National Autonomous University of Mexico

About: National Autonomous University of Mexico is a education organization based out in Mexico City, Distrito Federal, Mexico. It is known for research contribution in the topics: Population & Galaxy. The organization has 72868 authors who have published 127797 publications receiving 2285543 citations. The organization is also known as: UNAM & Universidad Nacional Autónoma de México.

Flexible Control of Mutual Inhibition: A Neural Model of Two-Interval Discrimination

Abstract: Networks adapt to environmental demands by switching between distinct dynamical behaviors. The activity of frontal-lobe neurons during two-interval discrimination tasks is an example of these adaptable dynamics. Subjects first perceive a stimulus, then hold it in working memory, and finally make a decision by comparing it with a second stimulus. We present a simple mutual-inhibition network model that captures all three task phases within a single framework. The model integrates both working memory and decision making because its dynamical properties are easily controlled without changing its connectivity. Mutual inhibition between nonlinear units is a useful design motif for networks that must display multiple behaviors.

RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation

Abstract: RegulonDB (http://regulondb.ccg.unam.mx/) is the primary reference database offering curated knowledge of the transcriptional regulatory network of Escherichia coli K12, currently the best-known electronically encoded database of the genetic regulatory network of any free-living organism. This paper summarizes the improvements, new biology and new features available in version 6.0. Curation of original literature is, from now on, up to date for every new release. All the objects are supported by their corresponding evidences, now classified as strong or weak. Transcription factors are classified by origin of their effectors and by gene ontology class. We have now computational predictions for σ54 and five different promoter types of the σ70 family, as well as their corresponding −10 and −35 boxes. In addition to those curated from the literature, we added about 300 experimentally mapped promoters coming from our own high-throughput mapping efforts. RegulonDB v.6.0 now expands beyond transcription initiation, including RNA regulatory elements, specifically riboswitches, attenuators and small RNAs, with their known associated targets. The data can be accessed through overviews of correlations about gene regulation. RegulonDB associated original literature, together with more than 4000 curation notes, can now be searched with the Textpresso text mining engine.

Phenoloxidase: a key component of the insect immune system

Abstract: The innate immune system in insects is composed of a large variety of specific and non-specific responses that are activated in response to the presence of foreign agents. One important element in such responses is the enzyme phenoloxidase (PO). Here, we review recent progress in PO research and discuss new applications in the emerging field of ecological immunology. Phenoloxidase produces indole groups, which are subsequently polymerized to melanin. The enzymatic reactions in turn produce a set of intermediate products such as quinones, diphenols, superoxide, hydrogen peroxide, and reactive nitrogen intermediates, which are important during defense against bacterial (gram+ and )), fungal, and viral agents. Phenoloxidase requires a complex system of activation and inhibition that involves various cell types, PO zymogens, inhibitor enzymes, and signaling molecules. Finally, research in evolutionary ecology has studied the costs of PO in terms of resource use and pleiotropic relations with other key traits and functions. These studies indicate that PO is a costly trait, whose production and maintenance have fitness costs for hosts. Phenoloxidase does not seem to be anindicatorofresistancebut rather ofhostcondition. Finally, we putforwardsome basicdirectionsforfutureinvestigationofPOaimedatexplainingitsactivatingsystem,itssubstrates,itscoordination with other immune components to fight off pathogens, and variation in PO in relation to gender,lifestages, seasonality, andacross different host species.

Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology

Abstract: Organellar DNA sequences are widely used in evolutionary and population genetic studies, however, the conservative nature of chloroplast gene and genome evolution often limits phylogenetic resolution and statistical power. To gain maximal access to the historical record contained within chloroplast genomes, we have adapted multiplex sequencing-by-synthesis (MSBS) to simultaneously sequence multiple genomes using the Illumina Genome Analyzer. We PCR-amplified ∼120 kb plastomes from eight species (seven Pinus, one Picea) in 35 reactions. Pooled products were ligated to modified adapters that included 3 bp indexing tags and samples were multiplexed at four genomes per lane. Tagged microreads were assembled by de novo and reference-guided assembly methods, using previously published Pinus plastomes as surrogate references. Assemblies for these eight genomes are estimated at 88–94% complete, with an average sequence depth of 55× to 186×. Mononucleotide repeats interrupt contig assembly with increasing repeat length, and we estimate that the limit for their assembly is 16 bp. Comparisons to 37 kb of Sanger sequence show a validated error rate of 0.056%, and conspicuous errors are evident from the assembly process. This efficient sequencing approach yields high-quality draft genomes and should have immediate applicability to genomes with comparable complexity.