Displaying publications 161 - 180 of 8233 in total

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  1. Chromosome-level genome sequence of the Genetically Improved Farmed Tilapia (GIFT, Oreochromis niloticus) highlights regions of introgression with O. mossambicus
    Etherington GJ, Nash W, Ciezarek A, Mehta TK, Barria A, Peñaloza C, et al.
    BMC Genomics, 2022 Dec 15;23(1):832.
    PMID: 36522771 DOI: 10.1186/s12864-022-09065-8
    BACKGROUND: The Nile tilapia (Oreochromis niloticus) is the third most important freshwater fish for aquaculture. Its success is directly linked to continuous breeding efforts focusing on production traits such as growth rate and weight. Among those elite strains, the Genetically Improved Farmed Tilapia (GIFT) programme initiated by WorldFish is now distributed worldwide. To accelerate the development of the GIFT strain through genomic selection, a high-quality reference genome is necessary.

    RESULTS: Using a combination of short (10X Genomics) and long read (PacBio HiFi, PacBio CLR) sequencing and a genetic map for the GIFT strain, we generated a chromosome level genome assembly for the GIFT. Using genomes of two closely related species (O. mossambicus, O. aureus), we characterised the extent of introgression between these species and O. niloticus that has occurred during the breeding process. Over 11 Mb of O. mossambicus genomic material could be identified within the GIFT genome, including genes associated with immunity but also with traits of interest such as growth rate.

    CONCLUSION: Because of the breeding history of elite strains, current reference genomes might not be the most suitable to support further studies into the GIFT strain. We generated a chromosome level assembly of the GIFT strain, characterising its mixed origins, and the potential contributions of introgressed regions to selected traits.

    Matched MeSH terms: Chromosomes/genetics
  2. Development and Evaluation of Real-Time Quantitative PCR Assays for Detection of Phellinus noxius Causing Brown Root Rot Disease
    Liu TY, Chen CH, Ko YC, Wu ZC, Liao TZ, Lee HH, et al.
    Plant Dis, 2024 Nov;108(11):3288-3299.
    PMID: 38944685 DOI: 10.1094/PDIS-01-24-0238-RE
    Brown root rot disease (BRRD) is a highly destructive tree disease. Early diagnosis of BRRD has been challenging because the first symptoms and signs are often observed after extensive tissue colonization. Existing molecular detection methods, all based on the internal transcribed spacer (ITS) region, were developed without testing against global Phellinus noxius isolates, other wood-decay fungi, or host plant tissues. This study aimed to develop SYBR Green real-time quantitative PCR (qPCR) assays for P. noxius. The primer pair Pn_ITS_F/Pn_ITS_R targets the ITS, and the primer pair Pn_NLR_F/Pn_NLR_R targets a P. noxius-unique group of homologous genes identified through a comparative genomics analysis. The homologous genes belong to the nucleotide-binding-oligomerization-domain-like receptor (NLR) superfamily. The new primer pairs and a previous primer pair G1F/G1R were optimized for qPCR conditions and tested for specificity using 61 global P. noxius isolates, 5 other Phellinus species, and 22 non-Phellinus wood-decay fungal species. Although all three primer pairs could detect as little as 100 fg (approximately 2.99 copies) of P. noxius genomic DNA, G1F/G1R had the highest specificity and Pn_NLR_F/Pn_NLR_R had the highest efficiency. To avoid false positives, the cutoff quantification cycle values were determined as 34 for G1F/G1R, 29 for Pn_ITS_F/Pn_ITS_R, and 32 for Pn_NLR_F/Pn_NLR_R. We further validated these qPCR assays using Ficus benjamina seedlings artificially inoculated with P. noxius, six tree species naturally infected by P. noxius, rhizosphere soil, and bulk soil. The newly developed qPCR assays provide sensitive detection and quantification of P. noxius, which is useful for long-term monitoring of BRRD status.
    Matched MeSH terms: DNA, Fungal/genetics
  3. Transient Expression of Green Fluorescent Protein in Integrase-Defective Lentiviral Vector-Transduced 293T Cell Line
    Nordin F, Hamid ZA, Chan L, Farzaneh F, Hamid MK
    Methods Mol Biol, 2016;1448:159-73.
    PMID: 27317180 DOI: 10.1007/978-1-4939-3753-0_12
    Non-integrating lentiviral vectors or also known as integrase-defective lentiviral (IDLV) hold a great promise for gene therapy application. They retain high transduction efficiency for efficient gene transfer in various cell types both in vitro and in vivo. IDLV is produced via a combined mutations introduced on the HIV-based lentiviral to disable their integration potency. Therefore, IDLV is considered safer than the wild-type integrase-proficient lentiviral vector as they could avoid the potential insertional mutagenesis associated with the nonspecific integration of transgene into target cell genome afforded by the wild-type vectors.Here we describe the system of IDLV which is produced through mutation in the integrase enzymes at the position of D64 located within the catalytic core domain. The efficiency of the IDLV in expressing the enhanced green fluorescent protein (GFP) reporter gene in transduced human monocyte (U937) cell lines was investigated. Expression of the transgene was driven by the spleen focus-forming virus (SFFV) LTRs. Transduction efficiency was studied using both the IDLV (ID-SFFV-GFP) and their wild-type counterparts (integrase-proficient SFFV-GFP). GFP expression was analyzed by fluorescence microscope and FACS analysis.Based on the results, the number of the GFP-positive cells in ID-SFFV-GFP-transduced U937 cells decreased rapidly over time. The percentage of GFP-positive cells decreased from ~50 % to almost 0, up to 10 days post-transduction. In wild-type SFFV-GFP-transduced cells, GFP expression is remained consistently at about 100 %. These data confirmed that the transgene expression in the ID-SFFV-GFP-transduced cells is transient in dividing cells. The lack of an origin of replication due to mutation of integrase enzymes in the ID-SFFV-GFP virus vector has caused the progressive loss of the GFP expression in dividing cells.Integrase-defective lentivirus will be a suitable choice for safer clinical applications. It preserves the advantages of the wild-type lentiviral vectors but with the benefit of transgene expression without stable integration into host genome, therefore reducing the potential risk of insertional mutagenesis.
    Matched MeSH terms: Lentivirus/genetics*; Transgenes/genetics; Integrases/genetics; Green Fluorescent Proteins/genetics*
  4. Fulltext Complete genome sequence and comparative genomic analysis of Mycobacterium massiliense JCM 15300 in the Mycobacterium abscessus group reveal a conserved genomic island MmGI-1 related to putative lipid metabolism
    Sekizuka T, Kai M, Nakanaga K, Nakata N, Kazumi Y, Maeda S, et al.
    PLoS One, 2014;9(12):e114848.
    PMID: 25503461 DOI: 10.1371/journal.pone.0114848
    Mycobacterium abscessus group subsp., such as M. massiliense, M. abscessus sensu stricto and M. bolletii, are an environmental organism found in soil, water and other ecological niches, and have been isolated from respiratory tract infection, skin and soft tissue infection, postoperative infection of cosmetic surgery. To determine the unique genetic feature of M. massiliense, we sequenced the complete genome of M. massiliense type strain JCM 15300 (corresponding to CCUG 48898). Comparative genomic analysis was performed among Mycobacterium spp. and among M. abscessus group subspp., showing that additional ß-oxidation-related genes and, notably, the mammalian cell entry (mce) operon were located on a genomic island, M. massiliense Genomic Island 1 (MmGI-1), in M. massiliense. In addition, putative anaerobic respiration system-related genes and additional mycolic acid cyclopropane synthetase-related genes were found uniquely in M. massiliense. Japanese isolates of M. massiliense also frequently possess the MmGI-1 (14/44, approximately 32%) and three unique conserved regions (26/44; approximately 60%, 34/44; approximately 77% and 40/44; approximately 91%), as well as isolates of other countries (Malaysia, France, United Kingdom and United States). The well-conserved genomic island MmGI-1 may play an important role in high growth potential with additional lipid metabolism, extra factors for survival in the environment or synthesis of complex membrane-associated lipids. ORFs on MmGI-1 showed similarities to ORFs of phylogenetically distant M. avium complex (MAC), suggesting that horizontal gene transfer or genetic recombination events might have occurred within MmGI-1 among M. massiliense and MAC.
    Matched MeSH terms: Mycobacterium/genetics*; Nontuberculous Mycobacteria/genetics*; Genomic Islands/genetics*; Lipid Metabolism/genetics
  5. Characteristics of complete mitogenome of the lesser short-nosed fruit bat Cynopterus brachyotis (Chiroptera: Pteropodidae) in Malaysia
    Yoon KB, Kim JY, Park YC
    Mitochondrial DNA A DNA Mapp Seq Anal, 2016 05;27(3):2091-2.
    PMID: 25418628 DOI: 10.3109/19401736.2014.982571
    We describe the characteristics of complete mitogenome of C. brachyotis in this article. The complete mitogenome of C. brachyotis is 16,701 bp long with a total base composition of 32.4% A, 25.7% T, 27.7% C and 14.2% G. The mitogenome consists of 13 protein-coding genes (11,408 bp), (KM659865) two rRNA (12S rRNA and 16S rRNA) genes (2,539 bp), 22 tRNA genes (1518 bp) and one control region (1239 bp).
    Matched MeSH terms: Base Composition/genetics; Chiroptera/genetics*; RNA, Transfer/genetics; Base Pairing/genetics
  6. The complete mitogenome of the ghost crab Ocypode ceratophthalmus (Pallas, 1772) (Crustacea: Decapoda: Ocypodidae)
    Tan MH, Gan HM, Lee YP, Austin CM
    Mitochondrial DNA A DNA Mapp Seq Anal, 2016 05;27(3):2123-4.
    PMID: 25423512 DOI: 10.3109/19401736.2014.982587
    The mitochondrial genome sequence of the ghost crab, Ocypode ceratophthalmus, is documented (GenBank accession number: LN611669) in this article. This is the first mitogenome for the family Ocypodidae and the second for the order Ocypodoidea. Ocypode ceratophthalmus has a mitogenome of 15,564 base pairs consisting of 13 protein-coding genes, two ribosomal subunit genes, 22 transfer RNAs and a non-coding AT-rich region. The base composition of the O. ceratophthalmus mitogenome is 35.78% for T, 19.36% for C, 33.73% for A and 11.13% for G, with an AT bias of 69.51% and the gene order is the typical arrangement for brachyuran crabs.
    Matched MeSH terms: Brachyura/genetics*; DNA, Mitochondrial/genetics; RNA, Transfer/genetics; Base Pairing/genetics
  7. The complete mitogenome of the soldier crab Mictyris longicarpus (Latreille, 1806) (Crustacea: Decapoda: Mictyridae)
    Tan MH, Gan HM, Lee YP, Austin CM
    Mitochondrial DNA A DNA Mapp Seq Anal, 2016 05;27(3):2121-2.
    PMID: 25423510 DOI: 10.3109/19401736.2014.982585
    The Mictyris longicarpus (soldier crab) complete mitochondrial genome sequence is reported making it the first for the family Mictyridae and the second for the superfamily Ocypodoidea. The mitogenome is 15,548 base pairs made up of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs and a non-coding AT-rich region. The soldier crab mitogenome gene order is characteristic of brachyuran crabs with a base composition of 36.58% for T, 19.15% for C, 32.43% for A and 11.83% for G, with an AT bias of 69.01%.
    Matched MeSH terms: Base Composition/genetics; Brachyura/genetics*; RNA, Transfer/genetics; Base Pairing/genetics
  8. The complete mitogenome of the bluespotted ribbontail ray Taeniura lymma (Forsskål, 1775) (Elasmobranchii: Myliobatiformes: Dasyatidae)
    Austin CM, Tan MH, Croft LJ, Meekan MG, Gan HY, Gan HM
    Mitochondrial DNA A DNA Mapp Seq Anal, 2016 09;27(5):3205-7.
    PMID: 25693694 DOI: 10.3109/19401736.2015.1007348
    The complete mitogenome of the ray Taeniura lymma was recovered from genome skimming using the HiSeq sequencing system. The T. lymma mitogenome has 17,652 base pairs (59.13% A + T content) made up of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs and a 1906 bp non-coding AT-rich region. This mitogenome sequence is the second for a ray from Australian waters, the first for the genus Taeniura and the ninth for the family Dasyatidae.
    Matched MeSH terms: Fishes/genetics*; RNA, Ribosomal/genetics; RNA, Transfer/genetics; Fish Proteins/genetics
  9. Fulltext Genetic variability and selection criteria in rice mutant lines as revealed by quantitative traits
    Oladosu Y, Rafii MY, Abdullah N, Abdul Malek M, Rahim HA, Hussin G, et al.
    ScientificWorldJournal, 2014;2014:190531.
    PMID: 25431777 DOI: 10.1155/2014/190531
    Genetic based knowledge of different vegetative and yield traits play a major role in varietal improvement of rice. Genetic variation gives room for recombinants which are essential for the development of a new variety in any crop. Based on this background, this work was carried out to evaluate genetic diversity of derived mutant lines and establish relationships between their yield and yield components using multivariate analysis. To achieve this objective, two field trials were carried out on 45 mutant rice genotypes to evaluate their growth and yield traits. Data were taken on vegetative traits and yield and its components, while genotypic and phenotypic coefficients, variance components, expected genetic advance, and heritability were calculated. All the genotypes showed variations for vegetative traits and yield and its components. Also, there was positive relationship between the quantitative traits and the final yield with the exception of number of tillers. Finally, the evaluated genotypes were grouped into five major clusters based on the assessed traits with the aid of UPGMA dendrogram. So hybridization of group I with group V or group VI could be used to attain higher heterosis or vigour among the genotypes. Also, this evaluation could be useful in developing reliable selection indices for important agronomic traits in rice.
    Matched MeSH terms: Mutation/genetics*; Oryza/genetics*; Selection, Genetic/genetics*; Genetic Variation/genetics*
  10. Fulltext Molecular phylogeny of the bamboo sharks (Chiloscyllium spp.)
    Masstor NH, Samat A, Nor SM, Md-Zain BM
    Biomed Res Int, 2014;2014:213896.
    PMID: 25013766 DOI: 10.1155/2014/213896
    Chiloscyllium, commonly called bamboo shark, can be found inhabiting the waters of the Indo-West Pacific around East Asian countries such as Malaysia, Myanmar, Thailand, Singapore, and Indonesia. The International Union for Conservation of Nature (IUCN) Red List has categorized them as nearly threatened sharks out of their declining population status due to overexploitation. A molecular study was carried out to portray the systematic relationships within Chiloscyllium species using 12S rRNA and cytochrome b gene sequences. Maximum parsimony and Bayesian were used to reconstruct their phylogeny trees. A total of 381 bp sequences' lengths were successfully aligned in the 12S rRNA region, with 41 bp sites being parsimony-informative. In the cytochrome b region, a total of 1120 bp sites were aligned, with 352 parsimony-informative characters. All analyses yield phylogeny trees on which C. indicum has close relationships with C. plagiosum. C. punctatum is sister taxon to both C. indicum and C. plagiosum while C. griseum and C. hasseltii formed their own clade as sister taxa. These Chiloscyllium classifications can be supported by some morphological characters (lateral dermal ridges on the body, coloring patterns, and appearance of hypobranchials and basibranchial plate) that can clearly be used to differentiate each species.
    Matched MeSH terms: Genetics, Population; RNA, Ribosomal/genetics*; Sharks/genetics*; Cytochromes b/genetics*
  11. A nucleotide signature for identification of Aglaia stellatopilosa Pannell
    Ng BL, Omarzuki M, Lau GS, Pannell CM, Yeo TC
    Mol Biotechnol, 2014 Jul;56(7):671-9.
    PMID: 24623047 DOI: 10.1007/s12033-014-9746-0
    Members of the genus Aglaia have been reported to contain bioactive phytochemicals. The genus, belonging to the Meliaceae family, is represented by at least 120 known species of woody trees or shrubs in the tropical rain forest. As some of these species are very similar in their morphology, taxonomic identification can be difficult. A reliable and definitive molecular method which can identify Aglaia to the level of the species will hence be useful in comparing the content of specific bioactive compounds between the species of this genus. Here, we report the analysis of DNA sequences in the internal transcribed spacer (ITS) of the nuclear ribosomal DNA and the observation of a unique nucleotide signature in the ITS that can be used for the identification of Aglaia stellatopilosa. The nucleotide signature consists of nine bases over the length of the ITS sequence (654 bp). This uniqueness was validated in 37 samples identified as Aglaia stellatopilosa by an expert taxonomist, whereas the nucleotide signature was lacking in a selection of other Aglaia species and non-Aglaia genera. This finding suggests that molecular typing could be utilized in the identification of Aglaia stellatopilosa.
    Matched MeSH terms: DNA, Ribosomal/genetics*; Nucleotides/genetics; DNA, Ribosomal Spacer/genetics*; Aglaia/genetics*
  12. MicroRNA pathways: an emerging role in identification of therapeutic strategies
    Vijayarathna S, Oon CE, Jothy SL, Chen Y, Kanwar JR, Sasidharan S
    Curr Gene Ther, 2014;14(2):112-20.
    PMID: 24588707
    For years researchers have exerted every effort to improve the influential roles of microRNA (miRNA) in regulating genes that direct mammalian cell development and function. In spite of numerous advancements, many facets of miRNA generation remain unresolved due to the perplexing regulatory networks. The biogenesis of miRNA, eminently endures as a mystery as no universal pathway defines or explicates the variegation in the rise of miRNAs. Early evidence in biogenesis ignited specific steps of being omitted or replaced that eventuate in the individual miRNAs of different mechanisms. Understanding the basic foundation concerning how miRNAs are generated and function will help with diagnostic tools and therapeutic strategies. This review encompasses the canonical and the non-canonical pathways involved in miRNA biogenesis, while elucidating how miRNAs regulate genes at the nuclear level and also the mechanism that lies behind circulating miRNAs.
    Matched MeSH terms: Cell Nucleus/genetics; Signal Transduction/genetics*; MicroRNAs/genetics*; Gene Regulatory Networks/genetics
  13. Fulltext Genetic structure and preliminary findings of cryptic diversity of the Malaysian Mahseer (Tor tambroides Valenciennes: Cyprinidae) inferred from mitochondrial DNA and microsatellite analyses
    Esa Y, Abdul Rahim KA
    Biomed Res Int, 2013;2013:170980.
    PMID: 24455674 DOI: 10.1155/2013/170980
    This study examines the population genetic structure of Tor tambroides, an important freshwater fish species in Malaysia, using fifteen polymorphic microsatellite loci and sequencing of 464 base pairs of the mitochondrial cytochrome c oxidase I (COI) gene. A total of 152 mahseer samples were collected from eight populations throughout the Malaysia river system. Microsatellites results found high levels of intrapopulation variations, but mitochondrial COI results found high levels of interpopulations differentiation. The possible reasons for their discrepancies might be the varying influence of genetic drift on each marker or the small sample sizes used in most of the populations. The Kelantan population showed very low levels of genetic variations using both mitochondrial and microsatellite analyses. Phylogenetic analysis of the COI gene found a unique haplotype (ER8∗), possibly representing a cryptic lineage of T. douronensis, from the Endau-Rompin population. Nevertheless, the inclusion of nuclear microsatellite analyses could not fully resolve the genetic identity of haplotype ER8∗ in the present study. Overall, the findings showed a serious need for more comprehensive and larger scale samplings, especially in remote river systems, in combination with molecular analyses using multiple markers, in order to discover more cryptic lineages or undescribed "genetic species" of mahseer.
    Matched MeSH terms: Cyprinidae/genetics*; DNA, Mitochondrial/genetics*; Haplotypes/genetics; Microsatellite Repeats/genetics
  14. Molecular basis of transfusion dependent beta-thalassemia major patients in Sabah
    Teh LK, George E, Lai MI, Tan JA, Wong L, Ismail P
    J Hum Genet, 2014 Mar;59(3):119-23.
    PMID: 24369358 DOI: 10.1038/jhg.2013.131
    Beta-thalassemia is one of the most prevalent inherited diseases and a public health problem in Malaysia. Malaysia is geographically divided into West and East Malaysia. In Sabah, a state in East Malaysia, there are over 1000 estimated cases of β-thalassemia major patients. Accurate population frequency data of the molecular basis of β-thalassemia major are needed for planning its control in the high-risk population of Sabah. Characterization of β-globin gene defects was done in 252 transfusion dependent β-thalassemia patients incorporating few PCR techniques. The study demonstrates that β-thalassemia mutations inherited are ethnically dependent. It is important to note that 86.9% of transfusion-dependent β-thalassemia major patients in Sabah were of the indigenous population and homozygous for a single mutation. The Filipino β(0)-deletion was a unique mutation found in the indigenous population of Sabah. Mutations common in West Malaysia were found in 11 (4.3%) patients. Four rare mutations (Hb Monroe, CD 8/9, CD 123/124/125 and IVS I-2) were also found. This study is informative on the population genetics of β-thalassemia major in Sabah.
    Matched MeSH terms: Ethnic Groups/genetics; Gene Frequency/genetics; beta-Thalassemia/genetics*; beta-Globins/genetics
  15. Fulltext Haplotype analysis of the 185delAG BRCA1 mutation in ethnically diverse populations
    Laitman Y, Feng BJ, Zamir IM, Weitzel JN, Duncan P, Port D, et al.
    Eur J Hum Genet, 2013 Feb;21(2):212-6.
    PMID: 22763381 DOI: 10.1038/ejhg.2012.124
    The 185delAG* BRCA1 mutation is encountered primarily in Jewish Ashkenazi and Iraqi individuals, and sporadically in non-Jews. Previous studies estimated that this is a founder mutation in Jewish mutation carriers that arose before the dispersion of Jews in the Diaspora ~2500 years ago. The aim of this study was to assess the haplotype in ethnically diverse 185delAG* BRCA1 mutation carriers, and to estimate the age at which the mutation arose. Ethnically diverse Jewish and non-Jewish 185delAG*BRCA1 mutation carriers and their relatives were genotyped using 15 microsatellite markers and three SNPs spanning 12.5 MB, encompassing the BRCA1 gene locus. Estimation of mutation age was based on a subset of 11 markers spanning a region of ~5 MB, using a previously developed algorithm applying the maximum likelihood method. Overall, 188 participants (154 carriers and 34 noncarriers) from 115 families were included: Ashkenazi, Iraq, Kuchin-Indians, Syria, Turkey, Iran, Tunisia, Bulgaria, non-Jewish English, non-Jewish Malaysian, and Hispanics. Haplotype analysis indicated that the 185delAG mutation arose 750-1500 years ago. In Ashkenazim, it is a founder mutation that arose 61 generations ago, and with a small group of founder mutations was introduced into the Hispanic population (conversos) ~650 years ago, and into the Iraqi-Jewish community ~450 years ago. The 185delAG mutation in the non-Jewish populations in Malaysia and the UK arose at least twice independently. We conclude that the 185delAG* BRCA1 mutation resides on a common haplotype among Ashkenazi Jews, and arose about 61 generations ago and arose independently at least twice in non-Jews.
    Matched MeSH terms: Ethnic Groups/genetics; Genetics, Population; Jews/genetics*; BRCA1 Protein/genetics*
  16. Fulltext Identification of introgressed alien chromosome segments associated with grain quality in Oryza rufipogon x MR219 advanced breeding lines using SSR markers
    Fasahat P, Muhammad K, Abdullah A, Wickneswari R
    Genet. Mol. Res., 2012;11(3):3534-46.
    PMID: 23079848 DOI: 10.4238/2012.September.26.10
    A limited backcross procedure was utilized to introgress genes associated with grain quality traits from Oryza rufipogon (Accession No. IRGC 105491), a wild rice from Malaysia, to the cultivated rice O. sativa cv. MR219, a popular high yielding Malaysian rice cultivar. A set of 10 BC(2)F(7) progenies were selected based on the field performance and phenotypic appearance in BC(2)F(5) and BC(2)F(6) generations, which initially started with 266 progenies in the BC(2)F(2) generation. These 10 advanced breeding lines are similar to each other but differ in several important grain quality traits, which can be traced to O. rufipogon introgressions. Phenotyping and genotyping of BC(2)F(7) variants were considered for QTL analysis. The introgressed lines did not show any significant changes compared to the recurrent parent MR219 for the traits grain density and milled rice percentage. All 10 progenies showed significantly higher head rice percentages (70-88%) than the recurrent parent MR219. Variants G13 and G15 had higher amylose contents than MR219. All variants were analyzed using polymorphic SSR markers. Of the 34 SSR markers, only 18 showed introgression from O. rufipogon for chromosomes 1, 2, 3, 5, 6, 8, 10, and 11. Graphical genotypes were prepared for each variant, and association between the introgression regions and the traits that increased grain quality was visualized. Based on marker trait association, some of the QTLs are stable across environments and genetic backgrounds and could be used universally.
    Matched MeSH terms: Oryza/genetics*; Seeds/genetics*; Microsatellite Repeats/genetics*; Chromosomes, Plant/genetics*
  17. Application of 16s rDNA and cytochrome b ribosomal markers in studies of lineage and fish populations structure of aquatic species
    Baharum SN, Nurdalila AA
    Mol Biol Rep, 2012 May;39(5):5225-32.
    PMID: 22167328 DOI: 10.1007/s11033-011-1320-2
    The most economically important form of aquaculture is fish farming, which is an industry that accounts for an ever increasing share of world fishery production. Molecular markers can be used to enhance the productivity of the aquaculture and fish industries to meet the increasing demand. Molecular markers can be identified via a DNA test regardless of the developmental stage, age or environmental challenges experienced by the organism. The application of 16s and cytochrome b markers has enabled rapid progress in investigations of genetic variability and inbreeding, parentage assignments, species and strain identification and the construction of high resolution genetic linkage maps for aquaculture fisheries. In this review, the advantages of principles and potential power tools of 16s and cytochrome b markers are discussed. Main findings in term of trend, aspects and debates on the reviewed issue made from the model of aquatic species for the benefit of aquaculture genomics and aquaculture genetics research are discussed. The concepts in this review are illustrated with various research examples and results that relate theory to reality and provide a strong review of the current status of these biotechnology topics.
    Matched MeSH terms: DNA, Ribosomal/genetics*; Fishes/genetics*; Cytochromes b/genetics*; Aquatic Organisms/genetics*
  18. Fulltext A rare X-linked inherited mucocutaneous syndrome in two siblings
    Chong LA, Ariffin H
    Med J Malaysia, 2009 Dec;64(4):327-9.
    PMID: 20954562 MyJurnal
    We report on an 11 year-old boy with dyskeratosis congenita who presented with dystrophic nails, dysphagia, hyperpigmentation and oral leukoplakia. He had a brother who died 14 years earlier with similar presenting symptoms and aplastic anaemia. Genetic studies of our patient demonstrated the presence of a DKC1 mutation and confirmed our diagnosis. Further genetic screening revealed that his mother and one of his four sisters are heterozygous for the same mutation.
    Matched MeSH terms: Nuclear Proteins/genetics; Cell Cycle Proteins/genetics; Dyskeratosis Congenita/genetics*; Rare Diseases/genetics*
  19. Isozyme analysis and relationships among three species in Malaysian Trichoderma isolates
    Siddiquee S, Tan SG, Yusof UK
    J Microbiol Biotechnol, 2010 Sep;20(9):1266-75.
    PMID: 20890090
    Isozyme and protein electrophoresis data from mycelial extracts of 27 isolates of Trichoderma harzianum, 10 isolates of T. aureoviride and 10 isolates of T. longibrachiatum from Southern Peninsular Malaysia were investigated. The eight enzyme and a single protein pattern systems were analyzed. Three isozyme and total protein patterns were shown to be useful for the detection of three Trichoderma species. The isozyme and protein data were analyzed using the Nei and Li Dice similarity coefficient for pairwise comparison between individual isolates, species isolate group, and for generating a distance matrix. The UPGMA cluster analysis showed a higher degree of relationship between T. harzianum and T. aureoviride than to T. longibrachiatum. These results suggested that the T. harzianum isolates had high levels of genetic variation compared to the other isolates of Trichoderma species.
    Matched MeSH terms: Fungal Proteins/genetics*; Isoenzymes/genetics; Trichoderma/genetics*; Mycelium/genetics
  20. Fulltext Phylogenetic relationships of leaf monkeys (Presbytis; Colobinae) based on cytochrome b and 12S rRNA genes
    Vun VF, Mahani MC, Lakim M, Ampeng A, Md-Zain BM
    Genet. Mol. Res., 2011;10(1):368-81.
    PMID: 21365553 DOI: 10.4238/vol10-1gmr1048
    Little is known about the classification and phylogenetic relationships of the leaf monkeys (Presbytis). We analyzed mitochondrial DNA sequences of cytochrome b (Cyt b) and 12S rRNA to determine the phylogenetic relationships of the genus Presbytis. Gene fragments of 388 and 371 bp of Cyt b and 12S rRNA, respectively, were sequenced from samples of Presbytis melalophos (subspecies femoralis, siamensis, robinsoni, and chrysomelas), P. rubicunda and P. hosei. The genus Trachypithecus (Cercopithecidae) was used as an outgroup. The Cyt b NJ and MP phylogeny trees showed P. m. chrysomelas to be the most primitive, followed by P. hosei, whereas 12S rRNA tree topology only indicated that these two species have close relationships with the other members of the genus. In our analysis, chrysomelas, previously classified as a subspecies of P. melalophos, was not included in either the P. m. femoralis clade or the P. m. siamensis clade. Whether or not there should be a separation at the species level remains to be clarified. The tree topologies also showed that P. m. siamensis is paraphyletic with P. m. robinsoni, and P. m. femoralis with P. rubicunda, in two different clades. Cyt b and 12S rRNA are good gene candidates for the study of phylogenetic relationships at the species level. However, the systematic relationships of some subspecies in this genus remain unclear.
    Matched MeSH terms: Cercopithecidae/genetics*; DNA, Mitochondrial/genetics; RNA, Ribosomal/genetics*; Cytochromes b/genetics*
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