Search

Your search keyword '"Mat Isa, Mohd Noor"' showing total 40 results
Start Over Author "Mat Isa, Mohd Noor"
40 results on '"Mat Isa, Mohd Noor"'

2. The molecular epidemiology of multiple zoonotic origins of SARS-CoV-2

Author

Pekar, Jonathan E, Magee, Andrew, Parker, Edyth, Moshiri, Niema, Izhikevich, Katherine, Havens, Jennifer L, Gangavarapu, Karthik, Malpica Serrano, Lorena Mariana, Crits-Christoph, Alexander, Matteson, Nathaniel L, Zeller, Mark, Levy, Joshua I, Wang, Jade C, Hughes, Scott, Lee, Jungmin, Park, Heedo, Park, Man-Seong, Ching Zi Yan, Katherine, Lin, Raymond Tzer Pin, Mat Isa, Mohd Noor, Noor, Yusuf Muhammad, Vasylyeva, Tetyana I, Garry, Robert F, Holmes, Edward C, Rambaut, Andrew, Suchard, Marc A, Andersen, Kristian G, Worobey, Michael, and Wertheim, Joel O

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Clinical Sciences, Infectious Diseases, Coronaviruses, Emerging Infectious Diseases, Lung, 2.2 Factors relating to the physical environment, Infection, Good Health and Well Being, Animals, COVID-19, Computer Simulation, Genetic Variation, Genomics, Humans, Molecular Epidemiology, Pandemics, Phylogeny, SARS-CoV-2, Viral Zoonoses, General Science & Technology
Abstract

Understanding the circumstances that lead to pandemics is important for their prevention. We analyzed the genomic diversity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) early in the coronavirus disease 2019 (COVID-19) pandemic. We show that SARS-CoV-2 genomic diversity before February 2020 likely comprised only two distinct viral lineages, denoted "A" and "B." Phylodynamic rooting methods, coupled with epidemic simulations, reveal that these lineages were the result of at least two separate cross-species transmission events into humans. The first zoonotic transmission likely involved lineage B viruses around 18 November 2019 (23 October to 8 December), and the separate introduction of lineage A likely occurred within weeks of this event. These findings indicate that it is unlikely that SARS-CoV-2 circulated widely in humans before November 2019 and define the narrow window between when SARS-CoV-2 first jumped into humans and when the first cases of COVID-19 were reported. As with other coronaviruses, SARS-CoV-2 emergence likely resulted from multiple zoonotic events.

Published
2022

3. Hairpin in a haystack: In silico identification and characterization of plant-conserved microRNA in Rafflesiaceae.

Author

Wicaksono, Adhityo, Meitha, Karlia, Wan, Kiew-Lian, Mat Isa, Mohd Noor, Parikesit, Arli Aditya, and Molina, Jeanmaire

Subjects
HAIRPIN (Genetics), NON-coding RNA, GENE expression, ENDANGERED plants, GRAPES
Abstract

Rafflesiaceae is a family of endangered plants whose members are solely parasitic to the tropical grape vine Tetrastigma (Vitaceae). Currently, the genetics of their crosstalk with the host remains unexplored. In this study, we use homology-based in silico approaches to characterize micro-RNAs (miRNAs) expressed by Sapria himalayana and Rafflesia cantleyi from published omics data. Derived from secondary structures or hairpins, miRNAs are small regulators of gene expression. We found that some plant-conserved miRNA still exists in Rafflesiaceae. Out of 9 highly conserved miRNA families in plants, 7 families (156/157, 159/319, 160, 165/166, 171, 172, 390) were identified with a total of 22 variants across Rafflesiaceae. Some miRNAs were missing endogenous targets and may have evolved to target host miRNA, though this requires experimental verification. Rafflesiaceae miRNA promoters are mostly inducible by ethylene that mediates stress response in the host but could be perceived by the parasites as a signal for growth. This study provides evidence that certain miRNAs with ancient origins in land plants still exist in Rafflesiaceae, though some may have been coopted by parasites to target host genes. [ABSTRACT FROM AUTHOR]

Published
2025
Full Text
View/download PDF

8. Topographically Distinguished Microbiome Taxonomy and Stress-Response Genes of Royal Belum Rainforest and Raja Muda Musa Peat Swamp Revealed through Metagenomic Inquisition

Author

Ahmad, Mohd Fadzli, primary, Abdullah, Hasdianty, additional, Hassan, Muhammad Naim, additional, Jamaludin, Muhammad Imran, additional, Sivam, Ashvini, additional, Komatsu, Kazuhiro, additional, Sapian, Irni Suhayu, additional, Alias, Halimah, additional, Mat Isa, Mohd Noor, additional, Kuwahara, Victor S., additional, and Yaacob, Nor Suhaila, additional

Published
2023
Full Text
View/download PDF

11. SARS-CoV-2 emergence very likely resulted from at least two zoonotic events

Author

Pekar, Jonathan E., Magee, Andrew, Parker, Edyth, Moshiri, Niema, Izhikevich, Katherine, Havens, Jennifer L., Gangavarapu, Karthik, Malpica Serrano, Lorena M., Crits-Christoph, Alexander, Matteson, Nathaniel L., Zeller, Mark, Levy, Joshua I., Wang, Jade C., Hughes, Scott, Lee, Jungmin, Park, Heedo, Park, Man-Seong, Ching Zi Yan, Katherine, Tzer Pin Lin, Raymond, Mat Isa, Mohd Noor, Muhammad Noor, Yusuf, Vasylyeva, Tetyana I., Garry, Robert F., Holmes, Edward C., Rambaut, Andrew, Suchard, Marc A., Andersen, Kristian G., Worobey, Michael, and Wertheim, Joel O.

Subjects
SARS-CoV-2, zoonosis, phylodynamics, molecular clock, viruses
Abstract

Understanding the circumstances that lead to pandemics is critical to their prevention. Here, we analyze the pattern and origin of genomic diversity of SARS-CoV-2 early in the COVID-19 pandemic. We show that the SARS-CoV-2 genomic diversity prior to February 2020 comprised only two distinct viral lineages—denoted A and B—with no transitional haplotypes. Novel phylodynamic rooting methods, coupled with epidemic simulations, indicate that these two lineages were the result of at least two separate cross-species transmission events into humans. The first zoonotic transmission likely involved lineage B viruses and occurred in late-November/early-December 2019 and no earlier than the beginning of November 2019, while the introduction of lineage A likely occurred within weeks of the first event. These findings define the narrow window between when SARS-CoV-2 first jumped into humans and when the first cases of COVID-19 were reported. Hence, as with SARS-CoV-1 in 2002 and 2003, SARS-CoV-2 emergence likely resulted from multiple zoonotic events.

Published
2022
Full Text
View/download PDF

13. WITHDRAWN: Gut microbiome dataset of captive Giant Pandas (Ailuropoda melanoleuca) in Zoo Negara Malaysia

Author

Nik Maheran Nik Muhammad, Mat Naim Ramli, Yang Haidi, Bryan Raveen Nelson, Jayaraj Vijaya Kumaran, Suganthi Appalasamy, Fong Pooi Har, Mat Isa Mohd Noor, Deng Tao, Wan Mohd Nazdrol Wan Mohd Nasir, Dennis Ten ChoonYung, Chong Ju Lian, Seri Intan Mokhtar, Mohamad Nur Arifuddin Mad Yusof, and Hafiz Yazid

Subjects
Multidisciplinary, biology, PANDAS, biology.animal, medicine, Zoology, medicine.disease, Gut microbiome, Ailuropoda melanoleuca
Published
2021
Full Text
View/download PDF

17. Effect of inorganic fertilizer application on soil microbial diversity in an oil palm plantation

Author

Salamat, Siti Suliza, Hassan, Mohd Ali, Shirai, Yoshihito, Mohd. Hanif, Ahmad Husni, Norizan, Mohd Shahkhirat, Mohd Zainudin, Mohd Huzairi, Mustapha, Nurul Asyifah, Mat Isa, Mohd Noor, Abu Bakar, Mohd Faizal, Salamat, Siti Suliza, Hassan, Mohd Ali, Shirai, Yoshihito, Mohd. Hanif, Ahmad Husni, Norizan, Mohd Shahkhirat, Mohd Zainudin, Mohd Huzairi, Mustapha, Nurul Asyifah, Mat Isa, Mohd Noor, and Abu Bakar, Mohd Faizal

Abstract

Excessive fertilizer applications in oil palm plantations are conventionally done to increase the oil yield, but they result in high production cost and environmental pollution. There have been only separate reports on the effects of fertilizer application on soil physical, chemical characteristics, and microbial biodiversity. Therefore, this study was conducted to determine the correlation between soil characteristics and soil microbial biodiversity in oil palm plantation after long-term frequent chemical fertilizer application compared with secondary soil, using molecular methods of polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE) and MiSeq. Secondary forest soil was chosen as the control. The results showed that after 25 years of fertilizer application, the total nitrogen and organic carbon contents decreased from low to very low scale, indicating soil infertility condition. Reduction of Firmicutes was related to suppression of soil borne diseases, and Bacteroidetes which is an indicator of soil health were both almost eliminated after 25 years of fertilizer application. In conclusion, long-term inorganic fertilizer application reduced the soil nitrogen, and organic carbon, altered beneficial microbes in the soil.

Published
2021

19. Sequencing and analysis of chromosome 1 of Eimeria tenella reveals a unique segmental organization

Author

King-Hwa Ling, Rajandream, Marie-Adele, Rivailler, Pierre, Ivens, Alasdair, Soon-Joo Yap, Madeira, Alda M.B.N., Mungall, Karen, Billington, Karen, Wai-Yan Yee; Bankier, Alan T., Carroll, FionnadhDurham, Alan M.; Peters, Nicholas, Shu-San Loo, Mat Isa, Mohd Noor, Novaes, Jeniffer, Quail, Michael, Rosli, Rozita, Nor Shamsudin, Mariana, Sobreira, Tiago J.P., Tivey, Adrian R., Siew-Fun Wai, White, Sarah, Xikun Wu, Kerhornou, Arnaud, Blake, Damer, Mohamed, Rahmah, Shirley, Martin, Gruber, Arthur, Berriman, Matthew, Tomley, Fiona, Dear, Paul H., and Wan, Kiew-Lian

Subjects
Protozoa -- Genetic aspects, Protozoa -- Research, Chromosomes -- Structure, Chromosomes -- Research, Bacterial genetics -- Research, Health
Abstract

The sequencing and analysis of the first chromosome of Eimeria tenella, a chromosome believed to carry loci associated with drug resistance and known to differ between virulent and attenuated strains of the parasite infecting the intestinal tracts of domestic fowls is reported. The chromosome is found to show most striking segmentation of repeat-rich regions peppered with transposon-like elements and telomere-like repeats, alternating with repeat-free regions.

Published
2007

20. New insights on the evolution of the sweet taste receptor of primates adapted to harsh environments

Author

Md Tamrin, Nur Aida, Zainudin, Ramlah, Esa, Yuzine, Alias, Halimah, Mat Isa, Mohd Noor, Croft, Laurence, Abdullah, Mohd Tajuddin, Md Tamrin, Nur Aida, Zainudin, Ramlah, Esa, Yuzine, Alias, Halimah, Mat Isa, Mohd Noor, Croft, Laurence, and Abdullah, Mohd Tajuddin

Abstract

Taste perception is an essential function that provides valuable dietary and sensory information, which is crucial for the survival of animals. Studies into the evolution of the sweet taste receptor gene (TAS1R2) are scarce, especially for Bornean endemic primates such as Nasalis larvatus (proboscis monkey), Pongo pygmaeus (Bornean orangutan), and Hylobates muelleri (Muller’s Bornean gibbon). Primates are the perfect taxa to study as they are diverse dietary feeders, comprising specialist folivores, frugivores, gummivores, herbivores, and omnivores. We constructed phylogenetic trees of the TAS1R2 gene for 20 species of anthropoid primates using four different methods (neighbor-joining, maximum parsimony, maximum-likelihood, and Bayesian) and also established the time divergence of the phylogeny. The phylogeny successfully separated the primates into their taxonomic groups as well as by their dietary preferences. Of note, the reviewed time of divergence estimation for the primate speciation pattern in this study was more recent than the previously published estimates. It is believed that this difference may be due to environmental changes, such as food scarcity and climate change, during the late Miocene epoch, which forced primates to change their dietary preferences. These findings provide a starting point for further investigation.

Published
2020

25. Contribution of transposable elements in the plant's genome

Author

Sahebi, Mahbod, Musa, Mohamed Hanafi, van Wijnen, Andre J., Rice, David, Yusop, Mohd Rafii, Azizi, Parisa, Osman, Mohamad Anuar, Taheri, Sima, Abu Bakar, Mohd Faizal, Mat Isa, Mohd Noor, Muhammad Noor, Yusuf, Sahebi, Mahbod, Musa, Mohamed Hanafi, van Wijnen, Andre J., Rice, David, Yusop, Mohd Rafii, Azizi, Parisa, Osman, Mohamad Anuar, Taheri, Sima, Abu Bakar, Mohd Faizal, Mat Isa, Mohd Noor, and Muhammad Noor, Yusuf

Abstract

Plants maintain extensive growth flexibility under different environmental conditions, allowing them to continuously and rapidly adapt to alterations in their environment. A large portion of many plant genomes consists of transposable elements (TEs) that create new genetic variations within plant species. Different types of mutations may be created by TEs in plants. Many TEs can avoid the host's defense mechanisms and survive alterations in transposition activity, internal sequence and target site. Thus, plant genomes are expected to utilize a variety of mechanisms to tolerate TEs that are near or within genes. TEs affect the expression of not only nearby genes but also unlinked inserted genes. TEs can create new promoters, leading to novel expression patterns or alternative coding regions to generate alternate transcripts in plant species. TEs can also provide novel cis-acting regulatory elements that act as enhancers or inserts within original enhancers that are required for transcription. Thus, the regulation of plant gene expression is strongly managed by the insertion of TEs into nearby genes. TEs can also lead to chromatin modifications and thereby affect gene expression in plants. TEs are able to generate new genes and modify existing gene structures by duplicating, mobilizing and recombining gene fragments. They can also facilitate cellular functions by sharing their transposase-coding regions. Hence, TE insertions can not only act as simple mutagens but can also alter the elementary functions of the plant genome. Here, we review recent discoveries concerning the contribution of TEs to gene expression in plant genomes and discuss the different mechanisms by which TEs can affect plant gene expression and reduce host defense mechanisms.

Published
2018

27. The Glaciozyma antarctica genome reveals an array of systems that provide sustained responses towards temperature variations in a persistently cold habitat

Author

Firdaus-Raih, Mohd, primary, Hashim, Noor Haza Fazlin, additional, Bharudin, Izwan, additional, Abu Bakar, Mohd Faizal, additional, Huang, Kie Kyon, additional, Alias, Halimah, additional, Lee, Bernard K. B., additional, Mat Isa, Mohd Noor, additional, Mat-Sharani, Shuhaila, additional, Sulaiman, Suhaila, additional, Tay, Lih Jinq, additional, Zolkefli, Radziah, additional, Muhammad Noor, Yusuf, additional, Law, Douglas Sie Nguong, additional, Abdul Rahman, Siti Hamidah, additional, Md-Illias, Rosli, additional, Abu Bakar, Farah Diba, additional, Najimudin, Nazalan, additional, Abdul Murad, Abdul Munir, additional, and Mahadi, Nor Muhammad, additional

Published
2018
Full Text
View/download PDF

34. Draft genome sequence of Pasteurella multocida subsp. multocida strain PMTB, isolated from a buffalo

Author

Yap, Huan Yong, Ghazali, Kamal, Wan Mohamad Nazarie, Wan Fahmi, Mat Isa, Mohd Noor, Zakaria, Zunita, Omar, Abdul Rahman, Yap, Huan Yong, Ghazali, Kamal, Wan Mohamad Nazarie, Wan Fahmi, Mat Isa, Mohd Noor, Zakaria, Zunita, and Omar, Abdul Rahman

Abstract

Pasteurella multocida serotypes B:2 and E:2 are the main causative agents of ruminant hemorrhagic septicemia in Asia and Africa, respectively. Pasteurella multocida strain PMTB was isolated from a buffalo with hemorrhagic septicemia and has been determined to be serotype B:2. Here we report the draft genome sequence of strain PMTB.

Published
2013

37. Sequencing and analysis of chromosome 1 of Eimeria tenella reveals a unique segmental organization

Author

Ling, King-Hwa, primary, Rajandream, Marie-Adele, additional, Rivailler, Pierre, additional, Ivens, Alasdair, additional, Yap, Soon-Joo, additional, Madeira, Alda M.B.N., additional, Mungall, Karen, additional, Billington, Karen, additional, Yee, Wai-Yan, additional, Bankier, Alan T., additional, Carroll, Fionnadh, additional, Durham, Alan M., additional, Peters, Nicholas, additional, Loo, Shu-San, additional, Mat Isa, Mohd Noor, additional, Novaes, Jeniffer, additional, Quail, Michael, additional, Rosli, Rozita, additional, Nor Shamsudin, Mariana, additional, Sobreira, Tiago J.P., additional, Tivey, Adrian R., additional, Wai, Siew-Fun, additional, White, Sarah, additional, Wu, Xikun, additional, Kerhornou, Arnaud, additional, Blake, Damer, additional, Mohamed, Rahmah, additional, Shirley, Martin, additional, Gruber, Arthur, additional, Berriman, Matthew, additional, Tomley, Fiona, additional, Dear, Paul H., additional, and Wan, Kiew-Lian, additional

Published
2007
Full Text
View/download PDF

38. Full genome SNP-based phylogenetic analysis reveals the origin and global spread of Brucella melitensis.

Author

Kim-Kee Tan, Yung-Chie Tan, Li-Yen Chang, Kok Wei Lee, Nore, Siti Sarah, Wai-Yan Yee, Mat Isa, Mohd Noor, Lela Jafar, Faizatul, Chee-Choong Hoh, and AbuBakar, Sazaly

Subjects
BRUCELLOSIS, ZOONOSES, BRUCELLA melitensis, SINGLE nucleotide polymorphisms, PHYLOGENY
Abstract

Background: Brucellosis is an important zoonotic disease that affects both humans and animals. We sequenced the full genome and characterised the genetic diversity of two Brucella melitensis isolates from Malaysia and the Philippines. In addition, we performed a comparative whole-genome single nucleotide polymorphism (SNP) analysis of B. melitensis strains collected from around the world, to investigate the potential origin and the history of the global spread of B. melitensis. Results: Single sequencing runs of each genome resulted in draft genome sequences of MY1483/09 and Phil 1136/12, which covered 99.85% and 99.92% of the complete genome sequences, respectively. The B. melitensis genome sequences, and two B. abortus strains used as the outgroup strains, yielded a total of 13,728 SNP sites. Phylogenetic analysis using whole-genome SNPs and geographical distribution of the isolates revealed spatial clustering of the B. melitensis isolates into five genotypes, I, II, III, IV and V. The Mediterranean strains, identified as genotype I, occupied the basal node of the phylogenetic tree, suggesting that B. melitensis may have originated from the Mediterranean regions. All of the Asian B. melitensis strains clustered into genotype II with the SEA strains, including the two isolates sequenced in this study, forming a distinct clade denoted here as genotype IId. Genotypes III, IV and V of B. melitensis demonstrated a restricted geographical distribution, with genotype III representing the African lineage, genotype IV representing the European lineage and genotype V representing the American lineage. Conclusion: We showed that SNPs retrieved from the B. melitensis draft full genomes were sufficient to resolve the interspecies relationships between B. melitensis strains and to discriminate between the vaccine and endemic strains. Phylogeographic reconstruction of the history of B. melitensis global spread at a finer scale by using whole-genome SNP analyses supported the origin of all B. melitensis strains from the Mediterranean region. The possible global distribution of B. melitensis following the ancient trade routes was also consistent with whole-genome SNP phylogeny. The whole genome SNP phylogenetics analysis, hence is a powerful tool for intraspecies discrimination of closely related species. [ABSTRACT FROM AUTHOR]

Published
2015
Full Text
View/download PDF

39. RNA-seq data from different developmental stages of Rafflesia cantleyifloral buds

Author

Amini, Safoora, Alias, Halimah, Aizat-Juhari, Mohd Afiq, Mat-Isa, Mohd-Noor, Adam, Jumaat Haji, Goh, Hoe-Han, and Wan, Kiew-Lian

Abstract

Rafflesia cantleyi, known as one of the world's largest flowers, is a specialised holoparasite due to dramatic morphological modifications. It possesses highly reduced vegetative structure and only appears as a flower for sexual reproduction. Moreover, it has an unusual life cycle in that its floral bud development takes up to nine months. In order to fully understand the highly modified floral organ structure and long life cycle of R. cantleyi, we used Illumina sequencing technology (HiSeq) for sequence generation followed by de novoassembly of sequence reads. We obtained the RNA-seq data from three different stages of floral bud, representing the early, mid and advanced developmental stages. These data are available viaBioProject accession number PRJNA378435. More than 10.3Gb raw sequence data were generated, corresponding to 102,203,042 raw reads. Following removal of low-quality reads and trimming of adapter sequences, a total of 91,638,836 reads were obtained. De novoassembly of these sequences using Trinity resulted in 89,690 unique transcripts with an N50 of 1653bp. The obtained transcriptomic data will be useful for further study to understand the molecular interactions that result in R. cantleyifloral development.

Published
2017
Full Text
View/download PDF

40. Expression and characterization of thermostable glycogen branching enzyme from Geobacillus mahadia Geo-05.

Author

Mohtar NS, Abdul Rahman MB, Raja Abd Rahman RN, Leow TC, Salleh AB, and Mat Isa MN

Abstract

The glycogen branching enzyme (EC 2.4.1.18), which catalyses the formation of α -1,6-glycosidic branch points in glycogen structure, is often used to enhance the nutritional value and quality of food and beverages. In order to be applicable in industries, enzymes that are stable and active at high temperature are much desired. Using genome mining, the nucleotide sequence of the branching enzyme gene ( glgB ) was extracted from the Geobacillus mahadia Geo-05 genome sequence provided by the Malaysia Genome Institute. The size of the gene is 2013 bp, and the theoretical molecular weight of the protein is 78.43 kDa. The gene sequence was then used to predict the thermostability, function and the three dimensional structure of the enzyme. The gene was cloned and overexpressed in E. coli to verify the predicted result experimentally. The purified enzyme was used to study the effect of temperature and pH on enzyme activity and stability, and the inhibitory effect by metal ion on enzyme activity. This thermostable glycogen branching enzyme was found to be most active at 55 °C, and the half-life at 60 °C and 70 °C was 24 h and 5 h, respectively. From this research, a thermostable glycogen branching enzyme was successfully isolated from Geobacillus mahadia Geo-05 by genome mining together with molecular biology technique., Competing Interests: The authors declare there are no competing interests.

Published
2016
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results