Matching SOX: partner proteins and co-factors of the SOX family of transcriptional regulators

SOX transcription factors perform a remarkable variety of important roles in vertebrate development, either activating or repressing specific target genes through interaction with different partner proteins. Surprisingly, these interactions are often mediated by the conserved, DNA-binding HMG domain, raising questions as to how each factor's specificity is generated. We propose a model whereby non-HMG domains may influence partner protein selection and/or binding stability.

The interaction of water flow and nutrients on aquatic plant growth

A long-term experiment was conducted to compare the effects of flowing and still water on growth, and the relationship between water flow and nutrients, in Aponogeton elongatus, a submerged aquatic macrophyte. A. elongatus plants were grown for 23 weeks with three levels of nutrition (0, 0.5 and 1g Osmocote Plus(R) fertiliser pot(-1)) in aquaria containing stirred or unstirred water. Fertilized plants grew much better than non-fertilized. The highest fertilizer level produced 29% wider leaves and 58% higher total dry weight in stirred water. Stirred water increased leaf area by 40% and tuber size by 81%, but only with the highest level of nutrition. These results suggest that this plant depends on its roots for mineral uptake, rather than from the open water, and the major limitation to growth in still water is the supply of dissolved inorganic carbon. It was the combined effects of nutrient availability and stirring that produced the strongest response in plant growth, morphology and composition. This study provides some explanation for the observations of others that these plants grow best in creeks or river systems with permanently flowing water.

Competition and resource availability in an annual plant community dominated by an invasive species, Carrichtera annua (L. Aschers.), in South Australia

The last decade has seen spirited debates about how resource availability affect the intensity of competition. This paper examines the effect that a dominant introduced species, Carrichtera annua, has upon the winter annual community in the arid chenopod shrublands of South Australia. Manipulative field experiments were conducted to assess plant community response to changing below-ground resource levels and to the manipulation of the density of C. annua. Changes in the density of C. annua had little effect on the abundance of all other species in the guild. Nutrient addition produced an increase in the biomass of the most abundant native species, Crassula colorata. An analysis of the root distribution of the main species suggested that the areas of soil resource capture of C. annua and C. colorata are largely segregated. Our results suggest that intraspecific competition may be stronger than interspecific competition, controlling the species responses to increased resource availability. The results are consistent with a two-phase resource dynamics systems, with pulses of high resource availability triggering growth, followed by pulses of stress. Smaller plants were nutrient limited under natural field conditions, suggesting that stress experienced during long interpulse phases may override competitive effects after short pulse phases. The observed differences in root system structure will determine when plants of a different species are experiencing a pulse or an interpulse phase. We suggest that the limitations to plant recruitment and growth are the product of a complex interplay between the length and intensity of the pulse of resource availability, the duration and severity of the interpulse periods, and biological characters of the species.

A genomewide survey of developmentally relevant genes in Ciona intestinalis - IV. Genes for HMG transcriptional regulators, bZip and GATA/Gli/Zic/Snail

Many kinds of transcription factors and regulators play key roles in a variety of developmental processes. In the present survey, genes encoding proteins with conserved HMG-box, bZip domains, and some types of zinc finger motifs were surveyed in the completely sequenced genome of Ciona intestinalis. In the present analysis, 21 HMG-box-containing genes and 26 bZip genes were identified as well as four small groups of zinc finger genes in the Ciona genome. The results also showed that a less redundant set of genes is present in the Ciona genome compared with vertebrate genomes. In addition, cDNA clones for almost all genes identified have been cloned and distributed as a Ciona intestinalis Gene Collection Release I. The present comprehensive analysis therefore provides a means to study the role of these transcription factors in developmental processes of basal chordates.

Database technologies for l-system simulations in virtual plant applications on bioinformatics

One of the most important advantages of database systems is that the underlying mathematics is rich enough to specify very complex operations with a small number of statements in the database language. This research covers an aspect of biological informatics that is the marriage of information technology and biology, involving the study of real-world phenomena using virtual plants derived from L-systems simulation. L-systems were introduced by Aristid Lindenmayer as a mathematical model of multicellular organisms. Not much consideration has been given to the problem of persistent storage for these simulations. Current procedures for querying data generated by L-systems for scientific experiments, simulations and measurements are also inadequate. To address these problems the research in this paper presents a generic process for data-modeling tools (L-DBM) between L-systems and database systems. This paper shows how L-system productions can be generically and automatically represented in database schemas and how a database can be populated from the L-system strings. This paper further describes the idea of pre-computing recursive structures in the data into derived attributes using compiler generation. A method to allow a correspondence between biologists' terms and compiler-generated terms in a biologist computing environment is supplied. Once the L-DBM gets any specific L-systems productions and its declarations, it can generate the specific schema for both simple correspondence terminology and also complex recursive structure data attributes and relationships.

Evaluating plant breeding strategies by simulating gene action and dryland environment effects

Functional genomics is the systematic study of genome-wide effects of gene expression on organism growth and development with the ultimate aim of understanding how networks of genes influence traits. Here, we use a dynamic biophysical cropping systems model (APSIM-Sorg) to generate a state space of genotype performance based on 15 genes controlling four adaptive traits and then search this spice using a quantitative genetics model of a plant breeding program (QU-GENE) to simulate recurrent selection. Complex epistatic and gene X environment effects were generated for yield even though gene action at the trait level had been defined as simple additive effects. Given alternative breeding strategies that restricted either the cultivar maturity type or the drought environment type, the positive (+) alleles for 15 genes associated with the four adaptive traits were accumulated at different rates over cycles of selection. While early maturing genotypes were favored in the Severe-Terminal drought environment type, late genotypes were favored in the Mild-Terminal and Midseason drought environment types. In the Severe-Terminal environment, there was an interaction of the stay-green (SG) trait with other traits: Selection for + alleles of the SG genes was delayed until + alleles for genes associated with the transpiration efficiency and osmotic adjustment traits had been fixed. Given limitations in our current understanding of trait interaction and genetic control, the results are not conclusive. However, they demonstrate how the per se complexity of gene X gene X environment interactions will challenge the application of genomics and marker-assisted selection in crop improvement for dryland adaptation.

SPAnDX: a process-based population dynamics model to explore management and climate change impacts on an invasive alien plant, Acacia nilotica

This paper describes a process-based metapopulation dynamics and phenology model of prickly acacia, Acacia nilotica, an invasive alien species in Australia. The model, SPAnDX, describes the interactions between riparian and upland sub-populations of A. nilotica within livestock paddocks, including the effects of extrinsic factors such as temperature, soil moisture availability and atmospheric concentrations of carbon dioxide. The model includes the effects of management events such as changing the livestock species or stocking rate, applying fire, and herbicide application. The predicted population behaviour of A. nilotica was sensitive to climate. Using 35 years daily weather datasets for five representative sites spanning the range of conditions that A. nilotica is found in Australia, the model predicted biomass levels that closely accord with expected values at each site. SPAnDX can be used as a decision-support tool in integrated weed management, and to explore the sensitivity of cultural management practices to climate change throughout the range of A. nilotica. The cohort-based DYMEX modelling package used to build and run SPAnDX provided several advantages over more traditional population modelling approaches (e.g. an appropriate specific formalism (discrete time, cohort-based, process-oriented), user-friendly graphical environment, extensible library of reusable components, and useful and flexible input/output support framework). (C) 2003 Published by Elsevier Science B.V.

Uniformity of liquid distribution in the canopy of the bean plant, using the spectrophotometric analysis

Fungal diseases are important factors limiting common bean yield. White mold is one of the main diseases caused by soil pathogens. The objective of this study was to quantify the distribution of a fungicide solution sprayed into the canopy of bean plants by spectrophotometry, using a boom sprayer with and without air assistance. The experiment was arranged in a 2 x 2 x 2 factorial (two types of nozzles, two application rates, and air assistance on and off) randomized block design with four replications. Air assistance influenced the deposition of solution on the bean plant and yield increased significantly with the increased rate of application and air assistance in the boom sprayer.

Adventitious rooting in cuttings of croton and hibiscus in response to indolbutyric acid and humic acid

Adventitious rooting of ornamental plants can be accelerated by the application of growth regulators, such as auxin. Humic acids, organic matter in soil and organic compounds also have a biostimulant effect. This work evaluated the rooting in cuttings of croton (Codianeum variegatum L. Rumph) and hibiscus (Hibiscus rosa-sinensis L) in response to the application of different concentrations of indolbutyric acid (IBA) and humic acid (HA). The experiment was carried out in a greenhouse. Apical stem cuttings were treated with solutions at concentrations of: 0, 250, 500, 1000, 2000 mg L-1 IBA and 0, 10, 20, 30, 40 mmol L-1 HA carbon isolated from vermicomposting. Forty-five days after the applications, the cuttings were removed from the pots containing carbonized rice hull and the following variables were measured: rooting number, length and width of leaves, fresh and dry matter of root and aerial part and root area. The results were subjected to analysis of variance and the qualitative and quantitative effects of the treatments were compared by contrast and regression, respectively. Regression equations were used to determine the maximum efficiency level of root dry matter according to IBA and HA. Higher accumulation of root dry matter was recorded for the treatments with the doses 579 mg L-1 IBA and 14 mmol L-1 HA and 970 mg L-1 IBA and 50 mmol L-1 HA for root cuttings of croton and hibiscus, respectively. It was found that the application of eiher IBA or HA at the indicated doses accelerates rooting in cuttings of croton and hibiscus and contributes to the formation of vigorous plants.

Gladiolus development in response to bulb treatment with different concentrations of humic acids

Gladiolus is an ornamental species produced for cut flowers and propagated by corms. The early flowering and increase in the number of flower buds, besides the production of commercial corms are constant challenges to be addressed in the crop improvement. Commercial production of ornamentals is technologically accelerated by means of growth regulators. Among them, the auxins stand out for their key role in the adventitious rooting and cell elongation. Alternatively, the humic substances present in the organic matter also have biostimulating effect, which is very similar to the auxinic effect. Therefore, this work aimed to study the growth and development of gladiolus in response to application of different concentrations of humic acids (HA) isolated from vermicompost. Corms were soaked for 24 hours in solutions containing 0, 10, 20, 30 and 40 mmol L-1 of C from HA. The corms were planted in 10-dm³ plastic bags filled with substrate and kept in a greenhouse. Growth of shoots and roots was evaluated. The results showed that the use of HA accelerates growth, and anticipates and increases flowering of Gladiolus.

Lignification of the plant and seed quality of RR soybeans sprayed with herbicide glyphosate

Differences in levels of lignin in the plant between conventional and transgenic cultivars RR has been reported by several authors, however, there are few studies evaluating the influence of spraying of glyphosate on the lignin in the plant and RR soybean seeds. The aim of this study was to evaluate the physiological quality of RR transgenic soybean seeds and the lignin contents of plants sprayed with the herbicide glyphosate. The assays were conducted both in greenhouse and field in the municipality of Lavras, MG, in the agricultural year 2007/08. The experiment was arranged in a splitplot design with four replicates, considering the treatments hand weeding and herbicide glyphosate as plots, and five RR soybean cultivars (BRS 245 RR, BRS 247 RR, Valiosa RR, Silvânia RR and Baliza RR) as splitplots. In the greenhouse, the cultivars tested were BRS 245 RR and Valiosa RR in a randomized block design with four replicates. The sprayings were carried out at stages V3, V7 and early R5 (3L/ha). The 1000 seed weight, mechanical injury, germination and germination velocity index, emergence velocity index, accelerated aging, electrical conductivity and water soaking seed test, lignin content in the seed coat, in the stem and legumes were determined. The spraying of glyphosate herbicide, in greenhouse and field, did not alter the physiological quality of seeds and the lignin contents in the plant.

Agronomic performance of 27 cocoa progenies and plant selection based on productivity, self-compatibility and disease resistance

The objective of the present work was to evaluate 27 progenies of cocoa crosses considering the agronomic traits and select F1 plants within superior crosses. The experiment was installed in March 2005, in the Experimental Station Joaquim Bahiana (ESJOB), in Itajuipe, Bahia. The area of the experiment is of approximately 3 ha, with a total of 3240 plants. Thirteen evaluations of vegetative brooms, five of cushion brooms and 15 of number of pods per plant were accomplished. Thirty pollinations were made for each selected plant to test for self-compatibility. The production, based on the number of pods per plant, and resistance to witches´ broom indicated CEPEC 94 x CCN 10, RB 39 x CCN 51 and CCN 10 x VB 1151 as superior progenies. All selections tested were self-compatible. The analyses of progenies and individual tree data, associated to visual field observations, allowed the selection of 17 plants which were included in a network of regional tests to determine the phenotypic stability.

Effect of biostimulant application on production and flavonoid content of marigold (Calendula officinalis L.)

The production of medicinal plants as raw material for industry must associate quality with biomass formation and, with this purpose, the application of plant growth regulators has been studied in these crops. The objective of this study was to evaluate the effect of a biostimulant on growth, inflorescence production and flavonoid content in marigold. The experiment was conducted in a greenhouse and the treatments consisted of increasing doses of the biostimulant (0, 3, 6, 9, 12 and 15 mL L-1) applied by foliar spraying in ten consecutive applications. The experiment was arranged in a completely randomized design, with six treatments and ten repetitions. The number of leaves and flowerheads and dry matter of roots increased linearly with increasing doses of the growth promoter, with 20%, 36.97% and 97.28% increases, respectively, compared with the control. The total dry mass and shoot dry mass showed maximum values at the highest dose tested of 15 mL L-1 (with increases of 40.09% and 46.30%, respectively). Plant height and flavonoid content reached the highest values at a dose of 6 mL L-1. The biostimulant promoted the development of marigold and positively influenced the synthesis of the secondary compound of medicinal interest. Among the tested doses, the application of rates between 6 and 9 mL L-1 of the biostimulant is recommended for more efficient large-scale production of marigold.

Acclimation of croton and hibiscus seedlings in response to the application of indobultiric acid and humic acid for rooting

The vegetative propagation of ornamental plants can be accelerated by applying plant growth regulators. Amongst them, the use of auxins, plant hormones with physiological effects on cell elongation and rooting have stood out. Alternatively, the application of humic acids, bioactive fraction of soil organic matter, also results in increases in rooting cuttings of ornamental plants. The objective of this work was to study the growth characteristics and the nutritional contents of croton and hibiscus plants during acclimation of seedlings in response to different concentrations of indolebutyric acid (IBA) and humic acid (HA) applied to cuttings for rooting. The experiment was conducted in greenhouse, and the apical stem cuttings were treated with solutions with concentrations of 0, 250, 500, 1000 and 2000 mg L-1of IBA and 0, 10, 20, 30 and 40 mg L-1 of C from HA. At 45 days of rooting in carbonized rice husk, they were individually transferred to plastic bags of 2.0 dm3 containing a mixture of soil: sand: manure (2: 1: 1) as substrate. At 90 days of acclimation, the plants were collected for measurement of growth and nutritional variables. The results showed that the application of the IBA stimulates the absorption of nutrients and growth of croton cuttings and transplanted hibiscus, contributing to formation of vigorous seedlings. A similar response occurred with the application of HA in hibiscus cuttings