Norovirus ; chemistry ; genetics ; physiology ; ultrastructure ; Open Reading Frames ; Virus Replication

With the development of modern sequencing techniques and bioinformatics, genomes that were once thought to be noncoding have been found to encode abundant functional micropeptides (miPs), a kind of small polypeptides. Although miPs are difficult to analyze and identify, a number of studies have begun to focus on them. More and more miPs have been revealed as essential for energy metabolism homeostasis, immune regulation, and tumor growth and development. Many reports have shown that miPs are especially essential for regulating glucose and lipid metabolism and regulating mitochondrial function. MiPs are also involved in the progression of related diseases. This paper reviews the sources and identification of miPs, as well as the functional significance of miPs for metabolism-related diseases, with the aim of revealing their potential clinical applications.
Humans ; Open Reading Frames ; Peptides ; Glucose ; Genome ; Metabolic Diseases

Reynoutria japonica Houtt., belonging to Polygoneae of Polygonaceae, is a Chinese medicinal herb with the functions of draining dampness and relieving jaundice, clearing heat and detoxifying, dispersing blood stasis and relieving pain, and relieving cough and resolving phlegm. In this study, we carried out high-throughput sequencing for the chloroplast genome sequences of five cultivars of R. japonica and analyzed the genome structure and variations. The chloroplast genomes of the five R. japonica cultivars had two sizes (163 376 bp and 163 371 bp) and a typical circular tetrad structure composed of a large single-copy (LSC) region of 85 784 bp, a small single-copy (SSC) region of 18 616 bp, and a pair of inverted repeat (IR) regions (IRa/IRb) which are spaced apart. A total of 161 genes were obtained by annotation, which consisted of 106 protein-coding genes, 10 rRNA-coding genes, and 45 tRNA-coding genes. The total GC content was 36.7%. Specifically, the GC content in the LSC, SSC, and IR regions were 34.8%, 30.7%, and 42.7%, respectively. Comparison of the whole chloroplast genome among the five cultivars showed that trnk-UUU, rpoC1, petD, rpl16, ndhA, and rpl12 in coding regions had sequence variations. In the phylogenetic tree constructed for the 11 samples of Polygoneae, the five cultivars of R. japonica clustered into one clade near the root and was a sister group of Fallopia multiflora (Thunb.).
Base Composition ; Genome, Chloroplast/genetics* ; Open Reading Frames ; Phylogeny ; Reynoutria

HExDB is a database for analyzing exon and splicing pattern information in Homo sapiens. HExDB is useful for specific purposes: 1) to design primers for exon amplification from cDNA and 2) to understand the change of ORFs by alternative splicing. HExDB was constructed by integrating data from AltExtron which is the computationally predicted exon database, Ensemble cDNA annotation, and Affymetrix genome tile published recently. Although it may contain false positive data, HExDB is good starting point due to its sensitivity. At present, there are as many as 2,046,519 exons stored in the HExDB. We found that 16.8% of the exons in the database was constitutive exons and 83.1% were novel gene exons.
Alternative Splicing* ; Animals ; DNA, Complementary ; Ecthyma, Contagious ; Exons* ; Genome ; Humans* ; Open Reading Frames

Enterotoxigenic B. pagilis (ETBF) strains which produce a 20 kDa zinc metalloprotease toxin (BFI) have been associated with diarrheal disease of animals and young children. Using B. pngilis toxin gene (bfi) from strain 86-5443-2-2 (piglet isolate) as a probe, the gene was identified in 74/77 human and animal ETBF strains but only 2/97 non-toxigenic B. fragilis (NTBF) strains. The region flanking bp was mapped with several restriction enzymes and 8 resriction fragments aacent to bft were used to probe colony blots of 77 KTBF and 97 NTBF strains. All 74 bft-positive ETBF strains hybridized to the 8 probes spanning a ca. 18 kb chromosomal region; however, this 18 kb region was absent in the 3 ETBF strains lacking p, and 47 of the 97 (48%) NTBF strains lacked the entire 18 kb region. Of note, the 2 NTBF strains containing btf did not have a ca. 12 kb region upstream of btfp. A ca. 9 kb fragment flanking the btf gene has been sequenced. Analysis of this data revealed several open reading frames (ORF) of which 3 are of particular interest (ORFs 1, 2 and 3). ORF1 and ORF3 encode proteins with significant homology to mobilization proteins, and ORF2 encodes a protein with significant homology to metalloprotease proteins, but only 50% similarity and 30% identity to BFf. These results suggest: 1) the btf genes are flanked by at least 18 kb of DNA largely unique to ETBF strains indicating a putative pathogenic island, 2) another metalloprotease protein present in ETBF strains may contribute to the pathogenicity and variable virulence of these diarrheagenic strains and 3) the pathogenic island may be mobiTized among different Bacteroides strains, and possibly among different species of intestinal bacteria.
Animals ; Bacteria ; Bacteroides fragilis* ; Bacteroides* ; Child ; DNA ; Genomic Islands* ; Humans ; Open Reading Frames ; Virulence* ; Zinc

Turnip yellow mosaic virus (TYMV) is a spherical plant virus that has a single 6.3 kb positive strand RNA genome. Information for TYMV replication is limited, except that the 3'-terminal sequence and 5'-untranslated region are required for genome replication. When a foreign sequence was inserted at the position upstream of the coat protein (CP) open reading frame (ORF), replication of the recombinant TYMV was comparable to wild type, as long as an RNAi suppressor was provided. In contrast, when the foreign sequence was inserted between the CP ORF and the 3'-terminal tRNA-like structure, replication of the recombinant virus was not detected. This result suggests that the CP ORF contains an essential replication element which should be appropriately spaced with respect to the 3'-end. Analysis of TYMV constructs containing a part or a full additional CP ORF indicates that the 3' quarter of the CP ORF is required for TYMV replication.
Animals ; Brassica napus ; Ecthyma, Contagious ; Genome ; Open Reading Frames ; Plant Viruses ; RNA ; Tymovirus ; Viruses

Human norovirus (HuNoV) is the major etiological agent of nonbacterial gastroenteritis worldwide. However, due to the absence of a rapid and sensitive diagnostic system, detection and monitoring have been limited. The HuNoV genome is composed of three open reading frames (ORFs). And major capsid protein, ORF2, is designated as a viral protein 1 (VP1). In this study, the baculovirus expression system was used for expression of the HuNoV capsid protein, VP1. Recombinant baculoviruses can be used as potent tools in HuNoV studies.
Baculoviridae ; Capsid ; Capsid Proteins ; Gastroenteritis ; Genome ; Humans ; Norovirus ; Open Reading Frames

Human papillomavirus (HPV) 16, E7 proteins derived from the prototype (Bac73) and natural variant (Bac101) E7 open reading frame were produced in Sf9 insect cells. The variant E7 gene occurred naturally by substitution mutation at the position of 88 nucleotide, resulting serine instead of asparagine. Using E7 specific monoclonal antibody (VD6), both E7 proteins were identified in recombinant baculovirus infected SF9 cells. Radiolabelling and immunoprecipitation analysis revealed that both E7 proteins were phosphoproteins. Immunostaining result showed that E7 proteins were mainly localized in the cytoplasm. Nuclear form of E7 proteins was also detected after a sequential fractionation procedure for removing chromatin structure. Considering that the VD6 recognition site in E7 protein is located within 10 amino acid at the N-terminus, this region appears to be blocked by the nuclear component. Western blot analysis revealed that nuclear form was more abundant than cytoplasmic E7 proteins. Time course immunostaining showed that the primary location of E7 protein was the nucleus and exported to the cytoplasm as proteins were accumulated. These events occurred similarly in both Bac73 and Bac101 infected Sf9 cells, suggesting that these two proteins may have similar biological functions.
Asparagine ; Baculoviridae* ; Blotting, Western ; Chromatin ; Cytoplasm ; Humans* ; Immunoprecipitation ; Insects ; Open Reading Frames ; Phosphoproteins ; Serine ; Sf9 Cells

Incorporation of unique barcodes into fission yeast gene deletion collections has enabled the identification of gene functions by growth fitness analysis. For fine tuning, it is important to examine barcode sequences, because mutations arise during strain construction. Out of 8,708 barcodes (4,354 strains) covering 88.5% of all 4,919 open reading frames, 7,734 barcodes (88.8%) were validated as high-fidelity to be inserted at the correct positions by Sanger sequencing. Sequence examination of the 7,734 high-fidelity barcodes revealed that 1,039 barcodes (13.4%) deviated from the original design. In total, 1,284 mutations (mutation rate of 16.6%) exist within the 1,039 mutated barcodes, which is comparable to budding yeast (18%). When the type of mutation was considered, substitutions accounted for 845 mutations (10.9%), deletions accounted for 319 mutations (4.1%), and insertions accounted for 121 mutations (1.6%). Peculiarly, the frequency of substitutions (67.6%) was unexpectedly higher than in budding yeast (~28%) and well above the predicted error of Sanger sequencing (~2%), which might have arisen during the solid-phase oligonucleotide synthesis and PCR amplification of the barcodes during strain construction. When the mutation rate was analyzed by position within 20-mer barcodes using the 1,284 mutations from the 7,734 sequenced barcodes, there was no significant difference between up-tags and down-tags at a given position. The mutation frequency at a given position was similar at most positions, ranging from 0.4% (32/7,734) to 1.1% (82/7,734), except at position 1, which was highest (3.1%), as in budding yeast. Together, well-defined barcode sequences, combined with the next-generation sequencing platform, promise to make the fission yeast gene deletion library a powerful tool for understanding gene function.
DNA* ; Gene Deletion* ; Mutation Rate ; Open Reading Frames ; Polymerase Chain Reaction ; Saccharomycetales ; Schizosaccharomyces*

Cervical carcinoma, the second most common malignancy in Malaysian females, is aetiologically linked to the human papillomavirus (HPV). A study was conducted at the Department of Pathology, University of Malaya Medical Centre to compare the identification of HPV 6, 11, 16 and 18 in 40 archived formalin-fixed, paraffin-embedded cervical carcinoma by non-isotopic in-situ hybridisation (NISH) and polymerase chain reaction (PCR). HPV L1 ORF consensus PCR was also carried in cases which were negative on HPV type-specific PCR. NISH detected HPV 16 in 13 (32.5%) cases with one case demonstrating a concomitant HPV 18. beta-globin DNA PCR was carried out on the same paraffin block as for NISH in 27 cases and on a different paraffin block in 13, with amplification in 9 of the former and 3 of the latter. Thus only 12 cases were subjected to further HPV PCR. HPV was detected in 10 (83.3%) with HPV 16 in 9 cases and HPV L1 ORF in one. When using the same paraffin block for both methods of HPV detection, NISH detected HPV in 6 and PCR in 7. NISH failed to detect HPV in a case detected by PCR. 2 cases were negative for HPV using both methods. Hence, HPV detection results by NISH and PCR were concordant in 88.9%. Interestingly, NISH detected HPV in 2 cases with non-amplifiable beta-globin DNA. Using an alternative paraffin block for HPV PCR from NISH, HPV DNA was detected in 3 cases, two of which also showed type-specific positivity on NISH. The third case did not reveal type-specific positivity with NISH or PCR but demonstrated HPV DNA on L1 ORF consensus PCR. It thus appears that PCR and NISH can be successfully used to detect HPV in formalin-fixed, paraffin-embedded tissue and in the presence of intact DNA NISH may be as sensitive as PCR.
Papillomavirus, Human ; Polymerase Chain Reaction ; DNA ; Open Reading Frames ; Cervical Cancer