Plasmid vector pSP189
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ABSTRACT:
PROVIDER: PRJNA302825 | ENA |
REPOSITORIES: ENA
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Project description:As vector-borne pathogens transit between the arthropod and vertebrate, adaptation is key for survival as each host varies and initiates unique defense mechanisms. An environmental signal that relapsing fever (RF) and Lyme causing spirochetes detect is the change of temperature between vector and mammal, yet incomplete genomes have hindered progress in understanding the genetic constituents expressed during tick colonization. We conducted a combined transcriptional and genomic sequence analysis to further assemble the ~150 kb linear plasmid (lp150) of Borrelia turicatae, a causative agent of RF borreliosis. Contiguous sequences (contigs), which were originally generated by Sanger sequencing, contained open reading frames (ORFs) identified to be up-regulated by the spirochetes when grown under tick-like conditions compared to the mammal. To aid in assembling the contigs, a PacBio RS I Single Molecule Real-Time DNA sequencing approach was used, given extended nucleotide reads over several thousand base pairs. A 36 kb locus was identified toward the 3‘ end of lp150, and expression of the ORFs was verified in the tick and mammal. We report the most complete version of lp150, and this study indicates that the plasmid likely facilitates vector colonization and establishing early mammalian infection
2017-02-09 | GSE69041 | GEO
Project description:To understand the response of host cells to rAAV vector production via plasmid transfection, samples were collected throughout the course of three 50 L production batches and analyzed by bulk RNA sequencing of polyadenylated transcripts (RNA-seq). Gene ontology analysis determined that upregulated pathways included inflammatory and antiviral responses. Systematic analyses of the cellular transcriptional response to rAAV production indicates that these host cells are not passively supporting vector manufacture, and therefore may illuminate genes and pathways that influence rAAV production, thereby enabling the rational design of next-generation manufacturing platforms to support safe, effective, and affordable AAV-based gene therapies.
2023-02-06 | GSE224405 | GEO
Project description:Plasmid pKJK172 Genome sequencing and assembly
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Project description:We analysed gene expression profiles in dental follicle cells after 48 hours of overexpression with the transcription factor DLX3. Total RNAs were isolated from dental follicle cells after 48 hours of transfection with a DLX3 expressions plasmid and for control with an empty vector.
2011-06-07 | E-GEOD-29753 | biostudies-arrayexpress
Project description:The debilitating disease kala-azar or visceral leishmaniasis (VL) is caused by the kinetoplastid protozoan parasite Leishmania donovani. The parasite is transmitted by the hematophagous sandfly vector of the genus Phlebotomus in the old world and Lutzomyia in the new world. The predominant Phlebotomine species associated with transmission of kala-azar are Phlebotomus papatasi and Phlebotomus argentipes. The infected female sandfly transmits the parasite when it takes a blood meal. Understanding the molecular interaction of the sand fly-Leishmania during the development of parasite within the gut of the sandfly is crucial to understanding parasite life cycle. The complete genome sequences of sandfly vectors (Phlebotomus and Lutzomyia) are currently not available and sequencing efforts are underway. Non-availability of genome sequence can hamper identification of proteins in the sandfly vector. In the present study we have carried out proteogenomic analysis of unsequenced sandfly vector P. paptasi cell line using high-resolution mass spectrometry and comparative homology-based searches using related dipteran protein data (mosquitoes and fruit fly). This study resulted in identification of 1,312 proteins from P. papatasi based on homology. Our study demonstrates the power of proteogenomic approaches in mapping the proteomes of unsequenced organisms.
2015-08-31 | PXD002115 | Pride
Project description:We generated a collection of 13 plasmids, with each plasmid containing a variant of a CRISPR protospacer targeted by spacer 8 of the E. coli CRISPR-I array. We transformed the plasmids as a pool into delta cas3 E. coli cells expressing all other cas genes constitutively. We then transformed these cells with either an empty vector or a plasmid expressing the Cas3 nuclease. DNA surrounding the protospacers was PCR-amplified and sequenced.
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Project description:We report the genome-wide analysis from chromatin immunoprecipitated DNA (ChIP-sequencing) at very high resolution of the DNA binding pattern of ParBF (SopB) either on the full length plasmid F or on E. coli chromosome carrying the parSF centromere sequence. We also varied the intracellular ParBF concentration to discriminate between the several proposed mechanism of partition complexes assembly.
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