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Containers and aggregates, mutators and isolates for reactive programming

Aleksandar Prokopec, Philipp Haller, Martin Odersky
2014 Proceedings of the Fifth Anuual Scala Workshop on - SCALA '14  
This paper presents a generic framework for reactive programming that extends first-class reactive values with the concept of lazy reactive containers, backed by several concrete implementations.  ...  Our framework addresses concurrency by introducing reactive isolates. We show examples that our programming model is efficient and convenient to use.  ...  We compared Reactive Collections against RxJava and Scala.React implementations on an Intel i5-2500 3.30 GHz Acknowledgements We would like to thank Erik Meijer for the discussions we had, his useful  ... 
doi:10.1145/2637647.2637656 dblp:conf/ecoop/ProkopecHO14 fatcat:ai2dxqzoynbjnfjoo5p727urd4

DnaK/DnaJ chaperone system reactivates endogenous E coli thermostable FBP aldolase in vivo and in vitro; the effect is enhanced by GroE heat shock proteins

Sabina Kedzierska, Grzegorz Jezierski, Alina Taylor
2001 Cell stress & chaperones (Print)  
The dnaK756 and dnaJ259 mutations had a negative effect on the reactivation of thermally inactivated Fda.  ...  GroEL/GroES alone were inefficient in the resolubilization or reactivation of the heat-aggregated Fda.  ...  Ż ylicz, and P. Lund for E coli strains and T. Kaczorowski for M13/T7 phage. We thank K. Liberek and M. Ż ylicz for generous gifts of purified DnaK, DnaJ, GroES, and GroEL proteins.  ... 
doi:10.1379/1466-1268(2001)006<0029:ddcsre>;2 pmid:11525240 pmcid:PMC434380 fatcat:msm6d7fvtrbzbi3cmmtawowixm

An integrated view of p53 dynamics, function, and reactivation

Özlem Demir, Emilia P Barros, Tavina L Offutt, Mia Rosenfeld, Rommie E Amaro
2021 Current Opinion in Structural Biology  
Expression level alterations and mutational frequency implicates p53 in most human cancers.  ...  In this review, we show how both computational and experimental methods have been used to provide an integrated view of p53 dynamics, function, and reactivation potential.  ...  The authors thank Chloe (Xiaoyi) Ma at the University of Toronto for the figure illustrations.  ... 
doi:10.1016/ pmid:33401096 pmcid:PMC8985518 fatcat:p7j7yw4glrhwvmten5rlakbqgm

Antigen-Driven Oligoclonal Expansion of Tumor-Infiltrating B Cells in Infiltrating Ductal Carcinoma of the Breast

J. A. Coronella, C. Spier, M. Welch, K. T. Trevor, A. T. Stopeck, H. Villar, E. M. Hersh
2002 Journal of Immunology  
Clones 1-35 and 2-26 contained no V gene mutations in comparison with germline. Clones 2-38 and 1-18 shared a single common mutation from germline. B and C, Patient 2, clonal groups 3, 5.  ...  TIL-B IgG H chains contained somatic mutations that clustered in the Ag-contacting CDRs, as is observed in affinity-matured Abs (reviewed in Refs. 30 and 43) , and as was also seen in tumor-draining lymph  ... 
doi:10.4049/jimmunol.169.4.1829 pmid:12165506 fatcat:b52feks3rzd6hjpwatdiverlge

The Genetics of Development in Dictyostelium Discoideum

S S Godfrey, M Sussman
1982 Annual Review of Genetics  
For example, a strain isolated as Agg-proved to carry mutant alleles defining the loci devA and devB (98).  ...  Mutations Affecting Aggregative Performance Mutations affecting call aggregation constitute the largest group among unselected survivors of mutagenesis (58) .  ... 
doi:10.1146/ pmid:6760801 fatcat:4vbql4fdybexli6svreqij6bxe

Analysis of Functional Domains of the Enterococcus faecalis Pheromone-Induced Surface Protein Aggregation Substance

C. M. Waters, G. M. Dunny
2001 Journal of Bacteriology  
Pheromone-inducible aggregation substance (AS) proteins of Enterococcus faecalis are essential for highefficiency conjugation of the sex pheromone plasmids and also serve as virulence factors during host  ...  Analysis of these insertions revealed a domain necessary for donor-recipient aggregation that extends further into the amino terminus of the protein than previously reported.  ...  We thank Pat Cleary for reading the manuscript and Pat Schlievert, Helmut Hirt, and John McCormick for providing antibodies, other reagents, and helpful discussion.  ... 
doi:10.1128/jb.183.19.5659-5667.2001 pmid:11544229 pmcid:PMC95458 fatcat:45k23z6obzha5k46xf6ddj3gwi

Reactivation of FMR1 by CRISPR/Cas9-Mediated Deletion of the Expanded CGG-Repeat of the Fragile X Chromosome

Nina Xie, He Gong, Joshua A. Suhl, Pankaj Chopra, Tao Wang, Stephen T. Warren, Barbara Bardoni
2016 PLoS ONE  
We observed transcriptional reactivation in approximately 67% of the CRISPR cut hybrid colonies and in 20% of isolated human FXS iPSC colonies.  ...  The reactivated cells produced FMRP and exhibited a decline in DNA methylation at the FMR1 locus.  ...  We thank Oskar Laur for generating CRISPR plasmid constructs and Robert B. Isett for methylation profiling array, whose work was supported by the Emory Integrated Genomics Core (EIGC).  ... 
doi:10.1371/journal.pone.0165499 pmid:27768763 pmcid:PMC5074572 fatcat:egwjazcucralvn6cn5dko3wvgy

Conserved Distal Loop Residues in the Hsp104 and ClpB Middle Domain Contact Nucleotide-binding Domain 2 and Enable Hsp70-dependent Protein Disaggregation

Morgan E. DeSantis, Elizabeth A. Sweeny, David Snead, Eunice H. Leung, Michelle S. Go, Kushol Gupta, Petra Wendler, James Shorter
2013 Journal of Biological Chemistry  
Conclusion: Distal loop does not project out into solution and Hsp104 and ClpB are tuned differently for Hsp70 collaboration.  ...  How Hsp104 and ClpB coordinate polypeptide handover with Hsp70 to dissolve disordered protein aggregates is unknown.  ...  Isolated MD Does Not Interact with Hsp70 or Inhibit Disaggregation in Trans-Another possibility for how specific distal loop mutations impair Hsp70 collaboration is that mutation in this region disrupts  ... 
doi:10.1074/jbc.m113.520759 pmid:24280225 pmcid:PMC3887210 fatcat:b2pniowdgjcf7bf3j5ok5lhv54

Single amino acid substitutions of alpha 1-antitrypsin that confer enhancement in thermal stability

K S Kwon, J Kim, H S Shin, M H Yu
1994 Journal of Biological Chemistry  
Characterization of various single amino acid substitutions at position 51 suggests that volume and flexibility of hydrophobic side chain at the site are critical factors for enhancing the stability of  ...  The mutation site is particularly interesting in that some genetic variants mapped at adjacent positions were shown previously to cause aggregation of the polypeptides, while the Phe51-->Cys mutation decreased  ...  Kim for helpful discussion and comments. We also thank Dr. F. William Studier for providing PET-8c plasmid and bacterial strains, Dr. David P.  ... 
pmid:8144550 fatcat:tdukwgd63ncorjjun6ean3ehuq

N-Terminal Domain of Yeast Hsp104 Chaperone Is Dispensable for Thermotolerance and Prion Propagation but Necessary for Curing Prions by Hsp104 Overexpression

G.-C. Hung
2006 Genetics  
Inactivating Hsp104 cures cells of [PSI 1 ] and other amyloidlike yeast prions. Overexpressing Hsp104 also eliminates [PSI 1 ], presumably by completely resolubilizing prion aggregates.  ...  Hsp104D147, engineered to lack the NTD, supported [PSI 1 ] and functioned normally in thermotolerance and protein disaggregation.  ...  We thank Yury Chernoff (Georgia Institute of Technology) for plasmids and John Glover (University of Toronto) for plasmids and Hsp104 antibody.  ... 
doi:10.1534/genetics.106.056820 pmid:16582428 pmcid:PMC1526498 fatcat:kb7suvvz2vaonhigwhplxubykq

Dynamic Diagnosis of Familial Prion Diseases Supports the β2-α2 Loop as a Universal Interference Target

Massimiliano Meli, Maria Gasset, Giorgio Colombo, Annalisa Pastore
2011 PLoS ONE  
However they variably have impact on the thermodynamic stability and metabolism of PrP C and on the properties of PrP Sc aggregates.  ...  of the patches for intermolecular recognition, as the disappearance of those for conversion inhibitors and the emergence of an interaction site at the b2-a2 loop region.  ...  [14] , whereby the structural properties of the isolate a2-a3 region, which recapitulates the amyloidogenic features of the whole protein and contains the mutations herein studied, have been elucidated  ... 
doi:10.1371/journal.pone.0019093 pmid:21552571 pmcid:PMC3084259 fatcat:c2vtsbki5ncvbejqvn4flf2jeu

Mutation of Mycobacterium tuberculosis and Implications for Using Whole-Genome Sequencing for Investigating Recent Tuberculosis Transmission

Kristin N. Nelson, Sarah Talarico, Shameer Poonja, Clinton J. McDaniel, Martin Cilnis, Alicia H. Chang, Kala Raz, Wendy S. Noboa, Lauren Cowan, Tambi Shaw, James Posey, Benjamin J. Silk
2022 Frontiers in Public Health  
Tuberculosis (TB) control programs use whole-genome sequencing (WGS) of Mycobacterium tuberculosis (Mtb) for detecting and investigating TB case clusters.  ...  However, the variable and sometimes long duration of latent infection, combined with uncertainty in the Mtb mutation rate during latency, can complicate interpretation of WGS results.  ...  to disease, allowing the TB program to conclude a recent TB case is attributable to reactivation of latent infection.  ... 
doi:10.3389/fpubh.2021.790544 pmid:35096744 pmcid:PMC8793027 fatcat:gfyulphumvb6vggo7dme2ztbha

Overexpression of mutated Cu,Zn-SOD in neuroblastoma cells results in cytoskeletal change

Rina Takamiya, Motoko Takahashi, Yong Seek Park, Yoshie Tawara, Noriko Fujiwara, Yasuhide Miyamoto, Jianguo Gu, Keiichiro Suzuki, Naoyuki Taniguchi
2005 American Journal of Physiology - Cell Physiology  
Yoshitaka Ikeda for technical support and critical discussion.  ...  of the Ministry of Education, Science, Culture, Sports, and Technology, and a Grant-in-Aid for Scientific Research (C) No. 15500237.  ...  Cells were incubated in DMEM containing 10% FBS for 1 day and then incubated with or without serum for an additional 48 h.  ... 
doi:10.1152/ajpcell.00014.2004 pmid:15456693 fatcat:wrellzbdxjadrfhf7b54h3jh3m

Role of chaperones and ATP synthase in DNA gyrase reactivation in Escherichia coli stationary-phase cells after nutrient addition

Alejandra Gutiérrez-Estrada, Jesús Ramírez-Santos, María del Gómez-Eichelmann
2014 SpringerPlus  
Escherichia coli stationary-phase (SP) cells contain relaxed DNA molecules and recover DNA supercoiling once nutrients become available.  ...  In these cells, the reactivation of DNA gyrase, which is a DNA topoisomerase type IIA enzyme, is responsible for the recovery of DNA supercoiling.  ...  We also thank L Camarena and C Domenzain for assistance in preparing the Figures and I Pérez-Montfort for editorial assistance.  ... 
doi:10.1186/2193-1801-3-656 pmid:25485196 pmcid:PMC4230433 fatcat:xs2ja5amlrhtxjlclig6ts7vpy

Molecular Evolution of the Thermosensitive PAb1620 Epitope of Human p53 by DNA Shuffling

Dimitris P. Xirodimas, David P. Lane
1999 Journal of Biological Chemistry  
For this purpose, we applied a recently developed random mutagenesis technique called DNA shuffling and screened for p53 variants that could retain reactivity to the native conformation-specific anti-p53  ...  Mutational analysis identified 20 amino acid residues in the core domain of p53 (amino acids 101-120) responsible for the thermostable phenotype.  ...  Scott, and C. Stephen for helpful discussions and critical reading of the manuscript. We also thank A. Sparks for providing anti-p53 antibodies.  ... 
doi:10.1074/jbc.274.39.28042 pmid:10488156 fatcat:m7hb3wocszcxljpj5o7qj45z3m
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