Progressive Mauve: Multiple alignment of genomes with gene flux and rearrangement

Multiple genome alignment remains a challenging problem. Effects of recombination including rearrangement, segmental duplication, gain, and loss can create a mosaic pattern of homology even among closely related organisms. We describe a method to align two or more genomes that have undergone large-scale recombination, particularly genomes that have undergone substantial amounts of gene gain and loss (gene flux). The method utilizes a novel alignment objective score, referred to as a sum-of-pairs breakpoint score. We also apply a probabilistic alignment filtering method to remove erroneous alignments of unrelated sequences, which are commonly observed in other genome alignment methods. We describe new metrics for quantifying genome alignment accuracy which measure the quality of rearrangement breakpoint predictions and indel predictions. The progressive genome alignment algorithm demonstrates markedly improved accuracy over previous approaches in situations where genomes have undergone realistic amounts of genome rearrangement, gene gain, loss, and duplication. We apply the progressive genome alignment algorithm to a set of 23 completely sequenced genomes from the genera Escherichia, Shigella, and Salmonella. The 23 enterobacteria have an estimated 2.46Mbp of genomic content conserved among all taxa and total unique content of 15.2Mbp. We document substantial population-level variability among these organisms driven by homologous recombination, gene gain, and gene loss. Free, open-source software implementing the described genome alignment approach is available from http://gel.ahabs.wisc.edu/mauve .Comment: Revision dated June 19, 200

Injectable and Spatially Patterned Microporous Annealed Particle (MAP) Hydrogels for Tissue Repair Applications.

Spatially patterned hydrogels are becoming increasingly popular in the field of regenerative medicine and tissue repair because of their ability to guide cell infiltration and migration. However, postfabrication technologies are usually required to spatially pattern a hydrogel, making these hydrogels difficult to translate into the clinic. Here, an injectable spatially patterned hydrogel is reported using hyaluronic acid (HA)-based particle hydrogels. These particle hydrogels are sequentially loaded into a syringe to form a pattern and, once injected, they maintain the pattern. The applicability of this hydrogel in a wound healing skin model, a subcutaneous implant model, as well as a stroke brain model is examined and distinct patterning in all models tested is shown. This injectable and spatially patterned hydrogel can be used to create physical or biochemical gradients. Further, this design can better match the scaffold properties within the physical location of the tissue (e.g., wound border vs wound center). This allows for better design features within the material that promote repair and regeneration

An in vitro model to study immune activation, epithelial disruption and stromal remodelling in inflammatory bowel disease and fistulising Crohn’s disease

At present, preclinical models of inflammatory bowel disease (IBD) are insufficient, limiting translation between research and new therapeutics. This is especially true for fistulising Crohn’s disease (CD), as the severe lack of relevant models hinders research progression. To address this, we present in vitro human IBD mucosal models that recapitulate multiple pathological hallmarks of IBD simultaneously in one model system - immune cell infiltration, stromal remodelling and epithelial disruption. Stimulation of models induces epithelial aberrations common in IBD tissue including altered morphology, microvilli abnormalities, claudin gene expression changes and increased permeability. Inflammatory biomarkers are also significantly increased including cytokines and chemokines integral to IBD pathogenesis. Evidence of extracellular matrix remodelling, including upregulated matrix-metalloproteinases and altered basement membrane components, suggests the models simulate pathological stromal remodelling events that closely resemble fistulising CD. Importantly, MMP-9 is the most abundant MMP and mimics the unique localisation observed in IBD tissue. The inflamed models were subsequently used to elucidate the involvement of TNF-α and IFN- γ in intestinal stromal remodelling, in which TNF-α but not IFN- γ induced MMP upregulation, specifically of MMP-3 and MMP-9. Collectively, our results demonstrate the potential of the IBD models for use in preclinical research in IBD, particularly for fistulising CD

Identifying Relationships Between High‐Risk Sexual Behaviors and Screening Positive for Chlamydia and Gonorrhea in School‐Wide Screening Events

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/96430/1/josh12004.pd

Genome-wide detection and analysis of homologous recombination among sequenced strains of Escherichia coli

BACKGROUND: Comparisons of complete bacterial genomes reveal evidence of lateral transfer of DNA across otherwise clonally diverging lineages. Some lateral transfer events result in acquisition of novel genomic segments and are easily detected through genome comparison. Other more subtle lateral transfers involve homologous recombination events that result in substitution of alleles within conserved genomic regions. This type of event is observed infrequently among distantly related organisms. It is reported to be more common within species, but the frequency has been difficult to quantify since the sequences under comparison tend to have relatively few polymorphic sites. RESULTS: Here we report a genome-wide assessment of homologous recombination among a collection of six complete Escherichia coli and Shigella flexneri genome sequences. We construct a whole-genome multiple alignment and identify clusters of polymorphic sites that exhibit atypical patterns of nucleotide substitution using a random walk-based method. The analysis reveals one large segment (approximately 100 kb) and 186 smaller clusters of single base pair differences that suggest lateral exchange between lineages. These clusters include portions of 10% of the 3,100 genes conserved in six genomes. Statistical analysis of the functional roles of these genes reveals that several classes of genes are over-represented, including those involved in recombination, transport and motility. CONCLUSION: We demonstrate that intraspecific recombination in E. coli is much more common than previously appreciated and may show a bias for certain types of genes. The described method provides high-specificity, conservative inference of past recombination events

Development of a mammalian neurosensory full‐thickness skin equivalent and its application to screen sensitizing stimuli

Human skin equivalents (HSEs) are an increasingly popular research tool due to limitations associated with animal testing for dermatological research. They recapitulate many aspects of skin structure and function, however, many only contain two basic cell types to model dermal and epidermal compartments, which limits their application. We describe advances in the field skin tissue modeling to produce a construct containing sensory-like neurons that is responsive to known noxious stimuli. Through incorporation of mammalian sensory-like neurons, we were able to recapitulate aspects of the neuroinflammatory response including secretion of substance P and a range of pro-inflammatory cytokines in response to a well-characterized neurosensitizing agent: capsaicin. We observed that neuronal cell bodies reside in the upper dermal compartment with neurites extending toward the keratinocytes of the stratum basale where they exist in close proximity to one another. These data suggest that we are able to model aspects of the neuroinflammatory response that occurs during exposure to dermatological stimuli including therapeutics and cosmetics. We propose that this skin construct can be considered a platform technology with a wide range of applications including screening of actives, therapeutics, modeling of inflammatory skin diseases, and fundamental approaches to probe underlying cell and molecular mechanisms

Current state of screening highâ ACE youth and emerging adults in primary care

Background and purposeTrauma comes in many forms, including interpersonal, community, and institutional trauma. The adverse childhood event (ACE) studies demonstrated that adverse experiences in childhood can have a profound, cumulative impact on the course of health and development over a lifetime. It is critical for healthcare providers, such as nurse practitioners (NPs), working in primary care to screen adolescents and emerging adults for a history of ACEs and trauma. A review of current assessment tools used in assessing this population in health settings is needed to determine how screening for ACEs is being performed.ConclusionsClinically efficient tools for screening and assessment of highâ ACE youth in primary care settings are lacking.  Developing a process to assess ACEs, risk behaviors, and physical and mental health status that is efficient to use during a time limited clinical visit is an important step in providing holistic care to a challenging population.Implications for practicePrimary care NPs are in the perfect position to implement assessments of ACEs through traumaâ informed nursing care. ACE assessment in clinical practice will provide vital information to guide the development of tailored interventions for reducing risk behaviors and mitigate the longâ term impacts of ACEs.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/141423/1/jaan12531_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/141423/2/jaan12531.pd

Reordering contigs of draft genomes using the Mauve Aligner

Summary: Mauve Contig Mover provides a new method for proposing the relative order of contigs that make up a draft genome based on comparison to a complete or draft reference genome. A novel application of the Mauve aligner and viewer provides an automated reordering algorithm coupled with a powerful drill-down display allowing detailed exploration of results

What are we missing? Risk behaviors among Arabâ American adolescents and emerging adults

Background and purposeResearch on Arabâ Americans as a distinct ethnic group is limited, especially when considering the health of Arabâ American youth. This study describes health risk (substance use, violence); health promotive behaviors (hope, spirituality); and sexual activity (oral, vaginal, anal sex) of Arabâ American adolescents and emerging adults (aged 15â 23) within their life context, as well as the association between these behaviors.MethodsA secondary analysis of data on a subset of Arabâ American participants obtained from a randomizedâ control trial was utilized to conduct mixed methods analyses. Qualitative analyses completed on the openâ ended questions used the constant comparative method for a subsample (n = 24) of participants. Descriptive quantitative analyses of survey data utilized bivariate analyses and stepwise logistic regression to explore the relation between risk behaviors and sexual activity among the full sample (n = 57).ConclusionsQualitative analyses revealed two groups of participants: (a) multiple risk behaviors and negative lifeâ events, and (b) minimal risk behaviors and positive lifeâ events. Quantitative analyses indicated older youth, smokers, and those with higher hope pathways were more likely to report vaginal sex.Implications for practiceThe unique cultural and social contexts of Arabâ American youth provide a framework for recommendations for the prevention of risk behaviors.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/134166/1/jaan12352.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/134166/2/jaan12352_am.pd

ASAP: a resource for annotating, curating, comparing, and disseminating genomic data

ASAP is a comprehensive web-based system for community genome annotation and analysis. ASAP is being used for a large-scale effort to augment and curate annotations for genomes of enterobacterial pathogens and for additional genome sequences. New tools, such as the genome alignment program Mauve, have been incorporated into ASAP in order to improve display and analysis of related genomes. Recent improvements to the database and challenges for future development of the system are discussed. ASAP is available on the web at