tRNA signatures reveal polyphyletic origins of streamlined SAR11 genomes among the alphaproteobacteria

Phylogenomic analyses are subject to bias from compositional convergence and noise from horizontal gene transfer (HGT). Compositional convergence is a likely cause of controversy regarding phylogeny of the SAR11 group of Alphaproteobacteria that have extremely streamlined, A+T-biased genomes. While careful modeling can reduce artifacts caused by convergence, the most consistent and robust phylogenetic signal in genomes may lie distributed among encoded functional features that govern macromolecular interactions. Here we develop a novel phyloclassification method based on signatures derived from bioinformatically defined tRNA Class-Informative Features (CIFs). tRNA CIFs are enriched for features that underlie tRNA-protein interactions. Using a simple tRNA-CIF-based phyloclassifier, we obtained results consistent with those of bias-corrected whole proteome phylogenomic studies, rejecting monophyly of SAR11 and affiliating most strains with Rhizobiales with strong statistical support. Yet SAR11 and Rickettsiales tRNA genes share distinct patterns of A+T-richness, as expected from their elevated genomic A+T compositions. Using conventional supermatrix methods on total tRNA sequence data, we could recover the artifactual result of a monophyletic SAR11 grouping with Rickettsiales. Thus tRNA CIF-based phyloclassification is more robust to base content convergence than supermatrix phylogenomics on whole tRNA sequences. Also, given the notoriously promiscuous HGT of aminoacyl-tRNA synthetases, tRNA CIF-based phyloclassification may be relatively robust to HGT of network components. We describe how unique features of tRNA-protein interaction networks facilitate the mining of traits governing macromolecular interactions from genomic data, and discuss why interaction-governing traits may be especially useful to solve difficult problems in microbial classification and phylogeny

tRNA functional signatures classify plastids as late-branching cyanobacteria.

BackgroundEukaryotes acquired the trait of oxygenic photosynthesis through endosymbiosis of the cyanobacterial progenitor of plastid organelles. Despite recent advances in the phylogenomics of Cyanobacteria, the phylogenetic root of plastids remains controversial. Although a single origin of plastids by endosymbiosis is broadly supported, recent phylogenomic studies are contradictory on whether plastids branch early or late within Cyanobacteria. One underlying cause may be poor fit of evolutionary models to complex phylogenomic data.ResultsUsing Posterior Predictive Analysis, we show that recently applied evolutionary models poorly fit three phylogenomic datasets curated from cyanobacteria and plastid genomes because of heterogeneities in both substitution processes across sites and of compositions across lineages. To circumvent these sources of bias, we developed CYANO-MLP, a machine learning algorithm that consistently and accurately phylogenetically classifies ("phyloclassifies") cyanobacterial genomes to their clade of origin based on bioinformatically predicted function-informative features in tRNA gene complements. Classification of cyanobacterial genomes with CYANO-MLP is accurate and robust to deletion of clades, unbalanced sampling, and compositional heterogeneity in input tRNA data. CYANO-MLP consistently classifies plastid genomes into a late-branching cyanobacterial sub-clade containing single-cell, starch-producing, nitrogen-fixing ecotypes, consistent with metabolic and gene transfer data.ConclusionsPhylogenomic data of cyanobacteria and plastids exhibit both site-process heterogeneities and compositional heterogeneities across lineages. These aspects of the data require careful modeling to avoid bias in phylogenomic estimation. Furthermore, we show that amino acid recoding strategies may be insufficient to mitigate bias from compositional heterogeneities. However, the combination of our novel tRNA-specific strategy with machine learning in CYANO-MLP appears robust to these sources of bias with high accuracy in phyloclassification of cyanobacterial genomes. CYANO-MLP consistently classifies plastids as late-branching Cyanobacteria, consistent with independent evidence from signature-based approaches and some previous phylogenetic studies

Eliminating the Abattoir Pen Lairages to Decrease the Prevalence of Salmonella in Cull Sows

The study objective, to determine the role of abattoir antemortem pens in preharvest Salmonella enterica contamination, was conducted over 4 sampling periods, February-April 2002. A total of 40 sows were selected for each period at the same collection point and transported to the abattoir. Twenty (20) were unloaded and sent directly to harvest and 20 held in antemortem pen for 2 h before harvest. Samples collected included ileocecal and subiliac lymph nodes, cecal and transverse colon contents, pre-rinse carcass sponge swabs for the right and left carcass sections and chopped meat blocks composited from these carcasses. The percentage of positive samples (all tissues) and cecal content from sows held in the antemortem pens (59%, 55 %, respectively) were significantly higher (P \u3c 0.05) compared to direct delivered (44%, 39 % respectively). This study demonstrates that normal antemortem holding practices contributed to increased Salmonella enterica contamination of the digestive tract

High Discordance of Chest X-ray and CT for Detection of Pulmonary Opacities in ED Patients: Implications for Diagnosing Pneumonia

Objective To evaluate the diagnostic performance of chest x-ray (CXR) compared to computed tomography (CT) for detection of pulmonary opacities in adult emergency department (ED) patients. Methods We conducted an observational cross-sectional study of adult patients presenting to 12 EDs in the United States from July 1, 2003, through November 30, 2006, who underwent both CXR and chest CT for routine clinical care. CXRs and CT scans performed on the same patient were matched. CXRs and CT scans were interpreted by attending radiologists and classified as containing pulmonary opacities if the final radiologist report noted opacity, infiltrate, consolidation, pneumonia, or bronchopneumonia. Using CT as a criterion standard, the diagnostic test characteristics of CXR to detect pulmonary opacities were calculated. Results The study cohort included 3423 patients. Shortness of breath, chest pain and cough were the most common complaints, with 96.1% of subjects reporting at least one of these symptoms. Pulmonary opacities were visualized on 309 (9.0%) CXRs and 191 (5.6 %) CT scans. CXR test characteristics for detection of pulmonary opacities included: sensitivity 43.5% (95% CI, 36.4%-50.8%); specificity 93.0% (95% CI, 92.1%-93.9%); positive predictive value 26.9% (95% CI, 22.1%-32.2%); and negative predictive value 96.5% (95% CI, 95.8%-97.1%). Conclusion In this multicenter cohort of adult ED patients with acute cardiopulmonary symptoms, CXR demonstrated poor sensitivity and positive predictive value for detecting pulmonary opacities. Reliance on CXR to identify pneumonia may lead to significant rates of misdiagnosis

5′ Fluorogenic PCR Assay for the iap Gene of Listeria species

We developed a fluorogenic 5′ nuclease polymerase chain reaction (PCR) assay targeting the iap gene, which is highly conserved in all Listeria species. We used this assay to screen tissues obtained during a survey of cull sows. To date, we have detected Listeria species in in caecal contents (66%, 23 of 35 samples), tonsil homogenates (67%, 4 of 6 samples), and ileocaecal lymph nodes (75%, 6 of 8 samples), but infrequently in feces collected before slaughter (4.4%,1 of 23 samples). Taken together, these data indicate that second-generation 5′ nuclease PCR (TaqMan) assays accelerates detection and quantitation of Listeria during pork production. This may reduce product recalls as well as reduce human illness and deaths. The development of portable instruments for 5′ nuclease assays will expedite field surveys

The impact of oxidation on spore and pollen chemistry

Sporomorphs (pollen and spores) have an outer wall composed of sporopollenin. Sporopollenin chemistry contains both a signature of ambient ultraviolet-B flux and taxonomic information, but it is currently unknown how sensitive this is to standard palynological processing techniques. Oxidation in particular is known to cause physical degradation to sporomorphs, and it is expected that this should have a concordant impact on sporopollenin chemistry. Here, we test this by experimentally oxidizing Lycopodium (clubmoss) spores using two common oxidation techniques: acetolysis and nitric acid. We also carry out acetolysis on eight angiosperm (flowering plant) taxa to test the generality of our results. Using Fourier Transform infrared (FTIR) spectroscopy, we find that acetolysis removes labile, non-fossilizable components of sporomorphs, but has a limited impact upon the chemistry of sporopollenin under normal processing durations. Nitric acid is more aggressive and does break down sporopollenin and reorganize its chemical structure, but when limited to short treatments (i.e. ≤10 min) at room temperature sporomorphs still contain most of the original chemical signal. These findings suggest that when used carefully oxidation does not adversely affect sporopollenin chemistry, and that palaeoclimatic and taxonomic signatures contained within the sporomorph wall are recoverable from standard palynological preparations

Host cell restriction factors that limit transcription and replication of human papillomavirus

The life cycle of human papillomaviruses (HPV) is tightly regulated by the differentiation state of mucosal and cutaneous keratinocytes. To counteract viral infection, constitutively expressed cellular factors, which are defined herein as restriction factors, directly mitigate viral gene expression and replication. In turn, some HPV gene products target these restriction factors and abrogate their anti-viral effects to establish efficient gene expression and replication programs. Ironically, in certain circumstances, this delicate counterbalance between viral gene products and restriction factors facilitates persistent infection by HPVs. This review serves to recapitulate the current knowledge of nuclear restriction factors that directly affect the HPV infectious cycle

A spatial-temporal analysis of section 404 wetland permitting in Texas and Florida: Thirteen years of impact along the coast

Over the past 200 years, an estimated 53% (about 47 million ha) of the original wetlands in the conterminous United States have been lost, mainly as a result of various human activities. Despite the importance of wetlands (particularly along the coast), and a longstanding federal policy framework meant to protect their integrity, the cumulative impact on these natural systems over large areas is poorly understood. We address this lack of research by mapping and conducting descriptive spatial analyses of federal wetland alteration permits (pursuant to section 404 of the Clean Water Act) across 85 watersheds in Florida and coastal Texas from 1991 to 2003. Results show that more than half of the permits issued in both states (60%) fell under the Nationwide permitting category. Permits issued in Texas were typically located outside of urban areas (78%) and outside 100-year floodplains (61%). More than half of permits issued in Florida were within urban areas (57%) and outside of 100-year floodplains (51%). The most affected wetlands types were estuarine in Texas (47%) and palustrine in Florida (55%). We expect that an additional outcome of this work will be an increased awareness of the cumulative depletion of wetlands and loss of ecological services in these urbanized areas, perhaps leading to increased conservation efforts