Displaying publications 141 - 160 of 1890 in total

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  1. Fulltext Bacterial flora varies throughout the saltwater crocodile (Crocodylus porosus) gastrointestinal tract
    Siddiqui R, Maciver SK, Anuar TS, Khan NA
    Am J Vet Res, 2023 Aug 01;84(8).
    PMID: 37353216 DOI: 10.2460/ajvr.23.03.0061
    OBJECTIVE: The objective of this study was to determine bacterial flora throughout the gastrointestinal tract of a saltwater crocodile (Crocodylus porosus) using 16S rRNA gene analysis.

    ANIMALS: A convention on international trade in endangered species (CITES) of wild fauna and flora registered crocodile farm, provided a healthy male saltwater crocodile, Crocodylus porosus for this study.

    PROCEDURES: Three samples were taken from the oral cavity, 3 samples from the proximal region of the small intestine (jejunum), and 3 samples from the distal part of the large intestine of the gastrointestinal tract of C. porosus were obtained using sterile cotton swabs. Next, swabs were placed in 15 mL sterile centrifuge tubes, individually, and kept on ice for immediate transportation to the laboratory. This was followed by 16S rRNA gene analysis using specific primers (341F-CCTAYGGGRBGCASCAG, and 806R-GGACTACNNGGGTATCTAAT). Amplicons were sequenced on Illumina paired-end platform, and bacterial gastrointestinal communities, the relative abundance of taxa, and principal component and coordinate analysis were performed.

    RESULTS: The findings revealed that bacterial community structures from differing regions exhibited several differences. The number of observed bacterial operational taxonomic units (OTUs) was 153 in the oral cavity, 239 in the small intestine, and 119 in the large intestine of C. porosus. The small intestine reflects the highest richness. In contrast, the large intestine exhibited the least richness of microbial communities. Relative abundance of taxa showed that Proteobacteria, Bacteroidetes, and Firmicutes were dominant in all 3 sample sites. Pseudomonas differed in the oral cavity and the large intestine, with the latter exhibiting less distribution of Pseudomonas. Stenotrophomonas and Castellaniella were higher in the oral cavity, while the relative abundance of Comamonas and Salmonella was higher in the small intestine. Conversely, the relative abundance of Salmonella and Pannonibacter was augmented in the large intestine.

    CLINICAL RELEVANCE: For the first time, this study demonstrates the bacterial diversity along the segments of the gastrointestinal tract of C. porosus. Bacterial flora varies throughout the gastrointestinal tract. Although further studies using large cohorts are warranted; however, our findings suggest that microbiome composition may have the potential as a biomarker in determining the overall health and well-being of C. porosus.

    Matched MeSH terms: RNA, Ribosomal, 16S/genetics
  2. Fulltext Isolation of Spirosoma foliorum sp. nov. from the fallen leaf of Acer palmatum by a novel cultivation technique
    Han HL, Nurcahyanto DA, Muhammad N, Lee YJ, Nguyen TTH, Kim SG, et al.
    Sci Rep, 2023 Sep 06;13(1):14684.
    PMID: 37673882 DOI: 10.1038/s41598-023-35108-5
    In the effort of isolating novel microbial species, the strain PL0132T was isolated from a fallen leaf under fresh water at a stream, which glided when grown on a tap water medium (without nutrients). The strain was determined to be Gram-negative, strictly aerobic, and rod-shaped, which grew optimally at 25 °C, pH 6-7, and the strain tolerates 1% (w/v) NaCl concentration. The complete genome of strain PL0132T comprises one contig with a sequencing depth of 76×, consisting of 8,853,064 base pairs and the genomic DNA G + C content was 46.7% (genome). 16S rRNA gene sequence analysis revealed that strain PL0132T represents a member of the phylum Bacteroidetes and is affiliated with the genus Spirosoma. Based on genomic, phenotypic, and chemotaxonomic characteristics, the strain PL0132T represents a novel species of the genus Spirosoma, for which the name Spirosoma foliorum sp. nov. is proposed (= KCTC 72228 T = InaCC B1447T).
    Matched MeSH terms: RNA, Ribosomal, 16S/genetics
  3. Fulltext Isolation of Streptococcus cuniculi from corneal lesion in laboratory-raised mice
    Tiong V, Loong SK, Mohamad Wali HA, Tan KK, Jee PF, Lim FS, et al.
    J Vet Med Sci, 2021 Mar 05;83(2):280-284.
    PMID: 33441499 DOI: 10.1292/jvms.20-0070
    Corneal lesions appearing as white mass beneath intact epithelium, with ocular discharge in one mouse, was observed in a batch of laboratory-raised BALB/c mice (n=9 of 56). The affected mice remained active, well-groomed and had normal appetite. Isolates recovered from swab cultures of the external and internal contents of the eye had partial 16S rRNA gene sequence of 99.1% similarity to Streptococcus cuniculi. No previous report of S. cuniculi infection in laboratory rodents has been presented. The isolate was susceptible to all antibiotics tested. We suggest S. cuniculi is an opportunistic bacteria in laboratory mice but are uncertain of its source. Our findings revealed that S. cuniculi is able to colonize laboratory mice and should be considered when mice present with eye lesion or ocular discharge.
    Matched MeSH terms: RNA, Ribosomal, 16S/genetics
  4. 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*
  5. Fulltext Structural and functional insights into TRiC chaperonin from a psychrophilic yeast, Glaciozyma antarctica
    Yusof NA, Kamaruddin S, Abu Bakar FD, Mahadi NM, Abdul Murad AM
    Cell Stress Chaperones, 2019 Mar;24(2):351-368.
    PMID: 30649671 DOI: 10.1007/s12192-019-00969-1
    Studies on TCP1-1 ring complex (TRiC) chaperonin have shown its indispensable role in folding cytosolic proteins in eukaryotes. In a psychrophilic organism, extreme cold temperature creates a low-energy environment that potentially causes protein denaturation with loss of activity. We hypothesized that TRiC may undergo evolution in terms of its structural molecular adaptation in order to facilitate protein folding in low-energy environment. To test this hypothesis, we isolated G. antarctica TRiC (GaTRiC) and found that the expression of GaTRiC mRNA in G. antarctica was consistently expressed at all temperatures indicating their importance in cell regulation. Moreover, we showed GaTRiC has the ability of a chaperonin whereby denatured luciferase can be folded to the functional stage in its presence. Structurally, three categories of residue substitutions were found in α, β, and δ subunits: (i) bulky/polar side chains to alanine or valine, (ii) charged residues to alanine, and (iii) isoleucine to valine that would be expected to increase intramolecular flexibility within the GaTRiC. The residue substitutions observed in the built structures possibly affect the hydrophobic, hydrogen bonds, and ionic and aromatic interactions which lead to an increase in structural flexibility. Our structural and functional analysis explains some possible structural features which may contribute to cold adaptation of the psychrophilic TRiC folding chamber.
    Matched MeSH terms: RNA, Messenger/genetics
  6. Fulltext Diet, lifestyle and gut microbiota composition among Malaysian women with gestational diabetes mellitus: a prospective cohort study
    Kunasegaran T, Balasubramaniam VRMT, Thirunavuk Arasoo VJ, Palanisamy UD, Tan YK, Ramadas A
    Sci Rep, 2024 Mar 22;14(1):6891.
    PMID: 38519592 DOI: 10.1038/s41598-024-57627-5
    The study addressed a significant gap in the profiling and understanding of the gut microbiota's influence on Malaysian Malay women with gestational diabetes mellitus (GDM). This prospective cohort study aimed to explore the intricate relationship between gut microbiota, dietary choices, and lifestyle factors among Malay women, both with and without GDM. The research specifically focused on participants during the second (T0) and third (T1) trimesters of pregnancy in Johor Bahru, Malaysia. In Part 1 of the study, a diverse pool of pregnant women at T0 was categorized into two groups: those diagnosed with GDM and those without GDM, with a total sample size of 105 individuals. The assessments encompassed demographic, clinical, lifestyle, and dietary factors at the T0 and T1 trimesters. Part 2 of the study delved into microbiome analysis, targeting a better understanding of the gut microbiota among the participants. Stool samples were randomly collected from 50% of the individuals in each group (GDM and non-GDM) at T0 and T1. The collected samples underwent processing, and 16s rRNA metagenomic analysis was employed to study the microbial composition. The results suggested an association between elevated body weight and glucose levels, poor sleep quality, lack of physical activity, greater intake of iron and meat, and reduced fruit consumption among women with GDM compared to non-GDM groups. The microbiome analysis revealed changes in microbial composition over time, with reduced diversity observed in the GDM group during the third trimester. The genera Lactiplantibacillus, Parvibacter, Prevotellaceae UCG001, and Vagococcus positively correlated with physical activity levels in GDM women in the second trimester. Similarly, the genus Victivallis exhibited a strong positive correlation with gravida and parity. On the contrary, the genus Bacteroides and Roseburia showed a negative correlation with omega-3 polyunsaturated fatty acids (PUFAs) in women without GDM in the third trimester. The study highlighted the multifaceted nature of GDM, involving a combination of lifestyle factors, dietary choices, and changes in gut microbiota composition. The findings emphasized the importance of considering these interconnected elements in understanding and managing gestational diabetes among Malaysian Malay women. Further exploration is essential to comprehend the mechanisms underlying this relationship and develop targeted interventions for effective GDM management.
    Matched MeSH terms: RNA, Ribosomal, 16S/genetics
  7. 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
  8. 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
  9. Fulltext SARS-CoV-2 detection by targeting four loci of viral genome using graphene oxide and gold nanoparticle DNA biosensor
    Babadi AA, Rahmati S, Fakhlaei R, Heidari R, Baradaran S, Akbariqomi M, et al.
    Sci Rep, 2022 Nov 12;12(1):19416.
    PMID: 36371566 DOI: 10.1038/s41598-022-23996-y
    The current COVID-19 pandemic outbreak poses a serious threat to public health, demonstrating the critical need for the development of effective and reproducible detection tests. Since the RT-qPCR primers are highly specific and can only be designed based on the known sequence, mutation sensitivity is its limitation. Moreover, the mutations in the severe acute respiratory syndrome β-coronavirus (SARS-CoV-2) genome led to new highly transmissible variants such as Delta and Omicron variants. In the case of mutation, RT-qPCR primers cannot recognize and attach to the target sequence. This research presents an accurate dual-platform DNA biosensor based on the colorimetric assay of gold nanoparticles and the surface-enhanced Raman scattering (SERS) technique. It simultaneously targets four different regions of the viral genome for detection of SARS-CoV-2 and its new variants prior to any sequencing. Hence, in the case of mutation in one of the target sequences, the other three probes could detect the SARS-CoV-2 genome. The method is based on visible biosensor color shift and a locally enhanced electromagnetic field and significantly amplified SERS signal due to the proximity of Sulfo-Cyanine 3 (Cy3) and AuNPs intensity peak at 1468 cm-1. The dual-platform DNA/GO/AuNP biosensor exhibits high sensitivity toward the viral genome with a LOD of 0.16 ng/µL. This is a safe point-of-care, naked-eye, equipment-free, and rapid (10 min) detection biosensor for diagnosing COVID-19 cases at home using a nasopharyngeal sample.
    Matched MeSH terms: RNA, Viral/genetics
  10. Fulltext Loop-Mediated Isothermal Amplification Assay for Identification of Five Human Plasmodium Species in Malaysia
    Lau YL, Lai MY, Fong MY, Jelip J, Mahmud R
    Am J Trop Med Hyg, 2016 Feb;94(2):336-339.
    PMID: 26598573 DOI: 10.4269/ajtmh.15-0569
    The lack of rapid, affordable, and accurate diagnostic tests represents the primary hurdle affecting malaria surveillance in resource- and expertise-limited areas. Loop-mediated isothermal amplification (LAMP) is a sensitive, rapid, and cheap diagnostic method. Five species-specific LAMP assays were developed based on 18S rRNA gene. Sensitivity and specificity of LAMP results were calculated as compared with microscopic examination and nested polymerase chain reaction. LAMP reactions were highly sensitive with the detection limit of one copy for Plasmodium vivax, Plasmodium falciparum, and Plasmodium malariae and 10 copies for Plasmodium knowlesi and Plasmodium ovale. LAMP positively detected all human malaria species in all positive samples (N = 134; sensitivity = 100%) within 35 minutes. All negative samples were not amplified by LAMP (N = 67; specificity = 100%). LAMP successfully detected two samples with very low parasitemia. LAMP may offer a rapid, simple, and reliable test for the diagnosis of malaria in areas where malaria is prevalent.
    Matched MeSH terms: RNA, Ribosomal, 18S/genetics; RNA, Protozoan/genetics
  11. Transcriptome analysis of feline infectious peritonitis virus infection
    Mehrbod P, Harun MS, Shuid AN, Omar AR
    Methods Mol Biol, 2015;1282:241-50.
    PMID: 25720485 DOI: 10.1007/978-1-4939-2438-7_20
    Feline infectious peritonitis (FIP) is a lethal systemic disease caused by FIP virus (FIPV). There are no effective vaccines or treatment available, and the virus virulence determinants and pathogenesis are not fully understood. Here, we describe the sequencing of RNA extracted from Crandell Rees Feline Kidney (CRFK) cells infected with FIPV using the Illumina next-generation sequencing approach. Bioinformatics analysis, based on Felis catus 2X annotated shotgun reference genome, using CLC bio Genome Workbench is used to map both control and infected cells. Kal's Z test statistical analysis is used to analyze the differentially expressed genes from the infected CRFK cells. In addition, RT-qPCR analysis is used for further transcriptional profiling of selected genes in infected CRFK cells and Peripheral Blood Mononuclear Cells (PBMCs) from healthy and FIP-diagnosed cats.
    Matched MeSH terms: RNA, Messenger/genetics; RNA, Messenger/isolation & purification; RNA, Messenger/metabolism
  12. The complete mitogenome of the invasive spiny-cheek crayfish Orconectes limosus (Rafinesque, 1817) (Crustacea: Decapoda: Cambaridae)
    Gan HM, Gan HY, Lee YP, Grandjean F, Austin CM
    Mitochondrial DNA A DNA Mapp Seq Anal, 2016 09;27(5):3181-3.
    PMID: 25648916 DOI: 10.3109/19401736.2015.1007326
    The invasive freshwater crayfish Orconectes limosus mitogenome was recovered by genome skimming. The mitogenome is 16,223 base pairs in length consisting of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a non-coding AT-rich region. The O. limosus mitogenome has an AT bias of 71.37% and base composition of 39.8% for T, 10.3% for C, 31.5% for A, and 18.4% for G. The mitogene order is identical to two other genera of northern hemisphere crayfish that have been sequenced for this organelle.
    Matched MeSH terms: RNA, Ribosomal/genetics; RNA, Transfer/genetics
  13. Phylogenetic relationships and morphological evolution in Lentinus, Polyporellus and Neofavolus, emphasizing southeastern Asian taxa
    Seelan JS, Justo A, Nagy LG, Grand EA, Redhead SA, Hibbett D
    Mycologia, 2015 May-Jun;107(3):460-74.
    PMID: 25661717 DOI: 10.3852/14-084
    The genus Lentinus (Polyporaceae, Basidiomycota) is widely documented from tropical and temperate forests and is taxonomically controversial. Here we studied the relationships between Lentinus subg. Lentinus sensu Pegler (i.e. sections Lentinus, Tigrini, Dicholamellatae, Rigidi, Lentodiellum and Pleuroti and polypores that share similar morphological characters). We generated sequences of internal transcribed spacers (ITS) and partial 28S regions of nuc rDNA and genes encoding the largest subunit of RNA polymerase II (RPB1), focusing on Lentinus subg. Lentinus sensu Pegler and the Neofavolus group, combined these data with sequences from GenBank (including RPB2 gene sequences) and performed phylogenetic analyses with maximum likelihood and Bayesian methods. We also evaluated the transition in hymenophore morphology between Lentinus, Neofavolus and related polypores with ancestral state reconstruction. Single-gene phylogenies and phylogenies combining ITS and 28S with RPB1 and RPB2 genes all support existence of a Lentinus/Polyporellus clade and a separate Neofavolus clade. Polyporellus (represented by P. arcularius, P. ciliatus, P. brumalis) forms a clade with species representing Lentinus subg. Lentinus sensu Pegler (1983), excluding L. suavissimus. Lentinus tigrinus appears as the sister group of Polyporellus in the four-gene phylogeny, but this placement was weakly supported. All three multigene analyses and the single-gene analysis using ITS strongly supported Polyporus tricholoma as the sister group of the Lentinus/Polyporellus clade; only the 28S rRNA phylogeny failed to support this placement. Under parsimony the ancestral hymenophoral configuration for the Lentinus/Polyporellus clade is estimated to be circular pores, with independent transitions to angular pores and lamellae. The ancestral state for the Neofavolus clade is estimated to be angular pores, with a single transition to lamellae in L. suavissimus. We propose that Lentinus suavissimus (section Pleuroti) should be reclassified as Neofavolus suavissimus comb. nov.
    Matched MeSH terms: RNA Polymerase II/genetics; RNA, Ribosomal/genetics
  14. The complete mitogenome of the stone crab Myomenippe fornasinii (Bianconi, 1851) (Crustacea: Decapoda: Menippidae)
    Tan MH, Gan HM, Lee YP, Austin CM
    Mitochondrial DNA A DNA Mapp Seq Anal, 2016;27(2):1374-5.
    PMID: 25103431 DOI: 10.3109/19401736.2014.947587
    The mitochondrial genome sequence of the stone crab, Myomenippe fornasinii, second of the superfamily Eriphioidea is documented. Myomenippe fornasinii has a mitogenome of 15,658 base pairs consisting of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs and a non-coding AT-rich region. The base composition of the M. fornasinii mitogenome is 36.10% for T, 18.52% for C, 35.48% for A, and 9.90% for G, with an AT bias of 71.58%. The mitogenome gene order conforms to what is the standard arrangement for brachyuran crabs.
    Matched MeSH terms: RNA, Ribosomal/genetics; RNA, Transfer/genetics
  15. Fulltext 5' isomiR variation is of functional and evolutionary importance
    Tan GC, Chan E, Molnar A, Sarkar R, Alexieva D, Isa IM, et al.
    Nucleic Acids Res, 2014 Aug;42(14):9424-35.
    PMID: 25056318 DOI: 10.1093/nar/gku656
    We have sequenced miRNA libraries from human embryonic, neural and foetal mesenchymal stem cells. We report that the majority of miRNA genes encode mature isomers that vary in size by one or more bases at the 3' and/or 5' end of the miRNA. Northern blotting for individual miRNAs showed that the proportions of isomiRs expressed by a single miRNA gene often differ between cell and tissue types. IsomiRs were readily co-immunoprecipitated with Argonaute proteins in vivo and were active in luciferase assays, indicating that they are functional. Bioinformatics analysis predicts substantial differences in targeting between miRNAs with minor 5' differences and in support of this we report that a 5' isomiR-9-1 gained the ability to inhibit the expression of DNMT3B and NCAM2 but lost the ability to inhibit CDH1 in vitro. This result was confirmed by the use of isomiR-specific sponges. Our analysis of the miRGator database indicates that a small percentage of human miRNA genes express isomiRs as the dominant transcript in certain cell types and analysis of miRBase shows that 5' isomiRs have replaced canonical miRNAs many times during evolution. This strongly indicates that isomiRs are of functional importance and have contributed to the evolution of miRNA genes.
    Matched MeSH terms: RNA Precursors/chemistry; RNA, Messenger/metabolism
  16. Fulltext Probiotic potential of Lactobacillus strains with antimicrobial activity against some human pathogenic strains
    Shokryazdan P, Sieo CC, Kalavathy R, Liang JB, Alitheen NB, Faseleh Jahromi M, et al.
    Biomed Res Int, 2014;2014:927268.
    PMID: 25105147 DOI: 10.1155/2014/927268
    The objective of this study was to isolate, identify, and characterize some lactic acid bacterial strains from human milk, infant feces, and fermented grapes and dates, as potential probiotics with antimicrobial activity against some human pathogenic strains. One hundred and forty bacterial strains were isolated and, after initial identification and a preliminary screening for acid and bile tolerance, nine of the best isolates were selected and further identified using 16 S rRNA gene sequences. The nine selected isolates were then characterized in vitro for their probiotic characteristics and their antimicrobial activities against some human pathogens. Results showed that all nine isolates belonged to the genus Lactobacillus. They were able to tolerate pH 3 for 3 h, 0.3% bile salts for 4 h, and 1.9 mg/mL pancreatic enzymes for 3 h. They exhibited good ability to attach to intestinal epithelial cells and were not resistant to the tested antibiotics. They also showed good antimicrobial activities against the tested pathogenic strains of humans, and most of them exhibited stronger antimicrobial activity than the reference strain L. casei Shirota. Thus, the nine Lactobacillus strains could be considered as potential antimicrobial probiotic strains against human pathogens and should be further studied for their human health benefits.
    Matched MeSH terms: RNA, Bacterial/genetics; RNA, Ribosomal, 16S/genetics
  17. The complete mitogenome of the Macquarie perch, Macquaria australasica Cuvier, 1830 (Teleostei: Percichthyidae)
    Gan HM, Tan MH, Austin CM
    Mitochondrial DNA A DNA Mapp Seq Anal, 2016;27(1):383-4.
    PMID: 24617484 DOI: 10.3109/19401736.2014.895996
    The complete mitochondrial genome of the conservationally significant Macquarie perch (Macquaria australasica) was obtained from low-coverage shotgun sequencing using the MiSeq sequencer. The M. australasica mitogenome has 16,496 base pairs (55% A + T content) made up of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a 819 bp non-coding AT-rich region. This is the first mitogenome sequence for the genus Macquaria, and the third to be reported for the family Percichthyidae.
    Matched MeSH terms: RNA, Ribosomal/genetics; RNA, Transfer/genetics
  18. Fulltext Specialized Hydrocarbonoclastic Bacteria Prevailing in Seawater around a Port in the Strait of Malacca
    Teramoto M, Queck SY, Ohnishi K
    PLoS One, 2013;8(6):e66594.
    PMID: 23824553 DOI: 10.1371/journal.pone.0066594
    Major degraders of petroleum hydrocarbons in tropical seas have been indicated only by laboratory culturing and never through observing the bacterial community structure in actual environments. To demonstrate the major degraders of petroleum hydrocarbons spilt in actual tropical seas, indigenous bacterial community in seawater at Sentosa (close to a port) and East Coast Park (far from a port) in Singapore was analyzed. Bacterial species was more diverse at Sentosa than at the Park, and the composition was different: γ-Proteobacteria (57.3%) dominated at Sentosa, while they did not at the Park. Specialized hydrocarbonoclastic bacteria (SHCB), which use limited carbon sources with a preference for petroleum hydrocarbons, were found as abundant species at Sentosa, indicating petroleum contamination. On the other hand, SHCB were not the abundant species at the Park. The abundant species of SHCB at Sentosa were Oleibacter marinus and Alcanivorax species (strain 2A75 type), which have previously been indicated by laboratory culturing as important petroleum-aliphatic-hydrocarbon degraders in tropical seas. Together with the fact that SHCB have been identified as major degraders of petroleum hydrocarbons in marine environments, these results demonstrate that the O. marinus and Alcanivorax species (strain 2A75 type) would be major degraders of petroleum aliphatic hydrocarbons spilt in actual tropical seas.
    Matched MeSH terms: RNA, Bacterial/genetics; RNA, Ribosomal, 16S/genetics
  19. Complete mitochondrial genome of the Tioman Island rock gecko, Cnemaspis limi (Sauria, Gekkota, Gekkonidae)
    Yan J, Tian C, Zhou J, Bauer AM, Lee Grismer L, Zhou K
    Mitochondrial DNA, 2014 Jun;25(3):181-2.
    PMID: 23631365 DOI: 10.3109/19401736.2013.792066
    We sequenced the complete mitochondrial genome of the Tioman Island rock gecko, Cnemaspis limi, which is known as an endemic species to Malaysia. The complete mitogenome is 16,680 bp in size, consisting of 37 genes coding for 13 proteins, 22 transfer RNAs, two ribosomal RNAs and one control region. The A + T content of the overall base composition of H-strand is 53.09% (T: 23.20%, C: 32.48%, A: 29.89% and G: 14.43%). The major non-coding region (control region) is 1254 bp in length with the A + T content of 55.09% and four replicates of a 76-bp repeat within this region.
    Matched MeSH terms: RNA, Ribosomal/genetics; RNA, Transfer/genetics
  20. Genome sequences of a novel HIV-1 CRF53_01B identified in Malaysia
    Chow WZ, Al-Darraji H, Lee YM, Takebe Y, Kamarulzaman A, Tee KK
    J Virol, 2012 Oct;86(20):11398-9.
    PMID: 22997419
    A novel HIV-1 genotype designated CRF53_01B was recently characterized from three epidemiologically unrelated persons in Malaysia. Here we announced three recently isolated full-length genomes of CRF53_01B, which is likely to be phylogenetically linked to CRF33_01B, circulating widely in Southeast Asia. The genome sequences may contribute to HIV-1 molecular surveillance and future vaccine development in the region.
    Matched MeSH terms: RNA, Viral/analysis; RNA, Viral/genetics; Sequence Analysis, RNA
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