Genetic control of branching is a primary determinant of yield, regulating seed number and harvesting ability, yet little is known about the molecular networks that shape grain-bearing inflorescences of cereal crops. Here, we used the maize (Zea mays) inflorescence to investigate gene networks that modulate determinacy, specifically the decision to allow branch growth. We characterized developmental transitions by associating spatiotemporal expression profiles with morphological changes resulting from genetic perturbations that disrupt steps in a pathway controlling branching. Developmental dynamics of genes targeted in vivo by the transcription factor RAMOSA1, a key regulator of determinacy, revealed potential mechanisms for repressing branches in distinct stem cell populations, including interactions with KNOTTED1, a master regulator of stem cell maintenance. Our results uncover discrete developmental modules that function in determining grass-specific morphology and provide a basis for targeted crop improvement and translation to other cereal crops with comparable inflorescence architectures.
This webinar is the second in a two part series on high throughput field phenotyping. This presentation describes how to handle data generated by a field-based sensor array. The video was recorded live as a webinar October 31, 2013.
We spend the majority of our lives indoors where we are constantly exposed to bacteria residing on surfaces. However, the diversity of these surface-associated communities is largely unknown. We explored the biogeographical patterns exhibited by bacteria across ten surfaces within each of twelve public restrooms. Using high-throughput barcoded pyrosequencing of the 16 S rRNA gene, we identified 19 bacterial phyla across all surfaces. Most sequences belonged to four phyla: Actinobacteria, Bacteriodetes, Firmicutes and Proteobacteria. The communities clustered into three general categories: those found on surfaces associated with toilets, those on the restroom floor, and those found on surfaces routinely touched with hands. On toilet surfaces, gut-associated taxa were more prevalent, suggesting fecal contamination of these surfaces. Floor surfaces were the most diverse of all communities and contained several taxa commonly found in soils. Skin-associated bacteria, especially the Propionibacteriaceae, dominated surfaces routinely touched with our hands. Certain taxa were more common in female than in male restrooms as vagina-associated Lactobacillaceae were widely distributed in female restrooms, likely from urine contamination. Use of the SourceTracker algorithm confirmed many of our taxonomic observations as human skin was the primary source of bacteria on restroom surfaces. Overall, these results demonstrate that restroom surfaces host relatively diverse microbial communities dominated by human-associated bacteria with clear linkages between communities on or in different body sites and those communities found on restroom surfaces. More generally, this work is relevant to the public health field as we show that human-associated microbes are commonly found on restroom surfaces suggesting that bacterial pathogens could readily be transmitted between individuals by the touching of surfaces. Furthermore, we demonstrate that we can use high-throughput analyses of bacterial communities to determine sources of bacteria on indoor surfaces, an approach which could be used to track pathogen transmission and test the efficacy of hygiene practices.
Constraints in field phenotyping capability limit our ability to dissect the genetics of quantitative traits, particularly those related to yield and stress tolerance (e.g., yield potential as well as increased drought, heat tolerance, and nutrient efficiency, etc.). The development of effective field-based high-throughput phenotyping platforms (HTPPs) remains a bottleneck for future breeding advances. However, progress in sensors, aeronautics, and high-performance computing are paving the way. Here, we review recent advances in field HTPPs, which should combine at an affordable cost, high capacity for data recording, scoring and processing, and non-invasive remote sensing methods, together with automated environmental data collection. Laboratory analyses of key plant parts may complement direct phenotyping under field conditions. Improvements in user-friendly data management together with a more powerful interpretation of results should increase the use of field HTPPs, therefore increasing the efficiency of crop genetic improvement to meet the needs of future generations.
Controlling the atmospheric CO2 concentration may ultimately require recycling CO2 into liquid fuels and commodity chemicals using renewable energy as the power source. Arguably the greatest challenge for this vision is to develop efficient CO2 reduction catalysts. This talk will describe our development of “oxide-derived” metal nanoparticle electrocatalysts. These materials are prepared by reducing metal oxide precursors, which kinetically traps metastable nanoparticle structures with unique catalytic properties. I will describe examples of these catalysts that electrochemically reduce CO2 to CO at potentials close to the thermodynamic minimum as well as catalysts that selectively reduce CO to multi-carbon oxygenates. The catalysts operate in water at ambient temperature and pressure and are remarkably robust. The structural origins of the catalytic activity will be discussed based on diffraction and high-resolution electron microscopy. Oxide-derived metal nanoparticles enable a two-step electrochemical conversion of CO2 to ethanol that could make CO2 a valuable feedstock for synthetic liquid fuel.
7:30 BroadE: Trinity – How it works 5:20 BroadE: The General Approach to De novo RNA-Seq Assembly Using De Bruijn Graphs 5:38 BroadE: Introduction to De Novo RNA-Seq Assembly using Trinity 3:00 BroadE: Strand-specific RNA-Seq is Preferred ...
Saber Miresmailli, Murray B. Isman. • Chemical defense is not the only type of defense that plants use for protection. • Botanical pesticides are not directly comparable to synthetic pesticides. • L....
Live-cell imaging assisted by fluorescent markers has been fundamental to understanding the focused secretory 'warfare' that occurs between plants and biotrophic pathogens that feed on living plant cells. Pathogens succeed through the spatiotemporal deployment of a remarkably diverse range of effector proteins to control plant defences and cellular processes. Some effectors can be secreted by appressoria even before host penetration, many enter living plant cells where they target diverse subcellular compartments and others move into neighbouring cells to prepare them before invasion. This Review summarizes the latest advances in our understanding of the cell biology of biotrophic interactions between plants and their eukaryotic filamentous pathogens based on in planta analyses of effectors.
Quorum sensing is a chemical communication process that bacteria use to regulate collective behaviors. Disabling quorum-sensing circuits with small molecules has been proposed as a potential strategy to prevent bacterial pathogenicity. The human pathogen Pseudomonas aeruginosa uses quorum sensing to control virulence and biofilm formation. Here, we analyze synthetic molecules for inhibition of the two P. aeruginosaquorum-sensing receptors, LasR and RhlR. Our most effective compound, meta-bromo-thiolactone (mBTL), inhibits both the production of the virulence factor pyocyanin and biofilm formation. mBTL also protectsCaenorhabditis elegans and human lung epithelial cells from killing by P. aeruginosa. Both LasR and RhlR are partially inhibited by mBTL in vivo and in vitro; however, RhlR, not LasR, is the relevant in vivo target. More potent antagonists do not exhibit superior function in impeding virulence. Because LasR and RhlR reciprocally control crucial virulence factors, appropriately tuning rather than completely inhibiting their activities appears to hold the key to blocking pathogenesis in vivo.
from GenomeWeb Organizational Changes at Illumina Aimed at Growth, New Market Entries October 16, 2013 NEW YORK (GenomeWeb News) – Illumina today announced sweeping changes to its organization in order to maintain growth in its existing markets and...
RNA-Seq, a deep sequencing technique, promises to be a potential successor to microarrays for studying the transcriptome. One of many aspects of transcriptomics that are of interest to researchers is gene expression estimation.
New research from the University of California, Davis, shows that the tiny proportion of a cell's DNA that is located outside the cell nucleus has a disproportionately large effect on a cell's metabolism.
Nature Reviews Genetics. doi:10.1038/nrg3583 Authors: Wusheng Liu, Joshua S. Yuan & C. Neal Stewart Jr
Basic research has provided a much better understanding of the genetic networks and regulatory hierarchies in plants. To meet the challenges of agriculture, we must be able to rapidly translate this knowledge into generating improved plants. Therefore, in this Review, we discuss advanced tools that are currently available for use in plant biotechnology to produce new products in plants and to generate plants with new functions. These tools include synthetic promoters, 'tunable' transcription factors, genome-editing tools and site-specific recombinases. We also review some tools with the potential to enable crop improvement, such as methods for the assembly and synthesis of large DNA molecules, plant transformation with linked multigenes and plant artificial chromosomes. These genetic technologies should be integrated to realize their potential for applications to pressing agricultural and environmental problems.