Phage annealing proteins promote oligonucleotide-directed mutagenesis in Escherichia coli and mouse ES cells

BACKGROUND: The phage protein pairs, RecE/RecT from Rac or Redα/Redβ from λ, initiate efficient double strand break repair (DSBR) in Escherichia coli that has proven very useful for DNA engineering. These phage pairs initiate DSBR either by annealing or by another mechanism that is not defined. RESULTS: Here we report that these proteins also mediate single strand oligonucleotide repair (ssOR) at high efficiencies. The ssOR activity, unlike DSBR, does not require a phage exonuclease (RecE or Redα) but only requires a phage annealing protein (RecT or Redβ). Notably, the P22 phage annealing protein Erf, which does not mediate the same DSBR reactions, also delivers ssOR activity. By altering aspects of the oligonucleotides, we document length and design parameters that affect ssOR efficiency to show a simple relationship to homologies either side of the repair site. Notably, ssOR shows strand bias. Oligonucleotides that can prime lagging strand replication deliver more ssOR than their leading complements. This suggests a model in which the annealing proteins hybridize the oligonucleotides to single stranded regions near the replication fork. We also show that ssOR is a highly efficient way to engineer BACs and can be detected in a eukaryotic cell upon expression of a phage annealing protein. CONCLUSION: Phage annealing proteins can initiate the recombination of single stranded oligonucleotides into endogenous targets in Escherichia coli at very high efficiencies. This expands the repertoire of useful DNA engineering strategies, shows promise for applications in eukaryotic cells, and has implications for the unanswered questions regarding DSBR mediated by RecE/RecT and Redα/Redβ

Micromagnetic simulations of current-induced magnetization switching in Co/Cu/Co nanopillars

Author name used in this publication: S. Q. Shi2007-2008 > Academic research: refereed > Publication in refereed journalVersion of RecordPublishe

Current-induced magnetization dynamics in Co/Cu/Co nanopillars

Author name used in this publication: S. Q. Shi2007-2008 > Academic research: refereed > Publication in refereed journalVersion of RecordPublishe

Does the initiation of urate lowering treatment during an acute gout attack prolong the current episode and precipitate recurrent attacks: a systematic literature review

Objectives: To systematically review the literature on effect of initiating urate lowering treatment (ULT) during an acute attack of gout on duration of index attack and persistence on ULT. Methods: OVID (MEDLINE), EMBASE and AMED were searched to identify randomized controlled trials (RCTs) of ULT initiation during acute gout attack published in English language. Two reviewers appraised the study quality and extracted data independently. Standardised mean difference (SMD) and relative risk (RR) were used to pool continuous and categorical data. Meta-analysis was carried out using STATA v14. Results: 537 studies were selected. 487 titles and abstracts were reviewed after removing duplicates. Three RCTs were identified. There was evidence from two high quality studies that early initiation of allopurinol did not increase pain severity at days 10 to 15 (SMDpooled (95%CI) 0.18(-0.58, 0.93)). Data from three studies suggested that initiation of ULT during an acute attack of gout did not associate with drop-outs (RRpooled (95%CI) 1.16(0.58, 2.31)). Conclusion: There is moderate-quality evidence that the initiation of ULT during an acute attack of gout does not increase pain severity and risk of ULT discontinuation. Larger studies are required to confirm these findings so that patients with acute gout can be initiated on ULT with confidence

Emergence of structural and dynamical properties of ecological mutualistic networks

Mutualistic networks are formed when the interactions between two classes of species are mutually beneficial. They are important examples of cooperation shaped by evolution. Mutualism between animals and plants plays a key role in the organization of ecological communities. Such networks in ecology have generically evolved a nested architecture independent of species composition and latitude - specialists interact with proper subsets of the nodes with whom generalists interact. Despite sustained efforts to explain observed network structure on the basis of community-level stability or persistence, such correlative studies have reached minimal consensus. Here we demonstrate that nested interaction networks could emerge as a consequence of an optimization principle aimed at maximizing the species abundance in mutualistic communities. Using analytical and numerical approaches, we show that because of the mutualistic interactions, an increase in abundance of a given species results in a corresponding increase in the total number of individuals in the community, as also the nestedness of the interaction matrix. Indeed, the species abundances and the nestedness of the interaction matrix are correlated by an amount that depends on the strength of the mutualistic interactions. Nestedness and the observed spontaneous emergence of generalist and specialist species occur for several dynamical implementations of the variational principle under stationary conditions. Optimized networks, while remaining stable, tend to be less resilient than their counterparts with randomly assigned interactions. In particular, we analytically show that the abundance of the rarest species is directly linked to the resilience of the community. Our work provides a unifying framework for studying the emergent structural and dynamical properties of ecological mutualistic networks.Comment: 10 pages, 4 figure

Three-Dimensional Manganese Oxide@Carbon Networks as Free-Standing, High-Loading Cathodes for High-Performance Zinc-Ion Batteries

Zinc-ion batteries (ZIBs), which are inexpensive and environmentally friendly, have a lot of potential for use in grid-scale energy storage systems, but their use is constrained by the availability of suitable cathode materials. MnO2-based cathodes are emerging as a promising contenders, due to the great availability and safety, as well as the device's stable output voltage platform (1.5 V). Improving the slow kinetics of MnO2-based cathodes caused by low electrical conductivity and mass diffusion rate is a challenge for their future use in next-generation rapid charging devices. Herein, the aforementioned challenges are overcome by proposing a sodium-intercalated manganese oxide (NMO) with 3D varying thinness carbon nanotubes (VTCNTs) networks as appropriate free-standing, binder-free cathodes (NMO/VTCNTs) without any heat treatment. A network construction strategy based on CNTs of different diameters is proposed for the first time to provide high specific capacity while achieving high mass loading. The specific capacity of as-prepared cathodes is significantly increased. The resulting free-standing binder-free cathodes achieve excellent capacity (329 mAh g−1 after 120 cycles at 0.2 A g−1 and 225 mAh g−1 after 200 cycles at 1 A g−1) and long-term cycling stability (158 mAh g−1 at 2 A g−1 after 1000 cycles)