Helicase ATPase activity of the Tobacco mosaic virus 126-kDa protein modulates replicase complex assembly

AbstractMutations disrupting helicase domain motifs of the Tobacco mosaic virus 126/183-kDa proteins were investigated for their effect on replicase function and assembly. These mutations inhibited virus replication but did not affect 126-kDa induced N gene resistance or RNAi suppression. However, in vivo expressed 126-kDa motif mutants yielded two distinct cytoplasmic phenotypes that correlated with ATPase activity. Specifically, ATPase active 126-kDa proteins produced small cytoplasmic bodies that resembled the ovoid granular-like bodies found early in virus infection while 126-kDa proteins defective in ATPase activity produced large tubule containing cytoplasmic bodies similar to those observed late in infection. Additional studies indicate that the helicase ATPase activity resides predominantly within monomer and dimer helicase forms and that motifs affecting ATPase activity induce alterations in helicase assembly. Combined these findings indicate that helicase ATPase activity modulates the progression of replicase complex assembly and maturation

Participatory Action Research for Dealing with Disasters on Islands

Much disaster research has a basis in non-island case studies, although mono-disciplinary disaster-related research across past decades has often used case studies of individual islands. Both sets of work contribute to contemporary ‘participatory action research’ which investigates ways of dealing with disasters on islands. This paper asks what might be gained through combining disaster research, island studies, and participatory action research. What value does island studies bring to participatory action research for dealing with disasters? Through a critical (not comprehensive) overview of participatory action research for dealing with disasters on islands, three main lessons emerge. First, the island context matters to a certain degree for disaster-related research and action. Second, islandness has much more to offer disaster-related research than is currently appreciated. Third, more studies are needed linking theory to evidence found on the ground on islanders’ terms. Limitations of the analyses here and future research directions are provided

Research on plant disease and pest management is essential to sustainable agriculture

In the United States, a country with food in great abundance, it is difficult to realize that, were it not for the current level of plant disease and pest management, most human resources would be needed to obtain enough food and other plant and animal products merely to survive. Instead, there are surpluses, markets for many agricultural products are depressed, and funds available for research on plant disease and pest management-and for agricultural research generally-have plateaued or are declining. Why does the United States need more research on plant disease and pest management? Because the health and productivity of the crops and cropping systems upon which the people depend for their own consumption and for export cannot be sustained without continuing research and development. This continued investment is needed to manage ever threatening, changing, and rebounding diseases and pest populations. Moreover, disease and pest management of the future must be improved while simultaneously reducing our dependence on pesticides as one of many steps toward the goal of sustainable agriculture. The goal of plant disease and pest management is to ensure that crops are healthy enough to yield to their full genetic potential within the physical limits imposed by the uncontrolled variables of climate, weather, and soils. Management is defined as limiting damage from diseases or pests to a level at or below an acceptable economic or aesthetic threshold. This process does not require total elimination or eradication of the pest or disease problem

Research on plant disease and pest management is essential to sustainable agriculture

In the United States, a country with food in great abundance, it is difficult to realize that, were it not for the current level of plant disease and pest management, most human resources would be needed to obtain enough food and other plant and animal products merely to survive. Instead, there are surpluses, markets for many agricultural products are depressed, and funds available for research on plant disease and pest management-and for agricultural research generally-have plateaud or are declining. Why does the United States need more research on plant disease and pest management? Because the health and productivity of the crops and cropping systems upon which the people depend for their own consumption and for export cannot be sustained without continuing research and development. This continued investment is needed to manage ever threatening, changing, and rebounding diseases and pest populations. Moreover, disease and pest management of the future must be improved while simultaneously reducing our dependence on pesticides as one of many steps toward the goal of sustainable agriculture. The goal of plant disease and pest management is to ensure that crops are healthy enough to yield to their full genetic potential within the physical limits imposed by the uncontrolled variables of climate, weather, and soils. Management is defined as limiting damage from diseases or pests to a level at or below an acceptable economic or aesthetic threshold. This process does not require total elimination or eradication of the pest or disease problem. Reducing the use of pesticides is a desirable goal, but it depends on continued and increased investments in research on alternatives. For many chemical pesticides, the alternatives either are not yet developed or are less effective than chemicals. This research must be broadly based across the biological, physical, and social sciences. Moreover, the United States and the world depend not only on sustainable agriculture but also on sustainable growth in agriculture to meet a long-term increase in demand for quality and quantity of agricultural products expected from increases in both numbers and economic status of people (Rutan 1992). Furthermore. these increases must \u27be attained at the same time that available agricultural land is decreasing to satisfy other needs such as more land for recreation and urbanization; restoration of some wetlands, grasslands, and woodlands; and diversions of land from farming to other uses. Improved disease and pest management offers one of the few effective means by which the necessary increases in crop productivity can be accomplished while natural resources, including the remaining forests, are protected. These same principles apply to other uses of plants as well, including as ornamentals, for landscapes, and in parks and golf courses

Capacity building lessons from a decade of transitional settlement and shelter

This paper examines 23 recent case studies of post‐disaster settlement and shelter across Africa, Asia, and Latin America to provide examples of implementing transitional settlement and shelter as a process and how to build more capacity for such programmes. The case studies are examined by using a four‐part framework: (i) Safety, security, and livelihoods; (ii) the question “Transition to what?” in order to understand better how to connect post‐disaster programmes to permanent communities and housing; (iii) fairness and equity; and (iv) connecting relief and development, which also explores root causes of vulnerability. The main lessons identify six specific activities that should be highlighted for capacity building in transitional settlement and shelter: site selection, good governance, participatory and consultative processes, land ownership, logistics, and monitoring and evaluation. Santruka Šiame darbe analizuojami 23 neseniai atliktu nelaimes ištiktu žmoniu apgyvendinimo ir prieglaudu jiems suteikimo Afrikoje, Azijoje ir Lotynu Amerikoje tyrimu rezultatai, pateikiami efektyvaus aprūpinimo laikinosiomis gyvenamosiomis vietomis ir prieglaudomis programu igyvendinimo pavyzdžiai, patariama, kaip didinti šiu programu potenciala. Tyrimu rezultatai nagrinejami remiantis keturiu daliu struktūra: 1) saugumas, apsauga ir pragyvenimo šaltinis; 2) klausimas “Jei laikinas, tai kas po to?”, siekis ištikus nelaimei vykdomas apgyvendinimo programas susieti su pastoviomis bendruomenemis ir nuolatiniu būstu; 3) teisingumas ir lygybe; 4) paramos ir pletros sasaja, pagrindines pažeidžiamumo priežastys. Išskiriamos šešios konkrečios veiklos rūšys, kurias reiketu akcentuoti didinat aprūpinimo laikinosiomis gyvenamosiomis vietomis ir prieglaudu suteikimo potenciala: vietos parinkimas, geras valdymas, dalyvavimo ir konsultavimo procesai, žemes nuosavybe, logistika, stebejimas bei vertinimas. First Publish Online: 18 Oct 201

Bog plant/lichen tissue nitrogen and sulfur concentrations as indicators of emissions from oil sands development in Alberta, Canada

Increasing gaseous emissions of nitrogen (N) and sulfur (S) associated with oil sands development in northern Alberta (Canada) has led to changing regional wet and dry N and S deposition regimes. We assessed the potential for using bog plant/lichen tissue chemistry (N and S concentrations, C:N and C:S ratios, in 10 plant/lichen species) to monitor changing atmospheric N and S deposition through sampling at five bog sites, 3-6 times per growing season from 2009 to 2016. During this 8-year period, oil sands N emissions steadily increased, while S emissions steadily decreased. We examined the following: (1) whether each species showed changes in tissue chemistry with increasing distance from the Syncrude and Suncor upgrader stacks (the two largest point sources of N and S emissions); (2) whether tissue chemistry changed over the 8 year period in ways that were consistent with increasing N and decreasing S emissions from oil sands facilities; and (3) whether tissue chemistry was correlated with growing season wet deposition of NH4+-N, NO3--N, or SO42--S. Based on these criteria, the best biomonitors of a changing N deposition regime were Evernia mesomorpha, Sphagnum fuscum, and Vaccinium oxycoccos. The best biomonitors of a changing S deposition regime were Evernia mesomorpha, Cladonia mitis, Sphagnum fuscum, Sphagnum capillifolium, Vaccinium oxycoccos, and Picea mariana. Changing N and S deposition regimes in the oil sands region appear to be influencing N and S cycling in what once were pristine ombrotrophic bogs, to the extent that these bogs may effectively monitor future spatial and temporal patterns of deposition

Experimental nitrogen addition alters structure and function of a boreal poor fen: Implications for critical loads

Bogs and fens cover 6 and 21%, respectively, of the 140,329 km2 Oil Sands Administrative Area in northern Alberta. Regional background atmospheric N deposition is low (b2 kg N ha−1 yr−1 ), but oil sands development has led to increasing N deposition (as high as 17 kg N ha−1 yr−1 ). To examine responses to N deposition, over five years, we experimentally applied N (as NH4NO3) to a poor fen near Mariana Lake, Alberta, unaffected by oil sands activities, at rates of 0, 5, 10, 15, 20, and 25 kg N ha−1 yr−1 , plus controls (no water or N addition). At Mariana Lake Poor Fen (MLPF), increasing N addition: 1) progressively inhibited N2-fixation; 2) had no effect on net primary production (NPP) of Sphagnum fuscum or S. angustifolium, while stimulating S. magellanicum NPP; 3) led to decreased abundance of S. fuscum and increased abundance of S. angustifolium, S. magellanicum, Andromeda polifolia, Vaccinium oxycoccos, and of vascular plants in general; 4) led to an increase in stem N concentrations in S. angustifolium and S. magellanicum, and an increase in leaf N concentrations in Chamaedaphne calyculata, Andromeda polifolia, and Vaccinium oxycoccos; 5) stimulated root biomass and production;6) stimulated decomposition of cellulose, but not of Sphagnum or vascular plant litter; and 7) had no or minimal effects on net N mineralization in surface peat, NH4 +-N, NO3 −-N or DON concentrations in surface porewater, or peat microbial composition. Increasing N addition led to a switch from new N inputs being taken up primarily by Sphagnum to being taken up primarily by shrubs. MLPF responses to increasing N addition did not exhibit threshold triggers, but rather began as soon as N additions increased. Considering all responses to N addition, we recommend a critical load for poor fens in Alberta of 3 kg N ha−1 yr−1

Pyxel 1.0: an open source Python framework for detector and end-to-end instrument simulation

Detector modeling is becoming more and more critical for the development of new instruments in scientific space missions and ground-based experiments. Modeling tools are often developed from scratch by each individual project and not necessarily shared for reuse by a wider community. To foster knowledge transfer, reusability, and reliability in the instrumentation community, we developed Pyxel, a framework for the simulation of scientific detectors and instruments. Pyxel is an open-source and collaborative project, based on Python, developed as an easy-to-use tool that can host and pipeline any kind of detector effect model. Recently, Pyxel has achieved a new milestone: the public release and launch of version 1.0, which simplified third-party contributions and improved ease of use even further. Since its launch, Pyxel has been experiencing a growing user community and is being used to simulate a variety of detectors. We give a tour of Pyxel’s version 1.0 changes and new features, including a new interface, parallel computing, and new detectors and models. We continue with an example of using Pyxel as a tool for model optimization and calibration. Finally, we describe an example of how Pyxel and its features can be used to develop a full-scale end-to-end instrument simulator

A novel DNA nuclease is stimulated by association with the GINS complex

Chromosomal DNA replication requires the spatial and temporal coordination of the activities of several complexes that constitute the replisome. A previously uncharacterized protein, encoded by TK1252 in the archaeon Thermococcus kodakaraensis, was shown to stably interact with the archaeal GINS complex in vivo, a central component of the archaeal replisome. Here, we document that this protein (TK1252p) is a processive, single-strand DNA-specific exonuclease that degrades DNA in the 5′ → 3′ direction. TK1252p binds specifically to the GINS15 subunit of T. kodakaraensis GINS complex and this interaction stimulates the exonuclease activity in vitro. This novel archaeal nuclease, designated GINS-associated nuclease (GAN), also forms a complex in vivo with the euryarchaeal-specific DNA polymerase D. Roles for GAN in replisome assembly and DNA replication are discussed