Untersuchung von Veränderungen cerebraler Metaboliten bei depressiven Patienten im Laufe einer EKT-Serie mittels 1 H-Magnetresonanzspektroskopie

14 Patienten mit Indikation zur Elektrokrampftherapie (EKT) bei einer schweren depressiven Episode wurden vor EKT, nach 6 EKT und am Ende der EKT-Serie untersucht. Mittels Magnetresonanzspektroskopie wurde N-Acetyl-Aspartat, Cholin, Creatin, Glutamin/Glutamat (Glx) und myo-Inositol in Hippocampus und linkem Cingulum gemessen. Erfolgreiche EKT führt im Cingulum zu einem Anstieg von Cholin, erklärbar durch vermehrten Membranumsatz. Die Zunahme von Creatin im Hippocampus zeigt einen Zusammenhang zwischen Stimmung und Energieversorgung. Der gemessene Glx-Anstieg könnte mitverantwortlich für die Gedächtnisstörung nach EKT sein. Die vorliegende Arbeit zeigt, dass im Hippocampus und Cingulum metabolische Veränderungen unter EKT auftreten, die sowohl klinische Effizienz als auch Nebenwirkungen erklären können. Weitere Untersuchungen von Cholin, Creatin und Glx an großen Patientenzahlen können zum tieferen Verständnis der depressiven Störungen sowie der Wirkungsweise der EKT beitragen

Cross-Flow Filtration of Escherichia coli at a Nanofluidic Gap for Fast Immobilization and Antibiotic Susceptibility Testing

Infections with antimicrobial-resistant (AMR) bacteria are globally on the rise. In the future, multi-resistant infections will become one of the major problems in global health care. In order to enable reserve antibiotics to retain their effect as long as possible, broad-spectrum antibiotics must be used sparingly. This can be achieved by a rapid microfluidic phenotypic antibiotic susceptibility test, which provides the information needed for a targeted antibiotic therapy in less time than conventional tests. Such microfluidic tests must cope with a low bacteria concentration. On-chip filtering of the samples to accumulate bacteria can shorten the test time. By means of fluorescence microscopy, we examined a novel nanogap filtration principle to hold back Escherichia coli and to perform cultivation experiments with and without antibiotics present. Microfluidic chips based on the nanogap flow principle showed to be useful for the concentration and cultivation of E. coli. With a concentration of 106 cells/mL, a specific growth rate of 0.013 min−1 and a doubling time of 53 min were achieved. In the presence of an antibiotic, no growth was observed. The results prove that this principle can, in future, be used in fast and marker-free antimicrobial susceptibility testing (AST)

Functional renormalization group in the broken symmetry phase: momentum dependence and two-parameter scaling of the self-energy

We include spontaneous symmetry breaking into the functional renormalization group (RG) equations for the irreducible vertices of Ginzburg-Landau theories by augmenting these equations by a flow equation for the order parameter, which is determined from the requirement that at each RG step the vertex with one external leg vanishes identically. Using this strategy, we propose a simple truncation of the coupled RG flow equations for the vertices in the broken symmetry phase of the Ising universality class in D dimensions. Our truncation yields the full momentum dependence of the self-energy Sigma (k) and interpolates between lowest order perturbation theory at large momenta k and the critical scaling regime for small k. Close to the critical point, our method yields the self-energy in the scaling form Sigma (k) = k_c^2 sigma^{-} (k | xi, k / k_c), where xi is the order parameter correlation length, k_c is the Ginzburg scale, and sigma^{-} (x, y) is a dimensionless two-parameter scaling function for the broken symmetry phase which we explicitly calculate within our truncation.Comment: 9 pages, 4 figures, puplished versio

Transcriptome sequencing of the human pathogen Corynebacterium diphtheriae NCTC 13129 provides detailed insights into its transcriptional landscape and into DtxR-mediated transcriptional regulation

Wittchen M, Busche T, Gaspar AH, et al. Transcriptome sequencing of the human pathogen Corynebacterium diphtheriae NCTC 13129 provides detailed insights into its transcriptional landscape and into DtxR-mediated transcriptional regulation. BMC Genomics. 2018;19(1): 82.Background The human pathogen Corynebacterium diphtheriae is the causative agent of diphtheria. In the 1990s a large diphtheria outbreak in Eastern Europe was caused by the strain C. diphtheriae NCTC 13129. Although the genome was sequenced more than a decade ago, not much is known about its transcriptome. Our aim was to use transcriptome sequencing (RNA-Seq) to close this knowledge gap and gain insights into the transcriptional landscape of a C. diphtheriae tox+ strain. Results We applied two different RNA-Seq techniques, one to retrieve 5′-ends of primary transcripts and the other to characterize the whole transcriptional landscape in order to gain insights into various features of the C. diphtheriae NCTC 13129 transcriptome. By examining the data we identified 1656 transcription start sites (TSS), of which 1202 were assigned to genes and 454 to putative novel transcripts. By using the TSS data promoter regions recognized by the housekeeping sigma factor σA and its motifs were analyzed in detail, revealing a well conserved −10 but an only weakly conserved −35 motif, respectively. Furthermore, with the TSS data 5’-UTR lengths were explored. The observed 5’-UTRs range from zero length (leaderless transcripts), which make up 20% of all genes, up to over 450 nt long leaders, which may harbor regulatory functions. The C. diphtheriae transcriptome consists of 471 operons which are further divided into 167 sub-operon structures. In a differential expression analysis approach, we discovered that genetic disruption of the iron-sensing transcription regulator DtxR, which controls expression of diphtheria toxin (DT), causes a strong influence on general gene expression. Nearly 15% of the genome is differentially transcribed, indicating that DtxR might have other regulatory functions in addition to regulation of iron metabolism and DT. Furthermore, our findings shed light on the transcriptional landscape of the DT encoding gene tox and present evidence for two tox antisense RNAs, which point to a new way of transcriptional regulation of toxin production. Conclusions This study presents extensive insights into the transcriptome of C. diphtheriae and provides a basis for future studies regarding gene characterization, transcriptional regulatory networks, and regulation of the tox gene in particular

Nanofluidic Immobilization and Growth Detection of Escherichia coli in a Chip for Antibiotic Susceptibility Testing

Infections with antimicrobial resistant bacteria are a rising threat for global healthcare as more and more antibiotics lose their effectiveness against bacterial pathogens. To guarantee the long-term effectiveness of broad-spectrum antibiotics, they may only be prescribed when inevitably required. In order to make a reliable assessment of which antibiotics are effective, rapid point-of-care tests are needed. This can be achieved with fast phenotypic microfluidic tests, which can cope with low bacterial concentrations and work label-free. Here, we present a novel optofluidic chip with a cross-flow immobilization principle using a regular array of nanogaps to concentrate bacteria and detect their growth label-free under the influence of antibiotics. The interferometric measuring principle enabled the detection of the growth of Escherichia coli in under 4 h with a sample volume of 187.2 µL and a doubling time of 79 min. In proof-of-concept experiments, we could show that the method can distinguish between bacterial growth and its inhibition by antibiotics. The results indicate that the nanofluidic chip approach provides a very promising concept for future rapid and label-free antimicrobial susceptibility tests

Phage Genome Diversity in a Biogas-Producing Microbiome Analyzed by Illumina and Nanopore GridION Sequencing

The microbial biogas network is complex and intertwined, and therefore relatively stable in its overall functionality. However, if key functional groups of microorganisms are affected by biotic or abiotic factors, the entire efficacy may be impaired. Bacteriophages are hypothesized to alter the steering process of the microbial network. In this study, an enriched fraction of virus-like particles was extracted from a mesophilic biogas reactor and sequenced on the Illumina MiSeq and Nanopore GridION sequencing platforms. Metagenome data analysis resulted in identifying 375 metagenome-assembled viral genomes (MAVGs). Two-thirds of the classified sequences were only assigned to the superkingdom Viruses and the remaining third to the family Siphoviridae, followed by Myoviridae, Podoviridae, Tectiviridae, and Inoviridae. The metavirome showed a close relationship to the phage genomes that infect members of the classes Clostridia and Bacilli. Using publicly available biogas metagenomic data, a fragment recruitment approach showed the widespread distribution of the MAVGs studied in other biogas microbiomes. In particular, phage sequences from mesophilic microbiomes were highly similar to the phage sequences of this study. Accordingly, the virus particle enrichment approach and metavirome sequencing provided additional genome sequence information for novel virome members, thus expanding the current knowledge of viral genetic diversity in biogas reactors.BMBF, 031L0103, de.NBI - Partner - MetaProtServBMBF, 031A532B, de.NBI - Etablierungsphase - Koordinierungs- und Administrationseinheit - CAU - GeschäftsstelleBMBF, 031A533A, de.NBI - Etablierungsphase - Leistungszentrum - BiGi - Bioinformatisches Resourcenzentrum für mikrobielle Genomforschung in Biotechnologie und MedizinBMBF, 031A533B, de.NBI - Etablierungsphase - Leistungszentrum - BiGi - Bioinformatisches Resourcenzentrum für mikrobielle Genomforschung in Biotechnologie und MedizinBMBF, 031A534A, de.NBI - Etablierungsphase - Leistungszentrum - BioInfra.Prot - Bioinformatik der ProteomikBMBF, 031A535A, de.NBI - Etablierungsphase - Leistungszentrum CiBi - Zentrum für integrative BioinformatikBMBF, 031A537A, de.NBI - Etablierungsphase - Heidelberg Center for Human Bioinformatics - HD-HuB - Humane Genetik und Genomik, Humane Mikrobiomik, systematische Phänotypisierung humaner ZellenBMBF, 031A537B, de.NBI - Etablierungsphase-European Molecular Biology Laboratory-HD-HUBBMBF, 031A537C, de.NBI - Etablierungsphase - Heidelberg Center for Human Bioinformatics - HD-HuBBMBF, 031A537D, de.NBI - Etablierungsphase - Heidelberg Center for Human Bioinformatics - HD-HuB - Humane Genetik und Genomik, Humane Metagenomik, systematische Phänotypisierung humaner Zellen, Epigenetik und de.NBI Cloud Standort Heidelberg/BerlinBMBF, 031A538A, de.NBI - Etablierungsphase - Leistungszentrum: RBC - RNA Bioinformati

Genome sequencing in families with congenital limb malformations

The extensive clinical and genetic heterogeneity of congenital limb malformation calls for comprehensive genome-wide analysis of genetic variation. Genome sequencing (GS) has the potential to identify all genetic variants. Here we aim to determine the diagnostic potential of GS as a comprehensive one-test-for-all strategy in a cohort of undiagnosed patients with congenital limb malformations. We collected 69 cases (64 trios, 1 duo, 5 singletons) with congenital limb malformations with no molecular diagnosis after standard clinical genetic testing and performed genome sequencing. We also developed a framework to identify potential noncoding pathogenic variants. We identified likely pathogenic/disease-associated variants in 12 cases (17.4%) including four in known disease genes, and one repeat expansion in HOXD13. In three unrelated cases with ectrodactyly, we identified likely pathogenic variants in UBA2, establishing it as a novel disease gene. In addition, we found two complex structural variants (3%). We also identified likely causative variants in three novel high confidence candidate genes. We were not able to identify any noncoding variants. GS is a powerful strategy to identify all types of genomic variants associated with congenital limb malformation, including repeat expansions and complex structural variants missed by standard diagnostic approaches. In this cohort, no causative noncoding SNVs could be identified. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00439-021-02295-y

Identifizierung und Charakterisierung von Modulatoren der Interferon-[gamma]-Antwort

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Van der Woude and Popliteal Pterygium Syndromes: Broad intrafamilial variability in a three generation family with mutation inIRF6

Patients with Van der Woude syndrome typically present with cleft lip, cleft lip and palate, or with cleft palate only. In contrast to non-syndromic cleft lip and/or palate, Van der Woude syndrome typically is characterized by bilateral, paramedian lower-lip pits. Popliteal pterygium syndrome shares features with Van der Woude syndrome, but, in addition, is characterized by a popliteal pterygium, genital anomalies, cutaneous syndactyly of the fingers and the toes, and a characteristic pyramidal fold of skin overlying the nail of the hallux. In some patients oral synechiae or eyelid synechiae are present. Van der Woude Syndrome and Popliteal pterygium syndrome are autosomal dominantly inherited disorders caused by heterozygous mutations in IRF6. We present a three generation family with tremendous intrafamilial phenotypic variability. The newborn index patient had a diagnosis of Popliteal pterygium syndrome. The mother presented with a classic Van der Woude Syndrome, while the maternal grandfather had Van der Woude Syndrome as well as minor signs of Popliteal pterygium syndrome. In all three affecteds the known pathogenic mutation c.265A>G, p.Lys89Glu in IRF6 was identified. While inter-as well as intrafamilial variability has been described in IRF6-related disorders, the occurrence of a typical Van der Woude Syndrome without any other anomalies as well as a diagnosis of Popliteal pterygium syndrome in the same family is rare. (C) 2016 Wiley Periodicals, Inc