Heterophils are associated with resistance to systemic Salmonella enteritidis infections in genetically distinct chicken lines

Heterophils mediate acute protection against Salmonella in young poultry. We evaluated susceptibility of genetically distinct lines of broilers to systemic Salmonella enteritidis (SE) infections. SE was administered into the abdomen of day-old chickens (parental lines [A and B]; F1 reciprocal crosses [C and D]) to assess modulation of leukocytes and survivability of chickens. Line A was more resistant to SE than line B; likewise cross D was more resistant than cross C. Significantly more heterophils migrated to the abdominal cavity post-infection in the resistant lines. These data indicate that increased heterophil influx to the infection site contributes to increased resistance against systemic SE infections in neonatal chickens.     

Reconstructing tumor amplisomes

MOTIVATION: Duplication of genomic sequences is a common phenomenon in tumor cells. While many duplications associated with tumors have been identified (e.g. via techniques such as CGH), both the organization of the duplicated sequences and the process that leads to these duplications are less clear. One mechanism that has been observed to lead to duplication is the extraction of DNA from the chromosomes and aggregation of this DNA into small, independently replicating linear or circular DNA sequences (amplisomes). Parts of these amplisomes may later be reinserted back into the main chromosomes leading to duplication. Although amplisomes are known to play an important role in tumorigenesis, their architecture and even size remain largely unknown. RESULTS: We reconstruct the structure of tumor amplisomes by analyzing duplications in the tumor genome. Our approach relies on recently generated data from End Sequence Profiling (ESP) experiments, which allow us to examine the fine structure of duplications in a tumor on a genome-wide scale. Using ESP data, we formulate the Amplisome Reconstruction Problem, describe an algorithm for its solution, and derive a putative architecture of a tumor amplisome that is the source for duplicated material in the MCF7 breast tumor cell line.     

Molecular Survey of Bacterial Communities Associated with Bacterial Chondronecrosis with Osteomyelitis (BCO) in Broilers

Bacterial chondronecrosis with osteomyelitis (BCO) is recognized as an important cause of lameness in commercial broiler chickens (meat-type chickens). Relatively little is known about the microbial communities associated with BCO. This study was conducted to increase our understanding of the microbial factors associated with BCO using a culture-independent approach. Using Illumina sequencing of the hyper-variable region V6 in the 16S rRNA gene, we characterized the bacterial communities in 97 femoral or tibial heads from normal and lame broilers carefully selected to represent diverse variations in age, line, lesion type, floor type, clinical status and bone type. Our in-depth survey based on 14 million assembled sequence reads revealed that complex bacterial communities exist in all samples, including macroscopically normal bones from clinically healthy birds. Overall, Proteobacteria (mean 90.9%) comprised the most common phylum, followed by Firmicutes (6.1%) and Actinobacteria (2.6%), accounting for more than 99% of all reads. Statistical analyses demonstrated that there are differences in bacterial communities in different types of bones (femur vs. tibia), lesion types (macroscopically normal femora or tibiae vs. those with pathognomonic BCO lesions), and among individual birds. This analysis also showed that BCO samples overrepresented genera Staphylococcus, whose species have been frequently isolated in BCO samples in previous studies. Rarefaction analysis demonstrated the general tendency that increased severities of BCO lesions were associated with reduced species diversity in both femoral and tibial samples when compared to macroscopically normal samples. These observations suggest that certain bacterial subgroups are preferentially selected in association with the development of BCO lesions. Understanding the microbial species associated with BCO will identify opportunities for understanding and modulating the pathogenesis of this form of lameness in broilers.     

Evidence-based de-implementation for contradicted, unproven, and aspiring healthcare practices

Abandoning ineffective medical practices and mitigating the risks of untested practices are important for improving patient health and containing healthcare costs. Historically, this process has relied on the evidence base, societal values, cultural tensions, and political sway, but not necessarily in that order. We propose a conceptual framework to guide and prioritize this process, shifting emphasis toward the principles of evidence-based medicine, acknowledging that evidence may still be misinterpreted or distorted by recalcitrant proponents of entrenched practices and other biases.     

Associations between COPD related manifestations: a cross-sectional study

Background

Cardiovascular disease, osteoporosis and emphysema are associated with COPD. Associations between these factors and whether they predict all-cause mortality in COPD patients are not well understood. Therefore, we examined associations between markers of cardiovascular disease (coronary artery calcification [CAC], thoracic aortic calcification [TAC] and arterial stiffness), bone density (bone attenuation of the thoracic vertebrae), emphysema (PI-950 and 15th percentile) and all-cause mortality in a COPD cohort.

Methods

We assessed CAC, TAC, bone attenuation of the thoracic vertebrae, PI-950 and 15th percentile on low-dose chest computed tomography in COPD subjects. We measured arterial stiffness as carotid-radial pulse wave velocity (PWV), and identified deaths from the national register.

Results

We studied 119 COPD subjects; aged 67.8 ±7.3, 66% were males and mean FEV₁% predicted was 46.0 ±17.5. Subjects were classified into three pre-specificed groups: CAC = 0 (n = 14), 0 < CAC ≤ 400 (n = 41) and CAC > 400 (n = 64). Subjects with higher CAC were more likely to be older (p < 0.001) and male (p = 0.03), and more likely to have higher systolic blood pressure (p = 0.001) and a history of hypertension (p = 0.002) or ischemic heart disease (p = 0.003). Higher CAC was associated with higher PWV (OR 1.62, p = 0.04) and lower bone attenuation (OR 0.32, p = 0.02), but not with 15th percentile, after adjustment for age, sex and pack-years of smoking. In a Cox proportional hazards model, CAC, TAC and 15th percentile predicted all-cause mortality (HR 2.01, 2.09 and 0.66, respectively).

Conclusions

Increased CAC was associated with increased arterial stiffness and lower bone density in a COPD cohort. In addition, CAC, TAC and extent of emphysema predicted all-cause mortality.

Trial registration

Lothian NHS Board, Lothian Research Ethics Committee, LREC/2003/8/28.     

Paired de bruijn graphs: a novel approach for incorporating mate pair information into genome assemblers

The recent proliferation of next generation sequencing with short reads has enabled many new experimental opportunities but, at the same time, has raised formidable computational challenges in genome assembly. One of the key advances that has led to an improvement in contig lengths has been mate pairs, which facilitate the assembly of repeating regions. Mate pairs have been algorithmically incorporated into most next generation assemblers as various heuristic post-processing steps to correct the assembly graph or to link contigs into scaffolds. Such methods have allowed the identification of longer contigs than would be possible with single reads; however, they can still fail to resolve complex repeats. Thus, improved methods for incorporating mate pairs will have a strong effect on contig length in the future. Here, we introduce the paired de Bruijn graph, a generalization of the de Bruijn graph that incorporates mate pair information into the graph structure itself instead of analyzing mate pairs at a post-processing step. This graph has the potential to be used in place of the de Bruijn graph in any de Bruijn graph based assembler, maintaining all other assembly steps such as error-correction and repeat resolution. Through assembly results on simulated perfect data, we argue that this can effectively improve the contig sizes in assembly.     

Spectral archives: extending spectral libraries to analyze both identified and unidentified spectra

Tandem mass spectrometry (MS/MS) experiments yield multiple, nearly identical spectra of the same peptide in various laboratories, but proteomics researchers typically do not leverage the unidentified spectra produced in other labs to decode spectra they generate. We propose a spectral archives approach that clusters MS/MS datasets, representing similar spectra by a single consensus spectrum. Spectral archives extend spectral libraries by analyzing both identified and unidentified spectra in the same way and maintaining information about peptide spectra that are common across species and conditions. Thus archives offer both traditional library spectrum similarity-based search capabilities along with new ways to analyze the data. By developing a clustering tool, MS-Cluster, we generated a spectral archive from ～1.18 billion spectra that greatly exceeds the size of existing spectral repositories. We advocate that publicly available data should be organized into spectral archives rather than be analyzed as disparate datasets, as is mostly the case today.