Displaying publications 81 - 100 of 928 in total

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  1. The genus Cerithideopsis Thiele, 1929 (Gastropoda: Potamididae) in the Indo-West Pacific region
    Reid DG, Claremont M
    Zootaxa, 2014;3779:61-80.
    PMID: 24871714 DOI: 10.11646/zootaxa.3779.1.8
    The genus Cerithideopsis is most common in mangrove and salt marsh habitats of the New World tropics, but there is also a small radiation in the Indo-West Pacific region. Previously, these Indo-Pacific snails have generally been classified as Cerithidea largillierti (Philippi, 1848). Molecular phylogenetic analysis (partial sequences of mitochondrial COI and 16S rRNA, and nuclear 28S rRNA) of 15 specimens from 8 localities between Japan and Australia reveal three clades, among which there are small morphological differences and which show allopatric distributions. Cerithideopsis largillierti sensu stricto is restricted to Japan and China, while the two other species are described as new: C. australiensis occurs in tropical Australasia and C. malayensis is found from Malaysia to Java and the Philippines. All occur on mud and in pools with leaf litter, in the shaded landward and middle zones of mangrove forests, and do not climb the trees. The species accounts include full synonymies, detailed descriptions of shells based on 82 museum samples, descriptions of living animals, distribution records and maps, and notes on habitat and conservation status.
    Matched MeSH terms: Molecular Sequence Data
  2. Atomistic simulation studies of the α/β-glucoside and galactoside in anhydrous bilayers: effect of the anomeric and epimeric configurations
    Ahmadi S, Manickam Achari V, Nguan H, Hashim R
    J Mol Model, 2014 Mar;20(3):2165.
    PMID: 24623320 DOI: 10.1007/s00894-014-2165-0
    Fully atomistic molecular dynamics simulation studies of thermotropic bilayers were performed using a set of glycosides namely n-octyl-β-D-glucopyranoside (β-C8Glc), n-octyl-α-D-glucopyranoside (α-C8Glc), n-octyl-β-D-galactopyranoside (β-C8Gal), and n-octyl-α-D-galactopyranoside (α-C8Gal) to investigate the stereochemical relationship of the epimeric/anomeric quartet liner glycolipids with the same octyl chain group. The results showed that, the anomeric stereochemistry or the axial/equatorial orientation of C1-O1 (α/β) is an important factor controlling the area and d-spacing of glycolipid bilayer systems in the thermotropic phase. The head group tilt angle and the chain ordering properties are affected by the anomeric effect. In addition, the L(C) phase of β-C8Gal, is tilting less compared to those in the fluid L(α). The stereochemistry of the C4-epimeric (axial/equatorial) and anomeric (α/β) centers simultaneously influence the inter-molecular hydrogen bond. Thus, the trend in the values of the hydrogen bond for these glycosides is β-C8Gal > α-C8Glc > β-C8Glc > α-C8Gal. The four bilayer systems showed anomalous diffusion behavior with an observed trend for the diffusion coefficients; and this trend is β-C8Gal > β-C8Glc > α-C8Gal > α-C8Glc. The "bent" configuration of the α-anomer results in an increase of the hydrophobic area, chain vibration and chain disorganization. Since thermal energy is dispensed more entropically for the chain region, the overall molecular diffusion decreases.
    Matched MeSH terms: Molecular Sequence Data
  3. Fulltext First case of a naturally acquired human infection with Plasmodium cynomolgi
    Ta TH, Hisam S, Lanza M, Jiram AI, Ismail N, Rubio JM
    Malar J, 2014;13:68.
    PMID: 24564912 DOI: 10.1186/1475-2875-13-68
    Since 1960, a total of seven species of monkey malaria have been reported as transmissible to man by mosquito bite: Plasmodium cynomolgi, Plasmodium brasilianum, Plasmodium eylesi, Plasmodium knowlesi, Plasmodium inui, Plasmodium schwetzi and Plasmodium simium. With the exception of P. knowlesi, none of the other species has been found to infect humans in nature. In this report, it is described the first known case of a naturally acquired P. cynomolgi malaria in humans.The patient was a 39-year-old woman from a malaria-free area with no previous history of malaria or travel to endemic areas. Initially, malaria was diagnosed and identified as Plasmodium malariae/P. knowlesi by microscopy in the Terengganu State Health Department. Thick and thin blood films stained with 10% Giemsa were performed for microscopy examination. Molecular species identification was performed at the Institute for Medical Research (IMR, Malaysia) and in the Malaria & Emerging Parasitic Diseases Laboratory (MAPELAB, Spain) using different nested PCR methods.Microscopic re-examination in the IMR showed characteristics of Plasmodium vivax and was confirmed by a nested PCR assay developed by Snounou et al. Instead, a different PCR assay plus sequencing performed at the MAPELAB confirmed that the patient was infected with P. cynomolgi and not with P. vivax.This is the first report of human P. cynomolgi infection acquired in a natural way, but there might be more undiagnosed or misdiagnosed cases, since P. cynomolgi is morphologically indistinguishable from P. vivax, and one of the most used PCR methods for malaria infection detection may identify a P. cynomolgi infection as P. vivax.Simian Plasmodium species may routinely infect humans in Southeast Asia. New diagnostic methods are necessary to distinguish between the human and monkey malaria species. Further epidemiological studies, incriminating also the mosquito vector(s), must be performed to know the relevance of cynomolgi malaria and its implication on human public health and in the control of human malaria.The zoonotic malaria cannot be ignored in view of increasing interactions between man and wild animals in the process of urbanization.
    Matched MeSH terms: Molecular Sequence Data
  4. Use of COI, CytB and ND5 genes for intra- and inter-specific differentiation of Haematobia irritans and Haematobia exigua
    Low VL, Tan TK, Lim PE, Domingues LN, Tay ST, Lim YA, et al.
    Vet Parasitol, 2014 Aug 29;204(3-4):439-42.
    PMID: 24912955 DOI: 10.1016/j.vetpar.2014.05.036
    A multilocus sequence analysis using mitochondria-encoded cytochrome c oxidase subunit I (COI), cytochrome B (CytB), NADH dehydrogenase subunit 5 (ND5); nuclear encoded 18S ribosomal RNA (18S) and 28S ribosomal RNA (28S) genes was performed to determine the levels of genetic variation between the closely related species Haematobia irritans Linnaeus and Haematobia exigua de Meijere. Among these five genes, ND5 and CytB genes were found to be more variable and informative in resolving the interspecific relationships of both species. In contrast, the COI gene was more valuable in inferring the intraspecific relationships. The ribosomal 18S and 28S sequences of H. irritans and H. exigua were highly conserved with limited intra- and inter-specific variation. Molecular evidence presented in this study demonstrated that both flies are genetically distinct and could be differentiated based on sequence analysis of mitochondrial genes.
    Matched MeSH terms: Molecular Sequence Data
  5. Fulltext Genetic species identification and population structure of Halophila (Hydrocharitaceae) from the Western Pacific to the Eastern Indian Ocean
    Nguyen VX, Detcharoen M, Tuntiprapas P, Soe-Htun U, Sidik JB, Harah MZ, et al.
    BMC Evol. Biol., 2014 Apr 30;14:92.
    PMID: 24886000 DOI: 10.1186/1471-2148-14-92
    BACKGROUND: The Indo-Pacific region has the largest number of seagrass species worldwide and this region is considered as the origin of the Hydrocharitaceae. Halophila ovalis and its closely-related species belonging to the Hydrocharitaceae are well-known as a complex taxonomic challenge mainly due to their high morphological plasticity. The relationship of genetic differentiation and geographic barriers of H. ovalis radiation was not much studied in this region. Are there misidentifications between H. ovalis and its closely related species? Does any taxonomic uncertainty among different populations of H. ovalis persist? Is there any genetic differentiation among populations in the Western Pacific and the Eastern Indian Ocean, which are separated by the Thai-Malay peninsula? Genetic markers can be used to characterize and identify individuals or species and will be used to answer these questions.

    RESULTS: Phylogenetic analyses of the nuclear ribosomal internal transcribed spacer region based on materials collected from 17 populations in the Western Pacific and the Eastern Indian Ocean showed that some specimens identified as H. ovalis belonged to the H. major clade, also supported by morphological data. Evolutionary divergence between the two clades is between 0.033 and 0.038, much higher than the evolutionary divergence among H. ovalis populations. Eight haplotypes were found; none of the haplotypes from the Western Pacific is found in India and vice versa. Analysis of genetic diversity based on microsatellite analysis revealed that the genetic diversity in the Western Pacific is higher than in the Eastern Indian Ocean. The unrooted neighbor-joining tree among 14 populations from the Western Pacific and the Eastern Indian Ocean showed six groups. The Mantel test results revealed a significant correlation between genetic and geographic distances among populations. Results from band-based and allele frequency-based approaches from Amplified Fragment Length Polymorphism showed that all samples collected from both sides of the Thai-Malay peninsula were clustered into two clades: Gulf of Thailand and Andaman Sea.

    CONCLUSIONS: Our study documented the new records of H. major for Malaysia and Myanmar. The study also revealed that the Thai-Malay peninsula is a geographic barrier between H. ovalis populations in the Western Pacific and the Eastern Indian Ocean.

    Matched MeSH terms: Molecular Sequence Data
  6. The phylogenetic relationships of three new species of the Cyrtodactylus pulchellus complex (Squamata: Gekkonidae) from poorly explored regions in northeastern Peninsular Malaysia
    Grismer LL, Wood PL, Anuar S, Quah ES, Muin MA, Mohamed M, et al.
    Zootaxa, 2014;3786:359-81.
    PMID: 24869541 DOI: 10.11646/zootaxa.3786.3.6
    An integrative taxonomic analysis of three newly discovered populations of the gekkonid genus Cyrtodactylus Gray from Merapoh, Pahang; Gunung Stong, Kelantan; and Gunung Tebu, Terengganu indicate they are part of the C. pulchellus complex and each is a new species and thusly named Cyrtodactylus sharkari sp. nov., C. jelawangensis sp. nov., and C. timur sp. nov., respectively. Each species bears a unique suite of morphological and color pattern characters separating them from each other and all other nominal species in the C. pulchellus complex. Their phylogenetic relationships to each other and other species in the C. pulchellus complex were unexpected in that they are not in accordance with the general distribution of the species in this complex, underscoring the intricate historical biogeography of the Thai-Malay Peninsula. These descriptions highlight our current lack of knowledge concerning the herpetological diversity and distribution of species in northeastern Peninsular Malaysia.
    Matched MeSH terms: Molecular Sequence Data
  7. Fulltext DNA methylation and expression of the EgDEF1 gene and neighboring retrotransposons in mantled somaclonal variants of oil palm
    Jaligot E, Hooi WY, Debladis E, Richaud F, Beulé T, Collin M, et al.
    PLoS One, 2014;9(3):e91896.
    PMID: 24638102 DOI: 10.1371/journal.pone.0091896
    The mantled floral phenotype of oil palm (Elaeis guineensis) affects somatic embryogenesis-derived individuals and is morphologically similar to mutants defective in the B-class MADS-box genes. This somaclonal variation has been previously demonstrated to be associated to a significant deficit in genome-wide DNA methylation. In order to elucidate the possible role of DNA methylation in the transcriptional regulation of EgDEF1, the APETALA3 ortholog of oil palm, we studied this epigenetic mark within the gene in parallel with transcript accumulation in both normal and mantled developing inflorescences. We also examined the methylation and expression of two neighboring retrotransposons that might interfere with EgDEF1 regulation. We show that the EgDEF1 gene is essentially unmethylated and that its methylation pattern does not change with the floral phenotype whereas expression is dramatically different, ruling out a direct implication of DNA methylation in the regulation of this gene. Also, we find that both the gypsy element inserted within an intron of the EgDEF1 gene and the copia element located upstream from the promoter are heavily methylated and show little or no expression. Interestingly, we identify a shorter, alternative transcript produced by EgDEF1 and characterize its accumulation with respect to its full-length counterpart. We demonstrate that, depending on the floral phenotype, the respective proportions of these two transcripts change differently during inflorescence development. We discuss the possible phenotypical consequences of this alternative splicing and the new questions it raises in the search for the molecular mechanisms underlying the mantled phenotype in the oil palm.
    Matched MeSH terms: Molecular Sequence Data
  8. The complete mitogenome of the red claw crayfish Cherax quadricarinatus (Von Martens, 1868) (Crustacea: Decapoda: Parastacidae)
    Gan HM, Tan MH, Austin CM
    Mitochondrial DNA A DNA Mapp Seq Anal, 2016;27(1):385-6.
    PMID: 24617485 DOI: 10.3109/19401736.2014.895997
    The commercial freshwater crayfish Cherax quadricarinatus complete mitochondrial genome was recovered from partial genome sequencing using the MiSeq Personal Sequencer. The mitogenome has 15,869 base pairs consisting of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a non-coding AT-rich region. The base composition of C. quadricarinatus is 32.16% for T, 23.39% for C, 33.26% for A, and 11.19% for G, with an AT bias of 65.42%.
    Matched MeSH terms: Molecular Sequence Data
  9. Fulltext Characterization of affinity-purified isoforms of Acinetobacter calcoaceticus Y1 glutathione transferases
    Chee CS, Tan IK, Alias Z
    ScientificWorldJournal, 2014;2014:750317.
    PMID: 24892084 DOI: 10.1155/2014/750317
    Glutathione transferases (GST) were purified from locally isolated bacteria, Acinetobacter calcoaceticus Y1, by glutathione-affinity chromatography and anion exchange, and their substrate specificities were investigated. SDS-polyacrylamide gel electrophoresis revealed that the purified GST resolved into a single band with a molecular weight (MW) of 23 kDa. 2-dimensional (2-D) gel electrophoresis showed the presence of two isoforms, GST1 (pI 4.5) and GST2 (pI 6.2) with identical MW. GST1 was reactive towards ethacrynic acid, hydrogen peroxide, 1-chloro-2,4-dinitrobenzene, and trans,trans-hepta-2,4-dienal while GST2 was active towards all substrates except hydrogen peroxide. This demonstrated that GST1 possessed peroxidase activity which was absent in GST2. This study also showed that only GST2 was able to conjugate GSH to isoproturon, a herbicide. GST1 and GST2 were suggested to be similar to F0KLY9 (putative glutathione S-transferase) and F0KKB0 (glutathione S-transferase III) of Acinetobacter calcoaceticus strain PHEA-2, respectively.
    Matched MeSH terms: Molecular Sequence Data
  10. Structural and functional analysis of a novel psychrophilic β-mannanase from Glaciozyma antarctica PI12
    Parvizpour S, Razmara J, Ramli AN, Md Illias R, Shamsir MS
    J Comput Aided Mol Des, 2014 Jun;28(6):685-98.
    PMID: 24849507 DOI: 10.1007/s10822-014-9751-1
    The structure of a novel psychrophilic β-mannanase enzyme from Glaciozyma antarctica PI12 yeast has been modelled and analysed in detail. To our knowledge, this is the first attempt to model a psychrophilic β-mannanase from yeast. To this end, a 3D structure of the enzyme was first predicted using a threading method because of the low sequence identity (<30%) using MODELLER9v12 and simulated using GROMACS at varying low temperatures for structure refinement. Comparisons with mesophilic and thermophilic mannanases revealed that the psychrophilic mannanase contains longer loops and shorter helices, increases in the number of aromatic and hydrophobic residues, reductions in the number of hydrogen bonds and salt bridges and numerous amino acid substitutions on the surface that increased the flexibility and its efficiency for catalytic reactions at low temperatures.
    Matched MeSH terms: Molecular Sequence Data
  11. Fulltext Genetic diversity, haplotypes and allele groups of Duffy binding protein (PkDBPαII) of Plasmodium knowlesi clinical isolates from Peninsular Malaysia
    Fong MY, Lau YL, Chang PY, Anthony CN
    Parasit Vectors, 2014;7:161.
    PMID: 24693997 DOI: 10.1186/1756-3305-7-161
    The monkey malaria parasite Plasmodium knowlesi is now recognized as the fifth species of Plasmodium that can cause human malaria. Like the region II of the Duffy binding protein of P. vivax (PvDBPII), the region II of the P. knowlesi Duffy binding protein (PkDBPαII) plays an essential role in the parasite's invasion into the host's erythrocyte. Numerous polymorphism studies have been carried out on PvDBPII, but none has been reported on PkDBPαII. In this study, the genetic diversity, haplotyes and allele groups of PkDBPαII of P. knowlesi clinical isolates from Peninsular Malaysia were investigated.
    Matched MeSH terms: Molecular Sequence Data
  12. Fulltext Molecular cloning and characterization of novel phytocystatin gene from turmeric, Curcuma longa
    Chan SN, Abu Bakar N, Mahmood M, Ho CL, Shaharuddin NA
    Biomed Res Int, 2014;2014:973790.
    PMID: 25853138 DOI: 10.1155/2014/973790
    Phytocystatin, a type of protease inhibitor (PI), plays major roles in plant defense mechanisms and has been reported to show antipathogenic properties and plant stress tolerance. Recombinant plant PIs are gaining popularity as potential candidates in engineering of crop protection and in synthesizing medicine. It is therefore crucial to identify PI from novel sources like Curcuma longa as it is more effective in combating against pathogens due to its novelty. In this study, a novel cDNA fragment encoding phytocystatin was isolated using degenerate PCR primers, designed from consensus regions of phytocystatin from other plant species. A full-length cDNA of the phytocystatin gene, designated CypCl, was acquired using 5'/3' rapid amplification of cDNA ends method and it has been deposited in NCBI database (accession number KF545954.1). It has a 687 bp long open reading frame (ORF) which encodes 228 amino acids. BLAST result indicated that CypCl is similar to cystatin protease inhibitor from Cucumis sativus with 74% max identity. Sequence analysis showed that CypCl contains most of the motifs found in a cystatin, including a G residue, LARFAV-, QxVxG sequence, PW dipeptide, and SNSL sequence at C-terminal extension. Phylogenetic studies also showed that CypCl is related to phytocystatin from Elaeis guineensis.
    Matched MeSH terms: Molecular Sequence Data
  13. Novel angiotensin I-converting enzyme inhibitory peptides derived from edible mushroom Agaricus bisporus (J.E. Lange) Imbach identified by LC-MS/MS
    Lau CC, Abdullah N, Shuib AS, Aminudin N
    Food Chem, 2014 Apr 1;148:396-401.
    PMID: 24262574 DOI: 10.1016/j.foodchem.2013.10.053
    Angiotensin I-converting enzyme (ACE) inhibitors derived from foods are valuable auxiliaries to agents such as captopril. Eight highly functional ACE inhibitory peptides from the mushroom, Agaricus bisporus, were identified by LC-MS/MS. Among these peptides, the most potent ACE inhibitory activity was exhibited by AHEPVK, RIGLF and PSSNK with IC₅₀ values of 63, 116 and 129 μM, respectively. These peptides exhibited high ACE inhibitory activity after gastrointestinal digestion. Lineweaver-Burk plots suggested that AHEPVK and RIGLF act as competitive inhibitors against ACE, whereas PSSNK acts as a non-competitive inhibitor. Mushrooms can be a good component of dietary supplement due to their readily available source and, in addition, they rarely cause food allergy. Compared to ACE inhibitory peptides isolated from other edible mushrooms, AHEPVK, RIGLF and PSSNK have lower IC₅₀ values. Therefore, these peptides may serve as an ideal ingredient in the production of antihypertensive supplements.
    Matched MeSH terms: Molecular Sequence Data
  14. Fulltext A novel Bruton's tyrosine kinase gene (BTK) invariant splice site mutation in a Malaysian family with X-linked agammaglobulinemia
    Chear CT, Gill HK, Ramly NH, Dhaliwal JS, Bujang N, Ripen AM, et al.
    Asian Pac J Allergy Immunol, 2013 Dec;31(4):320-4.
    PMID: 24383975 DOI: 10.12932/AP0304.31.4.2013
    X-linked agammaglobulinemia (XLA) is a rare genetic disorder caused by mutations in the Bruton's tyrosine kinase (BTK) gene. These mutations cause defects in early B cell development. A patient with no circulating B cells and low serum immunoglobulin isotypes was studied as were his mother and sister. Monocyte BTK protein expression was evaluated by flow cytometry. The mutation was determined using PCR and followed by sequencing. Flow cytometry showed the patient lacked BTK protein expression in his monocytes while the mother and sister had 62% and 40% of the monocytes showing BTK protein expressions respectively. The patient had a novel base substitution in the first nucleotide of intron 9 in the BTK gene, and the mutation was IVS9+1G
    Matched MeSH terms: Molecular Sequence Data
  15. Phylogeography and molecular diversity analysis of Jatropha curcas L. and the dispersal route revealed by RAPD, AFLP and nrDNA-ITS analysis
    Sudheer Pamidimarri DV, Reddy MP
    Mol Biol Rep, 2014 May;41(5):3225-34.
    PMID: 24469734 DOI: 10.1007/s11033-014-3185-7
    Jatropha curcas L. (Euphorbiaceae) has acquired a great importance as a renewable source of energy with a number of environmental benefits. Very few attempts were made to understand the extent of genetic diversity and its distribution. This study was aimed to study the diversity and deduce the phylogeography of Jatropha curcas L. which is said to be the most primitive species of the genus Jatropha. Here we studied the intraspecific genetic diversity of the species distributed in different parts of the globe. The study also focused to understand the molecular diversity at reported probable center of origin (Mexico), and to reveal the dispersal route to other regions based on random amplified polymorphic DNA, amplified fragment length polymorphism and nrDNA-ITS sequences data. The overall genetic diversity of J. curcas found in the present study was narrow. The highest genetic diversity was observed in the germplasm collected from Mexico and supports the earlier hypothesis based on morphological data and natural distribution, it is the center for origin of the species. Least genetic diversity found in the Indian germplasm and clustering results revealed that the species was introduced simultaneously by two distinct germplasm and subsequently distributed in different parts of India. The present molecular data further revealed that J. curcas might have spread from the center of the origin to Cape Verde, than to Spain, Portuguese to other neighboring countries and simultaneously to Africa. The molecular evidence supports the Burkill et al. (A dictionary of the economic products of the Malay Peninsula, Governments of Malaysia and Singapore by the Ministry of Agriculture and Co-operatives. Kuala Lumpur, Malaysia, 1966) view of Portuguese might have introduced the species to India. The clustering pattern suggests that the distribution was interfered by human activity.
    Matched MeSH terms: Molecular Sequence Data
  16. Fulltext A phylogenomic approach to bacterial subspecies classification: proof of concept in Mycobacterium abscessus
    Tan JL, Khang TF, Ngeow YF, Choo SW
    BMC Genomics, 2013;14:879.
    PMID: 24330254 DOI: 10.1186/1471-2164-14-879
    Mycobacterium abscessus is a rapidly growing mycobacterium that is often associated with human infections. The taxonomy of this species has undergone several revisions and is still being debated. In this study, we sequenced the genomes of 12 M. abscessus strains and used phylogenomic analysis to perform subspecies classification.
    Matched MeSH terms: Molecular Sequence Data
  17. Phylogeny and classification of Dickeya based on multilocus sequence analysis
    Marrero G, Schneider KL, Jenkins DM, Alvarez AM
    Int J Syst Evol Microbiol, 2013 Sep;63(Pt 9):3524-3539.
    PMID: 24003072 DOI: 10.1099/ijs.0.046490-0
    Bacterial heart rot of pineapple reported in Hawaii in 2003 and reoccurring in 2006 was caused by an undetermined species of Dickeya. Classification of the bacterial strains isolated from infected pineapple to one of the recognized Dickeya species and their phylogenetic relationships with Dickeya were determined by a multilocus sequence analysis (MLSA), based on the partial gene sequences of dnaA, dnaJ, dnaX, gyrB and recN. Individual and concatenated gene phylogenies revealed that the strains form a clade with reference Dickeya sp. isolated from pineapple in Malaysia and are closely related to D. zeae; however, previous DNA-DNA reassociation values suggest that these strains do not meet the genomic threshold for consideration in D. zeae, and require further taxonomic analysis. An analysis of the markers used in this MLSA determined that recN was the best overall marker for resolution of species within Dickeya. Differential intraspecies resolution was observed with the other markers, suggesting that marker selection is important for defining relationships within a clade. Phylogenies produced with gene sequences from the sequenced genomes of strains D. dadantii Ech586, D. dadantii Ech703 and D. zeae Ech1591 did not place the sequenced strains with members of other well-characterized members of their respective species. The average nucleotide identity (ANI) and tetranucleotide frequencies determined for the sequenced strains corroborated the results of the MLSA that D. dadantii Ech586 and D. dadantii Ech703 should be reclassified as Dickeya zeae Ech586 and Dickeya paradisiaca Ech703, respectively, whereas D. zeae Ech1591 should be reclassified as Dickeya chrysanthemi Ech1591.
    Matched MeSH terms: Molecular Sequence Data
  18. A context evaluation approach for structural comparison of proteins using cross entropy over n-gram modelling
    Razmara J, Deris SB, Parvizpour S
    Comput Biol Med, 2013 Oct;43(10):1614-21.
    PMID: 24034753 DOI: 10.1016/j.compbiomed.2013.07.022
    The structural comparison of proteins is a vital step in structural biology that is used to predict and analyse a new unknown protein function. Although a number of different techniques have been explored, the study to develop new alternative methods is still an active research area. The present paper introduces a text modelling-based technique for the structural comparison of proteins. The method models the secondary and tertiary structure of proteins in two linear sequences and then applies them to the comparison of two structures. The technique used for pairwise comparison of the sequences has been adopted from computational linguistics and its well-known techniques for analysing and quantifying textual sequences. To this end, an n-gram modelling technique is used to capture regularities between sequences, and then, the cross-entropy concept is employed to measure their similarities. Several experiments are conducted to evaluate the performance of the method and compare it with other commonly used programs. The assessments for information retrieval evaluation demonstrate that the technique has a high running speed, which is similar to other linear encoding methods, such as 3D-BLAST, SARST, and TS-AMIR, whereas its accuracy is comparable to CE and TM-align, which are high accuracy comparison tools. Accordingly, the results demonstrate that the algorithm has high efficiency compared with other state-of-the-art methods.
    Matched MeSH terms: Molecular Sequence Data
  19. Fulltext Oil palm genome sequence reveals divergence of interfertile species in Old and New worlds
    Singh R, Ong-Abdullah M, Low ET, Manaf MA, Rosli R, Nookiah R, et al.
    Nature, 2013 Aug 15;500(7462):335-9.
    PMID: 23883927 DOI: 10.1038/nature12309
    Oil palm is the most productive oil-bearing crop. Although it is planted on only 5% of the total world vegetable oil acreage, palm oil accounts for 33% of vegetable oil and 45% of edible oil worldwide, but increased cultivation competes with dwindling rainforest reserves. We report the 1.8-gigabase (Gb) genome sequence of the African oil palm Elaeis guineensis, the predominant source of worldwide oil production. A total of 1.535 Gb of assembled sequence and transcriptome data from 30 tissue types were used to predict at least 34,802 genes, including oil biosynthesis genes and homologues of WRINKLED1 (WRI1), and other transcriptional regulators, which are highly expressed in the kernel. We also report the draft sequence of the South American oil palm Elaeis oleifera, which has the same number of chromosomes (2n = 32) and produces fertile interspecific hybrids with E. guineensis but seems to have diverged in the New World. Segmental duplications of chromosome arms define the palaeotetraploid origin of palm trees. The oil palm sequence enables the discovery of genes for important traits as well as somaclonal epigenetic alterations that restrict the use of clones in commercial plantings, and should therefore help to achieve sustainability for biofuels and edible oils, reducing the rainforest footprint of this tropical plantation crop.
    Matched MeSH terms: Molecular Sequence Data
  20. Novel complex re-arrangement of ARG1 commonly shared by unrelated patients with hyperargininemia
    Mohseni J, Boon Hock C, Abdul Razak C, Othman SN, Hayati F, Peitee WO, et al.
    Gene, 2014 Jan 1;533(1):240-5.
    PMID: 24103480 DOI: 10.1016/j.gene.2013.09.081
    Hyperargininemia is a very rare progressive neurometabolic disorder caused by deficiency of hepatic cytosolic arginase I, resulting from mutations in the ARG1 gene. Until now, some mutations were reported worldwide and none of them were of Southeast Asian origins. Furthermore, most reported mutations were point mutations and a few others deletions or insertions.
    Matched MeSH terms: Molecular Sequence Data
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