PyNAST: a flexible tool for aligning sequences to a template alignment

Motivation: The Nearest Alignment Space Termination (NAST) tool is commonly used in sequence-based microbial ecology community analysis, but due to the limited portability of the original implementation, it has not been as widely adopted as possible. Python Nearest Alignment Space Termination (PyNAST) is a complete reimplementation of NAST, which includes three convenient interfaces: a Mac OS X GUI, a command-line interface and a simple application programming interface (API)

NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes

Microbiologists conducting surveys of bacterial and archaeal diversity often require comparative alignments of thousands of 16S rRNA genes collected from a sample. The computational resources and bioinformatics expertise required to construct such an alignment has inhibited high-throughput analysis. It was hypothesized that an online tool could be developed to efficiently align thousands of 16S rRNA genes via the NAST (Nearest Alignment Space Termination) algorithm for creating multiple sequence alignments (MSA). The tool was implemented with a web-interface at . Each user-submitted sequence is compared with Greengenes' ‘Core Set’, comprising ∼10 000 aligned non-chimeric sequences representative of the currently recognized diversity among bacteria and archaea. User sequences are oriented and paired with their closest match in the Core Set to serve as a template for inserting gap characters. Non-16S data (sequence from vector or surrounding genomic regions) are conveniently removed in the returned alignment. From the resulting MSA, distance matrices can be calculated for diversity estimates and organisms can be classified by taxonomy. The ability to align and categorize large sequence sets using a simple interface has enabled researchers with various experience levels to obtain bacterial and archaeal community profiles

Loss of bacterial diversity during antibiotic treatment of intubated patients colonized with Pseudomonas aeruginosa

Management of airway infections caused by Pseudomonas aeruginosa is a serious clinical challenge, but little is known about the microbial ecology of airway infections in intubated patients. We analyzed bacterial diversity in endotracheal aspirates obtained from intubated patients colonized by P. aeruginosa by using 16S rRNA clone libraries and microarrays (PhyloChip) to determine changes in bacterial community compositions during antibiotic treatment. Bacterial 16S rRNA genes were absent from aspirates obtained from patients briefly intubated for elective surgery but were detected by PCR in samples from all patients intubated for longer periods. Sequencing of 16S rRNA clone libraries demonstrated the presence of many orally, nasally, and gastrointestinally associated bacteria, including known pathogens, in the lungs of patients colonized with P. aeruginosa. PhyloChip analysis detected the same organisms and many additional bacterial groups present at low abundance that were not detected in clone libraries. For each patient, both culture-independent methods showed that bacterial diversity decreased following the administration of antibiotics, and communities became dominated by a pulmonary pathogen. P. aeruginosa became the dominant species in six of seven patients studied, despite treatment of five of these six with antibiotics to which it was sensitive in vitro. Our data demonstrate that the loss of bacterial diversity under antibiotic selection is highly associated with the development of pneumonia in ventilated patients colonized with P. aeruginosa. Interestingly, PhyloChip analysis demonstrated reciprocal changes in abundance between P. aeruginosa and the class Bacilli, suggesting that these groups may compete for a similar ecological niche and suggesting possible mechanisms through which the loss of microbial diversity may directly contribute to pathogen selection and persistence

Is Pretenure Interdisciplinary Research a Career Risk?

Despite initiatives to promote interdisciplinary research, early-career academics continue to perceive professional risks to working at the interface between traditional disciplines. Unexpectedly, the inherent practical challenges of interdisciplinary scholarship, such as new methodologies and lexicons, are not the chief source of the perceived risk. The perception of risk is pervasive across disciplines, and it persists despite efforts to support career development for individuals with common interests [Mitchell and Weiler, 2011]. Suggestions that interdisciplinary work can go unrewarded in academia [Clark et al., 2011] foster a concern that targeting interdisciplinary questions, such as those presented by climate change, will pose problems for acquiring and succeeding in a tenure-track position. If self-preservation limits the questions posed by early-career academics, a perceived career risk is as damaging as a real one to new transdisciplinary initiatives. Thus, institutions should address the source of this perception whether real or specious

Extending colonic mucosal microbiome analysis - Assessment of colonic lavage as a proxy for endoscopic colonic biopsies

This study was supported through GI Research funds and MRC Grant Ref: MR/M00533X/1 to GH.Peer reviewedPublisher PD

Influence of Primary Care Physician Availability and Socioeconomic Deprivation on Breast Cancer from 1988 to 2008: A Spatio-Temporal Analysis

Breast cancer is the most commonly diagnosed cancer and the second leading cause of cancer death among women in the United States. It is unclear how county-level primary care physician (PCP) availability and socioeconomic deprivation affect the spatial and temporal variation of breast cancer incidence and mortality.We used the 1988-2008 public-use county-based data from nine Surveillance, Epidemiology, and End Results (SEER) programs to analyze the temporal and spatial disparity of PCP availability and socioeconomic deprivation on early-stage incidence, advanced-stage incidence and breast cancer mortality. The spatio-temporal analysis was implemented by a novel structural additive modeling approach.Greater PCP availability was significantly associated with higher early-stage incidence, advanced-stage incidence and mortality during the entire study period while socioeconomic deprivation was significantly negatively associated with early-stage incidence, advanced-stage incidence, and mortality up to 1992. However, the observed influence of PCP availability and socioeconomic deprivation varied by county.We showed important associations of PCP availability and socioeconomic deprivation with the three breast cancer indicators. However, the effect of these associations varied over time and across counties. The association of PCP availability and socioeconomic deprivation was stronger in selected counties

Measuring the context of care in an Australian acute care hospital: a nurse survey

BACKGROUND: This study set out to achieve three objectives: to test the application of a context assessment tool in an acute hospital in South Australia; to use the tool to compare context in wards that had undergone an evidence implementation process with control wards; and finally to test for relationships between demographic variables (in particular experience) of nurses being studied (n = 422) with the dimensions of context. METHODS: The Alberta Context Tool (ACT) was administered to all nursing staff on six control and six intervention wards. A total of 217 (62%) were returned (67% from the intervention wards and 56% from control wards). Data were analysed using Stata (v9). The effect of the intervention was analysed using nested (hierarchical) analysis of variance; relationships between nurses' experience and context was examined using canonical correlation analysis. RESULTS: Results confirmed the adaptation and fit of the ACT to one acute care setting in South Australia. There was no difference in context scores between control and intervention wards. However, the tool identified significant variation between wards in many of the dimensions of context. Though significant, the relationship between nurses' experience and context was weak, suggesting that at the level of the individual nurse, few factors are related to context. CONCLUSIONS: Variables operating at the level of the individual showed little relationship with context. However, the study indicated that some dimensions of context (e.g., leadership, culture) vary at the ward level, whereas others (e.g., structural and electronic resources) do not. The ACT also raised a number of interesting speculative hypotheses around the relationship between a measure of context and the capability and capacity of staff to influence it.Timothy J. Schultz and Alison L. Kitso