TY - THES A1 - Olas, Justyna Jadwiga T1 - Nutrients regulate flowering time Y1 - 2015 ER - TY - THES A1 - Menke, Sebastian T1 - Investigating the impact of intrinsic and extrinsic factors on gut bacterial communities in Namibian wildlife species using a large-scale next-generation sequencing approach Y1 - 2015 ER - TY - JOUR A1 - Lamanna, Francesco A1 - Kirschbaum, Frank A1 - Waurick, Isabelle A1 - Dieterich, Christoph A1 - Tiedemann, Ralph T1 - Cross-tissue and cross-species analysis of gene expression in skeletal muscle and electric organ of African weakly-electric fish (Teleostei; Mormyridae) JF - BMC Genomics N2 - Background African weakly-electric fishes of the family Mormyridae are able to produce and perceive weak electric signals (typically less than one volt in amplitude) owing to the presence of a specialized, muscle-derived electric organ (EO) in their tail region. Such electric signals, also known as Electric Organ Discharges (EODs), are used for objects/prey localization, for the identification of conspecifics, and in social and reproductive behaviour. This feature might have promoted the adaptive radiation of this family by acting as an effective pre-zygotic isolation mechanism. Despite the physiological and evolutionary importance of this trait, the investigation of the genetic basis of its function and modification has so far remained limited. In this study, we aim at: i) identifying constitutive differences in terms of gene expression between electric organ and skeletal muscle (SM) in two mormyrid species of the genus Campylomormyrus: C. compressirostris and C. tshokwe, and ii) exploring cross-specific patterns of gene expression within the two tissues among C. compressirostris, C. tshokwe, and the outgroup species Gnathonemus petersii. Results Twelve paired-end (100 bp) strand-specific RNA-seq Illumina libraries were sequenced, producing circa 330 M quality-filtered short read pairs. The obtained reads were assembled de novo into four reference transcriptomes. In silico cross-tissue DE-analysis allowed us to identify 271 shared differentially expressed genes between EO and SM in C. compressirostris and C.tshokwe. Many of these genes correspond to myogenic factors, ion channels and pumps, and genes involved in several metabolic pathways. Cross-species analysis has revealed that the electric organ transcriptome is more variable in terms of gene expression levels across species than the skeletal muscle transcriptome. Conclusions The data obtained indicate that: i) the loss of contractile activity and the decoupling of the excitation-contraction processes are reflected by the down-regulation of the corresponding genes in the electric organ’s transcriptome; ii) the metabolic activity of the EO might be specialized towards the production and turn-over of membrane structures; iii) several ion channels are highly expressed in the EO in order to increase excitability; iv) several myogenic factors might be down-regulated by transcription repressors in the EO. Y1 - 2015 U6 - https://doi.org/10.1186/s12864-015-1858-9 SN - 1471-2164 VL - 16 IS - 668 PB - Biomed Central CY - London ER - TY - THES A1 - Weits, Daniel T1 - Regulation of the molecular response to low oxygen in plants Y1 - 2015 ER - TY - THES A1 - Thieme, Christoph J. T1 - Sequence and structure determinants of microRNA maturation and the elucidation of RNA transport in plants Y1 - 2015 ER - TY - THES A1 - Heyneke, Elmien T1 - The role of the calcineurin B-like interacting protein kinase, CIPK14 in regulating plant nutrient metabolism Y1 - 2015 ER - TY - THES A1 - Shivanand, Lathe Rahul T1 - DUF1068 protein family members are involved in cell wall formation in Arabidopsis thaliana Y1 - 2015 ER - TY - JOUR A1 - Sbragaglia, Valerio A1 - Lamanna, Francesco A1 - Mat, Audrey M. A1 - Rotllant, Guiomar A1 - Joly, Silvia A1 - Ketmaier, Valerio A1 - de la Iglesia, Horacio O. A1 - Aguzzi, Jacopo T1 - Identification, Characterization, and Diel Pattern of Expression of Canonical Clock Genes in Nephrops norvegicus (Crustacea: Decapoda) Eyestalk JF - PLoS one N2 - The Norway lobster, Nephrops norvegicus, is a burrowing decapod with a rhythmic burrow emergence (24 h) governed by the circadian system. It is an important resource for European fisheries and its behavior deeply affects its availability. The current knowledge of Nephrops circadian biology is phenomenological as it is currently the case for almost all crustaceans. In attempt to elucidate the putative molecular mechanisms underlying circadian gene regulation in Nephrops, we used a transcriptomics approach on cDNA extracted from the eyestalk, a structure playing a crucial role in controlling behavior of decapods. We studied 14 male lobsters under 12–12 light-darkness blue light cycle. We used the Hiseq 2000 Illumina platform to sequence two eyestalk libraries (under light and darkness conditions) obtaining about 90 millions 100-bp paired-end reads. Trinity was used for the de novo reconstruction of transcriptomes; the size at which half of all assembled bases reside in contigs (N50) was equal to 1796 (light) and 2055 (darkness). We found a list of candidate clock genes and focused our attention on canonical ones: timeless, period, clock and bmal1. The cloning of assembled fragments validated Trinity outputs. The putative Nephrops clock genes showed high levels of identity (blastx on NCBI) with known crustacean clock gene homologs such as Eurydice pulchra (period: 47%, timeless: 59%, bmal1: 79%) and Macrobrachium rosenbergii (clock: 100%). We also found a vertebrate-like cryptochrome 2. RT-qPCR showed that only timeless had a robust diel pattern of expression. Our data are in accordance with the current knowledge of the crustacean circadian clock, reinforcing the idea that the molecular clockwork of this group shows some differences with the established model in Drosophila melanogaster. Y1 - 2015 U6 - https://doi.org/10.1371/journal.pone.0141893 SN - 1932-6203 VL - 10 IS - 11 PB - Public Library of Science CY - Lawrence ER - TY - THES A1 - Timofeeva, Nadezda T1 - Effect of ions and amino-acid sequence on collagen structure BT - a molecular dynamics study Y1 - 2015 ER - TY - THES A1 - Swiadek, Magdalena Agnieszka T1 - Hybrid necrosis in local populations of Arabidopsis thaliana Y1 - 2015 ER - TY - THES A1 - Grune, Jana T1 - Effects of a novel non-steroidal mineralocorticoid receptor antagonist on cardiac hypertrophy Y1 - 2015 ER - TY - THES A1 - Krishnamoorthy, Praveen T1 - Regulatory roles of Ptdlns(4,5)P2 in trafficking of the cellulose synthase complex and identification of distinct plasma membrane localisation patterns of Arabidopsis PiP5-kinases Y1 - 2015 ER - TY - THES A1 - Pfestorf, Hans T1 - Land use intensity and insect root herbivores BT - from spatial pattern to plant community feedback Y1 - 2015 ER - TY - THES A1 - Zupok, Arkadiusz T1 - The psbB-operon is a major locus for plastome-genome incompatibility in Oenothera Y1 - 2015 ER - TY - THES A1 - Adamla, Frauke T1 - Polyglutamine- and aging-dependent aberrancies in transcription and translation Y1 - 2015 ER - TY - THES A1 - Alseekh, Saleh T1 - Identification and mode of inheritance of quantitative trait loci (QTL) for metabolite abundance in tomato Y1 - 2015 ER - TY - THES A1 - Müller, Jörg T1 - Response of bryophyte diversity to land-use and management in forest and grassland habitats Y1 - 2014 ER - TY - THES A1 - Soja, Aleksandra Maria T1 - Transcriptomic and metabolomic analysis of Arabidopsis thaliana during abiotic stress Y1 - 2014 ER - TY - THES A1 - Sklodowski, Kamil T1 - Regulation of plant potassium channels Y1 - 2015 ER - TY - THES A1 - Zhao, Liming T1 - Characterization genes involved in leaf development and senescence of arabidopsis Y1 - 2015 ER - TY - THES A1 - Eggers, Ute T1 - Environmental impacts on white stork (Ciconia ciconia) breeding success BT - a long-term study with a focus on effects of weather conditions at the breeding grounds Y1 - 2014 ER - TY - JOUR A1 - Pietra, Stefano A1 - Lang, Patricia A1 - Grebe, Markus T1 - SABRE is required for stabilization of root hair patterning in Arabidopsis thaliana JF - Physiologia Plantarum N2 - Patterned differentiation of distinct cell types is essential for the development of multicellular organisms. The root epidermis of Arabidopsis thaliana is composed of alternating files of root hair and non-hair cells and represents a model system for studying the control of cell-fate acquisition. Epidermal cell fate is regulated by a network of genes that translate positional information from the underlying cortical cell layer into a specific pattern of differentiated cells. While much is known about the genes of this network, new players continue to be discovered. Here we show that the SABRE (SAB) gene, known to mediate microtubule organization, anisotropic cell growth and planar polarity, has an effect on root epidermal hair cell patterning. Loss of SAB function results in ectopic root hair formation and destabilizes the expression of cell fate and differentiation markers in the root epidermis, including expression of the WEREWOLF (WER) and GLABRA2 (GL2) genes. Double mutant analysis reveal that wer and caprice (cpc) mutants, defective in core components of the epidermal patterning pathway, genetically interact with sab. This suggests that SAB may act on epidermal patterning upstream of WER and CPC. Hence, we provide evidence for a role of SAB in root epidermal patterning by affecting cell-fate stabilization. Our work opens the door for future studies addressing SAB-dependent functions of the cytoskeleton during root epidermal patterning. Y1 - 2015 UR - http://onlinelibrary.wiley.com/doi/10.1111/ppl.12257/epdf U6 - https://doi.org/DOI: 10.1111/ppl.12257 VL - 153 IS - 3 SP - 440 EP - 453 ER - TY - JOUR A1 - Kiefer, Christian S. A1 - Claes, Andrea R. A1 - Nzayisenga, Jean-Claude A1 - Pietra, Stefano A1 - Stanislas, Thomas A1 - Ikeda, Yoshihisa A1 - Grebe, Markus T1 - Arabidopsis AIP1-2 restricted by WER-mediated patterning modulates planar polarity JF - Development N2 - The coordination of cell polarity within the plane of the tissue layer (planar polarity) is crucial for the development of diverse multicellular organisms. Small Rac/Rho-family GTPases and the actin cytoskeleton contribute to planar polarity formation at sites of polarity establishment in animals and plants. Yet, upstream pathways coordinating planar polarity differ strikingly between kingdoms. In the root of Arabidopsis thaliana, a concentration gradient of the phytohormone auxin coordinates polar recruitment of Rho-of-plant (ROP) to sites of polar epidermal hair initiation. However, little is known about cytoskeletal components and interactions that contribute to this planar polarity or about their relation to the patterning machinery. Here, we show that ACTIN7 (ACT7) represents a main actin isoform required for planar polarity of root hair positioning, interacting with the negative modulator ACTIN-INTERACTING PROTEIN1-2 (AIP1-2). ACT7, AIP1-2 and their genetic interaction are required for coordinated planar polarity of ROP downstream of ethylene signalling. Strikingly, AIP1-2 displays hair cell file-enriched expression, restricted by WEREWOLF (WER)-dependent patterning and modified by ethylene and auxin action. Hence, our findings reveal AIP1-2, expressed under control of the WER-dependent patterning machinery and the ethylene signalling pathway, as a modulator of actin-mediated planar polarity. KW - AIP1 KW - Actin KW - Arabidopsis KW - Patterning KW - Planar polarity Y1 - 2015 UR - http://dev.biologists.org/content/142/1/151.long U6 - https://doi.org/doi: 10.1242/dev.111013 IS - 142 SP - 151 EP - 161 ER - TY - THES A1 - Pinchasik, Bat-El Shani T1 - Manipulaton of Microbubbles Inspired by Bubble Use in Nature KW - fff Y1 - 2015 ER - TY - THES A1 - Prill, Sebastian T1 - Real-Time in vitro toxicity monotoring in a microfluidic bioreactor for drug and chemical safety assessment Y1 - 2015 ER - TY - THES A1 - Kocyan, Alexander T1 - Evolution within the speciose plant group of asparagales BT - insights from molecular and morphological data Y1 - 2014 ER - TY - THES A1 - Pagel, Jörn T1 - Statistical process-based models for the understanding and prediction of range dynamics Y1 - 2014 ER - TY - THES A1 - Sprenger, Heike T1 - Characterization of drought tolerance in potato cultivars for identification of molecular markers Y1 - 2014 ER - TY - THES A1 - Omidbakhshfard, Mohammad Amin T1 - Functional analysis of the role of GRF9 in leaf development and establishment of Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) in Arabidopsis thaliana Y1 - 2014 ER - TY - THES A1 - Omranian, Nooshin T1 - Inferring gene regulatory networks and cellular phases from time-resolved transcriptomics data Y1 - 2014 ER - TY - THES A1 - Heise, Robert T1 - Estimation of photosynthetic carbon fluxes in intact plants Y1 - 2014 PB - Universitätsverlag Potsdam CY - Potsdam ER - TY - THES A1 - Liu, Zengyu T1 - Going off the rails? Guidance of the cellulose synthase complex by cortical microtubules in Arabidopsis Y1 - 2015 PB - Universitätsverlag Potsdam CY - Potsdam ER - TY - THES A1 - Sachse, Rita T1 - Biological membranes in cell-free systems BT - characterisation and functionalisation of spodoptera frugiperda derived microsomes Y1 - 2014 ER - TY - THES A1 - Emadpour, Masoumeh T1 - Development of tools for inducible gene expression in choroplasts Y1 - 2014 ER - TY - THES A1 - Stech, Marlitt T1 - Investigations on the cell-free synthesis of single-chain antibody fragments using a cukaryotic translation system Y1 - 2014 ER - TY - THES A1 - Schulz, Elisa T1 - The role of flavonols and anthocyanins in the cold an UV-B acclimation of Arabidopsis thaliana (L.) Y1 - 2014 ER - TY - THES A1 - Jin, Chenyu T1 - Theoretical and experimental study of capillary effect on melting Y1 - 2015 ER - TY - THES A1 - Päpke, Carola T1 - Regulation of respiration during low oxygen availability Y1 - 2014 ER - TY - THES A1 - Röthlein, Christoph T1 - Investigation of polyglutamine fibril structure using a novel FRET-based approach Y1 - 2014 ER - TY - THES A1 - Peng, Lei T1 - Electrochemistry and biocatalysis of new peroxide-activating enzymes Y1 - 2015 ER -