Increased 8-hydroxyguanine content of chloroplast DNA from ozone-treated plants

The mechanism of ozone-mediated plant injury is not known but has been postulated to involve oxygen free radicals. Hydroxyl free radicals react with DNA causing formation of many products, one of which is 8-hydroxyguanine. By using high performance liquid chromatography with electrochemical detection, the 8-hydroxy-2′-deoxyguanosine (8-OHdG) content of a DNA enzymatic digest can be sensitively quantitated. Beans (Phaseolus vulgaris L.) and peas (Pisum sativum L.) were treated with an ozone regime that caused acute injury. Chloroplast DNA was obtained from plants harvested either immediately after ozone treatment or 24 hours later. Ozone-exposed plants in general had nearly two-fold higher levels of 8-OHdG as compared to control plants. In vitro treatment of DNA in buffer solution with ozone did not cause formation of 8-OHdG in DNA, even though ozone did react directly with the macromolecule per se. Exposure of isolated, illuminated chloroplasts to ozone caused nearly a seven-fold increase in the amount of 8-OHdG in the chloroplast DNA as compared to none-ozone-exposed chloroplasts. These results suggest that ozone exposure to plants causes formation of enhanced levels of oxygen free radicals, thus mediating formation of 8-OHdG in chloroplast DNA. The reaction of ozone with DNA per se did not cause formation of 8-OHdG. Therefore, it is the interaction of ozone with plant cells and isolated chloroplasts which mediates oxygen free radical formation.     

Water Stress Reduces Ozone Injury via a Stomatal Mechanism

Various studies have shown that water-stressed plants are more tolerant of ozone exposures than are unstressed plants. Two probable explanations for this tolerance are (a) stomatal closure which reduces ozone uptake and (b) biochemical or anatomical changes within the leaves. Phaseolus vulgaris cv Pinto bean plants were established and transferred to membrane systems which controlled the osmotic potential around the roots at −35 or −80 kilopascals for 5 days prior to ozone treatment (0 or 1.0 microliters per liter for 2 hours). Both water-stressed and unstressed plants were sprayed with various concentrations of abscisic acid to close the stomata or with fusicoccin to induce stomata opening. The abaxial stomatal resistances of primary and trifoliate leaves were measured just prior to ozone exposure. Plant response to ozone was determined by stress ethylene production and chlorophyll loss. Both water stress and abscisic acid induced stomatal closure and reduced ozone injury. In water-stressed plants, fusicoccin induced stomatal opening and those plants were as sensitive to ozone as were the non-water-stressed plants. These data suggest that water stress protects plants from ozone injury mainly through its influence on stomatal aperture rather than through biochemical or anatomical changes.     

Isolation of Polysaccharides Sulfated during Early Embryogenesis in Fucus

Beginning 10 hours after fertilization, zygotes of Fucus distichus L. Powell incorporate (35)S into polysaccharides as a sulfate ester of fucose. These sulfated polysaccharides are sequestered in only the rhizoid cell of the two-celled embryo and can serve as a marker of cellular differentiation. Zygotes were pulsed at different times after fertilization with Na(2) (35)SO(4) to identify and isolate the fucans localized within the region of cytoplasm destined to become the rhizoid cell. Low molecular weight pools of (35)S were saturated within 60 minutes, with the greatest incorporation into ethanol-soluble and insoluble fractions occurring with 0.1 mm Na(2)SO(4) in the artificial sea water medium. At the time of rhizoid formation, four fucose-containing polysaccharide fractions incorporated (35)S. When each fraction was subjected to diethylaminoethyl chromatography, two components were eluted with KCl that contained over 84% of the fucose and 93% of the (35)S of the particular fraction. Highvoltage paper electrophoresis of each fraction also resulted in the separation of these two major components. Both components from each of the four fractions behaved identically when separated by diethylaminoethyl chromatography and paper electrophoresis. By comparing the incorporation of (35)S into the polysaccharide fractions at 4 and 16 hours after fertilization, the fucan-sulfate components that are localized in the cytoplasm at the time of rhizoid formation were isolated. Although sulfated polysaccharides in brown algae are reported to be very heterogeneous in terms of their sugar composition and complexes with other heteropolymers, we propose that there are two major components that are sulfated during early embryogenesis in Fucus. The location of these two sulfated polysaccharides in different chemical fractions may reflect their subcellular localization (e.g., cytoplasmic vesicles or cell walls), or their association with other heteropolymers.     

Intratumor heterogeneity of biomarker expression in breast carcinomas

Small biopsy samples are used increasingly to assess the biomarker expression for prognostic information and for monitoring therapeutic responses prior to and during neoadjuvant therapy. The issue of intratumor heterogeneity of expression of biomarkers, however, has raised questions about the validity of the assessment of biomarker expression based on limited tissue samples. We examined immunohistochemically the expression of HER-2neu (p185^erbB-2), epidermal growth factor receptor (EGFR), Bcl-2, p53, and proliferating cell nuclear antigen (PCNA) in 30 breast carcinomas using archived, paraffin embedded tissue and determined the extent of intratumor heterogeneity. Each section was divided into four randomly oriented discrete regions, each containing a portion of the infiltrating carcinoma. For each tumor, the entire lesion and four regions were analyzed for the expression of these markers. Scores of both membrane and cytoplasmic staining of HER-2neu and EGFR, scores of cytoplasmic staining of Bcl-2, and scores of nuclear staining of both p53 and PCNA were recorded. The intensity of staining and the proportion of immunostained cells were determined. A semiquantitative immunoscore was calculated by determining the sum of the products of the intensity and corresponding proportion of stained tumor cells. We analyzed both invasive (IDC) and in situ (DCIS) carcinomas. The Wilcoxon signed-rank test was used for paired comparisons between overall and regional immunoscores and between overall and regional percentages of stained cells. Spearman's correlation coefficients were used to assess the level of agreement of overall biomarker expression with each of the regions. Generalized linear models were used to assess overall and pair-wise differences in the absolute values of percent changes between overall and regional expression of biomarkers. For IDCs, there were no statistically significant differences in the expression of the biomarkers in terms of either the percentage of cells staining or the immunoscores when comparing the entire tumor with each region except for the lower EGFR expression of arbitrarily selected region 1 and lower p53 expression of region 1 compared to that of the entire tumor section. For DCIS, there were no statistically significant differences in the expression of the biomarkers between the entire tumor and each region except in PCNA of region 2 compared to that of entire tumor section. Positive correlation of immunoscores was observed between the entire tumor and each region as well as across all four regions for IDC. Similar observations were noted with DCIS except for HER-2neu and PCNA. No statistically significant differences were observed in the absolute values of percent changes of biomarker expression between overall and the four regions for both DCIS and IDC. Therefore, no significant intratumor heterogeneity in the expression of HER-2neu, Bcl-2, and PCNA was observed in IDC. Minor regional variations were observed for EGFR and p53 in IDC. Similarly, no significant regional variation in the expression of markers was observed in DCIS except for PCNA.     

Nitrogen Export from Forested Watersheds in the Oregon Coast Range: The Role of N<Subscript>2</Subscript>-fixing Red Alder

Variations in plant community composition across the landscape can influence nutrient retention and loss at the watershed scale. A striking example of plant species importance is the influence of N₂-fixing red alder (Alnus rubra) on nutrient cycling in the forests of the Pacific Northwest. To understand the influence of red alder on watershed nutrient export, we studied the chemistry of 26 small watershed streams within the Salmon River basin of the Oregon Coast Range. Nitrate and dissolved organic nitrogen (DON) concentrations were positively related to broadleaf cover (dominated by red alder: 94% of basal area), particularly when near-coastal sites were excluded (r ² = 0.65 and 0.68 for nitrate-N and DON, respectively). Nitrate and DON concentrations were more strongly related to broadleaf cover within entire watersheds than broadleaf cover within the riparian area alone, which indicates that leaching from upland alder stands plays an important role in watershed nitrogen (N) export. Nitrate dominated over DON in hydrologic export (92% of total dissolved N), and nitrate and DON concentrations were strongly correlated. Annual N export was highly variable among watersheds (2.4–30.8 kg N ha^–1 y^–1), described by a multiple linear regression combining broadleaf and mixed broadleaf–conifer cover (r² = 0.74). Base cation concentrations were positively related to nitrate concentrations, which suggests that nitrate leaching increases cation losses. Our findings provide evidence for strong control of ecosystem function by a single plant species, where leaching from N saturated red alder stands is a major control on N export from these coastal watersheds.     

Conversion for Avicel and AFEX pretreated corn stover by Clostridium thermocellum and simultaneous saccharification and fermentation: insights into microbial conversion of pretreated cellulosic biomass

In this study, efforts were taken to compare solubilization of Avicel and AFEX pretreated corn stover (AFEX CS) by SSF and Clostridium thermocellum fermentation, with an aim to gain insights into microbial conversion of pretreated cellulosic biomass. Solubilization rates for AFEX CS are comparable for the two systems while solubilization of Avicel is much faster by C. thermocellum. Initial catalyst loading impacts final cellulose conversion for SSF but not for C. thermocellum. Hydrolysis of the two substrates using cell-free C. thermocellum fermentation broth revealed much smaller difference in cellulose conversion than the difference observed for growing cultures. Tests on hemicellulose removal and particle size reduction for AFEX CS indicated that substrate accessibility is very important for enhanced solubilization by C. thermocellum.     

Carbon catabolite repression in <Emphasis Type="Italic">Thermoanaerobacterium saccharolyticum</Emphasis>

Background

The thermophilic anaerobe Thermoanaerobacterium saccharolyticum is capable of directly fermenting xylan and the biomass-derived sugars glucose, cellobiose, xylose, mannose, galactose and arabinose. It has been metabolically engineered and developed as a biocatalyst for the production of ethanol.

Results

We report the initial characterization of the carbon catabolite repression system in this organism. We find that sugar metabolism in T. saccharolyticum is regulated by histidine-containing protein HPr. We describe a mutation in HPr, His15Asp, that leads to derepression of less-favored carbon source utilization.

Conclusion

Co-utilization of sugars can be achieved by mutation of HPr in T. saccharolyticum. Further manipulation of CCR in this organism will be instrumental in achieving complete and rapid conversion of all available sugars to ethanol.

     

Identification of the [FeFe]-Hydrogenase Responsible for Hydrogen Generation in Thermoanaerobacterium saccharolyticum and Demonstration of Increased Ethanol Yield via Hydrogenase Knockout

Three putative hydrogenase enzyme systems in Thermoanaerobacterium saccharolyticum were investigated at the genetic, mRNA, enzymatic, and phenotypic levels. A four-gene operon containing two [FeFe]-hydrogenase genes, provisionally termed hfs (hydrogenase-Fe-S), was found to be the main enzymatic catalyst of hydrogen production. hfsB, perhaps the most interesting gene of the operon, contains an [FeFe]-hydrogenase and a PAS sensory domain and has several conserved homologues among clostridial saccharolytic, cellulolytic, and pathogenic bacteria. A second hydrogenase gene cluster, hyd, exhibited methyl viologen-linked hydrogenase enzymatic activity, but hyd gene knockouts did not influence the hydrogen yield of cultures grown in closed-system batch fermentations. This result, combined with the observation that hydB contains NAD(P)+ and FMN binding sites, suggests that the hyd genes are specific to the transfer of electrons from NAD(P)H to hydrogen ions. A third gene cluster, a putative [NiFe]-hydrogenase with homology to the ech genes, did not exhibit hydrogenase activity under any of the conditions tested. Deletion of the hfs and hydA genes resulted in a loss of detectable methyl viologen-linked hydrogenase activity. Strains with a deletion of the hfs genes exhibited a 95% reduction in hydrogen and acetic acid production. A strain with hfs and ldh deletions exhibited an increased ethanol yield from consumed carbohydrates and represents a new strategy for engineering increased ethanol yields in T. saccharolyticum.Thermophilic anaerobic bacteria have long been of interest for studies of cellulosic biomass conversion due to their native hydrolytic and fermentative abilities (5, 33). However, all thermophilic anaerobes isolated to date have branched fermentation pathways which produce organic acids in addition to solvents such as ethanol (12). For cellulosic fuel production, significant yield loss is likely to be economically unfeasible (11).In their natural environments, saccharolytic fermentative bacteria participate in interspecies hydrogen transfer, producing hydrogen from carbohydrates that is rapidly consumed by methanogens and sulfate-reducing bacteria (30). As a result, the hydrogen partial pressure remains exceedingly low, allowing hydrogen (E₀′, −414 mV) to be produced not only from ferredoxin (E₀′, ∼−400 mV) but also from the less favorable electron source NAD(P)H (E₀′, −320 mV). Fermentative bacteria benefit from hydrogen production, because they are able to coproduce acetic acid and an additional ATP via acetate kinase (23). When grown in pure culture in a closed fermentation vessel, hydrogen is generated primarily from reduced ferredoxin, since generation from NAD(P)H becomes less favorable as the concentration of hydrogen increases (7).We have recently demonstrated high-yield ethanol production in the thermophilic anaerobe Thermoanaerobacterium saccharolyticum JW/SL-YS485 through deletion of the l-lactate dehydrogenase (ldh), phosphate acetyltransferase (pta), and acetate kinase (ack) genes (20). In addition to producing ethanol at high yield, this strain produced significantly less hydrogen, as is required to balance end product electron stoichiometry, although hydrogenase activity in cell extracts remained high. In this study, we used gene knockout to identify gene clusters that are implicated in hydrogenase activity in T. saccharolyticum and to identify the hfs gene operon, which is required for hydrogen production. The hfs operon contains a protein with [FeFe]-hydrogenase and PAS sensory domains that is conserved among a few members of the genera Clostridium and Thermoanaerobacter. Strains with hfs deletions showed decreased acetic acid production, and a strain with hfs and ldh deletions produced ethanol at an increased yield.