Showing papers by "National Autonomous University of Mexico published in 2012"

Averting biodiversity collapse in tropical forest protected areas

Abstract: The rapid disruption of tropical forests probably imperils global biodiversity more than any other contemporary phenomenon(1-3). With deforestation advancing quickly, protected areas are increasingly becoming final refuges for threatened species and natural ecosystem processes. However, many protected areas in the tropics are themselves vulnerable to human encroachment and other environmental stresses(4-9). As pressures mount, it is vital to know whether existing reserves can sustain their biodiversity. A critical constraint in addressing this question has been that data describing a broad array of biodiversity groups have been unavailable for a sufficiently large and representative sample of reserves. Here we present a uniquely comprehensive data set on changes over the past 20 to 30 years in 31 functional groups of species and 21 potential drivers of environmental change, for 60 protected areas stratified across the world's major tropical regions. Our analysis reveals great variation in reserve 'health': about half of all reserves have been effective or performed passably, but the rest are experiencing an erosion of biodiversity that is often alarmingly widespread taxonomically and functionally. Habitat disruption, hunting and forest-product exploitation were the strongest predictors of declining reserve health. Crucially, environmental changes immediately outside reserves seemed nearly as important as those inside in determining their ecological fate, with changes inside reserves strongly mirroring those occurring around them. These findings suggest that tropical protected areas are often intimately linked ecologically to their surrounding habitats, and that a failure to stem broad-scale loss and degradation of such habitats could sharply increase the likelihood of serious biodiversity declines.

Gait and cognition: a complementary approach to understanding brain function and the risk of falling.

Abstract: Until recently, clinicians and researchers have performed gait assessments and cognitive assessments separately when evaluating older adults, but increasing evidence from clinical practice, epidemiological studies, and clinical trials shows that gait and cognition are interrelated in older adults. Quantifiable alterations in gait in older adults are associated with falls, dementia, and disability. At the same time, emerging evidence indicates that early disturbances in cognitive processes such as attention, executive function, and working memory are associated with slower gait and gait instability during single- and dual-task testing and that these cognitive disturbances assist in the prediction of future mobility loss, falls, and progression to dementia. This article reviews the importance of the interrelationship between gait and cognition in aging and presents evidence that gait assessments can provide a window into the understanding of cognitive function and dysfunction and fall risk in older people in clinical practice. To this end, the benefits of dual-task gait assessments (e.g., walking while performing an attention-demanding task) as a marker of fall risk are summarized. A potential complementary approach for reducing the risk of falls by improving certain aspects of cognition through nonpharmacological and pharmacological treatments is also presented. Untangling the relationship between early gait disturbances and early cognitive changes may be helpful in identifying older adults at risk of experiencing mobility decline, falls, and progression to dementia.

Randomized trial of tocilizumab in systemic juvenile idiopathic arthritis.

Abstract: Background Systemic juvenile idiopathic arthritis (JIA) is the most severe subtype of JIA; treatment options are limited. Interleukin-6 plays a pathogenic role in systemic JIA. Methods We randomly assigned 112 children, 2 to 17 years of age, with active systemic JIA (duration of ≥6 months and inadequate responses to nonsteroidal antiinflammatory drugs and glucocorticoids) to the anti–interleukin-6 receptor antibody tocilizumab (at a dose of 8 mg per kilogram of body weight if the weight was ≥30 kg or 12 mg per kilogram if the weight was <30 kg) or placebo given intravenously every 2 weeks during the 12-week, double-blind phase. Patients meeting the predefined criteria for nonresponse were offered open-label tocilizumab. All patients could enter an open-label extension. Results At week 12, the primary end point (an absence of fever and an improvement of 30% or more on at least three of the six variables in the American College of Rheumatology [ACR] core set for JIA, with no more than one variable worsening...

Reconstructing Native American population history

Abstract: The peopling of the Americas has been the subject of extensive genetic, archaeological and linguistic research; however, central questions remain unresolved. One contentious issue is whether the settlement occurred by means of a single migration or multiple streams of migration from Siberia. The pattern of dispersals within the Americas is also poorly understood. To address these questions at a higher resolution than was previously possible, we assembled data from 52 Native American and 17 Siberian groups genotyped at 364,470 single nucleotide polymorphisms. Here we show that Native Americans descend from at least three streams of Asian gene flow. Most descend entirely from a single ancestral population that we call 'First American'. However, speakers of Eskimo-Aleut languages from the Arctic inherit almost half their ancestry from a second stream of Asian gene flow, and the Na-Dene-speaking Chipewyan from Canada inherit roughly one-tenth of their ancestry from a third stream. We show that the initial peopling followed a southward expansion facilitated by the coast, with sequential population splits and little gene flow after divergence, especially in South America. A major exception is in Chibchan speakers on both sides of the Panama isthmus, who have ancestry from both North and South America.

Identifying Luminous Active Galactic Nuclei in Deep Surveys: Revised IRAC Selection Criteria

Abstract: Spitzer/IRAC selection is a powerful tool for identifying luminous active galactic nuclei (AGNs). For deep IRAC data, however, the AGN selection wedges currently in use are heavily contaminated by star-forming galaxies, especially at high redshift. Using the large samples of luminous AGNs and high-redshift star-forming galaxies in COSMOS, we redefine the AGN selection criteria for use in deep IRAC surveys. The new IRAC criteria are designed to be both highly complete and reliable, and incorporate the best aspects of the current AGN selection wedges and of infrared power-law selection while excluding high-redshift star-forming galaxies selected via the BzK, distant red galaxy, Lyman-break galaxy, and submillimeter galaxy criteria. At QSO luminosities of log L_(2-10keV)(erg s^(–1)) ≥44, the new IRAC criteria recover 75% of the hard X-ray and IRAC-detected XMM-COSMOS sample, yet only 38% of the IRAC AGN candidates have X-ray counterparts, a fraction that rises to 52% in regions with Chandra exposures of 50-160 ks. X-ray stacking of the individually X-ray non-detected AGN candidates leads to a hard X-ray signal indicative of heavily obscured to mildly Compton-thick obscuration (log N H (cm^(–2)) = 23.5 ± 0.4). While IRAC selection recovers a substantial fraction of luminous unobscured and obscured AGNs, it is incomplete to low-luminosity and host-dominated AGNs.

Regulated virulence controls the ability of a pathogen to compete with the gut microbiota.

Abstract: The virulence mechanisms that allow pathogens to colonize the intestine remain unclear. Here, we show that germ-free animals are unable to eradicate Citrobacter rodentium, a model for human infections with attaching and effacing bacteria. Early in infection, virulence genes were expressed and required for pathogen growth in conventionally raised mice but not germ-free mice. Virulence gene expression was down-regulated during the late phase of infection, which led to relocation of the pathogen to the intestinal lumen where it was outcompeted by commensals. The ability of commensals to outcompete C. rodentium was determined, at least in part, by the capacity of the pathogen and commensals to grow on structurally similar carbohydrates. Thus, pathogen colonization is controlled by bacterial virulence and through competition with metabolically related commensals.

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.

Methods for mapping ecosystem service supply: a review

Abstract: Mapping key areas for ecosystem service (ES) supply is essential for the development of strategies that will ensure their future supply. Given the rapid development in this area of research, we performed a review of different approaches used to map ES, with a special focus on those that use social–ecological data. We used an analytical framework based on five criteria for analyzing and comparing the methodological approaches: the types of ES, availability of data sources, types of data sources, spatial scale, and methods used to model ES. We found that regulating services were the most commonly mapped, followed by provisioning, cultural, and supporting services. Secondary (readily available) data were used more frequently than primary data to map ES. Biophysical data (land-cover variables) and mixed sources (databases like global statistics) were the most commonly employed ones. Most studies were performed at the regional or at the national scale. The most commonly used method to model services was the de...

The Sample Analysis at Mars Investigation and Instrument Suite

Abstract: The Sample Analysis at Mars (SAM) investigation of the Mars Science Laboratory (MSL) addresses the chemical and isotopic composition of the atmosphere and volatiles extracted from solid samples. The SAM investigation is designed to contribute substantially to the mission goal of quantitatively assessing the habitability of Mars as an essential step in the search for past or present life on Mars. SAM is a 40 kg instrument suite located in the interior of MSL’s Curiosity rover. The SAM instruments are a quadrupole mass spectrometer, a tunable laser spectrometer, and a 6-column gas chromatograph all coupled through solid and gas processing systems to provide complementary information on the same samples. The SAM suite is able to measure a suite of light isotopes and to analyze volatiles directly from the atmosphere or thermally released from solid samples. In addition to measurements of simple inorganic compounds and noble gases SAM will conduct a sensitive search for organic compounds with either thermal or chemical extraction from sieved samples delivered by the sample processing system on the Curiosity rover’s robotic arm.

Arthropod diversity in a tropical forest

Abstract: Most eukaryotic organisms are arthropods. Yet, their diversity in rich terrestrial ecosystems is still unknown. Here we produce tangible estimates of the total species richness of arthropods in a tropical rainforest. Using a comprehensive range of structured protocols, we sampled the phylogenetic breadth of arthropod taxa from the soil to the forest canopy in the San Lorenzo forest, Panama. We collected 6144 arthropod species from 0.48 hectare and extrapolated total species richness to larger areas on the basis of competing models. The whole 6000-hectare forest reserve most likely sustains 25,000 arthropod species. Notably, just 1 hectare of rainforest yields >60% of the arthropod biodiversity held in the wider landscape. Models based on plant diversity fitted the accumulated species richness of both herbivore and nonherbivore taxa exceptionally well. This lends credence to global estimates of arthropod biodiversity developed from plant models.

What do we need to know about speciation

Abstract: Speciation has been a major focus of evolutionary biology research in recent years, with many important advances. However, some of the traditional organising principles of the subject area no longer provide a satisfactory framework, such as the classification of speciation mechanisms by geographical context into allopatric, parapatric and sympatry classes. Therefore, we have asked where speciation research should be directed in the coming years. Here, we present a distillation of questions about the mechanisms of speciation, the genetic basis of speciation and the relationship between speciation and diversity. Our list of topics is not exhaustive; rather we aim to promote discussion on research priorities and on the common themes that underlie disparate speciation processes.

Robust 4C-seq data analysis to screen for regulatory DNA interactions

Abstract: Regulatory DNA elements can control the expression of distant genes via physical interactions. Here we present a cost-effective methodology and computational analysis pipeline for robust characterization of the physical organization around selected promoters and other functional elements using chromosome conformation capture combined with high-throughput sequencing (4C-seq). Our approach can be multiplexed and routinely integrated with other functional genomics assays to facilitate physical characterization of gene regulation.

New insight into the history of domesticated apple: secondary contribution of the European wild apple to the genome of cultivated varieties.

Abstract: The apple is the most common and culturally important fruit crop of temperate areas. The elucidation of its origin and domestication history is therefore of great interest. The wild Central Asian species Malus sieversii has previously been identified as the main contributor to the genome of the cultivated apple (Malus domestica), on the basis of morphological, molecular, and historical evidence. The possible contribution of other wild species present along the Silk Route running from Asia to Western Europe remains a matter of debate, particularly with respect to the contribution of the European wild apple. We used microsatellite markers and an unprecedented large sampling of five Malus species throughout Eurasia (839 accessions from China to Spain) to show that multiple species have contributed to the genetic makeup of domesticated apples. The wild European crabapple M. sylvestris, in particular, was a major secondary contributor. Bidirectional gene flow between the domesticated apple and the European crabapple resulted in the current M. domestica being genetically more closely related to this species than to its Central Asian progenitor, M. sieversii. We found no evidence of a domestication bottleneck or clonal population structure in apples, despite the use of vegetative propagation by grafting. We show that the evolution of domesticated apples occurred over a long time period and involved more than one wild species. Our results support the view that self-incompatibility, a long lifespan, and cultural practices such as selection from open-pollinated seeds have facilitated introgression from wild relatives and the maintenance of genetic variation during domestication. This combination of processes may account for the diversification of several long-lived perennial crops, yielding domestication patterns different from those observed for annual species.

Database of diazotrophs in global ocean: abundance, biomass and nitrogen fixation rates

Abstract: . Marine N2 fixing microorganisms, termed diazotrophs, are a key functional group in marine pelagic ecosystems. The biological fixation of dinitrogen (N2) to bioavailable nitrogen provides an important new source of nitrogen for pelagic marine ecosystems and influences primary productivity and organic matter export to the deep ocean. As one of a series of efforts to collect biomass and rates specific to different phytoplankton functional groups, we have constructed a database on diazotrophic organisms in the global pelagic upper ocean by compiling about 12 000 direct field measurements of cyanobacterial diazotroph abundances (based on microscopic cell counts or qPCR assays targeting the nifH genes) and N2 fixation rates. Biomass conversion factors are estimated based on cell sizes to convert abundance data to diazotrophic biomass. The database is limited spatially, lacking large regions of the ocean especially in the Indian Ocean. The data are approximately log-normal distributed, and large variances exist in most sub-databases with non-zero values differing 5 to 8 orders of magnitude. Reporting the geometric mean and the range of one geometric standard error below and above the geometric mean, the pelagic N2 fixation rate in the global ocean is estimated to be 62 (52–73) Tg N yr−1 and the pelagic diazotrophic biomass in the global ocean is estimated to be 2.1 (1.4–3.1) Tg C from cell counts and to 89 (43–150) Tg C from nifH-based abundances. Reporting the arithmetic mean and one standard error instead, these three global estimates are 140 p 9.2 Tg N yr−1, 18 p 1.8 Tg C and 590 p 70 Tg C, respectively. Uncertainties related to biomass conversion factors can change the estimate of geometric mean pelagic diazotrophic biomass in the global ocean by about p70%. It was recently established that the most commonly applied method used to measure N2 fixation has underestimated the true rates. As a result, one can expect that future rate measurements will shift the mean N2 fixation rate upward and may result in significantly higher estimates for the global N2 fixation. The evolving database can nevertheless be used to study spatial and temporal distributions and variations of marine N2 fixation, to validate geochemical estimates and to parameterize and validate biogeochemical models, keeping in mind that future rate measurements may rise in the future. The database is stored in PANGAEA ( doi:10.1594/PANGAEA.774851 ).

Novel Applications of Ferrites

Abstract: The applications of ferrimagnetic oxides, or ferrites, in the last 10 years are reviewed, including thin films and nanoparticles. The general features of the three basic crystal systems and their magnetic structures are briefly discussed, followed by the most interesting applications in electronic circuits as inductors, in high-frequency systems, in power delivering devices, in electromagnetic interference suppression, and in biotechnology. As the field is considerably large, an effort has been made to include the original references discussing each particular application on a more detailed manner.

A ∼ 0.2-solar-mass protostar with a Keplerian disk in the very young L1527 IRS system

Abstract: In the earliest stage of star formation, protostars accrete mass from their surrounding envelopes through circumstellar disks; observations of the protostar L1527 IRS find a large, rotating proto-planetary disk from which the protostellar mass is measured to be 0.19 solar masses, with a protostar-to-envelope mass ratio of about 0.2. This paper reports the use of submillimetre interferometry to obtain the first detection of a large Keplerian disk around a protostar in the earliest phase of evolution, the class 0 phase. Hitherto the smallest observed protostar-to-envelope mass ratio was about 2.1. The newly discovered protostar, L1527 IRS, has a mass of approximately 0.2 solar masses and a protostar-to-envelope mass ratio of about 0.2. L1527 already has a proto-planetary disk of at least seven Jupiter masses, similar to presumed planet-forming disks, so it appears to have all the elements of a solar system in the making. In their earliest stages, protostars accrete mass from their surrounding envelopes through circumstellar disks. Until now, the smallest observed protostar-to-envelope mass ratio was about 2.1 (ref. 1). The protostar L1527 IRS is thought to be in the earliest stages of star formation2. Its envelope contains about one solar mass of material within a radius of about 0.05 parsecs (refs 3, 4), and earlier observations suggested the presence of an edge-on disk5. Here we report observations of dust continuum emission and 13CO (rotational quantum number J = 2 → 1) line emission from the disk around L1527 IRS, from which we determine a protostellar mass of 0.19 ± 0.04 solar masses and a protostar-to-envelope mass ratio of about 0.2. We conclude that most of the luminosity is generated through the accretion process, with an accretion rate of about 6.6 × 10−7 solar masses per year. If it has been accreting at that rate through much of its life, its age is approximately 300,000 years, although theory suggests larger accretion rates earlier6, so it may be younger. The presence of a rotationally supported disk is confirmed, and significantly more mass may be added to its planet-forming region as well as to the protostar itself in the future.

Common Features of Environmental and Potentially Beneficial Plant-Associated Burkholderia

Abstract: The genus Burkholderia comprises more than 60 species isolated from a wide range of niches. Although they have been shown to be diverse and ubiquitously distributed, most studies have thus far focused on the pathogenic species due to their clinical importance. However, the increasing number of recently described Burkholderia species associated with plants or with the environment has highlighted the division of the genus into two main clusters, as suggested by phylogenetical analyses. The first cluster includes human, animal, and plant pathogens, such as Burkholderia glumae, Burkholderia pseudomallei, and Burkholderia mallei, as well as the 17 defined species of the Burkholderia cepacia complex, while the other, more recently established cluster comprises more than 30 non-pathogenic species, which in most cases have been found to be associated with plants, and thus might be considered to be potentially beneficial. Several species from the latter group share characteristics that are of use when associating with plants, such as a quorum sensing system, the presence of nitrogen fixation and/or nodulation genes, and the ability to degrade aromatic compounds. This review examines the commonalities in this growing subgroup of Burkholderia species and discusses their prospective biotechnological applications.

Rerouting carbon flux to enhance photosynthetic productivity.

Abstract: The bioindustrial production of fuels, chemicals, and therapeutics typically relies upon carbohydrate inputs derived from agricultural plants, resulting in the entanglement of food and chemical commodity markets. We demonstrate the efficient production of sucrose from a cyanobacterial species, Synechococcus elongatus, heterologously expressing a symporter of protons and sucrose (cscB). cscB-expressing cyanobacteria export sucrose irreversibly to concentrations of >10 mM without culture toxicity. Moreover, sucrose-exporting cyanobacteria exhibit increased biomass production rates relative to wild-type strains, accompanied by enhanced photosystem II activity, carbon fixation, and chlorophyll content. The genetic modification of sucrose biosynthesis pathways to minimize competing glucose- or sucrose-consuming reactions can further improve sucrose production, allowing the export of sucrose at rates of up to 36.1 mg liter(-1) h illumination(-1). This rate of production exceeds that of previous reports of targeted, photobiological production from microbes. Engineered S. elongatus produces sucrose in sufficient quantities (up to ∼80% of total biomass) such that it may be a viable alternative to sugar synthesis from terrestrial plants, including sugarcane.

The Chandra COSMOS Survey. III. Optical and Infrared Identification of X-Ray Point Sources

Abstract: The Chandra COSMOS Survey (C-COSMOS) is a large, 1.8 Ms, Chandra program that has imaged the central 0.9 deg^2 of the COSMOS field down to limiting depths of 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. In this paper we report the i, K, and 3.6 μm identifications of the 1761 X-ray point sources. We use the likelihood ratio technique to derive the association of optical/infrared counterparts for 97% of the X-ray sources. For most of the remaining 3%, the presence of multiple counterparts or the faintness of the possible counterpart prevented a unique association. For only 10 X-ray sources we were not able to associate a counterpart, mostly due to the presence of a very bright field source close by. Only two sources are truly empty fields. The full catalog, including spectroscopic and photometric redshifts and classification described here in detail, is available online. Making use of the large number of X-ray sources, we update the "classic locus" of active galactic nuclei (AGNs) defined 20 years ago in soft X-ray surveys and define a new locus containing 90% of the AGNs in the survey with full-band luminosity >10^(42) erg s^(–1). We present the linear fit between the total i-band magnitude and the X-ray flux in the soft and hard bands, drawn over two orders of magnitude in X-ray flux, obtained using the combined C-COSMOS and XMM-COSMOS samples. We focus on the X-ray to optical flux ratio (X/O) and we test its known correlation with redshift and luminosity, and a recently introduced anti-correlation with the concentration index (C). We find a strong anti-correlation (though the dispersion is of the order of 0.5 dex) between X/O computed in the hard band and C and that 90% of the obscured AGNs in the sample with morphological information live in galaxies with regular morphology (bulgy and disky/spiral), suggesting that secular processes govern a significant fraction of the black hole growth at X-ray luminosities of 10^(43)-10^(44.5) erg s^(–1). We also investigate the degree of obscuration of the sample using the hardness ratio, and we compare the X-ray color with the near-infrared to optical color.

Decline of monarch butterflies overwintering in Mexico: is the migratory phenomenon at risk?

Abstract: During the 2009-2010 overwintering season and following a 15-year downward trend, the total area in Mexico occupied by the eastern North American population of overwintering monarch butterflies reached an all-time low. Despite an increase, it remained low in 2010-2011. 2. Although the data set is small, the decline in abundance is statistically signifi- cant using both linear and exponential regression models. 3. Three factors appear to have contributed to reduce monarch abundance: degra- dation of the forest in the overwintering areas; the loss of breeding habitat in the Uni- ted States due to the expansion of GM herbicide-resistant crops, with consequent loss of milkweed host plants, as well as continued land development; and severe weather. 4. This decline calls into question the long-term survival of the monarchs' migra- tory phenomenon. Resumen. 1. Durante la temporada invernal 2009-2010, y siguiendo una tenden- cia a la baja de 15 anos, la superficie total ocupada por mariposas monarca en Mexico, provenientes del este America del Norte, llegoa su punto mas bajo. A pesar de su incremento, dicha superficie siguiosiendo baja en 2010-2011. 2. Aunque que el conjunto de datos disponibles es aun pequeno, esta disminucion de la abundancia de mariposas es estadisticamente significativa, tanto si se usan modelos de regresion lineales como exponenciales. 3. Hay tres factores que parecen haber contribuido con esta tendencia de reduc- ciond el numero de mariposas: la degradacion de bosque en las areas de invernacion en Mexico; la perdida de habitat de reproduccion en los Estados Unidos, debido a la expansiond e cultivos geneticamente modificados resistentes a herbicidas, con la consiguiente perdida de las plantas hospederas de algodoncillo, y por continuos cambios en el uso del suelo no favorables para ellas; y, las recientes condiciones cli- maticas severas. 4. Esta disminucion hace que nos cuestionemos sobre la posibilidad de superviven- cia a largo plazo del fenomeno migratorio de las mariposas monarca.

Development of a selective chemical etch to improve the conversion efficiency of Zn-rich Cu2ZnSnS4 solar cells.

Abstract: Improvement of the efficiency of Cu2ZnSnS4 (CZTS)-based solar cells requires the development of specific procedures to remove or avoid the formation of detrimental secondary phases. The presence of these phases is favored by the Zn-rich and Cu-poor conditions that are required to obtain device-grade layers. We have developed a selective chemical etching process based on the use of hydrochloric acid solutions to remove Zn-rich secondary phases from the CZTS film surface, which are partly responsible for the deterioration of the series resistance of the cells and, as a consequence, the conversion efficiency. Using this approach, we have obtained CZTS-based devices with 5.2% efficiency, which is nearly twice that of the devices we have prepared without this etching process.