Displaying publications 1021 - 1040 of 1902 in total

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  1. Nik Norliza Nik Hassan, Rozita Rosli, Abdul Munir Abdul Murad, Nor Kaslina Kornain, Sabariah, A.R., Rohan Malek Johan, et al.
    MyJurnal
    DNA microarray technology has permitted large scale parallel analysis of gene expression of several diseases, including cancers. Real-time PCR has become a well-established procedure for
    quantifying levels of gene expression. We evaluated Real-Time PCR to validate differentially expressed genes identified by DNA arrays. Gene expression of three different grade of transitional cell carcinoma (TCC) of human bladder cancer was determined using microarray slide containing cancer-related genes. Data obtained were sorted according based on the ratios between Cy3 and Cy5 dyes used and revealed 119, 235 and 183 differentially expressed genes in TCC WHO Grades I, II and III, respectively. Real-time PCR used SYBR Green-1 dye detection to validate relative change in gene expression. Real- Time PCR confirmed the change in gene expression of 17 of 28 (75%) genes identified by microarray. Real-Time PCR also suggest that genes identified by microarray with two or higher fold change cannot be eliminated as false nor be accepted as true without validation. Real-Time PCR based on SYBR Green- 1 is well-suited to validate DNA array results because it is quantitative, rapid and requires less RNA compared to the conventional assays.
    Matched MeSH terms: RNA
  2. Ghazali, F., Jamal, R., Zakaria, S.Z., Ismail, Z.H., Malik, Y.
    MyJurnal
    The two vital aspects of treatment for patients with tha-lassaemia are regular blood transfusions and iron chela-tion therapy. Unfortunately, the use of blood transfu-sions exposes these patients to the risks of acquiring transfusion related viral infections such as hepatitis C. Patients who acquire the hepatitis C virus (HCV) may develop chronic hepatitis and later on hepatocellular carcinoma. Hence, patients with thalassaemia should be regularly screened for the presence of HCV. We report here the results of a cross-sectional study conducted in a typical day-care centre for thalassaemics at the Hospital Universiti Kebangsaan Malaysia, involving 85 multiply transfused patients. We found that 19 patients (22.4%) were seropositive for HCV and two of them had positive HCV-RNA. Those who had started receiv-ing their transfusions before 1995, i.e. the year routine screening for HCV amongst blood donors were com-menced, and those who received transfusions 2-4 week-ly had a significantly higher risk of acquiring HCV infection.
    Matched MeSH terms: RNA
  3. Lim, S.N., Zeenathul, N.A., Mohd Azmi, M.L., Abas Mazni, O., Fauziah, O.
    MyJurnal
    Microinjection is a powerful tool to deliver various substances, such as nucleic acids, proteins, peptides, RNA, and synthetic molecules into mammalian cells mechanically. Through microinjection, a controlled amount of protein can be delivered into the target cells to elucidate the specific functional
    effects in vitro. In this study, a series of protein microinjection optimization was performed in human breast cancer cells. The presence of Maltose Binding Protein (MBP) was microscopically monitored through indirect immunofluorescence assay. The optimization experimentation gave a high success rate when MBP protein was used at the minimum concentration of 1.5 mg/ml and at the injection pressures of 50 and 70 hPa. The average success rate of injections was 49.2±4.15% and 50.8±4.6%, while the average cell survivability was 50.98±4.67% and 49.72±5.48% at 50 and 70 hPa, respectively. The optimization of the MBP concentration and injection pressures successfully allowed an efficient delivery of precise protein dosage into breast cancer cells without any adverse effect. This microinjection optimization can be a practical guideline in any downstream applications of protein functional work.
    Matched MeSH terms: RNA
  4. Lew LC, Choi SB, Khoo BY, Sreenivasan S, Ong KL, Liong MT
    Korean J Food Sci Anim Resour, 2018 Apr;38(2):350-361.
    PMID: 29805284 DOI: 10.5851/kosfa.2018.38.2.350
    Hypercholesterolemia is one of the primary risk factors for cardiovascular diseases. The use of lactobacilli probiotics to reduce blood cholesterol levels have been extensively reported. However, more information is needed to evaluate the possible mechanisms involved and to identify possible targets for further therapeutic development. In this study, strains of lactobacilli were screened based on the ability to assimilate cholesterol, and prevention of cholesterol accumulation in hepatic (HepG2) and intestinal (HT-29) cells. Cell free supernatant (CFS) from Lactobacillus plantarum DR7 showed a higher ability to assimilate cholesterol, reduction in cholesterol accumulation in both HepG2 and HT-29 cells, accompanied by reduced mRNA expression of HMG-CoA reductase (HMGCR) in HepG2 (p<0.05), compared to other lactobacilli. The reduction of HMGCR expression was also diminished in the presence of an AMPK inhibitor (Compound C), suggesting that L. plantarum DR7 exerted its effect via the AMPK pathway, typically via the phosphorylation of AMPK instead of the AMPK mRNA expression in HepG2 (p<0.05). Altogether, our present study illustrated that lactobacilli could exert cholesterol lowering properties along the AMPK pathway, specifically via phosphorylation of AMPK that led to reduced expression of HMGCR.
    Matched MeSH terms: RNA, Messenger
  5. Chan CS, Chan KG, Ee R, Hong KW, Urbieta MS, Donati ER, et al.
    Front Microbiol, 2017;8:1252.
    PMID: 28729863 DOI: 10.3389/fmicb.2017.01252
    Malaysia has a great number of hot springs, especially along the flank of the Banjaran Titiwangsa mountain range. Biological studies of the Malaysian hot springs are rare because of the lack of comprehensive information on their microbial communities. In this study, we report a cultivation-independent census to describe microbial communities in six hot springs. The Ulu Slim (US), Sungai Klah (SK), Dusun Tua (DT), Sungai Serai (SS), Semenyih (SE), and Ayer Hangat (AH) hot springs exhibit circumneutral pH with temperatures ranging from 43°C to 90°C. Genomic DNA was extracted from environmental samples and the V3-V4 hypervariable regions of 16S rRNA genes were amplified, sequenced, and analyzed. High-throughput sequencing analysis showed that microbial richness was high in all samples as indicated by the detection of 6,334-26,244 operational taxonomy units. In total, 59, 61, 72, 73, 65, and 52 bacterial phyla were identified in the US, SK, DT, SS, SE, and AH hot springs, respectively. Generally, Firmicutes and Proteobacteria dominated the bacterial communities in all hot springs. Archaeal communities mainly consisted of Crenarchaeota, Euryarchaeota, and Parvarchaeota. In beta diversity analysis, the hot spring microbial memberships were clustered primarily on the basis of temperature and salinity. Canonical correlation analysis to assess the relationship between the microbial communities and physicochemical variables revealed that diversity patterns were best explained by a combination of physicochemical variables, rather than by individual abiotic variables such as temperature and salinity.
    Matched MeSH terms: RNA, Ribosomal, 16S
  6. Jaafar F, Abdullah A, Makpol S
    Sci Rep, 2018 Jul 11;8(1):10471.
    PMID: 29992988 DOI: 10.1038/s41598-018-28708-z
    Tocotrienol-rich fraction (TRF) is palm vitamin E that consists of tocopherol and tocotrienol. TRF is involved in important cellular regulation including delaying cellular senescence. A key regulator of cellular senescence, Sirtuin 1 (SIRT1) is involved in lipid metabolism. Thus, SIRT1 may regulate vitamin E transportation and bioavailability at cellular level. This study aimed to determine the role of SIRT1 on cellular uptake and bioavailability of TRF in human diploid fibroblasts (HDFs). SIRT1 gene in young HDFs was silenced by small interference RNA (siRNA) while SIRT1 activity was inhibited by sirtinol. TRF treatment was given for 24 h before or after SIRT1 inhibition. Cellular concentration of TRF isomers was determined according to the time points of before and after TRF treatment at 0, 24, 48, 72 and 96 h. Our results showed that all tocotrienol isomers were significantly taken up by HDFs after 24 h of TRF treatment and decreased 24 h after TRF treatment was terminated but remained in the cell up to 72 h. The uptake of α-tocopherol, α-tocotrienol and β-tocotrienol was significantly higher in senescent cells as compared to young HDFs indicating higher requirement for vitamin E in senescent cells. Inhibition of SIRT1 gene increased the uptake of all tocotrienol isomers but not α-tocopherol. However, SIRT1 inhibition at protein level decreased tocotrienol concentration. In conclusion, SIRT1 may regulate the cellular uptake and bioavailability of tocotrienol isomers in human diploid fibroblast cells while a similar regulation was not shown for α-tocopherol.
    Matched MeSH terms: RNA, Small Interfering
  7. Zarkasi KZ, Halim MA, Nazari TF, Daud F
    Data Brief, 2018 Aug;19:514-519.
    PMID: 29900350 DOI: 10.1016/j.dib.2018.05.052
    This article contains data on the bacterial communities and its diversity associated with Anadara granosa. The A. granosa samples were obtained from two major estuaries in Penang, Malaysia using a culture dependent and 16S rRNA Illumina sequencing approaches. A. granosa, a commercial blood cockles and popular seafoods, is fragile to the surrounding environments. Thus, our research focused to better understand the bacterial communities and it diversity in the A. granosa, as well as on the generation of a metagenomic library from A. granosa to further understanding on it diversity. The bacteria Vibrionaceae (34.1%) was predominant in the A. granosa from both environments followed by Enterobacteriaceae (33.3%) and Bacillaceae (16.75%). Vibrio sp., Klebsiella sp., and Bacillus subtilis were the most abundant species present. The data generated in this research is the first metagenomic examination of A. granosa and will provide as a baseline to understand the bacterial communities associated with A. granosa and its surrounding natural environments.
    Matched MeSH terms: RNA, Ribosomal, 16S
  8. Bartlett AW, Truong KH, Songtaweesin WN, Chokephaibulkit K, Hansudewechakul R, Ly PS, et al.
    AIDS, 2018 07 31;32(12):1689-1697.
    PMID: 29794827 DOI: 10.1097/QAD.0000000000001883
    OBJECTIVES: The aim of this study was to describe characteristics of perinatally HIV-infected adolescents (PHIVAs), factors associated with mortality, and outcomes at transition.

    DESIGN: Ongoing observational database collating clinical data on HIV-infected children and adolescents in Asia.

    METHODS: Data from 2001 to 2016 relating to adolescents (10-19 years) with perinatal HIV infection were analysed to describe characteristics at adolescent entry and transition and combination antiretroviral therapy (cART) regimens across adolescence. A competing risk regression analysis was used to determine characteristics at adolescent entry associated with mortality. Outcomes at transition were compared on the basis of age at cART initiation.

    RESULTS: Of 3448 PHIVA, 644 had reached transition. Median age at HIV diagnosis was 5.5 years, cART initiation 7.2 years and transition 17.9 years. At adolescent entry, 35.0% had CD4+ cell count less than 500 cells/μl and 51.1% had experienced a WHO stage III/IV clinical event. At transition, 38.9% had CD4+ cell count less than 500 copies/ml, and 53.4% had experienced a WHO stage III/IV clinical event. Mortality rate was 0.71 per 100 person-years, with HIV RNA ≥1000 copies/ml, CD4+ cell count less than 500 cells/μl, height-for-age or weight-for-age z-score less than -2, history of a WHO stage III/IV clinical event or hospitalization and at least second cART associated with mortality. For transitioning PHIVA, those who commenced cART age less than 5 years had better virologic and immunologic outcomes, though were more likely to be on at least second cART.

    CONCLUSION: Delayed HIV diagnosis and cART initiation resulted in considerable morbidity and poor immune status by adolescent entry. Durable first-line cART regimens to optimize disease control are key to minimizing mortality. Early cART initiation provides the best virologic and immunologic outcomes at transition.

    Matched MeSH terms: RNA
  9. Azizi A, Mohd Hanafi N, Basiran MN, Teo CH
    3 Biotech, 2018 Aug;8(8):321.
    PMID: 30034985 DOI: 10.1007/s13205-018-1354-4
    Information on the abiotic stress tolerance and ice-ice disease resistance properties of tissue-cultured Kappaphycus alvarezii is scarce and can pose a big hurdle to a wider use of tissue-cultured seaweed in the industry. Here, we reported on a study of seaweed-associated bacteria diversity in farmed and tissue-cultured K. alvarezii, and ice-ice disease resistance and elevated growth temperature tolerance of tissue-cultured K. alvarezii in laboratory conditions. A total of 40 endophytic seaweed-associated bacteria strains were isolated from 4 types of K. alvarezii samples based on their colony morphologies, Gram staining properties and 16S rRNA gene sequences. Bacteria strains isolated were found to belong to Alteromonas sp., Aestuariibacter sp., Idiomarina sp., Jejuia sp., Halomonas sp., Primorskyibacter sp., Pseudoalteromonas sp., Ruegeria sp., Terasakiella sp., Thalassospira sp. and Vibrio sp. Vibrio alginolyticus strain ABI-TU15 isolated in this study showed agar-degrading property when analyzed using agar depression assay. Disease resistance assay was performed by infecting healthy K. alvarezii with 105 cells/mL Vibrio sp. ABI-TU15. Severe ice-ice disease symptoms were detected in farmed seaweeds compared to the tissue-cultured K. alvarezii. Besides disease resistance, tissue-cultured K. alvarezii showed better tolerance to the elevated growth temperatures of 30 and 35 °C. In conclusion, our overall data suggests that tissue-cultured K. alvarezii exhibited better growth performance than farmed seaweeds when exposed to elevated growth temperature and ice-ice disease-causing agent.
    Matched MeSH terms: RNA, Ribosomal, 16S
  10. Yogarajah T, Ong KC, Perera D, Wong KT
    Arch Virol, 2017 Mar;162(3):727-737.
    PMID: 27878462 DOI: 10.1007/s00705-016-3157-4
    Enterovirus A71 (EV-A71) and coxsackievirus A16 (CV-A16) are closely related enteroviruses that cause hand, foot and mouth disease (HFMD) in children. Serious neurological complications almost always occur in EV-A71 infection, but are rare in CV-A16 infection. Based on the hypothesis that this may be because EV-A71 infects neuronal cells more easily than CV-A16, we compared virus infection, replication and spread of EV-A71 and CV-A16 in SK-N-SH cells. We found that CV-A16 invariably showed significantly lower replication and caused less necrotic cell death in SK-N-SH cells, compared with EV-A71. This was not due to a lower proportion of CV-A16-infected cells, since both viruses showed similar proportions of infected cells at all time points analyzed. Furthermore, reduced replication of CV-A16 in SK-N-SH cells does not appear to be due to limited viral receptor availability, which might limit viral entry, because experiments with viral RNA-transfected cells showed the same results as for live virus infections. On the other hand, no differences were observed between EV-A71 and CV-A16 in RD cells and results were generally similar in RD cells for both viruses. Taken together, our findings suggest that the poor growth of CV-A16 and EV-A71in SK-N-SH cells, compared with RD cells, may be due to cell type-specific restrictions on viral replication and spread. Furthermore, the lower viral replication and necrotic cell death in CV-A16-infected SK-N-SH cells, compared with EV-A71-infected SK-N-SH cells, is consistent with the lower prevalence of neurotropism observed in CV-A16-associated HFMD outbreaks. Nonetheless, in vivo data and more extensive comparisons of different viral strains are essential to confirm our findings.
    Matched MeSH terms: RNA, Viral
  11. Laith AA, Ambak MA, Hassan M, Sheriff SM, Nadirah M, Draman AS, et al.
    Vet World, 2017 Jan;10(1):101-111.
    PMID: 28246454 DOI: 10.14202/vetworld.2017.101-111
    AIM: The main objective of this study was to emphasize on histopathological examinations and molecular identification of Streptococcus agalactiae isolated from natural infections in hybrid tilapia (Oreochromis niloticus) in Temerloh Pahang, Malaysia, as well as to determine the susceptibility of the pathogen strains to various currently available antimicrobial agents.

    MATERIALS AND METHODS: The diseased fishes were observed for variable clinical signs including fin hemorrhages, alterations in behavior associated with erratic swimming, exophthalmia, and mortality. Tissue samples from the eyes, brain, kidney, liver, and spleen were taken for bacterial isolation. Identification of S. agalactiae was screened by biochemical methods and confirmed by VITEK 2 and 16S rRNA gene sequencing. The antibiogram profiling of the isolate was tested against 18 standard antibiotics included nitrofurantoin, flumequine, florfenicol, amoxylin, doxycycline, oleandomycin, tetracycline, ampicillin, lincomycin, colistin sulfate, oxolinic acid, novobiocin, spiramycin, erythromycin, fosfomycin, neomycin, gentamycin, and polymyxin B. The histopathological analysis of eyes, brain, liver, kidney, and spleen was observed for abnormalities related to S. agalactiae infection.

    RESULTS: The suspected colonies of S. agalactiae identified by biochemical methods was observed as Gram-positive chained cocci, β-hemolytic, and non-motile. The isolate was confirmed as S. agalactiae by VITEK 2 (99% similarity), reconfirmed by 16S rRNA gene sequencing (99% similarity) and deposited in GenBank with accession no. KT869025. The isolate was observed to be resistance to neomycin and gentamicin. The most consistent gross findings were marked hemorrhages, erosions of caudal fin, and exophthalmos. Microscopic examination confirmed the presence of marked congestion and infiltration of inflammatory cell in the eye, brain, kidney, liver, and spleen. Eye samples showed damage of the lens capsule, hyperemic and hemorrhagic choroid tissue, and retina hyperplasia accompanied with edema. Brain samples showed perivascular and pericellular edema and hemorrhages of the meninges. Kidney samples showed hemorrhage and thrombosis in the glomeruli and tubules along with atrophy in hematopoietic tissue. Liver samples showed congestion of the sinusoids and blood vessel, thrombosis of portal blood vessel, and vacuolar (fatty) degeneration of hepatocytes. Spleen samples showed large thrombus in the splenic blood vessel, multifocal hemosiderin deposition, congestion of blood vessels, and multifocal infiltration of macrophages.

    CONCLUSION: Therefore, it can be concluded that pathological changes in tissues and organs of fish occur proportionally to the pathogen invasion, and because of their high resistance, neomycin and gentamicin utilization in the prophylaxis or treatment of S. agalactiae infection should be avoided.

    Matched MeSH terms: RNA, Ribosomal, 16S
  12. Kathleen, M.M., Samuel, L., Felecia, C., Ng K. H., Lesley, M.B., Kasing, A.
    MyJurnal
    (GTG)5 PCR is a type of repetitive extragenic palindromic (rep)-PCR which amplifies the (GTG)5 repetitive element that lays throughout the bacterial genome. In this study, fifty, thirty-nine and forty-nine unknown bacteria were isolated from aquaculture farms in Miri, Limbang and Lundu, respectively. (GTG)5 PCR was used to screen for clonal diversity among the isolates according to sampling sites. Banding profiles obtained from electrophoresed (GTG)5 PCR products were analyzed by RAPDistance Software to generate a dendrogram of neighbor joining tree (NJT) format. Based on the constructed dendrogram, representative isolates were selected for further identification. Conserved 16S rRNA region of the selected bacteria isolates were amplified and purified DNA products were sequenced. (GTG)5 PCR is useful in differentiation of unknown bacterial isolates and 16S rRNA analysis species identity of the bacteria in Sarawak aquaculture environment. The high diversity of bacteria in aquaculture environment may be caused by contamination from various sources.
    Matched MeSH terms: RNA, Ribosomal, 16S
  13. Lim MP, Firdaus-Raih M, Nathan S
    Front Microbiol, 2016;7:1436.
    PMID: 27672387 DOI: 10.3389/fmicb.2016.01436
    Burkholderia pseudomallei, the causative agent of melioidosis, is among a growing number of bacterial pathogens that are increasingly antibiotic resistant. Antimicrobial peptides (AMPs) have been investigated as an alternative approach to treat microbial infections, as generally, there is a lower likelihood that a pathogen will develop resistance to AMPs. In this study, 36 candidate Caenorhabditis elegans genes that encode secreted peptides of <150 amino acids and previously shown to be overexpressed during infection by B. pseudomallei were identified from the expression profile of infected nematodes. RNA interference (RNAi)-based knockdown of 12/34 peptide-encoding genes resulted in enhanced nematode susceptibility to B. pseudomallei without affecting worm fitness. A microdilution test demonstrated that two peptides, NLP-31 and Y43C5A.3, exhibited anti-B. pseudomallei activity in a dose dependent manner on different pathogens. Time kill analysis proposed that these peptides were bacteriostatic against B. pseudomallei at concentrations up to 8× MIC90. The SYTOX green assay demonstrated that NLP-31 and Y43C5A.3 did not disrupt the B. pseudomallei membrane. Instead, gel retardation assays revealed that both peptides were able to bind to DNA and interfere with bacterial viability. In parallel, microscopic examination showed induction of cellular filamentation, a hallmark of DNA synthesis inhibition, of NLP-31 and Y43C5A.3 treated cells. In addition, the peptides also regulated the expression of inflammatory cytokines in B. pseudomallei infected macrophage cells. Collectively, these findings demonstrate the potential of NLP-31 and Y43C5A.3 as anti-B. pseudomallei peptides based on their function as immune modulators.
    Matched MeSH terms: RNA Interference
  14. Yeo KS, Tan MC, Wong WY, Loh SW, Lam YL, Tan CL, et al.
    Sci Rep, 2016 Sep 27;6:34125.
    PMID: 27671354 DOI: 10.1038/srep34125
    TNF-induced signaling mediates pleiotropic biological consequences including inflammation, immunity, cell proliferation and apoptosis. Misregulation of TNF signaling has been attributed as a major cause of chronic inflammatory diseases and cancer. Jumonji domain-containing protein 8 (JMJD8) belongs to the JmjC family. However, only part of the family members has been described as hydroxylase enzymes that function as histone demethylases. Here, we report that JMJD8 positively regulates TNF-induced NF-κB signaling. Silencing the expression of JMJD8 using RNA interference (RNAi) greatly suppresses TNF-induced expression of several NF-κB-dependent genes. Furthermore, knockdown of JMJD8 expression reduces RIP ubiquitination, IKK kinase activity, delays IκBα degradation and subsequently blocks nuclear translocation of p65. In addition, JMJD8 deficiency enhances TNF-induced apoptosis. Taken together, these findings indicate that JMJD8 functions as a positive regulator of TNF-induced NF-κB signaling.
    Matched MeSH terms: RNA Interference
  15. Ibitoye EB, Lokman IH, Hezmee MNM, Goh YM, Zuki ABZ, Jimoh AA, et al.
    Poult Sci, 2019 Feb 01;98(2):745-752.
    PMID: 30265345 DOI: 10.3382/ps/pey419
    Growth hormones (GH) alone does not explain the growth rate in the chicken as growth in an animal is multi-factorial. Normal morphology of the intestinal villus and crypt, with adequate regulation of intestinal nutrient transporters, is essential to a healthy gut. Nutrition plays a significant role in gut health management, but information on the effect of dietary chitin and chitosan on gut morphology, gene expression of nutrient transporter, and serum levels of GH in broiler chickens is scanty. Thus, this study aimed at evaluating the comparative effect of dietary chitin and chitosan from cricket and shrimp on the small intestinal morphology, relative gene expression of intestinal nutrient transporters and serum level of GH in the broiler. A total of 150 day-old male Cobb500 broiler chicks were randomly allotted to one of the five treatment groups (n = 30). Treatment 1 was fed basal diet only, treatments 2 to 5 were fed a basal diet with 0.5 g cricket chitin, cricket chitosan, shrimp chitin, and shrimp chitosan, respectively, per kg diet. At days 21 and 42, duodenal and jejunal samples were assessed for structural morphology and jejunum for the relative gene expression of PepT1, EAAT3, SGLT1, and SGLT5 using quantitative real-time PCR. Results bared that dietary cricket chitosan and shrimp chitosan significantly (P < 0.05) improved jejunal villus height and reduced crypt depth without improving the body weight (BW). The gut morphology of birds under cricket chitin was poor and significantly (P < 0.05) different from other treated groups. Both the dietary chitin and chitosan at day 21 and only dietary chitosan at day 42 significantly (P < 0.05) down-regulated the relative mRNA expression of PepT1, EAAT3, SGLT1, and SGLT5 of broiler chickens. Treated groups differ non-significantly at both phases, while cricket chitin numerically increased the relative expression of PepT1, EAAT3, and SGLT1. Therefore, the potential of cricket chitin to improve BW and to up-regulate nutrient transporters is worthy of further exploration.
    Matched MeSH terms: RNA, Messenger
  16. Kumaresan V, Pasupuleti M, Arasu MV, Al-Dhabi NA, Arshad A, Amin SMN, et al.
    Mol Biol Rep, 2018 Dec;45(6):2511-2523.
    PMID: 30306509 DOI: 10.1007/s11033-018-4418-y
    Snakehead murrel, Channa striatus is an economically important aquatic species in Asia and are widely cultured and captured because of its nutritious and medicinal values. Their growth is predominantly affected by epizootic ulcerative syndrome (EUS) which is primarily caused by an oomycete fungus, Aphanomyces invadans. However, the molecular mechanism of immune response in murrel against this infection is still not clear. In this study, transcriptome technique was used to understand the molecular changes involved in C. striatus during A. invadans infection. RNA from the control (CF) and infected fish (IF) groups were sequenced using Illumina Hi-seq sequencing technology. For control group, 28,952,608 clean reads were generated and de novo assembly was performed to produce 60,753 contigs. For fungus infected group, 25,470,920 clean reads were obtained and assembled to produce 58,654 contigs. Differential gene expression analysis revealed that a total of 146 genes were up-regulated and 486 genes were down regulated. Most of the differentially expressed genes were involved in innate immune mechanism such as pathogen recognition, signalling and antimicrobial mechanisms. Interestingly, few adaptive immune genes, especially immunoglobulins were also significantly up regulated during fungal infection. Also, the results were validated by qRT-PCR analysis. These results indicated the involvement of various immune genes involved in both innate and adaptive immune mechanism during fungal infection in C. striatus which provide new insights into murrel immune mechanisms against A. invadans.
    Matched MeSH terms: RNA
  17. Chan SN, Low END, Raja Ali RA, Mokhtar NM
    Intest Res, 2018 Jul;16(3):374-383.
    PMID: 30090036 DOI: 10.5217/ir.2018.16.3.374
    Inflammatory bowel disease (IBD), which comprises of Crohn's disease and ulcerative colitis, is an idiopathic relapsing and remitting disease in which the interplay of different environment, microbial, immunological and genetic factors that attribute to the progression of the disease. Numerous studies have been conducted in multiple aspects including clinical, endoscopy and histopathology for the diagnostics and treatment of IBD. However, the molecular mechanism underlying the aetiology and pathogenesis of IBD is still poorly understood. This review tries to critically assess the scientific evidence at the transcriptomic level as it would help in the discovery of RNA molecules in tissues or serum between the healthy and diseased or different IBD subtypes. These molecular signatures could potentially serve as a reliable diagnostic or prognostic biomarker. Researchers have also embarked on the study of transcriptome to be utilized in targeted therapy. We focus on the evaluation and discussion related to the publications reporting the different approaches and techniques used in investigating the transcriptomic changes in IBD with the intention to offer new perspectives to the landscape of the disease.
    Matched MeSH terms: RNA
  18. Nagappan J, Chin CF, Angel LPL, Cooper RM, May ST, Low EL
    Biotechnol Lett, 2018 Dec;40(11-12):1541-1550.
    PMID: 30203158 DOI: 10.1007/s10529-018-2603-7
    The first and most crucial step of all molecular techniques is to isolate high quality and intact nucleic acids. However, DNA and RNA isolation from fungal samples are usually difficult due to the cell walls that are relatively unsusceptible to lysis and often resistant to traditional extraction procedures. Although there are many extraction protocols for Ganoderma species, different extraction protocols have been applied to different species to obtain high yields of good quality nucleic acids, especially for genome and transcriptome sequencing. Ganoderma species, mainly G. boninense causes the basal stem rot disease, a devastating disease that plagues the oil palm industry. Here, we describe modified DNA extraction protocols for G. boninense, G. miniatocinctum and G. tornatum, and an RNA extraction protocol for G. boninense. The modified salting out DNA extraction protocol is suitable for G. boninense and G. miniatocinctum while the modified high salt and low pH protocol is suitable for G. tornatum. The modified DNA and RNA extraction protocols were able to produce high quality genomic DNA and total RNA of ~ 140 to 160 µg/g and ~ 80 µg/g of mycelia respectively, for Single Molecule Real Time (PacBio Sequel® System) and Illumina sequencing. These protocols will benefit those studying the oil palm pathogens at nucleotide level.
    Matched MeSH terms: RNA
  19. Yee W, Abdul-Kadir R, Lee LM, Koh B, Lee YS, Chan HY
    3 Biotech, 2018 Aug;8(8):354.
    PMID: 30105179 DOI: 10.1007/s13205-018-1381-1
    In this work, a simple and inexpensive physical lysis method using a cordless drill fitted with a plastic pellet pestle and 150 mg of sterile sea sand was established for the extraction of DNA from six strains of freshwater microalgae. This lysis method was also tested for RNA extraction from two microalgal strains. Lysis duration between 15 and 120 s using the cetyltrimethyl ammonium bromide (CTAB) buffer significantly increased the yield of DNA from four microalgalstrains (Monoraphidium griffithii NS16, Scenedesmus sp. NS6, Scenedesmus sp. DPBC1 and Acutodesmus sp. DPBB10) compared to control. It was also found that grinding was not required to obtain DNA from two strains of microalgae (Choricystis sp. NPA14 and Chlamydomonas sp. BM3). The average DNA yield obtained using this lysis method was between 62.5 and 78.9 ng/mg for M. griffithii NS16, 42.2-247.0 ng/mg for Scenedesmus sp. NS6, 70.2-110.9 ng/mg for Scenedesmus sp. DPBC1 and 142.8-164.8 ng/mg for Acutodesmus sp. DPBB10. DNA obtained using this method was sufficiently pure for PCR amplification. Extraction of total RNA from M. griffithii NS16 and Mychonastes sp. NPD7 using this lysis method yielded high-quality RNA suitable for RT-PCR. This lysis method is simple, cheap and would enable rapid nucleic acid extraction from freshwater microalgae without requiring costly materials and equipment such as liquid nitrogen or beadbeaters, and would facilitate molecular studies on microalgae in general.
    Matched MeSH terms: RNA
  20. Yakasai, H.M., Karamba, K.I., Yasid, N.A., Abd. Rahman, F., Shukor, M.Y., Halmi, M.I.E.
    MyJurnal
    Molybdenum, an emerging pollutant, has being demonstrated recently to be toxic to
    spermatogenesis in several animal model systems. Metal mines especially gold mine often use
    cyanide and hence isolation of metal-reducing and cyanide-degrading bacteria can be useful for
    the bioremediation of these pollutants. Preliminary screening shows that three cyanide-degrading
    bacteria were able to reduce molybdenum to molybdenum blue (Mo-blue) when grown on a
    molybdate low phosphate minimal salts media. Phylogenetic analyses of the 16S rRNA gene of
    the best reducer indicates that it belongs to the Serratia genus. A variety of mathematical models
    such as logistic, Gompertz, Richards, Schnute, Baranyi-Roberts, von Bertalanffy, Buchanan
    three-phase and Huang were used to model molybdenum reduction, and the best model based on
    statistical analysis was modified Gompertz with lowest values for RMSE and AICc, highest
    adjusted R2 values, with Bias Factor and Accuracy Factor nearest to unity (1.0). The reduction
    constants obtained from the model will be used to carry out secondary modelling to study the
    effect of various parameters such as substrate, pH and temperature to molybdenum reduction.
    Matched MeSH terms: RNA, Ribosomal, 16S
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