Cancer tumor sequencing

Transcripts are frequently modified by structural variations, which lead to fused transcripts of either multiple genes, known as a fusion gene, or a gene and a previously non-transcribed sequence. Detecting these modifications, called transcriptomic structural variations (TSVs), especially in cancer tumor sequencing, is an important and challenging computational problem.

16p vimichaelfaraday 25-03-2022 17 1   Download

Breast cancer (BC) is the most common malignancy in women, in whom it reaches 20% of the total neoplasia incidence. Most BCs are considered sporadic and a number of factors, including familiarity, age, hormonal cycles and diet, have been reported to be BC risk factors.

11p vielonmusk 21-01-2022 15 0   Download

Immune checkpoint inhibitors (ICIs) are currently one of the most promising therapy options in the field of oncology. Although the first pivotal ICI trial results were published in 2011, few biomarkers exist to predict their therapy outcome. PD-L1 expression and tumor mutational burden (TMB) were proven to be sometimes-unre‑ liable biomarkers.

13p vielonmusk 21-01-2022 13 1   Download

Retinoids are potent immune modulators that inhibit Fas ligand (FasL) expression and thereby repress the activationinduced apoptosis of immature thymocytes and T-cell hybridomas. In this study, we demonstrate that all-transretinoic acid (all-trans-RA) directly represses the transcriptional activity of the nuclear factors of activated T-cells (NFAT), which is an important transactivator of the FasL promoter.

9p research12 01-06-2013 42 5   Download

We have determined the nucleotide sequence of a zebrafish cDNAclone that codes for a cellular retinol-binding protein type II (CRBPII). Radiation hybrid mapping revealed that the zebrafish and human CRBPII genes are located in syntenic groups.In situhybridization and emulsion autora-diography localized theCRBPIImRNA to the intestine and the liver of adult zebrafish.

8p research12 23-04-2013 45 4   Download

Signal sequences often containa-helix-destabilizing amino acids within the hydrophobic core. In the precursor of the Escherichia coliouter-membrane protein PhoE,the glycine residue at position)10 (Gly )10 ) is thought to be responsible for the break in the a-helix. Previously,we showed that substitution of Gly )10 bya-helix-promoting residues (Ala, Cys or Leu) reduced the proton-motive force dependency of the translocation of the precursor,but the actual role of the helix breaker remained obscure. ...

8p tumor12 22-04-2013 34 3   Download

Antifreeze glycoproteins (AFGPs) constitute the major fraction of protein in the blood serum of Antarctic noto-thenioids and Arctic cod. Each AFGP consists of a varying number of repeating units of (Ala-Ala-Thr)n, withminor sequence variations, and the disaccharide b-D-galactosyl-(1fi3)-a-N-acetyl-D-galactosamine joined as a glycoside to the hydroxyl oxygen of the Thr residues. These compounds allow the fish to survive in subzero ice-laden polar oceans by kineticallydepressing the temperatureatwhich icegrows ina noncolligative manner....

12p tumor12 20-04-2013 39 4   Download

The signature amidase from the extremophile archeumSulfolobus solfatari-cusis an enantioselective enzyme that cleaves S-amides. We report here that this enzyme also converts nitriles in the corresponding organic acid, simi-larly to the well characterized amidase from Rhodococcus rhodochrousJ1. The archaeal and rhodococcal enzymes belong to the signature amidases and contain the typical serine-glycine rich motif. They work at different optimal temperature, share a high sequence similarity and both contain an additional CX3C motif. ...

9p fptmusic 12-04-2013 31 3   Download

In recent years major progress has been made in elucidating the mechanism and structure of catalytic RNA molecules, and we are now beginning to understand ribozymes well enough to turn them into useful tools. Work in our laboratory has focused on the development of twin ribozymes for site-specific RNA sequence alteration. To this end, we followed a strategy that relies on the combination of two ribozyme units into one molecule (hence dubbed twin ribozyme).

11p fptmusic 11-04-2013 40 2   Download

Eukaryotic genomes are composed of isochores, i.e. long sequences relat-ively homogeneous in GC content. In this paper, the isochore structure of Arabidopsis thalianagenome has been studied using a windowless technique based on theZcurve method and intuitive curves are drawn for all the five chromosomes. Using these curves, we can calculate the GC content at any resolution, even at the base level.

9p fptmusic 11-04-2013 40 3   Download

We report here the identification of a tachykinin-related peptide (TRP) in crustaceans. Direct MALDI-TOF MS withbrainslicesof the crayfishProcambarus clarkiiindicated the presence of a peptide having an MS number of around 934. Quadrupole orthogonal acceleration time-of-flight (Q-TOF) MS/MS analysis implied the sequence to be APSGFLGMRamide, identical to that of CabTRP Ia, isolated previously from the crab Cancer borealis,and Pev-tachykinin, from the shrimpPenaeus vannamei.

11p dell39 03-04-2013 36 2   Download

Integrase of the human immunodeficiency virus type-1 (HIV-1) recognizes specific sequences located in the U3 and U5 regions at the ends of viral DNA. We synthesizedDNA duplexes mimicking the U5 region and containing either 2¢-aminonucleosides or non-nucleoside 1,3-propanediol insertions at the third and terminal positions and studied their interactions with HIV-1 integrase. Both modifications introduced a local structural distortion in the DNA double helix.

7p dell39 03-04-2013 31 2   Download

Trans-splicing group I ribozymes have been introduced in order to mediate RNA reprogramming (including RNA repair) of therapeutically relevant RNA transcripts. Efficient RNA reprogramming depends on the appropri-ate efficiency of the reaction, and several attempts, including optimization of target recognition and ribozyme catalysis, have been performed.

12p dell39 27-03-2013 33 3   Download

The reactive center loop (RCL) of serpins plays an essential role in the inhibition mechanism acting as a substrate for their target proteases. Chan-ges within the RCL sequence modulate the specificity and reactivity of the serpin molecule. Recently, we reported the construction of a1-antichymo-

10p inspiron33 26-03-2013 34 3   Download

The peroxisomal enzyme urate oxidase plays a pivotal role in the degrada-tion of purines in both prokaryotes and eukaryotes. However, knowledge about the purine-induced expression of the encoding gene is lacking in vertebrates. These are the first published sequences of fish urate oxidase,

12p inspiron33 25-03-2013 57 5   Download

O-Fucosylation is a post-translational glycosylation in which anO-fucose is covalently attached to the hydroxyl group of a specific serine or threon-ine residue. This modification occurs within the consensus sequence C2X4)5(S⁄T)C3 present on epidermal growth factor-like repeats of several proteins, including the Notch receptors and their ligands.

10p galaxyss3 21-03-2013 45 4   Download

The expansion of DNA repeat sequences is associated with many genetic diseases in humans. Simple bulge DNA structures have been implicated as intermediates in DNA slippage within the DNA repeat regions. To probe the possible role of bulged structures in DNA slippage, we designed and synthesized a pair of simple chiral spirocyclic compounds [Xi Z, Ouyang D & Mu HT (2006)Bioorg Med Chem Lett16, 1180–1184],

12p galaxyss3 07-03-2013 28 3   Download

Upstream stimulatory factor and TFII-I are ubiquitously expressed helix-loop-helix transcription factors that interact with E-box sequences and or initiator elements. We previously demonstrated that upstream stimulatory factor is an activator of b-globin gene expression whereas TFII-I is a repressor.

9p media19 05-03-2013 37 2   Download