Anchoring the CerEla1.0 Genome Assembly to Red Deer (Cervus elaphus) and Cattle (Bos taurus) Chromosomes and Specification of Evolutionary Chromosome Rearrangements in Cervidae

Simple Summary

The red deer (Cervus elaphus) de novo genome assembly (CerEla1.0) has provided a great resource for genetic studies in various deer species. In this study, we used gene order comparisons between C. elaphus CerEla1.0 and B. taurus ARS-UCD1.2 genome assemblies and fluorescence in situ hybridization (FISH) with bovine BAC probes to verify the red deer-bovine chromosome relationships and anchor the CerEla1.0 C-scaffolds to karyotypes of both species. We showed the homology between bovine and deer chromosomes and determined the centromere-telomere orientation of the CerEla1.0 C-scaffolds. Using a set of BAC probes, we were able to narrow the positions of evolutionary chromosome breakpoints defining the family Cervidae. In addition, we revealed several errors in the current CerEla1.0 genome assembly. Finally, we expanded our analysis to other Cervidae and confirmed the locations of the cervid evolutionary fissions and orientation of the fused chromosomes in eight cervid species. Our results can serve as a basis for necessary improvements of the red deer genome assembly and provide support to other genetic studies in Cervidae.

Abstract

The family Cervidae groups a range of species with an increasing economic significance. Their karyotypes share 35 evolutionary conserved chromosomal segments with cattle (Bos taurus). Recent publication of the annotated red deer (Cervus elaphus) whole genome assembly (CerEla1.0) has provided a basis for advanced genetic studies. In this study, we compared the red deer CerEla1.0 and bovine ARS-UCD1.2 genome assembly and used fluorescence in situ hybridization with bovine BAC probes to verify the homology between bovine and deer chromosomes, determined the centromere-telomere orientation of the CerEla1.0 C-scaffolds and specified positions of the cervid evolutionary chromosome breakpoints. In addition, we revealed several incongruences between the current deer and bovine genome assemblies that were shown to be caused by errors in the CerEla1.0 assembly. Finally, we verified the centromere-to-centromere orientation of evolutionarily fused chromosomes in seven additional deer species, giving a support to previous studies on their chromosome evolution.

Statistical-learning method for predicting hydrodynamic drag, lift, and pitching torque on spheroidal particles

A statistical learning approach is presented to predict the dependency of steady hydrodynamic interactions of thin oblate spheroidal particles on particle orientation and Reynolds number. The conventional empirical correlations that approximate such dependencies are replaced by a neural-network-based correlation which can provide accurate predictions for high-dimensional input spaces occurring in flows with nonspherical particles. By performing resolved simulations of steady uniform flow at 1≤Re≤120 around a 1:10 spheroidal body, a database consisting of Reynolds number- and orientation-dependent drag, lift, and pitching torque acting on the particle is collected. A multilayer perceptron is trained and validated with the generated database. The performance of the neural network is tested in a point-particle simulation of the buoyancy-driven motion of a 1:10 disk. Our statistical approach outperforms existing empirical correlations in terms of accuracy. The agreement between the numerical results and the experimental observations prove the potential of the method.

Sequence Analysis and FISH Mapping of Four Satellite DNA Families among Cervidae

Centromeric and pericentromeric chromosome regions are occupied by satellite DNA. Satellite DNAs play essential roles in chromosome segregation, and, thanks to their extensive sequence variability, to some extent, they can also be used as phylogenetic markers. In this paper, we isolated and sequenced satellite DNA I-IV in 11 species of Cervidae. The obtained satellite DNA sequences and their chromosomal distribution were compared among the analysed representatives of cervid subfamilies Cervinae and Capreolinae. Only satI and satII sequences are probably present in all analysed species with high abundance. On the other hand, fluorescence in situ hybridisation (FISH) with satIII and satIV probes showed signals only in a part of the analysed species, indicating interspecies copy number variations. Several indices, including FISH patterns, the high guanine and cytosine (GC) content, and the presence of centromere protein B (CENP-B) binding motif, suggest that the satII DNA may represent the most important satellite DNA family that might be involved in the centromeric function in Cervidae. The absence or low intensity of satellite DNA FISH signals on biarmed chromosomes probably reflects the evolutionary reduction of heterochromatin following the formation of chromosome fusions. The phylogenetic trees constructed on the basis of the satellite I-IV DNA relationships generally support the present cervid taxonomy.

Recurrent gene mutations detected in canine mast cell tumours by next generation sequencing

Genetic causes of canine mast cell tumours (MCTs), except for mutations in the KIT gene detected in some MCTs, are generally unknown. We used whole exome sequencing to reveal mutation spectra in canine MCTs. We detected somatic mutations in 87 genes including 10 genes recognized as human cancer drivers. Besides KIT, 14 other genes were recurrently mutated. Subsequently, we performed next generation sequencing of a panel of 50 selected genes in additional MCT samples. In this group, the most frequently altered gene was GNB1 showing a recurrent dinucleotide substitution at position of Gly116 in 30% of the MCT samples (n = 6/20) and Ile80 substitution accompanied by a splice region mutation in one case. We extended the study by analysis of the above mentioned GNB1 regions in additional MCT samples by Sanger sequencing, and assessed the overall prevalence of GNB1 mutations to 17.3% (n = 14/81), which is similar to the prevalence of KIT alterations. Our results indicate that GNB1 mutations are probably involved in canine MCT pathogenesis in both cutaneous and subcutaneous MCT cases. As opposed to KIT alterations, the presence of GNB1 mutations did not negatively affect survival times, and our data even showed a trend towards positive prognosis. If our results are confirmed in a larger number of MCTs, an extension of molecular testing of canine MCTs by GNB1 analysis would help to refine the molecular stratification of MCTs, and become useful for targeted treatment strategies.

Mutation and methylation status of KIT and TP53 in canine cutaneous and subcutaneous mast cell tumours

Cutaneous and subcutaneous mast cell tumours (MCTs) are counted among the most frequent cancers in dogs. However, the genetic aetiology of their development is still mostly unknown, with the exception of KIT and tumor protein p53 (TP₅₃ ) mutations reported in less than a half of cutaneous MCTs. In subcutaneous MCTs, no gene alterations were previously detected. We analysed KIT and TP₅₃ mutations in cutaneous and subcutaneous MCTs, and identified methylated CpG sites in KIT and TP₅₃ promoters and adjacent exon 1 regions. The mutation analysis focused on KIT exons 8, 9 and 11, and TP₅₃ exons 5-8, and revealed mutations in 26% and 7% cutaneous MCT cases, respectively. Moreover, we report a first case of KIT mutation ever detected in subcutaneous MCTs. KIT exon 11 mutations and high Kiupel and Patnaik grades were associated with reduced survival in this study. Both KIT and TP₅₃ gene were generally unmethylated in canine cutaneous MCTs. A sporadic methylation of the CpG positions in KIT promoter and adjacent exon 1 was detected in 70.4% of cutaneous and 82% of subcutaneous MCTs. A sporadic methylation of the CpG positions in the TP₅₃ promoter and exon 1 was observed in 36.8% of the analysed cutaneous MCT samples. Only in two subcutaneous MCTs, we observed more than 30% of clones showing KIT methylation at the CpG positions 13 or 14. The CpG position 14 is involved in a predicted binding site for Sp1 transcription factor. However, the significance of KIT promoter methylation at this specific position needs further evaluation.

Comparative Study of the Bush Dog (Speothos venaticus) Karyotype and Analysis of Satellite DNA Sequences and Their Chromosome Distribution in Six Species of Canidae

The bush dog (Speothos venaticus, 2n = 74) is a near threatened species taxonomically classified among South American canids. We revised the bush dog karyotype and performed a comparative sequence analysis of satellite and satellite-like DNAs in 6 canids: the bush dog, domestic dog (Canis familiaris, 2n = 78), grey wolf (C. lupus, 2n = 78), Chinese raccoon dog (Nyctereutes procyonoides procyonoides, 2n = 54+B), red fox (Vulpes vulpes, 2n = 34+B), and arctic fox (V. lagopus, 2n = 48-50) to specify the species position among Canidae. Using FISH with painting and BAC probes, we found that the distribution of canid evolutionarily conserved chromosome segments in the bush dog karyotype is similar to that of the domestic dog and grey wolf. The bush dog karyotype differs by 2 acrocentric chromosome pairs formed by tandem fusions of the canine (29;34) and (26;35) orthologues. An interstitial signal of the telomeric probe was observed in the (26;35) fusion site in the bush dog indicating a recent evolutionary origin of this rearrangement. Sequences and hybridisation patterns of satellite DNAs were compared, and a phylogenetic tree of the 6 canid species was constructed which confirmed the bush dog position close to the wolf-like canids, and apart from the raccoon dog and foxes.

Prevalence and prognostic value of c-kit and TP53 mutations in canine mast cell tumours

Cutaneous mast cell tumours (MCT) are among the most frequent malignancies in dogs. Their clinical behaviour is highly variable and, with the exception of mutations in the c-kit gene, little is known about their genetic aetiology. The mutational status of the c-kit exons 8, 9 and 11, and exons 5-8 of the TP53 gene was analysed to find markers for molecular stratification of MCTs and predictors of clinical outcome. Mutations in the c-kit gene were detected in 19.5% (n = 8/41) samples and their presence was significantly associated with the high histopathological grade (P = 0.038). Mutations in the DNA binding domain of the TP53 gene were found in 14.6% (n = 6/41) of the analysed MCTs, and their frequency was similar in low and high grade MCTs (P > 0.05). TP53 mutations were not useful prognostic factors in this sample of canine cutaneous MCTs.

Meiotic Recombination in the Giraffe (G. reticulata)

Recently, the reticulated giraffe (G. reticulata) was identified as a distinct species, which emphasized the need for intensive research in this interesting animal. To shed light on the meiotic process as a source of biodiversity, we analysed the frequency and distribution of meiotic recombination in 2 reticulated giraffe males. We used immunofluorescence detection of synaptonemal complex protein (SYCP3), meiotic double strand breaks (DSB, marked as RAD51 foci) in leptonema, and crossovers (COs, as MLH1 foci) in pachynema. The mean number of autosomal MLH1 foci per cell (27), which resulted from a single, distally located MLH1 focus observed on most chromosome arms, is one of the lowest among mammalian species analysed so far. The CO/DSB conversion ratio was 0.32. The pseudoautosomal region was localised in the Xq and Yp termini by FISH and showed an MLH1 focus in 83% of the pachytene cells. Chromatin structures corresponding to the nucleolus organiser regions were observed in the pachytene spermatocytes. The results are discussed in the context of known data on meiosis in Cetartiodactyla, depicting that the variation in CO frequency among species of this taxonomic group is mostly associated with their diploid chromosome number.

Satellite DNA Sequences in Canidae and Their Chromosome Distribution in Dog and Red Fox

Satellite DNA is a characteristic component of mammalian centromeric heterochromatin, and a comparative analysis of its evolutionary dynamics can be used for phylogenetic studies. We analysed satellite and satellite-like DNA sequences available in NCBI for 4 species of the family Canidae (red fox, Vulpes vulpes, VVU; domestic dog, Canis familiaris, CFA; arctic fox, Vulpes lagopus, VLA; raccoon dog, Nyctereutes procyonoides procyonoides, NPR) by comparative sequence analysis, which revealed 86-90% intraspecies and 76-79% interspecies similarity. Comparative fluorescence in situ hybridisation in the red fox and dog showed signals of the red fox satellite probe in canine and vulpine autosomal centromeres, on VVUY, B chromosomes, and in the distal parts of VVU9q and VVU10p which were shown to contain nucleolus organiser regions. The CFA satellite probe stained autosomal centromeres only in the dog. The CFA satellite-like DNA did not show any significant sequence similarity with the satellite DNA of any species analysed and was localised to the centromeres of 9 canine chromosome pairs. No significant heterochromatin block was detected on the B chromosomes of the red fox. Our results show extensive heterogeneity of satellite sequences among Canidae and prove close evolutionary relationships between the red and arctic fox.

32nd International Austrian Winter Symposium : Zell am See, the Netherlands. 20-23 January 2016

A1 68Ga-PSMA PET/CT in staging and restaging of Prostate Cancer Patients: comparative study with 18F-Choline PET/CT

W Langsteger, A Rezaee, W Loidl, HS Geinitz, F Fitz, M Steinmair, G Broinger, L Pallwien-Prettner, M Beheshti

A2 F18 Choline PET – CT: an accurate diagnostic tool for the detection of parathyroid adenoma?

L Imamovic, M Beheshti, G Rendl, D Hackl, O Tsybrovsky, M Steinmair, K Emmanuel, F Moinfar, C Pirich, W Langsteger

A3 [18F]Fluoro-DOPA-PET/CT in the primary diagnosis of medullary thyroid carcinoma

A Bytyqi, G Karanikas, M Mayerhöfer, O Koperek, B Niederle, M Hartenbach

A4 Variations of clinical PET/MR operations: An international survey on the clinical utilization of PET/MRI

T Beyer, K Herrmann, J Czernin

A5 Standard Dixon-based attenuation correction in combined PET/MRI: Reproducibility and the possibility of Lean body mass estimation

I Rausch, P Rust, MD DiFranco, M Lassen, A Stadlbauer, ME Mayerhöfer, M Hartenbach, M Hacker, T Beyer

A6 High resolution digital FDG PET/MRI imaging for assessment of ACL graft viability

K Binzel, R Magnussen, W Wei, MU Knopp, DC Flanigan, C Kaeding, MV Knopp

A7 Using pre-existing hematotoxicity as predictor for severe side effects and number of treatment cycles of Xofigo therapy

A Leisser, M Nejabat, M Hartenbach, G Kramer, M Krainer, M Hacker, A Haug

A8 QDOSE – comprehensive software solution for internal dose assessment

Wencke Lehnert, Karl Schmidt, Sharok Kimiaei, Marcus Bronzel, Andreas Kluge

A9 Clinical impact of Time-of-Flight on next-generation digital PET imaging of Yttrium-90 radioactivity following liver radioembolization

CL Wright, K Binzel, J Zhang, Evan Wuthrick, Piotr Maniawski, MV Knopp

A10 Snakes in patients! Lessons learned from programming active contours for automated organ segmentation

M Blaickner, E Rados, A Huber, M Dulovits, H Kulkarni, S Wiessalla, C Schuchardt, RP Baum, B Knäusl, D Georg

A11 Influence of a genetic polymorphism on brain uptake of the dual ABCB1/ABCG2 substrate [11C]tariquidar

M Bauer, B Wulkersdorfer, W Wadsak, C Philippe, H Haslacher, M Zeitlinger, O Langer

A12 Outcome prediction of temporal lobe epilepsy surgery from P-glycoprotein activity. Pooled analysis of (R)-[11C]-verapamil PET data from two European centres

M Bauer, M Feldmann, R Karch, W Wadsak, M Zeitlinger, MJ Koepp, M-C Asselin, E Pataraia, O Langer

A13 In-vitro and in-vivo characterization of [18F]FE@SNAP and derivatives for the visualization of the melanin concentrating hormone receptor 1

M Zeilinger, C Philippe, M Dumanic, F Pichler, J Pilz, M Hacker, W Wadsak, M Mitterhauser

A14 Reducing time in quality control leads to higher specific radioactivity of short-lived radiotracers

L Nics, B Steiner, M Hacker, M Mitterhauser, W Wadsak

A15 In vitro 11C-erlotinib binding experiments in cancer cell lines with epidermal growth factor receptor mutations

A Traxl, Thomas Wanek, Kushtrim Kryeziu, Severin Mairinger, Johann Stanek, Walter Berger, Claudia Kuntner, Oliver Langer

A16 7-[11C]methyl-6-bromopurine, a PET tracer to measure brain Mrp1 function: radiosynthesis and first PET evaluation in mice

S Mairinger, T Wanek, A Traxl, M Krohn, J Stanek, T Filip, M Sauberer, C Kuntner, J Pahnke, O Langer

A17 18F labeled azidoglucose derivatives as “click” agents for pretargeted PET imaging

D Svatunek, C Denk, M Wilkovitsch, T Wanek, T Filip, C Kuntner-Hannes, J Fröhlich, H Mikula

A18 Bioorthogonal tools for PET imaging: development of radiolabeled 1,2,4,5-Tetrazines

C Denk, D Svatunek, T Wanek, S Mairinger, J Stanek, T Filip, J Fröhlich, H Mikula, C Kuntner-Hannes

A19 Preclinical evaluation of [18F]FE@SUPPY- a new PET-tracer for oncology

T Balber, J Singer, J Fazekas, C Rami-Mark, N Berroterán-Infante, E Jensen-Jarolim, W Wadsak, M Hacker, H Viernstein, M Mitterhauser

A20 Investigation of Small [18F]-Fluoroalkylazides for Rapid Radiolabeling and In Vivo Click Chemistry

C Denk, D Svatunek, B Sohr, H Mikula, J Fröhlich, T Wanek, C Kuntner-Hannes, T Filip

A21 Microfluidic 68Ga-radiolabeling of PSMA-HBED-CC using a flow-through reactor

S Pfaff, C Philippe, M Mitterhauser, M Hartenbach, M Hacker, W Wadsak

A22 Influence of 24-nor-ursodeoxycholic acid on hepatic disposition of [18F]ciprofloxacin measured with positron emission tomography

T Wanek, E Halilbasic, M Visentin, S Mairinger, B Stieger, C Kuntner, M Trauner, O Langer

A23 Automated 18F-flumazenil production using chemically resistant disposable cassettes

P Lam, M Aistleitner, R Eichinger, C Artner

A24 Similarities and differences in the synthesis and quality control of 177Lu-DOTA-TATE, 177Lu -HA-DOTA-TATE and 177Lu-DOTA-PSMA (PSMA-617)

H Eidherr, C Vraka, A Haug, M Mitterhauser, L Nics, M Hartenbach, M Hacker, W Wadsak

A25 68Ga- and 177Lu-labelling of PSMA-617

H Kvaternik, R Müller, D Hausberger, C Zink, RM Aigner

A26 Radiolabelling of liposomes with 67Ga and biodistribution studies after administration by an aerosol inhalation system

U Cossío, M Asensio, A Montes, S Akhtar, Y te Welscher, R van Nostrum, V Gómez-Vallejo, J Llop

A27 Fully automated quantification of DaTscan SPECT: Integration of age and gender differences

F VandeVyver, T Barclay, N Lippens, M Troch

A28 Lesion-to-background ratio in co-registered 18F-FET PET/MR imaging – is it a valuable tool to differentiate between low grade and high grade brain tumor?

L Hehenwarter, B Egger, J Holzmannhofer, M Rodrigues-Radischat, C Pirich

A29 [11C]-methionine PET in gliomas - a retrospective data analysis of 166 patients

N Pötsch, I Rausch, D Wilhelm, M Weber, J Furtner, G Karanikas, A Wöhrer, M Mitterhauser, M Hacker, T Traub-Weidinger

A30 18F-Fluorocholine versus 18F-Fluorodeoxyglucose for PET/CT imaging in patients with relapsed or progressive multiple myeloma: a pilot study

T Cassou-Mounat, S Balogova, V Nataf, M Calzada, V Huchet, K Kerrou, J-Y Devaux, M Mohty, L Garderet, J-N Talbot

A31 Prognostic benefit of additional SPECT/CT in sentinel lymph node mapping of breast cancer patients

S Stanzel, G Pregartner, T Schwarz, V Bjelic-Radisic, B Liegl-Atzwanger, R Aigner

A32 Evaluation of diagnostic value of TOF-18F-FDG PET/CT in patients with suspected pancreatic cancer

S Stanzel, F Quehenberger, RM Aigner

A33 New quantification method for diagnosis of primary hyperpatahyroidism lesions and differential diagnosis vs thyropid nodular disease in dynamic scintigraphy

A Koljević Marković, Milica Janković, V Miler Jerković, M Paskaš, G Pupić, R Džodić, D Popović

A34 A rare case of diffuse pancreatic involvement in patient with merkel cell carcinoma detected by 18F-FDG

MC Fornito, D Familiari

A35 TSH-stimulated 18F-FDG PET/CT in the diagnosis of recurrent/metastatic radioiodine-negative differentiated thyroid carcinomas in patients with various thyroglobuline levels

P Koranda, H Polzerová, I Metelková, L Henzlová, R Formánek, E Buriánková, M Kamínek

A36 Breast Dose from lactation following I131 treatment

WH Thomson, C Lewis

A37 A new concept for performing SeHCAT studies with the gamma camera

WH Thomson, J O’Brien, G James, A Notghi

A38 Whole body F-18-FDG-PET and tuberculosis: sensitivity compared to x-ray-CT

H Huber, I Stelzmüller, R Wunn, M Mandl, F Fellner, B Lamprecht, M Gabriel

A39 Emerging role 18F-FDG PET-CT in the diagnosis and follow-up of the infection in heartware ventricular assist system (HVAD)

MC Fornito, G Leonardi

A40 Validation of Poisson resampling software

WH Thomson, J O’Brien, G James

A41 Protection of PET nuclear medicine personnel: problems in satisfying dose limit requirements

J Hudzietzová, J Sabol, M Fülöp

Variation of Meiotic Recombination Rates and MLH1 Foci Distribution in Spermatocytes of Cattle, Sheep and Goats

Despite similar genome sizes, a great variability in recombination rates is observed in mammals. We used antibodies against SYCP3, MLH1 and centromeres to compare crossover frequency, position along chromosome arms and the effect of crossover interference in spermatocytes of 4 species from the family Bovidae (Bos taurus, 2n = 60, tribe Bovini; Ovis aries, 2n = 54, Capra hircus, 2n = 60 and Ammotragus lervia, 2n = 58, tribe Caprini). Despite significant individual variability, our results also show significant differences in both recombination rates and the total length of autosomal synaptonemal complexes (SC) between cattle (47.53 MLH1 foci/cell, 244.59 µm) and members of the tribe Caprini (61.83 MLH1 foci, 296.19 µm) which can be explained by the length of time that has passed since their evolutionary divergence. Sheep displayed the highest number of MLH1 foci per cell and recombination density, although they have a lower diploid chromosome number caused by centric fusions corresponding to cattle chromosomes 1;3, 2;8 and 5;11. However, the proportion of MLH1 foci observed on the fused chromosomes in sheep (26.14%) was significantly lower than on the orthologous acrocentrics in cattle (27.6%) and goats (28.2%), and their distribution along the SC arms differed significantly. The reduced recombination rate in metacentrics is probably caused by interference acting across the centromere.

[Risk consideration for peridural catheter removal in acute coronary syndrome. Epidural hematoma versus stent thrombosis]

Perioperative pain therapy using an epidural catheter is the standard operating procedure for numerous surgical interventions. The necessity of initiating anticoagulant therapy in a patient with an epidural catheter requires a careful weighing up between thromboembolic complications and epidural hematoma. The case presented here of a 47-year-old female patient who was operated on for mastectomy with a latissimus dorsi myocutaneous flap demonstrates a possible solution to this dilemma. The patient sustained a perioperative ST elevation myocardial infarction treated with drug-eluting stents while undergoing epidural pain therapy. By using the short-acting antiplatelet drug tirofiban over a time period of 7 days the gap for dual antiplatelet therapy was reduced with the help of specific platelet aggregation assays to a time frame of a few hours to minimize the risk of stent thrombosis. The epidural catheter was removed without complications under consideration of the current recommendations for regional anesthesia and antithrombotic agents.

Lipidspeicherung in permanenten Mäusefibroblasten (L-strain, Earle) in Abhängigkeit von der Serumkonzentration Histochemische und quantitative Untersuchungen

Es wird über Untersuchungen an einem permanenten Zellstamm (Mäusefibroblasten, L-strain, Earle) in der Gewebekultur berichtet, die sich mit der Lipidspeicherung dieser Zellen in Abhängigkeit von der Serumkonzentration befassen. Die Untersuchungen wurden morphologisch im Phasenkontrastmikroskop, histochemisch mittels der Sudanschwarz-B-Färbung sowie quantitativ vorgenommen.

Bei steigender Serumzugabe zeigt sich eine zunehmende Lipideinlagerung, die als Speicherungsprozeß gedeutet wird. Eine gewisse Absättigung der Lipidaufnahme scheint mit 20-proz. Serumzusatz erreicht zu sein, da sich darüber hinaus keine Zunahme mehr beobachten ließ.

Bei hohem Serumzusatz (ca. 40%) zum Nährmedium kommt es zu einer relativ verringerten Aufnahme von Phospholipiden bei Zunahme der Neutralfette.

On the pair correlation function in a bubble swarm

The paper presents results on the dynamics of bubbles in a mono- and in a bi-disperse bubble swarm. The radial pair correlation function provides insight into the characteristic bubble clustering length. The angular pair correlation function shows that for small distances the most probable alignment of a bubble pair is horizontal.

Large Eddy Simulation of the shear flow instability in a rod-bundle assembly

The paper presents a Large Eddy Simulation at high Reynolds number of a section of a sub-channel in a fuel rod-bundle assembly of square pattern inside a pressurized water reactor. The focus is on the instability generated by the geometry of the sub-channel.

Fast identification of wine related lactic acid bacteria by multiplex PCR

The microflora of must and wine consists of yeasts, acetic acid bacteria and lactic acid bacteria (LAB). The latter group plays an important role for wine quality. The malolactic fermentation carried out by LAB leads to deacidification and stabilisation of wines. Nevertheless, LAB are often associated with wine spoilage. They are mainly responsible for the formation of biogenic amines. Furthermore, some strains produce exopolysaccharide slimes, acetic acid, diacetyl and other off-flavours. In this context a better monitoring of the vinification process is crucial to improve wine quality. Moreover, a lot of biodiversity studies would also profit from a fast and reliable identification method. In this study, we propose a species-specific multiplex PCR system for a rapid and simultaneous detection of 13 LAB species, frequently occurring in must or wine: Lactobacillus brevis, Lb. buchneri, Lb. curvatus, Lb. hilgardii, Lb. plantarum, Leuconostoc mesenteroides, Oenococcus oeni, Pediococcus acidilactici, P. damnosus, P. inopinatus, P. parvulus, P. pentosaceus and Weissella paramesenteroides.

Fast and reproducible chemical synthesis of zearalenone-14-β,D-glucuronide

The Fusarium mycotoxin zearalenone (ZEA) is mainly converted to the conjugate zearalenone-14-β,D-glucuronide (ZEA-14-GlcA) during phase II detoxification in humans and animals. This metabolite - previously described as zearalenone-4-O-β,D-glucuronide - is excreted via urine and could therefore serve as possible biomarker for ZEA exposure to estimate its intake. Direct determination of this substance is limited by the availability of a reference substance. So far, only the production of small amounts by enzymatic synthesis has been described. In this work, a fast and reproducible protocol for the chemical synthesis of ZEA-14-GlcA was developed, using substituted β-resorcylic acid esters as mycotoxin mimics and different glucuronyl donors for optimising the glycosylation (Königs-Knorr, trifluoroacetimidate method) and the deprotection step. This cost-effective procedure should be easily reproducible in other labs using standard equipment and common reagents.

Synthesis of deoxynivalenol-3-ß-D-O-glucuronide for its use as biomarker for dietary deoxynivalenol exposure

Trichothecene mycotoxins are prevalent toxic secondary metabolic products of several fungal species and pose a serious threat to human and animal health. Deoxynivalenol (DON) is known to undergo rapid metabolisation after uptake. The formed glucuronides are urinary excreted and could therefore serve as possible biomarkers for daily uptake measurement. So far human exposure to the major toxin DON was estimated from dietary average intake or by measurement of the parent toxin after hydrolysis. These approaches are indirect and time-consuming. Due to the clear demand for a direct determination method and lack of an available reference substance we synthesised DON-3-O-ö-D-glucuronide. The Königs-Knorr procedure using acetobromo-α-D-glucuronic acid methyl ester as glucuronyl-donor was optimised to produce the target compound in mg scale allowing subsequent characterisation via nuclear magnetic resonance and LC-MS/MS.

Packing spheres tightly: influence of mechanical stability on close-packed sphere structures

Many experiments and simulations of packings of monodisperse hard spheres report a dominance of the face-centered cubic structure in the hexagonally close-packed limit, even though it has no significant energetic or entropic gain over other close-packed configurations. Combining simulations and experiments, we demonstrate that a simple mechanical instability which occurs during the packing process may play an important role in selecting the face-centered cubic structure over other close-packed alternatives. Our argument is supported by detailed quantitative analyses of key configurations in sphere packings and highlights the importance of the packing dynamics. The proposed mechanism is elementary and should therefore play a role in a wide range of sphere systems.

The lymphangiogenesis inhibitor esVEGFR-2 in human embryos: expression in sympatho-adrenal tissues and differentiation-induced up-regulation in neuroblastoma

Tumour-induced hem- and lymph-angiogenesis are frequently associated with tumour progression. Vascular endothelial growth factor-C (VEGF-C) is a potent inducer of lymphangiogenesis, while the endogenous soluble splice-variant of VEGF receptor-2, esVEGFR-2, acts as a natural inhibitor. Previously we have shown down-regulation of esVEGFR-2 mRNA in progressed stages of neuro-blastoma (NB), a tumour derived from sympatho-adrenal precursor cells. Here we studied the immunolocalization of esVEGFR-2 in human embryos, infantile adrenal gland and primary NB. We also quantified esVEGFR-2 mRNA in NB cell lines after differentiation-induction by all-trans retinoic acid (ATRA). By immunoperoxidase staining we observed expression of esVEGFR-2 in both the sympathetic trunk and the adrenal medulla. Additionally, esVEGFR-2 was found in spinal ganglia, floor plate of the neural tube, choroid plexus, notochord, arterial endothelium, skeletal muscle, epidermis and gut epithelium. Developing and circulating leukocytes showed the strongest signal. In NB, esVEGFR-2 was considerably stronger in differentiating low grade tumours with neuronal phenotype than in undifferentiated lesions. Differentiation-induction of the NB cell line SMS-Kan with 5-10 µM ATRA resulted in a significant increase of esVEGFR-2 mRNA after 6, 9 and 12 days. We show that esVEGFR-2 is widely expressed in embryonic tissues. Especially, the adrenal medulla and circulating leukocytes seem to be potent inhibitors of lymphangiogenesis. We provide additional evidence for a role of esVEGFR-2 in NB. Thereby, high levels of esVEGFR-2 correlate with a more differentiated phenotype, and may inhibit tumour progression by inhibition of lymphangiogenesis.

Dielectric properties of human placenta, umbilical cord and amniotic fluid

The dielectric properties of freshly delivered human placenta, umbilical cord and amniotic fluid have been acquired at 37 °C and in the frequency range of 200 MHz-10 GHz. The experimental data were fitted to a Cole-Cole expression. The results show that dielectric properties of the umbilical cord are significantly higher than placenta due to the presence of high water content Wharton's jelly. The results also demonstrate large differences in the dielectric properties of amniotic and cerebrospinal fluids. The data presented can be used in numerical simulations of the exposure of pregnant women to electromagnetic fields.

Oligonucleotide-based array CGH as a diagnostic tool in multiple myeloma patients

Multiple myeloma (MM) is a hematological disease caused by malignant proliferation of clonal plasma cells (PCs) known for its clinical and biological heterogeneity. Identification of chromosomal changes in genome of PCs plays a key role in MM pathogenesis and is supposed to have important prognostic significance for MM patients. There are two major genetic entities in MM. Hyperdiploid tumors (H-MM), which include about 50% of MM tumors, often have multiple trisomies involving chromosomes 3, 5, 7, 9, 11, 15, 19, and 21 and a substantially lower prevalence of IgH translocations. Nearly half of tumors are non-hyperdiploid (NH-MM), and mostly have one of five recurrent IgH translocations: 11ql13 (CCND1), 6p21 (CCND3), 16q23 (MAF), 20q12 (MAFB), and 4p16 (FGFR3 and MMSET). The development and expanded use of new technologies, such as genome-wide array-based comparative genomic hybridization (aCGH) has accelerated genomic research in MM. This technique is a powerful tool to globally analyze recurrent copy number changes in tumor genome in a single reaction and to study cancer biology and clinical behaviors. It widely overcame routinely used cytogenetic techniques (G-banding, FISH) both in minimal resolution of chromosomal changes and amount of obtained genomic data important for further analyses and clinical applications. Array CGH technique is now used to better understanding of molecular phenotypes, sensitivity to particular chemotherapeutic agents, and prognosis of these diseases. This paper brings brief literature and methodic overview of oligonucleotide-based array-CGH technique in MM diagnosis.

[Isolated lymph node metastasis in pericardial fat flap after bronchial stump coverage]

The occurrence of bronchopleural fistulas is a serious complication after pneumonectomy because of lung cancer and additional bronchial stump coverage within right-sided and left-sided pneumonectomy therefore constitutes the operative standard. This is a case report on the early diagnosis of a lymph node metastasis within the pedicled pericardial fat flap used for bronchial stump coverage. Primary resection of the left lung was carried out 8 months previously because of cancer. Early diagnosis was possible using FDG-PET/CT in the post-operative treatment. The recurrence was successfully treated by en bloc resection and adjuvant radiation.

[Prolactinoma of the sphenoid sinus. Case report and literature review]

In this case study, we report on a patient complaining of headache who, after CT and MRI, was found to have a neoplasia of the left sphenoid sinus. After a transnasal biopsy and histological examination, a prolactinoma was diagnosed. Based on this case, we discuss important aspects of tumor biology, diagnostic procedures, histology as well as differential diagnosis. Prolactinoma has to be considered as a differential diagnose in all sphenoid sinus neoplasias with close contact to the pituitary gland.

[Child is inattentive, cannot sit still, disturbs the classroom. Is it really a hyperkinetic disorder?]

The clarification of attention-deficit/hyperactivity disorder (ADHD) requires an unequivocal categorization of the diagnostic criteria and a differentiation of the condition from normal variations and other disorder patterns. The ICD-10 criteria comprise the main symptoms inattention, hyperactivity and impulsivity. In kindergarten and preschool children, hyperactivity predominates, while in schoolchildren poor attention and cognitive impulsivity tend to be to the fore. In adolescence, aggressiveness and dissocial behavior coupled with drug abuse become central. In adulthood, ADHD is associated in particular with a tendency towards a lower social status and more frequent delinquency. Establishment of the diagnosis of ADHD requires information from the person to whom the individual relates. In this connection, exploration schemas, check lists and questionnaires are often very helpful. With regard to the differential diagnosis, mental disturbances due to physical causes (e.g. hearing disorders, epilepsy, etc.) must be excluded. Consideration must also be given in particular to comorbidities--found in up to two-thirds of cases--in which disordered social behavior, affective disorders and anxiety disturbances dominate.

Dynamic patterns of USPIO enhancement can be observed in macrophages after ischemic brain damage

Cells of the mononuclear phagocytotic system (MPS) are often found near to or within ischemic tissue and can potentially aggravate cellular damage. Hence, visualization of those cells would allow demarcation of putatively affected from intact tissue. Experimental MRI studies have shown that ultrasmall particles of dextran-coated iron oxide (USPIO) are internalized into cells of the MPS. To test if this cell tagging method may be also applied to cerebral infarction, USPIOs were administered to Fisher rats 5.5 h after permanent occlusion of the middle cerebral artery (pMCAO). During the first 2 days USPIO were preferentially found in patches within the lesion and in surrounding areas. On day 4, USPIOs expanded within the core of the lesion. On day 7 they were found predominantly within the boundary area. Histological analysis showed large populations of macrophages containing iron particles in the infarcted tissue. We conclude, therefore, that it is possible to monitor MPS activity after focal cerebral ischemia using USPIOs.

Arterial first pass gadolinium-CM dynamics as a function of several intravenous saline flush and Gd volumes

This study was performed to evaluate the dynamics of an arterial first pass gadolinium (Gd) contrast medium (CM) bolus at the descending aorta (DAo), depending on various saline flush and Gd volumes. Using an ultra-fast two- dimensional GE-sequence (Siemens Vision, 1.5-T), 200 sequential cross-sectional images of the addressed vessel (1 slice/s) were obtained. Several saline flush volumes (15 mL, 30 mL, and 60 mL) were applied following the administration of 10 mL Gd (single dose) to a group of 4 normal volunteers (body weight 50-55 kg) using a mechanical MR injector (injection rate = 3.0 mL/s). Additionally, when performing a second test series, the saline volume remained constant, while the Gd volumes were varied from half doses to triple doses (5, 10, 20, and 30 mL Gd were given to every volunteer of the group). The signal intensity versus time (SI/T) curve at a measured region of interest (ROI) within the DAo was calculated. The bolus arrival time (BAT), the maximal signal-to-noise ratio (SNR(max)), the bolus time length (BL; 75% and 80% maximum intensity duration), the slope of the SI/T curve, and the areas below the SI/T curve for both the 80% and 75% maximum intensity duration level (INT(80%) and INT(75%)) were calculated. The increase of saline flush volume from 30 to 60 mL caused significant bolus lengthening of approximately 50% (mean BL = 9.5 s, 10.3 s, and 15.4 s for 15 mL, 30 mL, and 60 mL saline flush volumes, respectively, measured as SI/T duration at the 75% SNR(max) level). Using saline flush volumes equal to or higher than 30 mL increased the slope of the SI/T curve. A continuous increase of INT(75%/80%) by using higher saline flush volumes was found. Different saline and Gd volumes did not affect the SNR(max) and the BAT. Only the low dose (0.05 mmol/kg Gd) showed a 17%-21.6% significantly lower SNR(max). The BL and the INT increased mainly by enlarging of applied Gd volume from single to double dose (BL(75%) and INT(75%) were 9.6 s and 1305, 12.3 s and 2121, 38.5 s and 6181, 37.8 s and 6613 for 5, 10, 20, and 30 mL applied Gd volume, respectively). The arterial bolus length benefits from increasing Gd and saline flush volumes due to increased venous bolus length and wash out effects of Gd within the injection site of the vein. Doses larger than a single dose are not needed to increase the SNR in contrast-enhanced magnetic resonance angiography images of the thoracic aorta.

New techniques for isolation of single prokaryotic cells

Since the 1960s, several new attempts have been made to improve the management of single prokaryotic cells using micromanipulator techniques. In order to facilitate the isolation of pure cultures we have recently developed an improved micromanipulation method for routine work. With the aid of this method single prokaryotic cells can be picked out of a mixed community under direct visual control. The isolated aerobic or anaerobic cells can be grown in pure culture or can be subjected to single cell PCR. Other powerful and completely new approaches are the applications of laser micromanipulation systems, such as optical tweezers or laser microdissection techniques. Of the latter two methods only optical tweezers have been successfully applied to cloning prokaryotic cells.

Enantiomeric resolution of galanthamine and related drugs used in anti-Alzheimer therapy by means of capillary zone electrophoresis employing derivatized cyclodextrin selectors

An analytical assay is presented for the determination of the enantiomeric composition of galanthamine and related synthetic and natural compounds. (-)-Galanthamine is isolated from Galanthus nivalis and is used in this optical pure form in the therapy of Alzheimer's disease. Recent efforts for a total synthesis of unichiral (-)-galanthamine is connected with the need for a fast and reliable assay for the determination of the optical purity of the end product, as well as for optimizing and controlling the final steps in total synthesis particularly the asymmetric transformation of narwedine. In this paper the enantiomeric resolution of these compounds is reported employing a capillary electrophoretic system with beta-cyclodextrin derived chiral selectors. With the proposed system a number of galanthamine and narwedine derived analogous compounds could be separated, including 1-bromo- and N-alkyl-substituted compounds.

Rapid isolation of single microbial cells from mixed natural and laboratory populations with the aid of a micromanipulator

In order to facilitate the isolation of pure cultures from natural habitats we have developed a method for the isolation of single microbial cell clones from a mixed population, e.g. the flora of the termite gut, with the aid of a modern micromanipulator. The separated single prokaryotic or eukaryotic cells were grown after transfer in culture media or they were used for single cell PCR. The micromanipulator was also applied for the removal of nuclei from protozoa, of which the SSU rDNA was directly amplified.

Ethidium bromide: a fast fluorescent staining procedure for the detection of symbiotic partnership of flagellates and prokaryotes

The hindgut of 'lower' termites harbors a dense population of flagellates and bacteria. The flagellates possess ecto- and endosymbiotic prokaryotes. Most of them are hardly visible in the phase contrast microscope. Staining with the DNA-intercalating agent ethidium bromide visualizes the nuclei of the flagellates as well as the ecto- and endosymbiotic bacteria as red objects. Furthermore, it is possible to distinguish between endosymbiotic methanogens and other bacteria. Following UV excitation, the blue-green autofluorescence of the methanogenic bacteria eclipses the red fluorescence light of the intercalated ethidium bromide. The dye facilitates the observation of symbiotic bacteria and helps identify the number, shape, localization, and dividing status of the nuclei. Thus, it is a powerful tool for the examination of microorganisms in complex habitats, which are rich in strongly autofluorescent material, like wood.

Isolation of Desulfovibrio intestinalis sp. nov. from the hindgut' of the lower termite Mastotermes darwiniensis

A Gram-negative, anaerobic sulfate-reducing bacterium was isolated from hindgut contents of the lower termite Mastotermes darwiniensis Froggatt (strain KMS2). Strain KMS2 is motile by a single polar flagellum. The isolate possesses desulfoviridin and catalase activity. The G+C content of its DNA is in the range of 54.5-55.5 mol% (strain KMS2). It respires hydrogen and different low molecular weight organic compounds in the presence of sulfate, thiosulfate, and sulfite, and also oxygen. The isolated strain ferments pyruvate. Fastest growth with a doubling time of 12.5 h was obtained at 37 degrees C and not at 28 degrees C, the temperature at which the termites were grown. The isolate showed a 16S rDNA sequence homology of 95.9% to Desulfovibrio desulfuricans ATCC 27774 and a DNA-DNA homology of 44.6% to D. desulfuricans Essex 6 (type strain). Based on its biochemical properties and 16S rDNA sequence, the isolate was assigned to a new species named Desulfovibrio intestinalis.

Unusual explanation for the death of a car passenger

After collision of a car with the left rearside against a steel mast the 19-year-old front seat passenger was found comatose on the seat. CT imaging showed a depression fracture parietal on the left with an intracerebral haemorrhage on the opposite side. The cause of the injury was unknown to the surgeons at the time of operation. Despite neurosurgical intervention the patient died 24 h after the accident. The post-mortem showed an additional depression fracture at the base of the skull in the right temporal region arousing suspicion of an impalement injury. Only inspection of the car by the forensic pathologists revealed the gas pressure telescopic shock absorber to be the cause of the head injury.