Comparison of the coat protein, movement protein and RNA polymerase gene sequences of Australian, Chinese, and American isolates of barley yellow dwarf virus transmitted by Rhopalosiphum padi

Barley yellow dwarf luteovirus-GPV (BYDV-GPV) is a common problem in Chinese wheat crops but is unrecorded elsewhere. A defining characteristic of GPV is its capacity to be transmitted efficiently by both Schizaphis graminum and Rhopaloshiphum padi. This dual aphid species transmission contrasts with those of BYDV-RPV and BYDV-SGV, globally distributed viruses, which are efficiently transmitted only by Rhopaloshiphum padi and Schizaphis graminum respectively. The viral RNA sequences encoding the coat protein (22K) gene, the movement protein (17K) gene, the region surrounding the conserved GDD motif of the polymerase gene and the intergenic sequences between these genes were determined for GPV and an Australian isolate of BYDV-RPV (RPVa). In all three genes, the sequences of GPV and RPVa were more similar to those of an American isolate of BYDV-RPV (RPVu) than to any other luteovirus for which there is data available. RPVa and RPVu were very similar, especially their coat proteins which had 97% identity at the amino acid level. The coat protein of GPV had 76% and 78% amino acid identity with RPVa and RPVu respectively. The data suggest that RPVu and RPVa are correctly named as strains of the same serotype and that GPV is sufficiently different from either RPV strain to be considered a distinct BYDV type. The coat protein and movement protein genes of GPV are very dissimilar to SGV. The polymerase sequences of RPVu, RPVa and GPV show close affinities with those of the sobemo-like luteoviruses and little similarity with those of the carmo-like luteoviruses. The sequences of the coat proteins, movement proteins and the polymerase segments of BYDV serotypes, other than RPV and GPV, form a cluster that is separate from their counterpart sequences from dicot-infecting luteoviruses. The RPV and GPV isolates consistently fall within a dicot-infecting cluster. This suggests that RPV and GPV evolved from within this group of viruses. Since these other viruses all infect dicots it seems likely that their common ancestor infected a dicot and that RPV and GPV evolved from a virus that switched hosts from a dicot to a monocot.

Expression patterns of vascular-specific promoters RolC and Sh in transgenic potatoes and their use in engineering PLRV-resistant plants

The expression patterns of GUS fusion constructs driven by the Agrobacterium rhizogenes RolC and the maize Sh (Shrunken: sucrose synthase-1) promoters were examined in transgenic potatoes (cv. Atlantic). RolC drove high-level gene expression in phloem tissue, bundle sheath cells and vascular parenchyma, but not in xylem or non-vascular tissues. Sh expression was exclusively confined to phloem tissue. Potato leafroll luteovirus (PLRV) replicates only in phloem tissues, and we show that when RolC is used to drive expression of the PLRV coat protein gene, virus-resistant lines can be obtained. In contrast, no significant resistance was observed when the Sh promoter was used.

Putative full-length clones of the genomic DNA segments of subterranean clover stunt virus and identification of the segment coding for the viral coat protein

Subterranean clover stunt disease is an economically important aphid-borne virus disease affecting certain pasture and grain legumes in Australia. The virus associated with the disease, subterranean clover stunt virus (SCSV), was previously found to be representative of a new type of single-stranded DNA virus. Analysis of the virion DNA and restriction mapping of double-stranded cDNA synthesized from virion DNA suggested that SCSV has a segmented genome composed of 3 or 4 different species of circular ssDNA each of about 850-880 nucleotides. To further investigate the complexity of the SCSV genome, we have isolated the replicative form DNA from infected pea and from it prepared putative full-length clones representing the SCSV genome segments. Analysis of these clones by restriction mapping indicated that clones representing at least 4 distinct genomic segments were obtained. This method is thus suitable for generating an extensive genomic library of novel ssDNA viruses containing multiple genome segments such as SCSV and banana bunchy top virus. The N-terminal amino acid sequence and amino acid composition of the coat protein of SCSV were determined. Comparison of the amino acid sequence with partial DNA sequence data, and the distinctly different restriction maps obtained for the full-length clones suggested that only one of these clones contained the coat protein gene. The results confirmed that SCSV has a functionally divided genome composed of several distinct ssDNA circles each of about 1 kb.

Infectious in vitro transcripts from a cloned cDNA of barley yellow dwarf virus

A full-length cDNA clone of barley yellow dwarf virus (BYDV-PAV serotype) has been constructed and fused to the bacteriophage T7 RNA polymerase promoter. RNA transcripts produced in vitro, either capped or uncapped, were infectious in Triticum monococcum protoplasts. Protoplasts inoculated with in vitro-transcribed BYDV RNA accumulated coat protein, synthesized new viral RNAs, and produced virus particles. Aphid feeding on extracts from protoplasts inoculated with in vitro RNA transcripts can be used to transfer the virus progeny to whole plants. Introduction of mutations which interrupt specific BYDV-PAV open reading frames (ORFs) V and VI eliminated infectivity while an ORF I mutant remained infectious. Infectious RNA transcripts derived from BYDV cDNA clones will facilitate analysis of the molecular aspects of BYDV infection and further enhance our understanding of this economically important virus.

Carrot red leaf and carrot mottle viruses : observations on the composition of the particles in single and mixed infections

Particles of carrot red leaf virus (CRLV; luteovirus group) purified from chervil (Anthriscus cerefolium) contain a single ssRNA species of mol. wt. about 1.8 x 106 and a major protein of mol. wt. about 25000. CRLV acts as a helper for aphid transmission of carrot mottle virus (CMotV; ungrouped) from mixedly infected plants. Virus preparations purified from such plants possess the infectivity of both viruses but contain particles indistinguishable from those of CRLV; some of the particles are therefore thought to consist of CMotV RNA packaged in CRLV coat protein. When RNA from such preparations was electrophoresed in agarose/polyacrylamide gels, CMotV infectivity was associated with an RNA band that migrated ahead of the CRLV RNA band and had an estimated mol. wt. of about 1.5 x 106, similar to that previously found for the infective ssRNA extracted directly from Nicotiana clevelandii leaves infected with CMotV alone. Preparations of dsRNA from CMotV-infected N. clevelandii leaves contained two species: one of mol. wt. about 3.2 x 106, presumably the replicative form of the infective ssRNA, and the other, mol. wt. about 0.9 x 106, of unknown origin and function. The infective agent in buffer extracts of CMotV-infected N. clevelandii was resistant to RNase (although the enzyme acted as a reversible inhibitor of infection at high concentrations) and is therefore not unprotected RNA. It may be protected within the approximately 52 nm enveloped structures previously reported.

Purification of particles of subterranean clover red leaf virus using an industrial-grade cellulase

Particles of two isolates of subterranean clover red leaf virus were purified by a method in which infected plant tissue was digested with an industrial-grade cellulase, Celluclast® 2.0 L type X. The yields of virus particles using this enzyme were comparable with those obtained using either of two laboratory-grade cellulases, Cellulase type 1 (Sigma) and Driselase®. However, the specific infectivity or aphid transmissibility of the particles purified using Celluclast® was 10-100 times greater than those of preparations obtained using laboratory-grade cellulases or no enzyme. The main advantage of using Celluclast® is that at present in Australia its cost is only ca. 1% of laboratory-grade cellulases.

Scleral matrix metalloproteinases, serine proteinase activity and hydrational capacity are increased in myopia induced by retinal image degradation

In the avian model of myopia, retinal image degradation quickly leads to ocular enlargement. We now give evidence that regionally specific changes in ocular size are correlated with both biomechanical indices of scleral remodeling, e.g. hydration capacity and with biochemical changes in proteinase activities. The latter include a 72 kDa matrix metalloproteinase (putatively MMP-2), other gelatin-binding MMPs, an acid pH MMP and a serine protease. Specifically, we have found that increases in scleral hydrational capacity parallel increases in collagen degrading activities. Gelatin zymography reveals that eyes with 7 days of retinal image degradation have elevated levels (1.4-fold) of gelatinolytic activities at 72 and 67 kDa M(r) in equatorial and posterior pole regions of the sclera while, after 14 days of treatment, increases are no longer apparent. Lower M(r) zymographic activities at 50, 46 and 37 kDa M(r) are collectively increased in eyes treated for both 7 and 14 days (1.4- and 2.4-fold respectively) in the equator and posterior pole areas of enlarging eyes. Western blot analyses of scleral extracts with an antibody to human MMP-2 reveals immunoreactive bands at 65, 30 and 25 kDa. Zymograms incubated under slightly acidic conditions reveal that, in enlarging eyes, MMP activities at 25 and 28 kDa M(r) are increased in scleral equator and posterior pole (1.6- and 4.5-fold respectively). A TIMP-like protein is also identified in sclera and cornea by Western blot analysis. Finally, retinal-image degradation also increases (~2.6-fold) the activity of a 23.5 kDa serine proteinase in limbus, equator and posterior pole sclera that is inhibited by aprotinin and soybean trypsin inhibitor. Taken together, these results indicate that eye growth induced by retinal-image degradation involves increases in the activities of multiple scleral proteinases that could modify the biomechanical properties of scleral structural components and contribute to tissue remodeling and growth.

Pathological excretion patterns of urinary proteins in miners highly exposed to dinitrotoluene

A cohort of 161 underground miners who had been highly exposed to dinitrotoluene (DNT) in the copper-mining industry of the former German Democratic Republic was reinvestigated for signs of subclinical renal damage. The study included a screening of urinary proteins excreted by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), and quantitations of the specific urinary proteins α 1-microglobulin and glutathione-S-transferase α (GST α) as biomarkers for damage of the proximal tubule and glutathione-S-transferase π (GST π) for damage of the distal tubule. The exposures were categorized semiquantitatively (low, medium, high, and very high), according to the type and duration of professional contact with DNT. A straight dose-dependence of pathological protein excretion patterns with the semiquantitative ranking of DNT exposure was seen. Most of the previously reported cancer cases of the urinary tract, especially those in the higher exposed groups, were confined to pathological urinary protein excretion patterns. The damage from DNT was directed toward the tubular system. In many cases, the appearance of Tamm-Horsfall protein, a 105-kD protein marker, was noted. Data on the biomarkers α 1-microglobulin, GST α, and GST π consistently demonstrated a dose-dependent increase in tubular damage, which confirmed the results of screening by SDS-PAGE and clearly indicated a nephrotoxic effect of DNT under the given conditions of exposure. Within the cluster of cancer patients observed among the DNT-exposed workers, only in exceptional cases were normal biomarker excretions found.

Gene patent practice across plant and human genomes

The uses of genetic sequences to inform, enable or create products or services for human biomedicine are substantially different from their uses in crop-based agriculture. Here, we explore what similarities and differences may emerge in patent use and strategies, and map patent-disclosed sequences onto three important plant genomes: maize (corn), rice and soybean. We focus on those referenced in the granted patent claims to compare their uses to the approach used in human gene patenting.

The ownership question of plant gene and genome intellectual properties

The restructuring of the crop agriculture industry over the past two decades has enabled patent holders to exclude, prevent and deter others from using certain research tools and delay or block further follow-on inventions

Abacá mosaic virus: a distinct strain of Sugarcane mosaic virus

Abacá mosaic virus (AbaMV) is related to members of the sugarcane mosaic virus subgroup of the genus Potyvirus. The ~2 kb 3′ terminal region of the viral genome was sequenced and, in all areas analysed, found to be most similar to Sugarcane mosaic virus (SCMV) and distinct from Johnsongrass mosaic virus (JGMV), Maize dwarf mosaic virus (MDMV) and Sorghum mosaic virus (SrMV). Cladograms of the 3′ terminal region of the NIb protein, the coat protein core and the 3′ untranslated region showed that AbaMV clustered with SCMV, which was a distinct clade and separate from JGMV, MDMV and SrMV. The N-terminal region of the AbaMV coat protein had a unique amino acid repeat motif different from those previously published for other strains of SCMV. The first experimental transmission of AbaMV from abacá (Musa textilis) to banana (Musa sp.), using the aphid vectors Rhopalosiphum maidis and Aphis gossypii, is reported. Polyclonal antisera for the detection of AbaMV in western blot assays and ELISA were prepared from recombinant coat protein expressed in E. coli. A reverse transcriptase PCR diagnostic assay, with microtitre plate colourimetric detection, was developed to discriminate between AbaMV and Banana bract mosaic virus, another Musa-infecting potyvirus. Sequence data, host reactions and serological relationships indicate that AbaMV should be considered a distinct strain of SCMV, and the strain designation SCMV-Ab is suggested.

Construction, installation, and performance of two repacked weighing lysimeters

Weighing lysimeters are the standard method for directly measuring evapotranspiration (ET). This paper discusses the construction, installation, and performance of two (1.52 m × 1.52 m × 2.13-m deep) repacked weighing lysimeters for measuring ET of corn and soybean in West Central Nebraska. The cost of constructing and installing each lysimeter was approximately US $12,500, which could vary depending on the availability and cost of equipment and labor. The resolution of the lysimeters was 0.0001 mV V-1, which was limited by the data processing and storage resolution of the datalogger. This resolution was equivalent to 0.064 and 0.078 mm of ET for the north and south lysimeters, respectively. Since the percent measurement error decreases with the magnitude of the ET measured, this resolution is adequate for measuring ET for daily and longer periods, but not for shorter time steps. This resolution would result in measurement errors of less than 5% for measuring ET values of ≥3 mm, but the percent error rapidly increases for lower ET values. The resolution of the lysimeters could potentially be improved by choosing a datalogger that could process and store data with a higher resolution than the one used in this study.

Apparent digestibility of some nutrient sources by juvenile mud crab, Scylla serrata (Forskal 1775)

As part of preliminary work aimed at the development of a formulated diet for the mud crab, Scylla serrata, an experiment was conducted with juvenile mud crabs (95.65±2.17 g) to determine apparent digestibility coefficients (ADC) for cellulose, fish meal, shrimp meal, blood meal, soybean meal, wheat flour and cod liver oil. Apparent digestibility coefficients for dry matter (ADCdm), energy (ADCenergy) and protein (ADC protein) were in the ranges 70.0-95.7%, 77.4-97.1% and 57.7-97.9% respectively. Soybean meal had the highest ADCdm and wheat flour had the lowest value (P<0.05), while the ADCdm for fish meal, blood meal and shrimp meal were not different (P?0.05). Similarly, soybean meal had the same ADCenergy as that of fish meal, but higher than those of cod liver oil, blood meal and shrimp meal (P<0.05). Moreover, the ADC protein for blood meal or shrimp meal were not significantly different from fish meal (P?0.05); nevertheless, they were lower than that of soybean meal and higher than that of wheat flour (P<0.05). Of significant interest was the ADCdm (78.0%) and ADCenergy (77.4%) for cellulose, which indicates that plant-based nutrient sources may well be a useful component of formulated diets for mud crabs.

Abundance and mortality of overwintering pupae of Helicoverpa armigera (Hübner) (Lepidoptera: Noctuidae) on the Darling Downs, Queensland, Australia

Surveys were conducted between 1997 and 2001 to investigate the incidence of overwintering Helicoverpa spp. pupae under summer crop residues on the Darling Downs, Queensland. Only Helicoverpa armigera was represented in collections of overwintering pupae. The results indicated that late-season crops of cotton, sorghum, maize, soybean, mungbean and sunflower were equally likely to have overwintering pupae under them. In the absence of tillage practices, these crops had the potential to produce similar numbers of moths/ha in the spring. There were expected differences between years in the densities of overwintering pupae and the number of emerged moths/ha. Irrigated crops produced 2.5 times more moths/ha than dryland crops. Overall survival from autumn-formed pupae to emerged moths averaged 44%, with a higher proportion of pupae under maize surviving to produce moths than each of the other crops. Parasitoids killed 44.1% of pupae, with Heteropelma scaposum representing 83.3% of all parasitoids reared from pupae. Percentage parasitism levels were lower in irrigated crops (27.6%) compared with dryland crops (40.5%). Recent changes to Helicoverpa spp. management in cotton/grain-farming systems in south-eastern Queensland, including widespread adoption of Bt cotton, and use of more effective and more selective insecticides, could lead to lower densities of overwintering pupae under late summer crops.

Long-term response of corn to limited irrigation and crop rotations

Dwindling water supplies for irrigation are prompting alternative management choices by irrigators. Limited irrigation, where less water is applied than full crop demand, may be a viable approach. Application of limited irrigation to corn was examined in this research. Corn was grown in crop rotations with dryland, limited irrigation, or full irrigation management from 1985 to 1999. Crop rotations included corn following corn (continuous corn), corn following wheat, followed by soybean (wheat-corn-soybean), and corn following soybean (corn-soybean). Full irrigation was managed to meet crop evapotranspiration requirements (ETc). Limited irrigation was managed with a seasonal target of no more than 150 mm applied. Precipitation patterns influenced the outcomes of measured parameters. Dryland yields had the most variation, while fully irrigated yields varied the least. Limited irrigation yields were 80% to 90%> of fully irrigated yields, but the limited irrigation plots received about half the applied water. Grain yields were significantly different among irrigation treatments. Yields were not significantly different among rotation treatments for all years and water treatments. For soil water parameters, more statistical differences were detected among the water management treatments than among the crop rotation treatments. Economic projections of these management practices showed that full irrigation produced the most income if water was available. Limited irrigation increased income significantly from dryland management.