The metaphysical thought of Thomas Aquinas. From the concept of being and unity to the concept of whole and part

The subject-matter of the thesis is the metaphysical thought of the renowned medieval philosopher and theologian Thomas Aquinas (1224/5-1274). The main goal ofthe thesis is to expose Aquinas' part-whole doctrine (mereology) in the broad context of his metaphysical theory. In concrete, we mean to elucidate the part-whole relationship in the background ofthe key metaphysical principles and concepts, such as the notion of being and unity or the issue of the ontological structure of a categorial being. The whole thesis can be divided into two main parts. In the first part we tackle those issues, which must be outlined to comprehend Aquinas' mereology in the broad horizon of his metaphysics. In the second part we set forth the independent attempt to advance Aquinas' part-whole theory

Additional file 8: Table S7. of A quantitative genome-wide RNAi screen in C. elegans for antifungal innate immunity genes

Species used in phylogenetic clustering listed in the same order as in Fig. 8. (XLSX 47 kb

AKIR-1 binds preferentially to <i>nlp</i> gene promoters in the absence of infection.

<p><b>A.</b> Specific binding of AKIR-1::GFP onto promoters (left panels) or 3’ UTR (right panel) of <i>act-1</i> (left panel; 2 different PCR amplicons, A and B), and <i>nlp-29</i>, <i>nlp-31</i> and <i>nlp-34</i>, represented as the fold enrichment of the specific ChIP signal obtained using an anti-GFP antibody for immunoprecipitation relative to that when blocked beads were used, measured by quantitative PCR. Data is normalised to input; the average (and standard error) from three independent experiments is shown. ***, p < 0.0001; **, p < 0.001; ns, p > 0.1; paired 2-tail Student’s t test. <b>B.</b> Model for the role of AKIR-1 in the regulation of <i>nlp</i> AMP gene expression upon infection. Under normal conditions (left), the AKIR-1/NuRD complex is recruited to the <i>nlp-29</i> locus, leading to modification (red stars) of histones (ovoids), and formation of an open chromatin structure. Upon infection, STA-2 is activated and, following removal of the AKIR-1/NuRD complex, is responsible for expression of the <i>nlp</i> genes. Infection could impact chromatin structure, but here we assume that it does not. When AKIR-1 is absent (right), an open chromatin structure cannot be formed, precluding STA-2-dependent expression of the <i>nlp</i> genes following infection, but not affecting the low basal STA-2-independent gene expression. The images are adapted, with permission, from <a href="https://www.activemotif.com" target="_blank">https://www.activemotif.com</a>.</p

Evolutionary plasticity in the innate immune function of Akirin

<div><p>Eukaryotic gene expression requires the coordinated action of transcription factors, chromatin remodelling complexes and RNA polymerase. The conserved nuclear protein Akirin plays a central role in immune gene expression in insects and mammals, linking the SWI/SNF chromatin-remodelling complex with the transcription factor NFκB. Although nematodes lack NFκB, Akirin is also indispensable for the expression of defence genes in the epidermis of <i>Caenorhabditis elegans</i> following natural fungal infection. Through a combination of reverse genetics and biochemistry, we discovered that in <i>C</i>. <i>elegans</i> Akirin has conserved its role of bridging chromatin-remodellers and transcription factors, but that the identity of its functional partners is different since it forms a physical complex with NuRD proteins and the POU-class transcription factor CEH-18. In addition to providing a substantial step forward in our understanding of innate immune gene regulation in <i>C</i>. <i>elegans</i>, our results give insight into the molecular evolution of lineage-specific signalling pathways.</p></div

AKIR-1 interactors identified by label-free quantitative immunoprecipitation.

<p><b>A.</b> Experimental design. Protein extracts from mixed-stage worms expressing AKIR-1::GFP were incubated with anti-GFP conjugated or control resins before proteolytic release of peptides from the immunoprecipitated proteins. The relative abundance of co-precipitated proteins was assessed by mass spectrometry. <b>B.</b> Volcano plot showing specific interaction partners (in red) of AKIR-1::GFP. The mean values for fold change from 3 independent experiments are shown. The SAM (significance analysis of microarrays) algorithm was used to evaluate the enrichment of the detected proteins. Proteins that met the combined enrichment threshold (hyperbolic curves, <i>t</i>_<i>0</i> = 1.2) are colored in red. Proteins with the gene ontology annotation “DNA-binding” (GO:0003677) are depicted as triangles. Known members of the NuRD complex are shown in blue. <b>C.</b> NuRD complex and/or DNA-binding proteins among the 53 high confidence AKIR-1::GFP interaction partners.</p

Akirin acts downstream of Gα to regulate the expression of <i>nlp-29</i>.

<p><b>A.</b> Ratio of green fluorescence (GFP) to size (time of flight; TOF) in IG274 worms carrying the integrated array <i>frIs7</i> (containing <i>nlp-29p</i>::<i>gfp</i> and <i>col-12p</i>::<i>DsRed</i>) treated with RNAi against negative and positive controls (<i>sta-1</i>, <i>dcar-1</i>, respectively) or <i>akir-1</i> and infected by <i>D</i>. <i>coniospora</i> (Infected), wounded (Wound), treated with a 5 mM dihydrocaffeic acid solution (DHCA) or exposed to 300mM NaCl (High salt). Here and in subsequent figures representing Biosort results, unless otherwise stated, graphs are representative of at least 3 independent experiments. The black bar represents the mean value for (from left to right), n = 189, 164, 179, 184, 183, 169; 23, 21, 30, 29, 36, 68; 97, 86, 114, 111, 104, 94; 96, 85, 100, 150, 129, 113; **** p<0.0001, ns p>0.05, Dunn’s test. <b>B.</b> Fluorescent images of adult worms carrying <i>frIs7</i>, expressing a constitutively active Gα protein, GPA-12*, in the epidermis and treated with RNAi against the indicated genes. Almost all of the residual GFP expression seen upon <i>akir-1</i>(RNAi), most prominent in the vulval muscle cells, comes from <i>unc-53Bp</i>::<i>gfp</i> used as a transgenesis marker.</p

Validation of AKIR-1 interactors by Western blotting.

<p><b>A.</b> Complexes immunopurified using an anti-GFP antibody from control or infected worms with a single copy <i>AKIR-1</i>::<i>GFP</i> insertion (<i>wt; frSi12[pNP157(akir-1p</i>::<i>AKIR-1</i>::<i>GFP)] II)</i> were probed with specific antibodies. The results for two independent pull-downs are shown. The presence of HDA-1 and LET-418 (NuRD complex components) could be confirmed. Anti-ACT-1 was used to control the total input for each immunoprecipitation. <b>B.</b> Complexes immunopurified using an anti-FLAG antibody, from a strain co-expressing AKIR-1::GFP and FLAG-tagged CEH-18 (<i>wt; frSi12[pNP157(akir-1p</i>::<i>AKIR-1</i>::<i>GFP)] II; wgIs533[CEH-18</i>::<i>TY1</i>::<i>GFP</i>::<i>3xFLAG + unc-119(+)]</i>), were probed with anti-FLAG (top panel) and anti-GFP (bottom) antibodies. In addition to the immunopurified complex (IP), the extract before immunopurification (Input), the unbound fraction (flow-through: FT) and proteins immunopurified using an unrelated antibody (Mock) were also analysed.</p

Akirin regulates multiple <i>nlp</i> genes in the epidermis.

<p><b>A.</b> Confocal images of IG1485 transgenic worms expressing an <i>akir-1p</i>::<i>gfp</i> reporter gene showing epidermal and neuronal expression of GFP. The lateral epithelial seam cells are indicated by the arrowheads. Much of the fluorescence in the head and tail comes from neurons, seen more clearly in the right panel. Scale bar 50 μm. <b>B.</b> Ratio of green fluorescence (GFP) to size (TOF) in <i>rde-1</i>(<i>ne219</i>);<i>wrt-2p</i>::<i>RDE-1</i> worms that are largely resistant to RNAi except in the epidermis, carrying the array <i>frIs7</i>, treated with RNAi against the indicated genes and infected by <i>D</i>. <i>coniospora</i>. The black bar represents the mean value for (from left to right), n = 135, 49, 155, 102, 130, 94; **** p<0.0001, Dunn’s test. <b>C.</b> Quantitative RT-PCR analysis of the expression of genes in the <i>nlp-29</i> cluster in <i>rde-1</i>(<i>ne219</i>); <i>wrt-2p</i>::<i>RDE-1</i> worms treated with RNAi against the indicated genes and infected by <i>D</i>. <i>coniospora</i>; results are presented relative to those of uninfected worms. Data (with average and SD) are from three independent experiments (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1007494#pgen.1007494.s002" target="_blank">S2B Fig</a>). **, p < 0.001; *, p < 0.01; 1-tailed ratio paired t test.</p

CEH-18 plays a role in host defence.

<p><b>A.</b> Ratio of green fluorescence (GFP) to size (TOF) in wild-type (IG274) or <i>ceh-18</i>(<i>mg57</i>) mutant (IG1714) worms carrying <i>frIs7</i>, infected or not with <i>D</i>. <i>coniospora</i> for 16 h (yellow and blue, respectively; data for IG274 is as Fig 3B in [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1007494#pgen.1007494.ref053" target="_blank">53</a>]), and IG274 worms treated with RNAi against <i>sta-1</i> (control) or <i>ceh-18</i> and, from left to right, exposed to high salt (purple; <i>cpsf-2(RNAi)</i> is a positive control, <i>sta-2(RNAi)</i> a negative control [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1007494#pgen.1007494.ref011" target="_blank">11</a>]), in worms also expressing GPA-12* in the epidermis, and in the <i>rde-1</i>(<i>ne219</i>);<i>wrt-2p</i>::<i>RDE-1</i> background and infected by <i>D</i>. <i>coniospora</i>. For the latter 2 panels, <i>sta-2(RNAi)</i> is a positive control. A minimum of 45 worms was used for each condition. The black bar represents the mean value; *** p<0.001, **** p<0.0001, relative to <i>sta-1</i>(RNAi), Dunn’s test; for the other conditions there is not a significance decrease. The results of the 3 right panels are unpublished results from [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1007494#pgen.1007494.ref011" target="_blank">11</a>], representative of at least 4 independent experiments. <b>B.</b> Quantitative RT-PCR analysis of the expression of several genes in the <i>nlp-29</i> cluster in wild-type worms, <i>sta-2</i> and <i>ceh-18</i> mutants infected by <i>D</i>. <i>coniospora</i>; results are presented relative to those of uninfected worms. Data (with average and SD) are from three independent experiments. **, p < 0.001; *, p < 0.01; 1-tailed ratio paired t test. <b>C.</b> Results of 2 independent tests of survival of <i>rde-1</i>(<i>ne219</i>);<i>wrt-2p</i>::<i>RDE-1</i> worms treated with RNAi against <i>sta-1</i>, <i>sta-2</i>, <i>akir-1</i> or <i>ceh-18</i>, infected with <i>D</i>. <i>coniospora</i> and cultured at 25°C (n>65 for all tests). The difference between the <i>sta-1(RNAi)</i> and <i>ceh-18(RNAi)</i> animals is highly significant in both trials (p<0.0001; one-sided log rank test).</p