TY  - JOUR
A1  - Hopfner, Franziska
A1  - Schormair, Barbara
A1  - Knauf, Franziska
A1  - Berthele, Achim
A1  - Tölle, Thomas R.
A1  - Baron, Ralf
A1  - Maier, Christoph
A1  - Treede, Rolf-Detlef
A1  - Binder, Andreas
A1  - Sommer, Claudia
A1  - Maihöfner, Christian
A1  - Kunz, Wolfram
A1  - Zimprich, Friedrich
A1  - Heemann, Uwe
A1  - Pfeufer, Arne
A1  - Näbauer, Michael
A1  - Kääb, Stefan
A1  - Nowak, Barbara
A1  - Gieger, Christian
A1  - Lichtner, Peter
A1  - Trenkwalder, Claudia
A1  - Oexle, Konrad
A1  - Winkelmann, Juliane
T1  - Novel SCARB2 mutation in Action Myoclonus-Renal Failure syndrome and evaluation of SCARB2 mutations in isolated AMRF features
JF  - BMC Neurology
N2  - Background: 

Action myoclonus-renal failure syndrome is a hereditary form of progressive myoclonus epilepsy associated with renal failure. It is considered to be an autosomal-recessive disease related to loss-of-function mutations in SCARB2. We studied a German AMRF family, additionally showing signs of demyelinating polyneuropathy and dilated cardiomyopathy. To test the hypothesis whether isolated appearance of individual AMRF syndrome features could be related to heterozygote SCARB2 mutations, we screened for SCARB2 mutations in unrelated patients showing isolated AMRF features. 

Methods: 

In the AMRF family all exons of SCARB2 were analyzed by Sanger sequencing. The mutation screening of unrelated patients with isolated AMRF features affected by either epilepsy (n = 103, progressive myoclonus epilepsy or generalized epilepsy), demyelinating polyneuropathy (n = 103), renal failure (n = 192) or dilated cardiomyopathy (n = 85) was performed as high resolution melting curve analysis of the SCARB2 exons. 

Results: 

A novel homozygous 1 bp deletion (c.111delC) in SCARB2 was found by sequencing three affected homozygous siblings of the affected family. A heterozygous sister showed generalized seizures and reduction of nerve conduction velocity in her legs. No mutations were found in the epilepsy, renal failure or dilated cardiomyopathy samples. In the polyneuropathy sample two individuals with demyelinating disease were found to be carriers of a SCARB2 frameshift mutation (c.666delCCTTA). 

Conclusions: 

Our findings indicate that demyelinating polyneuropathy and dilated cardiomyopathy are part of the action myoclonus-renal failure syndrome. Moreover, they raise the possibility that in rare cases heterozygous SCARB2 mutations may be associated with PNP features.
KW  - Demyelinating peripheral neuropathy
KW  - Beta-glucocerebrosidase
KW  - Epilepsy
KW  - LIMP-2
KW  - Mice
Y1  - 2011
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-141209
VL  - 11
IS  - 134
ER  - 
TY  - JOUR
A1  - Schwaab, Bernhard
A1  - Bjarnason-Wehrens, Birna
A1  - Meng, Karin
A1  - Albus, Christian
A1  - Salzwedel, Annett
A1  - Schmid, Jean-Paul
A1  - Benzer, Werner
A1  - Metz, Matthes
A1  - Jensen, Katrin
A1  - Rauch, Bernhard
A1  - Bönner, Gerd
A1  - Brzoska, Patrick
A1  - Buhr-Schinner, Heike
A1  - Charrier, Albrecht
A1  - Cordes, Carsten
A1  - Dörr, Gesine
A1  - Eichler, Sarah
A1  - Exner, Anne-Kathrin
A1  - Fromm, Bernd
A1  - Gielen, Stephan
A1  - Glatz, Johannes
A1  - Gohlke, Helmut
A1  - Grilli, Maurizio
A1  - Gysan, Detlef
A1  - Härtel, Ursula
A1  - Hahmann, Harry
A1  - Herrmann-Lingen, Christoph
A1  - Karger, Gabriele
A1  - Karoff, Marthin
A1  - Kiwus, Ulrich
A1  - Knoglinger, Ernst
A1  - Krusch, Christian-Wolfgang
A1  - Langheim, Eike
A1  - Mann, Johannes
A1  - Max, Regina
A1  - Metzendorf, Maria-Inti
A1  - Nebel, Roland
A1  - Niebauer, Josef
A1  - Predel, Hans-Georg
A1  - Preßler, Axel
A1  - Razum, Oliver
A1  - Reiss, Nils
A1  - Saure, Daniel
A1  - von Schacky, Clemens
A1  - Schütt, Morten
A1  - Schultz, Konrad
A1  - Skoda, Eva-Maria
A1  - Steube, Diethard
A1  - Streibelt, Marco
A1  - Stüttgen, Martin
A1  - Stüttgen, Michaela
A1  - Teufel, Martin
A1  - Tschanz, Hansueli
A1  - Völler, Heinz
A1  - Vogel, Heiner
A1  - Westphal, Ronja
T1  - Cardiac rehabilitation in German speaking countries of Europe — evidence-based guidelines from Germany, Austria and Switzerland LLKardReha-DACH — part 2
JF  - Journal of Clinical Medicine
N2  - Background: Scientific guidelines have been developed to update and harmonize exercise based cardiac rehabilitation (ebCR) in German speaking countries. Key recommendations for ebCR indications have recently been published in part 1 of this journal. The present part 2 updates the evidence with respect to contents and delivery of ebCR in clinical practice, focusing on exercise training (ET), psychological interventions (PI), patient education (PE). In addition, special patients' groups and new developments, such as telemedical (Tele) or home-based ebCR, are discussed as well. Methods: Generation of evidence and search of literature have been described in part 1. Results: Well documented evidence confirms the prognostic significance of ET in patients with coronary artery disease. Positive clinical effects of ET are described in patients with congestive heart failure, heart valve surgery or intervention, adults with congenital heart disease, and peripheral arterial disease. Specific recommendations for risk stratification and adequate exercise prescription for continuous-, interval-, and strength training are given in detail. PI when added to ebCR did not show significant positive effects in general. There was a positive trend towards reduction in depressive symptoms for “distress management” and “lifestyle changes”. PE is able to increase patients’ knowledge and motivation, as well as behavior changes, regarding physical activity, dietary habits, and smoking cessation. The evidence for distinct ebCR programs in special patients’ groups is less clear. Studies on Tele-CR predominantly included low-risk patients. Hence, it is questionable, whether clinical results derived from studies in conventional ebCR may be transferred to Tele-CR. Conclusions: ET is the cornerstone of ebCR. Additional PI should be included, adjusted to the needs of the individual patient. PE is able to promote patients self-management, empowerment, and motivation. Diversity-sensitive structures should be established to interact with the needs of special patient groups and gender issues. Tele-CR should be further investigated as a valuable tool to implement ebCR more widely and effectively.
KW  - cardiac rehabilitation
KW  - scientific guidelines
KW  - secondary prevention
KW  - physical activity
KW  - exercise training
KW  - psychological interventions
KW  - education
KW  - gender
KW  - frailty
KW  - migration
KW  - old patients
KW  - young patients
KW  - tele-medicine
KW  - home-based-rehabilitation
Y1  - 2021
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-242645
SN  - 2077-0383
VL  - 10
IS  - 14
ER  - 
TY  - JOUR
A1  - Schubert-Unkmeir, Alexandra
A1  - Konrad, Christian
A1  - Slanina, Heiko
A1  - Czapek, Florian
A1  - Hebling, Sabrina
A1  - Frosch, Matthias
T1  - Neisseria meningitidis Induces Brain Microvascular Endothelial Cell Detachment from the Matrix and Cleavage of Occludin: A Role for MMP-8
N2  - Disruption of the blood-brain barrier (BBB) is a hallmark event in the pathophysiology of bacterial meningitis. Several inflammatory mediators, such as tumor necrosis factor alpha (TNF-a), nitric oxide and matrix metalloproteinases (MMPs), contribute to this disruption. Here we show that infection of human brain microvascular endothelial cells (HBMEC) with Neisseria meningitidis induced an increase of permeability at prolonged time of infection. This was paralleled by an increase in MMP-8 activity in supernatants collected from infected cells. A detailed analysis revealed that MMP-8 was involved in the proteolytic cleavage of the tight junction protein occludin, resulting in its disappearance from the cell periphery and cleavage to a lower-sized 50-kDa protein in infected HBMEC. Abrogation of MMP-8 activity by specific inhibitors as well as transfection with MMP-8 siRNA abolished production of the cleavage fragment and occludin remained attached to the cell periphery. In addition, MMP-8 affected cell adherence to the underlying matrix. A similar temporal relationship was observed for MMP activity and cell detachment. Injury of the HBMEC monolayer suggested the requirement of direct cell contact because no detachment was observed when bacteria were placed above a transwell membrane or when bacterial supernatant was directly added to cells. Inhibition of MMP-8 partially prevented detachment of infected HBMEC and restored BBB permeability. Together, we established that MMP-8 activity plays a crucial role in disassembly of cell junction components and cell adhesion during meningococcal infection.
KW  - Neisseria meningitidis
Y1  - 2010
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-68589
ER  - 
TY  - THES
A1  - Konrad, Christian
T1  - Molecular analysis of insulin signaling mechanisms in Echinococcus multilocularis and their role in the host-parasite interaction in the alveolar echinococcosis
T1  - Molekulare Analyse der Insulin-Signalmechanismen in Echinococcus multilocularis und ihre Rolle in der Wirt-Parasiten-Interaktion in der Alveolären Echinokokkose
N2  - The insulin receptor ortholog EmIR of the fox-tapeworm Echinococcus multilocularis displays significant structural homology to the human insulin receptor (HIR) and has been suggested to be involved in insulin sensing mechanisms of the parasite’s metacestode larval stage. In the present work, the effects of host insulin on Echinococcus metacestode vesicles and the proposed interaction between EmIR and mammalian insulin have been studied using biochemical and cell-biological approaches. Human insulin, exogenously added to in vitro cultivated parasite larvae, (i) significantly stimulated parasite survival and growth, (ii) induced DNA de novo synthesis in Echinococcus, (iii) affected overall protein phosphorylation in the parasite, and (iv) specifically induced the phosphorylation of the parasite’s Erk-like MAP kinase orthologue EmMPK1. These results clearly indicated that Echinococcus metacestode vesicles are able to sense exogenous host insulin which induces a mitogenic response. To investigate whether EmIR mediates these effects, anti-EmIR antibodies were produced and utilized in biochemical assays and immunohistochemical analyses. EmIR was shown to be expressed in the germinal layer of the parasite both on the surface of glycogen storing cells and undifferentiated germinal cells. Upon addition of exogenous insulin to metacestode vesicles, the phosphorylation of EmIR was significantly induced, an effect which was suppressed in the presence of specific inhibitors of insulin receptor-like tyrosine kinases. Furthermore, upon expression of EmIR/HIR receptor chimera containing the extracellular ligand binding domain of EmIR in HEK 293 cells, a specific autophosphorylation of the chimera could be induced through the addition of exogenous insulin. These results indicated the capability of EmIR to sense and to transmit host insulin signals to the Echinococcus signaling machinery. The importance of insulin signaling mechanisms for parasite survival and growth were underscored by in vitro cultivation experiments in which the addition of an inhibitor of insulin receptor tyrosine kinases led to vesicle degradation and death. Based on the above outlined molecular data on the interaction between EmIR and mammalian insulin, the parasite’s insulin receptor orthologue most probably mediates the insulin effects on parasite growth and is, therefore, a potential candidate factor for host-parasite communication via evolutionary conserved pathways. In a final set of experiments, signaling mechanisms that act downstream of EmIR have been analyzed. These studies revealed significant differences between insulin signaling in Echinococcus and the related cestode parasite Taenia solium. These differences could be associated with differences in the organo-tropism of both species.
N2  - Der orthologe Insulinrezeptor EmIR des Fuchsbandwurmes Echinococcus multilocularis weist signifikante strukturelle Homologie zum humanen Insulinrezeptor (HIR) auf. Es wurde schon seit geraumer Zeit vermutet, dass EmIR an den Mechanismen beteiligt sein könnte, die es dem Metacestoden Larvenstadium des Parasiten erlauben Insulin zu detektieren. In dieser Arbeit wurden die Effekte von Wirtsinsulin auf Echinococcus Metacestoden-Vesikel und die vermutete Interaktion zwischen EmIR und Insulin von Säugern mittels biochemischer und zellbiologischer experimenteller Ansätze untersucht. Die exogene Zugabe von humanem Insulin zu in vitro kultivierten Parasitenlarven hatte folgende Effekte: (i) das Überleben und das Wachstum des Parasiten wurde signifikant stimuliert; (ii) die DNA de novo Synthese in Echinococcus wurde induziert; (iii) die generelle Proteinphosphorylierung des Parasiten wurde beeinflusst; (iv) die Phosphorylierung der orthologen Erk-like MAP Kinase, EmMPK1, des Parasiten wurde spezifisch induziert. Diese Beobachtungen zeigen deutlich, dass Echinococcus Metacestoden-Vesikel exogenes Insulin des Wirtes detektieren können und dass dieses Insulin einen mitogenischen Effekt auf den Parasiten hat. Um zu untersuchen, ob diese Effekte durch EmIR vermittelt werden, wurden anti-EmIR Antikörper hergestellt und in biochemischen experimentellen Ansätzen und immunohistochemischen Analysen eingesetzt. Es konnte gezeigt werden, dass EmIR in der Germinalschicht des Parasiten expremiert wird, sowohl an der Oberfläche von Glykogen-Speicherzellen als auch von undifferenzierten Germinalzellen. Nach der Zugabe von exogenem Insulin konnte eine signifikante Zunahme der Phosphorylierung von EmIR festgestellt werden. Diese Stimulierung konnte durch die Zugabe eines spezifischen Inhibitors für Insulinrezeptor-ähnliche Tyrosinkinasen unterdrückt werden. Desweiteren konnte mittels der Expression eines chimären EmIR/HIR-Rezeptors, der die extrazelluläre Ligandenbindungsdomäne von EmIR enthielt, in HEK293 Zellen gezeigt werden, dass die Zugabe von exogenem Insulin eine spezifische Autophosphorylierung der Chimäre induziert. Diese Ergebnisse bezeugen die Fähigkeit von EmIR Insulin-abhängige Signale des Wirtes einerseits zu detektieren und andererseits an die Echinococcus Signalwege weiter zu leiten. Die Bedeutung von Insulin-Signalmechanismen für das Überleben und das Wachstum des Parasiten konnte durch in vitro Kultivierungsexperimente aufgezeigt werden. Die Zugabe eines Inhibitors spezifisch für Insulinrezeptor Tyrosinkinasen verursachte die Degradation und den Tod der Metacestoden-Vesikel. Basierend auf den dargelegten molekularen Daten bezüglich der Interaktion zwischen EmIR und Insulin von Säugern erscheint es sehr wahrscheinlich, dass der orthologe Insulinrezeptor des Parasiten die Effekte von Insulin auf das Wachstum des Parasiten vermittelt. Aus diesem Grund ist EmIR ein potentieller Kandidat für die Kommunikation zwischen Wirt und Parasiten mittels evolutionär konservierten Signalwegen. Die Signalmechanismen unterhalb von EmIR wurden in abschließenden Experimenten untersucht. Diese offenbarten deutliche Unterschiede in der Weiterleitung von Insulin induzierten Signalen zwischen Echinococcus und dem verwandten parasitären Zestoden Taenia solium. Diese Unterschiede könnten mit dem unterschiedlichen Organtropismus beider Arten in Verbindung stehen.
KW  - Fuchsbandwurm
KW  - Insulin
KW  - Echinokokkus
KW  - Insulin
KW  - Helminth
KW  - EmERK
KW  - Echinococcus
KW  - insulin
KW  - helminth
KW  - EmERK
Y1  - 2007
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-22636
ER  - 
TY  - JOUR
A1  - Brehm, Klaus
A1  - Hemer, Sarah
A1  - Konrad, Christian
A1  - Spiliotis, Markus
A1  - Koziol, Uriel
A1  - Schaack, Dominik
A1  - Förster, Sabine
A1  - Gelmedin, Verena
A1  - Stadelmann, Britta
A1  - Dandekar, Thomas
A1  - Hemphill, Andrew
T1  - Host insulin stimulates Echinococcus multilocularis insulin signalling pathways and larval development
N2  - Background

The metacestode of the tapeworm Echinococcus multilocularis is the causative agent of alveolar echinococcosis, a lethal zoonosis. Infections are initiated through establishment of parasite larvae within the intermediate host’s liver, where high concentrations of insulin are present, followed by tumour-like growth of the metacestode in host organs. The molecular mechanisms determining the organ tropism of E. multilocularis or the influences of host hormones on parasite proliferation are poorly understood.

Results

Using in vitro cultivation systems for parasite larvae we show that physiological concentrations (10 nM) of human insulin significantly stimulate the formation of metacestode larvae from parasite stem cells and promote asexual growth of the metacestode. Addition of human insulin to parasite larvae led to increased glucose uptake and enhanced phosphorylation of Echinococcus insulin signalling components, including an insulin receptor-like kinase, EmIR1, for which we demonstrate predominant expression in the parasite’s glycogen storage cells. We also characterized a second insulin receptor family member, EmIR2, and demonstrated interaction of its ligand binding domain with human insulin in the yeast two-hybrid system. Addition of an insulin receptor inhibitor resulted in metacestode killing, prevented metacestode development from parasite stem cells, and impaired the activation of insulin signalling pathways through host insulin.

Conclusions

Our data indicate that host insulin acts as a stimulant for parasite development within the host liver and that E. multilocularis senses the host hormone through an evolutionarily conserved insulin signalling pathway. Hormonal host-parasite cross-communication, facilitated by the relatively close phylogenetic relationship between E. multilocularis and its mammalian hosts, thus appears to be important in the pathology of alveolar echinococcosis. This contributes to a closer understanding of organ tropism and parasite persistence in larval cestode infections. Furthermore, our data show that Echinococcus insulin signalling pathways are promising targets for the development of novel drugs.
KW  - Cestode
KW  - Tapeworm
KW  - Echinococcus
KW  - Echinococcosis
KW  - Insulin
KW  - Receptor kinase
KW  - Kinase inhibitor
KW  - Host-parasite interaction
Y1  - 2014
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-110357
ER  - 
TY  - JOUR
A1  - Meier, Doreen
A1  - Kruse, Janis
A1  - Buttlar, Jann
A1  - Friedrich, Michael
A1  - Zenk, Fides
A1  - Boesler, Benjamin
A1  - Forstner, Konrad U.
A1  - Hammann, Christian
A1  - Nellen, Wolfgang
T1  - Analysis of the Microprocessor in Dictyostelium: The Role of RbdB, a dsRNA Binding Protein
JF  - PLoS Genetics
N2  - We identified the dsRNA binding protein RbdB as an essential component in miRNA processing in Dictyostelium discoideum. RbdB is a nuclear protein that accumulates, together with Dicer B, in nucleolar foci reminiscent of plant dicing bodies. Disruption of rbdB results in loss of miRNAs and accumulation of primary miRNAs. The phenotype can be rescued by ectopic expression of RbdB thus allowing for a detailed analysis of domain function. The lack of cytoplasmic dsRBD proteins involved in miRNA processing, suggests that both processing steps take place in the nucleus thus resembling the plant pathway. However, we also find features e.g. in the domain structure of Dicer which suggest similarities to animals. Reduction of miRNAs in the rbdB- strain and their increase in the Argonaute A knock out allowed the definition of new miRNAs one of which appears to belong to a new non-canonical class.
KW  - microprocessor
KW  - Dictyostelium discoideum
KW  - dsRNA binding protein
KW  - RbdB
Y1  - 2016
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-166687
VL  - 12
IS  - 6
ER  - 
TY  - JOUR
A1  - Weber-Lassalle, Nana
A1  - Hauke, Jan
A1  - Ramser, Juliane
A1  - Richters, Lisa
A1  - Groß, Eva
A1  - Blümcke, Britta
A1  - Gehrig, Andrea
A1  - Kahlert, Anne-Karin
A1  - Müller, Clemens R.
A1  - Hackmann, Karl
A1  - Honisch, Ellen
A1  - Weber-Lassalle, Konstantin
A1  - Niederacher, Dieter
A1  - Borde, Julika
A1  - Thiele, Holger
A1  - Ernst, Corinna
A1  - Altmüller, Janine
A1  - Neidhardt, Guido
A1  - Nürnberg, Peter
A1  - Klaschik, Kristina
A1  - Schroeder, Christopher
A1  - Platzer, Konrad
A1  - Volk, Alexander E.
A1  - Wang-Gohrke, Shan
A1  - Just, Walter
A1  - Auber, Bernd
A1  - Kubisch, Christian
A1  - Schmidt, Gunnar
A1  - Horvath, Judit
A1  - Wappenschmidt, Barbara
A1  - Engel, Christoph
A1  - Arnold, Norbert
A1  - Dworniczak, Bernd
A1  - Rhiem, Kerstin
A1  - Meindl, Alfons
A1  - Schmutzler, Rita K.
A1  - Hahnen, Eric
T1  - BRIP1 loss-of-function mutations confer high risk for familial ovarian cancer, but not familial breast cancer
JF  - Breast Cancer Research
N2  - Background
Germline mutations in the BRIP1 gene have been described as conferring a moderate risk for ovarian cancer (OC), while the role of BRIP1 in breast cancer (BC) pathogenesis remains controversial.

Methods
To assess the role of deleterious BRIP1 germline mutations in BC/OC predisposition, 6341 well-characterized index patients with BC, 706 index patients with OC, and 2189 geographically matched female controls were screened for loss-of-function (LoF) mutations and potentially damaging missense variants. All index patients met the inclusion criteria of the German Consortium for Hereditary Breast and Ovarian Cancer for germline testing and tested negative for pathogenic BRCA1/2 variants.

Results
BRIP1 LoF mutations confer a high OC risk in familial index patients (odds ratio (OR) = 20.97, 95% confidence interval (CI) = 12.02–36.57, P < 0.0001) and in the subgroup of index patients with late-onset OC (OR = 29.91, 95% CI = 14.99–59.66, P < 0.0001). No significant association of BRIP1 LoF mutations with familial BC was observed (OR = 1.81 95% CI = 1.00–3.30, P = 0.0623). In the subgroup of familial BC index patients without a family history of OC there was also no apparent association (OR = 1.42, 95% CI = 0.70–2.90, P = 0.3030). In 1027 familial BC index patients with a family history of OC, the BRIP1 mutation prevalence was significantly higher than that observed in controls (OR = 3.59, 95% CI = 1.43–9.01; P = 0.0168). Based on the negative association between BRIP1 LoF mutations and familial BC in the absence of an OC family history, we conclude that the elevated mutation prevalence in the latter cohort was driven by the occurrence of OC in these families. Compared with controls, predicted damaging rare missense variants were significantly more prevalent in OC (P = 0.0014) but not in BC (P = 0.0693) patients.

Conclusions
To avoid ambiguous results, studies aimed at assessing the impact of candidate predisposition gene mutations on BC risk might differentiate between BC index patients with an OC family history and those without. In familial cases, we suggest that BRIP1 is a high-risk gene for late-onset OC but not a BC predisposition gene, though minor effects cannot be excluded.
KW  - breast cancer
KW  - ovarian cancer
KW  - BRIP1 gene
KW  - germline mutations
Y1  - 2018
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-233433
VL  - 20
ER  - 
TY  - JOUR
A1  - Čuklina, Jelena
A1  - Hahn, Julia
A1  - Imakaev, Maxim
A1  - Omasits, Ulrich
A1  - Förstner, Konrad U.
A1  - Ljubimov, Nikolay
A1  - Goebel, Melanie
A1  - Pessi, Gabriella
A1  - Fischer, Hans-Martin
A1  - Ahrens, Christian H.
A1  - Gelfand, Mikhail S.
A1  - Evguenieva-Hackenberg, Elena
T1  - Genome-wide transcription start site mapping of Bradyrhizobium japonicum grown free-living or in symbiosis - a rich resource to identify new transcripts, proteins and to study gene regulation
JF  - BMC Genomics
N2  - Background

Differential RNA-sequencing (dRNA-seq) is indispensable for determination of primary transcriptomes. However, using dRNA-seq data to map transcriptional start sites (TSSs) and promoters genome-wide is a bioinformatics challenge. We performed dRNA-seq of Bradyrhizobium japonicum USDA 110, the nitrogen-fixing symbiont of soybean, and developed algorithms to map TSSs and promoters.

Results

A specialized machine learning procedure for TSS recognition allowed us to map 15,923 TSSs: 14,360 in free-living bacteria, 4329 in symbiosis with soybean and 2766 in both conditions. Further, we provide proteomic evidence for 4090 proteins, among them 107 proteins corresponding to new genes and 178 proteins with N-termini different from the existing annotation (72 and 109 of them with TSS support, respectively). Guided by proteomics evidence, previously identified TSSs and TSSs experimentally validated here, we assign a score threshold to flag 14 % of the mapped TSSs as a class of lower confidence. However, this class of lower confidence contains valid TSSs of low-abundant transcripts. Moreover, we developed a de novo algorithm to identify promoter motifs upstream of mapped TSSs, which is publicly available, and found motifs mainly used in symbiosis (similar to RpoN-dependent promoters) or under both conditions (similar to RpoD-dependent promoters). Mapped TSSs and putative promoters, proteomic evidence and updated gene annotation were combined into an annotation file.

Conclusions

The genome-wide TSS and promoter maps along with the extended genome annotation of B. japonicum represent a valuable resource for future systems biology studies and for detailed analyses of individual non-coding transcripts and ORFs. Our data will also provide new insights into bacterial gene regulation during the agriculturally important symbiosis between rhizobia and legumes.
KW  - Bradyrhizobium
KW  - RNA-seq
KW  - Promoter prediction
KW  - Genome re-annotation
KW  - Internal transcription start site
KW  - Nodule
KW  - Transcription start site
KW  - Proteogenomics
KW  - Antisense RNA
Y1  - 2016
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-164565
VL  - 17
ER  - 
TY  - JOUR
A1  - Lo Cascio, Christian M.
A1  - Goetze, Oliver
A1  - Latshang, Tsogyal D.
A1  - Bluemel, Sena
A1  - Frauenfelder, Thomas
A1  - Bloch, Konrad E.
T1  - Gastrointestinal Dysfunction in Patients with Duchenne Muscular Dystrophy
JF  - PLoS ONE
N2  - Background
In adult patients with Duchenne muscular dystrophy (DMD) life-threatening constipation has been reported. Since gastrointestinal function in DMD has not been rigorously studied we investigated objective and subjective manifestations of gastrointestinal disturbances in DMD patients.

Methods
In 33 patients with DMD, age 12–41 years, eating behavior and gastrointestinal symptoms were evaluated by questionnaires. Gastric emptying half time (T\(_{1/2}\)) and oro-cecal transit time (OCTT) were evaluated by analyzing \(^{13}\)CO\(_{2}\) exhalation curves after ingestion of \(^{13}\)C labeled test meals. Colonic transit time (CTT) was measured by abdominal radiography following ingestion of radiopaque markers.

Results
The median (quartiles) T\(_{1/2}\) was 187 (168, 220) minutes, the OCTT was 6.3 (5.0, 7.9) hours, both substantially longer than normal data (Goetze 2005, T\(_{1/2}\): 107±10; Geypens 1999, OCTT 4.3±0.1 hours). The median CTT was 60 (48, 82) hours despite extensive use of laxative measures (Meier 1995, upper limit of normal: 60 hours). T\(_{1/2}\) and OCTT did not correlate with symptoms evaluated by the Gastroparesis Cardinal Symptom Index (GCSI) (Spearman r = -0.3, p = 0.1; and r = -0.15, p = 0.4, respectively). CTT was not correlated with symptoms of constipation assessed by ROME III criteria (r = 0.12, p = 0.5).

Conclusions
DMD patients have a markedly disturbed gastrointestinal motor function. Since objective measures of impaired gastrointestinal transport are not correlated with symptoms of gastroparesis or constipation our findings suggest that measures assuring adequate intestinal transport should be taken independent of the patient’s perception in order to prevent potentially life threatening constipation, particularly in older DMD patients.
KW  - gastrointestinal dysfunction
KW  - Duchenne muscular dystrophy
Y1  - 2016
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-166793
VL  - 11
IS  - 10
ER  - 
TY  - JOUR
A1  - Ruf, Franziska
A1  - Fraunholz, Martin
A1  - Öchsner, Konrad
A1  - Kaderschabeck, Johann
A1  - Wegener, Christian
T1  - WEclMon - A simple and robust camera-based system to monitor Drosophila eclosion under optogenetic manipulation and natural conditions
JF  - PLoS ONE
N2  - Eclosion in flies and other insects is a circadian-gated behaviour under control of a central and a peripheral clock. It is not influenced by the motivational state of an animal, and thus presents an ideal paradigm to study the relation and signalling pathways between central and peripheral clocks, and downstream peptidergic regulatory systems. Little is known, however, about eclosion rhythmicity under natural conditions, and research into this direction is hampered by the physically closed design of current eclosion monitoring systems.
We describe a novel open eclosion monitoring system (WEclMon) that allows the puparia to come into direct contact with light, temperature and humidity. We demonstrate that the system can be used both in the laboratory and outdoors, and shows a performance similar to commercial closed funnel-type monitors. Data analysis is semi-automated based on a macro toolset for the open imaging software Fiji. Due to its open design, the WEclMon is also well suited for optogenetic experiments. A small screen to identify putative neuroendocrine signals mediating time from the central clock to initiate eclosion showed that optogenetic activation of ETH-, EH and myosuppressin neurons can induce precocious eclosion. Genetic ablation of myosuppressin-expressing neurons did, however, not affect eclosion rhythmicity.
KW  - chronobiology
KW  - infrared radiation
KW  - light pulses
KW  - molting
KW  - Drosophila melanogaster
KW  - optogenetics
KW  - eclosion
Y1  - 2017
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-170755
VL  - 12
IS  - 6
ER  - 
TY  - JOUR
A1  - Müller, Laura S. M.
A1  - Cosentino, Raúl O.
A1  - Förstner, Konrad U.
A1  - Guizetti, Julien
A1  - Wedel, Carolin
A1  - Kaplan, Noam
A1  - Janzen, Christian J.
A1  - Arampatzi, Panagiota
A1  - Vogel, Jörg
A1  - Steinbiss, Sascha
A1  - Otto, Thomas D.
A1  - Saliba, Antoine-Emmanuel
A1  - Sebra, Robert P.
A1  - Siegel, T. Nicolai
T1  - Genome organization and DNA accessibility control antigenic variation in trypanosomes
JF  - Nature
N2  - Many evolutionarily distant pathogenic organisms have evolved similar survival strategies to evade the immune responses of their hosts. These include antigenic variation, through which an infecting organism prevents clearance by periodically altering the identity of proteins that are visible to the immune system of the host1. Antigenic variation requires large reservoirs of immunologically diverse antigen genes, which are often generated through homologous recombination, as well as mechanisms to ensure the expression of one or very few antigens at any given time. Both homologous recombination and gene expression are affected by three-dimensional genome architecture and local DNA accessibility2,3. Factors that link three-dimensional genome architecture, local chromatin conformation and antigenic variation have, to our knowledge, not yet been identified in any organism. One of the major obstacles to studying the role of genome architecture in antigenic variation has been the highly repetitive nature and heterozygosity of antigen-gene arrays, which has precluded complete genome assembly in many pathogens. Here we report the de novo haplotype-specific assembly and scaffolding of the long antigen-gene arrays of the model protozoan parasite Trypanosoma brucei, using long-read sequencing technology and conserved features of chromosome folding4. Genome-wide chromosome conformation capture (Hi-C) reveals a distinct partitioning of the genome, with antigen-encoding subtelomeric regions that are folded into distinct, highly compact compartments. In addition, we performed a range of analyses—Hi-C, fluorescence in situ hybridization, assays for transposase-accessible chromatin using sequencing and single-cell RNA sequencing—that showed that deletion of the histone variants H3.V and H4.V increases antigen-gene clustering, DNA accessibility across sites of antigen expression and switching of the expressed antigen isoform, via homologous recombination. Our analyses identify histone variants as a molecular link between global genome architecture, local chromatin conformation and antigenic variation.
KW  - histone variants
KW  - genome architecture
KW  - single molecule real time (SMRT)
KW  - brucei genome
KW  - distance-dependent decay
Y1  - 2018
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-224265
VL  - 563
ER  -