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1.  Measuring the fate of plant diversity: towards a foundation for future monitoring and opportunities for urgent action 
Vascular plants are often considered to be among the better known large groups of organisms, but gaps in the available baseline data are extensive, and recent estimates of total known (described) seed plant species range from 200 000 to 422 000. Of these, global assessments of conservation status using International Union for the Conservation of Nature (IUCN) categories and criteria are available for only approximately 10 000 species. In response to recommendations from the Conference of the Parties to the Convention on Biological Diversity to develop biodiversity indicators based on changes in the status of threatened species, and trends in the abundance and distribution of selected species, we examine how existing data, in combination with limited new data collection, can be used to maximum effect. We argue that future work should produce Red List Indices based on a representative subset of plant species so that the limited resources currently available are directed towards redressing taxonomic and geographical biases apparent in existing datasets. Sampling the data held in the world's major herbaria, in combination with Geographical Information Systems techniques, can produce preliminary conservation assessments and help to direct selective survey work using existing field networks to verify distributions and gather population data. Such data can also be used to backcast threats and potential distributions through time. We outline an approach that could result in: (i) preliminary assessments of the conservation status of tens of thousands of species not previously assessed, (ii) significant enhancements in the coverage and representation of plant species on the IUCN Red List, and (iii) repeat and/or retrospective assessments for a significant proportion of these. This would result in more robust Sampled Red List Indices that can be defended as more representative of plant diversity as a whole; and eventually, comprehensive assessments at species level for one or more major families of angiosperms. The combined results would allow scientifically defensible generalizations about the current status of plant diversity by 2010 as well as tentative comments on trends. Together with other efforts already underway, this approach would establish a firmer basis for ongoing monitoring of the status of plant diversity beyond 2010 and a basis for comparison with the trend data available for vertebrates.
PMCID: PMC1569457  PMID: 15814350
global biodiversity; species richness; conservation assessments; extinction risk; IUCN Red List; Living Planet Index
2.  Faithful degradation of soybean rbcS mRNA in vitro. 
Molecular and Cellular Biology  1994;14(4):2640-2650.
The mRNA encoding the soybean rbcS gene, SRS4, is degraded into a set of discrete lower-molecular-weight products in light-grown soybean seedlings and in transgenic petunia leaves. The 5'-proximal products have intact 5' ends, lack poly(A) tails, lack various amounts of 3'-end sequences, and are found at higher concentrations in the polysomal fraction. To study the mechanisms of SRS4 mRNA decay more closely, we developed a cell-free RNA degradation system based on a polysomal fraction isolated from soybean seedlings or mature petunia leaves. In the soybean in vitro degradation system, endogenous SRS4 mRNA and proximal product levels decreased over a 6-h time course. When full-length in vitro-synthesized SRS4 RNAs were added to either in vitro degradation system, the RNAs were degraded into the expected set of proximal products, such as those observed for total endogenous RNA samples. When exogenously added SRS4 RNAs already truncated at their 3' ends were added to either system, they too were degraded into the expected subset of proximal products. A set of distal fragments containing intact 3' ends and lacking various portions of 5'-end sequences were identified in vivo when the heterogeneous 3' ends of the SRS4 RNAs were removed by oligonucleotide-directed RNase H cleavage. Significant amounts of distal fragments which comigrated with the in vivo products were also observed when exogenous SRS4 RNAs were degraded in either in vitro system. These proximal and distal products lacking various portions of their 3' and 5' sequences, respectively, were generated in essentially a random order, a result supporting a nonprocessive mechanism. Tagging of the in vitro-synthesized RNAs on their 5' and 3' ends with plasmid vector sequences or truncation of the 3' end had no apparent effect on the degradation pattern. Therefore, RNA sequences and/or structures in the immediate vicinity of each 3' end point may be important in the degradation machinery. Together, these data suggest that SRS4 mRNA is degraded by a stochastic mechanism and that endonucleolytic cleavage may be the initial event. These plant in vitro systems should be useful in identifying the cis- and trans-acting factors involved in the degradation of mRNAs.
PMCID: PMC358631  PMID: 8139564
3.  Using empirical data to model transgene dispersal. 
One element of the current public debate about genetically modified crops is that gene flow from transgenic cultivars into surrounding weed populations will lead to more problematic weeds, particularly for traits such as herbicide resistance. Evolutionary biologists can inform this debate by providing accurate estimates of gene flow potential and subsequent ecological performance of resulting hybrids. We develop a model for gene flow incorporating exponential distance and directional effects to be applied to windpollinated species. This model is applied to previously published data on gene flow in experimental plots of Agrostis stolonifera L. (creeping bentgrass), which assessed gene flow from transgenic plants resistant to the herbicide glufosinate to surrounding non-transgenic plants. Our results show that although pollen dispersal can be limited in some sites, it may be extensive in others, depending on local conditions such as exposure to wind. Thus, hybridization under field conditions is likely to occur. Given the nature of the herbicide resistance trait, we regard this trait as unlikely to persist in the absence of herbicide, and suggest that the ecological consequences of such gene flow are likely to be minimal.
PMCID: PMC1693198  PMID: 12831482
4.  Degradation of the soybean ribulose-1,5-bisphosphate carboxylase small-subunit mRNA, SRS4, initiates with endonucleolytic cleavage. 
Molecular and Cellular Biology  1995;15(12):6641-6652.
The degradation of the soybean SRS4 mRNA, which encodes the small subunit of ribulose-1,5-bisphosphate carboxylase, yields a set of proximal (5' intact) and distal (3' intact) products both in vivo and in vitro. These products are generated by endonucleolytic cleavages that occur essentially in a random order, although some products are produced more rapidly than others. Comparison of sizes of products on Northern (RNA) blots showed that the combined sizes of pairs of proximal and distal products form contiguous full-length SRS4 mRNAs. When the 3' ends of the proximal products and the 5' ends of the distal products were mapped by S1 nuclease and primer extension assays, respectively, both sets of ends mapped to the same sequences within the SRS4 mRNA. A small in vitro-synthesized RNA fragment containing one cleavage site inhibited cleavage of all major sites, equivalently consistent with one enzymatic activity generating the endonucleolytic cleavage products. These products were rich in GU nucleotides, but no obvious consensus sequence was found among several cleavage sites. Preliminary evidence suggested that secondary structure could play a role in site selection. The structures of the 5' ends of the proximal products and the 3' ends of the distal products were examined. Proximal products were found with approximately equal frequency in both m7G cap(+) and m7G cap(-) fractions, suggesting that the endonucleolytic cleavage events occurred independently of the removal of the 5' cap structure. Distal products were distributed among fractions with poly(A) tails ranging from undetectable to greater than 100 nucleotides in length, suggesting that the endonucleolytic cleavage events occurred independently of poly(A) tail shortening. Together, these data support a stochastic endonuclease model in which an endonucleolytic cleavage event is the initial step in SRS4 mRNA degradation.
PMCID: PMC230917  PMID: 8524229
5.  Expression of a gene encoding a glycine-rich protein in petunia. 
Molecular and Cellular Biology  1987;7(12):4273-4279.
We have investigated the expression of a gene that codes for a glycine-rich structural protein (GRP1) in petunia. This gene is expressed as a single polyadenylated RNA of approximately 1,600 bases which was found to be present in leaves, stems, and flowers of petunia but not in roots. In the organs in which GRP1-specific mRNA was expressed, its steady-state levels were highest in stems and leaves and lowest in flowers. This analysis also revealed that the pattern of organ-specific expression for several of the GRP1-related genes was distinctly different. In addition, it was found that the levels of GRP1 RNA were significantly higher in young leaves and stems than in old, implying developmental regulation of the gene. GRP1-specific RNA in both old and young tissue that had been wounded was found to be increased at least 25-fold over that in young unwounded tissue. Increased levels of GRP1 mRNA were seen within 5 min after wounding, with substantial increases apparent by 30 min. Maximal levels of accumulation of GRP1 transcripts occurred 90 min after wounding. The enhancement of GRP1 mRNA levels by wounding appears to be one of the earliest events of the plant wound response and is distinct from that which we observed for the PAL gene in petunia. Using S1 analysis and RNA primer extension, we demonstrated that the same transcriptional start site was used by the GRP1 gene in all organs and in wounded and unwounded tissue. The potential significance of these data with regard to wound signal transduction is discussed.
PMCID: PMC368109  PMID: 2449603
6.  Transcriptional regulation of a gene encoding the small subunit of ribulose-1,5-bisphosphate carboxylase in soybean tissue is linked to the phytochrome response. 
Molecular and Cellular Biology  1985;5(8):1910-1917.
The effects of white light, far-red light, and darkness on the transcription of a soybean ribulose-1,5-biphosphate carboxylase small subunit gene, SRS1, were investigated. RNA was labeled with [alpha-32P]UTP in nuclei isolated from plants grown under different conditions of light and darkness and used to probe Southern blots and dot blots. The levels of small subunit mRNA synthesis were normalized to ribosomal RNA synthesis. We demonstrate that the SRS1 gene is transcribed at a rate 16- to 32-fold higher in plants grown in the light than in those grown in darkness. Transcription of the small subunit increased dramatically when plants grown in darkness were given 30 min to 6 h of light and then leveled off after 24 to 48 h of exposure. When light-grown seedlings were exposed to greater than 2 h of darkness, a gradual decrease in transcription was detected. This decrease in transcription reached basal dark-grown levels after 48 h of exposure to darkness. The increase in transcription in etiolated seedlings treated with white light for 15 min could be reduced to basal levels if the treatment was followed by treatment with far-red light for 15 min. In addition, transcription in ligh-grown seedlings was reduced to basal levels when plants were exposed to far-red light for 15 min. The transcription of this ribulose-1,5-biphosphate carboxylase small subunit gene is strongly positively regulated by white light, is negatively regulated by far-red light, and exhibits a classic phytochrome-linked response.
PMCID: PMC366907  PMID: 3837851
7.  Isolation and Mapping of Small Cauliflower Mosaic Virus DNA Fragments Active as Promoters in Escherichia coli 
Journal of Virology  1981;37(2):673-682.
Small EcoRI* fragments of cauliflower mosiac virus DNA (strain CM4-184), which act as promoters for the tetracycline resistance gene on the promoter probe plasmid pBRH4 in Escherichia coli, have been isolated and mapped on the viral genome. Two regions of the viral genome contain DNA sequences with promoter activity in E. coli. Two independent cloned fragments from one region direct a high level of tetracycline resistance (up to 38 μg of tetracycline per ml). Two independent fragments from the second region of the viral genome also direct tetracycline resistance, but at lower levels. The activity of the two fragments with the strongest promoter activity in E. coli may direct transcription of the viral genome in a clockwise direction. This is consistent with the direction of transcription predicted from sequence analysis of the viral DNA (Franck et al., Cell 21: 285-294, 1980). One of these fragments maps at the start of a large open translational reading frame which is predicted to contain the coding sequence for the viral coat protein. Each promoter-active fragment is located in the 5′-terminal portion of one of the six open reading frames predicted from the DNA sequence.
PMCID: PMC171055  PMID: 16789206
8.  A new restriction endonuclease from the anaerobic bacterium, Desulfovibrio desulfuricans, Norway. 
Nucleic Acids Research  1980;8(14):3125-3131.
The purification and characterization of a new restriction endonuclease, Dde 1, from a sulfate-reducing, anaerobic bacterium, Desulfovibrio desulfuricans, Norway, is reported. The enzyme recognizes the sequence (see formula index) and cleaves at the position indicated by the arrows. The enzyme preparation obtained is suitable for restriction mapping an ligation.
PMCID: PMC324359  PMID: 6255409
9.  A potential role for RNA turnover in the light regulation of plant gene expression: ribulose-1,5-bisphosphate carboxylase small subunit in soybean. 
Nucleic Acids Research  1990;18(11):3377-3385.
Post-transcriptional regulation of the genes encoding the small subunit (rbcS) of ribulose-1,5-bisphosphate carboxylase was examined in soybean seedlings. Substantial discrepancies were detected between relative in vitro transcription rates and steady-state RNA levels in light- and dark-grown seedling leaves, indicating that rbcS RNA may be degraded more rapidly in light than in darkness. Additional data imply that the turnover mechanism is rapidly induced by light, maintained for some time in darkness, and that it may be negatively controlled by far-red light. The proposed RNA turnover system does not affect all RNAs equally since a soybean actin gene showed equivalent in vitro transcription rates and RNA levels in light and darkness. Soybean rbcS genes may be subject to a novel mode of control in which light-induced expression is accompanied by an increased rate of RNA degradation. Models for the specific regulation of rbcS RNA stability in response to light are presented.
PMCID: PMC330947  PMID: 2356127
10.  Transcriptional and post-transcriptional processes regulate expression of RNA encoding the small subunit of ribulose-1,5-biphosphate carboxylase differently in petunia and in soybean. 
Nucleic Acids Research  1990;18(12):3621-3629.
The effects of white light, far-red light and darkness on the in vitro transcription and RNA levels of the small subunit of ribulose-1,5-bisphosphate carboxylase (rbcS) were investigated in petunia and in soybean. In petunia plants treated with 48 hours of darkness the in vitro transcription rate of two of the rbcS subfamilies of petunia, rbcS A and rbcS C, declined 32- and 8-fold respectively, whereas treatment of dark-adapted plants with light caused the in vitro transcription rate of these subfamilies to return to their light-grown levels. Relative RNA levels of rbcS A and rbcS C declined in parallel with in vitro transcription rate changes upon treatment of petunia plants with darkness. However, while relative RNA levels of rbcS C changed in parallel with in vitro transcription rate under all conditions of far-red light and white light tested, there were differences between the changes in rbcS A in vitro transcription rate and RNA levels which were consistent with post-transcriptional regulation of rbcS A RNA. In addition we observed that nuclei isolated from the leaves of plants which were exposed to darkness for periods of 72 hours or longer were transcriptionally inactive. Similar experiments on the in vitro transcription and relative levels of the rbcS RNA in soybean seedlings have lead to the hypothesis that rbcS RNA is less stable in light than in darkness. In contrast, small decreases in rbcS in vitro transcription rate in mature soybean plants treated with darkness were accompanied by large decreases in rbcS RNA, suggesting that rbcS RNA was degraded more rapidly in darkness than in light in these plants. We have shown that differences in the modulation of rbcS RNA levels by post-transcriptional mechanisms exist between plants which belong to different orders, and between different developmental states of the same plant species.
PMCID: PMC331018  PMID: 1694578
11.  5' proximal sequences of a soybean ribulose-1,5-bisphosphate carboxylase small subunit gene direct light and phytochrome controlled transcription. 
Nucleic Acids Research  1987;15(16):6501-6514.
Two closely related ribulose-1,5-bisphosphate carboxylase small subunit (SSU) genes, SRS1 and SRS4, are transcribed at high levels in soybean plants in response to light. Transgenic petunia plants containing 5' sequences from SRS1 or SRS4 fused to the polypeptide encoding region of a neomycin phosphotransferase (NPTII) gene exhibit selectable kanamycin resistance. Deletion of three ATG codons from the region preceding the normal NPTII translation start site has little effect on the levels of kanamycin resistance in transformed plants. Run-on transcription assays in isolated nuclei demonstrate that transcription of the SRS1/NPTII chimera and the native petunia SSU11A gene subfamily is light regulated and under phytochrome control in leaves of transgenic plants. In young expanding leaves of fully light grown plants, transcription of these genes is markedly reduced within minutes of far-red treatment, while ribosomal DNA and actin gene transcription remains unchanged. This is analogous to the transcriptional response we observed for SRS1 and SRS4 in soybean seedlings. These data suggest (1) that transcription of SSU genes in both soybean and petunia require the continued presence or synthesis of phytochrome in the Pfr form and (2) that 5' sequences are sufficient to direct the phytochrome controlled transcriptional response of the SRS1 gene. In fully expanded mature leaves we found the transcription rates of the native SSU11A gene subfamily, the chimeric SRS1/NPTII gene, the rDNA genes, and several other control genes to be reduced markedly after far-red treatment or after extended periods of darkness. The contrast between results in young and mature leaves is discussed.
PMCID: PMC306119  PMID: 3627996

Results 1-11 (11)