Selection for Unequal Densities of σ(70) Promoter-Like Signals in Different Regions of Large Bacterial Genomes

The evolutionary processes operating in the DNA regions that participate in the regulation of gene expression are poorly understood. In Escherichia coli, we have established a sequence pattern that distinguishes regulatory from nonregulatory regions. The density of promoter-like sequences, that could be recognizable by RNA polymerase and may function as potential promoters, is high within regulatory regions, in contrast to coding regions and regions located between convergently transcribed genes. Moreover, functional promoter sites identified experimentally are often found in the subregions of highest density of promoter-like signals, even when individual sites with higher binding affinity for RNA polymerase exist elsewhere within the regulatory region. In order to see the generality of this pattern, we have analyzed 43 additional genomes belonging to most established bacterial phyla. Differential densities between regulatory and nonregulatory regions are detectable in most of the analyzed genomes, with the exception of those that have evolved toward extreme genome reduction. Thus, presence of this pattern follows that of genes and other genomic features that require weak selection to be effective in order to persist. On this basis, we suggest that the loss of differential densities in the reduced genomes of host-restricted pathogens and symbionts is an outcome of the process of genome degradation resulting from the decreased efficiency of purifying selection in highly structured small populations. This implies that the differential distribution of promoter-like signals between regulatory and nonregulatory regions detected in large bacterial genomes confers a significant, although small, fitness advantage. This study paves the way for further identification of the specific types of selective constraints that affect the organization of regulatory regions and the overall distribution of promoter-like signals through more detailed comparative analyses among closely related bacterial genomes

Relationships that Heal: Beyond the Patient-Healer Dyad in Mayan Therapy

Biomedicine fosters particular styles of interaction and behaviors, with the therapeutic relationship seen as occurring between a doctor and patient. In contrast, where alternative modalities of healing are practiced, relationships go beyond a dyadic interaction and include wider social networks. In this article, we propose the existence of a ‘therapeutic unit’ in Maya healing practices in Guatemala that binds healer, wellness seeker, family, and community members, along with the spiritual and natural realms, into a coherent system requiring all of these elements to achieve success. Drawing on interviews with 67 Maya healers, we describe healers’ understanding of raxnaq’il nuk’aslemal (well-being), and show how these interactions activate wider networks that play crucial roles during treatments. We highlight how holism is expressed in relationships typical of indigenous healing systems, and how an appreciation of this is important for developing culturally appropriate health care provision systems

Arquitectura y paleoambientes de los depósitos fluviales gravosos de la Formación Las Cumbres (Neógeno), en Villa Mervil, La Rioja, Argentina

Un corte de la ruta nacional 60, 500 m al oeste de Villa Mervil (Sierras de Mazán, La Rioja) muestra el contacto entre las Formaciones Salicas y Las Cumbres, con excelente exposición de la arquitectura fluvial que pudo ser extendida en tres dimensiones y por más de 700 m en sentido N-S, a ambos lados de la ruta. El corte muestra el contacto entre las Formaciones Salicas (Plioceno) y Las Cumbres (Plio-Pleistoceno). Pueden ser reconocidos cinco estadios de sedimentación: A-S, el inferior, constituido por areniscas friables fluviales y eólicas; F, de capas tabulares consistentes en limos de barreal y areniscas de planicie de distributarios (escorrenteras y barras efímeras) con abundantes calcretos y rizoconcreciones; B, el mejor preservado y que ha permitido el análisis 3D, de conglomerados arenosos, que corta profundamente los dos estadios inferiores. El Estadio B está organizado en una serie de mesoformas de canal, con barrancas izquierdas (al Oeste) bien definidas. En su etapa final de abandono (Estadio L), fue rellenado por capas tabulares de arenas finas limos pardos, que contienen una arcilita verde y una capa de micrita blanca, que pueden asignarse a un depósito lacustre somero. Finalmente yace sobre todo el conjunto anterior, el Estadio C, de conglomerados finos arenosos que forman un extenso sistema de canales y planicie aluvial pero mal representado en estos afloramientos. Las particularidades de estos depósitos pueden ser comparadas con expresiones locales del ambiente actual: el río Pituil (al oeste de la Sierra de Velasco) la llanura arenosa del Bolsón de Pipanaco y el barreal del Señor de la Peña, donde impera un clima árido con una escasas lluvias estivales, indicado condiciones climáticas similares

Fishing, pollution, climate change, and the long-term decline of coral reefs off Havana, Cuba

Understanding temporal and spatial variation of coral reef communities allows us to analyze the relative effects of local stressors, such as fishing and eutrophication, and global stressors, such as ocean warming. To test for spatial and temporal changes in coral reef communities, we combined recent benthic and fish surveys from 2016 with long-term data, dating back to the late 1990s, from four zones located at different distances from Central Havana, Cuba’s largest population center. These changes may indicate the shifting importance of local vs global stressors affecting reef communities. Regardless of the distance from Havana, we found that coral cover was uniformly low (approximately 10%), whereas macroalgal abundance was often high (approximately 65%). Similarly, fish biomass was low across zones, particularly for herbivorous fishes (approximately 12 g m−2) that are critical ecological drivers of reef structure and coral resilience. Analyses of longer-term trends revealed that coral cover near Havana has been below about 10% since at least 1995, potentially because of local stressors. In contrast, reefs farther from Havana maintained relatively high coral cover (approximately 30%) until the early 2000s, but declined more recently to approximately 15%, putting them near the Caribbean-wide average. These distinct spatial and temporal trajectories of reef communities may be the result of the expansion of local stressors away from Havana as the human population increased, or as fishers ventured farther away to exploit new resources. Alternatively, the more recent decline of reefs farther from population centers may have resulted from increasingly frequent global stressors, such as bleaching events and hurricanes

EcoCyc: a comprehensive database resource for Escherichia coli

The EcoCyc database (http://EcoCyc.org/) is a comprehensive source of information on the biology of the prototypical model organism Escherichia coli K12. The mission for EcoCyc is to contain both computable descriptions of, and detailed comments describing, all genes, proteins, pathways and molecular interactions in E.coli. Through ongoing manual curation, extensive information such as summary comments, regulatory information, literature citations and evidence types has been extracted from 8862 publications and added to Version 8.5 of the EcoCyc database. The EcoCyc database can be accessed through a World Wide Web interface, while the downloadable Pathway Tools software and data files enable computational exploration of the data and provide enhanced querying capabilities that web interfaces cannot support. For example, EcoCyc contains carefully curated information that can be used as training sets for bioinformatics prediction of entities such as promoters, operons, genetic networks, transcription factor binding sites, metabolic pathways, functionally related genes, protein complexes and protein–ligand interactions

EcoCyc: fusing model organism databases with systems biology.

EcoCyc (http://EcoCyc.org) is a model organism database built on the genome sequence of Escherichia coli K-12 MG1655. Expert manual curation of the functions of individual E. coli gene products in EcoCyc has been based on information found in the experimental literature for E. coli K-12-derived strains. Updates to EcoCyc content continue to improve the comprehensive picture of E. coli biology. The utility of EcoCyc is enhanced by new tools available on the EcoCyc web site, and the development of EcoCyc as a teaching tool is increasing the impact of the knowledge collected in EcoCyc

Programming gene expression with combinatorial promoters

Promoters control the expression of genes in response to one or more transcription factors (TFs). The architecture of a promoter is the arrangement and type of binding sites within it. To understand natural genetic circuits and to design promoters for synthetic biology, it is essential to understand the relationship between promoter function and architecture. We constructed a combinatorial library of random promoter architectures. We characterized 288 promoters in Escherichia coli, each containing up to three inputs from four different TFs. The library design allowed for multiple −10 and −35 boxes, and we observed varied promoter strength over five decades. To further analyze the functional repertoire, we defined a representation of promoter function in terms of regulatory range, logic type, and symmetry. Using these results, we identified heuristic rules for programming gene expression with combinatorial promoters

DISTILLER: a data integration framework to reveal condition dependency of complex regulons in Escherichia coli

DISTILLER, a data integration framework for the inference of transcriptional module networks, is presented and used to investigate the condition dependency and modularity in Escherichia coli networks

Multidimensional annotation of the Escherichia coli K-12 genome

The annotation of the Escherichia coli K-12 genome in the EcoCyc database is one of the most accurate, complete and multidimensional genome annotations. Of the 4460 E. coli genes, EcoCyc assigns biochemical functions to 76%, and 66% of all genes had their functions determined experimentally. EcoCyc assigns E. coli genes to Gene Ontology and to MultiFun. Seventy-five percent of gene products contain reviews authored by the EcoCyc project that summarize the experimental literature about the gene product. EcoCyc information was derived from 15 000 publications. The database contains extensive descriptions of E. coli cellular networks, describing its metabolic, transport and transcriptional regulatory processes. A comparison to genome annotations for other model organisms shows that the E. coli genome contains the most experimentally determined gene functions in both relative and absolute terms: 2941 (66%) for E. coli, 2319 (37%) for Saccharomyces cerevisiae, 1816 (5%) for Arabidopsis thaliana, 1456 (4%) for Mus musculus and 614 (4%) for Drosophila melanogaster. Database queries to EcoCyc survey the global properties of E. coli cellular networks and illuminate the extent of information gaps for E. coli, such as dead-end metabolites. EcoCyc provides a genome browser with novel properties, and a novel interactive display of transcriptional regulatory networks