'Where is the child I used to be?' Childhood remembered - Günter Grass’s The Tin Drum, Christa Wolf’s A Model Childhood and W.G. Sebald’s Austerlitz

Genes with reduced expression in Q 30 -YFP colonies versus Q 0 -YFP colonies. The table summarizes the expression differences of two data sets (Q0_3d, Q30_3d). Standard deviation and p-values were obtained as described above. Hits with a p-value greater than 0.05 are indicated in grey. (DOCX 16 kb

Patients' preference between two competing treatments: Carotid stenting and carotid surgery

There are two competing treatments for atherosclerotic stenosis of the carotid artery, a major cause of stroke carotid endarterectomy (CEA) and carotid artery stenting (CAS). There have been various studies of the comparative medical merits of both methods. However, there is a lack of research on factors affecting patients' preference, and the aim of this pilot- study was to attempt to determine the factors contributing to this. 15 patients, including International Carotid Stenting Study participants, and those from the Stroke unit ward and outpatients clinic, were given a standard questionnaire, covering safety, side- effects, personal fears and willingness to pay. After reading an information sheet, the patients were asked to fill in the questionnaire without intervention from myself. A 2 to 1 majority of interviewees stated a preference for stenting over surgery. The strongest factors in patients' choice appeared to be perceived risk, concern over side effects, and anxiety in regard to type of anaesthesia. It is clear that a larger study is required, perhaps with some modification to the questionnaire and a more representative sample of interviewees

Nematode lifespan is regulated by temperature amongst other influences.

<p>This temperature dependence is the result of transcriptional networks and DAF-41/p23, which influences the transcriptional activities of HSF-1, DAF-12, and DAF-16.</p

Nematode Sgt1-Homologue D1054.3 Binds Open and Closed Conformations of Hsp90 via Distinct Binding Sites

Heat shock protein 90 (Hsp90) is a highly conserved ATP-driven machine involved in client protein maturation, folding, and activation. The chaperone is supported by a set of cochaperones that confer client specificities. One of those proteins is the suppressor of G2 allele of <i>skp1</i> (Sgt1), which participates together with Hsp90 in the immune responses of plants. Sgt1 consists of three domains: a TPR-, CS-, and SGS-domain, conserved in plants, yeast, and humans. The TPR-domain though is lacking in nematodes and insects. We observe that the <i>Caenorhabditis elegans</i> Sgt1 homologue D1054.3 binds to Hsp90 in the absence of nucleotides but much stronger in the presence of ATP and ATPγS. The latter binding mode is similar to p23, another CS-domain containing Hsp90 cofactor, even though binding is not observable for p23 in the absence of nucleotides. We use point mutations in Hsp90, which accumulate different conformations in the ATPase cycle, to differentiate between binding to open and closed Hsp90 conformations. These data support a strong contribution of the Hsp90 conformation to Sgt1 binding and highlight the ability of this cofactor to interact with all known Hsp90 conformations albeit with different affinities

Transcriptional networks affected by RNAi against <i>daf-21</i>.

<p>Networks for upregulated (A) and downregulated (B) genes after Hsp90-depletion. The networks were constructed as described in the Materials and Methods section. The color code uses four shadings of blue and red to indicate the expression differences with darkest blue being log₂(DiffExp) < -1, lightest blue being log₂(DiffExp) < -0.25, darkest red being log₂(DiffExp) > 1 and lightest red being log₂(DiffExp) > 0.25. In between 0.25 and -0.25 the nodes are white as indicated in the legend. Large clusters have been subjected to GO-term enrichment analysis and the results are depicted adjacent to the respective cluster in the network figure.</p

Hsp90-downregulation influences the heat-shock response, innate immune response and onset of oocyte development in nematodes

<div><p>Hsp90 is a molecular chaperone involved in the regulation and maturation of kinases and transcription factors. In <i>Caenorhabditis elegans</i>, it contributes to the development of fertility, maintenance of muscle structure, the regulation of heat-shock response and <i>dauer</i> state. To understand the consequences of Hsp90-depletion, we studied Hsp90 RNAi-treated nematodes by DNA microarrays and mass spectrometry. We find that upon development of phenotypes the levels of chaperones and Hsp90 cofactors are increased, while specific proteins related to the innate immune response are depleted. In microarrays, we further find many differentially expressed genes related to gonad and larval development. These genes form an expression cluster that is regulated independently from the immune response implying separate pathways of Hsp90-involvement. Using fluorescent reporter strains for the differentially expressed immune response genes <i>skr-5</i>, <i>dod-24</i> and <i>clec-60</i> we observe that their activity in intestinal tissues is influenced by Hsp90-depletion. Instead, effects on the development are evident in both gonad arms. After Hsp90-depletion, changes can be observed in early embryos and adults containing fluorescence-tagged versions of SEPA-1, CAV-1 or PUD-1, all of which are downregulated after Hsp90-depletion. Our observations identify molecular events for Hsp90-RNAi induced phenotypes during development and immune responses, which may help to separately investigate independent Hsp90-influenced processes that are relevant during the nematode’s life and development.</p></div

Immune response genes respond to <i>daf-21</i>-RNAi in intestinal tissues.

<p>DIC and fluorescence images of Hsp90-treated (right panels) and control nematodes (left panels) are shown. A) SHK207 nematodes were imaged to visualize SKR-5::GFP protein. Control nematodes showed rare expression in Int5, Int6 and Int7 cells. Hsp90-depleted nematodes generally showed induction in the full intestine. B) qRT-PCR has been performed for <i>skr-5</i> in control nematodes and in Hsp90-depleted nematodes as described in Materials and Methods. C) AU185 nematodes were imaged to visualize <i>clec-60p</i>-driven GFP expression. Control nematodes express in Int8 and Int9 cells and rarely in more anterior intestinal cells (left panel). Hsp90-depleted nematodes show induction in most parts of the intestine (right panel). D) AU10 nematodes were imaged to visualize expression of <i>dod-24p</i>-driven GFP. Control nematodes show induction in all parts of the intestine (left panel). Expression is substantially reduced in Hsp90-depleted nematodes (right panel). The scale bar represents 100 μm.</p

Genes from cluster <i>daf-21</i>Down_2 are suppressed by Hsp90 RNAi in gonads and embryos.

<p>A) HZ455 nematodes were imaged to visualize the expression and subcellular localization of SEPA-1 protein. Yellow arrows indicate the position of developed embryos, while green arrows indicate the fluorescence prior to passage through the spermathecum. B) RT688 nematodes were imaged to visualize subcellular localization of CAV-1 protein. The CAV-1 protein in the meiotic zone of the gonad arm is indicated in both panels with a green arrow, while yellow arrows indicate the position of developed embryos. C) BC12422 nematodes were imaged to visualize the cells expressing <i>zip-8</i>. The scale bar represents 100 μm. Yellow arrows show the position of a <i>bzip-8</i>::GFP expressing embryo. D) GFP::PUD-1.1 can be observed in intestinal tissues in later larval stages. After Hsp90 RNAi this expression is strongly diminished. The scale bar represents 100 μm.</p

Influence of Hsp90-depletion on the <i>C</i>. <i>elegans</i> proteome.

<p>A) Control and Hsp90 RNAi treated N2 nematodes at the moment of harvesting for analysis. The developing phenotype can be seen at the vulva site (yellow arrow) and the Hsp90-depleted nematodes are slightly smaller at that stage. B) Proteomic changes based on isotope-labelled mass spectrometry. The two independent experiments are plotted in the two dimensions. Blue spots indicate genes, for which the identification scores based on the number of detected peptides imply a reliable quantification. C) Network of upregulated proteins and corresponding GO enrichment analysis. The network was generated based on hit-to-hit relationships in a coexpression database as described in the Materials and Methods section. D) Network of downregulated proteins and corresponding GO enrichment analysis. The network was constructed with identical settings as in C.</p

Regulation of separated clusters during <i>daf</i>-21 RNAi-response and other conditions.

<p>A) Comparison between the three replicates regarding the up- or downregulation of specific clusters. The included genes are used to determine the UpRegScore of the respective cluster in each of the experiments as described in Materials and Methods. The score was calculyted as described in the Materials and Methods section. The results for the respective replicate on the single-gene basis are show in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0186386#pone.0186386.s002" target="_blank">S2</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0186386#pone.0186386.s003" target="_blank">S3</a> Figs and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0186386#pone.0186386.s004" target="_blank">S4B Fig</a>) Calculation of the UpRegScore for each gene cluster in the microarray experiments for RNAi against <i>sams-1</i> or <i>sbp-1</i> (left side), <i>V</i>. <i>cholerae</i> VC109/VC110 exposure and <i>P</i>. <i>aeruginosa</i> exposure (right side). The corresponding results on the single-gene basis are shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0186386#pone.0186386.s005" target="_blank">S5</a>–<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0186386#pone.0186386.s008" target="_blank">S8 Fig</a>.</p