Displaying publications 141 - 160 of 8077 in total

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  1. Fulltext Functional prediction of de novo uni-genes from chicken transcriptomic data following infectious bursal disease virus at 3-days post-infection
    Azli B, Ravi S, Hair-Bejo M, Omar AR, Ideris A, Mat Isa N
    BMC Genomics, 2021 Jun 19;22(1):461.
    PMID: 34147086 DOI: 10.1186/s12864-021-07690-3
    BACKGROUND: Infectious bursal disease (IBD) is an economically very important issue to the poultry industry and it is one of the major threats to the nation's food security. The pathogen, a highly pathogenic strain of a very virulent IBD virus causes high mortality and immunosuppression in chickens. The importance of understanding the underlying genes that could combat this disease is now of global interest in order to control future outbreaks. We had looked at identified novel genes that could elucidate the pathogenicity of the virus following infection and at possible disease resistance genes present in chickens.

    RESULTS: A set of sequences retrieved from IBD virus-infected chickens that did not map to the chicken reference genome were de novo assembled, clustered and analysed. From six inbred chicken lines, we managed to assemble 10,828 uni-transcripts and screened 618 uni-transcripts which were the most significant sequences to known genes, as determined by BLASTX searches. Based on the differentially expressed genes (DEGs) analysis, 12 commonly upregulated and 18 downregulated uni-genes present in all six inbred lines were identified with false discovery rate of q-value

    Matched MeSH terms: Chickens/genetics
  2. Biochemical and in silico structural characterization of a cold-active arginase from the psychrophilic yeast, Glaciozyma antarctica PI12
    Yusof NY, Quay DHX, Kamaruddin S, Jonet MA, Md Illias R, Mahadi NM, et al.
    Extremophiles, 2024 Feb 01;28(1):15.
    PMID: 38300354 DOI: 10.1007/s00792-024-01333-7
    Glaciozyma antarctica PI12 is a psychrophilic yeast isolated from Antarctica. In this work, we describe the heterologous production, biochemical properties and in silico structure analysis of an arginase from this yeast (GaArg). GaArg is a metalloenzyme that catalyses the hydrolysis of L-arginine to L-ornithine and urea. The cDNA of GaArg was reversed transcribed, cloned, expressed and purified as a recombinant protein in Escherichia coli. The purified protein was active against L-arginine as its substrate in a reaction at 20 °C, pH 9. At 10-35 °C and pH 7-9, the catalytic activity of the protein was still present around 50%. Mn2+, Ni2+, Co2+ and K+ were able to enhance the enzyme activity more than two-fold, while GaArg is most sensitive to SDS, EDTA and DTT. The predicted structure model of GaArg showed a very similar overall fold with other known arginases. GaArg possesses predominantly smaller and uncharged amino acids, fewer salt bridges, hydrogen bonds and hydrophobic interactions compared to the other counterparts. GaArg is the first reported arginase that is cold-active, facilitated by unique structural characteristics for its adaptation of catalytic functions at low-temperature environments. The structure and function of cold-active GaArg provide insights into the potentiality of new applications in various biotechnology and pharmaceutical industries.
    Matched MeSH terms: Arginase/genetics
  3. Fulltext Exome sequencing identifies breast cancer susceptibility genes and defines the contribution of coding variants to breast cancer risk
    Wilcox N, Dumont M, González-Neira A, Carvalho S, Joly Beauparlant C, Crotti M, et al.
    Nat Genet, 2023 Sep;55(9):1435-1439.
    PMID: 37592023 DOI: 10.1038/s41588-023-01466-z
    Linkage and candidate gene studies have identified several breast cancer susceptibility genes, but the overall contribution of coding variation to breast cancer is unclear. To evaluate the role of rare coding variants more comprehensively, we performed a meta-analysis across three large whole-exome sequencing datasets, containing 26,368 female cases and 217,673 female controls. Burden tests were performed for protein-truncating and rare missense variants in 15,616 and 18,601 genes, respectively. Associations between protein-truncating variants and breast cancer were identified for the following six genes at exome-wide significance (P 
    Matched MeSH terms: Mutation, Missense/genetics
  4. Phylogenetic Relationships of Sun Bear (Helarctos malayanus) Based on Mitochondrial DNA from Sumatra and Other Southeast Asian Regions
    Roesma DI, Tjong DH, Syaifullah, Aidil DR, Maulana MR, Salis VM
    Pak J Biol Sci, 2023 Nov;26(12):615-627.
    PMID: 38334154 DOI: 10.3923/pjbs.2023.615.627
    <b>Background and Objective:</b> The <i>Helarctos malayanus</i> is the sole bear species-living in Indonesia (Sumatra and Borneo). The available biological data for sun bears (<i>H. malayanus</i>) in Sumatra is limited, especially for morphological and genetic data. A morphological approach is difficult to do. Therefore, a molecular approach is the most likely choice. Phylogenetic analysis was carried out on <i>H. malayanus</i> in Central Sumatra (Dharmasraya, South Solok and Riau) using the Cytochrome B gene. <b>Materials and Methods:</b> Blood samples from three individuals of <i>H. malayanus</i> were obtained at the Sumatran Tiger Rehabilitation Center, Dharmasraya. Three <i>H. malayanus</i> Central Sumatra sequences and 62 GenBank sequences were used in the analysis. The DNA sequences were analyzed using the DNA Star, AliView, Bioedit, DNA SP, haplotype network, IQ Tree and MEGA software. <b>Results:</b> Forty-one haplotypes were identified in 65 sequences, with 17 haplotypes belonging to <i>H. malayanus</i>. Haplotype network analysis divides <i>H. malayanus</i> into Haplogroup I (Sundaland) and Haplogroup II (Mainland). All individuals of <i>H. malayanus</i> in Central Sumatra have the same haplotype as Peninsular Malaysia sequence. The sun bear (<i>H. malayanus</i>) has a monophyletic relationship with other bear species. The <i>H. malayanus</i> has a higher genetic distance between the two lineages (1.0-2.3%) than the genetic distance within the subpopulations of each lineage. <b>Conclusion:</b> The study results supported sun bear (<i>H. malayanus</i>) divided into two different lineages: Mainland (subcluster 1) and Sundaland (subcluster 2 and 3). The geographic isolation causes the absence of gene flow, which results in high genetic distance between sun bears (<i>H. malayanus</i>) in Sundaland and Mainland lineages.
    Matched MeSH terms: DNA, Mitochondrial/genetics
  5. Increased genome size is caused by heterochromatin addition in two non-related bat species, Hesperoptenus doriae and Philetor brachypterus (Vespertilionidae, Chiroptera, Mammalia)
    Volleth M, Greilhuber J, Heller KG, Müller S, Yong HS, Loidl J
    Chromosoma, 2023 Nov;132(4):269-288.
    PMID: 37322170 DOI: 10.1007/s00412-023-00802-w
    The average genome size (GS) of bats, which are the only mammals capable of powered flight, is approximately 18% smaller than that of closely related mammalian orders. The low nuclear DNA content of Chiroptera is comparable to that of birds, which are also characterized by a high metabolic rate. Only a few chiropteran taxa possess notable amounts of constitutive heterochromatin. Here, we studied the karyotypes of two non-related vesper bat species with unusually high amounts of constitutive heterochromatin: Hesperoptenus doriae and Philetor brachypterus. Conventional staining methods and whole-chromosome painting with probes derived from Myotis myotis (2n = 44), showing a karyotype close to that of the presumed ancestor of Vespertilionidae, revealed Robertsonian fusions as the main type of rearrangement leading to the exceptionally reduced diploid chromosome number of 2n = 26 in both species. Moreover, both karyotypes are characterized by large blocks of pericentromeric heterochromatin composed of CMA-positive and DA-DAPI-positive segments. In H. doriae, the heterochromatin accumulation has resulted in a genome size of 3.22 pg (1C), which is 40% greater than the mean genome size for the family. For P. brachypterus, a genome size of 2.94 pg was determined, representing an increase of about 28%. Most notably, in H. doriae, the presence of additional constitutive heterochromatin correlates with an extended mitotic cell cycle duration in vitro. A reduction in diploid chromosome number to 30 or lower is discussed as a possible cause of the accumulation of pericentromeric heterochromatin in Vespertilionidae.
    Matched MeSH terms: Heterochromatin/genetics
  6. Fulltext The first draft reference genome of the American mink (Neovison vison)
    Cai Z, Petersen B, Sahana G, Madsen LB, Larsen K, Thomsen B, et al.
    Sci Rep, 2017 Nov 06;7(1):14564.
    PMID: 29109430 DOI: 10.1038/s41598-017-15169-z
    The American mink (Neovison vison) is a semiaquatic species of mustelid native to North America. It's an important animal for the fur industry. Many efforts have been made to locate genes influencing fur quality and color, but this search has been impeded by the lack of a reference genome. Here we present the first draft genome of mink. In our study, two mink individuals were sequenced by Illumina sequencing with 797 Gb sequence generated. Assembly yielded 7,175 scaffolds with an N50 of 6.3 Mb and length of 2.4 Gb including gaps. Repeat sequences constitute around 31% of the genome, which is lower than for dog and cat genomes. The alignments of mink, ferret and dog genomes help to illustrate the chromosomes rearrangement. Gene annotation identified 21,053 protein-coding sequences present in mink genome. The reference genome's structure is consistent with the microsatellite-based genetic map. Mapping of well-studied genes known to be involved in coat quality and coat color, and previously located fur quality QTL provide new knowledge about putative candidate genes for fur traits. The draft genome shows great potential to facilitate genomic research towards improved breeding for high fur quality animals and strengthen our understanding on evolution of Carnivora.
    Matched MeSH terms: Dogs/genetics; Ferrets/genetics; Mink/genetics*; Repetitive Sequences, Nucleic Acid/genetics; Genome/genetics*; Microsatellite Repeats/genetics; Quantitative Trait Loci/genetics
  7. Fulltext Echoes of ancient introgression punctuate stable genomic lineages in the evolution of figs
    Gardner EM, Bruun-Lund S, Niissalo M, Chantarasuwan B, Clement WL, Geri C, et al.
    Proc Natl Acad Sci U S A, 2023 Jul 11;120(28):e2222035120.
    PMID: 37399402 DOI: 10.1073/pnas.2222035120
    Studies investigating the evolution of flowering plants have long focused on isolating mechanisms such as pollinator specificity. Some recent studies have proposed a role for introgressive hybridization between species, recognizing that isolating processes such as pollinator specialization may not be complete barriers to hybridization. Occasional hybridization may therefore lead to distinct yet reproductively connected lineages. We investigate the balance between introgression and reproductive isolation in a diverse clade using a densely sampled phylogenomic study of fig trees (Ficus, Moraceae). Codiversification with specialized pollinating wasps (Agaonidae) is recognized as a major engine of fig diversity, leading to about 850 species. Nevertheless, some studies have focused on the importance of hybridization in Ficus, highlighting the consequences of pollinator sharing. Here, we employ dense taxon sampling (520 species) throughout Moraceae and 1,751 loci to investigate phylogenetic relationships and the prevalence of introgression among species throughout the history of Ficus. We present a well-resolved phylogenomic backbone for Ficus, providing a solid foundation for an updated classification. Our results paint a picture of phylogenetically stable evolution within lineages punctuated by occasional local introgression events likely mediated by local pollinator sharing, illustrated by clear cases of cytoplasmic introgression that have been nearly drowned out of the nuclear genome through subsequent lineage fidelity. The phylogenetic history of figs thus highlights that while hybridization is an important process in plant evolution, the mere ability of species to hybridize locally does not necessarily translate into ongoing introgression between distant lineages, particularly in the presence of obligate plant-pollinator relationships.
    Matched MeSH terms: Pollination/genetics
  8. Diving deep into fish allergen immunotherapy: Current knowledge and future directions
    Reginald K, Nadeem K, Yap EZY, Latiff AHA
    Asian Pac J Allergy Immunol, 2024 Mar;42(1):1-13.
    PMID: 38165149 DOI: 10.12932/AP-030923-1687
    Fish allergy is one of the "big nine" categories of food allergens worldwide, and its prevalence is increasing with the higher demand for this nutritious food source. Fish allergies are a significant health concern as it is a leading cause of food anaphylaxis, accounting for 9% of all deaths from anaphylaxis. The gaps in treating fish allergies at present are the incomplete identification of fish allergens, lack of component-resolved diagnosis of fish allergens in the clinical setting, and the variability in sensitization profiles based on different fish consumption practices. Allergen immunotherapy (AIT) improves tolerance towards accidental consumption of fish and is longer lasting than pharmacotherapy. Current practice or research of fish AIT ranges from the use of whole fish via oral desensitization, to the use of purified recombinant parvalbumin and its hypoallergenic variant, passive IgG immunization, and modifying the allergenicity of parvalbumin by changing the diet of farmed fish. However, the focus of fish allergen-based studies in the context of AIT has been restricted to parvalbumins. More research is required to understand the involvement of other fish allergens, and several other strategies of AIT including peptide vaccines, DNA vaccines, hybrid allergens, and the use of nanobodies that have the capacity to treat multiple allergens have been proposed. For AIT, other important aspects to consider are the route of desensitization, and the biomarkers to assess the success of immunotherapy. Finally, we also address several clinical considerations for fish AIT.
    Matched MeSH terms: Parvalbumins/genetics
  9. Extensive intragenomic variations of the 18S rDNA V4 region in the toxigenic diatom species Pseudo-nitzschia multistriata revealed through high-throughput sequencing
    Wang H, Liu K, He Z, Chen Y, Hu Z, Chen W, et al.
    Mar Pollut Bull, 2024 Apr;201:116198.
    PMID: 38428045 DOI: 10.1016/j.marpolbul.2024.116198
    Metabarcoding analysis is an effective technique for monitoring the domoic acid-producing Pseudo-nitzschia species in marine environments, uncovering high-levels of molecular diversity. However, such efforts may result in the overinterpretation of Pseudo-nitzschia species diversity, as molecular diversity not only encompasses interspecies and intraspecies diversities but also exhibits extensive intragenomic variations (IGVs). In this study, we analyzed the V4 region of the 18S rDNA of 30 strains of Pseudo-nitzschia multistriata collected from the coasts of China. The results showed that each P. multistriata strain harbored about a hundred of unique 18S rDNA V4 sequence varieties, of which each represented by a unique amplicon sequence variant (ASV). This study demonstrated the extensive degree of IGVs in P. multistriata strains, suggesting that IGVs may also present in other Pseudo-nitzschia species and other phytoplankton species. Understanding the scope and levels of IGVs is crucial for accurately interpreting the results of metabarcoding analysis.
    Matched MeSH terms: Phytoplankton/genetics
  10. 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*
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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*
  17. 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*
  18. 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*
  19. 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
  20. 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
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