Forest-Based Networks.

In evolutionary studies, it is common to use phylogenetic trees to represent the evolutionary history of a set of species. However, in case the transfer of genes or other genetic information between the species or their ancestors has occurred in the past, a tree may not provide a complete picture of their history. In such cases, tree-based phylogenetic networks can provide a useful, more refined representation of the species' evolution. Such a network is essentially a phylogenetic tree with some arcs added between the tree's edges so as to represent reticulate events such as gene transfer, hybridization and recombination. Even so, this model does not permit the direct representation of evolutionary scenarios where reticulate events have taken place between different subfamilies or lineages of species. To represent such scenarios, in this paper we introduce the notion of a forest-based network, that is, a collection of leaf-disjoint phylogenetic trees on a set of species with arcs added between the edges of distinct trees within the collection. Forest-based networks include the recently introduced class of overlaid species forests which can be used to model introgression. As we shall see, even though the definition of forest-based networks is closely related to that of tree-based networks, they lead to new mathematical theory which complements that of tree-based networks. As well as studying the relationship of forest-based networks with other classes of phylogenetic networks, such as tree-child networks and universal tree-based networks, we present some characterizations of some special classes of forest-based networks. We expect that our results will be useful for developing new models and algorithms to understand reticulate evolution, such as introgression and gene transfer between species.

Uprooted Phylogenetic Networks.

The need for structures capable of accommodating complex evolutionary signals such as those found in, for example, wheat has fueled research into phylogenetic networks. Such structures generalize the standard model of a phylogenetic tree by also allowing for cycles and have been introduced in rooted and unrooted form. In contrast to phylogenetic trees or their unrooted versions, rooted phylogenetic networks are notoriously difficult to understand. To help alleviate this, recent work on them has also centered on their "uprooted" versions. By focusing on such graphs and the combinatorial concept of a split system which underpins an unrooted phylogenetic network, we show that not only can a so-called (uprooted) 1-nested network N be obtained from the Buneman graph (sometimes also called a median network) associated with the split system [Formula: see text] induced on the set of leaves of N but also that that graph is, in a well-defined sense, optimal. Along the way, we establish the 1-nested analogue of the fundamental "splits equivalence theorem" for phylogenetic trees and characterize maximal circular split systems.

[Tapering and termination of immunosuppressive treatment in spondyloarthritides (including psoriatic arthritis)]. / Ausschleichen und Beenden von immunsuppressiven Therapien bei Spondyloarthritiden (einschließlich Psoriasisarthritis).

BACKGROUND: Immunomodulatory long-term treatment has also become the standard treatment for spondyloarthritides (SpA), including psoriatic arthritis (PsA); however, uncertainty exists about dose reduction or termination of treatment after remission or low disease activity. OBJECTIVE: When is it possible to reduce medication or terminate treatment for SpA? MATERIAL AND METHODS: An extensive non-systematic literature search was performed focusing on practice guidelines, systematic meta-analyses and clinical trials on medicinal long-term treatment and voluntary medication reduction in axial and peripheral SpA, including PsA. RESULTS: The chances of drug-free remission after treatment with biologics for axial SpA and in PsA are low; however, in remission or a state of low disease activity reduction of the cumulative dosage of biologics can be successful in 53-100% of cases without a significant increase in disease activity. The current state and duration of remission, with or without comedication with nonsteroidal anti-inflammatory drugs (NSAID), extra-articular disease manifestations and the results of previous treatment attempts have to be carefully taken into consideration before elective dose reduction. CONCLUSION: Reduction of long-term treatment is an individualized decision made jointly by patients and physicians. The risk of flares and especially of extra-articular disease manifestations needs to be weighed against the possible advantages of reduced medication. Maintainenance of mediction-free disease remission is too rare in SpA or PsA patients carefully selected for biologics treatment, to allow a later voluntary termination of therapy, without at least a prior cautious attempt at dose reduction.

Nanoscopic yttrium oxide fluorides: non-aqueous fluorolytic sol-gel synthesis and structural insights by 19F and 89Y MAS NMR.

Nanoscopic yttrium acetate fluorides Y(CH(3)COO)(3-z)F(z) and yttrium oxide fluorides YO(3-z)/(2)F(z )were prepared with tunable Y/F molar ratios via the fluorolytic sol-gel route. All samples were characterized by X-ray diffraction, elemental analysis and thermal analysis. In addition, local structures of all samples were studied by (19)F MAS, (19)F-(89)Y CP MAS and (1)H-(89)Y CP MAS NMR spectroscopy and the respective chemical shifts are given. For both classes of compounds, only the fluorination using one equivalent of F (z = 1) leads to defined, well crystalline matrices: yttrium acetate fluoride Y(CH(3)COO)(2)F and r-YOF.

Application of the local effect model to predict DNA double-strand break rejoining after photon and high-LET irradiation.

In the recent version of the local effect model (LEM), the biological effects of ionising radiation can be well described trough the consideration of DNA double-strand breaks (DSB) clustering at the micrometre scale. Assuming a giant-loop organisation for the chromatin higher-order structure, two classes of DSB are defined, namely isolated (iDSB) and clustered DSB (cDSB), according to whether exactly one or more than one DSB are induced in a loop, respectively. Here, a DSB kinetic rejoining model based on the LEM is applied to the description of two specific aspects of DSB rejoining, namely the dose dependence of the rejoining capacity after photon radiation and the residual damage observed at late times after ion irradiation. Based on the hypothesis that iDSB and cDSB can be associated to the fast and slow components of rejoining, the model is able to reproduce the experimental data, therefore supporting the relevance of micrometre scale clustering of damage for photon radiation as well as for high-LET radiation.

NF-κB-dependent DNA damage-signaling differentially regulates DNA double-strand break repair mechanisms in immature and mature human hematopoietic cells.

Hematopoietic stem and progenitor cells (HSPC), that is, the cell population giving rise not only to all mature hematopoietic lineages but also the presumed target for leukemic transformation, can transmit (adverse) genetic events, such as are acquired from chemotherapy or ionizing radiation. Data on the repair of DNA double-strand-breaks (DSB) and its accuracy in HSPC are scarce, in part contradictory, and mostly obtained in murine models. We explored the activity, quality and molecular components of DSB repair in human HSPC as compared with mature peripheral blood lymphocytes (PBL). To consider chemotherapy/radiation-induced compensatory proliferation, we established cycling HSPC cultures. Comparison of pathway-specific repair activities using reporter systems revealed that HSPC were severely compromised in non-homologous end joining and homologous recombination but not microhomology-mediated end joining. We observed a more pronounced radiation-induced accumulation of nuclear 53BP1 in HSPC relative to PBL, despite evidence for comparable DSB formation from cytogenetic analysis and γH2AX signal quantification, supporting differential pathway usage. Functional screening excluded a major influence of phosphatidylinositol-3-OH-kinase (ATM/ATR/DNA-PK)- and p53-signaling as well as chromatin remodeling. We identified diminished NF-κB signaling as the molecular component underlying the observed differences between HSPC and PBL, limiting the expression of DSB repair genes and bearing the risk of an inaccurate repair.

Cilengitide--exceptional pseudopolymorphism of a cyclic pentapeptide.

Cilengitide (Cil) represents a cyclic pentapeptide, cyclo-(Arg-Gly-Asp-D-Phe-N-MeVal). Existence of an anhydrate form (A1) and a tetrahydrate form Cil1(H2O)4 has been observed. Surprisingly the anhydrate form proved to be more stable in aqueous environment compared to the tetrahydrate form. Assessment of thermodynamic stability has been carried out by competitive slurry experiments as well as by investigation of thermodynamic solubility. The lower solubility of the anhydrate form A1 can be explained by the hydrogen bonding motifs within the crystal structures. The tetrahydrate form Cil1(H2O)4 represents a special manifestation of a class of non-stoichiometric water-alcohol solvates Cil1(H2O)x(alcohol)y where methanol and ethanol can substitute water molecules in the crystal lattice of the tetrahydrate form leading to the hydrate-solvate systems Cil1(H2O)x(methanol)y named S1 and Cil1(H2O)x(ethanol)y named S2 with x ⩽ 4, y ⩽ 1 and y ⩽ 2-0.5x. The non-stoichiometric water alcohol solvates exhibit a higher solubility compared to the anhydrate form but convert rapidly to the anhydrate form in aqueous environments. Accordingly, the better soluble non-stoichiometric water alcohol solvates cannot be obtained by crystallization from aqueous media. However slurries or crystallization from solvent mixtures containing methanol and ethanol represent a means to obtain the highly soluble pseudo-polymorphs S1 and S2 and to circumvent formation of the low soluble anhydrate form A1.

A DNA double-strand break kinetic rejoining model based on the local effect model.

We report here on a DNA double-strand break (DSB) kinetic rejoining model applicable to a wide range of radiation qualities based on the DNA damage pattern predicted by the local effect model (LEM). In the LEM this pattern is derived from the SSB and DSB yields after photon irradiation in combination with an amorphous track structure approach. Together with the assumption of a giant-loop organization to describe the higher order chromatin structure this allows the definition of two different classes of DSB. These classes are defined by the level of clustering on a micrometer scale, i.e., "isolated DSB" (iDSB) are characterized by a single DSB in a giant loop and "clustered DSB" (cDSB) by two or more DSB in a loop. Clustered DSB are assumed to represent a more difficult challenge for the cell repair machinery compared to isolated DSB, and we thus hypothesize here that the fraction of isolated DSB can be identified with the fast component of rejoining, whereas clustered DSB are identified with the slow component of rejoining. The resulting predicted bi-exponential decay functions nicely reproduce the experimental curves of DSB rejoining over time obtained by means of gel electrophoresis elution techniques as reported by different labs, involving different cell types and a wide spectrum of radiation qualities. New experimental data are also presented aimed at investigating the effects of the same ion species accelerated at different energies. The results presented here further support the relevance of the proposed two classes of DSB as a basis for understanding cell response to ion irradiation. Importantly the density of DSB within DNA giant loops of around 2 Mbp size, i.e., on a micrometer scale, is identified as a key parameter for the description of radiation effectiveness.

Application of gastrointestinal modelling to the study of the digestion and transformation of dietary glycidyl esters.

Glycidyl esters (GEs) are known to be formed during vegetable oil processing. Because of their structure, it has been hypothesised that GEs, like fatty acid esters of chloropropanols (MCPD esters), may be accepted as substrates by gut lipases to release the epoxide glycidol. If confirmed such a hypothesis would be important for risk assessment since glycidol is considered as a genotoxic carcinogen. In the present study, biotransformation was investigated using static and dynamic gastrointestinal models. During the experiments, aliquots were analysed for non-digested GEs using liquid chromatography-time-of-flight-mass spectrometry (LC-ToF-MS). In the static model, a fast hydrolysis of GEs was observed as a result of lipase action. Lipase was very efficient at pH 4.8, and totally inhibited at very low pH (1.7). In the absence of lipase, GEs were found to be relatively stable. The potential impact of food matrix was studied using milk in a dynamic model simulating human physiological conditions. The fast, pH-dependent hydrolysis of GEs was further confirmed. The possible transformation of the digestion products was then investigated using gas chromatography coupled to mass spectrometry (GC-MS), mainly the epoxide ring-opening to glycerol followed by additional reactions. In any conditions applied, neither 2- nor 3-mono-chloropropanediol (2- nor 3-MCPD) were formed, indicating that a ring-opening of the epoxide group of GEs or glycidol followed by a reaction with chloride was unlikely. A small transformation of glycidol into glycerol was observed after longer incubation time correlated with a low pH. This suggested that ring-opening and reaction with water is possible in strongly acidic conditions. Overall, it is concluded that GEs are rapidly digested by gut lipases to form glycidol. Consequently, GEs should be considered as sources of glycidol exposure. In addition, risk assessment of GEs can likely rely on hazard identification and characterisation data specific for glycidol.

Analytical approaches for MCPD esters and glycidyl esters in food and biological samples: a review and future perspectives.

Esters of 2 - and 3-monochloropropane-1,2-diol (MCPD) and glycidol esters are important contaminants of processed edible oils used as foods or food ingredients. This review describes the occurrence and analysis of MCPD esters and glycidol esters in vegetable oils and some other foods. The focus is on the analytical methods based on both direct and indirect methods. Methods of analysis applied to oils and lipid extracts of foods have been based on transesterification to free MCPD and determination by gas chromatography-mass spectrometry (indirect methods) and by high-performance liquid chromatography-mass spectrometry (direct methods). The evolution and performance of the different methods is described and their advantages and disadvantages are discussed. The application of direct and indirect methods to the analysis of foods and to research studies is described. The metabolism and fate of MCPD esters and glycidol esters in biological systems and the methods used to study these in body tissues studies are described. A clear understanding of the chemistry of the methods is important when choosing those suitable for the desired application, and will contribute to the mitigation of these contaminants.

Preparation and stabilization of aluminium trifluoroacetate fluoride sols for optical coatings.

For the first time, aluminium fluorides in liquid phase are available for optical applications. By modifying the conditions of the fluorolytic sol-gel synthesis of aluminium fluorides transparent sols with low viscosities were obtained. These sols consist mainly of small oligomeric or cluster units of aluminium fluoride which are not measurable by DLS, WAXS, SAXS and show unusual narrow signals in solid state NMR. Isolated particles with diameters up to five nanometers can be identified by TEM measurements and allow the use of their sols in optical and anti reflecting coatings. The sol particles were modified by trifluoroacetic acid to prevent agglomeration, and as a result, the obtained xerogels can be re-dispersed transparently in organic solvents.

[Vestibular dysfunction after cochlear implant in adults]. / Vestibuläre Störungen nach Cochleaimplantat bei Erwachsenen.

BACKGROUND: According to the literature, clinical vertigo after cochlear implant (CI) occurs in 0.33-75%, a peripheral vestibular loss of function in 20-75%. MATERIALS AND METHODS: Between 2006 and 2009, 30 adults were implanted with a 22-channel Nucleus Freedom CI (41 operations). Cochleostomy was performed anterocaudal of the round window and the electrode inserted using the "off-stylet" technique into the scala tympani. RESULTS: Clinical vertigo occurred after 10/41 (24.4%) operations: acutely in 5/41 (12.2%), continuous in 1/41 (2.4%), delayed for 6-18 months in 5/41 (12.2%). In the calorimetry, 3/27 (11.1%) vestibular organs displayed a loss of function (p = 0.16). Three of 8 patients (37.5%) with clinical vertigo after surgery showed a loss of vestibular function (p = 0.08). CONCLUSION: Using the described techniques and materials, the risk of loss of vestibular function and the incidence of clinical vertigo can be minimized. Postoperative vertigo did not occur more often in patients with preoperative diminished vestibular function than in patients with normal findings. Therefore, preoperative vestibular function tests cannot be an indicator for the frequency of vertigo after CI. If one vestibular organ shows preoperative dysfunction, the non-affected normal vestibular organ should not be implanted.

Mechanistic insight into formation and changes of nanoparticles in MgF2 sols evidenced by liquid and solid state NMR.

The fluorolytic sol-gel reaction of magnesium methoxide with HF in methanol was studied by (19)F, (1)H and (13)C liquid and solid state NMR. In (19)F NMR five different species were identified, three of which belong to magnesium fluoride nanoparticles, i.e. NMR gave access to local structures of solid particles in suspensions. The long-term evolution of (19)F signals was followed and along with (19)F MAS NMR experiments of sols rotating at 13 kHz mechanistic insights into the ageing processes were obtained.

New crystalline aluminum alkoxide oxide fluorides: evidence of the mechanism of the fluorolytic sol-gel reaction.

This study reports three new crystalline aluminum isopropoxide oxide fluorides with molar ratios of Al:F equal to 1:1 and 1:1.25. These are the first three representatives isolated without the incorporation of external donor molecules. Compound 1 Al(4)F(4)(µ(4)-O)(µ-O(i)Pr)(5)[H(O(i)Pr)(2)] contains a tetranuclear unit consisting of two different five fold coordinated AlFO(4)-units, with F exclusively in the terminal position. Compound 2, Al(4)F(4)(µ(4)-O)(µ-O(i)Pr)(5)[H(O(i)Pr)(2)]·Al(5)F(5)(µ(5)-O)(µ-O(i)Pr)(8), contains both a tetranuclear unit (as in 1) and a pentanuclear Al-unit. Al-atoms in the latter are five- and six fold coordinated. Compound 3, Al(16)F(20)(µ(4)-O)(4)(µ-O(i)Pr)(20)·2((i)PrOH), exhibits a slightly higher fluorination degree and contains an oligomeric chain of four F-linked tetranuclear Al-units. In addition to X-ray structure analysis, compound 1 was characterized by different solid state MAS NMR techniques, including (27)Al triple quantum MAS NMR and (1)H, (1)H→(13)C CP, (19)F and (27)Al MAS NMR. On the basis of the collected data, a reliable decomposition of (27)Al single pulse MAS NMR spectra and an unambiguous assignment of the resonances to the respective structural AlFO(4)-units are given. The new crystalline aluminum isopropoxide oxide fluorides are direct evidence of the fluorolytic sol-gel mechanism previously discussed.

Identification of nevadensin as an important herb-based constituent inhibiting estragole bioactivation and physiology-based biokinetic modeling of its possible in vivo effect.

Estragole is a natural constituent of several herbs and spices including sweet basil. In rodent bioassays, estragole induces hepatomas, an effect ascribed to estragole bioactivation to 1'-sulfooxyestragole resulting in DNA adduct formation. The present paper identifies nevadensin as a basil constituent able to inhibit DNA adduct formation in rat hepatocytes exposed to the proximate carcinogen 1'-hydroxyestragole and nevadensin. This inhibition occurs at the level of sulfotransferase (SULT)-mediated bioactivation of 1'-hydroxyestragole. The Ki for SULT inhibition by nevadensin was 4 nM in male rat and human liver fractions. Furthermore, nevadensin up to 20 microM did not inhibit 1'-hydroxyestragole detoxification by glucuronidation and oxidation. The inhibition of SULT by nevadensin was incorporated into the recently developed physiologically based biokinetic (PBBK) rat and human models for estragole bioactivation and detoxification. The results predict that co-administration of estragole at a level inducing hepatic tumors in vivo (50mg/kg bw) with nevadensin at a molar ratio of 0.06, representing the ratio of their occurrence in basil, results in almost 100% inhibition of the ultimate carcinogen 1'-sulfooxyestragole when assuming 100% uptake of nevadensin. Assuming 1% uptake, inhibition would still amount to more than 83%. Altogether these data point at a nevadensin-mediated inhibition of the formation of the ultimate carcinogenic metabolite of estragole, without reducing the capacity to detoxify 1'-hydroxyestragole via glucuronidation or oxidation. These data also point at a potential reduction of the cancer risk when estragole exposure occurs within a food matrix containing SULT inhibitors compared to what is observed upon exposure to pure estragole.

Biological dose estimation of UVA laser microirradiation utilizing charged particle-induced protein foci.

The induction of localized DNA damage within a discrete nuclear volume is an important tool in DNA repair studies. Both charged particle irradiation and laser microirradiation (LMI) systems allow for such a localized damage induction, but the results obtained are difficult to compare, as the delivered laser dose cannot be measured directly. Therefore, we revisited the idea of a biological dosimetry based on the microscopic evaluation of irradiation-induced Replication Protein A (RPA) foci numbers. Considering that local dose deposition is characteristic for both LMI and charged particles, we took advantage of the defined dosimetry of particle irradiation to estimate the locally applied laser dose equivalent. Within the irradiated nuclear sub-volumes, the doses were in the range of several hundreds of Gray. However, local dose estimation is limited by the saturation of the RPA foci numbers with increasing particle doses. Even high-resolution 4Pi microscopy did not abrogate saturation as it was not able to resolve single lesions within individual RPA foci. Nevertheless, 4Pi microscopy revealed multiple and distinct 53BP1- and gamma H2AX-stained substructures within the lesion flanking chromatin domains. Monitoring the local recruitment of the telomere repeat-binding factors TRF1 and TRF2 showed that both proteins accumulated at damage sites after UVA-LMI but not after densely ionizing charged particle irradiation. Hence, our results indicate that the local dose delivered by UVA-LMI is extremely high and cannot be accurately translated into an equivalent ionizing radiation dose, despite the sophisticated techniques used in this study.

[Fundus leucaemicus as first manifestation of chronic myeloid leukemia. Diagnosis and monitoring with OCT under treatment with imatinib and interferon-alpha]. / Fundus leucaemicus als Erstmanifestation einer chronischen myeloischen Leukämie. Diagnosestellung und Verlaufskontrolle mit OCT unter Therapie mit Imatinib und Interferon-alpha.

Fundus leucaemicus with reduction of visual acuity can be one of the first signs of chronic myeloid leukemia (CML). The ocular manifestations are unspecific, but characteristic for severe systemic diseases. Optical coherence tomography (OCT) is helpful for documentation and quantification of the pathological retinal changes. However, peripheral blood counts and differential haemograms are seminal for the diagnosis of CML and can be important for survival. First line therapy for CML is the application of the tyrosine kinase inhibitor imatinib (Glivec). Ophthalmological adverse effects of this therapy, such as periorbital edema, are possible. Therefore regular ophthalmic monitoring should be performed.

Lack of significant effects of the type 2 diabetes susceptibility loci JAZF1, CDC123/CAMK1D, NOTCH2, ADAMTS9, THADA, and TSPAN8/LGR5 on diabetes and quantitative metabolic traits.

Recently, several novel loci reaching genome-wide significance levels for type 2 diabetes (T2D) were identified through a meta-analysis of three genome-wide scans and large-scale follow-up. The aim of our study was to investigate the association of these loci with T2D and related subphenotypes in two cohorts from Germany. We performed an association study of 9 SNPs in or around JAZF1, CDC123/ CAMK1D, NOTCH2, BCL11A, ADAMTS9, VEGFA, DCD, THADA, and TSPAN8/ LGR5 with T2D and related quantitative traits (fasting insulin and glucose, indices derived from OGTT) in the isolated population of Sorbs (205 cases and 695 controls) and in a mixed German population (Leipzig) (938 subjects with and 918 without T2D). None of the variants was associated with T2D, but the meta-analysis of both cohorts revealed a modest trend of association of rs7578597 in THADA with T2D (p=0.055). Furthermore, Sorbian subjects homozygous for the rs7578597 T-allele had lower mean 30-minute plasma insulin when compared with carriers of the C-allele (p<0.05). The T-allele was also nominally associated with higher fasting plasma glucose in the Leipzig cohort (p<0.05). Although several other SNPs showed some evidence for association with T2D-related traits the effects were not replicated within our study. Associations of the T2D-risk alleles with T2D or related subphenotypes were overall very weak in the approximately 2 700 subjects studied. This is compatible with the modest effect size of these "second sweep" variants, which will require large-scale association studies on quantitative traits to clarify their role in the pathophysiology of T2D.

Spatiotemporal analysis of DNA repair using charged particle radiation.

Approaches to visualise the dynamics of the DNA lesion processing substantially contributes to the understanding of the hierarchical organisation of the DNA damage response pathways. Charged particle irradiation has recently emerged as a tool to generate discrete sites of subnuclear damage by its means of extremely localised dose deposition at low energies, thus facilitating the spatiotemporal analysis of repair events. In addition, they are of high interest for risk estimations of human space exploration (e.g. mars mission) in the high energy regime (HZE). In this short review we will give examples for the application of charged particle irradiation to study spatiotemporal aspects of DNA damage recognition and repair in the context of recent achievements in this field. Beamline microscopy allows determining the exact kinetics of repair-related proteins after irradiation with different charged particles that induce different lesion densities. The classification into fast recruited proteins like DNA-PK or XRCC1 or slower recruited ones like 53BP1 or MDC1 helps to establish the hierarchical organisation of damage recognition and subsequent repair events. Additionally, motional analysis of DNA lesions induced by traversing particles proved information about the mobility of DSBs. Increased mobility or the absence of large scale motion has direct consequences on the formation of chromosomal translocations and, thus, on mechanisms of cancer formation. Charged particle microbeams offer the interesting perspective of precise nuclear or subnuclear targeting with a defined number of ions, avoiding the Poisson distribution of traversals inherent to broad beam experiments. With the help of the microbeam, geometrical patterns of traversing ions can be applied facilitating the analysis of spatial organisation of repair.

Distribution of DNA fragment sizes after irradiation with ions.

Ionizing radiation is responsible for production of double-strand breaks (DSBs) in a DNA structure. In contrast to sparsely ionizing radiation, densely ionizing radiation produces DSBs that are non-randomly distributed along the DNA molecule and can form clusters of various size. The paper discusses minimalistic models that describe observable patterns of fragment length in DNA segments irradiated with heavy ions and applies the formalism to interpret the recent experimental data collected by use of atomic force microscope (AFM).