Cytoscape ESP: simple search of complex biological networks

Summary: Cytoscape enhanced search plugin (ESP) enables searching complex biological networks on multiple attribute fields using logical operators and wildcards. Queries use an intuitive syntax and simple search line interface. ESP is implemented as a Cytoscape plugin and complements existing search functions in the Cytoscape network visualization and analysis software, allowing users to easily identify nodes, edges and subgraphs of interest, even for very large networks

Compensatory hydraulic uptake of water by tomato due to variable root-zone salinity

Trabajo desarrollado bajo la financiación del proyecto “Soil Hydrology research platform underpinning innovation to manage water scarcity in European and Chinese cropping Systems” (773903), coordinado por José Alfonso Gómez Calero, investigador del Instituto de Agricultura Sostenible (IAS).Plant root systems are exposed to spatial and temporal heterogeneity regarding water availability. In the long-term, compensation, increased uptake by roots in areas with favorable conditions in response to decreased uptake in areas under stress, is driven by root growth and distribution. In the short-term (hours–days), compensative processes are less understood. We hypothesized hydraulic compensation where local lowered water availability is accompanied by increased uptake from areas where water remains available. Our objective was to quantify instantaneous hydraulic root uptake under conditions of differential water availability. Tomato (Solanum lycopersicum L.) plants were grown in split-root weighing-drainage lysimeters in which each half of the roots could alternatively be exposed to short-term conditions of salinity. Uptake was quantified from each of the two root zone compartments. One-sided exposure to salinity immediately led to less uptake from the salt-affected compartment and increased uptake from the nontreated compartment. Compensation occurred at salinity, caused by NaCl solution of 4 dS m−1, that did not decrease uptake in plants with entire root systems exposed. At higher salinity, 6.44 dS m−1, transpiration decreased by ∼50% when the total root system was exposed. When only half of the roots were exposed, total uptake was maintained at levels of nonstressed plants with as much as 85% occurring from the nontreated compartment. The extent of compensation was not absolute and apparently a function of salinity, atmospheric demand, and duration of exposure. As long as there is no hydraulic restriction in other areas, temporary reduction in water availability in some parts of a tomato's root zone will not affect plant-scale transpiration.This research was primarily funded by the Chief Scientist of Israel's Ministry of Agriculture and Rural Development (Grant number 20-16-0010). The project has also received funding from the European Union's Horizon 2020 research and innovation programme under Project SHui, grant agreement No. 773903.Peer reviewe

Transgenic crop plant useful for generating tissue culture comprises root cell and leaf cell transformed with DNA construct having polynucleotide encoding Nicotiana tabacum aquaporin-1

Abstract: NOVELTY - A transgenic crop plant (T1) comprises at least one root cell and at least one leaf cell transformed with a DNA construct having a polynucleotide encoding Nicotiana tabacum aquaporin-1 (NtAQP1), where the plant has increase yield compared to a corresponding non-transgenic plant. USE - As a transgenic crop plant (where the plant is selected from a plant producing fruit, flower and ornamental plant, grain producing plant (i.e. wheat, oats, barely, rye, rice, maize), legumes (i.e. peanuts, peas soybean lentil), plant producing forage, plant producing fiber (including cotton and flax), a tree for wood industry, plant producing tuber or root crop, sugar beet, sugar came, plant producing oil (i.e. canola, sunflower, sesame) and tomato plant useful for generating tissue culture (claimed). ADVANTAGE - The transgenic crop plant is grown under optimal water availability conditions or abiotic stress conditions selected from water stress (drought) (i.e. water content of less than 70%), high soil salinity (i.e. above 4 dS/m), extreme temperatures, low oxygen levels or presence of heavy metals; has a yield increase of at least 60% compared to a plant grown from a seed of corresponding non-transgenic plant; and shows an enhanced tolerance to drought stress compared to unmodified plants. DETAILED DESCRIPTION - INDEPENDENT CLAIMS are included for the following: (1) a seed of the plant (T1), where a plant grown from the seed comprises at least one root cell and at least one leaf cell comprising a DNA construct containing polynucleotide encoding NtAQP1; (2) a tissue culture (R1) comprising at least one transgenic cell of the plant (T1) or a protoplast derived from it; (3) a plant regenerated from the tissue culture (R1); (4) increasing (m1) the yield of a crop plant involving transforming a plant cell with a DNA construct comprising a polynucleotide encoding NtAPQ1, and regenerating the transformed cell into a transgenic plant comprising at least one root cell and at least one leaf cell expressing NtAQP1 having an increased yield compared to a corresponding non-transgenic plant; (5) screening (m2) for a plant capable of producing high yield when grown under abiotic stress conditions involving obtaining several samples from several plant lines and a control sample from a reference plant, the samples comprising genetic material, measuring the expression level of a polynucleotide encoding NtAQP1 or its ortholog in the samples, comparing the expression level of the polynucleotide encoding NtAQP1 or its ortholog in the samples to the control sample, where a plant line overexpressing the polynucleotide encoding NtAQP1 or its ortholog is capable of producing high yield when grown under abiotic stress conditions. Technology Focus/Extension Abstract: TECHNOLOGY FOCUS - BIOLOGY - Preferred Plant: The plant lines are selected from plants of the same species and plants of different species. The control plant is tobacco (Nicotiana tabacum). Preferred Method: The method (m2) further involves planting the plant line overexpressing the polynucleotide encoding NtAQP1 or its ortholog and a corresponding control plant having lower expression of the polynucleotide under abiotic stress conditions; comparing the crop yield of the plant line to the crop yield of the control plant; and selecting plant lines having increased crop yield compared to the control plant. In the method (m2), the expression level of the polynucleotide is measured using nucleic acid technology (NAT)-based assays selected from quantitative polymerase chain reaction (PCR), Quantitative real time PCR and Northern Blot. The NAT assay is PCR employing a primer pair having the nucleic acid sequence of 5'-tatccttcgcaagaccctcc-3' (SEQ ID NO: 3) and 5'-tgcctggtctgtgttgtagat-3' (SEQ ID NO: 4). Preferred Tissue Culture: The tissue culture (R1) regenerates a plant having at least one root cell and at least one leaf cell comprising a DNA construct containing polynucleotide encoding NtAQP1. TECHNOLOGY FOCUS - BIOTECHNOLOGY - Preferred Components: The polynucleotide encodes an NtATQP1 comprising the amino acids sequence of SEQ ID NO: 1, not given in specification. The polynucleotide comprises the nucleic acid sequence of SEQ ID NO: 2, not given in specification. The DNA construct further comprises a regulatory element selected from a promoter, an enhancer, a termination sequence and a polyadenylation signal. The promoter is a constitutive promoter. The promoter is a tissue specific promoter selected from root specific promoter and shoot specific promoter. The tissue specific promoter is selected from guard cell specific promoter (shoot); endodermis (root) and bundle sheath (shoot) scarecrow promoter; bundle sheath OSTMT1 promoter (shoot); and the green tissue Fbpase promoter (shoot). The polynucleotide encodes NtATQP1 having at least 75 (preferably greater than or equal to 85)% homology to the protein having the amino acids sequence of SEQ ID NO: 1. The polynucleotide comprises a nucleic acids sequence having at least 75 (preferably greater than or equal to 85)% homology to the nucleic acid sequence of SEQ ID NO: 2

Characterization of plant aquaporins.

Plants have been reported to contain a large set of aquaporins (38 for Arabidopsis), which has been divided into four subfamilies on the basis of similarities in their amino acid sequences. They belong to the large superfamily of major intrinsic proteins (MIP), which was the basis for the nomenclature PIP, TIP, and NIP, also indicating the subcellular localization plasma membrane, tonoplast, and nodule of the respective founding member. The fourth subfamily of small and basic intrinsic proteins is not well characterized so far. The increasing number of reports dealing with various aspects of plant aquaporins is starting to advance our understanding of aquaporin biology in plants. Fundamental questions include: what is the basic function of the different plant aquaporins, what is their primary substrate, and what is the consequence of function/malfunction of a particular aquaporin for the overall function of the plant? Biochemical and biophysical techniques can be employed to get information on the basic functional characteristics of plant aquaporins. An impressive set of techniques has been used to study aquaporin function on molecular, subcellular, and cellular levels in plants, as well as in heterologous expression systems. The physiological role of aquaporins in plants is much less well understood, but reports unraveling the physiological role of aquaporins, mainly employing genetic techniques and functional measurement on the whole plant level, are emerging. The goal of this chapter is to give an overview on the applied methods, together with some exemplary findings

Genetics of superior growth traits in trees are being mapped but will the faster-growing risk-taker make it in the wild?

Increased biomass production of trees is a research field of great contemporary interest. Estimates of future needs for production of fibre, wood and biofuel suggest a need for significantly increased production in forests (Ragauskas et al. 206). This demand can only be met through increased productivity and/or resource utilization efficiency of tree crops. That is, we must explore the potential to optimize the genetic makeup of trees to achieve greater productivity in their growing environments. Since the introduction of molecular biology in plant sciences, the interest in genetic improvement of both agricultural and tree crops has been increasing and is currently one of the most intense areas of plant research. At the same time, tree and stand growth have been studied within (and across) the fields of ecophysiology, ecology, silviculture and forest management. This work has resulted in statistical and process-based models that relate tree growth to availability of various resources, and that thus can inform management (Landsberg and Waring 1997). Process-based growth models have been developed largely independent of the expanding knowledge base in molecular biology and the findings that tree growth can be directly improved through genetic alterations of specific processes such as lignin synthesis, frost hardiness and nitrogen (N) assimilation (Ragauskas et al. 2006, Ye et al. 2011). Similarly, we have underutilized the potential for ecological theories and growth models to guide breeding programmes by predicting the performance of genetically altered trees in the field. This 'Invited issue' is designed to stimulate research targeted at explicitly linking molecular understanding and tools and growth of forest stands