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Search Results: 1 - 10 of 12615 matches for " Andreas Gl?ckner "
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Gain and loss of polyadenylation signals during evolution of green algae
Sabina Wodniok, Andreas Simon, Gernot Glckner, Burkhard Becker
BMC Evolutionary Biology , 2007, DOI: 10.1186/1471-2148-7-65
Abstract: We set out to investigate polyadenylation signal differences between streptophytes and chlorophytes that may have emerged shortly after the evolutionary split between Streptophyta and Chlorophyta. We therefore analyzed expressed genes (ESTs) from three streptophyte algae, Mesostigma viride, Klebsormidium subtile and Coleochaete scutata, and from two early-branching chlorophytes, Pyramimonas parkeae and Scherffelia dubia. In addition, to extend the database, our analyses included ESTs from six other chlorophytes (Acetabularia acetabulum, Chlamydomonas reinhardtii, Helicosporidium sp. ex Simulium jonesii, Prototheca wickerhamii, Scenedesmus obliquus and Ulva linza) and one streptophyte (Closterium peracerosum). Our results indicate that polyadenylation signals in green algae vary widely. The UGUAA motif is confined to late-branching Chlorophyta. Most streptophyte algae do not have an A-rich sequence motif like that in embryophytes, animals and fungi. We observed polyadenylation signals similar to those of Arabidopsis and other land plants only in Mesostigma.Polyadenylation signals in green algae show considerable variation. A new NUE (UGUAA) was invented in derived chlorophytes and replaced not only the A-rich NUE but the complete poly(A) signal in all chlorophytes investigated except Scherffelia (only NUE replaced) and Pyramimonas (UGUAA completely missing). The UGUAA element is completely absent from streptophytes. However, the structure of the poly(A) signal was often modified in streptophyte algae. In most species investigated, an A-rich NUE is missing; instead, these species seem to rely mainly on U-rich elements.In eukaryotes, a polyadenylate tail [poly(A)] is attached to the cleaved 3' end of the nuclear-encoded precursor mRNA of most genes [1]. Polyadenylation is important for the regulation of mRNA stability and also affects translational capacity [2]. The general mechanism of polyadenylation is well understood in yeast and animals [3]. It requires two major
A comprehensive transcriptome and immune-gene repertoire of the lepidopteran model host Galleria mellonella
Heiko Vogel, Boran Altincicek, Gernot Glckner, Andreas Vilcinskas
BMC Genomics , 2011, DOI: 10.1186/1471-2164-12-308
Abstract: We performed a Galleria transcriptome characterization on the Roche 454-FLX platform combined with traditional Sanger sequencing to obtain a comprehensive transcriptome. To maximize sequence diversity, we pooled RNA extracted from different developmental stages, larval tissues including hemocytes, and from immune-challenged larvae and normalized the cDNA pool. We generated a total of 789,105 pyrosequencing and 12,032 high-quality Sanger EST sequences which clustered into 18,690 contigs with an average length of 1,132 bases. Approximately 40% of the ESTs were significantly similar (E ≤ e-03) to proteins of other insects, of which 45% have a reported function. We identified a large number of genes encoding proteins with established functions in immunity related sensing of microbial signatures and signaling, as well as effector molecules such as antimicrobial peptides and inhibitors of microbial proteinases. In addition, we found genes known as mediators of melanization or contributing to stress responses. Using the transcriptomic data, we identified hemolymph peptides and proteins induced upon immune challenge by 2D-gelelectrophoresis combined with mass spectrometric analysis.Here, we have developed extensive transcriptomic resources for Galleria. The data obtained is rich in gene transcripts related to immunity, expanding remarkably our knowledge about immune and stress-inducible genes in Galleria and providing the complete sequences of genes whose primary structure have only partially been characterized using proteomic methods. The generated data provide for the first time access to the genetic architecture of immunity in this model host, allowing us to elucidate the molecular mechanisms underlying pathogen and parasite response and detailed analyses of both its immune responses against human pathogens, and its coevolution with entomopathogens.The introduction of novel high through-put sequencing technologies provides insight into the genetic architecture of an incr
EST analysis of the scaly green flagellate Mesostigma viride (Streptophyta): Implications for the evolution of green plants (Viridiplantae)
Andreas Simon, Gernot Glckner, Marius Felder, Michael Melkonian, Burkhard Becker
BMC Plant Biology , 2006, DOI: 10.1186/1471-2229-6-2
Abstract: The number of expressed genes shared by Mesostigma with the embryophytes (90.3 % of the expressed genes showing similarity to known proteins) is higher than with Chlamydomonas (76.1 %). In general, cytosolic metabolic pathways, and proteins involved in vesicular transport, transcription, regulation, DNA-structure and replication, cell cycle control, and RNA-metabolism are more conserved between Mesostigma and the embryophytes than between Mesostigma and Chlamydomonas. However, plastidic and mitochondrial metabolic pathways, cytoskeletal proteins and proteins involved in protein folding are more conserved between Mesostigma and Chlamydomonas than between Mesostigma and the embryophytes.Our EST-analysis of Mesostigma supports the notion that this organism should be a suitable unicellular model for the last flagellate common ancestor of the streptophytes. Mesostigma shares more genes with the embryophytes than with the chlorophyte Chlamydomonas reinhardtii, although both organisms are flagellate unicells. Thus, it seems likely that several major physiological changes (e.g. in the regulation of photosynthesis and photorespiration) took place early during the evolution of streptophytes, i.e. before the transition to land.The Viridiplantae (literally meaning green plants) include all green algae and embryophyte plants. They represent a monophyletic group of organisms, which display a surprising diversity with respect to their morphology, cell architecture, life histories and reproduction, and their biochemistry. The colonization of the terrestrial habitat by streptophyte algae 450 – 470 million years ago [reviewed in [1]] was undoubtedly one of the most important steps in the evolution of life on earth [2-4], which paved the way for the evolution of the various groups of land plants (embryophytes = bryophytes, pteridophytes and spermatophytes) resulting in our current terrestrial ecosystems [5].A thorough understanding of the evolution of land plants requires knowledge ab
Transcriptional response of the model planctomycete Rhodopirellula baltica SH1T to changing environmental conditions
Patricia Wecker, Christine Klockow, Andreas Ellrott, Christian Quast, Philipp Langhammer, Jens Harder, Frank Glckner
BMC Genomics , 2009, DOI: 10.1186/1471-2164-10-410
Abstract: Stress responses to salinity and temperature shifts were monitored in time series experiments. Chemostat cultures grown in mineral medium at 28°C were compared to cultures that were shifted to either elevated (37°C) or reduced (6°C) temperatures as well as high salinity (59.5‰) and observed over 300 min. Heat shock showed the induction of several known chaperone genes. Cold shock altered the expression of genes in lipid metabolism and stress proteins. High salinity resulted in the modulation of genes coding for compatible solutes, ion transporters and morphology. In summary, over 3000 of the 7325 genes were affected by temperature and/or salinity changes.Transcriptional profiling confirmed that R. baltica is highly responsive to its environment. The distinct responses identified here have provided new insights into the complex adaptation machinery of this environmentally relevant marine bacterium. Our transcriptome study and previous proteome data suggest a set of genes of unknown functions that are most probably involved in the global stress response. This work lays the foundation for further bioinformatic and genetic studies which will lead to a comprehensive understanding of the biology of a marine Planctomycete.Marine ecosystems, covering approximately 71% of the Earth's surface, host the majority of biomass and contribute significantly to global cycles of matter and energy. Microorganisms are known to be the 'gatekeepers' of these processes, and insight into their lifestyle and fitness enhances our ability to monitor, model and predict the course and effect of global changes. Nevertheless, specific knowledge about their functions is still sparse. The 'genomic revolution' [1] has opened the door to investigations targeting their genetic potential and activity on the molecular level.A particularly interesting representative of the marine picoplankton community is Rhodopirellula baltica SH1T, a free-living bacterium which was isolated from the water column of the
Epidemiology and Changes in Patient-Related Factors from 1997 to 2009 in Clinical Yeast Isolates Related to Dermatology, Gynaecology, and Paediatrics
Viktor Czaika,Pietro Nenoff,Andreas Glckner,Wolfgang Fegeler,Karsten Becker,Arno F. Schmalreck
International Journal of Microbiology , 2013, DOI: 10.1155/2013/703905
Abstract: From 1997 to 2009, 1,862 dermatology, gynaecology, and paediatrics (DGP) associated clinical yeast isolates were analysed for species occurrence, specimen origin and type, (multi-) resistance pattern, and testing period. The top seven of the isolated DGP-associated species remained the same as compared to total medical wards, with Candida albicans (45%) as most frequent pathogen. However, the DGP wards and DGP ICUs showed species-specific profiles; that is, the species distribution is clinic-specific similar and however differs in their percentage from ward to ward. By applying the “one fungus one name” principle, respectively, the appropriate current taxonomic species denominations, it has been shown that no trend to emerging species from 1998 to 2008 could be detected. In particular the frequently isolated non-Candida albicans species isolated in the DGP departments have already been detected in or before 1997. As yeasts are part of the cutaneous microbiota and play an important role as opportunistic pathogens for superficial infections, proper identification of the isolates according to the new nomenclature deems to be essential for specific and calculated antifungal therapy for yeast-like DGP-related infectious agents. 1. Introduction Superficial fungal infections are often chronic and recurring. It has been estimated that approximately 15% of the population has fungal infections of the skin (tinea pedis or athlete’s foot) or nails (onychomycosis) or of the feet. These infections are common in older children and adults [1]. Distal subungual, proximal, subungual, and white superficial onychomycoses are usually caused by dermatophytes, but Candida spp. may be present in all types in less than 1% of these cases [2]. In the past, yeasts are thought to be simply skin contaminants [3]; however, yeasts and nondermatophyte moulds may also cause toenail onychomycosis [4–8]. A higher proportion of yeasts is generally found in onychomycosis, where dermatophytes (68%), yeasts (29%), and moulds (3%) are the most causative fungal pathogens [9]. Some Candida spp. causing onychomycosis were reported to be partly resistant to oral antifungal agents (AFAs). In patients with chronic mucocutaneous infections, the main yeast pathogen is Candida (C.) albicans, but C. tropicalis, C parapsilosis, Issatchenkia (I.) orientalis, and Meyerozyma (M.) guilliermondii may also contribute to these infections [10]. It has been suggested by Clayton and Noble [11] that the spread of yeasts in the hospital ward occurs in a similar way to the spread of Staphylococcus aureus. In
Treatment and prophylaxis of invasive candidiasis with anidulafungin, caspofungin and micafungin - review of the literature
A Glckner
European Journal of Medical Research , 2011, DOI: 10.1186/2047-783x-16-4-167
Abstract: Candida spp. are prominent fungal pathogens causing invasive infections predominantly in neutropenic and severely ill non-neutropenic patients. Most patients with invasive candidiasis have candidemia without evidence of deep tissue or organ involvement. Despite efforts to advance treatment options and modalities, the mortality associated with invasive candidiasis is still high. Published figures of crude mortality reside in the range of 30-60%, attributable mortality is estimated at 25-40% [1-6].As several investigators have shown, mortality of candidemia is directly correlated with the delay of initiation of adequate antifungal therapy [7,8]. Thus, early treatment with a reliably active and safe drug is mandatory to achieve the optimum clinical outcomes. However, this is a difficult requirement to meet as the predominant challenges encountered in the management of invasive candidiasis include a lack of well-performing methods for early detection of infection and several shortcomings of the azole and polyene antifungals, the former mainstays of invasive candidiasis therapy. These include gaps in the antifungal spectrum and a multitude of drug interactions for the azoles, and nephrotoxicity or acute toxicity associated with the polyene antifungals.Beginning in 2002, the introduction of three echinocandin antifungals has significantly expanded the historically limited armamentarium of drugs available for the treatment of invasive candidiasis. Working by a distinct cell wall-specific mechanism of action, anidulafungin, caspofungin and micafungin are characterized by excellent antifungal activity against Candida spp. and Aspergillus spp., low toxicity, few or negligible drug-drug interactions and pharmacokinetic independence of renal (and mostly hepatic) function. Therefore they rapidly became established in guidelines and clinical practice as primary treatment options for severely ill patients with invasive candidiasis. After a brief overview of the epidemiology and ch
Identification and phylogenetic analysis of Dictyostelium discoideum kinesin proteins
Martin Kollmar, Gernot Glckner
BMC Genomics , 2003, DOI: 10.1186/1471-2164-4-47
Abstract: Here, we report the identification of thirteen kinesin genes exploiting the information from the raw shotgun reads of the Dictyostelium discoideum genome project. A phylogenetic tree of 390 kinesin motor domain sequences was built, grouping the Dictyostelium kinesins into nine subfamilies. According to known cellular functions or strong homologies to kinesins of other organisms, four of the Dictyostelium kinesins are involved in organelle transport, six are implicated in cell division processes, two are predicted to perform multiple functions, and one kinesin may be the founder of a new subclass.This analysis of the Dictyostelium genome led to the identification of eight new kinesin motor proteins. According to an exhaustive phylogenetic comparison, Dictyostelium contains the same subset of kinesins that higher eukaryotes need to perform mitosis. Some of the kinesins are implicated in intracellular traffic and a small number have unpredictable functions.Eukaryotic cells express three types of motor proteins: myosins, kinesins and dyneins [1]. Each constitutes a large superfamily based on the highly conserved motor domain [2-4]. All motors have in common that they use the energy derived by the hydrolysis of ATP to produce mechanical force. While myosins move on actin filaments, kinesins and dyneins are responsible for the retrograde and anterograde transport along microtubule tracks. The first kinesin was isolated from squid giant axons as a protein responsible for fast axonal transport [5,6]. This conventional kinesin (KHC) was shown to be a tetramer including two heavy and two light chains. The heavy chain consists of an N-terminal motor domain with microtubule affinity and ATPase activity followed by an extended coiled-coil region containing the light chain binding site [7] and a C-terminal domain that binds to the cargos. Like KHC, most kinesins have their motor domains at the N-terminus. However, in some kinesins, the motor domain is located in the centre of the
Loo.py: transformation-based code generation for GPUs and CPUs
Andreas Kl?ckner
Computer Science , 2014, DOI: 10.1145/2627373.2627387
Abstract: Today's highly heterogeneous computing landscape places a burden on programmers wanting to achieve high performance on a reasonably broad cross-section of machines. To do so, computations need to be expressed in many different but mathematically equivalent ways, with, in the worst case, one variant per target machine. Loo.py, a programming system embedded in Python, meets this challenge by defining a data model for array-style computations and a library of transformations that operate on this model. Offering transformations such as loop tiling, vectorization, storage management, unrolling, instruction-level parallelism, change of data layout, and many more, it provides a convenient way to capture, parametrize, and re-unify the growth among code variants. Optional, deep integration with numpy and PyOpenCL provides a convenient computing environment where the transition from prototype to high-performance implementation can occur in a gradual, machine-assisted form.
Loo.py: From Fortran to performance via transformation and substitution rules
Andreas Kl?ckner
Computer Science , 2015, DOI: 10.1145/2774959.2774969
Abstract: A large amount of numerically-oriented code is written and is being written in legacy languages. Much of this code could, in principle, make good use of data-parallel throughput-oriented computer architectures. Loo.py, a transformation-based programming system targeted at GPUs and general data-parallel architectures, provides a mechanism for user-controlled transformation of array programs. This transformation capability is designed to not just apply to programs written specifically for Loo.py, but also those imported from other languages such as Fortran. It eases the trade-off between achieving high performance, portability, and programmability by allowing the user to apply a large and growing family of transformations to an input program. These transformations are expressed in and used from Python and may be applied from a variety of settings, including a pragma-like manner from other languages.
Long-term follow-up and treatment of congenital alveolar proteinosis
Matthias Griese, Jan Ripper, Anke Sibbersen, Pia Lohse, Peter Lohse, Frank Brasch, Andrea Schams, Asli Pamir, Bianca Schaub, Oliver J Muensterer, Carola Sch?n, Judith Glckner-Pagel, Thomas Nicolai, Karl Reiter, Andreas Hector
BMC Pediatrics , 2011, DOI: 10.1186/1471-2431-11-72
Abstract: A 2 1/2 years old girl was diagnosed as having alveolar proteinosis. Whole lung lavages were performed with a new catheter balloon technique, feasible in small sized airways. Because of some interstitial inflammation in the lung biopsy and to further improve the condition, empirical therapy with systemic steroids and azathioprin, and inhaled and subcutaneous GMCSF, were used. Based on clinical measures, total protein and lipid recovered by whole lung lavages, all these treatments were without benefit. Conversely, severe respiratory viral infections and an invasive aspergillosis with aspergilloma formation occurred. Recently the novel homozygous stop mutation p.Ser25X of the GMCSF receptor alpha chain was identified in the patient. This mutation leads to a lack of functional GMCSF receptor and a reduced response to GMCSF stimulation of CD11b expression of mononuclear cells of the patient. Subsequently a very intense treatment with monthly lavages was initiated, resulting for the first time in complete resolution of partial respiratory insufficiency and a significant improvement of the overall somato-psychosocial condition of the child.The long term management from early childhood into young adolescence of severe alveolar proteinosis due to GMCSF receptor deficiency requires a dedicated specialized team to perform technically demanding whole lung lavages and cope with complications.Pulmonary alveolar proteinosis (PAP) is characterized by a substantial and persistent increase in surfactant pool size [1,2]. There are several causes of this rare condition; mouse models with deletion of granulocyte-macrophage-colony stimulating factor (GM-CSF) or the GM-CSF receptor (GM-CSFR) beta-chain showed the first evidence for involved molecularly mechanisms [3,4]. Autoantibodies against GM-CSF, blocking GM-CSF signaling, are the cause for the most frequent form of PAP, mainly found in adults and also called autoimmune PAP [5]. In 2008 the first two families with congenital PAP and
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