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 - Beisser, Daniela A1 - Grohme, Markus A1 - Kopka, Joachim A1 - Frohme, Marcus A1 - Schill, Ralph O. A1 - Hengherr, Steffen A1 - Dandekar, Thomas A1 - Klau, Gunnar W. A1 - Dittrich, Marcus A1 - Müller, Tobias T1 - Integrated pathway modules using time-course metabolic profiles and EST data from Milnesium tardigradum JF - BMC Systems Biology N2 - Tardigrades are multicellular organisms, resistant to extreme environmental changes such as heat, drought, radiation and freezing. They outlast these conditions in an inactive form (tun) to escape damage to cellular structures and cell death. Tardigrades are apparently able to prevent or repair such damage and are therefore a crucial model organism for stress tolerance. Cultures of the tardigrade Milnesium tardigradum were dehydrated by removing the surrounding water to induce tun formation. During this process and the subsequent rehydration, metabolites were measured in a time series by GC-MS. Additionally expressed sequence tags are available, especially libraries generated from the active and inactive state. The aim of this integrated analysis is to trace changes in tardigrade metabolism and identify pathways responsible for their extreme resistance against physical stress. KW - integrated network analysis KW - functional modules KW - metabolic profiles KW - metabolic pathways KW - trend test Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6146 SN - 1752-0509 VL - 6 IS - 72 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 - Janowski, Susann A1 - Gross, Ina A1 - Sauer-Gürth, Hedwig A1 - Tietze, Dieter Thomas A1 - Grohme, Markus A1 - Frohme, Marcus A1 - Becker, Peter A1 - Wink, Michael T1 - New Microsatellite Markers for the Common Tern (Sterna hirundo) Developed with 454 Shot-Gun Pyrosequencing JF - The Open Ornithology Journal N2 - Long term studies, focusing on population- and socio-biology research, require the unequivocal identification of individuals. DNA studies with Short Tandem Repeats (STR loci) became a widespread tool in population genetics. We used the next-generation sequencing (NGS) approach with 454 shot-gun pyrosequencing to identify 13 new polymorphic STR loci for the Common Tern, Sterna hirundo. To enlarge the marker set we added two more loci originally developed for Black-legged Kittiwake (Rissa tridactyla) and Red-billed Gull (Chroicocephalus scopulinus) and arranged these 15 loci into three multiplex PCR panels for high throughput genotyping. Loci characterization demonstrated that our marker set is of high quality. A PIC value of about 0.67 and a power of exclusion value of 0.99 were reached. Deviation from Hardy-Weinberg expectations of some loci and low frequencies for null alleles are interpreted as a result of inbreeding and founder effect in the investigated tern colony. We used a test data set of this well-studied breeding colony of Common Tern at Banter Lake, Wilhelmshaven, Germany, to perform a parentage test. Parent-chick relationships, known from the social pedigree of that colony, were compared with genetically calculated ones. In order to test our markers and the used parentage program COLONY, we conducted six competing data sets with varying completeness of included parental genotypes. By including fully sampled parent pairs of known family assignment, results were correct for nest mates, single parents and parent pairs. Our marker set provides a powerful tool to investigate life-time reproductive success and other issues of population and socio-biology for Common Terns, e.g. in the aforementioned colony monitored for decades. KW - common tern KW - COLONY software KW - genotyping KW - microsatellites KW - multiplex PCR KW - next-generation sequencing KW - parentage analysis KW - Sterna hirundo Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6789 SN - 1874-4532 VL - 9 SP - 50 EP - 59 ER - TY - GEN A1 - Michel, Stephanie A1 - Jork, Nadine A1 - Rockmann, Christian A1 - Grohme, Markus A1 - Franke, Philipp A1 - Menzel, Detlef A1 - Frohme, Marcus T1 - Charakterisierung des mikrobiellen Symbioms von Blutegeln T2 - Wissenschaftliche Beiträge 2013 N2 - Die medizinischen Blutegel, Hirudo medicinalis und Hirudo verbana, werden wegen ihrer kurativen Wirkung in der Humanmedizin angewandt. Während des Blutsaugens injizieren sie über ihren Speichel eine Vielzahl bioaktiver, derzeit noch unbekannter Moleküle. Eine vollständige Aufklärung aller Inhaltsstoffe mit Wirkmechanismen ist für die Entwicklung von neuen Pharmaka von großem Interesse. Vor diesem Hintergrund wurden verschiedene Organe beider Arten auf ihre Besiedlung durch symbiontische Bakterien untersucht. Dazu wurden die Bakterien zunächst unter geeigneten Bedingungen kultiviert und mittels biochemischer Methoden charakterisiert. Die Identifizierung der Symbionten erfolgte durch Polymerasekettenreaktion (PCR) und Sequenzierung der 16S rDNA. Die biochemischen Tests ergaben, dass die kultivierbaren Bakterien Amylase positiv, Gram negativ und Ornithin Decarboxylase negativ sind. Mit Hilfe von datenbankgestützten Analysen der 16S rDNA-Sequenzen konnte Aeromonas veronii biovar sobria nachgewiesen werden. Hochdurchsatzsequenzierungen der gesamtgenomischen DNA des Bakteriums aus H. medicinalis zeigten deutliche Abweichungen zum Referenzgenom von Aeromonas veronii B565. Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-3084 SN - 0949-8214 VL - 17 SP - 8 EP - 12 ER - TY - JOUR A1 - Förster, Frank A1 - Beisser, Daniela A1 - Grohme, Markus A1 - Liang, Chunguang A1 - Mali, Brahim A1 - Siegl, Alexander Matthias A1 - Engelmann, Julia C. A1 - Shkumatov, Alexander A1 - Schokraie, Elham A1 - Müller, Tobias A1 - Schnölzer, Martina A1 - Schill, Ralph O. A1 - Frohme, Marcus A1 - Dandekar, Thomas T1 - Transcriptome Analysis in Tardigrade Species Reveals Specific Molecular Pathways for Stress Adaptations JF - Bioinformatics and Biology Insights N2 - Tardigrades have unique stress-adaptations that allow them to survive extremes of cold, heat, radiation and vacuum. To study this, encoded protein clusters and pathways from an ongoing transcriptome study on the tardigrade Milnesium tardigradum were analyzed using bioinformatics tools and compared to expressed sequence tags (ESTs) from Hypsibius dujardini, revealing major pathways involved in resistance against extreme environmental conditions. ESTs are available on the Tardigrade Workbench along with software and databank updates. Our analysis reveals that RNA stability motifs for M. tardigradum are different from typical motifs known from higher animals. M. tardigradum and H. dujardini protein clusters and conserved domains imply metabolic storage pathways for glycogen, glycolipids and specific secondary metabolism as well as stress response pathways (including heat shock proteins, bmh2, and specific repair pathways). Redox-, DNA-, stress- and protein protection pathways complement specific repair capabilities to achieve the strong robustness of M. tardigradum. These pathways are partly conserved in other animals and their manipulation could boost stress adaptation even in human cells. However, the unique combination of resistance and repair pathways make tardigrades and M. tardigradum in particular so highly stress resistant. KW - RNA KW - expressed sequence tag KW - cluster KW - protein family KW - adaptation KW - tardigrade KW - transcriptome Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6153 SN - 1177-9322 VL - 2012 IS - 6 SP - 69 EP - 96 ER - TY - JOUR A1 - Janowski, Susann A1 - Grohme, Markus A1 - Frohme, Marcus A1 - Wink, Michael T1 - Development of New Microsatellite (STR) Markers for Montagu’s Harrier (Circus pygargus) via 454 Shot-Gun Pyrosequencing JF - The Open Ornithology Journal N2 - During the last decades the ground-breeding Montagu’s harrier ( Circus pygargus , Linnaeus, 1758) has changed its breeding habitats in Europe to agricultural areas in which many local populations would be close to extinction without a special nest protection regime. Although Montagu’s harrier is a well-studied species in terms of ecology and breeding biology, its genetic structure and population genetics are almost unknown. As there is a lack of good genetic markers we developed a set of 19 microsatellite markers comprising 16 new STR markers which were identified by next-generation sequencing (NGS) using 454 shot-gun pyrosequencing of genomic DNA. The STR markers were arranged into three multiplex PCR sets for high throughput genotyping and characterised. The marker set provides a powerful tool for kinship analysis. The combined non-exclusion probability for parent pairs was 1.13* 10-11. Only three loci showed PIC values < 0.50. In total, 121 known family relationships were compared with genetically calculated ones to test the markers suitability for parentage analysis. In 97.5% of all cases full-sibships were accurately determined and 97.6% of all mothers were assigned correctly to their chicks. The present multiplex PCR panels can be used to investigate several hypotheses concerning breeding behaviour, kinship, exchange rates between populations and phylogeography. KW - Circus pygargus KW - Dipetalogaster maxima KW - genotyping KW - microsatellites KW - Montagu’s harrier KW - multiplex PCR KW - next-generation sequencing KW - parentage analysis Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-5966 SN - 1874-4532 VL - 7 SP - 11 EP - 18 ER -