Light-harvesting antenna function of phycoerythrin in Prochlorococcus marinus

AbstractProchlorococcus marinus strain CCMP 1375 is the sole prokaryote to possess phycoerythrin in addition to (divinyl-)chlorophyll a/b binding antenna complexes. Here we demonstrate, employing a spectrofluorimetric assay, that phycoerythrin serves a light-harvesting antenna function (transfers energy to chlorophylls)

CoVennTree: a new method for the comparative analysis of large datasets

The visualization of massive datasets, such as those resulting from comparative metatranscriptome analyses or the analysis of microbial population structures using ribosomal RNA sequences, is a challenging task. We developed a new method called CoVennTree (Comparative weighted Venn Tree) that simultaneously compares up to three multifarious datasets by aggregating and propagating information from the bottom to the top level and produces a graphical output in Cytoscape. With the introduction of weighted Venn structures, the contents and relationships of various datasets can be correlated and simultaneously aggregated without losing information. We demonstrate the suitability of this approach using a dataset of 16S rDNA sequences obtained from microbial populations at three different depths of the Gulf of Aqaba in the Red Sea. CoVennTree has been integrated into the Galaxy ToolShed and can be directly downloaded and integrated into the user instance

Nitrogen deprivation strongly affects Photosystem II but not phycoerythrin level in the divinyl-chlorophyll b-containing cyanobacterium Prochlorococcus marinus

AbstractEffects of nitrogen limitation on Photosystem II (PSII) activities and on phycoerythrin were studied in batch cultures of the marine oxyphotobacterium Prochlorococcus marinus. Dramatic decreases in photochemical quantum yields (FV/FM), the amplitude of thermoluminescence (TL) B-band, and the rate of QA reoxidation were observed within 12 h of growth in nitrogen-limited conditions. The decline in FV/FM paralleled changes in the TL B-band amplitude, indicative of losses in PSII activities and formation of non-functional PSII centers. These changes were accompanied by a continuous reduction in D1 protein content. In contrast, nitrogen deprivation did not cause any significant reduction in phycoerythrin content. Our results refute phycoerythrin as a nitrogen storage complex in Prochlorococcus. Regulation of phycoerythrin gene expression in Prochlorococcus is different from that in typical phycobilisome-containing cyanobacteria and eukaryotic algae investigated so far

5‐Hydroxymethyl‐, 5‐Formyl‐ and 5‐Carboxydeoxycytidines as Oxidative Lesions and Epigenetic Marks

Funder: LightDyNAmicsFunder: Volkswagen Foundation; Id: http://dx.doi.org/10.13039/501100001663Abstract: The four non‐canonical nucleotides in the human genome 5‐methyl‐, 5‐hydroxymethyl‐, 5‐formyl‐ and 5‐carboxydeoxycytidine (mdC, hmdC, fdC and cadC) form a second layer of epigenetic information that contributes to the regulation of gene expression. Formation of the oxidized nucleotides hmdC, fdC and cadC requires oxidation of mdC by ten‐eleven translocation (Tet) enzymes that require oxygen, Fe(II) and α‐ketoglutarate as cosubstrates. Although these oxidized forms of mdC are widespread in mammalian genomes, experimental evidence for their presence in fungi and plants is ambiguous. This vagueness is caused by the fact that these oxidized mdC derivatives are also formed as oxidative lesions, resulting in unclear basal levels that are likely to have no epigenetic function. Here, we report the xdC levels in the fungus Amanita muscaria in comparison to murine embryonic stem cells (mESCs), HEK cells and induced pluripotent stem cells (iPSCs), to obtain information about the basal levels of hmdC, fdC and cadC as DNA lesions in the genome

Helmholtz Open Science Workshop „Zugang zu und Nachnutzung von wissenschaftlicher Software“ #hgfos16, Report; November 2016

Der Report des Helmholtz Open Science Workshops „Zugang zu und Nachnutzung von wissenschaftlicher Software“ #hgfos16 behandelt die Themen Standards und Qualitätssicherung; Reproduzierbarkeit; Lizenzierung und weitere rechtliche Aspekte; Zitation und Anerkennung; Sichtbarkeit und Modularität; Geschäftsmodelle; Personal, Ausbildung, Karrierewege. Diese Themen sind eng miteinander verzahnt. Für jeden Themenbereich werden jeweils die Relevanz, Fragestellungen, Herausforderungen, mögliche Lösungsansätze und Handlungsempfehlungen betrachtet

Magnon-magnon interactions in the Spin-Peierls compound CuGeO_3

In a magnetic substance the gap in the Raman spectrum, Delta_R, is approximatively twice the value of the neutron scattering gap, Delta_S, if the the magnetic excitations (magnons) are only weakly interacting. But for CuGeO_3 the experimentally observed ratio Delta_R/Delta_S is approximatively 1.49-1.78, indicating attractive magnon-magnon interactions in the quasi-1D Spin-Peierls compound CuGe_3. We present numerical estimates for Delta_R/Delta_S from exact diagonalization studies for finite chains and find agreement with experiment for intermediate values of the frustration parameter alpha. An analysis of the numerical Raman intensity leads us to postulate a continuum of two-magnon bound states in the Spin-Peierls phase. We discuss in detail the numerical method used, the dependence of the results on the model parameters and a novel matrix-element effect due to the dimerization of the Raman-operator in the Spin-Peierls phase.Comment: submitted to PRB, Phys. Rev. B, in pres

Frustration induced Raman scattering in CuGeO_3

We present experimental data for the Raman intensity in the spin-Peierls compound CuGeO_3 and theoretical calculations from a one-dimensional frustrated spin model. The theory is based on (a) exact diagonalization and (b) a recently developed solitonic mean field theory. We find good agreement between the 1D-theory in the homogeneous phase and evidence for a novel dimerization of the Raman operator in the spin-Peierls state. Finally we present evidence for a coupling between the interchain exchange, the spin-Peierls order parameter and the magnetic excitations along the chains.Comment: Phys. Rev. B, Rapid Comm, in Pres

Methodik

Die vegetationskundliche und strukturelle Zuordnung der Lebensraumtypen erfolgt nach der vorrangig von Braun-Blanquet entwickelten Vegetationsklassifizierung, einer hierarchischen Gliederung der Vegetationstypen (Syntaxonomie), die die Ebenen der Assoziation, des Verbandes, der Ordnung und der Klasse umfasst. Hierbei ist die Assoziation die grundlegende Einheit, in der die Pflanzengesellschaften zusammengefasst werden, die sich durch gleiche charakteristische Arten(gruppen)kombinationen auszeichnen. Der Verband vereinigt ähnliche Assoziationen. Das sind bereits umfassendere, jedoch standörtlich noch recht einheitliche Vegetationseinheiten. In Ordnungen werden ähnliche Verbände zusammengefasst. Die Klasse vereinigt ähnliche Ordnungen

Scientific Software – the role of best practices and recommendations

In Geosciences – like in most other communities – scientific work strongly depends on software. For big data analysis, existing (closed or open source) program packages are often mixed with newly developed codes. Different versions of software components and varying configurations can influence the result of data analysis. This often makes reproducibility of results and reuse of codes very difficult. Policies for publication and documentation of used and newly developed software, along with best practices, can help tackle this problem. Within the Helmholtz Association a Task Group “Access to and Re-use of scientific software” was implemented by the Open ScienceWorking Group in 2016. The aim of the Task Group is to foster the discussion about scientific software in the Open Science context and to formulate recommendations for the production and publication of scientific software, ensuring open access to it. As a first step, a workshop gathered interested scientists from institutions across Germany. The workshop brought together various existing initiatives from different scientific communities to analyse current problems, share established best practices and come up with possible solutions. The subjects in the working groups covered a broad range of themes, including technical infrastructures, standards and quality assurance, citation of software and reproducibility. Initial recommendations are presented and discussed in the talk. They are the foundation for further discussions in the Helmholtz Association and the Priority Initiative “Digital Information” of the Alliance of Science Organisations in Germany. The talk aims to inform about the activities and to link with other initiatives on the national or international level

The Challenge of Regulation in a Minimal Photoautotroph: Non-Coding RNAs in Prochlorococcus

Prochlorococcus, an extremely small cyanobacterium that is very abundant in the world's oceans, has a very streamlined genome. On average, these cells have about 2,000 genes and very few regulatory proteins. The limited capability of regulation is thought to be a result of selection imposed by a relatively stable environment in combination with a very small genome. Furthermore, only ten non-coding RNAs (ncRNAs), which play crucial regulatory roles in all forms of life, have been described in Prochlorococcus. Most strains also lack the RNA chaperone Hfq, raising the question of how important this mode of regulation is for these cells. To explore this question, we examined the transcription of intergenic regions of Prochlorococcus MED4 cells subjected to a number of different stress conditions: changes in light qualities and quantities, phage infection, or phosphorus starvation. Analysis of Affymetrix microarray expression data from intergenic regions revealed 276 novel transcriptional units. Among these were 12 new ncRNAs, 24 antisense RNAs (asRNAs), as well as 113 short mRNAs. Two additional ncRNAs were identified by homology, and all 14 new ncRNAs were independently verified by Northern hybridization and 5′RACE. Unlike its reduced suite of regulatory proteins, the number of ncRNAs relative to genome size in Prochlorococcus is comparable to that found in other bacteria, suggesting that RNA regulators likely play a major role in regulation in this group. Moreover, the ncRNAs are concentrated in previously identified genomic islands, which carry genes of significance to the ecology of this organism, many of which are not of cyanobacterial origin. Expression profiles of some of these ncRNAs suggest involvement in light stress adaptation and/or the response to phage infection consistent with their location in the hypervariable genomic islands