Response of a Thin Flat Scored Metallic Disc Under Pressure Impulse

This paper presents the large deformation, and failure response of a thin flat scored metallic disc (FSMD) subjected to a pressure impulse as experienced in a break-away disc or an explosion vent. The response of this thin FSMD is numerically simulated for a loading rate and validated with an experiment, where a good agreement is found on plastic strains, burst pressure, and deformation pattern. The loading rate and several geometric parameters of FSMD significantly influence its response. Therefore, the influence of loading rate ( P& ), score depth and width-todisc thickness ratio (t 1 /t and b/t), diameter-to-disc thickness ratio (D/t), score length-to-disc radius ratio (l/R), score pattern, and score geometry on the deformation and failure response of the thin FSMD is thoroughly investigated. The studies demonstrate that 1) the failure initiation point shifts from disc centre to between 1/5th and 1/3rd radius for loading rates ≤ 25 MPa/s; 2) the responses such as burst pressure, burst time, central deflection, and equivalent strain are i) sensitive to the loading rates up to 100 MPa/s, ii) sensitive to score’s depth, only up to 0.6t and insensitive to score’s width, iii) significantly unaffected for the number of scores N > 8, iv) stabilised for l/R > 0.5 and D/t > 250, v) almost the same for semi-circular, rectangular and triangular score geometries, and vi) very minimal for the number of scores N = 3; and 3) the failure do not initiate and propagate along all scores for N > 4 in the disc.

Adaptations and Safety Modifications to Perform Safe Minimal Access Surgery (MIS: Laparoscopy and Robotic) During the COVID-19 Pandemic: Practice Modifications Expert Panel Consensus Guidelines from Academia of Minimal Access Surgical Oncology (AMASO)

The pandemic of COVID-19 across the globe triggered national lockdowns hampering normal working for all the essential services including healthcare. In order to reduce transmission and safety of patients and healthcare workers, the elective surgeries have been differed. The visits to the hospitals for follow-ups and consultations received temporary halt. However, we cannot halt the treatment for cancer patients who may or may not be COVID-19 positives. These are emergencies and should be treated ASAP. Conducting emergency surgeries during pandemic like COVID-19 is challenge for surgeons and the entire hospital infrastructure. The available information about COVID-19 and its propensity of contamination through droplets and aerosol need some modifications for conducting surgeries successfully without contaminating the hospital buildings, protecting healthcare teams and the patient. With these objectives, some modifications in the operating theater including surgical techniques for minimal access, laparoscopy, and robotic surgery are proposed in this review article. This review article also discusses the safety measures to be followed for the suspected or confirmed COVID-19 patient and the guidelines and recommendations for healthcare teams while treating these patients. Although there is little evidence of viral transmission through laparoscopic or open approaches, modifications to surgical practice such as the use of safe smoke evacuation and minimizing energy device used to reduce the risk of exposure to aerosolized particles to healthcare team are proposed in this review article.

Characterization of microstructural changes due to prolonged thermal exposure of directionally solidified Ni-base super alloy CM 247LC using ultrasonic

The high temperature strength of directionally solidified Ni-base super alloy CM 247LC strongly depends on the morphology, volume fraction, size and size distribution of γ' precipitate (Ni₃Al) in the FCC γ matrix. The microstructure of the alloy is engineered to achieve the right combination of these parameters that provides the required high temperature strength and creep resistance. The alloy contains high volume fraction of coherent γ' precipitates having near cubic shape. High temperature exposure of gas turbine components made out of the alloy leads to coarsening of the γ' precipitates and broadening of the γ matrix channel. This in turn, adversely affects the high temperature mechanical properties of the alloy. The present study endeavours to non-destructively characterize such detrimental changes in the microstructure that controls the mechanical properties and limits the life of components. The microstructural changes of the fully heat treated alloy exposed at 980 °C for different hours (100-1200) of thermal exposure have been characterized using ultrasonic methods. Changes in microstructural parameters due to different hours of thermal exposure have been correlated with changes in ultrasonic velocity, ultrasonic attenuation coefficient and second order acoustic nonlinearity parameter. It is observed that the change in attenuation is predominantly by absorption of the ultrasonic wave due to dislocation damping in the γ channels. Nonlinear ultrasonic parameter changes with thermal exposure predominantly due to the alteration of dislocation precipitate interaction. A dislocation precipitation interaction model for ultrasonic wave distortion has been used to explain the observed variation in nonlinear parameter. A microstructural parameter has been identified that varies in a similar way as ultrasonic attenuation and second order ultrasonic parameter. It is shown that variations in the acoustic non-linearity parameter follow the trend more closely with the identified microstructural parameter.

Plant pathogenic fungus F. solani mediated biosynthesis of nanoceria: antibacterial and antibiofilm activity

The present study reports the synthesis of CeO₂ nanoparticles using Fusarium solani. The biosynthesized CeO₂ nanoparticles were subjected to different characterization techniques and also showed potential antibacterial and antibiofilm activities.

5' Regulatory region of ubiquitin 2 gene from Porteresia coarctata makes efficient promoters for transgene expression in monocots and dicots

KEY MESSAGE

Porteresia ubiquitin 5' regulatory region drives transgene expression in monocots and dicots. Ubiquitin promoters are promising candidates for constitutive transgene expression in plants. In this study, we isolated and characterized a novel 5' regulatory sequence of a ubiquitin gene from Porteresia coarctata, a stress-tolerant wild grass species. Through functional analysis in heterologous plant systems, we have demonstrated that full length (Port Ubi2.3) or truncated sequence (PD2) of the isolated regulatory fragment can drive constitutive expression of GUS in monocots and/or dicots. In silico analysis of Port Ubi2.3 has revealed the presence of a 640 bp core promoter region followed by two exons and two introns with numerous putative cis-acting sites scattered throughout the regulatory region. Transformation and expression studies of six different deletion constructs in rice, tobacco and sugarcane revealed that the proximal intron has an enhancing effect on the activity of the core promoter in both monocots and dicots, whereas, Port Ubi2.3 was able to render strong expression only in monocots. This regulatory sequence is quite distinct from the other reported ubiquitin promoters in structure and performs better in monocots compared to other commonly used promoters-maize Ubi1 and Cauliflower Mosaic Virus 35S.

Naringin modulates oxidative stress and inflammation in 3-nitropropionic acid-induced neurodegeneration through the activation of nuclear factor-erythroid 2-related factor-2 signalling pathway

Nuclear factor-erythroid 2-related factor-2 (Nrf2) mediated regulation of cellular antioxidant production and the anti-inflammatory mechanism play an important role in neuroprotection against neurodegenerative diseases. Naringin a citrus flavonone, has been reported to possess neuroprotective effect against Huntington's disease, and other neurodegenerative disorders, however the mechanisms underlying its beneficial effects on 3-nitropropionic acid (3-NP)-induced neurodegeneration are poorly defined. The objective of the present study was to investigate the neuroprotective role of naringin and delineate the mechanism of action on 3-NP-induced neurodegeneration. Rats were injected with 3-NP (10mg/kg body weight/day, i.p.) for 2 weeks to develop neurodegeneration, while naringin (80 mg/kg body weight/day, orally) was administered throughout the experimental period, 1h prior to 3-NP exposure. Thereafter rats were euthanized for biochemical, histological, and molecular studies. Treatment with naringin ameliorated the reduced glutathione/oxidized glutathione ratio with concomitant decrease in the levels of hydroxyl radical, hydroperoxide and nitrite in 3-NP-induced rats. Nissl staining and transmission electron microscopic studies showed that naringin modulated 3-NP-induced histological changes. Naringin induces NAD(P)H:quinone oxidoreductase-1, heme oxygenase-1, glutathione S-transferase P1 and gamma-glutamylcysteine ligase mRNA expressions through the activation of Nrf2 and decreased the expressions of pro-inflammatory mediators like tumour necrosis factor-alpha, cyclooxygenase-2 and inducible nitric oxide synthase. These results indicate that naringin might be beneficial in mitigating 3-NP-induced neurodegeneration through the enhancement of phase II and antioxidant gene expressions via Nrf2 activation; thereby modulating the oxidative stress and inflammatory responses.

Multiplex PCR assay for simultaneous detection and differentiation of Mycobacterium tuberculosis, Mycobacterium avium complexes and other Mycobacterial species directly from clinical specimens

AIMS

Polymerase chain reaction (PCR) is the most rapid and sensitive method for diagnosing mycobacterial infections and identifying the aetiological Mycobacterial species in order to administer the appropriate therapy and for better patient management.

METHODS AND RESULTS

Two hundred and thirty-five samples from 145 clinically suspected cases of tuberculosis were processed for the detection of Mycobacterial infections by ZN (Ziehl Neelsen) smear examination, L-J & BACTEC MGIT-960 culture and multiplex PCR tests. The multiplex PCR comprised of genus-specific primers targeting hsp65 gene, Mycobacterium tuberculosis complex-specific primer targeting cfp10 (Rv3875, esxB) region and Mycobacterium avium complex-specific primer pairs targeting 16S-23S Internal Transcribed Spacer sequences. The multiplex PCR developed had an analytical sensitivity of 10 fg (3-4 cells) of mycobacterial DNA. The multiplex PCR test showed the highest (77.24%) detection rate, while ZN smear examination had the lowest (20%) detection rate, which was bettered by L-J culture (34.4%) and BACTEC MGIT-960 culture (50.34%) methods. The mean isolation time for M. tuberculosis was 19.03 days in L-J culture and 8.7 days in BACTEC MGIT-960 culture. Using the multiplex PCR, we could establish M. tuberculosis + M. avium co-infection in 1.3% HIV-negative and 2.9% HIV-positive patients. The multiplex PCR was also highly useful in diagnosing mycobacteraemia in 38.09% HIV-positive and 15.38% HIV-negative cases.

CONCLUSIONS

The developed in-house multiplex PCR could identify and differentiate the M. tuberculosis and M. avium complexes from other Mycobacterial species directly from clinical specimens.

SIGNIFICANCE AND IMPACT OF THE STUDY

The triplex PCR developed by us could be used to detect and differentiate M. tuberculosis, M. avium and other mycobacteria in a single reaction tube.

Prevalence of mycobacteremia in Indian HIV-infected patients detected by the MB/BacT automated culture system

The use of automated blood cultures system, such as MB/BacT, has provided a novel opportunity for laboratories to diagnose mycobacteremia in HIV-infected patients. However, no such study has been carried out in India so far. This prospective study was conducted on 52 HIV-positive patients with suspected tuberculosis who were referred to our tertiary care hospital in New Delhi. In these patients, the prevalence of mycobacteremia was evaluated using the MB/BacT automated culture system (bioMérieux, France). Twenty-seven HIV-negative but suspected tuberculosis patients were also included for comparison. Mycobacteria could be isolated from sputa or fecal samples of 20 HIV-positive patients (38.4%), and in nine (45%) of these 20 cases, mycobacteria could also be isolated simultaneously from their blood specimens. In the remaining 32 patients, all relevant non-hematological clinical samples remained negative for mycobacteria, but the pathogen could be detected from the blood samples of seven (21.87%) of these 32 patients. Therefore, only 25 (48%) clinically suspected patients remained negative in both Löwenstein-Jensen (L-J) and MB/BacT culture methods, and 12 of these responded to anti-tubercular treatment, while in the rest either non-tubercular diagnosis was established or they were lost to follow-up. The study revealed that low CD+(4) counts and poor or no reactivity to purified protein derivative (PPD) were the best clinical predictors for the occurrence of mycobacteremia in HIV-positive patients. Of the 16 isolates from blood, 13 were diagnosed as Mycobacterium tuberculosis and one each were identified as M. avium, M. kansasii, and a mixed infection of M. tuberculosis and M. avium complex. The prevalence rate of mycobacteremia was significantly low (11.1%) in HIV-negative patients. In conclusion, this study showed that blood culture could be an important adjunct investigation for confirming the clinical diagnosis of tuberculosis in HIV-positive patients.

Selective repression of translation by the brome mosaic virus 1a RNA replication protein

Differential expression of viral replication proteins is essential for successful infection. We report here that overexpression of the brome mosaic virus (BMV) 1a protein can repress viral RNA replication in a dosage-dependent manner. Using RNA replication-incompetent reporter constructs, repression of translation from BMV RNA1 and RNA2 was observed, suggesting that the effect on translation of the BMV RNA replication proteins is responsible for the decrease in RNA levels. Furthermore, repression of translation by 1a required the B box in the 5'-untranslated region (5' UTR); BMV RNA3 that lacks a B box in its 5' UTR is not subject to 1a-mediated translational inhibition. Mutations in either the methyltransferase or the helicase-like domains of 1a reduced the repression of replication and translation. These results suggest that in addition to its known functions in BMV RNA synthesis, 1a also regulates viral gene expression.

Interaction between Brome mosaic virus proteins and RNAs: effects on RNA replication, protein expression, and RNA stability

Brome mosaic virus (BMV) RNA replication has been examined in a number of systems, including Saccharomyces cerevisiae. We developed an efficient T-DNA-based gene delivery system using Agrobacterium tumefaciens to transiently express BMV RNAs in Nicotiana benthamiana. The expressed RNAs can systemically infect plants and provide material to extract BMV replicase that can perform template-dependent RNA-dependent RNA synthesis in vitro. We also expressed the four BMV-encoded proteins from nonreplicating RNAs and analyzed their effects on BMV RNA accumulation. The capsid protein that coinfiltrated with constructs expressing RNA1 and RNA2 suppressed minus-strand levels but increased plus-strand RNA accumulation. The replication proteins 1a and 2a could function in trans to replicate and transcribe the BMV RNAs. None of the BMV proteins or RNA could efficiently suppress posttranscriptional silencing. However, 1a expressed in trans will suppress the production of a recombinant green fluorescent protein expressed from the nontranslated portions of BMV RNA1 and RNA2, suggesting that 1a may regulate translation from BMV RNAs. BMV replicase proteins 1a did not affect the accumulation of the BMV RNAs in the absence of RNA replication, unlike the situation reported for S. cerevisiae. This work demonstrates that the Agrobacterium-mediated gene delivery system can be used to study the cis- and trans-acting requirements for BMV RNA replication in plants and that significant differences can exist for BMV RNA replication in different hosts.

Repair of the tRNA-like CCA sequence in a multipartite positive-strand RNA virus

The 3' portions of plus-strand brome mosaic virus (BMV) RNAs mimic cellular tRNAs. Nucleotide substitutions or deletions in the 3'CCA of the tRNA-like sequence (TLS) affect minus-strand initiation unless repaired. We observed that 2-nucleotide deletions involving the CCA 3' sequence in one or all BMV RNAs still allowed RNA accumulation in barley protoplasts at significant levels. Alterations of CCA to GGA in only BMV RNA3 also allowed RNA accumulation at wild-type levels. However, substitutions in all three BMV RNAs severely reduced RNA accumulation, demonstrating that substitutions have different repair requirements than do small deletions. Furthermore, wild-type BMV RNA1 was required for the repair and replication of RNAs with nucleotide substitutions. Results from sequencing of progeny viral RNA from mutant input RNAs demonstrated that RNA1 did not contribute its sequence to the mutant RNAs. Instead, the repaired ends were heterogeneous, with one-third having a restored CCA and others having sequences with the only commonality being the restoration of one cytidylate. The role of BMV RNA1 in increased repair was examined.

Replicase-binding sites on plus- and minus-strand brome mosaic virus RNAs and their roles in RNA replication in plant cells

The cis-acting elements for Brome mosaic virus (BMV) RNA synthesis have been characterized primarily for RNA3. To identify additional replicase-binding elements, nested fragments of all three of the BMV RNAs, both plus- and minus-sense fragments, were constructed and tested for binding enriched BMV replicase in a template competition assay. Ten RNA fragments containing replicase-binding sites were identified; eight were characterized further because they were more effective competitors. All eight mapped to noncoding regions of BMV RNAs, and the positions of seven localized to sequences containing previously characterized core promoter elements (C. C. Kao, Mol. Plant Pathol. 3:55-62, 2001), thus suggesting the identities of the replicase-binding sites. Three contained the tRNA-like structures that direct minus-strand RNA synthesis, three were within the 3' region of each minus-strand RNA that contained the core promoter for genomic plus-strand initiation, and one was in the core subgenomic promoter. Single-nucleotide mutations known previously to abolish RNA synthesis in vitro prevented replicase binding. When tested in the context of the respective full-length RNAs, the same mutations abolished BMV RNA synthesis in transfected barley protoplasts. The eighth site was within the intercistronic region (ICR) of plus-strand RNA3. Further mapping showed that a sequence of 22 consecutive adenylates was responsible for binding the replicase, with 16 being the minimal required length. Deletion of the poly(A) sequence was previously shown to severely debilitate BMV RNA replication in plants (E. Smirnyagina, Y. H. Hsu, N. Chua, and P. Ahlquist, Virology 198:427-436, 1994). Interestingly, the B box motif in the ICR of RNA3, which has previously been determined to bind the 1a protein, does not bind the replicase. These results identify the replicase-binding sites in all of the BMV RNAs and suggest that the recognition of RNA3 is different from that of RNA1 and RNA2.

Intracellular distribution of cowpea mosaic virus movement protein as visualised by green fluorescent protein fusions

Cowpea mosaic virus (CPMV) derivatives expressing movement protein (MP) green fluorescent protein (GFP) fusions (MP:GFP) were used to study the intracellular targeting and localization of the MP in cowpea protoplasts and plants. In protoplasts, a virus coding for a wild type MP:GFP (MPfGFP) induced the formation of fluorescent tubular structures, which shows that subcellular targeting and tubule formation are not affected by fusion of GFP to the C-terminus of the MP. In plants, MPfGFP infections were mostly confined to single epidermal cells and failed to achieve a systemic infection, probably because the fusion of GFP to the MP interfered with MP-virion interaction. MP:GFP mainly accumulated in fluorescent spots in the cell wall of epidermal cells of inoculated leaves, which may represent short tubular structures in modified plasmodesmata. At the cuticle-side of epidermal cells tubular structures were detected indicating that tubule formation in plants, as in protoplasts, does not require the presence of functional plasmodesmata. Furthermore, results were obtained which indicate that CPMV MP:GFP is able to traffic from cell-to-cell by itself. The possible significance of this finding is discussed.

Complete nucleotide sequence of Sesbania mosaic virus: a new virus species of the genus Sobemovirus

The complete nucleotide sequence of the Sesbania mosaic virus (SeMV) genomic RNA was determined by sequencing overlapping cDNA clones. The SeMV genome is 4149 nucleotides in length and encodes four potential overlapping open reading frames (ORFs). Comparison of the nucleotide sequence and the deduced amino acid sequence of the four ORFs of SeMV with that of other sobemoviruses revealed that SeMV was closest to southern bean mosaic virus Arkansas isolate (SBMV-Ark, 73% identity). The 5' non-coding regions of SeMV, SBMV and southern cowpea mosaic virus (SCPMV) are nearly identical. However ORF1 of SeMV which encodes for a putative movement protein of M(r) 18370 has only 34% identity with SBMV-Ark. ORF 2 encodes a polyprotein containing the serine protease, genome linked viral protein (VPg) and RNA dependent RNA polymerase domains and shows 78% identity with SBMV-Ark. The N-terminal amino acid sequence of VPg was found to be TLPPELSIIEIP, which mapped to the region 326-337 of ORF2 product and the cleavage site between the protease domain and VPg was identified to be E325-T326. The cleavage site between VPg and RNA dependent RNA polymerase was predicted to be E445-T446 based on the amino acid sequence analysis of the polyprotein from different sobemoviruses. ORF3 is nested within ORF2 in a--1 reading frame. The potential ribosomal frame shift signal and the downstream stem-loop structure found in other sobemoviruses are also conserved in SeMV RNA sequence, indicating that ORF3 might be expressed via--1 frame shifting mechanism. ORF4 encodes the coat protein of SeMV, which shows 76 and 66% identity with SBMV-Ark and SCPMV, respectively. Thus the comparison of the non-coding regions and the ORFs of SeMV with other sobemoviruses clearly revealed that it is not a strain of SBMV. Phylogenetic analysis of six different sobemoviruses, including SeMV, suggests that recombination event is not frequent in this group and that SeMV is a distinct member of the genus sobemovirus. The analysis also shows sobemoviruses infecting monocotyledons and dicotyledons fall into two distinct clusters.

Engineering cowpea mosaic virus RNA-2 into a vector to express heterologous proteins in plants

A series of new cowpea mosaic virus (CPMV) RNA-2-based expression vectors were designed. The jellyfish green fluorescent protein (GFP) was introduced between the movement protein (MP) and the large (L) coat protein or downstream of the small (S) coat protein. Release of the GFP inserted between the MP and L proteins was achieved by creating artificial processing sites each side of the insert, either by duplicating the MP-L cleavage site or by introducing a sequence encoding the foot-and-mouth disease virus (FMDV) 2A catalytic peptide. Eight amino acids derived from the C-terminus of the MP and 14-19 amino acids from the N-terminus of the L coat protein were necessary for efficient processing of the artificial Gln/Met sites. Insertion of the FMDV 2A sequence at the C-terminus of the GFP resulted in a genetically stable construct, which produced particles containing about 10 GFP-2A-L fusion proteins. Immunocapture experiments indicated that some of the GFP is present on the virion surface. Direct fusion of GFP to the C-terminus of the S coat protein resulted in a virus which was barely viable. However, when the sequence of GFP was linked to the C-terminus by an active FMDV 2A sequence, a highly infectious construct was obtained.

Molecular characterization and interviral relationships of a flexuous filamentous virus causing mosaic disease of sugarcane (Saccharum officinarum L.) in India

A virus isolate causing mosaic disease of commercial sugarcane was purified to homogeneity. Electron microscopy revealed flexuous filamentous virus particles of ca 890 x 15 nm. The virus isolate reacted positively with heterologous antiserum to narcissus latent virus form UK, but failed to react with potyvirus group specific antiserum. N-terminal sequencing of the intact coat protein (CP) and the tryptic peptides indicated that the virus was probably a potyvirus but distinct from several reported potyviruses. Comparison of the 3'-terminal 1084 nucleotide sequence of the RNA genome of this virus revealed 93.6% sequence identity in the coat protein coding region with the recently described sugarcane streak mosaic virus (Pakistani isolate). The molecular weight of the coat protein (40 kDa) was higher than that deduced from the amino acid sequence (34 kDa). The apparent increase in size was shown to be due to glycosylation of the coat protein which has not been reported thus far in the family, Potyviridae. This is the first report on the molecular characterization of a virus causing mosaic disease of sugarcane in India and the results demonstrate that the virus is a strain of sugarcane streak mosaic virus, a member of the Tritimovirus genus of the Potyviridae. We have named it sugarcane streak mosaic virus--Andhra Pradesh isolate (SCSMV-AP).

Genomic sequence of physalis mottle virus and its evolutionary relationship with other tymoviruses

The genome of physalis mottle tymovirus (PhMV) is 6673 nucleotides long and is rich in cytosine residues (40.58%) like other tymoviruses. The organization of the genes is also similar to that of five other tymoviruses whose sequences are known. However, PhMV has the longest 3' noncoding region as well as the longest replicase (RP) ORF. The RP sequences are similar to those of other tymoviruses (48-60% identity) whereas the coat proteins (CP) and the overlapping proteins (OP) are conserved to a lesser extent (30-50% and 26-34% respectively). A tetra peptide "GILG" was found to be present in all the tymoviral OPs. The PhMV RP also possesses the methyl transferase, polymerase and the helicase motifs found in all the Sindbis-like super group of plant viruses. A phylogenetic analysis of the six tymoviral sequences revealed that they do not have a rigid hierarchical similarity relationship.

Studies on the movement of cowpea mosaic virus using the jellyfish green fluorescent protein

The jellyfish green fluorescent protein (GFP) coding sequence was used to replace the coat protein (CP) genes in a full-length cDNA clone of CPMV RNA-2. Transcripts of this construct were replicated in the presence of RNA-1 in cowpea protoplasts, and GFP expression could be readily detected by fluorescent microscopy. It was not possible to infect cowpea plants with these transcripts, but combined with a mutant RNA-2, in which the 48-kDa movement protein (MP) gene has been deleted infection did occur. With this tripartite virus (CPMV-TRI) green fluorescent spots were visible under UV light on the inoculated leaf after 3 days and a few days later on the higher leaves. These results show that the polyproteins encoded by RNA-2 do not possess an essential function in the virus infection cycle and that there is, contrary to what we have found so far for the proteins encoded by RNA-1, no need for a tight regulation of the amounts of MP and CPs produced in a cell. Subsequently, the GFP gene was introduced between the MP and CP genes of RNA-2 utilizing artificial proteolytic processing sites for the viral proteinase. This CPMV-GFP was highly infectious on cowpea plants and the green fluorescent spots that developed on the inoculated leaves were larger and brighter than those produced by CPMV-TRI described above. When cowpea plants were inoculated with CPMV RNA-1 and RNA-2 mutants containing the GFP gene but lacking the CP or MP genes, only single fluorescent epidermal cells were detected between 2 and 6 days postinoculation. This experiment clearly shows that both the capsid proteins and the MP are absolutely required for cell-to-cell movement.

Assembly of physalis mottle virus capsid protein in Escherichia coli and the role of amino and carboxy termini in the formation of the icosahedral particles

The coat protein gene of physalis mottle tymovirus (PhMV) was over expressed in Escherichia coli using pET-3d vector. The recombinant protein was found to self assemble into capsids in vivo. The purified recombinant capsids had an apparent s value of 56.5 S and a diameter of 29(+/-2) nm. In order to establish the role of amino and carboxy-terminal regions in capsid assembly, two amino-terminal deletions clones lacking the first 11 and 26 amino acid residues and two carboxy-terminal deletions lacking the last five and ten amino acid residues were constructed and overexpressed. The proteins lacking N-terminal 11 (PhCPN1) and 26 (PhCPN2) amino acid residues self assembled into T=3 capsids in vivo, as evident from electron microscopy, ultracentrifugation and agarose gel electrophoresis. The recombinant, PhCPN1 and PhCPN2 capsids were as stable as the empty capsids formed in vivo and encapsidated a small amount of mRNA. The monoclonal antibody PA3B2, which recognizes the epitope within region 22 to 36, failed to react with PhCPN2 capsids while it recognized the recombinant and PhCPN1 capsids. Disassembly of the capsids upon treatment with urea showed that PhCPN2 capsids were most stable. These results demonstrate that the N-terminal 26 amino acid residues are not essential for T=3 capsid assembly in PhMV. In contrast, both the proteins lacking the C-terminal five and ten amino acid residues were present only in the insoluble fraction and could not assemble into capsids, suggesting that these residues are crucial for folding and assembly of the particles.

Structure of Sesbania mosaic virus at 3 A resolution

Sesbania mosaic virus (SMV) is an isometric, ss-RNA plant virus found infecting Sesbania grandiflora plants in fields near Tirupathi, South India. The virus particles, which sediment at 116 S at pH 5.5, swell upon treatment with EDTA at pH 7.5 resulting in the reduction of the sedimentation coefficient to 108 S. SMV coat protein amino acid sequence was determined and found to have approximately 60% amino acid sequence identity with that of southern bean mosaic virus (SBMV). The amino terminal 60 residue segment, which contains a number of positively charged residues, is less well conserved between SMV and SBMV when compared to the rest of the sequence. The 3D structure of SMV was determined at 3.0 A resolution by molecular replacement techniques using SBMV structure as the initial phasing model. The icosahedral asymmetric unit was found to contain four calcium ions occurring in inter subunit interfaces and three protein subunits, designated A, B and C. The conformation of the C subunit appears to be different from those of A and B in several segments of the polypeptide. These observations coupled with structural studies on SMV partially depleted of calcium suggest a plausible mechanism for the initiation of the disassembly of the virus capsid.

Structure of sesbania mosaic virus at 3 A resolution

BACKGROUND

Sobemoviruses are a group of RNA plant viruses that have a narrow host range. They are characterized in vitro by their stability, high thermal inactivation point and longevity. The three-dimensional structure of only one virus belonging to this group, southern bean mosaic virus (SBMV), is known. Structural studies on sesbania mosaic virus (SMV), which is closely related to SBMV, will provide details of the molecular interactions that are likely to be important in the stability and assembly of sobemoviruses.

RESULTS

We have determined the three-dimensional structure of SMV at 3 A resolution. The polypeptide fold and quaternary organization are very similar to those of SBMV. The capsid consists of sixty icosahedral asymmetric units, each comprising three copies of a chemically identical coat protein subunit, which are designated as A, B and C and are in structurally different environments. Four cation-binding sites have been located in the icosahedral asymmetric unit. Of these, the site at the quasi-threefold axis is not found in SBMV. Structural differences are observed in loops and regions close to this cation-binding site. Preliminary studies on ethylene diamine tetra acetic acid (EDTA) treated crystals suggest asymmetry in removal of the quasi-equivalent cations at the AB, BC, and AC subunit interfaces.

CONCLUSIONS

Despite the overall similarity between SMV and SBMV in the nature of the polypeptide fold, these viruses show a number of differences in intermolecular interactions. The polar interactions at the quasi-threefold axis are substantially less in SMV and positively charged residues on the RNA-facing side of the protein and in the N-terminal arm are not particularly well conserved. This suggests that protein-RNA interactions are likely to be different between the two viruses.

Primary structure of sesbania mosaic virus coat protein: its implications to the assembly and architecture of the virus

Sesbania mosaic virus (SMV) is a plant virus that infects Sesbania grandiflora plants in Andhra Pradesh, India. The amino acid sequence of the coat protein of SMV was determined using purified peptides generated by cleavage with trypsin, chymotrypsin, V8 protease and clostripain. The 230 residues so far determined were compared to the corresponding residues of southern bean mosaic virus (SBMV), the type member of sobemoviruses. The overall identity between the sequences is 61.7%. The amino terminal 64 residues, which constitute an independent domain (R-domain) known to interact with RNA, are conserved to a lower extent (52.5%). Comparison of the positively charged residues in this domain suggests that the RNA-protein interactions are considerably weaker in SMV. The residues that constitute the major domain of the coat protein, the surface domain (S-domain, residues 65-260), are better conserved (66.5%). The positively charged residues of this domain that face the nucleic acid are well conserved. The longest conserved stretch of residues (131- 142) corresponds to the loop involved in intersubunit interactions between subunits related by the quasi 3-fold symmetry. A unique cation binding site located on the quasi 3-fold axis contributes to the stability of SMV. These differences are reflected in the increased stability of the SMV coat protein and its ability to be reconstituted with RNA at pH 7.5. A major epitope was identified using monoclonal antibodies to SMV in the segment 201-223 which contains an exposed helix in the capsid structure.(ABSTRACT TRUNCATED AT 250 WORDS)

Structure of Sesbania mosaic virus at 4.7 A resolution and partial sequence of the coat protein

Sesbania mosaic virus (SMV) is a plant virus infecting Sesbania grandiflora plants in Andhra Pradesh, India. Amino acid sequence of the tryptic peptides of SMV coat protein were determined using a gas phase sequenator. These sequences showed identical amino acids at 69% of the positions when aligned with the corresponding residues of southern bean mosaic virus (SBMV). Crystals diffracting to better than 3 A resolution were obtained by precipitating the virus with ammonium sulphate. The crystals belonged to rhombohedral space group R3 with a = 291.4 A and alpha = 61.9 degrees. Three-dimensional X-ray diffraction data on these crystals were collected to a resolution of 4.7 A, using a Siemens-Nicolet area detector system. Self-rotation function studies revealed the icosahedral symmetry of the virus particles, as well as their precise orientation in the unit cell. Cross-rotation function and modelling studies with SBMV showed that it is a valid starting model for SMV structure determination. Low resolution phases computed using a polyalanine model of SBMV were subjected to refinement and extension by real-space electron density averaging and solvent flattening. The final electron density map revealed a polypeptide fold similar to SBMV. The single disulphide bridge of SBMV coat protein is retained in SMV. Four icosahedrally independent cation binding sites have been tentatively identified. Three of these sites, related by a quasi threefold axis, are also found in SBMV. The fourth site is situated on the quasi threefold axis. Aspartic acid residues, which replace Ile218 of SBMV from the quasi threefold-related subunits are suitable ligands to the cation at this site.