This study was carried out to determine the effects of hepatitis B virus genotypes, core promoter mutations (A1762G1764-->T1762A1764) as well as precore stop codon mutations (TGG-->TAG) on HBeAg expression and HBeAg/ anti-HBe status. Study was also performed on the effects of codon 15 variants (C1858/ T1858) on the predisposition of precore stop codon mutations (TGG-->TAG). A total of 77 sera samples were analyzed. Fifty one samples were successfully genotyped of which the predominant genotype was genotype B (29/ 51, 56.9 %), followed by genotype C (16/ 51, 31.4 %). Co-infections by genotypes B and C were observed in four samples (7.8 %). To a lesser degree, genotypes D and E (2.0 % each) were also observed. For core promoter mutations, the prevalence was 68.8 % (53/ 77) for A1762G1764 wild-type and 14.3 % (11/ 77) for T1762A1764 mutant while 9.1 % (7/ 77) was co-infected by both strains. The prevalence of codon 15 variants was found to be 42.9 % (33/ 77) for T1858 variant and 16.9 % (13/ 77) for C1858 variant. No TAG mutation was found. In our study, no associations were found between genotypes (B and C) and core promoter mutations as well as codon 15 variants. Also no correlation was observed between HBeAg/ anti-HBe status with genotypes (B and C) and core promoter mutations.
Here, we present the first complete mitochondrial genome of Malayan Gaur (Bos gaurus hubbacki) inferred using next-generation sequencing. The mitogenome is 16,367 bp in length with the structural organization of a typical bovine mitochondrial arrangement comprising 13 protein-coding genes, 21 tRNAs, and 2 rRNAs. No internal stop codon was found in the protein-coding genes. Phylogenetic tree analysis revealed that Malayan gaur is more closely related to Burmese banteng instead of gaur.
Angiostrongylus malaysiensis is a nematode parasite of various rat species. When first documented in Malaysia, it was referred to as A. cantonensis. Unlike A. cantonensis, the complete mitochondrial genome of A. malaysiensis has not been documented. We report here its complete mitogenome, its differentiation from A. cantonensis, and the phylogenetic relationships with its congeners and other Metastrongyloid taxa. The whole mitogenome of A. malaysiensis had a total length of 13,516bp, comprising 36 genes (12 PCGs, 2 rRNA and 22 tRNA genes) and a control region. It is longer than that of A. cantonensis (13,509bp). Its control region had a long poly T-stretch of 12bp which was not present in A. cantonensis. A. malaysiensis and A. cantonensis had identical start codon for the 12 PCGs, but four PCGs (atp6, cob, nad2, nad6) had different stop codon. The cloverleaf structure for the 22 tRNAs was similar in A. malaysiensis and A. cantonensis except the TΨC-arm was absent in trnV for A. malaysiensis but present in A. cantonensis. The Angiostrongylus genus was monophyletic, with A. malaysiensis and A. cantonensis forming a distinct lineage from that of A. costaricensis and A. vasorum. The genetic distance between A. malaysiensis and A. cantonensis was p=11.9% based on 12 PCGs, p=9.5% based on 2 rRNA genes, and p=11.6% based on 14 mt-genes. The mitogenome will prove useful for studies on phylogenetics and systematics of Angiostrongylus lungworms and other Metastrongyloid nematodes.
Familial multiple intestinal atresias is an autosomal recessive disease with or without combined immunodeficiency. In the last year, several reports have described mutations in the gene TTC7A as causal to the disease in different populations. However, exact correlation between different genotypes and various phenotypes are not clear. In this study, we report identification of novel compound heterozygous mutations in TTC7A gene in a Malay girl with familial multiple intestinal atresias and severe combined immunodeficiency (MIA-SCID) by whole exome sequencing. We found two mutations in TTC7A: one that destroyed a putative splicing acceptor at the junction of intron 17/exon 18 and one that introduced a stop codon that would truncate the last two amino acids of the encoded protein. Reviewing the recent reports on TTC7A mutations reveals correlation between the position and nature of the mutations with patient survival and clinical manifestations. Examination of public databases also suggests carrier status for healthy individuals, making a case for population screening on this gene, especially in populations with suspected frequent founder mutations.
The cavity-nesting honeybee Apis nuluensis inhabits only the highlands of Mount Kinabalu of Sabah, Borneo Island. The mitochondrial genome is a circular molecule of approximately 1.6 kb that includes 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and one AT-rich control region. The average AT content was 84.5%. The start codons ATC, ATG, and ATT were found in one, three, and nine genes, respectively, whereas the stop codon TAA was observed in all genes. The phylogenetic relationship, inferred using 13 PCGs, was consistent with that reported in previous studies that predicted a sister taxon relationship between A. nuluensis and A. cerana.
Infection by hepatitis B virus (HBV) is a major global health-care problem. HBV is an accepted factor in the elevated risks for liver disease such as cirrhosis and development of hepatocellular carcinoma. This problem is particularly prevalent in the Asia-Pacific region which includes Malaysia. During infection, the hepatitis B e antigen (HBeAg) is produced in the hosts. This antigen is an important serological marker for diagnosing chronic hepatitis B. Seroconversion to anti-body (anti-HBe) corresponds to the improvement of disease prognosis. However, certain mutations such as the core promoter dual mutations (A1762G1764→T1762A1764), the codon 15 variants (C1858/ T1858) and the precore stop codon mutations (TGG→TAG) can affect the HBeAg expression. This has diagnostic and clinical implications. Besides that, the HBV can be grouped into eight genotypes (A to H). Moreover, genotypic subtypes and recombinants have been observed as well. Studies have observed that these can differ in their affiliations with the mutations above as well as with disease prognosis.
Gymnothorax minor is a moray eel of the family Muraenidae found in the Western Pacific Ocean. We report here
its complete mitogenome as determined by Illumina next-generation sequencing and the phylogenetic relationship
with its congeners and other taxa of the family Muraenidae. The whole mitogenome of G. minor had a total length
of 16,574 bp, comprising 37 genes - 13 protein-coding genes (PCGs), two ribosomal ribonucleic acid (rRNA) and 22
transfer ribonucleic acid (tRNA) genes - and a control region. Excepting cox1 with GTG, the other 12 PCGs had ATG
start codon. Seven of its PCGs had incomplete stop codon - five (nad2; cox1; cox2; nad3 and nad4) with T and two
(atp6 and cox3) with TA. Molecular phylogeny based on 13 PCGs was concordant with 15 mitochondrial genes (13 PCGs
and 2 rRNA genes). The subfamily Muraeninae as well as the subfamily Uropterygiinae were monophyletic. However,
the genus Gymnothorax was paraphyletic, with G. minor forming a sister group with Rhinomuraena quaesita in the
lineage containing also G. kidako and G. formosus forming a sister group with Enchelynassa canina. The phylogenetic
relationship of the genus Gymnothorax and related taxa of the family Muraenidae, based on the mitochondrial cob
gene, was in general similar to that based on 15 mt-genes. The mitogenome is useful for future studies on phylogenetics
and systematics of eels of the family Muraenidae and other taxa of the order Anguilliformes.
The mitochondrial genome sequence of the purple mottled shore crab, Cyclograpsus granulosus, is documented (GenBank accession number: LN624373), which makes it the third for genera of the superfamily Grapsoidea. Cyclograpsus granulosus has a mitogenome of 16,300 bp 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 C. granulosus mitogenome is 36.15% for T, 19.54% for C, 33.14% for A and 11.17% for G, with an AT bias of 69.29%. The mitogenome gene order is atypical for the brachyuran crabs, but is identical to species of the genus Eriocheir from the same family.
The mitochondrial genome sequence of the porcellanid crab, Petrolisthes haswelli is provided, making it the second for the family Porcellanidae and the third for the superfamily Galatheoidea. Petrolisthes haswelli has a mitogenome of 15,348 bp 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 P. haswelli mitogenome is 35.66% for T, 18.65% for C, 34.35% for A and 11.34% for G, with an AT bias of 70.01%. The mitogenome gene order is identical to the mitogenome of Neopetrolisthes maculatus, the only other species of the family with a sequenced mitogenome.
The whole mitochondrial genome of the pest fruit fly Bactrocera arecae was obtained from next-generation sequencing of genomic DNA. It had a total length of 15,900 bp, consisting of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and a non-coding region (A + T-rich control region). The control region (952 bp) was flanked by rrnS and trnI genes. The start codons included 6 ATG, 3 ATT and 1 each of ATA, ATC, GTG and TCG. Eight TAA, two TAG, one incomplete TA and two incomplete T stop codons were represented in the protein-coding genes. The cloverleaf structure for trnS1 lacked the D-loop, and that of trnN and trnF lacked the TΨC-loop. Molecular phylogeny based on 13 protein-coding genes was concordant with 37 mitochondrial genes, with B. arecae having closest genetic affinity to B. tryoni. The subgenus Bactrocera of Dacini tribe and the Dacinae subfamily (Dacini and Ceratitidini tribes) were monophyletic. The whole mitogenome of B. arecae will serve as a useful dataset for studying the genetics, systematics and phylogenetic relationships of the many species of Bactrocera genus in particular, and tephritid fruit flies in general.
The interactions between transcription factors (TFs) and cis-acting regulatory elements (CREs) provide crucial information on the regulation of gene expression. The determination of TF-binding sites and CREs experimentally is costly and time intensive. An in silico identification and annotation of TFs, and the prediction of CREs from rice are made possible by the availability of whole genome sequence and transcriptome data. In this study, we tested the applicability of two algorithms developed for other model systems for the identification of biologically significant CREs of co-expressed genes from rice. CREs were identified from the DNA sequences located upstream from the transcription start sites, untranslated regions (UTRs), and introns, and downstream from the translational stop codons of co-expressed genes. The biologically significance of each CRE was determined by correlating their absence and presence in each gene with that gene's expression profile using a meta-database constructed from 50 rice microarray data sets. The reliability of these methods in the predictions of CREs and their corresponding TFs was supported by previous wet lab experimental data and a literature review. New CREs corresponding to abiotic stresses, biotic stresses, specific tissues, and developmental stages were identified from rice, revealing new pieces of information for future experimental testing. The effectiveness of some-but not all-CREs was found to be affected by copy number, position, and orientation. The corresponding TFs that were most likely correlated with each CRE were also identified. These findings not only contribute to the prioritization of candidates for further analysis, the information also contributes to the understanding of the gene regulatory network.
The EphA4 receptor tyrosine kinase is involved in numerous cell-signalling activities during embryonic development. EphA4 has the ability to bind to both types of ephrin ligands, the ephrinAs and ephrinBs. The C57BL/6J-Epha4rb-2J/GrsrJ strain, denoted Epha4(rb-2J/rb-2J), is a spontaneous mouse mutant that arose at The Jackson Laboratory. These mutants exhibited a synchronous hind limb locomotion defect or "hopping gait" phenotype, which is also characteristic of EphA4 null mice. Genetic complementation experiments suggested that Epha4(rb-2J) corresponds to an allele of EphA4, but details of the genomic defect in this mouse mutant are currently unavailable. We found a single base-pair deletion in exon 9 resulting in a frame shift mutation that subsequently resulted in a premature stop codon. Analysis of the predicted structure of the truncated protein suggests that both the kinase and sterile α motif (SAM) domains are absent. Definitive determination of genotype is needed for experimental studies of mice carrying the Epha4(rb-2J) allele, and we have also developed a method to ease detection of the mutation through RFLP. Eph-ephrin family members are reportedly expressed as numerous isoforms. Hence, delineation of the specific mutation in EphA4 in this strain is important for further functional studies, such as protein-protein interactions, immunostaining and gene compensatory studies, investigating the mechanism underlying the effects of altered function of Eph family of receptor tyrosine kinases on phenotype.
As most published studies on precore mutants have been carried out on isolates from patients with liver diseases, and it is unclear whether HBsAg carriers with viraemia in the absence of HBeAg are also generally infected by such mutants, it was decided to sequence the precore region in some HBV-DNA isolated from HBsAg-positive carriers. Precore sequences of HBV-DNA from 43 HBsAg carriers in Malaysia were studied. Three HBV subtypes were identified according to the nucleotide sequence of the precore region. Most of the carriers were found to be infected by the subtype adr. Mutations were detected in the precore regions. The most common conserved mutation was a silent mutation involving conversion from T to C (CCT to CCC) at position 1858 at codon 15 (proline). It was found that 4/43 (9.3%) had a mutation at the penultimate codon where TGG was changed to TAG. All 4 isolates with the TAG mutation had nt T at position 1858. Of the 4 carriers who were infected by these mutant viruses, 2 were coinfected with the wild type, 1 was infected only by a variant with the mutation at position 1896, while another was infected by a variant with mutations at positions 1896 and 1899. Three of the 4 were anti-HBe positive while 1 was HBeAg positive. Alanine aminotransaminase activities in all 4 carriers were normal. This study therefore demonstrated that variants with stop codons at the penultimate codon could be found in asymptomatic carriers in Malaysia.
The release of DNA into the cytoplasm upon damage to the nucleus or during viral infection triggers an interferon-mediated defense response, inflammation and cell death. In human cells cytoplasmic DNA is sensed by cyclic GMP-AMP Synthase (cGAS) and Absent In Melanoma 2 (AIM2). Here, we report the identification of a "natural knockout" model of cGAS. Comparative genomics of phylogenetically diverse mammalian species showed that cGAS and its interaction partner Stimulator of Interferon Genes (STING) have been inactivated by mutations in the Malayan pangolin whereas other mammals retained intact copies of these genes. The coding sequences of CGAS and STING1 are also disrupted by premature stop codons and frame-shift mutations in Chinese and tree pangolins, suggesting that expression of these genes was lost in a common ancestor of all pangolins that lived more than 20 million years ago. AIM2 is retained in a functional form in pangolins whereas it is inactivated by mutations in carnivorans, the phylogenetic sister group of pangolins. The deficiency of cGAS and STING points to the existence of alternative mechanisms of controlling cytoplasmic DNA-associated cell damage and viral infections in pangolins.