ruvA Mutants that resolve Holliday junctions but do not reverse replication forks

RuvAB and RuvABC complexes catalyze branch migration and resolution of Holliday junctions (HJs) respectively. In addition to their action in the last steps of homologous recombination, they process HJs made by replication fork reversal, a reaction which occurs at inactivated replication forks by the annealing of blocked leading and lagging strand ends. RuvAB was recently proposed to bind replication forks and directly catalyze their conversion into HJs. We report here the isolation and characterization of two separation-of-function ruvA mutants that resolve HJs, based on their capacity to promote conjugational recombination and recombinational repair of UV and mitomycin C lesions, but have lost the capacity to reverse forks. In vivo and in vitro evidence indicate that the ruvA mutations affect DNA binding and the stimulation of RuvB helicase activity. This work shows that RuvA's actions at forks and at HJs can be genetically separated, and that RuvA mutants compromised for fork reversal remain fully capable of homologous recombination

Исследование оптических спектров химически модифицированного поливинилиденфторида

The present study aims to extend insights of surf zone turbulence dynamics to wave groups. In a large-scale wave flume, bichromatic wave groups were produced with 31.5 s group period, 4.2 s mean wave period, and a 0.58 m maximum wave height near the paddle. This condition resulted in plunging-type wave breaking over a fixed, gravel-bed, barred profile. Optic, acoustic and electromagnetic instruments were used to measure the flow and the spatial and temporal distributions of turbulent kinetic energy (TKE). The measurements showed that turbulence in the shoaling region is primarily bed-generated and decays almost fully within one wave cycle, leading to TKE variations at the short wave frequency. The wave breaking-generated turbulence, in contrast, decays over multiple wave cycles, leading to a gradual increase and decay of TKE during a wave group cycle. In the wave breaking region, TKE dynamics are driven by the production and subsequent downward transport of turbulence under the successive breaking waves in the group. Consequently, the maximum near-bed TKE in the breaking region can lag the highest breaking wave by up to 2.5 wave cycles. The net cross-shore transport of TKE is in the shoaling region primarily driven by short-wave velocities and is shoreward-directed; in the wave breaking region, the TKE transport is seaward-directed by the undertow and the long-wave velocities. Downward transport of TKE is driven by the vertical component of the time-averaged flow. The cross-shore and vertical diffusive transport rates are small relative to the advective transport rates

Mutations in maltose-binding protein that alter affinity and solubility properties

Maltose-binding protein (MBP) from Escherichia coli has been shown to be a good substrate for protein engineering leading to altered binding (Marvin and Hellinga, Proc Natl Acad Sci U S A 98:4955–4960, 2001a) and increased affinity (Marvin and Hellinga, Nat Struct Biol 8:795–798, 2001b; Telmer and Shilton, J Biol Chem 278:34555–34567, 2003). It is also used in recombinant protein expression as both an affinity tag and a solubility tag. We isolated mutations in MBP that enhance binding to maltodextrins 1.3 to 15-fold, using random mutagenesis followed by screening for enhanced yield in a microplate-based affinity purification. We tested the mutations for their ability to enhance the yield of a fusion protein that binds poorly to immobilized amylose and their ability to enhance the solubility of one or more aggregation-prone recombinant proteins. We also measured dissociation constants of the mutant MBPs that retain the solubility-enhancing properties of MBP and combined two of the mutations to produce an MBP with a dissociation constant 10-fold tighter than wild-type MBP. Some of the mutations we obtained can be rationalized based on the previous work, while others indicate new ways in which the function of MBP can be modified

Laboratory Evolution of Fast-Folding Green Fluorescent Protein Using Secretory Pathway Quality Control

Green fluorescent protein (GFP) has undergone a long history of optimization to become one of the most popular proteins in all of cell biology. It is thermally and chemically robust and produces a pronounced fluorescent phenotype when expressed in cells of all types. Recently, a superfolder GFP was engineered with increased resistance to denaturation and improved folding kinetics. Here we report that unlike other well-folded variants of GFP (e.g., GFPmut2), superfolder GFP was spared from elimination when targeted for secretion via the SecYEG translocase. This prompted us to hypothesize that the folding quality control inherent to this secretory pathway could be used as a platform for engineering similar ‘superfolded’ proteins. To test this, we targeted a combinatorial library of GFPmut2 variants to the SecYEG translocase and isolated several superfolded variants that accumulated in the cytoplasm due to their enhanced folding properties. Each of these GFP variants exhibited much faster folding kinetics than the parental GFPmut2 protein and one of these, designated superfast GFP, folded at a rate that even exceeded superfolder GFP. Remarkably, these GFP variants exhibited little to no loss in specific fluorescence activity relative to GFPmut2, suggesting that the process of superfolding can be accomplished without altering the proteins' normal function. Overall, we demonstrate that laboratory evolution combined with secretory pathway quality control enables sampling of largely unexplored amino-acid sequences for the discovery of artificial, high-performance proteins with properties that are unparalleled in their naturally occurring analogues

Quantifying annual spatial consistency in chick-rearing seabirds to inform important site identification

Animal tracking has afforded insights into patterns of space use in numerous species and thereby informed area-based conservation planning. A crucial consideration when estimating spatial distributions from tracking data is whether the sample of tracked animals is representative of the wider population. However, it may also be important to track animals in multiple years to capture changes in distribution in response to varying environmental conditions. Using GPS-tracking data from 23 seabird species, we assessed the importance of multi-year sampling for identifying important sites for conservation during the chick-rearing period, when seabirds are most spatially constrained. We found a high degree of spatial overlap among distributions from different years in most species. Multi-year sampling often captured a significantly higher portion of reference distributions (based on all data for a population) than sampling in a single year. However, we estimated that data from a single year would on average miss only 5 % less of the full distribution of a population compared to equal-sized samples collected across three years (min: −0.3 %, max: 17.7 %, n = 23). Our results suggest a key consideration for identifying important sites from tracking data is whether enough individuals were tracked to provide a representative estimate of the population distribution during the sampling period, rather than that tracking necessarily take place in multiple years. By providing an unprecedented multi-species perspective on annual spatial consistency, this work has relevance for the application of tracking data to informing the conservation of seabirds.Fundação para a Ciência e Tecnologia - FCT; ARNETinfo:eu-repo/semantics/publishedVersio

Global assessment of marine plastic exposure risk for oceanic birds

Plastic pollution is distributed patchily around the world’s oceans. Likewise, marine organisms that are vulnerable to plastic ingestion or entanglement have uneven distributions. Understanding where wildlife encounters plastic is crucial for targeting research and mitigation. Oceanic seabirds, particularly petrels, frequently ingest plastic, are highly threatened, and cover vast distances during foraging and migration. However, the spatial overlap between petrels and plastics is poorly understood. Here we combine marine plastic density estimates with individual movement data for 7137 birds of 77 petrel species to estimate relative exposure risk. We identify high exposure risk areas in the Mediterranean and Black seas, and the northeast Pacific, northwest Pacific, South Atlantic and southwest Indian oceans. Plastic exposure risk varies greatly among species and populations, and between breeding and non-breeding seasons. Exposure risk is disproportionately high for Threatened species. Outside the Mediterranean and Black seas, exposure risk is highest in the high seas and Exclusive Economic Zones (EEZs) of the USA, Japan, and the UK. Birds generally had higher plastic exposure risk outside the EEZ of the country where they breed. We identify conservation and research priorities, and highlight that international collaboration is key to addressing the impacts of marine plastic on wide-ranging species

Quantifying annual spatial consistency in chick-rearing seabirds to inform important site identification

Animal tracking has afforded insights into patterns of space use in numerous species and thereby informed area-based conservation planning. A crucial consideration when estimating spatial distributions from tracking data is whether the sample of tracked animals is representative of the wider population. However, it may also be important to track animals in multiple years to capture changes in distribution in response to varying environmental conditions. Using GPS-tracking data from 23 seabird species, we assessed the importance of multi-year sampling for identifying important sites for conservation during the chick-rearing period, when seabirds are most spatially constrained. We found a high degree of spatial overlap among distributions from different years in most species. Multi-year sampling often captured a significantly higher portion of reference distributions (based on all data for a population) than sampling in a single year. However, we estimated that data from a single year would on average miss only 5 % less of the full distribution of a population compared to equal-sized samples collected across three years (min: −0.3 %, max: 17.7 %, n = 23). Our results suggest a key consideration for identifying important sites from tracking data is whether enough individuals were tracked to provide a representative estimate of the population distribution during the sampling period, rather than that tracking necessarily take place in multiple years. By providing an unprecedented multi-species perspective on annual spatial consistency, this work has relevance for the application of tracking data to informing the conservation of seabirds

Global assessment of marine plastic exposure risk for oceanic birds

Plastic pollution is distributed patchily around the world’s oceans. Likewise, marine organisms that are vulnerable to plastic ingestion or entanglement have uneven distributions. Understanding where wildlife encounters plastic is crucial for targeting research and mitigation. Oceanic seabirds, particularly petrels, frequently ingest plastic, are highly threatened, and cover vast distances during foraging and migration. However, the spatial overlap between petrels and plastics is poorly understood. Here we combine marine plastic density estimates with individual movement data for 7137 birds of 77 petrel species to estimate relative exposure risk. We identify high exposure risk areas in the Mediterranean and Black seas, and the northeast Pacific, northwest Pacific, South Atlantic and southwest Indian oceans. Plastic exposure risk varies greatly among species and populations, and between breeding and non-breeding seasons. Exposure risk is disproportionately high for Threatened species. Outside the Mediterranean and Black seas, exposure risk is highest in the high seas and Exclusive Economic Zones (EEZs) of the USA, Japan, and the UK. Birds generally had higher plastic exposure risk outside the EEZ of the country where they breed. We identify conservation and research priorities, and highlight that international collaboration is key to addressing the impacts of marine plastic on wide-ranging species

Global assessment of marine plastic exposure risk for oceanic birds

Plastic pollution is distributed patchily around the world's oceans. Likewise, marine organisms that are vulnerable to plastic ingestion or entanglement have uneven distributions. Understanding where wildlife encounters plastic is crucial for targeting research and mitigation. Oceanic seabirds, particularly petrels, frequently ingest plastic, are highly threatened, and cover vast distances during foraging and migration. However, the spatial overlap between petrels and plastics is poorly understood. Here we combine marine plastic density estimates with individual movement data for 7137 birds of 77 petrel species to estimate relative exposure risk. We identify high exposure risk areas in the Mediterranean and Black seas, and the northeast Pacific, northwest Pacific, South Atlantic and southwest Indian oceans. Plastic exposure risk varies greatly among species and populations, and between breeding and non-breeding seasons. Exposure risk is disproportionately high for Threatened species. Outside the Mediterranean and Black seas, exposure risk is highest in the high seas and Exclusive Economic Zones (EEZs) of the USA, Japan, and the UK. Birds generally had higher plastic exposure risk outside the EEZ of the country where they breed. We identify conservation and research priorities, and highlight that international collaboration is key to addressing the impacts of marine plastic on wide-ranging species.B.L.C., C.H., and A.M. were funded by the Cambridge Conservation Initiative’s Collaborative Fund sponsored by the Prince Albert II of Monaco Foundation. E.J.P. was supported by the Natural Environment Research Council C-CLEAR doctoral training programme (Grant no. NE/S007164/1). We are grateful to all those who assisted with the collection and curation of tracking data. Further details are provided in the Supplementary Acknowledgements. Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the U.S. Government.Peer reviewe