Cilj je rada analizirati pjesme Konstantina P. Kavafija koje tematiziraju smrt, a kroz vizuru teorijskih i hermeneutičkih književnih načela i igara riječi na temelju grčkih pojmova sema („grob”) i ...soma („tijelo”). Cilj je proučiti njihove oblike i simbolizme, promišljajući o njima kao o temeljnim motivima Kavafijeva stvaralaštva. Pritom će se primijeniti komparativno načelo povezivanja pjesničkih simbola s antičkom filozofijom smrti (oprimjerenom Platonom) te s kasnijim, simbolističkim promišljanjem smrti autora (npr. kod Stéphanea Mallarméa), iz kojih se Kavafijevo moderno pjesništvo i izrodilo. Tekstualnom analizom njegove poezije usmjerene na smrt, istražit će se pjesnikov utjecaj i osjećaj razornosti koji pobuđuje u čitatelju. Nadalje, rad će se usmjeriti na timotičku snagu njegove poezije kroz tvrdnju da se pjesnik naslanja na povijesno naslijeđe ponajprije Erosa, ali i Tanatosa.
Spontaneously fermented dairy products have a long history, and present diverse microorganisms and unique flavors. To provide insight into the bacterial diversity, 80 different types of spontaneously ...fermented dairy product samples’ sequence data that were downloaded from MG-RAST and NCBI and 8 koumiss and 4 shubat were sequenced by the PacBio SMRT sequencing platform. All samples including butter, sour cream, cottage cheese, yogurt, koumiss, shubat, and cheese, were collected from various regions in Russia, Kazakhstan, Mongolia and Inner Mongolia (China). The results revealed that Firmicutes and Proteobacteria were the most dominant phyla (>99%), and 11 species were identified with a relative abundance exceeding 1%. Furthermore, Streptococcus salivarius, Lactobacillus helveticus, Lactobacillus delbrueckii, Enterobacter xiangfangensis, and Acinetobacter baumannii were the primary bacterial species in the fermented dairy product samples. Principal coordinates analysis showed that koumiss and shubat stood out from the other samples. Moreover, permutational ANOVA tests revealed that the types of fermented dairy products and geographical origin significantly affected microbial diversity. However, different processing techniques did not affect microbial diversity. In addition, results of hierarchical clustering and canonical analysis of the principal coordinates were consistent. In conclusion, geographical origin and types of fermented dairy products determined the bacterial diversity in spontaneously fermented dairy product samples.
The study investigated methylation of each cytosine within a fragment of the
YJEFN3
gene located at one of the index loci of schizophrenia risk with the aim to determine whether methylation of this ...fragment is associated with the level of cognitive deficit in patients and to what extent it depends on the risk haplotype. Peripheral blood samples from 70 schizophrenia spectrum patients and 72 healthy subjects who underwent cognitive testing were examined using single-molecule real-time bisulfite sequencing. A negative correlation was found between methylation of the CpG site at chr19:19532203, hg38 (Illumina ID: cg08623644) and the cognitive index in patients. Methylation at cg08623644 was associated with the risk haplotype in the pooled sample and in healthy subjects. The patients showed a weakening of this association. The findings suggest that methylation at cg08623644 may be a peripheral marker of molecular processes associated with the severity of the disease, which deserves further investigation.
We hypothesized that key antiproliferative target genes for the vitamin D receptor (VDR) were repressed by an epigenetic mechanism in prostate cancer cells resulting in apparent hormonal ...insensitivity. To explore this possibility, we examined nuclear receptor corepressor expression in a panel of nonmalignant and malignant cell lines and primary cultures, and found frequently elevated SMRT corepressor mRNA expression often associated with reduced sensitivity to 1alpha,25-dihydroxyvitamin D(3) (1alpha,25(OH)2D3). For example, PC-3 and DU-145 prostate cancer cell lines had 1.8-fold and twofold increases in SMRT mRNA relative to normal PrEC cells (P<0.05). Similarly, 10/15 primary tumour cultures (including three matched to normal cells from the same donors) had elevated SMRT mRNA levels; generally NCoR1 and Alien were not as commonly elevated. Corepressor proteins often have associated histone deacetylases (HDAC) and reflectively the antiproliferative action of 1alpha,25(OH)2D3 can be 'restored' by cotreatment with low doses of HDAC inhibitors such as trichostatin A (TSA, 15 nM) to induce apoptosis in prostate cancer cell lines. To decipher the transcriptional events that lead to these cellular responses, we undertook gene expression studies in PC-3 cells after cotreatment of 1alpha,25(OH)2D3 plus TSA after 6 h. Examination of known VDR target genes and cDNA microarray analyses revealed cotreatment of 1alpha,25(OH)2D3 plus TSA cooperatively upregulated eight (out of 1176) genes, including MAPK-APK2 and GADD45alpha. MRNA and protein time courses and inhibitor studies confirmed these patterns of regulation. Subsequently, we knocked down SMRT levels in PC-3 cells using a small interfering RNA (siRNA) approach and found that GADD45alpha induction by 1alpha,25(OH)2D3 alone became very significantly enhanced. The same distortion of gene responsiveness, with repressed induction of GADD45alpha was found in primary tumour cultures compared and to matched peripheral zone (normal) cultures from the same donor. These data demonstrate that elevated SMRT levels are common in prostate cancer cells, resulting in suppression of target genes associated with antiproliferative action and apparent 1alpha,25(OH)2D3-insensitivity. This can be targeted therapeutically by combination treatments with HDAC inhibitors.
As a result of a high rate of mutations and recombination events, an RNA-virus exists as a heterogeneous "swarm" of mutant variants. The long read length offered by single-molecule sequencing ...technologies allows each mutant variant to be sequenced in a single pass. However, high error rate limits the ability to reconstruct heterogeneous viral population composed of rare, related mutant variants. In this article, we present two single-nucleotide variants (2SNV), a method able to tolerate the high error rate of the single-molecule protocol and reconstruct mutant variants. 2SNV uses linkage between single-nucleotide variations to efficiently distinguish them from read errors. To benchmark the sensitivity of 2SNV, we performed a single-molecule sequencing experiment on a sample containing a titrated level of known viral mutant variants. Our method is able to accurately reconstruct clone with frequency of 0.2% and distinguish clones that differed in only two nucleotides distantly located on the genome. 2SNV outperforms existing methods for full-length viral mutant reconstruction.
PacBio’s single-molecule real-time (SMRT) sequencing technology offers important advantages over the short-read DNA sequencing technologies that currently dominate the market. This includes ...exceptionally long read lengths (20 kb or more), unparalleled consensus accuracy, and the ability to sequence native, non-amplified DNA molecules. From fungi to insects to humans, long reads are now used to create highly accurate reference genomes by de novo assembly of genomic DNA and to obtain a comprehensive view of transcriptomes through the sequencing of full-length cDNAs. Besides reducing biases, sequencing native DNA also permits the direct measurement of DNA base modifications. Therefore, SMRT sequencing has become an attractive technology in many fields, such as agriculture, basic science, and medical research. The boundaries of SMRT sequencing are continuously being pushed by developments in bioinformatics and sample preparation. This book contains a collection of articles showcasing the latest developments and the breadth of applications enabled by SMRT sequencing technology.
: Tadpole tail develops from the tailbud, an apparently homogenous mass of cells at the posterior of the embryo. While much progress has been made in understanding the origin and the induction of the ...tailbud, the subsequent outgrowth and differentiation have received much less attention, particularly with regard to global gene expression changes.
: By using RNA-seq with SMRT and further analyses, we report the transcriptome profiles at four key stages of tail development, from a small tailbud to the onset of feeding (S18, S19, S21 and S28) in
, an anuran with a number of advantages for developmental and genetic studies.
: We obtained 48,826 transcripts and discovered 8807 differentially expressed transcripts (DETs, q < 0.05) among these four developmental stages. We functionally classified these DETs by using GO and KEGG analyses and revealed 110 significantly enriched GO categories and 6 highly enriched KEGG pathways (Protein digestion and absorption; ECM-receptor interaction; Pyruvate metabolism; Fatty acid degradation; Valine, leucine and isoleucine degradation; and Glyoxylate and dicarboxylate metabolism) that are likely critically involved in developmental changes in the tail. In addition, analyses of DETs between any two individual stages demonstrated the involvement of distinct biological pathways/GO terms at different stages of tail development. Furthermore, the most dramatic changes in gene expression profile are those between S28 and any of the other three stages. The upregulated DETs at S28 are highly enriched in "myosin complex" and "potassium channel activity", which are important for muscle contraction, a critical function of the tail that the animal needs by the end of embryogenesis. Additionally, many DETs and enriched pathways discovered here during tail development, such as HDAC1, Hes1 and Hippo signaling pathway, have also been reported to be vital for the tissue/organ regeneration, suggesting conserved functions between development and regeneration.
: The present staudy provides a golbal overview of gene expression patterns and new insights into the mechanism involved in anuran tail development and regeneration.
Strategies for sequencing fungal genomes on next-generation sequencing (NGS) platforms depend on the characteristics of the genome of the targeted species, quantity and quality of the genomic DNA, ...and cost considerations. Massively parallel sequencing with sequencing by synthesis (SBS) approach by Illumina produces terabases of short read sequences (i.e., ~300 bp) in a time and cost-effective manner, though the read length can limit the assembly particularly in repetitive regions. The single molecule, real-time (SMRT) sequencing approach by Pacific Biosciences (PacBio) produces longer reads (i.e., ~12,500 bp) which can facilitate de novo assembly of genomes that contain long repetitive sequences, though due to the lower-throughput of this platform achieving the coverage needed for assembly is more expensive than by SBS. Additionally, the Illumina SBS platforms can handle low quantity/quality of genomic DNA materials, while the SMRT system requires undamaged long DNA fragments as input to ensure that high-quality data is produced. Both platforms are discussed in this chapter including key decision-making points.
Bactrocera dorsalis (Hendel), as one of the most notorious and destructive invasive agricultural pests in the world, causes damage to over 250 different types of fruits and vegetables throughout ...tropical and subtropical areas. PacBio single-molecule real-time (SMRT) sequencing was used to generate the full-length transcriptome data of B. dorsalis. A total of 40,319,890 subreads (76.6 Gb, clean reads) were generated, including 535,241 circular consensus sequences (CCSs) and 386,916 full-length non-concatemer reads (FLNCs). Transcript cluster analysis of the FLNC reads revealed 22,780 high-quality reads (HQs). In total, 12,274 transcripts were functionally annotated based on four different databases. A total of 1978 SSR loci were distributed throughout 1714 HQ transcripts, of which 1926 were complete SSRs and 52 were complex SSRs. Among the total SSR loci, 2–3 nucleotide repeats were dominant, occupying 83.62%, of which di- and tri- nucleotide repeats were 39.38% and 44.24%, respectively. We detected 105 repeat motifs, of which AT/AT (50.19%), AC/GT (39.15%), CAA/TTG (32.46%), and ACA/TGT (10.86%) were the most common in di- and tri-nucleotide repeats. The repeat SSR motifs were 12–190 bp in length, and 1638 (88.02%) were shorter than 20 bp. According to the randomly selected microsatellite sequence, 80 pairs of primers were designed, and 174 individuals were randomly amplified by PCR using primers. The number of primers that had amplification products with clear bands and showed good polymorphism came to 41, indicating that this was a feasible way to explore SSR markers from the transcriptomic data of B. dorsalis. These results lay a foundation for developing highly polymorphic microsatellites for researching the functional genomics, population genetic structure, and genetic diversity of B. dorsalis.
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