Showing papers by "National Autonomous University of Mexico published in 2000"

Global biodiversity scenarios for the year 2100.

Abstract: Scenarios of changes in biodiversity for the year 2100 can now be developed based on scenarios of changes in atmospheric carbon dioxide, climate, vegetation, and land use and the known sensitivity of biodiversity to these changes. This study identified a ranking of the importance of drivers of change, a ranking of the biomes with respect to expected changes, and the major sources of uncertainties. For terrestrial ecosystems, land-use change probably will have the largest effect, followed by climate change, nitrogen deposition, biotic exchange, and elevated carbon dioxide concentration. For freshwater ecosystems, biotic exchange is much more important. Mediterranean climate and grassland ecosystems likely will experience the greatest proportional change in biodiversity because of the substantial influence of all drivers of biodiversity change. Northern temperate ecosystems are estimated to experience the least biodiversity change because major land-use change has already occurred. Plausible changes in biodiversity in other biomes depend on interactions among the causes of biodiversity change. These interactions represent one of the largest uncertainties in projections of future biodiversity change.

Single cell gel/comet assay: guidelines for in vitro and in vivo genetic toxicology testing.

Abstract: Atthe International Workshop on Genotoxicity Test Procedures (IWGTP) held in Washington, DC, March 25-26, 1999, an expert panel met to develop guidelines for the use of the single-cell gel (SCG)/Comet assay in genetic toxicology. The expert panel reached a consensus that the optimal version of the Comet assay for identifying agents with genotoxic activity was the alkaline (pH > 13) version of the assay developed by Singh et al. [1988]. The pH > 13 version is capable of detecting DNA single-strand breaks (SSB), alkali-labile sites (ALS), DNA-DNA/DNA-protein cross-linking, and SSB associated with incomplete excision repair sites. Relative to other genotoxicity tests, the advantages of the SCG assay include its demonstrated sensitivity for detecting low levels of DNA damage, the requirement for small numbers of cells per sample, its flexibility, its low costs, its ease of application, and the short time needed to complete a study. The expert panel decided that no single version of the alkaline (pH > 13) Comet assay was clearly superior. However, critical technical steps within the assay were discussed and guidelines developed for preparing slides with agarose gels, lysing cells to liberate DNA, exposing the liberated DNA to alkali to produce single-stranded DNA and to express ALS as SSB, electrophoresing the DNA using pH > 13 alkaline conditions, alkali neutralization, DNA staining, comet visualization, and data collection. Based on the current state of knowledge, the expert panel developed guidelines for conducting in vitro or in vivo Comet assays. The goal of the expert panel was to identify minimal standards for obtaining reproducible and reliable Comet data deemed suitable for regulatory submission. The expert panel used the current Organization for Economic Co-operation and Development (OECD) guidelines for in vitro and in vivo genetic toxicological studies as guides during the development of the corresponding in vitro and in vivo SCG assay guidelines. Guideline topics considered included initial considerations, principles of the test method, description of the test method, procedure, results, data analysis and reporting. Special consideration was given by the expert panel to the potential adverse effect of DNA degradation associated with cytotoxicity on the interpretation of Comet assay results. The expert panel also discussed related SCG methodologies that might be useful in the interpretation of positive Comet data. The related methodologies discussed included: (1) the use of different pH conditions during electrophoreses to discriminate between DNA strand breaks and ALS; (2) the use of repair enzymes or antibodies to detect specific classes of DNA damage; (3) the use of a neutral diffusion assay to identify apoptotic/necrotic cells; and (4) the use of the acellular SCG assay to evaluate the ability of a test substance to interact directly with DNA. The alkaline (pH > 13) Comet assay guidelines developed by the expert panel represent a work in progress. Additional information is needed before the assay can be critically evaluated for its utility in genetic toxicology. The information needed includes comprehensive data on the different sources of variability (e.g., cell to cell, gel to gel, run to run, culture to culture, animal to animal, experiment to experiment) intrinsic to the alkaline (pH > 3) SCG assay, the generation of a large database based on in vitro and in vivo testing using these guidelines, and the results of appropriately designed multilaboratory international validation studies.

Comparison of Upper Gastrointestinal Toxicity of Rofecoxib and Naproxen in Patients with Rheumatoid Arthritis

Abstract: Background Each year, clinical upper gastrointestinal events occur in 2 to 4 percent of patients who are taking nonselective nonsteroidal antiinflammatory drugs (NSAIDs). We assessed whether rofecoxib, a selective inhibitor of cyclooxygenase-2, would be associated with a lower incidence of clinically important upper gastrointestinal events than is the nonselective NSAID naproxen among patients with rheumatoid arthritis. Methods We randomly assigned 8076 patients who were at least 50 years of age (or at least 40 years of age and receiving long-term glucocorticoid therapy) and who had rheumatoid arthritis to receive either 50 mg of rofecoxib daily or 500 mg of naproxen twice daily. The primary end point was confirmed clinical upper gastrointestinal events (gastroduodenal perforation or obstruction, upper gastrointestinal bleeding, and symptomatic gastroduodenal ulcers). Results Rofecoxib and naproxen had similar efficacy against rheumatoid arthritis. During a median follow-up of 9.0 months, 2.1 confirmed ga...

The Stellar Population Histories of Early-Type Galaxies. II. Controlling Parameters of the Stellar Populations

Abstract: This paper analyzes single stellar population (SSP)–equivalent parameters for 50 local elliptical galaxies as a function of their structural parameters. The galaxy sample is drawn from the high-quality spectroscopic surveys of Gonzalez (1993) and Kuntschner (1998). The basic data are central values of SSP-equivalent ages, t, metallicities, [Z/H], and enhancement ratios, [E/Fe], derived in Paper I, together with global structural parameters including velocity dispersions, radii, surface brightnesses, masses, and luminosities. The galaxies fill a two-dimensional plane in the four-dimensional space of [Z/H], log t, log σ, and [E/Fe]. SSP age, t, and velocity dispersion, σ, can be taken as the two independent parameters that specify a galaxy's location in this hyperplane. The hyperplane can be decomposed into two subrelations: (1) a Z-plane, in which [Z/H] is a linear function of log σ and log t and (2) a relation between [E/Fe] and σ in which [E/Fe] is larger in high-σ galaxies. Velocity dispersion is the only structural parameter that is found to modulate the stellar populations; adding other structural variables such as Ie or re does not predict [Z/H] or [E/Fe] more accurately. Cluster and field ellipticals follow the same hyperplane, but their (σ,t) distributions within it differ. Most Fornax and Virgo cluster galaxies are old, with a only a small sprinkling of galaxies to younger ages. The field ellipticals span a larger range in SSP age, with a tendency for lower σ galaxies to be younger. The present sample thus suggests that the distribution of local ellipticals in the (σ,t) plane may depend on environment. Since the (σ,t) distribution affects all two-dimensional projections involving SSP parameters, many of the familiar scaling laws attributed to ellipticals may also depend on environment. Some evidence for this is seen in the current sample. For example, only Fornax ellipticals show the classic mass-metallicity relation, whereas other subsamples do not. The tight Mg-σ relations of these ellipticals can be understood as two-dimensional projections of the metallicity hyperplane showing it edge-on. At fixed σ, young age tends to be offset by high [Z/H], preserving Mg nearly constant. The tightness of the Mg-σ relations does not necessarily imply a narrow range of ages at fixed σ. Although SSP parameters are heavily weighted by young stars, modeling them still places tight constraints on the total star formation history of elliptical galaxies. The relation between [E/Fe] and σ is consistent with a higher effective yield of Type II SNe elements at higher σ. This might occur if the IMF is enhanced in massive stars at high σ, or if more SNe II–enriched gas is retained by deeper galactic potential wells. Either way, modulating Type II yields versus σ seems to fit the data better than modulating Type Ia yields. The Z-plane is harder to explain and may be a powerful clue to star formation in elliptical galaxies if it proves to be general. Present data favor a frosting model in which low apparent SSP ages are produced by adding a small frosting of younger stars to an older base population (assuming no change in σ). If the frosting abundances are close to or slightly greater than the base population, simple two-component models run along lines of constant σ in the Z-plane, as required. This favors star formation from well-mixed pre-enriched gas rather than unmixed low-metallicity gas from an accreted object.

The Stellar Population Histories of Local Early-Type Galaxies. I. Population Parameters

Abstract: This paper commences a series of investigations into the stellar populations of local elliptical galaxies as determined from their integrated spectra. The goal of the series is to determine the star formation and chemical evolution histories of present-day elliptical galaxies. The primary galaxy sample analyzed is that of Gonzalez, which consists of 39 elliptical galaxies drawn primarily from the local field and nearby groups, plus the bulge of Messier 31. Single-burst stellar population (SSP)–equivalent ages, metallicities, and abundance ratios are derived from Hβ, Mg b, and Fe line strengths using an extension of the Worthey models that incorporates nonsolar line-strength "response functions" by Tripicco & Bell. These functions account for changes in the Lick/IDS indices caused by nonsolar abundance ratios, allowing us to correct the Worthey models for the enhancements of Mg and other α-like elements relative to the Fe-peak elements. SSP-equivalent ages of the Gonzalez elliptical galaxies are found to vary widely, 1.5 Gyr t 18 Gyr, while metallicities [Z/H] and enhancement ratios [E/Fe] are strongly peaked around [Z/H] = +0.26 and [E/Fe] = +0.20 (in an aperture of radius re/8). The enhancement ratios [E/Fe] are milder than previous estimates because of the application of nonsolar abundance corrections to both Mg b and Fe for the first time. While [E/Fe] is usually greater than zero, it is not the "E" elements that are actually enhanced but rather the Fe-peak elements that are depressed; this serves not only to weaken Fe but also to strengthen Mg b, accounting for the overall generally mild enhancements. Based on index strengths from the Lick/IDS galaxy library (Trager et al.), C is not depressed with Fe but rather seems to be on a par with other elements such as Mg in the E group. Gradients in stellar populations within galaxies are found to be mild, with SSP-equivalent age increasing by 25%, metallicity decreasing by [Z/H] = 0.20 dex, and [E/Fe] remaining nearly constant out to an aperture of radius re/2 for nearly all systems. Our ages have an overall zero-point uncertainty of at least ~25% because of uncertainties in the stellar evolution prescription, the oxygen abundance, the effect of [E/Fe] ≠ 0 on the isochrones, and other unknowns. However, the relative age rankings of stellar populations should be largely unaffected by these errors. In particular, the large spread in ages appears to be real and cannot be explained by contamination of Hβ by blue stragglers or hot horizontal-branch stars, or by fill-in of Hβ by emission. Correlations between these derived SSP-equivalent parameters and other galaxy observables will be discussed in future papers.

Pseudomonas aeruginosa rhamnolipids: biosynthesis and potential applications

Abstract: Pseudomonas aeruginosa produces and secretes rhamnose-containing glycolipid biosurfactants called rhamnolipids. This review describes rhamnolipid biosynthesis and potential industrial and environmental applications of rhamnolipids. Rhamnolipid production is dependent on central metabolic pathways, such as fatty acid synthesis and dTDP-activated sugars, as well as on enzymes participating in the production of the exopolysaccharide alginate. Synthesis of these surfactants is regulated by a very complex genetic regulatory system that also controls different P. aeruginosa virulence-associated traits. Rhamnolipids have several potential industrial and environmental applications including the production of fine chemicals, the characterization of surfaces and surface coatings, as additives for environmental remediation, and as a biological control agent. Realization of this wide variety of applications requires economical commercial-scale production of rhamnolipids.

D2 Dopamine Receptors in Striatal Medium Spiny Neurons Reduce L-Type Ca2+ Currents and Excitability via a Novel PLCβ1–IP3–Calcineurin-Signaling Cascade

Abstract: In spite of the recognition that striatal D(2) receptors are critical determinants in a variety of psychomotor disorders, the cellular mechanisms by which these receptors shape neuronal activity have remained a mystery. The studies presented here reveal that D(2) receptor stimulation in enkephalin-expressing medium spiny neurons suppresses transmembrane Ca(2+) currents through L-type Ca(2+) channels, resulting in diminished excitability. This modulation is mediated by G(beta)(gamma) activation of phospholipase C, mobilization of intracellular Ca(2+) stores, and activation of the calcium-dependent phosphatase calcineurin. In addition to providing a unifying mechanism to explain the apparently divergent effects of D(2) receptors in striatal medium spiny neurons, this novel signaling linkage provides a foundation for understanding how this pivotal receptor shapes striatal excitability and gene expression.

The Stellar Population Histories of Local Early-Type Galaxies. I. Population Parameters

Abstract: We present single stellar population (SSP) equivalent ages, metallicities, and abundance ratios for local elliptical galaxies derived from Hbeta, Mgb, and absorption line strengths. We use an extension of the Worthey (1994) stellar population models that incorporates non-solar line-strength "response functions" by Tripicco & Bell (1995), allowing us to correct the models for the enhancements of Mg and other alpha-like elements relative to the Fe-peak elements. SSP-equivalent ages of local ellipticals from Gonzalez (1993) are found to vary widely, 1.5 =+0.26 and =+0.20 (in an aperture of radius Re/8). The enhancement ratios are milder than previous estimates, owing to the application of non-solar abundance corrections to both Mgb and for the first time. Gradients in stellar populations within galaxies are found to be mild, with SSP-equivalent age decreasing by 25%, metallicity decreasing by =0.20 dex, and [E/Fe] remaining nearly constant out to an aperture of radius Re/2 for nearly all systems. Our ages have an overall zeropoint uncertainty of at least 25% due to uncertainties in the stellar evolution prescription, the oxygen abundance, the effect of non-solar abundances on the isochrones, and other unknowns. However, the relative age rankings of stellar populations should be largely unaffected by these errors. In particular, the large spread in ages appears to be real and cannot be explained by contamination of Hbeta by blue stragglers or hot horizontal branch stars, or by fill-in of Hbeta by emission. Correlations between these derived SSP-equivalent parameters and other galaxy observables will be discussed in future papers. (Abridged)

Analysis of Arabidopsis glucose insensitive mutants, gin5 and gin6, reveals a central role of the plant hormone ABA in the regulation of plant vegetative development by sugar

Abstract: Sugars have signaling roles in a wide variety of developmental processes in plants. To elucidate the regulatory components that constitute the glucose signaling network governing plant growth and development, we have isolated and characterized two Arabidopsis glucose insensitive mutants, gin5 and gin6, based on a glucose-induced developmental arrest during early seedling morphogenesis. The T-DNA-tagged gin6 mutant abrogates the glucose-induced expression of a putative transcription factor, ABI4, previously shown to be involved in seed-specific abscisic acid (ABA) responses. Thus, ABI4 might be a regulator involved in both glucose- and seed-specific ABA signaling. The characterization of the gin5 mutant, on the other hand, reveals that glucose-specific accumulation of ABA is essential for hexokinase-mediated glucose responses. Consistent with this result, we show that three ABA-deficient mutants (aba1-1, aba2-1, and aba3-2) are also glucose insensitive. Exogenous ABA can restore normal glucose responses in gin5 and aba mutants but not in gin6 plants. Surprisingly, only abi4 and abi5-1 but not other ABA-insensitive signaling mutants (abi1-1, abi2-1, and abi3-1) exhibit glucose insensitivity, indicating the involvement of a distinct ABA signaling pathway in glucose responses. These results provide the first direct evidence to support a novel and central role of ABA in plant glucose responses mediated through glucose regulation of both ABA levels by GIN5 and ABA signaling by GIN6/ABI4.

Art Gallery and Illumination Problems

Abstract: In 1973, Victor Klee posed the following question: How many guards are necessary, and how many are sufficient to patrol the paintings and works of art in an art gallery with n walls? This wonderfully naive question of combinatorial geometry has, since its formulation, stimulated a plethora of papers, surveys and a book, most of them written in the last fifteen years. The first result in this area, due to V. Chvatal, asserts that n 3 guards are occasionally necessary and always sufficient to guard an art gallery represented by a simple polygon with n vertices. Since ChvataFs result, numerous variations on the art gallery problem have been studied, including mobile guards, guards with limited visibility or mobility, illumination of families of convex sets on the plane, guarding of rectilinear polygons, and others. In this paper, we survey most of these results.

Bat Diversity and Abundance as Indicators of Disturbance in Neotropical Rainforests

Abstract: Evaluating the degree of disturbance of any region to determine its relative importance for conservation purposes requires procedures that are relatively inexpensive and that yield accurate results fast. Because bats are abundant, diverse, and easy to sample, especially in the Neotropical rainforest, they fulfill several of the requirements of indicator species as identified in the literature. For 10 months we sampled bat communities in the Selva Lacandona in Chiapas, Mexico, at 15 sites representing five habitats. We also measured 10 variables representing vegetation structure and diversity at each site. With fuzzy-set techniques we produced a gradient classification of disturbance for the 15 sites based on the vegetation data. We explored the relationship between vegetation conditions, described as the membership degrees in the construct “fuzzy forest set” (the complementary fuzzy set of “disturbance”), and four bat community variables. Bat species richness, number of rare bat species, and the bat diversity index were positively correlated with the vegetation scores, and relative abundance of the most abundant bat species was negatively correlated with vegetation scores. A high number of phyllostomine species in a community is a good indicator of low levels of disturbance. Although a single indicator group will probably not be sufficient for decision-making processes in conservation, evaluating bat populations may be a good first step in assessing an area's conservation value, especially in rainforest regions.

Quantum gravity corrections to neutrino propagation

Abstract: Massive spin-1/2 fields are studied in the framework of loop quantum gravity by considering a state approximating, at a length scale L much greater than Planck length lP = 1.2 × 10 33 cm, a spin-1/2 field in flat spacetime. The discrete structure of spacetime at lP yields corrections to the field propagation at scale L. Next, Neutrino Bursts (¯ p � 10 5 GeV) accompaning Gamma Ray Bursts that have travelled cosmological distances, L � 10 10 l.y., are considered. The dominant correction is helicity independent and leads to a time delay w.r.t. the speed of light, c, of order (¯ p lP)L/c � 10 4 s. To next order in ¯ lP the correction has the form of the Gambini and Pullin effect for photons. Its contribution to time delay is comparable to that caused by the mass term. Finally, a dependence L 1 os / ¯ p 2 lP is found for a two-flavour neutrino oscillation length.

Structure and electronic properties of MoS2 nanotubes

Abstract: Structural and electronic properties as well as the stability of MoS2 nanotubes are studied using the density-functional-based tight-binding method. It is found that MoS2 zigzag ( n,0) nanotubes exhibit a narrow direct band gap and MoS2 armchair ( n,n) possess a nonzero moderate direct gap. Interestingly, the ( n,n) tubes show a small indirect gap similar to the direct gap of ( n,0) nanotubes. Simulated electron diffraction patterns confirm the existence of armchair and zigzag disulphide nanotubes. The structure of the MoS2 nanotube tips is explained by introducing topological defects which produce positive and negative curvature.

New metallic allotropes of planar and tubular carbon

Abstract: We propose a new family of layered sp(2)-like carbon crystals, incorporating five-, six-, and seven-membered rings in 2D Bravais lattices. These periodic sheets can be rolled so as to generate nanotubes of different diameter and chirality. We demonstrate that these sheets and tubes are metastable and more favorable than C-60, and it is also shown that their mechanical properties are similar to those of graphene. Density of states calculations of all structures revealed an intrinsic metallic behavior, independent of orientation, tube diameter, and chirality.

Coalescence of Single-Walled Carbon Nanotubes

Abstract: The coalescence of single-walled nanotubes is studied in situ under electron irradiation at high temperature in a transmission electron microscope. The merging process is investigated at the atomic level, using tight-binding molecular dynamics and Monte Carlo simulations. Vacancies induce coalescence via a zipper-like mechanism, imposing a continuous reorganization of atoms on individual tube lattices along adjacent tubes. Other topological defects induce the polymerization of tubes. Coalescence seems to be restricted to tubes with the same chirality, explaining the low frequency of occurrence of this event.

Impact of fishing on size composition and diversity of demersal fish communities

Abstract: By analysing data sets from different world regions we add evidence to documented changes in demersal fish community structure that may be related to fishing. Changes are analysed by community properties that might be expected to capture relevant overall changes – size spectra slopes and intercepts, Shannon-Wiener diversity, and dominance. Cross-system differences in the shape of the integrated community size spectra appear to be related to ecosystem productivity. The slope of size spectra appears to respond in a consistent way to changes in exploitation levels. In most areas studied, but particularly in high-latitude regions, we observe a decreasing trend in the slope, reflecting changes in size composition toward a relative decline in larger fish. The results from tropical regions are less conclusive, partly owing to the difficulty in obtaining consistent data series, but probably also because the generally higher growth rates of the constituent species make the slope less sensitive to changes in fishing. No evidence was found of any decline in species richness, while changes in diversity (richness and evenness) were caused either by changes in patterns of dominance or by changes in the number of species identified resulting from improved survey protocols.

TIMP-1,-2,-3, and-4 in idiopathic pulmonary fibrosis. A prevailing nondegradative lung microenvironment?

Abstract: Fibroblast proliferation and extracellular matrix accumulation characterize idiopathic pulmonary fibrosis (IPF). We evaluated the presence of tissue inhibitor of metalloproteinase (TIMP)-1, -2, -3, and -4; collagenase-1, -2, and -3; gelatinases A and B; and membrane type 1 matrix metalloproteinase (MMP) in 12 IPF and 6 control lungs. TIMP-1 was found in interstitial macrophages and TIMP-2 in fibroblast foci. TIMP-3 revealed an intense staining mainly decorating the elastic lamina in vessels. TIMP-4 was expressed in IPF lungs by epithelial and plasma cells. TIMP-2 colocalized with Ki67 in fibroblasts, whereas TIMP-3 colocalized with p27 in inflammatory and epithelial cells. Collagenase-1 was localized in macrophages and alveolar epithelial cells, collagenase-2 was localized in a few neutrophils, and collagenase-3 was not detected. MMP-9 was found in neutrophils and subepithelial myofibroblasts. Myofibroblast expression of MMP-9 was corroborated in vitro by RT-PCR. MMP-2 was noticed in myofibroblasts, some of them close to areas of basement membrane disruption, and membrane type 1 MMP was noticed in interstitial macrophages. These findings suggest that in IPF there is higher expression of TIMPs compared with collagenases, supporting the hypothesis that a nondegrading fibrillar collagen microenvironment is prevailing.

Substructure and Halo Density Profiles in a Warm Dark Matter Cosmology

Abstract: We performed a series of high-resolution collisionless N-body simulations designed to study the substructure of Milky Way-size galactic halos (host halos) and the density profiles of halos in a warm dark matter (WDM) scenario with a nonvanishing cosmological constant. The virial masses of the host halos range from 3.5 × 1012 to 1.7 × 1012 h-1 M☉, and they have more than 105 particles each. A key feature of the WDM power spectrum is the free-streaming length Rf,WDM, which fixes an additional parameter for the model of structure formation. We analyze the substructure of host halos using three Rf,WDM values: 0.2, 0.1, and 0.05 Mpc, and compare results to the predictions of the cold dark matter (CDM) model. We find that guest halos (satellites) do form in the WDM scenario, but are more easily destroyed by dynamical friction and tidal disruption than their counterparts in a CDM model. The small number of guest halos that we find in the WDM models with respect to the CDM one is the result of a lower guest halo accretion and a higher satellite destruction rate. These two phenomena operate almost with the same intensity in delivering a reduced number of guest halos at z = 0. For the model with Rf,WDM = 0.1 Mpc, the number of accreted small halos is a factor of 2.5 below that of the CDM model, while the fraction of destroyed satellites is almost twice as large as that of the CDM model. The larger the Rf,WDM value, the greater the size of these two effects and the smaller the abundance of satellites. Under the assumption that each guest halo hosts a luminous galaxy, we find that the observed circular velocity function of satellites around the Milky Way and Andromeda is well described by the Rf,WDM = 0.1 Mpc WDM model. In the Rf,WDM = 0.1-0.2 Mpc models, the surviving guest halos at z = 0, whose masses are in the range Mh ≈ 109-1011 h-1 M☉, have an average concentration parameter c1/5 = r(Mh)/r(Mh/5), which is approximately twice as small as that of the corresponding CDM guest halos. This difference very likely produces the higher satellite destruction rate found in the WDM models. The density profile of host halos is well described by the Navarro, Frenk, & White (NFW) fit, whereas guest halos show a wide variety of density profiles. A tendency to form shallow cores is not evident; the profiles, however, are limited by a poor mass resolution in the innermost regions where shallow cores could be expected.

Operons in Escherichia coli: genomic analyses and predictions.

Abstract: The rich knowledge of operon organization in Escherichia coli, together with the completed chromosomal sequence of this bacterium, enabled us to perform an analysis of distances between genes and of functional relationships of adjacent genes in the same operon, as opposed to adjacent genes in different transcription units. We measured and demonstrated the expected tendencies of genes within operons to have much shorter intergenic distances than genes at the borders of transcription units. A clear peak at short distances between genes in the same operon contrasts with a flat frequency distribution of genes at the borders of transcription units. Also, genes in the same operon tend to have the same physiological functional class. The results of these analyses were used to implement a method to predict the genomic organization of genes into transcription units. The method has a maximum accuracy of 88% correct identification of pairs of adjacent genes to be in an operon, or at the borders of transcription units, and correctly identifies around 75% of the known transcription units when used to predict the transcription unit organization of the E. coli genome. Based on the frequency distance distributions, we estimated a total of 630 to 700 operons in E. coli. This step opens the possibility of predicting operon organization in other bacteria whose genome sequences have been finished.

MADS-box gene evolution beyond flowers: expression in pollen, endosperm, guard cells, roots and trichomes

Abstract: MADS-box genes encode transcriptional regulators involved in diverse aspects of plant development. Here we describe the cloning and mRNA spatio-temporal expression patterns of five new MADS-box genes from Arabidopsis: AGL16, AGL18, AGL19, AGL27 and AGL31. These genes will probably become important molecular tools for both evolutionary and functional analyses of vegetative structures. We mapped our data and previous expression patterns onto a new MADS-box phylogeny. These analyses suggest that the evolution of the MADS-box family has involved a rapid and simultaneous functional diversification in vegetative as well as reproductive structures. The hypothetical ancestral genes had broader expression patterns than more derived ones, which have been co-opted for putative specialized functions as suggested by their expression patterns. AGL27 and AGL31, which are closely related to the recently described flowering-time gene FLC (previously AGL25), are expressed in most plant tissues. AGL19 is specifically expressed in the outer layers of the root meristem (lateral root cap and epidermis) and in the central cylinder cells of mature roots. AGL18, which is most similar in sequence to the embryo-expressed AGL15 gene, is expressed in the endosperm and in developing male and female gametophytes, suggesting a role for AGL18 that is distinct from previously characterized MADS-box genes. Finally, AGL16 RNA accumulates in leaf guard cells and trichomes. Our new phylogeny reveals seven new monophyletic clades of MADS-box sequences not specific to flowers, suggesting that complex regulatory networks involving several MADS-box genes, similar to those that control flower development, underlie development of vegetative structures.

Eigenvector 1: An Optimal Correlation Space for Active Galactic Nuclei.

Abstract: We identify a correlation space involving optical and UV emission-line parameters as well as the soft X-ray spectral index that provides optimal discrimination between all principal classes of active galactic nuclei (AGNs). Most of the sources in our three high-quality data samples show a strong intercorrelation with narrow-line Seyfert 1 (NLSy1) galaxies and steep-spectrum radio galaxies occupying opposite extrema in the space. NLSy1 sources show a clear continuity with broader line sources, indicating that they are not a disjoint class of AGN as is sometimes suggested. We interpret the principal intercorrelation in the parameter space as being driven by the AGN luminosity-to-black hole mass ratio (L/M is proportional to the Eddington ratio). Source orientation no doubt also plays an important role, but it is not yet clear whether FWHM Hβ or C IV λ1549 line shift is the better indicator. We tentatively identify two radio-quiet populations: an almost pure radio-quiet population A, with FWHM ≤ 4000, and population B, which occupies the same parameter domain as the flat-spectrum radio-loud sources. A possible interpretation sees population A/NLSy1 as lower mass/high accretion rate sources and population B/radio-loud sources as the opposite.

Periodicity and Firing Rate As Candidate Neural Codes for the Frequency of Vibrotactile Stimuli

Abstract: The flutter sensation is felt when mechanical vibrations between 5 and 50 Hz are applied to the skin. Neurons with rapidly adapting properties in the somatosensory system of primates are driven very effectively by periodic flutter stimuli; their evoked spike trains typically have a periodic structure with highly regular time differences between spikes. A long-standing conjecture is that, such periodic structure may underlie a subject's capacity to discriminate the frequencies of periodic vibrotactile stimuli and that, in primary somatosensory areas, stimulus frequency is encoded by the regular time intervals between evoked spikes, not by the mean rate at which these are fired. We examined this hypothesis by analyzing extracellular recordings from primary (S1) and secondary (S2) somatosensory cortices of awake monkeys performing a frequency discrimination task. We quantified stimulus-driven modulations in firing rate and in spike train periodicity, seeking to determine their relevance for frequency discrimination. We found that periodicity was extremely high in S1 but almost absent in S2. We also found that periodicity was enhanced when the stimuli were relevant for behavior. However, periodicity did not covary with psychophysical performance in single trials. On the other hand, rate modulations were similar in both areas, and with periodic and aperiodic stimuli, they were enhanced when stimuli were important for behavior, and were significantly correlated with psychophysical performance in single trials. Thus, the exquisitely timed, stimulus-driven spikes of primary somatosensory neurons may or may not contribute to the neural code for flutter frequency, but firing rate seems to be an important component of it.

The repertoire of DNA-binding transcriptional regulators in Escherichia coli K-12

Abstract: Using a combination of several approaches we estimated and characterized a total of 314 regulatory DNA-binding proteins in Escherichia coli, which might represent its minimal set of transcription factors. The collection is comprised of 35% activators, 43% repressors and 22% dual regulators. Within many regulatory protein families, the members are homogeneous in their regulatory roles, physiology of regulated genes, regulatory function, length and genome position, showing that these families have evolved homogeneously in prokaryotes, particularly in E.coli. This work describes a full characterization of the repertoire of regulatory interactions in a whole living cell. This repertoire should contribute to the interpretation of global gene expression profiles in both prokaryotes and eukaryotes.