplicons from 16 studies comprising three major ethnic groups in Malaysia were analysed, covering 636 Chinese, 248 Indian and 123 Malay individuals from four countries (China, India, Indonesia and Malaysia). A confounder-adjusted permutational multivariate analysis of variance (PERMANOVA) detected a significant association between ethnicity and the gut microbiota (PERMANOVA
MeSH term(s)	China ; Ethnicity ; Gastrointestinal Microbiome/genetics ; High-Throughput Nucleotide Sequencing ; Humans ; India ; Indonesia ; Malaysia ; RNA, Ribosomal, 16S
Chemical Substances	RNA, Ribosomal, 16S
Language	English
Publishing date	2021-08-26
Publishing country	England
Document type	Journal Article ; Meta-Analysis ; Research Support, Non-U.S. Gov't ; Systematic Review
ZDB-ID	2835258-0
ISSN	2057-5858 ; 2057-5858
ISSN (online)	2057-5858
ISSN	2057-5858
DOI	10.1099/mgen.0.000619
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Article: Naegleria fowleri: differential genetic expression following treatment with Hesperidin conjugated with silver nanoparticles using RNA-Seq

Siddiqui, Ruqaiyyah / Rajendran, Kavitha / Abdella, Bahaa / Ayub, Qasim / Lim, Shu Yong / Khan, Naveed Ahmed

Parasitology research. 2020 July, v. 119, no. 7

2020

Abstract: Naegleria fowleri causes a deadly infection known as primary amoebic meningoencephalitis (PAM). To our knowledge, there are very few transcriptome studies conducted on these brain-eating amoebae, despite rise in the number of cases. Although the ... ...

Abstract	Naegleria fowleri causes a deadly infection known as primary amoebic meningoencephalitis (PAM). To our knowledge, there are very few transcriptome studies conducted on these brain-eating amoebae, despite rise in the number of cases. Although the Naegleria genome has been sequenced, currently, it is not well annotated. Transcriptome level studies are needed to help understand the pathology and biology of this fatal parasitic infection. Recently, we showed that nanoparticles loaded with the flavonoid Hesperidin (HDN) are potential novel antimicrobial agents. N. fowleri trophozoites were treated with and without HDN-conjugated with silver nanoparticles (AgNPs) and silver only, and then, 50% minimum inhibitory concentration (MIC) was determined. The results revealed that the MIC of HDN-conjugated AgNPs was 12.5 microg/mL when treated for 3 h. As no reference genome exists for N. fowleri, de novo RNA transcriptome analysis using RNA-Seq and differential gene expression analysis was performed using the Trinity software. Analysis revealed that more than 2000 genes were differentially expressed in response to N. fowleri treatment with HDN-conjugated AgNPs. Some of the genes were linked to oxidative stress response, DNA repair, cell division, cell signalling and protein synthesis. The downregulated genes were linked with processes such as protein modification, synthesis of aromatic amino acids, when compared with untreated N. fowleri. Further transcriptome studies will lead to understanding of genetic mechanisms of the biology and pathogenesis and/or the identification of much needed drug candidates.
Keywords	DNA repair ; Naegleria fowleri ; RNA ; cell division ; computer software ; drugs ; gene expression regulation ; hesperidin ; meningoencephalitis ; minimum inhibitory concentration ; nanosilver ; oxidative stress ; parasitology ; parasitoses ; pathogenesis ; protein synthesis ; research ; sequence analysis ; silver ; stress response ; transcriptome ; transcriptomics ; trophozoites
Language	English
Dates of publication	2020-07
Size	p. 2351-2358.
Publishing place	Springer Berlin Heidelberg
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	284966-5
ISSN	1432-1955 ; 0932-0113 ; 0044-3255
ISSN (online)	1432-1955
ISSN	0932-0113 ; 0044-3255
DOI	10.1007/s00436-020-06711-6
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Article ; Online: The gut virome in two indigenous populations from Malaysia.

Lee, Chuen Zhang / Zoqratt, Muhammad Zarul Hanifah Md / Phipps, Maude E / Barr, Jeremy J / Lal, Sunil K / Ayub, Qasim / Rahman, Sadequr

Scientific reports

2022 Volume 12, Issue 1, Page(s) 1824

Abstract: The human gut contains a complex microbiota dominated by bacteriophages but also containing other viruses and bacteria and fungi. There are a growing number of techniques for the extraction, sequencing, and analysis of the virome but currently no ... ...

Abstract	The human gut contains a complex microbiota dominated by bacteriophages but also containing other viruses and bacteria and fungi. There are a growing number of techniques for the extraction, sequencing, and analysis of the virome but currently no standardized protocols. This study established an effective workflow for virome analysis to investigate the virome of stool samples from two understudied ethnic groups from Malaysia: the Jakun and Jehai Orang Asli. By using the virome extraction and analysis workflow with the Oxford Nanopore Technology, long-read sequencing successfully captured close to full-length viral genomes. The virome composition of the two indigenous Malaysian communities were remarkably different from those found in other parts of the world. Additionally, plant viruses found in the viromes of these individuals were attributed to traditional food-seeking methods. This study establishes a human gut virome workflow and extends insights into the healthy human gut virome, laying the groundwork for comparative studies.
MeSH term(s)	Feces/virology ; Female ; Gastrointestinal Microbiome/genetics ; Genome, Viral ; High-Throughput Nucleotide Sequencing ; Humans ; Indigenous Peoples ; Malaysia ; Metagenomics/methods ; Phylogeny ; Virome/genetics ; Viruses/classification ; Viruses/genetics
Language	English
Publishing date	2022-02-03
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-022-05656-3
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