Visualition of Great War in the Weekly Světozor

The bachelor thesis deals with the issue of imaging of Great War in czech weekly "Světozor". It will examine how much space during years 1914-1918 is given to war events, what sides of the war conflict are shown and with what frequency. The thesis also wants to cover whether there is any change in the manner of imaging during the course of the war. Last section of the thesis will be on the topic how could the reader perceive the Great War based on the photographs of this weekly

Supplementary tables “The plastid genome of some eustigmatophyte algae harbours a bacteria-derived six-gene cluster for biosynthesis of a novel secondary metabolite” by Tatiana Yurchenko et al

Supplementary tables S1 to S

Expression of the <i>RbcS</i> and <i>rbcL</i> genes in <i>Euglena gracilis</i> and <i>Euglena longa</i>.

<p>Expression levels of <i>RbcS</i> and <i>rbcL</i> mRNAs were analyzed by quantitative RT-PCR and normalized over the 18S ribosomal RNA. Cultivation conditions and species are denoted as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0158790#pone.0158790.g002" target="_blank">Fig 2</a>.</p

Additional file 1: Table S1. of A paneukaryotic genomic analysis of the small GTPase RABL2 underscores the significance of recurrent gene loss in eukaryote evolution

The list of RABL2 genes analyzed. Table S2. RABL2 sequences identified as contaminations. Table S3. Ciliary genes in species with RABL2 yet unknown to have flagellated stages. (XLS 77 kb

Stability of RBCS and RBCL proteins in <i>Euglena gracilis</i> and <i>Euglena longa</i>.

<p>Cell cultures were treated with 20 μg/ml of cycloheximide, aliquots were taken at 0, 1, 4, 8, and 24 h post treatment, and analyzed by western blotting using anti-RBCS, anti-RBCL and anti-Tubulin antibodies. Molecular weights (in kDa) are indicated on the left of each panel. The identity of the RBCL protein (arrowhead in the anti-RBCL panel) was confirmed by mass-spectrometry. Tubulin served as a loading control. Cultivation conditions and species are denoted as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0158790#pone.0158790.g002" target="_blank">Fig 2</a>.</p

Phylogenetic tree of RBCL protein sequences.

<p>The maximum-likelihood tree was inferred with RAxML using the LG+Γ substitution model. The bootstrap support values and posterior probabilities (from PhyloBayes) are indicated at branches when higher than 50% and 0.95, respectively. Highlighted in white boxes are non-photosynthetic species. <i>E</i>. <i>longa</i> is in bold.</p

RuBisCO in Non-Photosynthetic Alga <i>Euglena longa</i>: Divergent Features, Transcriptomic Analysis and Regulation of Complex Formation

<div><p><i>Euglena longa</i>, a close relative of the photosynthetic model alga <i>Euglena gracilis</i>, possesses an enigmatic non-photosynthetic plastid. Its genome has retained a gene for the large subunit of the enzyme RuBisCO (<i>rbcL</i>). Here we provide new data illuminating the putative role of RuBisCO in <i>E</i>. <i>longa</i>. We demonstrated that the <i>E</i>. <i>longa</i> RBCL protein sequence is extremely divergent compared to its homologs from the photosynthetic relatives, suggesting a possible functional shift upon the loss of photosynthesis. Similarly to <i>E</i>. <i>gracilis</i>, <i>E</i>. <i>longa</i> harbors a nuclear gene encoding the small subunit of RuBisCO (RBCS) as a precursor polyprotein comprising multiple RBCS repeats, but one of them is highly divergent. Both RBCL and the RBCS proteins are synthesized in <i>E</i>. <i>longa</i>, but their abundance is very low compared to <i>E</i>. <i>gracilis</i>. No RBCS monomers could be detected in <i>E</i>. <i>longa</i>, suggesting that processing of the precursor polyprotein is inefficient in this species. The abundance of RBCS is regulated post-transcriptionally. Indeed, blocking the cytoplasmic translation by cycloheximide has no immediate effect on the RBCS stability in photosynthetically grown <i>E</i>. <i>gracilis</i>, but in <i>E</i>. <i>longa</i>, the protein is rapidly degraded. Altogether, our results revealed signatures of evolutionary degradation (becoming defunct) of RuBisCO in <i>E</i>. <i>longa</i> and suggest that its biological role in this species may be rather unorthodox, if any.</p></div

Abundance of the RBCS and RBCL proteins in <i>Euglena gracilis</i> and <i>Euglena longa</i>.

<p>Protein immunodetection was performed using anti-RBCS, anti-RBCL, and anti-Tubulin antibodies. Three bands with different molecular weights were observed in anti-RBCS immunoblotting. The ~130 kDa band (marked *1) corresponds to polyprotein synthesized in the nucleus. The ~15 kDa band (marked *3) corresponds to the processed monomer after cleavage of the signal sequence and excision of decapeptides. The ~22 kDa band (marked *2) possibly corresponds to a monomer still attached to the transit peptide. The identity of the RBCL protein (arrowhead in the anti-RBCL panel) was confirmed by mass-spectrometry. Tubulin served as a loading control. Molecular weights in kDa are indicated on the left. EG-, <i>E</i>. <i>gracilis</i> cultivated photosynthetically (without ethanol); EG+, <i>E</i>. <i>gracilis</i> cultivated mixotrophically (with ethanol); EL, <i>E</i>. <i>longa</i>.</p

The revisited structure of the <i>SEC10</i> locus in <i>Arabidopsis thaliana</i>.

<p>The revisited arrangement of the <i>SEC10</i> locus (At5g12370) depicts <i>SEC10a</i>, <i>SEC10b</i>, and parts of two neighboring genes (At5g12360, At5g12380). Coding exons are shown as black boxed, 5′UTR as gray boxes, and 3′ UTR as white boxes. Arrows indicate the position and orientation of primers used for cloning of the <i>SEC10</i> locus in four overlapping parts (a-I, a-II, b-I and b-II; lines at the bottom represent the ranges of the cloned PCR products). The orange strip marks the region omitted from the reference sequence of the <i>A. thaliana</i> genome.</p

Dissecting a Hidden Gene Duplication: The <i>Arabidopsis thaliana SEC10</i> Locus

<div><p>Repetitive sequences present a challenge for genome sequence assembly, and highly similar segmental duplications may disappear from assembled genome sequences. Having found a surprising lack of observable phenotypic deviations and non-Mendelian segregation in <i>Arabidopsis thaliana</i> mutants in <i>SEC10</i>, a gene encoding a core subunit of the exocyst tethering complex, we examined whether this could be explained by a hidden gene duplication. Re-sequencing and manual assembly of the <i>Arabidopsis thaliana SEC10</i> (At5g12370) locus revealed that this locus, comprising a single gene in the reference genome assembly, indeed contains two paralogous genes in tandem, <i>SEC10a</i> and <i>SEC10b</i>, and that a sequence segment of 7 kb in length is missing from the reference genome sequence. Differences between the two paralogs are concentrated in non-coding regions, while the predicted protein sequences exhibit 99% identity, differing only by substitution of five amino acid residues and an indel of four residues. Both <i>SEC10</i> genes are expressed, although varying transcript levels suggest differential regulation. Homozygous T-DNA insertion mutants in either paralog exhibit a wild-type phenotype, consistent with proposed extensive functional redundancy of the two genes. By these observations we demonstrate that recently duplicated genes may remain hidden even in well-characterized genomes, such as that of <i>A. thaliana</i>. Moreover, we show that the use of the existing <i>A. thaliana</i> reference genome sequence as a guide for sequence assembly of new <i>Arabidopsis</i> accessions or related species has at least in some cases led to error propagation.</p></div