TY - GEN A1 - Lisdat, Fred A1 - Beissenhirtz, Moritz K. A1 - Scheller, Frieder W. A1 - Viezzoli, Maria S. T1 - Cystein-Mutanten der Cu,Zn-Superoxiddismutase und ihre Anwendung in Proteinelektroden für die Detektion von freien Sauerstoffradikalen T2 - Wissenschaftliche Beiträge 2006 N2 - Das Enzym Superoxiddismutase (SOD) bietet wegen seiner hohen Reaktionsrate und seiner extrem hohen Substratspezifi tät große Vorteile für eine Anwendung als Superoxidbiosensor. In dieser Arbeit wurden durch molekularbiologische Methoden Mutanten der humanen Cu,Zn-SOD gewonnen, welche ein oder zwei zusätzliche Cystein-Reste enthielten, die eine einfache Immobilisierung des Proteins durch Bindung des Cystein-Schwefels auf Goldelektroden ermöglichten. Sechs solcher Mutanten wurden entworfen, exprimiert, aufgereinigt und elektrochemisch charakterisiert. Alle Mutanten konnten durch einen einfachen Inkubationsschritt auf Goldelektroden gebunden werden und zeigten ein quasi-reversibles elektrochemisches Ansprechen. Für eine Mutante wurde die Anwendung als Superoxidsensor genauer untersucht und für beide Teilreaktionen der Dismutation ein Ansprechen des Sensors auf das Radikal gefunden. Bei Verwendung einer Teilreaktion konnte die Empfindlichkeit herkömmlicher Monoschichtsensoren um etwa eine Größenordnung übertroffen werden. Y1 - 2006 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus-216 SN - 0949-8214 VL - 11 SP - 7 EP - 11 ER - TY - GEN A1 - Balkenhohl, Thomas A1 - Beutler, Falko A1 - Schäfer, Daniel A1 - Lisdat, Fred T1 - Entwicklung eines impedimetrischen Biosensors für den Nachweis von Antigliadin Autoantikörpern T2 - Wissenschaftliche Beiträge 2007 N2 - In der vorliegenden Arbeit wurde ein Biosensor für den Nachweis von Antikörpern gegen Gliadin entwickelt. Gliadine sind Bestandteile der Getreideglutene und verantwortlich für die Manifestation der Zöliakie (Gluten-Unverträglichkeit). Der Biosensor basiert auf der Immobilisierung von Gliadin auf Goldelektroden, die zuvor mit Polystyrensulfonsäure beschichtet worden waren. Die erfolgreiche Immobilisierung wurde mit Hilfe der Quarzmikrowaage dokumentiert. Die Antigen-Antikörper-Bindung konnte durch die Inkubation mit einem Peroxidase-markierten Zweitantikörper und der enzymatischen Oxidation von 3-Amino-9- Ethylcarbazol (AEC) verstärkt werden. Die Zunahme in der Elektrodenisolierung durch die Bindungs- und Ablagerungsreaktion konnte durch elektrochemische Impedanzspektroskopie (EIS) in Anwesenheit des Hexacyanoferrat- Redoxsystems gemessen werden. Die Spektren wurden mit Hilfe eines Randles-Ersatzschaltbildes ausgewertet. Hierbei konnte eine Zunahme im Ladungstransferwiderstand festgestellt werden, die pro portional zur Antigliadin-Antikörperkonzentration, im Bereich von 10-8 M bis 10-6 M, war. Mit Hilfe dieses Sensors wurden schließlich humane Seren hinsichtlich ihrer Konzentration an Gliadinantikörpern, sowohl für Immunglobuline vom Typ IgG als auch IgA, untersucht. N2 - In this study an immunosensor was developed for the analysis of anti-gliadin antibodies. These antibodies can serve as an early diagnostic marker for celiac disease. The sensor is based on polystyrenesulfonic acid modifi ed gold electrodes on which gliadin was immobilized. The anti-gliadin antibody recognition was amplifi ed by a second binding step with a peroxidase- labeled antibody and subsequent peroxidase-catalyzed oxidation of 3-amino-9-ethylcarbazole (AEC) resulting in a precipitate formation on the electrode. The change of the electrode surface properties was followed by impedance spectroscopy in the presence of ferri-/ferrocyanide. By evaluating the impedance spectra the charge transfer resistance was found to be a suitable sensor parameter. A calibration curve for the detection of anti-gliadin antibodies was established for antibody concentrations between 10-8 M and 10-6 M and the sensor was also applied for the analysis of serum samples. Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus-522 SN - 0949-8214 VL - 12 SP - 48 EP - 57 ER - TY - GEN A1 - Hellmann, Michél A1 - Offermann, Judith A1 - Wildenauer, Franz-Xaver T1 - Cyanobakterienkultivierung zur Extraktion toxischer Metabolite T2 - Wissenschaftliche Beiträge 2007 N2 - Im Rahmen des Projektes »CyToTest« soll, in Kooperation mit der Firma BioTeZ Berlin-Buch GmbH, ein System entwickelt werden, mit dem direkt am Gewässer auf einfache Art und Weise die Cyanobakterientoxinkonzentration ermittelt werden kann. Dazu ist es nötig Cyanobakterien zu kultivieren und die Toxine zu isolieren. Beides wird gebraucht, um einerseits das Messsystem entwickeln zu können und andererseits an der TFH Wildau ein Verfahren zu entwickeln, mit dem die Cyanobakterien direkt am Gewässer aufgeschlossen und die Toxine extrahiert werden können. Im Rahmen dessen wurden sechs Gattungen Cyanobakterien kultiviert und ein Verfahren etabliert, um die Biomasse kalkulieren zu können. Weiterhin wurde mit der Kalibration der HPLC mit Toxinen begonnen, um die Extrakte später prüfen zu können. N2 - Within the project (in cooperation with BioTeZ Berlin- Buch GmbH) »CyToTest« a system shall be developed which allows to detect the concentration of cyanotoxins directly at the waterbody in a simple way. Therefore it is necessary to cultivate cyanobacteria and to isolate their toxins. This is essential for developing the measuring system and a procedure for digest the cyanobacteria and for extract the toxins directly at the waterbody. Therefore six species of cyanobacteria were cultivated and a method was developed for calculating the biomass. Furthermore the calibration of the HPLC with the toxins was begun for checking the extracts. Y1 - 2007 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus-518 SN - 0949-8214 VL - 12 SP - 41 EP - 47 ER - TY - GEN A1 - Tanne, Christoph K. A1 - Göbel, Gero A1 - Lisdat, Fred T1 - Entwicklung einer Glucosedehydrogenase-basierten Anode und deren Anwendung in einer Glucose/O2-Biobrennstoffzelle T2 - Wissenschaftliche Beiträge 2011 N2 - Unter Verwendung von mehrwandigen Kohlenstoffnanoröhren wurde in dieser Studie eine neuartige Anode zum Einsatz in Biobrennstoffzellen entwickelt. Dazu wurde das rekombinante Enzym Pyrrolochinolinchinon(PQQ)- abhängige Glucosedehydrogenase kovalent an eine aus PQQ bestehenden Zwischenschicht gekoppelt, welche zuvor an die Kohlenstoffnanoröhren adsorbiert war. Die Nanoröhren wurden aufgrund ihrer Thiolmodifikation chemisorptiv auf einer Goldelektrode gebunden. In glucosehaltiger Lösung konnte der Start eines katalytischen Stroms bei einem Potential von -80 mV vs. Ag/AgCl (1 MKCl) beobachtet werden. Unter Substratsättigung wurden Stromdichten im Bereich von 170 bis 200 μA/cm2 gemessen. Dieses System basiert auf einem mediatorvermittelten Elektronentransfer. Die entwickelte (PQQ)-GDH-MWCNT-Elektrode wurde mit einer MWCNT-modifizierten Elektrode kombiniert, bei der Bilirubinoxidase (BOD) als Biokatalysator fungiert. Daraus resultierte eine membranfreie Biobrennstoffzelle mit einem leichgewichtspotential von 600 mV und Leistungsdichten im Bereich von 20-25 μW/cm2. N2 - In this study a biofuel cell anode is developed on the basis of multi-walled carbon nanotubes (MWCNTs). Recombinant pyrroloquinoline quinone (PQQ) dependent glucose dehydrogenase is covalently coupled to a PQQ-layer which is adsorbed onto thiolmodified MWCNTs. The MWCNTs are chemisorbed to a gold electrode. In the presence of glucose a catalytic current starts at a potential of -80 mV vs. Ag/AgCl, 1 M KCl. Under substrate saturation current densities of 170 to 200 μA/cm2 can be achieved. The operation is based on mediated electron transfer of the enzyme. This (PQQ)-GDH-MWCNT-electrode is combined with a MWCNT-modifi ed electrode to which bilirubin oxidase (BOD) is covalently coupled. The resulting membrane-free biofuel cell has an open cell potential of 600 mV and can achieve power densities in the range of 20-25 μW/cm2. Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus-1039 SN - 0949-8214 VL - 15 SP - 13 EP - 21 ER - TY - JOUR A1 - Endrullat, Christoph A1 - Glökler, Jörn A1 - Franke, Philipp A1 - Frohme, Marcus T1 - Standardization and quality management in next-generation sequencing JF - Applied & Translational Genomics N2 - DNA sequencing continues to evolve quickly even after > 30 years. Many new platforms suddenly appeared and former established systems have vanished in almost the same manner. Since establishment of next-generation sequencing devices, this progress gains momentum due to the continually growing demand for higher throughput, lower costs and better quality of data. In consequence of this rapid development, standardized procedures and data formats as well as comprehensive quality management considerations are still scarce. Here, we listed and summarized current standardization efforts and quality management initiatives from companies, organizations and societies in form of published studies and ongoing projects. These comprise on the one hand quality documentation issues like technical notes, accreditation checklists and guidelines for validation of sequencing workflows. On the other hand, general standard proposals and quality metrics are developed and applied to the sequencing workflow steps with the main focus on upstream processes. Finally, certain standard developments for downstream pipeline data handling, processing and storage are discussed in brief. These standardization approaches represent a first basis for continuing work in order to prospectively implement next-generation sequencing in important areas such as clinical diagnostics, where reliable results and fast processing is crucial. Additionally, these efforts will exert a decisive influence on traceability and reproducibility of sequence data. KW - next-generation sequencing KW - quality management KW - data quality KW - standardization KW - validation KW - guideline Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6637 SN - 2212-0661 VL - 10 SP - 2 EP - 9 ER - TY - JOUR A1 - Thiemann, Alexander A1 - Fu, Junjie A1 - Seifert, Felix A1 - Grant-Downton, Robert T A1 - Schrag, Tobias A A1 - Pospisil, Heike A1 - Frisch, Matthias A1 - Melchinger, Albrecht E A1 - Scholten, Stefan T1 - Genome-wide meta-analysis of maize heterosis reveals the potential role of additive gene expression at pericentromeric loci JF - BMC Plant Biology N2 - The identification of QTL involved in heterosis formation is one approach to unravel the not yet fully understood genetic basis of heterosis - the improved agronomic performance of hybrid F1 plants compared to their inbred parents. The identification of candidate genes underlying a QTL is important both for developing markers and determining the molecular genetic basis of a trait, but remains difficult owing to the large number of genes often contained within individual QTL. To address this problem in heterosis analysis, we applied a meta-analysis strategy for grain yield (GY) of Zea mays L. as example, incorporating QTL-, hybrid field-, and parental gene expression data. KW - heterosis KW - maize KW - QTL KW - grain yield KW - additive gene expression Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-5999 SN - 1471-2229 VL - 14 IS - 88 ER - TY - JOUR A1 - Tillich, Ulrich M. A1 - Wolter, Nick A1 - Schulze, Katja A1 - Kramer, Dan A1 - Brödel, Oliver A1 - Frohme, Marcus T1 - High-throughput cultivation and screening platform for unicellular phototrophs JF - BMC Microbiology N2 - In this work we describe and test high-throughput methods with the model organism Synechocystis sp. PCC6803. The required technical automation for these processes was achieved with a Tecan Freedom Evo 200 pipetting robot. The cultivation was performed in 2.2 ml deepwell microtiter plates within a cultivation chamber outfitted with programmable shaking conditions, variable illumination, variable temperature, and an adjustable CO2 atmosphere. Each microtiter-well within the chamber functions as a separate cultivation vessel with reproducible conditions. The automated measurement of various parameters such as growth, full absorption spectrum, chlorophyll concentration, MALDI-TOF-MS, as well as a novel vitality measurement protocol, have already been established and can be monitored during cultivation. Measurement of growth parameters can be used as inputs for the system to allow for periodic automatic dilutions and therefore a semi-continuous cultivation of hundreds of cultures in parallel. The system also allows the automatic generation of mid and long term backups of cultures to repeat experiments or to retrieve strains of interest. KW - cyanobacteria KW - synechocystis KW - HTS KW - high throughput KW - automated cultivation Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6007 SN - 1471-2180 VL - 14 IS - 239 ER - TY - JOUR A1 - Wang, Chong A1 - Grohme, Markus A1 - Mali, Brahim A1 - Schill, Ralph O. A1 - Frohme, Marcus T1 - Towards Decrypting Cryptobiosis—Analyzing Anhydrobiosis in the Tardigrade Milnesium tardigradum Using Transcriptome Sequencing JF - PLoS ONE N2 - Many tardigrade species are capable of anhydrobiosis; however, mechanisms underlying their extreme desiccation resistance remain elusive. This study attempts to quantify the anhydrobiotic transcriptome of the limno-terrestrial tardigrade Milnesium tardigradum. Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6029 SN - 1932-6203 VL - 9 IS - 3 ER - TY - JOUR A1 - Balzer, Susanne A1 - Malde, Ketil A1 - Grohme, Markus A1 - Jonassen, Inge T1 - Filtering duplicate reads from 454 pyrosequencing data JF - Bioinformatics N2 - Throughout the recent years, 454 pyrosequencing has emerged as an efficient alternative to traditional Sanger sequencing and is widely used in both de novo whole-genome sequencing and metagenomics. Especially the latter application is extremely sensitive to sequencing errors and artificially duplicated reads. Both are common in 454 pyrosequencing and can create a strong bias in the estimation of diversity and composition of a sample. To date, there are several tools that aim to remove both sequencing noise and duplicates. Nevertheless, duplicate removal is often based on nucleotide sequences rather than on the underlying flow values, which contain additional information. Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6080 SN - 1367-4811 VL - 29 IS - 7 SP - 830 EP - 836 ER - TY - JOUR A1 - Grohme, Markus A1 - Mali, Brahim A1 - Wełnicz, Weronika A1 - Michel, Stephanie A1 - Schill, Ralph O. A1 - Frohme, Marcus T1 - The Aquaporin Channel Repertoire of the Tardigrade Milnesium tardigradum JF - Bioinformatics and Biology Insights N2 - Limno-terrestrial tardigrades are small invertebrates that are subjected to periodic drought of their micro-environment. They have evolved to cope with these unfavorable conditions by anhydrobiosis, an ametabolic state of low cellular water. During drying and rehydration, tardigrades go through drastic changes in cellular water content. By our transcriptome sequencing effort of the limno-terrestrial tardigrade Milnesium tardigradum and by a combination of cloning and targeted sequence assembly, we identified transcripts encoding eleven putative aquaporins. Analysis of these sequences proposed 2 classical aquaporins, 8 aquaglyceroporins and a single potentially intracellular unorthodox aquaporin. Using quantitative real-time PCR we analyzed aquaporin transcript expression in the anhydrobiotic context. We have identified additional unorthodox aquaporins in various insect genomes and have identified a novel common conserved structural feature in these proteins. Analysis of the genomic organization of insect aquaporin genes revealed several conserved gene clusters. KW - unorthodox aquaporin KW - anhydrobiosis KW - tardigrade Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6092 SN - 1177-9322 VL - 2013 IS - 7 SP - 153 EP - 165 ER - TY - JOUR A1 - Schokraie, Elham A1 - Warnken, Uwe A1 - Hotz-Wagenblatt, Agnes A1 - Grohme, Markus A1 - Hengherr, Steffen A1 - Förster, Frank A1 - Schill, Ralph O. A1 - Frohme, Marcus A1 - Dandekar, Thomas A1 - Schnölzer, Martina T1 - Comparative proteome analysis of Milnesium tardigradum in early embryonic state versus adults in active and anhydrobiotic state JF - PLoS ONE N2 - Tardigrades have fascinated researchers for more than 300 years because of their extraordinary capability to undergo cryptobiosis and survive extreme environmental conditions. However, the survival mechanisms of tardigrades are still poorly understood mainly due to the absence of detailed knowledge about the proteome and genome of these organisms. Our study was intended to provide a basis for the functional characterization of expressed proteins in different states of tardigrades. High-throughput, high-accuracy proteomics in combination with a newly developed tardigrade specific protein database resulted in the identification of more than 3000 proteins in three different states: early embryonic state and adult animals in active and anhydrobiotic state. This comprehensive proteome resource includes protein families such as chaperones, antioxidants, ribosomal proteins, cytoskeletal proteins, transporters, protein channels, nutrient reservoirs, and developmental proteins. A comparative analysis of protein families in the different states was performed by calculating the exponentially modified protein abundance index which classifies proteins in major and minor components. This is the first step to analyzing the proteins involved in early embryonic development, and furthermore proteins which might play an important role in the transition into the anhydrobiotic state. Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6392 SN - 1932-6203 VL - 7 IS - 9 ER - TY - JOUR A1 - Böttcher, René A1 - Amberg, Ronny A1 - Ruzius, F. P. A1 - Guryev, V. A1 - Verhaegh, Wim F. J. A1 - Beyerlein, Peter A1 - van der Zaag, P. J. T1 - Using a priori knowledge to align sequencing reads to their exact genomic position JF - Nucleic Acids Research N2 - The use of a priori knowledge in the alignment of targeted sequencing data is investigated using computational experiments. Adapting a Needleman–Wunsch algorithm to incorporate the genomic position information from the targeted capture, we demonstrate that alignment can be done to just the target region of interest. When in addition use is made of direct string comparison, an improvement of up to a factor of 8 in alignment speed compared to the fastest conventional aligner (Bowtie) is obtained. This results in a total alignment time in targeted sequencing of around 7 min for aligning approximately 56 million captured reads. For conventional aligners such as Bowtie, BWA or MAQ, alignment to just the target region is not feasible as experiments show that this leads to an additional 88% SNP calls, the vast majority of which are false positives (∼92%). Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6407 SN - 1362-4962 VL - 40 IS - 16 ER - TY - JOUR A1 - Hammer, Paul A1 - Banck, Michaela S. A1 - Amberg, Ronny A1 - Wang, Cheng A1 - Petznick, Gabriele A1 - Luo, Shujun A1 - Khrebtukova, Irina A1 - Schroth, Gary P. A1 - Beyerlein, Peter A1 - Beutler, Andreas S. T1 - mRNA-seq with agnostic splice site discovery for nervous system transcriptomics tested in chronic pain JF - Genome Research N2 - mRNA-seq is a paradigm-shifting technology because of its superior sensitivity and dynamic range and its potential to capture transcriptomes in an agnostic fashion, i.e., independently of existing genome annotations. Implementation of the agnostic approach, however, has not yet been fully achieved. In particular, agnostic mapping of pre-mRNA splice sites has not been demonstrated. The present study pursued dual goals: (1) to advance mRNA-seq bioinformatics toward unbiased transcriptome capture and (2) to demonstrate its potential for discovery in neuroscience by applying the approach to an in vivo model of neurological disease. We have performed mRNA-seq on the L4 dorsal root ganglion (DRG) of rats with chronic neuropathic pain induced by spinal nerve ligation (SNL) of the neighboring (L5) spinal nerve. We found that 12.4% of known genes were induced and 7% were suppressed in the dysfunctional (but anatomically intact) L4 DRG 2 wk after SNL. These alterations persisted chronically (2 mo). Using a read cluster classifier with strong test characteristics (ROC area 97%), we discovered 10,464 novel exons. A new algorithm for agnostic mapping of pre-mRNA splice junctions (SJs) achieved a precision of 97%. Integration of information from all mRNA-seq read classes including SJs led to genome reannotations specifically relevant for the species used (rat), the anatomical site studied (DRG), and the neurological disease considered (pain); for example, a 64-exon coreceptor for the nociceptive transmitter substance P was identified, and 21.9% of newly discovered exons were shown to be dysregulated. Thus, mRNA-seq with agnostic analysis methods appears to provide a highly productive approach for in vivo transcriptomics in the nervous system. Y1 - 2010 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6446 SN - 1549-5469 VL - 20 IS - 6 ER - TY - JOUR A1 - Förster, Frank A1 - Liang, Chunguang A1 - Shkumatov, Alexander A1 - Beisser, Daniela A1 - Engelmann, Julia C. A1 - Schnölzer, Martina A1 - Frohme, Marcus A1 - Müller, Tobias A1 - Schill, Ralph O. A1 - Dandekar, Thomas T1 - Tardigrade workbench: comparing stress-related proteins, sequence-similar and functional protein clusters as well as RNA elements in tardigrades JF - BMC Genomics N2 - Background Tardigrades represent an animal phylum with extraordinary resistance to environmental stress. Results To gain insights into their stress-specific adaptation potential, major clusters of related and similar proteins are identified, as well as specific functional clusters delineated comparing all tardigrades and individual species (Milnesium tardigradum, Hypsibius dujardini, Echiniscus testudo, Tulinus stephaniae, Richtersius coronifer) and functional elements in tardigrade mRNAs are analysed. We find that 39.3% of the total sequences clustered in 58 clusters of more than 20 proteins. Among these are ten tardigrade specific as well as a number of stress-specific protein clusters. Tardigrade-specific functional adaptations include strong protein, DNA- and redox protection, maintenance and protein recycling. Specific regulatory elements regulate tardigrade mRNA stability such as lox P DICE elements whereas 14 other RNA elements of higher eukaryotes are not found. Further features of tardigrade specific adaption are rapidly identified by sequence and/or pattern search on the web-tool tardigrade analyzer http://waterbear.bioapps.biozentrum.uni-wuerzburg.de. The work-bench offers nucleotide pattern analysis for promotor and regulatory element detection (tardigrade specific; nrdb) as well as rapid COG search for function assignments including species-specific repositories of all analysed data. Conclusion Different protein clusters and regulatory elements implicated in tardigrade stress adaptations are analysed including unpublished tardigrade sequences. Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6461 SN - 1471-2164 VL - 10 IS - 469 ER - TY - JOUR A1 - Meinel, Thomas A1 - Krause, Antje A1 - Luz, Hannes A1 - Vingron, Martin A1 - Staub, Eike T1 - The SYSTERS Protein Family Database in 2005 JF - Nucleic Acids Research N2 - The SYSTERS project aims to provide a meaningful partitioning of the whole protein sequence space by a fully automatic procedure. A refined two-step algorithm assigns each protein to a family and a superfamily. The sequence data underlying SYSTERS release 4 now comprise several protein sequence databases derived from completely sequenced genomes (ENSEMBL, TAIR, SGD and GeneDB), in addition to the comprehensive Swiss-Prot/TrEMBL databases. The SYSTERS web server (http://systers.molgen.mpg.de) provides access to 158 153 SYSTERS protein families. To augment the automatically derived results, information from external databases like Pfam and Gene Ontology are added to the web server. Furthermore, users can retrieve pre-processed analyses of families like multiple alignments and phylogenetic trees. New query options comprise a batch retrieval tool for functional inference about families based on automatic keyword extraction from sequence annotations. A new access point, PhyloMatrix, allows the retrieval of phylogenetic profiles of SYSTERS families across organisms with completely sequenced genomes. Y1 - 2004 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6476 SN - 1362-4962 VL - 33 SP - D226 EP - D229 ER - TY - JOUR A1 - Kipkorir, R. A1 - Muhoho, S. A1 - Muliro, P. A1 - Mugendi, Beatrice A1 - Frohme, Marcus A1 - Brödel, Oliver T1 - Effects of Coffee Processing Technologies on Aroma Profiles and Sensory Quality of Ruiru 11 and SL 28 Kenyan Coffee Varieties JF - Asian Journal of Agriculture and Food Sciences N2 - The study aimed at comparing the effects of three coffee processing methods on aroma profiles and sensory quality of Ruiru 11 and SL 28 coffee varieties. The processing methods varied on stages of processing and method of mucilage removal. The green coffee beans obtained from the three processing methods were graded and roasted, ground and analyzed for the aroma profiles and sensory quality. Headspace Solid phase Microextraction fibre (SPME) technique were used for the extraction of aroma compounds from coffee samples and characterization of the compounds with use of gas chromatography mass spectrometry (GC-MS). Sensory quality were analyzed by an expert panelist. Various volatile aroma compounds were identified in roasted coffee and classified into their chemical classes involving furans, ketones, pyrazines ketones pyridines, pyrroles and acids. The intensity of aroma compounds were compared in terms of their peak areas and variations were noted between the processing methods with the ecopulper showing higher levels of pyrazines such as 2-methylpyrazine, 2-ethyl-6-methylpyrazine, and wet pulper showing higher levels of furans such as furfuryl formate and furfuryl alcohol, acetate. The hand pulper was high in the level of acids and esters such as acetic acid and propanoic acid, ethyl ester. Similar aroma compounds were identified in headspace of Ruiru 11 and SL 28 and there were variations in the intensities of aroma groups such as pyrroles and pyridines. It was concluded that the eco-pulper and hand pulper methods gives better aroma quality than the wet pulper while SL 28 variety gives higher sensory quality than Ruiru 11. KW - coffee KW - processing KW - aroma KW - sensory quality Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6482 UR - https://ajouronline.com/index.php/AJAFS/article/view/2551 SN - 2321-1571 VL - 3 IS - 2 SP - 178 EP - 188 ER - TY - JOUR A1 - Graw, Stefan A1 - Meier, Richard A1 - Minn, Kay A1 - Bloomer, Clark A1 - Godwin, Andrew K. A1 - Fridley, Brooke A1 - Vlad, Anda A1 - Beyerlein, Peter A1 - Chien, Jeremy T1 - Robust gene expression and mutation analyses of RNA-sequencing of formalin-fixed diagnostic tumor samples JF - Scientific Reports N2 - Current genomic studies are limited by the availability of fresh tissue samples. Here, we show that Illumina RNA sequencing of formalin-fixed diagnostic tumor samples produces gene expression that is strongly correlated with matched frozen tumor samples (r > 0.89). In addition, sequence variations identified from FFPE RNA show 99.67% concordance with that from exome sequencing of matched frozen tumor samples. Because FFPE is a routine diagnostic sample preparation, the feasibility results reported here will facilitate the setup of large-scale research and clinical studies in medical genomics that are currently limited by the availability of fresh frozen samples. Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6319 SN - 2045-2322 VL - 5 ER - TY - JOUR A1 - Silbermann, Jascha A1 - Wernicke, Catrin A1 - Pospisil, Heike A1 - Frohme, Marcus T1 - RefPrimeCouch—a reference gene primer CouchApp JF - Database: The Journal of Biological Databases and Curation N2 - To support a quantitative real-time polymerase chain reaction standardization project, a new reference gene database application was required. The new database application was built with the explicit goal of simplifying not only the development process but also making the user interface more responsive and intuitive. To this end, CouchDB was used as the backend with a lightweight dynamic user interface implemented client-side as a one-page web application. Data entry and curation processes were streamlined using an OpenRefine-based workflow. The new RefPrimeCouch database application provides its data online under an Open Database License. Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6330 SN - 1758-0463 VL - 2013 ER - TY - JOUR A1 - Falckenhayn, Cassandra A1 - Boerjan, Bart A1 - Raddatz, Günter A1 - Frohme, Marcus A1 - Schoofs, Liliane A1 - Lyko, Frank T1 - Characterization of genome methylation patterns in the desert locust Schistocerca gregaria JF - The Journal of Experimental Biology N2 - DNA methylation is a widely conserved epigenetic modification. The analysis of genome-scale DNA methylation patterns in various organisms suggests that major features of animal methylomes are widely conserved. However, based on the variation of DNA methyltransferase genes in invertebrates, it has also been proposed that DNA methylation could provide a molecular mechanism for ecological adaptation. We have now analyzed the methylome of the desert locust, Schistocerca gregaria, which represents an organism with a high degree of phenotypic plasticity. Using genome-scale bisulfite sequencing, we show here that the S. gregaria methylome is characterized by CpG- and exon-specific methylation and thus shares two major features with other animal methylomes. In contrast to other invertebrates, however, overall methylation levels were substantially higher and a significant fraction of transposons was methylated. Additionally, genic sequences were densely methylated in a pronounced bimodal pattern, suggesting a role for DNA methylation in the regulation of locust gene expression. Our results thus uncover a unique pattern of genome methylation in locusts and provide an important foundation for investigating the role of DNA methylation in locust phase polyphenism. KW - DNA methylation KW - Schistocerca gregaria KW - locust KW - methylome Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6350 SN - 0022-0949 VL - 216 SP - 1423 EP - 1429 ER - TY - JOUR A1 - Schulze, Katja A1 - Tillich, Ulrich M. A1 - Dandekar, Thomas A1 - Frohme, Marcus T1 - PlanktoVision - an automated analysis system for the identification of phytoplankton JF - BMC Bioinformatics N2 - Phytoplankton communities are often used as a marker for the determination of fresh water quality. The routine analysis, however, is very time consuming and expensive as it is carried out manually by trained personnel. The goal of this work is to develop a system for an automated analysis. Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6364 SN - 1471-2105 VL - 14 IS - 115 ER -