The emergence and fate of horizontally acquired genes in Escherichia coli

Bacterial species, and even strains within species, can vary greatly in their gene contents and metabolic capabilities. We examine the evolution of this diversity by assessing the distribution and ancestry of each gene in 13 sequenced isolates of Escherichia coli and Shigella. We focus on the emergence and demise of two specific classes of genes, ORFans (genes with no homologs in present databases) and HOPs (genes with distant homologs), since these genes, in contrast to most conserved ancestral sequences, are known to be a major source of the novel features in each strain. We find that the rates of gain and loss of these genes vary greatly among strains as well as through time, and that ORFans and HOPs show very different behavior with respect to their emergence and demise. Although HOPs, which mostly represent gene acquisitions from other bacteria, originate more frequently, ORFans are much more likely to persist. This difference suggests that many adaptive traits are conferred by completely novel genes that do not originate in other bacterial genomes. With respect to the demise of these acquired genes, we find that strains of Shigella lose genes, both by disruption events and by complete removal, at accelerated rates

Factors Associated with the Diversification of the Gut Microbial Communities within Chimpanzees from Gombe National Park.

The gastrointestinal tract harbors large and diverse populations of bacteria that vary among individuals and within individuals over time. Numerous internal and external factors can influence the contents of these microbial communities, including diet, geography, physiology, and the extent of contact among hosts. To investigate the contributions of such factors to the variation and changes in gut microbial communities, we analyzed the distal gut microbiota of individual chimpanzees from two communities in Gombe National Park, Tanzania. These samples, which were derived from 35 chimpanzees, many of whom have been monitored for multiple years, provide an unusually comprehensive longitudinal depth for individuals of known genetic relationships. Although the composition of the great-ape microbiota has been shown to codiversify with host species, indicating that host genetics and phylogeny have played a major role in its differentiation over evolutionary timescales, the geneaological relationships of individual chimpanzees did not coincide with the similarity in their gut microbial communities. However, the inhabitants from adjacent chimpanzee communities could be distinguished based on the contents of their gut microbiota. Despite the broad similarity of community members, as would be expected from shared diet or interactions, long-term immigrants to a community often harbored the most distinctive gut microbiota, suggesting that individuals retain hallmarks of their previous gut microbial communities for extended periods. This pattern was reinforced in several chimpanzees sampled over long temporal scales, in which the major constituents of the gut microbiota were maintained for nearly a decade

Characterizing Scales of Genetic Recombination and Antibiotic Resistance in Pathogenic Bacteria Using Topological Data Analysis

Pathogenic bacteria present a large disease burden on human health. Control of these pathogens is hampered by rampant lateral gene transfer, whereby pathogenic strains may acquire genes conferring resistance to common antibiotics. Here we introduce tools from topological data analysis to characterize the frequency and scale of lateral gene transfer in bacteria, focusing on a set of pathogens of significant public health relevance. As a case study, we examine the spread of antibiotic resistance in Staphylococcus aureus. Finally, we consider the possible role of the human microbiome as a reservoir for antibiotic resistance genes.Comment: 12 pages, 6 figures. To appear in AMT 2014 Special Session on Advanced Methods of Interactive Data Mining for Personalized Medicin

Social behavior shapes the chimpanzee pan-microbiome

Animal sociality facilitates the transmission of pathogenic microorganisms among hosts, but the extent to which sociality enables animals’ beneficial microbial associations is poorly understood. The question is critical because microbial communities, particularly those in the gut, are key regulators of host health. We show evidence that chimpanzee social interactions propagate microbial diversity in the gut microbiome both within and between host generations. Frequent social interaction promotes species richness within individual microbiomes as well as homogeneity among the gut community memberships of different chimpanzees. Sampling successive generations across multiple chimpanzee families suggests that infants inherited gut microorganisms primarily through social transmission. These results indicate that social behavior generates a pan-microbiome, preserving microbial diversity across evolutionary time scales and contributing to the evolution of host species–specific gut microbial communities

Experimental Fracture Model versus Osteotomy Model in Metacarpal Bone Plate Fixation

Introduction. Osteotomy or fracture models can be used to evaluate mechanical properties of fixation techniques of the hand skeleton in vitro. Although many studies make use of osteotomy models, fracture models simulate the clinical situation more realistically. This study investigates monocortical and bicortical plate fixation on metacarpal bones considering both aforementioned models to decide which method is best suited to test fixation techniques. Methods. Porcine metacarpal bones (n = 40) were randomized into 4 groups. In groups I and II bones were fractured with a modified 3-point bending test. The intact bones represented a further control group to which the other groups after fixation were compared. In groups III and IV a standard osteotomy was carried out. Bones were fixated with plates monocortically (group I, III) and bicortically (group II, IV) and tested for failure. Results. Bones fractured at a mean maximum load of 482.8 N ± 104.8 N with a relative standard deviation (RSD) of 21.7%, mean stiffness was 122.3 ± 35 N/mm. In the fracture model, there was a significant difference (P = 0.01) for maximum load of monocortically and bicortically fixed bones in contrast to the osteotomy model (P = 0.9). Discussion. In the fracture model, because one can use the same bone for both measurements in the intact state and the bone-plate construct states, the impact of inter-individual differences is reduced. In contrast to the osteotomy model there are differences between monocortical and bicortical fixations in the fracture model. Thus simulation of the in vivo situation is better and seems to be suitable for the evaluation of mechanical properties of fixation techniques on metacarpals

Efficient inference of bacterial strain trees from genome-scale multilocus data

Motivation: In bacterial evolution, inferring a strain tree, which is the evolutionary history of different strains of the same bacterium, plays a major role in analyzing and understanding the evolution of strongly isolated populations, population divergence and various evolutionary events, such as horizontal gene transfer and homologous recombination. Inferring a strain tree from multilocus data of these strains is exceptionally hard since, at this scale of evolution, processes such as homologous recombination result in a very high degree of gene tree incongruence

A Simple PCR Method for Rapid Genotype Analysis of the TH-MYCN Transgenic Mouse

BACKGROUND: The TH-MYCN transgenic mouse is the most widely used murine model of human neuroblastoma, in which a human MYCN oncogene is targeted to neuroectodermal cells of developing mice under the influence of the rat tyrosine hydroxylase promoter. So far, homozygous transgenic mice have been identified by either Southern blot or quantitative real-time PCR. PRINCIPAL FINDINGS: To establish a simple and reliable genotyping method by conventional PCR, we confirmed the integration of the transgene in the TH-MYCN transgenic mouse by Southern blot and inverse PCR analyses. Our results showed that either five or six copies were found to be inserted in a head-to-tail tandem configuration at a single locus. The MYCN transgene/host DNA junction was sequenced and the integration site was identified at chromosome 18qE4. Finally, we succeeded in designing rapid, simple and reliable genotyping method by common PCR using primers flanking the integrated TH-MYCN transgene. CONCLUSION: We established a simple and reliable genotyping PCR method for determining the integration site of the TH-MYCN transgene that enables all possible genotypes to be distinguished within several hours. TH-MYCN mice are excellent model for human neuroblastoma study, thus our results will largely be useful for facilitating the pace of neuroblastoma study, including in the study of the tumourigenic process, and in the development of therapies to treat patients suffering from neuroblastoma

Biomechanical Analysis of the Efficacy of Locking Plates during Cyclic Loading in Metacarpal Fractures

Purpose. To analyse the biomechanical characteristics of locking plates under cyclic loading compared to a nonlocking plate in a diaphyseal metacarpal fracture. Methods. Oblique diaphyseal shaft fractures in porcine metacarpal bones were created in a biomechanical fracture model. An anatomical reduction and stabilization with a nonlocking and a comparable locking plate in mono- or bicortical screw fixation followed. Under cyclic loading, the displacement, and in subsequent load-to-failure tests, the maximum load and stiffness were measured. Results. For the monocortical screw fixation of the locking plate, a similar displacement, maximum load, and stiffness could be demonstrated compared to the bicortical screw fixation of the nonlocking plate. Conclusions. Locking plates in monocortical configuration may function as a useful alternative to the currently common treatment with bicortical fixations. Thereby, irritation of the flexor tendons would be avoided without compromising the stability, thus enabling the necessary early functional rehabilitation