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Functional clones and expressibility of partition functions

Andrei Bulatov, Leslie Ann Goldberg, Mark Jerrum, David Richerby, Stanislav Živný
2017 Theoretical Computer Science  
We identify a sublattice of interesting functional clones and investigate the relationships and properties of the functional clones in this sublattice.  ...  We study functional clones, which are sets of non-negative pseudo-Boolean functions (functions {0,1}^k→R_≥ 0) closed under (essentially) multiplication, summation and limits.  ...  In their weighted form, counting CSPs are general enough to express many partition functions occurring in statistical physics.  ... 
doi:10.1016/j.tcs.2017.05.001 fatcat:pllce63mvva4zpkjp4j3ojh2xu

Structural and genetic analyses of a par locus that regulates plasmid partition in Bacillus subtilis

S Chang, S Y Chang, O Gray
1987 Journal of Bacteriology  
The cloned par fragment regulated the partition of several different Bacillus replicons, and it only functioned in cis; it did not contain the replication function nor elevate the plasmid copy number in  ...  Using a partition-deficient plasmid vector, we randomly cloned DNA fragments of plasmid pLS11 and identified the locus that regulates plasmid partition (par) by cis complementation in Bacillus subtilis  ...  Ho for construction of some of the plasmids used in these studies, and S. D. Ehrlich and R. P.  ... 
doi:10.1128/jb.169.9.3952-3962.1987 pmid:3040669 pmcid:PMC213693 fatcat:2njdwdkb3baknd34ual275f5wm

Objective Clustering of Proteins Based on Subcellular Location Patterns

Xiang Chen, Robert F. Murphy
2005 Journal of Biomedicine and Biotechnology  
We describe an automated method that selects the best feature set to describe images for a given collection of proteins and constructs an effective partitioning of the proteins by location.  ...  The goal of proteomics is the complete characterization of all proteins. Efforts to characterize subcellular location have been limited to assigning proteins to general categories of organelles.  ...  ACKNOWLEDGMENTS We thank Jonathan Jarvik, Peter Berget, and all of our colleagues in the CD-tagging project for helpful discussions and providing images of tagged cell lines.  ... 
doi:10.1155/jbb.2005.87 pmid:16046813 pmcid:PMC1184054 fatcat:rjnnds4aevesppdxs4qhx2ilam

Sharing Duties in the Family

C.-K. J. Shen
2001 Genome Research  
Also, in the DDC model, partitioning of the functions and sites of expression among the paralogs are associated with mutations in the regulatory as well as in the coding regions.  ...  Did partitioning of the sites of expression occur first, or the partitioning of the function? Were critical mutations in the regulatory regions fixed prior to those in the coding regions?  ... 
doi:10.1101/gr.211701 pmid:11591636 fatcat:zzu23vsp3ravbgvmpbvyggb6me

Rapid, continuous purification of proteins in a microfluidic device using genetically-engineered partition tags

Robert J. Meagher, Yooli K. Light, Anup K. Singh
2008 Lab on a Chip  
Figure S1 : Genetic constructs used for creation of GFP or GST modified with partitioning tags.  ...  Figure S2 : S2 (A) spreading of different analytes as a function of position downstream, at a total flow rate of 7 µL/min.  ... 
doi:10.1039/b716462a pmid:18369506 fatcat:a5n6znt3rveerol6w55bivvayi

Molecular characterization and functional analysis of sucrose-cleaving enzymes in carrot (Daucus carota L.)

Arnd Sturm
1996 Journal of Experimental Botany  
The source/sink balance of these plants was manipulated and only the expression of these two genes was markedly altered, indicating their importance in sucrose partitioning.  ...  The expression patterns of each gene were different and were organ-and development-specific.  ...  Only the expression of isoenzyme II of vacuolar invertase and sucrose synthase markedly changed, supporting their involvement in sucrose partitioning.  ... 
doi:10.1093/jxb/47.special_issue.1187 pmid:21245247 fatcat:zmgh4xog5fhmbnb7kauidw637q

Expression of BamHI-A Rightward Transcripts in Epstein-Barr Virus-Associated Gastric Cancers

Bo-Gun Jang, Eun Ji Jung, Woo Ho Kim
2011 Cancer research and treatment : official journal of Korean Cancer Association  
Sequence reaction was carried out for the EBVassociated clones. Reverse transcription-polymerase chain reaction was performed after cells were partitioned into nuclear and cytoplasmic fractions.  ...  Results Using bioinformatic tools, we selected 13 EBV-associated clones from cDNA libraries of SNU719.  ...  Clones 1, 2, 4, 6, 10, 11 and 13 showed two fragments of 1.2 kb and 0.4 kb because of their EcoR I recognition sites. Sequence alignment of three groups of clones to the RPMS1 cDNA.  ... 
doi:10.4143/crt.2011.43.4.250 pmid:22247711 pmcid:PMC3253868 fatcat:4kty2jyrvzfujehmmfl3zihqqu

Fine-structure analysis of the P7 plasmid partition site

F Hayes, M A Davis, S J Austin
1993 Journal of Bacteriology  
Although the P7 site shares 55% sequence identity with its counterpart in bacteriophage P1, functional interactions between the partition sites and the Par proteins of the two plasmids were entirely species  ...  No evidence was found for the existence of a functional P7 analog of the P1 parS core, a small subregion of the P1 site that, in isolation, acts as an enfeebled partition site with modified incompatibility  ...  The P1 and P7 partition sites are therefore plasmid specific, both in their abilities to support the active partition process and in the expression of partition-mediated incompatibility towards P1 and  ... 
doi:10.1128/jb.175.11.3443-3451.1993 pmid:8501048 pmcid:PMC204743 fatcat:zyl24onl2jfjjfizooidh4cofm

Cortical aPKC kinase activity distinguishes neural stem cells from progenitor cells by ensuring asymmetric segregation of Numb

Jill M. Haenfler, Chaoyuan Kuang, Cheng-Yu Lee
2012 Developmental Biology  
In the absence of lgl function, elevated cortical aPKC kinase activity perturbs unequal partitioning of the fate determinants including Numb and induces supernumerary neuroblasts in larval brains.  ...  To investigate how increased cortical aPKC function induces formation of excess neuroblasts, we analyzed the fate of cells in neuroblast lineage clones in lgl mutant brains.  ...  We thank the anonymous reviewer and members of the Lee lab for reading the manuscript and providing critical comments.  ... 
doi:10.1016/j.ydbio.2012.02.027 pmid:22394487 pmcid:PMC3322243 fatcat:4jlziabedjgsta4lzgwxzbwa44

DNA microarrays for functional plant genomics [chapter]

Asaph Aharoni, Oscar Vorst
2001 Functional Genomics  
To date, the main applications of microarrays are in comprehensive, simultaneous gene expression monitoring and in DNA variation analyses for the identification and genotyping of mutations and polymorphisms  ...  arising from complementary functional genomics tools for 'profiling' the genome, proteome, metabolome and phenome.  ...  Acknowledgements We would like to thank Robert Hall and Ruud de Maagd for critical reading of the manuscript.  ... 
doi:10.1007/978-94-010-0448-0_7 fatcat:avk4ml3wpbbhlduz66k4layf2i

Convenient broad-host-range unstable vectors for studying stabilization cassettes in diverse bacteria

Aneta A. Bartosik, Krzysztof Glabski, Anna Kulinska, Ewa Lewicka, Jolanta Godziszewska, Aleksandra Markowska, Grazyna Jagura-Burdzy
2016 BMC Microbiology  
The vectors are suitable for testing of various stabilization functions, including plasmid and chromosomal partitioning cassettes encoding ParB homologues capable of spreading on DNA.  ...  The efficiency of stabilization may vary depending on the plasmid host so a thorough analysis of stabilization functions is required before use.  ...  III/Cloning the partitioning cassettes into the test vectors Chromosomal parA-parB operon of P. aeruginosa had been cloned earlier under the control of tacp and lacI q in pKLB3 [29] .  ... 
doi:10.1186/s12866-016-0674-y pmid:27044351 pmcid:PMC4820964 fatcat:bnk7akz2gfa4top4v6pzzytmzu

Page 696 of The Plant Journal Vol. 20, Issue 6 [page]

1999 The Plant Journal  
However, the level of expression differed significantly, with the highest level of expression found in stems, followed by medium levels in inflorescence and root tissues.  ...  In plants, regulated nucleo-cytoplasmic partitioning has also been described for a number of proteins, e.g. COP1, PHYB and GBFs (Nagatani, 1998; Yamamoto and Deng, 1999).  ... 

Global optimization based on a statistical model and simplicial partitioning

A. Žilinskas, J. Žilinskas
2002 Computers and Mathematics with Applications  
The convergence of an algorithm based on the constructed statistical model and simplicial partitioning is proved. Several versions of the algorithm are implemented and investigated.  ...  An approach to the construction of global optimization algorithms is developed using the proposed statistical model.  ...  However, many versions of partitioning may be applied instead of cloning.  ... 
doi:10.1016/s0898-1221(02)00206-7 fatcat:kel6puf7mjf4rnbwe6ajagoule

A detailed transcript map of the human chromosome 12p12.3 tumor suppressor locus: the usefulness of an integrative approach

Alexandre Montpetit, Nathalie Trudel, Daniel Sinnett
2001 Nature Genetics  
Partitioning the genes into functional classes revealed the activation of multiple pathways (including those for glucose metabolism, biosynthesis, transcriptional regulation, protein degradation and stress  ...  Analysis of the genomic sequence of BAC clones from this region revealed 34 additional Unigene clusters and 43 individual expressed sequence tags.  ...  Partitioning the genes into functional classes revealed the activation of multiple pathways (including those for glucose metabolism, biosynthesis, transcriptional regulation, protein degradation and stress  ... 
doi:10.1038/87218 fatcat:ut4wbkeaorbxncnzdijsrx4nk4

Optimization of plasmid maintenance in the attenuated live vector vaccine strain Salmonella typhi CVD 908-htrA

J E Galen, J Nair, J Y Wang, S S Wasserman, M K Tanner, M B Sztein, M M Levine
1999 Infection and Immunity  
We also included at least one naturally occurring plasmid partition function in our expression plasmids, which eliminates random segregation of these plasmids, thereby enhancing their inheritance and stability  ...  In this report, we demonstrate the utility of this novel plasmid maintenance system in enhancing the stability of our expression plasmids and go on to show that as the copy number of stabilized plasmids  ...  ACKNOWLEDGMENTS This research was supported by grants 5 RO1 AI29471, RO1 AI40297, and Research contract NO1 AI45251 (M. M. Levine, principal investigator).  ... 
pmid:10569759 pmcid:PMC97051 fatcat:wiw4uobgqnbmpihbiygqmm2ncq
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