Read by QxMD icon Read


Matteo Allegretti, Beatrice Casini, Chiara Mandoj, Stefania Benini, Laurent Alberti, Mariangela Novello, Elisa Melucci, Laura Conti, Renato Covello, Edoardo Pescarmona, Giuseppe Maria Milano, Alessio Annovazzi, Vincenzo Anelli, Virginia Ferraresi, Roberto Biagini, Patrizio Giacomini
Background: Limited information is available on the applicative value of liquid biopsy (LB) in rare tumors, including Ewing's sarcoma (ES). The accepted precision diagnostics standards would greatly benefit from a non-invasive LB test monitoring pathognomonic gene rearrangements in the bloodstream. Methods: Tissue and blood samples were collected from six and four ES patients, respectively. Plasma was cleared by two successive rounds of centrifugation and stored frozen until RNA extraction by the QIAmp CNA kit...
2018: Therapeutic Advances in Medical Oncology
Toshiyuki Ishiba, Andreas-Claudius Hoffmann, Joshua Usher, Yahya Elshimali, Todd Sturdevant, Mai Dang, Yolanda Jaimes, Rama Tyagi, Ronald Gonzales, Mary Grino, Jacek K Pinski, Afsaneh Barzi, Luis E Raez, Wilfried E Eberhardt, Dirk Theegarten, Heinz-Josef Lenz, Hiroyuki Uetake, Peter V Danenberg, Kathleen Danenberg
BACKGROUND: Precision medicine and prediction of therapeutic response requires monitoring potential biomarkers before and after treatment. Liquid biopsies provide noninvasive prognostic markers such as circulating tumor DNA and RNA. Circulating tumor RNA (ctRNA) in blood is also used to identify mutations in genes of interest, but additionally, provides information about relative expression levels of important genes. In this study, we analyzed PD-L1 expression in ctRNA isolated from various cancer types...
June 7, 2018: Biochemical and Biophysical Research Communications
Yongqing Tong, Zhijun Zhao, Bei Liu, Anyu Bao, Hongyun Zheng, Jian Gu, Mary McGrath, Ying Xia, Bihua Tan, Chunhua Song, Yan Li
BACKGROUND: Detecting an ALK fusion gene in patients with non-small cell lung cancer (NSCLC) could provide evidence to guide individualized therapy. METHODS: The 5'/3' imbalance strategy for quantitative reverse transcription-PCR (RT-qPCR) was developed to detect ALK fusion genes in circulating tumor RNA (ctRNA) of NSCLC patients. RESULTS: This method was validated in patients with the ALK fusion gene confirmed by next generation sequencing (NGS)...
March 27, 2018: Journal of Experimental & Clinical Cancer Research: CR
I S Batth, A Mitra, S Manier, I M Ghobrial, D Menter, S Kopetz, S Li
Current trajectory of clinical care is heading in the direction of personalized medicine. In an ideal scenario, clinicians can obtain extensive diagnostic and prognostic information via minimally-invasive assays. Information available in the peripheral blood has the potential to bring us closer to this goal. In this review we highlight the contributions of circulating tumor cells and circulating tumor DNA and RNA (ctDNA/ctRNA) towards cancer therapeutic field. We discuss clinical relevance, summarize available and upcoming technologies, and hypothesize how future care could be impacted by a combined study...
March 1, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
América Rivera-Urbalejo, Ángeles Pérez-Oseguera, Ofelia E Carreón-Rodríguez, Miguel A Cevallos
The maintenance of large plasmid in a wide variety of alpha-proteobacteria depends on the repABC replication/segregation unit. The intergenic repB-repC region of these plasmids encodes a countertranscribed RNA (ctRNA) that modulates the transcription/translation rate of RepC, the initiator protein. The ctRNA acts as a strong incompatibility factor when expressed in trans. We followed a site directed mutagenesis approach to map those sequences of the ctRNA that are required for plasmid incompatibility and for plasmid replication control...
March 2015: Plasmid
Cynthia B Yip, Hao Ding, Michael F Hynes
The six plasmids of Rhizobium leguminosarum VF39SM comprise nearly 35% of the bacterium's genome and are all repABC replicons. The repABC operons of the three largest plasmids of VF39SM were found to have strong incompatibility determinants in the non-protein coding regions. However, in all three repABC operons, the intergenic region between repB and repC was the strongest incompatibility factor; this intergenic region has been shown, for most repABC plasmids, to encode a counter-transcribed RNA (ctRNA) that regulates RepC abundance and therefore also rate of initiation of replication...
March 2015: Plasmid
Gabriela Pérez-Segura, Angeles Pérez-Oseguera, Miguel A Cevallos
The repABC replication/partitioning systems are commonly found in alpha-proteobacteria plasmids and in secondary chromosomes. All of the elements required for their replication and stable maintenance are encoded within a single transcription unit: the repABC operon. The repC gene encodes an initiator protein, while RepA, RepB and centromere-like sequence (parS) direct plasmid segregation. Strains containing two or more repABC plasmids are a common feature in some alpha proteobacteria groups, indicating that the repABC plasmid family embraces several incompatibility groups...
January 2013: Plasmid
Ramón Cervantes-Rivera, Cristina Romero-López, Alfredo Berzal-Herranz, Miguel A Cevallos
Replication and segregation of the Rhizobium etli symbiotic plasmid (pRetCFN42d) depend on the presence of a repABC operon, which carries all the plasmid-encoded elements required for these functions. All repABC operons share three protein-encoding genes (repA, repB, and repC), an antisense RNA (ctRNA) coding gene, and at least one centromere-like region (parS). The products of repA and repB, in conjunction with the parS region, make up the segregation system, and they negatively regulate operon transcription...
July 2010: Journal of Bacteriology
Sam Woong Kim, In Sil Jeong, Eun Ju Jeong, Je Il Tak, John Hwa Lee, Seong Kug Eo, Ho Young Kang, Jeong Dong Bahk
The plasmid pJB01, a member of the pMV158 family isolated from Enterococcus faecium JC1, contains three open reading frames, copA, repB, and repC. Plasmids included in this family produce counter-transcribed RNA (ctRNA) that contributes to copy number control. The pJB01 ctRNA, a transcript which consists of 54 nucleotides (nts), is encoded on the opposite strand from the copA/repB intergenic region and partially overlaps an atypical ribosome binding site (ARBS) for repB. The ARBS is integrated by the two underlined conserved regions: 5'-TTTTTGTNNNNTAANNNNN NNNNATG-3', and the ctRNA is complementary only to the 5' conserved sequence 5'-TTTTTGT-3'...
July 31, 2008: Molecules and Cells
Shiao-Ming Chang, Tsong-Rong Yan
A cryptic plasmid pL2 was isolated from Lactococcus lactis subsp. lactis and its complete nucleotide sequence was determined (5,299 bp, GenBank accession No. DQ917780). Its replication mode was identified as a theta-type belonging to the pAM beta 1 family. Analysis of the nucleotide sequence revealed that pL2 contained a transfer origin, a replication origin, and five putative open reading frames (ORF1-5). ORF1 (386 amino acids) was homologous to replication protein RepB. The other open reading frames were cryptic...
October 2007: Biotechnology Letters
A R Raha, W Y Hooi, N S Mariana, S Radu, N R S Varma, K Yusoff
A small plasmid designated pAR141 was isolated from Lactococcus lactis subsp. lactis M14 and its complete 1,594 base pair nucleotide sequence was determined. Analysis of the sequence indicated that this plasmid does not carry any industrially important determinants besides the elements involved in plasmid replication and control. The transcriptional repressor CopG and replication initiation protein RepB appeared as a single operon. A small countertranscribed RNA (ctRNA) coding region was found between the copG and repB genes...
July 2006: Plasmid
Javier Izquierdo, Tatiana Venkova-Canova, Miguel A Ramírez-Romero, Juan Téllez-Sosa, Ismael Hernández-Lucas, Juan Sanjuan, Miguel A Cevallos
The widespread replicons of repABC and repC families from alpha-proteobacteria share high similarity in their replication initiator proteins (RepC). Here we describe the minimal region required for stable replication of a member of the repC family, the low copy-number plasmid pRmeGR4a from Sinorizobium meliloti GR4. This region contains only two genes: one encoding the initiator protein RepC (46.8 kDa) and other, an antisense RNA (67 nt). Mapping of transcriptional start sites and promoter regions of both genes showed that the antisense RNA is nested within the repC mRNA leader...
November 2005: Plasmid
Penka Petrova, Vanya Miteva, Jose Angel Ruiz-Masó, Gloria del Solar
The cryptic plasmid pt38 (2911 bp) of Streptococcus thermophilus ST2783, a strain isolated from Bulgarian yogurt, was subcloned and sequenced. Five ORFs (ORF1 to ORF5) were identified, although putative transcription initiation and termination signals, and Shine-Dalgarno sequence could only be localized for three of them (ORF1, ORF2, and ORF5). ORF2 would specify a 142-amino acid protein sharing a high degree of homology with plasmid-born low-molecular-weight heat stress proteins described in a variety of S...
November 2003: Plasmid
Tatiana Venkova-Canova, Miroslav Pátek, Jan Nesvera
The cryptic multicopy plasmid pGA1 (4,826 bp) from Corynebacterium glutamicum LP-6 belongs to the fifth group of rolling-circle-replicating plasmids. A determinant, which negatively controls pGA1 replication, was localized in the leader region of the rep gene coding for the initiator of plasmid replication. This region, when cloned into the compatible vector pEC6, was found to cause decrease of segregational stability of the pGA1 derivative pKG48. A promoter and a single transcriptional start site were found in the rep leader region in orientation opposite to the rep gene...
April 2003: Journal of Bacteriology
E. Doran, R. A. Cattolico
Light acts as a complex regulator of cellular development and gene expression in photoautotrophs. Although light signals are highly effective in controlling cellular division and chloroplast biogenesis in the toxic marine alga Heterosigma carterae, their influence on gene expression has not been well characterized. To address this need cultures of H. carterae synchronized by an alternating light-dark regime were sampled through 12 h of light and 12 h of dark to characterize cell division, chloroplast complement, and chloroplast RNA abundance...
October 1997: Plant Physiology
D Takamatsu, M Osaki, T Sekizaki
A small cryptic plasmid designated pSSU1 was isolated from Streptococcus suis serotype 2 strain DAT1. The complete sequence of pSSU1 was 4975 bp and contained six major open reading frames (ORFs). ORF1 and ORF2 encode for proteins highly homologous to CopG and RepB of the pMV158 family, respectively. ORF5 encodes for a protein highly homologous to Mob of pMV158. ORF4 encodes for a protein highly homologous to orf3 of pVA380-1 of S. ferus, but its function is unknown. There was no similarity between ORF3 and ORF6 and other protein sequences...
January 2000: Current Microbiology
K Duan, C Q Liu, S Supple, N W Dunn
pND324 belongs to a family of closely related theta-type plasmids from Lactococcus lactis. An antisense RNA, termed countertranscript (ctRNA), was identified which is complementary to the leader sequence of the mRNA that encodes RepB, a protein essential for plasmid replication. When the synthesis of ctRNA was abolished by site-directed mutagenesis within its promoter region, the mutant replicon showed a 1.8-fold increase in copy number. Similar ctRNA promoter sequences are readily identifiable in 12 other published lactococcal theta-type plasmids, suggesting that they all encode a similar ctRNA-mediated regulatory mechanism...
July 15, 1998: FEMS Microbiology Letters
J Pérez-Martín, M Espinosa
Plasmid pLS1 replicates in both Gram-positive and Gram-negative bacteria. One of the elements controlling plasmid replication is an antisense RNA (ctRNA II), transcribed from promoter PctII, which should be expressed in all the hosts where the plasmid replicates. We show here that expression from PctII and the presence of curved DNA regions located upstream of this promoter are related. DNA fragments containing these upstream regions exhibit anomalous electrophoretic mobility, and their presence increases in vivo and in vitro transcription, apparently with an independence of any activator protein...
August 5, 1994: Journal of Molecular Biology
J H Kwak, B Weisblum
The cop-rep region of plasmid pE194 contains two tandem structural genes, cop and repF, as well as the plus and minus origins of replication. The two structural genes comprise an operon whose expression is repressed by the binding of Cop protein to a 28-bp inverted complementary repeat sequence that overlaps the cop-repF promoter. From its position relative to the promoter and the experimentally determined footprint made by the Cop protein, the 28-bp inverted complementary repeat sequence is presumed to function as the cop operator...
August 1994: Journal of Bacteriology
M Blanc, J F Briat, J P Laulhere
The in vitro transcription of chloroplast DNA (ctDNA) is studied using a DNA-protein complex isolated from spinach plastids. The RNA products are compared to the in vivo synthesized ctRNA by competition for hybridization. At least 80% of the in vitro RNA sequences are present in vivo. Modifications of ionic strength or introduction of heparin in the reaction medium has an important effect on transcriptional activity of the complex. Furthermore, the length of the RNA chains increases ionic strength and amount of heparin...
October 27, 1981: Biochimica et Biophysica Acta
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"