The Arabidopsis Information Resource (TAIR): a comprehensive database and web-based information retrieval, analysis, and visualization system for a model plant.

Arabidopsis thaliana, a small annual plant belonging to the mustard family, is the subject of study by an estimated 7000 researchers around the world. In addition to the large body of genetic, physiological and biochemical data gathered for this plant, it will be the first higher plant genome to be completely sequenced, with completion expected at the end of the year 2000. The sequencing effort has been coordinated by an international collaboration, the Arabidopsis Genome Initiative (AGI). The rationale for intensive investigation of Arabidopsis is that it is an excellent model for higher plants. In order to maximize use of the knowledge gained about this plant, there is a need for a comprehensive database and information retrieval and analysis system that will provide user-friendly access to Arabidopsis information. This paper describes the initial steps we have taken toward realizing these goals in a project called The Arabidopsis Information Resource (TAIR) (www.arabidopsis.org).

M-side electron transfer in reaction center mutants with a lysine near the nonphotoactive bacteriochlorophyll.

We report the primary charge separation events in a series of Rhodobacter capsulatus reaction centers (RCs) that have been genetically modified to contain a lysine near the bacteriochlorophyll molecule, BChl(M), on the nonphotoactive M-side of the RC. Using wild type and previously constructed mutants as templates, we substituted Lys for the native Ser residue at position 178 on the L polypeptide to make the S(L178)K single mutant, the S(L178)K/G(M201)D and S(L178)K/L(M212)H double mutants, and the S(L178)K/G(M201)D/L(M212)H triple mutant. In the triple mutant, the decay of the photoexcited primary electron donor (P) occurs with a time constant of 15 ps and is accompanied by 15% return to the ground state, 62% electron transfer to the L-side bacteriopheophytin, BPh(L), and 23% electron transfer to the M-side analogue, BPh(M). The data supporting electron transfer to the M-side include bleaching of the Q(X) band of BPh(M) at 528 nm and a spectrally and kinetically resolved anion band with a maximum at 640 nm assigned to BPh(M)(-). The decay of these features and concomitant approximately 20% decay of bleaching of the 850 nm band of P give a P(+)BPh(M)(-) lifetime on the order of 1-2 ns that reflects deactivation to give the ground state. These data and additional findings are compared to those from parallel experiments on the G(M201)D/L(M212)H double mutant, in which 15% electron transfer to BPh(M) has been reported previously and is reproduced here. We also compare the above results with the primary electron-transfer processes in S(L178)K, S(L178)K/G(M201)D, and S(L178)K /L(M212)H RCs and with those for the L(M212)H and G(M201)D single mutants and wild-type RCs. The comparison of extensive results that track the primary events in these eight RCs helps to elucidate key factors underlying the directionality and high yield of charge separation in the bacterial photosynthetic RC.

Epithelial injury induces egr-1 and fos expression by a pathway involving protein kinase C and ERK.

The signaling pathways activated in response to gastrointestinal injury remain poorly understood. Previous work has implicated the extracellular signal-regulated kinase (ERK) mitogen-activated protein kinase as a mediator of wound-signal transduction and a possible regulator of epithelial restitution. Monolayer injury resulted in rapid activation of p42 and p44 ERK. Injury-induced ERK activation was blocked by protein kinase C inhibition or by disruption of the cell cytoskeleton. Significant increases in Fos and early growth response (Egr)-1 mRNA levels were stimulated by injury, peaking by 20 min. ERK activation and the induction of Egr-1 mRNA were inhibited in a dose-dependent fashion with PD-98059. Fos mRNA expression was partially blocked by PD-98059. Western blot analysis demonstrated strong expression and nuclear localization of Fos and Egr after wounding. Electrophoretic mobility shift assays demonstrated that nuclear extracts contained a protein that specifically bound double-stranded oligonucleotides containing the Egr consensus binding element. Gel supershift assays demonstrated that the protein-DNA complexes were recognized by anti-Egr antibody. Inhibition of injury-induced ERK activation by PD-98059 or direct interference with Egr by expression of a dominant negative mutant led to significantly reduced in vitro monolayer restitution.

ERK and p38 MAP kinase pathways are mediators of intestinal epithelial wound-induced signal transduction.

Repair of gastrointestinal epithelial injury involves cell migration, proliferation, and specific gene expression. The pathways responsible for epithelial wound signal transduction are poorly understood. Mechanical wounding of IEC-6 cell monolayers resulted in rapid activation of the extracellular signal-regulated kinase (ERK) and p38 MAP kinase pathways, while c-Jun amino-terminal protein kinases were not significantly activated. Two minutes after wounding cells at the wound edge strongly expressed cytoplasmic phospho-ERK. By five minutes, immunostaining was concentrated within the nucleus. Consistent with activated MAP kinase signaling cascades (which phosphorylate transcription factors implicated in immediate-early gene induction), monolayer wounding resulted in greater than 30- and 8-fold increases in c-Fos and early growth response-1 mRNA by Northern blot analysis, peaking at 20 minutes. Only slight increases in c-Jun mRNA were detected. Thus, intestinal epithelial wound signal transduction is, at least in part, mediated by activation of ERK and p38 MAP kinase signaling cascades. ERK and p38 pathways may regulate pathophysiologically relevant genes in wound repair by the induction of transcription factors.

Squamous cell carcinoma of the supraglottic larynx treated with surgery and/or radiation therapy.

This is an analysis of 195 patients with squamous cell carcinoma of the supraglottic larynx treated with curative intent at the University of Florida between October 1964 and February 1984. The patients were staged according to the AJCC staging system. There was a minimum follow-up of 2 years, with 76% having at least a 5-year follow-up. Patients were treated with preoperative irradiation and resection (28), surgery and postoperative irradiation (35), surgery alone (26), or radiation therapy alone, with or without neck dissection(s) (106). This paper will compare the rate of local-regional control, the incidence of complications, voice preservation, and survival for radical irradiation, as opposed to surgery, with or without adjuvant irradiation.

Rainfall and decomposition in the chihuahuan desert.

We tested the hypotheses that rates of decomposition in a desert should be higher following single large rain events of 25 mm than evenly spaced 6 mm events and that supplemental rainfall should result in higher populations of soil biota. There were no significant differences in mass losses of creosotebush, Larrea tridentata, leaf litter on plots receiving water supplementation and no added water. On some sampling dates, there were higher mass losses in the 6 mm·week-1 treatment. Weekly rainfall produced higher coefficients of variation in mass losses than the other rainfall regimes. A single event pulse compared with weekly pulses of rainfall during the normal "dry" period resulted in no differences in mass losses. Microarthropods and nematodes exhibited numerical responses to supplemental rainfall but the litter microflora did not. These studies provide direct experimental evidence that the conventional wisdom linking decomposition to rainfall in deserts is wrong. The studies also suggest that the effects of litter fauna on surface litter decomposition are minimal; therefore, future studies should focus on activites of the microflora.

Carcinoma of the intact uterine cervix, stage IB-IIA-B, greater than or equal to 6 cm in diameter: irradiation alone vs preoperative irradiation and surgery.

This is an analysis of 123 patients with Stage IB-IIA-B carcinoma of the intact uterine cervix, 6 cm or greater in diameter, who were treated with curative intent at the University of Florida with radiation alone or radiation followed by a hysterectomy between October 1964 and February 1982. There is a minimum follow-up of 2 years in all patients; 87% of all recurrences and 91% of pelvic recurrences occurred within this time period. Examination of pelvic control rates, as well as disease-free survival, showed no significant advantage in pelvic control, disease-free survival, or absolute survival for either treatment group when compared by stage and tumor size. The incidence of severe complications was 6% for patients treated with irradiation alone and 15% for those treated with irradiation and surgery (p = 0.119).