Evaluating ecological condition using soil biogeochemical parameters and near infrared reflectance spectra.

Rapid, repeatable assessment of ecological condition is critical for quantitative ecosystem monitoring. Soils provide a sensitive, integrative indicator for which sampling and analysis techniques are well defined. We evaluated soil properties as indicators of ecological condition (subjectively classified into minimally/moderately/severely degraded based on vegetative, hydrologic and edaphic cues) at 526 sites within Ft. Benning military installation (Georgia, USA). For each sample, we measured 17 biogeochemical parameters, and collected high-resolution diffuse reflectance spectra using visible/near infrared reflectance spectroscopy (VNIRS). VNIR spectra have been related to numerous soil attributes - we examine them here for diagnosing integrated response (i.e., ecological condition). We used ordinal logistic regression (OLR) and classification trees (CT) to discriminate between condition categories using both sets of predictors (biogeochemistry and spectra). Sixteen biogeochemical parameters were significantly different across condition categories; however, multivariate models greatly improved discrimination ([calibration, validation] accuracy of [69%, 66%] and [96%, 73%] for OLT and CT models, respectively). Important predictors included total C, total P, and Mehlich K/Ca/Mg. VNIR spectra further improved discrimination ([calibration, validation] accuracy of [74%, 70%] and [96%, 75%] for OLR and CT models, respectively). While spectra were comparably effective at discriminating minimally degraded sites, they were significantly more effective at discriminating severely degraded sites. Error rates across confounding factors suggest that watershed of origin and landscape position were the only important confounders, likely due to imbalanced sampling. We conclude that multivariate diagnosis improves accuracy, and that VNIR spectroscopy, which yields substantial cost and logistical improvements over conventional analyses, provides an effective tool for rapid condition diagnosis.

Analysis of the genes encoding the largest subunit of RNA polymerase II in Arabidopsis and soybean.

We have cloned and sequenced the gene encoding the largest subunit of RNA polymerase II (RPB1) from Arabidopsis thaliana and partially sequenced genes from soybean (Glycine max). We have also determined the nucleotide sequence for a number of cDNA clones which encode the carboxyl terminal domains (CTDs) of RNA polymerase II from both soybean and Arabidopsis. The Arabidopsis RPB1 gene encodes a polypeptide of approximately 205 kDa, consists of 12 exons, and encompasses more than 8 kb. Predicted amino acid sequence shows eight regions of similarity with the largest subunit of other prokaryotic and eukaryotic RNA polymerases, as well as a highly conserved CTD unique to RNA polymerase II. The CTDs in plants, like those in most other eukaryotes, consist of tandem heptapeptide repeats with the consensus amino acid sequence PTSPSYS. The portion of RPB1 which encodes the CTD in plants differs from that of RPB1 of animals and lower eukaryotes. All the plant genes examined contain 2-3 introns within the CTD encoding regions, and at least two plant genes contain an alternatively spliced intron in the 3' untranslated region. Several clustered amino acid substitutions in the CTD are conserved in the two plant species examined, but are not found in other eukaryotes. RPB1 is encoded by a multigene family in soybean, but a single gene encodes this subunit in Arabidopsis and most other eukaryotes.

Purification and immunological analysis of RNA polymerase II from Caenorhabditis elegans.

We describe a rapid procedure for obtaining highly purified RNA polymerase II from the nematode Caenorhabditis elegans. The structure of the enzyme was examined by denaturing gel electrophoresis and found to consist of three large polypeptides (molecular weights 200,000, 175,000, and 135,000) and eight smaller polypeptides (molecular weights 29,500, 20,000, 16,000, 15,000, 13,000, 11,500, 10,500, and 9,500). As observed for the analogous enzyme from other organisms, the 175,000 polypeptide (II175) appeared to be a degraded form of the 200,000 polypeptide (II200). The structure of nematode RNA polymerase II closely resembles that of the corresponding enzyme from other animals. Four of its larger subunits shared antigenicity with Drosophila RNA polymerase II. Antibody raised against purified RNA polymerase II reacted with several enzyme subunits in "Western" blots of purified polymerase and impure enzyme fractions. Immunofluorescence staining was used to visualize RNA polymerase II in the nuclei of a nematode squash preparation and the nucleoplasm of cultured mammalian cells.