New Gromov-Inspired Metrics on Phylogenetic Tree Space

We present a new class of metrics for unrooted phylogenetic X-trees inspired by the Gromov–Hausdorff distance for (compact) metric spaces. These metrics can be efficiently computed by linear or quadratic programming. They are robust under NNI operations, too. The local behaviour of the metrics shows that they are different from any previously introduced metrics. The performance of the metrics is briefly analysed on random weighted and unweighted trees as well as random caterpillars.     

No Fabry Disease in Patients Presenting with Isolated Small Fiber Neuropathy

Objective

Screening for Fabry disease in patients with small fiber neuropathy has been suggested, especially since Fabry disease is potentially treatable. However, the diagnostic yield of testing for Fabry disease in isolated small fiber neuropathy patients has never been systematically investigated. Our aim is to determine the presence of Fabry disease in patients with small fiber neuropathy.

Methods

Patients referred to our institute, who met the criteria for isolated small fiber neuropathy were tested for Fabry disease by measurement of alpha-Galactosidase A activity in blood, lysosomal globotriaosylsphingosine in urine and analysis on possible GLA gene mutations.

Results

725 patients diagnosed with small fiber neuropathy were screened for Fabry disease. No skin abnormalities were seen except for redness of the hands or feet in 30.9% of the patients. Alfa-Galactosidase A activity was tested in all 725 patients and showed diminished activity in eight patients. Lysosomal globotriaosylsphingosine was examined in 509 patients and was normal in all tested individuals. Screening of GLA for mutations was performed for 440 patients, including those with diminished α-Galactosidase A activity. Thirteen patients showed a GLA gene variant. One likely pathogenic variant was found in a female patient. The diagnosis Fabry disease could not be confirmed over time in this patient. Eventually none of the patients were diagnosed with Fabry disease.

Conclusions

In patients with isolated small fiber neuropathy, and no other signs compatible with Fabry disease, the diagnostic yield of testing for Fabry disease is extremely low. Testing for Fabry disease should be considered only in cases with additional characteristics, such as childhood onset, cardiovascular disease, renal failure, or typical skin lesions.     

Associations of Whole Blood n-3 and n-6 Polyunsaturated Fatty Acids with Blood Pressure in Children and Adolescents – Results from the IDEFICS/I.Family Cohort

BackgroundPolyunsaturated n-3 and n-6 polyunsaturated fatty acids (PUFA) are precursors of biologically active metabolites that affect blood pressure (BP) regulation. This study investigated the association of n-3 and n-6 PUFA and BP in children and adolescents.MethodsIn a subsample of 1267 children aged 2–9 years at baseline of the European IDEFICS (Identification and prevention of dietary- and lifestyle-induced health effects in children and infants) cohort whole blood fatty acids were measured by a validated gas chromatographic method. Systolic and diastolic BP was measured at baseline and after two and six years. Mixed-effects models were used to assess the associations between fatty acids at baseline and BP z-scores over time adjusting for relevant covariables. Models were further estimated stratified by sex and weight status.ResultsThe baseline level of arachidonic acid was positively associated with subsequent systolic BP (β = 0.08, P = 0.002) and diastolic BP (β = 0.07, P<0.001). In thin/normal weight children, baseline alpha-linolenic (β = -1.13, P = 0.003) and eicosapentaenoic acid (β = -0.85, P = 0.003) levels were inversely related to baseline and also to subsequent systolic BP and alpha-linolenic acid to subsequent diastolic BP. In overweight/obese children, baseline eicosapentaenoic acid level was positively associated with baseline diastolic BP (β = 0.54, P = 0.005).ConclusionsLow blood arachidonic acid levels in the whole sample and high n-3 PUFA levels in thin/normal weight children are associated with lower and therefore healthier BP. The beneficial effects of high n-3 PUFA on BP were not observed in overweight/obese children, suggesting that they may have been overlaid by the unfavorable effects of excess weight.     

Improved bio-energy yields via sequential ethanol fermentation and biogas digestion of steam exploded oat straw

Using standard laboratory equipment, thermochemically pretreated oat straw was enzymatically saccharified and fermented to ethanol, and after removal of ethanol the remaining material was subjected to biogas digestion. A detailed mass balance calculation shows that, for steam explosion pretreatment, this combined ethanol fermentation and biogas digestion converts 85-87% of the higher heating value (HHV) of holocellulose (cellulose and hemicellulose) in the oat straw into biofuel energy. The energy (HHV) yield of the produced ethanol and methane was 9.5-9.8 MJ/(kg dry oat straw), which is 28-34% higher than direct biogas digestion that yielded 7.3-7.4 MJ/(kg dry oat straw). The rate of biogas formation from the fermentation residues was also higher than from the corresponding pretreated but unfermented oat straw, indicating that the biogas digestion could be terminated after only 24 days. This suggests that the ethanol process acts as an additional pretreatment for the biogas process.     

Design and synthesis of ATP-based nucleotide analogues and profiling of nucleotide-binding proteins

Two nucleotide-based probes were designed and synthesized in order to enrich samples for specific classes of proteins by affinity-based protein profiling. We focused on the profiling of adenine nucleotide-binding proteins. Two properties were considered in the design of the probes: the bait needs to bind adenine nucleotide-binding proteins with high affinity and carry a second functional group suitable and easily accessible for coupling to a chromatography resin. For this purpose, we synthesized p-biotinyl amidobenzoic acid-ATP (p-BABA-ATP) and p-biotinyl aminomethylbenzoic acid-ATP (p-BAMBA-ATP). p-BABA-ATP and p-BAMBA-ATP both bind to ATP-binding cassette (ABC) proteins with at least 10-fold higher affinity than ATP. Several ABC transporters could be enriched using p-BABA-ATP or p-BAMBA-ATP.     

Recent insights into iron import by bacteria

Bacteria are confronted with a low availability of iron owing to its insolubility in the Fe3+ form or its being bound to host proteins. The bacteria cope with the iron deficiency by using host heme or siderophores synthesized by themselves or other microbes. In contrast to most other nutrients, iron compounds are tightly bound to proteins at the cell surfaces, from which they are further translocated by highly specific proteins across the cell wall of gram-positive bacteria and the outer membrane of gram-negative bacteria. Once heme and iron siderophores arrive at the cytoplasmic membrane, they are taken up across the cytoplasmic membrane by ABC transporters. Here we present an outline of bacterial heme and iron siderophore transport exemplified by a few selected cases in which recent progress in the understanding of the transport mechanisms has been achieved.     

Ligand Binding and Crystal Structures of the Substrate-Binding Domain of the ABC Transporter OpuA

Background

The ABC transporter OpuA from Lactococcus lactis transports glycine betaine upon activation by threshold values of ionic strength. In this study, the ligand binding characteristics of purified OpuA in a detergent-solubilized state and of its substrate-binding domain produced as soluble protein (OpuAC) was characterized.

Principal Findings

The binding of glycine betaine to purified OpuA and OpuAC (K_D = 4–6 µM) did not show any salt dependence or cooperative effects, in contrast to the transport activity. OpuAC is highly specific for glycine betaine and the related proline betaine. Other compatible solutes like proline and carnitine bound with affinities that were 3 to 4 orders of magnitude lower. The low affinity substrates were not noticeably transported by membrane-reconstituted OpuA. OpuAC was crystallized in an open (1.9 Å) and closed-liganded (2.3 Å) conformation. The binding pocket is formed by three tryptophans (Trp-prism) coordinating the quaternary ammonium group of glycine betaine in the closed-liganded structure. Even though the binding site of OpuAC is identical to that of its B. subtilis homolog, the affinity for glycine betaine is 4-fold higher.

Conclusions

Ionic strength did not affect substrate binding to OpuA, indicating that regulation of transport is not at the level of substrate binding, but rather at the level of translocation. The overlap between the crystal structures of OpuAC from L.lactis and B.subtilis, comprising the classical Trp-prism, show that the differences observed in the binding affinities originate from outside of the ligand binding site.     

Gene Cluster Involved in the Biosynthesis of Griseobactin,a Catechol-Peptide Siderophore of Streptomyces sp. ATCC 700974

The main siderophores produced by streptomycetes are desferrioxamines. Here we show that Streptomyces sp. ATCC 700974 and several Streptomyces griseus strains, in addition, synthesize a hitherto unknown siderophore with a catechol-peptide structure, named griseobactin. The production is repressed by iron. We sequenced a 26-kb DNA region comprising a siderophore biosynthetic gene cluster encoding proteins similar to DhbABCEFG, which are involved in the biosynthesis of 2,3-dihydroxybenzoate (DHBA) and in the incorporation of DHBA into siderophores via a nonribosomal peptide synthetase. Adjacent to the biosynthesis genes are genes that encode proteins for the secretion, uptake, and degradation of siderophores. To correlate the gene cluster with griseobactin synthesis, the dhb genes in ATCC 700974 were disrupted. The resulting mutants no longer synthesized DHBA and griseobactin; production of both was restored by complementation with the dhb genes. Heterologous expression of the dhb genes or of the entire griseobactin biosynthesis gene cluster in the catechol-negative strain Streptomyces lividans TK23 resulted in the synthesis and secretion of DHBA or griseobactin, respectively, suggesting that these genes are sufficient for DHBA and griseobactin biosynthesis. Griseobactin was purified and characterized; its structure is consistent with a cyclic and, to a lesser extent, linear form of the trimeric ester of 2,3-dihydroxybenzoyl-arginyl-threonine complexed with aluminum under iron-limiting conditions. This is the first report identifying the gene cluster for the biosynthesis of DHBA and a catechol siderophore in Streptomyces.Iron is an essential element for the growth and proliferation of nearly all microorganisms. In the presence of oxygen, the soluble ferrous iron is readily oxidized to its ferric form, which exists predominantly as a highly insoluble hydroxide complex at neutral pH. To overcome iron limitation, many bacteria synthesize and secrete low-molecular-weight, high-affinity ferric iron chelators, called siderophores (38, 53). Following the chelation of Fe³⁺ in the medium, the iron-siderophore complex is actively taken up by its cognate ABC transport system, and Fe³⁺ is subsequently released by reduction to Fe²⁺ and/or by hydrolysis of the siderophore (28, 32, 36). The three main classes of siderophores contain catecholates, hydroxamates, or (α-hydroxy-)carboxylates as iron-coordinating ligands, but mixed siderophores and siderophores containing other functional groups, such as diphenolates, imidazoles, and thiazolines, have also been found (16, 38).Siderophores containing peptide moieties are synthesized by proteins belonging to the nonribosomal peptide synthetase (NRPS) family (16, 38). These multimodular enzymes function as enzymatic assembly lines in which the order of the modules usually determines the order of the amino acids incorporated into the peptide (19, 34). Each module contains the complete information for an elongation step combining the catalytic functions for the activation of the amino acid by the adenylation (A) domain, the tethering of the corresponding adenylate to the terminal thiol of the enzyme-bound 4′-phosphopantetheinyl (4′-PP) cofactor by the peptidyl carrier protein (PCP) domain, and the formation of the peptide bond by the condensation (C) domain (26, 34, 52). At the end, the product is released by the C-terminal thioesterase (TE) domain by hydrolysis or by cyclization via intramolecular condensation. Each adenylation domain recognizes a specific amino acid, and its substrate specificity can be predicted by its sequence. An NRPS specificity-conferring code consisting of 10 nonadjacent amino acid residues in the A domain has been proposed (49). Exceptions to the “colinearity-rule” (19) have been discovered. For example, in the biosynthesis of the siderophores enterobactin and bacillibactin, all the modules in the NRPS are used iteratively, and the TE domain stitches the chains together into a cyclic product (35, 45). Enterobactin is the trilactone of 2,3-dihydroxybenzoyl-serine, and bacillibactin is the lactone of 2,3-dihydroxybenzoyl-glycyl-threonine.The typical siderophores produced by streptomycetes are desferrioxamines (24), and the genes encoding the enzymes for their biosynthesis have been identified (5). Recently, structurally different siderophores have been reported to be coproduced with desferrioxamines in some species, e.g., coelichelin in Streptomyces coelicolor (9, 30) and enterobactin in Streptomyces tendae (18). The genes encoding the proteins for the biosynthesis of enterobactin in S. tendae remain unknown.Here we describe the gene cluster for the biosynthesis of a new siderophore, named griseobactin, produced by Streptomyces sp. strain ATCC 700974 and some strains of Streptomyces griseus. By sequencing two cosmids isolated from a Streptomyces sp. strain ATCC 700974 genomic library, we assigned the encoded proteins to enzymes that convert chorismate to 2,3-dihydroxybenzoate (DHBA), and to proteins involved in nonribosomal peptide biosynthesis and in the export, uptake, and utilization of siderophores. Knockout mutagenesis and heterologous expression confirmed the requirement of this gene cluster for the biosynthesis of griseobactin. This is the first report on the identification of the genes responsible for DHBA and catechol siderophore biosynthesis in Streptomyces.     

Imaging and tracking of single hyaluronan molecules diffusing in solution

Hyaluronan is an important soluble component of the extracellular matrix of many tissues with well known space-filling, lubricating and signaling functions. As such, hyaluronan can regulate cell adhesion, migration, differentiation and proliferation. Ultrastructural studies showed the existence of fibers and networks of hyaluronan molecules at surfaces, while bulk studies of hyaluronan in solution indicated that the polymer forms random coils. Here, we show that single hyaluronan molecules can be visualized and tracked in three-dimensional samples at room temperature in aqueous buffer. Using a wide-field fluorescence microscope equipped with laser excitation and an sensitive and fast EMCCD camera for fluorescence detection, single FITC-labeled hyaluronan molecules from rooster comb were detected in aqueous solutions. Freely moving hyaluronan-FITC could be tracked over up to 20 images acquired at a frame rate of 98 Hz. Analysis of the trajectories revealed Brownian motion of hyaluronan in tris-buffered saline with an average diffusion coefficient D = 3.0 ± 0.2 μm²/s. These observations confirm the concept that hyaluronan molecules form random coils in solution. The possibility of following the tracks of single hyaluronan molecules in solution facilitates the analysis of processes that lead to the formation of more organized forms of hyaluronan and its interactions with cells with very high spatial and temporal accuracy. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.