High-throughput phenotyping of multicellular organisms: finding the link between genotype and phenotype

High-throughput phenotyping approaches (phenomics) are being combined with genome-wide genetic screens to identify alterations in phenotype that result from gene inactivation. Here we highlight promising technologies for 'phenome-scale' analyses in multicellular organisms

Insights into root development from Arabidopsis root mutants

The root provides a useful system for the analysis of plant organ formation. Mutations that affect root development and physiology have been identified in Arabidopsis thaliana. Affected processes include embryonic root formation, cell expansion, cell differentiation and response to environmental stimuli. Analysis of these mutations is providing insight into fundamental questions of plant development.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/75185/1/j.1365-3040.1994.tb00159.x.pd

Optimal swimming speeds reflect preferred swimming speeds of brook charr (Salvelinus fontinalis Mitchill, 1874)

Several measures have been developed to quantify swimming performance to understand various aspects of ecology and behaviour, as well as to help design functional applications for fishways and aquaculture. One of those measures, the optimal swimming speed, is the speed at which the cost of transport (COT) is minimal, where COT is defined as the cost of moving unit mass over unit distance. The experimental protocol to determine the optimal swimming speed involves forced-swimming in a flume or respirometer. In this study, a 4.5–m-long tilted raceway with gradually increasing upstream water speed is used to determine a novel, behaviourally based swimming parameter: the preferred swimming speed. The optimal swimming speed and the preferred swimming speed of brook charr were determined and a comparison of the two reveals that the optimal swimming speed (25.9 ± 4.5 cm s−1 or 1.02 ± 0.47 bl s−1) reflected the preferred swimming speed (between 20 cm s−1 or 0.78 ± 0.02 bl s−1 and 25 cm s−1 or 0.95 ± 0.03 bl s−1). The preferred swimming speed can be advantageous for the determination of swimming speeds for the use in aquaculture studies

Stephen Crane\u27s Father and the Holiness Movement

Stephen Crane was the son and grandson of prominent Methodist ministers, and it is often assumed that his colorful life of excess and adventure was an understandable rejection of that legacy. But his father\u27s prominence during Crane\u27s childhood was tinged with something close to scandal, and what the son rejected is not entirely clear. Indeed, Crane the novelist seems to have inherited certain traits of character from Crane the minister-tenacity of purpose, intellectual integrity, iconoclastic fearlessness-and adapted them to his own ends. This article attempts to answer the question: Why did Stephen Crane\u27s father, Jonathan Townley Crane (1819-1880), give up the prestigious position of presiding elder in the Elizabeth (New Jersey) district of the Methodist Episcopal Church, in 1876, and return to the itinerant ministry? The answer may tum out to have a bearing on issues central to Crane studies, such as the reputed differences between the conceptions of God held by Crane\u27s father and his ma~ temal grandfather, and Stephen Crane\u27s own obsessive search for intense experience. It may also help to convey the atmosphere in the Crane household during the years when Stephen, born in 1871, was growing up. I propose, in short, to reveal a momentous and hitherto unsuspected episode in J. T. Crane\u27s life

Memories As Old As Outer Space

My paintings draw from personal memory, as well as the nostalgic longing and nightmarish foreboding of the irrational psyche. Cosmic ruptures, cliffs, cemeteries, and parking lots appear alongside snowglobes and canopy beds. I aim to suggest things to be wary of, while giving space for optimistic fantasy and reflective wonder

A SIMPLE Pipeline for Mapping Point Mutations

A forward genetic screen is one of the best methods for revealing the function of genes. In plants, this technique is highly efficient, as it is relatively easy to grow and screen hundreds or thousands of individuals. The cost efficiency and ease of data production afforded by next-generation sequencing have created new opportunities for rapid mapping of induced mutations. Current mapping tools are often not user friendly, are complicated, or require extensive preparation steps. To simplify the process of mapping new mutations, we developed a pipeline that takes next-generation sequencing fastq files as input, calls on several well-established and freely available genome-analysis tools, and outputs the most likely causal DNA changes. The pipeline has been validated in Arabidopsis thaliana (Arabidopsis) and can be readily applied to other species, with the possibility of mapping either dominant or recessive mutations

MicroRNA MIR396 regulates the switch between stem cells and transit-amplifying cells in arabidopsis roots

To ensure an adequate organ mass, the daughters of stem cells progress through a transit-amplifying phase displaying rapid cell division cycles before differentiating. Here, we show that Arabidopsis thaliana microRNA miR396 regulates the transition of root stem cells into transit-amplifying cells by interacting with GROWTH-REGULATING FACTORs (GRFs). The GRFs are expressed in transit-amplifying cells but are excluded from the stem cells through inhibition by miR396. Inactivation of the GRFs increases the meristem size and induces periclinal formative divisions in transit-amplifying cells. The GRFs repress PLETHORA (PLT) genes, regulating their spatial expression gradient. Conversely, PLT activates MIR396 in the stem cells to repress the GRFs. We identified a pathway regulated by GRF transcription factors that represses stem cell-promoting genes in actively proliferating cells, which is essential for the progression of the cell cycle and the orientation of the cell division plane. If unchecked, the expression of the GRFs in the stem cell niche suppresses formative cell divisions and distorts the organization of the quiescent center. We propose that the interactions identified here between miR396 and GRF and PLT transcription factors are necessary to establish the boundary between the stem cell niche and the transit-amplifying region.Fil: Rodriguez Virasoro, Ramiro Esteban. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Biología Molecular y Celular de Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario; ArgentinaFil: Ercoli, María Florencia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Biología Molecular y Celular de Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario; ArgentinaFil: Debernardi, Juan Manuel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Biología Molecular y Celular de Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario; ArgentinaFil: Breakfield, Natalie W.. University of Duke; Estados UnidosFil: Mecchia, Martin Alejandro. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Biología Molecular y Celular de Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario; ArgentinaFil: Sabatini, Martín. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Biología Molecular y Celular de Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario; ArgentinaFil: Cools, Toon. University of Ghent; BélgicaFil: De Veylder, Lieven. University of Ghent; BélgicaFil: Benfey, Philip N.. University of Duke; Estados UnidosFil: Palatnik, Javier Fernando. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Biología Molecular y Celular de Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario; Argentin

A broad competence to respond to SHORT-­‐ROOT as revealed by tissue-­‐specific ectopic expressions

In plants, cell fate specification depends primarily on position rather than lineage. Recent results indicate that positional information can be transmitted through intercellular trafficking of transcription factors. The SHORT ROOT (SHR) gene, a member of the GRAS family of putative transcription factors, is involved in root radial patterning in Arabidopsis. Correct radial patterning depends on the positional information transmitted through limited SHR intercellular movement and translated into cell division and specification by competent target cells. To investigate the regulation of SHR movement and the competence to respond to it, we drove expression of a translational fusion SHR::GFP using four different tissue-specific promoters. In a wild-type background, SHR::GFP was not able to move from either phloem companion cells or epidermal cells, both of which have been shown to support movement of other proteins, suggesting a requirement for tissue-specific factors for SHR movement. When expressed from its native promoter in plants with multiple endodermal layers, SHR::GFP was not able to move beyond the first endodermal layer, indicating that movement is not limited by a mechanism that recognizes boundaries between cell types. Surprisingly, movement of SHR::GFP was observed when ectopic expression from an epidermal promoter was placed in a scarecrow (scr) mutant background, revealing a possible role for SCR in limiting movement. Analysis of the competence to respond to SHR-mediated cell specification activity indicated that it was broadly distributed in the epidermal lineage, while competence to respond to the cell division activity of SHR appeared limited to the initials and involved induction of SCR. The spatial distribution of competence to respond to SHR highlights the importance of tightly regulated movement in generating the root radial pattern