Phylogenetic support values are not necessarily informative: the case of the Serialia hypothesis (a mollusk phylogeny)

Background: Molecular phylogenies are being published increasingly and many biologists rely on the most recent topologies. However, different phylogenetic trees often contain conflicting results and contradict significant background data. Not knowing how reliable traditional knowledge is, a crucial question concerns the quality of newly produced molecular data. The information content of DNA alignments is rarely discussed, as quality statements are mostly restricted to the statistical support of clades. Here we present a case study of a recently published mollusk phylogeny that contains surprising groupings, based on five genes and 108 species, and we apply new or rarely used tools for the analysis of the information content of alignments and for the filtering of noise (masking of random-like alignment regions, split decomposition, phylogenetic networks, quartet mapping). Results: The data are very fragmentary and contain contaminations. We show that that signal-like patterns in the data set are conflicting and partly not distinct and that the reported strong support for a "rather surprising result" (monoplacophorans and chitons form a monophylum Serialia) does not exist at the level of primary homologies. Split-decomposition, quartet mapping and neighbornet analyses reveal conflicting nucleotide patterns and lack of distinct phylogenetic signal for the deeper phylogeny of mollusks. Conclusion: Even though currently a majority of molecular phylogenies are being justified with reference to the 'statistical' support of clades in tree topologies, this confidence seems to be unfounded. Contradictions between phylogenies based on different analyses are already a strong indication of unnoticed pitfalls. The use of tree-independent tools for exploratory analyses of data quality are highly recommended. Concerning the new mollusk phylogeny more convincing evidence is needed

Psychometric Evaluation of the German Version of the Demoralization Scale-II and the Association Between Demoralization, Sociodemographic, Disease- and Treatment-Related Factors in Patients With Cancer

Objective: To test the psychometric properties, internal consistency, dimensional structure, and convergent validity of the German version of the Demoralization Scale- II (DS-II), and to examine the association between demoralization, sociodemographic, disease- and treatment-related variables in patients with cancer. Methods: We recruited adult patients with cancer at a Psychosocial Counseling Center and at oncological wards. Participants completed the 16-item DS-II, Patient Health Questionnaire-9 (PHQ-9), Generalized Anxiety Disorder Screener-2 (GAD-2), Distress Thermometer (DT), and Body Image Scale (BIS). We analyzed internal consistency of the DS-II using Cronbach‘s Alpha (a). We tested the dimensional structure of the DS-II with Confirmatory Factor Analyses (CFA). Convergent validity was expressed through correlation coefficients with established measures of psychological distress. The associations between demoralization, sociodemographic, disease- and treatmentrelated variables were examined with ANOVAs. Results: Out of 942 eligible patients, 620 participated. The average DS-II total score was M = 5.78, SD = 6.34, the Meaning and Purpose subscale M = 2.20, SD = 3.20, and the Distress and Coping Ability subscale M = 3.58, SD = 3.45. Internal consistency ranged from high to excellent with a = 0.93 for the DS-II total scale, a = 0.90 for the Meaning and Purpose subscale, and a = 0.87 for the Distress and Coping Ability subscale. The one-factor and the two-factor model yielded similar model fits, with CFI and TLI ranging between 0.910 and 0.933, SRMR < 0.05. The DS-II correlated significantly with depression (PHQ-9: r = 0.69), anxiety (GAD-2: r = 0.72), mental distress (DT: r = 0.36), and body image disturbance (BIS: r = 0.58). High levels of demoralization were reported by patients aged between 18 and 49 years (M = 7.77, SD = 6.26), patients who were divorced/separated (M = 7.64, SD = 7.29), lung cancer patients (M = 9.29, SD = 8.20), and those receiving no radiotherapy (M = 7.46, SD = 6.60). Conclusion: The DS-II has very good psychometric properties and can be recommended as a reliable tool for assessing demoralization in patients with cancer. The results support the implementation of a screening for demoralization in specific risk groups due to significantly increased demoralization scores

Potential pitfalls of modelling ribosomal RNA data in phylogenetic tree reconstruction: Evidence from case studies in the Metazoa

<p>Abstract</p> <p>Background</p> <p>Failure to account for covariation patterns in helical regions of ribosomal RNA (rRNA) genes has the potential to misdirect the estimation of the phylogenetic signal of the data. Furthermore, the extremes of length variation among taxa, combined with regional substitution rate variation can mislead the alignment of rRNA sequences and thus distort subsequent tree reconstructions. However, recent developments in phylogenetic methodology now allow a comprehensive integration of secondary structures in alignment and tree reconstruction analyses based on rRNA sequences, which has been shown to correct some of these problems. Here, we explore the potentials of RNA substitution models and the interactions of specific model setups with the inherent pattern of covariation in rRNA stems and substitution rate variation among loop regions.</p> <p>Results</p> <p>We found an explicit impact of RNA substitution models on tree reconstruction analyses. The application of specific RNA models in tree reconstructions is hampered by interaction between the appropriate modelling of covarying sites in stem regions, and excessive homoplasy in some loop regions. RNA models often failed to recover reasonable trees when single-stranded regions are excessively homoplastic, because these regions contribute a greater proportion of the data when covarying sites are essentially downweighted. In this context, the RNA6A model outperformed all other models, including the more parametrized RNA7 and RNA16 models.</p> <p>Conclusions</p> <p>Our results depict a trade-off between increased accuracy in estimation of interdependencies in helical regions with the risk of magnifying positions lacking phylogenetic signal. We can therefore conclude that caution is warranted when applying rRNA covariation models, and suggest that loop regions be independently screened for phylogenetic signal, and eliminated when they are indistinguishable from random noise. In addition to covariation and homoplasy, other factors, like non-stationarity of substitution rates and base compositional heterogeneity, can disrupt the signal of ribosomal RNA data. All these factors dictate sophisticated estimation of evolutionary pattern in rRNA data, just as other molecular data require similarly complicated (but different) corrections.</p

High correlation of the proteome patterns in bone marrow and peripheral blood blast cells in patients with acute myeloid leukemia

<p>Abstract</p> <p>Background</p> <p>When comparing myelogenous blasts from bone marrow and peripheral blood, immunophenotyping usually show a strong correlation of expression of surface antigens. However, it remains to be determined, whether this correlation also exists on the level of protein expression.</p> <p>Method</p> <p>Therefore, we investigated both bone marrow and peripheral blood blast cells from six patients with newly diagnosed acute myeloid leukemia (AML) using conventional two-dimensional electrophoresis in the first dimension and linear polyacrylamide gels (12%) in the second dimension. Proteins were visualized using the silver staining method and image analysis was performed using the PDQuest system.</p> <p>Results</p> <p>For each patient over 80 proteins were evaluated in the sample from peripheral blood and bone marrow. We could demonstrate that the protein expression profile of bone marrow did not significantly differ from the expression patterns of peripheral blast cells.</p> <p>Conclusion</p> <p>The proteome-set of leukemic blast cells from marrow and blood, does not differ substantially when drawn from AML patients with over 80 percent blast cells in both compartments. This indicates that in AML, blasts from peripheral blood samples can be considered suitable for investigations of the proteome using 2D-electrophoresis.</p

Harmonization of the intracellular cytokine staining assay

Active immunotherapy for cancer is an accepted treatment modality aiming to reinforce the T-cell response to cancer. T-cell reactivity is measured by various assays and used to guide the clinical development of immunotherapeutics. However, data obtained across different institutions may vary substantially making comparative conclusions difficult. The Cancer Immunotherapy Immunoguiding Program organizes proficiency panels to identify key parameters influencing the outcome of commonly used T-cell assays followed by harmonization. Our successes with IFNγ-ELISPOT and peptide HLA multimer analysis have led to the current study on intracellular cytokine staining (ICS). We report the results of three successive panels evaluating this assay. At the beginning, 3 out of 9 participants (33 %) were able to detect >6 out of 8 known virus-specific T-cell responses in peripheral blood of healthy individuals. This increased to 50 % of the laboratories in the second phase. The reported percentages of cytokine-producing T cells by the different laboratories were highly variable with coefficients of variation well over 60 %. Variability could partially be explained by protocol-related differences in background cytokine production leading to sub-optimal signal-to-noise ratios. The large number of protocol variables prohibited identification of prime guidelines to harmonize the assays. In addition, the gating strategy used to identify reactive T cells had a major impact on assay outcome. Subsequent harmonization of the gating strategy considerably reduced the variability within the group of participants. In conclusion, we propose that first basic guidelines should be applied for gating in ICS experiments before harmonizing assay protocol variables

CCL25-CCR9 interaction modulates ovarian cancer cell migration, metalloproteinase expression, and invasion

<p>Abstract</p> <p>Background</p> <p>Ovarian carcinoma (OvCa) is the most lethal gynecological malignancy among women and its poor prognosis is mainly due to metastasis. Chemokine receptor CCR9 is primarily expressed by a small subset of immune cells and its only natural ligand, CCL25, is largely expressed in the thymus, which involutes with age. Other than the thymus, CCL25 is expressed by the small bowel. Interactions between CCL25 and CCR9 have been implicated in leukocyte trafficking to the small bowel, a frequent metastatic site for OvCa cells. The current study shows OvCa tissue and cells significantly express CCR9, which interacts with CCL25 to support carcinoma cell migration and invasion.</p> <p>Methods</p> <p>RT-PCR and flow cytometry techniques were used to quantify the expression CCR9 by OvCa cells. OvCa tissue microarrays (TMA) was used to confirm CCR9 expression in clinical samples. The Aperio ScanScope scanning system was used to quantify immunohistochemical staining. Cell invasion and migration assays were performed using cell migration and matrigel invasion chambers. Matrix metalloproteinase (MMP) mRNAs were quantified by RT-PCR and active MMPs were quantified by ELISA.</p> <p>Results</p> <p>Our results show significantly (<it>p </it>< 0.001) higher expression of CCR9 by mucinous adenocarcinoma, papillary serous carcinoma, and endometriod ovarian carcinoma cases, than compared to non-neoplastic ovarian tissue. Furthermore, CCR9 expression was significantly elevated in OvCa cell lines (OVCAR-3 and CAOV-3) in comparison to normal adult ovarian epithelial cell mRNA. OvCa cells showed higher migratory and invasive potential towards chemotactic gradients of CCL25, which was inhibited by anti-CCR9 antibodies. Expression of collagenases (MMP-1, -8, and -13), gelatinases (MMP-2 and -9), and stromelysins (MMP-3, -10, and -11) by OvCa cells were modulated by CCL25 in a CCR9-dependent fashion.</p> <p>Conclusions</p> <p>These results demonstrate both biological significance and clinical relevance of CCL25 and CCR9 interactions in OvCa cell metastasis.</p

Shipping blood to a central laboratory in multicenter clinical trials: effect of ambient temperature on specimen temperature, and effects of temperature on mononuclear cell yield, viability and immunologic function

<p>Abstract</p> <p>Background</p> <p>Clinical trials of immunologic therapies provide opportunities to study the cellular and molecular effects of those therapies and may permit identification of biomarkers of response. When the trials are performed at multiple centers, transport and storage of clinical specimens become important variables that may affect lymphocyte viability and function in blood and tissue specimens. The effect of temperature during storage and shipment of peripheral blood on subsequent processing, recovery, and function of lymphocytes is understudied and represents the focus of this study.</p> <p>Methods</p> <p>Peripheral blood samples (n = 285) from patients enrolled in 2 clinical trials of a melanoma vaccine were shipped from clinical centers 250 or 1100 miles to a central laboratory at the sponsoring institution. The yield of peripheral blood mononuclear cells (PBMC) collected before and after cryostorage was correlated with temperatures encountered during shipment. Also, to simulate shipping of whole blood, heparinized blood from healthy donors was collected and stored at 15°C, 22°C, 30°C, or 40°C, for varied intervals before isolation of PBMC. Specimen integrity was assessed by measures of yield, recovery, viability, and function of isolated lymphocytes. Several packaging systems were also evaluated during simulated shipping for the ability to maintain the internal temperature in adverse temperatures over time.</p> <p>Results</p> <p>Blood specimen containers experienced temperatures during shipment ranging from -1 to 35°C. Exposure to temperatures above room temperature (22°C) resulted in greater yields of PBMC. Reduced cell recovery following cryo-preservation as well as decreased viability and immune function were observed in specimens exposed to 15°C or 40°C for greater than 8 hours when compared to storage at 22°C. There was a trend toward improved preservation of blood specimen integrity stored at 30°C prior to processing for all time points tested. Internal temperatures of blood shipping containers were maintained longer in an acceptable range when warm packs were included.</p> <p>Conclusions</p> <p>Blood packages shipped overnight by commercial carrier may encounter extreme seasonal temperatures. Therefore, considerations in the design of shipping containers should include protecting against extreme ambient temperature deviations and maintaining specimen temperature above 22°C or preferably near 30°C.</p