Displaying publications 361 - 380 of 398 in total

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  1. Miglani S, Ansari I, Patro S, Mohanty A, Mansoori S, Ahuja B, et al.
    PeerJ, 2021;9:e12214.
    PMID: 34631321 DOI: 10.7717/peerj.12214
    OBJECTIVE: The goal of this systematic review and meta-analysis is to determine the performance of 4% Articaine vs. 2% Lidocaine for mandibular and maxillary block and infiltration anaesthesia in patients with irreversible pulpitis (IP).

    METHODS: PubMed/MEDLINE, Cochrane Central Register of Controlled Trials, Web of Science, Google Scholar, and Open Gray were used to conduct a thorough literature search. A manual search of the reference lists of the publications found was also carried out. Two reviewers critically evaluated the papers for inclusion and exclusion criteria, and data extraction was done on the selected publications. The Cochrane Collaboration Tool and the Minors checklist were used to assess the quality of the selected studies for randomised controlled trials (RCTs) and non-randomised studies, respectively. The RevMan software was used to perform a meta-analysis of the pooled data and subgroups according to the technique of anaesthetic solution delivery, as well as a sensitivity analysis (P 

  2. Low CF, Shamsir MS, Mohamed-Hussein ZA, Baharum SN
    PeerJ, 2019;7:e6568.
    PMID: 30984478 DOI: 10.7717/peerj.6568
    Pathologically relevant behaviors of Vibrio, such as the expression of virulence factors, biofilm production, and swarming motility, have been shown to be controlled by quorum sensing. The autoinducer-2 quorum sensing receptor protein LuxP is one of the target proteins for drug development to suppress the virulence of Vibrio. Here, we reported the potential molecular interaction of fatty acids identified in vibriosis-resistant grouper with LuxP. Fatty acid, 4-oxodocosahexaenoic acid (4R8) showed significant binding affinity toward LuxP (-6.0 kcal/mol) based on molecular docking analysis. The dynamic behavior of the protein-ligand complex was illustrated by molecular dynamic simulations. The fluctuation of the protein backbone, the stability of ligand binding, and hydrogen bond interactions were assessed, suggesting 4R8 possesses potential interaction with LuxP, which was supported by the low binding free energy (-29.144 kJ/mol) calculated using the molecular mechanics Poisson-Boltzmann surface area.
  3. Ibrahim NF, Abd Hamid M, Mohd Akhir MF, Chuan Ong M, Wan Talaat WIA, Idris I
    PeerJ, 2023;11:e16203.
    PMID: 38025728 DOI: 10.7717/peerj.16203
    BACKGROUND: The natural hydrodynamic process of Kuala Nerus, Terengganu, has changed since the extension of Sultan Mahmud Airport runway in 2008. Consequently, severe coastal erosion has occurred in the area, particularly during the northeast monsoon season (NEM). Numerous types of coastal defense structures (CDS) have been constructed to protect the coastline. Despite the loss of esthetic values, the effect of CDS construction on marine organisms in the area remains unknown. Hence, this study aims to assess the ecological aspects of macrobenthic compositions at the CDS area of Kuala Nerus, Terengganu, based on the differences between the southwest (SWM) and northeast (NEM) monsoon seasons.

    METHODS: Macrobenthos were collected from the sediment in July (SWM) and December 2021 (NEM) using the Ponar grab at 12 substations from five sampling stations.

    RESULTS: The density of macrobenthos was higher in SWM (48,190.82 ind./m2) than in NEM (24,504.83 ind./m2), with phylum Mollusca recording the highest species composition (60-99.3%). The macrobenthos species had a low to moderate level of diversity (H' = 1.4-3.1) with the species were almost evenly distributed (J' = 0.2-0.8). Windward substations exhibited coarser grain sizes (38.56%-86.84%), whereas landward substations exhibited very fine grain sizes (44.26%-86.70%). The SWM season recorded a higher organic matter content (1.6%-6.33%) than the NEM season (0.4%-3.1%). However, metal concentrations in the surface sediment were within the safe range and permissible limits for both seasons, inferring that the macrobenthos composition was unaffected.

    DISCUSSION: This study demonstrated that the CDS associated with the monsoon system has controlled the hydrodynamics and nearshore sedimentary processes in the Kuala Nerus coastal zone, thereby affecting the macrobenthos population, in terms of richness and density. The ecological and energetic effects of the coastal structures in different seasons have resulted in a more significant result, with the SWM exhibiting a higher macrobenthos composition than the NEM.

  4. Beh YH, Halim MS, Ariffin Z
    PeerJ, 2023;11:e16469.
    PMID: 38025677 DOI: 10.7717/peerj.16469
    BACKGROUND: This study aimed to evaluate the load capacity of maxillary central incisors with simulated flared root canal restored with different fiber-reinforced composite (FRC) post cemented with either self-adhesive or self-etch resin cement and its mode of fracture.

    METHODS: Sixty-five extracted maxillary incisors were decoronated, its canal was artificially flared and randomly categorized into group tFRC (tapered FRC post) (n = 22), mFRC (multi-FRC post) (n = 21), and DIS-FRC (direct individually shaped-FRC (DIS-FRC) post) (n = 22), which were further subdivided based on cementation resin. The posts were cemented and a standardized resin core was constructed. After thermocycling, the samples were loaded statically and the maximum load was recorded.

    RESULTS: The load capacity of the maxillary central incisor was influenced by the different FRC post system and not the resin cement (p = 0.289), and no significant interaction was found between them. Group mFRC (522.9N) yielded a significantly higher load capacity compared to DIS-FRC (421.1N). Overall, a 55% favorable fracture pattern was observed, and this was not statistically significant.

    CONCLUSION: Within the limitation of the study, it can be concluded that prefabricated FRC posts outperform DIS-FRC posts in terms of the load capacity of a maxillary central incisor with a simulated flared root canal. The cementation methods whether a self-adhesive or self-etch resin cement, was not demonstrated to influence the load capacity of a maxillary central incisor with a flared root canal. There were no significant differences between the favorable and non-favorable fracture when FRC post systems were used to restored a maxillary central incisor with a flared root canal.

  5. 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.
  6. Deng N, Soh KG, Abdullah B, Huang D
    PeerJ, 2023;11:e16638.
    PMID: 38111665 DOI: 10.7717/peerj.16638
    BACKGROUND: Over the past decade, the popularity of racket sports has surged. Plyometric training (PT) has been the focus of extensive research because of the proven benefits it provides to athletes. However, there is a lack of systematic reviews and meta-analyses specifically evaluating the impact of PT on physical fitness metrics in racket sport athletes. This study aimed to conduct a comprehensive review and analysis of evidence derived from randomized controlled trials (RCTs) to evaluate the effects of PT on measures of physical fitness among racket sports athletes.

    METHODS: The electronic databases PubMed, Web of Science, SCOPUS, and SPORTDiscus were systematically searched up to June 2023 without placing any restrictions on the publication dates. The PICOS method was adopted to establish the inclusion criteria: (a) healthy athletes who participate in racket sports; (b) a PT program; (c) a control group; (d) assessment of physical fitness components pre- and post-PT; and (e) RCTs. The records' methodological quality was assessed utilizing the Physiotherapy Evidence Database (PEDro) scale. The certainty in the evidence related to each outcome was evaluated using the Grading of Recommendations Assessment, Development, and Evaluation (GRADE) assessment. A random-effects model was used to calculate effect sizes (ES; Hedges' g) between experimental and control groups.

    RESULTS: There were 14 eligible studies of moderate-to-high-quality, involving 746 athletes in total. The results revealed small-to-moderate effects (p < 0.05) of PT on muscle power (ES = 0.46), muscle strength (ES = 0.50), sprint speed (ES = 0.45), change of direction ability (ES = 0.76), and reaction time (ES = 0.67), while no clear evidence was found on balance and flexibility. The training-induced changes in muscle power showed no significant difference (p > 0.05) between youth (ES = 0.72) and adults (ES = 0.40). There were also similar muscle power improvements (ES = 0.36-0.54 vs 0.38-0.56, all p > 0.05) for a length of ≤7 weeks with ≤14 total PT sessions vs >7 weeks with >14 total PT sessions, and ≤2 weekly sessions vs >2 sessions. No adverse effects were reported in the included studies regarding the PT intervention. The certainty of evidence varied from very low to moderate. Conclusions: Our findings demonstrated that PT has positive effects on important indices of physical fitness among athletes participating in racket sports. Future studies are required to clarify the optimal doses and examine interactions among training variables to further promote the physical fitness of this specific population.

  7. Song K, Chen L, Suo N, Kong X, Li J, Wang T, et al.
    PeerJ, 2023;11:e16476.
    PMID: 38084141 DOI: 10.7717/peerj.16476
    BACKGROUND: Pseudomonas aeruginosa is a highly prevalent bacterial species known for its ability to cause various infections and its remarkable adaptability and biofilm-forming capabilities. In earlier work, we conducted research involving the screening of 33 metabolites obtained from a commercial source against two prevalent bacterial strains, Escherichia coli and Staphylococcus aureus. Through screening assays, we discovered a novel malic acid combination (MAC) consisting of malic acid, citric acid, glycine, and hippuric acid, which displayed significant inhibitory effects. However, the precise underlying mechanism and the potential impact of the MAC on bacterial biofilm formation remain unknown and warrant further investigation.

    METHODS: To determine the antibacterial effectiveness of the MAC against Pseudomonas aeruginosa, we conducted minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) assays. Transmission electron microscopy (TEM) and scanning electron microscopy (SEM) techniques were employed to observe bacterial morphology and biofilm formation. We further performed a biofilm inhibition assay to assess the effect of the MAC on biofilm formation. Whole-transcriptome sequencing and bioinformatics analysis were employed to elucidate the antibacterial mechanism of the MAC. Additionally, the expression levels of differentially expressed genes were validated using the real-time PCR approach.

    RESULTS: Our findings demonstrated the antibacterial activity of the MAC against P. aeruginosa. SEM analysis revealed that the MAC can induce morphological changes in bacterial cells. The biofilm assay showed that the MAC could reduce biofilm formation. Whole-transcriptome analysis revealed 1093 differentially expressed genes consisting of 659 upregulated genes and 434 downregulated genes, in response to the MAC treatment. Mechanistically, the MAC inhibited P. aeruginosa growth by targeting metabolic processes, secretion system, signal transduction, and cell membrane functions, thereby potentially compromising the survival of this human pathogen. This study provides valuable insights into the antibacterial and antibiofilm activities of the MAC, a synergistic and cost-effective malic acid combination, which holds promise as a potential therapeutic drug cocktail for treating human infectious diseases in the future.

  8. Chen A, Jiang J, Luo Y, Zhang G, Hu B, Wang X, et al.
    PeerJ, 2023;11:e16337.
    PMID: 38130929 DOI: 10.7717/peerj.16337
    Drought monitoring is crucial for assessing and mitigating the impacts of water scarcity on various sectors and ecosystems. Although traditional drought monitoring relies on soil moisture data, remote sensing technology has have significantly augmented the capabilities for drought monitoring. This study aims to evaluate the accuracy and applicability of two temperature vegetation drought indices (TVDI), TVDINDVI and TVDIEVI, constructed using the Normalized Difference Vegetation Index (NDVI) and the Enhanced Vegetation Index (EVI) vegetation indices for drought monitoring. Using Guangdong Province as a case, enhanced versions of these indices, developed through Savitzky-Golay filtering and terrain correction were employed. Additionally, Pearson correlation analysis and F-tests were utilized to determine the suitability of the Standardized Precipitation Index (SPI) and the Standardized Precipitation Evapotranspiration Index (SPEI) in correlation with TVDINDVI and TVDIEVI. The results show that TVDINDVI had more meteorological stations passing both significance test levels (P 
  9. Ng YH, Moy FM, Hairi NN, Bulgiba A
    PeerJ, 2024;12:e16778.
    PMID: 38274329 DOI: 10.7717/peerj.16778
    BACKGROUND: Teachers are responsible for educating future generations and therefore play an important role in a country's education system. Teachers constitute about 2.6% of all employees in Malaysia, making it one of the largest workforces in the country. While health and well-being are crucial to ensuring teachers' work performance, reports on non-communicable diseases such as type 2 diabetes mellitus (T2DM) among Malaysian teachers are scarce. Hence, this study focused on the prevalence of T2DM, undiagnosed diabetes mellitus (DM), impaired fasting glucose (IFG), and underlying lifestyle factors associated with these outcomes among Malaysian teachers.

    METHODS: This is a cross-sectional study from the CLUSTer cohort. There were 14144 teachers from the Peninsular Malaysia included in this study. The teachers' sociodemographic and lifestyle characteristics were described using a weighted complex analysis. A matched age group comparison was carried out between teachers and the Malaysian general population on T2DM, undiagnosed DM, and IFG status. Next, the researchers examined the association of lifestyle factors with T2DM and IFG using multivariable logistic regression.

    RESULTS: The prevalence of T2DM, undiagnosed DM, and IFG among the Malaysian teachers were 4.1%, 5.1%, and 5.6%, respectively. The proportions of teachers with T2DM (both diagnosed and undiagnosed) and the IFG increased linearly with age. Teachers had a lower weighted prevalence of T2DM (known and undiagnosed) than the general population. However, teachers were more inclined to have IFG than the general population, particularly those aged 45 years and older. Among all lifestyle indicators, only waist circumference (aOR: 1.14, 95% CI: 1.08, 1.20) was found to be associated with T2DM, whereas waist circumference (aOR: 1.10, 95% CI: 1.05, 1.15) and physical activity [moderately active = (aOR: 0.71, 95% CI: 0.52, 0.98); highly active = (aOR: 0.56, 95% CI: 0.40, 0.80)] were associated with IFG.

    CONCLUSIONS: Modifiable lifestyle factors such as abdominal obesity and physical activity were associated with T2DM and IFG. Intervention programs targeting these factors could help reduce future treatment costs and increase productivity.

  10. Mohd Shaha FR, Liew PL, Qamaruz Zaman F, Nulit R, Barin J, Rolland J, et al.
    PeerJ, 2024;12:e16570.
    PMID: 38313025 DOI: 10.7717/peerj.16570
    BACKGROUND: Oil palm (Elaeis guineensis Jacq.) is one of the major oil-producing crops. Improving the quality and increasing the production yield of oil palm have been the primary focuses of both conventional and modern breeding approaches. However, the conventional breeding approach for oil palm is very challenging due to its longevity, which results in a long breeding cycle. Thus, the establishment of marker assisted selection (MAS) for oil palm breeding programs would speed up the breeding pipeline by generating new oil palm varieties that possess high commercial traits. With the decreasing cost of sequencing, Genotyping-by-sequencing (GBS) is currently feasible to many researchers and it provides a platform to accelerate the discovery of single nucleotide polymorphism (SNP) as well as insertion and deletion (InDel) markers for the construction of a genetic linkage map. A genetic linkage map facilitates the identification of significant DNA regions associated with the trait of interest via quantitative trait loci (QTL) analysis.

    METHODS: A mapping population of 112 F1 individuals from a cross of Deli dura and Serdang pisifera was used in this study. GBS libraries were constructed using the double digestion method with HindIII and TaqI enzymes. Reduced representation libraries (RRL) of 112 F1 progeny and their parents were sequenced and the reads were mapped against the E. guineensis reference genome. To construct the oil palm genetic linkage map, informative SNP and InDel markers were used to discover significant DNA regions associated with the traits of interest. The nine traits of interest in this study were fresh fruit bunch (FFB) yield, oil yield (OY), oil to bunch ratio (O/B), oil to dry mesocarp ratio (O/DM) ratio, oil to wet mesocarp ratio (O/WM), mesocarp to fruit ratio (M/F), kernel to fruit ratio (K/F), shell to fruit ratio (S/F), and fruit to bunch ratio (F/B).

    RESULTS: A total of 2.5 million SNP and 153,547 InDel markers were identified. However, only a subset of 5,278 markers comprising of 4,838 SNPs and 440 InDels were informative for the construction of a genetic linkage map. Sixteen linkage groups were produced, spanning 2,737.6 cM for the maternal map and 4,571.6 cM for the paternal map, with average marker densities of one marker per 2.9 cM and one per 2.0 cM respectively, were produced. A QTL analysis was performed on nine traits; however, only QTL regions linked to M/F, K/F and S/F were declared to be significant. Of those QTLs were detected: two for M/F, four for K/F and one for S/F. These QTLs explained 18.1-25.6% of the phenotypic variance and were located near putative genes, such as casein kinase II and the zinc finger CCCH domain, which are involved in seed germination and growth. The identified QTL regions for M/F, K/F and S/F from this study could be applied in an oil palm breeding program and used to screen palms with desired traits via marker assisted selection (MAS).

  11. Suhaimi AH, Kobayashi MJ, Satake A, Ng CC, Lee SL, Muhammad N, et al.
    PeerJ, 2023;11:e16368.
    PMID: 38047035 DOI: 10.7717/peerj.16368
    Climatic factors have commonly been attributed as the trigger of general flowering, a unique community-level mass flowering phenomenon involving most dipterocarp species that forms the foundation of Southeast Asian tropical rainforests. This intriguing flowering event is often succeeded by mast fruiting, which provides a temporary yet substantial burst of food resources for animals, particularly frugivores. However, the physiological mechanism that triggers general flowering, particularly in dipterocarp species, is not well understood largely due to its irregular and unpredictable occurrences in the tall and dense forests. To shed light on this mechanism, we employed ecological transcriptomic analyses on an RNA-seq dataset of a general flowering species, Shorea curtisii (Dipterocarpaceae), sequenced from leaves and buds collected at multiple vegetative and flowering phenological stages. We assembled 64,219 unigenes from the transcriptome of which 1,730 and 3,559 were differentially expressed in the leaf and the bud, respectively. Differentially expressed unigene clusters were found to be enriched with homologs of Arabidopsis thaliana genes associated with response to biotic and abiotic stresses, nutrient level, and hormonal treatments. When combined with rainfall data, our transcriptome data reveals that the trees were responding to a brief period of drought prior to the elevated expression of key floral promoters and followed by differential expression of unigenes that indicates physiological changes associated with the transition from vegetative to reproductive stages. Our study is timely for a representative general flowering dipterocarp species that occurs in forests that are under the constant threat of deforestation and climate change as it pinpoints important climate sensitive and flowering-related homologs and offers a glimpse into the cascade of gene expression before and after the onset of floral initiation.
  12. 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.

  13. Abd Hamid M, Md Sah ASR, Idris I, Mohd Nor SA, Mansor M
    PeerJ, 2023;11:e15986.
    PMID: 38144186 DOI: 10.7717/peerj.15986
    BACKGROUND: The Temengor Reservoir is the second largest reservoir in Peninsular Malaysia. Located in the northwestern state of Perak, it was selected to develop a large-scale tilapia (Oreochromis niloticus) aquaculture facility within the Aquaculture Industrial Zone (AIZ) in 2008 due to its favourable environmental conditions. No record of tilapia has ever been reported in the natural waters prior to this. However, a post-establishment study recorded tilapia sightings in the natural waters of this lake. The cultured tilapia was easily recognizable with the elongated mouth and body, and long caudal fin. It is postulated that these were escapees from the floating cages that had invaded the natural waters and would negatively impact the native fish species. To test our hypothesis, we investigated the impact of the aquaculture facility on native fish diversity through a spatial design.

    METHODS: The study was focused on assessing the impact of tilapia culture at sites nearer to the AIZ vs more distant sites, the former with a greater likelihood of receiving escapees. Two major sites were chosen; within 5 km (near-cage) and within 5-15 km (far-cage) radii from the AIZ. Fish sampling was conducted using multiple mesh sizes of gill nets (3.7, 5.1, 6.5, 7.6, and 10.2 cm) deployed at the littoral zone of the sampling points. Species diversity, abundance, dietary habits, and habitat preference were investigated.

    RESULTS: The CPUE (individual/hour) of native fish species at the far-cage site of the AIZ Reservoir was found to be significantly higher (p < 0.05) than that at the near-cage site. Principal component analysis (PCA) based on diet and habitat preferences showed that the tilapia, O. niloticus had almost overlapping diet resources and habitat with native fish species.

    CONCLUSION: We conclude that there is a correlation between the reduced catches of native species (based on CPUE) and the high presence of tilapia. Thus, appropriate actions must be implemented for strategic and effective planning in terms of native fish conservation.

  14. Govender N, Zulkifli NS, Badrul Hisham NF, Ab Ghani NS, Mohamed-Hussein ZA
    PeerJ, 2022;10:e14168.
    PMID: 36518265 DOI: 10.7717/peerj.14168
    BACKGROUND: Pea eggplant (Solanum torvum Swartz) commonly known as turkey berry or 'terung pipit' in Malay is a vegetable plant widely consumed by the local community in Malaysia. The shrub bears pea-like turkey berry fruits (TBFs), rich in phytochemicals of medicinal interest. The TBF phytochemicals hold a wide spectrum of pharmacological properties. In this study, the TBF phytochemicals' potential inhibitory properties were evaluated against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) of the Coronavirus disease 2019 (COVID-19). The TBF polyphenols were screened against SARS-CoV receptors via molecular docking and the best receptor-ligand complex was validated further by molecular dynamics (MD) simulation.

    METHOD: The SARS-CoV receptor structure files (viral structural components) were retrieved from the Protein Data Bank (PDB) database: membrane protein (PDB ID: 3I6G), main protease (PDB ID: 5RE4), and spike glycoproteins (PDB ID: 6VXX and 6VYB). The receptor binding pocket regions were identified by Discovery Studio (BIOVIA) for targeted docking with TBF polyphenols (genistin, kaempferol, mellein, rhoifolin and scutellarein). The ligand and SARS-CoV family receptor structure files were pre-processed using the AutoDock tools. Molecular docking was performed with the Lamarckian genetic algorithm using AutoDock Vina 4.2 software. The best pose (ligand-receptor complex) from the molecular docking analysis was selected based on the minimum binding energy (MBE) and extent of structural interactions, as indicated by BIOVIA visualization tool. The selected complex was validated by a 100 ns MD simulation run using the GROMACS software. The dynamic behaviour and stability of the receptor-ligand complex were evaluated by the root mean square displacement (RMSD), root mean square fluctuation (RMSF), radius of gyration (Rg), solvent accessible surface area (SASA), solvent accessible surface volume (SASV) and number of hydrogen bonds.

    RESULTS: At RMSD = 0, the TBF polyphenols showed fairly strong physical interactions with SARS-CoV receptors under all possible combinations. The MBE of TBF polyphenol-bound SARS CoV complexes ranged from -4.6 to -8.3 kcal/mol. Analysis of the structural interactions showed the presence of hydrogen bonds, electrostatic and hydrophobic interactions between the receptor residues (RR) and ligands atoms. Based on the MBE values, the 3I6G-rhoifolin (MBE = -8.3 kcal/mol) and 5RE4-genistin (MBE = -7.6 kcal/mol) complexes were ranked with the least value. However, the latter showed a greater extent of interactions between the RRs and the ligand atoms and thus was further validated by MD simulation. The MD simulation parameters of the 5RE4-genistin complex over a 100 ns run indicated good structural stability with minimal flexibility within genistin binding pocket region. The findings suggest that S. torvum polyphenols hold good therapeutics potential in COVID-19 management.

  15. Li J, Guo X, Cai D, Xu Y, Wang Y
    PeerJ, 2023;11:e15925.
    PMID: 37641595 DOI: 10.7717/peerj.15925
    Quinoa (Chenopodium quinoa Willd.) is a highly nutritious food product with a comprehensive development prospect. Here, we discussed the effect of Bacillus amyloliquefaciens 11B91 on the growth, development and salt tolerance (salt concentrations: 0, 150, 300 mmol·L-1) of quinoa and highlighted a positive role for the application of plant growth-promoting rhizobacteria bacteria in quinoa. In this artical, the growth-promoting effect of Bacillus amyloliquefaciens 11B91 on quinoa (Longli No.1) and the changes in biomass, chlorophyll content, root activity and total phosphorus content under salt stress were measured. The results revealed that plants inoculated with 11B91 exhibited increased maximum shoot fresh weight (73.95%), root fresh weight (75.36%), root dry weight (136%), chlorophyll a (65.32%) contents and chlorophyll b (58.5%) contents, root activity (54.44%) and total phosphorus content (16.66%). Additionally, plants inoculated with 11B91 under salt stress plants showed significantly improved, fresh weight (107%), dry weight (133%), chlorophyll a (162%) contents and chlorophyll b (76.37%) contents, root activity (33.07%), and total phosphorus content (42.73%).
  16. Liu B, Lee CW, Bong CW, Wang AJ
    PeerJ, 2024;12:e16556.
    PMID: 38223759 DOI: 10.7717/peerj.16556
    BACKGROUND: Escherichia coli is a commonly used faecal indicator bacterium to assess the level of faecal contamination in aquatic habitats. However, extensive studies have reported that sediment acts as a natural reservoir of E. coli in the extraintestinal environment. E. coli can be released from the sediment, and this may lead to overestimating the level of faecal contamination during water quality surveillance. Thus, we aimed to investigate the effects of E. coli habitat transition from sediment to water on its abundance in the water column.

    METHODS: This study enumerated the abundance of E. coli in the water and sediment at five urban lakes in the Kuala Lumpur-Petaling Jaya area, state of Selangor, Malaysia. We developed a novel method for measuring habitat transition rate of sediment E. coli to the water column, and evaluated the effects of habitat transition on E. coli abundance in the water column after accounting for its decay in the water column.

    RESULTS: The abundance of E. coli in the sediment ranged from below detection to 12,000 cfu g-1, and was about one order higher than in the water column (1 to 2,300 cfu mL-1). The habitat transition rates ranged from 0.03 to 0.41 h-1. In contrast, the E. coli decay rates ranged from 0.02 to 0.16 h-1. In most cases (>80%), the habitat transition rates were higher than the decay rates in our study.

    DISCUSSION: Our study provided a possible explanation for the persistence of E. coli in tropical lakes. To the best of our knowledge, this is the first quantitative study on habitat transition of E. coli from sediments to water column.

  17. Abdullah NI, Elias NA, Ohte N, Vincenot C
    PeerJ, 2024;12:e16657.
    PMID: 38250723 DOI: 10.7717/peerj.16657
    Resource partitioning among tropical bats in agricultural areas of Peninsular Malaysia remains unclear. This study was conducted to evaluate resource partitioning among bats by examining their fecal samples. The main bat species sampled included: Rhinolophus coelophyllus, Rhinolophus malayanus, Rhinolophus pusillus, Rhinolophus refulgens, Taphozous melanopogon and Hipposideros larvatus. Two harp traps were set at different elevations on a hilltop (Gunung Keriang) and two high nets were used in neighboring rice fields at three sites, for three consecutive nights per sampling from April 2021 to February 2022. A total of 301 bats and 1,505 pellets were analyzed using a conventional approach which examined the fecal sample under the microscope. All of the bat species within the study had insects from the order Coleoptera, Lepidoptera, Diptera and Hemiptera in their diet. Larger bats exhibited a greater variety of prey consumption. Male individuals were observed to be generalists while female individuals were specialists, particularly during pregnancy and lactating reproductive stages. Bat species and insect order had a significant impact on the percentage fragment frequency of the insects consumed. Rhinolophus coelophyllus specialized in feeding on Coleoptera and Diptera, H. larvatus fed on Coleoptera, R. malayanus fed on Hemiptera, R. pusillus and T. melanopogon fed on Lepidoptera. Future molecular analysis can be carried out to further identify the insect pests consumed by these bats up to species level. These findings enhance our understanding of bats' ecological roles in agricultural landscapes and contribute to conservation and pest management strategies.
  18. Kong ZX, N Karunakaran R, Abdul Jabar K, Ponnampalavanar S, Chong CW, Teh CSJ
    PeerJ, 2022;10:e12830.
    PMID: 35223201 DOI: 10.7717/peerj.12830
    BACKGROUND: Carbapenem resistant Enterobacteriaceae (CRE) has rapidly disseminated worldwide and has become a global threat to the healthcare system due to its resistance towards "last line" antibiotics. This study aimed to investigate the prevalence of CRE and the resistance mechanism as well as the risk factors associated with in-hospital mortality.

    METHODS: A total of 168 CRE strains isolated from a tertiary teaching hospital from 2014-2015 were included in this study. The presence of carbapenemase genes and minimum inhibitory concentration of imipenem, meropenem and colistin were investigated. All carbapenem-resistant Klebsiella pneumoniae (K. pneumoniae) strains were characterised by PFGE. The risk factors of patients infected by CRE associated with in-hospital mortality were determined statistically.

    RESULTS: The predominant CRE species isolated was K. pneumoniae. The carbapenemases detected were blaOXA-48, blaOXA-232, blaVIM and blaNDM of which blaOXA-48 was the predominant carbapenemase detected among 168 CRE strains. A total of 40 CRE strains harboured two different carbapenemase genes. A total of seven clusters and 48 pulsotypes were identified among 140 CRKp strains. A predominant pulsotype responsible for the transmission from 2014 to 2015 was identified. Univariate statistical analysis identified that the period between CRE isolation and start of appropriate therapy of more than 3 days was statistically associated with in-hospital mortality.

  19. Mohd Shukri MF, Norhayati MN, Badrin S, Abdul Kadir A
    PeerJ, 2022;10:e13992.
    PMID: 36132218 DOI: 10.7717/peerj.13992
    BACKGROUND: Polycystic ovary syndrome (PCOS) is a disorder in reproductive age women and is characterized by hyperandrogenic anovulation and oligo-amenorrhea, which leads to infertility. Anovulation in PCOS is associated with low follicle-stimulating hormone levels and the arrest of antral follicle development in the final stages of maturation. L-carnitine (LC) plays a role in fatty acid metabolism, which is found to be lacking in PCOS patients. This systematic review and meta-analysis aimed to determine the effectiveness of LC supplementation for patients with PCOS.

    METHODS: We searched the Cochrane Central Register of Controlled Trials (CENTRAL), MEDLINE, Embase, Cumulative Index to Nursing and Allied Health Literature (CINAHL), Psychological Information Database (PsycINFO), and the World Health Organization International Clinical Trials Registry Platform for all randomized control trials, comparing LC alone or in combination with other standard treatments for the treatment of PCOS from inception till June 2021. We independently screened titles and abstracts to identify available trials, and complete texts of the trials were checked for eligibility. Data on the methods, interventions, outcomes, and risk of bias from the included trials were independently extracted by the authors. The estimation of risk ratios and mean differences with a 95 percent confidence interval (CI) was performed using a random-effects model.

    RESULTS: Nine studies with 995 participants were included in this review. Five comparison groups were involved. In one comparison group, LC reduced the fasting plasma glucose (FPG) (mean differences (MD) -5.10, 95% CI [-6.25 to -3.95]; P = 0.00001), serum low-density lipoprotein (LDL) (MD -25.00, 95% CI [-27.93 to -22.07]; P = 0.00001), serum total cholesterol (MD -21.00, 95% CI [-24.14 to -17.86]; P = 0.00001), and serum triglyceride (TG) (MD -9.00, 95% CI [-11.46 to -6.54]; P = 0.00001) with moderate certainty of evidence. Another comparison group demonstrated that LC lowers the LDL (MD -12.00, 95% CI [-15.80 to -8.20]; P = 0.00001), serum total cholesterol (MD -24.00, 95% CI [-27.61 to -20.39]; P = 0.00001), and serum TG (MD -19.00, 95% CI [-22.79 to -15.21]; P = 0.00001) with moderate certainty of evidence.

    CONCLUSION: There was low to moderate certainty of evidence that LC improves Body Mass Index (BMI) and serum LDL, TG, and total cholesterol levels in women with PCOS.

  20. Khalaf TK, Ismail N, Nazri NA, Ahmed N, Yajid AI, Mohamud R, et al.
    PeerJ, 2024;12:e18420.
    PMID: 39619199 DOI: 10.7717/peerj.18420
    BACKGROUND: Natural killer cells (NK cells) are essential in cancer immunosurveillance in the body as they can recognize cancer cells that lacking MHC class 1 on their surface. Regulatory cytokines, including interleukin (IL)-18, IL-12, IL-10, IL-8, interferon-γ (IFN-γ), and secretory granules like perforin and granzyme are involved in NK cell-mediated cytotoxicity. Stimulating NK cells cytotoxicity towards cancer cells is an ideal strategy to combat cancer naturally. Medicinal plants have been reported to enhance immunity, with Pereskia bleo (P. bleo) particularly noteworthy due to its abundant bioactive compounds and ability to activate immune cells. This study aimed to evaluate the potential of methanol extract of P. bleo leaves (MEPB) for enhancing NK cell cytotoxicity against triple-negative human breast cancer cells (MDA-MB-231).

    METHODS: The optimal concentration of MEPB to activate NK cells was determined using healthy blood samples, assessing the expression of IL-12, IL-18, IL-10, IL-8, IFN-γ, perforin, and granzyme B via an enzyme-linked immunosorbent assay (ELISA). NK cell purity from healthy donors and breast cancer patients was determined using specific antibodies, and the number of NK cells was assessed using flow cytometry and a hemocytometer. A co-culture experiment, ELISA, and apoptosis assay were used to evaluate NK-mediated cytotoxicity pathways.

    RESULTS: ELISA data indicated that MEPB at 7.5 µg/ml significantly increased the expression of IFN-γ, IL-12, IL-18, perforin, and granzyme B while decreasing IL-8 and IL-10 expression after 20 hrs of incubation. The average NK cell purity was 87.09 ± 0.043%. Breast cancer patients exhibited lower NK cell counts than healthy donors. Co-culture experiments demonstrated that NK cells induced apoptosis in MDA-MB-231 breast cancer cells in the presence of MEPB by increasing perforin, granzyme B, and IFN-γ expression in both healthy donors and breast cancer patients-experimental groups. P. bleo enhances NK cell activation, promoting the apoptosis of triple-negative human breast cancer cells (MDA-MB-231), suggesting the potential use of MEPB leaves as an anti-cancer immunostimulant.

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