Showing papers by "National Autonomous University of Mexico published in 2009"

A DNA barcode for land plants.

Abstract: DNA barcoding involves sequencing a standard region of DNA as a tool for species identification. However, there has been no agreement on which region(s) should be used for barcoding land plants. To provide a community recommendation on a standard plant barcode, we have compared the performance of 7 leading candidate plastid DNA regions (atpF–atpH spacer, matK gene, rbcL gene, rpoB gene, rpoC1 gene, psbK–psbI spacer, and trnH–psbA spacer). Based on assessments of recoverability, sequence quality, and levels of species discrimination, we recommend the 2-locus combination of rbcL+matK as the plant barcode. This core 2-locus barcode will provide a universal framework for the routine use of DNA sequence data to identify specimens and contribute toward the discovery of overlooked species of land plants.

Science for managing ecosystem services: Beyond the Millennium Ecosystem Assessment

Abstract: The Millennium Ecosystem Assessment (MA) introduced a new framework for analyzing social-ecological systems that has had wide influence in the policy and scientific communities. Studies after the MA are taking up new challenges in the basic science needed to assess, project, and manage flows of ecosystem services and effects on human well-being. Yet, our ability to draw general conclusions remains limited by focus on discipline-bound sectors of the full social-ecological system. At the same time, some polices and practices intended to improve ecosystem services and human well-being are based on untested assumptions and sparse information. The people who are affected and those who provide resources are increasingly asking for evidence that interventions improve ecosystem services and human well-being. New research is needed that considers the full ensemble of processes and feedbacks, for a range of biophysical and social systems, to better understand and manage the dynamics of the relationship between humans and the ecosystems on which they rely. Such research will expand the capacity to address fundamental questions about complex social-ecological systems while evaluating assumptions of policies and practices intended to advance human well-being through improved ecosystem services.

Oxidative stress as a mediator of life history trade-offs: mechanisms, measurements and interpretation

Abstract: The concept of trade-offs is central to our understanding of life-history evolution. The underlying mechanisms, however, have been little studied. Oxidative stress results from a mismatch between the production of damaging reactive oxygen species (ROS) and the organism's capacity to mitigate their damaging effects. Managing oxidative stress is likely to be a major determinant of life histories, as virtually all activities generate ROS. There is a recent burgeoning of interest in how oxidative stress is related to different components of animal performance. The emphasis to date has been on immediate or short-term effects, but there is an increasing realization that oxidative stress will influence life histories over longer time scales. The concept of oxidative stress is currently used somewhat loosely by many ecologists, and the erroneous assumption often made that dietary antioxidants are necessarily the major line of defence against ROS-induced damage. We summarize current knowledge on how oxidative stress occurs and the different methods for measuring it, and highlight where ecologists can be too simplistic in their approach. We critically review the potential role of oxidative stress in mediating life-history trade-offs, and present a framework for formulating appropriate hypotheses and guiding experimental design. We indicate throughout potentially fruitful areas for further research.

Microbial drug discovery: 80 years of progress

Abstract: Microbes have made a phenomenal contribution to the health and well-being of people throughout the world. In addition to producing many primary metabolites, such as amino acids, vitamins and nucleotides, they are capable of making secondary metabolites, which constitute half of the pharmaceuticals on the market today and provide agriculture with many essential products. This review centers on these beneficial secondary metabolites, the discovery of which goes back 80 years to the time when penicillin was discovered by Alexander Fleming.

The development of Assessment of SpondyloArthritis international Society classification criteria for axial spondyloarthritis (part I): classification of paper patients by expert opinion including uncertainty appraisal

Abstract: Objective: Non-radiographic axial spondyloarthritis (SpA) is characterised by a lack of definitive radiographic sacroiliitis and is considered an early stage of ankylosing spondylitis. The objective of this study was to develop candidate classification criteria for axial SpA that include patients with but also without radiographic sacroiliitis. Methods: Seventy-one patients with possible axial SpA, most of whom were lacking definite radiographic sacroiliitis, were reviewed as “paper patients” by 20 experts from the Assessment of SpondyloArthritis international Society (ASAS). Unequivocally classifiable patients were identified based on the aggregate expert opinion in conjunction with the expert-reported level of certainty of their judgement. Draft criteria for axial SpA were formulated and tested using classifiable patients. Results: Active sacroiliitis on magnetic resonance imaging (MRI) (odds ratio 45, 95% CI 5.3 to 383; p x rays in conjunction with one SpA feature or, if sacroilitiis is absent, in the presence of at least three SpA features. In a second set of candidate criteria, inflammatory back pain is obligatory in the clinical arm (sensitivity 86.1%; specificity 94.7%). Conclusion: The ASAS group has developed candidate criteria for the classification of axial SpA that include patients without radiographic sacroiliitis. The candidate criteria need to be validated in an independent international study.

The role of antioxidants and antioxidant-related enzymes in protective responses to environmentally induced oxidative stress

Abstract: In aerobic organisms, oxygen is essential for efficient energy production but paradoxically, produces chronic toxic stress in cells. Diverse protective systems must exist to enable adaptation to oxidative environments. Oxidative stress (OS) results when production of reactive oxidative species (ROS) exceeds the capacity of cellular antioxidant defenses to remove these toxic species. Epidemiological and clinical studies have linked environmental factors such as diet and lifestyle to cancer, diabetes, atherosclerosis, and neurodegenerative disorders. All of these conditions, as well as the aging process, are associated with OS due to elevation of ROS or insufficient ROS detoxification. Many environmental pollutants engage signaling pathways that are activated in response to OS. The same sequences of events are also associated with the etiology and early pathology of many chronic diseases. Investigations of oxidative responses in different in vivo models suggest that, in complex organisms such as mammals, organs and tissues contain distinct antioxidant systems, and this may form the basis for differential susceptibility to environmental toxic agents Thus, understanding the pathways leading to the induction of antioxidant responses will enable development of strategies to protect against oxidative damage. We shall review evidence of organ-specific antioxidant responses elicited by environmental pollutants in humans and animal models.

The Chandra COSMOS Survey. I. Overview and Point Source Catalog

Abstract: The Chandra COSMOS Survey (C-COSMOS) is a large, 1.8 Ms, Chandra program that has imaged the central 0.5 deg^2 of the COSMOS field (centered at 10 ^h , +02 ^o ) with an effective exposure of ~160 ks, and an outer 0.4 deg^2 area with an effective exposure of ~80 ks. The limiting source detection depths are 1.9 × 10^(–16) erg cm^(–2) s^(–1) in the soft (0.5-2 keV) band, 7.3 × 10^(–16) erg cm^(–2) s^(–1) in the hard (2-10 keV) band, and 5.7 × 10^(–16) erg cm^(–2) s^(–1) in the full (0.5-10 keV) band. Here we describe the strategy, design, and execution of the C-COSMOS survey, and present the catalog of 1761 point sources detected at a probability of being spurious of <2 × 10^(–5) (1655 in the full, 1340 in the soft, and 1017 in the hard bands). By using a grid of 36 heavily (~50%) overlapping pointing positions with the ACIS-I imager, a remarkably uniform (±12%) exposure across the inner 0.5 deg^2 field was obtained, leading to a sharply defined lower flux limit. The widely different point-spread functions obtained in each exposure at each point in the field required a novel source detection method, because of the overlapping tiling strategy, which is described in a companion paper. This method produced reliable sources down to a 7-12 counts, as verified by the resulting logN-logS curve, with subarcsecond positions, enabling optical and infrared identifications of virtually all sources, as reported in a second companion paper. The full catalog is described here in detail and is available online.

One Hundred Questions of Importance to the Conservation of Global Biological Diversity

Abstract: We identified 100 scientific questions that, if answered, would have the greatest impact on conservation practice and policy. Representatives from 21 international organizations, regional sections and working groups of the Society for Conservation Biology, and 12 academics, from all continents except Antarctica, compiled 2291 questions of relevance to conservation of biological diversity worldwide. The questions were gathered from 761 individuals through workshops, email requests, and discussions. Voting by email to short-list questions, followed by a 2-day workshop, was used to derive the final list of 100 questions. Most of the final questions were derived through a process of modification and combination as the workshop progressed. The questions are divided into 12 sections: ecosystem functions and services, climate change, technological change, protected areas, ecosystem management and restoration, terrestrial ecosystems, marine ecosystems, freshwater ecosystems, species management, organizational systems and processes, societal context and change, and impacts of conservation interventions. We anticipate that these questions will help identify new directions for researchers and assist funders in directing funds.

Beyond Reserves: A Research Agenda for Conserving Biodiversity in Human‐modified Tropical Landscapes

Abstract: To truly understand the current status of tropical diversity and to forecast future trends, we need to increase emphasis on the study of biodiversity in rural landscapes that are actively managed or modified by people. We present an integrated landscape approach to promote research in human-modified landscapes that includes the effects of landscape structure and dynamics on conservation of biodiversity, provision of ecosystem services, and sustainability of rural livelihoods. We propose research priorities encompassing three major areas: biodiversity, human–environment interactions, and restoration ecology. We highlight key areas where we lack knowledge and where additional understanding is most urgent for promoting conservation and sustaining rural livelihoods. Finally, we recommend participatory and multidisciplinary approaches in research and management. Lasting conservation efforts demand new alliances among conservation biologists, agroecologists, agronomists, farmers, indigenous peoples, rural social movements, foresters, social scientists, and land managers to collaborate in research, co-design conservation programs and policies, and manage human-modified landscapes in ways that enhance biodiversity conservation and promote sustainable livelihoods.

Idiopathic pulmonary fibrosis

Abstract: Masculino de 60 anos, exfumador (tabaquismo por espacio de 10 anos consumiendo 10 cigarros al dia, el cual suspendio hace 30 anos). Sin antecedentes heredofamiliares ni personales de importancia. Sin evidencia de exposicion laboral o ambiental con excepcion del tabaquismo. Inicia su padecimiento actual hace un ano y medio con tos seca en accesos, habitualmente relacionada con el esfuerzo. Un ano antes de consultar se agrega disnea de esfuerzo la que progreso de los grandes a los medianos esfuerzos, sin ortopnea. A la exploracion fisica de torax se auscultaron estertores crepitantes sub-escapulares bilaterales, y ruidos cardiacos ritmicos con reforzamiento del segundo ruido en foco pulmonar. Presenta hipocratismo digital, sin cianosis y sin edemas de miembros pelvicos

Angiosperm diversification through time.

Abstract: The extraordinary diversity of angiosperms is the ultimate outcome of the interplay of speciation and extinction, which determine the net diversification of different lineages. We document the temporal trends of angiosperm diversification rates during their early history. Absolute diversification rates were estimated for order-level clades using ages derived from relaxed molecular clock analyses that included or excluded a maximal constraint to angiosperm age. Diversification rates for angiosperms as a whole ranged from 0.0781 to 0.0909 net speciation events per million years, with dates from the constrained analysis. Diversification through time plots show an inverse relationship between clade age and rate, where the younger clades tend to have the highest rates. Angiosperm diversity is found to have mixed origins: slightly less than half of the living species belong to lineages with low to moderate diversification rates, which appeared between 130 and 102 Mya (Barremian-uppermost Albian; Lower Cretaceous). Slightly over half of the living species belong to lineages with moderate to high diversification rates, which appeared between 102 and 77 Mya (Cenomanian-mid Campanian; Upper Cretaceous). Terminal lineages leading to living angiosperm species, however, may have originated soon or long after the phylogenetic differentiation of the clade to which they belong.

EcoCyc: A comprehensive view of Escherichia coli biology

Abstract: EcoCyc (http://EcoCyc.org) provides a comprehensive encyclopedia of Escherichia coli biology. EcoCyc integrates information about the genome, genes and gene products; the metabolic network; and the regulatory network of E. coli. Recent EcoCyc developments include a new initiative to represent and curate all types of E. coli regulatory processes such as attenuation and regulation by small RNAs. EcoCyc has started to curate Gene Ontology (GO) terms for E. coli and has made a dataset of E. coli GO terms available through the GO Web site. The curation and visualization of electron transfer processes has been significantly improved. Other software and Web site enhancements include the addition of tracks to the EcoCyc genome browser, in particular a type of track designed for the display of ChIP-chip datasets, and the development of a comparative genome browser. A new Genome Omics Viewer enables users to paint omics datasets onto the full E. coli genome for analysis. A new advanced query page guides users in interactively constructing complex database queries against EcoCyc. A Macintosh version of EcoCyc is now available. A series of Webinars is available to instruct users in the use of EcoCyc.

Multiple ecological pathways to extinction in mammals

Abstract: As human population and resource demands continue to grow, biodiversity conservation has never been more critical. About one-quarter of all mammals are in danger of extinction, and more than half of all mammal populations are in decline. A major priority for conservation science is to understand the ecological traits that predict extinction risk and the interactions among those predictors that make certain species more vulnerable than others. Here, using a new database of nearly 4,500 mammal species, we use decision-tree models to quantify the multiple interacting factors associated with extinction risk. We show that the correlates of extinction risk vary widely across mammals and that there are unique pathways to extinction for species with different lifestyles and combinations of traits. We find that risk is relative and that all kinds of mammals, across all body sizes, can be at risk depending on their specific ecologies. Our results increase the understanding of extinction processes, generate simple rules of thumb that identify species at greatest risk, and highlight the potential of decision-tree analyses to inform conservation efforts.

Genomic Analysis of the Basal Lineage Fungus Rhizopus oryzae Reveals a Whole-Genome Duplication

Abstract: Rhizopus oryzae is the primary cause of mucormycosis, an emerging, life-threatening infection characterized by rapid angioinvasive growth with an overall mortality rate that exceeds 50%. As a representative of the paraphyletic basal group of the fungal kingdom called ‘‘zygomycetes,’’ R. oryzae is also used as a model to study fungal evolution. Here we report the genome sequence of R. oryzae strain 99–880, isolated from a fatal case of mucormycosis. The highly repetitive 45.3 Mb genome assembly contains abundant transposable elements (TEs), comprising approximately 20% of the genome. We predicted 13,895 protein-coding genes not overlapping TEs, many of which are paralogous gene pairs. The order and genomic arrangement of the duplicated gene pairs and their common phylogenetic origin provide evidence for an ancestral whole-genome duplication (WGD) event. The WGD resulted in the duplication of nearly all subunits of the protein complexes associated with respiratory electron transport chains, the V-ATPase, and the ubiquitin–proteasome systems. The WGD, together with recent gene duplications, resulted in the expansion of multiple gene families related to cell growth and signal transduction, as well as secreted aspartic protease and subtilase protein families, which are known fungal virulence factors. The duplication of the ergosterol biosynthetic pathway, especially the major azole target, lanosterol 14ademethylase (ERG11), could contribute to the variable responses of R. oryzae to different azole drugs, including voriconazole and posaconazole. Expanded families of cell-wall synthesis enzymes, essential for fungal cell integrity but absent in mammalian hosts, reveal potential targets for novel and R. oryzae-specific diagnostic and therapeutic treatments.

Dynamics of range margins for metapopulations under climate change

Abstract: We link spatially explicit climate change predictions to a dynamic metapopulation model. Predictions of species' responses to climate change, incorporating metapopulation dynamics and elements of dispersal, allow us to explore the range margin dynamics for two lagomorphs of conservation concern. Although the lagomorphs have very different distribution patterns, shifts at the edge of the range were more pronounced than shifts in the overall metapopulation. For Romerolagus diazi (volcano rabbit), the lower elevation range limit shifted upslope by approximately 700 m. This reduced the area occupied by the metapopulation, as the mountain peak currently lacks suitable vegetation. For Lepus timidus (European mountain hare), we modelled the British metapopulation. Increasing the dispersive estimate caused the metapopulation to shift faster on the northern range margin (leading edge). By contrast, it caused the metapopulation to respond to climate change slower, rather than faster, on the southern range margin (trailing edge). The differential responses of the leading and trailing range margins and the relative sensitivity of range limits to climate change compared with that of the metapopulation centroid have important implications for where conservation monitoring should be targeted. Our study demonstrates the importance and possibility of moving from simple bioclimatic envelope models to second-generation models that incorporate both dynamic climate change and metapopulation dynamics.

Review: Immunity mechanisms in crustaceans.

Abstract: Crustacean aquaculture represents a major industry in tropical developing countries. As a result of high culture densities and increasing extension of aquaculture farms, the presence of diseases has also increased, inducing economic losses. Invertebrates, which lack adaptive immune systems, have developed defense systems that respond against antigens on the surface of potential pathogens. The defense mechanisms of crustaceans depend completely on the innate immune system that is activated when pathogen-associated molecular patterns are recognized by soluble or by cell surface host proteins, such as lectins, antimicrobial, clotting, and pattern recognition proteins, which, in turn, activate cellular or humoral effector mechanisms to destroy invading pathogens. This work is aimed at presenting the main characteristics of the crustacean proteins that participate in immune defense by specific recognition of carbohydrate containing molecules, i.e. glycans, glycolipids, glycoproteins, peptidoglycans, or lipopol...

Cell death mechanisms induced by cytotoxic lymphocytes.

Abstract: One of the functions of the immune system is to recognize and destroy abnormal or infected cells to maintain homeostasis. This is accomplished by cytotoxic lymphocytes. Cytotoxicity is a highly organized multifactor process. Here, we reviewed the apoptosis pathways induced by the two main cytotoxic lymphocyte subsets, natural killer (NK) cells and CD8+ T cells. In base to recent experimental evidence, we reviewed NK receptors involved in recognition of target-cell, as well as lytic molecules such as perforin, granzymes-A and -B, and granulysin. In addition, we reviewed the Fas-FasL intercellular linkage mediated pathway, and briefly the cross-linking of tumor necrosis factor (TNF) and TNF receptor pathway. We discussed three models of possible molecular interaction between lytic molecules from effector cytotoxic cells and target-cell membrane to induction of apoptosis.

The XMM-Newton wide-field survey in the COSMOS field - The point-like X-ray source catalogue

Abstract: Context. The COSMOS survey is a multiwavelength survey aimed to study the evolution of galaxies, AGN and large scale structures. Within this survey XMM-COSMOS a powerful tool to detect AGN and galaxy clusters. The XMM-COSMOS is a deep X-ray survey over the full 2 deg^2 of the COSMOS area. It consists of 55 XMM-Newton pointings for a total exposure of ~1.5 Ms with an average vignetting-corrected depth of 40 ks across the field of view and a sky coverage of 2.13 deg^2. Aims. We present the catalogue of point-like X-ray sources detected with the EPIC CCD cameras, the log N − log S relations and the X-ray colour–colour diagrams. Methods. The analysis was performed using the XMM-SAS data analysis package in the 0.5–2 keV, 2–10 keV and 5–10 keV energy bands. Source detection has been performed using a maximum likelihood technique especially designed for raster scan surveys. The completeness of the catalogue as well as log N − log S and source density maps have been calibrated using Monte Carlo simulations. Results. The catalogs contains a total of 1887 unique sources detected in at least one band with likelihood parameter det_ml > 10. The survey, which shows unprecedented homogeneity, has a flux limit of ~1.7×10^(−15) erg cm^(−2) s^(−1), ~9.3×10^(−15) erg cm^(−2) s^(−1) and ~1.3×10^(−14) erg cm^(−2) s^(−1) over 90% of the area (1.92 deg^2) in the 0.5–2 keV, 2–10 keV and 5–10 keV energy band, respectively. Thanks to the rather homogeneous exposure over a large area, the derived log N − log S relations are very well determined over the flux range sampled by XMM-COSMOS. These relations have been compared with XRB synthesis models, which reproduce the observations with an agreement of ~10% in the 5–10 keV and 2–10 keV band, while in the 0.5–2 keV band the agreement is of the order of ~20%. The hard X-ray colors confirmed that the majority of the extragalactic sources in a bright subsample are actually type I or type II AGN. About 20% of the sources have a X-ray luminosity typical of AGN (L_X > 10^(42) erg/s) although they do not show any clear signature of nuclear activity in the optical spectrum.

Structure of Monomeric Yeast and Mammalian Sec61 Complexes Interacting with the Translating Ribosome

Abstract: The trimeric Sec61/SecY complex is a protein-conducting channel (PCC) for secretory and membrane proteins. Although Sec complexes can form oligomers, it has been suggested that a single copy may serve as an active PCC. We determined subnanometer-resolution cryo-electron microscopy structures of eukaryotic ribosome-Sec61 complexes. In combination with biochemical data, we found that in both idle and active states, the Sec complex is not oligomeric and interacts mainly via two cytoplasmic loops with the universal ribosomal adaptor site. In the active state, the ribosomal tunnel and a central pore of the monomeric PCC were occupied by the nascent chain, contacting loop 6 of the Sec complex. This provides a structural basis for the activity of a solitary Sec complex in cotranslational protein translocation.

Optically active metal nanoparticles

Abstract: Optical activity and its relation with chiral metal nanoparticles are revised in this tutorial review. The experimental evidence as well as the different mechanisms to explain the optical activity of ligand-protected nanoparticles are described, emphasizing the aspects that provide insights into this novel phenomenon at the nanoscale. The perspectives of this research field and a list of unsolved problems are presented. This tutorial review provides information for an interdisciplinary community working in synthesis, characterization and utilization of chiral metal nanoparticles.

Observation of Half-Quantum Vortices in an Exciton-Polariton Condensate

Abstract: Singly quantized vortices have already been observed in many systems, including the superfluid helium, Bose-Einstein condensates of dilute atomic gases, and condensates of exciton-polaritons in the solid state. Two-dimensional superfluids carrying spin are expected to demonstrate a different type of elementary excitations referred to as half-quantum vortices, characterized by a π rotation of the phase and a π rotation of the polarization vector when circumventing the vortex core. We detect half-quantum vortices in an exciton-polariton condensate by means of polarization-resolved interferometry, real-space spectroscopy, and phase imaging. Half-quantum vortices coexist with single-quantum vortices in our sample.

Patterns and causes of species richness: a general simulation model for macroecology

Abstract: Understanding the causes of spatial variation in species richness is a major research focus of biogeography and macroecology. Gridded environmental data and species richness maps have been used in increasingly sophisticated curve-fitting analyses, but these methods have not brought us much closer to a mechanistic understanding of the patterns. During the past two decades, macroecologists have successfully addressed technical problems posed by spatial autocorrelation, intercorrelation of predictor variables and non-linearity. However, curve-fitting approaches are problematic because most theoretical models in macroecology do not make quantitative predictions, and they do not incorporate interactions among multiple forces. As an alternative, we propose a mechanistic modelling approach. We describe computer simulation models of the stochastic origin, spread, and extinction of species' geographical ranges in an environmentally heterogeneous, gridded domain and describe progress to date regarding their implementation. The output from such a general simulation model (GSM) would, at a minimum, consist of the simulated distribution of species ranges on a map, yielding the predicted number of species in each grid cell of the domain. In contrast to curve-fitting analysis, simulation modelling explicitly incorporates the processes believed to be affecting the geographical ranges of species and generates a number of quantitative predictions that can be compared to empirical patterns. We describe three of the 'control knobs' for a GSM that specify simple rules for dispersal, evolutionary origins and environmental gradients. Binary combinations of different knob settings correspond to eight distinct simulation models, five of which are already represented in the literature of macroecology. The output from such a GSM will include the predicted species richness per grid cell, the range size frequency distribution, the simulated phylogeny and simulated geographical ranges of the component species, all of which can be compared to empirical patterns. Challenges to the development of the GSM include the measurement of goodness of fit (GOF) between observed data and model predictions, as well as the estimation, optimization and interpretation of the model parameters. The simulation approach offers new insights into the origin and maintenance of species richness patterns, and may provide a common framework for investigating the effects of contemporary climate, evolutionary history and geometric constraints on global biodiversity gradients. With further development, the GSM has the potential to provide a conceptual bridge between macroecology and historical biogeography.