Four cytosolic-type CuZn-superoxide dismutases in germinating seeds of Pinus sylvestris

A differential analysis of CuZn-superoxide dismutase (SOD. EC 1.15.1.1) isozymes after native-polyacry lamide gel elecrrophoresis (PAGE) and isoelectric focusing (IEF) indicated that germinating seeds of Scots pine (Pinus sylvestris L.) 3 days after the start of imbibition (3 DAI) contain five CuZn-SOD isozymes. Two isozymes co-migrated on native–PAGE but were separated after IEF. CuZn-SODs of Scots pine were purified from germinating seeds (3 DAI) by anion-exchange chromatography, hydrophobic interaction chromatography and chromatofocusing. The final separation of CuZn-SOD isozymes was accomplished by native-PAGE. CuZn-SOD isozymes were electroblotted and their NH₂-terminal amino acid sequence was determined. Comparisons of the amino acid sequences with sequences of CuZn-SOD isozymes from other plant sources indicated that one CuZn-SOD isozyme was of the chloroplastic type whereas the other four isozymes belonged to the cytosolic-type CuZn-SODs, The NH₂-terminal amino acid sequence of the chloroplastic CuZn-SOD and of one cytosolic-type CuZn-SOD were identical to those of two previously isolated, sequenced and localized CuZn-SOD isozymes from Scots pine needles. Two cytosolic-type CuZn-SOD isozymes showed a homology at 20 out of 21 NH₂-terminal amino acids. Mitochondria and glyoxysomes were isolated by differential and Percoll density-gradient centrifugation from germinating seeds (3 DAI). The cell fractionation experiments did not suggest that a major part of the CuZn-SOD activity in germinating seeds was derived from glyoxysomes or mitochondria.     

Association of the Decline of Nashi Pears with an MLO

Mycoplasma-like organisms (MLOs) were constantly detected by the DAPI technique and by restriction fragment length polymorphism (RFLP) analysis of PCR-amplified DNA in trees of Pyrus pyrifolia cvs Hosui and Kosui grafted on P. communis, seedlings rootstock with symptoms similar to the slow form of pear decline. These symptoms included upward curling of the leaves along the midrib. Leaves were abnormally thick and later turned reddish while major veins became swollen and brown. Trees with symptoms were usually 4–5 years old and were growing in the major pear areas of central Italy. The incidence of affected trees was particularly high in one orchard adjacent to a pear orchard strongly affected with the slow form of pear decline. In this case the distribution pattern of affected Nashi trees suggests that the causal agent was introduced from the adjacent pear orchard by an aerial vector. Although oriental pears are well-known hosts of the pear-decline agent when used as rootstocks of French cultivars, this is the first report of pear decline in P. pyrifolia varieties.     

Scarless skin wound repair in the fetus.

The ability of a fetus to heal without scar formation depends on its gestational age at the time of injury and the size of the wound defect. In general, linear incisions heal without scar until late in gestation whereas excisional wounds heal with scar at an earlier gestational age. The profiles of fetal proteoglycans, collagens, and growth factors are different from those in adult wounds. The less-differentiated state of fetal skin is probably an important characteristic responsible for scarless repair. There is minimal inflammation in fetal wounds. Fetal wounds are characterized by high levels of hyaluronic acid and its stimulator(s) with more rapid, highly organized collagen deposition. The roles of peptide growth factors such as transforming growth factor-beta and basic fibroblast growth factor are less prominent in fetal than in adult wound healing. Platelet-derived growth factor has been detected in scarless fetal skin wounds, but its role is unknown. An understanding of scarless tissue repair has possible clinical application in the modulation of adult fibrotic diseases and abnormal scar-forming conditions.     

Use of polymerase chain reaction and electroporation of Escherichia coli to monitor the persistence of extracellular plasmid DNA introduced into natural soils.

A modified protocol for DNA amplification by polymerase chain reaction (PCR) coupled with laser densitometric determination of the amount of PCR products, which allowed quantitation of target sequence numbers in soil extracts, was developed. The method was applied to monitor target loss during incubation of purified plasmid DNA in natural nonsterile soils. It revealed soil-specific kinetics of target loss. After 60 days, 0.2, 0.05, and 0.01% of the initially added nahA genes on plasmids were detectable by PCR in a loamy sand soil, a clay soil, and a silty clay soil, respectively. Electroporation of Escherichia coli was used in parallel to quantitate plasmid molecules in soil extracts by their transforming activity. It was found that transformation by electroporation was about 20 times more efficient and much less inhibited by constituents of soil extracts than transformation of Ca(2+)-treated cells (G. Romanowski, M.G. Lorenz, G. Sayler, and W. Wackernagel, Appl. Environ. Microbiol. 58:3012-3019, 1992). By electroporation, greater than 10,000-fold plasmid loss was monitored in nonsterile soils. Transforming activity was found up to 60 days after inoculation of the soils. The studies indicate that PCR and electroporation are sensitive methods for monitoring the persistence of extracellular plasmid DNA in soil. It is proposed that plasmid transformation by electroporation can be used for the monitoring in soil and other environments of genetically engineered organisms with recombinant plasmids. The data suggest that genetic material may persist in soil for weeks and even for months after its release from cells.     

Complete ammonia oxidization in agricultural soils: High ammonia fertilizer loss but low N2O production

The contribution of agriculture to the sustainable development goals requires climate-smart and profitable farm innovations. Increasing the ammonia fertilizer applications to meet the global food demands results in high agricultural costs, environmental quality deterioration, and global warming, without a significant increase in crop yield. Here, we reported that a third microbial ammonia oxidation process, complete ammonia oxidation (comammox), is contributing to a significant ammonia fertilizer loss (41.9 ± 4.8%) at the rate of 3.53 ± 0.55 mg N kg⁻¹ day⁻¹ in agricultural soils around the world. The contribution of comammox to ammonia fertilizer loss, occurring mainly in surface agricultural soil profiles (0–0.2 m), was equivalent to that of bacterial ammonia oxidation (48.6 ± 4.5%); both processes were significantly more important than archaeal ammonia oxidation (9.5 ± 3.6%). In contrast, comammox produced less N₂O (0.98 ± 0.44 μg N kg⁻¹ day⁻¹, 11.7 ± 3.1%), comparable to that produced by archaeal ammonia oxidation (16.4 ± 4.4%) but significantly lower than that of bacterial ammonia oxidation (72.0 ± 5.1%). The efficiency of ammonia conversion to N₂O by comammox (0.02 ± 0.01%) was evidently lower than that of bacterial (0.24 ± 0.06%) and archaeal (0.16 ± 0.04%) ammonia oxidation. The comammox rate increased with increasing soil pH values, which is the only physicochemical characteristic that significantly influenced both comammox bacterial abundance and rates. Ammonia fertilizer loss, dominated by comammox and bacterial ammonia oxidation, was more intense in soils with pH >6.5 than in soils with pH <6.5. Our results revealed that comammox plays a vital role in ammonia fertilizer loss and sustainable development in agroecosystems that have been previously overlooked for a long term.     

PocketOptimizer 2.0: A modular framework for computer-aided ligand-binding design

The ability to design customized proteins to perform specific tasks is of great interest. We are particularly interested in the design of sensitive and specific small molecule ligand-binding proteins for biotechnological or biomedical applications. Computational methods can narrow down the immense combinatorial space to find the best solution and thus provide starting points for experimental procedures. However, success rates strongly depend on accurate modeling and energetic evaluation. Not only intra- but also intermolecular interactions have to be considered. To address this problem, we developed PocketOptimizer, a modular computational protein design pipeline, that predicts mutations in the binding pockets of proteins to increase affinity for a specific ligand. Its modularity enables users to compare different combinations of force fields, rotamer libraries, and scoring functions. Here, we present a much-improved version––PocketOptimizer 2.0. We implemented a cleaner user interface, an extended architecture with more supported tools, such as force fields and scoring functions, a backbone-dependent rotamer library, as well as different improvements in the underlying algorithms. Version 2.0 was tested against a benchmark of design cases and assessed in comparison to the first version. Our results show how newly implemented features such as the new rotamer library can lead to improved prediction accuracy. Therefore, we believe that PocketOptimizer 2.0, with its many new and improved functionalities, provides a robust and versatile environment for the design of small molecule-binding pockets in proteins. It is widely applicable and extendible due to its modular framework. PocketOptimizer 2.0 can be downloaded at https://github.com/Hoecker-Lab/pocketoptimizer .     

GROWTH AND DEVELOPMENT OF REPRODUCTIVE AND VEGETATIVE TISSUES OF BOUGAINVILLEA CULTURED IN VITRO AS A FUNCTION OF CARBOHYDRATE

Inflorescence meristems and vegetative tissues, excised from noninduced Bougainvillea ‘San Diego Red’ plants, were cultured in vitro in media containing either 3% fructose, glucose or sucrose as carbon sources. Growth and development of young leaves were equivalent whether sucrose or fructose was used whereas floret initiation on inflorescence meristems was much greater when fructose or glucose was the carbon sources. Brief (1-3 days) exposure of inflorescence meristems to fructose at the beginning of culture and subsequent transfer to sucrose did not increase development over continuous culture in sucrose. Longer exposures (4-7 days) to fructose with subsequent transfer to sucrose did, however, increase the percentage of meristems developing florets, but such treatment did not increase development to the same level as those exposed to fructose for the entire period in vitro. During the first 18 days of culture, growth of meristems in sucrose was linear while that in fructose was exponential. There was no difference in carbohydrate requirements for floret initiation on meristems excised from short-day induced or noninduced plants, suggesting that induction does not enhance the ability of meristems to utilize sucrose.     

Immunogold Localisation of the Intermediate Chain within the Protein Complex of Cytoplasmic Dynein

It was our goal to determine the location of the intermediate chain within the complex of cytoplasmic dynein by immunoelectron microscopy. To do so we generated two monoclonal antibodies (m74-1 and m74-2) specific for the intermediate chain. Both antibodies recognised the intermediate chain by sodium dodecyl sulphate–polyacrylamide gel electrophoresis immunoblot and ELISA assays of native and denatured proteins. When sucrose density gradient-purified cytoplasmic dynein from bovine brain was incubated with the gold-conjugated monoclonal antibodies, m74-1 and m74-2, and examined by negative staining, the gold label was found opposite the globular heads at the base of the V-shaped stalk of the motor complex. The labelling of the intermediate chain is the first mapping of a component within cytoplasmic dynein. The identification of the intermediate chain at the base of the complex supports a possible docking function of the intermediate chain.     

Global vegetation models: incorporating transient changes to structure and composition

Abstract. We describe an approach for developing a Dynamic Global Vegetation Model (DGVM) that accounts for transient changes in vegetation distribution over a decadal time scale. The DGVM structure is based on a linkage between an equilibrium global vegetation model and smaller scale ecosystem dynamics modules that simulate the rate of vegetation change. Vegetation change is classified into four basic types, based largely on the projected change in above-ground biomass of the vegetation. These four types of change are: (1) dieback of forest, shrubland or grassland; (2) successional replacement within forest, shrubland or grassland; (3) invasion of forest, shrubland or grassland; (4) change in tree/grass ratio. We then propose an approach in which the appropriate ecosystem dynamics module for each type of change is applied and the grid cells of the global model updated accordingly. An approach for accounting for fire, as an example of a disturbance which may strongly influence the rate and spatial pattern of forest dieback, is incorporated. We also discuss data needs for the development, calibration and validation of the model.     

Increased chilling tolerance and altered carbon metabolism in tomato leaves following application of mechanical stress

We investigated the effects of brushing on the chilling tolerance and metabolism of nonstructural carbohydrates (soluble sugars and starch) in tomato leaves before, during and after a chilling stress. Tomato plants ( Lycopersicon esculentum Mill. cv. Caruso) were cultivated either without mechanical stress application (control plants) or with daily brushing treatments for 15 days (brushed plants), prior to a 7-day chilling treatment (8/5°C day/night). Brushing resulted in shorter plants with a 34% reduction in leaf dry weight per area and a 59% reduction of soluble sugars and starch, on a dry weight basis. The sugar to starch ratio was not affected by brushing. A greater chilling tolerance in the brushed plants was demonstrated by the maintenance of a significantly higher PSII efficiency in brushed plants (42%) compared to that of the control plants (30%) after 7 days of chilling treatment, less visible damage to the leaf tissue, and a more rapid resumption of growth during 3 days of recovery as compared to control plants. During the chilling treatment levels of soluble sugars per leaf dry weight increased 15-fold in the brushed plants and 5-fold in control plants. In the present study we have demonstrated that brushing can increase chilling tolerance in tomato plants. The observed differences in chilling tolerance and concentration of soluble sugars in the leaves may indicate an involvement of soluble sugar levels in acclimation to chilling.