Displaying publications 1 - 20 of 364 in total

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  1. Zulkefli NJ, Mariappan V, Vellasamy KM, Chong CW, Thong KL, Ponnampalavanar S, et al.
    PeerJ, 2016;4:e1802.
    PMID: 26998408 DOI: 10.7717/peerj.1802
    Background. Central intermediary metabolism (CIM) in bacteria is defined as a set of metabolic biochemical reactions within a cell, which is essential for the cell to survive in response to environmental perturbations. The genes associated with CIM are commonly found in both pathogenic and non-pathogenic strains. As these genes are involved in vital metabolic processes of bacteria, we explored the efficiency of the genes in genotypic characterization of Burkholderia pseudomallei isolates, compared with the established pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) schemes. Methods. Nine previously sequenced B. pseudomallei isolates from Malaysia were characterized by PFGE, MLST and CIM genes. The isolates were later compared to the other 39 B. pseudomallei strains, retrieved from GenBank using both MLST and sequence analysis of CIM genes. UniFrac and hierachical clustering analyses were performed using the results generated by both MLST and sequence analysis of CIM genes. Results. Genetic relatedness of nine Malaysian B. pseudomallei isolates and the other 39 strains was investigated. The nine Malaysian isolates were subtyped into six PFGE profiles, four MLST profiles and five sequence types based on CIM genes alignment. All methods demonstrated the clonality of OB and CB as well as CMS and THE. However, PFGE showed less than 70% similarity between a pair of morphology variants, OS and OB. In contrast, OS was identical to the soil isolate, MARAN. To have a better understanding of the genetic diversity of B. pseudomallei worldwide, we further aligned the sequences of genes used in MLST and genes associated with CIM for the nine Malaysian isolates and 39 B. pseudomallei strains from NCBI database. Overall, based on the CIM genes, the strains were subtyped into 33 profiles where majority of the strains from Asian countries were clustered together. On the other hand, MLST resolved the isolates into 31 profiles which formed three clusters. Hierarchical clustering using UniFrac distance suggested that the isolates from Australia were genetically distinct from the Asian isolates. Nevertheless, statistical significant differences were detected between isolates from Malaysia, Thailand and Australia. Discussion. Overall, PFGE showed higher discriminative power in clustering the nine Malaysian B. pseudomallei isolates and indicated its suitability for localized epidemiological study. Compared to MLST, CIM genes showed higher resolution in distinguishing those non-related strains and better clustering of strains from different geographical regions. A closer genetic relatedness of Malaysian isolates with all Asian strains in comparison to Australian strains was observed. This finding was supported by UniFrac analysis which resulted in geographical segregation between Australia and the Asian countries.
  2. Zhu C, Li Y, Liu G, Abdullah AL, Jiang Q
    PeerJ, 2024;12:e16743.
    PMID: 38188162 DOI: 10.7717/peerj.16743
    Nanoplastics (NPs) are an abundant, long-lasting, and widespread type of environmental pollution that is of increasing concern because of the serious threats they might pose to ecosystems and species. Identifying the ecological effects of plastic pollution requires understanding the effects of NPs on aquatic organisms. Here, we used the Pacific white shrimp (Litopenaeus vannamei) as a model species to investigate whether ingestion of polystyrene NPs affects gut microbes and leads to metabolic changes in L. vannamei. The abundance of Proteobacteria increased and that of Bacteroidota decreased after NPs treatment. Specifically, Vibrio spp., photobacterium spp., Xanthomarina spp., and Acinetobacter spp. increased in abundance, whereas Sulfitobacter spp. and Pseudoalteromonas spp. decreased. Histological observations showed that L. vannamei exposed to NP displayed a significantly lower intestinal fold height and damaged intestinal structures compared with the control group. Exposure to NPs also stimulated alkaline phosphatase, lysozyme, and acid phosphatase activity, resulting in an immune response in L. vannamei. In addition, the content of triglycerides, total cholesterol, and glucose were significantly altered after NP exposure. These results provided significant ecotoxicological data that can be used to better understand the biological fate and effects of NPs in L. vannamei.
  3. Zheng W, Mutha NV, Heydari H, Dutta A, Siow CC, Jakubovics NS, et al.
    PeerJ, 2016;4:e1698.
    PMID: 27017950 DOI: 10.7717/peerj.1698
    Background. The gram-negative Neisseria is associated with two of the most potent human epidemic diseases: meningococcal meningitis and gonorrhoea. In both cases, disease is caused by bacteria colonizing human mucosal membrane surfaces. Overall, the genus shows great diversity and genetic variation mainly due to its ability to acquire and incorporate genetic material from a diverse range of sources through horizontal gene transfer. Although a number of databases exist for the Neisseria genomes, they are mostly focused on the pathogenic species. In this present study we present the freely available NeisseriaBase, a database dedicated to the genus Neisseria encompassing the complete and draft genomes of 15 pathogenic and commensal Neisseria species. Methods. The genomic data were retrieved from National Center for Biotechnology Information (NCBI) and annotated using the RAST server which were then stored into the MySQL database. The protein-coding genes were further analyzed to obtain information such as calculation of GC content (%), predicted hydrophobicity and molecular weight (Da) using in-house Perl scripts. The web application was developed following the secure four-tier web application architecture: (1) client workstation, (2) web server, (3) application server, and (4) database server. The web interface was constructed using PHP, JavaScript, jQuery, AJAX and CSS, utilizing the model-view-controller (MVC) framework. The in-house developed bioinformatics tools implemented in NeisseraBase were developed using Python, Perl, BioPerl and R languages. Results. Currently, NeisseriaBase houses 603,500 Coding Sequences (CDSs), 16,071 RNAs and 13,119 tRNA genes from 227 Neisseria genomes. The database is equipped with interactive web interfaces. Incorporation of the JBrowse genome browser in the database enables fast and smooth browsing of Neisseria genomes. NeisseriaBase includes the standard BLAST program to facilitate homology searching, and for Virulence Factor Database (VFDB) specific homology searches, the VFDB BLAST is also incorporated into the database. In addition, NeisseriaBase is equipped with in-house designed tools such as the Pairwise Genome Comparison tool (PGC) for comparative genomic analysis and the Pathogenomics Profiling Tool (PathoProT) for the comparative pathogenomics analysis of Neisseria strains. Discussion. This user-friendly database not only provides access to a host of genomic resources on Neisseria but also enables high-quality comparative genome analysis, which is crucial for the expanding scientific community interested in Neisseria research. This database is freely available at http://neisseria.um.edu.my.
  4. Zanul Abidin Z, Mohd Salleh N, Himratul-Aznita WH, Ahmad SF, Lim GS, Raja Mohd N, et al.
    PeerJ, 2023;11:e15750.
    PMID: 37601266 DOI: 10.7717/peerj.15750
    BACKGROUND: The study's objective is to assess the adherence of C. albicans in different types of denture polymers and the effectiveness of eugenol and commercialized denture cleansers in the removal of C. albicans. Three types of denture base polymers (Lucitone® 199 (High-Impact PMMA), Impact® (conventional PMMA) and Eclipse® (UDMA)) and two hard denture reline materials (Kooliner® and Tokuyama® Rebase II Fast) were used in this study.

    METHODS: Three hundred samples were prepared (6 × 2 mm disc shape) and divided into five groups of denture polymers (n = 60) and further subjected into five treatment groups (Polident®, Steradent, distilled water, eugenol 5-minutes, and eugenol 10-min). Three samples were extracted from each treatment group for baseline data (n = 12). Baseline data were used to calculate the initial number of C. albicans adherence. A 0.5 ml immersion solution from each specimen was cultured on YPD agar and incubated for 48 h at 37 °C. Visible colonies were counted using a colony counter machine (ROCKER Galaxy 230).

    RESULTS: The result showed that the denture base polymer significantly affected the initial adherence (p = 0.007). The removal of C. albicans was also considerably affected by the denture base polymers and denture cleansers (p 

  5. Zakaria MH, Ramaiya SD, Bidin N, Syed NNF, Bujang JS
    PeerJ, 2023;11:e15496.
    PMID: 37456903 DOI: 10.7717/peerj.15496
    BACKGROUND: The social acceptability of wild freshwater macrophytes as locally consumed vegetables is widespread. Freshwater macrophytes have several uses; for example, they can be used as food for humans. This study determined the proximate composition and mineral content of three freshwater macrophyte species, i.e., Eichhornia crassipes, Limnocharis flava, and Neptunia oleracea.

    METHODS: Young shoots of E. crassipes, L. flava, and N. oleracea were collected from shallow channels of Puchong (3°00'11.89″N, 101°42'43.12″E), Ladang 10, Universiti Putra Malaysia (2°58'44.41″N, 101°42'44.45″E), and Kampung Alur Selibong, Langgar (06°5'50.9″N, 100°26'49.8″E), Kedah, Peninsular Malaysia. The nutritional values of these macrophytes were analysed by using a standard protocol from the Association of Official Analytical Chemists. Eight replicates of E. crassipes and L. flava and four replicates of N. oleracea were used for the subsequent analyses.

    RESULTS: In the proximate analysis, N. oleracea possessed the highest percentage of crude protein (29.61%) and energy content (4,269.65 cal g-1), whereas L. flava had the highest percentage of crude fat (5.75%) and ash (18.31%). The proximate composition trend for each species was different; specifically, all of the species possessed more carbohydrates and fewer crude lipids. All of the species demonstrated a similar mineral trend, with high nitrogen and potassium and lower copper contents. Nitrogen and potassium levels ranged from 12,380-40,380 mg kg-1 and from 11,212-33,276 mg kg-1, respectively, and copper levels ranged from 16-27 mg kg-1. The results showed that all three plant species, i.e., E. crassipes, N. oleracea, and L. flava are plant-based sources of macro- and micronutrient beneficial supplements for human consumption.

  6. Zainuddin MF, Kar Fai C, Mohamed MS, Abdul Rahman N', Halim M
    PeerJ, 2022;10:e12833.
    PMID: 35251776 DOI: 10.7717/peerj.12833
    Nowadays, the replacement of petro-diesel with biodiesel has raised the concern among the community for the utilization of improper feedstocks and the cost involved. However, these issues can be solved by producing single cell oil (SCO) from lignocellulosic biomass hydrolysates by oleaginous microorganisms. This study introduced Yarrowia lipolytica JCM 2320 with a desiccated coconut residue (DCR) hydrolysate (obtained from the 2% dilute sulphuric acid pretreatment) as a carbon source in generating SCO. However, common inhibitors formed during acid pretreatment of biomass such as five-hydroxymethylfurfural (HMF), furfural, acetic acid and levulinic acid resulting from the sugar degradations may have detrimental effects towards the fermentation process. To visualize the effect of inhibitors on Y. lipolytica, an inhibitory study was conducted by adding 0.5-5.0 g/L of potential inhibitors to the YPD (yeast, peptone and D-glucose) medium. It was found that the presence of furfural at 0.5 g/L would increase the lag phase, which beyond that was detrimental to Y. lipolytica. Furthermore, increasing the five-hydroxymethylfurfural (HMF) concentration would increase the lag phase of Y. lipolytica, whereas, for acetic acid and levulinic acid, it showed a negligible effect. Detoxification was hence conducted to remove the potential inhibitors from the DCR hydrolysate prior its utilization in the fermentation. To examine the possibility of using adsorption resins for the detoxification of DCR hydrolysate, five different resins were tested (Amberlite® XAD-4, Amberlite® XAD-7, Amberlite® IR 120, Amberlite® IRA 96 and Amberlite® IRA 402) with five different concentrations of 1%, 3%, 5%, 10% and 15% (w/v), respectively. At resin concentration of 10%, Amberlite® XAD-4 recorded the highest SCO yield, 2.90 ± 0.02 g/L, whereas the control and the conventional overliming detoxification method, recorded only 1.29 ± 0.01 g/L and 1.27 ± 0.02 g/L SCO accumulation, respectively. Moreover, the fatty acid profile of the oil produced was rich in oleic acid (33.60%), linoleic acid (9.90%), and palmitic acid (14.90%), which indicates the potential as a good biodiesel raw material.
  7. Zainal Baharin NH, Khairil Mokhtar NF, Mohd Desa MN, Gopalsamy B, Mohd Zaki NN, Yuswan MH, et al.
    PeerJ, 2021;9:e12193.
    PMID: 35003909 DOI: 10.7717/peerj.12193
    The emergence of antibiotic-resistant bacteria has become a significant and ever-increasing threat to global public health, increasing both morbidity and mortality rates, and the financial burden on health services. Infection by drug-resistant bacteria is anticipated to contribute to the demise of almost 10 million people by the year 2050 unless a competent and effective response is devised to engage with this issue. The emergence and spread of resistance are commonly caused by the excessive or inappropriate use of antibiotics and substandard pharmaceuticals. It arises when pathogens adapt to different conditions and develop self-defence mechanisms. Currently, novel antimicrobial peptides (AMPs) have been reported to be the sole cure for some clinical cases of infectious diseases such as sepsis and skin infections, although these agents may, on occasion, require administration together with an adjunctive low-dose antibiotic. Although AMPs are a promising alternative form of anti-microbial therapy and easily applied in the medical sector, they still have limitations that should not be taken lightly. Hence, this review explores the characteristics, advantages and disadvantages of AMPs for their potential in treating antibiotic-resistant pathogens.
  8. Zainal Ariffin SH, Lim KW, Megat Abdul Wahab R, Zainal Ariffin Z, Rus Din RD, Shahidan MA, et al.
    PeerJ, 2022;10:e14174.
    PMID: 36275474 DOI: 10.7717/peerj.14174
    BACKGROUND: There have been promising results published regarding the potential of stem cells in regenerative medicine. However, the vast variety of choices of techniques and the lack of a standard approach to analyse human osteoblast and osteoclast differentiation may reduce the utility of stem cells as a tool in medical applications. Therefore, this review aims to systematically evaluate the findings based on stem cell differentiation to define a standard gene expression profile approach.

    METHODS: This review was performed following the PRISMA guidelines. A systematic search of the study was conducted by retrieving articles from the electronic databases PubMed and Web of Science to identify articles focussed on gene expression and approaches for osteoblast and osteoclast differentiation.

    RESULTS: Six articles were included in this review; there were original articles of in vitro human stem cell differentiation into osteoblasts and osteoclasts that involved gene expression profiling. Quantitative polymerase chain reaction (qPCR) was the most used technique for gene expression to detect differentiated human osteoblasts and osteoclasts. A total of 16 genes were found to be related to differentiating osteoblast and osteoclast differentiation.

    CONCLUSION: Qualitative information of gene expression provided by qPCR could become a standard technique to analyse the differentiation of human stem cells into osteoblasts and osteoclasts rather than evaluating relative gene expression. RUNX2 and CTSK could be applied to detect osteoblasts and osteoclasts, respectively, while RANKL could be applied to detect both osteoblasts and osteoclasts. This review provides future researchers with a central source of relevant information on the vast variety of gene expression approaches in analysing the differentiation of human osteoblast and osteoclast cells. In addition, these findings should enable researchers to conduct accurately and efficiently studies involving isolated human stem cell differentiation into osteoblasts and osteoclasts.

  9. Zahari Z, Lee CS, Tan SC, Mohamad N, Lee YY, Ismail R
    PeerJ, 2015;3:e839.
    PMID: 25870765 DOI: 10.7717/peerj.839
    Aim. Poor sleep quality due to pain has been reported among opioid-dependent male patients on methadone maintenance therapy (MMT) but objective pain data are lacking. This study aimed to investigate the rate of pain-sensitivity using cold pressor test (CPT) and the relationship between pain-sensitivity and sleep quality in this population.
    Methods. A total of 168 male participants were included into the study. Objective pain-tolerance was evaluated at 0 h and at 24 h after the first CPT. Malay version of the Pittsburgh Sleep Quality Index (PSQI) and the subjective opiate withdrawal scale (SOWS) questionnaires were administered to evaluate the quality of sleep and withdrawal symptoms, respectively.
    Results. The mean age of study participants was 37.22 (SD 6.20) years old. Mean daily methadone dose was 76.64 (SD 37.63) mg/day, mean global PSQI score was 5.47 (SD 2.74) and mean averaged SOWS score was 5.43 (SD 6.91). The averaged pain-tolerance time ranged from 7 to 300 s with a mean time of 32.16 (SE 2.72) s, slightly below the cut-off score of 37.53 s. More specifically, 78.6% (n = 132) of participants were identified as pain-sensitive (averaged pain-tolerance time ≤37.53 s), and 36 (21.4%) participants were pain-tolerant (averaged pain-tolerance time >37.53 s). The pain-sensitive group reported poorer sleep quality with mean (SD) PSQI of 5.78 (2.80) compared with the pain-tolerant group with mean (SD) PSQI of 4.31 (2.18) (p = 0.005). With analysis of covariance, pain-sensitive group was found to have higher global PSQI scores (adjusted mean 5.76, 95% CI 5.29; 6.22) than pain-tolerant participants (adjusted mean 4.42, 95% CI 3.52; 5.32) (p = 0.010).
    Conclusions. Majority of opioid-dependent male patients on methadone treatment are pain-sensitive with CPT. Poor sleep quality is associated with cold pressor pain-sensitivity. Pain and sleep complaints in this male population should not be overlooked.
    Study site: Hospital Universiti Sains Malaysia (HUSM) and other MMT clinics (Kota Bharu, Pasir Mas, Pasir Puteh and Bachok), Kelantan, Malaysia
  10. Yusah KM, Foster WA, Reynolds G, Fayle TM
    PeerJ, 2018;6:e4231.
    PMID: 29423344 DOI: 10.7717/peerj.4231
    Background: Competitive interactions in biological communities can be thought of as giving rise to "assembly rules" that dictate the species that are able to co-exist. Ant communities in tropical canopies often display a particular pattern, an "ant mosaic", in which competition between dominant ant species results in a patchwork of mutually exclusive territories. Although ant mosaics have been well-documented in plantation landscapes, their presence in pristine tropical forests remained contentious until recently. Here we assess presence of ant mosaics in a hitherto under-investigated forest stratum, the emergent trees of the high canopy in primary tropical rain forest, and explore how the strength of any ant mosaics is affected by spatial scale, time of day, and sampling method.

    Methods: To test whether these factors might impact the detection of ant mosaics in pristine habitats, we sampled ant communities from emergent trees, which rise above the highest canopy layers in lowland dipterocarp rain forests in North Borneo (38.8-60.2 m), using both baiting and insecticide fogging. Critically, we restricted sampling to only the canopy of each focal tree. For baiting, we carried out sampling during both the day and the night. We used null models of species co-occurrence to assess patterns of segregation at within-tree and between-tree scales.

    Results: The numerically dominant ant species on the emergent trees sampled formed a diverse community, with differences in the identity of dominant species between times of day and sampling methods. Between trees, we found patterns of ant species segregation consistent with the existence of ant mosaics using both methods. Within trees, fogged ants were segregated, while baited ants were segregated only at night.

    Discussion: We conclude that ant mosaics are present within the emergent trees of the high canopy of tropical rain forest in Malaysian Borneo, and that sampling technique, spatial scale, and time of day interact to determine observed patterns of segregation. Restricting sampling to only emergent trees reveals segregatory patterns not observed in ground-based studies, confirming previous observations of stronger segregation with increasing height in the canopy.

  11. Yong CY, Ong HK, Tang HC, Yeap SK, Omar AR, Ho KL, et al.
    PeerJ, 2019;7:e7151.
    PMID: 31341728 DOI: 10.7717/peerj.7151
    The aquaculture of salmonid fishes is a multi-billion dollar industry with production over 3 million tons annually. However, infectious hematopoietic necrosis virus (IHNV), which infects and kills salmon and trout, significantly reduces the revenue of the salmon farming industry. Currently, there is no effective treatment for IHNV infected fishes; therefore, early detection and depopulation of the infected fishes remain the most common practices to contain the spread of IHNV. Apart from hygiene practices in aquaculture and isolation of infected fishes, loss of fishes due to IHNV infection can also be significantly reduced through vaccination programs. In the current review, some of the diagnostic methods for IHNV, spanning from clinical diagnosis to cell culture, serological and molecular methods are discussed in detail. In addition, some of the most significant candidate vaccines for IHNV are also extensively discussed, particularly the DNA vaccines.
  12. Yong CY, Yeap SK, Omar AR, Tan WS
    PeerJ, 2017;5:e3841.
    PMID: 28970971 DOI: 10.7717/peerj.3841
    Nodaviruses are small bipartite RNA viruses which belong to the family of Nodaviridae. They are categorized into alpha-nodavirus, which infects insects, and beta-nodavirus, which infects fishes. Another distinct group of nodavirus infects shrimps and prawns, which has been proposed to be categorized as gamma-nodavirus. Our current review focuses mainly on recent studies performed on nodaviruses. Nodavirus can be transmitted vertically and horizontally. Recent outbreaks have been reported in China, Indonesia, Singapore and India, affecting the aquaculture industry. It also decreased mullet stock in the Caspian Sea. Histopathology and transmission electron microscopy (TEM) are used to examine the presence of nodaviruses in infected fishes and prawns. For classification, virus isolation followed by nucleotide sequencing are required. In contrast to partial sequence identification, profiling the whole transcriptome using next generation sequencing (NGS) offers a more comprehensive comparison and characterization of the virus. For rapid diagnosis of nodavirus, assays targeting the viral RNA based on reverse-transcription PCR (RT-PCR) such as microfluidic chips, reverse-transcription loop-mediated isothermal amplification (RT-LAMP) and RT-LAMP coupled with lateral flow dipstick (RT-LAMP-LFD) have been developed. Besides viral RNA detections, diagnosis based on immunological assays such as enzyme-linked immunosorbent assay (ELISA), immunodot and Western blotting have also been reported. In addition, immune responses of fish and prawn are also discussed. Overall, in fish, innate immunity, cellular type I interferon immunity and humoral immunity cooperatively prevent nodavirus infections, whereas prawns and shrimps adopt different immune mechanisms against nodavirus infections, through upregulation of superoxide anion, prophenoloxidase, superoxide dismutase (SOD), crustin, peroxinectin, anti-lipopolysaccharides and heat shock proteins (HSP). Potential vaccines for fishes and prawns based on inactivated viruses, recombinant proteins or DNA, either delivered through injection, oral feeding or immersion, are also discussed in detail. Lastly, a comprehensive review on nodavirus virus-like particles (VLPs) is presented. In recent years, studies on prawn nodavirus are mainly focused on Macrobrachium rosenbergii nodavirus (MrNV). Recombinant MrNV VLPs have been produced in prokaryotic and eukaryotic expression systems. Their roles as a nucleic acid delivery vehicle, a platform for vaccine development, a molecular tool for mechanism study and in solving the structures of MrNV are intensively discussed.
  13. Yew CT, Gurumoorthy N, Nordin F, Tye GJ, Wan Kamarul Zaman WS, Tan JJ, et al.
    PeerJ, 2022;10:e13704.
    PMID: 35979475 DOI: 10.7717/peerj.13704
    HIV-1 derived lentiviral vector is an efficient transporter for delivering desired genetic materials into the targeted cells among many viral vectors. Genetic material transduced by lentiviral vector is integrated into the cell genome to introduce new functions, repair defective cell metabolism, and stimulate certain cell functions. Various measures have been administered in different generations of lentiviral vector systems to reduce the vector's replicating capabilities. Despite numerous demonstrations of an excellent safety profile of integrative lentiviral vectors, the precautionary approach has prompted the development of integrase-deficient versions of these vectors. The generation of integrase-deficient lentiviral vectors by abrogating integrase activity in lentiviral vector systems reduces the rate of transgenes integration into host genomes. With this feature, the integrase-deficient lentiviral vector is advantageous for therapeutic implementation and widens its clinical applications. This short review delineates the biology of HIV-1-erived lentiviral vector, generation of integrase-deficient lentiviral vector, recent studies involving integrase-deficient lentiviral vectors, limitations, and prospects for neoteric clinical use.
  14. Yeong KC, Takizawa H, Liew TS
    PeerJ, 2018;6:e5811.
    PMID: 30386703 DOI: 10.7717/peerj.5811
    Sabah is a province of Malaysia located on the northern part of the island of Borneo. Most of the leaf beetle fauna studies from this region conducted over the past 15 years have focussed on the mainland habitats while the leaf beetle fauna from island habitats (ca. 500 islands) have largely been overlooked. This study looks into the leaf beetle fauna of 13 small satellite islands off the west coast of Sabah. All specimens were first sorted into morpho-species operational taxonomic unit (OTU) before being identified to species rank where possible based on morphological characters and species names assigned when the specimens fitted the description of species in the literature. We collected 75 OTUs from 35 genera and five subfamilies according to morphology, 12 of which were identifiable to species level. In addition, the DNA barcode for each OTU was cross checked with records in GenBank and Barcoding of Life Data system (BOLD) to verify their identity. The number of species recorded was reduced from 12 species and 63 OTUs (total 75 OTUs) to 12 species and 56 OTUs (total 68 OTUs) after removal of the colour polymorphic species based on DNA barcode analyses. Pulau Gaya has the highest species richness and Pulau Sulug has the lowest species richness. A total of 64 Barcode Index Numbers consisting of 101 DNA barcodes were obtained from the 12 leaf beetle species and 48 OTUs. Based on the DNA barcode analyses, it was possible to confirm several polymorphic OTUs and cryptic species. The mean intraspecific and interspecific genetic divergence were determined as 0.77% and 16.11%, respectively. DNA barcodes of this study show a low similarity with records in GenBank and BOLD, highlighting the lack of representation and the urgency of studying leaf beetles from this region. The study provides the first documentation of leaf beetle fauna from island habitats of Sabah and the first DNA barcoding data for leaf beetles from this part of the world, with the next steps being larger scale sampling over a wider geographical scale for a better understanding of tropical arthropod diversity.
  15. Yeoh Y, Low TY, Abu N, Lee PY
    PeerJ, 2021;9:e12338.
    PMID: 34733591 DOI: 10.7717/peerj.12338
    Resistance to anti-cancer treatments is a critical and widespread health issue that has brought serious impacts on lives, the economy and public policies. Mounting research has suggested that a selected spectrum of patients with advanced colorectal cancer (CRC) tend to respond poorly to both chemotherapeutic and targeted therapeutic regimens. Drug resistance in tumours can occur in an intrinsic or acquired manner, rendering cancer cells insensitive to the treatment of anti-cancer therapies. Multiple factors have been associated with drug resistance. The most well-established factors are the emergence of cancer stem cell-like properties and overexpression of ABC transporters that mediate drug efflux. Besides, there is emerging evidence that signalling pathways that modulate cell survival and drug metabolism play major roles in the maintenance of multidrug resistance in CRC. This article reviews drug resistance in CRC as a result of alterations in the MAPK, PI3K/PKB, Wnt/β-catenin and Notch pathways.
  16. Yek SH, Sethu Pathy T, Yeo DYC, Gan JYS
    PeerJ, 2023;11:e16157.
    PMID: 37868047 DOI: 10.7717/peerj.16157
    Anthropogenic disturbances and seasonal changes significantly impact diversity and community composition of ants, but their effects are often intertwined. We investigated these drivers on Lang Tengah Island, a location with a pronounced monsoon season and three resorts that close during this period. We surveyed four sites, two disturbed and two undisturbed, before and after the monsoon season, using pitfall traps to sample epigaeic ant communities. Undisturbed habitats had higher species diversity, but both habitats (undisturbed and disturbed sites) have a high proportion of ants with characteristics of being encroached by generalist and invasive/tramp ant species. Post-monsoon sampling yielded an increase in species richness and diversity. Seasonal changes, such as monsoonal rains, can temporarily alter ant interactions and resource distribution, potentially maintaining diversity. Future studies should validate these findings for ant communities under similar pressures, using ant composition and functional roles for conservation and management purposes.
  17. Yee CS, Okomoda VT, Hashim F, Waiho K, Sheikh Abdullah SR, Alamanjo C, et al.
    PeerJ, 2021;9:e11217.
    PMID: 33981498 DOI: 10.7717/peerj.11217
    This study investigated the effect of co-culturing microalgae with a floc-forming bacterium. Of the six microalgae isolated from a biofloc sample, only Thalassiosira weissflogii, Chlamydomonas sp. and Chlorella vulgaris were propagated successfully in Conway medium. Hence, these species were selected for the experiment comparing microalgae axenic culture and co-culture with the floc-forming bacterium, Bacillus infantis. Results obtained showed that the co-culture had higher microalgae biomass compared to the axenic culture. A similar trend was also observed concerning the lipid content of the microalgae-bacterium co-cultures. The cell number of B. infantis co-cultured with T. weissflogii increased during the exponential stage until the sixth day, but the other microalgae species experienced a significant early reduction in cell density of the bacteria at the exponential stage. This study represents the first attempt at co-culturing microalgae with B. infantis, a floc-forming bacterium, and observed increased biomass growth and lipid accumulation compared to the axenic culture.
  18. Yap PSX, Chong CW, Ponnampalavanar S, Ramli R, Harun A, Tengku Jamaluddin TZM, et al.
    PeerJ, 2023;11:e16393.
    PMID: 38047021 DOI: 10.7717/peerj.16393
    BACKGROUND: The high burden of extended-spectrum beta-lactamase-producing (ESBL)-producing Enterobacterales worldwide, especially in the densely populated South East Asia poses a significant threat to the global transmission of antibiotic resistance. Molecular surveillance of ESBL-producing pathogens in this region is vital for understanding the local epidemiology, informing treatment choices, and addressing the regional and global implications of antibiotic resistance.

    METHODS: Therefore, an inventory surveillance of the ESBL-Escherichia coli (ESBL-EC) isolates responsible for infections in Malaysian hospitals was conducted. Additionally, the in vitro efficacy of flomoxef and other established antibiotics against ESBL-EC was evaluated.

    RESULTS: A total of 127 non-repetitive ESBL-EC strains isolated from clinical samples were collected during a multicentre study performed in five representative Malaysian hospitals. Of all the isolates, 33.9% were isolated from surgical site infections and 85.8% were hospital-acquired infections. High rates of resistance to cefotaxime (100%), cefepime (100%), aztreonam (100%) and trimethoprim-sulfamethoxazole (100%) were observed based on the broth microdilution test. Carbapenems remained the most effective antibiotics against the ESBL-EC, followed by flomoxef. Antibiotic resistance genes were identified by PCR. The blaCTX-M-1 was the most prevalent ESBL gene, with 28 isolates (22%) harbouring blaCTX-M-1 only, 27 isolates (21.3%) co-harbouring blaCTX-M-1 and blaTEM, and ten isolates (7.9%) co-harbouring blaCTX-M-1, blaTEM and blaSHV. A generalised linear model showed significant antibacterial activity of imipenem against different types of infection. Besides carbapenems, this study also demonstrated a satisfactory antibacterial activity of flomoxef (81.9%) on ESBL-EC, regardless of the types of ESBL genes.

  19. Yap JF, Moy FM, Wan Ahmad WA, Lim YC
    PeerJ, 2024;12:e16906.
    PMID: 38361766 DOI: 10.7717/peerj.16906
    BACKGROUND: School teachers may have an increased risk of cardiovascular disease (CVD), potentially affecting their work productivity. However, limited data exists on the impact of CVD on teachers' productivity in Malaysia. Our objectives were to assess work productivity loss (absenteeism and presenteeism) as well as to determine the associated annual monetary loss among school teachers who experienced incident CVD in Peninsular Malaysia.

    METHODS: We adopted a nested case-control design within a cohort of school teachers. Working teachers from six states of Peninsular Malaysia, and had experienced incident CVD before a right-censored date (31st December 2021) were defined as cases. Incident CVD was operationally defined as the development of non-fatal acute coronary syndrome (ACS), stroke, congestive cardiac failure, deep vein thrombosis or peripheral arterial disease before the censored date. Controls were working teachers who did not acquire an incident CVD before the similar right-censored date. All controls were randomly selected, with a ratio of one case to four controls, from among the working teachers in one of the states in Peninsular Malaysia. We used a shortened version of the Malay-validated World Health Organization-Health and Work Performance Questionnaire (WHO-HPQ) to estimate the workplace productivity effect among teachers with incident CVD (cases). The same questionnaire was distributed to teachers in a single state of Peninsular Malaysia who did not experience incident CVD (controls). Absenteeism, presenteeism and annual monetary loss were computed based on the scoring rules in the WHO-HPQ. Analysis of covariance was performed with covariate adjustment using propensity scores. The bootstrapping method was applied to obtain better estimates of marginal mean differences, along with standard errors (SE) and appropriate effect sizes.

    RESULTS: We recruited 48 cases (baseline mean age = 42.4 years old, 54.2% females) and 192 randomly selected controls (baseline mean age = 36.2 years old, 99.0% females). The majority of the cases had ACS (73.9%). No significant difference was observed in absenteeism between cases and controls. The mean self-rated job performance score was lower for cases (7.63, SE = 0.21) compared to controls (8.60, SE = 0.10). Marginal mean scores of absolute presenteeism among cases (76.30) were lower (p 

  20. Yap HYY, Tan NH, Ng ST, Tan CS, Fung SY
    PeerJ, 2018;6:e4940.
    PMID: 29888137 DOI: 10.7717/peerj.4940
    Background: The highly valued medicinal tiger milk mushroom (also known as Lignosus rhinocerus) has the ability to cure numerous ailments. Its anticancer activities are well explored, and recently a partially purified cytotoxic protein fraction termed F5 from the mushroom's sclerotial cold water extract consisting mainly of fungal serine proteases was found to exhibit potent selective cytotoxicity against a human breast adenocarcinoma cell line (MCF7) with IC50 value of 3.00 μg/ml. However, characterization of its cell death-inducing activity has yet to be established.

    Methods: The mechanism involved in the cytotoxic activities of F5 against MCF7 cells was elucidated by flow cytometry-based apoptosis detection, caspases activity measurement, and expression profiling of apoptosis markers by western blotting. Molecular attributes of F5 were further mined from L. rhinocerus's published genome and transcriptome for future exploration.

    Results and Discussion: Apoptosis induction in MCF7 cells by F5 may involve a cross-talk between the extrinsic and intrinsic apoptotic pathways with upregulation of caspase-8 and -9 activities and a marked decrease of Bcl-2. On the other hand, the levels of pro-apoptotic Bax, BID, and cleaved BID were increased accompanied by observable actin cleavage. At gene level, F5 composed of three predicted non-synonymous single nucleotide polymorphisms (T > C) and an alternative 5' splice site.

    Conclusions: Findings from this study provide an advanced framework for further investigations on cancer therapeutics development from L. rhinocerus.

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