Displaying publications 1181 - 1200 of 1902 in total

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  1. Parasite speciation within or between host species?--phylogenetic evidence from site-specific polystome monogeneans
    Littlewood DT, Rohde K, Clough KA
    Int J Parasitol, 1997 Nov;27(11):1289-97.
    PMID: 9421713
    Partial nuclear 28S ribosomal RNA and mitochondrial cytochrome c oxidase subunit I (COI) gene sequences (953 and 385 nucleotides, respectively) of one fish monogenean (outgroup) and six polystome monogeneans (four Polystomoides spp. from the oral cavities and urinary bladders of freshwater turtles in Australia and Malaya, two Neopolystoma spp. from the urinary bladder and conjunctival sac of a freshwater turtle in Australia) were used to examine the question of whether congeneric species infecting different sites in the same host species have speciated in that host by adapting to different sites, or whether species infecting a particular site in one host have given rise to species infecting the same site in different hosts. Results show unequivocally that congeneric species infecting the same site, even of host species belonging to different suborders and occurring on different continents, are more closely related than congeneric species infecting different sites of the same host species. This is interpreted as meaning that speciation has not occurred in one host. Morphological evolution of polystomes has been very slow: few differences between species and even genera have evolved over a period of at least 150 Myr, and this is matched by low substitution rates of nucleotides, and the ambiguous position of species of different genera, depending on whether COI or 28S rDNA sequences are used.
    Matched MeSH terms: RNA, Ribosomal, 28S/genetics
  2. Fulltext Myxozoan infections in fishes of the Tasik Kenyir Water Reservoir, Terengganu, Malaysia
    Székely C, Shaharom-Harrison F, Cech G, Ostoros G, Molnár K
    Dis Aquat Organ, 2009 Jan 28;83(1):37-48.
    PMID: 19301635 DOI: 10.3354/dao01991
    During a survey on fishes of the Tasik Kenyir Reservoir, Malaysia, 5 new Myxobolus spp. and 2 known Henneguya spp. were found. The specific locations for 2 Myxobolus spp. were the host's muscles, while 2 other Myxobolus spp. were found to develop in the host's kidney and gills, respectively. Of the species developing intracellularly in muscle cells, M. terengganuensis sp. nov. was described from Osteochilus hasselti and M. tasikkenyirensis sp. nov. from Osteochilus vittatus. M. csabai sp. nov. and M. osteochili sp. nov. were isolated from the kidney of Osteochilus hasselti, while M. dykovae sp. nov. was found in the gill lamellae of Barbonymus schwanenfeldii. Henneguya shaharini and Henneguya hemibagri plasmodia were found on the gills of Oxyeleotris marmoratus and Hemibagrus nemurus, respectively. Description of the new and known species was based on morphological characterization of spores, histological findings on locations of plasmodia and DNA sequence data.
    Matched MeSH terms: RNA, Ribosomal, 18S/genetics
  3. Fulltext Host-specific microbial communities in three sympatric North Sea sponges
    Naim MA, Morillo JA, Sørensen SJ, Waleed AA, Smidt H, Sipkema D
    FEMS Microbiol Ecol, 2014 Nov;90(2):390-403.
    PMID: 25088929 DOI: 10.1111/1574-6941.12400
    The establishment of next-generation technology sequencing has deepened our knowledge of marine sponge-associated microbiota with the identification of at least 32 phyla of Bacteria and Archaea from a large number of sponge species. In this study, we assessed the diversity of the microbial communities hosted by three sympatric sponges living in a semi-enclosed North Sea environment using pyrosequencing of bacterial and archaeal 16S ribosomal RNA gene fragments. The three sponges harbor species-specific communities each dominated by a different class of Proteobacteria. An α-proteobacterial Rhodobacter-like phylotype was confirmed as the predominant symbiont of Halichondria panicea. The microbial communities of Haliclona xena and H. oculata are described for the first time in this study and are dominated by Gammaproteobacteria and Betaproteobacteria, respectively. Several common phylotypes belonging to Chlamydiae, TM6, Actinobacteria, and Betaproteobacteria were detected in all sponge samples. A number of phylotypes of the phylum Chlamydiae were present at an unprecedentedly high relative abundance of up to 14.4 ± 1.4% of the total reads, which suggests an important ecological role in North Sea sponges. These Chlamydiae-affiliated operational taxonomic units may represent novel lineages at least at the genus level as they are only 86-92% similar to known sequences.
    Matched MeSH terms: RNA, Ribosomal, 16S/genetics
  4. Fulltext The effects of daily fasting hours on shaping gut microbiota in mice
    Li L, Su Y, Li F, Wang Y, Ma Z, Li Z, et al.
    BMC Microbiol, 2020 03 24;20(1):65.
    PMID: 32209070 DOI: 10.1186/s12866-020-01754-2
    BACKGROUND: It has recently been reported that intermittent fasting shapes the gut microbiota to benefit health, but this effect may be influenced to the exact fasting protocols. The purpose of this study was to assess the effects of different daily fasting hours on shaping the gut microbiota in mice. Healthy C57BL/6 J male mice were subjected to 12, 16 or 20 h fasting per day for 1 month, and then fed ad libitum for an extended month. Gut microbiota was analyzed by 16S rRNA gene-based sequencing and food intake was recorded as well.

    RESULTS: We found that cumulative food intake was not changed in the group with 12 h daily fasting, but significantly decreased in the 16 and 20 h fasting groups. The composition of gut microbiota was altered by all these types of intermittent fasting. At genus level, 16 h fasting led to increased level of Akkermansia and decreased level of Alistipes, but these effects disappeared after the cessation of fasting. No taxonomic differences were identified in the other two groups.

    CONCLUSIONS: These data indicated that intermittent fasting shapes gut microbiota in healthy mice, and the length of daily fasting interval may influence the outcome of intermittent fasting.

    Matched MeSH terms: RNA, Ribosomal, 16S/genetics*
  5. Expression of ADR-α1, 2 and ADR-β2 in cumulus cell culture of infertile women with polycystic ovary syndrome and poor responder who are a candidate for IVF: the novel strategic role of clonidine in this expression
    Zangeneh FZ, Bagheri M, Shoushtari MS, Naghizadeh MM
    J Recept Signal Transduct Res, 2021 Jun;41(3):263-272.
    PMID: 32878560 DOI: 10.1080/10799893.2020.1806320
    OBJECTIVE: Alpha and beta-adrenoceptors (ADR-α1, 2, and β2) play a regulatory role in the folliculogenesis and steroidogenesis in the ovarian follicles. This study aimed to measure these adrenoceptors mRNA and its protein levels in cumulus cells (CCs) culture of poor ovarian reserve (POR) and polycystic ovarian syndrome (PCOS) infertile women (IVF candidate) and the effect of clonidine treatment at CCs culture.

    METHODS: This case/control study was conducted in 2017 includes a control (donation oocytes) and two studies (PCO and POR) groups. The ovulation induction drugs were prescribed in all groups. After the oocyte puncture, the follicular fluid was collected and CCs were isolated were cultured. RNA was extracted and cDNA was synthesized and designed the primer for the ADR-α1, 2 and ADR-β2 gene expression. The protein levels were investigated by Western Blot.

    RESULTS: The results showed a high level of three adrenergic expressions in PCO women compared to the control group (p-value

    Matched MeSH terms: RNA; RNA, Messenger
  6. Diversity and Coding Potential of the Microbiota in the Photic and Aphotic Zones of Tropical Man-Made Lake with Intensive Aquaculture Activities: a Case Study on Temengor Lake, Malaysia
    Lau NS, Zarkasi KZ, Md Sah ASR, Shu-Chien AC
    Microb Ecol, 2019 Jul;78(1):20-32.
    PMID: 30397794 DOI: 10.1007/s00248-018-1283-0
    Although freshwater biomes cover less than 1% of the Earth's surface, they have disproportionate ecological significances. Attempts to study the taxonomy and function of freshwater microbiota are currently limited to samples collected from temperate lakes. In this study, we investigated samples from the photic and aphotic of an aquaculture site (disturbed) of Temengor Lake, a tropical lake in comparison with the undisturbed site of the lake using 16S rRNA amplicon and shotgun metagenomic approaches. Vertical changes in bacterial community composition and function of the Temengor Lake metagenomes were observed. The photic water layer of Temengor Lake was dominated by typical freshwater assemblages consisting of Proteobacteria, Actinobacteria, Bacteroidetes, Verrucomicrobia, and Cyanobacteria lineages. On the other hand, the aphotic water featured in addition to Proteobacteria, Bacteroidetes, Verrucomicrobia, and two more abundant bacterial phyla that are typically ubiquitous in anoxic habitats (Chloroflexi and Firmicutes). The aphotic zone of Temengor Lake exhibited genetic potential for nitrogen and sulfur metabolisms for which terminal electron acceptors other than oxygen are used in the reactions. The aphotic water of the disturbed site also showed an overrepresentation of genes associated with the metabolism of carbohydrates, likely driven by the enrichment of nutrient resulting from aquaculture activities at the site. The results presented in this study can serve as a basis for understanding the structure and functional capacity of the microbial communities in the photic and aphotic zones/water layers of tropical man-made lakes.
    Matched MeSH terms: RNA, Ribosomal, 16S/genetics
  7. Differential abundance and core members of the bacterial community associated with wild male Zeugodacus cucurbitae fruit flies (Insecta: Tephritidae) from three geographical regions of Southeast Asia
    Yong HS, Song SL, Eamsobhana P, Pasartvit A, Lim PE
    Mol Biol Rep, 2019 Aug;46(4):3765-3776.
    PMID: 31012029 DOI: 10.1007/s11033-019-04818-3
    Zeugodacus cucurbitae (Coquillet) is one of the most significant and widespread tephritid pest species of agricultural crops. This study reports the bacterial communities associated with Z. cucurbitae from three geographical regions in Southeast Asia (Thailand, Peninsular Malaysia, and Sarawak). The bacterial microbiota were investigated by targeted 16S rRNA gene (V3-V4 region) sequencing using the Illumina Mi-Seq platform. At 97% similarity and filtering at 0.001%, there were seven bacterial phyla and unassigned bacteria, comprising 11 classes, 23 orders, 39 families and 67 genera. The bacterial diversity and richness varied within and among the samples from the three geographical regions. Five phyla were detected for the Sarawak sample, and six each for the Thailand and Peninsular Malaysia samples. Four phyla-Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria-were represented in all the fruit fly specimens, forming the core members of the bacterial community. Proteobacteria was the predominant phylum, followed by Bacteroidetes, Firmicutes, and Actinobacteria. Fifty-three genera were represented in the Thailand sample, 56 in the Peninsular Malaysia sample, and 55 in the Sarawak sample. Forty-two genera were present in all the three geographical regions. The predominant core members were order Enterobacteriales (Proeteobacteria), and family Enterobacteriaceae (Enterobacteriales). Klebsiella (Enterobacteriaceae) was the predominant genus and K. oxytoca the predominant species with all specimens having > 10% relative abundance. The results indicate the presence of a great diversity as well as core members of the bacterial community associated with different populations of Z. cucurbitae.
    Matched MeSH terms: RNA, Ribosomal, 16S/genetics*
  8. Transcriptome analysis of Burkholderia pseudomallei SCV reveals an association with virulence, stress resistance and intracellular persistence
    Al-Maleki AR, Vellasamy KM, Mariappan V, Venkatraman G, Tay ST, Vadivelu J
    Genomics, 2020 01;112(1):501-512.
    PMID: 30980902 DOI: 10.1016/j.ygeno.2019.04.002
    Differences in expression of potential virulence and survival genes were associated with B. pseudomallei colony morphology variants. Microarray was used to investigate B. pseudomallei transcriptome alterations among the wild type and small colony variant (SCV) pre- and post-exposed to A549 cells. SCV pre- and post-exposed have lower metabolic requirements and consume lesser energy than the wild type pre- and post-exposed to A549. However, both the wild type and SCV limit their metabolic activities post- infection of A549 cells and this is indicated by the down-regulation of genes implicated in the metabolism of amino acids, carbohydrate, lipid, and other amino acids. Many well-known virulence and survival factors, including T3SS, fimbriae, capsular polysaccharides and stress response were up-regulated in both the wild type and SCV pre- and post-exposed to A549 cells. Microarray analysis demonstrated essential differences in bacterial response associated with virulence and survival pre- and post-exposed to A549 cells.
    Matched MeSH terms: RNA, Bacterial/isolation & purification
  9. Fulltext Kisspeptin-1 regulates forebrain dopaminergic neurons in the zebrafish
    Abdul Satar NM, Ogawa S, Parhar IS
    Sci Rep, 2020 11 09;10(1):19361.
    PMID: 33168887 DOI: 10.1038/s41598-020-75777-0
    The habenula is a phylogenetically conserved epithalamic structure, which conveys negative information via inhibition of mesolimbic dopamine neurons. We have previously shown the expression of kisspeptin (Kiss1) in the habenula and its role in the modulation of fear responses in the zebrafish. In this study, to investigate whether habenular Kiss1 regulates fear responses via dopamine neurons in the zebrafish, Kiss1 peptides were intracranially administered close to the habenula, and the expression of dopamine-related genes (th1, th2 and dat) were examined in the brain using real-time PCR and dopamine levels using LC-MS/MS. th1 mRNA levels and dopamine levels were significantly increased in the telencephalon 24-h and 30-min after Kiss1 administration, respectively. In fish administered with Kiss1, expression of neural activity marker gene, npas4a and kiss1 gene were significantly decreased in the ventral habenula. Application of neural tracer into the median raphe, site of habenular Kiss1 neural terminal projections showed tracer-labelled projections in the medial forebrain bundle towards the telencephalon where dopamine neurons reside. These results suggest that Kiss1 negatively regulates its own neuronal activity in the ventral habenula via autocrine action. This, in turn affects neurons of the median raphe via interneurons, which project to the telencephalic dopaminergic neurons.
    Matched MeSH terms: RNA, Messenger/metabolism
  10. Effects of age on feeding response: Focus on the rostral C1 neuron and its glucoregulatory proteins
    Ramlan H, Damanhuri HA
    Exp Gerontol, 2020 01;129:110779.
    PMID: 31705967 DOI: 10.1016/j.exger.2019.110779
    BACKGROUND: Older people are likely to develop anorexia of aging. Rostral C1 (rC1) catecholaminergic neurons in rostral ventrolateral medulla (RVLM) are recently discovered its role in food intake control. It is well established that these neurons regulate cardiovascular function.

    OBJECTIVE: This study aims to determine the effect of age on the function of rostral C1 (rC1) neurons in mediating feeding response.

    METHOD: Male Sprague Dawley rats at 3-months (n = 22) and 24-months (n = 22) old were used and further divided into two subgroups; 1) treatment group with 2-deoxy-d-glucose (2DG) and 2) vehicle group. Feeding hormones such as cholecystokinin (CCK), ghrelin and leptin were analysed using enzyme-linked immunosorbent assay (ELISA). Rat brain was carefully dissected to obtain the brainstem RVLM region. Further analysis was carried out to determine the level of proteins and genes in RVLM that were associated with feeding pathway. Protein expression of tyrosine hydroxylase (TH), phosphorylated TH at Serine40 (pSer40TH), AMP-activated protein kinase (AMPK), phosphorylated AMPK (phospho AMPK) and neuropeptide Y Y5 receptor (NPY5R) were determined by western blot. Expression of TH, AMPK and NPY genes were determined by real-time PCR.

    RESULTS: This study showed that blood glucose level was elevated in young and old rats following 2DG administration. Plasma CCK-8 concentration was higher in the aged rats at basal and increased with 2DG administration in young rats, but the leptin and ghrelin showed no changes. Old rats showed higher TH and lower AMPK mRNA levels. Glucoprivation decreased AMPK mRNA level in young rats and decreased TH mRNA in old rats. Aged rC1 neurons showed higher NPY5R protein level. Following glucoprivation, rC1 neurons produced distinct molecular changes across age in which, in young rats, AMPK phosphorylation level was increased and in old rats, TH phosphorylation level was increased.

    CONCLUSION: These findings suggest that glucose-counterregulatory responses by rC1 neurons at least, contribute to the ability of young and old rats in coping glucoprivation. Age-induced molecular changes within rC1 neurons may attenuate the glucoprivic responses. This situation may explain the impairment of feeding response in the elderly.

    Matched MeSH terms: RNA, Messenger/metabolism
  11. Isolation and characterization of a phenol-degrading Rhodococcus sp. strain AQ5NOL 2 KCTC 11961BP
    Arif NM, Ahmad SA, Syed MA, Shukor MY
    J Basic Microbiol, 2013 Jan;53(1):9-19.
    PMID: 22581645 DOI: 10.1002/jobm.201100120
    In this work, we report on the isolation of a phenol-degrading Rhodococcus sp. with a high tolerance towards phenol. The isolate was identified as Rhodococcus sp. strain AQ5NOL 2, based on 16S rDNA analysis. The strain degraded phenol using the meta pathway, a trait shared by many phenol-degraders. In addition to phenol biodegradation, the strain was also capable of degrading diesel. Strain AQ5NOL 2 exhibited a broad optimum temperature for growth on phenol at between 20 °C and 35 °C. The best nitrogen sources were ammonium sulphate, glycine or phenylalanine, followed by proline, nitrate, leucine, and alanine (in decreasing efficiency). Strain AQ5NOL 2 showed a high tolerance and degradation capacity of phenol, for it was able to register growth in the presence of 2000 mg l(-1) phenol. The growth of this strain on phenol as sole carbon and energy source were modeled using Haldane kinetics with a maximal specific growth rate (μ(max)) of 0.1102 hr(-1), a half-saturation constant (K(s) ) of 99.03 mg l(-1) or 1.05 mmol l(-1), and a substrate inhibition constant (K(i)) of 354 mg l(-1) or 3.76 mmol l(-1). Aside from phenol, the strain could utilize diesel, 2,4-dinitrophenol and ρ-cresol as carbon sources for growth. Strain AQ5NOL 2 exhibited inhibition of phenol degradation by Zn(2+), Cu(2+), Cr(6+), Ag(+) and Hg(2+) at 1 mg l(-1).
    Matched MeSH terms: RNA, Ribosomal, 16S/genetics
  12. P-TEFb goes viral
    Zaborowska J, Isa NF, Murphy S
    Bioessays, 2016 07;38 Suppl 1:S75-85.
    PMID: 27417125 DOI: 10.1002/bies.201670912
    Positive transcription elongation factor b (P-TEFb), which comprises cyclin-dependent kinase 9 (CDK9) kinase and cyclin T subunits, is an essential kinase complex in human cells. Phosphorylation of the negative elongation factors by P-TEFb is required for productive elongation of transcription of protein-coding genes by RNA polymerase II (pol II). In addition, P-TEFb-mediated phosphorylation of the carboxyl-terminal domain (CTD) of the largest subunit of pol II mediates the recruitment of transcription and RNA processing factors during the transcription cycle. CDK9 also phosphorylates p53, a tumor suppressor that plays a central role in cellular responses to a range of stress factors. Many viral factors affect transcription by recruiting or modulating the activity of CDK9. In this review, we will focus on how the function of CDK9 is regulated by viral gene products. The central role of CDK9 in viral life cycles suggests that drugs targeting the interaction between viral products and P-TEFb could be effective anti-viral agents.
    Matched MeSH terms: RNA Polymerase II/metabolism
  13. Fulltext Multiple gene targeting siRNAs for down regulation of Immediate Early-2 (Ie2) and DNA polymerase genes mediated inhibition of novel rat Cytomegalovirus (strain All-03)
    Balakrishnan KN, Abdullah AA, Bala JA, Jesse FFA, Abdullah CAC, Noordin MM, et al.
    Virol J, 2020 Oct 27;17(1):164.
    PMID: 33109247 DOI: 10.1186/s12985-020-01436-5
    BACKGROUND: Cytomegalovirus (CMV) is an opportunistic pathogen that causes severe complications in congenitally infected newborns and non-immunocompetent individuals. Developing an effective vaccine is a major public health priority and current drugs are fronting resistance and side effects on recipients. In the present study, with the aim of exploring new strategies to counteract CMV replication, several anti-CMV siRNAs targeting IE2 and DNA polymerase gene regions were characterized and used as in combinations for antiviral therapy.

    METHODS: The rat embryo fibroblast (REF) cells were transfected with multi siRNA before infecting with CMV strain ALL-03. Viral growth inhibition was measured by tissue culture infectious dose (TCID50), cytopathic effect (CPE) and droplet digital PCR (ddPCR) while IE2 and DNA polymerase gene knockdown was determined by real-time PCR. Ganciclovir was deployed as a control to benchmark the efficacy of antiviral activities of respective individual siRNAs.

    RESULTS: There was no significant cytotoxicity encountered for all the combinations of siRNAs on REF cells analyzed by MTT colorimetric assay (P > 0.05). Cytopathic effects (CPE) in cells infected by RCMV ALL-03 had developed significantly less and at much slower rate compared to control group. The expression of targeted genes was downregulated successfully resulted in significant reduction (P 

    Matched MeSH terms: RNA, Messenger; RNA, Small Interfering
  14. Surveillance of adult Aedes mosquitoes in Selangor, Malaysia
    Lau SM, Vythilingam I, Doss JI, Sekaran SD, Chua TH, Wan Sulaiman WY, et al.
    Trop Med Int Health, 2015 Oct;20(10):1271-80.
    PMID: 26094839 DOI: 10.1111/tmi.12555
    To determine the effectiveness of using sticky traps and the NS1 dengue antigen kit for the surveillance of Aedes mosquitoes for dengue control.
    Matched MeSH terms: RNA, Viral/isolation & purification
  15. Heteroplasmy, length, and sequence characterization of the mitochondrial control region in Tomistoma schlegelii
    Kaur T, Ong AH
    Biochem Genet, 2011 Oct;49(9-10):562-75.
    PMID: 21461907 DOI: 10.1007/s10528-011-9431-y
    This study describes the organization of the repetitive pattern in the mtDNA control region of Tomistoma schlegelii. Using newly designed primers, we detected length variations of approximately 50-100 bp among individuals, and only one individual showed a heteroplasmic band. Sequencing the region after CSB III revealed two main patterns: a repeat motif and a variable number tandem repeat (VNTR) pattern. The VNTR region, with a core unit of 104 bp, consisting of four motifs and a short AT chain, is implicated in the length variation seen among individuals of Tomistoma. A conserved motif seen in a family unit indicated that the repeat pattern was stably inherited from the maternal parent to all offspring. A combination of VNTR patterns specific to different crocodilians was seen in Tomistoma, and the overall secondary structure was shown to be similar to that in Crocodylus and Gavialis.
    Matched MeSH terms: RNA, Ribosomal/genetics
  16. Protein kinase D2 regulates epithelial sodium channel activity and aldosterone non-genomic responses in renal cortical collecting duct cells
    Thomas W, Dooley R, Quinn S, Robles MY, Harvey BJ
    Steroids, 2020 03;155:108553.
    PMID: 31836481 DOI: 10.1016/j.steroids.2019.108553
    Protein kinase D2 (PKD2) is a serine/threonine protein kinase which plays an important role in vesicle fission at the trans-Golgi network (TGN) to coordinate subcellular trafficking with gene expression. We found that in the rat kidney, PKD2 is specifically expressed in collecting duct principal cells predominantly at the apical membrane and with lower basal expression in cytosolic compartments. When rats were maintained on a Na+ depleted diet (<0.87 mmol Na+/kg) to increase plasma aldosterone levels, PKD2 became internalized to a cytoplasmic compartment. Treatment of murine M1 cortical collecting duct (M1-CCD) cells with aldosterone (10 nM) promoted PKD2 co-localization with the trans-Golgi network within 30 min. PKD2 underwent autophosphorylation at Ser876 within 10 min of aldosterone treatment and remained phosphorylated (active) for at least 24 h. A stable PKD2 shRNA knock-down (PKD2 KD) M1-CCD cell line was developed to study the role of PKD2 in epithelial Na+ channel (ENaC) trafficking and transepithelial Na+ transport (SCC) in epithelial monolayers grown in Ussing chambers. The PKD2 KD cells developed transepithelial resistance with kinetics equivalent to wild-type cells, however the transepithelial voltage and Na+ current were significantly elevated in PKD2 knock-down CCD epithelia. The higher basal SCC was due to increased ENaC activity. Aldosterone treatment for 24 h resulted in a decline in ENaC activity in the PKD2 KD cells as opposed to the increase observed in the wild-type cells. The paradoxical inhibition of SCC by aldosterone in PKD2 KD epithelium was attributed to a reduction in ENaC current and lower membrane abundance of ENaC, demonstrating that PKD2 plays a critical tonic role in ENaC trafficking and channel subunit stability. The rapid activation of PKD2 by aldosterone is synergistic with the transcriptional activity of MR and contributes to increased ENaC activity.
    Matched MeSH terms: RNA, Small Interfering/pharmacology
  17. Fulltext Gene expression patterns distinguish breast carcinomas from normal breast tissues: the Malaysian context
    Pau Ni IB, Zakaria Z, Muhammad R, Abdullah N, Ibrahim N, Aina Emran N, et al.
    Pathol Res Pract, 2010 Apr 15;206(4):223-8.
    PMID: 20097481 DOI: 10.1016/j.prp.2009.11.006
    Genomic and transcriptomic alterations that affect cellular processes, such as cell proliferation, differentiation, apoptosis and invasion, commonly occur in breast oncogenesis. Epidemiological evidence has proven that the risk of breast cancer predisposition varies among different ethnicities. This study aims to identify the transcriptome changes that commonly occur during the transition of normal breast epithelium to carcinoma in three local ethnic groups (Malays, Chinese and Indians). The gene expression patterns of 43 breast carcinomas with 43 patient-matched normal breast tissues were investigated using Affymetrix U133A GeneChip (containing 22,283 probe sets targeting approximately 18,400 different transcripts) and analyzed with GeneSpring GX10. Our findings revealed a total of 33 significantly differentially expressed genes, which showed>2-fold change at a 99.9% confidence interval level (p<0.001). The significantly differentially expressed genes included CD24, CD36, CD9, TACSTD1, TACSTD2, HBB, LEP, LPL, AKR1C1, AKR1C2 and AKR1C3. Our results indicate that the vast majority of gene expression changes, from normal breast epithelial to carcinoma, found in our three major ethnic populations are similar to those in the Caucasian population. Further study of the differentially expressed genes identified in our present study is needed to search for potential breast tumor biomarkers. This will eventually help to improve the therapeutic and treatment strategies for breast cancer patients in the future.
    Matched MeSH terms: RNA, Messenger/genetics
  18. Fulltext Differences in the bacteriome of swab, saliva, and tissue biopsies in oral cancer
    Gopinath D, Menon RK, Wie CC, Banerjee M, Panda S, Mandal D, et al.
    Sci Rep, 2021 01 13;11(1):1181.
    PMID: 33441939 DOI: 10.1038/s41598-020-80859-0
    Microbial dysbiosis has been implicated in the pathogenesis of oral cancer. We analyzed the compositional and metabolic profile of the bacteriome in three specific niches in oral cancer patients along with controls using 16SrRNA sequencing (Illumina Miseq) and DADA2 software. We found major differences between patients and control subjects. Bacterial communities associated with the tumor surface and deep paired tumor tissue differed significantly. Tumor surfaces carried elevated abundances of taxa belonging to genera Porphyromonas, Enterobacteriae, Neisseria, Streptococcus and Fusobacteria, whereas Prevotella, Treponema, Sphingomonas, Meiothermus and Mycoplasma genera were significantly more abundant in deep tissue. The most abundant microbial metabolic pathways were those related to fatty-acid biosynthesis, carbon metabolism and amino-acid metabolism on the tumor surface: carbohydrate metabolism and organic polymer degradation were elevated in tumor tissues. The bacteriome of saliva from patients with oral cancer differed significantly from paired tumor tissue in terms of community structure, however remained similar at taxonomic and metabolic levels except for elevated abundances of Streptococcus, Lactobacillus and Bacteroides, and acetoin-biosynthesis, respectively. These shifts to a pro-inflammatory profile are consistent with other studies suggesting oncogenic properties. Importantly, selection of the principal source of microbial DNA is key to ensure reliable, reproducible and comparable results in microbiome studies.
    Matched MeSH terms: RNA, Ribosomal, 16S/genetics
  19. Non-coding RNAs as therapeutic targets for preventing myocardial ischemia-reperfusion injury
    Ong SB, Katwadi K, Kwek XY, Ismail NI, Chinda K, Ong SG, et al.
    Expert Opin Ther Targets, 2018 03;22(3):247-261.
    PMID: 29417868 DOI: 10.1080/14728222.2018.1439015
    INTRODUCTION: New treatments are required to improve clinical outcomes in patients with acute myocardial infarction (AMI), for reduction of myocardial infarct (MI) size and preventing heart failure. Following AMI, acute ischemia/reperfusion injury (IRI) ensues, resulting in cardiomyocyte death and impaired cardiac function. Emerging studies have implicated a fundamental role for non-coding RNAs (microRNAs [miRNA], and more recently long non-coding RNAs [lncRNA]) in the setting of acute myocardial IRI. Areas covered: In this article, we discuss the roles of miRNAs and lncRNAs as potential biomarkers and therapeutic targets for the detection and treatment of AMI, review their roles as mediators and effectors of cardioprotection, particularly in the settings of interventions such as ischemic pre- and post-conditioning (IPC & IPost) as well as remote ischemic conditioning (RIC), and highlight future strategies for targeting ncRNAs to reduce MI size and prevent heart failure following AMI. Expert opinion: Investigating the roles of miRNAs and lncRNAs in the setting of AMI has provided new insights into the pathophysiology underlying acute myocardial IRI, and has identified novel biomarkers and therapeutic targets for detecting and treating AMI. Pharmacological and genetic manipulation of these ncRNAs has the therapeutic potential to improve clinical outcomes in AMI patients.
    Matched MeSH terms: RNA, Long Noncoding/genetics
  20. High-temperature EBPR process: the performance, analysis of PAOs and GAOs and the fine-scale population study of Candidatus "Accumulibacter phosphatis"
    Ong YH, Chua ASM, Fukushima T, Ngoh GC, Shoji T, Michinaka A
    Water Res, 2014 Nov 01;64:102-112.
    PMID: 25046374 DOI: 10.1016/j.watres.2014.06.038
    The applicability of the enhanced biological phosphorus removal (EBPR) process for the removal of phosphorus in warm climates is uncertain due to frequent reports of EBPR deterioration at temperature higher than 25 °C. Nevertheless, a recent report on a stable and efficient EBPR process at 28 °C has inspired the present study to examine the performance of EBPR at 24 °C-32 °C, as well as the PAOs and GAOs involved, in greater detail. Two sequencing batch reactors (SBRs) were operated for EBPR in parallel at different temperatures, i.e., SBR-1 at 28 °C and SBR-2 first at 24 °C and subsequently at 32 °C. Both SBRs exhibited high phosphorus removal efficiencies at all three temperatures and produced effluents with phosphorus concentrations less than 1.0 mg/L during the steady state of reactor operation. Real-time quantitative polymerase chain reaction (qPCR) revealed Accumulibacter-PAOs comprised 64% of the total bacterial population at 24 °C, 43% at 28 °C and 19% at 32 °C. Based on fluorescent in situ hybridisation (FISH), the abundance of Competibacter-GAOs at both 24 °C and 28 °C was rather low (<10%), while it accounted for 40% of the total bacterial population at 32 °C. However, the smaller Accumulibacter population and larger population of Competibacter at 32 °C did not deteriorate the phosphorus removal performance. A polyphosphate kinase 1 (ppk1)-based qPCR analysis on all studied EBPR processes detected only Accumulibacter clade IIF. The Accumulibacter population shown by 16S rRNA and ppk1 was not significantly different. This finding confirmed the existence of single clade IIF in the processes and the specificity of the clade IIF primer sets designed in this study. Habitat filtering related to temperature could have contributed to the presence of a unique clade. The clade IIF was hypothesised to be able to perform the EBPR activity at high temperatures. The clade's robustness most likely helps it to fit the high-temperature EBPR sludge best and allows it not only to outcompete other Accumulibacter clades but coexist with GAOs without compromising EBPR activity.
    Matched MeSH terms: RNA, Ribosomal, 16S/metabolism
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