NewickTreeModifier: A simple web tool to prune and modify Newick trees

Large-scale selection analyses of protein-coding sequences and phylogenetic tree reconstructions require suitable trees in Newick format. We developed the NewickTreeModifier (NTM), a simple web-based tool to trim and modify Newick trees for such analyses. The users can choose provided master trees or upload a tree to prune it to selected species available in FASTA, NEXUS, or PHYLIP sequence format with an internal converter, a simple species list, or directly determined from a checklist interface of the master trees. Plant, insect, and vertebrate master trees comprise the maximum number of species in an up-to-date phylogenetic order directly transferable to the pruned Newick outfile. NTM is available at https://retrogenomics.uni-muenster.de/tools/ntm.

Evaluation of colour vision impairment during acute hypobaric hypoxia in aviation medicine: a randomized controlled trial

The digitization of aircraft cockpits places high demands on the colour vision of pilots. The present study investigates colour vision changes upon acute exposure to hypobaric hypoxia. The digital Waggoner Computerized Color Vision Test and the Waggoner D-15 were performed by 54 healthy volunteers in a decompression chamber. Respective altitude levels were sea level, 10,000 or 15,000 ft for exposure periods of 15 and 60 min, respectively. As for 60 min of exposure a significant decrease in colour perception was found between subjects at 15,000 ft as compared to the control group as well as between subjects at 15,000 ft as compared to subjects at 10,000 ft. No significant difference was found in the comparison within the 15,000 ft groups across time points pre-, peri-, and post-exposure. Thus, pilots appear to experience only minor colour vision impairment up to an exposure altitude of 15,000 ft over 60 min of exposure.

Homoplasy of Retrotransposon Insertions in Toothed Whales

Retrotransposon insertion patterns facilitate a virtually homoplasy-free picture of phylogenetic history. Still, a few most likely random parallel insertions or deletions result in rare cases of homoplasy in primates. The following question arises: how frequent is retrotransposon homoplasy in other phylogenetic clades? Here, we derived genome insertion data of toothed whales to evaluate the extension of homoplasy in a representative laurasiatherian group. Among more than a thousand extracted and aligned retrotransposon loci, we detected 37 cases of precise parallel insertions in species that are separated by over more than 10 million years, a time frame which minimizes the effects of incomplete lineage sorting. We compared the phylogenetic signal of insertions with the flanking sequences of these loci to further exclude potential polymorphic loci derived by incomplete lineage sorting. We found that the phylogenetic signals of retrotransposon insertion patterns exhibiting true homoplasy differ from the signals of their flanking sequences. In toothed whales, precise parallel insertions account for around 0.18-0.29% of insertion cases, which is about 12.5 times the frequency of such insertions among Alus in primates. We also detected five specific deletions of retrotransposons on various lineages of toothed whale evolution, a frequency of 0.003%, which is slightly higher than such occurrences in primates. Overall, the level of retrotransposon homoplasy in toothed whales is still marginal compared to the phylogenetic diagnostic retrotransposon presence/absence signal.

A 4-lineage Statistical Suite to Evaluate the Support of Large-Scale Retrotransposon Insertion Data to Reconstruct Evolutionary Trees

Retrophylogenomics makes use of genome-wide retrotransposon presence/absence insertion patterns to resolve questions in phylogeny and population genetics. In the genomics era, evaluating high-throughput data requires the associated development of appropriately powerful statistical tools. The currently used KKSC 3-lineage statistical test for estimating the significance of retrophylogenomic data is limited by the number of possible tree topologies it can assess in one step. To improve on this, we have extended the analysis to simultaneously compare four lineages, enabling us to evaluate ten distinct presence/absence insertion patterns for 26 possible tree topologies plus 129 trees with different incidences of hybridization or introgression. The new tool provides statistics for cases involving multiple ancestral hybridizations/introgressions, ancestral incomplete lineage sorting, bifurcation, and polytomy. The test is embedded in a user-friendly web R application (http://retrogenomics.uni-muenster.de:3838/hammlet/) and is available for use by the scientific community. [ancestral hybridization/introgression; ancestral incomplete lineage sorting (ILS); empirical distribution; KKSC-statistics; 4-lineage (4-LIN) insertion polymorphism; polytomy; retrophylogenomics.].

Unusual Combination of Gastrointestinal Pathogens Detected by Multiplex PCR

Introduction/Objective

Infectious gastroenteritis (IGE) is a common but complex entity which is a major cause of global morbidity and mortality. IGE is caused by a wide range of etiologic agents such as viruses, bacteria, and parasites. In the United States there are approximately 373 million of IGE cases per year. Most cases of IGE resolve without identification of a specific pathogen. Multiplex molecular assays allow identification of multiple possible pathogens with rapid turnaround time and increased sensitivity, facilitating to formulate an effective treatment plan and control measures.

Methods/Case Report

We present a case of a pediatric patient with no significant past medical history who has been having runny stools that have progressively worsened in the last 3 months and 2 days history of bloody stools with mucus before emergency room presentation. She had no fever, vomiting, joint pain, oral ulcer, and rash. Physical exam showed that the patient appeared well, nontoxic, and vital signs were within normal limit. Copious rhinorrhea was noted. She was at 50th percentile for age on the growth chart. Family denied any recent travel or sick contacts however stated that all the family members have been on well water. Complete blood count was obtained and showed a platelet count of 669 x 10(3)/mcL and WBC of 16.6 x 10(3)/mcL with differential showing absolute lymphocytosis, absolute monocytosis and absolute eosinophilia. Biofire FilmArray gastrointestinal panel performed on the stool detected Giardia lamblia, Campylobacter, Shiga-like toxin producing E. coli and Adenovirus F 40/41. Repeat of the panel per protocol detected the same four pathogens.

Results (if a Case Study enter NA)

N/A.

Conclusion

This case report highlights the significance of detecting multiple causative pathogens. While long term watery diarrhea may guide clinicians to malabsorptive process and the use of well water to Giardia, a sensitive and specific multiplex assay can detect all the pathogens involved in the disease process and greatly simplify the treatment plan for patients. This unusual combination of pathogens can explain the unique symptomology of the patient including long term watery diarrhea, recent bloody diarrhea as well as copious rhinorrhea and failure to thrive.

ExoPLOT: Representation of alternative splicing in human tissues and developmental stages with transposed element (TE) involvement

Advances in RNA high-throughput sequencing and large-scale functional assays yield new insights into the multifaceted activities of transposed elements (TE) and many other previously undiscovered sequence elements. Currently, no tool for easy access, analysis, quantification, and visualization of alternatively spliced exons across multiple tissues or developmental stages is available. Also, analysis pipelines demand computational skills or hardware requirements, which often are hard to meet by wet-lab scientists. We developed ExoPLOT to enable simplified access to massive RNA high throughput sequencing datasets to facilitate the analysis of alternative splicing across many biological samples. To demonstrate the functonality of ExoPLOT, we analyzed the contributon of exonized TEs to human coding sequences (CDS). mRNA splice variants containing the TE-derived exon were quantified and compared to expression levels of TE-free splice variants. For analysis, we utilized 313 human cerebrum, cerebellum, heart, kidney, liver, ovary, and testis transcriptomes, representing various pre- and postnatal developmental stages. ExoPLOT visualizes the relative expression levels of alternative transcripts, e.g., caused by the insertion of new TE-derived exons, across different developmental stages of and among multiple tissues. This tool also provides a unique link between evolution and function during exonization (gain of a new exon) and exaptation (recruitment/co-optation) of a new exon. As input for analysis, we derived a database of 1151 repeat-masked, exonized TEs, representing all prominent families of transposons in the human genome and the collection of human consensus coding sequences (CCDS). ExoPLOT screened preprocessed RNA high-throughput sequencing datasets from seven human tissues to quantify and visualize the dynamics in RNA splicing for these 1151 TE-derived exons during the entire human organ development. In addition, we successfully mapped and analyzed 993 recently described exonized sequences from the human frontal cortex onto these 313 transcriptome libraries. ExoPLOT's approach to preprocessing RNA deep sequencing datasets facilitates alternative splicing analysis and significantly reduces processing times. In addition, ExoPLOT's design allows studying alternative RNA isoforms other than TE-derived in a customized - coordinate-based manner and is available at http://retrogenomics3.uni-muenster.de:3838/exz-plot-d/.

Euarchontoglires Challenged by Incomplete Lineage Sorting

Euarchontoglires, once described as Supraprimates, comprise primates, colugos, tree shrews, rodents, and lagomorphs in a clade that evolved about 90 million years ago (mya) from a shared ancestor with Laurasiatheria. The rapid speciation of groups within Euarchontoglires, and the subsequent inherent incomplete marker fixation in ancestral lineages, led to challenged attempts at phylogenetic reconstructions, particularly for the phylogenetic position of tree shrews. To resolve this conundrum, we sampled genome-wide presence/absence patterns of transposed elements (TEs) from all representatives of Euarchontoglires. This specific marker system has the advantage that phylogenetic diagnostic characters can be extracted in a nearly unbiased fashion genome-wide from reference genomes. Their insertions are virtually free of homoplasy. We simultaneously employed two computational tools, the genome presence/absence compiler (GPAC) and 2-n-way, to find a maximum of diagnostic insertions from more than 3 million TE positions. From 361 extracted diagnostic TEs, 132 provide significant support for the current resolution of Primatomorpha (Primates plus Dermoptera), 94 support the union of Euarchonta (Primates, Dermoptera, plus Scandentia), and 135 marker insertion patterns support a variety of alternative phylogenetic scenarios. Thus, whole genome-level analysis and a virtually homoplasy-free marker system offer an opportunity to finally resolve the notorious phylogenetic challenges that nature produces in rapidly diversifying groups.

MACSima imaging cyclic staining (MICS) technology reveals combinatorial target pairs for CAR T cell treatment of solid tumors

Many critical advances in research utilize techniques that combine high-resolution with high-content characterization at the single cell level. We introduce the MICS (MACSima Imaging Cyclic Staining) technology, which enables the immunofluorescent imaging of hundreds of protein targets across a single specimen at subcellular resolution. MICS is based on cycles of staining, imaging, and erasure, using photobleaching of fluorescent labels of recombinant antibodies (REAfinity Antibodies), or release of antibodies (REAlease Antibodies) or their labels (REAdye_lease Antibodies). Multimarker analysis can identify potential targets for immune therapy against solid tumors. With MICS we analysed human glioblastoma, ovarian and pancreatic carcinoma, and 16 healthy tissues, identifying the pair EPCAM/THY1 as a potential target for chimeric antigen receptor (CAR) T cell therapy for ovarian carcinoma. Using an Adapter CAR T cell approach, we show selective killing of cells only if both markers are expressed. MICS represents a new high-content microscopy methodology widely applicable for personalized medicine.

OUP accepted manuscript

Although first posited to be of a single origin, the two superfamilies of phalangeriform marsupial possums (Phalangeroidea: brushtail possums and cuscuses and Petauroidea: possums and gliders) have long been considered, based on multiple sequencing studies, to have evolved from two separate origins. However, previous data from these sequence analyses suggested a variety of conflicting trees. Therefore, we reinvestigated these relationships by screening \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$\sim$\end{document}200,000 orthologous short interspersed element (SINE) loci across the newly available whole-genome sequences of phalangeriform species and their relatives. Compared to sequence data, SINE presence/absence patterns are evolutionarily almost neutral molecular markers of the phylogenetic history of species. Their random and highly complex genomic insertion ensures their virtually homoplasy-free nature and enables one to compare hundreds of shared unique orthologous events to determine the true species tree. Here, we identify 106 highly reliable phylogenetic SINE markers whose presence/absence patterns within multiple Australasian possum genomes unexpectedly provide the first significant evidence for the reunification of Australasian possums into one monophyletic group. Together, our findings indicate that nucleotide homoplasy and ancestral incomplete lineage sorting have most likely driven the conflicting signal distributions seen in previous sequence-based studies. [Ancestral incomplete lineage sorting; possum genomes; possum monophyly; retrophylogenomics; SINE presence/absence.]

Evolution of renal-disease factor APOL1 results in cis and trans orientations at the endoplasmic reticulum that both show cytotoxic effects

The recent and exclusively in humans and a few other higher primates expressed APOL1 (apolipoprotein L1) gene is linked to African human trypanosomiasis (also known as African sleeping sickness) as well as to different forms of kidney diseases. Whereas APOL1’s role as a trypanolytic factor is well established, pathobiological mechanisms explaining its cytotoxicity in renal cells remain unclear. In this study, we compared the APOL family members using a combination of evolutionary studies and cell biological experiments to detect unique features causal for APOL1 nephrotoxic effects.

We investigated available primate and mouse genome and transcriptome data to apply comparative phylogenetic and maximum likelihood selection analyses. We suggest that the APOL gene family evolved early in vertebrates and initial splitting occurred in ancestral mammals. Diversification and differentiation of functional domains continued in primates, including developing the two members APOL1 and APOL2. Their close relationship could be diagnosed by sequence similarity and a shared ancestral insertion of an AluY transposable element. Live-cell imaging analyses showed that both expressed proteins show a strong preference to localize at the endoplasmic reticulum (ER). However, glycosylation and secretion assays revealed that—unlike APOL2—APOL1 membrane insertion or association occurs in different orientations at the ER, with the disease-associated mutants facing either the luminal (cis) or cytoplasmic (trans) side of the ER. The various pools of APOL1 at the ER offer a novel perspective in explaining the broad spectrum of its observed toxic effects.

Microbiologic Proof-Of-Concept: A Novel Device Combining UV Light And Ozone For Human Skin Antisepsis

Introduction/Objective

Hand hygiene (HH) decreases healthcare-associated infections (HAI). Available products include alcohol-based gels, foams, wipes, and “gold-standard” hand-washing with soap and water. We tested an investigational device (HyLuxO3; GMI, LLC, patent pending) for antimicrobial effect (AME). HyLuxO3 was engineered to deliver UV-C light energy and high velocity O3 airflow to safely achieve human skin antisepsis within OSHA and EPA regulatory limits. Combined UV and O3 has yet to be evaluated for HH and may demonstrate synergistic AME.

Methods

HyLuxO3 was tested on LB agar to titrate device variables to ascertain intensities for optimal AME; later testing was performed on VITRO-SKIN (Florida Suncare Testing, Bunnell, FL), a human skin surrogate. ATCC strains of MRSA, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Candida albicans were used to test AME vs. vegetative microbes; Bacillus atrophaeus spores were used as a surrogate for C. difficile. Tested variables included time under device, [O3], airflow velocity, 222 and/or 254 nm UV light, sample distance from UV lamp, and UV beam width. Positive controls were used to calculate log-kill curves for AME.

Results

Similar results were seen on LB agar and VITRO-SKIN. >7 log-kill and >5 log-kill were acheived vs. vegetative microbes (<30 sec) and spores (60 sec), respectively, under optimized variables. Presence of UV light and sample distance from and time under the device were the most important variables. 254 nm UV had a significantly better AME than 222 nm; combining both UV lamps had a significant synergistic AME. The narrowest UV beam (2 mm) yielded the greatest AME (total energy input kept constant). Adding O3 to UV had a modest but significant synergistic effect; optimal [O3] was 0.3-0.8 ppm. Changing airflow velocity had no significant effect on AME.

Conclusion

HyLuxO3 is a novel device that achieves >7 log-kill vs. common pathogenic vegetative microbes and >5 log-kill vs. spores using combined UV light and [O3] safe for human skin antisepsis (and surface/fomite decontamination)- and- yields such impressive AME on faster timescales than those required by bleach/other chemical products unsuitable for human skin. Future studies on human hands (using many other microbes) will determine if HyLuxO3 meets regulatory and efficacy requirements for use in and beyond healthcare settings, especially with the specter of emerging respiratory viruses.

Complex segregation analysis of familial amyloidosis in Oriental shorthair cats

Amyloidosis in Siamese/Oriental cats is a lethal condition with variable age of clinical onset. There is no sex predisposition and clinical signs of disease usually become apparent by 1-7 years of age. In the terminal stages, the liver is enlarged and pale, and contains parenchymal hemorrhages. In the present study, pedigree data from 17 cats with clinical signs consistent with amyloidosis underwent genetic analysis. Necropsy and histopathological data were available for 10 of the 17 cats. Necropsy findings included pale, fragile and enlarged livers with capsular ruptures and parenchymal hemorrhages, and sanguineous effusions in the abdominal cavity. Congo red staining with birefringence confirmed systemic amyloidosis mostly involving the liver and thyroid gland. In four of the 10 cases, protein deposits were classified as amyloid A protein (AA-amyloid) by immunostaining. Pedigree data for all 17 affected cats indicated a familial trait. Animal threshold model analysis demonstrated that the heritability for amyloidosis was 0.56 ± 0.09 (standard error). Complex segregation analysis was used for statistical comparisons among models to determine environmental or sex dependent effects, and Mendelian, polygenic, or mixed Mendelian and polygenic inheritance patterns. A mixed model with a Mendelian and polygenic component provided the best fit to the data and thus was most likely. All other models of inheritance were rejected due to their insufficient ability to explain segregation of amyloidosis. In conclusion, we found evidence for a complex genetic basis for amyloidosis in Oriental shorthair cats.

Examination of preliminary behavioral and effective connectivity findings from treatment response to citalopram in cocaine use disorder: A dynamic causal modeling study

We sought effective (directional) connectivity parameters associated with response to citalopram in cocaine use disorder (CUD) by conducting a functional magnetic resonance imaging (fMRI) experiment with participants diagnosed with CUD (n = 13) and matched healthy controls (HC; n = 17). CUD participants showed a positive correlation between bilateral DLPFC-to-putamen effective connectivity and treatment effectiveness score. These preliminary results support further investigation of prefrontal-striatal interactions in response to treatment in CUD.

SARS-CoV-2-reactive T cells in healthy donors and patients with COVID-19

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused the rapidly unfolding coronavirus disease 2019 (COVID-19) pandemic^1,2. Clinical manifestations of COVID-19 vary, ranging from asymptomatic infection to respiratory failure. The mechanisms that determine such variable outcomes remain unresolved. Here we investigated CD4⁺ T cells that are reactive against the spike glycoprotein of SARS-CoV-2 in the peripheral blood of patients with COVID-19 and SARS-CoV-2-unexposed healthy donors. We detected spike-reactive CD4⁺ T cells not only in 83% of patients with COVID-19 but also in 35% of healthy donors. Spike-reactive CD4⁺ T cells in healthy donors were primarily active against C-terminal epitopes in the spike protein, which show a higher homology to spike glycoproteins of human endemic coronaviruses, compared with N-terminal epitopes. Spike-protein-reactive T cell lines generated from SARS-CoV-2-naive healthy donors responded similarly to the C-terminal region of the spike proteins of the human endemic coronaviruses 229E and OC43, as well as that of SARS-CoV-2. This results indicate that spike-protein cross-reactive T cells are present, which were probably generated during previous encounters with endemic coronaviruses. The effect of pre-existing SARS-CoV-2 cross-reactive T cells on clinical outcomes remains to be determined in larger cohorts. However, the presence of spike-protein cross-reactive T cells in a considerable fraction of the general population may affect the dynamics of the current pandemic, and has important implications for the design and analysis of upcoming trials investigating COVID-19 vaccines.

Auswirkung der Implementierung eines Schockraumkoordinators auf Prozessparameter der Polytraumaversorgung im Schockraum eines Maximalversorgers

Hintergrund

In der Altersgruppe bis 40 Jahre stellt das schwere Trauma die häufigste Todesursache in Deutschland dar. Entsprechend der S3-Leitlinie „Polytrauma/Schwerverletztenbehandlung“ ist seit 2011 die Anwesenheit eines Schockraumkoordinators in Erwägung zu ziehen, der durch optimierte Versorgungs- und Behandlungsabläufe das Überleben der Patienten verbessern kann. Ziel der vorliegenden Untersuchung war die Analyse unterschiedlicher Prozessparameter zur Schockraumversorgung polytraumatisierter Patienten vor und nach Implementierung eines Schockraumkoordinators für die Polytraumaversorgung.

Material und Methoden

Um einen ausreichenden zeitlichen Abstand zum Zeitpunkt der Neueinführungen (2011) einzuhalten, wurden die Jahre 2009 und 2012 zum Vergleich herangezogen: Alle eingescannten Schockraumprotokolle der Jahre 2009 (01.01.2009–31.12.2009) und 2012 (01.01.2012–31.12.2012) wurden gesichtet und ausgewertet.

Ergebnisse

Aus dem Jahr 2009 wurden 213 und aus dem Jahr 2012 wurden 420 Schockraumeinsätze in die Auswertung einbezogen. Die durchschnittliche Schockraumanzahl lag im Jahr 2009 bei 17,8/Monat und im Jahr 2012 bei 35/Monat. Die mittlere Anzahl der Schockraumeinsätze hat sich nahezu verdoppelt (p < 0,001). Die mittlere Schockraumdauer lag im Jahr 2012 im Durchschnitt 5,8 min unter der im Jahr 2009 (p = 0,56).

Schlussfolgerungen

Die Patientenversorgung war in Anwesenheit eines Schockraumkoordinators bzw. nach Implementierung der SOP weder statistisch signifikant noch klinisch relevant verkürzt.

Risk factors for Cesarean delivery in pregnancy with small-for-gestational-age fetus undergoing induction of labor

OBJECTIVES

To identify risk factors for Cesarean delivery and non-reassuring fetal heart tracing (NRFHT) in pregnancies with a small-for-gestational-age (SGA) fetus undergoing induction of labor and to design and validate a prediction model, combining antenatal and intrapartum variables known at the time of labor induction, to identify pregnancies at increased risk of Cesarean delivery.

METHODS

This was a retrospective cohort study of non-anomalous, singleton gestations with a SGA fetus that underwent induction of labor, delivered in a single tertiary referral center between January 2011 and December 2016. SGA was defined as estimated fetal weight (EFW) < 10^th percentile. The primary outcome was to identify risk factors associated with Cesarean delivery. The secondary outcome was to identify risk factors associated with NRFHT. Univariate and multivariate analyses were used to determine which clinical characteristics, available at the time of admission, had the strongest association with Cesarean delivery and NRFHT during labor induction. The predictive value of the final models was assessed by the area under the receiver-operating-characteristics curve (AUC). Sensitivity and specificity of the models were also assessed. Internal validation of the models was performed using 10 000 bootstrap replicates of the original cohort. The adequacy of the models was evaluated using the Hosmer-Lemeshow goodness-of-fit test.

RESULTS

A total of 594 pregnancies were included. Cesarean delivery was performed in 243 (40.9%) pregnancies. Significant risk factors associated with Cesarean delivery, and included in the final model, were maternal age, gestational age at delivery and initial method of labor induction. The bootstrap estimate of the AUC of the final prediction model for Cesarean delivery was 0.82 (95% CI, 0.78-0.86). The model had sensitivity of 64.2%, specificity of 86.9%, positive likelihood ratio (LR) of 4.9 and negative LR of 0.41. The model had good fit (P = 0.617). NRFHT complicated 117 (19.7%) pregnancies. Significant risk factors for NRFHT included EFW < 5^th percentile, abnormal umbilical artery Doppler studies (pulsatility index > 95^th percentile or absent/reversed end-diastolic flow) and gestational age at delivery. The final prediction model for NRFHT had an AUC of 0.69 (95% CI, 0.63-0.75) and specificity of 97.0%.

CONCLUSION

We identified several significant risk factors for Cesarean delivery and NRFHT among SGA pregnancies undergoing induction of labor. Clinicians may use these risk factors to guide patient counseling and to help anticipate the potential need for operative delivery. Copyright © 2019 ISUOG. Published by John Wiley & Sons Ltd.

Determination of Low-Level Pesticide Residues in Soft Drinks and Sports Drinks by Liquid Chromatography with Tandem Mass Spectrometry: Collaborative Study

A collaborative study was conducted on a method for the measurement of 11 low-level pesticide residues in soft drinks and sports drinks by liquid chromatography with tandem mass spectrometry. The pesticide residues determined in this study were alachlor, atrazine, butachlor, isoproturon, malaoxon, monocrotophos, methyl paraoxon, phorate, phorate sulfone, phorate sulfoxide, and 2,4-dichlorophenoxyacetic acid (2,4-D). Blind fortification solutions containing 3 different levels of pesticide residues were provided to 9 collaborating laboratories to create test samples at concentrations of 0, 0.1, and 0.5 g/L with a 10-fold concentration for phorate in a total of 6 matrixes (2 colas, 1 diet cola, 1 clear lemon-lime soft drink, 1 orange soft drink, and 1 sports drink). Good qualitative performance of the method was demonstrated for all pesticide residues. Reproducibility relative standard deviation (RSDR) ranged from 7 to 151 for alachlor, atrazine, butachlor, isoproturon, malaoxon, monocrotophos, methyl paraoxon, phorate, phorate sulfone, phorate sulfoxide, and 2,4-D at the 0.1 g/L level (1.0 g/L for phorate). At 0.5 g/L (5.0 g/L for phorate), RSDR ranged from 9 to 57 for alachlor, atrazine, butachlor isoproturon, malaoxon, monocrotophos, methyl paraoxon, phorate, phorate sulfone, phorate sulfoxide, and 2,4-D in all matrixes. Repeatability relative standard deviation (RSDr), applicable to the diet cola and sports drink, ranged from 0 to 124 for the 11 pesticide residues at the 0.1 g/L level (1.0 g/L for phorate). At 0.5 g/L (5.0 g/L for phorate), RSDr ranged from 4 to 26. Recoveries for the 11 pesticide residues in all matrixes ranged from 84 to 300 at the 0.1 g/L level (1.0 g/L for phorate) and from 66 to 127 at the 0.5 g/L (5.0 g/L for phorate) level. Coefficients of determination (r2) of the matrix-matched calibration curves were 0.95. It is recommended that the method be accepted by AOAC as Official First Action with a limit of quantification of 0.5 g/L for alachlor, atrazine, butachlor, isoproturon, malaoxon, methyl paraoxon, monocrotophos, phorate sulfone, phorate sulfoxide, and 2,4-D and 5.0 g/L for phorate.

Kidney injury enhances renal G-CSF expression and modulates granulopoiesis and human neutrophil CD177 in vivo

Kidney injury significantly increases overall mortality. Neutrophilic granulocytes (neutrophils) are the most abundant human blood leukocytes. They are characterized by a high turnover rate, chiefly controlled by granulocyte colony stimulating factor (G‐CSF). The role of kidney injury and uremia in regulation of granulopoiesis has not been reported. Kidney transplantation, which inherently causes ischemia–reperfusion injury of the graft, elevated human neutrophil expression of the surface glycoprotein CD177. CD177 is among the most G‐CSF‐responsive neutrophil genes and reversibly increased on neutrophils of healthy donors who received recombinant G‐CSF. In kidney graft recipients, a transient rise in neutrophil CD177 correlated with renal tubular epithelial G‐CSF expression. In contrast, CD177 was unaltered in patients with chronic renal impairment and independent of renal replacement therapy. Under controlled conditions of experimental ischemia–reperfusion and unilateral ureteral obstruction injuries in mice, renal G‐CSF mRNA and protein expression significantly increased and systemic neutrophilia developed. Human renal tubular epithelial cell G‐CSF expression was promoted by hypoxia and proinflammatory cytokine interleukin 17A in vitro. Clinically, recipients of ABO blood group‐incompatible kidney grafts developed a larger rise in neutrophil CD177. Their grafts are characterized by complement C4d deposition on the renal endothelium, even in the absence of rejection. Indeed, complement activation, but not hypoxia, induced primary human endothelial cell G‐CSF expression. Our data demonstrate that kidney injury induces renal G‐CSF expression and modulates granulopoiesis. They delineate differential G‐CSF regulation in renal epithelium and endothelium. Altered granulopoiesis may contribute to the systemic impact of kidney injury.

True Homoplasy of Retrotransposon Insertions in Primates

How reliable are the presence/absence insertion patterns of the supposedly homoplasy-free retrotransposons, which were randomly inserted in the quasi infinite genomic space? To systematically examine this question in an up-to-date, multigenome comparison, we screened millions of primate transposed Alu SINE elements for incidences of homoplasious precise insertions and deletions. In genome-wide analyses, we identified and manually verified nine cases of precise parallel Alu insertions of apparently identical elements at orthologous positions in two ape lineages and twelve incidences of precise deletions of previously established SINEs. Correspondingly, eight precise parallel insertions and no exact deletions were detected in a comparison of lemuriform primate and human insertions spanning the range of primate diversity. With an overall frequency of homoplasious Alu insertions of only 0.01% (for human-chimpanzee-rhesus macaque) and 0.02-0.04% (for human-bushbaby-lemurs) and precise Alu deletions of 0.001-0.002% (for human-chimpanzee-rhesus macaque), real homoplasy is not considered to be a quantitatively relevant source of evolutionary noise. Thus, presence/absence patterns of Alu retrotransposons and, presumably, all LINE1-mobilized elements represent indeed the virtually homoplasy-free markers they are considered to be. Therefore, ancestral incomplete lineage sorting and hybridization remain the only serious sources of conflicting presence/absence patterns of retrotransposon insertions, and as such are detectable and quantifiable. [Homoplasy; precise deletions; precise parallel insertions; primates; retrotransposons.].

The Volcano Rabbit in the Phylogenetic Network of Lagomorphs

The order Lagomorpha unifies pikas (Ochotonidae) and the hares plus rabbits (Leporidae). Phylogenetic reconstructions of the species within Leporidae based on traditional morphological or molecular sequence data provide support for conflicting hypotheses. The retroposon presence/absence patterns analyzed in this study revealed strong support for the broadly accepted splitting of lagomorphs into ochotonids and leporids with Pronolagus as the first divergence in the leporid tree. Furthermore, the retroposon presence/absence patterns nested the rare volcano rabbit, Romerolagus diazi, within an unresolved network of deeper leporid relationships and provide the first homoplasy-free image of incomplete lineage sorting and/or ancestral hybridization/introgression in rapidly radiated Leporidae. At the same time, the strongest retroposon presence/absence signal supports the volcano rabbit as a separate branch between the Pronolagus junction and a unified cluster of the remaining leporids.

The impact of transposable elements in adaptive evolution

The growing knowledge about the influence of transposable elements (TEs) on (a) long-term genome and transcriptome evolution; (b) genomic, transcriptomic and epigenetic variation within populations; and (c) patterns of somatic genetic differences in individuals continues to spur the interest of evolutionary biologists in the role of TEs in adaptive evolution. As TEs can trigger a broad range of molecular variation in a population with potentially severe fitness and phenotypic consequences for individuals, different mechanisms evolved to keep TE activity in check, allowing for a dynamic interplay between the host, its TEs and the environment in evolution. Here, we review evidence for adaptive phenotypic changes associated with TEs and the basic molecular mechanisms by which the underlying genetic changes arise: (a) domestication, (b) exaptation, (c) host gene regulation, (d) TE-mediated formation of intronless gene copies-so-called retrogenes and (e) overall increased genome plasticity. Furthermore, we review and discuss how the stress-dependent incapacitation of defence mechanisms against the activity of TEs might facilitate adaptive responses to environmental challenges and how such mechanisms might be particularly relevant in species frequently facing novel environments, such as invasive, pathogenic or parasitic species.

Biochemical control systems for small molecule damage in plants

As a system, plant metabolism is far from perfect: small molecules (metabolites, cofactors, coenzymes, and inorganic molecules) are frequently damaged by unwanted enzymatic or spontaneous reactions. Here, we discuss the emerging principles in small molecule damage biology. We propose that plants evolved at least three distinct systems to control small molecule damage: (i) repair, which returns a damaged molecule to its original state; (ii) scavenging, which converts reactive molecules to harmless products; and (iii) steering, in which the possible formation of a damaged molecule is suppressed. We illustrate the concept of small molecule damage control in plants by describing specific examples for each of these three categories. We highlight interesting insights that we expect future research will provide on those systems, and we discuss promising strategies to discover new small molecule damage-control systems in plants.

De-novo emergence of SINE retroposons during the early evolution of passerine birds

Background

Passeriformes (“perching birds” or passerines) make up more than half of all extant bird species. The genome of the zebra finch, a passerine model organism for vocal learning, was noted previously to contain thousands of short interspersed elements (SINEs), a group of retroposons that is abundant in mammalian genomes but considered largely inactive in avian genomes.

Results

Here we resolve the deep phylogenetic relationships of passerines using presence/absence patterns of SINEs. The resultant retroposon-based phylogeny provides a powerful and independent corroboration of previous sequence-based analyses. Notably, SINE activity began in the common ancestor of Eupasseres (passerines excluding the New Zealand wrens Acanthisittidae) and ceased before the rapid diversification of oscine passerines (suborder Passeri – songbirds). Furthermore, we find evidence for very recent SINE activity within suboscine passerines (suborder Tyranni), following the emergence of a SINE via acquisition of a different tRNA head as we suggest through template switching.

Conclusions

We propose that the early evolution of passerines was unusual among birds in that it was accompanied by de-novo emergence and activity of SINEs. Their genomic and transcriptomic impact warrants further study in the light of the massive diversification of passerines.

Electronic supplementary material

The online version of this article (10.1186/s13100-017-0104-1) contains supplementary material, which is available to authorized users.

Genome of the Tasmanian tiger provides insights into the evolution and demography of an extinct marsupial carnivore

The Tasmanian tiger or thylacine (Thylacinus cynocephalus) was the largest carnivorous Australian marsupial to survive into the modern era. Despite last sharing a common ancestor with the eutherian canids ~160 million years ago, their phenotypic resemblance is considered the most striking example of convergent evolution in mammals. The last known thylacine died in captivity in 1936 and many aspects of the evolutionary history of this unique marsupial apex predator remain unknown. Here we have sequenced the genome of a preserved thylacine pouch young specimen to clarify the phylogenetic position of the thylacine within the carnivorous marsupials, reconstruct its historical demography and examine the genetic basis of its convergence with canids. Retroposon insertion patterns placed the thylacine as the basal lineage in Dasyuromorphia and suggest incomplete lineage sorting in early dasyuromorphs. Demographic analysis indicated a long-term decline in genetic diversity starting well before the arrival of humans in Australia. In spite of their extraordinary phenotypic convergence, comparative genomic analyses demonstrated that amino acid homoplasies between the thylacine and canids are largely consistent with neutral evolution. Furthermore, the genes and pathways targeted by positive selection differ markedly between these species. Together, these findings support models of adaptive convergence driven primarily by cis-regulatory evolution.

Speciation network in Laurasiatheria: retrophylogenomic signals

Rapid species radiation due to adaptive changes or occupation of new ecospaces challenges our understanding of ancestral speciation and the relationships of modern species. At the molecular level, rapid radiation with successive speciations over short time periods-too short to fix polymorphic alleles-is described as incomplete lineage sorting. Incomplete lineage sorting leads to random fixation of genetic markers and hence, random signals of relationships in phylogenetic reconstructions. The situation is further complicated when you consider that the genome is a mosaic of ancestral and modern incompletely sorted sequence blocks that leads to reconstructed affiliations to one or the other relative, depending on the fixation of their shared ancestral polymorphic alleles. The laurasiatherian relationships among Chiroptera, Perissodactyla, Cetartiodactyla, and Carnivora present a prime example for such enigmatic affiliations. We performed whole-genome screenings for phylogenetically diagnostic retrotransposon insertions involving the representatives bat (Chiroptera), horse (Perissodactyla), cow (Cetartiodactyla), and dog (Carnivora), and extracted among 162,000 preselected cases 102 virtually homoplasy-free, phylogenetically informative retroelements to draw a complete picture of the highly complex evolutionary relations within Laurasiatheria. All possible evolutionary scenarios received considerable retrotransposon support, leaving us with a network of affiliations. However, the Cetartiodactyla-Carnivora relationship as well as the basal position of Chiroptera and an ancestral laurasiatherian hybridization process did exhibit some very clear, distinct signals. The significant accordance of retrotransposon presence/absence patterns and flanking nucleotide changes suggest an important influence of mosaic genome structures in the reconstruction of species histories.

Recombinantly engineered antibodies for reproducible and background free flow cytometry analysis

Antibodies are key reagents for numerous cell analysis applications. Therefore, the contribution of antibodies in experimental irreproducibility is being critically looked at. The majority of antibodies used in basic research are still derived from hybridoma technology established in 1975. As highlighted during recent debates, hybridoma-based antibodies are prone to quality issues, i.e., lot-to-lot variability and lack of specificity. In addition, the technology itself doesn’t allow any improvements in the quality and the properties of the antibodies.

Recombinantly generated antibodies possess highly defined characteristics and are produced under standardized culture conditions leading to products that are reproducible in nature. This saves users the time associated with standardizing analysis and decreases the financial burden associated with working with inconsistent reagents. Recombinant technology also opens up myriads of possibilities to improve antibody properties. REAfinity™ Antibodies provided by Miltenyi Biotec are recombinantly engineered to lack background binding and share a single isotype. This solves the two common problems associated with flow cytometry: non-specific signals and complicated experiment planning with multiple antibody isotypes.

T3SS-Independent Uptake of the Short-Trip Toxin-Related Recombinant NleC Effector of Enteropathogenic Escherichia coli Leads to NF-κB p65 Cleavage

Effector proteins secreted by the type 3 secretion system (T3SS) of pathogenic bacteria have been shown to precisely modulate important signaling cascades of the host for the benefit of the pathogens. Among others, the non-LEE encoded T3SS effector protein NleC of enteropathogenic Escherichia coli (EPEC) is a Zn-dependent metalloprotease and suppresses innate immune responses by directly targeting the NF-κB signaling pathway. Many pathogenic bacteria release potent bacterial toxins of the A-B type, which-in contrast to the direct cytoplasmic injection of T3SS effector proteins-are released first into the environment. In this study, we found that NleC displays characteristics of bacterial A-B toxins, when applied to eukaryotic cells as a recombinant protein. Although lacking a B subunit, that typically mediates the uptake of toxins, recombinant NleC (rNleC) induces endocytosis via lipid rafts and follows the endosomal-lysosomal pathway. The conformation of rNleC is altered by low pH to facilitate its escape from acidified endosomes. This is reminiscent of the homologous A-B toxin AIP56 of the fish pathogen Photobacterium damselae piscicida (Phdp). The recombinant protease NleC is functional inside eukaryotic cells and cleaves p65 of the NF-κB pathway. Here, we describe the endocytic uptake mechanism of rNleC, characterize its intracellular trafficking and demonstrate that its specific activity of cleaving p65 requires activation of host cells e.g., by IL1β. Further, we propose an evolutionary link between some T3SS effector proteins and bacterial toxins from apparently unrelated bacteria. In summary, these properties might suggest rNleC as an interesting candidate for future applications as a potential therapeutic against immune disorders.

The Beaver's Phylogenetic Lineage Illuminated by Retroposon Reads

Solving problematic phylogenetic relationships often requires high quality genome data. However, for many organisms such data are still not available. Among rodents, the phylogenetic position of the beaver has always attracted special interest. The arrangement of the beaver's masseter (jaw-closer) muscle once suggested a strong affinity to some sciurid rodents (e.g., squirrels), placing them in the Sciuromorpha suborder. Modern molecular data, however, suggested a closer relationship of beaver to the representatives of the mouse-related clade, but significant data from virtually homoplasy-free markers (for example retroposon insertions) for the exact position of the beaver have not been available. We derived a gross genome assembly from deposited genomic Illumina paired-end reads and extracted thousands of potential phylogenetically informative retroposon markers using the new bioinformatics coordinate extractor fastCOEX, enabling us to evaluate different hypotheses for the phylogenetic position of the beaver. Comparative results provided significant support for a clear relationship between beavers (Castoridae) and kangaroo rat-related species (Geomyoidea) (p < 0.0015, six markers, no conflicting data) within a significantly supported mouse-related clade (including Myodonta, Anomaluromorpha, and Castorimorpha) (p < 0.0015, six markers, no conflicting data).

Multistate Outbreak of Human Salmonella Typhimurium Infections Linked to Pet Hedgehogs - United States, 2011-2013

Zoonotic Salmonella infections cause approximately 130 000 illnesses annually in the United States. Of 72.9 million US households owning at least one pet, five million own small mammals; 3000 hedgehogs were documented by USDA in USDA-licensed breeding facilities and pet stores in 2012. State health department collaborators and PulseNet, the national bacterial subtyping network, identified human infections of a Salmonella Typhimurium outbreak strain, which were investigated by CDC, USDA-APHIS and state public and animal health officials. A case was defined as an illness in a person infected with the outbreak strain identified between 1 December 2011 and 3 June 2013. Investigators collected information on patient exposures, cultured animal and environmental specimens for Salmonella, and conducted traceback investigations of USDA-licensed hedgehog facilities. There were 26 cases in 12 states. Illness onset dates ranged from 26 December 2011 to 8 April 2013. The median patient age was 15 years (range = <1-91 years); 58% were female. Among 23 persons with available information, 8 (35%) were hospitalized and one outbreak strain-associated death was reported. Of 25 patients with available information, 20 (80%) reported pet hedgehog contact in the week before illness onset. The outbreak strain was isolated from animal and environmental samples collected from three ill persons' homes in three states. Hedgehogs were purchased in geographically distant states from USDA-licensed breeders (10/17, 59%); a USDA-licensed pet store (1/17, 6%); unlicensed or unknown status breeders (3/17, 18%); and private individuals (3/17, 18%). Traceback investigations of USDA-licensed facilities did not reveal a single source of infection. Public and animal health collaboration linked pet hedgehog contact to human infections of Salmonella Typhimurium, highlighting the importance of a One Health investigative approach to zoonotic salmonellosis outbreaks. More efforts are needed to increase awareness among multiple stakeholders on the risk of illness associated with pet hedgehogs.

Genomic analysis reveals hidden biodiversity within colugos, the sister group to primates

Colugos are among the most poorly studied mammals despite their centrality to resolving supraordinal primate relationships. Two described species of these gliding mammals are the sole living members of the order Dermoptera, distributed throughout Southeast Asia. We generated a draft genome sequence for a Sunda colugo and a Philippine colugo reference alignment, and used these to identify colugo-specific genetic changes that were enriched in sensory and musculoskeletal-related genes that likely underlie their nocturnal and gliding adaptations. Phylogenomic analysis and catalogs of rare genomic changes overwhelmingly support the contested hypothesis that colugos are the sister group to primates (Primatomorpha), to the exclusion of treeshrews. We captured ~140 kb of orthologous sequence data from colugo museum specimens sampled across their range and identified large genetic differences between many geographically isolated populations that may result in a >300% increase in the number of recognized colugo species. Our results identify conservation units to mitigate future losses of this enigmatic mammalian order.

A nitride-based epitaxial surface layer formed by ammonia treatment of silicene-terminated ZrB2

We present a method for the formation of an epitaxial  surface layer involving B, N, and Si atoms on a ZrB2(0001) thin film on Si(111). It has the potential to be an insulating growth template for 2D semiconductors. The chemical reaction of NH3 molecules with the silicene-terminated ZrB2  surface was characterized by synchrotron-based, high-resolution core-level photoelectron spectroscopy and low-energy electron diffraction. In particular, the dissociative chemisorption of NH3 at 400 °C leads to surface  nitridation, and subsequent annealing up to 830 °C results in a solid phase reaction with the ZrB2 subsurface layers. In this way, a new nitride-based epitaxial  surface layer is formed with hexagonal symmetry and a single in-plane crystal orientation.

Treatment history and placebo responses to experimental and clinical pain in chronic pain patients

BACKGROUND

Placebo analgesia refers to the reduction in pain due to the administration of an inert treatment. It is induced by expectations of pain relief which are enhanced by learning mechanisms. In healthy humans, prior positive experiences enhance the placebo response. However, the effects of patients' prior experiences with treatment on placebo responses have not yet been examined. This study investigated how verbal information, learning and treatment history influence the magnitude of placebo analgesia in chronic pain.

METHODS

We administered a pharmacological placebo intervention in a sample of chronic pain patients (n = 49) who were seeking treatment in an outpatient pain clinic. Analyses were based on placebo responders.

RESULTS

We found that verbal information about a potent pain-relieving effect of the intervention induced a large placebo analgesic response to both acute experimental (F(1,44) = 43.35, p < 0.001) and chronic pain (F(1,44) = 37.72, p < 0.001). However, the placebo responses to experimental and chronic pain were not significantly related (r = 0.012, p = 0.95). An additional conditioning procedure did not significantly enhance placebo analgesia. Treatment history modulated the magnitude of the placebo response: patients with a more negative pain-related treatment history reported significantly larger placebo responses to their own chronic pain (τ = 0.271, p = 0.044).

CONCLUSIONS

We could show that placebo responses to both acute and chronic pain are high in pain treatment settings and that treatment history modulates this effect. Different mechanisms might underlie placebo responses to acute and chronic pain. Our findings highlight the necessity of considering placebo responses and treatment history in the treatment of chronic pain. WHAT DOES THIS STUDY ADD?: Placebo analgesia following verbal information of potent pain relief is high in chronic pain patients in a clinical setting. It is modulated by treatment history. Different mechanisms might underlie placebo analgesia to acute and chronic pain.

Incomplete Lineage Sorting and Hybridization Statistics for Large-Scale Retroposon Insertion Data

Ancient retroposon insertions can be used as virtually homoplasy-free markers to reconstruct the phylogenetic history of species. Inherited, orthologous insertions in related species offer reliable signals of a common origin of the given species. One prerequisite for such a phylogenetically informative insertion is that the inserted element was fixed in the ancestral population before speciation; if not, polymorphically inserted elements may lead to random distributions of presence/absence states during speciation and possibly to apparently conflicting reconstructions of their ancestry. Fortunately, such misleading fixed cases are relatively rare but nevertheless, need to be considered. Here, we present novel, comprehensive statistical models applicable for (1) analyzing any pattern of rare genomic changes, (2) testing and differentiating conflicting phylogenetic reconstructions based on rare genomic changes caused by incomplete lineage sorting or/and ancestral hybridization, and (3) differentiating between search strategies involving genome information from one or several lineages. When the new statistics are applied, in non-conflicting cases a minimum of three elements present in both of two species and absent in a third group are considered significant support (p<0.05) for the branching of the third from the other two, if all three of the given species are screened equally for genome or experimental data. Five elements are necessary for significant support (p<0.05) if a diagnostic locus derived from only one of three species is screened, and no conflicting markers are detected. Most potentially conflicting patterns can be evaluated for their significance and ancestral hybridization can be distinguished from incomplete lineage sorting by considering symmetric or asymmetric distribution of rare genomic changes among possible tree configurations. Additionally, we provide an R-application to make the new KKSC insertion significance test available for the scientific community at http://retrogenomics.uni-muenster.de:3838/KKSC_significance_test/.

The presence/absence patterns of transposed elements, so called jumping genes, provide invaluable information about evolution. Unfortunately, there is still no clear all-encompassing analysis of the statistical significance of insertion patterns, and the single existing model of insertion data is no longer sufficient for the emerging genomic era. Here, we have provided a comprehensive statistical framework for testing the significance of support for phylogenetic hypotheses derived from genome-level presence/absence data such as retroposon insertions and for evaluating such data for different evolutionary scenarios, including polytomy, incomplete lineage sorting, and ancestral hybridization. This statistical framework is especially important for high-throughput applications of current and upcoming genome projects due to its treatment of unlimited numbers of testable markers, and is embedded in a user-friendly R-application available to the scientific community online. Finally, a reliable, adaptable calculation for the significance of support for phylogenetic trees derived from retroposon presence/absence data is now available.

Obesogenic memory can confer long-term increases in adipose tissue but not liver inflammation and insulin resistance after weight loss

Objective

Obesity represents a major risk factor for the development of type 2 diabetes mellitus, atherosclerosis and certain cancer entities. Treatment of obesity is hindered by the long-term maintenance of initially reduced body weight, and it remains unclear whether all pathologies associated with obesity are fully reversible even upon successfully maintained weight loss.

Methods

We compared high fat diet-fed, weight reduced and lean mice in terms of body weight development, adipose tissue and liver insulin sensitivity as well as inflammatory gene expression. Moreover, we assessed similar parameters in a human cohort before and after bariatric surgery.

Results

Compared to lean animals, mice that demonstrated successful weight reduction showed increased weight gain following exposure to ad libitum control diet. However, pair-feeding weight-reduced mice with lean controls efficiently stabilized body weight, indicating that hyperphagia was the predominant cause for the observed weight regain. Additionally, whereas glucose tolerance improved rapidly after weight loss, systemic insulin resistance was retained and ameliorated only upon prolonged pair-feeding. Weight loss enhanced insulin action and resolved pro-inflammatory gene expression exclusively in the liver, whereas visceral adipose tissue displayed no significant improvement of metabolic and inflammatory parameters compared to obese mice. Similarly, bariatric surgery in humans (n = 55) resulted in massive weight reduction, improved hepatic inflammation and systemic glucose homeostasis, while adipose tissue inflammation remained unaffected and adipocyte-autonomous insulin action only exhibit minor improvements in a subgroup of patients (42%).

Conclusions

These results demonstrate that although sustained weight loss improves systemic glucose homeostasis, primarily through improved inflammation and insulin action in liver, a remarkable obesogenic memory can confer long-term increases in adipose tissue inflammation and insulin resistance in mice as well as in a significant subpopulation of obese patients.

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Upon weight loss in mice liver insulin sensitivity rapidly improves.

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Upon weight loss in mice fat retains metabolic inflammation and insulin resistance.

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Weight gain upon successful weight reduction in mice is driven by increased food intake.

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A proportion of human subjects undergoing bariatric surgery retain AT-inflammation.

LC-MS/MS based determination of basal- and ACTH-stimulated plasma concentrations of 11 steroid hormones: implications for detecting heterozygote CYP21A2 mutation carriers

OBJECTIVE

Heterozygosity in 21-hydroxylase deficiency (21OHD) has been associated with hyperandrogenemic symptoms in children and adults. Moreover, the carrier status is mandatory for genetic counseling. We aimed at defining a hormonal parameter for carrier detection by mass spectrometry.

DESIGN

Eleven basal and ACTH-stimulated steroid hormones of heterozygous carriers of CYP21A2 mutations and control individuals were compared.

METHOD

Hormones were determined in plasma samples by liquid chromatography tandem mass spectrometry (LC-MS/MS) in 58 carriers (35 males, 23 females, age range 6-78 years) and 44 random controls (25 males, 19 females, age range 8-58 years).

RESULTS

Heterozygotes could be identified best applying the 17-hydroxyprogesterone+21-deoxycortisol/cortisol×1000 ((17OHP+21S)/F×1000) equation 30  min after ACTH injection. An optimal cut-off value of 8.4 provided 89% sensitivity and specificity. Considering this data and a published frequency of heterozygotes of 1/50 to 1/61, the positive predictive value (PPV) of this cut-off is 12%. Of note, the negative predictive value (NPV) excluding heterozygosity in a given patient is 99.8%.

CONCLUSION

Considering only marginal biochemical effects anticipated from heterozygosity, the stimulated ((17OHP+21S)/F×1000) identifies and excludes heterozygotes remarkably well. Nevertheless, LC-MS/MS cannot replace genetic testing, since sensitivity and specificity did not reach 100%. However, due to the considerably high NPV of the optimal cut-off and to a specificity of even 100% applying a cut-off higher than 14.7, hormonal assessment of heterozygosity can be of significant aid in conditions with limited access to genetic testing, as in some health care systems. The ((17OHP+21S)/F×1000) equation can guide diagnostic considerations in the differential diagnosis of hyperandrogenism.

Exploring Massive Incomplete Lineage Sorting in Arctoids (Laurasiatheria, Carnivora)

Freed from the competition of large raptors, Paleocene carnivores could expand their newly acquired habitats in search of prey. Such changing conditions might have led to their successful distribution and rapid radiation. Today, molecular evolutionary biologists are faced, however, with the consequences of such accelerated adaptive radiations, because they led to sequential speciation more rapidly than phylogenetic markers could be fixed. The repercussions being that current genealogies based on such markers are incongruent with species trees.Our aim was to explore such conflicting phylogenetic zones of evolution during the early arctoid radiation, especially to distinguish diagnostic from misleading phylogenetic signals, and to examine other carnivore-related speciation events. We applied a combination of high-throughput computational strategies to screen carnivore and related genomes in silico for randomly inserted retroposed elements that we then used to identify inconsistent phylogenetic patterns in the Arctoidea group, which is well known for phylogenetic discordances.Our combined retrophylogenomic and in vitro wet lab approach detected hundreds of carnivore-specific insertions, many of them confirming well-established splits or identifying and solving conflicting species distributions. Our systematic genome-wide screens for Long INterspersed Elements detected homoplasy-free markers with insertion-specific truncation points that we used to distinguish phylogenetically informative markers from conflicting signals. The results were independently confirmed by phylogenetic diagnostic Short INterspersed Elements. As statistical analysis ruled out ancestral hybridization, these doubly verified but still conflicting patterns were statistically determined to be genomic remnants from a time of ancestral incomplete lineage sorting that especially accompanied large parts of Arctoidea evolution.