Using ESTs for phylogenomics: Can one accurately infer a phylogenetic tree from a gappy alignment?

<p>Abstract</p> <p>Background</p> <p>While full genome sequences are still only available for a handful of taxa, large collections of partial gene sequences are available for many more. The alignment of partial gene sequences results in a multiple sequence alignment containing large gaps that are arranged in a staggered pattern. The consequences of this pattern of missing data on the accuracy of phylogenetic analysis are not well understood. We conducted a simulation study to determine the accuracy of phylogenetic trees obtained from gappy alignments using three commonly used phylogenetic reconstruction methods (Neighbor Joining, Maximum Parsimony, and Maximum Likelihood) and studied ways to improve the accuracy of trees obtained from such datasets.</p> <p>Results</p> <p>We found that the pattern of gappiness in multiple sequence alignments derived from partial gene sequences substantially compromised phylogenetic accuracy even in the absence of alignment error. The decline in accuracy was beyond what would be expected based on the amount of missing data. The decline was particularly dramatic for Neighbor Joining and Maximum Parsimony, where the majority of gappy alignments contained 25% to 40% incorrect quartets. To improve the accuracy of the trees obtained from a gappy multiple sequence alignment, we examined two approaches. In the first approach, alignment masking, potentially problematic columns and input sequences are excluded from from the dataset. Even in the absence of alignment error, masking improved phylogenetic accuracy up to 100-fold. However, masking retained, on average, only 83% of the input sequences. In the second approach, alignment subdivision, the missing data is statistically modelled in order to retain as many sequences as possible in the phylogenetic analysis. Subdivision resulted in more modest improvements to alignment accuracy, but succeeded in including almost all of the input sequences.</p> <p>Conclusion</p> <p>These results demonstrate that partial gene sequences and gappy multiple sequence alignments can pose a major problem for phylogenetic analysis. The concern will be greatest for high-throughput phylogenomic analyses, in which Neighbor Joining is often the preferred method due to its computational efficiency. Both approaches can be used to increase the accuracy of phylogenetic inference from a gappy alignment. The choice between the two approaches will depend upon how robust the application is to the loss of sequences from the input set, with alignment masking generally giving a much greater improvement in accuracy but at the cost of discarding a larger number of the input sequences.</p

Influence of Immune Status on the Airborne Colonization of Piglets with Methicillin-Resistant Staphylococcus aureus (MRSA) Clonal Complex (CC) 398

Colonized vertebrates including humans and pigs are to date the main reservoirs of livestock-associated Methicillin-resistant Staphylococcus aureus (LA-MRSA). Currently, the mechanisms underlying colonization of pigs are not fully understood. We investigated the influence of piglet pre-immune status on airborne MRSA colonization. Three groups of MRSA-negative piglets were primed and exposed to airborne LA-MRSA (104 colony forming units (cfu)/m3) in an aerosol chamber for 24 h. One group was treated intramuscularly with dexamethasone (1 mg/kg body weight) to imitate weaning stress. The second group was exposed to bacterial endotoxin containing MRSA aerosol. Both conditions play a role in the development of multifactorial diseases and may promote MRSA colonization success. The third group served as control. The piglets' MRSA status was monitored for 21 days via swab samples. At necropsy, specific tissues and organs were analyzed. Blood was collected to examine specific immunological parameters. The duration of MRSA colonization was not extended in both treated groups compared to the control group, indicating the two immune-status influencing factors do not promote MRSA colonization. Blood sample analysis confirmed a mild dexamethasone-induced immune suppression and typical endotoxin-related changes in peripheral blood. Of note, the low-dose dexamethasone treatment showed a trend of increased MRSA clearance

Novel potential interacting partners of fibronectin in spontaneous animal model of interstitial cystitis

Feline idiopathic cystitis (FIC) is the only spontaneous animal model for human interstitial cystitis (IC), as both possess a distinctive chronical and relapsing character. Underlying pathomechanisms of both diseases are not clearly established yet. We recently detected increased urine fibronectin levels in FIC cases. The purpose of this study was to gain further insight into the pathogenesis by assessing interacting partners of fibronectin in urine of FIC affected cats. Several candidate proteins were identified via immunoprecipitation and mass spectrometry. Considerable changes in FIC conditions compared to physiological expression of co-purified proteins were detected by Western blot and immunohistochemistry. Compared to controls, complement C4a and thioredoxin were present in higher levels in urine of FIC patients whereas loss of signal intensity was detected in FIC affected tissue. Galectin-7 was exclusively detected in urine of FIC cats, pointing to an important role of this molecule in FIC pathogenesis. Moderate physiological signal intensity of galectin-7 in transitional epithelium shifted to distinct expression in transitional epithelium under pathophysiological conditions. I-FABP expression was reduced in urine and urinary bladder tissue of FIC cats. Additionally, transduction molecules of thioredoxin, NF-κB p65 and p38 MAPK, were examined. In FIC affected tissue, colocalization of thioredoxin and NF-κB p65 could be demonstrated compared to absent coexpression of thioredoxin and p38 MAPK. These considerable changes in expression level and pattern point to an important role for co-purified proteins of fibronectin and thioredoxin-regulated signal transduction pathways in FIC pathogenesis. These results could provide a promising starting point for novel therapeutic approaches in the future

Sustainability as Sales Argument in the Fruit Juice Industry? An Analysis of On-Product Communication

Purpose/Value – The objective of this paper is to determine (1) the extent to which sustainability serves as a sales argument and (2) which areas of sustainability are communicated in the fruit juice industry. This seems promising against the background that there are several ethical challenges the fruit juice chain is increasingly confronted with and consumers demand for sustainable products is also rising.Design/Methodology – A market investigation at the Point-of Sale (POS) was conducted in July 2013. On-product communication of all fruit juice products (direct fruit juices, fruit juices from concentrate, fruit nectars and smoothies) from five retailers (two full-range retailers, two discounters, one organic store) was analyzed. The data was evaluated using content analysis.Results/Findings – Overall, 562 fruit juices were examined. Results reveal that nearly one quarter of the prod-ucts has labels signaling sustainable aspects. However, most of those products were found in the organic food retailer and are organic juices. Only a small number of products consider other areas of sustainability, such as social concerns or regional production.Discussion/Conclusion – Communicating sustainability aspects of fruit juice production via on-package labels is scarce in conventional retail stores. In view of the ethical challenges present in the fruit juice chain and dis-cussed in the paper, the increasing demand of consumers for sustainable products and the high competition in the sector, communicating different sustainability aspects can be an opportunity for fruit juice producers and retailers to differentiate their products on the highly saturated fruit juice market

Phytome: a platform for plant comparative genomics

Phytome is an online comparative genomics resource that can be applied to functional plant genomics, molecular breeding and evolutionary studies. It contains predicted protein sequences, protein family assignments, multiple sequence alignments, phylogenies and functional annotations for proteins from a large, phylogenetically diverse set of plant taxa. Phytome serves as a glue between disparate plant gene databases both by identifying the evolutionary relationships among orthologous and paralogous protein sequences from different species and by enabling cross-references between different versions of the same gene curated independently by different database groups. The web interface enables sophisticated queries on lineage-specific patterns of gene/protein family proliferation and loss. This rich dataset is serving as a platform for the unification of sequence-anchored comparative maps across taxonomic families of plants. The Phytome web interface can be accessed at the following URL: . Batch homology searches and bulk downloads are available upon free registration

Wellbeing, quality of life, presence of concurrent diseases, and survival times in untreated and treated German Shepherd dogs with dwarfism

Background Pituitary dwarfism (PD) in German Shepherd dogs (GSD) is a rare endocrinopathy. Cause and inheritance of the disease are well characterized, but the overall survival time, presence of concurrent diseases, quality of life (QoL) and influence of different treatment options on those parameters is still not well investigated. The aim of this study was to obtain data regarding the disease pattern of GSD with PD and to investigate the impact of treatment. Methods 47 dogs with dwarfism (presumably PD) and 94 unaffected GSD serving as controls were enrolled. Data were collected via a standardized questionnaire, which every owner of a participating dog had completed. Dogs with PD were grouped based on three categories of treatment: Group 1 (untreated), group 2 (treated with levothyroxine), group 3 (treated with thyroxine and progestogens or with growth hormone (GH)). Groups were compared using One-Way-Anova, Kruskal-Wallis test or Wilcoxon-rank-sum test. Categorical analysis was performed using Two-Sample-Chi-Squared-test. Results Dogs treated with thyroxine and gestagen or GH were significantly taller and heavier compared to all other dogs with PD. Quality of life was best in dogs with PD treated with thyroxine and similar to unaffected GSD. Treatment increased survival time in dogs with PD independent of the treatment strategy. Dogs receiving thyroxine and progestogens or GH did not develop chronic kidney disease (CKD). Conclusion GSD with PD should be treated at least for their secondary hypothyroidism to increase survival time. Additional treatment with progestogens or GH improves body size and seems to protect against the occurrence of CKD

Investigation into the utility of an immunocytochemical assay in body cavity effusions for diagnosis of feline infectious peritonitis

Objectives Feline coronaviruses (FCoVs) exist as two biotypes, feline enteric coronavirus and feline infectious peritonitis virus. Although feline infectious peritonitis (FIP) is a very common disease, the ante-mortem diagnosis of this disease still remains a challenge. Immunofluorescence staining of FCoV in macrophages in effusion has been considered as the reference standard for the diagnosis, but recently this method has been shown to have lower specificity than previously reported. In addition, this method is not widely available and requires the use of fluorescence microscopes. Therefore, it was the aim of this study to evaluate the diagnostic potential of an immunocytochemical (ICC) assay using body cavity effusion. Methods Effusion samples from 27 cats with immunohistochemically confirmed FIP and 29 cats with suspected FIP but a definitive diagnosis of another disease were examined. ICC specimens were evaluated with respect to positive immunostaining. In addition, effusion samples were stained with haematoxylin and eosin and evaluated cytologically. Results A diagnostic sensitivity of 85.2% was recorded for effusion specimens (95% confidence interval [CI] 66.3-95.8), while the diagnostic specificity was only 72.4% (95% CI 52.8-87.3). Conclusions and relevance Once the clinical disease of FIP develops in a cat, it always leads to death, and most of the cats are euthanased within a few days or weeks. As false-positive results might lead to euthanasia of cats suffering from potentially treatable diseases, the diagnostic specificity of a diagnostic tool is the most important factor in a fatal disease like FIP. Thus, the diagnostic utility of this test proved to be insufficient and positive ICC results should be interpreted with caution. Nevertheless, full-body necropsy could not be performed in 13/29 control cats. It is possible that these cats actually suffered from early-stage FIP and that this fact might have influenced the diagnostic specificity of the ICC. Based on the results of the present study, however, ICC of effusion samples currently cannot be recommended to confirm a suspicion of FIP

Ecophysiological, morphological, and biochemical traits of free-living Diplosphaera chodatii (Trebouxiophyceae) reveal adaptation to harsh environmental conditions

Single-celled green algae within the Trebouxiophyceae (Chlorophyta) are typical components of terrestrial habitats, which often exhibit harsh environmental conditions for these microorganisms. This study provides a detailed overview of the ecophysiological, biochemical, and ultrastructural traits of an alga living on tree bark. The alga was isolated from a cypress tree in the Botanical Garden of Innsbruck (Austria) and identified by morphology and molecular phylogeny as Diplosphaera chodatii. Transmission electron microscopy after high-pressure freezing (HPF) showed an excellent preservation of the ultrastructure. The cell wall was bilayered with a smooth inner layer and an outer layer of polysaccharides with a fuzzy hair-like appearance that could possibly act as cell-cell adhesion mechanism and hence as a structural precursor supporting biofilm formation together with the mucilage observed occasionally. The photosynthetic-irradiance curves of D. chodatii indicated low light requirements without photoinhibition at high photon flux densities (1580 μmol photons m−2 s−1) supported by growth rate measurements. D. chodatii showed a high desiccation tolerance, as 85% of its initial value was recovered after controlled desiccation at a relative humidity of ~10%. The alga contained the low molecular weight carbohydrates sucrose and sorbitol, which probably act as protective compounds against desiccation. In addition, a new but chemically not elucidated mycosporine-like amino acid was detected with a molecular mass of 332 g mol−1 and an absorption maximum of 324 nm. The presented data provide various traits which contribute to a better understanding of the adaptive mechanisms of D. chodatii to terrestrial habitats

Diagnostic utility of cerebrospinal fluid immunocytochemistry for diagnosis of feline infectious peritonitis manifesting in the central nervous system

Objectives The aim of the study was to evaluate whether an ante-mortem diagnosis of central nervous system (CNS) feline infectious peritonitis (FIP) is possible via immunocytochemical staining (ICC) of feline coronavirus antigen (FCoV) within macrophages of cerebrospinal fluid (CSF). Methods Prospectively, CSF samples of 41 cats were investigated, including cats with histopathologically confirmed FIP and neurological signs (n = 10), cats with confirmed FIP without CNS involvement (n = 11), cats with neurological signs but another confirmed CNS disease (n = 17), and cats without neurological signs and a disease other than FIP (n = 3). ICC staining of CSF macrophages was performed in all cats. Sensitivity, specificity, positive (PPV) and negative predictive values (NPV) of CSF ICC were calculated. Results Of 10 samples from cats with CNS FIP, eight had detectable CSF macrophages, seven of which were positive for FCoV. Ten of 11 samples from cats with confirmed FIP without neurological signs had macrophages in the CSF, with all 10 being ICC-positive. In cats with other CNS disorders, 11/17 had macrophages, two of which stained positively. In cats with diseases other than FIP and without neurological disorders, 2/3 revealed macrophages, with one cat showing positive ICC staining. Diagnosis of FIP via CSF ICC had a sensitivity of 85.0% and a specificity of 83.3%. PPV and NPV were 85.0% and 83.3%. Conclusions and relevance CSF ICC is a highly sensitive test for ante-mortem diagnosis of FIP manifesting in the CNS. However, CNS ICC specificity is too low to confirm FIP and the method should only be applied in conjunction with other features such as CSF cytology. CNS ICC could be helpful to discover pre-neurological stages of CNS FIP