Displaying publications 1 - 20 of 417 in total

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  1. Ghaznavi-Rad E, Goering RV, Nor Shamsudin M, Weng PL, Sekawi Z, Tavakol M, et al.
    Eur J Clin Microbiol Infect Dis, 2011 Nov;30(11):1365-9.
    PMID: 21479532 DOI: 10.1007/s10096-011-1230-1
    The usefulness of mec-associated dru typing in the epidemiological analysis of methicillin-resistant Staphylococcus aureus (MRSA) isolated in Malaysia was investigated and compared with pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), and spa and SCCmec typing. The isolates studied included all MRSA types in Malaysia. Multilocus sequence type ST188 and ST1 isolates were highly clonal by all typing methods. However, the dru typing of ST239 isolates produced the clearest discrimination between SCCmec IIIa and III isolates, yielding more subtypes than any other method. Evaluation of the discriminatory power for each method identified dru typing and PFGE as the most discriminatory, with Simpson's index of diversity (SID) values over 89%, including an isolate which was non-typeable by spa, but dru-typed as dt13j. The discriminatory ability of dru typing, especially with closely related MRSA ST239 strains (e.g., Brazilian and Hungarian), underscores its utility as a tool for the epidemiological investigation of MRSA.
    Matched MeSH terms: Cluster Analysis
  2. Chew TH, Joyce-Tan KH, Akma F, Shamsir MS
    Bioinformatics, 2011 May 1;27(9):1320-1.
    PMID: 21398666 DOI: 10.1093/bioinformatics/btr109
    birgHPC, a bootable Linux Live CD has been developed to create high-performance clusters for bioinformatics and molecular dynamics studies using any Local Area Network (LAN)-networked computers. birgHPC features automated hardware and slots detection as well as provides a simple job submission interface. The latest versions of GROMACS, NAMD, mpiBLAST and ClustalW-MPI can be run in parallel by simply booting the birgHPC CD or flash drive from the head node, which immediately positions the rest of the PCs on the network as computing nodes. Thus, a temporary, affordable, scalable and high-performance computing environment can be built by non-computing-based researchers using low-cost commodity hardware.
    Matched MeSH terms: Cluster Analysis
  3. Sing, Lui Lo, Chen, Cheng Ann, Tzuen, Kiat Yap, Teruaki Yoshida
    MyJurnal
    A comparison of zooplankton abundance and community in the seagrass and non-seagrass areas of Limau-limauan and Bak- Bak waters within the newly established Tun Mustapha Marine Park was made during 15-17 May 2017. Samples were collected via horizontal tow of a 140 μm plankton net. Environmental variables (temperature, salinity, DO, pH, turbidity) showed no significant differences among the study sites. However, zooplankton showed increasing abundance from non-seagrass, seagrass edge, to seagrass areas at Limau-limauan, while abundance values were comparable among the stations at Bak-bak. Overall zooplankton abundance was significantly higher at the seagrass areas relative to the non-seagrass station at Limau-limauan (p < 0.005), while no statistical difference was found at Bak-Bak (p < 0.21). Mean canopy height was 3-fold higher (p < 0.001) at Limau-limauan than Bak-Bak, suggesting the importance of seagrass bed structural complexity in habitat preference for zooplankton. Cluster analysis revealed the zooplankton community from the seagrass area at Limau-limauan was different from that at seagrass edge and non-seagrass areas, which may be attributed to the influence of seagrass meadows in forming characteristic zooplankton compositions. Marked differences in zooplankton composition and abundance even in close vicinity of sites suggest the importance of local small-scale variations in seagrass habitats in shaping the zooplankton community.
    Matched MeSH terms: Cluster Analysis
  4. Koo HC, Kaur S, Chan KQ, Soh WH, Ang YL, Chow WS, et al.
    J Hum Nutr Diet, 2020 10;33(5):670-677.
    PMID: 32250007 DOI: 10.1111/jhn.12753
    INTRODUCTION: Little is known about the relationship of whole-grain intake with dietary fatty acids intake. The present study aimed to assess the whole-grain intake and its relationships with dietary fatty acids intake among multiethnic schoolchildren in Kuala Lumpur, Malaysia.

    METHODS: This cross-sectional study was conducted among 392 schoolchildren aged 9-11 years, cluster sampled from five randomly selected schools in Kuala Lumpur. Whole-grain and fatty acids intakes were assessed by 3-day, 24-h diet recalls. All whole-grain foods were considered irrespective of the amount of whole grain they contained.

    RESULTS: In total, 55.6% (n = 218) were whole-grain consumers. Mean (SD) daily intake of whole grain in the total sample was 5.13 (9.75) g day-1 . In the whole-grain consumer's only sample, mean (SD) intakes reached 9.23 (11.55) g day-1 . Significant inverse associations were found between whole-grain intake and saturated fatty acid (SAFA) intake (r = -0.357; P 

    Matched MeSH terms: Cluster Analysis
  5. Foong CP, Lau NS, Deguchi S, Toyofuku T, Taylor TD, Sudesh K, et al.
    BMC Microbiol, 2014;14:318.
    PMID: 25539583 DOI: 10.1186/s12866-014-0318-z
    Special features of the Japanese ocean include its ranges of latitude and depth. This study is the first to examine the diversity of Class I and II PHA synthases (PhaC) in DNA samples from pelagic seawater taken from the Japan Trench and Nankai Trough from a range of depths from 24 m to 5373 m. PhaC is the key enzyme in microorganisms that determines the types of monomer units that are polymerized into polyhydroxyalkanoate (PHA) and thus affects the physicochemical properties of this thermoplastic polymer. Complete putative PhaC sequences were determined via genome walking, and the activities of newly discovered PhaCs were evaluated in a heterologous host.
    Matched MeSH terms: Cluster Analysis
  6. Saeed F, Ahmed A, Shamsir MS, Salim N
    J Comput Aided Mol Des, 2014 Jun;28(6):675-84.
    PMID: 24830925 DOI: 10.1007/s10822-014-9750-2
    The cluster-based compound selection is used in the lead identification process of drug discovery and design. Many clustering methods have been used for chemical databases, but there is no clustering method that can obtain the best results under all circumstances. However, little attention has been focused on the use of combination methods for chemical structure clustering, which is known as consensus clustering. Recently, consensus clustering has been used in many areas including bioinformatics, machine learning and information theory. This process can improve the robustness, stability, consistency and novelty of clustering. For chemical databases, different consensus clustering methods have been used including the co-association matrix-based, graph-based, hypergraph-based and voting-based methods. In this paper, a weighted cumulative voting-based aggregation algorithm (W-CVAA) was developed. The MDL Drug Data Report (MDDR) benchmark chemical dataset was used in the experiments and represented by the AlogP and ECPF_4 descriptors. The results from the clustering methods were evaluated by the ability of the clustering to separate biologically active molecules in each cluster from inactive ones using different criteria, and the effectiveness of the consensus clustering was compared to that of Ward's method, which is the current standard clustering method in chemoinformatics. This study indicated that weighted voting-based consensus clustering can overcome the limitations of the existing voting-based methods and improve the effectiveness of combining multiple clusterings of chemical structures.
    Matched MeSH terms: Cluster Analysis*
  7. Wahab IR, Blagojević PD, Radulović NS, Boylan F
    Chem Biodivers, 2011 Nov;8(11):2005-14.
    PMID: 22083913 DOI: 10.1002/cbdv.201100135
    Analysis by GC and GC/MS of the essential oil obtained from Malaysian Curcuma mangga Val. & Zijp (Zingiberaceae) rhizomes allowed the identification of 97 constituents, comprising 89.5% of the total oil composition. The major compounds were identified as myrcene (1; 46.5%) and β-pinene (2; 14.6%). The chemical composition of this and additional 13 oils obtained from selected Curcuma L. taxa were compared using multivariate statistical analyses (agglomerative hierarchical cluster analysis and principal component analysis). The results of the statistical analyses of this particular data set pointed out that 1 could be potentially used as a valuable infrageneric chemotaxonomical marker for C. mangga. Moreover, it seems that C. mangga, C. xanthorrhiza Roxb., and C. longa L. are, with respect to the volatile secondary metabolites, closely related. In addition, comparison of the essential oil profiles revealed a potential influence of the environmental (geographical) factors, alongside with the genetic ones, on the production of volatile secondary metabolites in Curcuma taxa.
    Matched MeSH terms: Cluster Analysis
  8. Ng KT, Oong XY, Lim SH, Chook JB, Takebe Y, Chan YF, et al.
    Clin Infect Dis, 2018 07 02;67(2):261-268.
    PMID: 29385423 DOI: 10.1093/cid/ciy063
    Background: Rhinovirus (RV) is one of the main viral etiologic agents of acute respiratory illnesses. Despite the heightened disease burden caused by RV, the viral factors that increase the severity of RV infection, the transmission pattern, and seasonality of RV infections remain unclear.

    Methods: An observational study was conducted among 3935 patients presenting with acute upper respiratory illnesses in the ambulatory settings between 2012 and 2014.

    Results: The VP4/VP2 gene was genotyped from all 976 RV-positive specimens, where the predominance of RV-A (49%) was observed, followed by RV-C (38%) and RV-B (13%). A significant regression in median nasopharyngeal viral load (VL) (P < .001) was observed, from 883 viral copies/µL at 1-2 days after symptom onset to 312 viral copies/µL at 3-4 days and 158 viral copies/µL at 5-7 days, before declining to 35 viral copies/µL at ≥8 days. In comparison with RV-A (median VL, 217 copies/µL) and RV-B (median VL, 275 copies/µL), RV-C-infected subjects produced higher VL (505 copies/µL; P < .001). Importantly, higher RV VL (median, 348 copies/µL) was associated with more severe respiratory symptoms (Total Symptom Severity Score ≥17, P = .017). A total of 83 phylogenetic-based transmission clusters were identified in the population. It was observed that the relative humidity was the strongest environmental predictor of RV seasonality in the tropical climate.

    Conclusions: Our findings underline the role of VL in increasing disease severity attributed to RV-C infection, and unravel the factors that fuel the population transmission dynamics of RV.

    Matched MeSH terms: Cluster Analysis
  9. Muhammad SA, Seow EK, Mohd Omar AK, Rodhi AM, Mat Hassan H, Lalung J, et al.
    Sci Justice, 2018 Jan;58(1):59-66.
    PMID: 29332695 DOI: 10.1016/j.scijus.2017.05.008
    A total of 33 crude palm oil samples were randomly collected from different regions in Malaysia. Stable carbon isotopic composition (δ13C) was determined using Flash 2000 elemental analyzer while hydrogen and oxygen isotopic compositions (δ2H and δ18O) were analyzed by Thermo Finnigan TC/EA, wherein both instruments were coupled to an isotope ratio mass spectrometer. The bulk δ2H, δ18O and δ13C of the samples were analyzed by Hierarchical Cluster Analysis (HCA), Principal Component Analysis (PCA) and Orthogonal Partial Least Square-Discriminant Analysis (OPLS-DA). Unsupervised HCA and PCA methods have demonstrated that crude palm oil samples were grouped into clusters according to respective state. A predictive model was constructed by supervised OPLS-DA with good predictive power of 52.60%. Robustness of the predictive model was validated with overall accuracy of 71.43%. Blind test samples were correctly assigned to their respective cluster except for samples from southern region. δ18O was proposed as the promising discriminatory marker for discerning crude palm oil samples obtained from different regions. Stable isotopes profile was proven to be useful for origin traceability of crude palm oil samples at a narrower geographical area, i.e. based on regions in Malaysia. Predictive power and accuracy of the predictive model was expected to improve with the increase in sample size. Conclusively, the results in this study has fulfilled the main objective of this work where the simple approach of combining stable isotope analysis with chemometrics can be used to discriminate crude palm oil samples obtained from different regions in Malaysia. Overall, this study shows the feasibility of this approach to be used as a traceability assessment of crude palm oils.
    Matched MeSH terms: Cluster Analysis
  10. Chai LC, Kong BH, Elemfareji OI, Thong KL
    PLoS One, 2012;7(5):e36201.
    PMID: 22662115 DOI: 10.1371/journal.pone.0036201
    Salmonella enterica serovar Typhi (S. Typhi) is strictly a human intracellular pathogen. It causes acute systemic (typhoid fever) and chronic infections that result in long-term asymptomatic human carriage. S. Typhi displays diverse disease manifestations in human infection and exhibits high clonality. The principal factors underlying the unique lifestyle of S. Typhi in its human host during acute and chronic infections remain largely unknown and are therefore the main objective of this study.
    Matched MeSH terms: Cluster Analysis
  11. Roslan R, Othman RM, Shah ZA, Kasim S, Asmuni H, Taliba J, et al.
    Comput Biol Med, 2010 Jun;40(6):555-64.
    PMID: 20417930 DOI: 10.1016/j.compbiomed.2010.03.009
    Protein-protein interactions (PPIs) play a significant role in many crucial cellular operations such as metabolism, signaling and regulations. The computational methods for predicting PPIs have shown tremendous growth in recent years, but problem such as huge false positive rates has contributed to the lack of solid PPI information. We aimed at enhancing the overlap between computational predictions and experimental results in an effort to partially remove PPIs falsely predicted. The use of protein function predictor named PFP() that are based on shared interacting domain patterns is introduced in this study with the purpose of aiding the Gene Ontology Annotations (GOA). We used GOA and PFP() as agents in a filtering process to reduce false positive pairs in the computationally predicted PPI datasets. The functions predicted by PFP() were extracted from cross-species PPI data in order to assign novel functional annotations for the uncharacterized proteins and also as additional functions for those that are already characterized by the GO (Gene Ontology). The implementation of PFP() managed to increase the chances of finding matching function annotation for the first rule in the filtration process as much as 20%. To assess the capability of the proposed framework in filtering false PPIs, we applied it on the available S. cerevisiae PPIs and measured the performance in two aspects, the improvement made indicated as Signal-to-Noise Ratio (SNR) and the strength of improvement, respectively. The proposed filtering framework significantly achieved better performance than without it in both metrics.
    Matched MeSH terms: Cluster Analysis
  12. Drinkwater R, Schnell IB, Bohmann K, Bernard H, Veron G, Clare E, et al.
    Mol Ecol Resour, 2019 Jan;19(1):105-117.
    PMID: 30225935 DOI: 10.1111/1755-0998.12943
    The application of high-throughput sequencing (HTS) for metabarcoding of mixed samples offers new opportunities in conservation biology. Recently, the successful detection of prey DNA from the guts of leeches has raised the possibility that these, and other blood-feeding invertebrates, might serve as useful samplers of mammals. Yet little is known about whether sympatric leech species differ in their feeding preferences, and whether this has a bearing on their relative suitability for monitoring local mammalian diversity. To address these questions, we collected spatially matched samples of two congeneric leech species Haemadipsa picta and Haemadipsa sumatrana from lowland rainforest in Borneo. For each species, we pooled ~500 leeches into batches of 10 individuals, performed PCR to target a section of the mammalian 16S rRNA locus and undertook sequencing of amplicon libraries using an Illumina MiSeq. In total, we identified sequences from 14 mammalian genera, spanning nine families and five orders. We found greater numbers of detections, and higher diversity of OTUs, in H. picta compared with H. sumatrana, with rodents only present in the former leech species. However, comparison of samples from across the landscape revealed no significant difference in mammal community composition between the leech species. We therefore suggest that H. picta is the more suitable iDNA sampler in this degraded Bornean forest. We conclude that the choice of invertebrate sampler can influence the detectability of different mammal groups and that this should be accounted for when designing iDNA studies.
    Matched MeSH terms: Cluster Analysis
  13. Juhlin K, Karimi G, Andér M, Camilli S, Dheda M, Har TS, et al.
    Drug Saf, 2015 Apr;38(4):373-82.
    PMID: 25687792 DOI: 10.1007/s40264-015-0271-2
    Substandard medicines, whether the result of intentional manipulation or lack of compliance with good manufacturing practice (GMP) or good distribution practice (GDP), pose a significant potential threat to patient safety. Spontaneous adverse drug reaction reporting systems can contribute to identification of quality problems that cause unwanted and/or harmful effects, and to identification of clusters of lack of efficacy. In 2011, the Uppsala Monitoring Centre (UMC) constructed a novel algorithm to identify reporting patterns suggestive of substandard medicines in spontaneous reporting, and applied it to VigiBase(®), the World Health Organization's global individual case safety report database. The algorithm identified some historical clusters related to substandard products, which were later able to be confirmed in the literature or by contact with national centres (NCs). As relevant and detailed information is often lacking in the VigiBase reports but might be available at the reporting NC, further evaluation of the algorithm was undertaken with involvement from NCs.
    Matched MeSH terms: Cluster Analysis
  14. Htet AS, Bjertness MB, Sherpa LY, Kjøllesdal MK, Oo WM, Meyer HE, et al.
    BMC Public Health, 2016 12 05;16(1):1225.
    PMID: 27919240
    BACKGROUND: Recent societal and political reforms in Myanmar may upturn the socio-economy and, thus, contribute to the country's health transition. Baseline data on urban-rural disparities in non-communicable disease (NCD) risk factors are not thoroughly described in this country which has been relatively closed for more than five decades. We aim to investigate urban-rural differences in mean values and the prevalence of selected behavioral and metabolic risk factors for non-communicable diseases and 10-years risk in development of coronary heart diseases (CHD).

    METHODS: Two cross-sectional studies were conducted in urban and rural areas of Yangon Region in 2013 and 2014 respectively, using the WHO STEPwise approach to surveillance of risk factors of NCDs. Through a multi-stage cluster sampling method, 1486 participants were recruited.

    RESULTS: Age-standardized prevalence of the behavioral risk factors tended to be higher in the rural than urban areas for all included factors and significantly higher for alcohol drinking (19.9% vs. 13.9%; p = 0.040) and low fruit & vegetable consumption (96.7% vs. 85.1%; p = 0.001). For the metabolic risk factors, the tendency was opposite, with higher age-standardized prevalence estimates in urban than rural areas, significantly for overweight and obesity combined (40.9% vs. 31.2%; p = 0.023), obesity (12.3% vs.7.7%; p = 0.019) and diabetes (17.2% vs. 9.2%; p = 0.024). In sub-group analysis by gender, the prevalence of hypercholesterolemia and hypertriglyceridemia were significantly higher in urban than rural areas among males, 61.8% vs. 40.4%; p = 0.002 and 31.4% vs. 20.7%; p = 0.009, respectively. Mean values of age-standardized metabolic parameters showed higher values in urban than rural areas for both male and female. Based on WHO age-standardized Framingham risk scores, 33.0% (95% CI = 31.7-34.4) of urban dwellers and 27.0% (95% CI = 23.5-30.8) of rural dwellers had a moderate to high risk of developing CHD in the next 10 years.

    CONCLUSION: The metabolic risk factors, as well as a moderate or high ten-year risk of CHD were more common among urban residents whereas behavioral risk factors levels were higher in among the rural people of Yangon Region. The high prevalences of NCD risk factors in both urban and rural areas call for preventive measures to reduce the future risk of NCDs in Myanmar.

    Matched MeSH terms: Cluster Analysis
  15. May Z, Alam MK, Mahmud MS, Rahman NAA
    PLoS One, 2020;15(11):e0242022.
    PMID: 33186372 DOI: 10.1371/journal.pone.0242022
    Damage assessment is a key element in structural health monitoring of various industrial applications to understand well and predict the response of the material. The big uncertainty in carbon fiber composite materials response is because of variability in the initiation and propagation of damage. Developing advanced tools to design with composite materials, methods for characterizing several damage modes during operation are required. While there is a significant amount of work on the analysis of acoustic emission (AE) from different composite materials and many loading cases, this research focuses on applying an unsupervised clustering method for separating AE data into several groups with distinct evolution. In this paper, we develop an adaptive sampling and unsupervised bivariate data clustering techniques to characterize the several damage initiations of a composite structure in different lay-ups. An adaptive sampling technique pre-processes the AE features and eliminates redundant AE data samples. The reduction of unnecessary AE data depends on the requirements of the proposed bivariate data clustering technique. The bivariate data clustering technique groups the AE data (dependent variable) with respect to the mechanical data (independent variable) to assess the damage of the composite structure. Tensile experiments on carbon fiber reinforced composite laminates (CFRP) in different orientations are carried out to collect mechanical and AE data and demonstrate the damage modes. Based on the mechanical stress-strain data, the results show the dominant damage regions in different lay-ups of specimens and the definition of the different states of damage. In addition, the states of the damage are observed using Scanning Electron Microscope (SEM) analysis. Based on the AE data, the results show that the strong linear correlation between AE and mechanical energy, and the classification of various modes of damage in all lay-ups of specimens forming clusters of AE energy with respect to the mechanical energy. Furthermore, the validation of the cluster-based characterization and improvement of the sensitivity of the damage modes classification are observed by the combined knowledge of AE and mechanical energy and time-frequency spectrum analysis.
    Matched MeSH terms: Cluster Analysis
  16. Tee KK, Kantor R, Sungkanuparph S, Takebe Y, Li P, Ditangco R, et al.
    J Acquir Immune Defic Syndr, 2015 Sep 01;70(1):e28-30.
    PMID: 25835606 DOI: 10.1097/QAI.0000000000000614
    Matched MeSH terms: Cluster Analysis
  17. Ilias IA, Negishi K, Yasue K, Jomura N, Morohashi K, Baharum SN, et al.
    J Plant Res, 2019 Mar;132(2):159-172.
    PMID: 30341720 DOI: 10.1007/s10265-018-1067-0
    Expansin is a non-enzymatic protein which plays a pivotal role in cell wall loosening by inducing stress relaxation and extension in the plant cell wall. Previous studies on Arabidopsis, Petunia × hybrida, and tomato demonstrated that the suppression of expansin gene expression reduced plant growth but expansin overexpression does not necessarily promotes growth. In this study, both expansin gene suppression and overexpression in dark-grown transgenic Arabidopsis seedlings resulted in reduced hypocotyl length at late growth stages with a more pronounced effect for the overexpression. This defect in hypocotyl elongation raises questions about the molecular effect of expansin gene manipulation. RNA-seq analysis of the transcriptomic changes between day 3 and day 5 seedlings for both transgenic lines found numerous differentially expressed genes (DEGs) including transcription factors and hormone-related genes involved in different aspects of cell wall development. These DEGs imply that the observed hypocotyl growth retardation is a consequence of the concerted effect of regulatory factors and multiple cell-wall related genes, which are important for cell wall remodelling during rapid hypocotyl elongation. This is further supported by co-expression analysis through network-centric approach of differential network cluster analysis. This first transcriptome-wide study of expansin manipulation explains why the effect of expansin overexpression is greater than suppression and provides insights into the dynamic nature of molecular regulation during etiolation.
    Matched MeSH terms: Cluster Analysis
  18. Lokanathan Y, Mohd-Adnan A, Wan KL, Nathan S
    BMC Genomics, 2010;11:76.
    PMID: 20113487 DOI: 10.1186/1471-2164-11-76
    Cryptocaryon irritans is a parasitic ciliate that causes cryptocaryonosis (white spot disease) in marine fish. Diagnosis of cryptocaryonosis often depends on the appearance of white spots on the surface of the fish, which are usually visible only during later stages of the disease. Identifying suitable biomarkers of this parasite would aid the development of diagnostic tools and control strategies for C. irritans. The C. irritans genome is virtually unexplored; therefore, we generated and analyzed expressed sequence tags (ESTs) of the parasite to identify genes that encode for surface proteins, excretory/secretory proteins and repeat-containing proteins.
    Matched MeSH terms: Cluster Analysis
  19. Waiho K, Fazhan H, Shahreza MS, Moh JH, Noorbaiduri S, Wong LL, et al.
    PLoS One, 2017;12(1):e0171095.
    PMID: 28135340 DOI: 10.1371/journal.pone.0171095
    Adequate genetic information is essential for sustainable crustacean fisheries and aquaculture management. The commercially important orange mud crab, Scylla olivacea, is prevalent in Southeast Asia region and is highly sought after. Although it is a suitable aquaculture candidate, full domestication of this species is hampered by the lack of knowledge about the sexual maturation process and the molecular mechanisms behind it, especially in males. To date, data on its whole genome is yet to be reported for S. olivacea. The available transcriptome data published previously on this species focus primarily on females and the role of central nervous system in reproductive development. De novo transcriptome sequencing for the testes of S. olivacea from immature, maturing and mature stages were performed. A total of approximately 144 million high-quality reads were generated and de novo assembled into 160,569 transcripts with a total length of 142.2 Mb. Approximately 15-23% of the total assembled transcripts were annotated when compared to public protein sequence databases (i.e. UniProt database, Interpro database, Pfam database and Drosophila melanogaster protein database), and GO-categorised with GO Ontology terms. A total of 156,181 high-quality Single-Nucleotide Polymorphisms (SNPs) were mined from the transcriptome data of present study. Transcriptome comparison among the testes of different maturation stages revealed one gene (beta crystallin like gene) with the most significant differential expression-up-regulated in immature stage and down-regulated in maturing and mature stages. This was further validated by qRT-PCR. In conclusion, a comprehensive transcriptome of the testis of orange mud crabs from different maturation stages were obtained. This report provides an invaluable resource for enhancing our understanding of this species' genome structure and biology, as expressed and controlled by their gonads.
    Matched MeSH terms: Cluster Analysis
  20. Lim JJ, Wan Zurinah WN, Mouly V, Norwahidah AK
    Oxid Med Cell Longev, 2019;2019:9141343.
    PMID: 30774750 DOI: 10.1155/2019/9141343
    Human skeletal muscle is a vital organ involved in movement and force generation. It suffers from deterioration in mass, strength, and regenerative capacity in sarcopenia. Skeletal muscle satellite cells are involved in the regeneration process in response to muscle loss. Tocotrienol, an isomer of vitamin E, was reported to have a protective effect on cellular aging. This research is aimed at determining the modulation of tocotrienol-rich fraction (TRF) on the gene expressions of stress-induced premature senescence (SIPS) human skeletal muscle myoblasts (CHQ5B). CHQ5B cells were divided into three groups, i.e., untreated young control, SIPS control (treated with 1 mM hydrogen peroxide), and TRF-posttreated groups (24 hours of 50 μg/mL TRF treatment after SIPS induction). The differential gene expressions were assessed using microarray, GSEA, and KEGG pathway analysis. Results showed that TRF treatment significantly regulated the gene expressions, i.e., p53 (RRM2B, SESN1), ErbB (EREG, SHC1, and SHC3), and FoxO (MSTN, SMAD3) signalling pathways in the SIPS myoblasts compared to the SIPS control group (p < 0.05). TRF treatment modulated the proliferation capacity of SIPS myoblasts through regulation of ErbB (upregulation of expression of EREG, SHC1, and SHC3) and FoxO (downregulation of expression of MSTN and SMAD3) and maintaining the renewal of satellite cells through p53 signalling (upregulation of RRM2B and SESN1), MRF, cell cycle, and Wnt signalling pathways.
    Matched MeSH terms: Cluster Analysis
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