Result verification, code verification and computation of support values in phylogenetics

Verification in phylogenetics represents an extremely difficult subject. Phylogenetic analysis deals with the reconstruction of evolutionary histories of species, and as long as mankind is not able to travel in time, it will not be possible to verify deep evolutionary histories reconstructed with modern computational methods. Here, we focus on two more tangible issues that are related to verification in phylogenetics (i) the inference of support values on trees that provide some notion about the 'correctness' of the tree within narrow limits and, more importantly; (ii) issues pertaining to program verification, especially with respect to codes that rely heavily on floating-point arithmetics. Program verification represents a largely underestimated problem in computational science that can have fatal effects on scientific conclusions.     

A functional phylogenomic view of the seed plants

A novel result of the current research is the development and implementation of a unique functional phylogenomic approach that explores the genomic origins of seed plant diversification. We first use 22,833 sets of orthologs from the nuclear genomes of 101 genera across land plants to reconstruct their phylogenetic relationships. One of the more salient results is the resolution of some enigmatic relationships in seed plant phylogeny, such as the placement of Gnetales as sister to the rest of the gymnosperms. In using this novel phylogenomic approach, we were also able to identify overrepresented functional gene ontology categories in genes that provide positive branch support for major nodes prompting new hypotheses for genes associated with the diversification of angiosperms. For example, RNA interference (RNAi) has played a significant role in the divergence of monocots from other angiosperms, which has experimental support in Arabidopsis and rice. This analysis also implied that the second largest subunit of RNA polymerase IV and V (NRPD2) played a prominent role in the divergence of gymnosperms. This hypothesis is supported by the lack of 24nt siRNA in conifers, the maternal control of small RNA in the seeds of flowering plants, and the emergence of double fertilization in angiosperms. Our approach takes advantage of genomic data to define orthologs, reconstruct relationships, and narrow down candidate genes involved in plant evolution within a phylogenomic view of species' diversification.     

Neutrophil gelatinase-associated lipocalin in dehydrated patients: a preliminary report

Background

Acute kidney injury has been recognized as a major contributor to end stage renal disease. Although neutrophil gelatinase-associated lipocalin (Ngal) has been reported as a promising biomarker for early detection of acute kidney injury, no study has yet examined its potential clinical impact in patients with normal renal function. The purpose of current study is to investigate possible difference in serum Ngal levels between dehydrated and control patients.

Findings

A total of twelve patients presented with symptoms of mild dehydration defined by history of diarrheas or vomiting and orthostatic (postural) hypotension and an age and sex matched group of twelve control patients were included. The two groups of patients did not seem to differ in basic clinical and laboratory parameters. Serum Ngal was higher in dehydrated patients when compared to control group (Ngal = 129.4 ± 25.7 ng/mL vs 60.6 ± 0.4 ng/mL, p = 0.02). Ngal was not correlated with age, hemoglobin, white blood cell count, red blood cell count, urea or creatinine.

Conclusions

The presence of elevated Ngal levels in dehydrated patients may suggest its role as a very sensitive biomarker in even minimal and "silent" prerenal kidney dysfunction     

Serum VEGF levels and tissue activation of VEGFR2/KDR receptors in patients with breast and gynecologic cancer

ObjectivesVascular endothelial cell growth factor (VEGF) plays an important role in the biology of gynecological cancer, usually linked with aggressive tumour behaviour and a poor postoperative outcome. Yet, its role in benign breast/gynecological conditions is less clear.MethodsSerum VEGF was analysed in a series of 49 patients with gynecological cancer and 61 patients with benign disease and compared to those of 12 normal female subjects. In addition, the activation status of VEGFR2/KDR receptors was investigated in formalin-fixed paraffin embedded tissues and related to VEGF.ResultsMean serum levels of VEGF were significantly higher in patients with breast, endometrial and ovarian cancer compared to healthy controls and those with benign breast/gynecologic disease in the respective organs. A similar trend was noted in some cases of simple endometrial hyperplasia, fibroadenoma and fibrocystic disease of the breast. The expression of phosphorylated VEGFR2/KDR receptors was higher in breast, endometrial, ovarian cancer in patients with high VEGF serum levels and this reached a level of statistical significance when all malignancies were combined.ConclusionsSerum VEGF levels are increased in patients with breast and gynecological malignancies, but this can not be considered pathognomonic for cancer as it is also increased in certain benign conditions, including cases of fibroadenoma, fibrocystic disease of breast and simple endometrial hyperplasia. Furthermore, high serum VEGF levels are closely related to the activation status of the VEGFR2/KDR receptor in cancer cells, indicating a stimulatory effect of serum VEGF on the VEGF pathway contributing to tumor progression.     

A cervical ligamentum flavum cyst in an 82-year-old woman presenting with spinal cord compression: a case report and review of the literature

Introduction

Legionnaires' disease is recognized as a multi-systemic illness. Afflicted patients may have pulmonary, renal, gastrointestinal tract and central nervous system complications. However, renal insufficiency is uncommon. The spectrum of renal involvement may range from a mild and transient elevation of serum creatinine levels to anuric renal failure requiring dialysis and may be linked to several causes. In our present case report, we would like to draw attention to the importance of the pathological documentation of acute renal failure by reporting a case of a patient with acute tubulointerstitial nephritis complicating Legionnaires' disease.

Case presentation

A 55-year-old Caucasian man was admitted to our hospital for community-acquired pneumonia complicated by acute renal failure. Legionella pneumophila serogroup type 1 was diagnosed. Although the patient's respiratory illness responded to intravenous erythromycin and ofloxacin therapy, his renal failure worsened, he became anuric, and hemodialysis was started. A renal biopsy was performed, which revealed severe tubulointerstitial nephritis. After initiation of steroid therapy, his renal function improved dramatically.

Conclusions

This case highlights the importance of kidney biopsies in cases where acute renal failure is a complicating factor in Legionnaires' disease. If the presence of acute tubulointerstitial nephritis can be confirmed, it will likely respond favorably to steroidal treatment and thus irreversible renal damage and chronic renal failure will be avoided.     

Pancrustacean phylogeny in the light of new phylogenomic data: support for Remipedia as the possible sister group of Hexapoda

Remipedes are a small and enigmatic group of crustaceans, first described only 30 years ago. Analyses of both morphological and molecular data have recently suggested a close relationship between Remipedia and Hexapoda. If true, the remipedes occupy an important position in pancrustacean evolution and may be pivotal for understanding the evolutionary history of crustaceans and hexapods. However, it is important to test this hypothesis using new data and new types of analytical approaches. Here, we assembled a phylogenomic data set of 131 taxa, incorporating newly generated 454 expressed sequence tag (EST) data from six species of crustaceans, representing five lineages (Remipedia, Laevicaudata, Spinicaudata, Ostracoda, and Malacostraca). This data set includes all crustacean species for which EST data are available (46 species), and our largest alignment encompasses 866,479 amino acid positions and 1,886 genes. A series of phylogenomic analyses was performed to evaluate pancrustacean relationships. We significantly improved the quality of our data for predicting putative orthologous genes and for generating data subsets by matrix reduction procedures, thereby improving the signal to noise ratio in the data. Eight different data sets were constructed, representing various combinations of orthologous genes, data subsets, and taxa. Our results demonstrate that the different ways to compile an initial data set of core orthologs and the selection of data subsets by matrix reduction can have marked effects on the reconstructed phylogenetic trees. Nonetheless, all eight data sets strongly support Pancrustacea with Remipedia as the sister group to Hexapoda. This is the first time that a sister group relationship of Remipedia and Hexapoda has been inferred using a comprehensive phylogenomic data set that is based on EST data. We also show that selecting data subsets with increased overall signal can help to identify and prevent artifacts in phylogenetic analyses.     

A critical assessment of storytelling: gene ontology categories and the importance of validating genomic scans

In the age of whole-genome population genetics, so-called genomic scan studies often conclude with a long list of putatively selected loci. These lists are then further scrutinized to annotate these regions by gene function, corresponding biological processes, expression levels, or gene networks. Such annotations are often used to assess and/or verify the validity of the genome scan and the statistical methods that have been used to perform the analyses. Furthermore, these results are frequently considered to validate "true-positives" if the identified regions make biological sense a posteriori. Here, we show that this approach can be potentially misleading. By simulating neutral evolutionary histories, we demonstrate that it is possible not only to obtain an extremely high false-positive rate but also to make biological sense out of the false-positives and construct a sensible biological narrative. Results are compared with a recent polymorphism data set from Drosophila melanogaster.     

Investigating the entire course of telithromycin binding to Escherichia coli ribosomes

Applying kinetics and footprinting analysis, we show that telithromycin, a ketolide antibiotic, binds to Escherichia coli ribosomes in a two-step process. During the first, rapidly equilibrated step, telithromycin binds to a low-affinity site (K(T) = 500 nM), in which the lactone ring is positioned at the upper portion of the peptide exit tunnel, while the alkyl-aryl side chain of the drug inserts a groove formed by nucleotides A789 and U790 of 23S rRNA. During the second step, telithromycin shifts slowly to a high-affinity site (K(T)* = 8.33 nM), in which the lactone ring remains essentially at the same position, while the side chain interacts with the base pair U2609:A752 and the extended loop of protein L22. Consistently, mutations perturbing either the base pair U2609:A752 or the L22-loop hinder shifting of telithromycin to the final position, without affecting the initial step of binding. In contrast, mutation Lys63Glu in protein L4 placed on the opposite side of the tunnel, exerts only a minor effect on telithromycin binding. Polyamines disfavor both sequential steps of binding. Our data correlate well with recent crystallographic data and rationalize the changes in the accessibility of ribosomes to telithromycin in response to ribosomal mutations and ionic changes.