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Fulltext The first Malay database toward the ethnic-specific target molecular variation

Halim-Fikri H, Etemad A, Abdul Latif AZ, Merican AF, Baig AA, Annuar AA, et al.

BMC Res Notes, 2015;8:176.
PMID: 25925844 DOI: 10.1186/s13104-015-1123-y

The Malaysian Node of the Human Variome Project (MyHVP) is one of the eighteen official Human Variome Project (HVP) country-specific nodes. Since its inception in 9(th) October 2010, MyHVP has attracted the significant number of Malaysian clinicians and researchers to participate and contribute their data to this project. MyHVP also act as the center of coordination for genotypic and phenotypic variation studies of the Malaysian population. A specialized database was developed to store and manage the data based on genetic variations which also associated with health and disease of Malaysian ethnic groups. This ethnic-specific database is called the Malaysian Node of the Human Variome Project database (MyHVPDb).

Matched MeSH terms: Ethnic Groups/genetics*
Fulltext Molecular and morphological analyses reveal phylogenetic relationships of stingrays focusing on the family Dasyatidae (Myliobatiformes)

Lim KC, Lim PE, Chong VC, Loh KH

PLoS One, 2015;10(4):e0120518.
PMID: 25867639 DOI: 10.1371/journal.pone.0120518

Elucidating the phylogenetic relationships of the current but problematic Dasyatidae (Order Myliobatiformes) was the first priority of the current study. Here, we studied three molecular gene markers of 43 species (COI gene), 33 species (ND2 gene) and 34 species (RAG1 gene) of stingrays to draft out the phylogenetic tree of the order. Nine character states were identified and used to confirm the molecularly constructed phylogenetic trees. Eight or more clades (at different hierarchical level) were identified for COI, ND2 and RAG1 genes in the Myliobatiformes including four clades containing members of the present Dasyatidae, thus rendering the latter non-monophyletic. The uncorrected p-distance between these four 'Dasytidae' clades when compared to the distance between formally known families confirmed that these four clades should be elevated to four separate families. We suggest a revision of the present classification, retaining the Dasyatidae (Dasyatis and Taeniurops species) but adding three new families namely, Neotrygonidae (Neotrygon and Taeniura species), Himanturidae (Himantura species) and Pastinachidae (Pastinachus species). Our result indicated the need to further review the classification of Dasyatis microps. By resolving the non-monophyletic problem, the suite of nine character states enables the natural classification of the Myliobatiformes into at least thirteen families based on morphology.

Matched MeSH terms: Skates (Fish)/genetics
Molecular characterization of Nipah virus, a newly emergent paramyxovirus

Harcourt BH, Tamin A, Ksiazek TG, Rollin PE, Anderson LJ, Bellini WJ, et al.

Virology, 2000 Jun 5;271(2):334-49.
PMID: 10860887

Recently, a new paramyxovirus, now known as Nipah virus (NV), emerged in Malaysia and Singapore, causing fatal encephalitis in humans and a respiratory syndrome in pigs. Initial studies had indicated that NV is antigenically and genetically related to Hendra virus (HV). We generated the sequences of the N, P/C/V, M, F, and G genes of NV and compared these sequences with those of HV and other members of the family Paramyxoviridae. The intergenic regions of NV were identical to those of HV, and the gene start and stop sequences of NV were nearly identical to those of HV. The open reading frames (ORFs) for the V and C proteins within the P gene were found in NV, but the ORF encoding a potential short basic protein found in the P gene of HV was not conserved in NV. The N, P, C, V, M, F, and G ORFs in NV have nucleotide homologies ranging from 88% to 70% and predicted amino acid homologies ranging from 92% to 67% in comparison with HV. The predicted fusion cleavage sequence of the F protein of NV had a single amino acid substitution (K to R) in comparison with HV. Phylogenetic analysis demonstrated that although HV and NV are closely related, they are clearly distinct from any of the established genera within the Paramyxoviridae and should be considered a new genus.

Matched MeSH terms: Glycoproteins/genetics; Nucleoproteins/genetics; Phosphoproteins/genetics; Viral Fusion Proteins/genetics; Viral Matrix Proteins/genetics; Viral Proteins/genetics; Paramyxovirinae/genetics*
Fulltext Autosomal dominant thrombocytopenia with microthrombocytes: a family study

Jackson N, Mohammad S, Zainal N, Jamaluddin N, Hishamuddin M

Med J Malaysia, 1995 Dec;50(4):421-4.
PMID: 8668069

A family demonstrating autosomal dominant thrombocytopenia is described. A 28-year-old Malay housewife was found to have a platelet count of 40 x 10(9)/l with a low mean platelet volume (6.8 fl) while being investigated prior to ovarian cystectomy. The bone marrow was consistent with immune thrombocytopenia but she failed to respond to appropriate therapy. Five siblings, one parent and one nephew have easy bruising and platelet counts of 39-82 x 10(9)/l. Platelet aggregation studies excluded a major functional defect. Survival of homologous platelets in the circulation was normal. Familial thrombocytopenias are rare but important to differentiate from the common acquired thrombocytopenias in order to spare the patient unnecessary treatments.

Matched MeSH terms: Thrombocytopenia/genetics*
Fulltext Transferable antibiotic resistance in clinical isolates of Enterobacteriaceae in Malaysia

Khor SY, Jegathesan M

Med J Malaysia, 1983 Mar;38(1):19-22.
PMID: 6633328

Enterobacteriaceae isolated from clinical sources were examined for antibiotic resistance and the ability to transfer resistance to Escherichia coli. Twenty-nine out of 80 strains tested transferred part or all oftheir resistance genes. The strains carrying R plasmids included the genera Escherichia, Klebsiella, Salmonella, Enterobacter, Proteus, Providencia and Citrobacter. These results indicate that R plasmids possibly play a major role in the emergence of antibiotic resistance among clinical isolates of Enterobacteriaceae.

Matched MeSH terms: Enterobacteriaceae/genetics*
Fulltext Acrodermatitis continua of Hallopeau--a report of a case

Ismail R, Chan SP

Med J Malaysia, 1983 Sep;38(3):191-3.
PMID: 6672560
Matched MeSH terms: Acrodermatitis/genetics
Karyotypes of Hapalomys and Pithecheir (rodentia: Muridae) from peninsular Malaysia

Yong HS, Dhaliwal SS, Lim BL

Cytologia (Tokyo), 1982 Dec;47(3-4):535-8.
PMID: 7166052
Matched MeSH terms: Rodentia/genetics*
Chromosomal Locations of a Non-LTR Retrotransposon, Menolird18, in Cucumis melo and Cucumis sativus, and Its Implication on Genome Evolution of Cucumis Species

Setiawan AB, Teo CH, Kikuchi S, Sassa H, Kato K, Koba T

Cytogenet Genome Res, 2020;160(9):554-564.
PMID: 33171461 DOI: 10.1159/000511119

Mobile elements are major regulators of genome evolution through their effects on genome size and chromosome structure in higher organisms. Non-long terminal repeat (non-LTR) retrotransposons, one of the subclasses of transposons, are specifically inserted into repetitive DNA sequences. While studies on the insertion of non-LTR retrotransposons into ribosomal RNA genes and other repetitive DNA sequences have been reported in the animal kingdom, studies in the plant kingdom are limited. Here, using FISH, we confirmed that Menolird18, a member of LINE (long interspersed nuclear element) in non-LTR retrotransposons and found in Cucumis melo, was inserted into ITS and ETS (internal and external transcribed spacers) regions of 18S rDNA in melon and cucumber. Beside the 18S rDNA regions, Menolird18 was also detected in all centromeric regions of melon, while it was located at pericentromeric and sub-telomeric regions in cucumber. The fact that FISH signals of Menolird18 were found in centromeric and rDNA regions of mitotic chromosomes suggests that Menolird18 is a rDNA and centromere-specific non-LTR retrotransposon in melon. Our findings are the first report on a non-LTR retrotransposon that is highly conserved in 2 different plant species, melon and cucumber. The clear distinction of chromosomal localization of Menolird18 in melon and cucumber implies that it might have been involved in the evolutionary processes of the melon (C. melo) and cucumber (C. sativus) genomes.

Matched MeSH terms: Centromere/genetics; RNA, Ribosomal, 18S/genetics; Cucumis sativus/genetics*; DNA, Plant/genetics; RNA, Plant/genetics; Cucumis melo/genetics*; Chromosomes, Plant/genetics
Differential abundance and core members of the bacterial community associated with wild male Zeugodacus cucurbitae fruit flies (Insecta: Tephritidae) from three geographical regions of Southeast Asia

Yong HS, Song SL, Eamsobhana P, Pasartvit A, Lim PE

Mol Biol Rep, 2019 Aug;46(4):3765-3776.
PMID: 31012029 DOI: 10.1007/s11033-019-04818-3

Zeugodacus cucurbitae (Coquillet) is one of the most significant and widespread tephritid pest species of agricultural crops. This study reports the bacterial communities associated with Z. cucurbitae from three geographical regions in Southeast Asia (Thailand, Peninsular Malaysia, and Sarawak). The bacterial microbiota were investigated by targeted 16S rRNA gene (V3-V4 region) sequencing using the Illumina Mi-Seq platform. At 97% similarity and filtering at 0.001%, there were seven bacterial phyla and unassigned bacteria, comprising 11 classes, 23 orders, 39 families and 67 genera. The bacterial diversity and richness varied within and among the samples from the three geographical regions. Five phyla were detected for the Sarawak sample, and six each for the Thailand and Peninsular Malaysia samples. Four phyla-Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria-were represented in all the fruit fly specimens, forming the core members of the bacterial community. Proteobacteria was the predominant phylum, followed by Bacteroidetes, Firmicutes, and Actinobacteria. Fifty-three genera were represented in the Thailand sample, 56 in the Peninsular Malaysia sample, and 55 in the Sarawak sample. Forty-two genera were present in all the three geographical regions. The predominant core members were order Enterobacteriales (Proeteobacteria), and family Enterobacteriaceae (Enterobacteriales). Klebsiella (Enterobacteriaceae) was the predominant genus and K. oxytoca the predominant species with all specimens having > 10% relative abundance. The results indicate the presence of a great diversity as well as core members of the bacterial community associated with different populations of Z. cucurbitae.

Matched MeSH terms: Firmicutes/genetics; Klebsiella/genetics; RNA, Ribosomal, 16S/genetics*; Proteobacteria/genetics; Actinobacteria/genetics; Bacteroidetes/genetics; Microbiota/genetics*
Transcriptional analysis of nitrogen fixation in Paenibacillus durus during growth in nitrogen-enriched medium

Halim MA, Choo QC, Ghazali AHA, Wajidi MFF, Najimudin N

Lett Appl Microbiol, 2021 May;72(5):610-618.
PMID: 33525052 DOI: 10.1111/lam.13455

Paenibacillus durus strain ATCC 35681T is a Gram-positive diazotroph that displayed capability of fixing nitrogen even in the presence of nitrate or ammonium. However, the nitrogen fixation activity was detected only at day 1 of growth when cultured in liquid nitrogen-enriched medium. The transcripts of all the nifH homologues were present throughout the 9-day study. When grown in nitrogen-depleted medium, nitrogenase activities occurred from day 1 until day 6 and the nifH transcripts were also present during the course of the study albeit at different levels. In both studies, the absence of nitrogen fixation activity regardless of the presence of the nifH transcripts raised the possibility of a post-transcriptional or post-translational regulation of the system. A putative SigA box sequence was found upstream of the transcription start site of nifB1, the first gene in the major nitrogen fixation cluster. The upstream region of nifB2 showed a promoter recognizable by SigE, a sigma factor normally involved in sporulation.

Matched MeSH terms: Bacterial Proteins/genetics; Nitrogen Fixation/genetics*; Oxidoreductases/genetics*; Promoter Regions, Genetic/genetics; Sigma Factor/genetics; Transcription, Genetic/genetics*; Paenibacillus/genetics*
Contribution of TIMP4 rs3755724 polymorphism to susceptibility to focal epilepsy in Malaysian Chinese

Haerian BS, Sha'ari HM, Fong CY, Tan HJ, Wong SW, Ong LC, et al.

J Neuroimmunol, 2015 Jan 15;278:137-43.
PMID: 25595263 DOI: 10.1016/j.jneuroim.2014.12.016

Neuroinflammation can damage the brain and plays a critical role in the pathophysiology of epilepsy. Tissue inhibitor of metalloproteinase 4 (TIMP4) is an inflammation-induced apoptosis and matrix turnover factor involved in several neuronal disorders and inflammatory diseases. Evidence has shown linkage disequilibrium between rs3755724 (-55C/T) of this gene with synapsin 2 (SYN2) rs3773364 and peroxisome proliferator-activated G receptor (PPARG) rs2920502 loci, which contribute to epilepsy in Caucasians. The aim of this study was to examine the association of these loci alone or their haplotypes with the risk of epilepsy in the Malaysian population. Genomic DNA of 1241 Malaysian Chinese, Indian, and Malay subjects (670 patients with epilepsy and 571 healthy individuals) was genotyped for the candidate loci by using the Sequenom MassArray method. Allele and genotype association of rs3755724 with susceptibility to epilepsy was significant in the Malaysian Chinese with focal epilepsy under codominant and dominant models (C vs. T: 1.5 (1.1-2.0), p=0.02; CT vs. TT: 1.8 (1.2-2.8), p=0.007 and 1.8 (1.2-2.7), p=0.006, respectively). The T allele and the TT genotype were more common in patients than in controls. No significant association was found between rs2920502 and rs3773364-rs3755724-rs2920502 haplotypes for susceptibility to epilepsy in each ethnicity. This study provides evidence that the promoter TIMP4 rs3755724 is a new focal epilepsy susceptibility variant that is plausibly involved in inflammation-induced seizures in Malaysian Chinese.

Matched MeSH terms: Epilepsies, Partial/genetics*; Synapsins/genetics; Tissue Inhibitor of Metalloproteinases/genetics*; Genetic Predisposition to Disease/genetics*; Polymorphism, Single Nucleotide/genetics*; Asian Continental Ancestry Group/genetics; PPAR gamma/genetics
Rapid shifts in methanotrophic bacterial communities mitigate methane emissions from a tropical hydropower reservoir and its downstream river

Reis PCJ, Ruiz-González C, Crevecoeur S, Soued C, Prairie YT

Sci Total Environ, 2020 Dec 15;748:141374.
PMID: 32823225 DOI: 10.1016/j.scitotenv.2020.141374

Methane-oxidizing bacteria (MOB) present in the water column mitigate methane (CH4) emissions from hydropower complexes to the atmosphere. By creating a discontinuity in rivers, dams cause large environmental variations, including in CH4 and oxygen concentrations, between upstream, reservoir, and downstream segments. Although highest freshwater methanotrophic activity is often detected at low oxygen concentrations, CH4 oxidation in well-oxygenated downstream rivers below dams has also been reported. Here we combined DNA and RNA high-throughput sequencing with microscopic enumeration (by CARD-FISH) and biogeochemical data to investigate the abundance, composition, and potential activity of MOB taxa from upstream to downstream waters in the tropical hydropower complex Batang Ai (Malaysia). High relative abundance of MOB (up to 61% in 16S rRNA sequences and 19% in cell counts) and enrichment of stable isotopic signatures of CH4 (up to 0‰) were detected in the hypoxic hypolimnion of the reservoir and in the outflowing downstream river. MOB community shifts along the river-reservoir system reflected environmental sorting of taxa and an interrupted hydrologic connectivity in which downstream MOB communities resembled reservoir's hypolimnetic communities but differed from upstream and surface reservoir communities. In downstream waters, CH4 oxidation was accompanied by fast cell growth of particular MOB taxa. Our results suggest that rapid shifts in active MOB communities allow the mitigation of CH4 emissions from different zones of hydropower complexes, including in quickly re-oxygenated rivers downstream of dams.

Matched MeSH terms: RNA, Ribosomal, 16S/genetics
Gene expression changes associated with malignant transformation of oral potentially malignant disorders

Sathasivam HP, Casement J, Bates T, Sloan P, Thomson P, Robinson M, et al.

J Oral Pathol Med, 2021 Jan;50(1):60-67.
PMID: 32740996 DOI: 10.1111/jop.13090

BACKGROUND: A large number of oral squamous cell carcinomas (OSCCs) are believed to be preceded by oral potentially malignant disorders (OPMD) that have an increased likelihood of malignant transformation compared to clinically normal mucosa. This study was performed to identify differentially expressed genes between OPMDs that underwent malignant transformation (MT) and those that did not, termed "non-transforming" (NT) cases.
METHODS: Total RNA was extracted from formalin-fixed paraffin-embedded tissue biopsies of 20 OPMD cases with known clinical outcomes (10 MT vs. 10 NT). Samples were assessed for quantity, quality and integrity of RNA prior to sequencing. Analysis for differential gene expression between MT and NT was performed using statistical packages in R. Genes were considered to be significantly differentially expressed if the False Discovery Rate corrected P-value was 1.90). Analysis of RNA-Sequencing outputs revealed 41 genes (34 protein-coding; 7 non-coding) that were significantly differentially expressed between MT and NT cases. The log2 fold change for the statistically significant differentially expressed genes ranged from -2.63 to 2.48, with 23 protein-coding genes being downregulated and 11 protein-coding genes being upregulated in MT cases compared to NT cases.
CONCLUSION: Several candidate genes that may play a role in malignant transformation of OPMD have been identified. Experiments to validate these candidates are underway. It is anticipated that this work will contribute to better understanding of the etiopathogenesis of OPMD and development of novel biomarkers.

Matched MeSH terms: Cell Transformation, Neoplastic/genetics
CYP2C19 Genotype-Guided Antiplatelet Therapy Among Asian Patients with Ischaemic Stroke

Kow CS, Zaihan AF, Hasan SS

Clin Drug Investig, 2021 01;41(1):115-116.
PMID: 33237558 DOI: 10.1007/s40261-020-00985-5
Matched MeSH terms: Cytochrome P-450 CYP2C19/genetics
Unravelling the diagnostic and therapeutic potentialities of a novel RNA aptamer isolated against human pituitary tumour transforming gene 1 (PTTG1) protein

Prabu SS, Ch'ng ES, Woon PY, Chen JH, Tang TH, Citartan M

Anal Chim Acta, 2020 Nov 22;1138:181-190.
PMID: 33161980 DOI: 10.1016/j.aca.2020.09.038

Human Pituitary Tumour Transforming Gene 1 (PTTG1) is an oncoprotein involved in maintaining chromosome stability and acts as a biomarker for a panel of cancers. In this study, we endeavoured to generate an RNA aptamer against PTTG1. The RNA aptamer, SECURA-3 has an estimated equilibrium dissociation constant of 16.41 ± 6.4 nM. The aptamer was successfully harnessed in several diagnostic platforms including ELASA, aptamer-based dot blot and aptamer-based western blot. SECURA-3 was also unveiled as a potential probe that could replace its counterpart antibody in the histostaining-based detection of PTTG1 in HeLa and MCF-7 formalin-fixed paraffin-embedded cell blocks. In the aspect of therapeutics, SECURA-3 RNA aptamer demonstrates an antagonistic effect by antagonizing the interaction between PTTG1 and CXCR2, as revealed in the in vitro competitive nitrocellulose filter binding assay and dual-luciferase reporter assay in HeLa cells. As the first anti-PTTG1 aptamer, SECURA-3 RNA aptamer has immense diagnostic and therapeutic properties.

Matched MeSH terms: Securin/genetics*
Differentiated sap (4-6) gene expression of Candida albicans isolates from HIV-positive patients with oral candidiasis and commensals in healthy individuals

Meylani V, Sembiring L, Fudholi A, Wibawa T

Microb Pathog, 2021 Sep;158:105075.
PMID: 34224845 DOI: 10.1016/j.micpath.2021.105075

Gene expression of SAP 4-6 based on the detection of mRNA was observed in Candida albicans isolates from HIV-positive patients with oral candidiasis and commensal from healthy individuals. The species of C. albicans strains were selectively isolated from both sources using CHROMagar Chromogenic Media. The obtained isolates were then induced to express SAP 4-6 using SAP 4-6 gene inducer media. Analysis of gene expression was performed on a molecular basis using the RT-PCR method. Molecular analysis of gene expression showed that the isolates CH3 from HIV-positive patients with oral candidiasis could express SAP 4-6 gene, while commensal isolates from healthy people could not. Based on the results of this study, it could be concluded that, in terms of molecular detection, only isolates from HIV-positive patients (CH3) could express their SAP 4-6 gene.

Matched MeSH terms: Candida albicans/genetics
Fulltext Noonan syndrome in diverse populations

Kruszka P, Porras AR, Addissie YA, Moresco A, Medrano S, Mok GTK, et al.

Am J Med Genet A, 2017 Sep;173(9):2323-2334.
PMID: 28748642 DOI: 10.1002/ajmg.a.38362

Noonan syndrome (NS) is a common genetic syndrome associated with gain of function variants in genes in the Ras/MAPK pathway. The phenotype of NS has been well characterized in populations of European descent with less attention given to other groups. In this study, individuals from diverse populations with NS were evaluated clinically and by facial analysis technology. Clinical data and images from 125 individuals with NS were obtained from 20 countries with an average age of 8 years and female composition of 46%. Individuals were grouped into categories of African descent (African), Asian, Latin American, and additional/other. Across these different population groups, NS was phenotypically similar with only 2 of 21 clinical elements showing a statistically significant difference. The most common clinical characteristics found in all population groups included widely spaced eyes and low-set ears in 80% or greater of participants, short stature in more than 70%, and pulmonary stenosis in roughly half of study individuals. Using facial analysis technology, we compared 161 Caucasian, African, Asian, and Latin American individuals with NS with 161 gender and age matched controls and found that sensitivity was equal to or greater than 94% for all groups, and specificity was equal to or greater than 90%. In summary, we present consistent clinical findings from global populations with NS and additionally demonstrate how facial analysis technology can support clinicians in making accurate NS diagnoses. This work will assist in earlier detection and in increasing recognition of NS throughout the world.

Matched MeSH terms: Genetics, Population*; Noonan Syndrome/genetics*; ras Proteins/genetics; Mitogen-Activated Protein Kinase Kinases/genetics; African Continental Ancestry Group/genetics; European Continental Ancestry Group/genetics
Genetic architecture of Al3+ toxicity tolerance in rice F2:3 populations determined through QTL mapping

Jahan N, Javed MA, Khan A, Manan FA, Tabassum B

Ecotoxicology, 2021 Jul;30(5):794-805.
PMID: 33871748 DOI: 10.1007/s10646-021-02413-6

Aluminum (Al3+) toxicity is one of the factors limiting crop production in acidic soils. Identifying quantitative trait loci (QTLs)/genes for tolerance to Al3+ toxicity at seed germination can aid the development of new tolerant cultivars. The segregating population derived from Pak Basmati (Indica) × Pokkali (Indica) was used for mapping QTLs linked with tolerance to Al3+ toxicity ranging from 0 to 20 mM at pH 4 ± 0.2 at germination. The favorable alleles for all new QTLs were analyzed based on germination traits, i.e., final germination percentage (FG%), germination energy (GE), germination speed (GS), germination index (GI), mean germination time (MGT), germination value (GV), germination velocity (GVe), peak value of germination (GPV), and germination capacity (GC), and growth traits, such as root length (RL), shoot length (SL), total dry biomass (TDB) and germination vigor index (GVI). The phenotypic evolution showed transgressive variations. For genome-wide mapping, 90 polymorphic SSRs with 4 gene-specific markers and Win QTL Cart were used for QTL analysis. In all, 35 QTLs for germination and 11 QTLs for seedling growth were detected in distinct chromosomal regions by composite interval mapping (CIM), and multiple interval mapping (MIM) confirmed the pleiotropy at region RM128 on chromosome 1. Based on our genetic mapping studies, the genes/QTLs underlying tolerance to Al3+ toxicity could differ for both the germination and seedling stages in segregated populations. The QTLs identified in this study could be a source of new alleles for improving tolerance to Al3+ toxicity in rice.

Matched MeSH terms: Seedlings/genetics
Regulation of Glycine Cleavage and Detoxification by a Highly Conserved Glycine Riboswitch in Burkholderia spp

Munyati-Othman N, Appasamy SD, Damiri N, Emrizal R, Alipiah NM, Ramlan EI, et al.

Curr Microbiol, 2021 Aug;78(8):2943-2955.
PMID: 34076709 DOI: 10.1007/s00284-021-02550-5

The glycine riboswitch is a known regulatory element that is unique in having two aptamers that are joined by a linker region. In this study, we investigated a glycine riboswitch located in the 5' untranslated region of a glycine cleavage system homolog (gcvTHP) in Burkholderia spp. Structure prediction using the sequence generated a model with a glycine binding pocket composed of base-triple interactions (G62-A64-A86 and G65-U84-C85) that are supported by A/G minor interactions (A17-C60-G88 and G16-C61-G87, respectively) and two ribose-zipper motifs (C11-G12 interacting with A248-A247 and C153-U154 interacting with A79-A78) which had not been previously reported. The capacity of the riboswitch to bind to glycine was experimentally validated by native gel assays and the crucial role of interactions that make up the glycine binding pocket were proven by mutations of A17U and G16C which resulted in conformational differences that may lead to dysfunction. Using glycine supplemented minimal media, we were able to prove that the expression of the gcvTHP genes found downstream of the riboswitch responded to the glycine concentrations introduced thus confirming the role of this highly conserved Burkholderia riboswitch and its associated genes as a putative glycine detoxification system in Burkholderia spp.

Matched MeSH terms: Glycine/genetics
Fulltext The Crown Pearl: a draft genome assembly of the European freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758)

Gomes-Dos-Santos A, Lopes-Lima M, Machado AM, Marcos Ramos A, Usié A, Bolotov IN, et al.

DNA Res, 2021 May 02;28(2).
PMID: 33755103 DOI: 10.1093/dnares/dsab002

Since historical times, the inherent human fascination with pearls turned the freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758) into a highly valuable cultural and economic resource. Although pearl harvesting in M. margaritifera is nowadays residual, other human threats have aggravated the species conservation status, especially in Europe. This mussel presents a myriad of rare biological features, e.g. high longevity coupled with low senescence and Doubly Uniparental Inheritance of mitochondrial DNA, for which the underlying molecular mechanisms are poorly known. Here, the first draft genome assembly of M. margaritifera was produced using a combination of Illumina Paired-end and Mate-pair approaches. The genome assembly was 2.4 Gb long, possessing 105,185 scaffolds and a scaffold N50 length of 288,726 bp. The ab initio gene prediction allowed the identification of 35,119 protein-coding genes. This genome represents an essential resource for studying this species' unique biological and evolutionary features and ultimately will help to develop new tools to promote its conservation.

Matched MeSH terms: Bivalvia/genetics*

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