Transduplication resulted in the incorporation of two protein-coding sequences into the Turmoil-1 transposable element of C. elegans

Transposable elements may acquire unrelated gene fragments into their sequences in a process called transduplication. Transduplication of protein-coding genes is common in plants, but is unknown of in animals. Here, we report that the Turmoil-1 transposable element in C. elegans has incorporated two protein-coding sequences into its inverted terminal repeat (ITR) sequences. The ITRs of Turmoil-1 contain a conserved RNA recognition motif (RRM) that originated from the rsp- 2 gene and a fragment from the protein-coding region of the cpg-3 gene. We further report that an open reading frame specific to C. elegans may have been created as a result of a Turmoil-1 insertion. Mutations at the 5' splice site of this open reading frame may have reactivated the transduplicated RRM moti

Computational identification of transposable elements in the mouse genome

Repeat sequences cover about 39 percent of the mouse genome and completion of sequencing of the mouse genome [1] has enabled extensive research on the role of repeat sequences in mammalian genomics. This research covers the identification of Transposable elements (TEs) within the mouse transcriptome, based on available sequence information on mouse cDNAs (complementary DNAs) from GenBank [28]. The transcripts are screened for repeats using RepeatMasker [23], whose results are sieved to retain only Interspersed repeats (IRS). Using various bioinformatics software tools as well as tailor made programming, the research establishes: (i) the absolute location coordinates of the TEs on the transcript. (ii) The location of the IRs with respect to the 5’UTR, CDS and 3’UTR sequence features. (iii) The quality of alignment of the TE’s consensus sequence on the transcripts where they exist, (iv) the frequencies and distributions of the TEs on the cDNAs, (v) descriptions of the types and roles of transcripts containing TEs. This information has been collated and stored in a relational database (MTEDB) at http://warta.bio.psu.edu/htt_doc/M TEDB/homepage.htm)

Der chimäre Antigen Rezeptor (CAR) mit Spezifität für das Tumorstammzell-Antigen NY-Eso-1 hat eine höhere Aktivierungsschwelle für T-Zellen als der T-Zell Rezeptor (TCR)

In der adoptiven Immuntherapie von Tumorerkrankungen wird T-Zellen eine definierte Spezifität durch die Expression eines Antigen-spezifischen rekombinanten T-Zell Rezeptors (TCR) oder eines chimären Antigen-Rezeptors (CAR) verliehen. Die adoptive Zelltherapie mit CAR und TCR modifizierten T-Zellen erzielte Tumorremissionen, beispielsweise CAR T-Zellen bei der Therapie leukämischer Erkrankungen und TCR T-Zellen in der Behandlung solider Tumore und Myelomen. Die Bindedomäne der CARs zur Erkennung der Tumorzellen ist von einem Antikörper abgeleitet, der TCR erkennt MHC präsentiertes Antigen durch die variable TCR α- und β-Kette. In dieser Arbeit wurde ein Vergleich der T-Zell Aktivierung durch CAR und TCR durchgeführt. Als Modell Antigen wurde NY-Eso-1 verwendet, da NY-Eso-1 von Tumorzellen vieler solider und hämatologischer Erkrankungen exprimiert wird. Um bei der unterschiedlichen Struktur des CAR und TCR eine Vergleichbarkeit herzustellen, wurden CARs verwendet, deren Antikörper-abgeleitete Bindedomäne wie der verwendete TCR das HLA-A2 präsentierte NY-Eso-1(157-165) Antigen erkennt. CAR und TCR erkennen spezifisch das Antigen, jedoch mit unterschiedlicher Affinität; die CARs binden mit einer etwa 30fach oder 350fach höheren Affinität als der TCR. Sowohl der CAR als auch der TCR induzieren eine Antigen-abhängige T-Zell Aktivierung, erkenntlich an der Sekretion proinflammatorischer Zytokine und der zytolytischen Aktivität der modifizierten T-Zellen. Trotz höherer Affinität ist die Antigen-abhängige Aktivierungsschwelle der CAR T-Zellen höher als die der TCR T-Zellen. Die CD28 Kostimulation im CD28CD3ζ CAR verändert nicht die Aktivierungsschwelle, auch eine Steigerung der Affinität der CAR Bindedomäne verändert nicht die Aktivierungsschwelle. Jedoch verstärken sowohl die CD28 Kostimulation als auch die höhere Affinität die Effektorfunktionen der T-Zelle. Eine Trennung des ζ Primärsignals und der CD28 Kostimulation auf zwei koexprimierte CAR Moleküle verringert die T-Zell Aktivierung im Vergleich zum CAR mit kombinierter CD28CD3ζ Signaldomäne. Unsere Ergebnisse zeigen, dass T-Zellen gegen intrazelluläre Antigene sowohl durch einen TCR als auch einen CAR gerichtet werden können, jedoch sind CAR T-Zellen trotz höherer Affinität weniger sensitiv in der Erkennung geringer Antigenmengen als TCR modifizierte T-Zellen und bieten dadurch eine höhere Selektivität für Zielzellen mit hoher Antigendichte. Bei geringer Antigenexpression, wie sie auf NY-Eso-1 exprimierenden Tumorzellen vorkommen kann, ist jedoch eine TCR gerichtete T-Zell Therapie gegenüber CAR T-Zellen zu bevorzugen.The chimeric antigen receptor (CAR) with specificity for the tumor stem cell associated antigen NY-Eso-1 has a higher activation threshold than the NY-Eso-1 specific T cell receptor (TCR) In adoptive immunotherapy T cells are engineered to express an antigen-specific receptor with defined specificity for a tumor-associated antigen (TAA). T cells can be modified with a recombinant T cell receptor (TCR) or a chimeric antigen receptor (CAR). Current studies with either CAR or TCR modified T cells showed lasting and complete tumor regression; CAR redirected T cells exhibited success in the therapy of leukemia, for example, and TCR redirected T cells showed efficacy in the therapy of solid tumors or myeloma. The CAR recognizes the respective antigen by an antibody derived binding domain while the TCR recognizes the antigen by the variable regions of the α and β chains. In contrast to the TCR, the CAR recognizes the antigen in a MHC independent manner and is restricted to the recognition of cell surface antigens. We here compared CAR and TCR driven T cell activation. For a site-by-site comparison, we engineered a “TCR-like” CAR which recognizes the same MHC presented peptide as the recombinant TCR. As model antigen we used the tumor-associated antigen NY-Eso-1 which is presented by the HLA-A2 on solid and hematologic tumor cells. Both the anti-NY-Eso-1 TCR and anti-NY-Eso-1 CAR induced antigen-dependent T cell activation indicated by secretion of proinflammatory cytokines and cytolysis. The binding affinity of the two used CARs is 30-fold and 350-fold higher than the affinity of the TCR. Although the CAR has a higher binding affinity, the CAR modified T cells showed a higher activation threshold than the TCR redirected T cells. The integration of the costimulatory domain CD28 into the CAR and the increase of binding affinity had no impact on the activation threshold of CAR modified T cells; albeit, both CD28 costimulatory domain and improved affinity increased the magnitude in T cell effector functions. Splitting the primary ζ signal and the CD28 costimulatory domain onto two receptors lowered the T cell activation against target cells compared to the CD28CD3ζ CAR with one polypeptide chain. Our data show that both TCR and CAR redirect a T cell response towards intracellular antigens presented in the MHC context. Despite higher binding affinity, CAR T cells are less sensitive in recognizing the antigen than TCR modified T cells. Therefore CAR modified T cells are more selective in recognizing target cells with high antigen density levels while TCR redirected T cells are more effective in targeting tumor cells with low antigen amounts, like NY-Eso-1 positive tumors

U12 intron positions are more strongly conserved between animals and plants than U2 intron positions

We report that the positions of minor, U12 introns are conserved in orthologous genes from human and Arabidopsis to an even greater extent than the positions of the major, U2 introns. The U12 introns, especially, conserved ones are concentrated in 5'-portions of plant and animal genes, where the U12 to U2 conversions occurs preferentially in the 3'-portions of genes. These results are compatible with the hypothesis that the high level of conservation of U12 intron positions and their persistence in genomes despite the unidirectional U12 to U2 conversion are explained by the role of the slowly excised U12 introns in down-regulation of gene expression

Patients’ Radiation Doses During the Implantation of Stents in Carotid, Renal, Iliac, Femoral and Popliteal Arteries

AbstractObjectives and DesignThe aim of the study was to document the radiation doses to patients during the implantation of stents in various arteries and to discuss potential reasons for prolongation of radiological procedures.Materials and MethodsMeasurements of air kerma (Gy) and dose–area product (Gy cm2) (DAP) were carried out simultaneously on a sample of 345 patients, who underwent different interventional radiological procedures involving angioplasty with stenting of 73 carotid (21.5%), 22 renal (6.5%), 160 iliac (45%), 63 femoral (18.6%) and 27 popliteal (7.9%) arteries.ResultsThe highest mean air kerma values for fluoroscopy and exposure were found for renal angioplasty (340 and 420 mGy, respectively). With regard to total DAP values, the highest were obtained for renal (148 Gy cm2) and iliac/The Inter-Society Consensus for Management of Peripheral Arterial Disease (TASC) II C (199 Gy cm2) stent implantation. The lowest values were for carotid (53 Gy cm2), iliac/TASC II A (6.3 Gy cm2) and femoral/TASC II A (53 Gy cm2) arteries. For 3.5% of the patients, the air kerma was between 1 and 1.5 Gy and for 1.5%, it was between 1.5 and 2 Gy.ConclusionsIn procedures performed on the arteries of the lower limbs, a significantly higher dose was received by patients with TASC II C lesions. With regard to the number of stents implanted, the total DAP value was 50% higher for simultaneous three-stent implantation than for one or two stents

Retrophylogenomics place tarsiers on the evolutionary branch of anthropoids

One of the most disputed issues in primate evolution and thus of our own primate roots, is the phylogenetic position of the Southeast Asian tarsier. While much molecular data indicate a basal place in the primate tree shared with strepsirrhines (prosimian monophyly hypothesis), data also exist supporting either an earlier divergence in primates (tarsier-first hypothesis) or a close relationship with anthropoid primates (Haplorrhini hypothesis). The use of retroposon insertions embedded in the Tarsius genome afforded us the unique opportunity to directly test all three hypotheses via three pairwise genome alignments. From millions of retroposons, we found 104 perfect orthologous insertions in both tarsiers and anthropoids to the exclusion of strepsirrhines, providing conflict-free evidence for the Haplorrhini hypothesis, and none supporting either of the other two positions. Thus, tarsiers are clearly the sister group to anthropoids in the clade Haplorrhini