Training grapevines generates a metabolomic signature of wine.

Training systems are an option to handle the pronounced apical dominance of grapevines and to influence diverse traits of the corresponding wine. However, it is still unclear if different training systems generate signatures in the metabolome of the wine. By an untargeted metabolomics approach using (SPME) GC-MS wine (volatiles) and leaves were evaluated. Different training directions such as vertical shoot positioning systems, hanging shoot systems, and minimal pruning systems were distinguishable in wine. It was shown, that different training systems generate a metabolomic signature in the wine which was more pronounced than in leaves. Moreover, the sensory analysis showed some changes in the aroma of the different training systems. Thus, the influence of the training system ranges from the leaf metabolome to the wine metabolome.

Mixture effects of azole fungicides on the adrenal gland in a broad dose range.

Consumers are exposed to low concentrations of a variety of pesticide residues in or on food. Some of them might interfere with the endocrine system. While each individual active substance has been extensively tested for toxicity and safety, potential combination effects possibly resulting from combined exposure to different pesticides have seldomly been tested so far, especially in vivo. Since the adrenal gland is a key endocrine organ, we investigated if and how substances of a group of fungicides presumed to interfere with the biosynthesis of steroid hormones affect this organ when applied individually and in combination in a broad dose range. A 28-day feeding study was conducted in Wistar rats by using three (tri)azole fungicides considered to potentially affect the endocrine system (cyproconazole, epoxiconazole and prochloraz) individually at five dose levels, ranging from 0.9ppm to 2400ppm, and in combination at three dose levels. The parameters analysed included classical toxicology (pathology, histopathology, clinical chemistry) and molecular toxicology endpoints (gene expression arrays and quantitative real time PCR e.g. of Star, HSD3ß, Cyp11a1, Cyp11b1, Cyp11b2, Cyp 21, ApoE), as well as hormone analysis. A dose-dependent decrease in the adrenal gland weight of rats treated with epoxiconazole alone, which was accompanied by an atrophy of the adrenal gland as well as by an increase in the serum cholesterol level and which only became statistically significant at the top dose levels, was observed. These effects were attenuated in the combination experiments, although the same epoxiconazole concentration was used.

Successful diagnosis of lymphangioleiomyomatosis with transbronchial lung cryobiopsy.

A 47-year old female was evaluated in our clinic for an incidental discovery of diffuse cystic lung disease on high-resolution computed tomography (CT) scan of the chest. There was no personal or family history of tuberous sclerosis complex (TSC), sicca symptoms, pneumothorax, or skin or renal tumors. Review of her chest CT scan showed bilateral, round, uniform, thin-walled cysts present in a diffuse distribution characteristic of lymphangioleiomyomatosis (LAM). CT scan of the abdomen and pelvis did not reveal angiomyolipomas, lymphangioleiomyomas, abnormal lymphadenopathy, or chylous fluid collections. Serum vascular endothelial growth factor-D was non-diagnostic. In order to achieve diagnostic confirmation, the patient underwent transbronchial cryobiopsy of the lung, revealing changes consistent with LAM. Our case highlights the utility of transbronchial lung cryobiopsy in the evaluation of patients with suspected LAM and suggests that further investigation of this diagnostic technique is warranted in patients presenting with diffuse cystic lung disease.

A consolidated analysis of the physiologic and molecular responses induced under acid stress in the legume-symbiont model-soil bacterium Sinorhizobium meliloti.

Abiotic stresses in general and extracellular acidity in particular disturb and limit nitrogen-fixing symbioses between rhizobia and their host legumes. Except for valuable molecular-biological studies on different rhizobia, no consolidated models have been formulated to describe the central physiologic changes that occur in acid-stressed bacteria. We present here an integrated analysis entailing the main cultural, metabolic, and molecular responses of the model bacterium Sinorhizobium meliloti growing under controlled acid stress in a chemostat. A stepwise extracellular acidification of the culture medium had indicated that S. meliloti stopped growing at ca. pH 6.0-6.1. Under such stress the rhizobia increased the O2 consumption per cell by more than 5-fold. This phenotype, together with an increase in the transcripts for several membrane cytochromes, entails a higher aerobic-respiration rate in the acid-stressed rhizobia. Multivariate analysis of global metabolome data served to unequivocally correlate specific-metabolite profiles with the extracellular pH, showing that at low pH the pentose-phosphate pathway exhibited increases in several transcripts, enzymes, and metabolites. Further analyses should be focused on the time course of the observed changes, its associated intracellular signaling, and on the comparison with the changes that operate during the sub lethal acid-adaptive response (ATR) in rhizobia.

Maleic anhydride proton sponge as a novel MALDI matrix for the visualization of small molecules (<250 m/z) in brain tumors by routine MALDI ToF imaging mass spectrometry.

A novel vacuum stable proton sponge, 4-maleicanhydridoproton sponge (MAPS), was prepared and applied as the matrix in Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging (MALDI-MSI) of an aggressive brain tumor tissue (glioblastoma multiforme). Ionic maps of lactate, 2-hydroxyglutarate and chloride anions (m/z 89, 147, 35, respectively) were obtained using a routine MALDI ToF mass spectrometer.

A safe and feasible "clock-face" duct-to-mucosa pancreaticojejunostomy with a very low incidence of anastomotic failure: A single center experience of 248 patients.

INTRODUCTION: Postoperative pancreatic fistula (POPF) is one of the most frequent and serious postoperative complications of pancreatoduodenectomy (PD). We sought to assess the impact of a novel pancreaticojejunostomy (PJ) on the rates of POPF and overall postoperative complications. METHODS: Between 01/2010 and 12/2013, a total of 248 consecutive patients who underwent PD with a modified PJ were identified from our database and retrospectively analyzed. POPF cases were divided into three categories (ISGPF-international study group-guidelines): biochemical fistula without clinical sequelae (grade A), fistula requiring any therapeutic intervention (grade B), and fistula with severe clinical sequelae (grade C). Perioperative outcomes were recorded and analyzed. RESULTS: The overwhelming majority of patients had no evidence of fistula. Grade A POPF was observed in 9 (3.62%), grade B in 1 (0.40%), and grade C in 0 patients. There were no postoperative deaths. Overall complications occurred in 61 patients (24.59%) of patients after PD. CONCLUSIONS: This modified pancreaticojejunostomy is widely applicable and is associated with very low rates of POPF, low postoperative morbidity and mortality. Overall, it is a feasible and safe novel approach with excellent short-term outcomes.

Health Informatics via Machine Learning for the Clinical Management of Patients.

OBJECTIVES: To review how health informatics systems based on machine learning methods have impacted the clinical management of patients, by affecting clinical practice. METHODS: We reviewed literature from 2010-2015 from databases such as Pubmed, IEEE xplore, and INSPEC, in which methods based on machine learning are likely to be reported. We bring together a broad body of literature, aiming to identify those leading examples of health informatics that have advanced the methodology of machine learning. While individual methods may have further examples that might be added, we have chosen some of the most representative, informative exemplars in each case. RESULTS: Our survey highlights that, while much research is taking place in this high-profile field, examples of those that affect the clinical management of patients are seldom found. We show that substantial progress is being made in terms of methodology, often by data scientists working in close collaboration with clinical groups. CONCLUSIONS: Health informatics systems based on machine learning are in their infancy and the translation of such systems into clinical management has yet to be performed at scale.

[Perihilar cholangiocarcinoma (Klatskin tumor)]. / Zentrales Gallengangskarzinom (Klatskin-Tumor).

Perihilar cholangiocarcinoma or Klatskin tumors are a rare entity arising from the extrahepatic bile duct bifurcation. Considering the close anatomical relationship of the bile duct bifurcation with the portal vein bifurcation and hepatic arteries, surgical treatment is demanding. With an incidence of only 2-4 cases/100,000 population/year patients should be referred to a specialized center. The tumors are usually poorly differentiated adenocarcinomas growing diffusely along the duct and also the perineural sheath. Only radical surgery offers a curative option and currently surgical strategy usually consists of en bloc resection of the bile duct, extended liver resection and portal vein resection. Proximal and lateral safety margin R0 resections are technically very demanding procedures because of the local anatomy.

Metabolite fingerprinting of barley whole seeds, endosperms, and embryos during industrial malting.

Samples of whole seeds, isolated endosperms including the aleurone layer and isolated embryos with attached scutellum from an industrial scale barley malting process (variety Braemar) were analysed for their water soluble metabolites by gas chromatography-mass spectrometry (GC-MS). 73 known metabolites and about 350 unknown signals were detected. Principal component analysis (PCA) showed a time dependent shift of sample profiles. Whole seeds and endosperm samples showed very similar patterns with nearly all compounds rising until the end of germination. In the embryos a maximum concentration of compounds was reached after 72-96 h of malting. Most concentrations decreased afterwards. The kilning step, namely the drying and roasting of germinated seeds, induced variable effects of increases, stability or decreases of metabolites and thereby separated kilned samples from germinated seeds in the PCA. A second barley cultivar (Quench) underwent the same malting and analysis procedures and gave nearly identical results. Fructose, malate, myo-inositol and raffinose exhibited the potential to serve as markers for specific developmental stages of seeds in both varieties. Biological markers represent targets for industrial process control. Their potential application would meet the maltsters' demand to flatten variances in germination properties and to produce equal composed malt by directed malting management.

Two differentially expressed MATE factor genes from apple complement the Arabidopsis transparent testa12 mutant.

Proanthocyanidins (PAs) are a class of flavonoids with numerous functions in plant ecology and development, including protection against microbial infection, animal foraging and damage by UV light. PAs are also beneficial in the human diet and livestock farming, preventing diseases of the cardiovascular system and lowering the risk of cancer, asthma and diabetes. Apples (Malus x domestica Borkh.) are naturally rich in flavonoids, but the flavonoid content and composition varies significantly between cultivars. In this work, we applied knowledge from the model plant Arabidopsis thaliana, for which the main features of flavonoid biosynthesis have been elucidated, to investigate PA accumulation in apple. We identified functional homologues of the Multidrug And Toxic compound Extrusion (MATE) gene TRANSPARENT TESTA12 from A. thaliana using a comparative genomics approach. MdMATE1 and MdMATE2 were differentially expressed, and the function of the encoded proteins was verified by complementation of the respective A. thaliana mutant. In addition, MdMATE genes have a different gene structure in comparison to homologues from other species. Based on our findings, we propose that MdMATE1 and MdMATE2 are vacuolar flavonoid/H(+) -antiporters, active in PA accumulating cells of apple fruit. The identification of these flavonoid transporter genes expands our understanding of secondary metabolite biosynthesis and transport in apple, and is a prerequisite to improve the nutritional value of apples and apple-derived beverages.

CARMEN - Comparative Analysis and in silico Reconstruction of organism-specific MEtabolic Networks.

New sequencing technologies provide ultra-fast access to novel microbial genome data. For their interpretation, an efficient bioinformatics pipeline that facilitates in silico reconstruction of metabolic networks is highly desirable. The software tool CARMEN performs in silico reconstruction of metabolic networks to interpret genome data in a functional context. CARMEN supports the visualization of automatically derived metabolic networks based on pathway information from the KEGG database or from user-defined SBML templates; this software also enables comparative genomics. The reconstructed networks are stored in standardized SBML format. We demonstrated the functionality of CARMEN with a major application example focusing on the reconstruction of glycolysis and related metabolic reactions of Xanthomonas campestris pv. campestris B100. The curation of such pathways facilitates enhanced visualization of experimental results, simulations and comparative genomics. A second application of this software was performed on a set of corynebacteria to compare and to visualize their carbohydrate metabolism. In conclusion, using CARMEN, we developed highly automated data analysis software that rapidly converts sequence data into new knowledge, replacing the time-consuming manual reconstruction of metabolic networks. This tool is particularly useful for obtaining an overview of newly sequenced genomes and their metabolic blueprints and for comparative genome analysis. The generated pathways provide automated access to modeling and simulation tools that are compliant with the SBML standard. A user-friendly web interface of CARMEN is available at http://carmen.cebitec.uni-bielefeld.de.

Heat shock protein 27 modification is increased in the human diabetic failing heart.

Chronic conditions like diabetes mellitus (DM) leading to altered metabolism might cause cardiac dysfunction. Hyperglycemia plays an important role in the pathogenesis of diabetic complications including accumulation of methylglyoxal (MG), a highly reactive alpha-dicarbonyl metabolite of glucose degradation pathways and increased generation of advanced glycation endproducts (AGEs). The aim of this investigation was to study the extent of the MG-modification argpyrimidine in human diabetic heart and in rat cardiomyoblasts grown under hyperglycemic conditions. Left ventricular myocardial samples from explanted hearts of patients with cardiomyopathy with (n=8) or without DM (n=8) as well as nonfailing donor organs (n=6), and rat cardiac myoblasts H9c2 treated with glucose were screened for the MG-modification argpyrimidine. The small heat shock protein 27 (Hsp27) revealed to be the major argpyrimidine containing protein in cardiac tissue. Additionally, the modification of arginine leading to argpyrimidine and the phosphorylation of Hsp27 are increased in the myocardium of patients with DM. In H9c2 cells hyperglycemia leads to a decrease of the Hsp27-expression and an increase in argpyrimidine content and phosphorylation of Hsp27, which was accompanied by the induction of oxidative stress and apoptosis. This study shows an association between diabetes and increased argpyrimidine-modification of myocardial Hsp27, a protein which is involved in apoptosis, oxidative stress, and cytoskeleton stabilization.

Identification and characterization of a nodH ortholog from the alfalfa-nodulating Or191-like rhizobia.

Nodulation of Medicago sativa (alfalfa) is known to be restricted to Sinorhizobium meliloti and a few other rhizobia that include the poorly characterized isolates related to Rhizobium sp. strain Or191. Distinctive features of the symbiosis between alfalfa and S. meliloti are the marked specificity from the plant to the bacteria and the strict requirement for the presence of sulfated lipochitooligosaccharides (Nod factors [NFs]) at its reducing end. Here, we present evidence of the presence of a functional nodH-encoded NF sulfotransferase in the Or191-like rhizobia. The nodH gene, present in single copy, maps to a high molecular weight megaplasmid. As in S. meliloti, a nodF homolog was identified immediately upstream of nodH that was transcribed in the opposite direction (local synteny). This novel nodH ortholog was cloned and shown to restore both NF sulfation and the Nif+Fix+ phenotypes when introduced into an S. meliloti nodH mutant. Unexpectedly, however, nodH disruption in the Or191-like bacteria did not abolish their ability to nodulate alfalfa, resulting instead in a severely delayed nodulation. In agreement with evidence from other authors, the nodH sequence analysis strongly supports the idea that the Or191-like rhizobia most likely represent a genetic mosaic resulting from the horizontal transfer of symbiotic genes from a sinorhizobial megaplasmid to a not yet clearly identified ancestor.

Sinorhizobium meliloti strain 1021 produces a low-molecular-mass capsular polysaccharide that is a homopolymer of 3-deoxy-D-manno-oct-2-ulosonic acid harboring a phospholipid anchor.

Sinorhizobium meliloti strain 1021 possesses the particularity to synthesize biologically inefficient capsular polysaccharides (KPS). It has been assumed that this class of compounds is not produced in high-molecular-mass (HMM) forms, even if many genetic analyses show the existence of expression of genes involved in the biosynthesis of capsular polysaccharides. The expression of these genes that are involved in the export of a KPS throughout the membrane and in the attachment of a lipid moiety has never been related to a structurally characterized surface polysaccharide. It is now reported that S. meliloti strain 1021 produces low-molecular-mass polysaccharides (4-4.5 kDa) that are exclusively composed of beta-(2-->7)-linked 3-deoxy-d-manno-oct-2-ulopyranosonic acid (Kdo) residues. These compounds are considered precursor molecules of HMM KPS, whose biosynthesis is arrested in the case of S. meliloti strain 1021. For the first time, the phospholipid anchor of a rhizobial KPS has been found, and its structure could be partially identified-namely, a phosphoglycerol moiety bearing a hydroxy-octacosanoic acid. When compared to other rhizobial KPS (composed of dimeric hexose-Kdo-like sugar repeating units), the Kdo homopolymer described here may explain why a complementation of S. meliloti strain 1021 Exo B mutant with an effective rkpZ gene restoring an active higher KPS size does not completely lead to the fully effective nitrogen fixing phenotype.

A Rab-related small GTP binding protein is predominantly expressed in root nodules of Medicago sativa.

Rab-related small GTP-binding proteins are known to be involved in the regulation of the vesicular transport system in eucaryotic cells. In this paper we report the isolation of the cDNA clone MS- rab11f from Medicago sativa (alfalfa) root nodules using a combination of RT-PCR and SSCP analysis. MS- rab11f shows high homology to the Rab-related cDNA clone LJ- rab11f from Lotus japonicus root nodules. The MS-Rab11F protein expressed in Escherichia coli was found to bind GTP, confirming that the isolated cDNA indeed codes for a small GTP-binding protein. Expression analysis by RT-PCR demonstrated that MS- rab11f is preferentially expressed in root nodules of alfalfa. Using the cDNA-sequence of MS-rab11f, a peptide-specific antibody was generated. Western blot analysis with this antibody revealed that two Rab11F isoforms, designated MS-Rab11FA and MS-Rab11FB, are found in M. sativa root nodules.

Comparison of two Xanthomonas campestris pathovar campestris genomes revealed differences in their gene composition.

For the Xanthomonas campestris pathovar campestris wild-type strain B100 a plasmid-based clone library was constructed. The plasmids carried chromosomal fragments of 3-4 kb in size that were tagged in vitro with the artificial transposon KAN-2. More than 3000 of the transposon target sites were characterized by DNA sequencing. The sequences obtained were compared to the recently published genome of Xanthomonas campestris pathovar campestris strain ATCC 33913. Most of the sequenced clones derived from strain B100 matched the chromosomal sequence of strain ATCC 33913. An alignment to the circular map of this chromosome revealed that the similarities were statistically distributed over the entire genome of strain ATCC 33913. The similarity was obvious for protein coding sequences, as well as for mobile genetic elements. However, four regions in the genome of Xanthomonas campestris pathovar campestris strain ATCC 33913, ranging in size from 11 to 37 kb, were not represented in the sequenced clone library of Xanthomonas campestris pathovar campestris strain B100. On the other hand, 1.2% of the sequenced clones originating from Xanthomonas campestris pathovar campestris strain B100 showed no or insignificant similarities to the genome of strain ATCC 33913.

Lipopolysaccharide biosynthesis in Xanthomonas campestris pv. campestris: a cluster of 15 genes is involved in the biosynthesis of the LPS O-antigen and the LPS core.

As a result of mutational and DNA sequence analysis, a wxc gene cluster involved in the synthesis of the surface lipopolysaccharide (LPS) was identified in Xanthomonas campestris pv. campestris. This gene cluster comprises 15 genes. It was located on a cloned 35-kb fragment of chromosomal DNA, close, but not directly adjacent, to previously characterized genes for LPS biosynthesis. The G + C content of all but one of the wxc genes was atypically low for X. campestris pv. campestris, while the G + C distribution was uniform throughout the cluster. An SDS-PAGE analysis of mutant strains defective in various wxc genes confirmed that genes from this cluster were involved in LPS biosynthesis. The mutant phenotypes allowed the differentiation of three regions within the wxc cluster. Genes from wxc region 1 are necessary for the biosynthesis of the water-soluble LPS O-antigen. Analysis of DNA and deduced amino acid sequences led to the identification of two glycosyltransferases, two components of an ABC transport system, and a possible kinase among the seven putative proteins encoded by genes constituting wxc region 1. The two genes in wxc region 2 were similar to gmd and rmd, which direct the synthesis of the sugar nucleotide GDP-D-rhamnose. Mutations affecting wxc region 2 demonstrated its involvement in the formation of the LPS core. Genes from wxc region 3 showed similarities to genes that code for enzymes that modify nucleotide sugars, and to components of sugar translocation systems that have so far been rarely described in bacteria.

The lipopolysaccharides of the phytopathogen Xanthomonas campestris pv. campestris induce an oxidative burst reaction in cell cultures of Nicotiana tabacum.

The lipopolysaccharides (LPSXcc) of the phytopathogenic bacteria Xanthomonas campestris pv. campestris (X.c.c.) were purified from an exopolysaccharide-deficient mutant strain. The isolated LPSxcc induced an oxidative burst reaction in cell-suspension cultures of the non-host plant tobacco (Nicotiana tabacum L.) SRI. The oxidative burst elicited by LPSXcc differed from that induced by yeast elicitor (YE), a cell wall preparation of baker's yeast. The LPSXcc-induced oxidative burst was characterised by a slow increase in H2O2 production and an extended decline. Both the LPSXcc-and YE-induced oxidative bursts were completely blocked by the NAD(P)H-oxidase inhibitor diphenylene-iodonium. When LPSXcc and YE were applied in combination, a synergistic effect and the establishment of refractory states in the generation of H2O2 were observed. The amount of cytosolic calcium was measured in transgenic tobacco cell cultures carrying the apoaequorin gene by coelenterazine-derived chemiluminescence. Whereas YE induced a calcium peak within 1 min after application, LPSXcc induced a long-term calcium signal without transients. To our knowledge this is the first report on the elicitation of an oxidative burst in plant cell cultures by isolated LPS of a phytopathogenic bacterium.