ALBERT

Description: Surveys of the Milky Way (MW) and M31 enable detailed studies of stellar populations across ages and metallicities, with the goal of reconstructing formation histories across cosmic time. These surveys motivate key questions for galactic archaeology in a cosmological context: When did the main progenitor of an MW/M31-mass galaxy form, and what were the galactic building blocks that formed it? We investigate the formation times and progenitor galaxies of MW/M31-mass galaxies using the Feedback In Realistic Environments-2 cosmological simulations, including six isolated MW/M31-mass galaxies and six galaxies in Local Group (LG)-like pairs at z = 0. We examine main progenitor ‘formation’ based on two metrics: (1) transition from primarily ex-situ to in-situ stellar mass growth and (2) mass dominance compared to other progenitors. We find that the main progenitor of an MW/M31-mass galaxy emerged typically at z ∼ 3–4 ($11.6!!-!!12.2, m {Gyr}$ ago), while stars in the bulge region (inner 2 kpc) at z = 0 formed primarily in a single main progenitor at z ≲ 5 (${lesssim} !12.6, m {Gyr}$ ago). Compared with isolated hosts, the main progenitors of LG-like paired hosts emerged significantly earlier (Δz ∼ 2, $Delta t!sim !1.6, m {Gyr}$), with ∼4× higher stellar mass at all z ≳ 4 (${gtrsim} !12.2, m {Gyr}$ ago). This highlights the importance of environment in MW/M31-mass galaxy formation, especially at early times. On average, about 100 galaxies with $ m {it{ M}}_ m {star}!gtrsim !10^5, m {M}_odot$ went into building a typical MW/M31-mass system. Thus, surviving satellites represent a highly incomplete census (by ∼5×) of the progenitor population.

Description: Trees killed by natural disturbances have been recognized by the International Panel on Climate Change (IPCC) as a promising resource for bioenergy at the global scale. In the eastern boreal forest of Canada, there are two major types of natural disturbances that can generate large amounts of biomass for the production of bioenergy: wildfire and spruce budworm outbreak. For example, the mean burned area between 1970 and 2010 was estimated at 2900 km 2 per year. Following such disturbances, typically only trees and stands with a merchantable value, i.e., of acceptable quality for traditional forest products (lumber and pulp) are salvaged. However, adding bioenergy to the potential basket of products may both divert trees of marginal quality and profitability away from traditional products and to bioenergy facilities and lengthen the window of opportunity during which salvage operations can occur. This review shows how the dynamics of wood characteristics of trees affected by natural disturbances can be used to predict through time the basket of wood products that can be taken out of a salvaged stand and ensure the best fit between sources of fibre and types of processing facilities. The most important factors influencing fibre quality include degradation caused by fungi and insects. The most suitable time to salvage trees for the production of lumber in stands killed by either spruce budworm or fire is generally limited to 1–2 years after death. For the production of pulp and paper, trees can usually be salvaged for as long as the wood moisture content remains above the fibre saturation point, but usually is not recommended after 3 or 4 years following death. Thus, past this period, salvaged trees may yield better opportunities for the bioenergy sector. Information on wood as bioenergy feedstock (wood chips, wood pellets and liquid biofuel) highlights the importance of wood chemical components in the chemical reactivity of biofuel. This study offers background knowledge and a framework of analysis that highlights the potential of dead wood from natural disturbances for the production of forest and bioenergy products, which can be further adapted to other regions of the world, building on the Canadian experience of adapting practices to natural disturbances.

Description: The large repABC plasmids of the order Rhizobiales with Class I quorum-regulated conjugative transfer systems often define the nature of the bacterium that harbors them. These otherwise diverse plasmids contain a core of highly conserved genes for replication and conjugation raising the question of their evolutionary relationships. In an analysis of 18 such plasmids these elements fall into two organizational classes, Group I and Group II, based on the sites at which cargo DNA is located. Cladograms constructed from proteins of the transfer and quorum-sensing components indicated that those of the Group I plasmids, while coevolving, have diverged from those coevolving proteins of the Group II plasmids. Moreover, within these groups the phylogenies of the proteins usually occupy similar, if not identical, tree topologies. Remarkably, such relationships were not seen among proteins of the replication system; although RepA and RepB coevolve, RepC does not. Nor do the replication proteins coevolve with the proteins of the transfer and quorum-sensing systems. Functional analysis was mostly consistent with phylogenies. TraR activated promoters from plasmids within its group, but not between groups and dimerized with TraR proteins from within but not between groups. However, oriT sequences, which are highly conserved, were processed by the transfer system of plasmids regardless of group. We conclude that these plasmids diverged into two classes based on the locations at which cargo DNA is inserted, that the quorum-sensing and transfer functions are coevolving within but not between the two groups, and that this divergent evolution extends to function.

Description: Cys 2 His 2 zinc fingers (C2H2-ZFs) comprise the largest class of metazoan DNA-binding domains. Despite this domain's well-defined DNA-recognition interface, and its successful use in the design of chimeric proteins capable of targeting genomic regions of interest, much remains unknown about its DNA-binding landscape. To help bridge this gap in fundamental knowledge and to provide a resource for design-oriented applications, we screened large synthetic protein libraries to select binding C2H2-ZF domains for each possible three base pair target. The resulting data consist of 〉160 000 unique domain–DNA interactions and comprise the most comprehensive investigation of C2H2-ZF DNA-binding interactions to date. An integrated analysis of these independent screens yielded DNA-binding profiles for tens of thousands of domains and led to the successful design and prediction of C2H2-ZF DNA-binding specificities. Computational analyses uncovered important aspects of C2H2-ZF domain–DNA interactions, including the roles of within-finger context and domain position on base recognition. We observed the existence of numerous distinct binding strategies for each possible three base pair target and an apparent balance between affinity and specificity of binding. In sum, our comprehensive data help elucidate the complex binding landscape of C2H2-ZF domains and provide a foundation for efforts to determine, predict and engineer their DNA-binding specificities.

Description: Motivated by the recent discovery of several dwarfs near the Large Magellanic Cloud (LMC), we study the accretion of massive satellites onto Milky Way (MW)/M31-like haloes using the ELVIS suite of N -body simulations. We identify 25 surviving LMC-mass subhaloes, and investigate the lower-mass satellites that were associated with these subhaloes before they fell into the MW/M31 haloes. Typically, 7 per cent of the overall z  = 0 satellite population of MW/M31 haloes were in a surviving LMC-group before falling into the MW/M31 halo. This fraction can vary between 1 and 25 per cent, being higher for groups with higher mass and/or more recent infall times. Groups of satellites disperse rapidly in phase space after infall, and their distances and velocities relative to the group centre become statistically similar to the overall satellite population after 4–8 Gyr. We quantify the likelihood that satellites were associated with an LMC-mass group as a function of both distance and velocity relative to the LMC at z  = 0. The close proximity in distance of the nine Dark Energy Survey candidate dwarf galaxies to the LMC suggest that ~2–4 are likely associated with the LMC. Furthermore, if several of these dwarfs are genuine members, then the LMC-group probably fell into the MW very recently, 2 Gyr ago. If the connection with the LMC is established with follow-up velocity measurements, these ‘satellites of satellites’ represent prime candidates to study the effects of group pre-processing on lower mass dwarfs.

Description: Galaxies that are several virial radii beyond groups/clusters show preferentially quiescent star formation rates (SFR). Using a galaxy group/cluster catalogue from the Sloan Digital Sky Survey, together with a cosmological N -body simulation, we examine the origin of this environmental quenching beyond the virial radius. Accounting for the clustering of groups/clusters, we show that central galaxies show enhanced SFR quenching out to 2.5 virial radii beyond groups/clusters, and we demonstrate that this extended environmental enhancement can be explained simply by ‘ejected’ satellite galaxies that orbit beyond their host halo's virial radius. We show that ejected satellites typically orbit for several Gyr beyond the virial radius before falling back in, and thus they compose up to 40 per cent of all central galaxies near groups/clusters. We show that a model in which ejected satellites experience the same SFR quenching as satellites within a host halo can explain essentially all environmental dependence of galaxy quenching. Furthermore, ejected satellites (continue to) lose significant halo mass, an effect that is potentially observable via gravitational lensing. The SFRs/colours and stellar-to-halo masses of ejected satellites highlight the importance of environmental history and present challenges to models of galaxy occupation that ignore such history.

Description: Spontaneous neural activity promotes axon growth in many types of developing neurons, including motoneurons. In motoneurons from a mouse model of spinal muscular atrophy (SMA), defects in axonal growth and presynaptic function correlate with a reduced frequency of spontaneous Ca 2+ transients in axons which are mediated by N-type Ca 2+ channels. To characterize the mechanisms that initiate spontaneous Ca 2+ transients, we investigated the role of voltage-gated sodium channels (VGSCs). We found that low concentrations of the VGSC inhibitors tetrodotoxin (TTX) and saxitoxin (STX) reduce the rate of axon growth in cultured embryonic mouse motoneurons without affecting their survival. STX was 5- to 10-fold more potent than TTX and Ca 2+ imaging confirmed that low concentrations of STX strongly reduce the frequency of spontaneous Ca 2+ transients in somatic and axonal regions. These findings suggest that the Na V 1.9, a VGSC that opens at low thresholds, could act upstream of spontaneous Ca 2+ transients. qPCR from cultured and laser-microdissected spinal cord motoneurons revealed abundant expression of Na V 1.9. Na V 1.9 protein is preferentially localized in axons and growth cones. Suppression of Na V 1.9 expression reduced axon elongation. Motoneurons from Na V 1.9 –/– mice showed the reduced axon growth in combination with reduced spontaneous Ca 2+ transients in the soma and axon terminals. Thus, Na V 1.9 function appears to be essential for activity-dependent axon growth, acting upstream of spontaneous Ca 2+ elevation through voltage-gated calcium channels (VGCCs). Na V 1.9 activation could therefore serve as a target for modulating axonal regeneration in motoneuron diseases such as SMA in which presynaptic activity of VGCCs is reduced.

Description: Motivated by the recent discovery of several dwarfs near the Large Magellanic Cloud (LMC), we study the accretion of massive satellites onto Milky Way (MW)/M31-like haloes using the ELVIS suite of N -body simulations. We identify 25 surviving LMC-mass subhaloes, and investigate the lower-mass satellites that were associated with these subhaloes before they fell into the MW/M31 haloes. Typically, 7 per cent of the overall z  = 0 satellite population of MW/M31 haloes were in a surviving LMC-group before falling into the MW/M31 halo. This fraction can vary between 1 and 25 per cent, being higher for groups with higher mass and/or more recent infall times. Groups of satellites disperse rapidly in phase space after infall, and their distances and velocities relative to the group centre become statistically similar to the overall satellite population after 4–8 Gyr. We quantify the likelihood that satellites were associated with an LMC-mass group as a function of both distance and velocity relative to the LMC at z  = 0. The close proximity in distance of the nine Dark Energy Survey candidate dwarf galaxies to the LMC suggest that ~2–4 are likely associated with the LMC. Furthermore, if several of these dwarfs are genuine members, then the LMC-group probably fell into the MW very recently, 2 Gyr ago. If the connection with the LMC is established with follow-up velocity measurements, these ‘satellites of satellites’ represent prime candidates to study the effects of group pre-processing on lower mass dwarfs.

Description: Satellite galaxies in groups and clusters are more likely to have low star formation rates (SFRs) and lie on the ‘red sequence’ than central (‘field’) galaxies. Using galaxy group/cluster catalogues from the Sloan Digital Sky Survey Data Release 7, together with a high-resolution, cosmological N -body simulation to track satellite orbits, we examine the star formation histories and quenching time-scales of satellites of M star  〉 5  x 10 9 M at z 0. We first explore satellite infall histories: group preprocessing and ejected orbits are critical aspects of satellite evolution, and properly accounting for these, satellite infall typically occurred at z  ~ 0.5, or ~5 Gyr ago. To obtain accurate initial conditions for the SFRs of satellites at their time of first infall, we construct an empirical parametrization for the evolution of central galaxy SFRs and quiescent fractions. With this, we constrain the importance and efficiency of satellite quenching as a function of satellite and host halo mass, finding that satellite quenching is the dominant process for building up all quiescent galaxies at M star  〈 10 10 M . We then constrain satellite star formation histories, finding a ‘delayed-then-rapid’ quenching scenario: satellite SFRs evolve unaffected for 2–4 Gyr after infall, after which star formation quenches rapidly, with an e-folding time of 〈0.8 Gyr. These quenching time-scales are shorter for more massive satellites but do not depend on host halo mass: the observed increase in the satellite quiescent fraction with halo mass arises simply because of satellites quenching in a lower mass group prior to infall (group preprocessing), which is responsible for up to half of quenched satellites in massive clusters. Because of the long time delay before quenching starts, satellites experience significant stellar mass growth after infall, nearly identical to central galaxies. This fact provides key physical insight into the subhalo abundance matching method.

Description: Ending overfishing and rebuilding fish stocks to levels that provide for optimum sustainable yield is a concern for fisheries management worldwide. In the United States, fisheries managers are legally mandated to end overfishing and to implement rebuilding plans for fish stocks that fall below minimum stock size thresholds. Rebuilding plans should lead to recovery to target stock sizes within 10 years, except in situations where the life history of the stock or environmental conditions dictate otherwise. Federally managed groundfish species along the US West Coast have diverse life histories where some are able to rebuild quickly from overfished status, while others, specifically rockfish ( Sebastes spp.), may require decades for rebuilding. A management strategy evaluation which assumed limited estimation error was conducted to evaluate the performance of alternative strategies for rebuilding overfished stocks for these alternative US West Coast life histories. Generally, the results highlight the trade-off between the reduction of catches during rebuilding vs. the length of rebuilding. The most precautionary rebuilding plans requiring the greatest harvest reduction resulted in higher average catches over the entire projection period compared with strategies that required a longer rebuilding period with less of a reduction in rebuilding catch. Attempting to maintain a 50% probability of rebuilding was the poorest performing rebuilding strategy for all life histories, resulting in a large number of changes to the rebuilding plan, increased frequency of failing to meet rebuilding targets, and higher variation in catch. The rebuilding plans that implemented a higher initial rebuilding probability (≥60%) for determining rebuilding fishing mortality and targets generally resulted in fewer changes to the rebuilding plans and rebuilt by the target rebuilding year, particularly for stocks with the longer rebuilding plans (e.g. rockfishes).