Local adaptation optimizes photoprotection strategies in a Neotropical legume tree under drought stress.

Photoprotection is a plant functional mechanism to prevent photooxidative damage by excess light. This is most important when carbon assimilation is limited by drought, and as such, it entails a trade-off between carbon assimilation vs stress avoidance. The ecological adaptation of plants to local water availability can lead to different photoprotective strategies.

Developmental Analysis of Seed Transcriptomes Reveals Functional Gene Expression Clusters and Four Imprinted, Endosperm-Expressed Genes.

The double fertilization of the female gametophyte initiates embryogenesis and endosperm development in seeds the activation of genes involved in cell differentiation, organ patterning, and growth. A subset of genes expressed in endosperm exhibit imprinted expression, and the correct balance of gene expression between parental alleles is critical for proper endosperm and seed development. We use a transcriptional time series analysis to identify genes that are associated with key shifts in seed development, including genes associated with secondary cell wall synthesis, mitotic cell cycle, chromatin organization, auxin synthesis, fatty acid metabolism, and seed maturation.

Stem-cell-ubiquitous genes spatiotemporally coordinate division through regulation of stem-cell-specific gene networks.

Stem cells are responsible for generating all of the differentiated cells, tissues, and organs in a multicellular organism and, thus, play a crucial role in cell renewal, regeneration, and organization. A number of stem cell type-specific genes have a known role in stem cell maintenance, identity, and/or division. Yet, how genes expressed across different stem cell types, referred to here as stem-cell-ubiquitous genes, contribute to stem cell regulation is less understood.

tuxnet: a simple interface to process RNA sequencing data and infer gene regulatory networks.

Predicting gene regulatory networks (GRNs) from expression profiles is a common approach for identifying important biological regulators. Despite the increased use of inference methods, existing computational approaches often do not integrate RNA-sequencing data analysis, are not automated or are restricted to users with bioinformatics backgrounds. To address these limitations, we developed tuxnet, a user-friendly platform that can process raw RNA-sequencing data from any organism with an existing reference genome using a modified tuxedo pipeline (hisat 2 + cufflinks package) and infer GRNs from these processed data.

Characterizing the involvement of FaMADS9 in the regulation of strawberry fruit receptacle development.

FaMADS9 is the strawberry (Fragaria x ananassa) gene that exhibits the highest homology to the tomato (Solanum lycopersicum) RIN gene. Transgenic lines were obtained in which FaMADS9 was silenced. The fruits of these lines did not show differences in basic parameters, such as fruit firmness or colour, but exhibited lower Brix values in three of the four independent lines.

DOF2.1 Controls Cytokinin-Dependent Vascular Cell Proliferation Downstream of TMO5/LHW.

To create a three-dimensional structure, plants rely on oriented cell divisions and cell elongation. Oriented cell divisions are specifically important in procambium cells of the root to establish the different vascular cell types [1, 2]. These divisions are in part controlled by the auxin-controlled TARGET OF MONOPTEROS5 (TMO5) and LONESOME HIGHWAY (LHW) transcription factor complex [3-7].

Tracking Gene Expression via Light Sheet Microscopy and Computer Vision in Living Organisms.

Automated tracking of spatiotemporal gene expression using in vivo microscopy images have given great insight into understanding developmental processes in multicellular organisms. Many existing analysis tools rely on the fluorescent tagging of cell wall or cell nuclei localized proteins to assess position, orientation, and overall shape of an organism; information necessary for determining locations of gene expression activity. Particularly in plants, organism lines that have fluorescent tags can take months to develop, which can be time consuming and costly.

Predicting gene regulatory networks by combining spatial and temporal gene expression data in root stem cells.

Identifying the transcription factors (TFs) and associated networks involved in stem cell regulation is essential for understanding the initiation and growth of plant tissues and organs. Although many TFs have been shown to have a role in the root stem cells, a comprehensive view of the transcriptional signature of the stem cells is lacking. In this work, we used spatial and temporal transcriptomic data to predict interactions among the genes involved in stem cell regulation.

Inferring Gene Regulatory Networks in the Arabidopsis Root Using a Dynamic Bayesian Network Approach.

Gene regulatory network (GRN) models have been shown to predict and represent interactions among sets of genes. Here, we first show the basic steps to implement a simple but computationally efficient algorithm to infer GRNs based on dynamic Bayesian networks (DBNs), and we then explain how to approximate DBN-based GRN models with continuous models. In addition, we show a MATLAB implementation of the key steps of this method, which we use to infer an Arabidopsis root GRN.

Unusual positional effects on flower sex in an andromonoecious tree: Resource competition, architectural constraints, or inhibition by the apical flower?

Premise Of The Study: Two, nonmutually exclusive, mechanisms-competition for resources and architectural constraints-have been proposed to explain the proximal to distal decline in flower size, mass, and/or femaleness in indeterminate, elongate inflorescences. Whether these mechanisms also explain unusual positional effects such as distal to proximal declines of floral performance in determinate inflorescences, is understudied.

Methods: We tested the relative influence of these mechanisms in the andromonoecious wild olive tree, where hermaphroditic flowers occur mainly on apical and the most proximal positions in determinate inflorescences.

Multi-sample Arabidopsis Growth and Imaging Chamber (MAGIC) for long term imaging in the ZEISS Lightsheet Z.1.

Time-course imaging experiments on live organisms are critical for understanding the dynamics of growth and development. Light-sheet microscopy has advanced the field of long-term imaging of live specimens by significantly reducing photo-toxicity and allowing fast acquisition of three-dimensional data over time. However, current light-sheet technology does not allow the imaging of multiple plant specimens in parallel.

The expression of light-related leaf functional traits depends on the location of individual leaves within the crown of isolated Olea europaea trees.

Background: The spatial arrangement and expression of foliar syndromes within tree crowns can reflect the coupling between crown form and function in a given environment. Isolated trees subjected to high irradiance and concomitant stress may adjust leaf phenotypes to cope with environmental gradients that are heterogeneous in space and time within the tree crown. The distinct expression of leaf phenotypes among crown positions could lead to complementary patterns in light interception at the crown scale.

The effects of phenotypic plasticity and local adaptation on forecasts of species range shifts under climate change.

Species are the unit of analysis in many global change and conservation biology studies; however, species are not uniform entities but are composed of different, sometimes locally adapted, populations differing in plasticity. We examined how intraspecific variation in thermal niches and phenotypic plasticity will affect species distributions in a warming climate. We first developed a conceptual model linking plasticity and niche breadth, providing five alternative intraspecific scenarios that are consistent with existing literature.

Experimental data and computational modeling link auxin gradient and development in the Arabidopsis root.

The presence of an auxin gradient in the Arabidopsis root is crucial for proper root development and importantly, for stem cell niche (SCN) maintenance. Subsequently, developmental pathways in the root SCN regulate the formation of the auxin gradient. Combinations of experimental data and computational modeling enable the identification of pathways involved in establishing and maintaining the auxin gradient.

Hierarchical modularization of biochemical pathways using fuzzy-c means clustering.

Biological systems that are representative of regulatory, metabolic, or signaling pathways can be highly complex. Mathematical models that describe such systems inherit this complexity. As a result, these models can often fail to provide a path toward the intuitive comprehension of these systems.

Leaf-trait responses to irrigation of the endemic fog-oasis tree Myrcianthes ferreyrae: can a fog specialist benefit from regular watering?

Myrcianthes ferreyrae is an endemic, endangered species, with a small number of individuals located only in hyperarid, fog-oases known as lomas along the Peruvian desert in southern Peru, where fog is the main source of water. Following centuries of severe deforestation, reforestation with this native species was conducted in the Atiquipa lomas, Arequipa-Perú. On five slopes, five 2-year-old seedlings were irrigated monthly with water trapped by raschel-mesh fog collectors, supplementing natural rainfall with 0, 20, 40, 60 and 80 mm month(-1) from February to August 2008.

Forest restoration in a fog oasis: evidence indicates need for cultural awareness in constructing the reference.

Background: In the Peruvian Coastal Desert, an archipelago of fog oases, locally called lomas, are centers of biodiversity and of past human activity. Fog interception by a tree canopy, dominated by the legume tree tara (Caesalpinia spinosa), enables the occurrence in the Atiquipa lomas (southern Peru) of an environmental island with a diverse flora and high productivity. Although this forest provides essential services to the local population, it has suffered 90% anthropogenic reduction in area.

Phenotypic plasticity and integration across the canopy of Olea europaea subsp. guanchica (Oleaceae) in populations with different wind exposures.

Woody plants, as sessile and long-lived organisms, are expected to have effective mechanisms for dealing with recurrent environmental stresses. In the present study, we hypothesized that phenotypic plasticity (the ability to express alternative phenotypes) and integration (covariation among functionally related traits) are elicited in plants under stressful wind speed conditions. We investigated the within-crown variation of nine vegetative traits of a tree species (Olea europaea subsp.

Alternative methods for sampling and preservation of photosynthetic pigments and tocopherols in plant material from remote locations.

Current methods for the study of pigments involve freezing in liquid nitrogen and storage at -80 degrees C or lyophilization until HPLC analysis. These requirements greatly restrict ecophysiological research in remote areas where such resources are hardly available. We aimed to overcome such limitations by developing several techniques not requiring freezing or lyophilization.

Dark induction of the photoprotective xanthophyll cycle in response to dehydration.

Some plants tolerate tissue dehydration. Dehydration conditions suppress photosynthesis, exacerbating photooxidative stress. In this study, fern samples were collected from the field, desiccated in darkness, and subsequently re-watered.

Field patterns of leaf plasticity in adults of the long-lived evergreen Quercus coccifera.

Background And Aims: Quercus coccifera, as a long-lived sprouter, responds plastically to environmental variation. In this study, the role of foliar plasticity as a mechanism of habitat selection and modification within the canopy and across contrasted habitats was characterized. An examination was made of the differential contribution of inner and outer canopy layers to the crown plasticity expressed in the field by adult individuals and its dependence on environmental and genetic factors.

Extensive gene flow blurs phylogeographic but not phylogenetic signal in Olea europaea L.

Genetic structure and evolutionary patterns of the wild olive tree (Olea europaea L.) were investigated with AFLP fingerprinting data at three geographic levels: (a) phylogenetic relationships of the six currently recognized subspecies in Eurasia and Africa; (b) lineage identification in subsp. europaea of the Mediterranean basin; and (c) phylogeography in the western Mediterranean.

Mechanisms underlying the amelioration of O3-induced damage by elevated atmospheric concentrations of CO2.

There is growing evidence that rising atmospheric CO2 concentrations will reduce or prevent reductions in the growth and productivity of C3 crops attributable to ozone (O3) pollution. In this study, the role of pollutant exclusion in mediating this response was investigated through growth chamber-based investigations on leaves 4 and 7 of spring wheat (Triticum aestivum cv. Hanno).

Plasticity, instability and canalization: is the phenotypic variation in seedlings of sclerophyll oaks consistent with the environmental unpredictability of Mediterranean ecosystems?

•   Evergreen oaks from the Mediterranean basin exhibit a conservative resource-use strategy based on a reduced expression of phenotypic variation (i.e. canalization).