Conformational properties of the ?35 region of the trp promoter in solution: comparison of the wild-type sequence with an AT transversion

1993 ◽  
Vol 22 (2) ◽  
Author(s):  
AndrewN. Lane ◽  
ChristopherJ. Bauer ◽  
ThomasA. Frenkiel ◽  
AndrewJ. Birchall
2001 ◽  
Vol 155 (4) ◽  
pp. 641-641 ◽  
Author(s):  
Wolfgang Eicheler ◽  
Michael Baumann

Blood ◽  
2009 ◽  
Vol 114 (22) ◽  
pp. 2634-2634
Author(s):  
Bill H Chang ◽  
Stephanie G Willis ◽  
Linda C. Stork ◽  
Stephen P Hunger ◽  
William L. Carroll ◽  
...  

Abstract Abstract 2634 Poster Board II-610 Background: Philadelphia chromosome positive Acute Lymphoblastic Leukemia (Ph+ALL) occurs in 2–5% of pediatric ALL and is associated with a poor prognosis. COG AALL0031 treated children with an intensified chemotherapy backbone plus imatinib. All subjects received imatinib at 340mg/m^2 daily. Exposure to imatinib progressively increased in each of five cohorts. Patients had a total imatinib exposure (before maintenance) of 42 days in cohort 1, 63 days in cohort 2, 84 days in cohort 3, 126 days in cohort 4, and 280 days in cohort 5. All groups received an additional 336 days of imatinib exposure in maintenance cycles 1 through 12 for approximately 2 years (with imatinb given on 21 day cycles for maintenance cycles 1 – 4, and a two-week on/two-week off schedule for maintenance cycles 5 - 12). Early results of this trial show encouraging outcome with a 3-year event free survival of 80±11% (95% CI 64 – 90%) for patients in cohort 5. In studies of adults with Ph+ALL treated with imatinib many patients recurred with imatinib resistant BCR-Abl mutations. To date, there are no data on the occurrence of BCR-Abl mutations in pediatric Ph+ALL. Patients and Methods: We performed nested PCR to identify BCR-Abl point mutations in nine samples obtained at bone marrow (BM) relapse from Ph+ALL subjects on AALL0031. Results: (Table 1) Three samples from cohort 1 that had no exposure to imatinib prior to relapse showed wild-type sequence. There were 5 of 6 samples that also showed wild-type sequence. One sample was from cohort 2 and 3 samples were from cohort 3. Each subject relapsed 1 to 2 years after diagnosis while receiving varying amounts of imatinib with continued intensive therapy. One subject recurred after stem cell transplant in first remission. One sample from cohort 4 recurred after the completion of chemotherapy and imatinib. One subject from cohort 5 carried the histidine 396 to proline (H396P) mutation. This mutation, which increases the imatinib IC50 by 10-fold, has been previously described to occur in adults with CML and Ph+ALL treated with imatinib. The subject from cohort 5 recurred 1 year after diagnosis on therapy with imatinib. Conclusions: Only 1 resistant mutation in BCR-Abl has been identified among nine children with Ph+ALL treated on AALL0031. Therefore, unlike results in the adults, resistant mutations do not appear to drive early recurrence in Ph+ALL. Further studies will be needed to identify whether BCR-Abl mutations are identified in subjects who develop a late relapse after treatment with AALL0031 or subsequent treatment studies. Disclosures: Druker: OHSU patent #843 - Mutate ABL Kinase Domains: Patents & Royalties; MolecularMD: Equity Ownership; Roche: Consultancy; Cylene Pharmaceuticals: Consultancy; Calistoga Pharmaceuticals: Consultancy; Avalon Pharmaceuticals: Consultancy; Ambit Biosciences: Consultancy; Millipore via Dana-Farber Cancer Institute: Patents & Royalties; Novartis, ARIAD, Bristol-Myers Squibb: Research Funding. Schultz:novartis: Membership on an entity's Board of Directors or advisory committees.


2004 ◽  
Vol 50 (4) ◽  
pp. 694-701 ◽  
Author(s):  
Ourania Nasis ◽  
Shanel Thompson ◽  
Tom Hong ◽  
Margaret Sherwood ◽  
Shawn Radcliffe ◽  
...  

Abstract Background: Cell-free fetal DNA circulating in maternal blood has potential as a safer alternative to invasive methods of prenatal testing for paternally inherited genetic alterations, such as cystic fibrosis (CF) mutations. Methods: We used allele-specific PCR to detect mutated CF D1152H DNA in the presence of an excess of the corresponding wild-type sequence. Pfx buffer (Invitrogen) containing replication accessory proteins and Taq polymerase with no proofreading activity was combined with TaqMaster PCR Enhancer (Eppendorf) to suppress nonspecific amplification of the wild-type allele. The procedure was tested on DNA isolated from plasma drawn from 11 pregnant women (gestational age, 11–19.2 weeks), with mutation confirmation by chorionic villus sampling. Results: The method detected 5 copies of the CF D1152H mutant allele in the presence of up to ∼100 000 copies of wild-type allele without interference from the wild-type sequence. The D1152H mutation was correctly identified in one positive sample; the only false-positive result was seen in a mishandled sample. Conclusions: This procedure allows for reliable detection of the paternally inherited D1152H mutation and has potential application for detection of other mutations, which may help reduce the need for invasive testing.


2002 ◽  
Vol 168 (3) ◽  
pp. 1338-1347 ◽  
Author(s):  
Thomas K. Hoffmann ◽  
Douglas J. Loftus ◽  
Koji Nakano ◽  
Markus J. Maeurer ◽  
Kazuaki Chikamatsu ◽  
...  

2021 ◽  
Author(s):  
Luca Sesta ◽  
Guido Uguzzoni ◽  
Jorge Ferndadez-de-Cossio-Diaz ◽  
Andrea Pagnani

We present Annealed Mutational approximated landscape (AMaLa), a new method to infer fitness landscapes from Directed Evolution experiment sequencing data. Directed Evolution experiments typically start from a single wild-type sequence, which undergoes Darwinian in vitro evolution acted via multiple rounds of mutation and selection with respect to a target phenotype. In the last years, Directed Evolution is emerging as a powerful instrument to probe fitness landscapes under controlled experimental condition and, thanks to the use of high-throughput sequencing of the different rounds, as a relevant testing ground to develop accurate statistical models and inference algorithms. Fitness landscape modeling strategies, either use as input data the enrichment of variants abundances and hence require observing the same variants at different rounds, or they simply assume that the variants at the last sequenced round are the results of a sampling process at equilibrium. AMaLa aims at leveraging effectively the information encoded in the time evolution of all sequenced rounds. To do so, on the one hand we assume statistical sampling independence between sequenced rounds, and on the other we gauge all possible trajectories in sequence space with a time-dependent statistical weight consisting of two contributions: (i) a statistical energy term accounting for the selection process, (ii) a simple generalized Jukes-Cantor model to describe the purely mutational step. This simple scheme allows us to accurately describe the Directed Evolution dynamics in a concrete experimental setup and to infer a fitness landscape that reproduces correctly the measures of the phenotype under selection (e.g. antibiotic drug resistance), notably outperforming widely used inference strategies. We assess the reliability of AMaLa by showing how the inferred statistical model could be used to predict relevant structural properties of the wild-type sequence, and to reproduce the mutational effects of large scale functional screening not used to train the model.


2010 ◽  
Vol 55 (2) ◽  
pp. 762-766 ◽  
Author(s):  
Noboru Nakata ◽  
Masanori Kai ◽  
Masahiko Makino

ABSTRACTDiaminodiphenylsulfone (dapsone) has long been used as a first-line drug worldwide for the treatment of leprosy. Diagnosis for dapsone resistance ofMycobacterium lepraeby DNA tests would be of great clinical value, but the relationship between the nucleotide substitutions and susceptibility to dapsone must be clarified before use. In this study, we constructed recombinant strains of cultivableMycobacterium smegmatiscarrying theM. leprae folP1gene with or without a point mutation, disrupting their ownfolPgene on the chromosome. Dapsone susceptibilities of the recombinant bacteria were measured to examine influence of the mutations. Dapsone MICs for most of the strains with mutations at codon 53 or 55 ofM. leprae folP1were 2 to 16 times as high as the MIC for the strain with the wild-typefolP1sequence, but mutations that changed Thr to Ser at codon 53 showed somewhat lower MIC values than the wild-type sequence. Strains with mutations at codon 48 or 54 showed levels of susceptibility to dapsone comparable to the susceptibility of the strain with the wild-type sequence. This study confirmed that point mutations at codon 53 or 55 of theM. leprae folP1gene result in dapsone resistance.


Toxicon ◽  
2014 ◽  
Vol 88 ◽  
pp. 11-20 ◽  
Author(s):  
Morena Simonato ◽  
Laura Morbiato ◽  
Veronica Zorzi ◽  
Paola Caccin ◽  
Julián Fernández ◽  
...  

Blood ◽  
2009 ◽  
Vol 114 (22) ◽  
pp. 474-474
Author(s):  
Alessandro Zarpellon ◽  
Antonella Zampolli ◽  
Loredana Mendolicchio ◽  
James R Roberts ◽  
Zaverio M. Ruggeri

Abstract Abstract 474 Thrombin (Th) is a pleiotropic protease with prothrombotic, anticoagulant and proinflammatory functions. We have characterized the mechanisms through which the binding of Th to glycoprotein (GP) Ibα, a component of the GPIb-IX-V complex on platelets, may regulate these activities. First, we tested the hypothesis, based on crystallographic evidence, that both exosite I and II of α-Th are required for binding to GPIbα. For these studies, in addition to α-Th we used meizothrombin (M-Th), a precursor with functional exosite I but without exosite II, and γ-Th, a degradation product of α-Th with intact exosite II but structurally deranged exosite I. For experiments with purified components, we used a fully sulphated recombinant fragment of human GPIbα (residues -2-290; herein designated GPIbαN) with wild-type sequence (WT) or with the single mutations Y279F (prevents sulphation) or D277N. These residues are predicted to influence predominantly or exclusively the interaction with thrombin exosite I or II, respectively. In experiments measuring the formation of a stable complex in solution, GPIbαN-WT bound α-Th and γ-Th with similar characteristics, while there was no complex formed with M-Th under the same conditions. The mutation Y279F had only a modest effect, while the mutation D277N abolished formation of all complexes, indicating that exosite II is predominantly involved in binding a GPIbα fragment in solution. To obtain more biologically relevant findings, we generated BL6 mice with platelets expressing human GPIbα replacing the corresponding murine component in the GPIb-IX-V complex, either with wild-type sequence (h-WT strain) or with the mutations Y279F (h-279F strain) or D277N (h-277N strain). All had comparable surface expression of GPIbα (∼7,000 molecules/platelet). Platelets from h-WT mice bound α-Th and γ-Th in a saturable manner and with a similar apparent kd (∼50 nM) as human platelets. Because we could not label thrombin directly without affecting binding to platelet GPIbα, we used an indirect approach with biotin-PPACK inserted into the active site of α-Th, γ-Th or M-Th detected by fluorescent streptavidin-PE. With this method, there was no demonstrable M-Th binding to platelet GPIbα. Platelets from h-279F mice showed a markedly decreased binding of α-Th (∼16% of that seen with h-WT platelets and kd of 450 nM) and no binding of γ-Th. Neither α-Th or γ-Th bound to h-277N platelets. Altogether, these results show that α-Th binding to platelet GPIbα concurrently involves exosite I and II, and suggest that the deranged exosite I of γ-Th can contribute to the interaction but is not fully functional, as shown by the greater effect of the mutation Y279F on the binding with γ-Th than α-Th. Functionally, h-279F and h-277N platelets showed a significantly decreased response to stimulation by α-Th and decreased aggregation as compared to h-WT platelets, indicating that GPIbα contributes to this prothrombotic function of α-Th. In contrast, h-WT but not h-279F or h-277N platelets inhibited fibrinogen clotting, likely a consequence of GPIbα competing with fibrinogen for binding to α-Th exosite I, indicating that α-Th binding to GPIbα can also have anticoagulant consequences. Thus, we have shown that GPIbα is a relevant modulator of α-Th activity with potentially opposite effects on thrombogenesis possibly depending on the type of vascular lesion involved. Effects on inflammation remain to be explored. Disclosures: No relevant conflicts of interest to declare.


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