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杨, 乐. « Discussion and Selection of Several Effectiveness Evaluation Methods ». Operations Research and Fuzziology 11, no 04 (2021) : 448–52. http://dx.doi.org/10.12677/orf.2021.114050.
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曾, 杰. « Method of Intelligent Selection of Building Materials Based on Analytic Hierarchy Process ». Operations Research and Fuzziology 08, no 01 (2018) : 1–8. http://dx.doi.org/10.12677/orf.2018.81001.
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Yang, Li, Jiang Chen, Catherine C. Y. Chang, Xin-Ying Yang, Zhen-Zhen Wang, Ta-Yuan Chang et Bo-Liang Li. « A Stable Upstream Stem-loop Structure Enhances Selection of the First 5′-ORF-AUG as a Main Start Codon for Translation Initiation of Human ACAT1 mRNA ». Acta Biochimica et Biophysica Sinica 36, no 4 (1 avril 2004) : 259–68. http://dx.doi.org/10.1093/abbs/36.4.259.
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Abstract Human ACAT1 cDNA K1 was first cloned and functionally expressed in 1993. There are two adjacent in-frame AUG codons, AUG1397–1399 and AUG1415–1417, at 5′-terminus of the open reading frame (ORF, nt 1397–3049) of human ACAT1 mRNA corresponding to cDNA K1. In current work, these two adjacent inframe AUGs at 5′-terminus of the predicted ORF (5′-ORF-AUGs) as start codons for translation initiation of human ACAT1 mRNA were characterized in detail. Codon mutations indicated that both of these two adjacent 5′-ORF-AUGs can be selected as start codons but the first 5′-ORF-AUG1397–1399 is a main start codon consistent with that of the predicted ORF of human ACAT1 mRNA. Further deletion and mutation analyses demonstrated that a stable upstream stem-loop structure enhanced the selection of the first 5′-ORF-AUG1397–1399 as a main start codon, in addition to upstream nucleotide A in the –3 position, which is a key site of Kozak sequence. In addition, result of ACAT1 enzymatic activity assay showed no obvious difference between these two ACAT1 proteins respectively initiated from the two adjacent 5′-ORF-AUGs. This work showed that a stable upstream stem-loop structure could modulate the start codon selection during translation initiation of mRNAs that contain adjacent multi-5′-ORF-AUGs.
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魏, 志铭. « Research on LRP Site Selection of Emergency Materials in Guizhou Province under Major Epidemic ». Operations Research and Fuzziology 13, no 01 (2023) : 315–21. http://dx.doi.org/10.12677/orf.2023.131034.
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刘, 若男. « Research on the Methods of Improving the Quality and Speed of College Students’ Course Selection ». Operations Research and Fuzziology 11, no 02 (2021) : 147–52. http://dx.doi.org/10.12677/orf.2021.112018.
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鞠, 大伟. « Location Selection Model of Front Distribution Center Based on Regret Theory under Heterogeneous Group Information ». Operations Research and Fuzziology 11, no 01 (2021) : 81–96. http://dx.doi.org/10.12677/orf.2021.111011.
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Aleksandrov, Vadim, Marsel Kadyrov, Andrey Ponomarev, Denis Drugov et Evgeniya Neelova. « Oil Recovery Factor Assessment Results for Sites of the Sredne-Ugutskoye Field ». Key Engineering Materials 785 (octobre 2018) : 27–33. http://dx.doi.org/10.4028/www.scientific.net/kem.785.27.
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Oil recovery factor (ORF) assessment for sites of the Sredne-Ugutskoye field was performed applying various methods. For this field, the ORF prognostic assessment applying the existing methodological approaches is very relevant, as well as the selection of the most appropriate and accurate ORF calculation methods, taking into account the specific features of the geological structure of formations and reservoirs. The research objective is to obtain an adequate assessment of the ORF for productive sites of the Sredne-Ugutskoye field. With the help of a whole group of methods (analogy, empirical-analytical and empirical-statistical methods), predictive calculations of the ORF value for a number of Jurassic-age development sites were performed.
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侯, 杰. « Variable Selection for Soft-Sensing Model Based on False Nearest Neighbors in Self-Organizing Feature Mapping Feature Space ». Operations Research and Fuzziology 01, no 01 (2011) : 16–21. http://dx.doi.org/10.12677/orf.2011.11004.
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Snustad, D. P., J. P. Hunsperger, B. M. Chereskin et J. Messing. « Maize glutamine synthetase cDNAs : isolation by direct genetic selection in Escherichia coli. » Genetics 120, no 4 (1 décembre 1988) : 1111–23. http://dx.doi.org/10.1093/genetics/120.4.1111.
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Abstract Maize glutamine synthetase cDNA clones were isolated by genetic selection for functional rescue of an Escherichia coli delta glnA mutant growing on medium lacking glutamine. The Black Mexican Sweet cDNA library used in this study was constructed in pUC13 such that cDNA sense strands were transcribed under the control of the lac promoter. E. coli delta glnA cells were transformed with cDNA library plasmid DNA, grown briefly in rich medium to allow phenotypic expression of the cDNAs and the pUC13 ampr gene, and challenged to grow on agar medium lacking glutamine. Large numbers of glutamine synthetase cDNA clones have been identified in individual 150-mm Petri dishes; all characterized cDNA clones carry complete coding sequences. Two cDNAs identical except for different 5' and 3' termini have been sequenced. The major open reading frame predicts a protein with an amino acid sequence that exhibits striking similarity to the amino acid sequences of the predicted products of previously sequenced eukaryotic glutamine synthetase cDNAs and genes. In addition, the maize glutamine synthetase cDNAs were shown to contain a 5' mini-ORF of 29 codons separated by 37 nucleotide pairs from the major ORF. This mini-ORF was shown not to be essential for the functional rescue of the E. coli delta glnA mutant. Expression of the cDNAs in E. coli is presumed to be due to the function of a polycistronic hybrid lac messenger RNA or translational fusions encoded by the pUC plasmids. Proteins of the expected sizes encoded by two different pUC clones were shown to react with antibodies to tobacco glutamine synthetase.
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GIERLIK, AGNIESZKA, PAWEŁ MACKIEWICZ, MARIA KOWALCZUK, STANISŁAW CEBRAT et MIROSŁAW R. DUDEK. « SOME HINTS ON OPEN READING FRAME STATISTICS — HOW ORF LENGTH DEPENDS ON SELECTION ». International Journal of Modern Physics C 10, no 04 (juin 1999) : 635–43. http://dx.doi.org/10.1142/s0129183199000474.
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Coding sequences of DNA generate Open Reading Frames (ORFs) inside them with much higher frequency than random DNA sequences do, especially in the antisense strand. This is a specific feature of the genetic code. Since coding sequences are selected for their length, the generated ORFs are indirect results of this selection and their length is also influenced by selection. That is why ORFs found in any genome, even much longer ones than those spontaneously generated in random DNA sequences, should be considered as two different sets of ORFs: The first one coding for proteins, the second one generated by the coding ORFs. Even intergenic sequences possess greater capacity for generating ORFs than random DNA sequences of the same nucleotide composition, which seems to be a premise that intergenic sequences were generated from coding sequences by recombinational mechanisms.
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Spatz, Stephen J., Lawrence Petherbridge, Yuguang Zhao et Venugopal Nair. « Comparative full-length sequence analysis of oncogenic and vaccine (Rispens) strains of Marek's disease virus ». Journal of General Virology 88, no 4 (1 avril 2007) : 1080–96. http://dx.doi.org/10.1099/vir.0.82600-0.
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The complete DNA sequence of the Marek's disease virus serotype 1 vaccine strain CVI988 was determined and consists of 178 311 bp with an overall gene organization identical to that of the oncogenic strains. In examining open reading frames (ORFs), nine differ between vaccine and oncogenic strains. A 177 bp insertion was identified in the overlapping genes encoding the Meq, RLORF6 and 23 kDa proteins of CVI988. Three ORFs are predicted to encode truncated proteins. One, designated 49.1, overlaps the gene encoding the large tegument protein UL36 and encodes a severely truncated protein of 34 aa. The others, ORF5.5/ORF75.91 and ORF3.0/78.0, located in the repeat regions (diploid), encode a previously unidentified ORF of 52 aa and a truncated version of the virus-encoded chemokine (vIL-8), respectively. Subtle genetic changes were identified in the two ORFs encoding tegument proteins UL36 and UL49. Only one diploid ORF (ORF6.2/ORF75.6) present in the genomes of the three virulent strains is absent in the CVI988-BAC genome. Seventy non-synonymous amino acid substitutions were identified that could differentiate CVI988-BAC from all three oncogenic strains collectively. Estimates of the non-synonymous to synonymous substitution ratio (ω) indicate that CVI988 ORFs are generally under purifying selection (ω<1), whereas UL39, UL49, UL50, RLORF6 and RLORF7 (Meq) appear to evolve under relaxed selective constraints. No CVI988 ORF was found to be under positive evolutionary selection (ω≫1).
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Verma, Vaishali, Gopal Joshi, Amita Gupta et Vijay K. Chaudhary. « An efficient ORF selection system for DNA fragment libraries based on split beta-lactamase complementation ». PLOS ONE 15, no 7 (23 juillet 2020) : e0235853. http://dx.doi.org/10.1371/journal.pone.0235853.
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Cassan, Elodie, Anne-Muriel Arigon-Chifolleau, Jean-Michel Mesnard, Antoine Gross et Olivier Gascuel. « Concomitant emergence of the antisense protein gene of HIV-1 and of the pandemic ». Proceedings of the National Academy of Sciences 113, no 41 (28 septembre 2016) : 11537–42. http://dx.doi.org/10.1073/pnas.1605739113.
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Recent experiments provide sound arguments in favor of the in vivo expression of the AntiSense Protein (ASP) of HIV-1. This putative protein is encoded on the antisense strand of the provirus genome and entirely overlapped by the env gene with reading frame −2. The existence of ASP was suggested in 1988, but is still controversial, and its function has yet to be determined. We used a large dataset of ∼23,000 HIV-1 and SIV sequences to study the origin, evolution, and conservation of the asp gene. We found that the ASP ORF is specific to group M of HIV-1, which is responsible for the human pandemic. Moreover, the correlation between the presence of asp and the prevalence of HIV-1 groups and M subtypes appeared to be statistically significant. We then looked for evidence of selection pressure acting on asp. Using computer simulations, we showed that the conservation of the ASP ORF in the group M could not be due to chance. Standard methods were ineffective in disentangling the two selection pressures imposed by both the Env and ASP proteins—an expected outcome with overlaps in frame −2. We thus developed a method based on careful evolutionary analysis of the presence/absence of stop codons, revealing that ASP does impose significant selection pressure. All of these results support the idea that asp is the 10th gene of HIV-1 group M and indicate a correlation with the spread of the pandemic.
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Narechania, Apurva, Masanori Terai et Robert D. Burk. « Overlapping reading frames in closely related human papillomaviruses result in modular rates of selection within E2 ». Journal of General Virology 86, no 5 (1 mai 2005) : 1307–13. http://dx.doi.org/10.1099/vir.0.80747-0.
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A core group of four open reading frames (ORFs) is present in all known papillomaviruses (PVs): the E1 and E2 replication/transcription proteins and the L1 and L2 structural proteins. Because they are involved in processes that are essential to PV propagation, the sequences of these proteins are well-conserved. However, sequencing of novel subtypes for human papillomaviruses (HPV) 54 (AE9) and 82 (AE2/IS39), coupled to analysis of four other closely related genital HPV pairs, indicated that E2 has a higher dN/dS ratio than E1, L1 or L2. The elevated ratio is not homogeneous across the length of the ORF, but instead varies with respect to E2's three domains. The E2 hinge region is of particular interest, because its hypervariability (dN/dS>1) differs markedly from the two domains that it joins: the transcription-activation domain and the DNA-binding domain. Deciphering whether the hinge region's high rate of non-synonymous change is the result of positive Darwinian selection or relaxed constraint depends on the evolutionary behaviour of E4, an ORF that overlaps E2. The E2 hinge region is contained within E4 and non-synonymous changes in the hinge are associated with a disproportionate amount of synonymous change in E4, a case of simultaneous positive and purifying selection in overlapping reading frames. Modular rates of selection among E2 domains are a likely consequence of the presence of an embedded E4. E4 appears to be positioned in a part of the HPV genome that can tolerate non-synonymous change and purifying selection of E4 may be indicative of its functional importance.
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Odom, Obed W., Stephen P. Holloway, Nita N. Deshpande, Jaesung Lee et David L. Herrin. « Mobile Self-Splicing Group I Introns from thepsbA Gene of Chlamydomonas reinhardtii : Highly Efficient Homing of an Exogenous Intron Containing Its Own Promoter ». Molecular and Cellular Biology 21, no 10 (15 mai 2001) : 3472–81. http://dx.doi.org/10.1128/mcb.21.10.3472-3481.2001.
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ABSTRACT Introns 2 and 4 of the psbA gene of Chlamydomonas reinhardtii chloroplasts (Cr.psbA2 andCr.psbA4, respectively) contain large free-standing open reading frames (ORFs). We used transformation of an intronless-psbA strain (IL) to test whether these introns undergo homing. Each intron, plus short exon sequences, was cloned into a chloroplast expression vector in both orientations and then cotransformed into IL along with a spectinomycin resistance marker (16Srrn). For Cr.psbA2, the sense construct gave nearly 100% cointegration of the intron whereas the antisense construct gave 0%, consistent with homing. For Cr.psbA4, however, both orientations produced highly efficient cointegration of the intron. Efficient cointegration of Cr.psbA4 also occurred when the intron was introduced as a restriction fragment lacking any known promoter. Deletion of most of the ORF, however, abolished cointegration of the intron, consistent with homing. TheCr.psbA4 constructs also contained a 3-(3,4-dichlorophenyl)-1,1-dimethylurea resistance marker in exon 5, which was always present when the intron integrated, thus demonstrating exon coconversion. Remarkably, primary selection for this marker gave >100-fold more transformants (>10,000/μg of DNA) than did the spectinomycin resistance marker. A trans homing assay was developed for Cr.psbA4; the ORF-minus intron integrated when the ORF was cotransformed on a separate plasmid. This assay was used to identify an intronic region between bp −88 and −194 (relative to the ORF) that stimulated homing and contained a possible bacterial (−10, −35)-type promoter. Primer extension analysis detected a transcript that could originate from this promoter. Thus, this mobile, self-splicing intron also contains its own promoter for ORF expression. The implications of these results for horizontal intron transfer and organelle transformation are discussed.
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Papamichos, Spyros I., Dimitrios Margaritis et Ioannis Kotsianidis. « Adaptive Evolution Coupled with Retrotransposon Exaptation Allowed for the Generation of a Human-Protein-Specific Coding Gene That Promotes Cancer Cell Proliferation and Metastasis in Both Haematological Malignancies and Solid Tumours : The Extraordinary Case ofMYEOVGene ». Scientifica 2015 (2015) : 1–10. http://dx.doi.org/10.1155/2015/984706.
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The incidence of cancer in human is high as compared to chimpanzee. However previous analysis has documented that numerous human cancer-related genes are highly conserved in chimpanzee. Till date whether human genome includes species-specific cancer-related genes that could potentially contribute to a higher cancer susceptibility remains obscure. This study focuses onMYEOV, an oncogene encoding for two protein isoforms, reported as causally involved in promoting cancer cell proliferation and metastasis in both haematological malignancies and solid tumours. First we document, via stringentin silicoanalysis, thatMYEOVarosede novoin Catarrhini. We show that MYEOV short-isoform start codon was evolutionarily acquired after Catarrhini/Platyrrhini divergence. Throughout the course of Catarrhini evolutionMYEOVacquired a gradually elongated translatable open reading frame (ORF), a gradually shortened translation-regulatory upstream ORF, and alternatively spliced mRNA variants. A point mutation introduced in human allowed for the acquisition of MYEOV long-isoform start codon. Second, we demonstrate the precious impact of exonized transposable elements on the creation ofMYEOVgene structure. Third, we highlight that the initial part of MYEOV long-isoform coding DNA sequence was under positive selection pressure during Catarrhini evolution.MYEOVrepresents a Primate Orphan Gene that acquired, via ORF expansion, a human-protein-specific coding potential.
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杰, 侯. « 基于SOM特征映射空间相似度判别的软传感器建模变量选择<br>Variable Selection for Soft-Sensing Model Based on False Nearest Neighbors in Self-Organizing Feature Mapping Feature Space ». Operations Research and Fuzziology 01, no 01 (2011) : 16–21. http://dx.doi.org/10.4236/orf.2011.11004.
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Nikolaidis, Marios, Athanasios Papakyriakou, Katerina Chlichlia, Panayotis Markoulatos, Stephen G. Oliver et Grigorios D. Amoutzias. « Comparative Analysis of SARS-CoV-2 Variants of Concern, Including Omicron, Highlights Their Common and Distinctive Amino Acid Substitution Patterns, Especially at the Spike ORF ». Viruses 14, no 4 (29 mars 2022) : 707. http://dx.doi.org/10.3390/v14040707.
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In order to gain a deeper understanding of the recently emerged and highly divergent Omicron variant of concern (VoC), a study of amino acid substitution (AAS) patterns was performed and compared with those of the other four successful variants of concern (Alpha, Beta, Gamma, Delta) and one closely related variant of interest (VoI—Lambda). The Spike ORF consistently emerges as an AAS hotspot in all six lineages, but in Omicron this enrichment is significantly higher. The progenitors of each of these VoC/VoI lineages underwent positive selection in the Spike ORF. However, once they were established, their Spike ORFs have been undergoing purifying selection, despite the application of global vaccination schemes from 2021 onwards. Our analyses reject the hypothesis that the heavily mutated receptor binding domain (RBD) of the Omicron Spike was introduced via recombination from another closely related Sarbecovirus. Thus, successive point mutations appear as the most parsimonious scenario. Intriguingly, in each of the six lineages, we observed a significant number of AAS wherein the new residue is not present at any homologous site among the other known Sarbecoviruses. Such AAS should be further investigated as potential adaptations to the human host. By studying the phylogenetic distribution of AAS shared between the six lineages, we observed that the Omicron (BA.1) lineage had the highest number (8/10) of recurrent mutations.
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Śmietanka, Beata, Marek Lubośny, Aleksandra Przyłucka, Karin Gérard et Artur Burzyński. « Mitogenomics of Perumytilus purpuratus (Bivalvia : Mytilidae) and its implications for doubly uniparental inheritance of mitochondria ». PeerJ 6 (18 septembre 2018) : e5593. http://dx.doi.org/10.7717/peerj.5593.
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Animal mitochondria are usually inherited through the maternal lineage. The exceptional system allowing fathers to transmit their mitochondria to the offspring exists in some bivalves. Its taxonomic spread is poorly understood and new mitogenomic data are needed to fill the gap. Here, we present for the first time the two divergent mitogenomes from Chilean mussel Perumytilus purpuratus. The existence of these sex-specific mitogenomes confirms that this species has the doubly uniparental inheritance (DUI) of mitochondria. The genetic distance between the two mitochondrial lineages in P. purpuratus is not only much bigger than in the Mytilus edulis species complex but also greater than the distance observed in Musculista senhousia, the only other DUI-positive member of the Mytilidae family for which both complete mitochondrial genomes were published to date. One additional, long ORF (open reading frame) is present exclusively in the maternal mitogenome of P. purpuratus. This ORF evolves under purifying selection, and will likely be a target for future DUI research.
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Gourlay, Louise J., Clelia Peano, Cecilia Deantonio, Lucia Perletti, Alessandro Pietrelli, Riccardo Villa, Elena Matterazzo et al. « Selecting soluble/foldable protein domains through single-gene or genomic ORF filtering : structure of the head domain of Burkholderia pseudomallei antigen BPSL2063 ». Acta Crystallographica Section D Biological Crystallography 71, no 11 (31 octobre 2015) : 2227–35. http://dx.doi.org/10.1107/s1399004715015680.
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The 1.8 Å resolution crystal structure of a conserved domain of the potential Burkholderia pseudomallei antigen and trimeric autotransporter BPSL2063 is presented as a structural vaccinology target for melioidosis vaccine development. Since BPSL2063 (1090 amino acids) hosts only one conserved domain, and the expression/purification of the full-length protein proved to be problematic, a domain-filtering library was generated using β-lactamase as a reporter gene to select further BPSL2063 domains. As a result, two domains (D1 and D2) were identified and produced in soluble form in Escherichia coli. Furthermore, as a general tool, a genomic open reading frame-filtering library from the B. pseudomallei genome was also constructed to facilitate the selection of domain boundaries from the entire ORFeome. Such an approach allowed the selection of three potential protein antigens that were also produced in soluble form. The results imply the further development of ORF-filtering methods as a tool in protein-based research to improve the selection and production of soluble proteins or domains for downstream applications such as X-ray crystallography.
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Hasan, Md Junayed, et Jong-Myon Kim. « Bearing Fault Diagnosis under Variable Rotational Speeds Using Stockwell Transform-Based Vibration Imaging and Transfer Learning ». Applied Sciences 8, no 12 (22 novembre 2018) : 2357. http://dx.doi.org/10.3390/app8122357.
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In this paper, discrete orthonormal Stockwell transform (DOST)-based vibration imaging is proposed as a preprocessing step for supporting load and rotational speed invariant scenarios for signals of various health conditions. For any health condition, features can easily be extracted from its generated health pattern. To automate the feature selection process, a convolutional neural network (CNN)-based transfer learning (TL) approach for diagnosis has also been introduced. Transfer learning allows an established model to use feature knowledge obtained under one set of working conditions through hidden layers to diagnose faults that occur under other working conditions. The network learns from the massive source dataset, and that knowledge is applied to the target data to identify faults. Using the bearing dataset of Case Western Reserve University, the proposed approach yields an average 99.8% classification accuracy and, specifically, 99.99% for healthy condition (HC), 99.95% for inner race fault (IRF), 99.96% for ball fault (BF), 99.68% for outer race fault for 12 o’clock sensor position (ORF@12), 99.93% for outer race fault for 3 o’clock sensor position (ORF@3), and 99.89% for outer race fault for 6 o’clock sensor position (ORF@6). In this paper, the proposed approach is compared with conventional artificial neural networks (ANNs), support vector machines (SVMs), hierarchical CNNs, and deep autoencoders. The proposed approach outperforms these conventional methods in the accuracy under all working conditions.
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An, Yingfeng, Hayretin Yumerefendi, Philippe J. Mas, Alban Chesneau et Darren J. Hart. « ORF-selector ESPRIT : A second generation library screen for soluble protein expression employing precise open reading frame selection ». Journal of Structural Biology 175, no 2 (août 2011) : 189–97. http://dx.doi.org/10.1016/j.jsb.2011.04.004.
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Abrahams, Liam, et Laurence D. Hurst. « A Depletion of Stop Codons in lincRNA is Owing to Transfer of Selective Constraint from Coding Sequences ». Molecular Biology and Evolution 37, no 4 (16 décembre 2019) : 1148–64. http://dx.doi.org/10.1093/molbev/msz299.
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Abstract Although the constraints on a gene’s sequence are often assumed to reflect the functioning of that gene, here we propose transfer selection, a constraint operating on one class of genes transferred to another, mediated by shared binding factors. We show that such transfer can explain an otherwise paradoxical depletion of stop codons in long intergenic noncoding RNAs (lincRNAs). Serine/arginine-rich proteins direct the splicing machinery by binding exonic splice enhancers (ESEs) in immature mRNA. As coding exons cannot contain stop codons in one reading frame, stop codons should be rare within ESEs. We confirm that the stop codon density (SCD) in ESE motifs is low, even accounting for nucleotide biases. Given that serine/arginine-rich proteins binding ESEs also facilitate lincRNA splicing, a low SCD could transfer to lincRNAs. As predicted, multiexon lincRNA exons are depleted in stop codons, a result not explained by open reading frame (ORF) contamination. Consistent with transfer selection, stop codon depletion in lincRNAs is most acute in exonic regions with the highest ESE density, disappears when ESEs are masked, is consistent with stop codon usage skews in ESEs, and is diminished in both single-exon lincRNAs and introns. Owing to low SCD, the maximum lengths of pseudo-ORFs frequently exceed null expectations. This has implications for ORF annotation and the evolution of de novo protein-coding genes from lincRNAs. We conclude that not all constraints operating on genes need be explained by the functioning of the gene but may instead be transferred owing to shared binding factors.
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Majumder, S., et V. K. Baranwal. « First Report of Garlic common latent virus in Garlic from India ». Plant Disease 93, no 1 (janvier 2009) : 106. http://dx.doi.org/10.1094/pdis-93-1-0106c.
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Garlic (Allium sativum L.) is one of the most important culinary herbs in the Indian subcontinent. Several viruses belonging to genera Potyvirus, Carlavirus, and Allexivirus are known to infect garlic (2,3). Garlic accessions grown on the research farm of the Indian Agricultural Research Institute, New Delhi, were tested for the presence of Onion yellow dwarf virus (OYDV), Shallot latent virus (SLV), and Garlic common latent virus (GarCLV). Leaves showing mild to severe mosaic symptoms were collected in January of 2008 from five accessions of garlic (Pusa Selection-34, G-1, Selection-17, G-282, and PGS-14) from the experimental plots. Direct antigen coated (DAC)-ELISA was performed with antisera to OYDV, GarCLV (Bioreba, Reinach, Switzerland), and Garlic latent virus (GarLV) (synonym for SLV) obtained from D. E. Lesemann, (Braunschweig, Germany). Total RNA was extracted from 100 mg of leaves with the RNeasy Plant Mini kit (Qiagen, Maryland) according to the manufacturer's protocol. Reverse transcription (RT)-PCR and DAC-ELISA confirmed the presence of OYDV and SLV in all selection lines, both of which were reported previously from garlic in India (1). The occurrence of GarCLV was confirmed by DAC-ELISA and RT- PCR using a primer pair 5′-AAATGTTAATCGCTAAACGACC-3′ and 5′-CTTTGTGGATTTTCGGTAAG-3′ designed from the conserved region of open reading frame (ORF) 5 (coat protein) and ORF 6 (nucleic acid binding protein) of GarCLV (GenBank Accession Nos. AB004566, X81138, and X81139). Expected amplicons of ∼500 bp for GarCLV were obtained from all garlic lines tested, confirming that all five garlic lines had mixed infections of OYDV, SLV, and GarCLV. The amplicons obtained from Pusa Selection-34 were directly sequenced and the 536-bp nucleotide sequence (GenBank Accession No. FJ154841) showed a sequence identity of 87% compared with GarCLV (GenBank Accession No. AB004566). To our knowledge, this is the first report of GarCLV in garlic cultivars in India. Our study demonstrates that GarCLV occurs frequently in mixed infections with OYDV and SLV and the potential impact of these mixed infections on garlic production needs to be evaluated. References: (1) S. Majumder et al. J. Plant Pathol. 90:369, 2008. (2) P. Van Dijk. Acta Hortic. 358:299, 1994. (3) D. G. A. Walkey and D. N. Antill. J. Hortic. Sci, 64:53, 1989.
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Cornman, Robert S. « Relative abundance and molecular evolution of Lake Sinai Virus (Sinaivirus) clades ». PeerJ 7 (21 mars 2019) : e6305. http://dx.doi.org/10.7717/peerj.6305.
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Lake Sinai Viruses (Sinaivirus) are commonly detected in honey bees (Apis mellifera) but no disease phenotypes or fitness consequences have yet been demonstrated. This viral group is genetically diverse, lacks obvious geographic structure, and multiple lineages can co-infect individual bees. While phylogenetic analyses have been performed, the molecular evolution of LSV has not been studied extensively. Here, I use LSV isolates from GenBank as well as contigs assembled from honey bee Sequence Read Archive (SRA) accessions to better understand the evolutionary history of these viruses. For each ORF, substitution rate variation, codon usage, and tests of positive selection were evaluated. Outlier regions of high or low diversity were sought with sliding window analysis and the role of recombination in creating LSV diversity was explored. Phylogenetic analysis consistently identified two large clusters of sequences that correspond to the current LSV1 and LSV2 nomenclature, however lineages sister to LSV1 were the most frequently detected in honey bee SRA accessions. Different expression levels among ORFs suggested the occurrence of subgenomic transcripts. ORF1 and RNA-dependent RNA polymerase had higher evolutionary rates than the capsid and ORF4. A hypervariable region of the ORF1 protein-coding sequence was identified that had reduced selective constraint, but a site-based model of positive selection was not significantly more likely than a neutral model for any ORF. The only significant recombination signals detected between LSV1 and LSV2 initiated within this hypervariable region, but assumptions of the test (single-frame coding and independence of substitution rate by site) were violated. LSV codon usage differed strikingly from that of honey bees and other common honey-bee viruses, suggesting LSV is not strongly co-evolved with that host. LSV codon usage was significantly correlated with that of Varroa destructor, however, despite the relatively weak codon bias exhibited by the latter. While codon usage between the LSV1 and LSV2 clusters was similar for three ORFs, ORF4 codon usage was uncorrelated between these clades, implying rapid divergence of codon use for this ORF only. Phylogenetic placement and relative abundance of LSV isolates reconstructed from SRA accessions suggest that detection biases may be over-representing LSV1 and LSV2 in public databases relative to their sister lineages.
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Hsiao, Yi-Yuong, Chorng-Horng Lin, Jong-Kang Liu, Tit-Yee Wong et Jimmy Kuo. « Analysis of Codon Usage Patterns in Toxic DinoflagellateAlexandrium tamarensethrough Expressed Sequence Tag Data ». Comparative and Functional Genomics 2010 (2010) : 1–9. http://dx.doi.org/10.1155/2010/138538.
Texte intégralRésumé :
We have analyzed synonymous codon usage in the genome ofA. tamarenseCCMP 1598 for protein-coding sequences from 10865 expressed sequence tags (ESTs). We reconstructed a total of 4284 unigenes, including 74 ribosomal protein and 40 plastid-related genes, from ESTs using FrameDP, an open reading frame (ORF) prediction program. Correspondence analysis ofA. tamarensegenes based on codon usage showed that the GC content at the third base of synonymous codons (GC3s) was strongly correlated with the first axis (r=0.93withP<.001). On the other hand, the second axis discriminated between presumed highly and low expressed genes, with expression levels being confirmed by the analysis of EST frequencies (r=−0.89withP<.001). Our results suggest that mutational bias is the major factor in shaping codon usage inA. tamarensegenome, but other factors, namely, translational selection, hydropathy, and aromaticity, also appear to influence the selection of codon usage in this species.
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Wang, Jinbo, Abhineet M. Sharma, Siobain Duffy et Rodrigo P. P. Almeida. « Genetic Diversity in the 3′ Terminal 4.7-kb Region of Grapevine leafroll-associated virus 3 ». Phytopathology® 101, no 4 (avril 2011) : 445–50. http://dx.doi.org/10.1094/phyto-07-10-0173.
Texte intégralRésumé :
Grapevine leafroll-associated virus 3 (GLRaV-3; Ampelovirus, Closteroviridae), associated with grapevine leafroll disease, is an important pathogen found across all major grape-growing regions of the world. The genetic diversity of GLRaV-3 in Napa Valley, CA, was studied by sequencing 4.7 kb in the 3′ terminal region of 50 isolates obtained from Vitis vinifera ‘Merlot’. GLRaV-3 isolates were subdivided into four distinct phylogenetic clades. No evidence of positive selection was observed in the data set, although neutral selection (ratio of nonsynonymous to synonymous substitution rates = 1.1) was observed in one open reading frame (ORF 11, p4). Additionally, the four clades had variable degrees of overall nucleotide diversity. Moreover, no geographical structure among isolates was observed, and isolates belonging to different phylogenetic clades were found in distinct vineyards, with one exception. Considered with the evidence of purifying selection (i.e., against deleterious mutations), these data indicate that the population of GLRaV-3 in Napa Valley is not expanding and its effective population size is not increasing. Furthermore, research on the biological characterization of GLRaV-3 strains might provide valuable insights on the biology of this species that may have epidemiological relevance.
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Istiana, Rohma, Hermin Pancasakti Kusumaningrum et Rejeki Siti Ferniah. « Analysis of The Open Reading Frame (ORF) 29-TrnC (GCA) Sequence to Detect Indica and Japonica Sub Species on Upland Rice of Situ Bagendit and Inbred Rice of Ciherang ». Biosaintifika : Journal of Biology & ; Biology Education 10, no 1 (2 avril 2018) : 153–59. http://dx.doi.org/10.15294/biosaintifika.v10i1.12626.
Texte intégralRésumé :
The identification and the characterization of genetic diversity of rice was the first step in the rice plant breeding program. This study aimed to detect indica or japonica sub-species on upland rice Situ Bagendit and inbred rice Ciherang using molecular markers ORF 29-TrnC (GCA) on the chloroplast genome. Rice was included to the indica sub-species if the 32 bp insertion on ORF 29-TrnC (GCA) sequence was found, on the contrary, if the deletion 32 bp on ORF 29-TrnC (GCA) was found then it was included to the japonica sub-species. DNA isolation was examined from the leaves of the rice plants, and then it tested quantitatively to determine the transparency and DNA concentration from the isolation results. PCR amplification was performed using a pair of primers CP2 and it was followed by agarose gel electrophoresis. The visualization of the DNA bands used the gel documentation. Sequencing of PCR products produced a long base 390 bp in Situ Bagendit rice and 390 bp in Ciherang rice. Analysis of the sequences showed that the insertions occurred throughout the 32 bp in Situ Bagendit rice and the insertions occurred throughout the 32 bp in Ciherang rice. The results showed that upland rice Situ Bagendit and inbred rice Ciherang were included in the indica sub-species. The knowledge of variety of genetics of rice can be used as bio-information in the plant breeding program. Further, the knowledge can be used to protect in genetic power source, the selection and the composing of superior varieties of rice which is tolerant with kinds of biotic and abiotic factor.
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Chantrel, Yann, Mauricette Gaisne, Claire Lions et Jacqueline Verdière. « The Transcriptional Regulator Hap1p (Cyp1p) Is Essential for Anaerobic or Heme-Deficient Growth of Saccharomyces cerevisiae : Genetic and Molecular Characterization of an Extragenic Suppressor that Encodes a WD Repeat Protein ». Genetics 148, no 2 (1 février 1998) : 559–69. http://dx.doi.org/10.1093/genetics/148.2.559.
Texte intégralRésumé :
Abstract We report here that Hap1p (originally named Cyp1p) has an essential function in anaerobic or heme-deficient growth. Analysis of intragenic revertants shows that this function depends on the amino acid preceding the first cysteine residue of the DNA-binding domain of Hap1p. Selection of recessive extragenic suppressors of a hap1−hem1− strain allowed the identification, cloning, and molecular analysis of ASC1 (Cyp1 Absence of growth Supressor). The sequence of ASC1 reveals that its ORF is interrupted by an intron that shelters the U24 snoRNA. Deletion of the intron, inactivation of the ORF, and molecular localization of the mutations show unambiguously that it is the protein and not the snoRNA that is involved in the suppressor phenotype. ASC1, which is constitutively transcribed, encodes an abundant, cytoplasmically localized 35-kD protein that belongs to the WD repeat family, which is found in a large variety of eucaryotic organisms. Polysome profile analysis supports the involvement of this protein in translation. We propose that the absence of functional Asc1p allows the growth of hap1−hem1− cells by reducing the efficiency of translation. Based on sequence comparisons, we discuss the possibility that the protein intervenes in a kinase-dependent signal transduction pathway involved in this last function.
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Klymiuk, Nikolai, Mathias Müller, Gottfried Brem et Bernhard Aigner. « Characterization of Porcine Endogenous Retrovirus γ pro-pol Nucleotide Sequences ». Journal of Virology 76, no 22 (15 novembre 2002) : 11738–43. http://dx.doi.org/10.1128/jvi.76.22.11738-11743.2002.
Texte intégralRésumé :
ABSTRACT Endogenous retroviral sequences in the pig genome (PERV) represent a potential infectious risk in xenotransplantation. All known infectious PERV have been asssigned to the PERV γ1 family, consisting of the subfamilies A, B, and C. The aim of the study was the concise examination of PERV γ by the analysis of the retroviral pro-pol sequences. The analysis of 52 pro-pol clones amplified in this study revealed eight PERV γ families. In addition to four already-described families (γ1, γ4, γ5, γ6), four novel families (γ7, γ8, γ9, γ10) were identified. Quantitative analysis of the novel PERV γ sequences in selected breeds revealed variations in the endogenous retroviral load. Open reading frames (ORF) in the amplified proviral fragment were only found for PERV γ1. In addition, novel ORF-containing PERV γ1 clones consisting of hybrid sequences were revealed. Sequence comparison from published full-length PERV γ1 clones of the PERV subfamilies A, B, and C resulted in a lack of strict correlation of the classification of pro-pol and env. The results indicated the occurrence of causative recombination events between retroviral genomes. Thus, our study on PERV γ provides new data for the evaluation and selection of pigs intended to be used in xenotransplantation.
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Lin, X., P. J. Nelson, B. Frankfort, E. Tombler, R. Johnson et I. H. Gelman. « Isolation and characterization of a novel mitogenic regulatory gene, 322, which is transcriptionally suppressed in cells transformed by src and ras. » Molecular and Cellular Biology 15, no 5 (mai 1995) : 2754–62. http://dx.doi.org/10.1128/mcb.15.5.2754.
Texte intégralRésumé :
In an attempt to isolate novel regulatory and/or tumor suppressor genes, we identified cDNAs whose abundance is low in NIH 3T3 cells and further decreased following the expression of the activated oncogene, v-src. The transcription of one such gene, 322, is suppressed at least 15-fold in src-, ras-, and fos-transformed cells and 3-fold in myc-transformed cells but is unaffected in raf-, mos-, or neu-transformed cells. Activation of a ts-v-src allele in confluent 3Y1 fibroblasts resulted in an initial increase in 322 mRNA levels after 1 to 2 h followed by a rapid decrease to suppressed levels after 4 to 8 h. Morphological transformation was not detected until 12 h later, indicating that the accumulation of 322 transcripts is regulated by v-src and not as a consequence of transformation. Addition of fetal calf serum to starved subconfluent NIH 3T3 or 3Y1 fibroblasts resulted in a similar biphasic regulation of 322, indicating that 322 transcription is responsive to mitogenic factors. Sequence analysis of a putative full-length 322 cDNA clone (5.4 kb) identified a large open reading frame (ORF) encoding a 148.1-kDa product. In vitro transcription and translation of the 322 cDNA from a T7 promoter resulted in a 207-kDa product whose electrophoretic mobility on a sodium dodecyl sulfate-polyacrylamide gel electrophoresis gel was unaffected by digestion with endoglycosidase F. The discrepancy in predicted versus measured molecular weights may result from the high percentage of acidic residues (roughly 20% Glu or Asp) in the 322 ORF product. Comparison of the 322 cDNA ORF with sequences in data banks indicates that this gene is novel. The 322 ORF product contains a potential Cys-1-His-3 Zn finger, at least five nuclear localization signals of the adenovirus E1a motif K(R/K)X(R/K), and alternating acidic and basic domains. Overexpression of the 322 cells resulted in the selection of rapidly growing cells which had lost the transduced 322 cDNA. Thus, 322 represent a novel src- and ras-regulated gene which encodes a potential regulator of mitogenesis and/or tumor suppressor.
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Roy, Bijoyita, Westley J. Friesen, Yuki Tomizawa, John D. Leszyk, Jin Zhuo, Briana Johnson, Jumana Dakka et al. « Ataluren stimulates ribosomal selection of near-cognate tRNAs to promote nonsense suppression ». Proceedings of the National Academy of Sciences 113, no 44 (4 octobre 2016) : 12508–13. http://dx.doi.org/10.1073/pnas.1605336113.
Texte intégralRésumé :
A premature termination codon (PTC) in the ORF of an mRNA generally leads to production of a truncated polypeptide, accelerated degradation of the mRNA, and depression of overall mRNA expression. Accordingly, nonsense mutations cause some of the most severe forms of inherited disorders. The small-molecule drug ataluren promotes therapeutic nonsense suppression and has been thought to mediate the insertion of near-cognate tRNAs at PTCs. However, direct evidence for this activity has been lacking. Here, we expressed multiple nonsense mutation reporters in human cells and yeast and identified the amino acids inserted when a PTC occupies the ribosomal A site in control, ataluren-treated, and aminoglycoside-treated cells. We find that ataluren’s likely target is the ribosome and that it produces full-length protein by promoting insertion of near-cognate tRNAs at the site of the nonsense codon without apparent effects on transcription, mRNA processing, mRNA stability, or protein stability. The resulting readthrough proteins retain function and contain amino acid replacements similar to those derived from endogenous readthrough, namely Gln, Lys, or Tyr at UAA or UAG PTCs and Trp, Arg, or Cys at UGA PTCs. These insertion biases arise primarily from mRNA:tRNA mispairing at codon positions 1 and 3 and reflect, in part, the preferred use of certain nonstandard base pairs, e.g., U-G. Ataluren’s retention of similar specificity of near-cognate tRNA insertion as occurs endogenously has important implications for its general use in therapeutic nonsense suppression.
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Chen, Zigui, Rob DeSalle, Mark Schiffman, Rolando Herrero et Robert D. Burk. « Evolutionary Dynamics of Variant Genomes of Human Papillomavirus Types 18, 45, and 97 ». Journal of Virology 83, no 3 (26 novembre 2008) : 1443–55. http://dx.doi.org/10.1128/jvi.02068-08.
Texte intégralRésumé :
ABSTRACT Human papillomavirus type 18 (HPV18) and HPV45 account for approximately 20% of all cervix cancers. We show that HPV18, HPV45, and the recently discovered HPV97 comprise a clade sharing a most recent common ancestor within HPV α7 species. Variant lineages of these HPV types were classified by sequence analysis of the upstream regulatory region/E6 region among cervical samples from a population-based study in Costa Rica, and 27 representative genomes from each major variant lineage were sequenced. Nucleotide variation within HPV18 and HPV45 was 3.82% and 2.39%, respectively, and amino acid variation was 4.73% and 2.87%, respectively. Only 18 nucleotide variations, of which 10 were nonsynonymous, were identified among three HPV97 genomes. Full-genome comparisons revealed maximal diversity between HPV18 African and non-African variants (2.6% dissimilarity), whereas HPV18 Asian-American [E1 (AA)] and European (E2) variants were closely related (less than 0.5% dissimilarity); HPV45 genomes had a maximal difference of 1.6% nucleotides. Using a Bayesian Markov chain Monte Carlo (MCMC) method, the divergence times of HPV18, -45, and -97 from their most recent common ancestors indicated that HPV18 diverged approximately 7.7 million years (Myr) ago, whereas HPV45 and HPV97 split off around 5.7 Myr ago, in a period encompassing the divergence of the great ape species. Variants within the HPV18/45/97 lineages were estimated to have diverged from their common ancestors in the genus Homo within the last 1 Myr (<0.7 Myr). To investigate the molecular basis of HPV18, HPV45, and HPV97 evolution, regression models of codon substitution were used to identify lineages and amino acid sites under selective pressure. The E5 open reading frame (ORF) of HPV18 and the E4 ORFs of HPV18, HPV45, and HPV18/45/97 had nonsynonymous/synonymous substitution rate ratios (dN /dS ) over 1 indicative of positive Darwinian selection. The L1 ORF of HPV18 genomes had an increased proportion of nonsynonymous substitutions (4.93%; average dN /dS ratio [M3] = 0.3356) compared to HPV45 (1.86%; M3 = 0.1268) and HPV16 (2.26%; M3 = 0.1330) L1 ORFs. In contrast, HPV18 and HPV16 genomes had similar amino acid substitution rates within the E1 ORF (2.89% and 3.24%, respectively), while HPV45 E1 was highly conserved (amino acid substitution rate was 0.77%). These data provide an evolutionary history of this medically important clade of HPVs and identify an unexpected divergence of the L1 gene of HPV18 that may have clinical implications for the long-term use of an L1-virus-like particle-based prophylactic vaccine.
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Lucaci, Alexander G., Jordan D. Zehr, Stephen D. Shank, Dave Bouvier, Alexander Ostrovsky, Han Mei, Anton Nekrutenko, Darren P. Martin et Sergei L. Kosakovsky Pond. « RASCL : Rapid Assessment of Selection in CLades through molecular sequence analysis ». PLOS ONE 17, no 11 (2 novembre 2022) : e0275623. http://dx.doi.org/10.1371/journal.pone.0275623.
Texte intégralRésumé :
An important unmet need revealed by the COVID-19 pandemic is the near-real-time identification of potentially fitness-altering mutations within rapidly growing SARS-CoV-2 lineages. Although powerful molecular sequence analysis methods are available to detect and characterize patterns of natural selection within modestly sized gene-sequence datasets, the computational complexity of these methods and their sensitivity to sequencing errors render them effectively inapplicable in large-scale genomic surveillance contexts. Motivated by the need to analyze new lineage evolution in near-real time using large numbers of genomes, we developed the Rapid Assessment of Selection within CLades (RASCL) pipeline. RASCL applies state of the art phylogenetic comparative methods to evaluate selective processes acting at individual codon sites and across whole genes. RASCL is scalable and produces automatically updated regular lineage-specific selection analysis reports: even for lineages that include tens or hundreds of thousands of sampled genome sequences. Key to this performance is (i) generation of automatically subsampled high quality datasets of gene/ORF sequences drawn from a selected “query” viral lineage; (ii) contextualization of these query sequences in codon alignments that include high-quality “background” sequences representative of global SARS-CoV-2 diversity; and (iii) the extensive parallelization of a suite of computationally intensive selection analysis tests. Within hours of being deployed to analyze a novel rapidly growing lineage of interest, RASCL will begin yielding JavaScript Object Notation (JSON)-formatted reports that can be either imported into third-party analysis software or explored in standard web-browsers using the premade RASCL interactive data visualization dashboard. By enabling the rapid detection of genome sites evolving under different selective regimes, RASCL is well-suited for near-real-time monitoring of the population-level selective processes that will likely underlie the emergence of future variants of concern in measurably evolving pathogens with extensive genomic surveillance.
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ROY, S., A. BANERJEE, J. TARAFDAR, B. K. SENAPATI et I. DASGUPTA. « Transfer of transgenes for resistance to rice tungro disease into high-yielding rice cultivars through gene-based marker-assisted selection ». Journal of Agricultural Science 150, no 5 (octobre 2012) : 610–18. http://dx.doi.org/10.1017/s0021859611000827.
Texte intégralRésumé :
SUMMARYRice tungro disease (RTD), caused by the simultaneous infection of rice tungro bacilliform virus (RTBV) and rice tungro spherical virus (RTSV), is one of the major threats to sustainable rice production in South and Southeast Asia. Transgenic resistance against RTBV has been reported previously using an RNA interference (RNAi) construct (ORF IV of RTBV, placed both in sense and anti-sense orientation under CaMV 35S promoter), in the scented rice line Pusa Basmati-1 (PB-1). This construct was transferred to two high-yielding tungro-susceptible indica rice cultivars (IET4094 and IET4786) from the transgenic PB-1 rice line using back cross breeding till the BC2F3 stage. On challenge inoculation, the progenies (BC2F1) showed mild symptoms of tungro, in contrast to severe symptoms displayed by the recurrent parents. Segregation of the transgene indicated near homozygosity of the plants at the BC2F3 stage, implying that the lines can be used as a valuable resistance source for further breeding against RTD.
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Yero, Daniel, Caroline Vipond, Yanet Climent, Gretel Sardiñas, Ian M. Feavers et Rolando Pajón. « Variation in the Neisseria meningitidis FadL-like protein : an evolutionary model for a relatively low-abundance surface antigen ». Microbiology 156, no 12 (1 décembre 2010) : 3596–608. http://dx.doi.org/10.1099/mic.0.043182-0.
Texte intégralRésumé :
The molecular diversity of a novel Neisseria meningitidis antigen, encoded by the ORF NMB0088 of MC58 (FadL-like protein), was assessed in a panel of 64 diverse meningococcal strains. The panel consisted of strains belonging to different serogroups, serotypes, serosubtypes and MLST sequence types, of different clinical sources, years and countries of isolation. Based on the sequence variability of the protein, the FadL-like protein has been divided into four variant groups in this species. Antigen variants were associated with specific serogroups and MLST clonal complexes. Maximum-likelihood analyses were used to determine the relationships among sequences and to compare the selection pressures acting on the encoded protein. Furthermore, a model of population genetics and molecular evolution was used to detect natural selection in DNA sequences using the non-synonymous : synonymous substitution (d N : d S) ratio. The meningococcal sequences were also compared with those of the related surface protein in non-pathogenic commensal Neisseria species to investigate potential horizontal gene transfer. The N. meningitidis fadL gene was subject to only weak positive selection pressure and was less diverse than meningococcal major outer-membrane proteins. The majority of the variability in fadL was due to recombination among existing alleles from the same or related species that resulted in a discrete mosaic structure in the meningococcal population. In general, the population structuring observed based on the FadL-like membrane protein indicates that it is under intermediate immune selection. However, the emergence of a new subvariant within the hyperinvasive lineages demonstrates the phenotypic adaptability of N. meningitidis, probably in response to selective pressure.
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Chen, Zigui, Masanori Terai, Leiping Fu, Rolando Herrero, Rob DeSalle et Robert D. Burk. « Diversifying Selection in Human Papillomavirus Type 16 Lineages Based on Complete Genome Analyses ». Journal of Virology 79, no 11 (1 juin 2005) : 7014–23. http://dx.doi.org/10.1128/jvi.79.11.7014-7023.2005.
Texte intégralRésumé :
ABSTRACT Human papillomavirus type 16 (HPV16) is the primary etiological agent of cervical cancer, the second most common cancer in women worldwide. Complete genomes of 12 isolates representing the major lineages of HPV16 were cloned and sequenced from cervicovaginal cells. The sequence variations within the open reading frames (ORFs) and noncoding regions were identified and compared with the HPV16R reference sequence (50). This whole-genome approach gives us unprecedented precision in detailing sequence-level changes that are under selection on a whole-viral-genome scale. Of 7,908 base pair nucleotide positions, 313 (4.0%) were variable. Within the 2,452 amino acids (aa) comprising 8 ORFs, 243 (9.9%) amino acid positions were variable. In order to investigate the molecular evolution of HPV16 variants, maximum likelihood models of codon substitution were used to identify lineages and amino acid sites under selective pressure. Five codon sites in the E5 (aa 48, 65) and E6 (aa 10, 14, 83) ORFs were demonstrated to be under diversifying selective pressure. The E5 ORF had the overall highest nonsynonymous/synonymous substitution rate (ω) ratio (M3 = 0.7965). The E2 gene had the next-highest ω ratio (M3 = 0.5611); however, no specific codons were under positive selection. These data indicate that the E6 and E5 ORFs are evolving under positive Darwinian selection and have done so in a relatively short time period. Whether response to selective pressure upon the E5 and E6 ORFs contributes to the biological success of HPV16, its specific biological niche, and/or its oncogenic potential remains to be established.
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Stedman, Kenneth M., Christa Schleper, Evelyn Rumpf et Wolfram Zillig. « Genetic Requirements for the Function of the Archaeal Virus SSV1 in Sulfolobus solfataricus : Construction and Testing of Viral Shuttle Vectors ». Genetics 152, no 4 (1 août 1999) : 1397–405. http://dx.doi.org/10.1093/genetics/152.4.1397.
Texte intégralRésumé :
Abstract Directed open reading frame (ORF) disruption and a serial selection technique in Escherichia coli and the extremely thermophilic archaeon Sulfolobus solfataricus allowed the identification of otherwise cryptic crucial and noncrucial viral open reading frames in the genome of the archaeal virus SSV1. It showed that the 15.5-kbp viral genome can incorporate a 2.96-kbp insertion without loss of viral function and package this DNA properly into infectious virus particles. The selection technique, based on the preferential binding of ethidium bromide to relaxed DNA and the resulting inhibition of endonuclease cleavage to generate a pool of mostly singly cut molecules, should be generally applicable. A fully functional viral shuttle vector for S. solfataricus and E. coli was made. This vector spreads efficiently through infected cultures of S. solfataricus, its replication is induced by UV irradiation, it forms infectious virus particles, and it is stable at high copy number in both S. solfataricus and E. coli. The classification of otherwise unidentifiable ORFs in SSV1 facilitates genetic analysis of this virus, and the shuttle vector should be useful for the development of genetic systems for Crenarchaeota.
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Chen, Yi-Ywan M., Hui-Ru Shieh, Cheng-Tzer Lin et Shin-Yi Liang. « Properties and Construction of Plasmid pFW213, a Shuttle Vector with the Oral Streptococcus Origin of Replication ». Applied and Environmental Microbiology 77, no 12 (29 avril 2011) : 3967–74. http://dx.doi.org/10.1128/aem.02828-10.
Texte intégralRésumé :
ABSTRACTStreptococcus parasanguinisis among the most successful colonizers of the human body. Strain FW213 harbors a 7.0-kb cryptic plasmid, pFW213, with a copy number at 5 to 10 per chromosome. Sequence and functional analyses of pFW213 revealed that the open reading frame (ORF) encoding the replication protein (Rep) is essential for the replication of pFW213, and the putative plasmid addiction system (RelB and RelE) and an ORF (ORF6) with no known function are required for its stability. The minimal replicon of pFW213 contains therepgene and its 5′-flanking 390-bp region. Within the minimal replicon, an A/T-rich region followed by 5 contiguous 22-bp repeats was located 5′ of the ATG ofrep.No single-stranded replication intermediates were detected in the derivatives of pFW213, suggesting that pFW213 replicates via the theta replication mechanism. The minimal replicon was unstable in streptococcal hosts without selection, but the stability was greatly enhanced in derivatives containing the intactrelBEgenes. AStreptococcus-Escherichia colishuttle vector, pCG1, was constructed with the pFW213 replicon. Plasmid pCG1 features a multiple cloning region and a spectinomycin resistance determinant that is expressed in bothStreptococcusspp. andE. coli. Various streptococcal DNA fragments were cloned in pCG1, and the recombinant constructs were stably maintained in the streptococcal hosts. Since pCG1 is compatible with the most widely used streptococcal replicon, pVA380-1, pCG1 will provide a much needed tool allowing the cloning of two genes that work in concert in the same host.
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Lothert, Keven, Felix Pagallies, Thomas Feger, Ralf Amann et Michael W. Wolff. « Selection of chromatographic methods for the purification of cell culture-derived Orf virus for its application as a vaccine or viral vector ». Journal of Biotechnology 323 (novembre 2020) : 62–72. http://dx.doi.org/10.1016/j.jbiotec.2020.07.023.
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Dahl, Kristin Hegstad, Gunnar Skov Simonsen, Ørjan Olsvik et Arnfinn Sundsfjord. « Heterogeneity in the vanB Gene Cluster of Genomically Diverse Clinical Strains of Vancomycin-Resistant Enterococci ». Antimicrobial Agents and Chemotherapy 43, no 5 (1 mai 1999) : 1105–10. http://dx.doi.org/10.1128/aac.43.5.1105.
Texte intégralRésumé :
ABSTRACT Molecular analysis of 17 genomically unrelated clinical VanB-type vancomycin-resistant enterococcus isolates from hospital patients in Germany, Norway, Sweden, the United Kingdom and the United States revealed three subtypes of the vanB gene cluster—vanB1, vanB2, andvanB3—which was in accordance with previous subtyping of the ligase gene sequence. There was no correlation betweenvanB subtype and levels of vancomycin resistance. All strains studied carried a structurally conserved vanB gene cluster as shown by long-range PCR (long PCR) covering 5,959 bp of the published sequence in vanB1 strain V583. Restriction analysis of long PCR amplicons displayed one unique vanB1pattern and a second vanB2- and vanB3-specific pattern. The vanSB-vanYB intergenic sequences with flanking coding regions were identical within eachvanB subtype with one exception. A U.S. vanB2isolate had a 789-bp enlargement of this region containing a putative open reading frame (ORF) with substantial homology to an ORF in theClostridium perfringens IS1469 insertion element. The molecular heterogeneity within the vanB gene cluster has implications for the selection of PCR primers, as the primers must ensure detection of all vanB subtypes, and is of importance when considering reservoirs and dissemination ofvanB resistance. The molecular identity within thevanB1 and the vanB2 subtype indicates horizontal transmission of both gene clusters between isolates in different geographical areas. Restriction analysis of long PCRvanB amplicons may reveal specific varieties that can be used as epidemiological markers for mobile determinants conferring VanB-type resistance. The finding of three distinct vanBgene clusters should encourage a search for different environmental reservoirs of vanB resistance determinants.
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Mérai, Zsuzsanna, Zoltán Kerényi, Attila Molnár, Endre Barta, Anna Válóczi, György Bisztray, Zoltán Havelda, József Burgyán et Dániel Silhavy. « Aureusvirus P14 Is an Efficient RNA Silencing Suppressor That Binds Double-Stranded RNAs without Size Specificity ». Journal of Virology 79, no 11 (1 juin 2005) : 7217–26. http://dx.doi.org/10.1128/jvi.79.11.7217-7226.2005.
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ABSTRACT RNA silencing is a conserved eukaryotic gene regulatory system in which sequence specificity is determined by small RNAs. Plant RNA silencing also acts as an antiviral mechanism; therefore, viral infection requires expression of a silencing suppressor. The mechanism and the evolution of silencing suppression are still poorly understood. Tombusvirus open reading frame (ORF) 5-encoded P19 is a size-selective double-stranded RNA (dsRNA) binding protein that suppresses silencing by sequestering double-stranded small interfering RNAs (siRNAs), the specificity determinant of the antiviral silencing system. To better understand the evolution of silencing suppression, we characterized the suppressor of the type member of Aureusviruses, the closest relatives of the genus Tombusvirus. We show that the Pothos latent virus (PoLV) ORF 5-encoded P14 is an efficient suppressor of both virus- and transgene-induced silencing. Findings that in vitro P14 binds dsRNAs and double-stranded siRNAs without obvious size selection suggest that P14, unlike P19, can suppress silencing by sequestering both long dsRNA and double-stranded siRNA components of the silencing machinery. Indeed, P14 prevents the accumulation of hairpin transcript-derived siRNAs, indicating that P14 inhibits inverted repeat-induced silencing by binding the long dsRNA precursors of siRNAs. However, viral siRNAs accumulate to high levels in PoLV-infected plants; therefore, P14 might inhibit virus-induced silencing by sequestering double-stranded siRNAs. Finally, sequence analyses suggest that P14 and P19 suppressors diverged from an ancient dsRNA binding suppressor that evolved as a nested protein within the common ancestor of aureusvirus-tombusvirus movement proteins.
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Yao, Xiaoting, Ming Pang, Tianxing Wang, Xi Chen, Xidian Tang, Jianjun Chang, Dekun Chen et Wentao Ma. « Genomic Features and Evolution of the Parapoxvirus during the Past Two Decades ». Pathogens 9, no 11 (27 octobre 2020) : 888. http://dx.doi.org/10.3390/pathogens9110888.
Texte intégralRésumé :
Parapoxvirus (PPV) has been identified in some mammals and poses a great threat to both the livestock production and public health. However, the prevalence and evolution of this virus are still not fully understood. Here, we performed an in silico analysis to investigate the genomic features and evolution of PPVs. We noticed that although there were significant differences of GC contents between orf virus (ORFV) and other three species of PPVs, all PPVs showed almost identical nucleotide bias, that is GC richness. The structural analysis of PPV genomes showed the divergence of different PPV species, which may be due to the specific adaptation to their natural hosts. Additionally, we estimated the phylogenetic diversity of seven different genes of PPV. According to all available sequences, our results suggested that during 2010–2018, ORFV was the dominant virus species under the selective pressure of the optimal gene patterns. Furthermore, we found the substitution rates ranged from 3.56 × 10−5 to 4.21 × 10−4 in different PPV segments, and the PPV VIR gene evolved at the highest substitution rate. In these seven protein-coding regions, purifying selection was the major evolutionary pressure, while the GIF and VIR genes suffered the greatest positive selection pressure. These results may provide useful knowledge on the virus genetic evolution from a new perspective which could help to create prevention and control strategies.
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Zhou, Yu, Lin Zhang, Xiaoming Zhang, Hongyue Zu, Hong Di, Ling Dong, Xianjun Liu et al. « Rice black-streaked dwarf virus Genome in China : Diversification, Phylogeny, and Selection ». Plant Disease 101, no 9 (septembre 2017) : 1588–96. http://dx.doi.org/10.1094/pdis-12-16-1814-re.
Texte intégralRésumé :
Rice black-streaked dwarf virus (RBSDV), a Fijivirus, causes maize rough dwarf disease and rice black-streaked dwarf disease in the summer maize-growing regions of the Yellow and Huai rivers, respectively, in China. Nevertheless, the diversification and selection of the entire genome from S1 to S10 have not been illuminated. Molecular variation, evolution, conserved regions, and other genomic properties were analyzed in 21 RBSDV isolates from maize (Zea mays L.) and rice (Oryza sativa) hosts sampled from nine geographic locations in China. Low codon adaptation index values ranging from 0.1878 to 0.2918 indicated a low degree of codon-usage bias and low potential expression for all 13 RBSDV open reading frames (ORFs). ORF9-2 showed a stronger effect of codon usage bias than did other ORFs, as the majority of points for this ORF lay close to the standard curve in the Nc plot (the effective number of codons [Nc] versus the frequency of G+C at synonymous third-base positions [GC3]). A 9-bp deletion mutation was detected in the RBSDV genome in the 3′ UTR of S8. Nucleotide diversity analysis indicated that the structural proteins of RBSDV, such as S2 and S4, were all more conserved than nonstructural proteins such as S9. Nucleotide diversity (π) was highest among S9 sequences (0.0656), and was significantly higher than among S4 sequences (0.0225, P < 0.01). The number of conserved regions among the 10 segments varied substantially. The highest number of conserved regions (5) was found in S5, whereas no conserved regions were identified in S9. Nucleotide diversity and the number of conserved regions were independent of the lengths of segments. Nucleotide diversity was also not correlated with the number of conserved regions in segments. Ten recombination events in 21 isolates were found in seven segments with breakpoint positions in UTRs, intergenic spacer regions, and gene coding regions. The number of recombination events was also independent of the lengths of segments. RBSDV isolates from China could be phylogenetically classified into two groups using either 10 segment sequences or the concatenated sequence of S1 through S10, regardless of host or geographical location. The phylogenetic tree generated from pairwise nucleotide identities of individual RBSDV segments such as S9 and S3, with nucleotide identity values of 93.74% and 95.86%, respectively, is similar to the tree constructed from the concatenated sequences of the entire RBSDV genome. The 13 RBSDV ORFs were under negative and purifying selection (Ka/Ks < 1). ORF5-2 was under the greatest selection pressure; however, ORF2, which encodes the core protein of RBSDV, was under the lowest selection pressure.
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McLysaght, Aoife, et Daniele Guerzoni. « New genes from non-coding sequence : the role of de novo protein-coding genes in eukaryotic evolutionary innovation ». Philosophical Transactions of the Royal Society B : Biological Sciences 370, no 1678 (26 septembre 2015) : 20140332. http://dx.doi.org/10.1098/rstb.2014.0332.
Texte intégralRésumé :
The origin of novel protein-coding genes de novo was once considered so improbable as to be impossible. In less than a decade, and especially in the last five years, this view has been overturned by extensive evidence from diverse eukaryotic lineages. There is now evidence that this mechanism has contributed a significant number of genes to genomes of organisms as diverse as Saccharomyces , Drosophila , Plasmodium , Arabidopisis and human. From simple beginnings, these genes have in some instances acquired complex structure, regulated expression and important functional roles. New genes are often thought of as dispensable late additions; however, some recent de novo genes in human can play a role in disease. Rather than an extremely rare occurrence, it is now evident that there is a relatively constant trickle of proto-genes released into the testing ground of natural selection. It is currently unknown whether de novo genes arise primarily through an ‘RNA-first’ or ‘ORF-first’ pathway. Either way, evolutionary tinkering with this pool of genetic potential may have been a significant player in the origins of lineage-specific traits and adaptations.
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Kuznetsova, Irina, Anna-Polina Shurygina, Brigitte Wolf, Markus Wolschek, Florian Enzmann, Abylay Sansyzbay, Berik Khairullin et al. « Adaptive mutation in nuclear export protein allows stable transgene expression in a chimaeric influenza A virus vector ». Journal of General Virology 95, no 2 (1 février 2014) : 337–49. http://dx.doi.org/10.1099/vir.0.056036-0.
Texte intégralRésumé :
The development of influenza virus vectors with long insertions of foreign sequences remains difficult due to the small size and instable nature of the virus. Here, we used the influenza virus inherent property of self-optimization to generate a vector stably expressing long transgenes from the NS1 protein ORF. This was achieved by continuous selection of bright fluorescent plaques of a GFP-expressing vector during multiple passages in mouse B16f1 cells. The newly generated vector acquired stability in IFN-competent cell lines and in vivo in murine lungs. Although improved vector fitness was associated with the appearance of four coding mutations in the polymerase (PB2), haemagglutinin and non-structural (NS) segments, the stability of the transgene expression was dependent primarily on the single mutation Q20R in the nuclear export protein (NEP). Importantly, a longer insert, such as a cassette of 1299 nt encoding two Mycobacterium tuberculosis Esat6 and Ag85A proteins, could substitute for the GFP transgene. Thus, the inherent property of the influenza virus to adapt can also be used to adjust a vector backbone to give stable expression of long transgenes.
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Reguzova, Alena, Michael Ghosh, Melanie Müller, Hanns-Joachim Rziha et Ralf Amann. « Orf Virus-Based Vaccine Vector D1701-V Induces Strong CD8+ T Cell Response against the Transgene but Not against ORFV-Derived Epitopes ». Vaccines 8, no 2 (10 juin 2020) : 295. http://dx.doi.org/10.3390/vaccines8020295.
Texte intégralRésumé :
The potency of viral vector-based vaccines depends on their ability to induce strong transgene-specific immune response without triggering anti-vector immunity. Previously, Orf virus (ORFV, Parapoxvirus) strain D1701-V was reported as a novel vector mediating protection against viral infections. The short-lived ORFV-specific immune response and the absence of virus neutralizing antibodies enables repeated immunizations and enhancement of humoral immune responses against the inserted antigens. However, only limited information exists about the D1701-V induced cellular immunity. In this study we employed major histocompatibility complex (MHC) ligandomics and immunogenicity analysis to identify ORFV-specific epitopes. Using liquid chromatography-tandem mass spectrometry we detected 36 ORFV-derived MHC I peptides, originating from various proteins. Stimulated splenocytes from ORFV-immunized mice did not exhibit specific CD8+ T cell responses against the tested peptides. In contrast, immunization with ovalbumin-expressing ORFV recombinant elicited strong SIINFEKL-specific CD8+ T lymphocyte response. In conclusion, our data indicate that cellular immunity to the ORFV vector is negligible, while strong CD8+ T cell response is induced against the inserted transgene. These results further emphasize the ORFV strain D1701-V as an attractive vector for vaccine development. Moreover, the presented experiments describe prerequisites for the selection of T cell epitopes exploitable for generation of ORFV-based vaccines by reverse genetics.
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Simpson, J’Zaria, Christine A. Kozak et Guney Boso. « Cross-species transmission of an ancient endogenous retrovirus and convergent co-option of its envelope gene in two mammalian orders ». PLOS Genetics 18, no 10 (14 octobre 2022) : e1010458. http://dx.doi.org/10.1371/journal.pgen.1010458.
Texte intégralRésumé :
Endogenous retroviruses (ERVs) found in vertebrate genomes are remnants of retroviral invasions of their ancestral species. ERVs thus represent molecular fossil records of ancient retroviruses and provide a unique opportunity to study viral-host interactions, including cross-species transmissions, in deep time. While most ERVs contain the mutated remains of the original retrovirus, on rare occasions evolutionary selection pressures lead to the co-option/exaptation of ERV genes for a host function. Here, we report the identification of two ancient related non-orthologous ERV env genes, ARTenvV and CARenvV, that are preserved with large open reading frames (ORFs) in the mammalian orders Artiodactyla and Carnivora, respectively, but are not found in other mammals. These Env proteins lack a transmembrane motif, but phylogenetic analyses show strong sequence preservation and positive selection of the env surface ORF in their respective orders, and transcriptomic analyses show a broad tissue expression pattern for both ARTenvV and CARenvV, suggesting that these genes may be exapted for a host function. Multiple lines of evidence indicate that ARTenvV and CARenvV were derived from an ancient ancestral exogenous gamma-like retrovirus that was independently endogenized in two mammalian orders more than 60 million years ago, which roughly coincides with the K-Pg mass extinction event and subsequent mammalian diversification. Thus, these findings identify the oldest known retroviral cross-ordinal transmission of a gamma-like retrovirus with no known extant infectious counterpart in mammals, and the first discovery of the convergent co-option of an ERV gene derived from the same ancestral retrovirus in two different mammalian orders.
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Pignatelli, S., P. Dal Monte, G. Rossini, S. Chou, T. Gojobori, K. Hanada, J. J. Guo et al. « Human cytomegalovirus glycoprotein N (gpUL73-gN) genomic variants : identification of a novel subgroup, geographical distribution and evidence of positive selective pressure ». Journal of General Virology 84, no 3 (1 mars 2003) : 647–55. http://dx.doi.org/10.1099/vir.0.18704-0.
Texte intégralRésumé :
Human cytomegalvirus (HCMV) ORF UL73 is a polymorphic locus, encoding the viral glycoprotein gpUL73-gN, a component of the gC-II envelope complex. The previously identified gN genomic variants, denoted gN-1, gN-2, gN-3 and gN-4, were further investigated in this work by analysing a large panel of HCMV clinical isolates collected from all over the world (223 samples). Sequencing and phylogenetic analysis confirmed the existence of the four gN genotypes, but also allowed the identification of a novel subgroup belonging to the gN-3 genotype, which was designated gN-3b. The number of non-synonymous (dN) and synonymous (dS) nucleotide substitutions and their ratio (dN/dS) were estimated among the gN genotypes to evaluate the possibility of positive selection. Results showed that the four variants evolved by neutral (random) selection, but that the gN-3 and gN-4 genotypes are maintained by positive selective pressure. The 223 HCMV clinical isolates were subdivided according to their geographical origin, and four main regions of gN prevalence were identified: Europe, China, Australia and Northern America. The gN variants were found to be widespread and represented within the regions analysed without any significant difference, and no new genotype was detected. Finally, for clinical and epidemiological purposes, a rapid and low-cost method for genetic grouping of the HCMV clinical isolates was developed based on the RFLP revealed by SacI, ScaI and SalI digestion of the PCR-amplified UL73 sequence. This technique enabled us to distinguish all four gN genomic variants and also their subtypes.
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Adams, Cynthia R., Vicki S. Blazer, Jim Sherry, Robert Scott Cornman et Luke R. Iwanowicz. « Phylogeographic Genetic Diversity in the White Sucker Hepatitis B Virus across the Great Lakes Region and Alberta, Canada ». Viruses 13, no 2 (12 février 2021) : 285. http://dx.doi.org/10.3390/v13020285.
Texte intégralRésumé :
Hepatitis B viruses belong to a family of circular, double-stranded DNA viruses that infect a range of organisms, with host responses that vary from mild infection to chronic infection and cancer. The white sucker hepatitis B virus (WSHBV) was first described in the white sucker (Catostomus commersonii), a freshwater teleost, and belongs to the genus Parahepadnavirus. At present, the host range of WSHBV and its impact on fish health are unknown, and neither genetic diversity nor association with fish health have been studied in any parahepadnavirus. Given the relevance of genomic diversity to disease outcome for the orthohepadnaviruses, we sought to characterize genomic variation in WSHBV and determine how it is structured among watersheds. We identified WSHBV-positive white sucker inhabiting tributaries of Lake Michigan, Lake Superior, Lake Erie (USA), and Lake Athabasca (Canada). Copy number in plasma and in liver tissue was estimated via qPCR. Templates from 27 virus-positive fish were amplified and sequenced using a primer-specific, circular long-range amplification method coupled with amplicon sequencing on the Illumina MiSeq. Phylogenetic analysis of the WSHBV genome identified phylogeographical clustering reminiscent of that observed with human hepatitis B virus genotypes. Notably, most non-synonymous substitutions were found to cluster in the pre-S/spacer overlap region, which is relevant for both viral entry and replication. The observed predominance of p1/s3 mutations in this region is indicative of adaptive change in the polymerase open reading frame (ORF), while, at the same time, the surface ORF is under purifying selection. Although the levels of variation we observed do not meet the criteria used to define sub/genotypes of human and avian hepadnaviruses, we identified geographically associated genome variation in the pre-S and spacer domain sufficient to define five WSHBV haplotypes. This study of WSHBV genetic diversity should facilitate the development of molecular markers for future identification of genotypes and provide evidence in future investigations of possible differential disease outcomes.