Potential Open Reading Frames Research Articles

Genomic and molecular characterization of a cyprinid herpesvirus 2 YC-01 strain isolated from gibel carp

Cyprinid herpesvirus 2 (CyHV-2) is the pathogen of herpesviral hematopoietic necrosis (HVHN), causing the severe economic losses in farmed gibel carp (Carassius gibelio). Further exploration of the genome structure and potential molecular pathogenesis of CyHV-2 through complete genome sequencing, comparative genomics, and molecular characterization is required. Herein, the genome of a CyHV-2 YC-01 strain isolated from diseased gibel carp collected in Yancheng, Jiangsu Province, China was sequenced, then we analyzed the genomic structure, genetic properties, and molecular characterization. First, the complete YC-01 genome comprises 275,367 bp without terminal repeat (TR) regions, with 151 potential open reading frames (ORFs). Second, compared with other representative published strains of the genus Cyvirus, several evident variations are found in YC-01, particularly the orientation and position of ORF25 and ORF25B. ORF107 and ORF156 are considered as potential molecular genetic markers for YC-01. ORF55 (encoding thymidine kinase) might be used to distinguish YC-01 and ST-J1 from other CyHV-2 isolates. Third, phylogenetically, YC-01 clusters with the members of the genus Cyvirus (together with the other six CyHV-2 isolates). Fourth, 43 putative proteins are predicted to be functional and are mainly divided into five categories. Several conserved motifs are found in nucleotide, amino acid, and promoter sequences including cis-acting elements identification of YC-01. Finally, the potential virulence factors and linear B cell epitopes of CyHV-2 are predicted to supply possibilities for designing novel vaccines rationally. Our results provide insights for further understanding genomic structure, genetic evolution, and potential molecular mechanisms of CyHV-2.

Abstract 472: Long non-coding RNA MIR31HG-derived circRNA enhances the oncogenicity of oral carcinoma

Abstract Introduction: Oral carcinoma (OC) represents a significant health challenge, with the role of non-coding RNAs, particularly microRNAs and long non-coding RNAs (LncRNAs), being well-established in its progression. However, the implications of circular RNAs (circRNAs) in this context are less well understood, presenting a notable gap in current research. Our study focuses on the MIR31HG LncRNA, identified as crucial in OC, particularly its role in producing circRNA, as evidenced by sequencing. This specific MIR31HG-derived circRNA, designated 31HGcircR, which contains a potential open reading frame (ORF), and may demonstrate phenotypic significances. Alterations to 31HGcircR, either through knockout or ORF mutation, result in remarkable phenotypic changes, highlighting its potential importance in the pathogenesis of OC. Methods: We implemented 31HGcircR overexpression in OC cell lines, utilizing the TetOff system for gene expression control. CRISPR/Cas9 was employed for gene knockout, and siRNA for gene knockdown. Gene expression was quantified using qPCR. Additionally, the BaseScope assay was used to label and detect the spatial expression of overexpressed 31HGcircR within the cells. Assays to assess cell proliferation, invasion, migration, anchorage-independent growth (AIG), and clonogenicity were conducted. Results: The findings revealed specific junctions of 31HGcircR and varied expression levels across different OC cell lines. There was a significant correlation among the expression of 31HGcircR, MIR31HG and miR-31-5p. Notably, the knockdown of 31HGcircR led to pronounced inhibition of cell growth, migration, invasion, AIG, and clonogenic activity. Conversely, overexpression of 31HGcircR or its ORFs augmented invasion and clonogenic potential in certain cell lines. The TetOff system demonstrated that minimal concentrations of Doxycycline effectively suppressed 31HGcircR expression, with reversible effects upon removal. Knocking out 31HGcircR resulted in reduced invasion and clonogenic capabilities. Conclusion: This study provides clues demonstrating the oncogenic roles of 31HGcircR in OC, which simulate the functions of MIR31HG or miR-31-5p. The changes in cell phenotypes following 31HGcircR manipulation suggest its potential as a therapeutic target or biomarker in OC. These findings offer valuable insights, contributing to the evolving understanding of circRNAs in cancer research and potential treatment avenues. Citation Format: Chung-Hsien Chou, Hsi-Feng Tu, Kuo-Wei Chang, Shu-Chun Lin. Long non-coding RNA MIR31HG-derived circRNA enhances the oncogenicity of oral carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 472.

Analysis of unintended open reading frame ORF-130 expression in maize event MZIR098 by LC-MS as part of the allergenicity risk assessment of genetically modified crops

Rigorous safety assessments are required for genetically modified (GM) crops to support their use as food or feed. These assessments include bioinformatics analysis of the amino acid sequences of all potential open reading frames (ORFs) encoded in the exogenous DNA introduced into the plant through genetic modification. Sequence similarities of potential DNA products to known or potential toxins and allergens trigger subsequent assessments of potential hazards for the consumer or the environment. The bioinformatic analysis of Syngenta maize event MZIR098 insert DNA revealed a total of 415 ORFs. One putative ORF (ORF-130) triggered further risk assessment based on its sequence similarities with known allergens, including peanut allergen Ara h 1, wheat glutenin, and others. We examined the potential expression of ORF-130 at a protein level to exclude the possibility of exposure during consumption of MZIR098 maize. Specifically, we developed and validated a liquid chromatography approach coupled to a tandem mass spectrometry (LC-MS/MS) method, called parallel reaction monitoring (PRM). This measure of expression was quantitative and targeted against the peptides unique to ORF-130. The linear range of the method was 25-5000 amol ORF-130/µl. Both, limit of detection (LOD) and lower limit of quantitation (LLOQ) of the method, were 12 μg ORF-130 per gram of dry MZIR098 maize leaf. The method was accurate and specific to ORF-130. PRM analysis of MZIR098 extracts did not detect putative ORF-130 above the limits of detection/quantitation. Furthermore, the broad proteomic data dependent acquisition (DDA) analysis of the MZIR098 extracts demonstrated no evidence of ORF-130 corroborating the PRM analysis. Our results confirm that ORF-130 is not characterized as a functional gene in Syngenta maize event MZIR098 insert DNA and does not express gene products at detectable levels.

Sequencing, Analysis and Organization of the Complete Genome of a Novel Baculovirus Calliteara abietis Nucleopolyhedrovirus (CaabNPV).

Baculoviridae, a virus family characterized by a single large double stranded DNA, encompasses the majority of viral bioinsecticides, representing a highly promising and environmentally friendly pesticide approach to insect control. This study focuses on the characterization of a baculovirus isolated from larvae of Calliteara abietis (Erebidae, Lymantriidae) collected in Mongolian pinaceae forests. This new isolate was called Calliteara abietis nucleopolyhedrovirus (CaabNPV). CaabNPV exhibits an irregular polyhedron shape, and significant variation in the diameter of its occlusion bodies (OBs) was observed. Nucleotide distance calculations confirmed CaabNPV as a novel baculovirus. The CaabNPV genome spans 177,161 bp with a G+C content of 45.12% and harbors 150 potential open reading frames (ORFs), including 38 core genes. A comprehensive genomic analysis categorizes CaabNPV within Group II alphabaculovirus, revealing a close phylogenetic relationship with Alphabaculovirus orleucostigmae (OrleNPV). Additionally, repeat sequence analysis identified three highly repetitive sequences consisting of 112 bp repeat units, known as homologous regions (hrs). This research contributes valuable insights into CaabNPV's phylogenetic placement, genomic structure, and its potential applications in insect biocontrol.

ASFV antigens selected from genotype I immunised pigs are immunogenic, but do not protect against genotype II challenge.

African swine fever virus (ASFV) has recent caused outbreaks of viral haemorrhagic fever in domestic pigs and wild boar in Africa, Asia, Europe, Oceania and North America. Control measures for African swine fever are limited in most countries to biosecurity at the farm gate followed by movement restrictions and selective or complete culling of pigs on affected premises. Modified live vaccines are being trialled in several countries, however development of safe and effective African swine fever subunit vaccines has been restricted by a poor understanding of the key antigens required for protection, particularly for the panzootic genotype II viruses. The cellular immune response is thought to be critical for protection against African swine fever and therefore to develop an effective subunit vaccine that stimulates an anti-ASFV T-cell response we screened lymphocytes from pigs which survived challenge with Georgia 2007/1. Using an overlapping peptide library corresponding to 168 annotated open reading frames and 24 potential minor open reading frames we identified seventeen proteins with strongly stimulated secretion of interferon gamma in an ELISpot assay. The phenotype of the T cells which were stimulated by these pools of peptides were then investigated by flow cytometry. Proteins stimulating predominantly CD8+ T cells were incorporated into bivalent replication deficient adenovirus vectors and tested as potential vaccine candidates in immunisation and challenge experiments in pigs.

Translational control of murine adiponectin expression by an upstream open reading frame element

ABSTRACT Adiponectin, an adipocyte-specific secretory protein encoded by the ADIPOQ gene has a causal role in insulin resistance. Anti-diabetic drugs increase plasma adiponectin by a poorly understood, post-transcriptional mechanism enhancing insulin sensitivity. Deletion analysis of a reporter bearing the mouse Adipoq mRNA 5’-leader identified an inhibitory cis-regulatory sequence. The 5’-leader harbours two potential upstream open reading frames (uORFs) overlapping the principal downstream ORF. Mutation of the uORF ATGs increased reporter translation ~3-fold, indicative of a functional uORF. uORFs are common in mammalian mRNAs; however, only a select group resist translational repression by the integrated stress response (ISR). Thapsigargin (TG), which induces endoplasmic reticulum (ER) stress and the ISR, enhanced expression of a reporter bearing the Adipoq 5’-leader; polysome profiling verified translation-stimulation. TG-stimulated translation was absent in cells defective in Ser51 phosphorylation of eukaryotic initiation factor 2α (eIF2α), required for the ISR. To determine its role in expression and function of endogenous adiponectin, the upstream uORF was disrupted by CRISPR-Cas9-mediated mutagenesis of differentiated mouse 3T3-L1 adipocytes. uORF disruption in adipocytes increased adiponectin expression, triacylglycerol accumulation, and glucose uptake, and inhibited paracrine muscle and liver cell expression of gluconeogenic enzymes, establishing an important role of the uORF in adiponectin-mediated responses to stress.

Characterization and genomic analysis of an oceanic cyanophage infecting marine Synechococcus reveal a novel genus.

Cyanophages play a crucial role in the biogeochemical cycles of aquatic ecosystems by affecting the population dynamics and community structure of cyanobacteria. In this study, a novel cyanophage, Nanhaivirus ms29, that infects Synechococcus sp. MW02 was isolated from the ocean basin in the South China Sea. It was identified as a T4-like phage using transmission electron microscopy. Phylogenetic analysis demonstrated that this cyanophage is distinct from other known T4-like cyanophage, belonging to a novel genus named Nanhaivirus within the family Kyanoviridae, according to the most recent classification proposed by the International Committee on Taxonomy of Viruses (ICTV). The genome of this novel cyanophage is composed of 178,866 bp of double-stranded DNA with a G + C content of 42.5%. It contains 217 potential open reading frames (ORFs) and 6 tRNAs. As many as 30 auxiliary metabolic genes (AMGs) were identified in the genome, which related to photosynthesis, carbon metabolism, nutrient uptake and stress tolerance, possibly reflecting a genomic adaption to the oligotrophic environment. Read-mapping analysis showed that Nanhaivirus ms29 mainly distributed in temperate and tropical epipelagic waters. This study enriches of the virus gene database of cyanophages and provides valuable insights into the phylogeny of cyanophages and their interactions with their hosts.

Unraveling the genome and gene expression of Hibiscus chlorotic ringspot virus isolated from Hibiscus rosa-sinensis in Southwest Iran

Hibiscus chlorotic ringspot virus (HCRSV; genus Betacarmovirus, family Tombusviridae) is one of the pathogens causing disease on Hibiscus rosa-sinensis (Chinese rose), an ornamental plant grown throughout the tropic and subtropic regions of the world. In a survey on Chinese hibiscus plants showing chlorotic ring spots leaves in Khuzestan Province, Southwestern Iran, HCRSV was identified and the complete genome of the first Iranian isolate of the virus, HCRSV-IR, was determined using Illumina RNA-Seq. The genome of HCRSV-IR was 3911 nucleotides long and potentially encodes seven open reading frames (ORFs) similar to previously known HCRSV isolates. Iranian isolate of virus showed the highest nucleotide sequence identity, 94.39 %, to the Brazil isolate (MK279671.1) Hibiscus chlorotic ringspot virus (HCRSV; genus Betacarmovirus, family Tombusviridae) is one of the pathogens causing disease on Hibiscus rosa-sinensis (Chinese rose), an ornamental plant grown throughout the tropic and subtropic regions of the world. In a survey on Chinese hibiscus plants showing chlorotic ring spots leaves in Khuzestan Province, Southwestern Iran, HCRSV was identified and the complete genome of the first Iranian isolate of virus, HCRSV-IR, was determined using Illumina RNA-Seq. The genome of HCRSV-IR was 3911 nucleotides long and potentially encodes seven open reading frames (ORFs) similar to previously known HCRSV isolates. Iranian isolate of the virus showed the highest nucleotide sequence identity, 94.39 %, to Brazil isolate (MK279671.1) Chinese hibiscus plants exhibiting chlorotic ringspot symptoms were surveyed in southwestern Iran to determine the presence of Hibiscus chlorotic ringspot virus (HCRSV; genus Betacarmovirus, family Tombusviridae). The complete sequence of the Iranian isolate of the virus, HCRSV-IR, was obtained using Illumina RNA-Seq, marking the first time this sequence has been documented. HCRSV-IR (Accession No. OP779319) has a genome comprising 3911 nucleotides, which encodes seven potential open reading frames (ORFs). Comparative analysis revealed that HCRSV-IR shares the highest nucleotide sequence identity (94.39 %) with an isolate from Brazil (MK279671.1). Analysis of the gene expression profile of the HCRSV-IR population infecting hibiscus plants indicated increased expression of the coat protein gene. Additionally, seventeen single nucleotide polymorphisms (SNPs) were identified within the viral variant populations from the infected hibiscus plants. These SNPs were located in coding regions across the entire genome, implying potential evolutionary significance. To the best of our knowledge, this study represents the first investigation into the molecular characterization of the complete genome of HCRSV, specifically infecting Chinese hibiscus in Iran.

Differential sense and antisense expression profiles of Syrista parreyssi (Hymenoptera: Cephidae) mitochondrial transcripts.

The transcription of the mitogenome shows a unique pattern that is both similar to and different from the nuclear and bacterial patterns. Mitochondrial transcription generates five polycistronic units from three promoters in Drosophila melanogaster, and different expression levels of genes were observed in both different and, interestingly, the same polycistronic units in D. melanogaster. This study was conducted to test this phenomenon in the mitogenome of Syrista parreyssi (Hymenoptera: Cephidae). RNA isolation and DNase digestion were performed using only one whole individual, and real-time polymerase chain reaction analyses were performed with complementary DNAs of 11 gene regions using gene-specific primers. It was found that the expression level of each gene exhibited differences from each other, and some genes (e.g., cox genes, and rrnS) were interestingly expressed at significant levels in the corresponding antisense chain. Additionally, the mitogenome of S. parreyssi was found to have the capacity to encode 169 additional peptides from 13 known protein-coding genes, most of which were encoded in antisense transcript units. One of the unique findings was a potential open reading frame sequence that was potentially encoded in the antisense rrnL gene and included a conserved cox3 domain.

Characterization and genomic analysis of a novel Synechococcus phage S-H9–2 belonging to Bristolvirus genus isolated from the Yellow Sea

Cyanophages are known to influence the population dynamics and community structure of cyanobacteria and thus play an important role in biogeochemical cycles in aquatic ecosystems. In this study, a novel Synechococcus phage S-H9–2 infecting Synechococcus sp. WH 8102 was isolated from the coastal water of the Yellow Sea. Synechococcus phage S-H9–2 contains a 187,320 bp genome of double-stranded DNA with a G + C content of 40.3%, 202 potential open reading frames (ORFs), and 15 tRNAs. Phylogenetic analysis and nucleotide-based intergenomic similarity suggest that Synechococcus phage S-H9–2 belongs to the Bristolvirus genus under the family Kyanoviridae. Homologs of the S-H9–2 open reading frame can be found in a variety of marine environments, as shown by the results of mapping the genome sequence of S-H9–2 to the Global Ocean Viromes 2.0 dataset. The presence of auxiliary metabolic genes (AMGs) related to photosynthesis, carbon metabolism, and phosphorus assimilation, as well as phylogenetic relationships based on complete genome sequences, reflect the mechanism of phage-host interaction and host-specific strategies for adaptation to environmental conditions. This study enriches the current genomic database of cyanophage and contributed to our understanding of the virus-host interactions and their adaption to the environment.

The cytosolic lncRNA dutA affects STATa signaling and developmental commitment in Dictyostelium.

STATa is a pivotal transcription factor for Dictyostelium development. dutA is the most abundant RNA transcribed by RNA polymerase II in Dictyostelium, and its functional interplay with STATa has been suggested. This study demonstrates that dutA RNA molecules are distributed as spot-like structures in the cytoplasm, and that its cell type-specific expression changes dramatically during development. dutA RNA was exclusively detectable in the prespore region of slugs and then predominantly localized in prestalk cells, including the organizer region, at the Mexican hat stage before most dutA transcripts, excluding those in prestalk O cells, disappeared as culmination proceeded. dutA RNA was not translated into small peptides from any potential open reading frame, which confirmed that it is a cytoplasmic lncRNA. Ectopic expression of dutA RNA in the organizer region of slugs caused a prolonged slug migration period. In addition, buffered suspension-cultured cells of the strain displayed reduced STATa nuclear translocation and phosphorylation on Tyr702. Analysis of gene expression in various dutA mutants revealed changes in the levels of several STATa-regulated genes, such as the transcription factors mybC and gtaG, which might affect the phenotype. dutA RNA may regulate several mRNA species, thereby playing an indirect role in STATa activation.

A novel virus in the family Marnaviridae as a potential pathogen of Penaeus vannamei glass post-larvae disease

As an aquatic animal of great commercial relevance, Penaeus vannamei is currently the dominant species of cultured shrimp in China and many other countries worldwide. In recent years, the outbreak of glass post-larvae disease (GPD), which accounts for more than 90% of the mortality of shrimp seedlings in serious cases, in many regions of China has caused significant losses and threatened the sustainability of the aquaculture industry and the economy. It is extremely urgent to determine the infectious agent of GPD in P. vannamei. In this work, we performed metagenomic sequencing of glass post-larvae collected from diseased prawns in Tangshan Hebei, where GPD broke out recently. An evolutionary tree was constructed by MEGA 7 to understand the evolutionary history and relationship of the pathogen genome. A novel virus in the family Marnaviridae was first identified in P. vannamei suffering from GPD, and we tentatively named this virus Baishivirus (GenBank: ON550424). The identified pathogen was validated according to Koch's rule with a pathogenic challenge assay and reverse transcription-polymerase chain reaction. There was only 8% query coverage with 64.96% identity in the Baishivirus genome when compared with its most closely related genome sequence of Wenzhou picorna-like virus 21 reported in 2016. Baishivirus genomic RNA is 9.895 kb in length and encodes three potential open reading frames (ORFs). The identification of Baishivirus in P. vannamei enriches the family Marnaviridae and potentially provides a new candidate to study and prevent GPD in the aquaculture industry.

Prolonged activity of HERV-K(HML2) in Old World Monkeys accounts for recent integrations and novel recombinant variants.

Around 8% of the human genome comprises Human Endogenous Retroviruses (HERVs) acquired over primate evolution. Some are specific to primates such as HERV-K, consisting of 10 HML subtypes and including the most recently acquired elements. Particularly, HML2 is the youngest clade, having some human-specific integrations, and while it has been widely described in humans its presence and distribution in non-human primates remain poorly characterized. To investigate HML2 distribution in non-human primates, the present study focused on the characterization of HML2 integrations in Macaca fascicularis and Macaca mulatta which are the most evolutionarily distant species related to humans in the Catarrhini parvorder. We identified overall 208 HML2 proviruses for M. fascicularis (77) and M. mulatta (131). Among them, 46 proviruses are shared by the two species while the others are species specific. Only 12 proviruses were shared with humans, confirming that the major wave of HML2 diffusion in humans occurred after macaques' divergence. Phylogenetic analysis confirmed structural variations between HML2 macaques' species-specific proviruses, and the ones shared between macaques and humans. The HML2 loci were characterized in terms of structure, focusing on potential residual open reading frames (ORFs) for gag, pol, and env genes for the latter being reported to be expressed in human pathological conditions. The analysis identified highly conserved gag and pol genes, while the env genes had a very divergent nature. Of the 208 HML2 proviral sequences present in Macaca species, 81 sequences form a cluster having a MER11A, a characteristic HML8 LTR sequence, insertion in the env region indicating a recombination event that occurred between the HML2 env gene and the HML8 LTR. This recombination event, which was shown to be present only in a subset of macaques' shared sequences and species-specific sequences, highlights a recent viral activity leading to the emergence of an env variant specific to the Old World Monkeys (OWMs). We performed an exhaustive analysis of HML2 in two species of OWMs, in terms of its evolutionary history, structural features, and potential residual coding capacity highlighting recent activity of HML2 in macaques that occurred after its split from the Catarrhini parvorder, leading to the emergence of viral variants, hence providing a better understanding of the endogenization and diffusion of HML2 along primate evolution.

Structural and functional organisation of the phytopathogenic fungi Phoma sp.1 mitochondrial genome

The article presents the results of the mitochondrial DNA (30 837 n. r.) sequencing of the phytopathogenic fungi Phoma sp.1 – causative agent of Phoma blight of the pine and spruce plants cultivated in the forest nurseries. Annotation of the Phoma sp.1 mitochondrion showed 43 coding loci. Potential open reading frames (orf89, orf87, orf76 and orf108) and gene introns (cox3, nad1) are described. A comparative single genes analysis in the NCBI GenBank database showed, that Phoma sp.1 belongs to the Didymella spp., which can have Phoma anamorph. It has been shown that mitohondrial genes can be used as DNA markers for the diagnosis of Phoma and phoma-like fungi. Analysis of the mitochondrial synthenia of Phoma sp.1 and a related species (including phoma-like fungi), revealed significant structural rearrangements in mtDNA during phylogenesis.

Complete Genome and Molecular Characterization of a New Cyprinid Herpesvirus 2 (CyHV-2) SH-01 Strain Isolated from Cultured Crucian Carp.

Cyprinid herpesvirus 2 (CyHV-2) is a causative factor of herpesviral hematopoietic necrosis (HVHN) in farmed crucian carp (Carassius carassius) and goldfish (Carassius auratus). In this study, we analyzed the genomic characteristics of a new strain, CyHV-2 SH-01, isolated during outbreaks in crucian carp at a local fish farm near Shanghai, China. CyHV-2 SH-01 exhibited a high sensitivity to goldfish and crucian carp in our previous research. The complete genome of SH-01 is 290,428 bp with 154 potential open reading frames (ORFs) and terminal repeat (TR) regions at both ends. Compared to the sequenced genomes of other CyHVs, Carassius auratus herpesvirus (CaHV) and Anguillid herpesvirus 1 (AngHV-1), several variations were found in SH-01, including nucleotide mutations, deletions, and insertions, as well as gene duplications, rearrangements, and horizontal transfers. Overall, the genome of SH-01 shares 99.60% of its identity with that of ST-J1. Genomic collinearity analysis showed that SH-01 has a high degree of collinearity with another three CyHV-2 isolates, and it is generally closely related to CaHV, CyHV-1, and CyHV-3, although it contains many differences in locally collinear blocks (LCBs). The lowest degree of collinearity was found with AngHV-1, despite some homologous LCBs, indicating that they are evolutionarily the most distantly related. The results provide new clues to better understand the CyHV-2 genome through sequencing and sequence mining.

Complete genomic sequences and comparative analysis of two Orf virus isolates from Guizhou Province and Jilin Province, China.

Orf virus (ORFV, species Orf virus) belongs to the typical species of the Parapoxvirus genus of the family Poxviridae, which infects sheep, goats, and humans with worldwide distribution. Although outbreaks of Orf have been reported sequentially in several Chinese provinces, the epidemiology of Orf and genetic diversity of ORFV strains still needs to be further characterized. To further reveal the genomic organization of the ORFV-GZ18 and ORFV-CL18 isolates, the complete genome sequences of two recently obtained ORFV isolates were sequenced using the next-generation sequencing technology and analyzed, which had been deposited in the GenBank database under accession number MN648218 and MN648219, respectively. The complete genomic sequence of ORFV-CL18 was 138,495bp in length, including 131 potential open reading frames (ORFs) flanked by inverted terminal repeats (ITRs) of 3481bp at both ends, which has genomic structure typical Parapoxviruses. The overall genomic organization of the fully sequenced genome of ORFV-GZ18 was consistent with ORFV-CL18 genome, with a complete genome size of 138,446 nucleotides, containing 131 ORFs flanked by ITRs of 3469bp. Additionally, the overall G + C contents of ORFV-GZ18 and ORFV-CL18 genome sequences were about 63.9% and 63.8%, respectively. The phylogenetic analysis showed that both ORFV-GZ18 and ORFV-CL18 were genetically closely related to ORFV-SY17 derived from sheep. In summary, the complete genomic sequences of ORFV-GZ18 and ORFV-CL18 are reported, with the hope it will be useful to investigate the host range, geographic distribution, and genetic evolution of the virus in Southern West and Northern East China.

CSCD2: an integrated interactional database of cancer-specific circular RNAs.

The significant function of circRNAs in cancer was recognized in recent work, so a well-organized resource is required for characterizing the interactions between circRNAs and other functional molecules (such as microRNA and RNA-binding protein) in cancer. We previously developed cancer-specific circRNA database (CSCD), a comprehensive database for cancer-specific circRNAs, which is widely used in circRNA research. Here, we updated CSCD to CSCD2 (http://geneyun.net/CSCD2 or http://gb.whu.edu.cn/CSCD2), which includes significantly more cancer-specific circRNAs identified from a large number of human cancer and normal tissues/cell lines. CSCD2 contains >1000 samples (825 tissues and 288 cell lines) and identifies a large number of circRNAs: 1 013 461 cancer-specific circRNAs, 1 533 704 circRNAs from only normal samples and 354 422 circRNAs from both cancer and normal samples. In addition, CSCD2 predicts potential miRNA–circRNA and RBP–circRNA interactions using binding motifs from >200 RBPs and 2000 microRNAs. Furthermore, the potential full-length and open reading frame sequence of these circRNAs were also predicted. Collectively, CSCD2 provides a significantly enhanced resource for exploring the function and regulation of circRNAs in cancer.

A Novel Polyvalent Bacteriophage vB_EcoM_swi3 Infects Pathogenic Escherichia coli and Salmonella enteritidis.

A novel virulent bacteriophage vB_EcoM_swi3 (swi3), isolated from swine feces, lyzed 9% (6/65) of Escherichia coli and isolates 54% (39/72) of Salmonella enteritidis isolates, which were all clinically pathogenic multidrug-resistant strains. Morphological observation showed that phage swi3 belonged to the Myoviridae family with an icosahedral head (80 nm in diameter) and a contractile sheathed tail (120 nm in length). At the optimal multiplicity of infection of 1, the one-step growth analysis of swi3 showed a 25-min latent period with a burst size of 25-plaque-forming units (PFU)/infected cell. Phage swi3 remained stable both at pH 6.0–8.0 and at less than 50°C for at least 1 h. Genomic sequencing and bioinformatics analysis based on genomic sequences and the terminase large subunit showed that phage swi3 was a novel member that was most closely related to Salmonella phages and belonged to the Rosemountvirus genus. Phage swi3 harbored a 52-kb double-stranded DNA genome with 46.02% GC content. Seventy-two potential open reading frames were identified and annotated, only 15 of which had been assigned to functional genes. No gene associated with pathogenicity and virulence was identified. The effects of phage swi3 in treating pathologic E. coli infections in vivo were evaluated using a mouse model. The administration of a single intraperitoneal injection of swi3 (106 PFU) at 2 h after challenge with the E. coli strain (serotype K88) (108 colony-forming units) sufficiently protected all mice without toxic side effects. This finding highlighted that phage swi3 might be used as an effective antibacterial agent to prevent E. coli and S. enteritidis infection.

Chromatin accessibility and translational landscapes of tea plants under chilling stress

Plants have evolved regulatory mechanisms at multiple levels to regulate gene expression in order to improve their cold adaptability. However, limited information is available regarding the stress response at the chromatin and translational levels. Here, we characterize the chromatin accessibility, transcriptional, and translational landscapes of tea plants in vivo under chilling stress for the first time. Chilling stress significantly affected both the transcription and translation levels as well as the translation efficiency of tea plants. A total of 3010 genes that underwent rapid and independent translation under chilling stress were observed, and they were significantly enriched in the photosynthesis-antenna protein and phenylpropanoid biosynthesis pathways. A set of genes that were significantly responsive to cold at the transcription and translation levels, including four (+)-neomenthol dehydrogenases (MNDs) and two (E)-nerolidol synthases (NESs) arranged in tandem on the chromosomes, were also found. We detected potential upstream open reading frames (uORFs) on 3082 genes and found that tea plants may inhibit the overall expression of genes by enhancing the translation of uORFs under chilling stress. In addition, we identified distal transposase hypersensitive sites (THSs) and proximal THSs and constructed a transcriptional regulatory network for tea plants under chilling stress. We also identified 13 high-confidence transcription factors (TFs) that may play a crucial role in cold regulation. These results provide valuable information regarding the potential transcriptional regulatory network in plants and help to clarify how plants exhibit flexible responses to chilling stress.

Utilizing Amino Acid Composition and Entropy of Potential Open Reading Frames to Identify Protein-Coding Genes.

One of the main steps in gene-finding in prokaryotes is determining which open reading frames encode for a protein, and which occur by chance alone. There are many different methods to differentiate the two; the most prevalent approach is using shared homology with a database of known genes. This method presents many pitfalls, most notably the catch that you only find genes that you have seen before. The four most popular prokaryotic gene-prediction programs (GeneMark, Glimmer, Prodigal, Phanotate) all use a protein-coding training model to predict protein-coding genes, with the latter three allowing for the training model to be created ab initio from the input genome. Different methods are available for creating the training model, and to increase the accuracy of such tools, we present here GOODORFS, a method for identifying protein-coding genes within a set of all possible open reading frames (ORFS). Our workflow begins with taking the amino acid frequencies of each ORF, calculating an entropy density profile (EDP), using KMeans to cluster the EDPs, and then selecting the cluster with the lowest variation as the coding ORFs. To test the efficacy of our method, we ran GOODORFS on 14,179 annotated phage genomes, and compared our results to the initial training-set creation step of four other similar methods (Glimmer, MED2, PHANOTATE, Prodigal). We found that GOODORFS was the most accurate (0.94) and had the best F1-score (0.85), while Glimmer had the highest precision (0.92) and PHANOTATE had the highest recall (0.96).