Nature Precedings - Subject feed for Plant Biology

BRAGOMAP – a new Perl script for high throughoutput blast results analysis including GO and MapMan automatic annotations

Rafal Woycicki — Mon, 26 Oct 2009 11:35:28 UTC

Analyzing of sequences similarities is the first and most important method used to find out the function of unknown nucleotides. Searching of homologs should be done carefully not to loose any important ones. Having thousands of results from various long-read sequencing projects (ie. differentially expressed tags, genomic polymorphons or BAC ends), the by-hand ability to retrieve interesting (to our goal) similarities in hundreds of Blast results decreases rapidly. Decreasing the number of retrieved sequences by giving more stringency in e-value threshold or displaying less results could lead to false deductions. Functional genomics, proteomics and metabolomics could give us answers to the role of nucleotide sequences. It makes the need to annotate as much of the homologies as we can, to proper molecular function, biological process and cellular component (as its proposed by widely accepted Gene Ontology Consortium annotations or MapMan mappings by Max-Planc-Institute). To facilitate fast retrieval of interesting Blast homologies and making right deductions about the biological role of sequences, in big sequencing projects, the new Perl script BRAGOMAP was written. The program make use of some of BioPerl modules as well as the power of regex text-mining in the Perl itself. The script gives us the possibility to find interesting sequence similarities by using keywords and giving points for each one found. It collects all important information from the GenBank data and puts it in different columns of tab-delimited file for further use. If we were interested (for example) in flower differentiation genes we could use the keywords (flower, ovule, anther, etc.) and/or filter all the homologies isolated from flower tissues in a special development stage. We can also filter results by choosing similarities to interesting genes or protein products. This script retrieve also all standard information from the Blast and GenBank files as Description, ACC no., E-value, Similarity positions, Query Length, Percent of Similarity etc. Automatic GO and MapMan annotations are done by looking for genes, protein products and /or DB references in the proper mappings files. Here we present the usefulness of the script in analyzing sequence similarities and annotations mapping of 3855 BAC ends obtained from the HindIII BAC genomic library of cucumber (Cucumis sativus L., line B10).

Mega- change gene copies are produced by reverse transcription of precursor RNA with replaced introns.

Drew Schwartz — Wed, 07 Oct 2009 15:36:36 UTC

This report describes the presence of copy genes in plants where the sequence similarity to their parental genes is almost completely limited to limited to the exons. Evidence is presented that indicates that they arose via a novel processing of transcribed precursor RNA during which the introns are replaced rather than excised, followed by reverse transcription and incorporation into the chromosomes. Intron replacement may play an important role in evolution as it results in megagene changes.

Nuclear DNA and protein content evaluation in Taxus plant cell cultures using multiparameter flow cytometry

Vishal Gaurav — Thu, 01 Oct 2009 08:33:37 UTC

Plant cell cultures of Taxus provide the most reliable production methods for the anti-cancer drug paclitaxel. In order to comprehend the inherent culture heterogeneity and production variability in cell cultures, it is essential that the cellular metabolism is studied at the genomic level. Genomic stability in plant cell cultures is crucial as it affects cell growth and division, metabolite accumulation and protein synthesis. A rapid and efficient method to prepare nuclei suspensions from aggregated cell cultures of Taxus was employed. Methods were subsequently developed to simultaneously stain them for DNA and protein content using Propidium Iodide and Fluorescein Isothiocyanate respectively. Flow cytometry was used to analyze and quantify the DNA content and genome size of Taxus using known reference species as standards. Furthermore, their genomic stability was evaluated by correlating DNA content and genome size with cell size and complexity, protein content, and elicitation effects using multiparameter flow cytometry. These techniques to evaluate and correlate various culture characteristics can be very useful in designing superior bio processes for enhanced production.

In silico microRNA identification from paprika (Capsicum annuum) ESTs

Thu, 24 Sep 2009 12:00:45 UTC

A total of 33,311 Expressed Sequence Tags (EST) of paprika were mined from the GenBank EST database. The redundancy of the EST sequences was removed using CAP3 and it resulted 4,541 contigs 8,539 singletons as nonredundant data sets. The microRNAs were predicted using the program miRNAfinder. This program predicted a total of 85 miRNAs miRNAs. Another study was carried out to find the homologes miRNA using blast based tool named “miRseeK’ A total of 13 miRNAs with significant similarity with the plant miRNAs were obtained from paprika ESTs. The targets of the predicted miRNAs were found using the program miRU2. Findings suggest that most miRNAs play an important role in plant development, signal transduction, protein degradation and in response to environmental stress. The miRNAs were found to be perfectly or nearly complementary to its target mRNAs.

Factors influencing impala distribution patterns in Nairobi National Park, Kenya

Vincent Obade — Tue, 22 Sep 2009 14:23:28 UTC

Monitoring the distribution of wild animals using appropriate methods and survey techniques is essential not only for sustainable management but also to avoid wastage of resources. This study applied remote sensing to investigate the factors influencing the distribution of herbivores in Nairobi National Park, Kenya. Impala was selected as indicator specie for the herbivores within the park, because the population of impala had drastically reduced over time. The influence of food availability, water and disturbance on herbivore presence was investigated. A positive significant statistical relationship between impala population density and feed availability was observed. However, the correlation between impala population density and water distance was negative, indicating less impalas as the distance from water sources increase. An interesting finding was the expectation of greater impala population presence next to roads. The study demonstrated a rapid method for gaining information useful for conservation and land use planning practices, such as in the determination of the carrying capacity or even for redistributing animals within the park.

Cost effective mass multiplication of Gymnema sylvestre in hydroponic system

Wed, 16 Sep 2009 09:52:03 UTC

Present experiment was designed with an objective to develop a cost efficient mass multiplication method for Gymnema sylvestre using hydroponic system. A plastic tub, with polyethylene cover, containing 1/10 strength of MS salts supplemented with Indole butyric acid (IBA) at different concentrations (0.5, 1.0, 2.5 mg/L) was studied. Medium containing 0.5mg/L of IBA produced highest rooting (66%) with 96 % survival. This protocol will serve as an alternative to the existing in vitro and clonal multiplication protocols.

CO2 Enhancement of Forest Productivity Constrained by Limited Nitrogen Availability

Richard J. Norby — Mon, 14 Sep 2009 16:07:44 UTC

Stimulation of terrestrial productivity by rising CO2 concentration is projected to reduce the airborne fraction of anthropogenic CO2 emissions; coupled climate-carbon (C) cycle models, including those used in the IPCC Fourth Assessment Report (AR4), are sensitive to this negative feedback on atmospheric CO21. The representation of the so-called CO2 fertilization effect in the 11 models used in AR4 and subsequent models2,3 was broadly consistent with experimental evidence from four free-air CO2 enrichment (FACE) experiments, which indicated that net primary productivity (NPP) of forests was increased by 23 +/- 2% in response to atmospheric CO2 enrichment to 550 ppm4. Substantial uncertainty remains, however, because of the expectation that feedbacks through the nitrogen (N) cycle will reduce the CO2 stimulation of NPP5,6; these feedbacks were not included in the AR4 models and heretofore have not been confirmed by experiments in forests7. Here, we provide new evidence from a FACE experiment in a deciduous Liquidambar styraciflua (sweetgum) forest stand in Tennessee, USA, that N limitation has significantly reduced the stimulation of NPP by elevated atmospheric CO2 concentration (eCO2). Isotopic evidence and N budget analysis support the premise that N availability in this forest ecosystem has been declining over time, and declining faster in eCO2. Model analyses and evidence from leaf- and stand-level observations provide mechanistic evidence that declining N availability constrained the tree response to eCO2. These results provide a strong rationale and process understanding for incorporating N limitation and N feedback effects in ecosystem and global models used in climate change assessments.

Overcoming high temperature inhibition of flower formation and fruit production without bees

Albert Liptay — Wed, 02 Sep 2009 10:34:33 UTC

Flower formation in the Cucurbitaceae family is compromised at high temperatures; both male and female flowers and therefore fruit productivity are greatly reduced as the growing temperatures for these vegetable crops are increased above 26C. This intractable phenomenon has been documented both with outdoor field experiments at various latitudes on the eastern seaboard in the USA and in a laboratory, temperature-regulated setting. We now report that an agricultural product, FP, which has been, and is used globally on many commercial crops to increase flower number and strength during blossom formation and development, overcomes the apparent refractory floral initiation and development at high temperatures. This is a new and unexpected finding. Additionally, in another facet of the experiments reported here, the parthenocarpic fruit development potential of FP was tested by eliminating bee pollination. This aspect of the study was addressed in part because of the recent concerns with bee colony collapse disorder. Flower formation, flower development and fruit yield were increased by FP over the bee-pollinated, untreated controls at high temperatures. FP was developed over a number of years of outdoor field trials as an approach to crop productivity that included hormonal regulation of floral strength and supported by mineral supplements through to the fruit production process.

Enhancing Jatropha Productivity by Canopy Management

Chalapathy K. Reddy — Tue, 01 Sep 2009 08:57:39 UTC

Jatropha seed and oil yield is function of planting material used, growing conditions, plant architecture development and maintenance. Jatropha is hardy plant; thrives well in arid and semi arid regions with an average rainfall ranging from 500 to 1200 mm. It has been planted in varied soil types, marginal and waste lands; where in utilization of in situ resources by agronomic practices and development and management of canopy by pruning are very crucial for harvesting higher seed for biodiesel production. Building ideal canopy by pruning during first growing season is very important. Pruning is done during winter season when plants are in dormant condition.

Urban Ecosystems: Alterations to Peakflow, Microclimate and the Natural Environment

Jason A. Hubbart — Fri, 14 Aug 2009 09:29:00 UTC

More than half of the world’s population now lives in urbanized ecosystems. Continued human population growth over the next several decades will place unprecedented demand on urban water resources, resulting in escalating water quality and supply challenges. Urbanization exacts significant impacts on stream ecosystems including increased magnitude and frequency of peak flows, altered microclimates and reduced biodiversity. Increased impervious surface area in urban settings reduces or eliminates soil infiltration and increases the amount of stormwater runoff delivered to stream channels. Stormwater routing networks in urban areas channelize runoff, reducing stormwater transit time. Stormwater flow serves as an important transport mechanism for non-point source pollutants, and impervious surfaces serve as conduits to flow, replacing soils and vegetation that would otherwise attenuate runoff and transport of pollutants. Stream channels typically broaden and deepen in response to increased volume, velocity and frequency of peak flows, leading to increased channel instability, accelerated erosion, and subsequent loss of habitat. Given these scenarios, urbanization can degrade freshwater resources, detrimentally impact in-stream and riparian biota, and destroy riparian wetland form and function. The following work quantifies peak flow and microclimate alteration due to urbanization in a large, multi-use watershed of the central U.S. A long-term stream flow monitoring program was established in the Hinkson Creek Watershed located in Boone County, mid-Missouri during the fall of 2008. Hydroclimate stations were installed at five locations along Hinkson Creek within predominantly forest, cropland, and urban environments. Continuous stream stage and flow data from these sites were used to quantify peak flow in different environments of the watershed. Preliminary results indicate that forested environments tend to attenuate peak flows from small precipitation events (< 0.80 mm), whereas events of similar magnitude in urban settings cause spikes in flow and a flashier hydrograph. With larger precipitation events (> 1.0 mm), the time from peak rainfall to peak flow is decreased by as much as 13% in urban settings accompanied by at least 4 cm higher peak flows and 15-20% greater flow volume. Average air temperatures in the urban region exceed the forested region by at least 15% during winter months, holding important implications for snow melt and runoff, peak flow and ecosystem processes. Continued monitoring and analyses will more precisely quantify the effects of urbanization on these phenomena and will provide critical information for the sustainable management of urban natural resources.