Xer Recombinase and Genome Integrity in Helicobacter pylori, a Pathogen without Topoisomerase IV

In the model organism E. coli, recombination mediated by the related XerC and XerD recombinases complexed with the FtsK translocase at specialized dif sites, resolves dimeric chromosomes into free monomers to allow efficient chromosome segregation at cell division. Computational genome analysis of Helicobacter pylori, a slow growing gastric pathogen, identified just one chromosomal xer gene (xerH) and its cognate dif site (difH). Here we show that recombination between directly repeated difH sites requires XerH, FtsK but not XerT, the TnPZ transposon associated recombinase. xerH inactivation was not lethal, but resulted in increased DNA per cell, suggesting defective chromosome segregation. The xerH mutant also failed to colonize mice, and was more susceptible to UV and ciprofloxacin, which induce DNA breakage, and thereby recombination and chromosome dimer formation. xerH inactivation and overexpression each led to a DNA segregation defect, suggesting a role for Xer recombination in regulation of replication. In addition to chromosome dimer resolution and based on the absence of genes for topoisomerase IV (parC, parE) in H. pylori, we speculate that XerH may contribute to chromosome decatenation, although possible involvement of H. pylori's DNA gyrase and topoisomerase III homologue are also considered. Further analyses of this system should contribute to general understanding of and possibly therapy development for H. pylori, which causes peptic ulcers and gastric cancer; for the closely related, diarrheagenic Campylobacter species; and for unrelated slow growing pathogens that lack topoisomerase IV, such as Mycobacterium tuberculosis

Nothing Lasts Forever: Environmental Discourses on the Collapse of Past Societies

The study of the collapse of past societies raises many questions for the theory and practice of archaeology. Interest in collapse extends as well into the natural sciences and environmental and sustainability policy. Despite a range of approaches to collapse, the predominant paradigm is environmental collapse, which I argue obscures recognition of the dynamic role of social processes that lie at the heart of human communities. These environmental discourses, together with confusion over terminology and the concepts of collapse, have created widespread aporia about collapse and resulted in the creation of mixed messages about complex historical and social processes

Towards an Archaeology of the Perception: ‘Looking’ at the Minoan Palaces

Architecture is perhaps one of the most important elements in the archaeology of Bronze Age Crete. It is employed as the archaeologist’s lens through which this society, its members and its social structures are viewed. While there are certain general laws concerning architecture and its relation to society, an approach is advocated here in which the visual perception of the ancient user is considered to be the key to the interpretation of the architecture. The human perception of architecture is significant in the mode of construction and the subsequent contextualization of a building within the social network. This principle is illustrated with a discussion of the visual impact of the palaces within Minoan society, possibly enhancing their monumentality and their ability to function as a stage for various performances

Funerary Pithoi in Bronze Age Crete: Their Introduction and Significance at the Threshold of Minoan Palatial Society

Toward the end of the third millennium B.C.E., Minoan funerary customs changed, and people began to favor the use of clay receptacles-pithoi or larnakes-for the bodies of the dead. This article offers a comprehensive study of the funerary pithoi of the period, comprising a review of the available material and its classification, distribution, and dating, the relation of container to tomb types, and the specific use of pithoi within funerary ritual. It also assesses the importance of pithoi as an investment in terms of the material wealth that they represent and the knowledge of the complex techniques of handling dead bodies that they require. Finally, it examines the symbolic connotations of the pithos and argues that its wide adoption was part of a general turn toward the concept of the regeneration of life. This concept shifted the emphasis of the funerary realm toward the social dimension-namely, toward the reallocation of the roles and resources of the dead among the living. Such a shift helped people come to terms with contemporary social reality and shaped the agency of emerging elites, which led to the establishment of the first Minoan palaces and transformed Crete from a series of kin-based communities to a group of proto-states

Assessing the unified airway hypothesis in children via transcriptional profiling of the airway epithelium

© 2020 American Academy of Allergy, Asthma & Immunology Background: Emerging evidence suggests that disease vulnerability is expressed throughout the airways, the so-called unified airway hypothesis, but the evidence to support this is predominantly indirect. Objectives: We sought to establish the transcriptomic profiles of the upper and lower airways and determine their level of similarity irrespective of airway symptoms (wheeze) and allergy. Methods: We performed RNA sequencing on upper and lower airway epithelial cells from 63 children with or without wheeze and accompanying atopy, using differential gene expression and gene coexpression analyses to determine transcriptional similarity. Results: We observed approximately 91% homology in the expressed genes between the 2 sites. When coexpressed genes were grouped into modules relating to biological functions, all were found to be conserved between the 2 regions, resulting in a consensus network containing 16 modules associated with ribosomal function, metabolism, gene expression, mitochondrial activity, and antiviral responses through IFN activity. Although symptom-associated gene expression changes were more prominent in the lower airway, they were reflected in nasal epithelium and included IL-1 receptor like 1, prostaglandin-endoperoxide synthase 1, CCL26, and periostin. Through network analysis we identified a cluster of coexpressed genes associated with atopic wheeze in the lower airway, which could equally distinguish atopic and nonatopic phenotypes in upper airway samples. Conclusions: We show that the upper and lower airways are significantly conserved in their transcriptional composition, and that variations associated with disease are present in both nasal and tracheal epithelium. Findings from this study supporting a unified airway imply that clinical insight regarding the lower airway in health and disease can be gained from studying the nasal epithelium

Traces of places: sacred sites in miniature on Minoan gold rings.

Sacred sites in Minoan Crete are known from both archaeological remains and iconography. Glyptic art is the most extensive body of Aegean Bronze Age representational art and consists of carved seals in the form of engraved metal signet rings, stone seals, and the clay impressions (sealings) that these were used to produce. Gold signet rings from the Cretan Neopalatial period (1750–1490 BCE) depict various types of sacred site including mountain, rural, cave, and urban sanctuaries. How should we understand the built structures depicted in these miniature cult scenes? Do they all depict variations of walls or buildings, or are they altars? This paper differentiates the built structures depicted in cult scenes on Minoan gold rings, correlates them to archaeological remains at Minoan sacred sites, and proposes an explanation of ephemeral cult structures now only recorded in the iconographic evidence. It will be demonstrated that these miniature art forms represent Minoan sacred sites in three ways: as natural places characterised by the presence of trees and stones and the absence of architecture; as outdoor sanctuaries surrounded by ashlar stone walls; and as shrines and altars, the shapes of which evoke natural cult locations such as mountains and sacred groves through abstract form. It will be argued that representation of Minoan cult structures that evoked the natural landscape within prestigious art forms was a method whereby Neopalatial elites naturalised their authority by depicting themselves in special relationship with the animate landscape