Here we present the Transcription Factor Encyclopedia (TFe), a new web-based compendium of mini review articles on transcription factors (TFs) that is founded on the principles of open access and collaboration.
Andres Zurita's insight:
Our consortium of over 100 researchers has collectively contributed over 130 mini review articles on pertinent human, mouse and rat TFs. Notable features of the TFe website include a high-quality PDF generator and web API for programmatic data retrieval. TFe aims to rapidly educate scientists about the TFs they encounter through the delivery of succinct summaries written and vetted by experts in the field. TFe is available at http://www.cisreg.ca/tfe webcite.
International Plant & Animal Genome XXI Conference, San Diego, CA Date: Monday, January 14, 2013 Time: 5-7pm Location: Garden Salon 2
The Plant Breeding and Genomics (PBG) Community of Practice on eXtension.org will highlight the need, both locally and globally, for technical continuing education in the field of genomic assisted crop improvement. The growth of publically available sequence data for numerous crop species, and increasing power of open access computational tools, has opened up new strategies for crop improvement for all plant breeders. Inquiry-based learning, through self-paced, how-to, educational modules is proving to be a successful way to connect breeding professionals to emerging technologies. This session will provide an introduction to the PBG community, its resources, and strategies to integrate and expand the community.
Genotypic Technology and National Institute of Plant Genome Research (NIPGR), India, have under an MoU launched chickpea DNA microarrays.
Andres Zurita's insight:
Pioneers in genomics and bioinformatics in India, Genotypic Technology in association with the National Institute of Plant Genome Research (NIPGR), New Delhi, India, has launched chickpea DNA microarrays. The newly developed microarray slide consists of eight arrays with about 60,000 annotated probes. These probes could be used further to develop functional molecular markers and in gene copy number studies.
Disintegrating ice, spectacular sunbursts and minuscule lizards are among 2012’s most striking pictures.
Andres Zurita's insight:
With every moment of our lives seemingly Instagram’d, Facebooked and Twitpic’d, has the power of the photographic image faded like a Polaroid ravaged by sunlight? Not a bit of it. The camera is always on hand to record the wonder of the natural world and the thrill of exploring it. This year it showed us a man falling to Earth faster than the speed of sound; the nightmarish denizens of the deep oceans; and the delicate tracery of a brain’s protective shield. These, and more, are some of Nature’s favourite pictures of 2012.
Agricultural research must be moved to the heart of efforts to limit climate change's impacts on those living in dry areas, says a report.
Andres Zurita's insight:
The report, released by a group of leading international experts in climate change and agriculture last month (30 November), is intended to inform policymakers and agricultural planners about the risks climate change poses to dry areas. It offers practical solutions to reduce these threats and boost the productivity of this type of land.
The GLV/RGF/CLEL small signaling peptide family is encoded by eleven genes in Arabidopsis thaliana. Some of them have already been shown to control root meristem maintenance (Matsuzaki et al., 2010), auxin fluxes and gravitropic responses (Whitford et al., 2012). As a basis for the detailed analysis of their function, we determined the expression domains for each of the eleven GLV genes with promoter-reporter lines. Although they are collectively active in all examined plant parts, GLV genes have highly specific transcription patterns, generally restricted to very few cells or cell types in the root and shoot, and in vegetative and reproductive tissues. GLV functions were further investigated with the comparative analysis of root phenotypes induced by gain- and loss-of-function mutants, or treatments with GLV-derived synthetic peptides. We identified functional classes that relate to the gene expression domains and suggest that different GLV signals trigger distinct downstream pathways. Interestingly, GLV genes transcribed in the early steps of lateral root development inhibited root branching to a larger extent when overexpressed. Furthermore, transcription patterns together with mutant phenotypes pointed to the involvement of GLV4 and GLV8 in root hair formation. Overall, our data suggest that nine GLV genes form three subgroups according to their expression and function within the root, and offer a comprehensive framework to study the role of the GLV signaling peptides in plant development.
For a comprehensive survey of the structure and dynamics of the Dutch Phytophthora infestans population, 652 P. infestans isolates were collected from commercial potato fields in the Netherlands during the 10-year period 2000–2009. Genotyping was performed using 12 highly informative microsatellite markers and mitochondrial haplotypes. In addition, for each isolate, the mating type was determined. STRUCTURE analysis grouped the 322 identified genotypes in three clusters. Cluster 1 consists of a single clonal lineage NL-001, known as “Blue_13”; all isolates in this cluster have the A2 mating type and the Ia mitochondrial haplotype. Clusters 2 and 3 display a more elaborate substructure containing many unique genotypes. In Cluster 3, several distinct clonal lineages were also identified. This survey witnesses that the Dutch population underwent dramatic changes in the 10 years under study. The most notable change was the emergence and spread of A2 mating type strain NL-001 (or “Blue_13”). The results emphasize the importance of the sexual cycle in generating genetic diversity and the importance of the asexual cycle as the propagation and dispersal mechanism for successful genotypes. Isolates were also screened for absence of the Avrblb1/ipiO class I gene, which is indicative for virulence on Rpi-blb1. This is also the first report of Rpi-blb1 breakers in the Netherlands. Superimposing the virulence screening on the SSR genetic backbone indicates that lack the Avrblb1/ipiO class I gene only occurred in sexual progeny. So far, the asexual spread of the virulent isolates identified has been limited.
Via Kamoun Lab @ TSL
The draft genome of the pear (Pyrus bretschneideri) using a combination of BAC-by-BAC and next-generation sequencing is reported. A 512.0-Mb sequence corresponding to 97.1% of the estimated genome size of this highly heterozygous species is assembled with 1943 coverage. High-density genetic maps comprising 2005 SNP markers anchored 75.5% of the sequence to all 17 chromosomes. The pear genome encodes 42,812 protein-coding genes, and of these, ~28.5% encode multiple isoforms. Repetitive sequences of 271.9 Mb in length, accounting for 53.1% of the pear genome, are identified. Simulation of eudicots to the ancestor of Rosaceae has reconstructed nine ancestral chromosomes. Pear and apple diverged from each other ~5.4–21.5 million years ago, and a recent whole-genome duplication (WGD) event must have occurred 30–45 MYA prior to their divergence, but following divergence from strawberry. When compared with the apple genome sequence, size differences between the apple and pear genomes are confirmed mainly due to the presence of repetitive sequences predominantly contributed by transposable elements (TEs), while genic regions are similar in both species. Genes critical for self-incompatibility, lignified stone cells (a unique feature of pear fruit), sorbitol metabolism, and volatile compounds of fruit have also been identified. Multiple candidate SFB genes appear as tandem repeats in the S-locus region of pear; while lignin synthesis-related gene family expansion and highly expressed gene families of HCT, C39H, and CCOMT contribute to high accumulation of both G-lignin and S-lignin. Moreover, alpha-linolenic acid metabolism is a key pathway for aroma in pear fruit.
Via Plant Breeding and Genomics News
Leaf senescence can impact crop production by either changing photosynthesis duration, or by modifying the nutrient remobilization efficiency and harvest index. The doubling of the grain yield in major cereals in the last 50 years was primarily achieved through the extension of photosynthesis duration and the increase in crop biomass partitioning, two things that are intrinsically coupled with leaf senescence. In this review, we consider the functionality of a leaf as a function of leaf age, and divide a leaf's life into three phases: the functionality increasing phase at the early growth stage, the full functionality phase, and the senescence and functionality decreasing phase. A genetic framework is proposed to describe gene actions at various checkpoints to regulate leaf development and senescence. Four categories of genes contribute to crop production: those which regulate (I) the speed and transition of early leaf growth, (II) photosynthesis rate, (III) the onset and (IV) the progression of leaf senescence. Current advances in isolating and characterizing senescence regulatory genes are discussed in the leaf aging and crop production context. We argue that the breeding of crops with leaf senescence ideotypes should be an essential part of further crop genetic improvement.
Phosphorus (P) is an essential element for plant growth and development but it is often a limiting nutrient in soils. Hence, P acquisition from soil by plant roots is a subject of considerable interest in agriculture, ecology and plant root biology. Root architecture, with its shape and structured development, can be considered as an evolutionary response to scarcity of resources.
Scope This review discusses the significance of root architecture development in response to low P availability and its beneficial effects on alleviation of P stress. It also focuses on recent progress in unravelling cellular, physiological and molecular mechanisms in root developmental adaptation to P starvation. The progress in a more detailed understanding of these mechanisms might be used for developing strategies that build upon the observed explorative behaviour of plant roots.
Conclusions The role of root architecture in alleviation of P stress is well documented. However, this paper describes how plants adjust their root architecture to low-P conditions through inhibition of primary root growth, promotion of lateral root growth, enhancement of root hair development and cluster root formation, which all promote P acquisition by plants. The mechanisms for activating alterations in root architecture in response to P deprivation depend on changes in the localized P concentration, and transport of or sensitivity to growth regulators such as sugars, auxins, ethylene, cytokinins, nitric oxide (NO), reactive oxygen species (ROS) and abscisic acid (ABA). In the process, many genes are activated, which in turn trigger changes in molecular, physiological and cellular processes. As a result, root architecture is modified, allowing plants to adapt effectively to the low-P environment. This review provides a framework for understanding how P deficiency alters root architecture, with a focus on integrated physiological and molecular signalling.
PLOS ONE: an inclusive, peer-reviewed, open-access resource from the PUBLIC LIBRARY OF SCIENCE. Reports of well-performed scientific studies from all disciplines freely available to the whole world.
Andres Zurita's insight:
Treatment differences observed following feeding of Bt maize to sows did not indicate inflammation or allergy and are unlikely to be of major importance. These results provide additional data for Bt maize safety assessment.
09 OCTUBRE, 2010El mapa de las rutas metabólicas… Animado!
Gastó cientos de ATP escribiendo: David Castro
¿Qué es una ruta o vía metabólica? De manera sencilla, es el flujo de reacciones que sigue un determinado compuesto al ingresar a la célula, de esta manera, se transforma en una molécula más compleja (biosíntesis o anabolismo) o en una más sencilla (degradación o catabolismo).
el Dr, Donald Nicholson, el mismo que creó este mapa de las rutas metabólicas que les acabo de poner, ha desarrollado unos mapas animados. A sus 80 años y con la ayuda de una computadora ha desarrollado los “Animaps”.
We at Science have once again had the challenge of choosing 10 scientific accomplishments to highlight in this final issue of the year. Our 10 choices reveal that 2012 has been a remarkable one for the physics of particles (the Higgs boson, neutrinos, and Majorana “quasiparticles”), as well as for biological discovery (the production of eggs from stem cells, the derivation of some modern human genes from Denisovan ancestors, and the greatly enhanced cataloging of human genetic regulation). Three technological breakthroughs also appear on our list: functional brain/machine interfaces, TALENS as a tool for genetic engineering, and the x-ray laser determination of a protein structure. And finally, there is one feat of physics and engineering virtuosity: the Curiosity rover's remarkably precise, gentle, “sky crane” landing on Mars.
The top Breakthrough of the Year—the discovery of the Higgs boson—was an unusually easy choice, representing both a triumph of the human intellect and the culmination of decades of work by many thousands of physicists and engineers. The two teams at the CERN Large Hadron Collider that detected this elusive particle have in this issue provided a more widely accessible version of their detailed findings published earlier this year in Physics Letters B. These articles are accompanied by a historical summary and overview of this seminal discovery (p. 1524).
LUNES, 17 DE DICIEMBRE DE 2012Buscando la rosa azul por @bioamaraUn extracto de la entrada: Estamos en unas fechas en las que una planta concreta cobra protagonismo. Hablamos del pascuero, flor de pascua o poinsetia. Su belleza y la particularidad de sus hojas rojas, me ha hecho pensar en los colores de las flores. Sin embargo, hoy no os voy a hablar de la flor de pascua sino de rosas, de leyendas, de fantasía hecha realidad...pero antes de entrar en materia, me vais a permitir que os ponga en situación. Para ello, tendremos que definir lo que son las antocianinas para aquellos que no lo sepan. La primera rosa azul que se comercializa en el mundo Las antocianinas (del griego anthos: ‘flor’ + kyáneos: ‘azul’) son pigmentos hidrosolubles que se hallan en las vacuolas de las células vegetales y que otorgan el color rojo, púrpura o azul a las hojas, flores y frutos. Desde el punto de vista químico, las antocianinas pertenecen al grupo de los flavonoides y son glucósidos de las antocianidinas, es decir, están constituidas por una molécula de antocianidina, que es la aglicona, a la que se le une un azúcar por medio de un enlace glucosídico. Sus funciones en las plantas son múltiples, desde la de protección de la radiación ultravioleta hasta la de atracción de insectos polinizadores. En JoF3 hablé de estas moléculas y otras implicadas en el metabolismo secundario de plantas. Si queréis saber más, podéis verlo en este enlace. Entrada completa en: http://lacienciadeamara.blogspot.com.es/2012/12/buscando-la-rosa-azul.html?m=1
In the coming decades, continued population growth, rising meat and dairy consumption and expanding biofuel use will dramatically increase the pressure on global agriculture. Even as we face these future burdens, there have been scattered reports of yield stagnation in the world’s major cereal crops, including maize, rice and wheat. Here we study data from ~2.5 million census observations across the globe extending over the period 1961–2008. We examined the trends in crop yields for four key global crops: maize, rice, wheat and soybeans. Although yields continue to increase in many areas, we find that across 24–39% of maize-, rice-, wheat- and soybean-growing areas, yields either never improve, stagnate or collapse. This result underscores the challenge of meeting increasing global agricultural demands. New investments in underperforming regions, as well as strategies to continue increasing yields in the high-performing areas, are required.
Most of the natural variation in wheat vernalization response is determined by allelic differences in the MADS-box transcription factorVERNALIZATION1 (VRN1). Extended exposures to low temperatures during the winter (vernalization) induce VRN1 expression and promote the transition of the apical meristem to the reproductive phase. In contrast to its Arabidopsis homolog (APETALA1), which is mainly expressed in the apical meristem, VRN1 is also expressed at high levels in the leaves, but its function in this tissue is not well understood. Using tetraploid wheat lines with truncation mutations in the two homoeologous copies of VRN1 (henceforth vrn1-null mutants), we demonstrate that a central role of VRN1 in the leaves is to maintain low transcript levels of the VRN2 flowering repressor after vernalization. Transcript levels of VRN2 were gradually down-regulated during vernalization in both mutant and wild-type genotypes, but were up-regulated after vernalization only in the vrn1-null mutants. The up-regulation of VRN2 delayed flowering by repressing the transcription of FT, a flowering-integrator gene that encodes a mobile protein that is transported from the leaves to the apical meristem to induce flowering. The role of VRN2 in the delayed flowering of the vrn1-null mutant was confirmed using double vrn1-vrn2-null mutants, which flowered two months earlier than the vrn1-null mutants. Both mutants produced normal flowers and seeds demonstrating that VRN1 is not essential for wheat flowering, which contradicts current flowering models. This result does not diminish the importance of VRN1 in the seasonal regulation of wheat flowering. The up-regulation of VRN1 during winter is required to maintain low transcript levels of VRN2, accelerate the induction of FT in the leaves, and regulate a timely flowering in the spring. Our results also demonstrate the existence of redundant wheat flowering genes that may provide new targets for engineering wheat varieties better adapted to changing environments.
Phytophthora infestans is the oomycete pathogen responsible for the devastating late blight disease on potato and tomato. There is presently an intense research focus on the role(s) of effectors in promoting late blight disease development. However, little is known about how they are regulated, or how diversity in their expression may be generated among different isolates. Here we present data from investigation of RNA silencing processes, characterized by non-coding small RNA molecules (sRNA) of 19–40 nt. From deep sequencing of sRNAs we have identified sRNAs matching numerous RxLR and Crinkler (CRN) effector protein genes in two isolates differing in pathogenicity. Effector gene-derived sRNAs were present in both isolates, but exhibited marked differences in abundance, especially for CRN effectors. Small RNAs in P. infestans grouped into three clear size classes of 21, 25/26 and 32 nt. Small RNAs from all size classes mapped to RxLR effector genes, but notably 21 nt sRNAs were the predominant size class mapping to CRN effector genes. Some effector genes, such as PiAvr3a, to which sRNAs were found, also exhibited differences in transcript accumulation between the two isolates. The P. infestans genome is rich in transposable elements, and the majority of sRNAs of all size classes mapped to these sequences, predominantly to long terminal repeat (LTR) retrotransposons. RNA silencing of Dicer and Argonaute genes provided evidence that generation of 21 nt sRNAs is Dicer-dependent, while accumulation of longer sRNAs was impacted by silencing of Argonaute genes. Additionally, we identified six microRNA (miRNA) candidates from our sequencing data, their precursor sequences from the genome sequence, and target mRNAs. These miRNA candidates have features characteristic of both plant and metazoan miRNAs.
Via Kamoun Lab @ TSL
FORTUNE -- After each Presidential election, The National Intelligence Council (NIC), the Washington, D.C., agency that provides long-term strategic analysis to America's intelligence community, releases a report on security risks. Its newest report, issued on December 10th and called Global Trends 2030: Alternative Worlds, covers many topics from cross-border conflict to terrorism to regional economic collapse.
Via International Maize and Wheat Improvement Center