DNA replication can still spring surprises

A report of the first EMBO conference in a biennial series 'Replication and Segregation of Chromosomes', Geilo, Norway, 16-20 June 2008

Chromosome Architecture and Evolution in Bacteria

Inferences of organismal molecular evolution have been dominated by comparisons of their constituent genes. Yet the evolutionary histories of genes within Bacterial genomes are not necessarily congruent. Here, Horizontal Gene Transfer (HGT) of sequences across species boundaries can confound these analyses. There does appear to be phylogenetic cohesion, where members of higher taxonomic groups share genotypic similarity despite gene transfer. Herein I examine the rules for governing HGT to determine the impact this process has played in the evolution of Bacteria and Archaea. Bacterial chromosomes are more than simple lists of genes. Genomes must maintain information beyond component genes to direct efficient replication and segregation of their chromosomes. I propose that this structure constrains the process of HGT so that transfer among certain pairs of donors and recipients is favored. I present methods to detect this structure and new theories of bacterial cell biology and evolution based on what this structure reveals. I present evidence that bacterial chromosomes are structured by repetitive sequences termed Architecture IMparting Sequences (AIMS). AIMS are found primarily on leading strands and increase in abundance towards the replication terminus. Bacteria with robustly-identified replication origins and termini all have AIMS, and related AIMS are conserved amongst families of bacteria. We propose that AIMS are under selection to provide DNA binding proteins with polarity information, facilitating identification of the location of the replication terminus. Although AIMS evolved to direct the biology of cell division and replication, the conservation of AIMS among related taxa leads to a secondary effect. Because AIMS are counterselected when in nonpermissive orientations, AIMS constrain both intragenomic and intergenomic rearrangements. Thus HGT frequency will depend on AIMS compatibility between different species. We predict that HGT is most common between bacterial genomes which are more closely related and will impede transfer between species which have dissimilar genome architecture. The additional level of selection reflected by AIMS has resulted in cohesive bacterial groups that reflect common gene pools as a result of biased rates of gene transfer

The evolution of spherical cell shape; progress and perspective

Bacterial cell shape is a key trait governing the extracellular and intracellular factors of bacterial life. Rod-like cell shape appears to be original which implies that the cell wall, division, and rod-like shape came together in ancient bacteria and that the myriad of shapes observed in extant bacteria have evolved from this ancestral shape. In order to understand its evolution, we must first understand how this trait is actively maintained through the construction and maintenance of the peptidoglycan cell wall. The proteins that are primarily responsible for cell shape are therefore the elements of the bacterial cytoskeleton, principally FtsZ, MreB, and the penicillin-binding proteins. MreB is particularly relevant in the transition between rod-like and spherical cell shape as it is often (but not always) lost early in the process. Here we will highlight what is known of this particular transition in cell shape and how it affects fitness before giving a brief perspective on what will be required in order to progress the field of cell shape evolution from a purely mechanistic discipline to one that has the perspective to both propose and to test reasonable hypotheses regarding the ecological drivers of cell shape change

Food Predictors of Plasma Carotenoids

Empirical prediction models that weight food frequency questionnaire (FFQ) food items by their relation to nutrient biomarker concentrations may estimate nutrient exposure better than nutrient intakes derived from food composition databases. Carotenoids may especially benefit because contributing foods vary in bioavailability and assessment validity. Our objective was to develop empirical prediction models for the major plasma carotenoids and total carotenoids and evaluate their validity compared with dietary intakes calculated from standard food composition tables. 4180 nonsmoking women in the Nurses’ Health Study (NHS) blood subcohort with previously measured plasma carotenoids were randomly divided into training (n = 2787) and testing (n = 1393) subsets. Empirical prediction models were developed in the training subset by stepwise selection from foods contributing ≥0.5% to intake of the relevant carotenoid. Spearman correlations between predicted and measured plasma concentrations were compared to Spearman correlations between dietary intake and measured plasma concentrations for each carotenoid. Three to 12 foods were selected for the α-carotene, β-carotene, β-cryptoxanthin, lutein/zeaxanthin, lycopene, and total carotenoids prediction models. In the testing subset, Spearman correlations with measured plasma concentrations for the calculated dietary intakes and predicted plasma concentrations, respectively, were 0.31 and 0.37 for α-carotene, 0.29 and 0.31 for β-carotene, 0.36 and 0.41 for β-cryptoxanthin, 0.28 and 0.31 for lutein/zeaxanthin, 0.22 and 0.23 for lycopene, and 0.22 and 0.27 for total carotenoids. Empirical prediction models may modestly improve assessment of some carotenoids, particularly α-carotene and β-cryptoxanthin

Complete genome sequences of three novel Pseudomonas fluorescens SBW25 bacteriophages, Noxifer, Phabio, and Skulduggery

Three novel bacteriophages, two of which are jumbophages, were isolated from compost in Auckland, New Zealand. Noxifer, Phabio, and Skulduggery are double-stranded DNA (dsDNA) phages with genome sizes of 278,136 bp (Noxifer), 309,157 bp (Phabio), and 62,978 bp (Skulduggery)

Early Intervention with Children at Risk of Emotional/Behavioral Disorders: A Critical Examination of Research Methodology and Practices

Children\u27s behavior problems pose challenges to families, schools, and society. The research literature argues that early detection/intervention is the most powerful course of action in ameliorating these problems in children at risk of emotional/behavioral disorders. However, specifying precisely what constitutes a quality program of early intervention is not a simple task. Current conceptualizations suggest that successful early intervention cannot be unidimensional in nature, but must consist of a complex series of interactions and transactions that synergistically serve to nurture and enhance both the development of the child and family. In this paper, we reviewed the accumulated research to learn more about the critical elements of early intervention. Specifically, we examined three major areas addressed in the literature. First, we describe literature search procedures and criteria for study inclusion, along with methods for analyzing these early intervention studies. Second, we examine the conduct of the intervention, including characteristics of study participants, types of interventions, types of measures, age of onset and length of intervention, treatment fidelity, and social validity measures. Finally, we draw upon that review to offer recommendations for future research

Phages in the Gut Ecosystem

Phages, short for bacteriophages, are viruses that specifically infect bacteria and are the most abundant biological entities on earth found in every explored environment, from the deep sea to the Sahara Desert. Phages are abundant within the human biome and are gaining increasing recognition as potential modulators of the gut ecosystem. For example, they have been connected to gastrointestinal diseases and the treatment efficacy of Fecal Microbiota Transplant. The ability of phages to modulate the human gut microbiome has been attributed to the predation of bacteria or the promotion of bacterial survival by the transfer of genes that enhance bacterial fitness upon infection. In addition, phages have been shown to interact with the human immune system with variable outcomes. Despite the increasing evidence supporting the importance of phages in the gut ecosystem, the extent of their influence on the shape of the gut ecosystem is yet to be fully understood. Here, we discuss evidence for phage modulation of the gut microbiome, postulating that phages are pivotal contributors to the gut ecosystem dynamics. We therefore propose novel research questions to further elucidate the role(s) that they have within the human ecosystem and its impact on our health and well-being

Manifold Routes to a Nucleus

It is widely assumed that there is a clear distinction between eukaryotes, with cell nuclei, and prokaryotes, which lack nuclei. This suggests the evolution of nuclear compartmentation is a singular event. However, emerging knowledge of the diversity of bacterial internal cell structures suggests the picture may not be as black-and-white as previously thought. For instance, some members of the bacterial PVC superphylum appear to have nucleus-like compartmentation, where transcription and translation are physically separated, and some jumbophages have recently been shown to create nucleus-like structures within their Pseudomonad hosts. Moreover, there is also tantalizing metagenomic identification of new Archaea that carry homologs of genes associated with internal cell membrane structure in eukaryotes. All these cases invite comparison with eukaryote cell biology. While the bacterial cases of genetic compartmentation are likely convergent, and thus viewed by many as not germane to the question of eukaryote origins, we argue here that, in addressing the broader question of the evolution of compartmentation, other instances are at least as important: they provide us with a point of comparison which is critical for a more general understanding of both the conditions favoring the emergence of intracellular compartmentation of DNA and the evolutionary consequences of such cellular architecture. Finally, we consider three classes of explanation for the emergence of compartmentation: physical protection, crosstalk avoidance and nonadaptive origins

MLK Historic District: 493 Auburn Ave. NE

Prepared by the Fall 2010 Conservation of Historic Building Materials class. This Historic Structure Report contains the history of the three double-shotgun houses located at 493 Auburn Avenue built by Alexander Daniel Hamilton and his father, Alexander Hamilton, African-American father-and-son builders. The existing conditions of the interior, exterior, infrastructure, and grounds of the buildings are detailed, as well as a master plan of recommendations for the site. The purpose of this report is to provide a current assessment of the condition of the property, recommendations for needed repairs and options for future consideration.https://scholarworks.gsu.edu/history_heritagepreservation/1052/thumbnail.jp