Accessing Soybase and Other Genome Databases Via the Internet

The Internet or World Wide Web is increasingly in the news. It seems to be much like Mark Twain\u27s comment about the weather - everyone talks about the Internet but no one knows much about it. In fact the Internet is full of useful information if one only can find it. This paper (and associated computer demonstration) will first describe some of the genome databases that are accessible via the Internet and then give some strategies for searching the Internet for other types of information

Salicornia as a crop plant in temperate regions: selection of genetically characterized ecotypes and optimization of their cultivation conditions

Rising sea levels and salinization of groundwater due to global climate change result in fast dwindling sources of fresh water. Therefore it is important to find alternatives to grow food crops and vegetables. Halophytes are naturally evolved salt-tolerant plants that are adapted to grow in environments that inhibit the growth of most glycophytic crop plants substantially. Members of the Salicornioideae are promising candidates for saline agriculture due to their high tolerance to salinity. Our aim was to develop genetically characterized lines of Salicornia and Sarcocornia for further breeding and to determine optimal cultivation conditions. To obtain a large and diverse genetic pool, seeds were collected from different countries and ecological conditions. The External Transcribed Spacer (ETS) sequence of 62 Salicornia and Sarcocornia accessions was analysed: ETS sequence data showed a clear distinction between the two genera and between different Salicornia taxa. However, in some cases the ETS was not sufficiently variable to resolve morphologically distinct species. For the determination of optimal cultivation conditions, experiments on germination, seedling establishment and growth to a harvestable size were performed using different accessions of Salicornia spp. Experiments revealed that the percentage germination was greatest at lower salinities and with temperatures of 20/10˚C (day/night). Salicornia spp. produced more harvestable biomass In hydroponic culture than in sand culture, but the nutrient concentration requires optimization as hydroponically grown plants showed symptoms of stress. Salicornia ramosissima produced more harvestable biomass than S. dolichostachya in artificial sea water containing 257 mM NaCl. Based on preliminary tests on ease of cultivation, gain in biomass, morphology and taste, S. dolichostachya was investigated in more detail and the optimal salinity for seedling establishment found to be 100 mM. Harvesting of S. dolichostachya twice in a growing season was successful but the interval between the harvests needs to be optimized to maximise biomass production

Quantitative determination of calcium oxalate and oxalate in developing seeds of soybean (Leguminosae)

Developing soybean seeds accumulate very large amounts of both soluble oxalate and insoluble crystalline calcium (Ca) oxalate. Use of two methods of detection for the determination of total, soluble, and insoluble oxalate revealed that at +16 d postfertilization, the seeds were 24% dry mass of oxalate, and three-fourths of this oxalate (18%) was bound Ca oxalate. During later seed development, the dry mass of oxalate decreased. Crystals were isolated from the seeds, and X-ray diffraction and polarizing microscopy identified them as Ca oxalate monohydrate. These crystals were a mixture of kinked and straight prismatics. Even though certain plant tissues are known to contain significant amounts of oxalate and Ca oxalate during certain periods of growth, the accumulation of oxalate during soybean seed development was surprising and raises interesting questions regarding its function

The response of the maize nitrate transport system to nitrogen demand and supply across the lifecycle

The definitive version is available at www.newphytologist.comAn understanding of nitrate (NO3-) uptake throughout the lifecycle of plants, and how this process responds to nitrogen (N) availability, is an important step towards the development of plants with improved nitrogen use efficiency (NUE). NO3- uptake capacity and transcript levels of putative high- and low-affinity NO3- transporters (NRTs) were profiled across the lifecycle of dwarf maize (Zea mays) plants grown at reduced and adequate NO3-. Plants showed major changes in high-affinity NO3- uptake capacity across the lifecycle, which varied with changing relative growth rates of roots and shoots. Transcript abundances of putative high-affinity NRTs (predominantly ZmNRT2.1 and ZmNRT2.2) were correlated with two distinct peaks in high-affinity root NO3- uptake capacity and also N availability. The reduction in NO3- supply during the lifecycle led to a dramatic increase in NO3- uptake capacity, which preceded changes in transcript levels of NRTs, suggesting a model with short-term post-translational regulation and longer term transcriptional regulation of NO3- uptake capacity. These observations offer new insight into the control of NO3- uptake by both plant developmental processes and N availability, and identify key control points that may be targeted by future plant improvement programmes to enhance N uptake relative to availability and/or demand.Trevor Garnett, Vanessa Conn, Darren Plett, Simon Conn, Juergen Zanghellini, Nenah Mackenzie, Akiko Enju, Karen Francis, Luke Holtham, Ute Roessner, Berin Boughton, Antony Bacic, Neil Shirley, Antoni Rafalski, Kanwarpal Dhugga, Mark Tester, and Brent N. Kaise

The importance of nodule CO2 fixation for the efficiency of symbiotic nitrogen fixation in pea at vegetative growth and during pod formation

Nodule CO2 fixation is of pivotal importance for N2 fixation. The process provides malate for bacteroids and oxaloacetate for nitrogen assimilation. The hypothesis of the present paper was that grain legume nodules would adapt to higher plant N demand and more restricted carbon availability at pod formation through increased nodule CO2 fixation and a more efficient N2 fixation. Growth, N2 fixation, and nodule composition during vegetative growth and at pod formation were studied in pea plants (Pisum sativum L.). In parallel experiments, 15N2 and 13CO2 uptake, as well as nodule hydrogen and CO2 release, was measured. Plants at pod formation showed higher growth rates and N2 fixation per plant when compared with vegetative growth. The specific activity of active nodules was about 25% higher at pod formation. The higher nodule activity was accompanied by higher amino acid concentration in nodules and xylem sap with a higher share of asparagine. Nodule 13CO2 fixation was increased at pod formation, both per plant and per 15N2 fixed unit. However, malate concentration in nodules was only 40% of that during vegetative growth and succinate was no longer detectable. The data indicate that increased N2 fixation at pod formation is connected with strongly increased nodule CO2 fixation. While the sugar concentration in nodules at pod formation was not altered, the concentration of organic acids, namely malate and succinate, was significantly lower. It is concluded that strategies to improve the capability of nodules to fix CO2 and form organic acids might prolong intensive N2 fixation into the later stages of pod formation and pod filling in grain legumes

Proteomic Analysis Reveals That Iron Availability Alters the Metabolic Status of the Pathogenic Fungus Paracoccidioides brasiliensis

Paracoccidioides brasiliensis is a thermodimorphic fungus and the causative agent of paracoccidioidomycosis (PCM). The ability of P. brasiliensis to uptake nutrients is fundamental for growth, but a reduction in the availability of iron and other nutrients is a host defense mechanism many pathogenic fungi must overcome. Thus, fungal mechanisms that scavenge iron from host may contribute to P. brasiliensis virulence. In order to better understand how P. brasiliensis adapts to iron starvation in the host we compared the two-dimensional (2D) gel protein profile of yeast cells during iron starvation to that of iron rich condition. Protein spots were selected for comparative analysis based on the protein staining intensity as determined by image analysis. A total of 1752 protein spots were selected for comparison, and a total of 274 out of the 1752 protein spots were determined to have changed significantly in abundance due to iron depletion. Ninety six of the 274 proteins were grouped into the following functional categories; energy, metabolism, cell rescue, virulence, cell cycle, protein synthesis, protein fate, transcription, cellular communication, and cell fate. A correlation between protein and transcript levels was also discovered using quantitative RT-PCR analysis from RNA obtained from P. brasiliensis under iron restricting conditions and from yeast cells isolated from infected mouse spleens. In addition, western blot analysis and enzyme activity assays validated the differential regulation of proteins identified by 2-D gel analysis. We observed an increase in glycolytic pathway protein regulation while tricarboxylic acid cycle, glyoxylate and methylcitrate cycles, and electron transport chain proteins decreased in abundance under iron limiting conditions. These data suggest a remodeling of P. brasiliensis metabolism by prioritizing iron independent pathways