Restoration of catalytic functions in Cre recombinase mutants by electrostatic compensation between active site and DNA substrate

Two conserved catalytic arginines, Arg-173 and Arg-292, of the tyrosine site-specific recombinase Cre are essential for the transesterification steps of strand cleavage and joining in native DNA substrates containing scissile phosphate groups. The active site tyrosine (Tyr-324) provides the nucleophile for the cleavage reaction, and forms a covalent 3′-phosphotyrosyl intermediate. The 5′-hydroxyl group formed during cleavage provides the nucleophile for the joining reaction between DNA partners, yielding strand exchange. Previous work showed that substitution of the scissile phosphate (P) by methylphosphonate (MeP) permits strand cleavage by a Cre variant lacking Arg-292. We now demonstrate that MeP activation and cleavage are not blocked by substitution of Arg-173 or even simultaneous substitutions of Arg-173 and Arg-292 by alanine. Furthermore, Cre(R173A) and Cre(R292A) are competent in strand joining, Cre(R173A) being less efficient. No joining activity is detected with Cre(R173A, R292A). Consistent with their ability to cleave and join strands, Cre(R173A) and Cre(R292A) can promote recombination between two MeP-full-site DNA partners. These findings shed light on the overall contribution of active site electrostatics, and tease apart distinctive contributions of the individual arginines, to the chemical steps of recombination. They have general implications in active site mechanisms that promote important phosphoryl transfer reactions in nucleic acids

An open prospective study on the efficacy of Navina Smart, an electronic system for transanal irrigation, in neurogenic bowel dysfunction

Background: Transanal irrigation (TAI) has emerged as a key option when more conservative bowel management does not help spinal cord injured (SCI) individuals with neurogenic bowel dysfunction (NBD). Aim: To investigate the short-term efficacy and safety of an electronic TAI system (Navina Smart) in subjects with NBD. Design: We present an open, prospective efficacy study on Navina Smart, in individuals with NBD secondary to SCI, studied at three months. Population: Eighty-nine consecutive consenting established SCI individuals (61 male; mean age 48, range 18–77) naïve to TAI treatment were recruited from ten centres in seven countries. Subjects had confirmed NBD of at least moderate severity (NBD score ≥10). Methods: Subjects were taught how to use the device at baseline assisted by the Navina Smart app, and treatment was tailored during phone calls until optimal TAI regime was achieved. The NBD score was measured at baseline and at three months follow up (mean 98 days). Safety analysis was performed on the complete population while per protocol (PP) analysis was performed on 52 subjects. Results: PP analysis showed a significant decrease in mean NBD score (17.8 to 10, p<0.00001). In subjects with severe symptoms (defined as NBD score ≥14), mean NBD scores decreased (19.4 to 10.9, p<0.0001). The number of subjects with severe symptoms decreased from 41 (79%) subjects at baseline to 16 (31%) at three months follow-up. Device failure accounted for the commonest cause for loss of data. Side effects possibly related to the device developed in 11 subjects (12%). Discontinuation due to failure of therapy to relieve symptoms was reported by 5 subjects (6%). Conclusion: Navina Smart is effective for individuals with NBD, even those with severe symptoms; long-term data will follow. Whilst there were some device problems (addressed by the later stages of subject recruitment) the treatment was generally safe

An open prospective study on the efficacy of Navina Smart, an electronic system for transanal irrigation, in neurogenic bowel dysfunction

Background: Transanal irrigation (TAI) has emerged as a key option when more conservative bowel management does not help spinal cord injured (SCI) individuals with neurogenic bowel dysfunction (NBD). Aim: To investigate the short-term efficacy and safety of an electronic TAI system (Navina Smart) in subjects with NBD. Design: We present an open, prospective efficacy study on Navina Smart, in individuals with NBD secondary to SCI, studied at three months. Population: Eighty-nine consecutive consenting established SCI individuals (61 male; mean age 48, range 18–77) naïve to TAI treatment were recruited from ten centres in seven countries. Subjects had confirmed NBD of at least moderate severity (NBD score ≥10). Methods: Subjects were taught how to use the device at baseline assisted by the Navina Smart app, and treatment was tailored during phone calls until optimal TAI regime was achieved. The NBD score was measured at baseline and at three months follow up (mean 98 days). Safety analysis was performed on the complete population while per protocol (PP) analysis was performed on 52 subjects. Results: PP analysis showed a significant decrease in mean NBD score (17.8 to 10, p<0.00001). In subjects with severe symptoms (defined as NBD score ≥14), mean NBD scores decreased (19.4 to 10.9, p<0.0001). The number of subjects with severe symptoms decreased from 41 (79%) subjects at baseline to 16 (31%) at three months follow-up. Device failure accounted for the commonest cause for loss of data. Side effects possibly related to the device developed in 11 subjects (12%). Discontinuation due to failure of therapy to relieve symptoms was reported by 5 subjects (6%). Conclusion: Navina Smart is effective for individuals with NBD, even those with severe symptoms; long-term data will follow. Whilst there were some device problems (addressed by the later stages of subject recruitment) the treatment was generally safe

Pseudomonas aeruginosa Adaptation to Lungs of Cystic Fibrosis Patients Leads to Lowered Resistance to Phage and Protist Enemies

Pathogenic life styles can lead to highly specialized interactions with host species, potentially resulting in fitness trade-offs in other ecological contexts. Here we studied how adaptation of the environmentally transmitted bacterial pathogen, Pseudomonas aeruginosa, to cystic fibrosis (CF) patients affects its survival in the presence of natural phage (14/1, ΦKZ, PNM and PT7) and protist (Tetrahymena thermophila and Acanthamoebae polyphaga) enemies. We found that most of the bacteria isolated from relatively recently intermittently colonised patients (1-25 months), were innately phage-resistant and highly toxic for protists. In contrast, bacteria isolated from long time chronically infected patients (2-23 years), were less efficient in both resisting phages and killing protists. Moreover, chronic isolates showed reduced killing of wax moth larvae (Galleria mellonella) probably due to weaker in vitro growth and protease expression. These results suggest that P. aeruginosa long-term adaptation to CF-lungs could trade off with its survival in aquatic environmental reservoirs in the presence of microbial enemies, while lowered virulence could reduce pathogen opportunities to infect insect vectors; factors that are both likely to result in poorer environmental transmission. From an applied perspective, phage therapy could be useful against chronic P. aeruginosa lung infections that are often characterized by multidrug resistance: chronic isolates were least resistant to phages and their poor growth will likely slow down the emergence of beneficial resistance mutations

A molecular insight into algal-oomycete warfare : cDNA analysis of Ectocarpus siliculosus infected with the basal oomycete Eurychasma dicksonii

Peer reviewedPublisher PD

Genomic-Bioinformatic Analysis of Transcripts Enriched in the Third-Stage Larva of the Parasitic Nematode Ascaris suum

Differential transcription in Ascaris suum was investigated using a genomic-bioinformatic approach. A cDNA archive enriched for molecules in the infective third-stage larva (L3) of A. suum was constructed by suppressive-subtractive hybridization (SSH), and a subset of cDNAs from 3075 clones subjected to microarray analysis using cDNA probes derived from RNA from different developmental stages of A. suum. The cDNAs (n = 498) shown by microarray analysis to be enriched in the L3 were sequenced and subjected to bioinformatic analyses using a semi-automated pipeline (ESTExplorer). Using gene ontology (GO), 235 of these molecules were assigned to ‘biological process’ (n = 68), ‘cellular component’ (n = 50), or ‘molecular function’ (n = 117). Of the 91 clusters assembled, 56 molecules (61.5%) had homologues/orthologues in the free-living nematodes Caenorhabditis elegans and C. briggsae and/or other organisms, whereas 35 (38.5%) had no significant similarity to any sequences available in current gene databases. Transcripts encoding protein kinases, protein phosphatases (and their precursors), and enolases were abundantly represented in the L3 of A. suum, as were molecules involved in cellular processes, such as ubiquitination and proteasome function, gene transcription, protein–protein interactions, and function. In silico analyses inferred the C. elegans orthologues/homologues (n = 50) to be involved in apoptosis and insulin signaling (2%), ATP synthesis (2%), carbon metabolism (6%), fatty acid biosynthesis (2%), gap junction (2%), glucose metabolism (6%), or porphyrin metabolism (2%), although 34 (68%) of them could not be mapped to a specific metabolic pathway. Small numbers of these 50 molecules were predicted to be secreted (10%), anchored (2%), and/or transmembrane (12%) proteins. Functionally, 17 (34%) of them were predicted to be associated with (non-wild-type) RNAi phenotypes in C. elegans, the majority being embryonic lethality (Emb) (13 types; 58.8%), larval arrest (Lva) (23.5%) and larval lethality (Lvl) (47%). A genetic interaction network was predicted for these 17 C. elegans orthologues, revealing highly significant interactions for nine molecules associated with embryonic and larval development (66.9%), information storage and processing (5.1%), cellular processing and signaling (15.2%), metabolism (6.1%), and unknown function (6.7%). The potential roles of these molecules in development are discussed in relation to the known roles of their homologues/orthologues in C. elegans and some other nematodes. The results of the present study provide a basis for future functional genomic studies to elucidate molecular aspects governing larval developmental processes in A. suum and/or the transition to parasitism

Molecular evolution of the membrane associated progesterone receptor in the Brachionus plicatilis (Rotifera, Monogononta) species complex

Author Posting. © Springer, 2010. This is the author's version of the work. It is posted here by permission of Springer for personal use, not for redistribution. The definitive version was published in Hydrobiologia 662 (2011): 99-106, doi:10.1007/s10750-010-0484-4.Many studies have investigated physiological roles of the membrane associated progesterone receptor (MAPR), but little is known of its evolution. Marked variations in response to exogenous progesterone have been reported for four brachionid rotifer species, suggesting differences in progesterone signaling and reception. Here we report sequence variation for the MAPR gene in the Brachionus plicatilis species complex. Phylogenetic analysis of this receptor is compared with relatedness based on cytochrome c oxidase subunit 1 sequences. Nonsynonymous to synonymous site substitution rate ratios, amino acid divergence, and variations in predicted phosphorylation sites are examined to assess evolution of the MAPR among brachionid clades.National Science Foundation grant BE/GenEn MCB-0412674E to TWS and DMW, and an NSF IGERT fellowship to HAS under DGE 0114400, supported this work

Exploring the Genetic Basis of Variation in Gene Predictions with a Synthetic Association Study

Identifying DNA polymorphisms that affect molecular processes like transcription, splicing, or translation typically requires genotyping and experimentally characterizing tissue from large numbers of individuals, which remains expensive and time consuming. Here we introduce an alternative strategy: a “synthetic association study” in which we computationally predict molecular phenotypes on artificial genomes containing randomly sampled combinations of polymorphic alleles, and perform a classical association study to identify genotypes underlying variation in these computationally predicted annotations. We applied this method to characterize the effects on gene structure of 32,792 single-nucleotide polymorphisms between two strains of the antibiotic producing fungus Penicilium chrysogenum. Although these SNPs represent only 0.1 percent of the nucleotides in the genome, they collectively altered 1.8 percent of predicted gene models between these strains. To determine which SNPs or combinations of SNPs were responsible for this variation, we predicted protein-coding genes in 500 intermediate genomes, each identical except for randomly chosen alleles at each SNP position. Of 30,468 gene models in the genome, 557 varied across these 500 genomes. 226 of these polymorphic gene models (40%) were perfectly correlated with individual SNPs, all of which were within or immediately proximal to the affected gene. The genetic architectures of the other 321 were more complex, with several examples of SNP epistasis that would have been difficult to predict a priori. We expect that many of the SNPs that affect computational gene structure reflect a biologically unrealistic sensitivity of the gene prediction algorithm to sequence changes, and we propose that genome annotation algorithms could be improved by minimizing their sensitivity to natural polymorphisms. However, many of the SNPs we identified are likely to affect transcript structure in vivo, and the synthetic association study approach can be easily generalized to any computed genome annotation to uncover relationships between genotype and important molecular phenotypes