Displaying publications 1 - 20 of 373 in total

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  1. Tamana S, Xenophontos M, Minaidou A, Stephanou C, Harteveld CL, Bento C, et al.
    Elife, 2022 Dec 01;11.
    PMID: 36453528 DOI: 10.7554/eLife.79713
    Haemoglobinopathies are the commonest monogenic diseases worldwide and are caused by variants in the globin gene clusters. With over 2400 variants detected to date, their interpretation using the American College of Medical Genetics and Genomics (ACMG)/Association for Molecular Pathology (AMP) guidelines is challenging and computational evidence can provide valuable input about their functional annotation. While many in silico predictors have already been developed, their performance varies for different genes and diseases. In this study, we evaluate 31 in silico predictors using a dataset of 1627 variants in HBA1, HBA2, and HBB. By varying the decision threshold for each tool, we analyse their performance (a) as binary classifiers of pathogenicity and (b) by using different non-overlapping pathogenic and benign thresholds for their optimal use in the ACMG/AMP framework. Our results show that CADD, Eigen-PC, and REVEL are the overall top performers, with the former reaching moderate strength level for pathogenic prediction. Eigen-PC and REVEL achieve the highest accuracies for missense variants, while CADD is also a reliable predictor of non-missense variants. Moreover, SpliceAI is the top performing splicing predictor, reaching strong level of evidence, while GERP++ and phyloP are the most accurate conservation tools. This study provides evidence about the optimal use of computational tools in globin gene clusters under the ACMG/AMP framework.
    Matched MeSH terms: Genomics*
  2. Onn CK, Abraham RK, Grismer JL, Grismer LL
    Zootaxa, 2018 Jun 15;4434(2):250-264.
    PMID: 30313185 DOI: 10.11646/zootaxa.4434.2.2
    Previously, only one species of torrent frog (Amolops larutensis) was thought to occur throughout Peninsular Malaysia. However, genomic work has demonstrated that populations from eastern Peninsular Malaysia form two separate lineages that are genetically distinct from A. larutensis that is now restricted to the western half of Peninsular Malaysia. This study demonstrates that all three lineages can be morphologically distinguished from each other, thereby providing additional support for the recognition of the eastern lineages as two distinct species. These lineages are described herein as Amolops gerutu sp. nov. from the eastern states of Kelantan, Terengganu, and Pahang, and A. australis sp. nov. from the southern-most state of Johor. In general, these two new species form a clade that is sister to A. larutensis and can be readily distinguished from it by having: (1) considerably denser and more pronounced dorsal tubercles, and (2) the posterodorsal surface of thighs having dense, dark stippling as opposed to broad vermiculations. Although differences in other morphometric characters were detected, their utility as diagnostic characters should be applied with caution due to the large intraspecific variation that overlaps among different species in many of the characters we measured. As such, we advocate for the use of tuberculation and pattern of the posterodorsal portion of the thighs as primary diagnostic characters. These characters can readily distinguish A. larutensis from the two new species. To differentiate A. australis sp. nov. from A. gerutu sp. nov. and A. larutensis, body size can be a good diagnostic character as A. australis sp. nov. is significantly smaller in both males (mean = 31.04 ± 1.59 mm) and females (mean = 46.48 ± 3.2 mm). Additionally, we show a strong positive correlation between body size and elevation, with populations from montane forests (>900 m asl) being considerably larger than populations at lower elevations.
    Matched MeSH terms: Genomics
  3. Kumar P, Pandey R, Sharma P, Dhar MS, A V, Uppili B, et al.
    Wellcome Open Res, 2020;5:184.
    PMID: 32995557 DOI: 10.12688/wellcomeopenres.16119.1
    Background: India first detected SARS-CoV-2, causal agent of COVID-19 in late January 2020, imported from Wuhan, China. From March 2020 onwards, the importation of cases from countries in the rest of the world followed by seeding of local transmission triggered further outbreaks in India. Methods: We used ARTIC protocol-based tiling amplicon sequencing of SARS-CoV-2 (n=104) from different states of India using a combination of MinION and MinIT sequencing from Oxford Nanopore Technology to understand how introduction and local transmission occurred. Results: The analyses revealed multiple introductions of SARS-CoV-2 genomes, including the A2a cluster from Europe and the USA, A3 cluster from Middle East and A4 cluster (haplotype redefined) from Southeast Asia (Indonesia, Thailand and Malaysia) and Central Asia (Kyrgyzstan). The local transmission and persistence of genomes A4, A2a and A3 was also observed in the studied locations. The most prevalent genomes with patterns of variance (confined in a cluster) remain unclassified, and are here proposed as A4-clade based on its divergence within the A cluster. Conclusions: The viral haplotypes may link their persistence to geo-climatic conditions and host response. Multipronged strategies including molecular surveillance based on real-time viral genomic data is of paramount importance for a timely management of the pandemic.
    Matched MeSH terms: Genomics
  4. Kannan M, Zainal Z, Ismail I, Baharum SN, Bunawan H
    Viruses, 2020 07 26;12(8).
    PMID: 32722532 DOI: 10.3390/v12080803
    Numerous potyvirus studies, including virus biology, transmission, viral protein function, as well as virus-host interaction, have greatly benefited from the utilization of reverse genetic techniques. Reverse genetics of RNA viruses refers to the manipulation of viral genomes, transfection of the modified cDNAs into cells, and the production of live infectious progenies, either wild-type or mutated. Reverse genetic technology provides an opportunity of developing potyviruses into vectors for improving agronomic traits in plants, as a reporter system for tracking virus infection in hosts or a production system for target proteins. Therefore, this review provides an overview on the breakthroughs achieved in potyvirus research through the implementation of reverse genetic systems.
    Matched MeSH terms: Genomics/methods*
  5. Yun SI, Song BH, Frank JC, Julander JG, Olsen AL, Polejaeva IA, et al.
    Viruses, 2018 08 11;10(8).
    PMID: 30103523 DOI: 10.3390/v10080422
    Zika virus (ZIKV) causes no-to-mild symptoms or severe neurological disorders. To investigate the importance of viral and host genetic variations in determining ZIKV infection outcomes, we created three full-length infectious cDNA clones as bacterial artificial chromosomes for each of three spatiotemporally distinct and genetically divergent ZIKVs: MR-766 (Uganda, 1947), P6-740 (Malaysia, 1966), and PRVABC-59 (Puerto Rico, 2015). Using the three molecularly cloned ZIKVs, together with 13 ZIKV region-specific polyclonal antibodies covering nearly the entire viral protein-coding region, we made three conceptual advances: (i) We created a comprehensive genome-wide portrait of ZIKV gene products and their related species, with several previously undescribed gene products identified in the case of all three molecularly cloned ZIKVs. (ii) We found that ZIKV has a broad cell tropism in vitro, being capable of establishing productive infection in 16 of 17 animal cell lines from 12 different species, although its growth kinetics varied depending on both the specific virus strain and host cell line. More importantly, we identified one ZIKV-non-susceptible bovine cell line that has a block in viral entry but fully supports the subsequent post-entry steps. (iii) We showed that in mice, the three molecularly cloned ZIKVs differ in their neuropathogenicity, depending on the particular combination of viral and host genetic backgrounds, as well as in the presence or absence of type I/II interferon signaling. Overall, our findings demonstrate the impact of viral and host genetic variations on the replication kinetics and neuropathogenicity of ZIKV and provide multiple avenues for developing and testing medical countermeasures against ZIKV.
    Matched MeSH terms: Genomics
  6. Vasilakis N, Tesh RB, Popov VL, Widen SG, Wood TG, Forrester NL, et al.
    Viruses, 2019 05 23;11(5).
    PMID: 31126128 DOI: 10.3390/v11050471
    In recent years, it has become evident that a generational gap has developed in the community of arbovirus research. This apparent gap is due to the dis-investment of training for the next generation of arbovirologists, which threatens to derail the rich history of virus discovery, field epidemiology, and understanding of the richness of diversity that surrounds us. On the other hand, new technologies have resulted in an explosion of virus discovery that is constantly redefining the virosphere and the evolutionary relationships between viruses. This paradox presents new challenges that may have immediate and disastrous consequences for public health when yet to be discovered arboviruses emerge. In this review we endeavor to bridge this gap by providing a historical context for the work being conducted today and provide continuity between the generations. To this end, we will provide a narrative of the thrill of scientific discovery and excitement and the challenges lying ahead.
    Matched MeSH terms: Genomics/methods
  7. Mat Isa N, Mohd Ayob J, Ravi S, Mustapha NA, Ashari KS, Bejo MH, et al.
    Virusdisease, 2019 Sep;30(3):426-432.
    PMID: 31803810 DOI: 10.1007/s13337-019-00530-9
    The main aim of our study was to explore the genome sequence of the inclusion body hepatitis associated Fowl adenovirus serotype 8b (FAdV-8b) UPM04217 and to study its genomic organisation. The nucleotide sequence of the whole genome of FAdV-8b UPM04217 was determined by using the 454 Pyrosequencing platform and the Sanger sequencing method. The complete genome was found to be 44,059 bp long with 57.9% G + C content and shared 97.5% genome identity with the reference FAdV-E genome (HG isolate). Interestingly, the genome analysis using ORF Finder, Glimmer3 and FGENESV predicted a total of 39 open reading frames (ORFs) compared to the FAdV-E HG that possessed 46 ORFs. Fourteen ORFs located within the central genomic region and 16 ORFs located within the left and right ends of the genome were assigned as being the high protein-coding regions. The fusion of the small ORFs at the right end terminal specifically in ORF22 and ORF33 could be the result of gene truncation in the FAdV-E HG. The frame shift mutation in ORF25 and other mutations in ORF13 and ORF17 might have lead to the emergence of genes that could have different functions. Besides, one of the minor capsid components, pVI, in FAdV-8b UPM04217 shared the highest similarity of 93% with that of FAdV-D, while only 47% similarity was found with FAdV-E. From the gene arrangement layout of the FAdV genome, FAdV-8b UPM04217 showed intermediate evolution between the FAdV-E HG and the FAdV-D although it was apparently more similar to the FAdV-E HG.
    Matched MeSH terms: Genomics
  8. Ge F, Guo R, Liang Y, Chen Y, Shao H, Sung YY, et al.
    Virus Res, 2023 Oct 15;336:199226.
    PMID: 37739268 DOI: 10.1016/j.virusres.2023.199226
    Stutzerimonas stutzeri is an opportunistic pathogenic bacterium belonging to the Gammaproteobacteria, exhibiting wide distribution in the environment and playing significant ecological roles such as nitrogen fixation or pollutant degradation. Despite its ecological importance, only two S. stutzeri phages have been isolated to date. Here, a novel S. stutzeri phage, vB_PstS_ZQG1, was isolated from the surface seawater of Qingdao, China. Transmission electron microscopy analysis indicates that vB_PstS_ZQG1 has a morphology characterized by a long non-contractile tail. The genomic sequence of vB_PstS_ZQG1 contains a linear, double-strand 61,790-bp with the G+C content of 53.24% and encodes 90 putative open reading frames. Two auxiliary metabolic genes encoding TolA protein and nucleotide pyrophosphohydrolase were identified, which are likely involved in host adaptation and phage reproduction. Phylogenetic and comparative genomic analyses demonstrated that vB_PstS_ZQG1 exhibits low similarity with previously isolated phages or uncultured viruses (average nucleotide identity values range from 21.7 to 29.4), suggesting that it represents a novel viral genus by itself, here named as Fuevirus. Biogeographic analysis showed that vB_PstS_ZQG1 was only detected in epipelagic and mesopelagic zone with low abundance. In summary, our findings of the phage vB_PstS_ZQG1 will provide helpful insights for further research on the interactions between S. stutzeri phages and their hosts, and contribute to discovering unknown viral sequences in the metagenomic database.
    Matched MeSH terms: Genomics
  9. Chen Y, Guo R, Liang Y, Luo L, Han Y, Wang H, et al.
    Virus Res, 2023 Sep;334:199183.
    PMID: 37499764 DOI: 10.1016/j.virusres.2023.199183
    Stutzerimonas stutzeri is an opportunistic pathogen widely distributed in the environment and displays diverse metabolic capabilities. In this study, a novel lytic S. stutzeri phage, named vB_PstM_ZRG1, was isolated from the seawater in the East China Sea (29°09'N, 123°39'E). vB_PstM_ZRG1 was stable at temperatures ranging from -20°C to 65°C and across a wide range of pH values from 3 to 10. The genome of vB_PstM_ZRG1 was determined to be a double-stranded DNA with a genome size of 52,767 bp, containing 78 putative open reading frames (ORFs). Three auxiliary metabolic genes encoded by phage vB_PstM_ZRG1 were predicted, including Toll/interleukin-1 receptor (TIR) domain, proline-alanine-alanine-arginine (PAAR) protein and SGNH (Ser-Gly-Asn-His) family hydrolase, especially TIR domain is not common in isolated phages. Phylogenic and network analysis showed that vB_PstM_ZRG1 has low similarity to other phage genomes in the GenBank and IMG/VR database, and might represent a novel viral genus, named Elithevirus. Additionally, the distribution map results indicated that vB_PstM_ZRG1 could infect both extreme colds- and warm-type hosts in the marine environment. In summary, our finding provided basic information for further research on the relationship between S. stutzeri and their phages, and expanded our understanding of genomic characteristics, phylogenetic diversity and distribution of Elithevirus.
    Matched MeSH terms: Genomics
  10. Mohandas S, Shete A, Sarkale P, Kumar A, Mote C, Yadav P
    Virulence, 2023 Dec;14(1):2224642.
    PMID: 37312405 DOI: 10.1080/21505594.2023.2224642
    Nipah virus (NiV) is a high-risk pathogen which can cause fatal infections in humans. The Indian isolate from the 2018 outbreak in the Kerala state of India showed ~ 4% nucleotide and amino acid difference in comparison to the Bangladesh strains of NiV and the substitutions observed were mostly not present in the region of any functional significance except for the phosphoprotein gene. The differential expression of viral genes was observed following infection in Vero (ATCC® CCL-81™) and BHK-21 cells. Intraperitoneal infection in the 10-12-week-old, Syrian hamster model induced dose dependant multisystemic disease characterized by prominent vascular lesions in lungs, brain, kidney and extra vascular lesions in brain and lungs. Congestion, haemorrhages, inflammatory cell infiltration, thrombosis and rarely endothelial syncitial cell formation were seen in the blood vessels. Intranasal infection resulted in respiratory tract infection characterised by pneumonia. The model showed disease characteristics resembling the human NiV infection except that of myocarditis similar to that reported by NiV-Malaysia and NiV-Bangladesh isolates in hamster model. The variation observed in the genome of the Indian isolate at the amino acid levels should be explored further for any functional significance.
    Matched MeSH terms: Genomics
  11. Zhou H, Liu L, Li R, Qin Y, Fang Q, Balasubramaniam VR, et al.
    Virol J, 2017 08 17;14(1):156.
    PMID: 28814340 DOI: 10.1186/s12985-017-0823-4
    BACKGROUND: Astroviruses (AstVs) have been reported to infect and cause gastroenteritis in most animal species. Human AstVs were regarded the causative agent of viral diarrhea in children. In dogs, little is known about the epidemiology and clinical significance of AstV infection.

    FINDINGS: In this study, we collected and tested 253 rectal swabs from pet dogs; of which 64 samples (25.3%) tested positive for AstVs with diarrhea and 15 more samples (5.9%) also was identified as AstVs, however without any clinical signs. Phylogenetic analysis of 39 partial ORF1b sequences from these samples revealed that they are similar to AstVs, which can be subdivided into three lineages. Interestingly, out of the 39 isolates sequenced, 16 isolates are shown to be in the Mamastrovirus 5/canine astrovirus (CAstV) lineage and the remaining 23 isolates displayed higher similarities with known porcine astrovirus (PoAstV) 5 and 2. Further, analysis of 13 capsid sequences from these isolates showed that they are closely clustered with Chinese or Italy CAstV isolates.

    CONCLUSIONS: The findings indicate that CAstVs commonly circulate in pet dogs, and our sequencing results have shown the genomic diversity of CAstVs leading to increasing number of clusters.

    Matched MeSH terms: Genomics
  12. Peng R, Li D, Wang J, Xiong G, Wang M, Liu D, et al.
    Virol J, 2023 Jun 22;20(1):135.
    PMID: 37349792 DOI: 10.1186/s12985-023-02064-5
    OBJECTIVE: To isolate a prevalent G9P[8] group A rotavirus (RVA) (N4006) in China and investigate its genomic and evolutionary characteristics, with the goal of facilitating the development of a new rotavirus vaccine.

    METHODS: The RVA G9P[8] genotype from a diarrhea sample was passaged in MA104 cells. The virus was evaluated by TEM, polyacrylamide gel electrophoresis, and indirect immunofluorescence assay. The complete genome of virus was obtained by RT-PCR and sequencing. The genomic and evolutionary characteristics of the virus were evaluated by nucleic acid sequence analysis with MEGA ver. 5.0.5 and DNASTAR software. The neutralizing epitopes of VP7 and VP4 (VP5* and VP8*) were analyzed using BioEdit ver. 7.0.9.0 and PyMOL ver. 2.5.2.

    RESULTS: The RVA N4006 (G9P[8] genotype) was adapted in MA104 cells with a high titer (105.5 PFU/mL). Whole-genome sequence analysis showed N4006 to be a reassortant rotavirus of Wa-like G9P[8] RVA and the NSP4 gene of DS-1-like G2P[4] RVA, with the genotype constellation G9-P[8]-I1-R1-C1-M1-A1-N1-T1-E2-H1 (G9P[8]-E2). Phylogenetic analysis indicated that N4006 had a common ancestor with Japanese G9P[8]-E2 rotavirus. Neutralizing epitope analysis showed that VP7, VP5*, and VP8* of N4006 had low homology with vaccine viruses of the same genotype and marked differences with vaccine viruses of other genotypes.

    CONCLUSION: The RVA G9P[8] genotype with the G9-P[8]-I1-R1-C1-M1-A1-N1-T1-E2-H1 (G9P[8]-E2) constellation predominates in China and may originate from reassortment between Japanese G9P[8] with Japanese DS-1-like G2P[4] rotaviruses. The antigenic variation of N4006 with the vaccine virus necessitates an evaluation of the effect of the rotavirus vaccine on G9P[8]-E2 genotype rotavirus.

    Matched MeSH terms: Genomics
  13. Sun B, Jia L, Liang B, Chen Q, Liu D
    Virol Sin, 2018 Oct;33(5):385-393.
    PMID: 30311101 DOI: 10.1007/s12250-018-0050-1
    Nipah virus (NiV), a zoonotic paramyxovirus belonging to the genus Henipavirus, is classified as a Biosafety Level-4 pathogen based on its high pathogenicity in humans and the lack of available vaccines or therapeutics. Since its initial emergence in 1998 in Malaysia, this virus has become a great threat to domestic animals and humans. Sporadic outbreaks and person-to-person transmission over the past two decades have resulted in hundreds of human fatalities. Epidemiological surveys have shown that NiV is distributed in Asia, Africa, and the South Pacific Ocean, and is transmitted by its natural reservoir, Pteropid bats. Numerous efforts have been made to analyze viral protein function and structure to develop feasible strategies for drug design. Increasing surveillance and preventative measures for the viral infectious disease are urgently needed.
    Matched MeSH terms: Genomics
  14. Thau, Wilson Lym Yon, Henry, Erle Stanley, Janna Ong Abdullah
    Trop Life Sci Res, 2010;21(2):-.
    MyJurnal
    Genetic engineering is a powerful tool for the improvement of plant traits. Despite reported successes in the plant kingdom, this technology has barely scratched the surface of the Melastomataceae family. Limited studies have led to some optimisation of parameters known to affect the transformation efficiency of these plants. The major finding of this study was to optimise the presence of selected enhancers [e.g., monosaccharides (D-glucose, D-galactose and D-fructose), tyrosine, aluminium chloride (AICI3) and ascorbic
    acid] to improve the transformation efficiency of Tibouchina semidecandra. Agrobacterium tumefaciens strain LBA4404 harbouring the disarmed plasmid pCAMBIA1304 was used to transform shoots and nodes of T. semidecandra. Different concentrations of the transformation enhancers were tested by using green fluorescent protein (GFP) as a reporter. The results obtained were based on the percentage of GFP expression, which was observed 14 days post-transformation. A combination of 120 µM galactose and 100
    µM tyrosine supplemented with 600 µM AICI3 in the presence of 15 mg/l ascorbic acid gave the highest percentage of positive transformants for T. semidecandra shoots. Whereas 60 µM galactose and 50 µM tyrosine with 200 µM AICI3 in the presence of 15 mg/l ascorbic acid was optimum for T. semidecandra nodes. The presence of the hygromycin phosphotransferase II (hptII) transgene in the genomic DNA of putative
    T. semidecandra transformants was verified by PCR amplification with specific primers.
    Matched MeSH terms: Genomics
  15. Zakiah Ramle, Rashidah Abdul Rahim
    Trop Life Sci Res, 2016;27(11):151-157.
    MyJurnal
    A lipase producer psychrophilic microorganism isolated from Arctic sample was
    studied. The genomic DNA of the isolate was extracted using modified CTAB method.
    Identification of the isolate by morphological and 16S rRNA sequence analysis revealed
    that the isolate is closely related to Arthrobacter gangotriensis (97% similarity).
    A. gangotriensis was determined as positive lipase producer based on the plate screening
    using specific and sensitive plate assay of Rhodamine B. The PCR result using
    Arthrobacter sp.’s full lipase gene sequence as the template primers emphasised a
    possible lipase gene at 900 bp band size. The gene is further cloned in a suitable vector
    system for expression of lipase.
    Matched MeSH terms: Genomics
  16. Leh TY, Yong CSY, Nulit R, Abdullah JO
    Trop Life Sci Res, 2019 Jan;30(1):149-159.
    PMID: 30847038 MyJurnal DOI: 10.21315/tlsr2019.30.1.9
    Stevia rebaudiana, a perennial herb native to northeastern Paraguay, has gained immense attention globally over the recent decades due to the natural sweetness of its leaves. Like in most plants, this particular species contains high amount of secondary metabolites, thus rendering the isolation of high quality and quantity RNA extract for molecular applications rather challenging. An effective, high-yield and high-quality RNA isolation protocol for this economically important plant species was devised here based on the cetyltrimethylammonium bromide (CTAB) extraction method, with an additional genomic DNA (gDNA) removal step. DNA and other contaminants that may affect downstream applications were effectively removed. Our results exhibited that RNA samples isolated from the leaves and stems of Stevia rebaudiana using this improvised method are high in integrity and quality with RNA integrity number (RIN) of more than 8 and low in contaminants.
    Matched MeSH terms: Genomics
  17. Sellvam D, Lau NS, Arip YM
    Trop Life Sci Res, 2018 Mar;29(1):37-50.
    PMID: 29644014 DOI: 10.21315/tlsr2018.29.1.3
    Malaysia is one of the countries that are loaded with mega biodiversity which includes microbial communities. Phages constitute the major component in the microbial communities and yet the numbers of discovered phages are just a minute fraction of its population in the biosphere. Taking into account of a huge numbers of waiting to be discovered phages, a new bacteriophage designated as Escherichia phage YD-2008.s was successfully isolated using Escherichia coli ATCC 11303 as the host. Phage YD-2008.s poses icosahedral head measured at 57nm in diameter with a long non-contractile flexible tail measured at 107nm; proving the phage as one of the members of Siphoviridae family under the order of Caudovirales. Genomic sequence analyses revealed phage YD-2008.s genome as linear dsDNA of 44,613 base pairs with 54.6% G+C content. Sixty-two open reading frames (ORFs) were identified on phage YD-2008.s full genome, using bioinformatics annotation software; Rapid Annotation using Subsystem Technology (RAST). Among the ORFs, twenty-eight of them code for functional proteins. Thirty two are classified as hypothetical proteins and there are two unidentified proteins. Even though majority of the coded putative proteins have high amino acids similarities to phages from the genus Hk578likevirus of the Siphoviridae family, yet phage YD-2008.s stands with its' own distinctiveness. Therefore, this is another new finding to Siphoviridae family as well as to the growing list of viruses in International Committee on Taxonomy of Viruses (ICTV) database.
    Matched MeSH terms: Genomics
  18. Sellvam, Dharmela, Yahya Mat Arip, Nyok, Sean Lau
    Trop Life Sci Res, 2018;29(1):37-50.
    MyJurnal
    Malaysia is one of the countries that are loaded with mega biodiversity which
    includes microbial communities. Phages constitute the major component in the microbial
    communities and yet the numbers of discovered phages are just a minute fraction of
    its population in the biosphere. Taking into account of a huge numbers of waiting to be
    discovered phages, a new bacteriophage designated as Escherichia phage YD-2008.s
    was successfully isolated using Escherichia coli ATCC 11303 as the host. Phage YD-2008.s poses icosahedral head measured at 57nm in diameter with a long non-contractile
    flexible tail measured at 107nm; proving the phage as one of the members of Siphoviridae
    family under the order of Caudovirales. Genomic sequence analyses revealed phage
    YD-2008.s genome as linear dsDNA of 44,613 base pairs with 54.6% G+C content.
    Sixty-two open reading frames (ORFs) were identified on phage YD-2008.s full genome,
    using bioinformatics annotation software; Rapid Annotation using Subsystem Technology
    (RAST). Among the ORFs, twenty-eight of them code for functional proteins. Thirty two are
    classified as hypothetical proteins and there are two unidentified proteins. Even though
    majority of the coded putative proteins have high amino acids similarities to phages from the
    genus Hk578likevirus of the Siphoviridae family, yet phage YD-2008.s stands with its’ own
    distinctiveness. Therefore, this is another new finding to Siphoviridae family as well as to the
    growing list of viruses in International Committee on Taxonomy of Viruses (ICTV) database.
    Matched MeSH terms: Genomics
  19. Fahmeeda Mohamad Jazamuddin, Wan Mohd Aizat, Hoe-Han Goh, Chen-Fei Low, Syarul Nataqain Baharum
    Trop Life Sci Res, 2019;30(2):2012-209.
    MyJurnal
    Vibriosis is a prevalent aquatic disease caused by Vibrio species and has led to massive loss of brown-marbled grouper, Epinephelus fuscoguttatus. The complexity of molecular mechanisms associated with immune defence can be studied through transcriptomics analysis. High quality and quantity of total RNAs are crucial for the veracity of RNA sequencing and gene expression analysis. A low quality RNA will compromise downstream analysis, resulting in loss of time and revenue to re-acquire the data again. Thus, a reliable and an efficient RNA isolation method is the first and most important step to obtain high quality RNA for gene expression studies. There are many aspects need to be considered when deciding an extraction method, such as the cost-effectiveness of the protocol, the duration of chemical exposure, the duration required for a complete extraction and the number of sample-transferring. A good RNA extraction protocol must be able to produce high yield and purity of RNA free from enzyme inhibitors, such as nucleases (RNase), phenols, alcohols or other chemicals carryover, apart from protein and genomic DNA contamination, to maintain isolated RNA integrity in storage condition. In this study, TransZolTM Up produced clean and pure RNA samples from control gills only but not from the infected gill and whole-body tissues. Modified conventional CTAB (conventional hexadecyltrimethylammonium bromide) method was then used as an alternative method to isolate RNA from gill and whole-body tissues of Vibrio-infected E. fuscoguttatus. Modified CTAB method produced intact RNA on gel electrophoresis with higher RIN number (>6.5) for infected gill and whole-body tissues, suggesting that this method could also be used to isolate high quality RNA from fish samples. Therefore, this method is potentially suitable to be used to extract RNA from other fish species especially those that have been infected.
    Matched MeSH terms: Genomics
  20. Zangooie F, Ganjali M, Keighobadi M, Nabavi R
    Trop Biomed, 2018 Dec 01;35(4):1140-1147.
    PMID: 33601861
    Trypanosomiasis is a disease caused by a flagellate protozoon called Trypanosoma and can be mechanically transmitted by vectors to humans and animals. Various species of Trypanosoma are found in livestock and poultry, which include Trypanosoma evansi, T. brucei, T. vivax and T. congolense. The camel is the most sensitive livestock for T. evansi, so the exact identification of infection is very important for epidemiological studies and the design of control programs. The present study was conducted with the aim of molecular detection of camel trypanosomiasis in the Sistan region in 2015. Previous studies have shown that internal transcribed spacer one (ITS1) of the ribosomal DNA is a reliable genetic marker for carrying out systematic molecular studies of trypanosomes. In order to investigate infections of camels with T. evansi, a total of 113 blood samples were collected randomly and the presence of parasites in each sample was evaluated using the microscopic method and polymerase chain reaction (PCR) test. Genomic DNA was extracted and the ITS-1 was amplified by PCR. In comparison to the nucleotide sequence obtained with the sequences recorded in GenBank, it was determined that there is a 99% homology with the recorded sequence of T. evansi. The obtained sequence was registered in Gen Bank with kx900449 code. The T. evansi sequences from different countries such as India, Taiwan, Thailand, the Philippines, China and Argentina and etc., were extracted from the Gene bank and aligned using the ClustalW2 sequence alignment tool and MEGA software. In this study the prevalence of T. evansi infection using the molecular method was 6.19% and no positive samples were found by microscopic observation.
    Matched MeSH terms: Genomics
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