Displaying publications 121 - 140 of 1896 in total

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  1. Fulltext Unexpectedly high levels of lineage diversity in Sundaland puddle frogs (Dicroglossidae: Occidozyga Kuhl and van Hasselt, 1822)
    Flury JM, Haas A, Brown RM, Das I, Pui YM, Boon-Hee K, et al.
    Mol Phylogenet Evol, 2021 10;163:107210.
    PMID: 34029720 DOI: 10.1016/j.ympev.2021.107210
    One of the most urgent contemporary tasks for taxonomists and evolutionary biologists is to estimate the number of species on earth. Recording alpha diversity is crucial for protecting biodiversity, especially in areas of elevated species richness, which coincide geographically with increased anthropogenic environmental pressures - the world's so-called biodiversity hotspots. Although the distribution of Puddle frogs of the genus Occidozyga in South and Southeast Asia includes five biodiversity hotspots, the available data on phylogeny, species diversity, and biogeography are surprisingly patchy. Samples analyzed in this study were collected throughout Southeast Asia, with a primary focus on Sundaland and the Philippines. A mitochondrial gene region comprising ~ 2000 bp of 12S and 16S rRNA with intervening tRNA Valine and three nuclear loci (BDNF, NTF3, POMC) were analyzed to obtain a robust, time-calibrated phylogenetic hypothesis. We found a surprisingly high level of genetic diversity within Occidozyga, based on uncorrected p-distance values corroborated by species delimitation analyses. This extensive genetic diversity revealed 29 evolutionary lineages, defined by the > 5% uncorrected p-distance criterion for the 16S rRNA gene, suggesting that species diversity in this clade of phenotypically homogeneous forms probably has been underestimated. The comparison with results of other anuran groups leads to the assumption that anuran species diversity could still be substantially underestimated in Southeast Asia in general. Many genetically divergent lineages of frogs are phenotypically similar, indicating a tendency towards extensive morphological conservatism. We present a biogeographic reconstruction of the colonization of Sundaland and nearby islands which, together with our temporal framework, suggests that lineage diversification centered on the landmasses of the northern Sunda Shelf. This remarkably genetically structured group of amphibians could represent an exceptional case for future studies of geographical structure and diversification in a widespread anuran clade spanning some of the most pronounced geographical barriers on the planet (e.g., Wallace's Line). Studies considering gene flow, morphology, ecological and bioacoustic data are needed to answer these questions and to test whether observed diversity of Puddle frog lineages warrants taxonomic recognition.
    Matched MeSH terms: RNA, Ribosomal, 16S/genetics
  2. Molecular identification and biofilm-forming ability of Elizabethkingia species
    Puah SM, Fong SP, Kee BP, Puthucheary SD, Chua KH
    Microb Pathog, 2022 Jan;162:105345.
    PMID: 34896547 DOI: 10.1016/j.micpath.2021.105345
    Recently, Elizabethkingia species have gained attention as a cause of life-threatening infections. The identification via phenotypic methods of three important species- Elizabethkingia meningoseptica, E. anophelis and E. miricola is difficult. Our objectives were to re-assess 30 archived Flavobacterium meningosepticum isolates using 16S rRNA gene sequencing, ERIC-PCR, and biofilm formation assay. Twenty-four isolates were re-identified as E. anophelis and 6 as E. miricola. All of them had the ability to form biofilm as shown in microtiter plate assay based on crystal violet staining. Overall, E. anophelis had a higher specific biofilm formation index compared to E. miricola. A total of 42% (10 out of 24) of E. anophelis were classified as strong, 29% (7 out of 24) as moderate and 29% (7 out of 24) as weak biofilm producers. E. miricola, 17% (1 out of 6) isolates were strong biofilm producers, 50% (3 out of 6) moderate and 33% (2 out of 6) were weak producers. E. anophelis from tracheal secretions were significantly associated with (p = 0.0361) strong biofilm formation. In summary, this study showed that the isolates originally identified as F. meningosepticum were re-classified using the 16S rRNA gene as one of two Elizabethkingia species. The ability of E. anophelis to form strong biofilm in endotracheal tubes indicates their probable role in the pathogenesis of Elizabethkingia infections.
    Matched MeSH terms: RNA, Ribosomal, 16S/genetics
  3. Fulltext Chloroplast Genome Analysis for Genetic Information and Authentication in Five Barleria Species
    Kaewdaungdee S, Sudmoon R, Tanee T, Lee SY, Chaveerach A
    Genes (Basel), 2022 Sep 22;13(10).
    PMID: 36292590 DOI: 10.3390/genes13101705
    In order to authenticate the genomic information of Barleriacristata L., B. lupulina Lindl., B. repens Nees, B. siamensis Craib, and B. strigosa Willd, cp genomes were investigated. They revealed a general structure with a total size of 151,997-152,324 bp. The genomes encoded a total of 131 genes, including 86 CDS, 37 tRNA, and 8 rRNA genes. Other details found were as follows: different numbers and types of SSRs; identical gene content, which is adjacent to the border regions, except for B. strigosa, that revealed a shorter ndhF gene sequence and lacked the ycf1 gene; slightly different genetic distance values, which can be used for species identification; three distinct gaps of nucleotide variations between the species located at the intergenic spacer regions of the LSC and CDS of the SSC; three effective molecular markers derived from divergent hotspot regions, including the ccsA-ndhD, ndhA-ndhH-rps15, and ycf1. The genetic relationships derived from the cp genome and the CDS phylogenetic trees of Barleria and the 13 genera in Acanthaceae and different families, Scrophulariaceae and Phrymaceae, showed similar results. The six Barleria species as monophyletic groups with inner and outer outgroups were found to have perfect discrimination. These results have helped to authenticate the five Barleria species and the six genera in Acanthaceae.
    Matched MeSH terms: RNA, Transfer/genetics
  4. Fulltext Aerobic Methanotrophy and Co-occurrence Networks of a Tropical Rainforest and Oil Palm Plantations in Malaysia
    Ho A, Zuan ATK, Mendes LW, Lee HJ, Zulkeflee Z, van Dijk H, et al.
    Microb Ecol, 2022 Nov;84(4):1154-1165.
    PMID: 34716776 DOI: 10.1007/s00248-021-01908-3
    Oil palm (OP) plantations are gradually replacing tropical rainforest in Malaysia, one of the largest palm oil producers globally. Conversion of lands to OP plantations has been associated with compositional shifts of the microbial community, with consequences on the greenhouse gas (GHG) emissions. While the impact of the change in land use has recently been investigated for microorganisms involved in N2O emission, the response of the aerobic methanotrophs to OP agriculture remains to be determined. Here, we monitored the bacterial community composition, focusing on the aerobic methanotrophs, in OP agricultural soils since 2012, 2006, and 1993, as well as in a tropical rainforest, in 2019 and 2020. High-affinity methane uptake was confirmed, showing significantly lower rates in the OP plantations than in the tropical rainforest, but values increased with continuous OP agriculture. The bacterial, including the methanotrophic community composition, was modified with ongoing OP agriculture. The methanotrophic community composition was predominantly composed of unclassified methanotrophs, with the canonical (Methylocystis) and putative methanotrophs thought to catalyze high-affinity methane oxidation present at higher relative abundance in the oldest OP plantation. Results suggest that the methanotrophic community was relatively more stable within each site, exhibiting less temporal variations than the total bacterial community. Uncharacteristically, a 16S rRNA gene-based co-occurrence network analysis revealed a more complex and connected community in the OP agricultural soil, which may influence the resilience of the bacterial community to disturbances. Overall, we provide a first insight into the ecology and role of the aerobic methanotrophs as a methane sink in OP agricultural soils.
    Matched MeSH terms: RNA, Ribosomal, 16S/genetics
  5. Fulltext Zonula occludens-1 expression is reduced in nasal epithelial cells of allergic rhinitis patients
    Siti Sarah CO, Nur Husna SM, Md Shukri N, Wong KK, Mohd Ashari NS
    PeerJ, 2022;10:e13314.
    PMID: 35480562 DOI: 10.7717/peerj.13314
    Allergic rhinitis (AR) is a common allergic disease characterized by disruption of nasal epithelial barrier. In this study, we investigated the mRNA expression of zonula occludens-1 (ZO-1), ZO-2 and ZO-3 and histone deacetylase 1 (HDAC1) and HDAC2 in AR patients compared to healthy controls. RNA samples were extracted from nasal epithelial cells of house dust mites (HDMs)-sensitized AR patients and healthy controls (n = 28 in each group). The RNAs were reverse transcribed into cDNAs for measurement of ZO-1, ZO-2, ZO-3, HDAC1 and HDAC2 expression levels by quantitative PCR. The mRNA expression of ZO-1 was significantly decreased in AR patients compared to healthy controls (p = 0.010). No significant difference was observed in the expression levels of ZO-2, ZO-3, HDAC1 and HDAC2 in AR patients compared to healthy controls. We found significant associations of higher HDAC2 levels in AR patients with lower frequency of changing bedsheet (p = 0.043) and with AR patients sensitized to Dermatophagoides farinae (p = 0.041). Higher expression of ZO-2 was observed in AR patients who had pets (p = 0.007). In conclusion, our data indicated that ZO-1 expression was lower in AR patients contributing to decreased integrity of nasal epithelial barrier integrity, and HDAC2 may be involved in the pathogenesis of the disease.
    Matched MeSH terms: RNA, Messenger/metabolism
  6. Revisiting miRNA-21 as a Therapeutic Strategy for Myocardial Infarction: A Systematic Review
    Sothivelr V, Hasan MY, Mohd Saffian S, Zainalabidin S, Ugusman A, Mahadi MK
    J Cardiovasc Pharmacol, 2022 Sep 01;80(3):393-406.
    PMID: 35767710 DOI: 10.1097/FJC.0000000000001305
    Several types of cardiovascular cells use microRNA-21 ( miR-21 ), which has been linked to cardioprotection. In this study, we systematically reviewed the results of published papers on the therapeutic effect of miR-21 for myocardial infarction. Studies described the cardioprotective effects of miR-21 to reduce infarct size by improving angiogenesis, antiapoptotic, and anti-inflammatory mechanisms. Results suggest that cardioprotective effects of miR-21 may work synergistically to prevent the deterioration of cardiac function during postischemia. However, there are other results that indicate that miR-21 positively regulates tissue fibrosis, potentially worsening a postischemic injury. The dual functionalities of miR-21 occur through the targeting of genes and signaling pathways, such as PTEN , PDCD4 , KBTBD7 , NOS3 , STRN , and Spry-1 . This review provides insights into the future advancement of safe miR-21 -based genetic therapy in the treatment of myocardial infarction.
    Matched MeSH terms: RNA-Binding Proteins/metabolism
  7. Fulltext Circular RNA- and microRNA-Mediated Post-Transcriptional Regulation of Preadipocyte Differentiation in Adipogenesis: From Expression Profiling to Signaling Pathway
    Huang CJ, Choo KB
    Int J Mol Sci, 2023 Feb 25;24(5).
    PMID: 36901978 DOI: 10.3390/ijms24054549
    Adipogenesis is an indispensable cellular process that involves preadipocyte differentiation into mature adipocyte. Dysregulated adipogenesis contributes to obesity, diabetes, vascular conditions and cancer-associated cachexia. This review aims to elucidate the mechanistic details on how circular RNA (circRNA) and microRNA (miRNA) modulate post-transcriptional expression of targeted mRNA and the impacted downstream signaling and biochemical pathways in adipogenesis. Twelve adipocyte circRNA profiling and comparative datasets from seven species are analyzed using bioinformatics tools and interrogations of public circRNA databases. Twenty-three circRNAs are identified in the literature that are common to two or more of the adipose tissue datasets in different species; these are novel circRNAs that have not been reported in the literature in relation to adipogenesis. Four complete circRNA-miRNA-mediated modulatory pathways are constructed via integration of experimentally validated circRNA-miRNA-mRNA interactions and the downstream signaling and biochemical pathways involved in preadipocyte differentiation via the PPARγ/C/EBPα gateway. Despite the diverse mode of modulation, bioinformatics analysis shows that the circRNA-miRNA-mRNA interacting seed sequences are conserved across species, supporting mandatory regulatory functions in adipogenesis. Understanding the diverse modes of post-transcriptional regulation of adipogenesis may contribute to the development of novel diagnostic and therapeutic strategies for adipogenesis-associated diseases and in improving meat quality in the livestock industries.
    Matched MeSH terms: RNA, Messenger/genetics
  8. Fulltext Detection of a Babesia sp. genotype closely related to marsupial-associated Babesia spp. in male Haemaphysalis shimoga from Sarawak, Malaysian Borneo
    Lau AC, Qiu Y, Moustafa MAM, Nakao R, Shimozuru M, Onuma M, et al.
    J Vet Med Sci, 2022 Nov 01;84(11):1469-1473.
    PMID: 36123016 DOI: 10.1292/jvms.22-0304
    In this study, Babesia screening was conducted in 55 rodents and 160 tick samples collected from primary forests and an oil palm plantation in Sarawak, Malaysian Borneo. PCR targeting the 18S ribosomal DNA revealed the presence of Babesia spp. DNA detected in two questing male Haemaphysalis shimoga ticks collected from the oil palm plantation. Sequence analysis revealed that both sequences were identical and had 98.6% identity to a Babesia macropus sequence obtained from Eastern grey kangaroos (Macropus giganteus) in Australia. Phylogenetic tree revealed clustering with marsupial-associated Babesia spp. in the Babesia sensu stricto clade. Whether or not H. shimoga is the competent vector and the importance of the Babesia sp. detected in this study warrants more investigation.
    Matched MeSH terms: RNA, Ribosomal, 18S/genetics
  9. Diversity and Distribution of Microbial Communities Associated with Reef Corals of the Malay Peninsula
    Kanisan DP, Quek ZBR, Oh RM, Afiq-Rosli L, Lee JN, Huang D, et al.
    Microb Ecol, 2023 Jan;85(1):37-48.
    PMID: 35043221 DOI: 10.1007/s00248-022-01958-1
    Coral-associated bacteria play critical roles in the regulation of coral health and function. Environmental perturbations that alter the bacterial community structure can render the coral holobiont more susceptible and less resilient to disease. Understanding the natural variation of the coral microbiome across space and host species provides a baseline that can be used to distinguish shifts in community structure. Using a 16S rRNA gene metabarcoding approach, this study examines bacterial community structure across three scleractinian coral hosts. Our results show that corals of three regions-eastern and western Peninsular Malaysia and Singapore-host distinct bacterial communities; despite these differences, we were able to identify a core microbiome shared across all three species. This core microbiome was also present in samples previously collected in Thailand, suggesting that these core microbes play an important role in promoting and maintaining host health. For example, several have been identified as dimethylsulfoniopropionate (DMSP) metabolizers that have roles in sulfur cycling and the suppression of bacterial pathogens. Pachyseris speciosa has the most variable microbiome, followed by Porites lutea, with the composition of the Diploastrea heliopora microbiome the least variable throughout all locations. Microbial taxa associated with each region or site are likely shaped by local environmental conditions. Taken together, host identity is a major driver of differences in microbial community structure, while environmental heterogeneity shapes communities at finer scales.
    Matched MeSH terms: RNA, Ribosomal, 16S/genetics
  10. Environmental surveillance of SARS-CoV-2 in municipal wastewater to monitor COVID-19 status in urban clusters in Malaysia
    Aziz MA, Norman S, Mohamed Zaid S, Simarani K, Sulaiman R, Mohd Aris A, et al.
    Arch Microbiol, 2023 Jan 28;205(2):76.
    PMID: 36708390 DOI: 10.1007/s00203-023-03417-y
    Wastewater monitoring for SARS-CoV-2 has attracted considerable attention worldwide to complement the existing clinical-based surveillance system. In this study, we report our first successful attempt to prove the circulation of SARS-CoV-2 genes in Malaysian urban wastewater. A total of 18 wastewater samples were obtained from a regional sewage treatment plant that received municipal sewage between February 2021 and May 2021. Using the quantitative PCR assay targeting the E and RdRp genes of SARS-CoV-2, we confirmed that both genes were detected in the raw sewage, while no viral RNA was found in the treated sewage. We were also able to show that the trend of COVID-19 cases in Kuala Lumpur and Selangor was related to the changes in SARS-CoV-2 RNA levels in the wastewater samples. Overall, our study highlights that monitoring wastewater for SARS-CoV-2 should help local health professionals to obtain additional information on the rapid and silent circulation of infectious agents in communities at the regional level.
    Matched MeSH terms: RNA, Viral/genetics
  11. Thermo-Responsive Polymer-siRNA Conjugates Enabling Artificial Control of Gene Silencing around Body Temperature
    Honda Y, Onodera S, Takemoto H, Harun NFC, Nomoto T, Matsui M, et al.
    Pharm Res, 2023 Jan;40(1):157-165.
    PMID: 36307662 DOI: 10.1007/s11095-022-03414-8
    PURPOSE: Controlling small interfering RNA (siRNA) activity by external stimuli is useful to exert a selective therapeutic effect at the target site. This study aims to develop a technology to control siRNA activity in a thermo-responsive manner, which can be utilized even at temperatures close to body temperature.

    METHODS: siRNA was conjugated with a thermo-responsive copolymer that was synthesized by copolymerization of N-isopropylacrylamide (NIPAAm) and hydrophilic N,N-dimethylacrylamide (DMAA) to permit thermally controlled interaction between siRNA and an intracellular gene silencing-related protein by utilizing the coil-to-globule phase transition of the copolymer. The composition of the copolymer was fine-tuned to obtain lower critical solution temperature (LCST) around body temperature, and the phase transition behavior was evaluated. The cellular uptake and gene silencing efficiency of the copolymer-siRNA conjugates were then investigated in cultured cells.

    RESULTS: The siRNA conjugated with the copolymer with LCST of 38.0°C exhibited ~ 11.5 nm of the hydrodynamic diameter at 37°C and ~ 9.8 nm of the diameter at 41°C, indicating the coil-globule transition above the LCST. In line with this LCST behavior, its cellular uptake and gene silencing efficiency were enhanced when the temperature was increased from 37°C to 41°C.

    CONCLUSION: By fine-tuning the LCST behavior of the copolymer that was conjugated with siRNA, siRNA activity could be controlled in a thermo-responsive manner around the body temperature. This technique may offer a promising approach to induce therapeutic effects of siRNA selectively in the target site even in the in vivo conditions.

    Matched MeSH terms: RNA, Small Interfering/genetics
  12. scGGAN: single-cell RNA-seq imputation by graph-based generative adversarial network
    Huang Z, Wang J, Lu X, Mohd Zain A, Yu G
    Brief Bioinform, 2023 Mar 19;24(2).
    PMID: 36733262 DOI: 10.1093/bib/bbad040
    Single-cell RNA sequencing (scRNA-seq) data are typically with a large number of missing values, which often results in the loss of critical gene signaling information and seriously limit the downstream analysis. Deep learning-based imputation methods often can better handle scRNA-seq data than shallow ones, but most of them do not consider the inherent relations between genes, and the expression of a gene is often regulated by other genes. Therefore, it is essential to impute scRNA-seq data by considering the regional gene-to-gene relations. We propose a novel model (named scGGAN) to impute scRNA-seq data that learns the gene-to-gene relations by Graph Convolutional Networks (GCN) and global scRNA-seq data distribution by Generative Adversarial Networks (GAN). scGGAN first leverages single-cell and bulk genomics data to explore inherent relations between genes and builds a more compact gene relation network to jointly capture the homogeneous and heterogeneous information. Then, it constructs a GCN-based GAN model to integrate the scRNA-seq, gene sequencing data and gene relation network for generating scRNA-seq data, and trains the model through adversarial learning. Finally, it utilizes data generated by the trained GCN-based GAN model to impute scRNA-seq data. Experiments on simulated and real scRNA-seq datasets show that scGGAN can effectively identify dropout events, recover the biologically meaningful expressions, determine subcellular states and types, improve the differential expression analysis and temporal dynamics analysis. Ablation experiments confirm that both the gene relation network and gene sequence data help the imputation of scRNA-seq data.
    Matched MeSH terms: Sequence Analysis, RNA/methods
  13. Biodegradation of monocrotophos by Brucella intermedia Msd2 isolated from cotton plant
    Shazmin, Ahmad SA, Naqvi TA, Munis MFH, Javed MT, Chaudhary HJ
    World J Microbiol Biotechnol, 2023 Mar 31;39(6):141.
    PMID: 37000294 DOI: 10.1007/s11274-023-03575-7
    Widespread and inadequate use of Monocrotophos has led to several environmental issues. Biodegradation is an ecofriendly method used for detoxification of toxic monocrotophos. In the present study, Msd2 bacterial strain was isolated from the cotton plant growing in contaminated sites of Sahiwal, Pakistan. Msd2 is capable of utilizing the monocrotophos (MCP) organophosphate pesticide as its sole carbon source for growth. Msd2 was identified as Brucella intermedia on the basis of morphology, biochemical characterization and 16S rRNA sequencing. B. intermedia showed tolerance of MCP up to 100 ppm. The presence of opd candidate gene for pesticide degradation, gives credence to B. intermedia as an effective bacterium to degrade MCP. Screening of the B. intermedia strain Msd2 for plant growth promoting activities revealed its ability to produce ammonia, exopolysaccharides, catalase, amylase and ACC-deaminase, and phosphorus, zinc and potassium solubilization. The optimization of the growth parameters (temperatures, shaking rpm, and pH level) of the MCP-degrading isolate was carried out in minimal salt broth supplemented with MCP. The optimal pH, temperature, and rpm for Msd2 growth were observed as pH 6, 35 °C, and 120 rpm, respectively. Based on optimization results, batch degradation experiment was performed. Biodegradation of MCP by B. intermedia was monitored using HPLC and recorded 78% degradation of MCP at 100 ppm concentration within 7 days of incubation. Degradation of MCP by Msd2 followed the first order reaction kinetics. Plant growth promoting and multi-stress tolerance ability of Msd2 was confirmed by molecular analysis. It is concluded that Brucella intermedia strain Msd2 could be beneficial as potential biological agent for an effective bioremediation for polluted environments.
    Matched MeSH terms: RNA, Ribosomal, 16S/genetics
  14. Fulltext Endometrial microbiota composition is associated with reproductive outcome in infertile patients
    Moreno I, Garcia-Grau I, Perez-Villaroya D, Gonzalez-Monfort M, Bahçeci M, Barrionuevo MJ, et al.
    Microbiome, 2022 Jan 04;10(1):1.
    PMID: 34980280 DOI: 10.1186/s40168-021-01184-w
    BACKGROUND: Previous evidence indicates associations between the female reproductive tract microbiome composition and reproductive outcome in infertile patients undergoing assisted reproduction. We aimed to determine whether the endometrial microbiota composition is associated with reproductive outcomes of live birth, biochemical pregnancy, clinical miscarriage or no pregnancy.

    METHODS: Here, we present a multicentre prospective observational study using 16S rRNA gene sequencing to analyse endometrial fluid and biopsy samples before embryo transfer in a cohort of 342 infertile patients asymptomatic for infection undergoing assisted reproductive treatments.

    RESULTS: A dysbiotic endometrial microbiota profile composed of Atopobium, Bifidobacterium, Chryseobacterium, Gardnerella, Haemophilus, Klebsiella, Neisseria, Staphylococcus and Streptococcus was associated with unsuccessful outcomes. In contrast, Lactobacillus was consistently enriched in patients with live birth outcomes.

    CONCLUSIONS: Our findings indicate that endometrial microbiota composition before embryo transfer is a useful biomarker to predict reproductive outcome, offering an opportunity to further improve diagnosis and treatment strategies. Video Abstract.

    Matched MeSH terms: RNA, Ribosomal, 16S/genetics
  15. Purification and Characterization of Desferrioxamine B of Pseudomonas fluorescens and Its Application to Improve Oil Content, Nutrient Uptake, and Plant Growth in Peanuts
    Nithyapriya S, Sundaram L, Eswaran SUD, Perveen K, Alshaikh NA, Sayyed RZ, et al.
    Microb Ecol, 2024 Apr 17;87(1):60.
    PMID: 38630182 DOI: 10.1007/s00248-024-02377-0
    Microorganisms produce siderophores, which are low-molecular-weight iron chelators when iron availability is limited. The present analyzed the role of LNPF1 as multifarious PGPR for improving growth parameters and nutrient content in peanut and soil nutrients. Such multifarious PGPR strains can be used as effective bioinoculants for peanut farming. In this work, rhizosphere bacteria from Zea mays and Arachis hypogaea plants in the Salem area of Tamil Nadu, India, were isolated and tested for biochemical attributes and characteristics that stimulate plant growth, such as the production of hydrogen cyanide, ammonia (6 µg/mL), indole acetic acid (76.35 µg/mL), and solubilizing phosphate (520 µg/mL). The 16S rRNA gene sequences identified the isolate LNPF1 as Pseudomonas fluorescens with a similarity percentage of 99% with Pseudomonas sp. Isolate LNPF1 was evaluated for the production of siderophore. Siderophore-rich supernatant using a Sep Pack C18 column and Amberlite-400 Resin Column (λmax 264) produced 298 mg/L and 50 mg/L of siderophore, respectively. The characterization of purified siderophore by TLC, HPLC, FTIR, and 2D-NMR analysis identified the compound as desferrioxamine, a hydroxamate siderophore. A pot culture experiment determined the potential of LNPF1 to improve iron and oil content and photosynthetic pigments in Arachis hypogaea L. and improve soil nutrient content. Inoculation of A. hypogea seeds with LNPF1 improved plant growth parameters such as leaf length (60%), shoot length (22%), root length (54.68%), fresh weight (47.28%), dry weight (37%), and number of nuts (66.66) compared to the control (untreated seeds). This inoculation also improved leaf iron content (43.42), short iron content (38.38%), seed iron (46.72%), seed oil (31.68%), carotenoid (64.40%), and total chlorophyll content (98.%) compared to control (untreated seeds). Bacterized seeds showed a substantial increase in nodulation (61.65%) and weight of individual nodules (95.97) vis-à-vis control. The results of the present study indicated that P. fluorescens might be utilized as a potential bioinoculant to improve growth, iron content, oil content, number of nuts and nodules of Arachishypogaea L., and enrich soil nutrients.
    Matched MeSH terms: RNA, Ribosomal, 16S/genetics
  16. Fulltext Two extraction-free reverse transcription loop-mediated isothermal amplification assays for detection of SARS-CoV-2
    Lai MY, Bukhari FDM, Zulkefli NZ, Ismail I, Mustapa NI, Soh TST, et al.
    BMC Infect Dis, 2021 Nov 17;21(1):1162.
    PMID: 34789179 DOI: 10.1186/s12879-021-06876-0
    BACKGROUND: Current assays for detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) rely on time consuming, costly and laboratory based methods for virus isolation, purification and removing inhibitors. To address this limitation, we propose a simple method for testing RNA from nasopharyngeal swab samples that bypasses the RNA purification step.

    METHODS: In the current project, we have described two extraction-free reverse transcription loop-mediated isothermal amplification (RT-LAMP) assays for the detection of SARS-CoV-2 by using E gene and RdRp gene as the targets.

    RESULTS: Here, results showed that reverse transcription loop-mediated isothermal amplification assays with 88.4% sensitive (95% CI: 74.9-96.1%) and 67.4% sensitive (95% CI: 51.5-80.9%) for E gene and RdRp gene, respectively.

    CONCLUSION: Without the need of RNA purification, our developed RT-LAMP assays for direct detection of SARS-CoV-2 from nasopharyngeal swab samples could be turned into alternatives to qRT-PCR for rapid screening.

    Matched MeSH terms: RNA, Viral/genetics
  17. First Report on Novel Psychrotrophic Phosphorus-Solubilizing Ochrobactrum thiophenivorans EU-KL94 from Keylong Region in Great Himalayas and Their Role in Plant Growth Promotion of Oats (Avena sativa L.)
    Kour D, Yadav AN
    Curr Microbiol, 2023 May 30;80(7):227.
    PMID: 37249717 DOI: 10.1007/s00284-023-03308-x
    Cold stress leads to the disruption of the cellular homeostasis in plants and generation of reactive oxygen species (ROS) and productivity losses. In the present study, 94 psychrotrophic phosphorus-solubilizing bacteria with multiple plant growth-promoting (PGP) capabilities were isolated from rhizosphere of wheat. The most efficient strain EU-KL94 showing highest amount of solubilized phosphorus and maximum number of PGP attributes was identified using 16S rRNA sequencing as Ochrobactrum thiophenivorans. Ochrobactrum thiophenivorans EU-KL94 along with recommended doses of the chemical fertilizers as controls were used for alleviation of cold stress in oats. The strain improved the root and shoot length, dry and fresh weight, proline, glycine betaine, chlorophyll content as well as the superoxide dismutase (SOD) and glutathione reductase (GR) activities of oats under cold stress conditions. Ochrobactrum thiophenivorans with all promising plant growth activities under cold stress could be used as an environmental friendly strategy for mitigation of low temperature stress. To the best of our knowledge, Ochrobactrum thiophenivorans has been reported for the first time as P-solubilizer and as bioinoculants in oats for cold stress mitigation.
    Matched MeSH terms: RNA, Ribosomal, 16S/genetics
  18. Small RNAs and Karma methylation in Elaeis guineensis mother palms are linked to high clonal mantling
    Ooi SE, Sarpan N, Taranenko E, Feshah I, Nuraziyan A, Roowi SH, et al.
    Plant Mol Biol, 2023 Mar;111(4-5):345-363.
    PMID: 36609897 DOI: 10.1007/s11103-022-01330-4
    The mantled phenotype is an abnormal somaclonal variant arising from the oil palm cloning process and severe phenotypes lead to oil yield losses. Hypomethylation of the Karma retrotransposon within the B-type MADS-box EgDEF1 gene has been associated with this phenotype. While abnormal Karma-EgDEF1 hypomethylation was detected in mantled clones, we examined the methylation state of Karma in ortets that gave rise to high mantling rates in their clones. Small RNAs (sRNAs) were proposed to play a role in Karma hypomethylation as part of the RNA-directed DNA methylation process, hence differential expression analysis of sRNAs between the ortet groups was conducted. While no sRNA was differentially expressed at the Karma-EgDEF1 region, three sRNA clusters were differentially regulated in high-mantling ortets. The first two down-regulated clusters were possibly derived from long non-coding RNAs while the third up-regulated cluster was derived from the intron of a DnaJ chaperone gene. Several predicted mRNA targets for the first two sRNA clusters conversely displayed increased expression in high-mantling relative to low-mantling ortets. These predicted mRNA targets may be associated with defense or pathogenesis response. In addition, several differentially methylated regions (DMRs) were identified in Karma and its surrounding regions, mainly comprising subtle CHH hypomethylation in high-mantling ortets. Four of the 12 DMRs were located in a region corresponding to hypomethylated areas at the 3'end of Karma previously reported in mantled clones. Further investigations on these sRNAs and DMRs may indicate the predisposition of certain ortets towards mantled somaclonal variation.
    Matched MeSH terms: RNA, Messenger/metabolism
  19. Fulltext A multiplexed RT-PCR assay for nanopore whole genome sequencing of Tilapia lake virus (TiLV)
    Delamare-Deboutteville J, Meemetta W, Pimsannil K, Sangpo P, Gan HM, Mohan CV, et al.
    Sci Rep, 2023 Nov 20;13(1):20276.
    PMID: 37985860 DOI: 10.1038/s41598-023-47425-w
    Tilapia lake virus (TiLV) is a highly contagious viral pathogen that affects tilapia, a globally significant and affordable source of fish protein. To prevent the introduction and spread of TiLV and its impact, there is an urgent need for increased surveillance, improved biosecurity measures, and continuous development of effective diagnostic and rapid sequencing methods. In this study, we have developed a multiplexed RT-PCR assay that can amplify all ten complete genomic segments of TiLV from various sources of isolation. The amplicons generated using this approach were immediately subjected to real-time sequencing on the Nanopore system. By using this approach, we have recovered and assembled 10 TiLV genomes from total RNA extracted from naturally TiLV-infected tilapia fish, concentrated tilapia rearing water, and cell culture. Our phylogenetic analysis, consisting of more than 36 TiLV genomes from both newly sequenced and publicly available TiLV genomes, provides new insights into the high genetic diversity of TiLV. This work is an essential steppingstone towards integrating rapid and real-time Nanopore-based amplicon sequencing into routine genomic surveillance of TiLV, as well as future vaccine development.
    Matched MeSH terms: RNA Viruses*
  20. Selecting the optimal gridded climate dataset for Nigeria using advanced time series similarity algorithms
    Tanimu B, Hamed MM, Bello AD, Abdullahi SA, Ajibike MA, Shahid S
    Environ Sci Pollut Res Int, 2024 Feb;31(10):15986-16010.
    PMID: 38308777 DOI: 10.1007/s11356-024-32128-0
    Choosing a suitable gridded climate dataset is a significant challenge in hydro-climatic research, particularly in areas lacking long-term, reliable, and dense records. This study used the most common method (Perkins skill score (PSS)) with two advanced time series similarity algorithms, short time series distance (STS), and cross-correlation distance (CCD), for the first time to evaluate, compare, and rank five gridded climate datasets, namely, Climate Research Unit (CRU), TERRA Climate (TERRA), Climate Prediction Center (CPC), European Reanalysis V.5 (ERA5), and Climatologies at high resolution for Earth's land surface areas (CHELSA), according to their ability to replicate the in situ rainfall and temperature data in Nigeria. The performance of the methods was evaluated by comparing the ranking obtained using compromise programming (CP) based on four statistical criteria in replicating in situ rainfall, maximum temperature, and minimum temperature at 26 locations distributed over Nigeria. Both methods identified CRU as Nigeria's best-gridded climate dataset, followed by CHELSA, TERRA, ERA5, and CPC. The integrated STS values using the group decision-making method for CRU rainfall, maximum and minimum temperatures were 17, 10.1, and 20.8, respectively, while CDD values for those variables were 17.7, 11, and 12.2, respectively. The CP based on conventional statistical metrics supported the results obtained using STS and CCD. CRU's Pbias was between 0.5 and 1; KGE ranged from 0.5 to 0.9; NSE ranged from 0.3 to 0.8; and NRMSE between - 30 and 68.2, which were much better than the other products. The findings establish STS and CCD's ability to evaluate the performance of climate data by avoiding the complex and time-consuming multi-criteria decision algorithms based on multiple statistical metrics.
    Matched MeSH terms: RNA, Long Noncoding*
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