Novel phenotype of RNA synthesis expressed by vesicular stomatitis virus isolated from persistent infection

Recent developments and potential of robotics in plant eco-phenotyping

Automated acquisition of plant eco-phenotypic information can serve as a decision-making basis for precision agricultural management and can also provide detailed insights into plant growth status, pest management, water and fertilizer management for plant breeders and plant physiologists. Because the microscopic components and macroscopic morphology of plants will be affected by the ecological environment, research on plant eco-phenotyping is more meaningful than the study of single-plant phenotyping. To achieve high-throughput acquisition of phenotyping information, the combination of high-precision sensors and intelligent robotic platforms have become an emerging research focus. Robotic platforms and automated systems are the important carriers of phenotyping monitoring sensors that enable large-scale screening. Through the diverse design and flexible systems, an efficient operation can be achieved across a range of experimental and field platforms. The combination of robot technology and plant phenotyping monitoring tools provides the data to inform novel artificial intelligence (AI) approaches that will provide steppingstones for new research breakthroughs. Therefore, this article introduces robotics and eco-phenotyping and examines research significant to this novel domain of plant eco-phenotyping. Given the monitoring scenarios of phenotyping information at different scales, the used intelligent robot technology, efficient automation platform, and advanced sensor equipment are summarized in detail. We further discuss the challenges posed to current research as well as the future developmental trends in the application of robot technology and plant eco-phenotyping. These include the use of collected data for AI applications and high-bandwidth data transfer, and large well-structured (meta) data storage approaches in plant sciences and agriculture.

The L protein of a VSV mutant isolated from a persistent infection is responsible for viral interference and dominance over the wild-type

The dominance of a mutant isolated from a persistent infection (VSV-Pi) over wild-type vesicular stomatitis virus (wt-VSV) in mixed infections was described previously (J. A. Jordan and J. S. Youngner, 1987, Virology, 158, 407-413). In an attempt to identify the VSV-Pi gene product responsible for transcriptional interference, various combinations of purified VSV-Pi and wt-VSV transcribing core proteins were analyzed in an in vitro transcription assay and compared to homologous wild-type controls. The reconstitution studies revealed that the VSV-Pi RNA dependent-RNA polymerase (L protein) has a dominant activity which works in trans to inhibit wt-VSV transcription.

Vesicular stomatitis virus in Drosophila melanogaster cells: regulation of viral transcription and replication

Vesicular stomatitis virus RNA synthesis was investigated during the establishment of persistent infection in Drosophila melanogaster cells. The transcription rate declined as early as 5 h after infection and was strongly inhibited after 7 h, leading to a decrease in viral mRNA levels and in viral protein synthesis rates. Full-length plus-strand antigenomes and minus-strand genomes were detected after a 3-h lag time and accumulated until 15 h after infection. Short encapsidated plus-strand molecules were also generated corresponding to the 5' end of viral defective antigenomes. Assembly and release of virions were not restricted, but their infectivity was extremely reduced. In persistently infected cells, an equilibrium was reached where the level of intracellular genomes maintained was constant and maximal even after the rate of all viral syntheses had decreased. These results are discussed with regard to the establishment of persistent infection.

Dominance of temperature-sensitive phenotypes. II. Vesicular stomatitis virus mutants from a persistent infection interfere with shut-off of host protein synthesis by wild-type virus

The dominance of a mutant (VSV-PI) isolated from a long-term persistent infection over wild-type vesicular stomatitis virus (wt-VSV) is reported. This dominance has some important differences from and similarities to the dominance of conventional ts mutants studied previously (J. S. Youngner, D. W. Frielle, and P. Whitaker-Dowling, 1986, Virology 155, 225-235). Unlike the ts mutants representing complementation groups I and IV, coinfection with VSV-PI does not reduce the yield of infectious wt-VSV at either the permissive (37 degrees) or nonpermissive (39.5 degrees) temperatures. However, in double infections with wt-VSV and VSV-PI at 37 degrees, viral RNA synthesis patterns were converted to those of the RNA synthesis phenotype of VSV-PI: reduced mRNA transcription and enhanced replication of genomic RNA. In addition, VSV-PI which shuts off host protein synthesis very inefficiently was able to interfere in double infections with the ability of wt-VSV to rapidly shut off host protein synthesis. This finding suggests that the mutant virus is not just missing the factor(s) responsible for the inhibition of host protein synthesis but has a dominant activity which works in trans to interfere with the shut-off function of wt-VSV. Ultraviolet irradiation of VSV-PI was used to determine the target size of the interference function. The calculated value for the uv target size is equal to that of the viral genome. This suggests that either viral replication or the expression of the last gene on the viral genome (encoding the L protein) is required for interference by VSV-PI with the shut-off of host cell protein synthesis by wt-VSV.

Dominance of temperature-sensitive phenotypes. I. Studies of the mechanism of inhibition of the growth of wild-type vesicular stomatitis virus

It has been reported previously that temperature-sensitive (ts) mutants of vesicular stomatitis virus (VSV) with an RNA- phenotype interfere with the growth of wild-type (wt)-VSV at both the permissive (34 degrees) and nonpermissive (39.5 degrees) temperatures (J. S. Youngner and D. O. Quagliana (1976) J. Virol. 19, 102-107). Investigation of the mechanism of this interference has revealed the following information. In double infection with RNA- ts mutants and wt-VSV, the cumulative synthesis of viral RNA is inhibited. By varying the relative multiplicities of the two viruses, it was observed that the level of RNA synthesis reflects the level of interference with wt-VSV growth. Although viral RNA synthesis was severely compromised in double infections, this inhibition was not at the level of primary transcription or the translation of primary transcripts. Rather, secondary transcription and genome RNA replication were drastically reduced. Sequential infection with wt-VSV and the ts mutants revealed that there is an early point in the replication cycle of wt-VSV (1 to 2 hr) after which the ts mutants can no longer interfere with the growth of wt-VSV. Ultraviolet irradiation of ts G 41, a mutant belonging to complementation group IV, was used to determine the target size of the interference function. The calculated value for the target size was very close to the target size of the N gene. Additional experiments showed that RNA+ ts mutants representing complementation groups III and V also were able to interfere with the growth of wt-VSV.

Vaccinia-mediated rescue of encephalomyocarditis virus from the inhibitory effects of interferon

Coinfection of mouse L cells with vaccinia virus rescues encephalomyocarditis virus (EMC) from the inhibitory effect of interferon (IFN). The vaccinia-mediated rescue of EMC growth increases the yield of EMC as much as 1000-fold and is optimum when vaccinia is used at a multiplicity of infection of 1. This rescue correlates with a vaccinia-dependent stimulation of EMC gene expression. Evidence is presented to indicate that the rescue by vaccinia does not involve a block of the 2'-5'A synthetase pathway. However, the vaccinia rescue function is correlated with a vaccinia-mediated inhibition of the IFN-induced protein kinase.

Persistent infection of a temperature-sensitive G31 vesicular stomatitis virus mutant in neural and nonneural cells: biological and virological characteristics

Mouse L-929 cells (L cells), human oligodendroglioma cells, and rat glioma cells were persistently infected with vesicular stomatitis virus (VSV) mutant tsG31 and maintained for at least 4 years at 37 degrees C. The striking observation in this study was that there is a marked difference in neurovirulence among the persistent infections (PIs) derived from the three cell lines. tsG31 VSV derived from persistently infected L cells and oligodendroglioma cells remained highly virulent as assayed by intracerebral (i.c.) inoculation into 3-week-old Swiss mice. In contrast, tsG31 VSV isolated from glioma cells lost neurovirulence by passage 20. Persistently infected glioma cells were carried through more than 180 passages without reemergence of neurovirulent virus. Importantly, glioma PI virus neurovirulence was restored quickly by i.c. passage in mice and more slowly by passage through normal L cells. In contrast, the neurovirulence of L-cell PI virus was enhanced by i.c. passage in mice and slowly reduced by passage through normal glioma cells. Furthermore, no alteration in neurovirulence was observed in the case of oligodendroglioma PI virus. Although the mechanism(s) underlying the loss of virulence in glioma cells is unclear, our studies suggest that either strict temperature sensitivity or the presence of a heat-labile transcriptase or both play a major role in this phenomenon.

Base mutations in the terminal noncoding regions of the genome of vesicular stomatitis virus isolated from persistent infections of L cells

The 3'-terminal regions of the genomes of vesicular stomatitis virus obtained from two long-term, independently initiated persistent infections of L cells were found to contain several sequence mutations. In contrast to the hypermutability displayed in the 5'-terminal regions of the genomes of viruses obtained from persistent infections of baby hamster kidney (BHK) cells (P. J. O'Hara, F. M. Horodyski, S. T. Nichol, and J. J. Holland, J. Virol. 49, 793-798, 1984), no 5' mutations were detected in viruses from L-cell carrier lines. The absence of detectable defective interfering (DI) particles in the L-cell carrier cultures may account for this difference. Plus-strand leader RNA made by the viruses from persistently infected L cells failed to accumulate from 5 to 8 hr postinfection unlike the accumulation noted for the leader RNA generated by wild-type VSV. Minus-strand leader RNA, on the other hand, accumulated at a similar or increased rate compared to wild type. The relationship of these observations to the processes of host shutoff, viral transcription, and replication are discussed.

Further studies of the RNA synthesis phenotype selected during persistent infection with vesicular stomatitis virus

Vesicular stomatitis virus (VSV) isolated from two independently established lines of persistently infected mouse L cells expressed an altered phenotype of RNA synthesis at 37 degrees, the temperature at which the persistently infected cultures were maintained (T.K. Frey and J.S. Youngner, 1982, J. Virol. 44, 167-174). In comparison to the viruses used to initiate the two lines, wild-type (wt) VSV and ts-0-23 (ts-, RNA+ complementation group III), the VSV expressing this RNA phenotype synthesized much less mRNA but equal or greater amounts of 40 S genomic RNA (rt- phenotype). In the line initiated with wt-VSV, at 17 days after initiation, when 85% of the clones were ts-, 36% of the ts- clones were rt-. By 63 days the VSV-PI population was uniformly ts- and rt- and this phenotype prevailed for at least 2 years of persistence. In the line initiated with ts-0-23, the rt- phenotype was stable for at least 3 years of persistence. To study the relationship of the ts- and rt- phenotypes which were coselected during persistence, ts+ revertants of a ts- rt- VSV-PI clone were isolated. All of the ts+ revertants expressed a wt-VSV phenotype of RNA synthesis at 37 degrees (rt+), indicating that the two phenotypic markers may be pleiotropic manifestations of the same mutation. rt-VSV inhibited host cell RNA and protein synthesis more slowly than did wt-VSV. However, rt-VSV synthesized equivalent or greater amounts of all the virus proteins, compared to wt-VSV, despite the reduced amount of mRNA transcription. The attenuated shutoff of host cell macromolecular synthesis by rt- VSV and the concomitant efficient 40 S genome replication and virus protein synthesis may in part explain the selective advantage of the rt- mutation during persistence. The rt- phenotype was not unique to persistent infection; ts- rt- mutants also evolved during serial undiluted passages of wt-VSV in L cells and one ts- rt- mutant was identified in a group of spontaneous mutants isolated from a wt-VSV stock.

Vesicular stomatitis virus mutants resistant to defective-interfering particles accumulate stable 5'-terminal and fewer 3'-terminal mutations in a stepwise manner

We have studied the evolution of sequences which include the RNA polymerase binding sites at the 5' and 3' termini of vesicular stomatitis virus mutants (Sdi-) resistant to defective-interfering particles. We observed a striking stepwise accumulation of stable base substitutions within the area of replication initiation at the 5'-terminal 54 nucleotides of Sdi- mutants isolated at intervals from persistent infections and undiluted lytic passage series. Fewer mutations accumulated in the region of transcription initiation at the 3' end and in those portions of the N and L protein coding cistrons examined. The termini changes are not strictly required to obtain the Sdi- phenotype. However, it is possible that they represent stepwise compensatory changes to accommodate Sdi- mutations affecting viral replication or encapsidation gene products or both. These results have important implications for RNA virus genome evolution.

Selection of a mutant S1 gene during reovirus persistent infection of L cells: role in maintenance of the persistent state

LR-7 cells, variant L cells derived from a type 3 reovirus persistently infected (p.i.) carrier culture (R. Ahmed, W. M. Canning, R. S. Kauffman, A. H. Sharpe, J. V. Hallum, and B. N. Fields, Cell 25, 325-332, 1983) were used to define the viral genes critical for maintenance of the persistent state. A cloned viral isolate (L/C virus) derived from the p.i. culture replicated normally in LR-7 cells, while wild-type (wt) viruses of the three reovirus serotypes replicated less efficiently. To identify the viral gene(s) permitting enhanced replication of L/C virus in LR-7 cells, viral reassortants were prepared by mixed infection of L cells with L/C virus and type 1 wt. Study of the one-step growth curves and final yields of large numbers of reassortants in both L cells and LR-7 cells revealed that the presence of the S1 gene from L/C virus was critical for normal viral replication in LR-7 cells. However, this phenotype was suppressed by the simultaneous presence in reassortants of both the M2 and S4 genes from the type 1 wt parent. The critical change in the S1 gene occurred by passage 13 (63 days) after initiation of the carrier culture. Although multiple mutations are present in the viral population from p.i. cultures, certain specific mutations can be identified as critical for maintenance of the persistent state.

Genetic variation during persistent reovirus infection: isolation of cold-sensitive and temperature-sensitive mutants from persistently infected L cells

We have examined the evolution of reovirus in two independently established persistently infected (p.i.) cell lines. We found that reovirus undergoes extensive mutation during persistent infection in L cells. However, there was no consistent pattern of virus evolution; in one p.i. cell line temperature-sensitive (ts) mutants were selected, whereas cold-sensitive (cs) mutants were isolated from the second p.i. culture. Neither the cs nor the ts mutants isolated from the carrier cultures expressed their defect at 37 degrees, the temperature at which the p.i. cells were maintained, indicating that the cs and ts phenotypes were nonselected markers. These results emphasize the point that emergence of the ts or cs mutants during persistent infection only signifies that the virus has changed; it does not necessarily imply that the particular mutant is essential for the maintenance of the persistent infection. Given the high mutation rate of viruses, and the wide spectrum of viral mutants present in carrier cultures, it is essential to distinguish the relevant changes from those which may simply represent an epiphenomenon. In the accompanying paper (R. S. Kauffman, R. Ahmed, and B. N. Fields Virology, 130, 79-87, 1983), we show that by using a genetic approach, it is possible to identify the viral gene(s) which are critical for the maintenance of persistent reovirus infection.