Targeting climate diversity in conservation planning to build resilience to climate change

USGS Publications Warehouse

Heller, Nicole E.; Kreitler, Jason R.; Ackerly, David; Weiss, Stuart; Recinos, Amanda; Branciforte, Ryan; Flint, Lorraine E.; Flint, Alan L.; Micheli, Elisabeth

2015-01-01

Climate change is raising challenging concerns for systematic conservation planning. Are methods based on the current spatial patterns of biodiversity effective given long-term climate change? Some conservation scientists argue that planning should focus on protecting the abiotic diversity in the landscape, which drives patterns of biological diversity, rather than focusing on the distribution of focal species, which shift in response to climate change. Climate is one important abiotic driver of biodiversity patterns, as different climates host different biological communities and genetic pools. We propose conservation networks that capture the full range of climatic diversity in a region will improve the resilience of biotic communities to climate change compared to networks that do not. In this study we used historical and future hydro-climate projections from the high resolution Basin Characterization Model to explore the utility of directly targeting climatic diversity in planning. Using the spatial planning tool, Marxan, we designed conservation networks to capture the diversity of climate types, at the regional and sub-regional scale, and compared them to networks we designed to capture the diversity of vegetation types. By focusing on the Conservation Lands Network (CLN) of the San Francisco Bay Area as a real-world case study, we compared the potential resilience of networks by examining two factors: the range of climate space captured, and climatic stability to 18 future climates, reflecting different emission scenarios and global climate models. We found that the climate-based network planned at the sub-regional scale captured a greater range of climate space and showed higher climatic stability than the vegetation and regional based-networks. At the same time, differences among network scenarios are small relative to the variance in climate stability across global climate models. Across different projected futures, topographically heterogeneous areas

IAA-Ala Resistant3, an Evolutionarily Conserved Target of miR167, Mediates Arabidopsis Root Architecture Changes during High Osmotic Stress[W

PubMed Central

Kinoshita, Natsuko; Wang, Huan; Kasahara, Hiroyuki; Liu, Jun; MacPherson, Cameron; Machida, Yasunori; Kamiya, Yuji; Hannah, Matthew A.; Chua, Nam-Hai

2012-01-01

The functions of microRNAs and their target mRNAs in Arabidopsis thaliana development have been widely documented; however, roles of stress-responsive microRNAs and their targets are not as well understood. Using small RNA deep sequencing and ATH1 microarrays to profile mRNAs, we identified IAA-Ala Resistant3 (IAR3) as a new target of miR167a. As expected, IAR3 mRNA was cleaved at the miR167a complementary site and under high osmotic stress miR167a levels decreased, whereas IAR3 mRNA levels increased. IAR3 hydrolyzes an inactive form of auxin (indole-3-acetic acid [IAA]-alanine) and releases bioactive auxin (IAA), a central phytohormone for root development. In contrast with the wild type, iar3 mutants accumulated reduced IAA levels and did not display high osmotic stress–induced root architecture changes. Transgenic plants expressing a cleavage-resistant form of IAR3 mRNA accumulated high levels of IAR3 mRNAs and showed increased lateral root development compared with transgenic plants expressing wild-type IAR3. Expression of an inducible noncoding RNA to sequester miR167a by target mimicry led to an increase in IAR3 mRNA levels, further confirming the inverse relationship between the two partners. Sequence comparison revealed the miR167 target site on IAR3 mRNA is conserved in evolutionarily distant plant species. Finally, we showed that IAR3 is required for drought tolerance. PMID:22960911

Readings in Wildlife and Fish Conservation, High School Conservation Curriculum Project.

ERIC Educational Resources Information Center

Ensminger, Jack

This publication is a tentative edition of readings on Wildlife and Fish Conservation in Louisiana, and as such it forms part of one of the four units of study designed for an experimental high school course, the "High School Conservation Curriculum Project." The other three units are concerned with Forest Conervation, Soil and Water…

Targeted conservation to safeguard a biodiversity hotspot from climate and land-cover change.

PubMed

Struebig, Matthew J; Wilting, Andreas; Gaveau, David L A; Meijaard, Erik; Smith, Robert J; Fischer, Manuela; Metcalfe, Kristian; Kramer-Schadt, Stephanie

2015-02-02

Responses of biodiversity to changes in both land cover and climate are recognized [1] but still poorly understood [2]. This poses significant challenges for spatial planning as species could shift, contract, expand, or maintain their range inside or outside protected areas [2-4]. We examine this problem in Borneo, a global biodiversity hotspot [5], using spatial prioritization analyses that maximize species conservation under multiple environmental-change forecasts. Climate projections indicate that 11%-36% of Bornean mammal species will lose ≥ 30% of their habitat by 2080, and suitable ecological conditions will shift upslope for 23%-46%. Deforestation exacerbates this process, increasing the proportion of species facing comparable habitat loss to 30%-49%, a 2-fold increase on historical trends. Accommodating these distributional changes will require conserving land outside existing protected areas, but this may be less than anticipated from models incorporating deforestation alone because some species will colonize high-elevation reserves. Our results demonstrate the increasing importance of upland reserves and that relatively small additions (16,000-28,000 km(2)) to the current conservation estate could provide substantial benefits to biodiversity facing changes to land cover and climate. On Borneo, much of this land is under forestry jurisdiction, warranting targeted conservation partnerships to safeguard biodiversity in an era of global change. Copyright © 2015 Elsevier Ltd. All rights reserved.

Cost-effective targeting of conservation investments to reduce the northern Gulf of Mexico hypoxic zone.

PubMed

Rabotyagov, Sergey S; Campbell, Todd D; White, Michael; Arnold, Jeffrey G; Atwood, Jay; Norfleet, M Lee; Kling, Catherine L; Gassman, Philip W; Valcu, Adriana; Richardson, Jeffrey; Turner, R Eugene; Rabalais, Nancy N

2014-12-30

A seasonally occurring summer hypoxic (low oxygen) zone in the northern Gulf of Mexico is the second largest in the world. Reductions in nutrients from agricultural cropland in its watershed are needed to reduce the hypoxic zone size to the national policy goal of 5,000 km(2) (as a 5-y running average) set by the national Gulf of Mexico Task Force's Action Plan. We develop an integrated assessment model linking the water quality effects of cropland conservation investment decisions on the more than 550 agricultural subwatersheds that deliver nutrients into the Gulf with a hypoxic zone model. We use this integrated assessment model to identify the most cost-effective subwatersheds to target for cropland conservation investments. We consider targeting of the location (which subwatersheds to treat) and the extent of conservation investment to undertake (how much cropland within a subwatershed to treat). We use process models to simulate the dynamics of the effects of cropland conservation investments on nutrient delivery to the Gulf and use an evolutionary algorithm to solve the optimization problem. Model results suggest that by targeting cropland conservation investments to the most cost-effective location and extent of coverage, the Action Plan goal of 5,000 km(2) can be achieved at a cost of $2.7 billion annually. A large set of cost-hypoxia tradeoffs is developed, ranging from the baseline to the nontargeted adoption of the most aggressive cropland conservation investments in all subwatersheds (estimated to reduce the hypoxic zone to less than 3,000 km(2) at a cost of $5.6 billion annually).

Systematic conservation planning for ecosystem services: Opportunities for improving spatial targeting of ecosystem service payments in Costa Rica

NASA Astrophysics Data System (ADS)

Ramos Bendana, Zayra Sherlly

Tropical forests are of high conservation priority world-wide due their high value for harboring biodiversity and providing ecosystem services from the local to global scale. Financial resources for conservation are scarce. This challenges practitioners to design conservation networks encompassing spatial synergies between biodiversity and ecosystem services. Furthermore, conservation networks need to be robust to climate change impacts and the unpredictability of biodiversity response to these impacts. Methodologies for selecting locations that can help achieve multiple conservation objectives and can be easily integrated in current conservation practices are urgently needed. The first chapter of this study was focused on exploring the effect of integrating into conservation assessments two climate adaptation approaches based on environmental heterogeneity, as well as the effect of the selection of planning unit size on resultant conservation networks. With Costa Rica as planning region, our results showed that protecting the representation of the geophysical diversity resulted in conservation networks with over 25% more internal environmental heterogeneity, but more fragmented. Incorporating cross-environmental connectivity, on the other hand, resulted in low increases in environmental heterogeneity. Increasing the planning unit size reduced the effect of emphasizing connectivity between environmentally different locations. These results highlight the importance of testing environmental-heterogeneity-based approaches in each context due the specific characteristics of planning regions prior integrating them into formal conservation assessments. The second chapter focused on exploring synergies between biodiversity and carbon storage priorities, when integrating environmental-heterogeneity-based climate adaptation approaches. Results revealed very low synergies between targeting the representation of regional biodiversity and areas of high carbon content. However

Cost-effective targeting of conservation investments to reduce the northern Gulf of Mexico hypoxic zone

PubMed Central

Rabotyagov, Sergey S.; Campbell, Todd D.; White, Michael; Arnold, Jeffrey G.; Atwood, Jay; Norfleet, M. Lee; Kling, Catherine L.; Gassman, Philip W.; Valcu, Adriana; Richardson, Jeffrey; Turner, R. Eugene; Rabalais, Nancy N.

2014-01-01

A seasonally occurring summer hypoxic (low oxygen) zone in the northern Gulf of Mexico is the second largest in the world. Reductions in nutrients from agricultural cropland in its watershed are needed to reduce the hypoxic zone size to the national policy goal of 5,000 km2 (as a 5-y running average) set by the national Gulf of Mexico Task Force’s Action Plan. We develop an integrated assessment model linking the water quality effects of cropland conservation investment decisions on the more than 550 agricultural subwatersheds that deliver nutrients into the Gulf with a hypoxic zone model. We use this integrated assessment model to identify the most cost-effective subwatersheds to target for cropland conservation investments. We consider targeting of the location (which subwatersheds to treat) and the extent of conservation investment to undertake (how much cropland within a subwatershed to treat). We use process models to simulate the dynamics of the effects of cropland conservation investments on nutrient delivery to the Gulf and use an evolutionary algorithm to solve the optimization problem. Model results suggest that by targeting cropland conservation investments to the most cost-effective location and extent of coverage, the Action Plan goal of 5,000 km2 can be achieved at a cost of $2.7 billion annually. A large set of cost-hypoxia tradeoffs is developed, ranging from the baseline to the nontargeted adoption of the most aggressive cropland conservation investments in all subwatersheds (estimated to reduce the hypoxic zone to less than 3,000 km2 at a cost of $5.6 billion annually). PMID:25512489

Protecting Important Sites for Biodiversity Contributes to Meeting Global Conservation Targets

PubMed Central

Butchart, Stuart H. M.; Scharlemann, Jörn P. W.; Evans, Mike I.; Quader, Suhel; Aricò, Salvatore; Arinaitwe, Julius; Balman, Mark; Bennun, Leon A.; Bertzky, Bastian; Besançon, Charles; Boucher, Timothy M.; Brooks, Thomas M.; Burfield, Ian J.; Burgess, Neil D.; Chan, Simba; Clay, Rob P.; Crosby, Mike J.; Davidson, Nicholas C.; De Silva, Naamal; Devenish, Christian; Dutson, Guy C. L.; Fernández, David F. Día z; Fishpool, Lincoln D. C.; Fitzgerald, Claire; Foster, Matt; Heath, Melanie F.; Hockings, Marc; Hoffmann, Michael; Knox, David; Larsen, Frank W.; Lamoreux, John F.; Loucks, Colby; May, Ian; Millett, James; Molloy, Dominic; Morling, Paul; Parr, Mike; Ricketts, Taylor H.; Seddon, Nathalie; Skolnik, Benjamin; Stuart, Simon N.; Upgren, Amy; Woodley, Stephen

2012-01-01

Protected areas (PAs) are a cornerstone of conservation efforts and now cover nearly 13% of the world's land surface, with the world's governments committed to expand this to 17%. However, as biodiversity continues to decline, the effectiveness of PAs in reducing the extinction risk of species remains largely untested. We analyzed PA coverage and trends in species' extinction risk at globally significant sites for conserving birds (10,993 Important Bird Areas, IBAs) and highly threatened vertebrates and conifers (588 Alliance for Zero Extinction sites, AZEs) (referred to collectively hereafter as ‘important sites’). Species occurring in important sites with greater PA coverage experienced smaller increases in extinction risk over recent decades: the increase was half as large for bird species with>50% of the IBAs at which they occur completely covered by PAs, and a third lower for birds, mammals and amphibians restricted to protected AZEs (compared with unprotected or partially protected sites). Globally, half of the important sites for biodiversity conservation remain unprotected (49% of IBAs, 51% of AZEs). While PA coverage of important sites has increased over time, the proportion of PA area covering important sites, as opposed to less important land, has declined (by 0.45–1.14% annually since 1950 for IBAs and 0.79–1.49% annually for AZEs). Thus, while appropriately located PAs may slow the rate at which species are driven towards extinction, recent PA network expansion has under-represented important sites. We conclude that better targeted expansion of PA networks would help to improve biodiversity trends. PMID:22457717

Elemental conservation units: communicating extinction risk without dictating targets for protection.

PubMed

Wood, Chris C; Gross, Mart R

2008-02-01

Conservation biologists mostly agree on the need to identify and protect biodiversity below the species level but have not yet resolved the best approach. We addressed 2 issues relevant to this debate. First, we distinguished between the abstract goal of preserving the maximum amount of unique biodiversity and the pragmatic goal of minimizing the loss of ecological goods and services given that further loss of biodiversity seems inevitable. Second, we distinguished between the scientific task of assessing extinction risk and the normative task of choosing targets for protection. We propose that scientific advice on extinction risk be given at the smallest meaningful scale: the elemental conservation unit (ECU). An ECU is a demographically isolated population whose probability of extinction over the time scale of interest (say 100 years) is not substantially affected by natural immigration from other populations. Within this time frame, the loss of an ECU would be irreversible without human intervention. Society's decision to protect an ECU ought to reflect human values that have social, economic, and political dimensions. Scientists can best inform this decision by providing advice about the probability that an ECU will be lost and the ecological and evolutionary consequences of that loss in a form that can be integrated into landscape planning. The ECU approach provides maximum flexibility to decision makers and ensures that the scientific task of assessing extinction risk informs, but remains distinct from, the normative social challenge of setting conservation targets.

Target validation of highly conserved Amblyomma americanum tick saliva serine protease inhibitor 19

PubMed Central

Kim, Tae K.; Radulovic, Zeljko; Mulenga, Albert

2016-01-01

Amblyomma americanum tick serine protease inhibitor (serpin, AAS) 19, is a highly conserved protein that is characterized by its functional domain being 100% conserved across tick species. We also reported that AAS19 was an immunogenic tick saliva protein with anti-haemostatic functions and an inhibitor of trypsin-like proteases including five of the eight serine protease factors in the blood clotting cascade. In this study the goal was to validate the importance of AAS19 in A. americanum tick physiology, assess immunogenicity and investigate tick vaccine efficacy of yeast-expressed recombinant (r) AAS19. We confirm that AAS19 is important to A. americanum fitness and blood meal feeding. AAS19 mRNA disruption by RNAi silencing caused ticks to obtain blood meals that were 50% smaller than controls, and treated ticks being morphologically deformed with 100% of the deformed ticks dying in incubation. We show that rAAS19 is highly immunogenic in that two 500 µg inoculations mixed with TiterMax Gold adjuvant provoked antibody titers of more than 1:320000 that specifically reacted with native AAS19 in unfed and partially fed tick tissue. Since AAS19 is injected into animals during tick feeding, we challenge infested immunized rabbits twice to test if tick infestations of immunized rabbits could act as booster. While in the first infestation significantly smaller tick blood meals were observed on one of the two immunized rabbits, smaller blood meals were observed on both rabbits, but 60% of ticks that engorged on immunized rabbits in the second infestation failed to lay eggs. It is notable that ticks fed faster on immunized animals despite obtaining smaller blood meals. We conclude that rAAS19 is a potential component of cocktail tick vaccine. PMID:26746129

A high density field reversed configuration (FRC) target for magnetized target fusion: First internal profile measurements of a high density FRC

NASA Astrophysics Data System (ADS)

Intrator, T.; Zhang, S. Y.; Degnan, J. H.; Furno, I.; Grabowski, C.; Hsu, S. C.; Ruden, E. L.; Sanchez, P. G.; Taccetti, J. M.; Tuszewski, M.; Waganaar, W. J.; Wurden, G. A.

2004-05-01

Magnetized target fusion (MTF) is a potentially low cost path to fusion, intermediate in plasma regime between magnetic and inertial fusion energy. It requires compression of a magnetized target plasma and consequent heating to fusion relevant conditions inside a converging flux conserver. To demonstrate the physics basis for MTF, a field reversed configuration (FRC) target plasma has been chosen that will ultimately be compressed within an imploding metal liner. The required FRC will need large density, and this regime is being explored by the FRX-L (FRC-Liner) experiment. All theta pinch formed FRCs have some shock heating during formation, but FRX-L depends further on large ohmic heating from magnetic flux annihilation to heat the high density (2-5×1022m-3), plasma to a temperature of Te+Ti≈500 eV. At the field null, anomalous resistivity is typically invoked to characterize the resistive like flux dissipation process. The first resistivity estimate for a high density collisional FRC is shown here. The flux dissipation process is both a key issue for MTF and an important underlying physics question.

Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites.

PubMed

Betel, Doron; Koppal, Anjali; Agius, Phaedra; Sander, Chris; Leslie, Christina

2010-01-01

mirSVR is a new machine learning method for ranking microRNA target sites by a down-regulation score. The algorithm trains a regression model on sequence and contextual features extracted from miRanda-predicted target sites. In a large-scale evaluation, miRanda-mirSVR is competitive with other target prediction methods in identifying target genes and predicting the extent of their downregulation at the mRNA or protein levels. Importantly, the method identifies a significant number of experimentally determined non-canonical and non-conserved sites.

Conserved and Variant Epitopes of Plasmodium vivax Duffy Binding Protein as Targets of Inhibitory Monoclonal Antibodies

PubMed Central

Ntumngia, Francis B.; Schloegel, Jesse; Barnes, Samantha J.; McHenry, Amy M.; Singh, Sanjay; King, Christopher L.

2012-01-01

The Duffy binding protein (DBP) is a vital ligand for Plasmodium vivax blood-stage merozoite invasion, making the molecule an attractive vaccine candidate against vivax malaria. Similar to other blood-stage vaccine candidates, DBP allelic variation eliciting a strain-specific immunity may be a major challenge for development of a broadly effective vaccine against vivax malaria. To understand whether conserved epitopes can be the target of neutralizing anti-DBP inhibition, we generated a set of monoclonal antibodies to DBP and functionally analyzed their reactivity to a panel of allelic variants. Quantitative analysis by enzyme-linked immunosorbent assay (ELISA) determined that some monoclonal antibodies reacted strongly with epitopes conserved on all DBP variants tested, while reactivity of others was allele specific. Qualitative analysis characterized by anti-DBP functional inhibition using an in vitro erythrocyte binding inhibition assay indicated that there was no consistent correlation between the endpoint titers and functional inhibition. Some monoclonal antibodies were broadly inhibitory while inhibition of others varied significantly by target allele. These data demonstrate a potential for vaccine-elicited immunization to target conserved epitopes but optimization of DBP epitope target specificity and immunogenicity may be necessary for protection against diverse P. vivax strains. PMID:22215740

Conserved and variant epitopes of Plasmodium vivax Duffy binding protein as targets of inhibitory monoclonal antibodies.

PubMed

Ntumngia, Francis B; Schloegel, Jesse; Barnes, Samantha J; McHenry, Amy M; Singh, Sanjay; King, Christopher L; Adams, John H

2012-03-01

The Duffy binding protein (DBP) is a vital ligand for Plasmodium vivax blood-stage merozoite invasion, making the molecule an attractive vaccine candidate against vivax malaria. Similar to other blood-stage vaccine candidates, DBP allelic variation eliciting a strain-specific immunity may be a major challenge for development of a broadly effective vaccine against vivax malaria. To understand whether conserved epitopes can be the target of neutralizing anti-DBP inhibition, we generated a set of monoclonal antibodies to DBP and functionally analyzed their reactivity to a panel of allelic variants. Quantitative analysis by enzyme-linked immunosorbent assay (ELISA) determined that some monoclonal antibodies reacted strongly with epitopes conserved on all DBP variants tested, while reactivity of others was allele specific. Qualitative analysis characterized by anti-DBP functional inhibition using an in vitro erythrocyte binding inhibition assay indicated that there was no consistent correlation between the endpoint titers and functional inhibition. Some monoclonal antibodies were broadly inhibitory while inhibition of others varied significantly by target allele. These data demonstrate a potential for vaccine-elicited immunization to target conserved epitopes but optimization of DBP epitope target specificity and immunogenicity may be necessary for protection against diverse P. vivax strains.

The Malarial Host-Targeting Signal Is Conserved in the Irish Potato Famine Pathogen

PubMed Central

Liolios, Konstantinos; Win, Joe; Kanneganti, Thirumala-Devi; Young, Carolyn; Kamoun, Sophien; Haldar, Kasturi

2006-01-01

Animal and plant eukaryotic pathogens, such as the human malaria parasite Plasmodium falciparum and the potato late blight agent Phytophthora infestans, are widely divergent eukaryotic microbes. Yet they both produce secretory virulence and pathogenic proteins that alter host cell functions. In P. falciparum, export of parasite proteins to the host erythrocyte is mediated by leader sequences shown to contain a host-targeting (HT) motif centered on an RxLx (E, D, or Q) core: this motif appears to signify a major pathogenic export pathway with hundreds of putative effectors. Here we show that a secretory protein of P. infestans, which is perceived by plant disease resistance proteins and induces hypersensitive plant cell death, contains a leader sequence that is equivalent to the Plasmodium HT-leader in its ability to export fusion of green fluorescent protein (GFP) from the P. falciparum parasite to the host erythrocyte. This export is dependent on an RxLR sequence conserved in P. infestans leaders, as well as in leaders of all ten secretory oomycete proteins shown to function inside plant cells. The RxLR motif is also detected in hundreds of secretory proteins of P. infestans, Phytophthora sojae, and Phytophthora ramorum and has high value in predicting host-targeted leaders. A consensus motif further reveals E/D residues enriched within ~25 amino acids downstream of the RxLR, which are also needed for export. Together the data suggest that in these plant pathogenic oomycetes, a consensus HT motif may reside in an extended sequence of ~25–30 amino acids, rather than in a short linear sequence. Evidence is presented that although the consensus is much shorter in P. falciparum, information sufficient for vacuolar export is contained in a region of ~30 amino acids, which includes sequences flanking the HT core. Finally, positional conservation between Phytophthora RxLR and P. falciparum RxLx (E, D, Q) is consistent with the idea that the context of their

Conserving rare species can have high opportunity costs for common species.

PubMed

Neeson, Thomas M; Doran, Patrick J; Ferris, Michael C; Fitzpatrick, Kimberly B; Herbert, Matthew; Khoury, Mary; Moody, Allison T; Ross, Jared; Yacobson, Eugene; McIntyre, Peter B

2018-04-13

Conservation practitioners face difficult choices in apportioning limited resources between rare species (to ensure their existence) and common species (to ensure their abundance and ecosystem contributions). We quantified the opportunity costs of conserving rare species of migratory fishes in the context of removing dams and retrofitting road culverts across 1,883 tributaries of the North American Great Lakes. Our optimization models show that maximizing total habitat gains across species can be very efficient in terms of benefits achieved per dollar spent, but disproportionately benefits common species. Conservation approaches that target rare species, or that ensure some benefits for every species (i.e., complementarity) enable strategic allocation of resources among species but reduce aggregate habitat gains. Thus, small habitat gains for the rarest species necessarily come at the expense of more than 20 times as much habitat for common ones. These opportunity costs are likely to occur in many ecosystems because range limits and conservation costs often vary widely among species. Given that common species worldwide are declining more rapidly than rare ones within major taxa, our findings provide incentive for triage among multiple worthy conservation targets. © 2018 John Wiley & Sons Ltd.

Interregional sharing of energy conservation targets in China: Efficiency and equity

NASA Astrophysics Data System (ADS)

Wei, Dan

implications differ across the applications of various equity criteria. However, for the energy production-based sovereignty and egalitarian equity criteria, the poorest region (in terms of per capita gross regional product) can enjoy net profits from trading, while the clustered region of wealthy coastal provinces shoulders the highest cost. This indicates that a conservation-quota trading system applying these two equity criteria is consistent with the national strategy in China to reduce regional income disparities and to develop the interior and western less-developed regions of the country. Third, compared with trading among conventional regions, trading among statistically clustered regions can more sharply apply the equity criteria to burden sharing and utilize larger differences in marginal conservation costs between regions to achieve a lower total net cost for the country as a whole. In sum, this research develops a useful methodology and identifies an operational way to attain energy conservation targets in China. It offers insights for similar interregional burden-sharing or benefit-sharing policies for China in the future, such as greenhouse gas emission trading, which is closely related to the energy conservation issue.

Identification of microRNAs and their targets in Finger millet by high throughput sequencing.

PubMed

Usha, S; Jyothi, M N; Sharadamma, N; Dixit, Rekha; Devaraj, V R; Nagesh Babu, R

2015-12-15

MicroRNAs are short non-coding RNAs which play an important role in regulating gene expression by mRNA cleavage or by translational repression. The majority of identified miRNAs were evolutionarily conserved; however, others expressed in a species-specific manner. Finger millet is an important cereal crop; nonetheless, no practical information is available on microRNAs to date. In this study, we have identified 95 conserved microRNAs belonging to 39 families and 3 novel microRNAs by high throughput sequencing. For the identified conserved and novel miRNAs a total of 507 targets were predicted. 11 miRNAs were validated and tissue specificity was determined by stem loop RT-qPCR, Northern blot. GO analyses revealed targets of miRNA were involved in wide range of regulatory functions. This study implies large number of known and novel miRNAs found in Finger millet which may play important role in growth and development. Copyright © 2015 Elsevier B.V. All rights reserved.

Studies of uranium carbide targets of a high density

NASA Astrophysics Data System (ADS)

Panteleev, V. N.; Alyakrinskiy, O.; Barbui, M.; Barzakh, A. E.; Dubois, M.; Eleon, C.; Essabaa, S.; Fedorov, D. V.; Gaubert, G.; Ionan, A. M.; Ivanov, V. S.; Jardin, P.; Lau, C.; Leroy, R.; Lhersonneau, G.; Mezilev, K. A.; Mhamed, C.; Molkanov, P. L.; Moroz, F. V.; Orlov, S. Yu.; Saint Laurent, M. G.; Stroe, L.; Tecchio, L. B.; Tonezzer, M.; Villari, A. C. C.; Volkov, Yu. M.

2008-10-01

Production of Cs and Fr isotopes from uranium carbide targets of a high density has been investigated at IRIS (Investigation Radioactive Isotopes at Synchrocyclotron), Gatchina. The UC target material with a density of 12 g/cm3 was prepared in a form of pellets. Two targets were tested on-line under the same temperature conditions: (a) a reference small target with a thickness of 4.5 g/cm2; (b) a heavier (so called intermediate) target with a thickness of 91 g/cm2. Yields and release efficiencies of nuclides with half-lives from some minutes to some milliseconds produced by 1 GeV protons in these targets are presented. It is remarkable that yields, even those of very short-lived isotopes such as 214Fr (T1/2 = 5 ms) and 219Fr (T1/2 = 20 ms), increase proportionally to the target thickness. A one month off-line heating test of the 91 g/cm2 target at a temperature of 2000 °C has been carried out successfully. The yields and release efficiencies of Cs and Fr measured on-line before and after the heating test coincided within the limits of measurement errors, thereby demonstrating the conservation of the target unit parameters. Based on these very promising results, a heavier target with a mass about 0.7 kg is prepared presently at IRIS.

Functional Targets of the Monogenic Diabetes Transcription Factors HNF-1α and HNF-4α Are Highly Conserved Between Mice and Humans

PubMed Central

Boj, Sylvia F.; Servitja, Joan Marc; Martin, David; Rios, Martin; Talianidis, Iannis; Guigo, Roderic; Ferrer, Jorge

2009-01-01

OBJECTIVE The evolutionary conservation of transcriptional mechanisms has been widely exploited to understand human biology and disease. Recent findings, however, unexpectedly showed that the transcriptional regulators hepatocyte nuclear factor (HNF)-1α and -4α rarely bind to the same genes in mice and humans, leading to the proposal that tissue-specific transcriptional regulation has undergone extensive divergence in the two species. Such observations have major implications for the use of mouse models to understand HNF-1α– and HNF-4α–deficient diabetes. However, the significance of studies that assess binding without considering regulatory function is poorly understood. RESEARCH DESIGN AND METHODS We compared previously reported mouse and human HNF-1α and HNF-4α binding studies with independent binding experiments. We also integrated binding studies with mouse and human loss-of-function gene expression datasets. RESULTS First, we confirmed the existence of species-specific HNF-1α and -4α binding, yet observed incomplete detection of binding in the different datasets, causing an underestimation of binding conservation. Second, only a minor fraction of HNF-1α– and HNF-4α–bound genes were downregulated in the absence of these regulators. This subset of functional targets did not show evidence for evolutionary divergence of binding or binding sequence motifs. Finally, we observed differences between conserved and species-specific binding properties. For example, conserved binding was more frequently located near transcriptional start sites and was more likely to involve multiple binding events in the same gene. CONCLUSIONS Despite evolutionary changes in binding, essential direct transcriptional functions of HNF-1α and -4α are largely conserved between mice and humans. PMID:19188435

Coevolution Pattern and Functional Conservation or Divergence of miR167s and their targets across Diverse Plant Species.

PubMed

Barik, Suvakanta; Kumar, Ashutosh; Sarkar Das, Shabari; Yadav, Sandeep; Gautam, Vibhav; Singh, Archita; Singh, Sharmila; Sarkar, Ananda K

2015-10-13

microRNAs (miRNAs), a class of endogenously produced small non-coding RNAs of 20-21 nt length, processed from precursor miRNAs, regulate many developmental processes by negatively regulating the target genes in both animals and plants. The coevolutionary pattern of a miRNA family and their targets underscores its functional conservation or diversification. The miR167 regulates various aspects of plant development in Arabidopsis by targeting ARF6 and ARF8. The evolutionary conservation or divergence of miR167s and their target genes are poorly understood till now. Here we show the evolutionary relationship among 153 MIR167 genes obtained from 33 diverse plant species. We found that out of the 153 of miR167 sequences retrieved from the "miRBase", 27 have been annotated to be processed from the 3' end, and have diverged distinctively from the other miR167s produced from 5' end. Our analysis reveals that gma-miR167h/i and mdm-miR167a are processed from 3' end and have evolved separately, diverged most resulting in novel targets other than their known ones, and thus led to functional diversification, especially in apple and soybean. We also show that mostly conserved miR167 sequences and their target AUXIN RESPONSE FACTORS (ARFs) have gone through parallel evolution leading to functional diversification among diverse plant species.

Achieving Aichi Biodiversity Target 11 to improve the performance of protected areas and conserve freshwater biodiversity

Treesearch

Diego Juffe-Bignoli; Ian Harrison; Stuart HM Butchart; Rebecca Flitcroft; Virgilio Hermoso; Harry Jonas; Anna Lukasiewicz; Michele Thieme; Eren Turak; Heather Bingham; James Dalton; William Darwall; Marine Deguignet; Nigel Dudley; Royal Gardner; Jonathan Higgins; Ritesh Kumar; Simon Linke; G Randy Milton; Jamie Pittock; Kevin G Smith; Arnout van Soesbergen

2016-01-01

1. The Strategic Plan for Biodiversity (2011–2020), adopted at the 10th meeting of the Conference of the Parties to the Convention on Biological Diversity, sets 20 Aichi Biodiversity Targets to be met by 2020 to address biodiversity loss and ensure its sustainable and equitable use. Aichi Biodiversity Target 11 describes what an improved conservation network would look...

Universal antibodies against the highly conserved influenza fusion peptide cross-neutralize several subtypes of influenza A virus

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hashem, Anwar M.; Department of Microbiology, Faculty of Medicine, King Abdulaziz University, Jeddah; Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON

Research highlights: {yields} The fusion peptide is the only universally conserved epitope in all influenza viral hemagglutinins. {yields} Anti-fusion peptide antibodies are universal antibodies that cross-react with all influenza HA subtypes. {yields} The universal antibodies cross-neutralize different influenza A subtypes. {yields} The universal antibodies inhibit the fusion process between the viruses and the target cells. -- Abstract: The fusion peptide of influenza viral hemagglutinin plays a critical role in virus entry by facilitating membrane fusion between the virus and target cells. As the fusion peptide is the only universally conserved epitope in all influenza A and B viruses, it couldmore » be an attractive target for vaccine-induced immune responses. We previously reported that antibodies targeting the first 14 amino acids of the N-terminus of the fusion peptide could bind to virtually all influenza virus strains and quantify hemagglutinins in vaccines produced in embryonated eggs. Here we demonstrate that these universal antibodies bind to the viral hemagglutinins in native conformation presented in infected mammalian cell cultures and neutralize multiple subtypes of virus by inhibiting the pH-dependant fusion of viral and cellular membranes. These results suggest that this unique, highly-conserved linear sequence in viral hemagglutinin is exposed sufficiently to be attacked by the antibodies during the course of infection and merits further investigation because of potential importance in the protection against diverse strains of influenza viruses.« less

Use of ancient sedimentary DNA as a novel conservation tool for high-altitude tropical biodiversity.

PubMed

Boessenkool, Sanne; McGlynn, Gayle; Epp, Laura S; Taylor, David; Pimentel, Manuel; Gizaw, Abel; Nemomissa, Sileshi; Brochmann, Christian; Popp, Magnus

2014-04-01

Conservation of biodiversity may in the future increasingly depend upon the availability of scientific information to set suitable restoration targets. In traditional paleoecology, sediment-based pollen provides a means to define preanthropogenic impact conditions, but problems in establishing the exact provenance and ecologically meaningful levels of taxonomic resolution of the evidence are limiting. We explored the extent to which the use of sedimentary ancient DNA (sedaDNA) may complement pollen data in reconstructing past alpine environments in the tropics. We constructed a record of afro-alpine plants retrieved from DNA preserved in sediment cores from 2 volcanic crater sites in the Albertine Rift, eastern Africa. The record extended well beyond the onset of substantial anthropogenic effects on tropical mountains. To ensure high-quality taxonomic inference from the sedaDNA sequences, we built an extensive DNA reference library covering the majority of the afro-alpine flora, by sequencing DNA from taxonomically verified specimens. Comparisons with pollen records from the same sediment cores showed that plant diversity recovered with sedaDNA improved vegetation reconstructions based on pollen records by revealing both additional taxa and providing increased taxonomic resolution. Furthermore, combining the 2 measures assisted in distinguishing vegetation change at different geographic scales; sedaDNA almost exclusively reflects local vegetation, whereas pollen can potentially originate from a wide area that in highlands in particular can span several ecozones. Our results suggest that sedaDNA may provide information on restoration targets and the nature and magnitude of human-induced environmental changes, including in high conservation priority, biodiversity hotspots, where understanding of preanthropogenic impact (or reference) conditions is highly limited. © 2013 Society for Conservation Biology.

Conservation genetics of high elevation five-needle white pines

Treesearch

Andrew D. Bower; Sierra C. McLane; Andrew Eckert; Stacy Jorgensen; Anna Schoettle; Sally Aitken

2011-01-01

Conservation genetics examines the biophysical factors influencing genetic processes and uses that information to conserve and maintain the evolutionary potential of species and populations. Here we review published and unpublished literature on the conservation genetics of seven North American high-elevation five-needle pines. Although these species are widely...

Coevolution Pattern and Functional Conservation or Divergence of miR167s and their targets across Diverse Plant Species

PubMed Central

Barik, Suvakanta; Kumar, Ashutosh; Sarkar Das, Shabari; Yadav, Sandeep; Gautam, Vibhav; Singh, Archita; Singh, Sharmila; Sarkar, Ananda K.

2015-01-01

microRNAs (miRNAs), a class of endogenously produced small non-coding RNAs of 20–21 nt length, processed from precursor miRNAs, regulate many developmental processes by negatively regulating the target genes in both animals and plants. The coevolutionary pattern of a miRNA family and their targets underscores its functional conservation or diversification. The miR167 regulates various aspects of plant development in Arabidopsis by targeting ARF6 and ARF8. The evolutionary conservation or divergence of miR167s and their target genes are poorly understood till now. Here we show the evolutionary relationship among 153 MIR167 genes obtained from 33 diverse plant species. We found that out of the 153 of miR167 sequences retrieved from the “miRBase”, 27 have been annotated to be processed from the 3′ end, and have diverged distinctively from the other miR167s produced from 5′ end. Our analysis reveals that gma-miR167h/i and mdm-miR167a are processed from 3′ end and have evolved separately, diverged most resulting in novel targets other than their known ones, and thus led to functional diversification, especially in apple and soybean. We also show that mostly conserved miR167 sequences and their target AUXIN RESPONSE FACTORS (ARFs) have gone through parallel evolution leading to functional diversification among diverse plant species. PMID:26459056

An assessment of high carbon stock and high conservation value approaches to sustainable oil palm cultivation in Gabon

NASA Astrophysics Data System (ADS)

Austin, Kemen G.; Lee, Michelle E.; Clark, Connie; Forester, Brenna R.; Urban, Dean L.; White, Lee; Kasibhatla, Prasad S.; Poulsen, John R.

2017-01-01

Industrial-scale oil palm cultivation is rapidly expanding in Gabon, where it has the potential to drive economic growth, but also threatens forest, biodiversity and carbon resources. The Gabonese government is promoting an ambitious agricultural expansion strategy, while simultaneously committing to minimize negative environmental impacts of oil palm agriculture. This study estimates the extent and location of suitable land for oil palm cultivation in Gabon, based on an analysis of recent trends in plantation permitting. We use the resulting suitability map to evaluate two proposed approaches to minimizing negative environmental impacts: a High Carbon Stock (HCS) approach, which emphasizes forest protection and climate change mitigation, and a High Conservation Value (HCV) approach, which focuses on safeguarding biodiversity and ecosystems. We quantify the forest area, carbon stock, and biodiversity resources protected under each approach, using newly developed maps of priority species distributions and forest biomass for Gabon. We find 2.7-3.9 Mha of suitable or moderately suitable land that avoid HCS areas, 4.4 million hectares (Mha) that avoid HCV areas, and 1.2-1.7 Mha that avoid both. This suggests that Gabon’s oil palm production target could likely be met without compromising important ecosystem services, if appropriate safeguards are put in place. Our analysis improves understanding of suitability for oil palm in Gabon, determines how conservation strategies align with national targets for oil palm production, and informs national land use planning.

Habitat Re-Creation (Ecological Restoration) as a Strategy for Conserving Insect Communities in Highly Fragmented Landscapes

PubMed Central

Shuey, John A.

2013-01-01

Because of their vast diversity, measured by both numbers of species as well as life history traits, insects defy comprehensive conservation planning. Thus, almost all insect conservation efforts target individual species. However, serious insect conservation requires goals that are set at the faunal level and conservation success requires strategies that conserve intact communities. This task is complicated in agricultural landscapes by high levels of habitat fragmentation and isolation. In many regions, once widespread insect communities are now functionally trapped on islands of ecosystem remnants and subject to a variety of stressors associated with isolation, small population sizes and artificial population fragmentation. In fragmented landscapes ecological restoration can be an effective strategy for reducing localized insect extinction rates, but insects are seldom included in restoration design criteria. It is possible to incorporate a few simple conservation criteria into restoration designs that enhance impacts to entire insect communities. Restoration can be used as a strategy to address fragmentation threats to isolated insect communities if insect communities are incorporated at the onset of restoration planning. Fully incorporating insect communities into restoration designs may increase the cost of restoration two- to three-fold, but the benefits to biodiversity conservation and the ecological services provided by intact insect communities justify the cost. PMID:26462535

Habitat Re-Creation (Ecological Restoration) as a Strategy for Conserving Insect Communities in Highly Fragmented Landscapes.

PubMed

Shuey, John A

2013-12-05

Because of their vast diversity, measured by both numbers of species as well as life history traits, insects defy comprehensive conservation planning. Thus, almost all insect conservation efforts target individual species. However, serious insect conservation requires goals that are set at the faunal level and conservation success requires strategies that conserve intact communities. This task is complicated in agricultural landscapes by high levels of habitat fragmentation and isolation. In many regions, once widespread insect communities are now functionally trapped on islands of ecosystem remnants and subject to a variety of stressors associated with isolation, small population sizes and artificial population fragmentation. In fragmented landscapes ecological restoration can be an effective strategy for reducing localized insect extinction rates, but insects are seldom included in restoration design criteria. It is possible to incorporate a few simple conservation criteria into restoration designs that enhance impacts to entire insect communities. Restoration can be used as a strategy to address fragmentation threats to isolated insect communities if insect communities are incorporated at the onset of restoration planning. Fully incorporating insect communities into restoration designs may increase the cost of restoration two- to three-fold, but the benefits to biodiversity conservation and the ecological services provided by intact insect communities justify the cost.

Silencing Effect of Hominoid Highly Conserved Noncoding Sequences on Embryonic Brain Development

PubMed Central

Mahmoudi Saber, Morteza

2017-01-01

Abstract Superfamily Hominoidea, which consists of Hominidae (humans and great apes) and Hylobatidae (gibbons), is well-known for sharing human-like characteristics, however, the genomic origins of these shared unique phenotypes have mainly remained elusive. To decipher the underlying genomic basis of Hominoidea-restricted phenotypes, we identified and characterized Hominoidea-restricted highly conserved noncoding sequences (HCNSs) that are a class of potential regulatory elements which may be involved in evolution of lineage-specific phenotypes. We discovered 679 such HCNSs from human, chimpanzee, gorilla, orangutan and gibbon genomes. These HCNSs were demonstrated to be under purifying selection but with lineage-restricted characteristics different from old CNSs. A significant proportion of their ancestral sequences had accelerated rates of nucleotide substitutions, insertions and deletions during the evolution of common ancestor of Hominoidea, suggesting the intervention of positive Darwinian selection for creating those HCNSs. In contrary to enhancer elements and similar to silencer sequences, these Hominoidea-restricted HCNSs are located in close proximity of transcription start sites. Their target genes are enriched in the nervous system, development and transcription, and they tend to be remotely located from the nearest coding gene. Chip-seq signals and gene expression patterns suggest that Hominoidea-restricted HCNSs are likely to be functional regulatory elements by imposing silencing effects on their target genes in a tissue-restricted manner during fetal brain development. These HCNSs, emerged through adaptive evolution and conserved through purifying selection, represent a set of promising targets for future functional studies of the evolution of Hominoidea-restricted phenotypes. PMID:28633494

Orchid conservation: further links.

PubMed

Fay, Michael F

2016-07-01

Due in great part to their often complex interactions with mycorrhizal fungi, pollinators and host trees, Orchidaceae present particular challenges for conservation. Furthermore, orchids, as potentially the largest family of angiosperms with >26000 species, species complexes and frequent hybrid formation, are complex to catalogue. Following a highlight in 2015, a further seven papers focusing on orchids, their interactions with beneficial organisms, pollinators and mycorrhiza, and other factors relating to their conservation, including threats from human utilization and changing land use, are presented here. The production of an online flora of all known plants and an assessment of the conservation status of all known plant species as far as possible, to guide conservation action are the first two targets of the Global Strategy for Plant Conservation Without knowing how many species there are and how they should be circumscribed, neither of these targets is achievable. Orchids are a fascinating subject for fundamental research with rapid species evolution, specific organ structure and development, but they also suffer from high levels of threat. Effective orchid conservation must take account of the beneficial interactions with fungi and pollinators and the potentially detrimental effects of over-collection and changes in land use. © The Author 2016. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Structural Basis for Conserved Regulation and Adaptation of the Signal Recognition Particle Targeting Complex.

PubMed

Wild, Klemens; Bange, Gert; Motiejunas, Domantas; Kribelbauer, Judith; Hendricks, Astrid; Segnitz, Bernd; Wade, Rebecca C; Sinning, Irmgard

2016-07-17

The signal recognition particle (SRP) is a ribonucleoprotein complex with a key role in targeting and insertion of membrane proteins. The two SRP GTPases, SRP54 (Ffh in bacteria) and FtsY (SRα in eukaryotes), form the core of the targeting complex (TC) regulating the SRP cycle. The architecture of the TC and its stimulation by RNA has been described for the bacterial SRP system while this information is lacking for other domains of life. Here, we present the crystal structures of the GTPase heterodimers of archaeal (Sulfolobus solfataricus), eukaryotic (Homo sapiens), and chloroplast (Arabidopsis thaliana) SRP systems. The comprehensive structural comparison combined with Brownian dynamics simulations of TC formation allows for the description of the general blueprint and of specific adaptations of the quasi-symmetric heterodimer. Our work defines conserved external nucleotide-binding sites for SRP GTPase activation by RNA. Structural analyses of the GDP-bound, post-hydrolysis states reveal a conserved, magnesium-sensitive switch within the I-box. Overall, we provide a general model for SRP cycle regulation by RNA. Copyright © 2016 Elsevier Ltd. All rights reserved.

Dynamic conservation of forest genetic resources in 33 European countries.

PubMed

Lefèvre, François; Koskela, Jarkko; Hubert, Jason; Kraigher, Hojka; Longauer, Roman; Olrik, Ditte C; Schüler, Silvio; Bozzano, Michele; Alizoti, Paraskevi; Bakys, Remigijus; Baldwin, Cathleen; Ballian, Dalibor; Black-Samuelsson, Sanna; Bednarova, Dagmar; Bordács, Sándor; Collin, Eric; de Cuyper, Bart; de Vries, Sven M G; Eysteinsson, Thröstur; Frýdl, Josef; Haverkamp, Michaela; Ivankovic, Mladen; Konrad, Heino; Koziol, Czesław; Maaten, Tiit; Notivol Paino, Eduardo; Oztürk, Hikmet; Pandeva, Ivanova Denitsa; Parnuta, Gheorghe; Pilipovič, Andrej; Postolache, Dragos; Ryan, Cathal; Steffenrem, Arne; Varela, Maria Carolina; Vessella, Federico; Volosyanchuk, Roman T; Westergren, Marjana; Wolter, Frank; Yrjänä, Leena; Zariŋa, Inga

2013-04-01

Dynamic conservation of forest genetic resources (FGR) means maintaining the genetic diversity of trees within an evolutionary process and allowing generation turnover in the forest. We assessed the network of forests areas managed for the dynamic conservation of FGR (conservation units) across Europe (33 countries). On the basis of information available in the European Information System on FGR (EUFGIS Portal), species distribution maps, and environmental stratification of the continent, we developed ecogeographic indicators, a marginality index, and demographic indicators to assess and monitor forest conservation efforts. The pan-European network has 1967 conservation units, 2737 populations of target trees, and 86 species of target trees. We detected a poor coincidence between FGR conservation and other biodiversity conservation objectives within this network. We identified 2 complementary strategies: a species-oriented strategy in which national conservation networks are specifically designed for key target species and a site-oriented strategy in which multiple-target units include so-called secondary species conserved within a few sites. The network is highly unbalanced in terms of species representation, and 7 key target species are conserved in 60% of the conservation units. We performed specific gap analyses for 11 tree species, including assessment of ecogeographic, demographic, and genetic criteria. For each species, we identified gaps, particularly in the marginal parts of their distribution range, and found multiple redundant conservation units in other areas. The Mediterranean forests and to a lesser extent the boreal forests are underrepresented. Monitoring the conservation efficiency of each unit remains challenging; however, <2% of the conserved populations seem to be at risk of extinction. On the basis of our results, we recommend combining species-oriented and site-oriented strategies. © 2012 Society for Conservation Biology.

Targeting Conserved Genes in Fusarium Species.

PubMed

Gil-Serna, Jéssica; Patiño, Belén; Jurado, Miguel; Mirete, Salvador; Vázquez, Covadonga; González-Jaén, M Teresa

2017-01-01

Fumonisins are important mycotoxins contaminating foods and feeds which are mainly produced by F. verticillioides and F. proliferatum. Additionally, both are pathogens of maize and other cereals. We describe two highly sensitive, rapid, and species-specific PCR protocols which enable detection and discrimination of these closely related species in cereal flour or grain samples. The specific primer pairs of these assays were based on the intergenic spacer region of the multicopy rDNA unit which highly improves the sensitivity of the PCR assay in comparison with single-copy target regions.

Methylated glycans as conserved targets of animal and fungal innate defense

PubMed Central

Wohlschlager, Therese; Butschi, Alex; Grassi, Paola; Sutov, Grigorij; Gauss, Robert; Hauck, Dirk; Schmieder, Stefanie S.; Knobel, Martin; Titz, Alexander; Dell, Anne; Haslam, Stuart M.; Hengartner, Michael O.; Aebi, Markus; Künzler, Markus

2014-01-01

Effector proteins of innate immune systems recognize specific non-self epitopes. Tectonins are a family of β-propeller lectins conserved from bacteria to mammals that have been shown to bind bacterial lipopolysaccharide (LPS). We present experimental evidence that two Tectonins of fungal and animal origin have a specificity for O-methylated glycans. We show that Tectonin 2 of the mushroom Laccaria bicolor (Lb-Tec2) agglutinates Gram-negative bacteria and exerts toxicity toward the model nematode Caenorhabditis elegans, suggesting a role in fungal defense against bacteria and nematodes. Biochemical and genetic analysis of these interactions revealed that both bacterial agglutination and nematotoxicity of Lb-Tec2 depend on the recognition of methylated glycans, namely O-methylated mannose and fucose residues, as part of bacterial LPS and nematode cell-surface glycans. In addition, a C. elegans gene, termed samt-1, coding for a candidate membrane transport protein for the presumptive donor substrate of glycan methylation, S-adenosyl-methionine, from the cytoplasm to the Golgi was identified. Intriguingly, limulus lectin L6, a structurally related antibacterial protein of the Japanese horseshoe crab Tachypleus tridentatus, showed properties identical to the mushroom lectin. These results suggest that O-methylated glycans constitute a conserved target of the fungal and animal innate immune system. The broad phylogenetic distribution of O-methylated glycans increases the spectrum of potential antagonists recognized by Tectonins, rendering this conserved protein family a universal defense armor. PMID:24879441

Incorporating Conservation Zone Effectiveness for Protecting Biodiversity in Marine Planning

PubMed Central

Makino, Azusa; Klein, Carissa J.; Beger, Maria; Jupiter, Stacy D.; Possingham, Hugh P.

2013-01-01

Establishing different types of conservation zones is becoming commonplace. However, spatial prioritization methods that can accommodate multiple zones are poorly understood in theory and application. It is typically assumed that management regulations across zones have differential levels of effectiveness (“zone effectiveness”) for biodiversity protection, but the influence of zone effectiveness on achieving conservation targets has not yet been explored. Here, we consider the zone effectiveness of three zones: permanent closure, partial protection, and open, for planning for the protection of five different marine habitats in the Vatu-i-Ra Seascape, Fiji. We explore the impact of differential zone effectiveness on the location and costs of conservation priorities. We assume that permanent closure zones are fully effective at protecting all habitats, open zones do not contribute towards the conservation targets and partial protection zones lie between these two extremes. We use four different estimates for zone effectiveness and three different estimates for zone cost of the partial protection zone. To enhance the practical utility of the approach, we also explore how much of each traditional fishing ground can remain open for fishing while still achieving conservation targets. Our results show that all of the high priority areas for permanent closure zones would not be a high priority when the zone effectiveness of the partial protection zone is equal to that of permanent closure zones. When differential zone effectiveness and costs are considered, the resulting marine protected area network consequently increases in size, with more area allocated to permanent closure zones to meet conservation targets. By distributing the loss of fishing opportunity equitably among local communities, we find that 84–88% of each traditional fishing ground can be left open while still meeting conservation targets. Finally, we summarize the steps for developing marine zoning

High-Throughput Sequencing and Characterization of the Small RNA Transcriptome Reveal Features of Novel and Conserved MicroRNAs in Panax ginseng

PubMed Central

Ma, Yimian; Yuan, Lichai; Lu, Shanfa

2012-01-01

microRNAs (miRNAs) play vital regulatory roles in many organisms through direct cleavage of transcripts, translational repression, or chromatin modification. Identification of miRNAs has been carried out in various plant species. However, no information is available for miRNAs from Panax ginseng, an economically significant medicinal plant species. Using the next generation high-throughput sequencing technology, we obtained 13,326,328 small RNA reads from the roots, stems, leaves and flowers of P. ginseng. Analysis of these small RNAs revealed the existence of a large, diverse and highly complicated small RNA population in P. ginseng. We identified 73 conserved miRNAs, which could be grouped into 33 families, and 28 non-conserved ones belonging to 9 families. Characterization of P. ginseng miRNA precursors revealed many features, such as production of two miRNAs from distinct regions of a precursor, clusters of two precursors in a transcript, and generation of miRNAs from both sense and antisense transcripts. It suggests the complexity of miRNA production in P. gingseng. Using a computational approach, we predicted for the conserved and non-conserved miRNA families 99 and 31 target genes, respectively, of which eight were experimentally validated. Among all predicted targets, only about 20% are conserved among various plant species, whereas the others appear to be non-conserved, indicating the diversity of miRNA functions. Consistently, many miRNAs exhibited tissue-specific expression patterns. Moreover, we identified five dehydration- and ten heat-responsive miRNAs and found the existence of a crosstalk among some of the stress-responsive miRNAs. Our results provide the first clue to the elucidation of miRNA functions in P. ginseng. PMID:22962612

The yan gene is highly conserved in Drosophila and its expression suggests a complex role throughout development.

PubMed

Price, M D; Lai, Z

1999-04-01

Competence for cell fate determination and cellular differentiation is under tight control of regulatory genes. Yan, a nuclear target of receptor tyrosine kinase (RTK) signaling, is an E twenty six (ETS) DNA-binding protein that functions as a negative regulator of cell differentiation and proliferation in Drosophila. Most members of RTK signaling pathways are highly conserved through evolution, yet no yan orthologues have been identified to date in vertebrates. To investigate the degree of yan conservation during evolution, we have characterized a yan homologue from a sibling species of D. melanogaster, D. virilis. Our results show that the organization, primary structure and expression pattern of yan are highly conserved. Both genes span over 20 kb and contain four exons with introns at identical positions. The areas with highest amino acid similarity include the Pointed and ETS domain but there are other discrete regions with a high degree of similarity. Phylogenetic analysis reveals that yan's closest relative is the human tel gene, a negative regulator of differentiation in hematopoetic precursors. In both species, Yan is dynamically expressed beginning as early as stage 4/5 and persisting throughout embryogenesis. In third instar larvae, Yan is expressed in and behind the morphogenetic furrow of the eye imaginal disc as well as in the laminar precursor cells of the brain. Ovarian follicle cells also contain Yan protein. Conservation of the structure and expression patterns of yan genes strongly suggests that regulatory mechanisms for their expression are also conserved in these two species.

Consumption‐Based Conservation Targeting: Linking Biodiversity Loss to Upstream Demand through a Global Wildlife Footprint

PubMed Central

Berlow, Eric; Conlisk, Erin; Erb, Karlheinz; Iha, Katsunori; Martinez, Neo; Newman, Erica A.; Plutzar, Christoph; Smith, Adam B.; Harte, John

2016-01-01

Abstract Although most conservation efforts address the direct, local causes of biodiversity loss, effective long‐term conservation will require complementary efforts to reduce the upstream economic pressures, such as demands for food and forest products, which ultimately drive these downstream losses. Here, we present a wildlife footprint analysis that links global losses of wild birds to consumer purchases across 57 economic sectors in 129 regions. The United States, India, China, and Brazil have the largest regional wildlife footprints, while per‐person footprints are highest in Mongolia, Australia, Botswana, and the United Arab Emirates. A US$100 purchase of bovine meat or rice products occupies approximately 0.1 km2 of wild bird ranges, displacing 1–2 individual birds, for 1 year. Globally significant importer regions, including Japan, the United Kingdom, Germany, Italy, and France, have large footprints that drive wildlife losses elsewhere in the world and represent important targets for consumption‐focused conservation attention. PMID:29104616

Effect of the target power density on high-power impulse magnetron sputtering of copper

NASA Astrophysics Data System (ADS)

Kozák, Tomáš

2012-04-01

We present a model analysis of high-power impulse magnetron sputtering of copper. We use a non-stationary global model based on the particle and energy conservation equations in two zones (the high density plasma ring above the target racetrack and the bulk plasma region), which makes it possible to calculate time evolutions of the averaged process gas and target material neutral and ion densities, as well as the fluxes of these particles to the target and substrate during a pulse period. We study the effect of the increasing target power density under conditions corresponding to a real experimental system. The calculated target current waveforms show a long steady state and are in good agreement with the experimental results. For an increasing target power density, an analysis of the particle densities shows a gradual transition to a metal dominated discharge plasma with an increasing degree of ionization of the depositing flux. The average fraction of target material ions in the total ion flux onto the substrate is more than 90% for average target power densities higher than 500 W cm-2 in a pulse. The average ionized fraction of target material atoms in the flux onto the substrate reaches 80% for a maximum average target power density of 3 kW cm-2 in a pulse.

Highly conserved type 1 pili promote enterotoxigenic E. coli pathogen-host interactions

PubMed Central

Rashu, Rasheduzzaman; Begum, Yasmin Ara; Ciorba, Matthew A.; Hultgren, Scott J.; Qadri, Firdausi

2017-01-01

Enterotoxigenic Escherichia coli (ETEC), defined by their elaboration of heat-labile (LT) and/or heat-stable (ST) enterotoxins, are a common cause of diarrheal illness in developing countries. Efficient delivery of these toxins requires ETEC to engage target host enterocytes. This engagement is accomplished using a variety of pathovar-specific and conserved E. coli adhesin molecules as well as plasmid encoded colonization factors. Some of these adhesins undergo significant transcriptional modulation as ETEC encounter intestinal epithelia, perhaps suggesting that they cooperatively facilitate interaction with the host. Among genes significantly upregulated on cell contact are those encoding type 1 pili. We therefore investigated the role played by these pili in facilitating ETEC adhesion, and toxin delivery to model intestinal epithelia. We demonstrate that type 1 pili, encoded in the E. coli core genome, play an essential role in ETEC virulence, acting in concert with plasmid-encoded pathovar specific colonization factor (CF) fimbriae to promote optimal bacterial adhesion to cultured intestinal epithelium (CIE) and to epithelial monolayers differentiated from human small intestinal stem cells. Type 1 pili are tipped with the FimH adhesin which recognizes mannose with stereochemical specificity. Thus, enhanced production of highly mannosylated proteins on intestinal epithelia promoted FimH-mediated ETEC adhesion, while conversely, interruption of FimH lectin-epithelial interactions with soluble mannose, anti-FimH antibodies or mutagenesis of fimH effectively blocked ETEC adhesion. Moreover, fimH mutants were significantly impaired in delivery of both heat-stable and heat-labile toxins to the target epithelial cells in vitro, and these mutants were substantially less virulent in rabbit ileal loop assays, a classical model of ETEC pathogenesis. Collectively, our data suggest that these highly conserved pili play an essential role in virulence of these diverse

Superior Control of HIV-1 Replication by CD8+ T Cells Targeting Conserved Epitopes: Implications for HIV Vaccine Design

PubMed Central

Kunwar, Pratima; Hawkins, Natalie; Dinges, Warren L.; Liu, Yi; Gabriel, Erin E.; Swan, David A.; Stevens, Claire E.; Maenza, Janine; Collier, Ann C.; Mullins, James I.; Hertz, Tomer; Yu, Xuesong; Horton, Helen

2013-01-01

A successful HIV vaccine will likely induce both humoral and cell-mediated immunity, however, the enormous diversity of HIV has hampered the development of a vaccine that effectively elicits both arms of the adaptive immune response. To tackle the problem of viral diversity, T cell-based vaccine approaches have focused on two main strategies (i) increasing the breadth of vaccine-induced responses or (ii) increasing vaccine-induced responses targeting only conserved regions of the virus. The relative extent to which set-point viremia is impacted by epitope-conservation of CD8+ T cell responses elicited during early HIV-infection is unknown but has important implications for vaccine design. To address this question, we comprehensively mapped HIV-1 CD8+ T cell epitope-specificities in 23 ART-naïve individuals during early infection and computed their conservation score (CS) by three different methods (prevalence, entropy and conseq) on clade-B and group-M sequence alignments. The majority of CD8+ T cell responses were directed against variable epitopes (p<0.01). Interestingly, increasing breadth of CD8+ T cell responses specifically recognizing conserved epitopes was associated with lower set-point viremia (r = - 0.65, p = 0.009). Moreover, subjects possessing CD8+ T cells recognizing at least one conserved epitope had 1.4 log10 lower set-point viremia compared to those recognizing only variable epitopes (p = 0.021). The association between viral control and the breadth of conserved CD8+ T cell responses may be influenced by the method of CS definition and sequences used to determine conservation levels. Strikingly, targeting variable versus conserved epitopes was independent of HLA type (p = 0.215). The associations with viral control were independent of functional avidity of CD8+ T cell responses elicited during early infection. Taken together, these data suggest that the next-generation of T-cell based HIV-1 vaccines should focus on strategies that

Structural flexibility at a major conserved antibody target on hepatitis C virus E2 antigen.

PubMed

Kong, Leopold; Lee, David E; Kadam, Rameshwar U; Liu, Tong; Giang, Erick; Nieusma, Travis; Garces, Fernando; Tzarum, Netanel; Woods, Virgil L; Ward, Andrew B; Li, Sheng; Wilson, Ian A; Law, Mansun

2016-10-24

Hepatitis C virus (HCV) is a major cause of liver disease, affecting over 2% of the world's population. The HCV envelope glycoproteins E1 and E2 mediate viral entry, with E2 being the main target of neutralizing antibody responses. Structural investigations of E2 have produced templates for vaccine design, including the conserved CD81 receptor-binding site (CD81bs) that is a key target of broadly neutralizing antibodies (bNAbs). Unfortunately, immunization with recombinant E2 and E1E2 rarely elicits sufficient levels of bNAbs for protection. To understand the challenges for eliciting bNAb responses against the CD81bs, we investigated the E2 CD81bs by electron microscopy (EM), hydrogen-deuterium exchange (HDX), molecular dynamics (MD), and calorimetry. By EM, we observed that HCV1, a bNAb recognizing the N-terminal region of the CD81bs, bound a soluble E2 core construct from multiple angles of approach, suggesting components of the CD81bs are flexible. HDX of multiple E2 constructs consistently indicated the entire CD81bs was flexible relative to the rest of the E2 protein, which was further confirmed by MD simulations. However, E2 has a high melting temperature of 84.8 °C, which is more akin to proteins from thermophilic organisms. Thus, recombinant E2 is a highly stable protein overall, but with an exceptionally flexible CD81bs. Such flexibility may promote induction of nonneutralizing antibodies over bNAbs to E2 CD81bs, underscoring the necessity of rigidifying this antigenic region as a target for rational vaccine design.

Targeting of nucleotide-binding proteins by HAMLET--a conserved tumor cell death mechanism.

PubMed

Ho, J C S; Nadeem, A; Rydström, A; Puthia, M; Svanborg, C

2016-02-18

HAMLET (Human Alpha-lactalbumin Made LEthal to Tumor cells) kills tumor cells broadly suggesting that conserved survival pathways are perturbed. We now identify nucleotide-binding proteins as HAMLET binding partners, accounting for about 35% of all HAMLET targets in a protein microarray comprising 8000 human proteins. Target kinases were present in all branches of the Kinome tree, including 26 tyrosine kinases, 10 tyrosine kinase-like kinases, 13 homologs of yeast sterile kinases, 4 casein kinase 1 kinases, 15 containing PKA, PKG, PKC family kinases, 15 calcium/calmodulin-dependent protein kinase kinases and 13 kinases from CDK, MAPK, GSK3, CLK families. HAMLET acted as a broad kinase inhibitor in vitro, as defined in a screen of 347 wild-type, 93 mutant, 19 atypical and 17 lipid kinases. Inhibition of phosphorylation was also detected in extracts from HAMLET-treated lung carcinoma cells. In addition, HAMLET recognized 24 Ras family proteins and bound to Ras, RasL11B and Rap1B on the cytoplasmic face of the plasma membrane. Direct cellular interactions between HAMLET and activated Ras family members including Braf were confirmed by co-immunoprecipitation. As a consequence, oncogenic Ras and Braf activity was inhibited and HAMLET and Braf inhibitors synergistically increased tumor cell death in response to HAMLET. Unlike most small molecule kinase inhibitors, HAMLET showed selectivity for tumor cells in vitro and in vivo. The results identify nucleotide-binding proteins as HAMLET targets and suggest that dysregulation of the ATPase/kinase/GTPase machinery contributes to cell death, following the initial, selective recognition of HAMLET by tumor cells. The findings thus provide a molecular basis for the conserved tumoricidal effect of HAMLET, through dysregulation of kinases and oncogenic GTPases, to which tumor cells are addicted.

Future battlegrounds for conservation under global change

PubMed Central

Lee, Tien Ming; Jetz, Walter

2008-01-01

Global biodiversity is under significant threat from the combined effects of human-induced climate and land-use change. Covering 12% of the Earth's terrestrial surface, protected areas are crucial for conserving biodiversity and supporting ecological processes beneficial to human well-being, but their selection and design are usually uninformed about future global change. Here, we quantify the exposure of the global reserve network to projected climate and land-use change according to the Millennium Ecosystem Assessment and set these threats in relation to the conservation value and capacity of biogeographic and geopolitical regions. We find that geographical patterns of past human impact on the land cover only poorly predict those of forecasted change, thus revealing the inadequacy of existing global conservation prioritization templates. Projected conservation risk, measured as regional levels of land-cover change in relation to area protected, is the greatest at high latitudes (due to climate change) and tropics/subtropics (due to land-use change). Only some high-latitude nations prone to high conservation risk are also of high conservation value, but their high relative wealth may facilitate additional conservation efforts. In contrast, most low-latitude nations tend to be of high conservation value, but they often have limited capacity for conservation which may exacerbate the global biodiversity extinction crisis. While our approach will clearly benefit from improved land-cover projections and a thorough understanding of how species range will shift under climate change, our results provide a first global quantitative demonstration of the urgent need to consider future environmental change in reserve-based conservation planning. They further highlight the pressing need for new reserves in target regions and support a much extended ‘north–south’ transfer of conservation resources that maximizes biodiversity conservation while mitigating global climate

Conservation and divergence of microRNAs in Populus

PubMed Central

Barakat, Abdelali; Wall, Phillip K; DiLoreto, Scott; dePamphilis, Claude W; Carlson, John E

2007-01-01

Background MicroRNAs (miRNAs) are small RNAs (sRNA) ~21 nucleotides in length that negatively control gene expression by cleaving or inhibiting the translation of target gene transcripts. miRNAs have been extensively analyzed in Arabidopsis and rice and partially investigated in other non-model plant species. To date, 109 and 62 miRNA families have been identified in Arabidopsis and rice respectively. However, only 33 miRNAs have been identified from the genome of the model tree species (Populus trichocarpa), of which 11 are Populus specific. The low number of miRNA families previously identified in Populus, compared with the number of families identified in Arabidopsis and rice, suggests that many miRNAs still remain to be discovered in Populus. In this study, we analyzed expressed small RNAs from leaves and vegetative buds of Populus using high throughput pyrosequencing. Results Analysis of almost eighty thousand small RNA reads allowed us to identify 123 new sequences belonging to previously identified miRNA families as well as 48 new miRNA families that could be Populus-specific. Comparison of the organization of miRNA families in Populus, Arabidopsis and rice showed that miRNA family sizes were generally expanded in Populus. The putative targets of non-conserved miRNA include both previously identified targets as well as several new putative target genes involved in development, resistance to stress, and other cellular processes. Moreover, almost half of the genes predicted to be targeted by non-conserved miRNAs appear to be Populus-specific. Comparative analyses showed that genes targeted by conserved and non-conserved miRNAs are biased mainly towards development, electron transport and signal transduction processes. Similar results were found for non-conserved miRNAs from Arabidopsis. Conclusion Our results suggest that while there is a conserved set of miRNAs among plant species, a large fraction of miRNAs vary among species. The non-conserved miRNAs may

Broadly neutralizing antibodies from human survivors target a conserved site in the Ebola virus glycoprotein HR2-MPER region.

PubMed

Flyak, Andrew I; Kuzmina, Natalia; Murin, Charles D; Bryan, Christopher; Davidson, Edgar; Gilchuk, Pavlo; Gulka, Christopher P; Ilinykh, Philipp A; Shen, Xiaoli; Huang, Kai; Ramanathan, Palaniappan; Turner, Hannah; Fusco, Marnie L; Lampley, Rebecca; Kose, Nurgun; King, Hannah; Sapparapu, Gopal; Doranz, Benjamin J; Ksiazek, Thomas G; Wright, David W; Saphire, Erica Ollmann; Ward, Andrew B; Bukreyev, Alexander; Crowe, James E

2018-05-07

Ebola virus (EBOV) in humans causes a severe illness with high mortality rates. Several strategies have been developed in the past to treat EBOV infection, including the antibody cocktail ZMapp, which has been shown to be effective in nonhuman primate models of infection 1 and has been used under compassionate-treatment protocols in humans 2 . ZMapp is a mixture of three chimerized murine monoclonal antibodies (mAbs) 3-6 that target EBOV-specific epitopes on the surface glycoprotein 7,8 . However, ZMapp mAbs do not neutralize other species from the genus Ebolavirus, such as Bundibugyo virus (BDBV), Reston virus (RESTV) or Sudan virus (SUDV). Here, we describe three naturally occurring human cross-neutralizing mAbs, from BDBV survivors, that target an antigenic site in the canonical heptad repeat 2 (HR2) region near the membrane-proximal external region (MPER) of the glycoprotein. The identification of a conserved neutralizing antigenic site in the glycoprotein suggests that these mAbs could be used to design universal antibody therapeutics against diverse ebolavirus species. Furthermore, we found that immunization with a peptide comprising the HR2-MPER antigenic site elicits neutralizing antibodies in rabbits. Structural features determined by conserved residues in the antigenic site described here could inform an epitope-based vaccine design against infection caused by diverse ebolavirus species.

Energy Conservation Featured in Illinois High School

ERIC Educational Resources Information Center

Modern Schools, 1976

1976-01-01

The William Fremd High School in Palatine, Illinois, scheduled to open in 1977, is being built with energy conservation uppermost in mind. In this system, 70 heat pumps will heat and cool 300,000 square feet of educational facilities. (Author/MLF)

Estimating climate resilience for conservation across geophysical settings.

PubMed

Anderson, Mark G; Clark, Melissa; Sheldon, Arlene Olivero

2014-08-01

Conservationists need methods to conserve biological diversity while allowing species and communities to rearrange in response to a changing climate. We developed and tested such a method for northeastern North America that we based on physical features associated with ecological diversity and site resilience to climate change. We comprehensively mapped 30 distinct geophysical settings based on geology and elevation. Within each geophysical setting, we identified sites that were both connected by natural cover and that had relatively more microclimates indicated by diverse topography and elevation gradients. We did this by scoring every 405 ha hexagon in the region for these two characteristics and selecting those that scored >SD 0.5 above the mean combined score for each setting. We hypothesized that these high-scoring sites had the greatest resilience to climate change, and we compared them with sites selected by The Nature Conservancy for their high-quality rare species populations and natural community occurrences. High-scoring sites captured significantly more of the biodiversity sites than expected by chance (p < 0.0001): 75% of the 414 target species, 49% of the 4592 target species locations, and 53% of the 2170 target community locations. Calcareous bedrock, coarse sand, and fine silt settings scored markedly lower for estimated resilience and had low levels of permanent land protection (average 7%). Because our method identifies-for every geophysical setting-sites that are the most likely to retain species and functions longer under a changing climate, it reveals natural strongholds for future conservation that would also capture substantial existing biodiversity and correct the bias in current secured lands. © 2014 The Authors. Conservation Biology published by Wiley Periodicals, Inc., on behalf of the Society for Conservation Biology.

LAKE PONTCHARTRAIN ESTUARY CONSERVATION PLAN

EPA Science Inventory

The Nature Conservancy will conduct a series of a least four science expert workshops to develop a Site Conservation Plan for the Lake Pontchartrain Estuary and adjacent wetlands. The objective of the Site Conservation Plan is to identify conservation targets, threats or stresse...

Profiling unauthorized natural resource users for better targeting of conservation interventions.

PubMed

Harrison, Mariel; Baker, Julia; Twinamatsiko, Medard; Milner-Gulland, E J

2015-12-01

Unauthorized use of natural resources is a key threat to many protected areas. Approaches to reducing this threat include law enforcement and integrated conservation and development (ICD) projects, but for such ICDs to be targeted effectively, it is important to understand who is illegally using which natural resources and why. The nature of unauthorized behavior makes it difficult to ascertain this information through direct questioning. Bwindi Impenetrable National Park, Uganda, has many ICD projects, including authorizing some local people to use certain nontimber forest resources from the park. However, despite over 25 years of ICD, unauthorized resource use continues. We used household surveys, indirect questioning (unmatched count technique), and focus group discussions to generate profiles of authorized and unauthorized resource users and to explore motivations for unauthorized activity. Overall, unauthorized resource use was most common among people from poor households who lived closest to the park boundary and farthest from roads and trading centers. Other motivations for unauthorized resource use included crop raiding by wild animals, inequity of revenue sharing, and lack of employment, factors that created resentment among the poorest communities. In some communities, benefits obtained from ICD were reported to be the greatest deterrents against unauthorized activity, although law enforcement ranked highest overall. Despite the sensitive nature of exploring unauthorized resource use, management-relevant insights into the profiles and motivations of unauthorized resource users can be gained from a combination of survey techniques, as adopted here. To reduce unauthorized activity at Bwindi, we suggest ICD benefit the poorest people living in remote areas and near the park boundary by providing affordable alternative sources of forest products and addressing crop raiding. To prevent resentment from driving further unauthorized activity, ICDs should be

High-resolution schemes for hyperbolic conservation laws

NASA Technical Reports Server (NTRS)

Harten, A.

1982-01-01

A class of new explicit second order accurate finite difference schemes for the computation of weak solutions of hyperbolic conservation laws is presented. These highly nonlinear schemes are obtained by applying a nonoscillatory first order accurae scheme to an appropriately modified flux function. The so derived second order accurate schemes achieve high resolution while preserving the robustness of the original nonoscillatory first order accurate scheme.

High throughput deep degradome sequencing reveals microRNAs and their targets in response to drought stress in mulberry (Morus alba).

PubMed

Li, Ruixue; Chen, Dandan; Wang, Taichu; Wan, Yizhen; Li, Rongfang; Fang, Rongjun; Wang, Yuting; Hu, Fei; Zhou, Hong; Li, Long; Zhao, Weiguo

2017-01-01

MicroRNAs (miRNAs) play important regulatory roles by targeting mRNAs for cleavage or translational repression. Identification of miRNA targets is essential to better understanding the roles of miRNAs. miRNA targets have not been well characterized in mulberry (Morus alba). To anatomize miRNA guided gene regulation under drought stress, transcriptome-wide high throughput degradome sequencing was used in this study to directly detect drought stress responsive miRNA targets in mulberry. A drought library (DL) and a contrast library (CL) were constructed to capture the cleaved mRNAs for sequencing. In CL, 409 target genes of 30 conserved miRNA families and 990 target genes of 199 novel miRNAs were identified. In DL, 373 target genes of 30 conserved miRNA families and 950 target genes of 195 novel miRNAs were identified. Of the conserved miRNA families in DL, mno-miR156, mno-miR172, and mno-miR396 had the highest number of targets with 54, 52 and 41 transcripts, respectively, indicating that these three miRNA families and their target genes might play important functions in response to drought stress in mulberry. Additionally, we found that many of the target genes were transcription factors. By analyzing the miRNA-target molecular network, we found that the DL independent networks consisted of 838 miRNA-mRNA pairs (63.34%). The expression patterns of 11 target genes and 12 correspondent miRNAs were detected using qRT-PCR. Six miRNA targets were further verified by RNA ligase-mediated 5' rapid amplification of cDNA ends (RLM-5' RACE). Gene Ontology (GO) annotations and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that these target transcripts were implicated in a broad range of biological processes and various metabolic pathways. This is the first study to comprehensively characterize target genes and their associated miRNAs in response to drought stress by degradome sequencing in mulberry. This study provides a framework for understanding

Direct and Indirect Targeting of PP2A by Conserved Bacterial Type-III Effector Proteins

PubMed Central

Jin, Lin; Ham, Jong Hyun; Hage, Rosemary; Zhao, Wanying; Soto-Hernández, Jaricelis; Lee, Sang Yeol; Paek, Seung-Mann; Kim, Min Gab; Boone, Charles; Coplin, David L.; Mackey, David

2016-01-01

Bacterial AvrE-family Type-III effector proteins (T3Es) contribute significantly to the virulence of plant-pathogenic species of Pseudomonas, Pantoea, Ralstonia, Erwinia, Dickeya and Pectobacterium, with hosts ranging from monocots to dicots. However, the mode of action of AvrE-family T3Es remains enigmatic, due in large part to their toxicity when expressed in plant or yeast cells. To search for targets of WtsE, an AvrE-family T3E from the maize pathogen Pantoea stewartii subsp. stewartii, we employed a yeast-two-hybrid screen with non-lethal fragments of WtsE and a synthetic genetic array with full-length WtsE. Together these screens indicate that WtsE targets maize protein phosphatase 2A (PP2A) heterotrimeric enzyme complexes via direct interaction with B’ regulatory subunits. AvrE1, another AvrE-family T3E from Pseudomonas syringae pv. tomato strain DC3000 (Pto DC3000), associates with specific PP2A B’ subunit proteins from its susceptible host Arabidopsis that are homologous to the maize B’ subunits shown to interact with WtsE. Additionally, AvrE1 was observed to associate with the WtsE-interacting maize proteins, indicating that PP2A B’ subunits are likely conserved targets of AvrE-family T3Es. Notably, the ability of AvrE1 to promote bacterial growth and/or suppress callose deposition was compromised in Arabidopsis plants with mutations of PP2A genes. Also, chemical inhibition of PP2A activity blocked the virulence activity of both WtsE and AvrE1 in planta. The function of HopM1, a Pto DC3000 T3E that is functionally redundant to AvrE1, was also impaired in specific PP2A mutant lines, although no direct interaction with B’ subunits was observed. These results indicate that sub-component specific PP2A complexes are targeted by bacterial T3Es, including direct targeting by members of the widely conserved AvrE-family. PMID:27191168

The precision problem in conservation and restoration

USGS Publications Warehouse

Hiers, J. Kevin; Jackson, Stephen T.; Hobbs, Richard J.; Bernhardt, Emily S.; Valentine, Leonie E.

2016-01-01

Within the varied contexts of environmental policy, conservation of imperilled species populations, and restoration of damaged habitats, an emphasis on idealized optimal conditions has led to increasingly specific targets for management. Overly-precise conservation targets can reduce habitat variability at multiple scales, with unintended consequences for future ecological resilience. We describe this dilemma in the context of endangered species management, stream restoration, and climate-change adaptation. Inappropriate application of conservation targets can be expensive, with marginal conservation benefit. Reduced habitat variability can limit options for managers trying to balance competing objectives with limited resources. Conservation policies should embrace habitat variability, expand decision-space appropriately, and support adaptation to local circumstances to increase ecological resilience in a rapidly changing world.

Tilapia and human CLIC2 structures are highly conserved.

PubMed

Zeng, Jiao; Li, Zhengjun; Lui, Eei Yin; Lam, Siew Hong; Swaminathan, Kunchithapadam

2018-01-08

Chloride intracellular channels (CLICs) exist in soluble and membrane bound forms. We have determined the crystal structure of soluble Clic2 from the euryhaline teleost fish Oreochromis mossambicus. Structural comparison of tilapia and human CLIC2 with other CLICs shows that these proteins are highly conserved. We have also compared the expression levels of clic2 in selected osmoregulatory organs of tilapia, acclimated to freshwater, seawater and hypersaline water. Structural conservation of vertebrate CLICs implies that they might play conserved roles. Also, tissue-specific responsiveness of clic2 suggests that it might be involved in iono-osmoregulation under extreme conditions in tilapia. Copyright © 2017 Elsevier Inc. All rights reserved.

Conservation Planning for Ecosystem Services

PubMed Central

Chan, Kai M. A; Shaw, M. Rebecca; Cameron, David R; Underwood, Emma C; Daily, Gretchen C

2006-01-01

Despite increasing attention to the human dimension of conservation projects, a rigorous, systematic methodology for planning for ecosystem services has not been developed. This is in part because flows of ecosystem services remain poorly characterized at local-to-regional scales, and their protection has not generally been made a priority. We used a spatially explicit conservation planning framework to explore the trade-offs and opportunities for aligning conservation goals for biodiversity with six ecosystem services (carbon storage, flood control, forage production, outdoor recreation, crop pollination, and water provision) in the Central Coast ecoregion of California, United States. We found weak positive and some weak negative associations between the priority areas for biodiversity conservation and the flows of the six ecosystem services across the ecoregion. Excluding the two agriculture-focused services—crop pollination and forage production—eliminates all negative correlations. We compared the degree to which four contrasting conservation network designs protect biodiversity and the flow of the six services. We found that biodiversity conservation protects substantial collateral flows of services. Targeting ecosystem services directly can meet the multiple ecosystem services and biodiversity goals more efficiently but cannot substitute for targeted biodiversity protection (biodiversity losses of 44% relative to targeting biodiversity alone). Strategically targeting only biodiversity plus the four positively associated services offers much promise (relative biodiversity losses of 7%). Here we present an initial analytical framework for integrating biodiversity and ecosystem services in conservation planning and illustrate its application. We found that although there are important potential trade-offs between conservation for biodiversity and for ecosystem services, a systematic planning framework offers scope for identifying valuable synergies. PMID

The Precision Problem in Conservation and Restoration.

PubMed

Hiers, J Kevin; Jackson, Stephen T; Hobbs, Richard J; Bernhardt, Emily S; Valentine, Leonie E

2016-11-01

Within the varied contexts of environmental policy, conservation of imperilled species populations, and restoration of damaged habitats, an emphasis on idealized optimal conditions has led to increasingly specific targets for management. Overly-precise conservation targets can reduce habitat variability at multiple scales, with unintended consequences for future ecological resilience. We describe this dilemma in the context of endangered species management, stream restoration, and climate-change adaptation. Inappropriate application of conservation targets can be expensive, with marginal conservation benefit. Reduced habitat variability can limit options for managers trying to balance competing objectives with limited resources. Conservation policies should embrace habitat variability, expand decision-space appropriately, and support adaptation to local circumstances to increase ecological resilience in a rapidly changing world. Copyright © 2016 Elsevier Ltd. All rights reserved.

Evaluating local benefits from conservation in Nepal's Annapurna Conservation Area.

PubMed

Spiteri, Arian; Nepal, Sanjay K

2008-09-01

Protected areas are integral to the global effort to conserve biodiversity, and, over the past two decades, protected area managers have begun to recognize that conservation objectives are next to impossible to achieve without considering the needs and concerns of local communities. Incentive-based programs (IBPs) have become a favored approach to protected area management, geared at fostering local stewardship by delivering benefits tied to conservation to local people. Effective IBPs require benefits to accrue to and be recognized by those experiencing the greatest consequences as a result of the protected area, and those likely to continue extractive activities if their livelihood needs are compromised. This research examines dispersal of IBP benefits, as perceived by local residents in Nepal's Annapurna Conservation Area. Results reported here are based on questionnaire interviews with 188 households conducted between September and December 2004. Results indicate that local residents primarily identify benefits from social development activities, provisions for resource extraction, and economic opportunities. Overall, benefits have been dispersed equally to households in villages on and off the main tourist route, and regardless of a household's participation in tourism. However, benefits are not effectively targeted to poorer residents, those highly dependent on natural resources, and those experiencing the most crop damage and livestock loss from protected wildlife. This article provides several suggestions for improving the delivery of conservation incentives.

Identification of miRNAs and their targets in wild tomato at moderately and acutely elevated temperatures by high-throughput sequencing and degradome analysis

PubMed Central

Zhou, Rong; Wang, Qian; Jiang, Fangling; Cao, Xue; Sun, Mintao; Liu, Min; Wu, Zhen

2016-01-01

MicroRNAs (miRNAs) are 19–24 nucleotide (nt) noncoding RNAs that play important roles in abiotic stress responses in plants. High temperatures have been the subject of considerable attention due to their negative effects on plant growth and development. Heat-responsive miRNAs have been identified in some plants. However, there have been no reports on the global identification of miRNAs and their targets in tomato at high temperatures, especially at different elevated temperatures. Here, three small-RNA libraries and three degradome libraries were constructed from the leaves of the heat-tolerant tomato at normal, moderately and acutely elevated temperatures (26/18 °C, 33/33 °C and 40/40 °C, respectively). Following high-throughput sequencing, 662 conserved and 97 novel miRNAs were identified in total with 469 conserved and 91 novel miRNAs shared in the three small-RNA libraries. Of these miRNAs, 96 and 150 miRNAs were responsive to the moderately and acutely elevated temperature, respectively. Following degradome sequencing, 349 sequences were identified as targets of 138 conserved miRNAs, and 13 sequences were identified as targets of eight novel miRNAs. The expression levels of seven miRNAs and six target genes obtained by quantitative real-time PCR (qRT-PCR) were largely consistent with the sequencing results. This study enriches the number of heat-responsive miRNAs and lays a foundation for the elucidation of the miRNA-mediated regulatory mechanism in tomatoes at elevated temperatures. PMID:27653374

PknB remains an essential and a conserved target for drug development in susceptible and MDR strains of M. Tuberculosis.

PubMed

Gupta, Anamika; Pal, Sudhir K; Pandey, Divya; Fakir, Najneen A; Rathod, Sunita; Sinha, Dhiraj; SivaKumar, S; Sinha, Pallavi; Periera, Mycal; Balgam, Shilpa; Sekar, Gomathi; UmaDevi, K R; Anupurba, Shampa; Nema, Vijay

2017-08-18

The Mycobacterium tuberculosis (M.tb) protein kinase B (PknB) which is now proved to be essential for the growth and survival of M.tb, is a transmembrane protein with a potential to be a good drug target. However it is not known if this target remains conserved in otherwise resistant isolates from clinical origin. The present study describes the conservation analysis of sequences covering the inhibitor binding domain of PknB to assess if it remains conserved in susceptible and resistant clinical strains of mycobacteria picked from three different geographical areas of India. A total of 116 isolates from North, South and West India were used in the study with a variable profile of their susceptibilities towards streptomycin, isoniazid, rifampicin, ethambutol and ofloxacin. Isolates were also spoligotyped in order to find if the conservation pattern of pknB gene remain consistent or differ with different spoligotypes. The impact of variation as found in the study was analyzed using Molecular dynamics simulations. The sequencing results with 115/116 isolates revealed the conserved nature of pknB sequences irrespective of their susceptibility status and spoligotypes. The only variation found was in one strains wherein pnkB sequence had G to A mutation at 664 position translating into a change of amino acid, Valine to Isoleucine. After analyzing the impact of this sequence variation using Molecular dynamics simulations, it was observed that the variation is causing no significant change in protein structure or the inhibitor binding. Hence, the study endorses that PknB is an ideal target for drug development and there is no pre-existing or induced resistance with respect to the sequences involved in inhibitor binding. Also if the mutation that we are reporting for the first time is found again in subsequent work, it should be checked with phenotypic profile before drawing the conclusion that it would affect the activity in any way. Bioinformatics analysis in our study

78 FR 20503 - Energy Conservation Program: Availability of the Interim Technical Support Document for High...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-04-05

... Conservation Program: Availability of the Interim Technical Support Document for High-Intensity Discharge Lamps... high-intensity discharge (HID) lamps energy conservation standards in the Federal Register. This... interim analysis for high- intensity discharge lamps energy conservation standards. The notice provided...

Increasing participation in incentive programs for biodiversity conservation.

PubMed

Sorice, Michael G; Oh, Chi-Ok; Gartner, Todd; Snieckus, Mary; Johnson, Rhett; Donlan, C Josh

2013-07-01

Engaging private landowners in conservation activities for imperiled species is critical to maintaining and enhancing biodiversity. Market-based approaches can incentivize conservation behaviors on private lands by shifting the benefit-cost ratio of engaging in activities that result in net conservation benefits for target species. In the United States and elsewhere, voluntary conservation agreements with financial incentives are becoming an increasingly common strategy. While the influence of program design and delivery of voluntary conservation programs is often overlooked, these aspects are critical to achieving the necessary participation to attain landscape-scale outcomes. Using a sample of family-forest landowners in the southeast United States, we show how preferences for participation in a conservation program to protect an at-risk species, the gopher tortoise (Gopherus polyphemus), are related to program structure, delivery, and perceived efficacy. Landowners were most sensitive to programs that are highly controlling, require permanent conservation easements, and put landowners at risk for future regulation. Programs designed with greater levels of compensation and that support landowners' autonomy to make land management decisions can increase participation and increase landowner acceptance of program components that are generally unfavorable, like long-term contracts and permanent easements. There is an inherent trade-off between maximizing participation and maximizing the conservation benefits when designing a conservation incentive program. For conservation programs targeting private lands to achieve landscape-level benefits, they must attract a critical level of participation that creates a connected mosaic of conservation benefits. Yet, programs with attributes that strive to maximize conservation benefits within a single agreement (and reduce risks of failure) are likely to have lower participation, and thus lower landscape benefits. Achieving

Global priorities for national carnivore conservation under land use change

PubMed Central

Di Minin, Enrico; Slotow, Rob; Hunter, Luke T. B.; Montesino Pouzols, Federico; Toivonen, Tuuli; Verburg, Peter H.; Leader-Williams, Nigel; Petracca, Lisanne; Moilanen, Atte

2016-01-01

Mammalian carnivores have suffered the biggest range contraction among all biodiversity and are particularly vulnerable to habitat loss and fragmentation. Therefore, we identified priority areas for the conservation of mammalian carnivores, while accounting for species-specific requirements for connectivity and expected agricultural and urban expansion. While prioritizing for carnivores only, we were also able to test their effectiveness as surrogates for 23,110 species of amphibians, birds, mammals and reptiles and 867 terrestrial ecoregions. We then assessed the risks to carnivore conservation within each country that makes a contribution to global carnivore conservation. We found that land use change will potentially lead to important range losses, particularly amongst already threatened carnivore species. In addition, the 17% of land targeted for protection under the Aichi Target 11 was found to be inadequate to conserve carnivores under expected land use change. Our results also highlight that land use change will decrease the effectiveness of carnivores to protect other threatened species, especially threatened amphibians. In addition, the risk of human-carnivore conflict is potentially high in countries where we identified spatial priorities for their conservation. As meeting the global biodiversity target will be inadequate for carnivore protection, innovative interventions are needed to conserve carnivores outside protected areas to compliment any proposed expansion of the protected area network. PMID:27034197

Designing coastal conservation to deliver ecosystem and human well-being benefits.

PubMed

Annis, Gust M; Pearsall, Douglas R; Kahl, Katherine J; Washburn, Erika L; May, Christopher A; Franks Taylor, Rachael; Cole, James B; Ewert, David N; Game, Edward T; Doran, Patrick J

2017-01-01

Conservation scientists increasingly recognize that incorporating human values into conservation planning increases the chances for success by garnering broader project acceptance. However, methods for defining quantitative targets for the spatial representation of human well-being priorities are less developed. In this study we employ an approach for identifying regionally important human values and establishing specific spatial targets for their representation based on stakeholder outreach. Our primary objective was to develop a spatially-explicit conservation plan that identifies the most efficient locations for conservation actions to meet ecological goals while sustaining or enhancing human well-being values within the coastal and nearshore areas of the western Lake Erie basin (WLEB). We conducted an optimization analysis using 26 features representing ecological and human well-being priorities (13 of each), and included seven cost layers. The influence that including human well-being had on project results was tested by running five scenarios and setting targets for human well-being at different levels in each scenario. The most important areas for conservation to achieve multiple goals are clustered along the coast, reflecting a concentration of existing or potentially restorable coastal wetlands, coastal landbird stopover habitat and terrestrial biodiversity, as well as important recreational activities. Inland important areas tended to cluster around trails and high quality inland landbird stopover habitat. Most concentrated areas of importance also are centered on lands that are already conserved, reflecting the lower costs and higher benefits of enlarging these conserved areas rather than conserving isolated, dispersed areas. Including human well-being features in the analysis only influenced the solution at the highest target levels.

Designing coastal conservation to deliver ecosystem and human well-being benefits

PubMed Central

Pearsall, Douglas R.; Kahl, Katherine J.; Washburn, Erika L.; May, Christopher A.; Franks Taylor, Rachael; Cole, James B.; Ewert, David N.; Game, Edward T.; Doran, Patrick J.

2017-01-01

Conservation scientists increasingly recognize that incorporating human values into conservation planning increases the chances for success by garnering broader project acceptance. However, methods for defining quantitative targets for the spatial representation of human well-being priorities are less developed. In this study we employ an approach for identifying regionally important human values and establishing specific spatial targets for their representation based on stakeholder outreach. Our primary objective was to develop a spatially-explicit conservation plan that identifies the most efficient locations for conservation actions to meet ecological goals while sustaining or enhancing human well-being values within the coastal and nearshore areas of the western Lake Erie basin (WLEB). We conducted an optimization analysis using 26 features representing ecological and human well-being priorities (13 of each), and included seven cost layers. The influence that including human well-being had on project results was tested by running five scenarios and setting targets for human well-being at different levels in each scenario. The most important areas for conservation to achieve multiple goals are clustered along the coast, reflecting a concentration of existing or potentially restorable coastal wetlands, coastal landbird stopover habitat and terrestrial biodiversity, as well as important recreational activities. Inland important areas tended to cluster around trails and high quality inland landbird stopover habitat. Most concentrated areas of importance also are centered on lands that are already conserved, reflecting the lower costs and higher benefits of enlarging these conserved areas rather than conserving isolated, dispersed areas. Including human well-being features in the analysis only influenced the solution at the highest target levels. PMID:28241018

Ecosystem services and opportunity costs shift spatial priorities for conserving forest biodiversity.

PubMed

Schröter, Matthias; Rusch, Graciela M; Barton, David N; Blumentrath, Stefan; Nordén, Björn

2014-01-01

Inclusion of spatially explicit information on ecosystem services in conservation planning is a fairly new practice. This study analyses how the incorporation of ecosystem services as conservation features can affect conservation of forest biodiversity and how different opportunity cost constraints can change spatial priorities for conservation. We created spatially explicit cost-effective conservation scenarios for 59 forest biodiversity features and five ecosystem services in the county of Telemark (Norway) with the help of the heuristic optimisation planning software, Marxan with Zones. We combined a mix of conservation instruments where forestry is either completely (non-use zone) or partially restricted (partial use zone). Opportunity costs were measured in terms of foregone timber harvest, an important provisioning service in Telemark. Including a number of ecosystem services shifted priority conservation sites compared to a case where only biodiversity was considered, and increased the area of both the partial (+36.2%) and the non-use zone (+3.2%). Furthermore, opportunity costs increased (+6.6%), which suggests that ecosystem services may not be a side-benefit of biodiversity conservation in this area. Opportunity cost levels were systematically changed to analyse their effect on spatial conservation priorities. Conservation of biodiversity and ecosystem services trades off against timber harvest. Currently designated nature reserves and landscape protection areas achieve a very low proportion (9.1%) of the conservation targets we set in our scenario, which illustrates the high importance given to timber production at present. A trade-off curve indicated that large marginal increases in conservation target achievement are possible when the budget for conservation is increased. Forty percent of the maximum hypothetical opportunity costs would yield an average conservation target achievement of 79%.

Ecosystem Services and Opportunity Costs Shift Spatial Priorities for Conserving Forest Biodiversity

PubMed Central

Schröter, Matthias; Rusch, Graciela M.; Barton, David N.; Blumentrath, Stefan; Nordén, Björn

2014-01-01

Inclusion of spatially explicit information on ecosystem services in conservation planning is a fairly new practice. This study analyses how the incorporation of ecosystem services as conservation features can affect conservation of forest biodiversity and how different opportunity cost constraints can change spatial priorities for conservation. We created spatially explicit cost-effective conservation scenarios for 59 forest biodiversity features and five ecosystem services in the county of Telemark (Norway) with the help of the heuristic optimisation planning software, Marxan with Zones. We combined a mix of conservation instruments where forestry is either completely (non-use zone) or partially restricted (partial use zone). Opportunity costs were measured in terms of foregone timber harvest, an important provisioning service in Telemark. Including a number of ecosystem services shifted priority conservation sites compared to a case where only biodiversity was considered, and increased the area of both the partial (+36.2%) and the non-use zone (+3.2%). Furthermore, opportunity costs increased (+6.6%), which suggests that ecosystem services may not be a side-benefit of biodiversity conservation in this area. Opportunity cost levels were systematically changed to analyse their effect on spatial conservation priorities. Conservation of biodiversity and ecosystem services trades off against timber harvest. Currently designated nature reserves and landscape protection areas achieve a very low proportion (9.1%) of the conservation targets we set in our scenario, which illustrates the high importance given to timber production at present. A trade-off curve indicated that large marginal increases in conservation target achievement are possible when the budget for conservation is increased. Forty percent of the maximum hypothetical opportunity costs would yield an average conservation target achievement of 79%. PMID:25393951

Targeting ecosystem features for conservation: Standing crops in the Florida Everglades

USGS Publications Warehouse

Turner, A.M.; Trexler, J.C.; Jordan, C.F.; Slack, S.J.; Geddes, P.; Chick, J.H.; Loftus, W.F.

1999-01-01

The Everglades in southern Florida, U.S.A., is a major focus of conservation activities. The freshwater wetlands of the Everglades do not have high species richness, and no species of threatened aquatic animals or plants live there. We have, however, identified a distinctive ecological feature of the Everglades that is threatened by canal construction, draining, and nutrient enrichment from agricultural runoff compared to values reported from other freshwater systems, standing stocks of periphyton in relatively undisturbed areas of the Everglades were unusually high, and standing stocks of invertebrates and fish were unusually low. Averaging data gathered from nine sites and five sampling periods spanning I year, we found that periphyton standing crop was 88.2 g/m2 (ash-free dry mass), invertebrate standing stock was 0.64 g/m2 (dry mass), and fish standing stock was 1.2 g/m2 (dry mass of large and small species combined). We found that fish standing stocks were much higher in phosphorus-enriched sites than in nearby reference sites but that invertebrate standing stocks were similar in enriched and reference sites. Our results support the notion that oligotrophy is at least partially responsible for the low standing stocks of fish, but they also suggest that species interactions and a paucity of deep-water refugia are important. Anthropogenic eutrophication in Everglades marshes will lead to the loss of distinctive ecosystem features. A focus on species richness and 'hot spots' of threatened species provides no basis for conservation of ecosystems like the Everglades. If oligotrophic ecosystems often have low species richness, they will be underrepresented in preservation networks based on some common criteria for establishing conservation priorities.

The Orinoco megadelta as a conservation target in the face of the ongoing and future sea level rise.

PubMed

Vegas-Vilarrúbia, T; Hernández, E; Rull, Valentí; Rull Vegas, Elisa

2015-05-15

Currently, risk assessments related to rising sea levels and the adoption of defensive or adaptive measures to counter these sea level increases are underway for densely populated deltas where economic losses might be important, especially in the developed world. However, many underpopulated deltas harbouring high biological and cultural diversity are also at risk but will most likely continue to be ignored as conservation targets. In this study, we explore the potential effects of erosion, inundation and salinisation on one of the world's comparatively underpopulated megadeltas, the Orinoco Delta. With a 1 m sea level rise expected to occur by 2100, several models predict a moderate erosion of the delta's shorelines, migration or loss of mangroves, general inundation of the delta with an accompanying submersion of wetlands, and an increase in the distance to which sea water intrudes into streams, resulting in harm to the freshwater biota and resources. The Warao people are the indigenous inhabitants of the Orinoco Delta and currently are subject to various socioeconomic stressors. Changes due to sea level rise will occur extremely rapidly and cause abrupt shifts in the Warao's traditional environments and resources, resulting in migrations and abandonment of their ancestral territories. However, evidence indicates that deltaic aggradation/accretion processes at the Orinoco delta due to allochthonous sediment input and vegetation growth could be elevating the surface of the land, keeping pace with the local sea level rise. Other underpopulated and large deltas of the world also may risk immeasurable biodiversity and cultural losses and should not be forgotten as important conservation targets. Copyright © 2015. Published by Elsevier B.V.

Targeting Conserved Genes in Penicillium Species.

PubMed

Peterson, Stephen W

2017-01-01

Polymerase chain reaction amplification of conserved genes and sequence analysis provides a very powerful tool for the identification of toxigenic as well as non-toxigenic Penicillium species. Sequences are obtained by amplification of the gene fragment, sequencing via capillary electrophoresis of dideoxynucleotide-labeled fragments or NGS. The sequences are compared to a database of validated isolates. Identification of species indicates the potential of the fungus to make particular mycotoxins.

The Adaptation for Conservation Targets (ACT) framework: a tool for incorporating climate change into natural resource management.

PubMed

Cross, Molly S; Zavaleta, Erika S; Bachelet, Dominique; Brooks, Marjorie L; Enquist, Carolyn A F; Fleishman, Erica; Graumlich, Lisa J; Groves, Craig R; Hannah, Lee; Hansen, Lara; Hayward, Greg; Koopman, Marni; Lawler, Joshua J; Malcolm, Jay; Nordgren, John; Petersen, Brian; Rowland, Erika L; Scott, Daniel; Shafer, Sarah L; Shaw, M Rebecca; Tabor, Gary M

2012-09-01

As natural resource management agencies and conservation organizations seek guidance on responding to climate change, myriad potential actions and strategies have been proposed for increasing the long-term viability of some attributes of natural systems. Managers need practical tools for selecting among these actions and strategies to develop a tailored management approach for specific targets at a given location. We developed and present one such tool, the participatory Adaptation for Conservation Targets (ACT) framework, which considers the effects of climate change in the development of management actions for particular species, ecosystems and ecological functions. Our framework is based on the premise that effective adaptation of management to climate change can rely on local knowledge of an ecosystem and does not necessarily require detailed projections of climate change or its effects. We illustrate the ACT framework by applying it to an ecological function in the Greater Yellowstone Ecosystem (Montana, Wyoming, and Idaho, USA)--water flows in the upper Yellowstone River. We suggest that the ACT framework is a practical tool for initiating adaptation planning, and for generating and communicating specific management interventions given an increasingly altered, yet uncertain, climate.

The Adaptation for Conservation Targets (ACT) Framework: A tool for incorporating climate change into natural resource management

USGS Publications Warehouse

Cross, Molly S.; Zavaleta, Erika S.; Bachelet, Dominique; Brooks, Marjorie L.; Enquist, Carolyn A.F.; Fleishman, Erica; Graumlich, Lisa J.; Groves, Craig R.; Hannah, Lee; Hansen, Lara J.; Hayward, Gregory D.; Koopman, Marni; Lawler, Joshua J.; Malcolm, Jay; Nordgren, John R.; Petersen, Brian; Rowland, Erika; Scott, Daniel; Shafer, Sarah L.; Shaw, M. Rebecca; Tabor, Gary

2012-01-01

As natural resource management agencies and conservation organizations seek guidance on responding to climate change, myriad potential actions and strategies have been proposed for increasing the long-term viability of some attributes of natural systems. Managers need practical tools for selecting among these actions and strategies to develop a tailored management approach for specific targets at a given location. We developed and present one such tool, the participatory Adaptation for Conservation Targets (ACT) framework, which considers the effects of climate change in the development of management actions for particular species, ecosystems and ecological functions. Our framework is based on the premise that effective adaptation of management to climate change can rely on local knowledge of an ecosystem and does not necessarily require detailed projections of climate change or its effects. We illustrate the ACT framework by applying it to an ecological function in the Greater Yellowstone Ecosystem (Montana, Wyoming, and Idaho, USA)—water flows in the upper Yellowstone River. We suggest that the ACT framework is a practical tool for initiating adaptation planning, and for generating and communicating specific management interventions given an increasingly altered, yet uncertain, climate.

Assessing conservation opportunity on private land: socio-economic, behavioral, and spatial dimensions.

PubMed

Raymond, Christopher M; Brown, Gregory

2011-10-01

This study presents a method for assessing conservation opportunity on private land based on landholders' socio-economic, behavioral, and farm characteristics. These characteristics include age, gender, education, level of off-farm income, farm size, proportion of remnant native vegetation on-farm, and ecological value of native vegetation on-farm. A sample of landholders who own greater than 2 ha of land in the South Australian Murray-Darling Basin region were sent a mail-based survey about their values and preferences for environmental management (N = 659, 52% response). Cross-tabulations and ANOVA statistical analysis techniques were used to compare the socio-economic attributes across three landholder classes: disengaged, moderately engaged, and highly engaged in native vegetation planting. Results indicate that highly engaged landholders were more likely to be female, formally educated, hobby farmers who managed small parcels of land and have high off-farm incomes, whereas disengaged landholders held significantly stronger farming connections (more farming experience, family have lived on the farm for more generations). Spatial analysis revealed area-specific differences in conservation opportunity and conservation priority. In some areas, properties of high ecological value were managed by highly engaged landholders, but nearby properties of high value were managed by moderately engaged or disengaged landholders. Environmental managers therefore cannot assume areas of high conservation priority will be areas of high conservation opportunity. At the regional scale, the potential for revegetation seems most promising within the moderately engaged landholder group considering the vast amount of land managed by this group in areas of high ecological value, particularly within the less represented Mallee and Coorong and Rangelands sub-regions. We suggest that incentive schemes which purchase conservation need to be targeted at disengaged landholders; mentoring

Adenovirus Delivered Short Hairpin RNA Targeting a Conserved Site in the 5′ Non-Translated Region Inhibits All Four Serotypes of Dengue Viruses

PubMed Central

Korrapati, Anil Babu; Swaminathan, Gokul; Singh, Aarti; Khanna, Navin; Swaminathan, Sathyamangalam

2012-01-01

Background Dengue is a mosquito-borne viral disease caused by four closely related serotypes of Dengue viruses (DENVs). This disease whose symptoms range from mild fever to potentially fatal haemorrhagic fever and hypovolemic shock, threatens nearly half the global population. There is neither a preventive vaccine nor an effective antiviral therapy against dengue disease. The difference between severe and mild disease appears to be dependent on the viral load. Early diagnosis may enable timely therapeutic intervention to blunt disease severity by reducing the viral load. Harnessing the therapeutic potential of RNA interference (RNAi) to attenuate DENV replication may offer one approach to dengue therapy. Methodology/Principal Findings We screened the non-translated regions (NTRs) of the RNA genomes of representative members of the four DENV serotypes for putative siRNA targets mapping to known transcription/translation regulatory elements. We identified a target site in the 5′ NTR that maps to the 5′ upstream AUG region, a highly conserved cis-acting element essential for viral replication. We used a replication-defective human adenovirus type 5 (AdV5) vector to deliver a short-hairpin RNA (shRNA) targeting this site into cells. We show that this shRNA matures to the cognate siRNA and is able to inhibit effectively antigen secretion, viral RNA replication and infectious virus production by all four DENV serotypes. Conclusion/Significance The data demonstrate the feasibility of using AdV5-mediated delivery of shRNAs targeting conserved sites in the viral genome to achieve inhibition of all four DENV serotypes. This paves the way towards exploration of RNAi as a possible therapeutic strategy to curtail DENV infection. PMID:22848770

High-resolution satellite imagery is an important yet underutilized resource in conservation biology.

PubMed

Boyle, Sarah A; Kennedy, Christina M; Torres, Julio; Colman, Karen; Pérez-Estigarribia, Pastor E; de la Sancha, Noé U

2014-01-01

Technological advances and increasing availability of high-resolution satellite imagery offer the potential for more accurate land cover classifications and pattern analyses, which could greatly improve the detection and quantification of land cover change for conservation. Such remotely-sensed products, however, are often expensive and difficult to acquire, which prohibits or reduces their use. We tested whether imagery of high spatial resolution (≤5 m) differs from lower-resolution imagery (≥30 m) in performance and extent of use for conservation applications. To assess performance, we classified land cover in a heterogeneous region of Interior Atlantic Forest in Paraguay, which has undergone recent and dramatic human-induced habitat loss and fragmentation. We used 4 m multispectral IKONOS and 30 m multispectral Landsat imagery and determined the extent to which resolution influenced the delineation of land cover classes and patch-level metrics. Higher-resolution imagery more accurately delineated cover classes, identified smaller patches, retained patch shape, and detected narrower, linear patches. To assess extent of use, we surveyed three conservation journals (Biological Conservation, Biotropica, Conservation Biology) and found limited application of high-resolution imagery in research, with only 26.8% of land cover studies analyzing satellite imagery, and of these studies only 10.4% used imagery ≤5 m resolution. Our results suggest that high-resolution imagery is warranted yet under-utilized in conservation research, but is needed to adequately monitor and evaluate forest loss and conversion, and to delineate potentially important stepping-stone fragments that may serve as corridors in a human-modified landscape. Greater access to low-cost, multiband, high-resolution satellite imagery would therefore greatly facilitate conservation management and decision-making.

A Framework for Effective Assessment of Model-based Projections of Biodiversity to Inform the Next Generation of Global Conservation Targets

NASA Astrophysics Data System (ADS)

Myers, B.; Beard, T. D.; Weiskopf, S. R.; Jackson, S. T.; Tittensor, D.; Harfoot, M.; Senay, G. B.; Casey, K.; Lenton, T. M.; Leidner, A. K.; Ruane, A. C.; Ferrier, S.; Serbin, S.; Matsuda, H.; Shiklomanov, A. N.; Rosa, I.

2017-12-01

Biodiversity and ecosystems services underpin political targets for the conservation of biodiversity; however, previous incarnations of these biodiversity-related targets have not relied on integrated model based projections of possible outcomes based on climate and land use change. Although a few global biodiversity models are available, most biodiversity models lie along a continuum of geography and components of biodiversity. Model-based projections of the future of global biodiversity are critical to support policymakers in the development of informed global conservation targets, but the scientific community lacks a clear strategy for integrating diverse data streams in developing, and evaluating the performance of, such biodiversity models. Therefore, in this paper, we propose a framework for ongoing testing and refinement of model-based projections of biodiversity trends and change, by linking a broad variety of biodiversity models with data streams generated by advances in remote sensing, coupled with new and emerging in-situ observation technologies to inform development of essential biodiversity variables, future global biodiversity targets, and indicators. Our two main objectives are to (1) develop a framework for model testing and refining projections of a broad range of biodiversity models, focusing on global models, through the integration of diverse data streams and (2) identify the realistic outputs that can be developed and determine coupled approaches using remote sensing and new and emerging in-situ observations (e.g., metagenomics) to better inform the next generation of global biodiversity targets.

A high yield neutron target

NASA Technical Reports Server (NTRS)

Alger, D. L.; Steinberg, R.; Weisenbach, P.

1974-01-01

Target, in cylinder form, rotates rapidly in front of beam. Titanium tritide film is much thicker than range of accelerated deutron. Sputtering electrode permits full use of thick film. Stream of high-velocity coolant provides efficient transfer of heat from target.

Distributed Relaxation for Conservative Discretizations

NASA Technical Reports Server (NTRS)

Diskin, Boris; Thomas, James L.

2001-01-01

A multigrid method is defined as having textbook multigrid efficiency (TME) if the solutions to the governing system of equations are attained in a computational work that is a small (less than 10) multiple of the operation count in one target-grid residual evaluation. The way to achieve this efficiency is the distributed relaxation approach. TME solvers employing distributed relaxation have already been demonstrated for nonconservative formulations of high-Reynolds-number viscous incompressible and subsonic compressible flow regimes. The purpose of this paper is to provide foundations for applications of distributed relaxation to conservative discretizations. A direct correspondence between the primitive variable interpolations for calculating fluxes in conservative finite-volume discretizations and stencils of the discretized derivatives in the nonconservative formulation has been established. Based on this correspondence, one can arrive at a conservative discretization which is very efficiently solved with a nonconservative relaxation scheme and this is demonstrated for conservative discretization of the quasi one-dimensional Euler equations. Formulations for both staggered and collocated grid arrangements are considered and extensions of the general procedure to multiple dimensions are discussed.

Conserved sequences in the current strains of HIV-1 subtype A in Russia are effectively targeted by artificial RNAi in vitro.

PubMed

Tchurikov, Nickolai A; Fedoseeva, Daria M; Gashnikova, Natalya M; Sosin, Dmitri V; Gorbacheva, Maria A; Alembekov, Ildar R; Chechetkin, Vladimir R; Kravatsky, Yuri V; Kretova, Olga V

2016-05-25

Highly active antiretroviral therapy has greatly reduced the morbidity and mortality of AIDS. However, many of the antiretroviral drugs are toxic with long-term use, and all currently used anti-HIV agents generate drug-resistant mutants. Therefore, there is a great need for new approaches to AIDS therapy. RNAi is a powerful means of inhibiting HIV-1 production in human cells. We propose to use RNAi for gene therapy of HIV/AIDS. Previously we identified a number of new biologically active siRNAs targeting several moderately conserved regions in HIV-1 transcripts. Here we analyze the heterogeneity of nucleotide sequences in three RNAi targets in sequences encoding the reverse transcriptase and integrase domains of current isolates of HIV-1 subtype A in Russia. These data were used to generate genetic constructs expressing short hairpin RNAs 28-30-bp in length that could be processed in cells into siRNAs. After transfection of the constructs we observed siRNAs that efficiently attacked the selected targets. We expect that targeting several viral genes important for HIV-1 reproduction will help overcome the problem of viral adaptation and will prevent the appearance of RNAi escape mutants in current virus strains, an important feature of gene therapy of HIV/AIDS. Copyright © 2016 Elsevier B.V. All rights reserved.

The highly conserved MraZ protein is a transcriptional regulator in Escherichia coli

DOE Office of Scientific and Technical Information (OSTI.GOV)

Eraso, Jesus M.; Markillie, Lye Meng; Mitchell, Hugh D.

2014-05-05

The mraZ and mraW genes are highly conserved in bacteria, both in sequence and location at the head of the division and cell wall (dcw) gene cluster. Although MraZ has structural similarity to the AbrB transition state regulator and the MazE antitoxin, and MraW is known to methylate ribosomal RNA, mraZ and mraW null mutants have no detectable growth phenotype in any species tested to date, hampering progress in understanding their physiological role. Here we show that overproduction of Escherichia coli MraZ perturbs cell division and the cell envelope, is more lethal at high levels or in minimal growth medium,more » and that MraW antagonizes these effects. MraZGFP localizes to the nucleoid, suggesting that it binds DNA. Indeed, purified MraZ directly binds a region upstream from its own promoter containing three direct repeats to regulate its own expression and that of downstream cell division and cell wall genes. MraZ-LacZ fusions are repressed by excess MraZ but not when DNA binding by MraZ is inhibited. RNAseq analysis indicates that MraZ is a global transcriptional regulator with numerous targets in addition to dcw genes. One of these targets, mioC, is directly bound by MraZ in a region with three direct repeats.« less

Evaluation of highly conserved hsp65-specific nested PCR primers for diagnosing Mycobacterium tuberculosis.

PubMed

Priyadarshini, P; Tiwari, K; Das, A; Kumar, D; Mishra, M N; Desikan, P; Nath, G

2017-02-01

To evaluate the sensitivity and specificity of a new nested set of primers designed for the detection of Mycobacterium tuberculosis complex targeting a highly conserved heat shock protein gene (hsp65). The nested primers were designed using multiple sequence alignment assuming the nucleotide sequence of the M. tuberculosis H37Rv hsp65 genome as base. Multidrug-resistant Mycobacterium species along with other non-mycobacterial and fungal species were included to evaluate the specificity of M. tuberculosis hsp65 gene-specific primers. The sensitivity of the primers was determined using serial 10-fold dilutions, and was 100% as shown by the bands in the case of M. tuberculosis complex. None of the other non M. tuberculosis complex bacterial and fungal species yielded any band on nested polymerase chain reaction (PCR). The first round of amplification could amplify 0.3 ng of the template DNA, while nested PCR could detect 0.3 pg. The present hsp65-specific primers have been observed to be sensitive, specific and cost-effective, without requiring interpretation of biochemical tests, real-time PCR, sequencing or high-performance liquid chromatography. These primer sets do not have the drawbacks associated with those protocols that target insertion sequence 6110, 16S rDNA, rpoB, recA and MPT 64.

Plant and yeast cornichon possess a conserved acidic motif required for correct targeting of plasma membrane cargos.

PubMed

Rosas-Santiago, Paul; Lagunas-Gomez, Daniel; Yáñez-Domínguez, Carolina; Vera-Estrella, Rosario; Zimmermannová, Olga; Sychrová, Hana; Pantoja, Omar

2017-10-01

The export of membrane proteins along the secretory pathway is initiated at the endoplasmic reticulum after proteins are folded and packaged inside this organelle by their recruiting into the coat complex COPII vesicles. It is proposed that cargo receptors are required for the correct transport of proteins to its target membrane, however, little is known about ER export signals for cargo receptors. Erv14/Cornichon belong to a well conserved protein family in Eukaryotes, and have been proposed to function as cargo receptors for many transmembrane proteins. Amino acid sequence alignment showed the presence of a conserved acidic motif in the C-terminal in homologues from plants and yeast. Here, we demonstrate that mutation of the C-terminal acidic motif from ScErv14 or OsCNIH1, did not alter the localization of these cargo receptors, however it modified the proper targeting of the plasma membrane transporters Nha1p, Pdr12p and Qdr2p. Our results suggest that mistargeting of these plasma membrane proteins is a consequence of a weaker interaction between the cargo receptor and cargo proteins caused by the mutation of the C-terminal acidic motif. Copyright © 2017 Elsevier B.V. All rights reserved.

Designing large-scale conservation corridors for pattern and process.

PubMed

Rouget, Mathieu; Cowling, Richard M; Lombard, Amanda T; Knight, Andrew T; Kerley, Graham I H

2006-04-01

A major challenge for conservation assessments is to identify priority areas that incorporate biological patterns and processes. Because large-scale processes are mostly oriented along environmental gradients, we propose to accommodate them by designing regional-scale corridors to capture these gradients. Based on systematic conservation planning principles such as representation and persistence, we identified large tracts of untransformed land (i.e., conservation corridors) for conservation that would achieve biodiversity targets for pattern and process in the Subtropical Thicket Biome of South Africa. We combined least-cost path analysis with a target-driven algorithm to identify the best option for capturing key environmental gradients while considering biodiversity targets and conservation opportunities and constraints. We identified seven conservation corridors on the basis of subtropical thicket representation, habitat transformation and degradation, wildlife suitability, irreplaceability of vegetation types, protected area networks, and future land-use pressures. These conservation corridors covered 21.1% of the planning region (ranging from 600 to 5200 km2) and successfully achieved targets for biological processes and to a lesser extent for vegetation types. The corridors we identified are intended to promote the persistence of ecological processes (gradients and fixed processes) and fulfill half of the biodiversity pattern target. We compared the conservation corridors with a simplified corridor design consisting of a fixed-width buffer along major rivers. Conservation corridors outperformed river buffers in seven out of eight criteria. Our corridor design can provide a tool for quantifying trade-offs between various criteria (biodiversity pattern and process, implementation constraints and opportunities). A land-use management model was developed to facilitate implementation of conservation actions within these corridors.

Toward target 2 of the global strategy for plant conservation: an expert analysis of the Puerto Rican flora to validate new streamlined methods for assessing conservation status

Treesearch

J.S. Miller; G.A. Krupnick; H. Stevens; H. Porter-Morgan; B. Boom; Pedro Acevedo-Rodriguez; J. Ackerman; D. Kolterman; E. Santiago; C. Torres; J. Velez; NO-VALUE

2013-01-01

Target 2 of the 2020 Global Strategy for Plant Conservation (GSPC) calls for a comprehensive list of the world’s threatened plant species. The lack of such a list is one of the greatest impediments to protecting the full complement of the world’s plant species, and work to achieve this has been slow. An efficient system for identifying those species that are at risk of...

Can private land conservation reduce wildfire risk to homes? A case study in San Diego County, California, USA

USGS Publications Warehouse

Butsic, Van; Syphard, Alexandra D.; Keeley, Jon E.; Bar-Massada, Avi

2017-01-01

The purchase of private land for conservation purposes is a common way to prevent the exploitation of sensitive ecological areas. However, private land conservation can also provide other benefits, one of these being natural hazard reduction. Here, we investigated the impacts of private land conservation on fire risk to homes in San Diego County, California. We coupled an econometric land use change model with a model that estimates the probability of house loss due to fire in order to compare fire risk at the county and municipality scale under alternative private land purchasing schemes and over a 20 year time horizon. We found that conservation purchases could reduce fire risk on this landscape, and the amount of risk reduction was related to the targeting approach used to choose which parcels were conserved. Conservation land purchases that targeted parcels designated as high fire hazard resulted in lower fire risk to homes than purchases that targeted low costs or high likelihood to subdivide. This result was driven by (1) preventing home placement in fire prone areas and (2) taking land off the market, and hence increasing development densities in other areas. These results raise the possibility that resource conservation and fire hazard reduction may benefit from combining efforts. With adequate planning, future conservation purchases could have synergistic effects beyond just protecting ecologically sensitive areas.

Quantifying progress toward a conservation assessment for all plants.

PubMed

Bachman, Steven P; Nic Lughadha, Eimear M; Rivers, Malin C

2018-06-01

The Global Strategy for Plant Conservation (GSPC) set an ambitious target to achieve a conservation assessment for all known plant species by 2020. We consolidated digitally available plant conservation assessments and reconciled their scientific names and assessment status to predefined standards to provide a quantitative measure of progress toward this target. The 241,919 plant conservation assessments generated represent 111,824 accepted land plant species (vascular plants and bryophytes, not algae). At least 73,081 and up to 90,321 species have been assessed at the global scale, representing 21-26% of known plant species. Of these plant species, at least 27,148 and up to 32,542 are threatened. Eighty plant families, including some of the largest, such as Asteraceae, Orchidaceae, and Rubiaceae, are underassessed and should be the focus of assessment effort if the GSPC target is to be met by 2020. Our data set is accessible online (ThreatSearch) and is a baseline that can be used to directly support other GSPC targets and plant conservation action. Although around one-quarter of a million plant assessments have been compiled, the majority of plants are still unassessed. The challenge now is to build on this progress and redouble efforts to document conservation status of unassessed plants to better inform conservation decisions and conserve the most threatened species. © 2017 The Authors. Conservation Biology published by Wiley Periodicals, Inc. on behalf of Society for Conservation Biology.

INCENP Centromere and Spindle Targeting: Identification of Essential Conserved Motifs and Involvement of Heterochromatin Protein HP1

PubMed Central

Ainsztein, Alexandra M.; Kandels-Lewis, Stefanie E.; Mackay, Alastair M.; Earnshaw, William C.

1998-01-01

The inner centromere protein (INCENP) has a modular organization, with domains required for chromosomal and cytoskeletal functions concentrated near the amino and carboxyl termini, respectively. In this study we have identified an autonomous centromere- and midbody-targeting module in the amino-terminal 68 amino acids of INCENP. Within this module, we have identified two evolutionarily conserved amino acid sequence motifs: a 13–amino acid motif that is required for targeting to centromeres and transfer to the spindle, and an 11–amino acid motif that is required for transfer to the spindle by molecules that have targeted previously to the centromere. To begin to understand the mechanisms of INCENP function in mitosis, we have performed a yeast two-hybrid screen for interacting proteins. These and subsequent in vitro binding experiments identify a physical interaction between INCENP and heterochromatin protein HP1Hsα. Surprisingly, this interaction does not appear to be involved in targeting INCENP to the centromeric heterochromatin, but may instead have a role in its transfer from the chromosomes to the anaphase spindle. PMID:9864353

Conserved herpesvirus protein kinases

PubMed Central

Gershburg, Edward; Pagano, Joseph S.

2008-01-01

Conserved herpesviral protein kinases (CHPKs) are a group of enzymes conserved throughout all subfamilies of Herpesviridae. Members of this group are serine/threonine protein kinases that are likely to play a conserved role in viral infection by interacting with common host cellular and viral factors; however along with a conserved role, individual kinases may have unique functions in the context of viral infection in such a way that they are only partially replaceable even by close homologues. Recent studies demonstrated that CHPKs are crucial for viral infection and suggested their involvement in regulation of numerous processes at various infection steps (primary infection, nuclear egress, tegumentation), although the mechanisms of this regulation remain unknown. Notwithstanding, recent advances in discovery of new CHPK targets, and studies of CHPK knockout phenotypes have raised their attractiveness as targets for antiviral therapy. A number of compounds have been shown to inhibit the activity of human cytomegalovirus (HCMV)-encoded UL97 protein kinase and exhibit a pronounced antiviral effect, although the same compounds are inactive against Epstein-Barr Virus (EBV)-encoded protein kinase BGLF4, illustrating the fact that low homology between the members of this group complicates development of compounds targeting the whole group, and suggesting that individualized, structure-based inhibitor design will be more effective. Determination of CHPK structures will greatly facilitate this task. PMID:17881303

The conservation pattern of short linear motifs is highly correlated with the function of interacting protein domains.

PubMed

Ren, Siyuan; Yang, Guang; He, Youyu; Wang, Yiguo; Li, Yixue; Chen, Zhengjun

2008-10-01

Many well-represented domains recognize primary sequences usually less than 10 amino acids in length, called Short Linear Motifs (SLiMs). Accurate prediction of SLiMs has been difficult because they are short (often < 10 amino acids) and highly degenerate. In this study, we combined scoring matrixes derived from peptide library and conservation analysis to identify protein classes enriched of functional SLiMs recognized by SH2, SH3, PDZ and S/T kinase domains. Our combined approach revealed that SLiMs are highly conserved in proteins from functional classes that are known to interact with a specific domain, but that they are not conserved in most other protein groups. We found that SLiMs recognized by SH2 domains were highly conserved in receptor kinases/phosphatases, adaptor molecules, and tyrosine kinases/phosphatases, that SLiMs recognized by SH3 domains were highly conserved in cytoskeletal and cytoskeletal-associated proteins, that SLiMs recognized by PDZ domains were highly conserved in membrane proteins such as channels and receptors, and that SLiMs recognized by S/T kinase domains were highly conserved in adaptor molecules, S/T kinases/phosphatases, and proteins involved in transcription or cell cycle control. We studied Tyr-SLiMs recognized by SH2 domains in more detail, and found that SH2-recognized Tyr-SLiMs on the cytoplasmic side of membrane proteins are more highly conserved than those on the extra-cellular side. Also, we found that SH2-recognized Tyr-SLiMs that are associated with SH3 motifs and a tyrosine kinase phosphorylation motif are more highly conserved. The interactome of protein domains is reflected by the evolutionary conservation of SLiMs recognized by these domains. Combining scoring matrixes derived from peptide libraries and conservation analysis, we would be able to find those protein groups that are more likely to interact with specific domains.

Conservative versus liberal oxygenation targets in critically ill children: the randomised multiple-centre pilot Oxy-PICU trial.

PubMed

Peters, Mark J; Jones, Gareth A L; Wiley, Daisy; Wulff, Jerome; Ramnarayan, Padmanabhan; Ray, Samiran; Inwald, David; Grocott, Michael; Griksaitis, Michael; Pappachan, John; O'Neill, Lauran; Eaton, Simon; Mouncey, Paul R; Harrison, David A; Rowan, Kathryn M

2018-06-04

Oxygen saturation monitoring for children receiving respiratory support is standard worldwide. No randomised clinical trials have compared peripheral oxygen saturation (SpO 2 ) targets for critically ill children. The harm of interventions to raise SpO 2 to > 94% may exceed their benefits. We undertook an open, parallel-group randomised trial of children > 38 weeks completed gestation and < 16 years of age receiving invasive or non-invasive respiratory support and supplemental oxygen who were admitted urgently to one of three paediatric intensive care units. A 'research without prior consent' approach was employed. Children were randomly assigned to a liberal oxygenation group (SpO 2 targets > 94%) or a conservative oxygenation group (SpO 2  = 88-92% inclusive). Outcomes were measures of feasibility: recruitment rate, protocol adherence and acceptability, between-group separation of SpO 2 and safety. The Oxy-PICU trial was registered before recruitment: ClinicalTrials.gov identifier NCT03040570. A total of 159 children met the inclusion criteria, of whom 119 (75%) were randomised between April and July 2017, representing a rate of 10 patients per month per site. The mean time to randomisation from first contact with an intensive care team was 1.9 (SD 2.2) h. Consent to continue in the study was obtained in 107 cases (90%); the children's parents/legal representatives were supportive of the consent process. The median (interquartile range, IQR) of time-weighted individual mean SpO 2 was 94.9% (92.6-97.1) in the conservative oxygenation group and 97.5% (96.2-98.4) in the liberal group [difference 2.7%, 95% confidence interval (95% CI) 1.3-4.0%, p < 0.001]. Median (IQR) time-weighted individual mean FiO 2 was 0.28 (0.24-0.37) in the conservative group and 0.37 (0.30-0.42) in the liberal group (difference 0.08, 95% CI 0.03-0.13, p < 0.001). There were no significant between-group differences in length of stay, duration of organ support or mortality

The Nature Conservancy's Gulf Wings Project – A Case Study in Conservation Planning for Migratory Birds

Treesearch

Charles Duncan; Becky Abel; Danny Kwan; David Mehlman

2005-01-01

The Nature Conservancy has adopted a framework for mission success called Conservation by Design. We plan at the ecoregional level to define conservation targets and the portfolio of sites needed to protect them. We consider threats and strategies for abating them at these key sites, and we define measures of success to hold ourselves accountable. Migratory birds...

Optimized spatial priorities for biodiversity conservation in China: a systematic conservation planning perspective.

PubMed

Wu, Ruidong; Long, Yongcheng; Malanson, George P; Garber, Paul A; Zhang, Shuang; Li, Diqiang; Zhao, Peng; Wang, Longzhu; Duo, Hairui

2014-01-01

By addressing several key features overlooked in previous studies, i.e. human disturbance, integration of ecosystem- and species-level conservation features, and principles of complementarity and representativeness, we present the first national-scale systematic conservation planning for China to determine the optimized spatial priorities for biodiversity conservation. We compiled a spatial database on the distributions of ecosystem- and species-level conservation features, and modeled a human disturbance index (HDI) by aggregating information using several socioeconomic proxies. We ran Marxan with two scenarios (HDI-ignored and HDI-considered) to investigate the effects of human disturbance, and explored the geographic patterns of the optimized spatial conservation priorities. Compared to when HDI was ignored, the HDI-considered scenario resulted in (1) a marked reduction (∼9%) in the total HDI score and a slight increase (∼7%) in the total area of the portfolio of priority units, (2) a significant increase (∼43%) in the total irreplaceable area and (3) more irreplaceable units being identified in almost all environmental zones and highly-disturbed provinces. Thus the inclusion of human disturbance is essential for cost-effective priority-setting. Attention should be targeted to the areas that are characterized as moderately-disturbed, <2,000 m in altitude, and/or intermediately- to extremely-rugged in terrain to identify potentially important regions for implementing cost-effective conservation. We delineated 23 primary large-scale priority areas that are significant for conserving China's biodiversity, but those isolated priority units in disturbed regions are in more urgent need of conservation actions so as to prevent immediate and severe biodiversity loss. This study presents a spatially optimized national-scale portfolio of conservation priorities--effectively representing the overall biodiversity of China while minimizing conflicts with economic

Optimized Spatial Priorities for Biodiversity Conservation in China: A Systematic Conservation Planning Perspective

PubMed Central

Wu, Ruidong; Long, Yongcheng; Malanson, George P.; Garber, Paul A.; Zhang, Shuang; Li, Diqiang; Zhao, Peng; Wang, Longzhu; Duo, Hairui

2014-01-01

By addressing several key features overlooked in previous studies, i.e. human disturbance, integration of ecosystem- and species-level conservation features, and principles of complementarity and representativeness, we present the first national-scale systematic conservation planning for China to determine the optimized spatial priorities for biodiversity conservation. We compiled a spatial database on the distributions of ecosystem- and species-level conservation features, and modeled a human disturbance index (HDI) by aggregating information using several socioeconomic proxies. We ran Marxan with two scenarios (HDI-ignored and HDI-considered) to investigate the effects of human disturbance, and explored the geographic patterns of the optimized spatial conservation priorities. Compared to when HDI was ignored, the HDI-considered scenario resulted in (1) a marked reduction (∼9%) in the total HDI score and a slight increase (∼7%) in the total area of the portfolio of priority units, (2) a significant increase (∼43%) in the total irreplaceable area and (3) more irreplaceable units being identified in almost all environmental zones and highly-disturbed provinces. Thus the inclusion of human disturbance is essential for cost-effective priority-setting. Attention should be targeted to the areas that are characterized as moderately-disturbed, <2,000 m in altitude, and/or intermediately- to extremely-rugged in terrain to identify potentially important regions for implementing cost-effective conservation. We delineated 23 primary large-scale priority areas that are significant for conserving China's biodiversity, but those isolated priority units in disturbed regions are in more urgent need of conservation actions so as to prevent immediate and severe biodiversity loss. This study presents a spatially optimized national-scale portfolio of conservation priorities – effectively representing the overall biodiversity of China while minimizing conflicts with economic

Fixism and conservation science.

PubMed

Robert, Alexandre; Fontaine, Colin; Veron, Simon; Monnet, Anne-Christine; Legrand, Marine; Clavel, Joanne; Chantepie, Stéphane; Couvet, Denis; Ducarme, Frédéric; Fontaine, Benoît; Jiguet, Frédéric; le Viol, Isabelle; Rolland, Jonathan; Sarrazin, François; Teplitsky, Céline; Mouchet, Maud

2017-08-01

The field of biodiversity conservation has recently been criticized as relying on a fixist view of the living world in which existing species constitute at the same time targets of conservation efforts and static states of reference, which is in apparent disagreement with evolutionary dynamics. We reviewed the prominent role of species as conservation units and the common benchmark approach to conservation that aims to use past biodiversity as a reference to conserve current biodiversity. We found that the species approach is justified by the discrepancy between the time scales of macroevolution and human influence and that biodiversity benchmarks are based on reference processes rather than fixed reference states. Overall, we argue that the ethical and theoretical frameworks underlying conservation research are based on macroevolutionary processes, such as extinction dynamics. Current species, phylogenetic, community, and functional conservation approaches constitute short-term responses to short-term human effects on these reference processes, and these approaches are consistent with evolutionary principles. © 2016 Society for Conservation Biology.

Improving spatial prioritisation for remote marine regions: optimising biodiversity conservation and sustainable development trade-offs

NASA Astrophysics Data System (ADS)

Moore, Cordelia H.; Radford, Ben T.; Possingham, Hugh P.; Heyward, Andrew J.; Stewart, Romola R.; Watts, Matthew E.; Prescott, Jim; Newman, Stephen J.; Harvey, Euan S.; Fisher, Rebecca; Bryce, Clay W.; Lowe, Ryan J.; Berry, Oliver; Espinosa-Gayosso, Alexis; Sporer, Errol; Saunders, Thor

2016-08-01

Creating large conservation zones in remote areas, with less intense stakeholder overlap and limited environmental information, requires periodic review to ensure zonation mitigates primary threats and fill gaps in representation, while achieving conservation targets. Follow-up reviews can utilise improved methods and data, potentially identifying new planning options yielding a desirable balance between stakeholder interests. This research explored a marine zoning system in north-west Australia-a biodiverse area with poorly documented biota. Although remote, it is economically significant (i.e. petroleum extraction and fishing). Stakeholder engagement was used to source the best available biodiversity and socio-economic data and advanced spatial analyses produced 765 high resolution data layers, including 674 species distributions representing 119 families. Gap analysis revealed the current proposed zoning system as inadequate, with 98.2% of species below the Convention on Biological Diversity 10% representation targets. A systematic conservation planning algorithm Maxan provided zoning options to meet representation targets while balancing this with industry interests. Resulting scenarios revealed that conservation targets could be met with minimal impacts on petroleum and fishing industries, with estimated losses of 4.9% and 7.2% respectively. The approach addressed important knowledge gaps and provided a powerful and transparent method to reconcile industry interests with marine conservation.

Improving spatial prioritisation for remote marine regions: optimising biodiversity conservation and sustainable development trade-offs.

PubMed

Moore, Cordelia H; Radford, Ben T; Possingham, Hugh P; Heyward, Andrew J; Stewart, Romola R; Watts, Matthew E; Prescott, Jim; Newman, Stephen J; Harvey, Euan S; Fisher, Rebecca; Bryce, Clay W; Lowe, Ryan J; Berry, Oliver; Espinosa-Gayosso, Alexis; Sporer, Errol; Saunders, Thor

2016-08-24

Creating large conservation zones in remote areas, with less intense stakeholder overlap and limited environmental information, requires periodic review to ensure zonation mitigates primary threats and fill gaps in representation, while achieving conservation targets. Follow-up reviews can utilise improved methods and data, potentially identifying new planning options yielding a desirable balance between stakeholder interests. This research explored a marine zoning system in north-west Australia-a biodiverse area with poorly documented biota. Although remote, it is economically significant (i.e. petroleum extraction and fishing). Stakeholder engagement was used to source the best available biodiversity and socio-economic data and advanced spatial analyses produced 765 high resolution data layers, including 674 species distributions representing 119 families. Gap analysis revealed the current proposed zoning system as inadequate, with 98.2% of species below the Convention on Biological Diversity 10% representation targets. A systematic conservation planning algorithm Maxan provided zoning options to meet representation targets while balancing this with industry interests. Resulting scenarios revealed that conservation targets could be met with minimal impacts on petroleum and fishing industries, with estimated losses of 4.9% and 7.2% respectively. The approach addressed important knowledge gaps and provided a powerful and transparent method to reconcile industry interests with marine conservation.

Improving spatial prioritisation for remote marine regions: optimising biodiversity conservation and sustainable development trade-offs

PubMed Central

Moore, Cordelia H.; Radford, Ben T.; Possingham, Hugh P.; Heyward, Andrew J.; Stewart, Romola R.; Watts, Matthew E.; Prescott, Jim; Newman, Stephen J.; Harvey, Euan S.; Fisher, Rebecca; Bryce, Clay W.; Lowe, Ryan J.; Berry, Oliver; Espinosa-Gayosso, Alexis; Sporer, Errol; Saunders, Thor

2016-01-01

Creating large conservation zones in remote areas, with less intense stakeholder overlap and limited environmental information, requires periodic review to ensure zonation mitigates primary threats and fill gaps in representation, while achieving conservation targets. Follow-up reviews can utilise improved methods and data, potentially identifying new planning options yielding a desirable balance between stakeholder interests. This research explored a marine zoning system in north-west Australia–a biodiverse area with poorly documented biota. Although remote, it is economically significant (i.e. petroleum extraction and fishing). Stakeholder engagement was used to source the best available biodiversity and socio-economic data and advanced spatial analyses produced 765 high resolution data layers, including 674 species distributions representing 119 families. Gap analysis revealed the current proposed zoning system as inadequate, with 98.2% of species below the Convention on Biological Diversity 10% representation targets. A systematic conservation planning algorithm Maxan provided zoning options to meet representation targets while balancing this with industry interests. Resulting scenarios revealed that conservation targets could be met with minimal impacts on petroleum and fishing industries, with estimated losses of 4.9% and 7.2% respectively. The approach addressed important knowledge gaps and provided a powerful and transparent method to reconcile industry interests with marine conservation. PMID:27556689

Conserved Regulation of p53 Network Dosage by MicroRNA–125b Occurs through Evolving miRNA–Target Gene Pairs

PubMed Central

Khaw, Swea Ling; Chin, Lingzi; Teh, Cathleen; Tay, Junliang; O'Day, Elizabeth; Korzh, Vladimir; Yang, Henry; Lal, Ashish; Lieberman, Judy; Lodish, Harvey F.; Lim, Bing

2011-01-01

MicroRNAs regulate networks of genes to orchestrate cellular functions. MiR-125b, the vertebrate homologue of the Caenorhabditis elegans microRNA lin-4, has been implicated in the regulation of neural and hematopoietic stem cell homeostasis, analogous to how lin-4 regulates stem cells in C. elegans. Depending on the cell context, miR-125b has been proposed to regulate both apoptosis and proliferation. Because the p53 network is a central regulator of both apoptosis and proliferation, the dual roles of miR-125b raise the question of what genes in the p53 network might be regulated by miR-125b. By using a gain- and loss-of-function screen for miR-125b targets in humans, mice, and zebrafish and by validating these targets with the luciferase assay and a novel miRNA pull-down assay, we demonstrate that miR-125b directly represses 20 novel targets in the p53 network. These targets include both apoptosis regulators like Bak1, Igfbp3, Itch, Puma, Prkra, Tp53inp1, Tp53, Zac1, and also cell-cycle regulators like cyclin C, Cdc25c, Cdkn2c, Edn1, Ppp1ca, Sel1l, in the p53 network. We found that, although each miRNA–target pair was seldom conserved, miR-125b regulation of the p53 pathway is conserved at the network level. Our results lead us to propose that miR-125b buffers and fine-tunes p53 network activity by regulating the dose of both proliferative and apoptotic regulators, with implications for tissue stem cell homeostasis and oncogenesis. PMID:21935352

Measuring the effectiveness of conservation: a novel framework to quantify the benefits of sage-grouse conservation policy and easements in Wyoming.

PubMed

Copeland, Holly E; Pocewicz, Amy; Naugle, David E; Griffiths, Tim; Keinath, Doug; Evans, Jeffrey; Platt, James

2013-01-01

Increasing energy and housing demands are impacting wildlife populations throughout western North America. Greater sage-grouse (Centrocercus urophasianus), a species known for its sensitivity to landscape-scale disturbance, inhabits the same low elevation sage-steppe in which much of this development is occurring. Wyoming has committed to maintain sage-grouse populations through conservation easements and policy changes that conserves high bird abundance "core" habitat and encourages development in less sensitive landscapes. In this study, we built new predictive models of oil and gas, wind, and residential development and applied build-out scenarios to simulate future development and measure the efficacy of conservation actions for maintaining sage-grouse populations. Our approach predicts sage-grouse population losses averted through conservation action and quantifies return on investment for different conservation strategies. We estimate that without conservation, sage-grouse populations in Wyoming will decrease under our long-term scenario by 14-29% (95% CI: 4-46%). However, a conservation strategy that includes the "core area" policy and $250 million in targeted easements could reduce these losses to 9-15% (95% CI: 3-32%), cutting anticipated losses by roughly half statewide and nearly two-thirds within sage-grouse core breeding areas. Core area policy is the single most important component, and targeted easements are complementary to the overall strategy. There is considerable uncertainty around the magnitude of our estimates; however, the relative benefit of different conservation scenarios remains comparable because potential biases and assumptions are consistently applied regardless of the strategy. There is early evidence based on a 40% reduction in leased hectares inside core areas that Wyoming policy is reducing potential for future fragmentation inside core areas. Our framework using build-out scenarios to anticipate species declines provides estimates

Measuring the Effectiveness of Conservation: A Novel Framework to Quantify the Benefits of Sage-Grouse Conservation Policy and Easements in Wyoming

PubMed Central

Copeland, Holly E.; Pocewicz, Amy; Naugle, David E.; Griffiths, Tim; Keinath, Doug; Evans, Jeffrey; Platt, James

2013-01-01

Increasing energy and housing demands are impacting wildlife populations throughout western North America. Greater sage-grouse (Centrocercus urophasianus), a species known for its sensitivity to landscape-scale disturbance, inhabits the same low elevation sage-steppe in which much of this development is occurring. Wyoming has committed to maintain sage-grouse populations through conservation easements and policy changes that conserves high bird abundance “core” habitat and encourages development in less sensitive landscapes. In this study, we built new predictive models of oil and gas, wind, and residential development and applied build-out scenarios to simulate future development and measure the efficacy of conservation actions for maintaining sage-grouse populations. Our approach predicts sage-grouse population losses averted through conservation action and quantifies return on investment for different conservation strategies. We estimate that without conservation, sage-grouse populations in Wyoming will decrease under our long-term scenario by 14–29% (95% CI: 4–46%). However, a conservation strategy that includes the “core area” policy and $250 million in targeted easements could reduce these losses to 9–15% (95% CI: 3–32%), cutting anticipated losses by roughly half statewide and nearly two-thirds within sage-grouse core breeding areas. Core area policy is the single most important component, and targeted easements are complementary to the overall strategy. There is considerable uncertainty around the magnitude of our estimates; however, the relative benefit of different conservation scenarios remains comparable because potential biases and assumptions are consistently applied regardless of the strategy. There is early evidence based on a 40% reduction in leased hectares inside core areas that Wyoming policy is reducing potential for future fragmentation inside core areas. Our framework using build-out scenarios to anticipate species declines

Low-enriched uranium high-density target project. Compendium report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vandegrift, George; Brown, M. Alex; Jerden, James L.

2016-09-01

At present, most 99Mo is produced in research, test, or isotope production reactors by irradiation of highly enriched uranium targets. To achieve the denser form of uranium needed for switching from high to low enriched uranium (LEU), targets in the form of a metal foil (~125-150 µm thick) are being developed. The LEU High Density Target Project successfully demonstrated several iterations of an LEU-fission-based Mo-99 technology that has the potential to provide the world’s supply of Mo-99, should major producers choose to utilize the technology. Over 50 annular high density targets have been successfully tested, and the assembly and disassemblymore » of targets have been improved and optimized. Two target front-end processes (acidic and electrochemical) have been scaled up and demonstrated to allow for the high-density target technology to mate up to the existing producer technology for target processing. In the event that a new target processing line is started, the chemical processing of the targets is greatly simplified. Extensive modeling and safety analysis has been conducted, and the target has been qualified to be inserted into the High Flux Isotope Reactor, which is considered above and beyond the requirements for the typical use of this target due to high fluence and irradiation duration.« less

Identifying conservation priorities and management strategies based on ecosystem services to improve urban sustainability in Harbin, China.

PubMed

Qu, Yi; Lu, Ming

2018-01-01

Rapid urbanization and agricultural development has resulted in the degradation of ecosystems, while also negatively impacting ecosystem services (ES) and urban sustainability. Identifying conservation priorities for ES and applying reasonable management strategies have been found to be effective methods for mitigating this phenomenon. The purpose of this study is to propose a comprehensive framework for identifying ES conservation priorities and associated management strategies for these planning areas. First, we incorporated 10 ES indicators within a systematic conservation planning (SCP) methodology in order to identify ES conservation priorities with high irreplaceability values based on conservation target goals associated with the potential distribution of ES indicators. Next, we assessed the efficiency of the ES conservation priorities for meeting the designated conservation target goals. Finally, ES conservation priorities were clustered into groups using a K-means clustering analysis in an effort to identify the dominant ES per location before formulating management strategies. We effectively identified 12 ES priorities to best represent conservation target goals for the ES indicators. These 12 priorities had a total areal coverage of 13,364 km 2 representing 25.16% of the study area. The 12 priorities were further clustered into five significantly different groups ( p -values between groups < 0.05), which helped to refine management strategies formulated to best enhance ES across the study area. The proposed method allows conservation and management plans to easily adapt to a wide variety of quantitative ES target goals within urban and agricultural areas, thereby preventing urban and agriculture sprawl and guiding sustainable urban development.

Identifying conservation priorities and management strategies based on ecosystem services to improve urban sustainability in Harbin, China

PubMed Central

2018-01-01

Rapid urbanization and agricultural development has resulted in the degradation of ecosystems, while also negatively impacting ecosystem services (ES) and urban sustainability. Identifying conservation priorities for ES and applying reasonable management strategies have been found to be effective methods for mitigating this phenomenon. The purpose of this study is to propose a comprehensive framework for identifying ES conservation priorities and associated management strategies for these planning areas. First, we incorporated 10 ES indicators within a systematic conservation planning (SCP) methodology in order to identify ES conservation priorities with high irreplaceability values based on conservation target goals associated with the potential distribution of ES indicators. Next, we assessed the efficiency of the ES conservation priorities for meeting the designated conservation target goals. Finally, ES conservation priorities were clustered into groups using a K-means clustering analysis in an effort to identify the dominant ES per location before formulating management strategies. We effectively identified 12 ES priorities to best represent conservation target goals for the ES indicators. These 12 priorities had a total areal coverage of 13,364 km2 representing 25.16% of the study area. The 12 priorities were further clustered into five significantly different groups (p-values between groups < 0.05), which helped to refine management strategies formulated to best enhance ES across the study area. The proposed method allows conservation and management plans to easily adapt to a wide variety of quantitative ES target goals within urban and agricultural areas, thereby preventing urban and agriculture sprawl and guiding sustainable urban development. PMID:29682412

Preferential Targeting of Conserved Gag Regions after Vaccination with a Heterologous DNA Prime-Modified Vaccinia Virus Ankara Boost HIV-1 Vaccine Regimen.

PubMed

Bauer, Asli; Podola, Lilli; Mann, Philipp; Missanga, Marco; Haule, Antelmo; Sudi, Lwitiho; Nilsson, Charlotta; Kaluwa, Bahati; Lueer, Cornelia; Mwakatima, Maria; Munseri, Patricia J; Maboko, Leonard; Robb, Merlin L; Tovanabutra, Sodsai; Kijak, Gustavo; Marovich, Mary; McCormack, Sheena; Joseph, Sarah; Lyamuya, Eligius; Wahren, Britta; Sandström, Eric; Biberfeld, Gunnel; Hoelscher, Michael; Bakari, Muhammad; Kroidl, Arne; Geldmacher, Christof

2017-09-15

Prime-boost vaccination strategies against HIV-1 often include multiple variants for a given immunogen for better coverage of the extensive viral diversity. To study the immunologic effects of this approach, we characterized breadth, phenotype, function, and specificity of Gag-specific T cells induced by a DNA-prime modified vaccinia virus Ankara (MVA)-boost vaccination strategy, which uses mismatched Gag immunogens in the TamoVac 01 phase IIa trial. Healthy Tanzanian volunteers received three injections of the DNA-SMI vaccine encoding a subtype B and AB-recombinant Gag p37 and two vaccinations with MVA-CMDR encoding subtype A Gag p55 Gag-specific T-cell responses were studied in 42 vaccinees using fresh peripheral blood mononuclear cells. After the first MVA-CMDR boost, vaccine-induced gamma interferon-positive (IFN-γ + ) Gag-specific T-cell responses were dominated by CD4 + T cells ( P < 0.001 compared to CD8 + T cells) that coexpressed interleukin-2 (IL-2) (66.4%) and/or tumor necrosis factor alpha (TNF-α) (63.7%). A median of 3 antigenic regions were targeted with a higher-magnitude median response to Gag p24 regions, more conserved between prime and boost, compared to those of regions within Gag p15 (not primed) and Gag p17 (less conserved; P < 0.0001 for both). Four regions within Gag p24 each were targeted by 45% to 74% of vaccinees upon restimulation with DNA-SMI-Gag matched peptides. The response rate to individual antigenic regions correlated with the sequence homology between the MVA- and DNA Gag-encoded immunogens ( P = 0.04, r 2 = 0.47). In summary, after the first MVA-CMDR boost, the sequence-mismatched DNA-prime MVA-boost vaccine strategy induced a Gag-specific T-cell response that was dominated by polyfunctional CD4 + T cells and that targeted multiple antigenic regions within the conserved Gag p24 protein. IMPORTANCE Genetic diversity is a major challenge for the design of vaccines against variable viruses. While including multiple variants for a

Conservation of transcription factor binding events predicts gene expression across species

PubMed Central

Hemberg, Martin; Kreiman, Gabriel

2011-01-01

Recent technological advances have made it possible to determine the genome-wide binding sites of transcription factors (TFs). Comparisons across species have suggested a relatively low degree of evolutionary conservation of experimentally defined TF binding events (TFBEs). Using binding data for six different TFs in hepatocytes and embryonic stem cells from human and mouse, we demonstrate that evolutionary conservation of TFBEs within orthologous proximal promoters is closely linked to function, defined as expression of the target genes. We show that (i) there is a significantly higher degree of conservation of TFBEs when the target gene is expressed in both species; (ii) there is increased conservation of binding events for groups of TFs compared to individual TFs; and (iii) conserved TFBEs have a greater impact on the expression of their target genes than non-conserved ones. These results link conservation of structural elements (TFBEs) to conservation of function (gene expression) and suggest a higher degree of functional conservation than implied by previous studies. PMID:21622661

The conservation pattern of short linear motifs is highly correlated with the function of interacting protein domains

PubMed Central

Ren, Siyuan; Yang, Guang; He, Youyu; Wang, Yiguo; Li, Yixue; Chen, Zhengjun

2008-01-01

Background Many well-represented domains recognize primary sequences usually less than 10 amino acids in length, called Short Linear Motifs (SLiMs). Accurate prediction of SLiMs has been difficult because they are short (often < 10 amino acids) and highly degenerate. In this study, we combined scoring matrixes derived from peptide library and conservation analysis to identify protein classes enriched of functional SLiMs recognized by SH2, SH3, PDZ and S/T kinase domains. Results Our combined approach revealed that SLiMs are highly conserved in proteins from functional classes that are known to interact with a specific domain, but that they are not conserved in most other protein groups. We found that SLiMs recognized by SH2 domains were highly conserved in receptor kinases/phosphatases, adaptor molecules, and tyrosine kinases/phosphatases, that SLiMs recognized by SH3 domains were highly conserved in cytoskeletal and cytoskeletal-associated proteins, that SLiMs recognized by PDZ domains were highly conserved in membrane proteins such as channels and receptors, and that SLiMs recognized by S/T kinase domains were highly conserved in adaptor molecules, S/T kinases/phosphatases, and proteins involved in transcription or cell cycle control. We studied Tyr-SLiMs recognized by SH2 domains in more detail, and found that SH2-recognized Tyr-SLiMs on the cytoplasmic side of membrane proteins are more highly conserved than those on the extra-cellular side. Also, we found that SH2-recognized Tyr-SLiMs that are associated with SH3 motifs and a tyrosine kinase phosphorylation motif are more highly conserved. Conclusion The interactome of protein domains is reflected by the evolutionary conservation of SLiMs recognized by these domains. Combining scoring matrixes derived from peptide libraries and conservation analysis, we would be able to find those protein groups that are more likely to interact with specific domains. PMID:18828911

High density laser-driven target

DOEpatents

Lindl, John D.

1981-01-01

A high density target for implosion by laser energy composed of a central quantity of fuel surrounded by a high-Z pusher shell with a low-Z ablator-pusher shell spaced therefrom forming a region filled with low-density material.

ABCE1 Is a Highly Conserved RNA Silencing Suppressor

PubMed Central

Kärblane, Kairi; Gerassimenko, Jelena; Nigul, Lenne; Piirsoo, Alla; Smialowska, Agata; Vinkel, Kadri; Kylsten, Per; Ekwall, Karl; Swoboda, Peter; Truve, Erkki; Sarmiento, Cecilia

2015-01-01

ATP-binding cassette sub-family E member 1 (ABCE1) is a highly conserved protein among eukaryotes and archaea. Recent studies have identified ABCE1 as a ribosome-recycling factor important for translation termination in mammalian cells, yeast and also archaea. Here we report another conserved function of ABCE1. We have previously described AtRLI2, the homolog of ABCE1 in the plant Arabidopsis thaliana, as an endogenous suppressor of RNA silencing. In this study we show that this function is conserved: human ABCE1 is able to suppress RNA silencing in Nicotiana benthamiana plants, in mammalian HEK293 cells and in the worm Caenorhabditis elegans. Using co-immunoprecipitation and mass spectrometry, we found a number of potential ABCE1-interacting proteins that might support its function as an endogenous suppressor of RNA interference. The interactor candidates are associated with epigenetic regulation, transcription, RNA processing and mRNA surveillance. In addition, one of the identified proteins is translin, which together with its binding partner TRAX supports RNA interference. PMID:25659154

The Universally Conserved Prokaryotic GTPases

PubMed Central

Verstraeten, Natalie; Fauvart, Maarten; Versées, Wim; Michiels, Jan

2011-01-01

Summary: Members of the large superclass of P-loop GTPases share a core domain with a conserved three-dimensional structure. In eukaryotes, these proteins are implicated in various crucial cellular processes, including translation, membrane trafficking, cell cycle progression, and membrane signaling. As targets of mutation and toxins, GTPases are involved in the pathogenesis of cancer and infectious diseases. In prokaryotes also, it is hard to overestimate the importance of GTPases in cell physiology. Numerous papers have shed new light on the role of bacterial GTPases in cell cycle regulation, ribosome assembly, the stress response, and other cellular processes. Moreover, bacterial GTPases have been identified as high-potential drug targets. A key paper published over 2 decades ago stated that, “It may never again be possible to capture [GTPases] in a family portrait” (H. R. Bourne, D. A. Sanders, and F. McCormick, Nature 348:125-132, 1990) and indeed, the last 20 years have seen a tremendous increase in publications on the subject. Sequence analysis identified 13 bacterial GTPases that are conserved in at least 75% of all bacterial species. We here provide an overview of these 13 protein subfamilies, covering their cellular functions as well as cellular localization and expression levels, three-dimensional structures, biochemical properties, and gene organization. Conserved roles in eukaryotic homologs will be discussed as well. A comprehensive overview summarizing current knowledge on prokaryotic GTPases will aid in further elucidating the function of these important proteins. PMID:21885683

Liquid lithium target as a high intensity, high energy neutron source

DOEpatents

Parkin, Don M.; Dudey, Norman D.

1976-01-01

This invention provides a target jet for charged particles. In one embodiment the charged particles are high energy deuterons that bombard the target jet to produce high intensity, high energy neutrons. To this end, deuterons in a vacuum container bombard an endlessly circulating, free-falling, sheet-shaped, copiously flowing, liquid lithium jet that gushes by gravity from a rectangular cross-section vent on the inside of the container means to form a moving web in contact with the inside wall of the vacuum container. The neutrons are produced via break-up of the beam in the target by stripping, spallation and compound nuclear reactions in which the projectiles (deuterons) interact with the target (Li) to produce excited nuclei, which then "boil off" or evaporate a neutron.

High-Throughput Sequencing Reveals Diverse Sets of Conserved, Nonconserved, and Species-Specific miRNAs in Jute

PubMed Central

Islam, Md. Tariqul; Ferdous, Ahlan Sabah; Najnin, Rifat Ara; Sarker, Suprovath Kumar; Khan, Haseena

2015-01-01

MicroRNAs play a pivotal role in regulating a broad range of biological processes, acting by cleaving mRNAs or by translational repression. A group of plant microRNAs are evolutionarily conserved; however, others are expressed in a species-specific manner. Jute is an agroeconomically important fibre crop; nonetheless, no practical information is available for microRNAs in jute to date. In this study, Illumina sequencing revealed a total of 227 known microRNAs and 17 potential novel microRNA candidates in jute, of which 164 belong to 23 conserved families and the remaining 63 belong to 58 nonconserved families. Among a total of 81 identified microRNA families, 116 potential target genes were predicted for 39 families and 11 targets were predicted for 4 among the 17 identified novel microRNAs. For understanding better the functions of microRNAs, target genes were analyzed by Gene Ontology and their pathways illustrated by KEGG pathway analyses. The presence of microRNAs identified in jute was validated by stem-loop RT-PCR followed by end point PCR and qPCR for randomly selected 20 known and novel microRNAs. This study exhaustively identifies microRNAs and their target genes in jute which will ultimately pave the way for understanding their role in this crop and other crops. PMID:25861616

High purity tungsten targets

NASA Technical Reports Server (NTRS)

1975-01-01

High purity tungsten, which is used for targets in X-ray tubes was considered for space processing. The demand for X-ray tubes was calculated using the growth rates for dental and medical X-ray machines. It is concluded that the cost benefits are uncertain.

Polarized targets in high energy physics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cates, G.D. Jr.

1994-12-01

Various approaches are discussed for producing polarized nuclear targets for high energy physics experiments. As a unifying theme, examples are drawn from experiments to measure spin dependent structure functions of nucleons in deep inelastic scattering. This single physics goal has, over roughly two decades, been a driving force in advances in target technology. Actual or planned approaches have included solid targets polarized by dynamic nuclear polarization (DNP), several types of internal targets for use in storage rings, and gaseous {sup 3}He targets polarized by spin-exchange optical pumping. This last approach is the type of target adopted for SLAC E-142, anmore » experiment to measure the spin structure function of the neutron, and is described in detail.« less

Predicting occurrence of juvenile shark habitat to improve conservation planning.

PubMed

Oh, Beverly Z L; Sequeira, Ana M M; Meekan, Mark G; Ruppert, Jonathan L W; Meeuwig, Jessica J

2017-06-01

Fishing and habitat degradation have increased the extinction risk of sharks, and conservation strategies recognize that survival of juveniles is critical for the effective management of shark populations. Despite the rapid expansion of marine protected areas (MPAs) globally, the paucity of shark-monitoring data on large scales (100s-1000s km) means that the effectiveness of MPAs in halting shark declines remains unclear. Using data collected by baited remote underwater video systems (BRUVS) in northwestern Australia, we developed generalized linear models to elucidate the ecological drivers of habitat suitability for juvenile sharks. We assessed occurrence patterns at the order and species levels. We included all juvenile sharks sampled and the 3 most abundant species sampled separately (grey reef [Carcharhinus amblyrhynchos], sandbar [Carcharhinus plumbeus], and whitetip reef sharks [Triaenodon obesus]). We predicted the occurrence of juvenile sharks across 490,515 km 2 of coastal waters and quantified the representation of highly suitable habitats within MPAs. Our species-level models had higher accuracy (ĸ ≥ 0.69) and deviance explained (≥48%) than our order-level model (ĸ = 0.36 and deviance explained of 10%). Maps of predicted occurrence revealed different species-specific patterns of highly suitable habitat. These differences likely reflect different physiological or resource requirements between individual species and validate concerns over the utility of conservation targets based on aggregate species groups as opposed to a species-focused approach. Highly suitable habitats were poorly represented in MPAs with the most restrictions on extractive activities. This spatial mismatch possibly indicates a lack of explicit conservation targets and information on species distribution during the planning process. Non-extractive BRUVS provided a useful platform for building the suitability models across large scales to assist conservation planning across

Enhancing Conservation with High Resolution Productivity Datasets for the Conterminous United States

NASA Astrophysics Data System (ADS)

Robinson, Nathaniel Paul

Human driven alteration of the earth's terrestrial surface is accelerating through land use changes, intensification of human activity, climate change, and other anthropogenic pressures. These changes occur at broad spatio-temporal scales, challenging our ability to effectively monitor and assess the impacts and subsequent conservation strategies. While satellite remote sensing (SRS) products enable monitoring of the earth's terrestrial surface continuously across space and time, the practical applications for conservation and management of these products are limited. Often the processes driving ecological change occur at fine spatial resolutions and are undetectable given the resolution of available datasets. Additionally, the links between SRS data and ecologically meaningful metrics are weak. Recent advances in cloud computing technology along with the growing record of high resolution SRS data enable the development of SRS products that quantify ecologically meaningful variables at relevant scales applicable for conservation and management. The focus of my dissertation is to improve the applicability of terrestrial gross and net primary productivity (GPP/NPP) datasets for the conterminous United States (CONUS). In chapter one, I develop a framework for creating high resolution datasets of vegetation dynamics. I use the entire archive of Landsat 5, 7, and 8 surface reflectance data and a novel gap filling approach to create spatially continuous 30 m, 16-day composites of the normalized difference vegetation index (NDVI) from 1986 to 2016. In chapter two, I integrate this with other high resolution datasets and the MOD17 algorithm to create the first high resolution GPP and NPP datasets for CONUS. I demonstrate the applicability of these products for conservation and management, showing the improvements beyond currently available products. In chapter three, I utilize this dataset to evaluate the relationships between land ownership and terrestrial production

Operationalizing biodiversity for conservation planning.

PubMed

Sarkar, Sahotra; Margules, Chris

2002-07-01

Biodiversity has acquired such a general meaning that people now find it difficult to pin down a precise sense for planning and policy-making aimed at biodiversity conservation. Because biodiversity is rooted in place, the task of conserving biodiversity should target places for conservation action; and because all places contain biodiversity, but not all places can be targeted for action, places have to be prioritized. What is needed for this is a measure of the extent to which biodiversity varies from place to place. We do not need a precise measure of biodiversity to prioritize places. Relative estimates of similarity or difference can be derived using partial measures, or what have come to be called biodiversity surrogates. Biodiversity surrogates are supposed to stand in for general biodiversity in planning applications. We distinguish between true surrogates, those that might truly stand in for general biodiversity, and estimator surrogates, which have true surrogates as their target variable. For example, species richness has traditionally been the estimator surrogate for the true surrogate, species diversity. But species richness does not capture the differences in composition between places; the essence of biodiversity. Another measure, called complementarity, explicitly captures the differences between places as we iterate the process of place prioritization, starting with an initial place. The relative concept of biodiversity built into the definition of complementarity has the level of precision needed to undertake conservation planning.

Antibody Recognition of a Highly Conserved Influenza Virus Epitope

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ekiert, Damian C.; Bhabha, Gira; Elsliger, Marc-André

2009-05-21

Influenza virus presents an important and persistent threat to public health worldwide, and current vaccines provide immunity to viral isolates similar to the vaccine strain. High-affinity antibodies against a conserved epitope could provide immunity to the diverse influenza subtypes and protection against future pandemic viruses. Cocrystal structures were determined at 2.2 and 2.7 angstrom resolutions for broadly neutralizing human antibody CR6261 Fab in complexes with the major surface antigen (hemagglutinin, HA) from viruses responsible for the 1918 H1N1 influenza pandemic and a recent lethal case of H5N1 avian influenza. In contrast to other structurally characterized influenza antibodies, CR6261 recognizes amore » highly conserved helical region in the membrane-proximal stem of HA1 and HA2. The antibody neutralizes the virus by blocking conformational rearrangements associated with membrane fusion. The CR6261 epitope identified here should accelerate the design and implementation of improved vaccines that can elicit CR6261-like antibodies, as well as antibody-based therapies for the treatment of influenza.« less

Prioritizing conservation areas for coastal plant diversity under increasing urbanization.

PubMed

Doxa, Aggeliki; Albert, Cécile Hélène; Leriche, Agathe; Saatkamp, Arne

2017-10-01

Coastal urban expansion will continue to drive further biodiversity losses, if conservation targets for coastal ecosystems are not defined and met. Prioritizing areas for future protected area networks is thus an urgent task in such urbanization-threatened ecosystems. Our aim is to quantify past and future losses of coastal vegetation priority areas due to urbanization and assess the effectiveness of the existing protected area network for conservation. We conduct a prioritization analysis, based on 82 coastal plants, including common and IUCN red list species, in a highly-urbanized but biotically diverse region, in South-Eastern France. We evaluate the role of protected areas, by taking into account both strict and multi-use areas. We assess the impact of past and future urbanization on high priority areas, by combining prioritization analyses and urbanization models. We show that half of the highly diverse areas have already been lost due to urbanization. Remaining top priority areas are also among the most exposed to future urban expansion. The effectiveness of the existing protected area (PA) network is only partial. While strict PAs coincide well with top priority areas, they only represent less than one third of priority areas. The effectiveness of multi-use PAs, such as the Natura 2000 network, also remains limited. Our approach highlights the impact of urbanization on plant conservation targets. By modelling urbanization, we manage to identify those areas where protection could be more efficient to limit further losses. We suggest to use our approach in the future to expand the PA network in order to achieve the 2020 Aichi biodiversity targets. Copyright © 2017 Elsevier Ltd. All rights reserved.

Identification of areas in Brazil that optimize conservation of forest carbon, jaguars, and biodiversity.

PubMed

De Barros, Alan E; MacDonald, Ewan A; Matsumoto, Marcelo H; Paula, Rogério C; Nijhawan, Sahil; Malhi, Y; MacDonald, David W

2014-04-01

A major question in global environmental policy is whether schemes to reduce carbon pollution through forest management, such as Reducing Emissions from Deforestation and Degradation (REDD+), can also benefit biodiversity conservation in tropical countries. We identified municipalities in Brazil that are priorities for reducing rates of deforestation and thus preserving carbon stocks that are also conservation targets for the endangered jaguar (Panthera onca) and biodiversity in general. Preliminary statistical analysis showed that municipalities with high biodiversity were positively associated with high forest carbon stocks. We used a multicriteria decision analysis to identify municipalities that offered the best opportunities for the conservation of forest carbon stocks and biodiversity conservation under a range of scenarios with different rates of deforestation and carbon values. We further categorized these areas by their representativeness of the entire country (through measures such as percent forest cover) and an indirect measure of cost (number of municipalities). The municipalities that offered optimal co-benefits for forest carbon stocks and conservation were termed REDDspots (n = 159), and their spatial distribution was compared with the distribution of current and proposed REDD projects (n = 135). We defined REDDspots as the municipalities that offer the best opportunities for co-benefits between the conservation of forest carbon stocks, jaguars, and other wildlife. These areas coincided in 25% (n = 40) of municipalities. We identified a further 95 municipalities that may have the greatest potential to develop additional REDD+ projects while also targeting biodiversity conservation. We concluded that REDD+ strategies could be an efficient tool for biodiversity conservation in key locations, especially in Amazonian and Atlantic Forest biomes. ©2013 Society for Conservation Biology.

Comparison of conservation metrics in a case study of lemurs.

PubMed

Gudde, Renske; Venditti, Chris

2016-12-01

Conservation planning is important to protect species from going extinct now that natural habitats are decreasing owing to human activity and climate change. However, there is considerable controversy in choosing appropriate metrics to weigh the value of species and geographic regions. For example, the added value of phylogenetic conservation-selection criteria remains disputed because high correlations between them and the nonphylogenetic criteria of species richness have been reported. We evaluated the commonly used conservation metrics species richness, endemism, phylogenetic diversity (PD), and phylogenetic endemism (PE) in a case study on lemurs of Madagascar. This enabled us to identify the conservation target of each metric and consider how they may be used in future conservation planning. We also devised a novel metric that uses a phylogeny scaled according to the rate of phenotypic evolution as a proxy for a species' ability to adapt to change. High rates of evolution may indicate generalization or specialization. Both specialization and low rates of evolution may result in an inability to adapt to changing environments. We examined conservation priorities by using the inverse of the rate of body mass evolution to account for species with low rates of evolution. In line with previous work, we found high correlations among species richness and PD (r = 0.96), and endemism and PE (r = 0.82) in Malagasy lemurs. Phylogenetic endemism in combination with rates of evolution and their inverse prioritized grid cells containing highly endemic and specialized lemurs at risk of extinction, such as Avahi occidentalis and Lepilemur edwardsi, 2 endangered lemurs with high rates of phenotypic evolution and low-quality diets, and Hapalemur aureus, a critically endangered species with a low rate of body mass evolution and a diet consisting of very high doses of cyanide. © 2016 Society for Conservation Biology.

Conservative Management for Stable High Ankle Injuries in Professional Football Players.

PubMed

Knapik, Derrick M; Trem, Anthony; Sheehan, Joseph; Salata, Michael J; Voos, James E

High ankle "syndesmosis" injuries are common in American football players relative to the general population. At the professional level, syndesmotic sprains represent a challenging and unique injury lacking a standardized rehabilitation protocol during conservative management. PubMed, Biosis Preview, SPORTDiscus, PEDro, and EMBASE databases were searched using the terms syndesmotic injuries, American football, conservative management, and rehabilitation. Clinical review. Level 3. When compared with lateral ankle sprains, syndesmosis injuries result in significantly prolonged recovery times and games lost. For stable syndesmotic injuries, conservative management features a brief period of immobilization and protected weightbearing followed by progressive strengthening exercises and running, and athletes can expect to return to competition in 2 to 6 weeks. Further research investigating the efficacy of dry needling and blood flow restriction therapy is necessary to evaluate the benefit of these techniques in the rehabilitation process. Successful conservative management of stable syndesmotic injuries in professional American football athletes requires a thorough understanding of the anatomy, injury mechanisms, diagnosis, and rehabilitation strategies utilized in elite athletes.

In-silico and in-vivo analyses of EST databases unveil conserved miRNAs from Carthamus tinctorius and Cynara cardunculus

PubMed Central

2012-01-01

Background MicroRNAs (miRNAs) are small RNAs (21-24 bp) providing an RNA-based system of gene regulation highly conserved in plants and animals. In plants, miRNAs control mRNA degradation or restrain translation, affecting development and responses to stresses. Plant miRNAs show imperfect but extensive complementarity to mRNA targets, making their computational prediction possible, useful when data mining is applied on different species. In this study we used a comparative approach to identify both miRNAs and their targets, in artichoke and safflower. Results Two complete expressed sequence tags (ESTs) datasets from artichoke (3.6·104 entries) and safflower (4.2·104), were analysed with a bioinformatic pipeline and in vitro experiments, identifying 17 potential miRNAs. For each EST, using RNAhybrid program and 953 non redundant miRNA mature sequences, available in mirBase as reference, we searched matching putative targets. 8730 out of 42011 ESTs from safflower and 7145 of 36323 ESTs from artichoke showed at least one predicted miRNA target. BLAST analysis showed that 75% of all ESTs shared at least a common homologous region (E-value < 10-4) and about 50% of these displayed 400 bp or longer aligned sequences as conserved homologous/orthologous (COS) regions. 960 and 890 ESTs of safflower and artichoke organized in COS shared 79 different miRNA targets, considered functionally conserved, and statistically significant when compared with random sequences (signal to noise ratio > 2 and specificity ≥ 0.85). Four highly significant miRNAs selected from in silico data were experimentally validated in globe artichoke leaves. Conclusions Mature miRNAs and targets were predicted within EST sequences of safflower and artichoke. Most of the miRNA targets appeared highly/moderately conserved, highlighting an important and conserved function. In this study we introduce a stringent parameter for the comparative sequence analysis, represented by the identification of the same

Uncovering leaf rust responsive miRNAs in wheat (Triticum aestivum L.) using high-throughput sequencing and prediction of their targets through degradome analysis.

PubMed

Kumar, Dhananjay; Dutta, Summi; Singh, Dharmendra; Prabhu, Kumble Vinod; Kumar, Manish; Mukhopadhyay, Kunal

2017-01-01

Deep sequencing identified 497 conserved and 559 novel miRNAs in wheat, while degradome analysis revealed 701 targets genes. QRT-PCR demonstrated differential expression of miRNAs during stages of leaf rust progression. Bread wheat (Triticum aestivum L.) is an important cereal food crop feeding 30 % of the world population. Major threat to wheat production is the rust epidemics. This study was targeted towards identification and functional characterizations of micro(mi)RNAs and their target genes in wheat in response to leaf rust ingression. High-throughput sequencing was used for transcriptome-wide identification of miRNAs and their expression profiling in retort to leaf rust using mock and pathogen-inoculated resistant and susceptible near-isogenic wheat plants. A total of 1056 mature miRNAs were identified, of which 497 miRNAs were conserved and 559 miRNAs were novel. The pathogen-inoculated resistant plants manifested more miRNAs compared with the pathogen infected susceptible plants. The miRNA counts increased in susceptible isoline due to leaf rust, conversely, the counts decreased in the resistant isoline in response to pathogenesis illustrating precise spatial tuning of miRNAs during compatible and incompatible interaction. Stem-loop quantitative real-time PCR was used to profile 10 highly differentially expressed miRNAs obtained from high-throughput sequencing data. The spatio-temporal profiling validated the differential expression of miRNAs between the isolines as well as in retort to pathogen infection. Degradome analysis provided 701 predicted target genes associated with defense response, signal transduction, development, metabolism, and transcriptional regulation. The obtained results indicate that wheat isolines employ diverse arrays of miRNAs that modulate their target genes during compatible and incompatible interaction. Our findings contribute to increase knowledge on roles of microRNA in wheat-leaf rust interactions and could help in rust

TargetSpy: a supervised machine learning approach for microRNA target prediction.

PubMed

Sturm, Martin; Hackenberg, Michael; Langenberger, David; Frishman, Dmitrij

2010-05-28

Virtually all currently available microRNA target site prediction algorithms require the presence of a (conserved) seed match to the 5' end of the microRNA. Recently however, it has been shown that this requirement might be too stringent, leading to a substantial number of missed target sites. We developed TargetSpy, a novel computational approach for predicting target sites regardless of the presence of a seed match. It is based on machine learning and automatic feature selection using a wide spectrum of compositional, structural, and base pairing features covering current biological knowledge. Our model does not rely on evolutionary conservation, which allows the detection of species-specific interactions and makes TargetSpy suitable for analyzing unconserved genomic sequences.In order to allow for an unbiased comparison of TargetSpy to other methods, we classified all algorithms into three groups: I) no seed match requirement, II) seed match requirement, and III) conserved seed match requirement. TargetSpy predictions for classes II and III are generated by appropriate postfiltering. On a human dataset revealing fold-change in protein production for five selected microRNAs our method shows superior performance in all classes. In Drosophila melanogaster not only our class II and III predictions are on par with other algorithms, but notably the class I (no-seed) predictions are just marginally less accurate. We estimate that TargetSpy predicts between 26 and 112 functional target sites without a seed match per microRNA that are missed by all other currently available algorithms. Only a few algorithms can predict target sites without demanding a seed match and TargetSpy demonstrates a substantial improvement in prediction accuracy in that class. Furthermore, when conservation and the presence of a seed match are required, the performance is comparable with state-of-the-art algorithms. TargetSpy was trained on mouse and performs well in human and drosophila

TargetSpy: a supervised machine learning approach for microRNA target prediction

PubMed Central

2010-01-01

Background Virtually all currently available microRNA target site prediction algorithms require the presence of a (conserved) seed match to the 5' end of the microRNA. Recently however, it has been shown that this requirement might be too stringent, leading to a substantial number of missed target sites. Results We developed TargetSpy, a novel computational approach for predicting target sites regardless of the presence of a seed match. It is based on machine learning and automatic feature selection using a wide spectrum of compositional, structural, and base pairing features covering current biological knowledge. Our model does not rely on evolutionary conservation, which allows the detection of species-specific interactions and makes TargetSpy suitable for analyzing unconserved genomic sequences. In order to allow for an unbiased comparison of TargetSpy to other methods, we classified all algorithms into three groups: I) no seed match requirement, II) seed match requirement, and III) conserved seed match requirement. TargetSpy predictions for classes II and III are generated by appropriate postfiltering. On a human dataset revealing fold-change in protein production for five selected microRNAs our method shows superior performance in all classes. In Drosophila melanogaster not only our class II and III predictions are on par with other algorithms, but notably the class I (no-seed) predictions are just marginally less accurate. We estimate that TargetSpy predicts between 26 and 112 functional target sites without a seed match per microRNA that are missed by all other currently available algorithms. Conclusion Only a few algorithms can predict target sites without demanding a seed match and TargetSpy demonstrates a substantial improvement in prediction accuracy in that class. Furthermore, when conservation and the presence of a seed match are required, the performance is comparable with state-of-the-art algorithms. TargetSpy was trained on mouse and performs well

Conservation agriculture in high tunnels: soil health and profit enhancement

USDA-ARS?s Scientific Manuscript database

In 2013, through the USDA’s Evans-Allen capacity grant, the high tunnel became an on-farm research laboratory for conservation agriculture. Dr. Manuel R. Reyes, Professor and his research team from the North Carolina Agriculture and Technology State University (NCATSU), Greensboro, North Carolina (1...

High order entropy conservative central schemes for wide ranges of compressible gas dynamics and MHD flows

NASA Astrophysics Data System (ADS)

Sjögreen, Björn; Yee, H. C.

2018-07-01

The Sjogreen and Yee [31] high order entropy conservative numerical method for compressible gas dynamics is extended to include discontinuities and also extended to equations of ideal magnetohydrodynamics (MHD). The basic idea is based on Tadmor's [40] original work for inviscid perfect gas flows. For the MHD four formulations of the MHD are considered: (a) the conservative MHD, (b) the Godunov [14] non-conservative form, (c) the Janhunen [19] - MHD with magnetic field source terms, and (d) a MHD with source terms by Brackbill and Barnes [5]. Three forms of the high order entropy numerical fluxes for the MHD in the finite difference framework are constructed. They are based on the extension of the low order form of Chandrashekar and Klingenberg [9], and two forms with modifications of the Winters and Gassner [49] numerical fluxes. For flows containing discontinuities and multiscale turbulence fluctuations the high order entropy conservative numerical fluxes as the new base scheme under the Yee and Sjogreen [31] and Kotov et al. [21,22] high order nonlinear filter approach is developed. The added nonlinear filter step on the high order centered entropy conservative spatial base scheme is only utilized at isolated computational regions, while maintaining high accuracy almost everywhere for long time integration of unsteady flows and DNS and LES of turbulence computations. Representative test cases for both smooth flows and problems containing discontinuities for the gas dynamics and the ideal MHD are included. The results illustrate the improved stability by using the high order entropy conservative numerical flux as the base scheme instead of the pure high order central scheme.

Endosidin2 targets conserved exocyst complex subunit EXO70 to inhibit exocytosis

DOE PAGES

Zhang, Chunhua; Brown, Michelle Q.; van de Ven, Wilhelmina; ...

2015-11-25

The exocyst complex regulates the last steps of exocytosis, which is essential to organisms across kingdoms. In humans, its dysfunction is correlated with several significant diseases, such as diabetes and cancer progression. Investigation of the dynamic regulation of the evolutionarily conserved exocyst-related processes using mutants in genetically tractable organisms such as Arabidopsis thaliana is limited by the lethality or the severity of phenotypes. We discovered that the small molecule Endosidin2 (ES2) binds to the EXO70 (exocyst component of 70 kDa) subunit of the exocyst complex, resulting in inhibition of exocytosis and endosomal recycling in both plant and human cells andmore » enhancement of plant vacuolar trafficking. An EXO70 protein with a C-terminal truncation results in dominant ES2 resistance, uncovering possible distinct regulatory roles for the N terminus of the protein. Ultimately, this study not only provides a valuable tool in studying exocytosis regulation but also offers a potentially new target for drugs aimed at addressing human disease.« less

Endosidin2 targets conserved exocyst complex subunit EXO70 to inhibit exocytosis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Chunhua; Brown, Michelle Q.; van de Ven, Wilhelmina

The exocyst complex regulates the last steps of exocytosis, which is essential to organisms across kingdoms. In humans, its dysfunction is correlated with several significant diseases, such as diabetes and cancer progression. Investigation of the dynamic regulation of the evolutionarily conserved exocyst-related processes using mutants in genetically tractable organisms such as Arabidopsis thaliana is limited by the lethality or the severity of phenotypes. We discovered that the small molecule Endosidin2 (ES2) binds to the EXO70 (exocyst component of 70 kDa) subunit of the exocyst complex, resulting in inhibition of exocytosis and endosomal recycling in both plant and human cells andmore » enhancement of plant vacuolar trafficking. An EXO70 protein with a C-terminal truncation results in dominant ES2 resistance, uncovering possible distinct regulatory roles for the N terminus of the protein. Ultimately, this study not only provides a valuable tool in studying exocytosis regulation but also offers a potentially new target for drugs aimed at addressing human disease.« less

Capturing neutral and adaptive genetic diversity for conservation in a highly structured tree species.

PubMed

Rodríguez-Quilón, Isabel; Santos-Del-Blanco, Luis; Serra-Varela, María Jesús; Koskela, Jarkko; González-Martínez, Santiago C; Alía, Ricardo

2016-10-01

Preserving intraspecific genetic diversity is essential for long-term forest sustainability in a climate change scenario. Despite that, genetic information is largely neglected in conservation planning, and how conservation units should be defined is still heatedly debated. Here, we use maritime pine (Pinus pinaster Ait.), an outcrossing long-lived tree with a highly fragmented distribution in the Mediterranean biodiversity hotspot, to prove the importance of accounting for genetic variation, of both neutral molecular markers and quantitative traits, to define useful conservation units. Six gene pools associated to distinct evolutionary histories were identified within the species using 12 microsatellites and 266 single nucleotide polymorphisms (SNPs). In addition, height and survival standing variation, their genetic control, and plasticity were assessed in a multisite clonal common garden experiment (16 544 trees). We found high levels of quantitative genetic differentiation within previously defined neutral gene pools. Subsequent cluster analysis and post hoc trait distribution comparisons allowed us to define 10 genetically homogeneous population groups with high evolutionary potential. They constitute the minimum number of units to be represented in a maritime pine dynamic conservation program. Our results uphold that the identification of conservation units below the species level should account for key neutral and adaptive components of genetic diversity, especially in species with strong population structure and complex evolutionary histories. The environmental zonation approach currently used by the pan-European genetic conservation strategy for forest trees would be largely improved by gradually integrating molecular and quantitative trait information, as data become available. © 2016 by the Ecological Society of America.

Building robust conservation plans.

PubMed

Visconti, Piero; Joppa, Lucas

2015-04-01

Systematic conservation planning optimizes trade-offs between biodiversity conservation and human activities by accounting for socioeconomic costs while aiming to achieve prescribed conservation objectives. However, the most cost-efficient conservation plan can be very dissimilar to any other plan achieving the set of conservation objectives. This is problematic under conditions of implementation uncertainty (e.g., if all or part of the plan becomes unattainable). We determined through simulations of parallel implementation of conservation plans and habitat loss the conditions under which optimal plans have limited chances of implementation and where implementation attempts would fail to meet objectives. We then devised a new, flexible method for identifying conservation priorities and scheduling conservation actions. This method entails generating a number of alternative plans, calculating the similarity in site composition among all plans, and selecting the plan with the highest density of neighboring plans in similarity space. We compared our method with the classic method that maximizes cost efficiency with synthetic and real data sets. When implementation was uncertain--a common reality--our method provided higher likelihood of achieving conservation targets. We found that χ, a measure of the shortfall in objectives achieved by a conservation plan if the plan could not be implemented entirely, was the main factor determining the relative performance of a flexibility enhanced approach to conservation prioritization. Our findings should help planning authorities prioritize conservation efforts in the face of uncertainty about future condition and availability of sites. © 2014 Society for Conservation Biology.

Efficiency of incentives to jointly increase carbon sequestration and species conservation on a landscape

PubMed Central

Nelson, Erik; Polasky, Stephen; Lewis, David J.; Plantinga, Andrew J.; Lonsdorf, Eric; White, Denis; Bael, David; Lawler, Joshua J.

2008-01-01

We develop an integrated model to predict private land-use decisions in response to policy incentives designed to increase the provision of carbon sequestration and species conservation across heterogeneous landscapes. Using data from the Willamette Basin, Oregon, we compare the provision of carbon sequestration and species conservation under five simple policies that offer payments for conservation. We evaluate policy performance compared with the maximum feasible combinations of carbon sequestration and species conservation on the landscape for various conservation budgets. None of the conservation payment policies produce increases in carbon sequestration and species conservation that approach the maximum potential gains on the landscape. Our results show that policies aimed at increasing the provision of carbon sequestration do not necessarily increase species conservation and that highly targeted policies do not necessarily do as well as more general policies. PMID:18621703

High-Order Entropy Stable Finite Difference Schemes for Nonlinear Conservation Laws: Finite Domains

NASA Technical Reports Server (NTRS)

Fisher, Travis C.; Carpenter, Mark H.

2013-01-01

Developing stable and robust high-order finite difference schemes requires mathematical formalism and appropriate methods of analysis. In this work, nonlinear entropy stability is used to derive provably stable high-order finite difference methods with formal boundary closures for conservation laws. Particular emphasis is placed on the entropy stability of the compressible Navier-Stokes equations. A newly derived entropy stable weighted essentially non-oscillatory finite difference method is used to simulate problems with shocks and a conservative, entropy stable, narrow-stencil finite difference approach is used to approximate viscous terms.

A multiple-alignment based primer design algorithm for genetically highly variable DNA targets

PubMed Central

2013-01-01

Background Primer design for highly variable DNA sequences is difficult, and experimental success requires attention to many interacting constraints. The advent of next-generation sequencing methods allows the investigation of rare variants otherwise hidden deep in large populations, but requires attention to population diversity and primer localization in relatively conserved regions, in addition to recognized constraints typically considered in primer design. Results Design constraints include degenerate sites to maximize population coverage, matching of melting temperatures, optimizing de novo sequence length, finding optimal bio-barcodes to allow efficient downstream analyses, and minimizing risk of dimerization. To facilitate primer design addressing these and other constraints, we created a novel computer program (PrimerDesign) that automates this complex procedure. We show its powers and limitations and give examples of successful designs for the analysis of HIV-1 populations. Conclusions PrimerDesign is useful for researchers who want to design DNA primers and probes for analyzing highly variable DNA populations. It can be used to design primers for PCR, RT-PCR, Sanger sequencing, next-generation sequencing, and other experimental protocols targeting highly variable DNA samples. PMID:23965160

Is antioxidant potential of the mitochondrial targeted ubiquinone derivative MitoQ conserved in cells lacking mtDNA?

PubMed

Lu, Chao; Zhang, Dawei; Whiteman, Matthew; Armstrong, Jeffrey S

2008-03-01

MitoQ has been developed as a mitochondrial targeted antioxidant for diseases associated with oxidative stress. Here we show that MitoQ blocks the generation of reactive oxygen species (ROS) and mitochondrial protein thiol oxidation, and preserves mitochondrial function and ultrastructure after glutathione (GSH) depletion. Furthermore, the antioxidant effect of MitoQ is conserved in cells lacking mitochondrial DNA, indicating that its antioxidant properties do not depend on a functional electron transport chain (ETC). Our results elucidate the antioxidant mechanism of MitoQ and suggest that it may be a useful therapeutic for disorders associated with a dysfunctional ETC and increased ROS production.

77 FR 11785 - Energy Conservation Program: Public Meeting and Availability of the Framework Document for High...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-02-28

... Conservation Program: Public Meeting and Availability of the Framework Document for High-Intensity Discharge...) is initiating the rulemaking and data collection process to consider establishing energy conservation... Policy and Conservation Act (EPCA) (42 U.S.C. 6291, et seq.; EPCA or ``the Act'') sets forth a variety of...

The Druggable Pocketome of Corynebacterium diphtheriae: A New Approach for in silico Putative Druggable Targets

PubMed Central

Hassan, Syed S.; Jamal, Syed B.; Radusky, Leandro G.; Tiwari, Sandeep; Ullah, Asad; Ali, Javed; Behramand; de Carvalho, Paulo V. S. D.; Shams, Rida; Khan, Sabir; Figueiredo, Henrique C. P.; Barh, Debmalya; Ghosh, Preetam; Silva, Artur; Baumbach, Jan; Röttger, Richard; Turjanski, Adrián G.; Azevedo, Vasco A. C.

2018-01-01

Diphtheria is an acute and highly infectious disease, previously regarded as endemic in nature but vaccine-preventable, is caused by Corynebacterium diphtheriae (Cd). In this work, we used an in silico approach along the 13 complete genome sequences of C. diphtheriae followed by a computational assessment of structural information of the binding sites to characterize the “pocketome druggability.” To this end, we first computed the “modelome” (3D structures of a complete genome) of a randomly selected reference strain Cd NCTC13129; that had 13,763 open reading frames (ORFs) and resulted in 1,253 (∼9%) structure models. The amino acid sequences of these modeled structures were compared with the remaining 12 genomes and consequently, 438 conserved protein sequences were obtained. The RCSB-PDB database was consulted to check the template structures for these conserved proteins and as a result, 401 adequate 3D models were obtained. We subsequently predicted the protein pockets for the obtained set of models and kept only the conserved pockets that had highly druggable (HD) values (137 across all strains). Later, an off-target host homology analyses was performed considering the human proteome using NCBI database. Furthermore, the gene essentiality analysis was carried out that gave a final set of 10-conserved targets possessing highly druggable protein pockets. To check the target identification robustness of the pipeline used in this work, we crosschecked the final target list with another in-house target identification approach for C. diphtheriae thereby obtaining three common targets, these were; hisE-phosphoribosyl-ATP pyrophosphatase, glpX-fructose 1,6-bisphosphatase II, and rpsH-30S ribosomal protein S8. Our predicted results suggest that the in silico approach used could potentially aid in experimental polypharmacological target determination in C. diphtheriae and other pathogens, thereby, might complement the existing and new drug-discovery pipelines

High-Resolution Genuinely Multidimensional Solution of Conservation Laws by the Space-Time Conservation Element and Solution Element Method

NASA Technical Reports Server (NTRS)

Himansu, Ananda; Chang, Sin-Chung; Yu, Sheng-Tao; Wang, Xiao-Yen; Loh, Ching-Yuen; Jorgenson, Philip C. E.

1999-01-01

In this overview paper, we review the basic principles of the method of space-time conservation element and solution element for solving the conservation laws in one and two spatial dimensions. The present method is developed on the basis of local and global flux conservation in a space-time domain, in which space and time are treated in a unified manner. In contrast to the modern upwind schemes, the approach here does not use the Riemann solver and the reconstruction procedure as the building blocks. The drawbacks of the upwind approach, such as the difficulty of rationally extending the 1D scalar approach to systems of equations and particularly to multiple dimensions is here contrasted with the uniformity and ease of generalization of the Conservation Element and Solution Element (CE/SE) 1D scalar schemes to systems of equations and to multiple spatial dimensions. The assured compatibility with the simplest type of unstructured meshes, and the uniquely simple nonreflecting boundary conditions of the present method are also discussed. The present approach has yielded high-resolution shocks, rarefaction waves, acoustic waves, vortices, ZND detonation waves, and shock/acoustic waves/vortices interactions. Moreover, since no directional splitting is employed, numerical resolution of two-dimensional calculations is comparable to that of the one-dimensional calculations. Some sample applications displaying the strengths and broad applicability of the CE/SE method are reviewed.

Evolutionary growth process of highly conserved sequences in vertebrate genomes.

PubMed

Ishibashi, Minaka; Noda, Akiko Ogura; Sakate, Ryuichi; Imanishi, Tadashi

2012-08-01

Genome sequence comparison between evolutionarily distant species revealed ultraconserved elements (UCEs) among mammals under strong purifying selection. Most of them were also conserved among vertebrates. Because they tend to be located in the flanking regions of developmental genes, they would have fundamental roles in creating vertebrate body plans. However, the evolutionary origin and selection mechanism of these UCEs remain unclear. Here we report that UCEs arose in primitive vertebrates, and gradually grew in vertebrate evolution. We searched for UCEs in two teleost fishes, Tetraodon nigroviridis and Oryzias latipes, and found 554 UCEs with 100% identity over 100 bps. Comparison of teleost and mammalian UCEs revealed 43 pairs of common, jawed-vertebrate UCEs (jUCE) with high sequence identities, ranging from 83.1% to 99.2%. Ten of them retain lower similarities to the Petromyzon marinus genome, and the substitution rates of four non-exonic jUCEs were reduced after the teleost-mammal divergence, suggesting that robust conservation had been acquired in the jawed vertebrate lineage. Our results indicate that prototypical UCEs originated before the divergence of jawed and jawless vertebrates and have been frozen as perfect conserved sequences in the jawed vertebrate lineage. In addition, our comparative sequence analyses of UCEs and neighboring regions resulted in a discovery of lineage-specific conserved sequences. They were added progressively to prototypical UCEs, suggesting step-wise acquisition of novel regulatory roles. Our results indicate that conserved non-coding elements (CNEs) consist of blocks with distinct evolutionary history, each having been frozen since different evolutionary era along the vertebrate lineage. Copyright © 2012 Elsevier B.V. All rights reserved.

A Bioinformatic Pipeline for Monitoring of the Mutational Stability of Viral Drug Targets with Deep-Sequencing Technology.

PubMed

Kravatsky, Yuri; Chechetkin, Vladimir; Fedoseeva, Daria; Gorbacheva, Maria; Kravatskaya, Galina; Kretova, Olga; Tchurikov, Nickolai

2017-11-23

The efficient development of antiviral drugs, including efficient antiviral small interfering RNAs (siRNAs), requires continuous monitoring of the strict correspondence between a drug and the related highly variable viral DNA/RNA target(s). Deep sequencing is able to provide an assessment of both the general target conservation and the frequency of particular mutations in the different target sites. The aim of this study was to develop a reliable bioinformatic pipeline for the analysis of millions of short, deep sequencing reads corresponding to selected highly variable viral sequences that are drug target(s). The suggested bioinformatic pipeline combines the available programs and the ad hoc scripts based on an original algorithm of the search for the conserved targets in the deep sequencing data. We also present the statistical criteria for the threshold of reliable mutation detection and for the assessment of variations between corresponding data sets. These criteria are robust against the possible sequencing errors in the reads. As an example, the bioinformatic pipeline is applied to the study of the conservation of RNA interference (RNAi) targets in human immunodeficiency virus 1 (HIV-1) subtype A. The developed pipeline is freely available to download at the website http://virmut.eimb.ru/. Brief comments and comparisons between VirMut and other pipelines are also presented.

Conserving migratory mule deer through the umbrella of sage-grouse

USGS Publications Warehouse

Copeland, H. E.; Sawyer, H.; Monteith, K. L.; Naugle, D.E.; Pocewicz, Amy; Graf, N.; Kauffman, Matthew J.

2014-01-01

Conserving migratory ungulates in increasingly human-dominated landscapes presents a difficult challenge to land managers and conservation practitioners. Nevertheless, ungulates may receive ancillary benefits from conservation actions designed to protect species of greater conservation priority where their ranges are sympatric. Greater Sage-Grouse (Centrocerus urophasianus), for example, have been proposed as an umbrella species for other sagebrush (Artemesia spp.)-dependent fauna. We examined a landscape where conservation efforts for sage-grouse overlap spatially with mule deer (Odocoileus hemionus) to determine whether sage-grouse conservation measures also might protect important mule deer migration routes and seasonal ranges. We conducted a spatial analysis to determine what proportion of migration routes, stopover areas, and winter ranges used by mule deer were located in areas managed for sage-grouse conservation. Conservation measures overlapped with 66–70% of migration corridors, 74–75% of stopovers, and 52–91% of wintering areas for two mule deer populations in the upper Green River Basin of Wyoming. Of those proportions, conservation actions targeted towards sage-grouse accounted for approximately half of the overlap in corridors and stopover areas, and nearly all overlap on winter ranges, indicating that sage-grouse conservation efforts represent an important step in conserving migratory mule deer. Conservation of migratory species presents unique challenges because although overlap with conserved lands may be high, connectivity of the entire route must be maintained as barriers to movement anywhere within the migration corridor could render it unviable. Where mule deer habitats overlap with sage-grouse core areas, our results indicate that increased protection is afforded to winter ranges and migration routes within the umbrella of sage-grouse conservation, but this protection is contingent on concentrated developments within core areas not

Evolutionary Origin and Conserved Structural Building Blocks of Riboswitches and Ribosomal RNAs: Riboswitches as Probable Target Sites for Aminoglycosides Interaction.

PubMed

Mehdizadeh Aghdam, Elnaz; Barzegar, Abolfazl; Hejazi, Mohammad Saeid

2014-01-01

Riboswitches, as noncoding RNA sequences, control gene expression through direct ligand binding. Sporadic reports on the structural relation of riboswitches with ribosomal RNAs (rRNA), raises an interest in possible similarity between riboswitches and rRNAs evolutionary origins. Since aminoglycoside antibiotics affect microbial cells through binding to functional sites of the bacterial rRNA, finding any conformational and functional relation between riboswitches/rRNAs is utmost important in both of medicinal and basic research. Analysis of the riboswitches structures were carried out using bioinformatics and computational tools. The possible functional similarity of riboswitches with rRNAs was evaluated based on the affinity of paromomycin antibiotic (targeting "A site" of 16S rRNA) to riboswitches via docking method. There was high structural similarity between riboswitches and rRNAs, but not any particular sequence based similarity between them was found. The building blocks including "hairpin loop containing UUU", "peptidyl transferase center conserved hairpin A loop"," helix 45" and "S2 (G8) hairpin" as high identical rRNA motifs were detected in all kinds of riboswitches. Surprisingly, binding energies of paromomycin with different riboswitches are considerably better than the binding energy of paromomycin with "16S rRNA A site". Therefore the high affinity of paromomycin to bind riboswitches in comparison with rRNA "A site" suggests a new insight about riboswitches as possible targets for aminoglycoside antibiotics. These findings are considered as a possible supporting evidence for evolutionary origin of riboswitches/rRNAs and also their role in the exertion of antibiotics effects to design new drugs based on the concomitant effects via rRNA/riboswitches.

The biology of Mur ligases as an antibacterial target.

PubMed

Kouidmi, Imène; Levesque, Roger C; Paradis-Bleau, Catherine

2014-10-01

With antibiotic resistance mechanisms increasing in diversity and spreading among bacterial pathogens, the development of new classes of antibacterial agents against judiciously chosen targets is a high-priority task. The biochemical pathway for peptidoglycan biosynthesis is one of the best sources of antibacterial targets. Within this pathway are the Mur ligases, described in this review as highly suitable targets for the development of new classes of antibacterial agents. The amide ligases MurC, MurD, MurE and MurF function with the same catalytic mechanism and share conserved amino acid regions and structural features that can conceivably be exploited for the design of inhibitors that simultaneously target more than one enzyme. This would provide multi-target antibacterial weapons with minimized likelihood of target-mediated resistance development. © 2014 John Wiley & Sons Ltd.

Potent influenza A virus entry inhibitors targeting a conserved region of hemagglutinin.

PubMed

Lin, Dongguo; Luo, Yinzhu; Yang, Guang; Li, Fangfang; Xie, Xiangkun; Chen, Daiwei; He, Lifang; Wang, Jingyu; Ye, Chunfeng; Lu, Shengsheng; Lv, Lin; Liu, Shuwen; He, Jian

2017-11-15

Influenza A viruses (IAVs) induce acute respiratory disease and cause significant morbidity and mortality throughout the world. With the emergence of drug-resistant viral strains, new and effective anti-IAV drugs with different modes of action are urgently needed. In this study, by conjugating cholesterol to the N-terminus of the short peptide KKWK, a lipopeptide named S-KKWK was created. The anti-IAV test indicated that S-KKWK and its derivatives displayed potent antiviral activities against a broad variety of influenza A viral strains including oseltamivir-resistant strains and clinically relevant isolates with IC 50 values ranging from 0.7 to 3.0µM. An extensive mechanistic study showed that these peptides functioned as viral "entry blockers" by inhibiting the conformational rearrangements of HA2 subunit, thereby interrupting the fusion of virus-host cell membranes. Significantly, a computer-aided docking simulation and protein sequence alignment identified conserved residues in the stem region of HA2 as the possible binding site of S-KKWK, which may be employed as a potential drug target for designing anti-IAVs with a broad-spectrum of activity. By targeting this region, a potent anti-IAV agent was subsequently created. In addition, the anti-IAV activity of S-KKWK was assessed by experiments with influenza A virus-infected mice, in which S-KKWK reduced the mortality of infected animals and extended survival time significantly. Overall, in addition to providing a strategy for designing broad-spectrum anti-IAV agents, these results indicate that S-KKWK and its derivatives are prospective candidates for potent antivirals. Copyright © 2017 Elsevier Inc. All rights reserved.

The alignment of agricultural and nature conservation policies in the European Union.

PubMed

Hodge, Ian; Hauck, Jennifer; Bonn, Aletta

2015-08-01

Europe is a region of relatively high population density and productive agriculture subject to substantial government intervention under the Common Agricultural Policy (CAP). Many habitats and species of high conservation interest have been created by the maintenance of agricultural practices over long periods. These practices are often no longer profitable, and nature conservation initiatives require government support to cover the cost for them to be continued. The CAP has been reformed both to reduce production of agricultural commodities at costs in excess of world prices and to establish incentives for landholders to adopt voluntary conservation measures. A separate nature conservation policy has established an extensive series of protected sites (Natura 2000) that has, as yet, failed to halt the loss of biodiversity. Additional broader scale approaches have been advocated for conservation in the wider landscape matrix, including the alignment of agricultural and nature conservation policies, which remains a challenge. Possibilities for alignment include further shifting of funds from general support for farmers toward targeted payments for biodiversity goals at larger scales and adoption of an ecosystem approach. The European response to the competing demands for land resources may offer lessons globally as demands on rural land increase. © 2015 Society for Conservation Biology.

Preferred conservation policies of shark researchers.

PubMed

Shiffman, David S; Hammerschlag, Neil

2016-08-01

There is increasing concern about the conservation status of sharks. However, the presence of numerous different (and potentially mutually exclusive) policies complicates management implementation and public understanding of the process. We distributed an online survey to members of the largest professional shark and ray research societies to assess member knowledge of and attitudes toward different conservation policies. Questions covered society member opinions on conservation and management policies, personal histories of involvement in advocacy and management, and perceptions of the approach of conservation nongovernmental organizations (NGOs) to shark conservation. One hundred and two surveys were completed (overall response rate 21%). Respondents considered themselves knowledgeable about and actively involved in conservation and management policy; a majority believed scientists have a responsibility to advocate for conservation (75%), and majorities have sent formal public comments to policymakers (54%) and included policy suggestions in their papers (53%). They believe sustainable shark fisheries are possible, are currently happening today (in a few places), and should be the goal instead of banning fisheries. Respondents were generally less supportive of newer limit-based (i.e., policies that ban exploitation entirely without a species-specific focus) conservation policy tools, such as shark sanctuaries and bans on the sale of shark fins, than of target-based fisheries management tools (i.e., policies that allow for sustainable harvest of species whose populations can withstand it), such as fishing quotas. Respondents were generally supportive of environmental NGO efforts to conserve sharks but raised concerns about some NGOs that they perceived as using incorrect information and focusing on the wrong problems. Our results show there is an ongoing debate in shark conservation and management circles relative to environmental policy on target-based natural

The global distribution of tetrapods reveals a need for targeted reptile conservation.

PubMed

Roll, Uri; Feldman, Anat; Novosolov, Maria; Allison, Allen; Bauer, Aaron M; Bernard, Rodolphe; Böhm, Monika; Castro-Herrera, Fernando; Chirio, Laurent; Collen, Ben; Colli, Guarino R; Dabool, Lital; Das, Indraneil; Doan, Tiffany M; Grismer, Lee L; Hoogmoed, Marinus; Itescu, Yuval; Kraus, Fred; LeBreton, Matthew; Lewin, Amir; Martins, Marcio; Maza, Erez; Meirte, Danny; Nagy, Zoltán T; de C Nogueira, Cristiano; Pauwels, Olivier S G; Pincheira-Donoso, Daniel; Powney, Gary D; Sindaco, Roberto; Tallowin, Oliver J S; Torres-Carvajal, Omar; Trape, Jean-François; Vidan, Enav; Uetz, Peter; Wagner, Philipp; Wang, Yuezhao; Orme, C David L; Grenyer, Richard; Meiri, Shai

2017-11-01

The distributions of amphibians, birds and mammals have underpinned global and local conservation priorities, and have been fundamental to our understanding of the determinants of global biodiversity. In contrast, the global distributions of reptiles, representing a third of terrestrial vertebrate diversity, have been unavailable. This prevented the incorporation of reptiles into conservation planning and biased our understanding of the underlying processes governing global vertebrate biodiversity. Here, we present and analyse the global distribution of 10,064 reptile species (99% of extant terrestrial species). We show that richness patterns of the other three tetrapod classes are good spatial surrogates for species richness of all reptiles combined and of snakes, but characterize diversity patterns of lizards and turtles poorly. Hotspots of total and endemic lizard richness overlap very little with those of other taxa. Moreover, existing protected areas, sites of biodiversity significance and global conservation schemes represent birds and mammals better than reptiles. We show that additional conservation actions are needed to effectively protect reptiles, particularly lizards and turtles. Adding reptile knowledge to a global complementarity conservation priority scheme identifies many locations that consequently become important. Notably, investing resources in some of the world's arid, grassland and savannah habitats might be necessary to represent all terrestrial vertebrates efficiently.

High volume fabrication of laser targets using MEMS techniques

NASA Astrophysics Data System (ADS)

Spindloe, C.; Arthur, G.; Hall, F.; Tomlinson, S.; Potter, R.; Kar, S.; Green, J.; Higginbotham, A.; Booth, N.; Tolley, M. K.

2016-04-01

The latest techniques for the fabrication of high power laser targets, using processes developed for the manufacture of Micro-Electro-Mechanical System (MEMS) devices are discussed. These laser targets are designed to meet the needs of the increased shot numbers that are available in the latest design of laser facilities. Traditionally laser targets have been fabricated using conventional machining or coarse etching processes and have been produced in quantities of 10s to low 100s. Such targets can be used for high complexity experiments such as Inertial Fusion Energy (IFE) studies and can have many complex components that need assembling and characterisation with high precision. Using the techniques that are common to MEMS devices and integrating these with an existing target fabrication capability we are able to manufacture and deliver targets to these systems. It also enables us to manufacture novel targets that have not been possible using other techniques. In addition, developments in the positioning systems that are required to deliver these targets to the laser focus are also required and a system to deliver the target to a focus of an F2 beam at 0.1Hz is discussed.

Conservation and the industry sector

NASA Technical Reports Server (NTRS)

1975-01-01

The following six highly energy intensive industries were studied as targets of energy conservation opportunity: food and kindred products, paper and allied products, chemicals and allied products, petroleum and coal products, stone, glass and clay products, and primary manufacturing. After studying conservation actions within each industry the actions were grouped under three broad categories: increased combustion efficiency, process improvement, and good housekeeping. Some of the results were: (1) approximately 2.18 quads could be saved in 1980 and 2.57 quads in 1985 by installing cogenerative facilities in 50% of the industries, (2) regenerative air-preheaters could result in a 10-15% increase in furnace efficiency representing a 15-25% fuel savings (2.3 to 3.9 quads in 1980 and 2.7 to 4.5 quads in 1985), (3) several major industries have potential for energy savings by recycling-aluminum (0.2 quads), steel (1 quad), glass (0.006 quads), paper and cement (0.08 quads).

Alkylation sensitivity screens reveal a conserved cross-species functionome

PubMed Central

Svilar, David; Dyavaiah, Madhu; Brown, Ashley R.; Tang, Jiang-bo; Li, Jianfeng; McDonald, Peter R.; Shun, Tong Ying; Braganza, Andrea; Wang, Xiao-hong; Maniar, Salony; St Croix, Claudette M.; Lazo, John S.; Pollack, Ian F.; Begley, Thomas J.; Sobol, Robert W.

2013-01-01

To identify genes that contribute to chemotherapy resistance in glioblastoma, we conducted a synthetic lethal screen in a chemotherapy-resistant glioblastoma derived cell line with the clinical alkylator temozolomide (TMZ) and an siRNA library tailored towards “druggable” targets. Select DNA repair genes in the screen were validated independently, confirming the DNA glycosylases UNG and MYH as well as MPG to be involved in the response to high dose TMZ. The involvement of UNG and MYH is likely the result of a TMZ-induced burst of reactive oxygen species. We then compared the human TMZ sensitizing genes identified in our screen with those previously identified from alkylator screens conducted in E. coli and S. cerevisiae. The conserved biological processes across all three species composes an Alkylation Functionome that includes many novel proteins not previously thought to impact alkylator resistance. This high-throughput screen, validation and cross-species analysis was then followed by a mechanistic analysis of two essential nodes: base excision repair (BER) DNA glycosylases (UNG, human and mag1, S. cerevisiae) and protein modification systems, including UBE3B and ICMT in human cells or pby1, lip22, stp22 and aim22 in S. cerevisiae. The conserved processes of BER and protein modification were dual targeted and yielded additive sensitization to alkylators in S. cerevisiae. In contrast, dual targeting of BER and protein modification genes in human cells did not increase sensitivity, suggesting an epistatic relationship. Importantly, these studies provide potential new targets to overcome alkylating agent resistance. PMID:23038810

Factoring attitudes towards armed conflict risk into selection of protected areas for conservation.

PubMed

Hammill, E; Tulloch, A I T; Possingham, H P; Strange, N; Wilson, K A

2016-03-30

The high incidence of armed conflicts in biodiverse regions poses significant challenges in achieving international conservation targets. Because attitudes towards risk vary, we assessed different strategies for protected area planning that reflected alternative attitudes towards the risk of armed conflicts. We find that ignoring conflict risk will deliver the lowest return on investment. Opting to completely avoid conflict-prone areas offers limited improvements and could lead to species receiving no protection. Accounting for conflict by protecting additional areas to offset the impacts of armed conflicts would not only increase the return on investment (an effect that is enhanced when high-risk areas are excluded) but also increase upfront conservation costs. Our results also demonstrate that fine-scale estimations of conflict risk could enhance the cost-effectiveness of investments. We conclude that achieving biodiversity targets in volatile regions will require greater initial investment and benefit from fine-resolution estimates of conflict risk.

Identification and characterization of microRNAs and their targets in high-altitude stress-adaptive plant maca (Lepidium meyenii Walp).

PubMed

Paul, Sujay

2017-06-01

MicroRNAs (miRNAs) are endogenous, short (~21-nucleotide), non-coding RNA molecules that play pivotal roles in plant growth, development, and stress response signaling. In this study using recently published draft genome sequence of a high-altitude plant maca (Lepidium meyenii Walp) and applying genome-wide computational-based approaches, a total of 62 potentially conserved miRNAs belonging to 28 families were identified and four (lme-miR160a, lme-miR164c, lme-miR 166a, and lme-miR 319a) of them further validated by RT-PCR. Deploying psRNATarget tool a total of 99 potential miRNA target transcripts were also identified in maca. Targets include a number of transcription factors like Squamosa promoter-binding, NAC, MYB, auxin response factor, APETALA, WRKY, and F-box protein. To the best of my knowledge, this is the first genome-based miRNA profiling of a high-altitude plant.

Species conservation and natural variation among populations [Chapter 5

Treesearch

Leonard F. Ruggiero; Michael K. Schwartz; Keith B. Aubry; Charles J. Krebs; Amanda Stanley; Steven W. Buskirk

2000-01-01

In conservation planning, the importance of natural variation is often given inadequate consideration. However, ignoring the implications of variation within species may result in conservation strategies that jeopardize, rather than conserve, target species (see Grieg 1979; Turcek 1951; Storfer 1999). Natural variation in the traits of individuals and populations is...

Drug repositioning for orphan genetic diseases through Conserved Anticoexpressed Gene Clusters (CAGCs)

PubMed Central

2013-01-01

Background The development of new therapies for orphan genetic diseases represents an extremely important medical and social challenge. Drug repositioning, i.e. finding new indications for approved drugs, could be one of the most cost- and time-effective strategies to cope with this problem, at least in a subset of cases. Therefore, many computational approaches based on the analysis of high throughput gene expression data have so far been proposed to reposition available drugs. However, most of these methods require gene expression profiles directly relevant to the pathologic conditions under study, such as those obtained from patient cells and/or from suitable experimental models. In this work we have developed a new approach for drug repositioning, based on identifying known drug targets showing conserved anti-correlated expression profiles with human disease genes, which is completely independent from the availability of ‘ad hoc’ gene expression data-sets. Results By analyzing available data, we provide evidence that the genes displaying conserved anti-correlation with drug targets are antagonistically modulated in their expression by treatment with the relevant drugs. We then identified clusters of genes associated to similar phenotypes and showing conserved anticorrelation with drug targets. On this basis, we generated a list of potential candidate drug-disease associations. Importantly, we show that some of the proposed associations are already supported by independent experimental evidence. Conclusions Our results support the hypothesis that the identification of gene clusters showing conserved anticorrelation with drug targets can be an effective method for drug repositioning and provide a wide list of new potential drug-disease associations for experimental validation. PMID:24088245

Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates

PubMed Central

Kikuta, Hiroshi; Laplante, Mary; Navratilova, Pavla; Komisarczuk, Anna Z.; Engström, Pär G.; Fredman, David; Akalin, Altuna; Caccamo, Mario; Sealy, Ian; Howe, Kerstin; Ghislain, Julien; Pezeron, Guillaume; Mourrain, Philippe; Ellingsen, Staale; Oates, Andrew C.; Thisse, Christine; Thisse, Bernard; Foucher, Isabelle; Adolf, Birgit; Geling, Andrea; Lenhard, Boris; Becker, Thomas S.

2007-01-01

We report evidence for a mechanism for the maintenance of long-range conserved synteny across vertebrate genomes. We found the largest mammal-teleost conserved chromosomal segments to be spanned by highly conserved noncoding elements (HCNEs), their developmental regulatory target genes, and phylogenetically and functionally unrelated “bystander” genes. Bystander genes are not specifically under the control of the regulatory elements that drive the target genes and are expressed in patterns that are different from those of the target genes. Reporter insertions distal to zebrafish developmental regulatory genes pax6.1/2, rx3, id1, and fgf8 and miRNA genes mirn9-1 and mirn9-5 recapitulate the expression patterns of these genes even if located inside or beyond bystander genes, suggesting that the regulatory domain of a developmental regulatory gene can extend into and beyond adjacent transcriptional units. We termed these chromosomal segments genomic regulatory blocks (GRBs). After whole genome duplication in teleosts, GRBs, including HCNEs and target genes, were often maintained in both copies, while bystander genes were typically lost from one GRB, strongly suggesting that evolutionary pressure acts to keep the single-copy GRBs of higher vertebrates intact. We show that loss of bystander genes and other mutational events suffered by duplicated GRBs in teleost genomes permits target gene identification and HCNE/target gene assignment. These findings explain the absence of evolutionary breakpoints from large vertebrate chromosomal segments and will aid in the recognition of position effect mutations within human GRBs. PMID:17387144

High affinity ligands from in vitro selection: Complex targets

PubMed Central

Morris, Kevin N.; Jensen, Kirk B.; Julin, Carol M.; Weil, Michael; Gold, Larry

1998-01-01

Human red blood cell membranes were used as a model system to determine if the systematic evolution of ligands by exponential enrichment (SELEX) methodology, an in vitro protocol for isolating high-affinity oligonucleotides that bind specifically to virtually any single protein, could be used with a complex mixture of potential targets. Ligands to multiple targets were generated simultaneously during the selection process, and the binding affinities of these ligands for their targets are comparable to those found in similar experiments against pure targets. A secondary selection scheme, deconvolution-SELEX, facilitates rapid isolation of the ligands to targets of special interest within the mixture. SELEX provides high-affinity compounds for multiple targets in a mixture and might allow a means for dissecting complex biological systems. PMID:9501188

Antibody to a conserved antigenic target is protective against diverse prokaryotic and eukaryotic pathogens

PubMed Central

Cywes-Bentley, Colette; Skurnik, David; Zaidi, Tanweer; Roux, Damien; DeOliveira, Rosane B.; Garrett, Wendy S.; Lu, Xi; O’Malley, Jennifer; Kinzel, Kathryn; Zaidi, Tauqeer; Rey, Astrid; Perrin, Christophe; Fichorova, Raina N.; Kayatani, Alexander K. K.; Maira-Litràn, Tomas; Gening, Marina L.; Tsvetkov, Yury E.; Nifantiev, Nikolay E.; Bakaletz, Lauren O.; Pelton, Stephen I.; Golenbock, Douglas T.; Pier, Gerald B.

2013-01-01

Microbial capsular antigens are effective vaccines but are chemically and immunologically diverse, resulting in a major barrier to their use against multiple pathogens. A β-(1→6)–linked poly-N-acetyl-d-glucosamine (PNAG) surface capsule is synthesized by four proteins encoded in genetic loci designated intercellular adhesion in Staphylococcus aureus or polyglucosamine in selected Gram-negative bacterial pathogens. We report that many microbial pathogens lacking an identifiable intercellular adhesion or polyglucosamine locus produce PNAG, including Gram-positive, Gram-negative, and fungal pathogens, as well as protozoa, e.g., Trichomonas vaginalis, Plasmodium berghei, and sporozoites and blood-stage forms of Plasmodium falciparum. Natural antibody to PNAG is common in humans and animals and binds primarily to the highly acetylated glycoform of PNAG but is not protective against infection due to lack of deposition of complement opsonins. Polyclonal animal antibody raised to deacetylated glycoforms of PNAG and a fully human IgG1 monoclonal antibody that both bind to native and deacetylated glycoforms of PNAG mediated complement-dependent opsonic or bactericidal killing and protected mice against local and/or systemic infections by Streptococcus pyogenes, Streptococcus pneumoniae, Listeria monocytogenes, Neisseria meningitidis serogroup B, Candida albicans, and P. berghei ANKA, and against colonic pathology in a model of infectious colitis. PNAG is also a capsular polysaccharide for Neisseria gonorrhoeae and nontypable Hemophilus influenzae, and protects cells from environmental stress. Vaccination targeting PNAG could contribute to immunity against serious and diverse prokaryotic and eukaryotic pathogens, and the conserved production of PNAG suggests that it is a critical factor in microbial biology. PMID:23716675

Factoring attitudes towards armed conflict risk into selection of protected areas for conservation

PubMed Central

Hammill, E.; Tulloch, A. I. T.; Possingham, H. P.; Strange, N.; Wilson, K. A.

2016-01-01

The high incidence of armed conflicts in biodiverse regions poses significant challenges in achieving international conservation targets. Because attitudes towards risk vary, we assessed different strategies for protected area planning that reflected alternative attitudes towards the risk of armed conflicts. We find that ignoring conflict risk will deliver the lowest return on investment. Opting to completely avoid conflict-prone areas offers limited improvements and could lead to species receiving no protection. Accounting for conflict by protecting additional areas to offset the impacts of armed conflicts would not only increase the return on investment (an effect that is enhanced when high-risk areas are excluded) but also increase upfront conservation costs. Our results also demonstrate that fine-scale estimations of conflict risk could enhance the cost-effectiveness of investments. We conclude that achieving biodiversity targets in volatile regions will require greater initial investment and benefit from fine-resolution estimates of conflict risk. PMID:27025894

High-frequency ultrasound-guided disruption of glycoprotein VI-targeted microbubbles targets atheroprogressison in mice.

PubMed

Metzger, Katja; Vogel, Sebastian; Chatterjee, Madhumita; Borst, Oliver; Seizer, Peter; Schönberger, Tanja; Geisler, Tobias; Lang, Florian; Langer, Harald; Rheinlaender, Johannes; Schäffer, Tilman E; Gawaz, Meinrad

2015-01-01

Targeted contrast-enhanced ultrasound (CEU) using microbubble agents is a promising non-invasive imaging technique to evaluate atherosclerotic lesions. In this study, we decipher the diagnostic and therapeutic potential of targeted-CEU with soluble glycoprotein (GP)-VI in vivo. Microbubbles were conjugated with the recombinant fusion protein GPVI-Fc (MBGPVI) that binds with high affinity to atherosclerotic lesions. MBGPVI or control microbubbles (MBC) were intravenously administered into ApoE(-/-) or wild type mice and binding of the microbubbles to the vessel wall was visualized by high-resolution CEU. CEU molecular imaging signals of MBGPVI were substantially enhanced in the aortic arch and in the truncus brachiocephalicus in ApoE(-/-) as compared to wild type mice. High-frequency ultrasound (HFU)-guided disruption of MBGPVI enhanced accumulation of GPVI in the atherosclerotic lesions, which may interfere with atheroprogression. Thus, we establish targeted-CEU with soluble GPVI as a novel non-invasive molecular imaging method for atherosclerosis. Further, HFU-guided disruption of GPVI-targeted microbubbles is an innovate therapeutic approach that potentially prevents progression of atherosclerotic disease. Copyright © 2014 Elsevier Ltd. All rights reserved.

Interpreting beta-diversity components over time to conserve metacommunities in highly dynamic ecosystems.

PubMed

Ruhí, Albert; Datry, Thibault; Sabo, John L

2017-12-01

The concept of metacommunity (i.e., a set of local communities linked by dispersal) has gained great popularity among community ecologists. However, metacommunity research mostly addresses questions on spatial patterns of biodiversity at the regional scale, whereas conservation planning requires quantifying temporal variation in those metacommunities and the contributions that individual (local) sites make to regional dynamics. We propose that recent advances in diversity-partitioning methods may allow for a better understanding of metacommunity dynamics and the identification of keystone sites. We used time series of the 2 components of beta diversity (richness and replacement) and the contributions of local sites to these components to examine which sites controlled source-sink dynamics in a highly dynamic model system (an intermittent river). The relative importance of the richness and replacement components of beta diversity fluctuated over time, and sample aggregation led to underestimation of beta diversity by up to 35%. Our literature review revealed that research on intermittent rivers would benefit greatly from examination of beta-diversity components over time. Adequately appraising spatiotemporal variability in community composition and identifying sites that are pivotal for maintaining biodiversity at the landscape scale are key needs for conservation prioritization and planning. Thus, our framework may be used to guide conservation actions in highly dynamic ecosystems when time-series data describing biodiversity across sites connected by dispersal are available. © 2017 Society for Conservation Biology.

Six Highly Conserved Targets of RNAi Revealed in HIV-1-Infected Patients from Russia Are Also Present in Many HIV-1 Strains Worldwide.

PubMed

Kretova, Olga V; Fedoseeva, Daria M; Gorbacheva, Maria A; Gashnikova, Natalya M; Gashnikova, Maria P; Melnikova, Nataliya V; Chechetkin, Vladimir R; Kravatsky, Yuri V; Tchurikov, Nickolai A

2017-09-15

RNAi has been suggested for use in gene therapy of HIV/AIDS, but the main problem is that HIV-1 is highly variable and could escape attack from the small interfering RNAs (siRNAs) due to even single nucleotide substitutions in the potential targets. To exhaustively check the variability in selected RNA targets of HIV-1, we used ultra-deep sequencing of six regions of HIV-1 from the plasma of two independent cohorts of patients from Russia. Six RNAi targets were found that are invariable in 82%-97% of viruses in both cohorts and are located inside the domains specifying reverse transcriptase (RT), integrase, vpu, gp120, and p17. The analysis of mutation frequencies and their characteristics inside the targets suggests a likely role for APOBEC3G (apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3G, A3G) in G-to-A mutations and a predominant effect of RT biases in the detected variability of the virus. The lowest frequency of mutations was detected in the central part of all six targets. We also discovered that the identical RNAi targets are present in many HIV-1 strains from many countries and from all continents. The data are important for both the understanding of the patterns of HIV-1 mutability and properties of RT and for the development of gene therapy approaches using RNAi for the treatment of HIV/AIDS. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Conservation in the face of climate change: recent developments.

PubMed

Lawler, Joshua; Watson, James; Game, Edward

2015-01-01

An increased understanding of the current and potential future impacts of climate change has significantly influenced conservation in practice in recent years. Climate change has necessitated a shift toward longer planning time horizons, moving baselines, and evolving conservation goals and targets. This shift has resulted in new perspectives on, and changes in, the basic approaches practitioners use to conserve biodiversity. Restoration, spatial planning and reserve selection, connectivity modelling, extinction risk assessment, and species translocations have all been reimagined in the face of climate change. Restoration is being conducted with a new acceptance of uncertainty and an understanding that goals will need to shift through time. New conservation targets, such as geophysical settings and climatic refugia, are being incorporated into conservation plans. Risk assessments have begun to consider the potentially synergistic impacts of climate change and other threats. Assisted colonization has gained acceptance in recent years as a viable and necessary conservation tool. This evolution has paralleled a larger trend in conservation-a shift toward conservation actions that benefit both people and nature. As we look forward, it is clear that more change is on the horizon. To protect biodiversity and essential ecosystem services, conservation will need to anticipate the human response to climate change and to focus not only on resistance and resilience but on transitions to new states and new ecosystems.

A Sensitive in Vitro High-Throughput Screen To Identify Pan-filoviral Replication Inhibitors Targeting the VP35–NP Interface

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Gai; Nash, Peter J.; Johnson, Britney

The 2014 Ebola outbreak in West Africa, the largest outbreak on record, highlighted the need for novel approaches to therapeutics targeting Ebola virus (EBOV). Within the EBOV replication complex, the interaction between polymerase cofactor, viral protein 35 (VP35), and nucleoprotein (NP) is critical for viral RNA synthesis. We recently identified a peptide at the N-terminus of VP35 (termed NPBP) that is sufficient for interaction with NP and suppresses EBOV replication, suggesting that the NPBP binding pocket can serve as a potential drug target. Here we describe the development and validation of a sensitive high-throughput screen (HTS) using a fluorescence polarizationmore » assay. Initial hits from this HTS include the FDA-approved compound tolcapone, whose potency against EBOV infection was validated in a nonfluorescent secondary assay. High conservation of the NP–VP35 interface among filoviruses suggests that this assay has the capacity to identify pan-filoviral inhibitors for development as antivirals.« less

Bird community conservation and carbon offsets in western North America.

PubMed

Schuster, Richard; Martin, Tara G; Arcese, Peter

2014-01-01

Conservation initiatives to protect and restore valued species and communities in human-dominated landscapes face huge challenges linked to the cost of acquiring habitat. We ask how the sale of forest carbon offsets could reduce land acquisition costs, and how the alternate goals of maximizing α or β-diversity in focal communities could affect the prioritization land parcels over a range of conservation targets. Maximizing total carbon storage and carbon sequestration potential reduced land acquisition costs by up to 48%. Maximizing β rather than α-diversity within forest and savannah bird communities reduced acquisition costs by up to 15%, and when these solutions included potential carbon credit revenues, acquisition cost reductions up to 32% were achieved. However, the total cost of conservation networks increased exponentially as area targets increased in all scenarios. Our results indicate that carbon credit sales have the potential to enhance conservation outcomes in human-dominated landscapes by reducing the net acquisition costs of land conservation in old and maturing forests essential for the persistence of old forest plant and animal communities. Maximizing β versus α-diversity may further reduce costs by reducing the total area required to meet conservation targets and enhancing landscape heterogeneity. Although the potential value of carbon credit sales declined as a fraction of total acquisition costs, even conservative scenarios using a carbon credit value of $12.5/T suggest reductions in acquisition cost of up to $235 M, indicating that carbon credit sales could substantially reduce the costs of conservation.

Bird Community Conservation and Carbon Offsets in Western North America

PubMed Central

Schuster, Richard; Martin, Tara G.; Arcese, Peter

2014-01-01

Conservation initiatives to protect and restore valued species and communities in human-dominated landscapes face huge challenges linked to the cost of acquiring habitat. We ask how the sale of forest carbon offsets could reduce land acquisition costs, and how the alternate goals of maximizing α or β-diversity in focal communities could affect the prioritization land parcels over a range of conservation targets. Maximizing total carbon storage and carbon sequestration potential reduced land acquisition costs by up to 48%. Maximizing β rather than α-diversity within forest and savannah bird communities reduced acquisition costs by up to 15%, and when these solutions included potential carbon credit revenues, acquisition cost reductions up to 32% were achieved. However, the total cost of conservation networks increased exponentially as area targets increased in all scenarios. Our results indicate that carbon credit sales have the potential to enhance conservation outcomes in human-dominated landscapes by reducing the net acquisition costs of land conservation in old and maturing forests essential for the persistence of old forest plant and animal communities. Maximizing β versus α-diversity may further reduce costs by reducing the total area required to meet conservation targets and enhancing landscape heterogeneity. Although the potential value of carbon credit sales declined as a fraction of total acquisition costs, even conservative scenarios using a carbon credit value of $12.5/T suggest reductions in acquisition cost of up to $235 M, indicating that carbon credit sales could substantially reduce the costs of conservation. PMID:24918621

smRNAome profiling to identify conserved and novel microRNAs in Stevia rebaudiana Bertoni

PubMed Central

2012-01-01

Background MicroRNAs (miRNAs) constitute a family of small RNA (sRNA) population that regulates the gene expression and plays an important role in plant development, metabolism, signal transduction and stress response. Extensive studies on miRNAs have been performed in different plants such as Arabidopsis thaliana, Oryza sativa etc. and volume of the miRNA database, mirBASE, has been increasing on day to day basis. Stevia rebaudiana Bertoni is an important perennial herb which accumulates high concentrations of diterpene steviol glycosides which contributes to its high indexed sweetening property with no calorific value. Several studies have been carried out for understanding molecular mechanism involved in biosynthesis of these glycosides, however, information about miRNAs has been lacking in S. rebaudiana. Deep sequencing of small RNAs combined with transcriptomic data is a powerful tool for identifying conserved and novel miRNAs irrespective of availability of genome sequence data. Results To identify miRNAs in S. rebaudiana, sRNA library was constructed and sequenced using Illumina genome analyzer II. A total of 30,472,534 reads representing 2,509,190 distinct sequences were obtained from sRNA library. Based on sequence similarity, we identified 100 miRNAs belonging to 34 highly conserved families. Also, we identified 12 novel miRNAs whose precursors were potentially generated from stevia EST and nucleotide sequences. All novel sequences have not been earlier described in other plant species. Putative target genes were predicted for most conserved and novel miRNAs. The predicted targets are mainly mRNA encoding enzymes regulating essential plant metabolic and signaling pathways. Conclusions This study led to the identification of 34 highly conserved miRNA families and 12 novel potential miRNAs indicating that specific miRNAs exist in stevia species. Our results provided information on stevia miRNAs and their targets building a foundation for future studies to

smRNAome profiling to identify conserved and novel microRNAs in Stevia rebaudiana Bertoni.

PubMed

Mandhan, Vibha; Kaur, Jagdeep; Singh, Kashmir

2012-11-01

MicroRNAs (miRNAs) constitute a family of small RNA (sRNA) population that regulates the gene expression and plays an important role in plant development, metabolism, signal transduction and stress response. Extensive studies on miRNAs have been performed in different plants such as Arabidopsis thaliana, Oryza sativa etc. and volume of the miRNA database, mirBASE, has been increasing on day to day basis. Stevia rebaudiana Bertoni is an important perennial herb which accumulates high concentrations of diterpene steviol glycosides which contributes to its high indexed sweetening property with no calorific value. Several studies have been carried out for understanding molecular mechanism involved in biosynthesis of these glycosides, however, information about miRNAs has been lacking in S. rebaudiana. Deep sequencing of small RNAs combined with transcriptomic data is a powerful tool for identifying conserved and novel miRNAs irrespective of availability of genome sequence data. To identify miRNAs in S. rebaudiana, sRNA library was constructed and sequenced using Illumina genome analyzer II. A total of 30,472,534 reads representing 2,509,190 distinct sequences were obtained from sRNA library. Based on sequence similarity, we identified 100 miRNAs belonging to 34 highly conserved families. Also, we identified 12 novel miRNAs whose precursors were potentially generated from stevia EST and nucleotide sequences. All novel sequences have not been earlier described in other plant species. Putative target genes were predicted for most conserved and novel miRNAs. The predicted targets are mainly mRNA encoding enzymes regulating essential plant metabolic and signaling pathways. This study led to the identification of 34 highly conserved miRNA families and 12 novel potential miRNAs indicating that specific miRNAs exist in stevia species. Our results provided information on stevia miRNAs and their targets building a foundation for future studies to understand their roles in key

The SPES High Power ISOL production target

NASA Astrophysics Data System (ADS)

Andrighetto, A.; Corradetti, S.; Ballan, M.; Borgna, F.; Manzolaro, M.; Scarpa, D.; Monetti, A.; Rossignoli, M.; Silingardi, R.; Mozzi, A.; Vivian, G.; Boratto, E.; De Ruvo, L.; Sattin, N.; Meneghetti, G.; Oboe, R.; Guerzoni, M.; Margotti, A.; Ferrari, M.; Zenoni, A.; Prete, G.

2016-11-01

SPES (Selective Production of Exotic Species) is a facility under construction at INFN-LNL (Istituto Nazionale di Fisica Nucleare - Laboratori Nazionali di Legnaro), aimed to produce intense neutron-rich radioactive ion beams (RIBs). These will be obtained using the ISOL (Isotope Separation On-Line) method, bombarding a uranium carbide target with a proton beam of 40MeV energy and currents up to 200μA. The target configuration was designed to obtain a high number of fissions, up to 1013 per second, low power deposition and fast release of the produced isotopes. The exotic isotopes generated in the target are ionized, mass separated and re-accelerated by the ALPI superconducting LINAC at energies of 10AMeV and higher, for masses in the region of A = 130 amu , with an expected rate on the secondary target up to 109 particles per second. In this work, recent results on the R&D activities regarding the SPES RIB production target-ion source system are reported.

Decentralizing conservation and diversifying livelihoods within Kanchenjunga Conservation Area, Nepal.

PubMed

Parker, Pete; Thapa, Brijesh; Jacob, Aerin

2015-12-01

To alleviate poverty and enhance conservation in resource dependent communities, managers must identify existing livelihood strategies and the associated factors that impede household access to livelihood assets. Researchers increasingly advocate reallocating management power from exclusionary central institutions to a decentralized system of management based on local and inclusive participation. However, it is yet to be shown if decentralizing conservation leads to diversified livelihoods within a protected area. The purpose of this study was to identify and assess factors affecting household livelihood diversification within Nepal's Kanchenjunga Conservation Area Project, the first protected area in Asia to decentralize conservation. We randomly surveyed 25% of Kanchenjunga households to assess household socioeconomic and demographic characteristics and access to livelihood assets. We used a cluster analysis with the ten most common income generating activities (both on- and off-farm) to group the strategies households use to diversify livelihoods, and a multinomial logistic regression to identify predictors of livelihood diversification. We found four distinct groups of household livelihood strategies with a range of diversification that directly corresponded to household income. The predictors of livelihood diversification were more related to pre-existing socioeconomic and demographic factors (e.g., more landholdings and livestock, fewer dependents, receiving remittances) than activities sponsored by decentralizing conservation (e.g., microcredit, training, education, interaction with project staff). Taken together, our findings indicate that without direct policies to target marginalized groups, decentralized conservation in Kanchenjunga will continue to exclude marginalized groups, limiting a household's ability to diversify their livelihood and perpetuating their dependence on natural resources. Copyright © 2015 Elsevier Ltd. All rights reserved.

Development of high resolution target monitor.

DOT National Transportation Integrated Search

2008-01-01

The proposed High-resolution Target Movement Monitor uses triangulation theory but in a unique way. Unlike the commercially available triangulation systems which use sensing diodes to perceive reflected laser signatures and are limited to very short ...

Invasive mammal eradication on islands results in substantial conservation gains

PubMed Central

Jones, Holly P.; Holmes, Nick D.; Butchart, Stuart H. M.; Tershy, Bernie R.; Kappes, Peter J.; Corkery, Ilse; Aguirre-Muñoz, Alfonso; Armstrong, Doug P.; Bonnaud, Elsa; Burbidge, Andrew A.; Campbell, Karl; Courchamp, Franck; Cowan, Philip E.; Cuthbert, Richard J.; Ebbert, Steve; Genovesi, Piero; Howald, Gregg R.; Keitt, Bradford S.; Kress, Stephen W.; Miskelly, Colin M.; Oppel, Steffen; Poncet, Sally; Rauzon, Mark J.; Rocamora, Gérard; Russell, James C.; Samaniego-Herrera, Araceli; Seddon, Philip J.; Spatz, Dena R.; Towns, David R.; Croll, Donald A.

2016-01-01

More than US$21 billion is spent annually on biodiversity conservation. Despite their importance for preventing or slowing extinctions and preserving biodiversity, conservation interventions are rarely assessed systematically for their global impact. Islands house a disproportionately higher amount of biodiversity compared with mainlands, much of which is highly threatened with extinction. Indeed, island species make up nearly two-thirds of recent extinctions. Islands therefore are critical targets of conservation. We used an extensive literature and database review paired with expert interviews to estimate the global benefits of an increasingly used conservation action to stem biodiversity loss: eradication of invasive mammals on islands. We found 236 native terrestrial insular faunal species (596 populations) that benefitted through positive demographic and/or distributional responses from 251 eradications of invasive mammals on 181 islands. Seven native species (eight populations) were negatively impacted by invasive mammal eradication. Four threatened species had their International Union for the Conservation of Nature (IUCN) Red List extinction-risk categories reduced as a direct result of invasive mammal eradication, and no species moved to a higher extinction-risk category. We predict that 107 highly threatened birds, mammals, and reptiles on the IUCN Red List—6% of all these highly threatened species—likely have benefitted from invasive mammal eradications on islands. Because monitoring of eradication outcomes is sporadic and limited, the impacts of global eradications are likely greater than we report here. Our results highlight the importance of invasive mammal eradication on islands for protecting the world's most imperiled fauna. PMID:27001852

Invasive mammal eradication on islands results in substantial conservation gains.

PubMed

Jones, Holly P; Holmes, Nick D; Butchart, Stuart H M; Tershy, Bernie R; Kappes, Peter J; Corkery, Ilse; Aguirre-Muñoz, Alfonso; Armstrong, Doug P; Bonnaud, Elsa; Burbidge, Andrew A; Campbell, Karl; Courchamp, Franck; Cowan, Philip E; Cuthbert, Richard J; Ebbert, Steve; Genovesi, Piero; Howald, Gregg R; Keitt, Bradford S; Kress, Stephen W; Miskelly, Colin M; Oppel, Steffen; Poncet, Sally; Rauzon, Mark J; Rocamora, Gérard; Russell, James C; Samaniego-Herrera, Araceli; Seddon, Philip J; Spatz, Dena R; Towns, David R; Croll, Donald A

2016-04-12

More than US$21 billion is spent annually on biodiversity conservation. Despite their importance for preventing or slowing extinctions and preserving biodiversity, conservation interventions are rarely assessed systematically for their global impact. Islands house a disproportionately higher amount of biodiversity compared with mainlands, much of which is highly threatened with extinction. Indeed, island species make up nearly two-thirds of recent extinctions. Islands therefore are critical targets of conservation. We used an extensive literature and database review paired with expert interviews to estimate the global benefits of an increasingly used conservation action to stem biodiversity loss: eradication of invasive mammals on islands. We found 236 native terrestrial insular faunal species (596 populations) that benefitted through positive demographic and/or distributional responses from 251 eradications of invasive mammals on 181 islands. Seven native species (eight populations) were negatively impacted by invasive mammal eradication. Four threatened species had their International Union for the Conservation of Nature (IUCN) Red List extinction-risk categories reduced as a direct result of invasive mammal eradication, and no species moved to a higher extinction-risk category. We predict that 107 highly threatened birds, mammals, and reptiles on the IUCN Red List-6% of all these highly threatened species-likely have benefitted from invasive mammal eradications on islands. Because monitoring of eradication outcomes is sporadic and limited, the impacts of global eradications are likely greater than we report here. Our results highlight the importance of invasive mammal eradication on islands for protecting the world's most imperiled fauna.

7 CFR 12.23 - Conservation plans and conservation systems.

Code of Federal Regulations, 2010 CFR

2010-01-01

... to produce agricultural commodities prior to December 23, 1985, the applicable conservation systems... available conservation technology; cost-effective; and shall not cause undue economic hardship on the person... containing highly erodible cropland which was used to produce an agricultural commodity prior to December 23...

Proteomic Analysis of Pathogenic Fungi Reveals Highly Expressed Conserved Cell Wall Proteins

PubMed Central

Champer, Jackson; Ito, James I.; Clemons, Karl V.; Stevens, David A.; Kalkum, Markus

2016-01-01

We are presenting a quantitative proteomics tally of the most commonly expressed conserved fungal proteins of the cytosol, the cell wall, and the secretome. It was our goal to identify fungi-typical proteins that do not share significant homology with human proteins. Such fungal proteins are of interest to the development of vaccines or drug targets. Protein samples were derived from 13 fungal species, cultured in rich or in minimal media; these included clinical isolates of Aspergillus, Candida, Mucor, Cryptococcus, and Coccidioides species. Proteomes were analyzed by quantitative MSE (Mass Spectrometry—Elevated Collision Energy). Several thousand proteins were identified and quantified in total across all fractions and culture conditions. The 42 most abundant proteins identified in fungal cell walls or supernatants shared no to very little homology with human proteins. In contrast, all but five of the 50 most abundant cytosolic proteins had human homologs with sequence identity averaging 59%. Proteomic comparisons of the secreted or surface localized fungal proteins highlighted conserved homologs of the Aspergillus fumigatus proteins 1,3-β-glucanosyltransferases (Bgt1, Gel1-4), Crf1, Ecm33, EglC, and others. The fact that Crf1 and Gel1 were previously shown to be promising vaccine candidates, underlines the value of the proteomics data presented here. PMID:26878023

Conservation in the face of climate change: recent developments

PubMed Central

Lawler, Joshua; Watson, James; Game, Edward

2015-01-01

An increased understanding of the current and potential future impacts of climate change has significantly influenced conservation in practice in recent years. Climate change has necessitated a shift toward longer planning time horizons, moving baselines, and evolving conservation goals and targets. This shift has resulted in new perspectives on, and changes in, the basic approaches practitioners use to conserve biodiversity. Restoration, spatial planning and reserve selection, connectivity modelling, extinction risk assessment, and species translocations have all been reimagined in the face of climate change. Restoration is being conducted with a new acceptance of uncertainty and an understanding that goals will need to shift through time. New conservation targets, such as geophysical settings and climatic refugia, are being incorporated into conservation plans. Risk assessments have begun to consider the potentially synergistic impacts of climate change and other threats. Assisted colonization has gained acceptance in recent years as a viable and necessary conservation tool. This evolution has paralleled a larger trend in conservation—a shift toward conservation actions that benefit both people and nature. As we look forward, it is clear that more change is on the horizon. To protect biodiversity and essential ecosystem services, conservation will need to anticipate the human response to climate change and to focus not only on resistance and resilience but on transitions to new states and new ecosystems. PMID:26937271

High power neutron production targets

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wender, S.

1996-06-01

The author describes issues of concern in the design of targets and associated systems for high power neutron production facilities. The facilities include uses for neutron scattering, accelerator driven transmutation, accelerator production of tritium, short pulse spallation sources, and long pulse spallation sources. Each of these applications requires a source with different design needs and consequently different implementation in practise.

The hot pepper (Capsicum annuum) microRNA transcriptome reveals novel and conserved targets: a foundation for understanding MicroRNA functional roles in hot pepper.

PubMed

Hwang, Dong-Gyu; Park, June Hyun; Lim, Jae Yun; Kim, Donghyun; Choi, Yourim; Kim, Soyoung; Reeves, Gregory; Yeom, Seon-In; Lee, Jeong-Soo; Park, Minkyu; Kim, Seungill; Choi, Ik-Young; Choi, Doil; Shin, Chanseok

2013-01-01

MicroRNAs (miRNAs) are a class of non-coding RNAs approximately 21 nt in length which play important roles in regulating gene expression in plants. Although many miRNA studies have focused on a few model plants, miRNAs and their target genes remain largely unknown in hot pepper (Capsicum annuum), one of the most important crops cultivated worldwide. Here, we employed high-throughput sequencing technology to identify miRNAs in pepper extensively from 10 different libraries, including leaf, stem, root, flower, and six developmental stage fruits. Based on a bioinformatics pipeline, we successfully identified 29 and 35 families of conserved and novel miRNAs, respectively. Northern blot analysis was used to validate further the expression of representative miRNAs and to analyze their tissue-specific or developmental stage-specific expression patterns. Moreover, we computationally predicted miRNA targets, many of which were experimentally confirmed using 5' rapid amplification of cDNA ends analysis. One of the validated novel targets of miR-396 was a domain rearranged methyltransferase, the major de novo methylation enzyme, involved in RNA-directed DNA methylation in plants. This work provides the first reliable draft of the pepper miRNA transcriptome. It offers an expanded picture of pepper miRNAs in relation to other plants, providing a basis for understanding the functional roles of miRNAs in pepper.

Targeting community-dwelling urinary incontinence sufferers: a multi-disciplinary community based model for conservative continence services.

PubMed

St John, Winsome; Wallis, Marianne; James, Heather; McKenzie, Shona; Guyatt, Sheridan

2004-10-01

This paper presents an argument that there is a need to provide services that target community-dwelling incontinence sufferers, and presents a demonstration case study of a multi-disciplinary, community-based conservative model of service delivery: The Waterworx Model. Rationale for approaches taken, implementation of the model, evaluation and lessons learned are discussed. In this paper community-dwelling sufferers of urinary incontinence are identified as an underserved group, and useful information is provided for those wishing to establish services for them. The Waterworx Model of continence service delivery incorporates three interrelated approaches. Firstly, client access is achieved by using community-based services via clinic and home visits, creating referral pathways and active promotion of services. Secondly, multi-disciplinary client care is provided by targeting a specific client group, multi-disciplinary assessment, promoting client self-management and developing client knowledge and health literacy. Finally, interdisciplinary collaboration and linkages is facilitated by developing multidisciplinary assessment tools, using interdisciplinary referrals, staff development, multi-disciplinary management and providing professional education. Implementation of the model achieved greater client access, improvement in urinary incontinence and client satisfaction. Our experiences suggest that those suffering urinary incontinence and living in the community are an underserved group and that continence services should be community focussed, multi-disciplinary, generalist in nature.

HIGH POWER BEAM DUMP AND TARGET / ACCELERATOR INTERFACE PROCEDURES

DOE Office of Scientific and Technical Information (OSTI.GOV)

Blokland, Willem; Plum, Michael A; Peters, Charles C

Satisfying operational procedures and limits for the beam target interface is a critical concern for high power operation at spallation neutron sources. At the Oak Ridge Spallation Neutron Source (SNS) a number of protective measures are instituted to ensure that the beam position, beam size and peak intensity are within acceptable limits at the target and high power Ring Injection Dump (RID). The high power beam dump typically handles up to 50 100 kW of beam power and its setup is complicated by the fact that there are two separate beam components simultaneously directed to the dump. The beam onmore » target is typically in the 800-1000 kW average power level, delivered in sub- s 60 Hz pulses. Setup techniques using beam measurements to quantify the beam parameters at the target and dump will be described. However, not all the instrumentation used for the setup and initial qualification is available during high power operation. Additional techniques are used to monitor the beam during high power operation to ensure the setup conditions are maintained, and these are also described.« less

REVIEW: The evolving linkage between conservation science and practice at The Nature Conservancy.

PubMed

Kareiva, Peter; Groves, Craig; Marvier, Michelle

2014-10-01

The Nature Conservancy (TNC) was founded by ecologists as a United States land trust to purchase parcels of habitat for the purpose of scientific study. It has evolved into a global organization working in 35 countries 'to conserve the lands and waters on which all life depends'. TNC is now the world 's largest conservation non-governmental organization (NGO), an early adopter of advances in ecological theory and a producer of new science as a result of practising conservation.The Nature Conservancy 's initial scientific innovation was the use of distributional data for rare species and ecological communities to systematically target lands for conservation. This innovation later evolved into a more rigorous approach known as 'Conservation by Design' that contained elements of systematic conservation planning, strategic planning and monitoring and evaluation.The next scientific transition at TNC was a move to landscape-scale projects, motivated by ideas from landscape ecology. Because the scale at which land could be set aside in areas untouched by humans fell far short of the spatial scale demanded by conservation, TNC became involved with best management practices for forestry, grazing, agriculture, hydropower and other land uses.A third scientific innovation at TNC came with the pursuit of multiobjective planning that accounts for economic and resource needs in the same plans that seek to protect biodiversity.The Millennium Ecosystem Assessment prompted TNC to become increasingly concerned with ecosystem services and the material risk to people posed by ecosystem deterioration.Finally, because conservation depends heavily upon negotiation, TNC has recently recruited social scientists, economists and communication experts. One aspect still missing, however, is a solid scientific understanding of thresholds that should be averted. Synthesis and applications . Over its 60-plus year history, scientific advances have informed The Nature Conservancy (TNC) 's actions

REVIEW: The evolving linkage between conservation science and practice at The Nature Conservancy

PubMed Central

Kareiva, Peter; Groves, Craig; Marvier, Michelle

2014-01-01

The Nature Conservancy (TNC) was founded by ecologists as a United States land trust to purchase parcels of habitat for the purpose of scientific study. It has evolved into a global organization working in 35 countries ‘to conserve the lands and waters on which all life depends’. TNC is now the world 's largest conservation non-governmental organization (NGO), an early adopter of advances in ecological theory and a producer of new science as a result of practising conservation.The Nature Conservancy 's initial scientific innovation was the use of distributional data for rare species and ecological communities to systematically target lands for conservation. This innovation later evolved into a more rigorous approach known as ‘Conservation by Design’ that contained elements of systematic conservation planning, strategic planning and monitoring and evaluation.The next scientific transition at TNC was a move to landscape-scale projects, motivated by ideas from landscape ecology. Because the scale at which land could be set aside in areas untouched by humans fell far short of the spatial scale demanded by conservation, TNC became involved with best management practices for forestry, grazing, agriculture, hydropower and other land uses.A third scientific innovation at TNC came with the pursuit of multiobjective planning that accounts for economic and resource needs in the same plans that seek to protect biodiversity.The Millennium Ecosystem Assessment prompted TNC to become increasingly concerned with ecosystem services and the material risk to people posed by ecosystem deterioration.Finally, because conservation depends heavily upon negotiation, TNC has recently recruited social scientists, economists and communication experts. One aspect still missing, however, is a solid scientific understanding of thresholds that should be averted.Synthesis and applications. Over its 60-plus year history, scientific advances have informed The Nature Conservancy (TNC) 's

Are conservation organizations configured for effective adaptation to global change?

USGS Publications Warehouse

Armsworth, Paul R.; Larson, Eric R.; Jackson, Stephen T.; Sax, Dov F.; Simonin, Paul W.; Blossey, Bernd; Green, Nancy; Lester, Liza; Klein, Mary L.; Ricketts, Taylor H.; Runge, Michael C.; Shaw, M. Rebecca

2015-01-01

Conservation organizations must adapt to respond to the ecological impacts of global change. Numerous changes to conservation actions (eg facilitated ecological transitions, managed relocations, or increased corridor development) have been recommended, but some institutional restructuring within organizations may also be needed. Here we discuss the capacity of conservation organizations to adapt to changing environmental conditions, focusing primarily on public agencies and nonprofits active in land protection and management in the US. After first reviewing how these organizations anticipate and detect impacts affecting target species and ecosystems, we then discuss whether they are sufficiently flexible to prepare and respond by reallocating funding, staff, or other resources. We raise new hypotheses about how the configuration of different organizations enables them to protect particular conservation targets and manage for particular biophysical changes that require coordinated management actions over different spatial and temporal scales. Finally, we provide a discussion resource to help conservation organizations assess their capacity to adapt.

Prioritizing bird conservation actions in the Prairie Hardwood transition of the Midwestern United States

USGS Publications Warehouse

Thogmartin, Wayne E.; Crimmins, Shawn M.; Pearce, Jennie

2014-01-01

Large-scale planning for the conservation of species is often hindered by a poor understanding of factors limiting populations. In regions with declining wildlife populations, it is critical that objective metrics of conservation success are developed to ensure that conservation actions achieve desired results. Using spatially explicit estimates of bird abundance, we evaluated several management alternatives for conserving bird populations in the Prairie Hardwood Transition of the United States. We designed landscapes conserving species at 50% of their current predicted abundance as well as landscapes attempting to achieve species population targets (which often required the doubling of current abundance). Conserving species at reduced (half of current) abundance led to few conservation conflicts. However, because of extensive modification of the landscape to suit human use, strategies for achieving regional population targets for forest bird species would be difficult under even ideal circumstances, and even more so if maintenance of grassland bird populations is also desired. Our results indicated that large-scale restoration of agricultural lands to native grassland and forest habitats may be the most productive conservation action for increasing bird population sizes but the level of landscape transition required to approach target bird population sizes may be societally unacceptable.

Business strategies for conservation on private lands: Koa forestry as a case study

PubMed Central

Goldstein, Joshua H.; Daily, Gretchen C.; Friday, James B.; Matson, Pamela A.; Naylor, Rosamond L.; Vitousek, Peter

2006-01-01

Innovative financial instruments are being created to reward conservation on private, working lands. Major design challenges remain, however, to make investments in biodiversity and ecosystem services economically attractive and commonplace. From a business perspective, three key financial barriers for advancing conservation land uses must frequently be addressed: high up-front costs, long time periods with no revenue, and high project risk due to long time horizons and uncertainty. We explored ways of overcoming these barriers on grazing lands in Hawaii by realizing a suite of timber and conservation revenue streams associated with their (partial) reforestation. We calculated the financial implications of alternative strategies, focusing on Acacia koa (“koa”) forestry because of its high conservation and economic potential. Koa’s timber value alone creates a viable investment (mean net present value = $453/acre), but its long time horizon and poor initial cash flow pose formidable challenges for landowners. At present, subsidy payments from a government conservation program targeting benefits for biodiversity, water quality, and soil erosion have the greatest potential to move landowners beyond the tipping point in favor of investments in koa forestry, particularly when combined with future timber harvest (mean net present value = $1,661/acre). Creating financial mechanisms to capture diverse ecosystem service values through time will broaden opportunities for conservation land uses. Governments, nongovernmental organizations, and private investors have roles to play in catalyzing this transition by developing new revenue streams that can reach a broad spectrum of landowners. PMID:16782816

Business strategies for conservation on private lands: Koa forestry as a case study.

PubMed

Goldstein, Joshua H; Daily, Gretchen C; Friday, James B; Matson, Pamela A; Naylor, Rosamond L; Vitousek, Peter

2006-06-27

Innovative financial instruments are being created to reward conservation on private, working lands. Major design challenges remain, however, to make investments in biodiversity and ecosystem services economically attractive and commonplace. From a business perspective, three key financial barriers for advancing conservation land uses must frequently be addressed: high up-front costs, long time periods with no revenue, and high project risk due to long time horizons and uncertainty. We explored ways of overcoming these barriers on grazing lands in Hawaii by realizing a suite of timber and conservation revenue streams associated with their (partial) reforestation. We calculated the financial implications of alternative strategies, focusing on Acacia koa ("koa") forestry because of its high conservation and economic potential. Koa's timber value alone creates a viable investment (mean net present value = $453/acre), but its long time horizon and poor initial cash flow pose formidable challenges for landowners. At present, subsidy payments from a government conservation program targeting benefits for biodiversity, water quality, and soil erosion have the greatest potential to move landowners beyond the tipping point in favor of investments in koa forestry, particularly when combined with future timber harvest (mean net present value = $1,661/acre). Creating financial mechanisms to capture diverse ecosystem service values through time will broaden opportunities for conservation land uses. Governments, nongovernmental organizations, and private investors have roles to play in catalyzing this transition by developing new revenue streams that can reach a broad spectrum of landowners.

UniDrug-target: a computational tool to identify unique drug targets in pathogenic bacteria.

PubMed

Chanumolu, Sree Krishna; Rout, Chittaranjan; Chauhan, Rajinder S

2012-01-01

Targeting conserved proteins of bacteria through antibacterial medications has resulted in both the development of resistant strains and changes to human health by destroying beneficial microbes which eventually become breeding grounds for the evolution of resistances. Despite the availability of more than 800 genomes sequences, 430 pathways, 4743 enzymes, 9257 metabolic reactions and protein (three-dimensional) 3D structures in bacteria, no pathogen-specific computational drug target identification tool has been developed. A web server, UniDrug-Target, which combines bacterial biological information and computational methods to stringently identify pathogen-specific proteins as drug targets, has been designed. Besides predicting pathogen-specific proteins essentiality, chokepoint property, etc., three new algorithms were developed and implemented by using protein sequences, domains, structures, and metabolic reactions for construction of partial metabolic networks (PMNs), determination of conservation in critical residues, and variation analysis of residues forming similar cavities in proteins sequences. First, PMNs are constructed to determine the extent of disturbances in metabolite production by targeting a protein as drug target. Conservation of pathogen-specific protein's critical residues involved in cavity formation and biological function determined at domain-level with low-matching sequences. Last, variation analysis of residues forming similar cavities in proteins sequences from pathogenic versus non-pathogenic bacteria and humans is performed. The server is capable of predicting drug targets for any sequenced pathogenic bacteria having fasta sequences and annotated information. The utility of UniDrug-Target server was demonstrated for Mycobacterium tuberculosis (H37Rv). The UniDrug-Target identified 265 mycobacteria pathogen-specific proteins, including 17 essential proteins which can be potential drug targets. UniDrug-Target is expected to accelerate

A framework for addressing bird conservation priorities in high-elevation vegetation communities of the Appalachian Mountains

Treesearch

Brian W. Smith; Dean Demarest; Ed. Laurent

2010-01-01

The Appalachian Mountains Joint Venture (AMJV) is a self-directed, nonregulatory bird conservation partnership with the mission of restoring and sustaining native bird populations and their habitats throughout Appalachia. In 2008, the AMJV formed an ad hoc "high-elevation" technical working group to identify and address conservation priorities of bird species...

Genomic perspectives of spider silk genes through target capture sequencing: Conservation of stabilization mechanisms and homology-based structural models of spidroin terminal regions.

PubMed

Collin, Matthew A; Clarke, Thomas H; Ayoub, Nadia A; Hayashi, Cheryl Y

2018-07-01

A powerful system for studying protein aggregation, particularly rapid self-assembly, is spider silk. Spider silks are proteinaceous and silk proteins are synthesized and stored within silk glands as liquid dope. As needed, liquid dope is near-instantaneously transformed into solid fibers or viscous adhesives. The dominant constituents of silks are spidroins (spider fibroins) and their terminal domains are vital for the tight control of silk self-assembly. To better understand spidroin termini, we used target capture and deep sequencing to identify spidroin gene sequences from six species representing the araneoid families of Araneidae, Nephilidae, and Theridiidae. We obtained 145 terminal regions, of which 103 are newly annotated here, as well as novel variants within nine diverse spidroin types. Our comparative analyses demonstrated the conservation of acidic, basic, and cysteine amino acid residues across spidroin types that had been proposed to be important for monomer stability, dimer formation, and self-assembly from a limited sampling of spidroins. Computational, protein homology modeling revealed areas of spidroin terminal regions that are highly conserved in three-dimensions despite sequence divergence across spidroin types. Analyses of our dense sampling of terminal regions suggest that most spidroins share stabilization mechanisms, dimer formation, and tertiary structure, despite producing functionally distinct materials. Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.

Crystal structure and size-dependent neutralization properties of HK20, a human monoclonal antibody binding to the highly conserved heptad repeat 1 of gp41.

PubMed

Sabin, Charles; Corti, Davide; Buzon, Victor; Seaman, Mike S; Lutje Hulsik, David; Hinz, Andreas; Vanzetta, Fabrizia; Agatic, Gloria; Silacci, Chiara; Mainetti, Lara; Scarlatti, Gabriella; Sallusto, Federica; Weiss, Robin; Lanzavecchia, Antonio; Weissenhorn, Winfried

2010-11-18

The human monoclonal antibody (mAb) HK20 neutralizes a broad spectrum of primary HIV-1 isolates by targeting the highly conserved heptad repeat 1 (HR1) of gp41, which is transiently exposed during HIV-1 entry. Here we present the crystal structure of the HK20 Fab in complex with a gp41 mimetic 5-Helix at 2.3 Å resolution. HK20 employs its heavy chain CDR H2 and H3 loops to bind into a conserved hydrophobic HR1 pocket that is occupied by HR2 residues in the gp41 post fusion conformation. Compared to the previously described HR1-specific mAb D5, HK20 approaches its epitope with a different angle which might favor epitope access and thus contribute to its higher neutralization breadth and potency. Comparison of the neutralization activities of HK20 IgG, Fab and scFv employing both single cycle and multiple cycle neutralization assays revealed much higher potencies for the smaller Fab and scFv over IgG, implying that the target site is difficult to access for complete antibodies. Nevertheless, two thirds of sera from HIV-1 infected individuals contain significant titers of HK20-inhibiting antibodies. The breadth of neutralization of primary isolates across all clades, the higher potencies for C-clade viruses and the targeting of a distinct site as compared to the fusion inhibitor T-20 demonstrate the potential of HK20 scFv as a therapeutic tool.

Diversity, expression and mRNA targeting abilities of Argonaute-targeting miRNAs among selected vascular plants.

PubMed

Jagtap, Soham; Shivaprasad, Padubidri V

2014-12-02

Micro (mi)RNAs are important regulators of plant development. Across plant lineages, Dicer-like 1 (DCL1) proteins process long ds-like structures to produce micro (mi) RNA duplexes in a stepwise manner. These miRNAs are incorporated into Argonaute (AGO) proteins and influence expression of RNAs that have sequence complementarity with miRNAs. Expression levels of AGOs are greatly regulated by plants in order to minimize unwarranted perturbations using miRNAs to target mRNAs coding for AGOs. AGOs may also have high promoter specificity-sometimes expression of AGO can be limited to just a few cells in a plant. Viral pathogens utilize various means to counter antiviral roles of AGOs including hijacking the host encoded miRNAs to target AGOs. Two host encoded miRNAs namely miR168 and miR403 that target AGOs have been described in the model plant Arabidopsis and such a mechanism is thought to be well conserved across plants because AGO sequences are well conserved. We show that the interaction between AGO mRNAs and miRNAs is species-specific due to the diversity in sequences of two miRNAs that target AGOs, sequence diversity among corresponding target regions in AGO mRNAs and variable expression levels of these miRNAs among vascular plants. We used miRNA sequences from 68 plant species representing 31 plant families for this analysis. Sequences of miR168 and miR403 are not conserved among plant lineages, but surprisingly they differ drastically in their sequence diversity and expression levels even among closely related plants. Variation in miR168 expression among plants correlates well with secondary structures/length of loop sequences of their precursors. Our data indicates a complex AGO targeting interaction among plant lineages due to miRNA sequence diversity and sequences of miRNA targeting regions among AGO mRNAs, thus leading to the assumption that the perturbations by viruses that use host miRNAs to target antiviral AGOs can only be species-specific. We also show

Conservation Genetics of Two Highly Endangered and Poorly Known Species of Zamia (Zamiaceae: Cycadales) in Colombia.

PubMed

Aristizábal, Arturo; Tuberquia, Dino J; Sanín, María José

2018-05-11

Genetic diversity is key in providing the variation needed to face stochastic change. Increased habitat loss alters population size and dynamics posing serious threats to the conservation of wild species. Colombia has undergone massive deforestation over the last century, but harbors extraordinary high species diversity of genus Zamia (Cycadales); however, most of the species are under threat. In this study, we targeted the largest accessible remaining populations of 2 closely related species growing as endemics in the Magdalena Valley region of Colombia. We successfully transferred the SSR loci used in previous Zamia studies to these species. In total, we amplified 13 microsatellite loci in 3 wild populations, aiming at: 1) assessing genetic diversity and 2) understanding if the structure found between the 3 populations reflected species and population boundaries due to ecological and historical genetic isolation. We found that the actual population size does not reflect population genetic diversity with a small population (Perales) harboring the highest genetic diversity. In addition, all populations are highly structured regardless of species containment, all showing signs of genetic isolation. Given the high degree of ecological threat, and the inherent biological traits of Cycads, we provide information regarding the prioritization of populations for ex situ management.

Alternative futures for Borneo show the value of integrating economic and conservation targets across borders

PubMed Central

Runting, Rebecca K.; Meijaard, Erik; Abram, Nicola K.; Wells, Jessie A.; Gaveau, David L.A.; Ancrenaz, Marc; Posssingham, Hugh P.; Wich, Serge A.; Ardiansyah, Fitrian; Gumal, Melvin T.; Ambu, Laurentius N.; Wilson, Kerrie A.

2015-01-01

Balancing economic development with international commitments to protect biodiversity is a global challenge. Achieving this balance requires an understanding of the possible consequences of alternative future scenarios for a range of stakeholders. We employ an integrated economic and environmental planning approach to evaluate four alternative futures for the mega-diverse island of Borneo. We show what could be achieved if the three national jurisdictions of Borneo coordinate efforts to achieve their public policy targets and allow a partial reallocation of planned land uses. We reveal the potential for Borneo to simultaneously retain ∼50% of its land as forests, protect adequate habitat for the Bornean orangutan (Pongo pygmaeus) and Bornean elephant (Elephas maximus borneensis), and achieve an opportunity cost saving of over US$43 billion. Such coordination would depend on enhanced information sharing and reforms to land-use planning, which could be supported by the increasingly international nature of economies and conservation efforts. PMID:25871635

Conservation plan based on the concept of integrity

NASA Astrophysics Data System (ADS)

Yen, Y. N.; Cheng, C. F.

2015-08-01

Value based concept has been accepted as a universal principle for the conservation of Cultural Heritage. Authenticity and integrity are two main issues protecting those values. Authenticity is the major tool in the value assessment and integrity plays an important role in the procedure of conservation plan. From the perspective of integrity, this research explores the principle of conservation plan and discusses its relation with the restoration plan and urban plan. A conservation plan in Quing-Lin village, Kinmen, will be taken as an example for implementation. The research shows that a conservation plan with integrity in mind helps to clarify the conservation target areas and their buffer zones. It also serves as a tool for developing control and risk management. Cultural mapping is an efficient tool for the communication with stakeholders in the process of the conservation plan.

Conservation of Mannan Synthesis in Fungi of the Zygomycota and Ascomycota Reveals a Broad Diagnostic Target.

PubMed

Burnham-Marusich, Amanda R; Hubbard, Breeana; Kvam, Alexander J; Gates-Hollingsworth, Marcellene; Green, Heather R; Soukup, Eric; Limper, Andrew H; Kozel, Thomas R

2018-01-01

Ascomycetes and zygomycetes account for the majority of (i) fungi responsible for cutaneous, subcutaneous, and invasive human fungal infections, (ii) plant fungal pathogens, (iii) fungi that threaten global biodiversity, (iv) fungal agents of agricultural spoilage, and (v) fungi in water-damaged buildings. Rapid recognition of fungal infection (or contamination) enables early treatment (or remediation). A bioinformatics search found homologues of Saccharomyces cerevisiae Mnn9p present in members of the Zygomycota and Ascomycota phyla and absent in members of the Chytridiomycota and Basidiomycota. Mnn9p is a component of the yeast mannan polymerization complex and is necessary for α-1,6 mannan production. A monoclonal antibody (2DA6) was produced that was reactive with purified mannans of Mucor , Rhizopus , Aspergillus , Fusarium , and Candida species. Experimentation using a 2DA6 antigen capture enzyme-linked immunosorbent assay (ELISA) and extracts of fungi from the four phyla found agreement between the presence or absence of Mnn9p homologues and production or lack of production of mannan reactive with 2DA6. Studies of cell extracts from yeast mannan mutants identified α-1,6 mannan as the epitope recognized by 2DA6. To translate this finding into a point-of-use diagnostic, a 2DA6 lateral flow immunoassay was constructed that detected mannan in (i) extracts of dermatophytes and fungi that produce trauma-related infection and (ii) tissue from plants infected with Grosmannia clavigera or Sclerotium cepivorum These studies (i) revealed that the conservation of α-1,6-linked mannan in fungi of the Zygomycota and Ascomycota can be exploited as a broad diagnostic target and (ii) have provided a means to detect that target in an immunoassay platform that is well suited for clinic or field use. IMPORTANCE A key question asked when faced with an infection, an infestation, or environmental damage is whether it is a fungus. Identification of fungi as the cause of the

Conservation of Mannan Synthesis in Fungi of the Zygomycota and Ascomycota Reveals a Broad Diagnostic Target

PubMed Central

Hubbard, Breeana; Kvam, Alexander J.; Gates-Hollingsworth, Marcellene; Green, Heather R.; Soukup, Eric; Limper, Andrew H.; Kozel, Thomas R.

2018-01-01

ABSTRACT Ascomycetes and zygomycetes account for the majority of (i) fungi responsible for cutaneous, subcutaneous, and invasive human fungal infections, (ii) plant fungal pathogens, (iii) fungi that threaten global biodiversity, (iv) fungal agents of agricultural spoilage, and (v) fungi in water-damaged buildings. Rapid recognition of fungal infection (or contamination) enables early treatment (or remediation). A bioinformatics search found homologues of Saccharomyces cerevisiae Mnn9p present in members of the Zygomycota and Ascomycota phyla and absent in members of the Chytridiomycota and Basidiomycota. Mnn9p is a component of the yeast mannan polymerization complex and is necessary for α-1,6 mannan production. A monoclonal antibody (2DA6) was produced that was reactive with purified mannans of Mucor, Rhizopus, Aspergillus, Fusarium, and Candida species. Experimentation using a 2DA6 antigen capture enzyme-linked immunosorbent assay (ELISA) and extracts of fungi from the four phyla found agreement between the presence or absence of Mnn9p homologues and production or lack of production of mannan reactive with 2DA6. Studies of cell extracts from yeast mannan mutants identified α-1,6 mannan as the epitope recognized by 2DA6. To translate this finding into a point-of-use diagnostic, a 2DA6 lateral flow immunoassay was constructed that detected mannan in (i) extracts of dermatophytes and fungi that produce trauma-related infection and (ii) tissue from plants infected with Grosmannia clavigera or Sclerotium cepivorum. These studies (i) revealed that the conservation of α-1,6-linked mannan in fungi of the Zygomycota and Ascomycota can be exploited as a broad diagnostic target and (ii) have provided a means to detect that target in an immunoassay platform that is well suited for clinic or field use. IMPORTANCE A key question asked when faced with an infection, an infestation, or environmental damage is whether it is a fungus. Identification of fungi as the cause of the

Reconciling nature conservation and traditional farming practices: a spatially explicit framework to assess the extent of High Nature Value farmlands in the European countryside

PubMed Central

Lomba, Angela; Alves, Paulo; Jongman, Rob H G; McCracken, David I

2015-01-01

Agriculture constitutes a dominant land cover worldwide, and rural landscapes under extensive farming practices acknowledged due to high biodiversity levels. The High Nature Value farmland (HNVf) concept has been highlighted in the EU environmental and rural policies due to their inherent potential to help characterize and direct financial support to European landscapes where high nature and/or conservation value is dependent on the continuation of specific low-intensity farming systems. Assessing the extent of HNV farmland by necessity relies on the availability of both ecological and farming systems' data, and difficulties associated with making such assessments have been widely described across Europe. A spatially explicit framework of data collection, building out from local administrative units, has recently been suggested as a means of addressing such difficulties. This manuscript tests the relevance of the proposed approach, describes the spatially explicit framework in a case study area in northern Portugal, and discusses the potential of the approach to help better inform the implementation of conservation and rural development policies. Synthesis and applications: The potential of a novel approach (combining land use/cover, farming and environmental data) to provide more accurate and efficient mapping and monitoring of HNV farmlands is tested at the local level in northern Portugal. The approach is considered to constitute a step forward toward a more precise targeting of landscapes for agri-environment schemes, as it allowed a more accurate discrimination of areas within the case study landscape that have a higher value for nature conservation. PMID:25798221

Effects of Spearfishing on Reef Fish Populations in a Multi-Use Conservation Area

PubMed Central

Frisch, Ashley J.; Cole, Andrew J.; Hobbs, Jean-Paul A.; Rizzari, Justin R.; Munkres, Katherine P.

2012-01-01

Although spearfishing is a popular method of capturing fish, its ecological effects on fish populations are poorly understood, which makes it difficult to assess the legitimacy and desirability of spearfishing in multi-use marine reserves. Recent management changes within the Great Barrier Reef Marine Park (GBRMP) fortuitously created a unique scenario by which to quantify the effects of spearfishing on fish populations. As such, we employed underwater visual surveys and a before-after-control-impact experimental design to investigate the effects of spearfishing on the density and size structure of target and non-target fishes in a multi-use conservation park zone (CPZ) within the GBRMP. Three years after spearfishing was first allowed in the CPZ, there was a 54% reduction in density and a 27% reduction in mean size of coral trout (Plectropomus spp.), the primary target species. These changes were attributed to spearfishing because benthic habitat characteristics and the density of non-target fishes were stable through time, and the density and mean size of coral trout in a nearby control zone (where spearfishing was prohibited) remained unchanged. We conclude that spearfishing, like other forms of fishing, can have rapid and substantial negative effects on target fish populations. Careful management of spearfishing is therefore needed to ensure that conservation obligations are achieved and that fishery resources are harvested sustainably. This is particularly important both for the GBRMP, due to its extraordinarily high conservation value and world heritage status, and for tropical island nations where people depend on spearfishing for food and income. To minimize the effects of spearfishing on target species and to enhance protection of functionally important fishes (herbivores), we recommend that fishery managers adjust output controls such as size- and catch-limits, rather than prohibit spearfishing altogether. This will preserve the cultural and social

Environmental service payments: evaluating biodiversity conservation trade-offs and cost-efficiency in the Osa Conservation Area, Costa Rica.

PubMed

Barton, D N; Faith, D P; Rusch, G M; Acevedo, H; Paniagua, L; Castro, M

2009-02-01

The cost-efficiency of payments for environmental services (PES) to private landowners in the Osa Conservation Area, Costa Rica, is evaluated in terms of the trade-off between biodiversity representation and opportunity costs of conservation to agricultural and forestry land-use. Using available GIS data and an 'off-the-shelf' software application called TARGET, we find that the PES allocation criteria applied by authorities in 2002-2003 were more than twice as cost-efficient as criteria applied during 1999-2001. Results show that a policy relevant assessment of the cost-effectiveness of PES relative to other conservation policies can be carried out at regional level using available studies and GIS data. However, there are a number of data and conceptual limitations to using heuristic optimisation algorithms in the analysis of the cost-efficiency of PES. Site specific data on probabilities of land-use change, and a detailed specification of opportunity costs of farm land, labour and capital are required to use algorithms such as TARGET for ranking individual sites based on cost-efficiency. Despite its conceptual soundness for regional conservation analysis, biodiversity complementarity presents a practical challenge as a criterion for PES eligibility at farm level because it varies depending on the set of areas under PES contracts at any one time.

Stable Binding of the Conserved Transcription Factor Grainy Head to its Target Genes Throughout Drosophila melanogaster Development

PubMed Central

Nevil, Markus; Bondra, Eliana R.; Schulz, Katharine N.; Kaplan, Tommy; Harrison, Melissa M.

2017-01-01

It has been suggested that transcription factor binding is temporally dynamic, and that changes in binding determine transcriptional output. Nonetheless, this model is based on relatively few examples in which transcription factor binding has been assayed at multiple developmental stages. The essential transcription factor Grainy head (Grh) is conserved from fungi to humans, and controls epithelial development and barrier formation in numerous tissues. Drosophila melanogaster, which possess a single grainy head (grh) gene, provide an excellent system to study this conserved factor. To determine whether temporally distinct binding events allow Grh to control cell fate specification in different tissue types, we used a combination of ChIP-seq and RNA-seq to elucidate the gene regulatory network controlled by Grh during four stages of embryonic development (spanning stages 5–17) and in larval tissue. Contrary to expectations, we discovered that Grh remains bound to at least 1146 genomic loci over days of development. In contrast to this stable DNA occupancy, the subset of genes whose expression is regulated by Grh varies. Grh transitions from functioning primarily as a transcriptional repressor early in development to functioning predominantly as an activator later. Our data reveal that Grh binds to target genes well before the Grh-dependent transcriptional program commences, suggesting it sets the stage for subsequent recruitment of additional factors that execute stage-specific Grh functions. PMID:28007888

Spatial Dynamics and Expanded Vertical Niche of Blue Sharks in Oceanographic Fronts Reveal Habitat Targets for Conservation

PubMed Central

Queiroz, Nuno; Humphries, Nicolas E.; Noble, Leslie R.; Santos, António M.; Sims, David W.

2012-01-01

Dramatic population declines among species of pelagic shark as a result of overfishing have been reported, with some species now at a fraction of their historical biomass. Advanced telemetry techniques enable tracking of spatial dynamics and behaviour, providing fundamental information on habitat preferences of threatened species to aid conservation. We tracked movements of the highest pelagic fisheries by-catch species, the blue shark Prionace glauca, in the North-east Atlantic using pop-off satellite-linked archival tags to determine the degree of space use linked to habitat and to examine vertical niche. Overall, blue sharks moved south-west of tagging sites (English Channel; southern Portugal), exhibiting pronounced site fidelity correlated with localized productive frontal areas, with estimated space-use patterns being significantly different from that of random walks. Tracked female sharks displayed behavioural variability in diel depth preferences, both within and between individuals. Diel depth use ranged from normal DVM (nDVM; dawn descent, dusk ascent), to reverse DVM (rDVM; dawn ascent, dusk descent), to behavioural patterns where no diel differences were apparent. Results showed that blue sharks occupy some of the most productive marine zones for extended periods and structure diel activity patterns across multiple spatio-temporal scales in response to particular habitat types. In so doing, sharks occupied an extraordinarily broad vertical depth range for their size (1.0–2.0 m fork length), from the surface into the bathypelagic realm (max. dive depth, 1160 m). The space-use patterns of blue sharks indicated they spend much of the time in areas where pelagic longlining activities are often highest, and in depth zones where these fisheries particularly target other species, which could account for the rapid declines recently reported for blue sharks in many parts of the world's oceans. Our results provide habitat targets for blue shark conservation

Mass Media Strategies Targeting High Sensation Seekers: What Works and Why

ERIC Educational Resources Information Center

Stephenson, Michael T.

2003-01-01

Objectives: To examine strategies for using the mass media effectively in drug prevention campaigns targeting high sensation seekers. Methods: Both experimental lab and field studies were used to develop a comprehensive audience segmentation strategy targeting high sensation seekers. Results: A 4-pronged targeting strategy employed in an…

High order filtering methods for approximating hyperbolic systems of conservation laws

NASA Technical Reports Server (NTRS)

Lafon, F.; Osher, S.

1991-01-01

The essentially nonoscillatory (ENO) schemes, while potentially useful in the computation of discontinuous solutions of hyperbolic conservation-law systems, are computationally costly relative to simple central-difference methods. A filtering technique is presented which employs central differencing of arbitrarily high-order accuracy except where a local test detects the presence of spurious oscillations and calls upon the full ENO apparatus to remove them. A factor-of-three speedup is thus obtained over the full-ENO method for a wide range of problems, with high-order accuracy in regions of smooth flow.

High-power liquid-lithium jet target for neutron production

DOE Office of Scientific and Technical Information (OSTI.GOV)

Halfon, S.; Feinberg, G.; Racah Institute of Physics, Hebrew University, Jerusalem 91904

2013-12-15

A compact liquid-lithium target (LiLiT) was built and tested with a high-power electron gun at the Soreq Nuclear Research Center. The lithium target, to be bombarded by the high-intensity proton beam of the Soreq Applied Research Accelerator Facility (SARAF), will constitute an intense source of neutrons produced by the {sup 7}Li(p,n){sup 7}Be reaction for nuclear astrophysics research and as a pilot setup for accelerator-based Boron Neutron Capture Therapy. The liquid-lithium jet target acts both as neutron-producing target and beam dump by removing the beam thermal power (>5 kW, >1 MW/cm{sup 3}) with fast transport. The target was designed based onmore » a thermal model, accompanied by a detailed calculation of the {sup 7}Li(p,n) neutron yield, energy distribution, and angular distribution. Liquid lithium is circulated through the target loop at ∼200 °C and generates a stable 1.5 mm-thick film flowing at a velocity up to 7 m/s onto a concave supporting wall. Electron beam irradiation demonstrated that the liquid-lithium target can dissipate electron power areal densities of >4 kW/cm{sup 2} and volume power density of ∼2 MW/cm{sup 3} at a lithium flow of ∼4 m/s while maintaining stable temperature and vacuum conditions. The LiLiT setup is presently in online commissioning stage for high-intensity proton beam irradiation (1.91–2.5 MeV, 1–2 mA) at SARAF.« less

Essentiality, conservation, evolutionary pressure and codon bias in bacterial genomes.

PubMed

Dilucca, Maddalena; Cimini, Giulio; Giansanti, Andrea

2018-07-15

Essential genes constitute the core of genes which cannot be mutated too much nor lost along the evolutionary history of a species. Natural selection is expected to be stricter on essential genes and on conserved (highly shared) genes, than on genes that are either nonessential or peculiar to a single or a few species. In order to further assess this expectation, we study here how essentiality of a gene is connected with its degree of conservation among several unrelated bacterial species, each one characterised by its own codon usage bias. Confirming previous results on E. coli, we show the existence of a universal exponential relation between gene essentiality and conservation in bacteria. Moreover, we show that, within each bacterial genome, there are at least two groups of functionally distinct genes, characterised by different levels of conservation and codon bias: i) a core of essential genes, mainly related to cellular information processing; ii) a set of less conserved nonessential genes with prevalent functions related to metabolism. In particular, the genes in the first group are more retained among species, are subject to a stronger purifying conservative selection and display a more limited repertoire of synonymous codons. The core of essential genes is close to the minimal bacterial genome, which is in the focus of recent studies in synthetic biology, though we confirm that orthologs of genes that are essential in one species are not necessarily essential in other species. We also list a set of highly shared genes which, reasonably, could constitute a reservoir of targets for new anti-microbial drugs. Copyright © 2018 Elsevier B.V. All rights reserved.

Large-scale conservation planning in a multinational marine environment: cost matters.

PubMed

Mazor, Tessa; Giakoumi, Sylvaine; Kark, Salit; Possingham, Hugh P

2014-07-01

Explicitly including cost in marine conservation planning is essential for achieving feasible and efficient conservation outcomes. Yet, spatial priorities for marine conservation are still often based solely on biodiversity hotspots, species richness, and/or cumulative threat maps. This study aims to provide an approach for including cost when planning large-scale Marine Protected Area (MPA) networks that span multiple countries. Here, we explore the incorporation of cost in the complex setting of the Mediterranean Sea. In order to include cost in conservation prioritization, we developed surrogates that account for revenue from multiple marine sectors: commercial fishing, noncommercial fishing, and aquaculture. Such revenue can translate into an opportunity cost for the implementation of an MPA network. Using the software Marxan, we set conservation targets to protect 10% of the distribution of 77 threatened marine species in the Mediterranean Sea. We compared nine scenarios of opportunity cost by calculating the area and cost required to meet our targets. We further compared our spatial priorities with those that are considered consensus areas by several proposed prioritization schemes in the Mediterranean Sea, none of which explicitly considers cost. We found that for less than 10% of the Sea's area, our conservation targets can be achieved while incurring opportunity costs of less than 1%. In marine systems, we reveal that area is a poor cost surrogate and that the most effective surrogates are those that account for multiple sectors or stakeholders. Furthermore, our results indicate that including cost can greatly influence the selection of spatial priorities for marine conservation of threatened species. Although there are known limitations in multinational large-scale planning, attempting to devise more systematic and rigorous planning methods is especially critical given that collaborative conservation action is on the rise and global financial crisis

Effects of management tactics on meeting conservation objectives for Western North American groundfish fisheries.

PubMed

Melnychuk, Michael C; Banobi, Jeannette A; Hilborn, Ray

2013-01-01

There is considerable variability in the status of fish populations around the world and a poor understanding of how specific management characteristics affect populations. Overfishing is a major problem in many fisheries, but in some regions the recent tendency has been to exploit stocks at levels below their maximum sustainable yield. In Western North American groundfish fisheries, the status of individual stocks and management systems among regions are highly variable. In this paper, we show the current status of groundfish stocks from Alaska, British Columbia, and the U.S. West Coast, and quantify the influence on stock status of six management tactics often hypothesized to affect groundfish. These tactics are: the use of harvest control rules with estimated biological reference points; seasonal closures; marine reserves; bycatch constraints; individual quotas (i.e., 'catch shares'); and gear type. Despite the high commercial value of many groundfish and consequent incentives for maintaining stocks at their most productive levels, most stocks were managed extremely conservatively, with current exploitation rates at only 40% of management targets and biomass 33% above target biomass on average. Catches rarely exceeded TACs but on occasion were far below TACs (mean catch:TAC ratio of 57%); approximately $150 million of potential landed value was foregone annually by underutilizing TACs. The use of individual quotas, marine reserves, and harvest control rules with estimated limit reference points had little overall effect on stock status. More valuable fisheries were maintained closer to management targets and were less variable over time than stocks with lower catches or ex-vessel prices. Together these results suggest there is no single effective management measure for meeting conservation objectives; if scientifically established quotas are set and enforced, a variety of means can be used to ensure that exploitation rates and biomass levels are near to or more

Increasing the Structural Coverage of Tuberculosis Drug Targets

PubMed Central

Baugh, Loren; Phan, Isabelle; Begley, Darren W.; Clifton, Matthew C.; Armour, Brianna; Dranow, David M.; Taylor, Brandy M.; Muruthi, Marvin M.; Abendroth, Jan; Fairman, James W.; Fox, David; Dieterich, Shellie H.; Staker, Bart L.; Gardberg, Anna S.; Choi, Ryan; Hewitt, Stephen N.; Napuli, Alberto J.; Myers, Janette; Barrett, Lynn K.; Zhang, Yang; Ferrell, Micah; Mundt, Elizabeth; Thompkins, Katie; Tran, Ngoc; Lyons-Abbott, Sally; Abramov, Ariel; Sekar, Aarthi; Serbzhinskiy, Dmitri; Lorimer, Don; Buchko, Garry W.; Stacy, Robin; Stewart, Lance J.; Edwards, Thomas E.; Van Voorhis, Wesley C.; Myler, Peter J.

2015-01-01

High-resolution three-dimensional structures of essential Mycobacterium tuberculosis (Mtb) proteins provide templates for TB drug design, but are available for only a small fraction of the Mtb proteome. Here we evaluate an intra-genus “homolog-rescue” strategy to increase the structural information available for TB drug discovery by using mycobacterial homologs with conserved active sites. Of 179 potential TB drug targets selected for x-ray structure determination, only 16 yielded a crystal structure. By adding 1675 homologs from nine other mycobacterial species to the pipeline, structures representing an additional 52 otherwise intractable targets were solved. To determine whether these homolog structures would be useful surrogates in TB drug design, we compared the active sites of 106 pairs of Mtb and non-TB mycobacterial (NTM) enzyme homologs with experimentally determined structures, using three metrics of active site similarity, including superposition of continuous pharmacophoric property distributions. Pair-wise structural comparisons revealed that 19/22 pairs with >55% overall sequence identity had active site Cα RMSD <1Å, >85% side chain identity, and ≥80% PSAPF (similarity based on pharmacophoric properties) indicating highly conserved active site shape and chemistry. Applying these results to the 52 NTM structures described above, 41 shared >55% sequence identity with the Mtb target, thus increasing the effective structural coverage of the 179 Mtb targets over three-fold (from 9% to 32%). The utility of these structures in TB drug design can be tested by designing inhibitors using the homolog structure and assaying the cognate Mtb enzyme; a promising test case, Mtb cytidylate kinase, is described. The homolog-rescue strategy evaluated here for TB is also generalizable to drug targets for other diseases. PMID:25613812

Pirating conserved phage mechanisms promotes promiscuous staphylococcal pathogenicity island transfer.

PubMed

Bowring, Janine; Neamah, Maan M; Donderis, Jorge; Mir-Sanchis, Ignacio; Alite, Christian; Ciges-Tomas, J Rafael; Maiques, Elisa; Medmedov, Iltyar; Marina, Alberto; Penadés, José R

2017-08-08

Targeting conserved and essential processes is a successful strategy to combat enemies. Remarkably, the clinically important Staphylococcus aureus pathogenicity islands (SaPIs) use this tactic to spread in nature. SaPIs reside passively in the host chromosome, under the control of the SaPI-encoded master repressor, Stl. It has been assumed that SaPI de-repression is effected by specific phage proteins that bind to Stl, initiating the SaPI cycle. Different SaPIs encode different Stl repressors, so each targets a specific phage protein for its de-repression. Broadening this narrow vision, we report here that SaPIs ensure their promiscuous transfer by targeting conserved phage mechanisms. This is accomplished because the SaPI Stl repressors have acquired different domains to interact with unrelated proteins, encoded by different phages, but in all cases performing the same conserved function. This elegant strategy allows intra- and inter-generic SaPI transfer, highlighting these elements as one of nature's most fascinating subcellular parasites.

High-efficiency-release targets for use at ISOL facilities: computational design

NASA Astrophysics Data System (ADS)

Liu, Y.; Alton, G. D.

1999-12-01

This report describes efforts made at the Oak Ridge National Laboratory to design high-efficiency-release targets that simultaneously incorporate the short diffusion lengths, high permeabilities, controllable temperatures, and heat-removal properties required for the generation of useful radioactive ion beam (RIB) intensities for nuclear physics and astrophysics research using the isotope separation on-line (ISOL) technique. Short diffusion lengths are achieved either by using thin fibrous target materials or by coating thin layers of selected target material onto low-density carbon fibers such as reticulated-vitreous-carbon fiber (RVCF) or carbon-bonded-carbon fiber (CBCF) to form highly permeable composite target matrices. Computational studies that simulate the generation and removal of primary beam deposited heat from target materials have been conducted to optimize the design of target/heat-sink systems for generating RIBs. The results derived from diffusion release-rate simulation studies for selected targets and thermal analyses of temperature distributions within a prototype target/heat-sink system subjected to primary ion beam irradiation are presented in this report.

Land market feedbacks can undermine biodiversity conservation

PubMed Central

Armsworth, Paul R.; Daily, Gretchen C.; Kareiva, Peter; Sanchirico, James N.

2006-01-01

The full or partial purchase of land has become a cornerstone of efforts to conserve biodiversity in countries with strong private property rights. Methods used to target areas for acquisition typically ignore land market dynamics. We show how conservation purchases affect land prices and generate feedbacks that can undermine conservation goals, either by displacing development toward biologically valuable areas or by accelerating its pace. The impact of these market feedbacks on the effectiveness of conservation depends on the ecological value of land outside nature reserves. Traditional, noneconomic approaches to site prioritization should perform adequately in places where land outside reserves supports little biodiversity. However, these approaches will perform poorly in locations where the countryside surrounding reserves is important for species’ persistence. Conservation investments can sometimes even be counterproductive, condemning more species than they save. Conservation is most likely to be compromised in the absence of accurate information on species distributions, which provides a strong argument for improving inventories of biodiversity. Accounting for land market dynamics in conservation planning is crucial for making smart investment decisions. PMID:16554375

Land market feedbacks can undermine biodiversity conservation.

PubMed

Armsworth, Paul R; Daily, Gretchen C; Kareiva, Peter; Sanchirico, James N

2006-04-04

The full or partial purchase of land has become a cornerstone of efforts to conserve biodiversity in countries with strong private property rights. Methods used to target areas for acquisition typically ignore land market dynamics. We show how conservation purchases affect land prices and generate feedbacks that can undermine conservation goals, either by displacing development toward biologically valuable areas or by accelerating its pace. The impact of these market feedbacks on the effectiveness of conservation depends on the ecological value of land outside nature reserves. Traditional, noneconomic approaches to site prioritization should perform adequately in places where land outside reserves supports little biodiversity. However, these approaches will perform poorly in locations where the countryside surrounding reserves is important for species' persistence. Conservation investments can sometimes even be counterproductive, condemning more species than they save. Conservation is most likely to be compromised in the absence of accurate information on species distributions, which provides a strong argument for improving inventories of biodiversity. Accounting for land market dynamics in conservation planning is crucial for making smart investment decisions.

Bacterial Transcription as a Target for Antibacterial Drug Development

PubMed Central

Ma, Cong; Yang, Xiao

2016-01-01

SUMMARY Transcription, the first step of gene expression, is carried out by the enzyme RNA polymerase (RNAP) and is regulated through interaction with a series of protein transcription factors. RNAP and its associated transcription factors are highly conserved across the bacterial domain and represent excellent targets for broad-spectrum antibacterial agent discovery. Despite the numerous antibiotics on the market, there are only two series currently approved that target transcription. The determination of the three-dimensional structures of RNAP and transcription complexes at high resolution over the last 15 years has led to renewed interest in targeting this essential process for antibiotic development by utilizing rational structure-based approaches. In this review, we describe the inhibition of the bacterial transcription process with respect to structural studies of RNAP, highlight recent progress toward the discovery of novel transcription inhibitors, and suggest additional potential antibacterial targets for rational drug design. PMID:26764017

Parallel Reaction Monitoring: A Targeted Experiment Performed Using High Resolution and High Mass Accuracy Mass Spectrometry

PubMed Central

Rauniyar, Navin

2015-01-01

The parallel reaction monitoring (PRM) assay has emerged as an alternative method of targeted quantification. The PRM assay is performed in a high resolution and high mass accuracy mode on a mass spectrometer. This review presents the features that make PRM a highly specific and selective method for targeted quantification using quadrupole-Orbitrap hybrid instruments. In addition, this review discusses the label-based and label-free methods of quantification that can be performed with the targeted approach. PMID:26633379

Determinants of bird conservation-action implementation and associated population trends of threatened species.

PubMed

Luther, David A; Brooks, Thomas M; Butchart, Stuart H M; Hayward, Matt W; Kester, Marieke E; Lamoreux, John; Upgren, Amy

2016-12-01

Conservation actions, such as habitat protection, attempt to halt the loss of threatened species and help their populations recover. The efficiency and the effectiveness of actions have been examined individually. However, conservation actions generally occur simultaneously, so the full suite of implemented conservation actions should be assessed. We used the conservation actions underway for all threatened and near-threatened birds of the world (International Union for Conservation of Nature Red List of Threatened Species) to assess which biological (related to taxonomy and ecology) and anthropogenic (related to geoeconomics) factors were associated with the implementation of different classes of conservation actions. We also assessed which conservation actions were associated with population increases in the species targeted. Extinction-risk category was the strongest single predictor of the type of conservation actions implemented, followed by landmass type (continent, oceanic island, etc.) and generation length. Species targeted by invasive nonnative species control or eradication programs, ex situ conservation, international legislation, reintroduction, or education, and awareness-raising activities were more likely to have increasing populations. These results illustrate the importance of developing a predictive science of conservation actions and the relative benefits of each class of implemented conservation action for threatened and near-threatened birds worldwide. © 2016 Society for Conservation Biology.

Aquaculture expansion in Brazilian freshwaters against the Aichi Biodiversity Targets.

PubMed

Lima Junior, Dilermando Pereira; Magalhães, André Lincoln Barroso; Pelicice, Fernando Mayer; Vitule, Jean Ricardo Simões; Azevedo-Santos, Valter M; Orsi, Mário Luís; Simberloff, Daniel; Agostinho, Angelo Antônio

2018-05-01

The Convention on Biological Diversity proposed the Aichi Biodiversity Targets to improve conservation policies and to balance economic development, social welfare, and the maintenance of biodiversity/ecosystem services. Brazil is a signatory of the Aichi Biodiversity Targets and is the most diverse country in terms of freshwater fish, but its national policies have supported the development of unsustainable commercial and ornamental aquaculture, which has led to serious disturbances to inland ecosystems and natural resources. We analyzed the development of Brazilian aquaculture to show how current aquaculture expansion conflicts with all 20 Aichi Targets. This case suggests that Brazil and many other megadiverse developing countries will not meet international conservation targets, stressing the need for new strategies, such as the environmental management system, to improve biodiversity conservation.

A novel program to design siRNAs simultaneously effective to highly variable virus genomes.

PubMed

Lee, Hui Sun; Ahn, Jeonghyun; Jun, Eun Jung; Yang, Sanghwa; Joo, Chul Hyun; Kim, Yoo Kyum; Lee, Heuiran

2009-07-10

A major concern of antiviral therapy using small interfering RNAs (siRNAs) targeting RNA viral genome is high sequence diversity and mutation rate due to genetic instability. To overcome this problem, it is indispensable to design siRNAs targeting highly conserved regions. We thus designed CAPSID (Convenient Application Program for siRNA Design), a novel bioinformatics program to identify siRNAs targeting highly conserved regions within RNA viral genomes. From a set of input RNAs of diverse sequences, CAPSID rapidly searches conserved patterns and suggests highly potent siRNA candidates in a hierarchical manner. To validate the usefulness of this novel program, we investigated the antiviral potency of universal siRNA for various Human enterovirus B (HEB) serotypes. Assessment of antiviral efficacy using Hela cells, clearly demonstrates that HEB-specific siRNAs exhibit protective effects against all HEBs examined. These findings strongly indicate that CAPSID can be applied to select universal antiviral siRNAs against highly divergent viral genomes.

Spatial relationship between climatic diversity and biodiversity conservation value.

PubMed

Wang, Junjun; Wu, Ruidong; He, Daming; Yang, Feiling; Hu, Peijun; Lin, Shiwei; Wu, Wei; Diao, Yixin; Guo, Yang

2018-06-04

Capturing the full range of climatic diversity in a reserve network is expected to improve the resilience of biodiversity to climate change. Therefore, a study on systematic conservation planning for climatic diversity that explicitly or implicitly hypothesizes that regions with higher climatic diversity will support greater biodiversity is needed. However, little is known about the extent and generality of this hypothesis. This study utilized the case of Yunnan, southwest China, to quantitatively classify climatic units and modeled 4 climatic diversity indicators, including the variety of climatic units (VCU), rarity of climatic units (RCU), endemism of climatic units (ECU) and a composite index of climatic units (CICD). We used 5 reliable priority conservation area (PCA) schemes to represent the areas with high biodiversity conservation value. We then investigated the spatial relationships between the 4 climatic diversity indicators and the 5 PCA schemes and assessed the representation of climatic diversity within the existing nature reserves. The CICD exhibited the best performance for indicating high conservation value areas, followed by the ECU and RCU. However, contrary to conventional knowledge, VCU did not show a positive association with biodiversity conservation value. The rarer or more endemic climatic units tended to have higher reserve coverage than the more common units. However, only 28 units covering 10.5% of the land in Yunnan had more than 17% of their areas protected. In addition to climatic factors, topography and human disturbances also significantly affected the relationship between climatic diversity and biodiversity conservation value. This analysis suggests that climatic diversity can be an effective surrogate for establishing a more robust reserve network under climate change in Yunnan. Our study improves the understanding of the relationship between climatic diversity and biodiversity and helps build an evidence-based foundation for

Spatial analysis of ecosystem service relationships to improve targeting of payments for hydrological services

PubMed Central

Manson, Robert H.; Ricketts, Taylor H.; Geissert, Daniel

2018-01-01

Payment for hydrological services (PHS) are popular tools for conserving ecosystems and their water-related services. However, improving the spatial targeting and impacts of PHS, as well as their ability to foster synergies with other ecosystem services (ES), remain challenging. We aimed at using spatial analyses to evaluate the targeting performance of México’s National PHS program in central Veracruz. We quantified the effectiveness of areas targeted for PHS in actually covering areas of high HS provision and social priority during 2003–2013. First, we quantified provisioning and spatial distributions of two target (water yield and soil retention), and one non-target ES (carbon storage) using InVEST. Subsequently, pairwise relationships among ES were quantified by using spatial correlation and overlap analyses. Finally, we evaluated targeting by: (i) prioritizing areas of individual and overlapping ES; (ii) quantifying spatial co-occurrences of these priority areas with those targeted by PHS; (iii) evaluating the extent to which PHS directly contribute to HS delivery; and (iv), testing if PHS targeted areas disproportionately covered areas with high ecological and social priority. We found that modelled priority areas exhibited non-random distributions and distinct spatial patterns. Our results show significant pairwise correlations between all ES suggesting synergistic relationships. However, our analysis showed a significantly lower overlap than expected and thus significant mismatches between PHS targeted areas and all types of priority areas. These findings suggest that the targeting of areas with high HS provisioning and social priority by Mexico’s PHS program could be improved significantly. This study underscores: (1) the importance of using maps of HS provisioning as main targeting criteria in PHS design to channel payments towards areas that require future conservation, and (2) the need for future research that helps balance ecological and

INTEGRATING REPRESENTATION AND VULNERABILITY: TWO APPROACHES FOR PRIORITIZING AREAS FOR CONSERVATION

EPA Science Inventory

One fundamental step in conservation planning involves determining where to concentrate efforts to protect conservation targets. Here we demonstrate two approaches to prioritizing areas based on both species composition and potential threats facing the species. The first approa...

Crystal Structure and Size-Dependent Neutralization Properties of HK20, a Human Monoclonal Antibody Binding to the Highly Conserved Heptad Repeat 1 of gp41

PubMed Central

Seaman, Mike S.; Lutje Hulsik, David; Hinz, Andreas; Vanzetta, Fabrizia; Agatic, Gloria; Silacci, Chiara; Mainetti, Lara; Scarlatti, Gabriella; Sallusto, Federica; Weiss, Robin; Lanzavecchia, Antonio; Weissenhorn, Winfried

2010-01-01

The human monoclonal antibody (mAb) HK20 neutralizes a broad spectrum of primary HIV-1 isolates by targeting the highly conserved heptad repeat 1 (HR1) of gp41, which is transiently exposed during HIV-1 entry. Here we present the crystal structure of the HK20 Fab in complex with a gp41 mimetic 5-Helix at 2.3 Å resolution. HK20 employs its heavy chain CDR H2 and H3 loops to bind into a conserved hydrophobic HR1 pocket that is occupied by HR2 residues in the gp41 post fusion conformation. Compared to the previously described HR1-specific mAb D5, HK20 approaches its epitope with a different angle which might favor epitope access and thus contribute to its higher neutralization breadth and potency. Comparison of the neutralization activities of HK20 IgG, Fab and scFv employing both single cycle and multiple cycle neutralization assays revealed much higher potencies for the smaller Fab and scFv over IgG, implying that the target site is difficult to access for complete antibodies. Nevertheless, two thirds of sera from HIV-1 infected individuals contain significant titers of HK20-inhibiting antibodies. The breadth of neutralization of primary isolates across all clades, the higher potencies for C-clade viruses and the targeting of a distinct site as compared to the fusion inhibitor T-20 demonstrate the potential of HK20 scFv as a therapeutic tool. PMID:21124990

Conservation planning under uncertainty in urban development and vegetation dynamics

PubMed Central

Carmel, Yohay

2018-01-01

Systematic conservation planning is a framework for optimally locating and prioritizing areas for conservation. An often-noted shortcoming of most conservation planning studies is that they do not address future uncertainty. The selection of protected areas that are intended to ensure the long-term persistence of biodiversity is often based on a snapshot of the current situation, ignoring processes such as climate change. Scenarios, in the sense of being accounts of plausible futures, can be utilized to identify conservation area portfolios that are robust to future uncertainty. We compared three approaches for utilizing scenarios in conservation area selection: considering a full set of scenarios (all-scenarios portfolio), assuming the realization of specific scenarios, and a reference strategy based on the current situation (current distributions portfolio). Our objective was to compare the robustness of these approaches in terms of their relative performance across future scenarios. We focused on breeding bird species in Israel’s Mediterranean region. We simulated urban development and vegetation dynamics scenarios 60 years into the future using DINAMICA-EGO, a cellular-automata simulation model. For each scenario, we mapped the target species’ available habitat distribution, identified conservation priority areas using the site-selection software MARXAN, and constructed conservation area portfolios using the three aforementioned strategies. We then assessed portfolio performance based on the number of species for which representation targets were met in each scenario. The all-scenarios portfolio consistently outperformed the other portfolios, and was more robust to ‘errors’ (e.g., when an assumed specific scenario did not occur). On average, the all-scenarios portfolio achieved representation targets for five additional species compared with the current distributions portfolio (approximately 33 versus 28 species). Our findings highlight the importance

Conservation planning under uncertainty in urban development and vegetation dynamics.

PubMed

Troupin, David; Carmel, Yohay

2018-01-01

Systematic conservation planning is a framework for optimally locating and prioritizing areas for conservation. An often-noted shortcoming of most conservation planning studies is that they do not address future uncertainty. The selection of protected areas that are intended to ensure the long-term persistence of biodiversity is often based on a snapshot of the current situation, ignoring processes such as climate change. Scenarios, in the sense of being accounts of plausible futures, can be utilized to identify conservation area portfolios that are robust to future uncertainty. We compared three approaches for utilizing scenarios in conservation area selection: considering a full set of scenarios (all-scenarios portfolio), assuming the realization of specific scenarios, and a reference strategy based on the current situation (current distributions portfolio). Our objective was to compare the robustness of these approaches in terms of their relative performance across future scenarios. We focused on breeding bird species in Israel's Mediterranean region. We simulated urban development and vegetation dynamics scenarios 60 years into the future using DINAMICA-EGO, a cellular-automata simulation model. For each scenario, we mapped the target species' available habitat distribution, identified conservation priority areas using the site-selection software MARXAN, and constructed conservation area portfolios using the three aforementioned strategies. We then assessed portfolio performance based on the number of species for which representation targets were met in each scenario. The all-scenarios portfolio consistently outperformed the other portfolios, and was more robust to 'errors' (e.g., when an assumed specific scenario did not occur). On average, the all-scenarios portfolio achieved representation targets for five additional species compared with the current distributions portfolio (approximately 33 versus 28 species). Our findings highlight the importance of

Targeted ENO schemes with tailored resolution property for hyperbolic conservation laws

NASA Astrophysics Data System (ADS)

Fu, Lin; Hu, Xiangyu Y.; Adams, Nikolaus A.

2017-11-01

In this paper, we extend the range of targeted ENO (TENO) schemes (Fu et al. (2016) [18]) by proposing an eighth-order TENO8 scheme. A general formulation to construct the high-order undivided difference τK within the weighting strategy is proposed. With the underlying scale-separation strategy, sixth-order accuracy for τK in the smooth solution regions is designed for good performance and robustness. Furthermore, a unified framework to optimize independently the dispersion and dissipation properties of high-order finite-difference schemes is proposed. The new framework enables tailoring of dispersion and dissipation as function of wavenumber. The optimal linear scheme has minimum dispersion error and a dissipation error that satisfies a dispersion-dissipation relation. Employing the optimal linear scheme, a sixth-order TENO8-opt scheme is constructed. A set of benchmark cases involving strong discontinuities and broadband fluctuations is computed to demonstrate the high-resolution properties of the new schemes.

A High-Order Finite Spectral Volume Method for Conservation Laws on Unstructured Grids

NASA Technical Reports Server (NTRS)

Wang, Z. J.; Liu, Yen; Kwak, Dochan (Technical Monitor)

2001-01-01

A time accurate, high-order, conservative, yet efficient method named Finite Spectral Volume (FSV) is developed for conservation laws on unstructured grids. The concept of a 'spectral volume' is introduced to achieve high-order accuracy in an efficient manner similar to spectral element and multi-domain spectral methods. In addition, each spectral volume is further sub-divided into control volumes (CVs), and cell-averaged data from these control volumes is used to reconstruct a high-order approximation in the spectral volume. Riemann solvers are used to compute the fluxes at spectral volume boundaries. Then cell-averaged state variables in the control volumes are updated independently. Furthermore, TVD (Total Variation Diminishing) and TVB (Total Variation Bounded) limiters are introduced in the FSV method to remove/reduce spurious oscillations near discontinuities. A very desirable feature of the FSV method is that the reconstruction is carried out only once, and analytically, and is the same for all cells of the same type, and that the reconstruction stencil is always non-singular, in contrast to the memory and CPU-intensive reconstruction in a high-order finite volume (FV) method. Discussions are made concerning why the FSV method is significantly more efficient than high-order finite volume and the Discontinuous Galerkin (DG) methods. Fundamental properties of the FSV method are studied and high-order accuracy is demonstrated for several model problems with and without discontinuities.

Large scale RNAi screen in Tribolium reveals novel target genes for pest control and the proteasome as prime target.

PubMed

Ulrich, Julia; Dao, Van Anh; Majumdar, Upalparna; Schmitt-Engel, Christian; Schwirz, Jonas; Schultheis, Dorothea; Ströhlein, Nadi; Troelenberg, Nicole; Grossmann, Daniela; Richter, Tobias; Dönitz, Jürgen; Gerischer, Lizzy; Leboulle, Gérard; Vilcinskas, Andreas; Stanke, Mario; Bucher, Gregor

2015-09-03

Insect pest control is challenged by insecticide resistance and negative impact on ecology and health. One promising pest specific alternative is the generation of transgenic plants, which express double stranded RNAs targeting essential genes of a pest species. Upon feeding, the dsRNA induces gene silencing in the pest resulting in its death. However, the identification of efficient RNAi target genes remains a major challenge as genomic tools and breeding capacity is limited in most pest insects impeding whole-animal-high-throughput-screening. We use the red flour beetle Tribolium castaneum as a screening platform in order to identify the most efficient RNAi target genes. From about 5,000 randomly screened genes of the iBeetle RNAi screen we identify 11 novel and highly efficient RNAi targets. Our data allowed us to determine GO term combinations that are predictive for efficient RNAi target genes with proteasomal genes being most predictive. Finally, we show that RNAi target genes do not appear to act synergistically and that protein sequence conservation does not correlate with the number of potential off target sites. Our results will aid the identification of RNAi target genes in many pest species by providing a manageable number of excellent candidate genes to be tested and the proteasome as prime target. Further, the identified GO term combinations will help to identify efficient target genes from organ specific transcriptomes. Our off target analysis is relevant for the sequence selection used in transgenic plants.

Macroeconomic policy, growth, and biodiversity conservation.

PubMed

Lawn, Philip

2008-12-01

To successfully achieve biodiversity conservation, the amount of ecosystem structure available for economic production must be determined by, and subject to, conservation needs. As such, the scale of economic systems must remain within the limits imposed by the need to preserve critical ecosystems and the regenerative and waste assimilative capacities of the ecosphere. These limits are determined by biophysical criteria, yet macroeconomics involves the use of economic instruments designed to meet economic criteria that have no capacity to achieve biophysically based targets. Macroeconomic policy cannot, therefore, directly solve the biodiversity erosion crisis. Nevertheless, good macroeconomic policy is still important given that bad macroeconomy policy is likely to reduce human well-being and increase the likelihood of social upheaval that could undermine conservation efforts.

77 FR 18963 - Energy Conservation Program: Public Meeting and Availability of the Framework Document for High...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-03-29

... the Framework Document for High-Intensity Discharge Lamps AGENCY: Office of Energy Efficiency and... availability of framework document for high-intensity discharge (HID) lamps, initiating the rulemaking and data... Availability of Framework Document Regarding Energy Conservation Standards for High-Intensity Discharge (HID...

Success and Design of Local Referenda for Land Conservation

ERIC Educational Resources Information Center

Banzhaf, H. Spencer; Oates, Wallace E.; Sanchirico, James N.

2010-01-01

From 1998 to 2006, over three-quarters of the more than 1,550 U.S. referenda targeting open space passed. We analyze the success of the conservation movement at holding referenda in areas with greater ecological value and greater likelihood of supporting conservation. To do so, we first analyze the patterns in where referenda are held and in which…

A comparison of global conservation prioritization models with spatial spending patterns of conservation nongovernmental organizations.

PubMed

Holmes, George; Scholfield, Katherine; Brockington, Dan

2012-08-01

In recent decades, various conservation organizations have developed models to prioritize locations for conservation. Through a survey of the spending patterns of 281 conservation nongovernmental organizations (NGOs), we examined the relation between 2 such models and spatial patterns of spending by conservation NGOs in 44 countries in sub-Saharan Africa. We tested whether, at the country level, the proportion of a country designated as a conservation priority was correlated with where NGOs spent money. For one model (the combination of Conservation International's hotspots and High Biodiversity Wilderness Areas, which are areas of high endemism with high or low levels of vegetation loss respectively), there was no relation between the proportion of a country designated as a priority and levels of NGO spending, including by the NGO associated with the model. In the second model (Global 200), the proportion of a country designated as a priority and the amount of money spent by NGOs were significantly and positively related. Less money was spent in countries in northern and western sub-Saharan Africa than countries in southern and eastern Africa, relative to the proportion of the country designated as a conservation priority. We suggest that on the basis of our results some NGOs consider increasing their spending on the areas designated as of conservation priority which are currently relatively underfunded, although there are economic, political, cultural, historical, biological, and practical reasons why current spending patterns may not align with priority sites. ©2012 Society for Conservation Biology.

The context and development of a global framework for plant conservation.

PubMed

Jackson, Peter Wyse; Sharrock, Suzanne

2011-01-01

A new international initiative for plant conservation was first called for as a resolution of the International Botanical Congress in 1999. The natural home for such an initiative was considered to be the Convention on Biological Diversity (CBD), and the Conference of the Parties (COP) to the CBD agreed to consider a Global Strategy for Plant Conservation (GSPC) at its 5th meeting in 2000. It was proposed that the GSPC could provide an innovative model approach for target setting within the CBD and, prior to COP5, a series of inter-sessional papers on proposed targets and their justification were developed by plant conservation experts. Key factors that ensured the adoption of the GSPC by the CBD in 2002 included: (1) ensuring that prior to and during COP5, key Parties in each region were supportive of the Strategy; (2) setting targets at the global level and not attempting to impose these nationally; and (3) the offer by Botanic Gardens Conservation International (BGCI) to support a GSPC position in the CBD Secretariat for 3 years, which provided a clear indication of the support for the GSPC from non-governmental organizations (NGO).

Elevated levels of Era GTPase improve growth, 16S rRNA processing, and 70S ribosome assembly of Escherichia coli lacking highly conserved multifunctional YbeY endoribonuclease.

PubMed

Ghosal, Anubrata; Babu, Vignesh M P; Walker, Graham C

2018-06-18

YbeY is a highly conserved, multifunctional endoribonuclease that plays a significant role in ribosome biogenesis and has several additional roles. Here, we show in Escherichia coli that overexpressing the conserved GTPase, Era, partially suppresses the growth defect of a ΔybeY strain while improving 16S rRNA processing and 70S ribosome assembly. This suppression requires both Era's ability to hydrolyze GTP and the function of three exoribonucleases, RNase II, RNase R and RNase PH, suggesting a model for Era's action. Overexpressing Vibrio cholerae Era similarly partially suppresses the defects of an E. coli ΔybeY strain indicating this property of Era is conserved in bacteria other than E. coli Importance This work provides additional insights into the critical, but still incompletely understood, mechanism of the processing of the E. coli 16S rRNA 3'-terminus. The highly conserved GTPase, Era, is known to bind to the precursor of the 16S rRNA near its 3-end. Both the endoribonuclease YbeY, which binds to Era, and four exoribonucleases have been implicated in this 3'-end processing. Results reported here offer additional insights into the role of Era in 16S rRNA 3'-maturation and into the relationship between the action of the endoribonuclease YbeY and the four exoribonucleases. This study also hints at why YbeY is only essential in some bacteria and suggests that the YbeY could be a target for a new class of antibiotic in these bacteria. Copyright © 2018 American Society for Microbiology.

Crowdfunding biodiversity conservation.

PubMed

Gallo-Cajiao, E; Archibald, C; Friedman, R; Steven, R; Fuller, R A; Game, E T; Morrison, T H; Ritchie, E G

2018-05-26

Raising funds is critical for conserving biodiversity and hence so too is scrutinizing emerging financial mechanisms that might help achieve this goal. In this context, anecdotal evidence indicates crowdfunding is being used to support a variety of activities needed for biodiversity conservation, yet its magnitude and allocation remain largely unknown. We conducted a global analysis to help address this knowledge gap, based on empirical data from conservation-focused projects extracted from crowdfunding platforms. For each project, we determined the funds raised, date, country of implementation, proponent characteristics, activity type, biodiversity realm, and target taxa. We identified 72 relevant platforms and 577 conservation-focused projects that have raised US$4 790 634 since 2009. Whilst proponents were based in 38 countries, projects were delivered across 80 countries, indicating a potential mechanism of resource mobilization. Proponents were from non-governmental organizations (35%), universities (30%), or were freelancers (26%). Most projects were for research (40%), persuasion (31%), and on-ground actions (21%). Projects have focused primarily on species (57.7%) and terrestrial ecosystems (20.3%), and less on marine (8.8%) and freshwater ecosystems (3.6%). Projects have focused on 208 species, including a disproportionate number of threatened bird and mammal species. Crowdfunding for biodiversity conservation has now become a global phenomenon and presents signals for potential expansion, despite possible pitfalls. Opportunities arise from its spatial amplifying effect, steady increase over time, inclusion of Cinderella species, adoption by multiple actors, and funding of a range of activities beyond research. Our study paves the way for further research on key questions, such as campaign success rates, effectiveness, and drivers of adoption. Even though the capital input of crowdfunding so far has been modest compared to other conservation finance

How to Go Green: Creating a Conservation Culture in a Public High School through Education, Modeling, and Communication

ERIC Educational Resources Information Center

Schelly, Chelsea; Cross, Jennifer E.; Franzen, William; Hall, Pete; Reeve, Stu

2012-01-01

This case study examines how energy conservation efforts in one public high school contributed to both sustainability education and the adoption of sustainable behavior within educational and organizational practice. Individual role models, school facilities, school governance and school culture together support both conservation and environmental…

A case study of assigning conservation value to dispersed habitat units for conservation planning

USGS Publications Warehouse

Rohweder, Jason J.; Sara C. Vacek,; Crimmins, Shawn M.; Thogmartin, Wayne E.

2015-01-01

Resource managers are increasingly tasked with developing habitat conservation plans in the face of numerous, sometimes competing, objectives. These plans must often be implemented across dispersed habitat conservation units that may contribute unequally to overall conservation objectives. Using U.S. Fish and Wildlife Service waterfowl production areas (WPA) in western Minnesota as our conservation landscape, we develop a landscape-scale approach for evaluating the conservation value of dispersed habitat conservation units with multiple conservation priorities. We evaluated conservation value based on a suite of variables directly applicable to conservation management practices, thus providing a direct link between conservation actions and outcomes. We developed spatial models specific to each of these conservation objectives and also developed two freely available prioritization tools to implement these analyses. We found that some WPAs provided high conservation value across a range of conservation objectives, suggesting that managing these specific areas would achieve multiple conservation goals. Conversely, other WPAs provided low conservation value for some objectives, suggesting they would be most effectively managed for a distinct set of specific conservation goals. Approaches such as ours provide a direct means of assessing the conservation value of dispersed habitat conservation units and could be useful in the development of habitat management plans, particularly when faced with multiple conservation objectives.

Influence of FGD gypsum on the properties of a highly erodible soil under conservation tillage

USDA-ARS?s Scientific Manuscript database

The performance of conservation tillage practices imposed on highly erodible soils may be improved by the use of amendments with a high solubility rate, and whose dissolution products are translocated at depth in the soil profile faster than normally used agricultural lime and fertilizer products. T...

Increasing the structural coverage of tuberculosis drug targets.

PubMed

Baugh, Loren; Phan, Isabelle; Begley, Darren W; Clifton, Matthew C; Armour, Brianna; Dranow, David M; Taylor, Brandy M; Muruthi, Marvin M; Abendroth, Jan; Fairman, James W; Fox, David; Dieterich, Shellie H; Staker, Bart L; Gardberg, Anna S; Choi, Ryan; Hewitt, Stephen N; Napuli, Alberto J; Myers, Janette; Barrett, Lynn K; Zhang, Yang; Ferrell, Micah; Mundt, Elizabeth; Thompkins, Katie; Tran, Ngoc; Lyons-Abbott, Sally; Abramov, Ariel; Sekar, Aarthi; Serbzhinskiy, Dmitri; Lorimer, Don; Buchko, Garry W; Stacy, Robin; Stewart, Lance J; Edwards, Thomas E; Van Voorhis, Wesley C; Myler, Peter J

2015-03-01

High-resolution three-dimensional structures of essential Mycobacterium tuberculosis (Mtb) proteins provide templates for TB drug design, but are available for only a small fraction of the Mtb proteome. Here we evaluate an intra-genus "homolog-rescue" strategy to increase the structural information available for TB drug discovery by using mycobacterial homologs with conserved active sites. Of 179 potential TB drug targets selected for x-ray structure determination, only 16 yielded a crystal structure. By adding 1675 homologs from nine other mycobacterial species to the pipeline, structures representing an additional 52 otherwise intractable targets were solved. To determine whether these homolog structures would be useful surrogates in TB drug design, we compared the active sites of 106 pairs of Mtb and non-TB mycobacterial (NTM) enzyme homologs with experimentally determined structures, using three metrics of active site similarity, including superposition of continuous pharmacophoric property distributions. Pair-wise structural comparisons revealed that 19/22 pairs with >55% overall sequence identity had active site Cα RMSD <1 Å, >85% side chain identity, and ≥80% PSAPF (similarity based on pharmacophoric properties) indicating highly conserved active site shape and chemistry. Applying these results to the 52 NTM structures described above, 41 shared >55% sequence identity with the Mtb target, thus increasing the effective structural coverage of the 179 Mtb targets over three-fold (from 9% to 32%). The utility of these structures in TB drug design can be tested by designing inhibitors using the homolog structure and assaying the cognate Mtb enzyme; a promising test case, Mtb cytidylate kinase, is described. The homolog-rescue strategy evaluated here for TB is also generalizable to drug targets for other diseases. Copyright © 2014 Elsevier Ltd. All rights reserved.

Increasing the structural coverage of tuberculosis drug targets

DOE Office of Scientific and Technical Information (OSTI.GOV)

Baugh, Loren; Phan, Isabelle; Begley, Darren W.

High-resolution three-dimensional structures of essential Mycobacterium tuberculosis (Mtb) proteins provide templates for TB drug design, but are available for only a small fraction of the Mtb proteome. Here we evaluate an intra-genus “homolog-rescue” strategy to increase the structural information available for TB drug discovery by using mycobacterial homologs with conserved active sites. We found that of 179 potential TB drug targets selected for x-ray structure determination, only 16 yielded a crystal structure. By adding 1675 homologs from nine other mycobacterial species to the pipeline, structures representing an additional 52 otherwise intractable targets were solved. To determine whether these homolog structuresmore » would be useful surrogates in TB drug design, we compared the active sites of 106 pairs of Mtb and non-TB mycobacterial (NTM) enzyme homologs with experimentally determined structures, using three metrics of active site similarity, including superposition of continuous pharmacophoric property distributions. Pair-wise structural comparisons revealed that 19/22 pairs with >55% overall sequence identity had active site Cα RMSD <1 Å, >85% side chain identity, and ≥80% PS APF (similarity based on pharmacophoric properties) indicating highly conserved active site shape and chemistry. Applying these results to the 52 NTM structures described above, 41 shared >55% sequence identity with the Mtb target, thus increasing the effective structural coverage of the 179 Mtb targets over three-fold (from 9% to 32%). The utility of these structures in TB drug design can be tested by designing inhibitors using the homolog structure and assaying the cognate Mtb enzyme; a promising test case, Mtb cytidylate kinase, is described. The homolog-rescue strategy evaluated here for TB is also generalizable to drug targets for other diseases.« less

Increasing the structural coverage of tuberculosis drug targets

DOE PAGES

Baugh, Loren; Phan, Isabelle; Begley, Darren W.; ...

2014-12-19

High-resolution three-dimensional structures of essential Mycobacterium tuberculosis (Mtb) proteins provide templates for TB drug design, but are available for only a small fraction of the Mtb proteome. Here we evaluate an intra-genus “homolog-rescue” strategy to increase the structural information available for TB drug discovery by using mycobacterial homologs with conserved active sites. We found that of 179 potential TB drug targets selected for x-ray structure determination, only 16 yielded a crystal structure. By adding 1675 homologs from nine other mycobacterial species to the pipeline, structures representing an additional 52 otherwise intractable targets were solved. To determine whether these homolog structuresmore » would be useful surrogates in TB drug design, we compared the active sites of 106 pairs of Mtb and non-TB mycobacterial (NTM) enzyme homologs with experimentally determined structures, using three metrics of active site similarity, including superposition of continuous pharmacophoric property distributions. Pair-wise structural comparisons revealed that 19/22 pairs with >55% overall sequence identity had active site Cα RMSD <1 Å, >85% side chain identity, and ≥80% PS APF (similarity based on pharmacophoric properties) indicating highly conserved active site shape and chemistry. Applying these results to the 52 NTM structures described above, 41 shared >55% sequence identity with the Mtb target, thus increasing the effective structural coverage of the 179 Mtb targets over three-fold (from 9% to 32%). The utility of these structures in TB drug design can be tested by designing inhibitors using the homolog structure and assaying the cognate Mtb enzyme; a promising test case, Mtb cytidylate kinase, is described. The homolog-rescue strategy evaluated here for TB is also generalizable to drug targets for other diseases.« less

High-Speed Incoming Infrared Target Detection by Fusion of Spatial and Temporal Detectors

PubMed Central

Kim, Sungho

2015-01-01

This paper presents a method for detecting high-speed incoming targets by the fusion of spatial and temporal detectors to achieve a high detection rate for an active protection system (APS). The incoming targets have different image velocities according to the target-camera geometry. Therefore, single-target detector-based approaches, such as a 1D temporal filter, 2D spatial filter and 3D matched filter, cannot provide a high detection rate with moderate false alarms. The target speed variation was analyzed according to the incoming angle and target velocity. The speed of the distant target at the firing time is almost stationary and increases slowly. The speed varying targets are detected stably by fusing the spatial and temporal filters. The stationary target detector is activated by an almost zero temporal contrast filter (TCF) and identifies targets using a spatial filter called the modified mean subtraction filter (M-MSF). A small motion (sub-pixel velocity) target detector is activated by a small TCF value and finds targets using the same spatial filter. A large motion (pixel-velocity) target detector works when the TCF value is high. The final target detection is terminated by fusing the three detectors based on the threat priority. The experimental results of the various target sequences show that the proposed fusion-based target detector produces the highest detection rate with an acceptable false alarm rate. PMID:25815448

Cost-effective conservation of amphibian ecology and evolution

PubMed Central

Campos, Felipe S.; Lourenço-de-Moraes, Ricardo; Llorente, Gustavo A.; Solé, Mirco

2017-01-01

Habitat loss is the most important threat to species survival, and the efficient selection of priority areas is fundamental for good systematic conservation planning. Using amphibians as a conservation target, we designed an innovative assessment strategy, showing that prioritization models focused on functional, phylogenetic, and taxonomic diversity can include cost-effectiveness–based assessments of land values. We report new key conservation sites within the Brazilian Atlantic Forest hot spot, revealing a congruence of ecological and evolutionary patterns. We suggest payment for ecosystem services through environmental set-asides on private land, establishing potential trade-offs for ecological and evolutionary processes. Our findings introduce additional effective area-based conservation parameters that set new priorities for biodiversity assessment in the Atlantic Forest, validating the usefulness of a novel approach to cost-effectiveness–based assessments of conservation value for other species-rich regions. PMID:28691084

High order filtering methods for approximating hyberbolic systems of conservation laws

NASA Technical Reports Server (NTRS)

Lafon, F.; Osher, S.

1990-01-01

In the computation of discontinuous solutions of hyperbolic systems of conservation laws, the recently developed essentially non-oscillatory (ENO) schemes appear to be very useful. However, they are computationally costly compared to simple central difference methods. A filtering method which is developed uses simple central differencing of arbitrarily high order accuracy, except when a novel local test indicates the development of spurious oscillations. At these points, the full ENO apparatus is used, maintaining the high order of accuracy, but removing spurious oscillations. Numerical results indicate the success of the method. High order of accuracy was obtained in regions of smooth flow without spurious oscillations for a wide range of problems and a significant speed up of generally a factor of almost three over the full ENO method.

Fabrication High Resolution Metrology Target By Step And Repeat Method

NASA Astrophysics Data System (ADS)

Dusa, Mircea

1983-10-01

Based on the photolithography process generally used to generate high resolution masks for semiconductor I.C.S, we found a very useful industrial application of laser technology.First, we have generated high resolution metrology targets which are used in industrial measurement laser interferometers as difra.ction gratings. Secondi we have generated these targets using step and repeat machine, with He-Ne laser interferometer controlled state, as a pattern generator, due to suitable computer programming.Actually, high resolution metrology target, means two chromium plates, one of which is called the" rule" the other one the "vernier". In Fig.1 we have the configuration of the rule and the vernier. The rule has a succesion of 3 μM lines generated as a difraction grating on a 4 x 4 inch chromium blank. The vernier has several exposed fields( areas) having 3 - 15 μm lines, fields placed on very precise position on the chromium blank surface. High degree of uniformity, tight CD tolerances, low defect density required by the targets, creates specialised problems during processing. Details of the processing, together with experimental results will be presented. Before we start to enter into process details, we have to point out that the dimensional requirements of the reticle target, are quite similar or perhaps more strict than LSI master casks. These requirements presented in Fig.2.

Characterization of STIP, a multi-domain nuclear protein, highly conserved in metazoans, and essential for embryogenesis in Caenorhabditis elegans.

PubMed

Ji, Qiongmei; Huang, Cheng-Han; Peng, Jianbin; Hashmi, Sarwar; Ye, Tianzhang; Chen, Ying

2007-04-15

We report here the identification and characterization of STIP, a multi-domain nuclear protein that contains a G-patch, a coiled-coil, and several short tryptophan-tryptophan repeats highly conserved in metazoan species. To analyze their functional role in vivo, we cloned nematode stip-1 genes and determined the spatiotemporal pattern of Caenorhabditis elegans STIP-1 protein. RNA analyses and Western blots revealed that stip-1 mRNA was produced via trans-splicing and translated as a 95-kDa protein. Using reporter constructs, we found STIP-1 to be expressed at all developmental stages and in many tissue/cell types including worm oocyte nuclei. We found that STIP-1 is targeted to the nucleus and forms large polymers with a rod-like shape when expressed in mammalian cells. Using deletion mutants, we mapped the regions of STIP-1 involved in nuclear import and polymer assembly. We further showed that knockdown of C. elegans stip-1 by RNA interference arrested development and resulted in morphologic abnormalities around the 16-cell stage followed by 100% lethality, suggesting its essential role in worm embryogenesis. Importantly, the embryonic lethal phenotype could be faithfully rescued with Drosophila and human genes via transgenic expression. Our data provide the first direct evidence that STIP have a conserved essential nuclear function across metazoans from worms to humans.

Regulation of ciliary motility: conserved protein kinases and phosphatases are targeted and anchored in the ciliary axoneme

PubMed Central

Wirschell, Maureen; Yamamoto, Ryosuke; Alford, Lea; Gokhale, Avanti; Gaillard, Anne; Sale, Winfield S.

2011-01-01

Recent evidence has revealed that the dynein motors and highly conserved signaling proteins are localized within the ciliary 9 + 2 axoneme. One key mechanism for regulation of motility is phosphorylation. Here, we review diverse evidence, from multiple experimental organisms, that ciliary motility is regulated by phosphorylation / dephosphorylation of the dynein arms through kinases and phosphatases that are anchored immediately adjacent to their axonemal substrates. PMID:21513695

Balancing forest-regeneration probabilities and maintenance costs in dry grasslands of high conservation priority

USGS Publications Warehouse

Bolliger, Janine; Edwards, Thomas C.; Eggenberg, Stefan; Ismail, Sascha; Seidl, Irmi; Kienast, Felix

2011-01-01

Abandonment of agricultural land has resulted in forest regeneration in species-rich dry grasslands across European mountain regions and threatens conservation efforts in this vegetation type. To support national conservation strategies, we used a site-selection algorithm (MARXAN) to find optimum sets of floristic regions (reporting units) that contain grasslands of high conservation priority. We sought optimum sets that would accommodate 136 important dry-grassland species and that would minimize forest regeneration and costs of management needed to forestall predicted forest regeneration. We did not consider other conservation elements of dry grasslands, such as animal species richness, cultural heritage, and changes due to climate change. Optimal sets that included 95–100% of the dry grassland species encompassed an average of 56–59 floristic regions (standard deviation, SD 5). This is about 15% of approximately 400 floristic regions that contain dry-grassland sites and translates to 4800–5300 ha of dry grassland out of a total of approximately 23,000 ha for the entire study area. Projected costs to manage the grasslands in these optimum sets ranged from CHF (Swiss francs) 5.2 to 6.0 million/year. This is only 15–20% of the current total estimated cost of approximately CHF30–45 million/year required if all dry grasslands were to be protected. The grasslands of the optimal sets may be viewed as core sites in a national conservation strategy.

Combining Natural History Collections with Fisher Knowledge for Community-Based Conservation in Fiji

PubMed Central

Golden, Abigail S.; Naisilsisili, Waisea; Ligairi, Isikele; Drew, Joshua A.

2014-01-01

Harnessing the traditional ecological knowledge (TEK) of local communities has the potential to enhance conservation planning in developing regions. Marine protected areas (MPAs) that incorporate traditional beliefs about reef tenure are generally more successful in reaching conservation goals and ensuring the participation of local fishermen on vulnerable tropical reef systems. Fiji possesses a unique system of traditional reef management in which local clans or villages, called mataqali, control individual units of a reef, known as qoliqoli, and make independent management decisions based on traditional beliefs and conservation concerns. This is an example of a system, known as customary marine tenure, which has attracted interest from conservation scientists hoping to set up MPAs in vulnerable regions. As one example of this grassroots participation, Nagigi village on the Fijian island of Vanua Levu has expressed interest in setting up an MPA in part of its qoliqoli because of concerns about overfishing. In response to this interest, we took a two-pronged approach to assessing Nagigi's fishery status and conservation needs, first conducting a fishery-independent species survey using destructive sampling and then focusing on fisheries targets identified through fisher interviews. These interviews allowed us to identify heavily targeted species, assess villagers' understanding of reef dynamics over 30 or 40 years of fisheries expansion, and evaluate village support and expectations for a proposed conservation program. Based on our findings we recommend a temporary closure to be in effect for at least three years, allowing one of the more important fishery targets, Lethrinus harak (Forsskål, 1775; Lethrinidae), to complete at least one generation within the reserve. The methodology of matching the proposed marine protected area with the life histories and ecologies of heavily targeted species identified through fisherman and -woman interviews can offer a template

Combining natural history collections with fisher knowledge for community-based conservation in Fiji.

PubMed

Golden, Abigail S; Naisilsisili, Waisea; Ligairi, Isikele; Drew, Joshua A

2014-01-01

Harnessing the traditional ecological knowledge (TEK) of local communities has the potential to enhance conservation planning in developing regions. Marine protected areas (MPAs) that incorporate traditional beliefs about reef tenure are generally more successful in reaching conservation goals and ensuring the participation of local fishermen on vulnerable tropical reef systems. Fiji possesses a unique system of traditional reef management in which local clans or villages, called mataqali, control individual units of a reef, known as qoliqoli, and make independent management decisions based on traditional beliefs and conservation concerns. This is an example of a system, known as customary marine tenure, which has attracted interest from conservation scientists hoping to set up MPAs in vulnerable regions. As one example of this grassroots participation, Nagigi village on the Fijian island of Vanua Levu has expressed interest in setting up an MPA in part of its qoliqoli because of concerns about overfishing. In response to this interest, we took a two-pronged approach to assessing Nagigi's fishery status and conservation needs, first conducting a fishery-independent species survey using destructive sampling and then focusing on fisheries targets identified through fisher interviews. These interviews allowed us to identify heavily targeted species, assess villagers' understanding of reef dynamics over 30 or 40 years of fisheries expansion, and evaluate village support and expectations for a proposed conservation program. Based on our findings we recommend a temporary closure to be in effect for at least three years, allowing one of the more important fishery targets, Lethrinus harak (Forsskål, 1775; Lethrinidae), to complete at least one generation within the reserve. The methodology of matching the proposed marine protected area with the life histories and ecologies of heavily targeted species identified through fisherman and -woman interviews can offer a template

Profiling unauthorized natural resource users for better targeting of conservation interventions

PubMed Central

Baker, Julia; Twinamatsiko, Medard; Milner‐Gulland, E.J.

2015-01-01

Abstract Unauthorized use of natural resources is a key threat to many protected areas. Approaches to reducing this threat include law enforcement and integrated conservation and development (ICD) projects, but for such ICDs to be targeted effectively, it is important to understand who is illegally using which natural resources and why. The nature of unauthorized behavior makes it difficult to ascertain this information through direct questioning. Bwindi Impenetrable National Park, Uganda, has many ICD projects, including authorizing some local people to use certain nontimber forest resources from the park. However, despite over 25 years of ICD, unauthorized resource use continues. We used household surveys, indirect questioning (unmatched count technique), and focus group discussions to generate profiles of authorized and unauthorized resource users and to explore motivations for unauthorized activity. Overall, unauthorized resource use was most common among people from poor households who lived closest to the park boundary and farthest from roads and trading centers. Other motivations for unauthorized resource use included crop raiding by wild animals, inequity of revenue sharing, and lack of employment, factors that created resentment among the poorest communities. In some communities, benefits obtained from ICD were reported to be the greatest deterrents against unauthorized activity, although law enforcement ranked highest overall. Despite the sensitive nature of exploring unauthorized resource use, management‐relevant insights into the profiles and motivations of unauthorized resource users can be gained from a combination of survey techniques, as adopted here. To reduce unauthorized activity at Bwindi, we suggest ICD benefit the poorest people living in remote areas and near the park boundary by providing affordable alternative sources of forest products and addressing crop raiding. To prevent resentment from driving further unauthorized activity, ICDs

Importance of Highly Conserved Peptide Sites of Human Cytomegalovirus gO for Formation of the gH/gL/gO Complex

PubMed Central

Stegmann, Cora; Abdellatif, Mohamed E. A.; Laib Sampaio, Kerstin; Walther, Paul

2016-01-01

ABSTRACT The glycoprotein O (gO) is betaherpesvirus specific. Together with the viral glycoproteins H and L, gO forms a covalent trimeric complex that is part of the viral envelope. This trimer is crucial for cell-free infectivity of human cytomegalovirus (HCMV) but dispensable for cell-associated spread. We hypothesized that the amino acids that are conserved among gOs of different cytomegaloviruses are important for the formation of the trimeric complex and hence for efficient virus spread. In a mutational approach, nine peptide sites, containing all 13 highly conserved amino acids, were analyzed in the context of HCMV strain TB40-BAC4 with regard to infection efficiency and formation of the gH/gL/gO complex. Mutation of amino acids (aa) 181 to 186 or aa 193 to 198 resulted in the loss of the trimer and a complete small-plaque phenotype, whereas mutation of aa 108 or aa 249 to 254 caused an intermediate phenotype. While individual mutations of the five conserved cysteines had little impact, their relevance was revealed in a combined mutation, which abrogated both complex formation and cell-free infectivity. C343 was unique, as it was sufficient and necessary for covalent binding of gO to gH/gL. Remarkably, however, C218 together with C167 rescued infectivity in the absence of detectable covalent complex formation. We conclude that all highly conserved amino acids contribute to the function of gO to some extent but that aa 181 to 198 and cysteines 343, 218, and 167 are particularly relevant. Surprisingly, covalent binding of gO to gH/gL is required neither for its incorporation into virions nor for proper function in cell-free infection. IMPORTANCE Like all herpesviruses, the widespread human pathogen HCMV depends on glycoproteins gB, gH, and gL for entry into target cells. Additionally, gH and gL have to bind gO in a trimeric complex for efficient cell-free infection. Homologs of gO are shared by all cytomegaloviruses, with 13 amino acids being highly conserved

Target of Rapamycin (TOR) in Nutrient Signaling and Growth Control

PubMed Central

Loewith, Robbie; Hall, Michael N.

2011-01-01

TOR (Target Of Rapamycin) is a highly conserved protein kinase that is important in both fundamental and clinical biology. In fundamental biology, TOR is a nutrient-sensitive, central controller of cell growth and aging. In clinical biology, TOR is implicated in many diseases and is the target of the drug rapamycin used in three different therapeutic areas. The yeast Saccharomyces cerevisiae has played a prominent role in both the discovery of TOR and the elucidation of its function. Here we review the TOR signaling network in S. cerevisiae. PMID:22174183

A high content, high throughput cellular thermal stability assay for measuring drug-target engagement in living cells.

PubMed

Massey, Andrew J

2018-01-01

Determining and understanding drug target engagement is critical for drug discovery. This can be challenging within living cells as selective readouts are often unavailable. Here we describe a novel method for measuring target engagement in living cells based on the principle of altered protein thermal stabilization / destabilization in response to ligand binding. This assay (HCIF-CETSA) utilizes high content, high throughput single cell immunofluorescent detection to determine target protein levels following heating of adherent cells in a 96 well plate format. We have used target engagement of Chk1 by potent small molecule inhibitors to validate the assay. Target engagement measured by this method was subsequently compared to target engagement measured by two alternative methods (autophosphorylation and CETSA). The HCIF-CETSA method appeared robust and a good correlation in target engagement measured by this method and CETSA for the selective Chk1 inhibitor V158411 was observed. However, these EC50 values were 23- and 12-fold greater than the autophosphorylation IC50. The described method is therefore a valuable advance in the CETSA method allowing the high throughput determination of target engagement in adherent cells.

3D model for Cancerous Inhibitor of Protein Phosphatase 2A armadillo domain unveils highly conserved protein-protein interaction characteristics.

PubMed

Dahlström, Käthe M; Salminen, Tiina A

2015-12-07

Cancerous Inhibitor of Protein Phosphatase 2A (CIP2A) is a human oncoprotein, which exerts its cancer-promoting function through interaction with other proteins, for example Protein Phosphatase 2A (PP2A) and MYC. The lack of structural information for CIP2A significantly prevents the design of anti-cancer therapeutics targeting this protein. In an attempt to counteract this fact, we modeled the three-dimensional structure of the N-terminal domain (CIP2A-ArmRP), analyzed key areas and amino acids, and coupled the results to the existing literature. The model reliably shows a stable armadillo repeat fold with a positively charged groove. The fact that this conserved groove highly likely binds peptides is corroborated by the presence of a conserved polar ladder, which is essential for the proper peptide-binding mode of armadillo repeat proteins and, according to our results, several known CIP2A interaction partners appropriately possess an ArmRP-binding consensus motif. Moreover, we show that Arg229Gln, which has been linked to the development of cancer, causes a significant change in charge and surface properties of CIP2A-ArmRP. In conclusion, our results reveal that CIP2A-ArmRP shares the typical fold, protein-protein interaction site and interaction patterns with other natural armadillo proteins and that, presumably, several interaction partners bind into the central groove of the modeled CIP2A-ArmRP. By providing essential structural characteristics of CIP2A, the present study significantly increases our knowledge on how CIP2A interacts with other proteins in cancer progression and how to develop new therapeutics targeting CIP2A. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

Conservation Genetics of the Philippine Tarsier: Cryptic Genetic Variation Restructures Conservation Priorities for an Island Archipelago Primate

PubMed Central

Brown, Rafe M.; Weghorst, Jennifer A.; Olson, Karen V.; Duya, Mariano R. M.; Barley, Anthony J.; Duya, Melizar V.; Shekelle, Myron; Neri-Arboleda, Irene; Esselstyn, Jacob A.; Dominy, Nathaniel J.; Ong, Perry S.; Moritz, Gillian L.; Luczon, Adrian; Diesmos, Mae Lowe L.; Diesmos, Arvin C.; Siler, Cameron D.

2014-01-01

Establishment of conservation priorities for primates is a particular concern in the island archipelagos of Southeast Asia, where rates of habitat destruction are among the highest in the world. Conservation programs require knowledge of taxonomic diversity to ensure success. The Philippine tarsier is a flagship species that promotes environmental awareness and a thriving ecotourism economy in the Philippines. However, assessment of its conservation status has been impeded by taxonomic uncertainty, a paucity of field studies, and a lack of vouchered specimens and genetic samples available for study in biodiversity repositories. Consequently, conservation priorities are unclear. In this study we use mitochondrial and nuclear DNA to empirically infer geographic partitioning of genetic variation and to identify evolutionarily distinct lineages for conservation action. The distribution of Philippine tarsier genetic diversity is neither congruent with expectations based on biogeographical patterns documented in other Philippine vertebrates, nor does it agree with the most recent Philippine tarsier taxonomic arrangement. We identify three principal evolutionary lineages that do not correspond to the currently recognized subspecies, highlight the discovery of a novel cryptic and range-restricted subcenter of genetic variation in an unanticipated part of the archipelago, and identify additional geographically structured genetic variation that should be the focus of future studies and conservation action. Conservation of this flagship species necessitates establishment of protected areas and targeted conservation programs within the range of each genetically distinct variant of the Philippine tarsier. PMID:25136854

Computational design of high efficiency release targets for use at ISOL facilities

NASA Astrophysics Data System (ADS)

Liu, Y.; Alton, G. D.; Middleton, J. W.

1999-06-01

This report describes efforts made at the Oak Ridge National Laboratory to design high-efficiency-release targets that simultaneously incorporate the short diffusion lengths, high permeabilities, controllable temperatures, and heat removal properties required for the generation of useful radioactive ion beam (RIB) intensities for nuclear physics and astrophysics research using the isotope separation on-line (ISOL) technique. Short diffusion lengths are achieved either by using thin fibrous target materials or by coating thin layers of selected target material onto low-density carbon fibers such as reticulated vitreous carbon fiber (RVCF) or carbon-bonded-carbon-fiber (CBCF) to form highly permeable composite target matrices. Computational studies which simulate the generation and removal of primary beam deposited heat from target materials have been conducted to optimize the design of target/heat-sink systems for generating RIBs. The results derived from diffusion release-rate simulation studies for selected targets and thermal analyses of temperature distributions within a prototype target/heat-sink system subjected to primary ion beam irradiation will be presented in this report.

Setting population targets for mammals using body mass as a predictor of population persistence.

PubMed

Hilbers, Jelle P; Santini, Luca; Visconti, Piero; Schipper, Aafke M; Pinto, Cecilia; Rondinini, Carlo; Huijbregts, Mark A J

2017-04-01

Conservation planning and biodiversity assessments need quantitative targets to optimize planning options and assess the adequacy of current species protection. However, targets aiming at persistence require population-specific data, which limit their use in favor of fixed and nonspecific targets, likely leading to unequal distribution of conservation efforts among species. We devised a method to derive equitable population targets; that is, quantitative targets of population size that ensure equal probabilities of persistence across a set of species and that can be easily inferred from species-specific traits. In our method, we used models of population dynamics across a range of life-history traits related to species' body mass to estimate minimum viable population targets. We applied our method to a range of body masses of mammals, from 2 g to 3825 kg. The minimum viable population targets decreased asymptotically with increasing body mass and were on the same order of magnitude as minimum viable population estimates from species- and context-specific studies. Our approach provides a compromise between pragmatic, nonspecific population targets and detailed context-specific estimates of population viability for which only limited data are available. It enables a first estimation of species-specific population targets based on a readily available trait and thus allows setting equitable targets for population persistence in large-scale and multispecies conservation assessments and planning. © 2016 The Authors. Conservation Biology published by Wiley Periodicals, Inc. on behalf of Society for Conservation Biology.

Conservation Action Planning: Lessons learned from the St. Marys River watershed biodiversity conservation planning process

USGS Publications Warehouse

Patterson, Tamatha A.; Grundel, Ralph

2014-01-01

Conservation Action Planning (CAP) is an adaptive management planning process refined by The Nature Conservancy (TNC) and embraced worldwide as the Open Standards for the Practice of Conservation. The CAP process facilitates open, multi-institutional collaboration on a common conservation agenda through organized actions and quantified results. While specifically designed for conservation efforts, the framework is adaptable and flexible to multiple scales and can be used for any collaborative planning effort. The CAP framework addresses inception; design and development of goals, measures, and strategies; and plan implementation and evaluation. The specific components of the CAP include defining the project scope and conservation targets; assessing the ecological viability; ascertaining threats and surrounding situation; identifying opportunities and designing strategies for action; and implementing actions and monitoring results. In 2007, TNC and a multidisciplinary graduate student team from the University of Michigan's School of Natural Resources and Environment initiated a CAP for the St. Marys River, the connecting channel between Lake Superior and Lake Huron, and its local watershed. The students not only gained experience in conservation planning, but also learned lessons that notably benefited the CAP process and were valuable for any successful collaborative effort—a dedicated core team improved product quality, accelerated the timeline, and provided necessary support for ongoing efforts; an academic approach in preparation for engagement in the planning process brought applicable scientific research to the forefront, enhanced workshop facilitation, and improved stakeholder participation; and early and continuous interactions with regional stakeholders improved cooperation and built a supportive network for collaboration.

Conserved stem fragment from H3 influenza hemagglutinin elicits cross-clade neutralizing antibodies through stalk-targeted blocking of conformational change during membrane fusion.

PubMed

Gong, Xin; Yin, He; Shi, Yuhua; Guan, Shanshan; He, Xiaoqiu; Yang, Lan; Yu, Yongjiao; Kuai, Ziyu; Jiang, Chunlai; Kong, Wei; Wang, Song; Shan, Yaming

2016-04-01

Currently available influenza vaccines typically fail to elicit/boost broadly neutralizing antibodies due to the mutability of virus sequences and conformational changes during protective immunity, thereby limiting their efficacy. This problem needs to be addressed by further understanding the mechanisms of neutralization and finding the desired neutralizing site during membrane fusion. This study specifically focused on viruses of the H3N2 subtype, which have persisted as a principal source of influenza-related morbidity and mortality in humans since the 1968 influenza pandemic. Through sequence alignment and epitope prediction, a series of highly conserved stem fragments (spanning 47 years) were found and coupled to the Keyhole Limpet Hemocyanin (KLH) protein. By application of a combinatorial display library and crystal structure modeling, a stem fragment immunogen, located at the turning point of the HA neck undergoing conformational change during membrane fusion with both B- and T-cell epitopes, was identified. After synthesis of the optimal stem fragment using a multiple antigen peptide (MAP) system, strong humoral immune responses and cross-clade neutralizing activities against strains from the H3 subtype of group 2 influenza viruses after animal immunizations were observed. By detection of nuclear protein immunofluorescence with acid bypass treatment, antisera raised against MAP4 immunogens of the stem fragment showed the potential to inhibit the conformational change of HA in stem-targeted virus neutralization. The identification of this conserved stem fragment provides great potential for exploitation of this site of vulnerability in therapeutic and vaccine design. Copyright © 2016 European Federation of Immunological Societies. Published by Elsevier B.V. All rights reserved.

Satellite remote sensing, biodiversity research and conservation of the future

PubMed Central

Pettorelli, Nathalie; Safi, Kamran; Turner, Woody

2014-01-01

Assessing and predicting ecosystem responses to global environmental change and its impacts on human well-being are high priority targets for the scientific community. The potential for synergies between remote sensing science and ecology, especially satellite remote sensing and conservation biology, has been highlighted by many in the past. Yet, the two research communities have only recently begun to coordinate their agendas. Such synchronization is the key to improving the potential for satellite data effectively to support future environmental management decision-making processes. With this themed issue, we aim to illustrate how integrating remote sensing into ecological research promotes a better understanding of the mechanisms shaping current changes in biodiversity patterns and improves conservation efforts. Added benefits include fostering innovation, generating new research directions in both disciplines and the development of new satellite remote sensing products. PMID:24733945

Reconciling Mining with the Conservation of Cave Biodiversity: A Quantitative Baseline to Help Establish Conservation Priorities.

PubMed

Jaffé, Rodolfo; Prous, Xavier; Zampaulo, Robson; Giannini, Tereza C; Imperatriz-Fonseca, Vera L; Maurity, Clóvis; Oliveira, Guilherme; Brandi, Iuri V; Siqueira, José O

2016-01-01

Caves pose significant challenges for mining projects, since they harbor many endemic and threatened species, and must therefore be protected. Recent discussions between academia, environmental protection agencies, and industry partners, have highlighted problems with the current Brazilian legislation for the protection of caves. While the licensing process is long, complex and cumbersome, the criteria used to assign caves into conservation relevance categories are often subjective, with relevance being mainly determined by the presence of obligate cave dwellers (troglobites) and their presumed rarity. However, the rarity of these troglobitic species is questionable, as most remain unidentified to the species level and their habitats and distribution ranges are poorly known. Using data from 844 iron caves retrieved from different speleology reports for the Carajás region (South-Eastern Amazon, Brazil), one of the world's largest deposits of high-grade iron ore, we assess the influence of different cave characteristics on four biodiversity proxies (species richness, presence of troglobites, presence of rare troglobites, and presence of resident bat populations). We then examine how the current relevance classification scheme ranks caves with different biodiversity indicators. Large caves were found to be important reservoirs of biodiversity, so they should be prioritized in conservation programs. Our results also reveal spatial autocorrelation in all the biodiversity proxies assessed, indicating that iron caves should be treated as components of a cave network immersed in the karst landscape. Finally, we show that by prioritizing the conservation of rare troglobites, the current relevance classification scheme is undermining overall cave biodiversity and leaving ecologically important caves unprotected. We argue that conservation efforts should target subterranean habitats as a whole and propose an alternative relevance ranking scheme, which could help simplify the

Reconciling Mining with the Conservation of Cave Biodiversity: A Quantitative Baseline to Help Establish Conservation Priorities

PubMed Central

Prous, Xavier; Zampaulo, Robson; Giannini, Tereza C.; Imperatriz-Fonseca, Vera L.; Maurity, Clóvis; Oliveira, Guilherme; Brandi, Iuri V.; Siqueira, José O.

2016-01-01

Caves pose significant challenges for mining projects, since they harbor many endemic and threatened species, and must therefore be protected. Recent discussions between academia, environmental protection agencies, and industry partners, have highlighted problems with the current Brazilian legislation for the protection of caves. While the licensing process is long, complex and cumbersome, the criteria used to assign caves into conservation relevance categories are often subjective, with relevance being mainly determined by the presence of obligate cave dwellers (troglobites) and their presumed rarity. However, the rarity of these troglobitic species is questionable, as most remain unidentified to the species level and their habitats and distribution ranges are poorly known. Using data from 844 iron caves retrieved from different speleology reports for the Carajás region (South-Eastern Amazon, Brazil), one of the world's largest deposits of high-grade iron ore, we assess the influence of different cave characteristics on four biodiversity proxies (species richness, presence of troglobites, presence of rare troglobites, and presence of resident bat populations). We then examine how the current relevance classification scheme ranks caves with different biodiversity indicators. Large caves were found to be important reservoirs of biodiversity, so they should be prioritized in conservation programs. Our results also reveal spatial autocorrelation in all the biodiversity proxies assessed, indicating that iron caves should be treated as components of a cave network immersed in the karst landscape. Finally, we show that by prioritizing the conservation of rare troglobites, the current relevance classification scheme is undermining overall cave biodiversity and leaving ecologically important caves unprotected. We argue that conservation efforts should target subterranean habitats as a whole and propose an alternative relevance ranking scheme, which could help simplify the

Traveling waves and conservation laws for highly nonlinear wave equations modeling Hertz chains

NASA Astrophysics Data System (ADS)

Przedborski, Michelle; Anco, Stephen C.

2017-09-01

A highly nonlinear, fourth-order wave equation that models the continuum theory of long wavelength pulses in weakly compressed, homogeneous, discrete chains with a general power-law contact interaction is studied. For this wave equation, all solitary wave solutions and all nonlinear periodic wave solutions, along with all conservation laws, are derived. The solutions are explicitly parameterized in terms of the asymptotic value of the wave amplitude in the case of solitary waves and the peak of the wave amplitude in the case of nonlinear periodic waves. All cases in which the solution expressions can be stated in an explicit analytic form using elementary functions are worked out. In these cases, explicit expressions for the total energy and total momentum for all solutions are obtained as well. The derivation of the solutions uses the conservation laws combined with an energy analysis argument to reduce the wave equation directly to a separable first-order differential equation that determines the wave amplitude in terms of the traveling wave variable. This method can be applied more generally to other highly nonlinear wave equations.

Phylogenetic analysis reveals conservation and diversification of micro RNA166 genes among diverse plant species.

PubMed

Barik, Suvakanta; SarkarDas, Shabari; Singh, Archita; Gautam, Vibhav; Kumar, Pramod; Majee, Manoj; Sarkar, Ananda K

2014-01-01

Similar to the majority of the microRNAs, mature miR166s are derived from multiple members of MIR166 genes (precursors) and regulate various aspects of plant development by negatively regulating their target genes (Class III HD-ZIP). The evolutionary conservation or functional diversification of miRNA166 family members remains elusive. Here, we show the phylogenetic relationships among MIR166 precursor and mature sequences from three diverse model plant species. Despite strong conservation, some mature miR166 sequences, such as ppt-miR166m, have undergone sequence variation. Critical sequence variation in ppt-miR166m has led to functional diversification, as it targets non-HD-ZIPIII gene transcript (s). MIR166 precursor sequences have diverged in a lineage specific manner, and both precursors and mature osa-miR166i/j are highly conserved. Interestingly, polycistronic MIR166s were present in Physcomitrella and Oryza but not in Arabidopsis. The nature of cis-regulatory motifs on the upstream promoter sequences of MIR166 genes indicates their possible contribution to the functional variation observed among miR166 species. Copyright © 2013 Elsevier Inc. All rights reserved.

Informing Extension Program Development through Audience Segmentation: Targeting High Water Users

ERIC Educational Resources Information Center

Huang, Pei-wen; Lamm, Alexa J.; Dukes, Michael D.

2016-01-01

Human reliance on water has led to water issues globally. Although extension professionals have made efforts successfully to educate the general public about water conservation to enhance water resource sustainability, difficulty has been found in reaching high water users, defined as residents irrigating excessively to their landscape irrigation…

Identification of microRNAs in Caragana intermedia by high-throughput sequencing and expression analysis of 12 microRNAs and their targets under salt stress.

PubMed

Zhu, Jianfeng; Li, Wanfeng; Yang, Wenhua; Qi, Liwang; Han, Suying

2013-09-01

142 miRNAs were identified and 38 miRNA targets were predicted, 4 of which were validated, in C. intermedia . The expression of 12 miRNAs in salt-stressed leaves was assessed by qRT-PCR. MicroRNAs (miRNAs) are endogenous small RNAs that play important roles in various biological and metabolic processes in plants. Caragana intermedia is an important ecological and economic tree species prominent in the desert environment of west and northwest China. To date, no investigation into C. intermedia miRNAs has been reported. In this study, high-throughput sequencing of small RNAs and analysis of transcriptome data were performed to identify both conserved and novel miRNAs, and also their target mRNA genes in C. intermedia. Based on sequence similarity and hairpin structure prediction, 132 putative conserved miRNAs (12 of which were confirmed to form hairpin precursors) belonging to 31 known miRNA families were identified. Ten novel miRNAs (including the miRNA* sequences of three novel miRNAs) were also discovered. Furthermore, 36 potential target genes of 17 known miRNA families and 2 potential target genes of 1 novel miRNA were predicted; 4 of these were validated by 5' RACE. The expression of 12 miRNAs was validated in different tissues, and these and five target mRNAs were assessed by qRT-PCR after salt treatment. The expression levels of seven miRNAs (cin-miR157a, cin-miR159a, cin-miR165a, cin-miR167b, cin-miR172b, cin-miR390a and cin-miR396a) were upregulated, while cin-miR398a expression was downregulated after salt treatment. The targets of cin-miR157a, cin-miR165a, cin-miR172b and cin-miR396a were downregulated and showed an approximately negative correlation with their corresponding miRNAs under salt treatment. These results would help further understanding of miRNA regulation in response to abiotic stress in C. intermedia.

Microstructured snow targets for high energy quasi-monoenergetic proton acceleration

NASA Astrophysics Data System (ADS)

Schleifer, E.; Nahum, E.; Eisenmann, S.; Botton, M.; Baspaly, A.; Pomerantz, I.; Abricht, F.; Branzel, J.; Priebe, G.; Steinke, S.; Andreev, A.; Schnuerer, M.; Sandner, W.; Gordon, D.; Sprangle, P.; Ledingham, K. W. D.; Zigler, A.

2013-05-01

Compact size sources of high energy protons (50-200MeV) are expected to be key technology in a wide range of scientific applications 1-8. One promising approach is the Target Normal Sheath Acceleration (TNSA) scheme 9,10, holding record level of 67MeV protons generated by a peta-Watt laser 11. In general, laser intensity exceeding 1018 W/cm2 is required to produce MeV level protons. Another approach is the Break-Out Afterburner (BOA) scheme which is a more efficient acceleration scheme but requires an extremely clean pulse with contrast ratio of above 10-10. Increasing the energy of the accelerated protons using modest energy laser sources is a very attractive task nowadays. Recently, nano-scale targets were used to accelerate ions 12,13 but no significant enhancement of the accelerated proton energy was measured. Here we report on the generation of up to 20MeV by a modest (5TW) laser system interacting with a microstructured snow target deposited on a Sapphire substrate. This scheme relax also the requirement of high contrast ratio between the pulse and the pre-pulse, where the latter produces the highly structured plasma essential for the interaction process. The plasma near the tip of the snow target is subject to locally enhanced laser intensity with high spatial gradients, and enhanced charge separation is obtained. Electrostatic fields of extremely high intensities are produced, and protons are accelerated to MeV-level energies. PIC simulations of this targets reproduce the experimentally measured energy scaling and predict the generation of 150 MeV protons from laser power of 100TW laser system18.

Cnidarian microRNAs frequently regulate targets by cleavage.

PubMed

Moran, Yehu; Fredman, David; Praher, Daniela; Li, Xin Z; Wee, Liang Meng; Rentzsch, Fabian; Zamore, Phillip D; Technau, Ulrich; Seitz, Hervé

2014-04-01

In bilaterians, which comprise most of extant animals, microRNAs (miRNAs) regulate the majority of messenger RNAs (mRNAs) via base-pairing of a short sequence (the miRNA "seed") to the target, subsequently promoting translational inhibition and transcript instability. In plants, many miRNAs guide endonucleolytic cleavage of highly complementary targets. Because little is known about miRNA function in nonbilaterian animals, we investigated the repertoire and biological activity of miRNAs in the sea anemone Nematostella vectensis, a representative of Cnidaria, the sister phylum of Bilateria. Our work uncovers scores of novel miRNAs in Nematostella, increasing the total miRNA gene count to 87. Yet only a handful are conserved in corals and hydras, suggesting that microRNA gene turnover in Cnidaria greatly exceeds that of other metazoan groups. We further show that Nematostella miRNAs frequently direct the cleavage of their mRNA targets via nearly perfect complementarity. This mode of action resembles that of small interfering RNAs (siRNAs) and plant miRNAs. It appears to be common in Cnidaria, as several of the miRNA target sites are conserved among distantly related anemone species, and we also detected miRNA-directed cleavage in Hydra. Unlike in bilaterians, Nematostella miRNAs are commonly coexpressed with their target transcripts. In light of these findings, we propose that post-transcriptional regulation by miRNAs functions differently in Cnidaria and Bilateria. The similar, siRNA-like mode of action of miRNAs in Cnidaria and plants suggests that this may be an ancestral state.

Target R and D for high power proton beam applications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fabich, A.

High power targets are one of the major issues in an accelerator complex for future HEP physic studies. The paper will review status of studies worldwide. It will focus on the status of the MERIT mercury-jet target experiment at CERN.

Highly efficient targeted mutagenesis in axolotl using Cas9 RNA-guided nuclease

PubMed Central

Flowers, G. Parker; Timberlake, Andrew T.; Mclean, Kaitlin C.; Monaghan, James R.; Crews, Craig M.

2014-01-01

Among tetrapods, only urodele salamanders, such as the axolotl Ambystoma mexicanum, can completely regenerate limbs as adults. The mystery of why salamanders, but not other animals, possess this ability has for generations captivated scientists seeking to induce this phenomenon in other vertebrates. Although many recent advances in molecular biology have allowed limb regeneration and tissue repair in the axolotl to be investigated in increasing detail, the molecular toolkit for the study of this process has been limited. Here, we report that the CRISPR-Cas9 RNA-guided nuclease system can efficiently create mutations at targeted sites within the axolotl genome. We identify individual animals treated with RNA-guided nucleases that have mutation frequencies close to 100% at targeted sites. We employ this technique to completely functionally ablate EGFP expression in transgenic animals and recapitulate developmental phenotypes produced by loss of the conserved gene brachyury. Thus, this advance allows a reverse genetic approach in the axolotl and will undoubtedly provide invaluable insight into the mechanisms of salamanders' unique regenerative ability. PMID:24764077

Targeting high-risk employees may reduce cardiovascular racial disparities.

PubMed

Burke, James F; Vijan, Sandeep; Chekan, Lynette A; Makowiec, Ted M; Thomas, Laurita; Morgenstern, Lewis B

2014-09-01

A possible remedy for health disparities is for employers to promote cardiovascular health among minority employees. We sought to quantify the financial return to employers of interventions to improve minority health, and to determine whether a race- or risk-targeted strategy was better. Retrospective claims-based cohort analysis. Unconditional per-person costs attributable to stroke and myocardial infarction (MI) were estimated for University of Michigan employees from 2006 to 2009 using a 2-part model. The model was then used to predict the costs of cardiovascular disease to the University for 2 subgroups of employees-minorities and high-risk patients-and to calculate cost-savings thresholds: the point at which the costs of hypothetical interventions (eg, workplace fitness programs) would equal the cost savings from stroke/ MI prevention. Of the 38,314 enrollees, 10% were African American. Estimated unconditional payments for stroke/MI were almost the same in African Americans ($128 per employee per year; 95% CI, $79-$177) and whites ($128 per employee per year; 95% CI, $101- $156), including higher event rates and lower payments per event in African Americans. Targeting the highest risk decile with interventions to reduce stroke/MI would result in a substantially higher cost-savings threshold ($81) compared with targeting African Americans ($13). An unanticipated consequence of risk-based targeting is that African Americans would substantially benefit: an intervention targeted at the top risk decile would prevent 75% of the events in African Americans, just as would an intervention that exclusively targeted African Americans. Targeting all high-risk employees for cardiovascular risk reduction may be a win-win-win situation for employers: improving health, decreasing costs, and reducing disparities.

Reef sharks: recent advances in ecological understanding to inform conservation.

PubMed

Osgood, G J; Baum, J K

2015-12-01

Sharks are increasingly being recognized as important members of coral-reef communities, but their overall conservation status remains uncertain. Nine of the 29 reef-shark species are designated as data deficient in the IUCN Red List, and three-fourths of reef sharks had unknown population trends at the time of their assessment. Fortunately, reef-shark research is on the rise. This new body of research demonstrates reef sharks' high site restriction, fidelity and residency on coral reefs, their broad trophic roles connecting reef communities and their high population genetic structure, all information that should be useful for their management and conservation. Importantly, recent studies on the abundance and population trends of the three classic carcharhinid reef sharks (grey reef shark Carcharhinus amblyrhynchos, blacktip reef shark Carcharhinus melanopterus and whitetip reef shark Triaenodon obesus) may contribute to reassessments identifying them as more vulnerable than currently realized. Because over half of the research effort has focused on only these three reef sharks and the nurse shark Ginglymostoma cirratum in only a few locales, there remain large taxonomic and geographic gaps in reef-shark knowledge. As such, a large portion of reef-shark biodiversity remains uncharacterized despite needs for targeted research identified in their red list assessments. A research agenda for the future should integrate abundance, life history, trophic ecology, genetics, habitat use and movement studies, and expand the breadth of such research to understudied species and localities, in order to better understand the conservation requirements of these species and to motivate effective conservation solutions. © 2015 The Fisheries Society of the British Isles.

Identification of influenza A nucleoprotein body domain residues essential for viral RNA expression expose antiviral target.

PubMed

Davis, Alicia M; Ramirez, Jose; Newcomb, Laura L

2017-02-07

Influenza A virus is controlled with yearly vaccination while emerging global pandemics are kept at bay with antiviral medications. Unfortunately, influenza A viruses have emerged resistance to approved influenza antivirals. Accordingly, there is an urgent need for novel antivirals to combat emerging influenza A viruses resistant to current treatments. Conserved viral proteins are ideal targets because conserved protein domains are present in most, if not all, influenza subtypes, and are presumed less prone to evolve viable resistant versions. The threat of an antiviral resistant influenza pandemic justifies our study to identify and characterize antiviral targets within influenza proteins that are highly conserved. Influenza A nucleoprotein (NP) is highly conserved and plays essential roles throughout the viral lifecycle, including viral RNA synthesis. Using NP crystal structure, we targeted accessible amino acids for substitution. To characterize the NP proteins, reconstituted viral ribonucleoproteins (vRNPs) were expressed in 293 T cells, RNA was isolated, and reverse transcription - quantitative PCR (RT-qPCR) was employed to assess viral RNA expressed from reconstituted vRNPs. Location was confirmed using cellular fractionation and western blot, along with observation of NP-GFP fusion proteins. Nucleic acid binding, oligomerization, and vRNP formation, were each assessed with native gel electrophoresis. Here we report characterization of an accessible and conserved five amino acid region within the NP body domain that plays a redundant but essential role in viral RNA synthesis. Our data demonstrate substitutions in this domain did not alter NP localization, oligomerization, or ability to bind nucleic acids, yet resulted in a defect in viral RNA expression. To define this region further, single and double amino acid substitutions were constructed and investigated. All NP single substitutions were functional, suggesting redundancy, yet different combinations of

Compound Structure-Independent Activity Prediction in High-Dimensional Target Space.

PubMed

Balfer, Jenny; Hu, Ye; Bajorath, Jürgen

2014-08-01

Profiling of compound libraries against arrays of targets has become an important approach in pharmaceutical research. The prediction of multi-target compound activities also represents an attractive task for machine learning with potential for drug discovery applications. Herein, we have explored activity prediction in high-dimensional target space. Different types of models were derived to predict multi-target activities. The models included naïve Bayesian (NB) and support vector machine (SVM) classifiers based upon compound structure information and NB models derived on the basis of activity profiles, without considering compound structure. Because the latter approach can be applied to incomplete training data and principally depends on the feature independence assumption, SVM modeling was not applicable in this case. Furthermore, iterative hybrid NB models making use of both activity profiles and compound structure information were built. In high-dimensional target space, NB models utilizing activity profile data were found to yield more accurate activity predictions than structure-based NB and SVM models or hybrid models. An in-depth analysis of activity profile-based models revealed the presence of correlation effects across different targets and rationalized prediction accuracy. Taken together, the results indicate that activity profile information can be effectively used to predict the activity of test compounds against novel targets. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Reductions in global biodiversity loss predicted from conservation spending.

PubMed

Waldron, Anthony; Miller, Daniel C; Redding, Dave; Mooers, Arne; Kuhn, Tyler S; Nibbelink, Nate; Roberts, J Timmons; Tobias, Joseph A; Gittleman, John L

2017-11-16

Halting global biodiversity loss is central to the Convention on Biological Diversity and United Nations Sustainable Development Goals, but success to date has been very limited. A critical determinant of success in achieving these goals is the financing that is committed to maintaining biodiversity; however, financing decisions are hindered by considerable uncertainty over the likely impact of any conservation investment. For greater effectiveness, we need an evidence-based model that shows how conservation spending quantitatively reduces the rate of biodiversity loss. Here we demonstrate such a model, and empirically quantify how conservation investment reduced biodiversity loss in 109 countries (signatories to the Convention on Biological Diversity and Sustainable Development Goals), by a median average of 29% per country between 1996 and 2008. We also show that biodiversity changes in signatory countries can be predicted with high accuracy, using a dual model that balances the effects of conservation investment against those of economic, agricultural and population growth (human development pressures). Decision-makers can use this model to forecast the improvement that any proposed biodiversity budget would achieve under various scenarios of human development pressure, and then compare these forecasts to any chosen policy target. We find that the impact of spending decreases as human development pressures grow, which implies that funding may need to increase over time. The model offers a flexible tool for balancing the Sustainable Development Goals of human development and maintaining biodiversity, by predicting the dynamic changes in conservation finance that will be needed as human development proceeds.

Reductions in global biodiversity loss predicted from conservation spending

NASA Astrophysics Data System (ADS)

Waldron, Anthony; Miller, Daniel C.; Redding, Dave; Mooers, Arne; Kuhn, Tyler S.; Nibbelink, Nate; Roberts, J. Timmons; Tobias, Joseph A.; Gittleman, John L.

2017-11-01

Halting global biodiversity loss is central to the Convention on Biological Diversity and United Nations Sustainable Development Goals, but success to date has been very limited. A critical determinant of success in achieving these goals is the financing that is committed to maintaining biodiversity; however, financing decisions are hindered by considerable uncertainty over the likely impact of any conservation investment. For greater effectiveness, we need an evidence-based model that shows how conservation spending quantitatively reduces the rate of biodiversity loss. Here we demonstrate such a model, and empirically quantify how conservation investment between 1996 and 2008 reduced biodiversity loss in 109 countries (signatories to the Convention on Biological Diversity and Sustainable Development Goals), by a median average of 29% per country. We also show that biodiversity changes in signatory countries can be predicted with high accuracy, using a dual model that balances the effects of conservation investment against those of economic, agricultural and population growth (human development pressures). Decision-makers can use this model to forecast the improvement that any proposed biodiversity budget would achieve under various scenarios of human development pressure, and then compare these forecasts to any chosen policy target. We find that the impact of spending decreases as human development pressures grow, which implies that funding may need to increase over time. The model offers a flexible tool for balancing the Sustainable Development Goals of human development and maintaining biodiversity, by predicting the dynamic changes in conservation finance that will be needed as human development proceeds.

Impact of High-Z Coatings on the Ablation Pressure of Laser Driven Targets.

NASA Astrophysics Data System (ADS)

Mostovych, Andrew; Oh, Jaechul; Schmitt, Andrew; Weaver, James

2007-11-01

Recent hydrodynamic experiments [1] with planar high-Z coated targets at the Naval Research Laboratory and spherical implosion experiments with high-Z coated shell targets [2] at the Omega facility all show significant improvement in target stability as a result of the high-Z coatings. For better understanding of the hydrodynamic processes it is important to know the changes in ablation pressure as a result of the high-Z layers. Using the Nike Laser, we have conducted new experiments to measure the change in shock speed of planar CH targets that are irradiated with and without the presence of a 200 Ang. gold high-Z coating. The evolution of shock propagation inside the targets is diagnosed with VISAR probing while average shock velocities are also measured by shock breakout detection from the stepped rear surface of the targets. We find that the high-Z layers produce a time dependent ablation pressure which is detected via the observation of non-steady shocks in the targets. Experimental results and comparisons to hydrodynamic simulations will be presented. Work supported by U. S. Department of Energy. [1] S.P. Obenschain et al., Phys. Plasmas 9, 2234 (2002). [2] A.N. Mostovych et al., APS Abstracts DPPFO3002M, (2005).

Planning for land use and conservation: Assessing GIS-based conservation software for land use planning

Treesearch

Rob Baldwin; Ryan Scherzinger; Don Lipscomb; Miranda Mockrin; Susan Stein

2014-01-01

Recent advances in planning and ecological software make it possible to conduct highly technical analyses to prioritize conservation investments and inform local land use planning. We review these tools, termed conservation planning tools, and assess the knowledge of a key set of potential users: the land use planning community. We grouped several conservation software...

Incorporating seascape connectivity in conservation prioritisation.

PubMed

Weeks, Rebecca

2017-01-01

In conservation prioritisation, it is often implicit that representation targets for individual habitat types act as surrogates for the species that inhabit them. Yet for many commercially and ecologically important coral reef fish species, connectivity among different habitats in a seascape may be more important than any single habitat alone. Approaches to conservation prioritisation that consider seascape connectivity are thus warranted. I demonstrate an approach that can be implemented within a relatively data-poor context, using widely available conservation planning software. Based on clearly stated assumptions regarding species' habitat usage and movement ability, this approach can be adapted to different focal species and contexts, or refined as further data become available. I first derive a seascape connectivity metric based on area-weighted proximity between juvenile and adult habitat patches, and then apply this during spatial prioritisation using the decision-support software Marxan. Using a case study from Micronesia, I present two applications: first, to inform prioritisation for a network of marine protected areas to achieve regional objectives for habitat representation; and second, to identify nursery habitat patches that are most likely to supply juveniles to adult populations on reefs within existing protected areas. Incorporating seascape connectivity in conservation prioritisation highlights areas where small marine protected areas placed on coral reefs might benefit from proximity to other habitats in the seascape, and thus be more effective. Within the context of community tenure over resources, identification of critical nursery habitats to improve the effectiveness of existing marine protected areas indicates where collaboration across community boundaries might be required. Outputs from these analyses are likely to be most useful in regions where management is highly decentralised, imposing spatial constraints on the size of individual

Incorporating seascape connectivity in conservation prioritisation

PubMed Central

2017-01-01

In conservation prioritisation, it is often implicit that representation targets for individual habitat types act as surrogates for the species that inhabit them. Yet for many commercially and ecologically important coral reef fish species, connectivity among different habitats in a seascape may be more important than any single habitat alone. Approaches to conservation prioritisation that consider seascape connectivity are thus warranted. I demonstrate an approach that can be implemented within a relatively data-poor context, using widely available conservation planning software. Based on clearly stated assumptions regarding species’ habitat usage and movement ability, this approach can be adapted to different focal species and contexts, or refined as further data become available. I first derive a seascape connectivity metric based on area-weighted proximity between juvenile and adult habitat patches, and then apply this during spatial prioritisation using the decision-support software Marxan. Using a case study from Micronesia, I present two applications: first, to inform prioritisation for a network of marine protected areas to achieve regional objectives for habitat representation; and second, to identify nursery habitat patches that are most likely to supply juveniles to adult populations on reefs within existing protected areas. Incorporating seascape connectivity in conservation prioritisation highlights areas where small marine protected areas placed on coral reefs might benefit from proximity to other habitats in the seascape, and thus be more effective. Within the context of community tenure over resources, identification of critical nursery habitats to improve the effectiveness of existing marine protected areas indicates where collaboration across community boundaries might be required. Outputs from these analyses are likely to be most useful in regions where management is highly decentralised, imposing spatial constraints on the size of individual

Controversies in cancer stem cells: targeting embryonic signaling pathways.

PubMed

Takebe, Naoko; Ivy, S Percy

2010-06-15

Selectively targeting cancer stem cells (CSC) or tumor-initiating cells (TIC; from this point onward referred to as CSCs) with novel agents is a rapidly emerging field of oncology. Our knowledge of CSCs and their niche microenvironments remains a nascent field. CSC's critical dependence upon self-renewal makes these regulatory signaling pathways ripe for the development of experimental therapeutic agents. Investigational agents targeting the Notch, Hedgehog, and Wnt pathways are currently in late preclinical development stages, with some early phase 1-2 testing in human subjects. This series of articles will provide an overview and summary of the current state of knowledge of CSCs, their interactive microenvironment, and how they may serve as important targets for antitumor therapies. We also examine the scope and stage of development of early experimental agents that specifically target these highly conserved embryonic signaling pathways. (c) 2010 AACR.

High-current fast electron beam propagation in a dielectric target.

PubMed

Klimo, Ondrej; Tikhonchuk, V T; Debayle, A

2007-01-01

Recent experiments demonstrate an efficient transformation of high intensity laser pulse into a relativistic electron beam with a very high current density exceeding 10(12) A cm(-2). The propagation of such a beam inside the target is possible if its current is neutralized. This phenomenon is not well understood, especially in dielectric targets. In this paper, we study the propagation of high current density electron beam in a plastic target using a particle-in-cell simulation code. The code includes both ionization of the plastic and collisions of newborn electrons. The numerical results are compared with a relatively simple analytical model and a reasonable agreement is found. The temporal evolution of the beam velocity distribution, the spatial density profile, and the propagation velocity of the ionization front are analyzed and their dependencies on the beam density and energy are discussed. The beam energy losses are mainly due to the target ionization induced by the self-generated electric field and the return current. For the highest beam density, a two-stream instability is observed to develop in the plasma behind the ionization front and it contributes to the beam energy losses.

Feedbacks between conservation and social-ecological systems

PubMed Central

Miller, Brian W.; Caplow, Susan C.; Leslie, Paul W.

2012-01-01

Robust ways to meet objectives of environmental conservation and social and economic development remain elusive. This struggle may in part be related to insufficient understanding of the feedbacks between conservation initiatives and social-ecological systems, specifically, the ways in which conservation initiatives result in social changes that have secondary effects on the environments targeted by conservation. To explore this idea we sampled peer-reviewed articles addressing the social and environmental dimensions of conservation and coded each paper according to its research focus and characterization of these feedbacks. The majority of articles in our sample focused either on the effect of conservation initiatives on people (e.g., relocation, employment) or the effect of people on the environment (e.g., fragmentation, conservation efficacy of traditional management systems). Few studies in our sample empirically addressed both the social dynamics resulting from conservation initiatives and subsequent environmental effects. In many cases, one was measured and the other was discussed anecdotally. Among the studies that describe feedbacks between social and environmental variables, there was more evidence of positive (amplifying) feedbacks between social and environmental outcomes (i.e., undesirable social outcomes yielded undesirable environmental effects, and desirable social outcomes yielded desirable environmental effects). The major themes within the sampled literature include conflict between humans and wild animals, social movements, adaptive comanagement, loss of traditional management systems, traditional ecological knowledge, human displacement and risks to livelihoods, and conservation and development. The narratives associated with each theme can serve as hypotheses for facilitating further discussion about conservation issues and for catalyzing future studies of the feedbacks between conservation and social-ecological systems. PMID:22443128

RNA expression in a cartilaginous fish cell line reveals ancient 3′ noncoding regions highly conserved in vertebrates

PubMed Central

Forest, David; Nishikawa, Ryuhei; Kobayashi, Hiroshi; Parton, Angela; Bayne, Christopher J.; Barnes, David W.

2007-01-01

We have established a cartilaginous fish cell line [Squalus acanthias embryo cell line (SAE)], a mesenchymal stem cell line derived from the embryo of an elasmobranch, the spiny dogfish shark S. acanthias. Elasmobranchs (sharks and rays) first appeared >400 million years ago, and existing species provide useful models for comparative vertebrate cell biology, physiology, and genomics. Comparative vertebrate genomics among evolutionarily distant organisms can provide sequence conservation information that facilitates identification of critical coding and noncoding regions. Although these genomic analyses are informative, experimental verification of functions of genomic sequences depends heavily on cell culture approaches. Using ESTs defining mRNAs derived from the SAE cell line, we identified lengthy and highly conserved gene-specific nucleotide sequences in the noncoding 3′ UTRs of eight genes involved in the regulation of cell growth and proliferation. Conserved noncoding 3′ mRNA regions detected by using the shark nucleotide sequences as a starting point were found in a range of other vertebrate orders, including bony fish, birds, amphibians, and mammals. Nucleotide identity of shark and human in these regions was remarkably well conserved. Our results indicate that highly conserved gene sequences dating from the appearance of jawed vertebrates and representing potential cis-regulatory elements can be identified through the use of cartilaginous fish as a baseline. Because the expression of genes in the SAE cell line was prerequisite for their identification, this cartilaginous fish culture system also provides a physiologically valid tool to test functional hypotheses on the role of these ancient conserved sequences in comparative cell biology. PMID:17227856

Energy conservation of the scattering from one-dimensional random rough surfaces in the high-frequency limit.

PubMed

Pinel, Nicolas; Bourlier, Christophe; Saillard, Joseph

2005-08-01

Energy conservation of the scattering from one-dimensional strongly rough dielectric surfaces is investigated using the Kirchhoff approximation with single reflection and by taking the shadowing phenomenon into account, both in reflection and transmission. In addition, because no shadowing function in transmission exists in the literature, this function is presented here in detail. The model is reduced to the high-frequency limit (or geometric optics). The energy conservation criterion is investigated versus the incidence angle, the permittivity of the lower medium, and the surface rms slope.

Strategic conservation planning for the Eastern North Carolina/Southeastern Virginia Strategic Habitat Conservation Team

USGS Publications Warehouse

Alexander-Vaughn, Louise B.; Collazo, Jaime A.; Drew, C. Ashton

2014-01-01

Fish and Wildlife Research Unit at North Carolina State University, is assisting the ENCSEVA team in developing a scientifically sound basis for the Plan though the elicitation of expert knowledge and the organization of that knowledge using the Open Standards for the Practice of Conservation. The Open Standards for the Practice of Conservation is a framework that is well suited to incorporating decision-making tools such as Structured Decision Making and provides a multi-step process to conceptually organize conservation projects in a manner that enhances the rigor and transparency of expert and knowledge-based plans. It helps define explicit pathways from 2 planned conservation activities and ultimate impact, as well as indicators to measure success (Stem et al. 2005). Specifically, the framework identifies conservation targets, key ecological attributes, threats, and associated indicators to monitor responses given the implementation of a conservation action (Conservation Measures Partnership 2007). This report serves to provide a scientific foundation for the Plan by summarizing the expert opinion of wildlife biologists, ecologists, hydrologists, researchers, natural resource managers, and conservation practitioners regarding five environments (wetlands, riverine systems, estuaries, uplands, and barrier islands) within the ENCSEVA geography. Specifically, this report describes (1) the approach to elicit expert knowledge meant to support the strategic plan, (2) how this knowledge can inform collaborative conservation planning, and (3) a summary of opportunities available for the ENCSEVA team to address threats and impacts associated with climate change within the ecoregion.

Assessing the shelf life of cost-efficient conservation plans for species at risk across gradients of agricultural land use.

PubMed

Robillard, Cassandra M; Kerr, Jeremy T

2017-08-01

High costs of land in agricultural regions warrant spatial prioritization approaches to conservation that explicitly consider land prices to produce protected-area networks that accomplish targets efficiently. However, land-use changes in such regions and delays between plan design and implementation may render optimized plans obsolete before implementation occurs. To measure the shelf life of cost-efficient conservation plans, we simulated a land-acquisition and restoration initiative aimed at conserving species at risk in Canada's farmlands. We accounted for observed changes in land-acquisition costs and in agricultural intensity based on censuses of agriculture taken from 1986 to 2011. For each year of data, we mapped costs and areas of conservation priority designated using Marxan. We compared plans to test for changes through time in the arrangement of high-priority sites and in the total cost of each plan. For acquisition costs, we measured the savings from accounting for prices during site selection. Land-acquisition costs and land-use intensity generally rose over time independent of inflation (24-78%), although rates of change were heterogeneous through space and decreased in some areas. Accounting for spatial variation in land price lowered the cost of conservation plans by 1.73-13.9%, decreased the range of costs by 19-82%, and created unique solutions from which to choose. Despite the rise in plan costs over time, the high conservation priority of particular areas remained consistent. Delaying conservation in these critical areas may compromise what optimized conservation plans can achieve. In the case of Canadian farmland, rapid conservation action is cost-effective, even with moderate levels of uncertainty in how to implement restoration goals. © 2016 Society for Conservation Biology.

Symmetrization of conservation laws with entropy for high-temperature hypersonic computations

NASA Technical Reports Server (NTRS)

Chalot, F.; Hughes, T. J. R.; Shakib, F.

1990-01-01

Results of Hughes, France, and Mallet are generalized to conservation law systems taking into account high-temperature effects. Symmetric forms of different equation sets are derived in terms of entropy variables. First, the case of a general divariant gas is studied; it can be specialized to the usual Navier-Stokes equations, as well as to situations where the gas is vibrationally excited, and undergoes equilibrium chemical reactions. The case of gas in thermochemical nonequilibrium is considered next. Transport phenomena, and in particular mass diffusion, are examined in the framework of symmetric advective-diffusive systems.

Conservation and diversification of the miR166 family in soybean and potential roles of newly identified miR166s.

PubMed

Li, Xuyan; Xie, Xin; Li, Ji; Cui, Yuhai; Hou, Yanming; Zhai, Lulu; Wang, Xiao; Fu, Yanli; Liu, Ranran; Bian, Shaomin

2017-02-01

microRNA166 (miR166) is a highly conserved family of miRNAs implicated in a wide range of cellular and physiological processes in plants. miR166 family generally comprises multiple miR166 members in plants, which might exhibit functional redundancy and specificity. The soybean miR166 family consists of 21 members according to the miRBase database. However, the evolutionary conservation and functional diversification of miR166 family members in soybean remain poorly understood. We identified five novel miR166s in soybean by data mining approach, thus enlarging the size of miR166 family from 21 to 26 members. Phylogenetic analyses of the 26 miR166s and their precursors indicated that soybean miR166 family exhibited both evolutionary conservation and diversification, and ten pairs of miR166 precursors with high sequence identity were individually grouped into a discrete clade in the phylogenetic tree. The analysis of genomic organization and evolution of MIR166 gene family revealed that eight segmental duplications and four tandem duplications might occur during evolution of the miR166 family in soybean. The cis-elements in promoters of MIR166 family genes and their putative targets pointed to their possible contributions to the functional conservation and diversification. The targets of soybean miR166s were predicted, and the cleavage of ATHB14-LIKE transcript was experimentally validated by RACE PCR. Further, the expression patterns of the five newly identified MIR166s and 12 target genes were examined during seed development and in response to abiotic stresses, which provided important clues for dissecting their functions and isoform specificity. This study enlarged the size of soybean miR166 family from 21 to 26 members, and the 26 soybean miR166s exhibited evolutionary conservation and diversification. These findings have laid a foundation for elucidating functional conservation and diversification of miR166 family members, especially during seed development or

Applications of very high-resolution imagery in the study and conservation of large predators in the Southern Ocean.

PubMed

Larue, Michelle A; Knight, Joseph

2014-12-01

The Southern Ocean is one of the most rapidly changing ecosystems on the planet due to the effects of climate change and commercial fishing for ecologically important krill and fish. Because sea ice loss is expected to be accompanied by declines in krill and fish predators, decoupling the effects of climate and anthropogenic changes on these predator populations is crucial for ecosystem-based management of the Southern Ocean. We reviewed research published from 2007 to 2014 that incorporated very high-resolution satellite imagery to assess distribution, abundance, and effects of climate and other anthropogenic changes on populations of predators in polar regions. Very high-resolution imagery has been used to study 7 species of polar animals in 13 papers, many of which provide methods through which further research can be conducted. Use of very high-resolution imagery in the Southern Ocean can provide a broader understanding of climate and anthropogenic forces on populations and inform management and conservation recommendations. We recommend that conservation biologists continue to integrate high-resolution remote sensing into broad-scale biodiversity and population studies in remote areas, where it can provide much needed detail. © 2014 Society for Conservation Biology.

Quantifying species recovery and conservation success to develop an IUCN Green List of Species.

PubMed

Akçakaya, H Resit; Bennett, Elizabeth L; Brooks, Thomas M; Grace, Molly K; Heath, Anna; Hedges, Simon; Hilton-Taylor, Craig; Hoffmann, Michael; Keith, David A; Long, Barney; Mallon, David P; Meijaard, Erik; Milner-Gulland, E J; Rodrigues, Ana S L; Rodriguez, Jon Paul; Stephenson, P J; Stuart, Simon N; Young, Richard P

2018-03-26

Stopping declines in biodiversity is critically important, but it is only a first step toward achieving more ambitious conservation goals. The absence of an objective and practical definition of species recovery that is applicable across taxonomic groups leads to inconsistent targets in recovery plans and frustrates reporting and maximization of conservation impact. We devised a framework for comprehensively assessing species recovery and conservation success. We propose a definition of a fully recovered species that emphasizes viability, ecological functionality, and representation; and use counterfactual approaches to quantify degree of recovery. This allowed us to calculate a set of 4 conservation metrics that demonstrate impacts of conservation efforts to date (conservation legacy); identify dependence of a species on conservation actions (conservation dependence); quantify expected gains resulting from conservation action in the medium term (conservation gain); and specify requirements to achieve maximum plausible recovery over the long term (recovery potential). These metrics can incentivize the establishment and achievement of ambitious conservation targets. We illustrate their use by applying the framework to a vertebrate, an invertebrate, and a woody and an herbaceous plant. Our approach is a preliminary framework for an International Union for Conservation of Nature (IUCN) Green List of Species, which was mandated by a resolution of IUCN members in 2012. Although there are several challenges in applying our proposed framework to a wide range of species, we believe its further development, implementation, and integration with the IUCN Red List of Threatened Species will help catalyze a positive and ambitious vision for conservation that will drive sustained conservation action. © 2018 The Authors. Conservation Biology published by Wiley Periodicals, Inc. on behalf of Society for Conservation Biology.

7 CFR 766.110 - Conservation Contract.

Code of Federal Regulations, 2010 CFR

2010-01-01

... floodplains; (iii) Areas of high water quality or scenic value; (iv) Historic or cultural properties listed in..., or 50 years. (e) Conservation management plan. The Agency, through the recommendations of the Conservation Contract review team, is responsible for approving the conservation management plan. (f...

7 CFR 766.110 - Conservation Contract.

Code of Federal Regulations, 2011 CFR

2011-01-01

... floodplains; (iii) Areas of high water quality or scenic value; (iv) Historic or cultural properties listed in..., or 50 years. (e) Conservation management plan. The Agency, through the recommendations of the Conservation Contract review team, is responsible for approving the conservation management plan. (f...

In vivo therapeutic potential of Dicer-hunting siRNAs targeting infectious hepatitis C virus.

PubMed

Watanabe, Tsunamasa; Hatakeyama, Hiroto; Matsuda-Yasui, Chiho; Sato, Yusuke; Sudoh, Masayuki; Takagi, Asako; Hirata, Yuichi; Ohtsuki, Takahiro; Arai, Masaaki; Inoue, Kazuaki; Harashima, Hideyoshi; Kohara, Michinori

2014-04-23

The development of RNA interference (RNAi)-based therapy faces two major obstacles: selecting small interfering RNA (siRNA) sequences with strong activity, and identifying a carrier that allows efficient delivery to target organs. Additionally, conservative region at nucleotide level must be targeted for RNAi in applying to virus because hepatitis C virus (HCV) could escape from therapeutic pressure with genome mutations. In vitro preparation of Dicer-generated siRNAs targeting a conserved, highly ordered HCV 5' untranslated region are capable of inducing strong RNAi activity. By dissecting the 5'-end of an RNAi-mediated cleavage site in the HCV genome, we identified potent siRNA sequences, which we designate as Dicer-hunting siRNAs (dh-siRNAs). Furthermore, formulation of the dh-siRNAs in an optimized multifunctional envelope-type nano device inhibited ongoing infectious HCV replication in human hepatocytes in vivo. Our efforts using both identification of optimal siRNA sequences and delivery to human hepatocytes suggest therapeutic potential of siRNA for a virus.

Cost-effectiveness of alternative conservation strategies with application to the Pacific leatherback turtle.

PubMed

Gjertsen, Heidi; Squires, Dale; Dutton, Peter H; Eguchi, Tomoharu

2014-02-01

Although holistic conservation addressing all sources of mortality for endangered species or stocks is the preferred conservation strategy, limited budgets require a criterion to prioritize conservation investments. We compared the cost-effectiveness of nesting site and at-sea conservation strategies for Pacific leatherback turtles (Dermochelys coriacea). We sought to determine which conservation strategy or mix of strategies would produce the largest increase in population growth rate per dollar. Alternative strategies included protection of nesters and their eggs at nesting beaches in Indonesia, gear changes, effort restrictions, and caps on turtle takes in the Hawaiian (U.S.A.) longline swordfish fishery, and temporal and area closures in the California (U.S.A.) drift gill net fishery. We used a population model with a biological metric to measure the effects of conservation alternatives. We normalized all effects by cost to prioritize those strategies with the greatest biological effect relative to its economic cost. We used Monte Carlo simulation to address uncertainty in the main variables and to calculate probability distributions for cost-effectiveness measures. Nesting beach protection was the most cost-effective means of achieving increases in leatherback populations. This result creates the possibility of noncompensatory bycatch mitigation, where high-bycatch fisheries invest in protecting nesting beaches. An example of this practice is U.S. processors of longline tuna and California drift gill net fishers that tax themselves to finance low-cost nesting site protection. Under certain conditions, fisheries interventions, such as technologies that reduce leatherback bycatch without substantially decreasing target species catch, can be cost-effective. Reducing bycatch in coastal areas where bycatch is high, particularly adjacent to nesting beaches, may be cost-effective, particularly, if fisheries in the area are small and of little commercial value. �

Global Conservation Priorities for Marine Turtles

PubMed Central

Wallace, Bryan P.; DiMatteo, Andrew D.; Bolten, Alan B.; Chaloupka, Milani Y.; Hutchinson, Brian J.; Abreu-Grobois, F. Alberto; Mortimer, Jeanne A.; Seminoff, Jeffrey A.; Amorocho, Diego; Bjorndal, Karen A.; Bourjea, Jérôme; Bowen, Brian W.; Briseño Dueñas, Raquel; Casale, Paolo; Choudhury, B. C.; Costa, Alice; Dutton, Peter H.; Fallabrino, Alejandro; Finkbeiner, Elena M.; Girard, Alexandre; Girondot, Marc; Hamann, Mark; Hurley, Brendan J.; López-Mendilaharsu, Milagros; Marcovaldi, Maria Angela; Musick, John A.; Nel, Ronel; Pilcher, Nicolas J.; Troëng, Sebastian; Witherington, Blair; Mast, Roderic B.

2011-01-01

Where conservation resources are limited and conservation targets are diverse, robust yet flexible priority-setting frameworks are vital. Priority-setting is especially important for geographically widespread species with distinct populations subject to multiple threats that operate on different spatial and temporal scales. Marine turtles are widely distributed and exhibit intra-specific variations in population sizes and trends, as well as reproduction and morphology. However, current global extinction risk assessment frameworks do not assess conservation status of spatially and biologically distinct marine turtle Regional Management Units (RMUs), and thus do not capture variations in population trends, impacts of threats, or necessary conservation actions across individual populations. To address this issue, we developed a new assessment framework that allowed us to evaluate, compare and organize marine turtle RMUs according to status and threats criteria. Because conservation priorities can vary widely (i.e. from avoiding imminent extinction to maintaining long-term monitoring efforts) we developed a “conservation priorities portfolio” system using categories of paired risk and threats scores for all RMUs (n = 58). We performed these assessments and rankings globally, by species, by ocean basin, and by recognized geopolitical bodies to identify patterns in risk, threats, and data gaps at different scales. This process resulted in characterization of risk and threats to all marine turtle RMUs, including identification of the world's 11 most endangered marine turtle RMUs based on highest risk and threats scores. This system also highlighted important gaps in available information that is crucial for accurate conservation assessments. Overall, this priority-setting framework can provide guidance for research and conservation priorities at multiple relevant scales, and should serve as a model for conservation status assessments and priority-setting for

Water Wisdom: 23 Stand-Alone Activities on Water Supply and Water Conservation for High School Students. 2nd Edition.

ERIC Educational Resources Information Center

Massachusetts State Water Resources Authority, Boston.

This water conservation education program for high schools consists of both stand-alone activities and teacher support materials. Lessons are divided into six broad categories: (1) The Water Cycle; (2) Water and Society; (3) Keeping Water Pure; (4) Visualizing Volumes; (5) The Economics of Water Use; and (6) Domestic Water Conservation. The…

Androgen receptor status is highly conserved during tumor progression of breast cancer.

PubMed

Grogg, André; Trippel, Mafalda; Pfaltz, Katrin; Lädrach, Claudia; Droeser, Raoul A; Cihoric, Nikola; Salhia, Bodour; Zweifel, Martin; Tapia, Coya

2015-11-09

highly conserved during tumor progression and a change only occurs in a small fraction (4.1 %). Our study supports the notion that targeting AR could be effective for many BC patients and that re-testing of AR status in formerly negative or mixed type BC's is recommended.

Systems and Trans-System Level Analysis Identifies Conserved Iron Deficiency Responses in the Plant Lineage[W][OA

PubMed Central

Urzica, Eugen I.; Casero, David; Yamasaki, Hiroaki; Hsieh, Scott I.; Adler, Lital N.; Karpowicz, Steven J.; Blaby-Haas, Crysten E.; Clarke, Steven G.; Loo, Joseph A.; Pellegrini, Matteo; Merchant, Sabeeha S.

2012-01-01

We surveyed the iron nutrition-responsive transcriptome of Chlamydomonas reinhardtii using RNA-Seq methodology. Presumed primary targets were identified in comparisons between visually asymptomatic iron-deficient versus iron-replete cells. This includes the known components of high-affinity iron uptake as well as candidates for distributive iron transport in C. reinhardtii. Comparison of growth-inhibited iron-limited versus iron-replete cells revealed changes in the expression of genes in chloroplastic oxidative stress response pathways, among hundreds of other genes. The output from the transcriptome was validated at multiple levels: by quantitative RT-PCR for assessing the data analysis pipeline, by quantitative proteomics for assessing the impact of changes in RNA abundance on the proteome, and by cross-species comparison for identifying conserved or universal response pathways. In addition, we assessed the functional importance of three target genes, VITAMIN C 2 (VTC2), MONODEHYDROASCORBATE REDUCTASE 1 (MDAR1), and CONSERVED IN THE GREEN LINEAGE AND DIATOMS 27 (CGLD27), by biochemistry or reverse genetics. VTC2 and MDAR1, which are key enzymes in de novo ascorbate synthesis and ascorbate recycling, respectively, are likely responsible for the 10-fold increase in ascorbate content of iron-limited cells. CGLD27/At5g67370 is a highly conserved, presumed chloroplast-localized pioneer protein and is important for growth of Arabidopsis thaliana in low iron. PMID:23043051

Mistaken identity: activating conservative political identities induces "conservative" financial decisions.

PubMed

Morris, Michael W; Carranza, Erica; Fox, Craig R

2008-11-01

Four studies investigated whether activating a social identity can lead group members to choose options that are labeled in words associated with that identity. When political identities were made salient, Republicans (but not Democrats) became more likely to choose the gamble or investment option labeled "conservative." This shift did not occur in a condition in which the same options were unlabeled. Thus, the mechanism underlying the effect appears to be not activated identity-related values prioritizing low risk, but rather activated identity-related language (the group label "conservative"). Indeed, when political identities were salient, Republicans favored options labeled "conservative" regardless of whether the options were low or high risk. Finally, requiring participants to explain the label "conservative" before making their choice did not diminish the effect, which suggests that it does not merely reflect inattention to content or construct accessibility. We discuss the implications of these results for the literatures on identity, priming, choice, politics, and marketing.

ECASTAR: Energy Conservation; an Assessment of Systems, Technologies and Requirements

NASA Technical Reports Server (NTRS)

1975-01-01

A methodology for a systems approach display and assessment of the potential for energy conservation actions and the impacts of those actions was presented. The U.S. economy is divided into four sectors: energy industry, industry, residential/commercial and transportation. Each sector is assessed with respect to energy conservation actions and impacts. The four sectors are combined and three strategies for energy conservation actions for the combined sectors are assessed. The three strategies (national energy conservation, electrification and diversification) represent energy conservation actions for the near term (now to 1985), the mid term (1985 to 2000) and the far term (2000 and beyond). The assessment procedure includes input/output analysis to bridge the flows between the sectors, and net economics and net energetics as performance criteria for the conservation actions. Targets of opportunity for large net energy net energy savings and the application of technology to achieve these savings are discussed.

Landscape Conservation Cooperatives: Creating a Collaborative Conservation Vision in the Face of Climate Change Uncertainty

NASA Astrophysics Data System (ADS)

Athearn, N.; Schlafmann, D.

2015-12-01

The 22 Landscape Conservation Cooperatives (LCCs) form a "network of networks," each defined by the characteristics of its ecoregion and its unique community of conservation managers, practitioners, and scientists. As self-directed partnerships, LCCs are strongly influenced not only by the landscape but by the evolving cultures and values that define the multi-faceted relationships between people and place. LCCs maintain an ecologically connected network across these diverse landscapes by transcending borders and leveraging resources. Natural resource managers are challenged to make decisions in the face of multiple uncertainties, and several partners across the network have recognized that climate change is one important uncertainty that spans boundaries - both across the conservation community and beyond. The impacts of climate change across the LCC Network are likely to be as diverse as the network itself - manifesting as, for example, sea level rise, ocean acidification, loss of sea ice, and shifts in climate patterns and timing - but synergies are being leveraged within and between LCCs and national climate-focused programs to systematically address the needs of the network to support a collaborative conservation vision that addresses multiple landscape-scale stressors in the face of climate uncertainties. This vision is being achieved by leveraging the convening power of the LCCs and collaborating with DOI Climate Science Centers and others. Selected case studies will demonstrate how the network finds strength in its differences, but also reveals powerful collaborative opportunities through integrated science, shared conservation strategies, and strategic approaches for translating targeted science to conservation action. These examples exemplify past successes as well as ongoing efforts as the network continues to bring about effective application of climate science to achieve conservation outcomes across the LCC Network in an uncertain future climate.

Tobacco industry targeting youth in Argentina.

PubMed

Braun, S; Mejia, R; Ling, P M; Pérez-Stable, E J

2008-04-01

Argentina has one of the highest cigarette smoking rates among both men and women in the Americas and no legislated restrictions on tobacco industry advertising. The tobacco industry has traditionally expanded markets by targeting adolescents and young adults. The objective of this study was to determine whether and how the tobacco industry promotes cigarettes to adolescents in Argentina. We conducted a systematic search of tobacco industry documents available through the internet dated between 1995 and 2004 using standard search terms to identify marketing strategies in Argentina. A selected review of the four leading newspapers and nine magazines with reported high readership among adolescents was completed. The selected print media were searched for tobacco images and these were classified as advertisements if associated with a commercial product or as a story if not. The tobacco industry used market segmentation as a strategy to target Argentinean consumers. British American Tobacco (BAT) undertook a young adult psychographic study and classified them as "progressives", "Jurassics" or "conservatives" and "crudos" or "spoiled brats". BAT marketed Lucky Strike to the "progressives" using Hollywood movies as a vehicle. The tobacco industry also targeted their national brands to the conservatives and linked these brands with "nationalistic values" in advertising campaigns. Philip Morris promoted Marlboro by sponsoring activities directed at young people and they launched the 10 cigarettes packet as a starter vehicle. The tobacco industry used psychographic segmentation of the population and developed advertising strategies focused on youth. Tobacco control researchers and advocates must be able to address these strategies in counter-marketing interventions.

Comparing pseudo-absences generation techniques in Boosted Regression Trees models for conservation purposes: A case study on amphibians in a protected area.

PubMed

Cerasoli, Francesco; Iannella, Mattia; D'Alessandro, Paola; Biondi, Maurizio

2017-01-01

Boosted Regression Trees (BRT) is one of the modelling techniques most recently applied to biodiversity conservation and it can be implemented with presence-only data through the generation of artificial absences (pseudo-absences). In this paper, three pseudo-absences generation techniques are compared, namely the generation of pseudo-absences within target-group background (TGB), testing both the weighted (WTGB) and unweighted (UTGB) scheme, and the generation at random (RDM), evaluating their performance and applicability in distribution modelling and species conservation. The choice of the target group fell on amphibians, because of their rapid decline worldwide and the frequent lack of guidelines for conservation strategies and regional-scale planning, which instead could be provided through an appropriate implementation of SDMs. Bufo bufo, Salamandrina perspicillata and Triturus carnifex were considered as target species, in order to perform our analysis with species having different ecological and distributional characteristics. The study area is the "Gran Sasso-Monti della Laga" National Park, which hosts 15 Natura 2000 sites and represents one of the most important biodiversity hotspots in Europe. Our results show that the model calibration ameliorates when using the target-group based pseudo-absences compared to the random ones, especially when applying the WTGB. Contrarily, model discrimination did not significantly vary in a consistent way among the three approaches with respect to the tree target species. Both WTGB and RDM clearly isolate the highly contributing variables, supplying many relevant indications for species conservation actions. Moreover, the assessment of pairwise variable interactions and their three-dimensional visualization further increase the amount of useful information for protected areas' managers. Finally, we suggest the use of RDM as an admissible alternative when it is not possible to individuate a suitable set of species as a

Water conservation in irrigation can increase water use

PubMed Central

Ward, Frank A.; Pulido-Velazquez, Manuel

2008-01-01

Climate change, water supply limits, and continued population growth have intensified the search for measures to conserve water in irrigated agriculture, the world's largest water user. Policy measures that encourage adoption of water-conserving irrigation technologies are widely believed to make more water available for cities and the environment. However, little integrated analysis has been conducted to test this hypothesis. This article presents results of an integrated basin-scale analysis linking biophysical, hydrologic, agronomic, economic, policy, and institutional dimensions of the Upper Rio Grande Basin of North America. It analyzes a series of water conservation policies for their effect on water used in irrigation and on water conserved. In contrast to widely-held beliefs, our results show that water conservation subsidies are unlikely to reduce water use under conditions that occur in many river basins. Adoption of more efficient irrigation technologies reduces valuable return flows and limits aquifer recharge. Policies aimed at reducing water applications can actually increase water depletions. Achieving real water savings requires designing institutional, technical, and accounting measures that accurately track and economically reward reduced water depletions. Conservation programs that target reduced water diversions or applications provide no guarantee of saving water. PMID:19015510

Constitutive nuclear lamina-genome interactions are highly conserved and associated with A/T-rich sequence.

PubMed

Meuleman, Wouter; Peric-Hupkes, Daan; Kind, Jop; Beaudry, Jean-Bernard; Pagie, Ludo; Kellis, Manolis; Reinders, Marcel; Wessels, Lodewyk; van Steensel, Bas

2013-02-01

In metazoans, the nuclear lamina is thought to play an important role in the spatial organization of interphase chromosomes, by providing anchoring sites for large genomic segments named lamina-associated domains (LADs). Some of these LADs are cell-type specific, while many others appear constitutively associated with the lamina. Constitutive LADs (cLADs) may contribute to a basal chromosome architecture. By comparison of mouse and human lamina interaction maps, we find that the sizes and genomic positions of cLADs are strongly conserved. Moreover, cLADs are depleted of synteny breakpoints, pointing to evolutionary selective pressure to keep cLADs intact. Paradoxically, the overall sequence conservation is low for cLADs. Instead, cLADs are universally characterized by long stretches of DNA of high A/T content. Cell-type specific LADs also tend to adhere to this "A/T rule" in embryonic stem cells, but not in differentiated cells. This suggests that the A/T rule represents a default positioning mechanism that is locally overruled during lineage commitment. Analysis of paralogs suggests that during evolution changes in A/T content have driven the relocation of genes to and from the nuclear lamina, in tight association with changes in expression level. Taken together, these results reveal that the spatial organization of mammalian genomes is highly conserved and tightly linked to local nucleotide composition.

Limitations of outsourcing on-the-ground biodiversity conservation.

PubMed

Iacona, Gwenllian D; Bode, Michael; Armsworth, Paul R

2016-12-01

costs of achieving conservation targets. © 2016 Society for Conservation Biology.

Private land manager capacity to conserve threatened communities under climate change.

PubMed

Raymond, C M; Lechner, A M; Lockwood, M; Carter, O; Harris, R M B; Gilfedder, L

2015-08-15

Major global changes in vegetation community distributions and ecosystem processes are expected as a result of climate change. In agricultural regions with a predominance of private land, biodiversity outcomes will depend on the adaptive capacity of individual land managers, as well as their willingness to engage with conservation programs and actions. Understanding adaptive capacity of landholders is critical for assessing future prospects for biodiversity conservation in privately owned agricultural landscapes globally, given projected climate change. This paper is the first to develop and apply a set of statistical methods (correlation and bionomial regression analyses) for combining social data on land manager adaptive capacity and factors associated with conservation program participation with biophysical data describing the current and projected-future distribution of climate suitable for vegetation communities. We apply these methods to the Tasmanian Midlands region of Tasmania, Australia and discuss the implications of the modelled results on conservation program strategy design in other contexts. We find that the integrated results can be used by environmental management organisations to design community engagement programs, and to tailor their messages to land managers with different capacity types and information behaviours. We encourage environmental agencies to target high capacity land managers by diffusing climate change and grassland management information through well respected conservation NGOs and farm system groups, and engage low capacity land managers via formalized mentoring programs. Copyright © 2015 Elsevier Ltd. All rights reserved.

High cumulants of conserved charges and their statistical uncertainties

NASA Astrophysics Data System (ADS)

Li-Zhu, Chen; Ye-Yin, Zhao; Xue, Pan; Zhi-Ming, Li; Yuan-Fang, Wu

2017-10-01

We study the influence of measured high cumulants of conserved charges on their associated statistical uncertainties in relativistic heavy-ion collisions. With a given number of events, the measured cumulants randomly fluctuate with an approximately normal distribution, while the estimated statistical uncertainties are found to be correlated with corresponding values of the obtained cumulants. Generally, with a given number of events, the larger the cumulants we measure, the larger the statistical uncertainties that are estimated. The error-weighted averaged cumulants are dependent on statistics. Despite this effect, however, it is found that the three sigma rule of thumb is still applicable when the statistics are above one million. Supported by NSFC (11405088, 11521064, 11647093), Major State Basic Research Development Program of China (2014CB845402) and Ministry of Science and Technology (MoST) (2016YFE0104800)

Fisheries conservation on the high seas: linking conservation physiology and fisheries ecology for the management of large pelagic fishes

PubMed Central

Horodysky, Andrij Z.; Cooke, Steven J.; Graves, John E.; Brill, Richard W.

2016-01-01

Populations of tunas, billfishes and pelagic sharks are fished at or over capacity in many regions of the world. They are captured by directed commercial and recreational fisheries (the latter of which often promote catch and release) or as incidental catch or bycatch in commercial fisheries. Population assessments of pelagic fishes typically incorporate catch-per-unit-effort time-series data from commercial and recreational fisheries; however, there have been notable changes in target species, areas fished and depth-specific gear deployments over the years that may have affected catchability. Some regional fisheries management organizations take into account the effects of time- and area-specific changes in the behaviours of fish and fishers, as well as fishing gear, to standardize catch-per-unit-effort indices and refine population estimates. However, estimates of changes in stock size over time may be very sensitive to underlying assumptions of the effects of oceanographic conditions and prey distribution on the horizontal and vertical movement patterns and distribution of pelagic fishes. Effective management and successful conservation of pelagic fishes requires a mechanistic understanding of their physiological and behavioural responses to environmental variability, potential for interaction with commercial and recreational fishing gear, and the capture process. The interdisciplinary field of conservation physiology can provide insights into pelagic fish demography and ecology (including environmental relationships and interspecific interactions) by uniting the complementary expertise and skills of fish physiologists and fisheries scientists. The iterative testing by one discipline of hypotheses generated by the other can span the fundamental–applied science continuum, leading to the development of robust insights supporting informed management. The resulting species-specific understanding of physiological abilities and tolerances can help to improve stock

Disruption of long-distance highly conserved noncoding elements in neurocristopathies.

PubMed

Amiel, Jeanne; Benko, Sabina; Gordon, Christopher T; Lyonnet, Stanislas

2010-12-01

One of the key discoveries of vertebrate genome sequencing projects has been the identification of highly conserved noncoding elements (CNEs). Some characteristics of CNEs include their high frequency in mammalian genomes, their potential regulatory role in gene expression, and their enrichment in gene deserts nearby master developmental genes. The abnormal development of neural crest cells (NCCs) leads to a broad spectrum of congenital malformation(s), termed neurocristopathies, and/or tumor predisposition. Here we review recent findings that disruptions of CNEs, within or at long distance from the coding sequences of key genes involved in NCC development, result in neurocristopathies via the alteration of tissue- or stage-specific long-distance regulation of gene expression. While most studies on human genetic disorders have focused on protein-coding sequences, these examples suggest that investigation of genomic alterations of CNEs will provide a broader understanding of the molecular etiology of both rare and common human congenital malformations. © 2010 New York Academy of Sciences.

Conservation of high-flux backbone in alternate optimal and near-optimal flux distributions of metabolic networks.

PubMed

Samal, Areejit

2008-12-01

Constraint-based flux balance analysis (FBA) has proven successful in predicting the flux distribution of metabolic networks in diverse environmental conditions. FBA finds one of the alternate optimal solutions that maximizes the biomass production rate. Almaas et al. have shown that the flux distribution follows a power law, and it is possible to associate with most metabolites two reactions which maximally produce and consume a given metabolite, respectively. This observation led to the concept of high-flux backbone (HFB) in metabolic networks. In previous work, the HFB has been computed using a particular optima obtained using FBA. In this paper, we investigate the conservation of HFB of a particular solution for a given medium across different alternate optima and near-optima in metabolic networks of E. coli and S. cerevisiae. Using flux variability analysis (FVA), we propose a method to determine reactions that are guaranteed to be in HFB regardless of alternate solutions. We find that the HFB of a particular optima is largely conserved across alternate optima in E. coli, while it is only moderately conserved in S. cerevisiae. However, the HFB of a particular near-optima shows a large variation across alternate near-optima in both organisms. We show that the conserved set of reactions in HFB across alternate near-optima has a large overlap with essential reactions and reactions which are both uniquely consuming (UC) and uniquely producing (UP). Our findings suggest that the structure of the metabolic network admits a high degree of redundancy and plasticity in near-optimal flow patterns enhancing system robustness for a given environmental condition.

Genome-wide identification of conserved microRNA and their response to drought stress in Dongxiang wild rice (Oryza rufipogon Griff.).

PubMed

Zhang, Fantao; Luo, Xiangdong; Zhou, Yi; Xie, Jiankun

2016-04-01

To identify drought stress-responsive conserved microRNA (miRNA) from Dongxiang wild rice (Oryza rufipogon Griff., DXWR) on a genome-wide scale, high-throughput sequencing technology was used to sequence libraries of DXWR samples, treated with and without drought stress. 505 conserved miRNAs corresponding to 215 families were identified. 17 were significantly down-regulated and 16 were up-regulated under drought stress. Stem-loop qRT-PCR revealed the same expression patterns as high-throughput sequencing, suggesting the accuracy of the sequencing result was high. Potential target genes of the drought-responsive miRNA were predicted to be involved in diverse biological processes. Furthermore, 16 miRNA families were first identified to be involved in drought stress response from plants. These results present a comprehensive view of the conserved miRNA and their expression patterns under drought stress for DXWR, which will provide valuable information and sequence resources for future basis studies.

The Role of High Dose Interleukin-2 in the Era of Targeted Therapy.

PubMed

Gills, Jessie; Parker, William P; Pate, Scott; Niu, Sida; Van Veldhuizen, Peter; Mirza, Moben; Holzbeierlein, Jeffery M; Lee, Eugene K

2017-09-01

We assessed survival outcomes following high dose interleukin-2 in a contemporary cohort of patients during the era of targeted agents. We retrospectively reviewed the records of patients with metastatic renal cell carcinoma treated with high dose interleukin-2 between July 2007 and September 2014. Clinicopathological data were abstracted and patient response to therapy was based on RECIST (Response Evaluation Criteria In Solid Tumors), version 1.1 criteria. The Kaplan-Meier method was used to estimate progression-free and overall survival in the entire cohort, the response to high dose interleukin-2 in regard to previous targeted agent therapy and the response to the targeted agent in relation to the response to high dose interleukin-2. We identified 92 patients, of whom 87 had documentation of a response to high dose interleukin-2. Median overall survival was 34.4 months from the initiation of high dose interleukin-2 therapy in the entire cohort. Patients who received targeted therapy before high dose interleukin-2 had overall survival (median 34.4 and 30.0 months, p = 0.88) and progression-free survival (median 1.5 and 1.7 months, p = 0.8) similar to those in patients who received no prior therapy, respectively. Additionally, patients with a complete or partial response to high dose interleukin-2 had similar outcomes for subsequent targeted agents compared to patients whose best response was stable or progressive disease (median overall survival 30.1 vs 25.4 months, p = 0.4). Our data demonstrate that patient responses to high dose interleukin-2 and to targeted agents before and after receiving high dose interleukin-2 are independent. As such, carefully selected patients should be offered high dose interleukin-2 for the possibility of a complete and durable response without the fear of limiting the treatment benefit of targeted agents. Copyright © 2017 American Urological Association Education and Research, Inc. Published by Elsevier Inc. All rights reserved.

Neglected wild life: Parasitic biodiversity as a conservation target☆

PubMed Central

Gómez, Andrés; Nichols, Elizabeth

2013-01-01

Parasites appropriate host resources to feed and/or to reproduce, and lower host fitness to varying degrees. As a consequence, they can negatively impact human and animal health, food production, economic trade, and biodiversity conservation. They can also be difficult to study and have historically been regarded as having little influence on ecosystem organization and function. Not surprisingly, parasitic biodiversity has to date not been the focus of much positive attention from the conservation community. However, a growing body of evidence demonstrates that parasites are extremely diverse, have key roles in ecological and evolutionary processes, and that infection may paradoxically result in ecosystem services of direct human relevance. Here we argue that wildlife parasites should be considered meaningful conservation targets no less relevant than their hosts. We discuss their numerical and functional importance, current conservation status, and outline a series of non-trivial challenges to consider before incorporating parasite biodiversity in conservation strategies. We also suggest that addressing the key knowledge gaps and communication deficiencies that currently impede broad discussions about parasite conservation requires input from wildlife parasitologists. PMID:24533340

Vulnerability of dynamic genetic conservation units of forest trees in Europe to climate change.

PubMed

Schueler, Silvio; Falk, Wolfgang; Koskela, Jarkko; Lefèvre, François; Bozzano, Michele; Hubert, Jason; Kraigher, Hojka; Longauer, Roman; Olrik, Ditte C

2014-05-01

A transnational network of genetic conservation units for forest trees was recently documented in Europe aiming at the conservation of evolutionary processes and the adaptive potential of natural or man-made tree populations. In this study, we quantified the vulnerability of individual conservation units and the whole network to climate change using climate favourability models and the estimated velocity of climate change. Compared to the overall climate niche of the analysed target species populations at the warm and dry end of the species niche are underrepresented in the network. However, by 2100, target species in 33-65 % of conservation units, mostly located in southern Europe, will be at the limit or outside the species' current climatic niche as demonstrated by favourabilities below required model sensitivities of 95%. The highest average decrease in favourabilities throughout the network can be expected for coniferous trees although they are mainly occurring within units in mountainous landscapes for which we estimated lower velocities of change. Generally, the species-specific estimates of favourabilities showed only low correlations to the velocity of climate change in individual units, indicating that both vulnerability measures should be considered for climate risk analysis. The variation in favourabilities among target species within the same conservation units is expected to increase with climate change and will likely require a prioritization among co-occurring species. The present results suggest that there is a strong need to intensify monitoring efforts and to develop additional conservation measures for populations in the most vulnerable units. Also, our results call for continued transnational actions for genetic conservation of European forest trees, including the establishment of dynamic conservation populations outside the current species distribution ranges within European assisted migration schemes. © 2013 John Wiley & Sons Ltd.

Improving Robotic Assembly of Planar High Energy Density Targets

NASA Astrophysics Data System (ADS)

Dudt, D.; Carlson, L.; Alexander, N.; Boehm, K.

2016-10-01

Increased quantities of planar assemblies for high energy density targets are needed with higher shot rates being implemented at facilities such as the National Ignition Facility and the Matter in Extreme Conditions station of the Linac Coherent Light Source. To meet this growing demand, robotics are used to reduce assembly time. This project studies how machine vision and force feedback systems can be used to improve the quantity and quality of planar target assemblies. Vision-guided robotics can identify and locate parts, reducing laborious manual loading of parts into precision pallets and associated teaching of locations. On-board automated inspection can measure part pickup offsets to correct part drop-off placement into target assemblies. Force feedback systems can detect pickup locations and apply consistent force to produce more uniform glue bond thickness, thus improving the performance of the targets. System designs and performance evaluations will be presented. Work supported in part by the US DOE under the Science Undergraduate Laboratory Internships Program (SULI) and ICF Target Fabrication DE-NA0001808.

Low-Intensity Agricultural Landscapes in Transylvania Support High Butterfly Diversity: Implications for Conservation

PubMed Central

Loos, Jacqueline; Dorresteijn, Ine; Hanspach, Jan; Fust, Pascal; Rakosy, László; Fischer, Joern

2014-01-01

European farmland biodiversity is declining due to land use changes towards agricultural intensification or abandonment. Some Eastern European farming systems have sustained traditional forms of use, resulting in high levels of biodiversity. However, global markets and international policies now imply rapid and major changes to these systems. To effectively protect farmland biodiversity, understanding landscape features which underpin species diversity is crucial. Focusing on butterflies, we addressed this question for a cultural-historic landscape in Southern Transylvania, Romania. Following a natural experiment, we randomly selected 120 survey sites in farmland, 60 each in grassland and arable land. We surveyed butterfly species richness and abundance by walking transects with four repeats in summer 2012. We analysed species composition using Detrended Correspondence Analysis. We modelled species richness, richness of functional groups, and abundance of selected species in response to topography, woody vegetation cover and heterogeneity at three spatial scales, using generalised linear mixed effects models. Species composition widely overlapped in grassland and arable land. Composition changed along gradients of heterogeneity at local and context scales, and of woody vegetation cover at context and landscape scales. The effect of local heterogeneity on species richness was positive in arable land, but negative in grassland. Plant species richness, and structural and topographic conditions at multiple scales explained species richness, richness of functional groups and species abundances. Our study revealed high conservation value of both grassland and arable land in low-intensity Eastern European farmland. Besides grassland, also heterogeneous arable land provides important habitat for butterflies. While butterfly diversity in arable land benefits from heterogeneity by small-scale structures, grasslands should be protected from fragmentation to provide

Voyager 2 Uranus and Neptune targeting

NASA Technical Reports Server (NTRS)

Gray, D. L.; Cesarone, R. J.; Van Allen, R. E.

1982-01-01

Targeting strategies are developed for the Voyager 2 flybys of Uranus and Neptune/Triton. The need to maximize science return, conserve propellant, and maintain spacecraft safety presents a challenge, given the difficulty in estimating the spacecraft orbit relative to these outer planets. Expected propellant usage, science return, and targeting complexity are presented for each targeting strategy. For the dual encounter of Neptune and its satellite Triton, split targeting conditions are proposed to fix the most important conditions at each body, and thus minimize science losses resulting from Triton ephemeris uncertainties.

Anticancer molecules targeting fibroblast growth factor receptors.

PubMed

Liang, Guang; Liu, Zhiguo; Wu, Jianzhang; Cai, Yuepiao; Li, Xiaokun

2012-10-01

The fibroblast growth factor receptor (FGFR) family includes four highly conserved receptor tyrosine kinases: FGFR1-4. Upon ligand binding, FGFRs activate an array of downstream signaling pathways, such as the mitogen activated protein kinase (MAPK) and the phosphoinositide-3-kinase (PI3K)/Akt pathways. These FGFR cascades play crucial roles in tumor cell proliferation, angiogenesis, migration, and survival. The combination of knockdown studies and pharmaceutical inhibition in preclinical models demonstrates that FGFRs are attractive targets for therapeutic intervention in cancer. Multiple FGFR inhibitors with various structural skeletons have been designed, synthesized, and evaluated. Reviews on FGFRs have recently focused on FGFR signaling, pathophysiology, and functions in cancer or other diseases. In this article, we review recent advances in structure-activity relationships (SAR) of FGFR inhibitors, as well as the FGFR-targeting drug design strategies currently employed in targeting deregulated FGFRs by antibodies and small molecule inhibitors. Copyright © 2012 Elsevier Ltd. All rights reserved.

Optimal fire histories for biodiversity conservation.

PubMed

Kelly, Luke T; Bennett, Andrew F; Clarke, Michael F; McCarthy, Michael A

2015-04-01

Fire is used as a management tool for biodiversity conservation worldwide. A common objective is to avoid population extinctions due to inappropriate fire regimes. However, in many ecosystems, it is unclear what mix of fire histories will achieve this goal. We determined the optimal fire history of a given area for biological conservation with a method that links tools from 3 fields of research: species distribution modeling, composite indices of biodiversity, and decision science. We based our case study on extensive field surveys of birds, reptiles, and mammals in fire-prone semi-arid Australia. First, we developed statistical models of species' responses to fire history. Second, we determined the optimal allocation of successional states in a given area, based on the geometric mean of species relative abundance. Finally, we showed how conservation targets based on this index can be incorporated into a decision-making framework for fire management. Pyrodiversity per se did not necessarily promote vertebrate biodiversity. Maximizing pyrodiversity by having an even allocation of successional states did not maximize the geometric mean abundance of bird species. Older vegetation was disproportionately important for the conservation of birds, reptiles, and small mammals. Because our method defines fire management objectives based on the habitat requirements of multiple species in the community, it could be used widely to maximize biodiversity in fire-prone ecosystems. © 2014 Society for Conservation Biology.

A free-jet Hg target operating in a high magnetic field intersecting a high-power proton beam

NASA Astrophysics Data System (ADS)

Graves, Van; Spampinato, Philip; Gabriel, Tony; Kirk, Harold; Simos, Nicholas; Tsang, Thomas; McDonald, Kirk; Peter Titus; Fabich, Adrian; Haseroth, Helmut; Lettry, Jacques

2006-06-01

A proof-of-principal experiment to investigate the interaction of a proton beam, high magnetic field, and high-Z target is planned to take place at CERN in early 2007. This experiment is part of the Muon Collider Collaboration, with participants from Brookhaven National Laboratory, Princeton University, Massachusetts Institute Of Technology, European Organization for Nuclear Research-CERN, Rutherford Appleton Laboratory, and Oak Ridge National Laboratory. An unconstrained mercury jet target system that interacts with a high power (1 MW) proton beam in a high magnetic field (15 T) is being designed. The Hg jet diameter is 1-cm with a velocity up to 20 m/s. A laser optical diagnostic system will be incorporated into the target design to permit observation of the dispersal of the jet resulting from interaction with a 24 GeV proton beam with up to 20×1012 ppp. The target system includes instruments for sensing mercury vapor, temperature, flow rate, and sump tank level, and the means to position the jet relative to the magnetic axis of a solenoid and the proton beam. The design considerations for the system include all issues dealing with safely handling approximately 23 l of Hg, transporting the target system and the mercury to CERN, decommissioning the experiment, and returning the mildly activated equipment and Hg to the US.

A free-jet Hg target operating in a high magnetic field intersecting a high-power proton beam

NASA Astrophysics Data System (ADS)

Van Graves; Spampinato, Philip; Gabriel, Tony; Kirk, Harold; Simos, Nicholas; Tsang, Thomas; McDonald, Kirk; Peter Titus; Fabich, Adrian; Haseroth, Helmut; Lettry, Jacques

2006-06-01

A proof-of-principal experiment to investigate the interaction of a proton beam, high magnetic field, and high- Z target is planned to take place at CERN in early 2007. This experiment is part of the Muon Collider Collaboration, with participants from Brookhaven National Laboratory, Princeton University, Massachusetts Institute Of Technology, European Organization for Nuclear Research-CERN, Rutherford Appleton Laboratory, and Oak Ridge National Laboratory. An unconstrained mercury jet target system that interacts with a high power (1 MW) proton beam in a high magnetic field (15 T) is being designed. The Hg jet diameter is 1-cm with a velocity up to 20 m/s. A laser optical diagnostic system will be incorporated into the target design to permit observation of the dispersal of the jet resulting from interaction with a 24 GeV proton beam with up to 20×10 12 ppp. The target system includes instruments for sensing mercury vapor, temperature, flow rate, and sump tank level, and the means to position the jet relative to the magnetic axis of a solenoid and the proton beam. The design considerations for the system include all issues dealing with safely handling approximately 23 l of Hg, transporting the target system and the mercury to CERN, decommissioning the experiment, and returning the mildly activated equipment and Hg to the US.

Bison conservation initiative: Bison conservation genetics workshop: report and recommendations

USGS Publications Warehouse

Gogan, Peter J.; Dratch, Peter

2010-01-01

targets, and develop a metapopulation structure between herds. Fourth and finally, the current methods used to evaluate the DOI bison herds, using mitochondrial DNA and a suite of nuclear DNA microsatellites, are highly informative at the herd level. They have confirmed relatedness of herds that we know from historical records have a common origin. They have detected cattle ancestry in most of the herds where it was suspected and have shown some loss of rare alleles. However, they do not sample across the bison genome, and the use of neutral genetic markers as the basis for selection of individual bison—either to breed or move to other herds—would be better supported by more high-resolution molecular methods currently under development.

Isolation and expression analysis of four HD-ZIP III family genes targeted by microRNA166 in peach.

PubMed

Zhang, C H; Zhang, B B; Ma, R J; Yu, M L; Guo, S L; Guo, L

2015-10-30

MicroRNA166 (miR166) is known to have highly conserved targets that encode proteins of the class III homeodomain-leucine zipper (HD-ZIP III) family, in a broad range of plant species. To further understand the relationship between HD-ZIP III genes and miR166, four HD-ZIP III family genes (PpHB14, PpHB15, PpHB8, and PpREV) were isolated from peach (Prunus persica) tissue and characterized. Spatio-temporal expression profiles of the genes were analyzed. Genes of the peach HD-ZIP III family were predicted to encode five conserved domains. Deduced amino acid sequences and tertiary structures of the four peach HD-ZIP III genes were highly conserved, with corresponding genes in Arabidopsis thaliana. The expression level of four targets displayed the opposite trend to that of miR166 throughout fruit development, with the exception of PpHB14 from 35 to 55 days after full bloom (DAFB). This finding indicates that miR166 may negatively regulate its four targets throughout fruit development. As for leaf and phloem, the same trend in expression level was observed between four targets and miR166 from 75 to 105 DAFB. However, the opposite trend was observed for the transcript level between four targets and miR166 from 35 to 55 DAFB. miRNA166 may negatively regulate four targets in some but not all developmental stages for a given tissue. The four genes studied were observed to have, exactly or generally, the same change tendency as individual tissue development, a finding that suggests genes of the HD-ZIP III family in peach may have complementary or cooperative functions in various tissues.

Comprehensive Non-Destructive Conservation Documentation of Lunar Samples Using High-Resolution Image-Based 3D Reconstructions and X-Ray CT Data

NASA Technical Reports Server (NTRS)

Blumenfeld, E. H.; Evans, C. A.; Oshel, E. R.; Liddle, D. A.; Beaulieu, K.; Zeigler, R. A.; Hanna, R. D.; Ketcham, R. A.

2015-01-01

Established contemporary conservation methods within the fields of Natural and Cultural Heritage encourage an interdisciplinary approach to preservation of heritage material (both tangible and intangible) that holds "Outstanding Universal Value" for our global community. NASA's lunar samples were acquired from the moon for the primary purpose of intensive scientific investigation. These samples, however, also invoke cultural significance, as evidenced by the millions of people per year that visit lunar displays in museums and heritage centers around the world. Being both scientifically and culturally significant, the lunar samples require a unique conservation approach. Government mandate dictates that NASA's Astromaterials Acquisition and Curation Office develop and maintain protocols for "documentation, preservation, preparation and distribution of samples for research, education and public outreach" for both current and future collections of astromaterials. Documentation, considered the first stage within the conservation methodology, has evolved many new techniques since curation protocols for the lunar samples were first implemented, and the development of new documentation strategies for current and future astromaterials is beneficial to keeping curation protocols up to date. We have developed and tested a comprehensive non-destructive documentation technique using high-resolution image-based 3D reconstruction and X-ray CT (XCT) data in order to create interactive 3D models of lunar samples that would ultimately be served to both researchers and the public. These data enhance preliminary scientific investigations including targeted sample requests, and also provide a new visual platform for the public to experience and interact with the lunar samples. We intend to serve these data as they are acquired on NASA's Astromaterials Acquisistion and Curation website at http://curator.jsc.nasa.gov/. Providing 3D interior and exterior documentation of astromaterial

The Most Deeply Conserved Noncoding Sequences in Plants Serve Similar Functions to Those in Vertebrates Despite Large Differences in Evolutionary Rates[W

PubMed Central

Burgess, Diane; Freeling, Michael

2014-01-01

In vertebrates, conserved noncoding elements (CNEs) are functionally constrained sequences that can show striking conservation over >400 million years of evolutionary distance and frequently are located megabases away from target developmental genes. Conserved noncoding sequences (CNSs) in plants are much shorter, and it has been difficult to detect conservation among distantly related genomes. In this article, we show not only that CNS sequences can be detected throughout the eudicot clade of flowering plants, but also that a subset of 37 CNSs can be found in all flowering plants (diverging ∼170 million years ago). These CNSs are functionally similar to vertebrate CNEs, being highly associated with transcription factor and development genes and enriched in transcription factor binding sites. Some of the most highly conserved sequences occur in genes encoding RNA binding proteins, particularly the RNA splicing–associated SR genes. Differences in sequence conservation between plants and animals are likely to reflect differences in the biology of the organisms, with plants being much more able to tolerate genomic deletions and whole-genome duplication events due, in part, to their far greater fecundity compared with vertebrates. PMID:24681619

The Physics of Advanced High-Gain Targets for Inertial Fusion Energy

NASA Astrophysics Data System (ADS)

Perkins, L. John

2010-11-01

In ca. 2011-2012, the National Ignition Facility is poised to demonstrate fusion ignition and gain in the laboratory for the first time. This key milestone in the development of inertial confinement fusion (ICF) can be expected to engender interest in the development of inertial fusion energy (IFE) and expanded efforts on a number of advanced targets that may achieve high fusion energy gain at lower driver energies. In this tutorial talk, we will discuss the physics underlying ICF ignition and thermonuclear burn, examine the requirements for high gain, and outline candidate R&D programs that will be required to assess the performance of these target concepts under various driver systems including lasers, heavy-ions and pulsed power. Such target concepts include those operating by fast ignition, shock ignition, impact ignition, dual-density, magnetically-insulated, one- and two-sided drive, etc., some of which may have potential to burn advanced, non-DT fusion fuels. We will then delineate the role of such targets in their application to the production of high average fusion power. Here, systems studies of IFE economics suggest that we should strive for target fusion gains of around 100 at drive energies of 1MJ, together with corresponding rep-rates of up to 10Hz and driver electrical efficiencies around 15%. In future years, there may be exciting opportunities to study such ``innovative confinement concepts'' with prospects of fielding them on facilities such as NIF to obtain high fusion energy gains on a single shot basis.

Crystal Structure of the Marburg Virus Nucleoprotein Core Domain Chaperoned by a VP35 Peptide Reveals a Conserved Drug Target for Filovirus.

PubMed

Zhu, Tengfei; Song, Hao; Peng, Ruchao; Shi, Yi; Qi, Jianxun; Gao, George F

2017-09-15

Filovirus nucleoprotein (NP), viral protein 35 (VP35), and polymerase L are essential for viral replication and nucleocapsid formation. Here, we identify a 28-residue peptide (NP binding peptide [NPBP]) from Marburg virus (MARV) VP35 through sequence alignment with previously identified Ebola virus (EBOV) NPBP, which bound to the core region (residues 18 to 344) of the N-terminal portion of MARV NP with high affinity. The crystal structure of the MARV NP core/NPBP complex at a resolution of 2.6 Å revealed that NPBP binds to the C-terminal region of the NP core via electrostatic and nonpolar interactions. Further structural analysis revealed that the MARV and EBOV NP cores hold a conserved binding pocket for NPBP, and this pocket could serve as a promising target for the design of universal drugs against filovirus infection. In addition, cross-binding assays confirmed that the NP core of MARV or EBOV can bind the NPBP from the other virus, although with moderately reduced binding affinities that result from termini that are distinct between the MARV and EBOV NPBPs. IMPORTANCE Historically, Marburg virus (MARV) has caused severe disease with up to 90% lethality. Among the viral proteins produced by MARV, NP and VP35 are both multifunctional proteins that are essential for viral replication. In its relative, Ebola virus (EBOV), an N-terminal peptide from VP35 binds to the NP N-terminal region with high affinity. Whether this is a common mechanism among filoviruses is an unsolved question. Here, we present the crystal structure of a complex that consists of the core domain of MARV NP and the NPBP peptide from VP35. As we compared MARV NPBP with EBOV NPBP, several different features at the termini were identified. Although these differences reduce the affinity of the NP core for NPBPs across genera, a conserved pocket in the C-terminal region of the NP core makes cross-species binding possible. Our results expand our knowledge of filovirus NP-VP35 interactions and

Tunable allosteric library of caspase-3 identifies coupling between conserved water molecules and conformational selection

PubMed Central

Maciag, Joseph J.; Mackenzie, Sarah H.; Tucker, Matthew B.; Schipper, Joshua L.; Swartz, Paul; Clark, A. Clay

2016-01-01

The native ensemble of caspases is described globally by a complex energy landscape where the binding of substrate selects for the active conformation, whereas targeting an allosteric site in the dimer interface selects an inactive conformation that contains disordered active-site loops. Mutations and posttranslational modifications stabilize high-energy inactive conformations, with mostly formed, but distorted, active sites. To examine the interconversion of active and inactive states in the ensemble, we used detection of related solvent positions to analyze 4,995 waters in 15 high-resolution (<2.0 Å) structures of wild-type caspase-3, resulting in 450 clusters with the most highly conserved set containing 145 water molecules. The data show that regions of the protein that contact the conserved waters also correspond to sites of posttranslational modifications, suggesting that the conserved waters are an integral part of allosteric mechanisms. To test this hypothesis, we created a library of 19 caspase-3 variants through saturation mutagenesis in a single position of the allosteric site of the dimer interface, and we show that the enzyme activity varies by more than four orders of magnitude. Altogether, our database consists of 37 high-resolution structures of caspase-3 variants, and we demonstrate that the decrease in activity correlates with a loss of conserved water molecules. The data show that the activity of caspase-3 can be fine-tuned through globally desolvating the active conformation within the native ensemble, providing a mechanism for cells to repartition the ensemble and thus fine-tune activity through conformational selection. PMID:27681633

Tunable allosteric library of caspase-3 identifies coupling between conserved water molecules and conformational selection.

PubMed

Maciag, Joseph J; Mackenzie, Sarah H; Tucker, Matthew B; Schipper, Joshua L; Swartz, Paul; Clark, A Clay

2016-10-11

The native ensemble of caspases is described globally by a complex energy landscape where the binding of substrate selects for the active conformation, whereas targeting an allosteric site in the dimer interface selects an inactive conformation that contains disordered active-site loops. Mutations and posttranslational modifications stabilize high-energy inactive conformations, with mostly formed, but distorted, active sites. To examine the interconversion of active and inactive states in the ensemble, we used detection of related solvent positions to analyze 4,995 waters in 15 high-resolution (<2.0 Å) structures of wild-type caspase-3, resulting in 450 clusters with the most highly conserved set containing 145 water molecules. The data show that regions of the protein that contact the conserved waters also correspond to sites of posttranslational modifications, suggesting that the conserved waters are an integral part of allosteric mechanisms. To test this hypothesis, we created a library of 19 caspase-3 variants through saturation mutagenesis in a single position of the allosteric site of the dimer interface, and we show that the enzyme activity varies by more than four orders of magnitude. Altogether, our database consists of 37 high-resolution structures of caspase-3 variants, and we demonstrate that the decrease in activity correlates with a loss of conserved water molecules. The data show that the activity of caspase-3 can be fine-tuned through globally desolvating the active conformation within the native ensemble, providing a mechanism for cells to repartition the ensemble and thus fine-tune activity through conformational selection.

Classifying Residents who use Landscape Irrigation: Implications for Encouraging Water Conservation Behavior

NASA Astrophysics Data System (ADS)

Warner, Laura A.; Lamm, Alexa J.; Rumble, Joy N.; Martin, Emmett T.; Cantrell, Randall

2016-08-01

Large amounts of water applied as urban irrigation can often be reduced substantially without compromising esthetics. Thus, encouraging the adoption of water-saving technologies and practices is critical to preserving water resources, yet difficult to achieve. The research problem addressed in this study is the lack of characterization of residents who use urban irrigation, which hinders the design of effective behavior change programs. This study examined audience segmentation as an approach to encouraging change using current residential landscape practices. K-means cluster analysis identified three meaningful subgroups among residential landscape irrigation users ( N = 1,063): the water considerate majority ( n = 479, 45 %), water savvy conservationists ( n = 378, 36 %), and unconcerned water users ( n = 201, 19 %). An important finding was that normative beliefs, attitudes, and perceived behavioral control characteristics of the subgroups were significantly different with large and medium practical effect sizes. Future water conservation behaviors and perceived importance of water resources were also significantly different among subgroups. The water considerate majority demonstrated capacity to conserve, placed high value on water, and were likely to engage in behavior changes. This article contributes to the literature on individuals who use residential landscape irrigation, an important target audience with potential to conserve water through sustainable irrigation practices and technologies. Findings confirm applicability of the capacity to conserve water to audience segmentation and extend this concept by incorporating perceived value of water resources and likelihood of conservation. The results suggest practical application to promoting residential landscape water conservation behaviors based on important audience characteristics.

Classifying Residents who use Landscape Irrigation: Implications for Encouraging Water Conservation Behavior.

PubMed

Warner, Laura A; Lamm, Alexa J; Rumble, Joy N; Martin, Emmett T; Cantrell, Randall

2016-08-01

Large amounts of water applied as urban irrigation can often be reduced substantially without compromising esthetics. Thus, encouraging the adoption of water-saving technologies and practices is critical to preserving water resources, yet difficult to achieve. The research problem addressed in this study is the lack of characterization of residents who use urban irrigation, which hinders the design of effective behavior change programs. This study examined audience segmentation as an approach to encouraging change using current residential landscape practices. K-means cluster analysis identified three meaningful subgroups among residential landscape irrigation users (N = 1,063): the water considerate majority (n = 479, 45 %), water savvy conservationists (n = 378, 36 %), and unconcerned water users (n = 201, 19 %). An important finding was that normative beliefs, attitudes, and perceived behavioral control characteristics of the subgroups were significantly different with large and medium practical effect sizes. Future water conservation behaviors and perceived importance of water resources were also significantly different among subgroups. The water considerate majority demonstrated capacity to conserve, placed high value on water, and were likely to engage in behavior changes. This article contributes to the literature on individuals who use residential landscape irrigation, an important target audience with potential to conserve water through sustainable irrigation practices and technologies. Findings confirm applicability of the capacity to conserve water to audience segmentation and extend this concept by incorporating perceived value of water resources and likelihood of conservation. The results suggest practical application to promoting residential landscape water conservation behaviors based on important audience characteristics.

Research on Evaluation of Conservation Planning Implementation of Nanshe Historic Village in Dongguan City

NASA Astrophysics Data System (ADS)

Yubin, Luo

2017-10-01

Conservation planning plays an important role in the protection and development of historic villages. The evaluation of conservation planning is helpful to find out the problems existing in the village protection work which helps to improve the conservation planning system. The paper briefly summarizes the conservation planning background of Nanshe historic village in Dongguan city, Guangdong province, China. The conservation planning guided the protection work of Nanshe village since 2002. It evaluates four aspects of the conservation planning implementation and effect such as protection and utilization of the ancient buildings, roadway repair, landscape and basic sanitation facilities improvement by ways of field research and questionnaire survey. There are only nineteen ancient buildings repaired and the rest of them are part of repaired or not repaired. Most of the roadways are well preserved. Only four of them are partly repaired or not repaired. Most of the villagers like to chat under the ancient banyan trees. Conservation Planning pays not much attention to the needs of the residents. Although conservation planning of Nanshe village developed the near, middle and long term target it actually took 14 years to carry out the near target. It enhances the social awareness of Nanshe village and the sense of belongings of the villagers. Most of the villagers are satisfied with the implementation of the conservation planning. Meanwhile, the paper exposes the conservation planning is too idealistic. It lacks of implementation details and the three phases of the investment funds and pays not much attention to the needs of residents.

Metapopulation effective size and conservation genetic goals for the Fennoscandian wolf (Canis lupus) population

PubMed Central

Laikre, L; Olsson, F; Jansson, E; Hössjer, O; Ryman, N

2016-01-01

The Scandinavian wolf population descends from only five individuals, is isolated, highly inbred and exhibits inbreeding depression. To meet international conservation goals, suggestions include managing subdivided wolf populations over Fennoscandia as a metapopulation; a genetically effective population size of Ne⩾500, in line with the widely accepted long-term genetic viability target, might be attainable with gene flow among subpopulations of Scandinavia, Finland and Russian parts of Fennoscandia. Analytical means for modeling Ne of subdivided populations under such non-idealized situations have been missing, but we recently developed new mathematical methods for exploring inbreeding dynamics and effective population size of complex metapopulations. We apply this theory to the Fennoscandian wolves using empirical estimates of demographic parameters. We suggest that the long-term conservation genetic target for metapopulations should imply that inbreeding rates in the total system and in the separate subpopulations should not exceed Δf=0.001. This implies a meta-Ne of NeMeta⩾500 and a realized effective size of each subpopulation of NeRx⩾500. With current local effective population sizes and one migrant per generation, as recommended by management guidelines, the meta-Ne that can be reached is ~250. Unidirectional gene flow from Finland to Scandinavia reduces meta-Ne to ~130. Our results indicate that both local subpopulation effective sizes and migration among subpopulations must increase substantially from current levels to meet the conservation target. Alternatively, immigration from a large (Ne⩾500) population in northwestern Russia could support the Fennoscandian metapopulation, but immigration must be substantial (5–10 effective immigrants per generation) and migration among Fennoscandian subpopulations must nevertheless increase. PMID:27328654

Treat to target in gout.

PubMed

Perez-Ruiz, Fernando; Moreno-Lledó, Aitana; Urionagüena, Irati; Dickson, Alastair J

2018-01-01

The treat-to-target (T2T) approach has been successfully implemented in a number of diseases. T2T has been proposed for rheumatic diseases such as RA, spondyloarthritis, lupus, and recently for gout. The level of evidence for such approaches differs from one condition to the other (moderate to high for hyperlipidaemia, for example). Practice is based on the best available evidence at any time, and in absence of good evidence for T2T in gout, some suggest a conservative only-treat-symptoms approach. Evidence suggests that not treating gout to target in the long term is overall associated with worsening outcomes, such as flares, tophi and structural damage, which is associated to loss of quality of life and mortality. Different targets have been proposed for hyperuricaemia in gout; lower than 6 mg/dl (0.36 mmol/l) for all patients, at least <5 mg/dl (0.30 mmol/l) for patients with severe-polyarticular or tophaceous-gout. © The Author 2018. Published by Oxford University Press on behalf of the British Society for Rheumatology. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

PACCMIT/PACCMIT-CDS: identifying microRNA targets in 3' UTRs and coding sequences.

PubMed

Šulc, Miroslav; Marín, Ray M; Robins, Harlan S; Vaníček, Jiří

2015-07-01

The purpose of the proposed web server, publicly available at http://paccmit.epfl.ch, is to provide a user-friendly interface to two algorithms for predicting messenger RNA (mRNA) molecules regulated by microRNAs: (i) PACCMIT (Prediction of ACcessible and/or Conserved MIcroRNA Targets), which identifies primarily mRNA transcripts targeted in their 3' untranslated regions (3' UTRs), and (ii) PACCMIT-CDS, designed to find mRNAs targeted within their coding sequences (CDSs). While PACCMIT belongs among the accurate algorithms for predicting conserved microRNA targets in the 3' UTRs, the main contribution of the web server is 2-fold: PACCMIT provides an accurate tool for predicting targets also of weakly conserved or non-conserved microRNAs, whereas PACCMIT-CDS addresses the lack of similar portals adapted specifically for targets in CDS. The web server asks the user for microRNAs and mRNAs to be analyzed, accesses the precomputed P-values for all microRNA-mRNA pairs from a database for all mRNAs and microRNAs in a given species, ranks the predicted microRNA-mRNA pairs, evaluates their significance according to the false discovery rate and finally displays the predictions in a tabular form. The results are also available for download in several standard formats. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

An optimization-based approach for high-order accurate discretization of conservation laws with discontinuous solutions

NASA Astrophysics Data System (ADS)

Zahr, M. J.; Persson, P.-O.

2018-07-01

This work introduces a novel discontinuity-tracking framework for resolving discontinuous solutions of conservation laws with high-order numerical discretizations that support inter-element solution discontinuities, such as discontinuous Galerkin or finite volume methods. The proposed method aims to align inter-element boundaries with discontinuities in the solution by deforming the computational mesh. A discontinuity-aligned mesh ensures the discontinuity is represented through inter-element jumps while smooth basis functions interior to elements are only used to approximate smooth regions of the solution, thereby avoiding Gibbs' phenomena that create well-known stability issues. Therefore, very coarse high-order discretizations accurately resolve the piecewise smooth solution throughout the domain, provided the discontinuity is tracked. Central to the proposed discontinuity-tracking framework is a discrete PDE-constrained optimization formulation that simultaneously aligns the computational mesh with discontinuities in the solution and solves the discretized conservation law on this mesh. The optimization objective is taken as a combination of the deviation of the finite-dimensional solution from its element-wise average and a mesh distortion metric to simultaneously penalize Gibbs' phenomena and distorted meshes. It will be shown that our objective function satisfies two critical properties that are required for this discontinuity-tracking framework to be practical: (1) possesses a local minima at a discontinuity-aligned mesh and (2) decreases monotonically to this minimum in a neighborhood of radius approximately h / 2, whereas other popular discontinuity indicators fail to satisfy the latter. Another important contribution of this work is the observation that traditional reduced space PDE-constrained optimization solvers that repeatedly solve the conservation law at various mesh configurations are not viable in this context since severe overshoot and

Function-based classification of carbohydrate-active enzymes by recognition of short, conserved peptide motifs.

PubMed

Busk, Peter Kamp; Lange, Lene

2013-06-01

Functional prediction of carbohydrate-active enzymes is difficult due to low sequence identity. However, similar enzymes often share a few short motifs, e.g., around the active site, even when the overall sequences are very different. To exploit this notion for functional prediction of carbohydrate-active enzymes, we developed a simple algorithm, peptide pattern recognition (PPR), that can divide proteins into groups of sequences that share a set of short conserved sequences. When this method was used on 118 glycoside hydrolase 5 proteins with 9% average pairwise identity and representing four characterized enzymatic functions, 97% of the proteins were sorted into groups correlating with their enzymatic activity. Furthermore, we analyzed 8,138 glycoside hydrolase 13 proteins including 204 experimentally characterized enzymes with 28 different functions. There was a 91% correlation between group and enzyme activity. These results indicate that the function of carbohydrate-active enzymes can be predicted with high precision by finding short, conserved motifs in their sequences. The glycoside hydrolase 61 family is important for fungal biomass conversion, but only a few proteins of this family have been functionally characterized. Interestingly, PPR divided 743 glycoside hydrolase 61 proteins into 16 subfamilies useful for targeted investigation of the function of these proteins and pinpointed three conserved motifs with putative importance for enzyme activity. Furthermore, the conserved sequences were useful for cloning of new, subfamily-specific glycoside hydrolase 61 proteins from 14 fungi. In conclusion, identification of conserved sequence motifs is a new approach to sequence analysis that can predict carbohydrate-active enzyme functions with high precision.

Biodiversity conservation in a changing climate: a review of threats and implications for conservation planning in Myanmar.

PubMed

Rao, Madhu; Saw Htun; Platt, Steven G; Tizard, Robert; Poole, Colin; Than Myint; Watson, James E M

2013-11-01

High levels of species richness and endemism make Myanmar a regional priority for conservation. However, decades of economic and political sanctions have resulted in low conservation investment to effectively tackle threats to biodiversity. Recent sweeping political reforms have placed Myanmar on the fast track to economic development-the expectation is increased economic investments focused on the exploitation of the country's rich, and relatively intact, natural resources. Within a context of weak regulatory capacity and inadequate environmental safeguards, rapid economic development is likely to have far-reaching negative implications for already threatened biodiversity and natural-resource-dependent human communities. Climate change will further exacerbate prevailing threats given Myanmar's high exposure and vulnerability. The aim of this review is to examine the implications of increased economic growth and a changing climate within the larger context of biodiversity conservation in Myanmar. We summarize conservation challenges, assess direct climatological impacts on biodiversity and conclude with recommendations for long-term adaptation approaches for biodiversity conservation.

High overlap between traditional ecological knowledge and forest conservation found in the Bolivian Amazon.

PubMed

Paneque-Gálvez, Jaime; Pérez-Llorente, Irene; Luz, Ana Catarina; Guèze, Maximilien; Mas, Jean-François; Macía, Manuel J; Orta-Martínez, Martí; Reyes-García, Victoria

2018-03-12

It has been suggested that traditional ecological knowledge (TEK) may play a key role in forest conservation. However, empirical studies assessing to what extent TEK is associated with forest conservation compared with other variables are rare. Furthermore, to our knowledge, the spatial overlap of TEK and forest conservation has not been evaluated at fine scales. In this paper, we address both issues through a case study with Tsimane' Amerindians in the Bolivian Amazon. We sampled 624 households across 59 villages to estimate TEK and used remote sensing data to assess forest conservation. We ran statistical and spatial analyses to evaluate whether TEK was associated and spatially overlapped with forest conservation at the village level. We find that Tsimane' TEK is significantly and positively associated with forest conservation although acculturation variables bear stronger and negative associations with forest conservation. We also find a very significant spatial overlap between levels of Tsimane' TEK and forest conservation. We discuss the potential reasons underpinning our results, which provide insights that may be useful for informing policies in the realms of development, conservation, and climate. We posit that the protection of indigenous cultural systems is vital and urgent to create more effective policies in such realms.

[Comparative chromosome painting shows the red panda (Ailurus fulgens) has a highly conserved karyotype].

PubMed

Tian, Ying; Nie, Wen-Hui; Wang, Jin-Huan; Yang, Yun-Fei; Yang, Feng-Tang

2002-02-01

We have established a comparative chromosome map between red panda (Ailurus fulgens, 2n = 36) and dog by chromosome painting with biotin-labelled chromosome-specific probes of the dog. Dog probes specific for the 38 automates delineated 71 homologous segments in the metaphase chromosomes of red panda. Of the 38 autosomal paints, 18 probes each delineated one homologous segment in red panda genome, while the other 20 ones each detected two to five homologous segments. The dog X chromosome-specific paint delineated the whole X chromosome of the red panda. The results indicate that at least 28 fissions (breaks), 49 fusions and 4 inversions were needed to "convert" the dog karyotype to that of the red panda, suggesting that extensive chromosome rearrangements differentiate the karyotypes of red panda and dog. Based on the established comparative chromosome homologies of dog and domestic cat, we could infer that there were 26 segments of conserved synteny between red panda and domestic cat. Comparative analysis of the distribution patterns of conserved segments defined by dog paints in red panda and domestic cat genomes revealed at least 2 cryptic inversions in two large chromosomal regions of conserved synteny between red panda and domestic cat. The karyotype of red panda shows high degree of homology with that of domestic cat.

New support vector machine-based method for microRNA target prediction.

PubMed

Li, L; Gao, Q; Mao, X; Cao, Y

2014-06-09

MicroRNA (miRNA) plays important roles in cell differentiation, proliferation, growth, mobility, and apoptosis. An accurate list of precise target genes is necessary in order to fully understand the importance of miRNAs in animal development and disease. Several computational methods have been proposed for miRNA target-gene identification. However, these methods still have limitations with respect to their sensitivity and accuracy. Thus, we developed a new miRNA target-prediction method based on the support vector machine (SVM) model. The model supplies information of two binding sites (primary and secondary) for a radial basis function kernel as a similarity measure for SVM features. The information is categorized based on structural, thermodynamic, and sequence conservation. Using high-confidence datasets selected from public miRNA target databases, we obtained a human miRNA target SVM classifier model with high performance and provided an efficient tool for human miRNA target gene identification. Experiments have shown that our method is a reliable tool for miRNA target-gene prediction, and a successful application of an SVM classifier. Compared with other methods, the method proposed here improves the sensitivity and accuracy of miRNA prediction. Its performance can be further improved by providing more training examples.

Identification and classification of structural soil conservation measures based on very high resolution stereo satellite data.

PubMed

Eckert, Sandra; Tesfay Ghebremicael, Selamawit; Hurni, Hans; Kohler, Thomas

2017-05-15

Land degradation affects large areas of land around the globe, with grave consequences for those living off the land. Major efforts are being made to implement soil and water conservation measures that counteract soil erosion and help secure vital ecosystem services. However, where and to what extent such measures have been implemented is often not well documented. Knowledge about this could help to identify areas where soil and water conservation measures are successfully supporting sustainable land management, as well as areas requiring urgent rehabilitation of conservation structures such as terraces and bunds. This study explores the potential of the latest satellite-based remote sensing technology for use in assessing and monitoring the extent of existing soil and water conservation structures. We used a set of very high resolution stereo Geoeye-1 satellite data, from which we derived a detailed digital surface model as well as a set of other spectral, terrain, texture, and filtered information layers. We developed and applied an object-based classification approach, working on two segmentation levels. On the coarser level, the aim was to delimit certain landscape zones. Information about these landscape zones is useful in distinguishing different types of soil and water conservation structures, as each zone contains certain specific types of structures. On the finer level, the goal was to extract and identify different types of linear soil and water conservation structures. The classification rules were based mainly on spectral, textural, shape, and topographic properties, and included object relationships. This approach enabled us to identify and separate from other classes the majority (78.5%) of terraces and bunds, as well as most hillside terraces (81.25%). Omission and commission errors are similar to those obtained by the few existing studies focusing on the same research objective but using different types of remotely sensed data. Based on our results

Effects of the light goose conservation order on non-target waterfowl distribution during spring migration

USGS Publications Warehouse

Dinges, Andrew J.; Webb, Elisabeth B.; Vrtiska, Mark P.

2015-01-01

The Light Goose Conservation Order (LGCO) was initiated in 1999 to reduce mid-continent populations of light geese (lesser snow geese Chen caerulescens and Ross's geese C. rossi). However, concern about potential for LGCO activities (i.e. hunting activities) to negatively impact non-target waterfowl species during spring migration in the Rainwater Basin (RWB) of Nebraska prompted agency personnel to limit the number of hunt days each week and close multiple public wetlands to LGCO activities entirely. To evaluate the effects of the LGCO in the RWB, we quantified waterfowl density at wetlands open and closed to LGCO hunting and recorded all hunter encounters during springs 2011 and 2012. We encountered a total of 70 hunting parties on 22 study wetlands, with over 90% of these encounters occurring during early season when the majority of waterfowl used the RWB region. We detected greater overall densities of dabbling ducks Anas spp., as well as for mallards A. platyrhynchos and northern pintails A. acuta on wetlands closed to the LGCO. We detected no effects of hunt day in the analyses of dabbling duck densities. We detected no differences in mean weekly dabbling duck densities among wetlands open to hunting, regardless of weekly or cumulative hunting encounter frequency throughout early season. Additionally, hunting category was not a predictor for the presence of greater white-fronted geese Anser albifronsin a logistic regression model. Given that dabbling duck densities were greater on wetlands closed to hunting, providing wetlands free from hunting disturbance as refugia during the LGCO remains an important management strategy at migration stopover sites. However, given that we did not detect an effect of hunt day or hunting frequency on dabbling duck density, our results suggest increased hunting frequency at sites already open to hunting would likely have minimal impacts on the distribution of non-target waterfowl species using the region for spring

The efficiency of ceramic-faced metal targets at high-velocity impact

NASA Astrophysics Data System (ADS)

Tolkachev, V. F.; Konyaev, A. A.; Pakhnutova, N. V.

2017-11-01

The paper represents experimental results and engineering evaluation concerning the efficiency of composite materials to be used as an additional protection during the high- velocity interaction of a tungsten rod with a target in the velocity range of 1...5 km/s. The main parameter that characterizes the high-velocity interaction of a projectile with a layered target is the penetration depth. Experimental data, numerical simulation and engineering evaluation by modified models are used to determine the penetration depth. Boron carbide, aluminum oxide, and aluminum nickelide are applied as a front surface of targets. Based on experimental data and numerical simulation, the main characteristics of ceramics are determined, which allows composite materials to be effectively used as additional elements of protection.

Targeted Capture and High-Throughput Sequencing Using Molecular Inversion Probes (MIPs).

PubMed

Cantsilieris, Stuart; Stessman, Holly A; Shendure, Jay; Eichler, Evan E

2017-01-01

Molecular inversion probes (MIPs) in combination with massively parallel DNA sequencing represent a versatile, yet economical tool for targeted sequencing of genomic DNA. Several thousand genomic targets can be selectively captured using long oligonucleotides containing unique targeting arms and universal linkers. The ability to append sequencing adaptors and sample-specific barcodes allows large-scale pooling and subsequent high-throughput sequencing at relatively low cost per sample. Here, we describe a "wet bench" protocol detailing the capture and subsequent sequencing of >2000 genomic targets from 192 samples, representative of a single lane on the Illumina HiSeq 2000 platform.

High-intensity laser-accelerated ion beam produced from cryogenic micro-jet target

DOE PAGES

Gauthier, M.; Kim, J. B.; Curry, C. B.; ...

2016-08-24

Here, we report on the successful operation of a newly developed cryogenic jet target at high intensity laser-irradiation. Using the frequency-doubled Titan short pulse laser system at Jupiter Laser Facility, Lawrence Livermore National Laboratory, we demonstrate the generation of a pure proton beam a with maximum energy of 2 MeV. Furthermore, we record a quasi-monoenergetic peak at 1.1 MeV in the proton spectrum emitted in the laser forward direction suggesting an alternative acceleration mechanism. Using a solid-density mixed hydrogen-deuterium target, we are also able to produce pure proton-deuteron ion beams. With its high purity, limited size, near-critical density, and high-repetitionmore » rate capability, this target is promising for future applications.« less

High-intensity laser-accelerated ion beam produced from cryogenic micro-jet target

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gauthier, M., E-mail: maxence.gauthier@stanford.edu; Kim, J. B.; Curry, C. B.

2016-11-15

We report on the successful operation of a newly developed cryogenic jet target at high intensity laser-irradiation. Using the frequency-doubled Titan short pulse laser system at Jupiter Laser Facility, Lawrence Livermore National Laboratory, we demonstrate the generation of a pure proton beam a with maximum energy of 2 MeV. Furthermore, we record a quasi-monoenergetic peak at 1.1 MeV in the proton spectrum emitted in the laser forward direction suggesting an alternative acceleration mechanism. Using a solid-density mixed hydrogen-deuterium target, we are also able to produce pure proton-deuteron ion beams. With its high purity, limited size, near-critical density, and high-repetition ratemore » capability, this target is promising for future applications.« less

Enhanced Membrane Pore Formation through High-Affinity Targeted Antimicrobial Peptides

PubMed Central

Arnusch, Christopher J.; Pieters, Roland J.; Breukink, Eefjan

2012-01-01

Many cationic antimicrobial peptides (AMPs) target the unique lipid composition of the prokaryotic cell membrane. However, the micromolar activities common for these peptides are considered weak in comparison to nisin, which follows a targeted, pore-forming mode of action. Here we show that AMPs can be modified with a high-affinity targeting module, which enables membrane permeabilization at low concentration. Magainin 2 and a truncated peptide analog were conjugated to vancomycin using click chemistry, and could be directed towards specific membrane embedded receptors both in model membrane systems and whole cells. Compared with untargeted vesicles, a gain in permeabilization efficacy of two orders of magnitude was reached with large unilamellar vesicles that included lipid II, the target of vancomycin. The truncated vancomycin-peptide conjugate showed an increased activity against vancomycin resistant Enterococci, whereas the full-length conjugate was more active against a targeted eukaryotic cell model: lipid II containing erythrocytes. This study highlights that AMPs can be made more selective and more potent against biological membranes that contain structures that can be targeted. PMID:22768121

Dynamic accommodation with simulated targets blurred with high order aberrations

PubMed Central

Gambra, Enrique; Wang, Yinan; Yuan, Jing; Kruger, Philip B.; Marcos, Susana

2010-01-01

High order aberrations have been suggested to play a role in determining the direction of accommodation. We have explored the effect of retinal blur induced by high order aberrations on dynamic accommodation by measuring the accommodative response to sinusoidal variations in accommodative demand (1–3 D). The targets were blurred with 0.3 and 1 μm (for a 3-mm pupil) of defocus, coma, trefoil and spherical aberration. Accommodative gain decreased significantly when 1-μm of aberration was induced. We found a strong correlation between the relative accommodative gain (and phase lag) and the contrast degradation imposed on the target at relevant spatial frequencies. PMID:20600230

Ecological-niche modeling and prioritization of conservation-area networks for Mexican herpetofauna.

PubMed

Urbina-Cardona, J Nicolás; Flores-Villela, Oscar

2010-08-01

One of the most important tools in conservation biology is information on the geographic distribution of species and the variables determining those patterns. We used maximum-entropy niche modeling to run distribution models for 222 amphibian and 371 reptile species (49% endemics and 27% threatened) for which we had 34,619 single geographic records. The planning region is in southeastern Mexico, is 20% of the country's area, includes 80% of the country's herpetofauna, and lacks an adequate protected-area system. We used probabilistic data to build distribution models of herpetofauna for use in prioritizing conservation areas for three target groups (all species and threatened and endemic species). The accuracy of species-distribution models was better for endemic and threatened species than it was for all species. Forty-seven percent of the region has been deforested and additional conservation areas with 13.7% to 88.6% more native vegetation (76% to 96% of the areas are outside the current protected-area system) are needed. There was overlap in 26 of the main selected areas in the conservation-area network prioritized to preserve the target groups, and for all three target groups the proportion of vegetation types needed for their conservation was constant: 30% pine and oak forests, 22% tropical evergreen forest, 17% low deciduous forest, and 8% montane cloud forests. The fact that different groups of species require the same proportion of habitat types suggests that the pine and oak forests support the highest proportion of endemic and threatened species and should therefore be given priority over other types of vegetation for inclusion in the protected areas of southeastern Mexico.

Small molecules targeting viral RNA.

PubMed

Hermann, Thomas

2016-11-01

Highly conserved noncoding RNA (ncRNA) elements in viral genomes and transcripts offer new opportunities to expand the repertoire of drug targets for the development of antiinfective therapy. Ligands binding to ncRNA architectures are able to affect interactions, structural stability or conformational changes and thereby block processes essential for viral replication. Proof of concept for targeting functional RNA by small molecule inhibitors has been demonstrated for multiple viruses with RNA genomes. Strategies to identify antiviral compounds as inhibitors of ncRNA are increasingly emphasizing consideration of drug-like properties of candidate molecules emerging from screening and ligand design. Recent efforts of antiviral lead discovery for RNA targets have provided drug-like small molecules that inhibit viral replication and include inhibitors of human immunodeficiency virus (HIV), hepatitis C virus (HCV), severe respiratory syndrome coronavirus (SARS CoV), and influenza A virus. While target selectivity remains a challenge for the discovery of useful RNA-binding compounds, a better understanding is emerging of properties that define RNA targets amenable for inhibition by small molecule ligands. Insight from successful approaches of targeting viral ncRNA in HIV, HCV, SARS CoV, and influenza A will provide a basis for the future exploration of RNA targets for therapeutic intervention in other viral pathogens which create urgent, unmet medical needs. Viruses for which targeting ncRNA components in the genome or transcripts may be promising include insect-borne flaviviruses (Dengue, Zika, and West Nile) and filoviruses (Ebola and Marburg). WIREs RNA 2016, 7:726-743. doi: 10.1002/wrna.1373 For further resources related to this article, please visit the WIREs website. © 2016 Wiley Periodicals, Inc.

High-resolution remotely sensed small target detection by imitating fly visual perception mechanism.

PubMed

Huang, Fengchen; Xu, Lizhong; Li, Min; Tang, Min

2012-01-01

The difficulty and limitation of small target detection methods for high-resolution remote sensing data have been a recent research hot spot. Inspired by the information capture and processing theory of fly visual system, this paper endeavors to construct a characterized model of information perception and make use of the advantages of fast and accurate small target detection under complex varied nature environment. The proposed model forms a theoretical basis of small target detection for high-resolution remote sensing data. After the comparison of prevailing simulation mechanism behind fly visual systems, we propose a fly-imitated visual system method of information processing for high-resolution remote sensing data. A small target detector and corresponding detection algorithm are designed by simulating the mechanism of information acquisition, compression, and fusion of fly visual system and the function of pool cell and the character of nonlinear self-adaption. Experiments verify the feasibility and rationality of the proposed small target detection model and fly-imitated visual perception method.

Conserving the Birds of Uganda’s Banana-Coffee Arc: Land Sparing and Land Sharing Compared

PubMed Central

Hulme, Mark F.; Vickery, Juliet A.; Green, Rhys E.; Phalan, Ben; Chamberlain, Dan E.; Pomeroy, Derek E.; Nalwanga, Dianah; Mushabe, David; Katebaka, Raymond; Bolwig, Simon; Atkinson, Philip W.

2013-01-01

Reconciling the aims of feeding an ever more demanding human population and conserving biodiversity is a difficult challenge. Here, we explore potential solutions by assessing whether land sparing (farming for high yield, potentially enabling the protection of non-farmland habitat), land sharing (lower yielding farming with more biodiversity within farmland) or a mixed strategy would result in better bird conservation outcomes for a specified level of agricultural production. We surveyed forest and farmland study areas in southern Uganda, measuring the population density of 256 bird species and agricultural yield: food energy and gross income. Parametric non-linear functions relating density to yield were fitted. Species were identified as “winners” (total population size always at least as great with agriculture present as without it) or “losers” (total population sometimes or always reduced with agriculture present) for a range of targets for total agricultural production. For each target we determined whether each species would be predicted to have a higher total population with land sparing, land sharing or with any intermediate level of sparing at an intermediate yield. We found that most species were expected to have their highest total populations with land sparing, particularly loser species and species with small global range sizes. Hence, more species would benefit from high-yield farming if used as part of a strategy to reduce forest loss than from low-yield farming and land sharing, as has been found in Ghana and India in a previous study. We caution against advocacy for high-yield farming alone as a means to deliver land sparing if it is done without strong protection for natural habitats, other ecosystem services and social welfare. Instead, we suggest that conservationists explore how conservation and agricultural policies can be better integrated to deliver land sparing by, for example, combining land-use planning and agronomic support for

Identifying Priority Areas for Conservation: A Global Assessment for Forest-Dependent Birds

PubMed Central

Buchanan, Graeme M.; Donald, Paul F.; Butchart, Stuart H. M.

2011-01-01

Limited resources are available to address the world's growing environmental problems, requiring conservationists to identify priority sites for action. Using new distribution maps for all of the world's forest-dependent birds (60.6% of all bird species), we quantify the contribution of remaining forest to conserving global avian biodiversity. For each of the world's partly or wholly forested 5-km cells, we estimated an impact score of its contribution to the distribution of all the forest bird species estimated to occur within it, and so is proportional to the impact on the conservation status of the world's forest-dependent birds were the forest it contains lost. The distribution of scores was highly skewed, a very small proportion of cells having scores several orders of magnitude above the global mean. Ecoregions containing the highest values of this score included relatively species-poor islands such as Hawaii and Palau, the relatively species-rich islands of Indonesia and the Philippines, and the megadiverse Atlantic Forests and northern Andes of South America. Ecoregions with high impact scores and high deforestation rates (2000–2005) included montane forests in Cameroon and the Eastern Arc of Tanzania, although deforestation data were not available for all ecoregions. Ecoregions with high impact scores, high rates of recent deforestation and low coverage by the protected area network included Indonesia's Seram rain forests and the moist forests of Trinidad and Tobago. Key sites in these ecoregions represent some of the most urgent priorities for expansion of the global protected areas network to meet Convention on Biological Diversity targets to increase the proportion of land formally protected to 17% by 2020. Areas with high impact scores, rapid deforestation, low protection and high carbon storage values may represent significant opportunities for both biodiversity conservation and climate change mitigation, for example through Reducing Emissions from

The existence of High Conservation Value Forest (HCVF) in Perum Perhutani KPH Kendal to support Implementation of FSC Certification

NASA Astrophysics Data System (ADS)

Sulistyowati, Sri; Hadi, Sudharto P.

2018-02-01

High Conservation Value Forest (HCVF) is the identification of High Conservation Values that are important and need to be protected. Under FSC certification mechanism, HCVF becomes one of Principles and Criteria to attain certification. In this study, we identify the existence of HCVF in Perum Perhutani KPH Kendal to support implementation process of FSC certification. Qualitative method was conducted through observation and secondary data from Perum Perhutani KPH Kendal. Data analysis showed through ecolabel certification, Perum Perhutani KPH Kendal has been identified HCVF area covering 2,715.5 hectares consists of HCV 1 until 6. Secondary Natural Forest (HAS) Subah and Kaliwungu for Ulolanang and Pagerwunung Nature Reserve buffer zone include as HCV 1.1, conservation area of leopard (Panthera pardus melas) and Pangolin (Manis javanica).for HCV 1.2, conservation area of lutung (Trachypiyhecus auratus) as endemic species for CITES App I and Critically Endangered species include as HCV 1.3, Goa kiskendo for bats species habitat include as HCV 1.4, regions of interest species for Deer (Cervus timorensis) and Kepodang (Oriolus chinensis) as HCV 2.3, Germplasm Protection Region/ KPPN area with high biodiversity include as HCV 3, river border area and water springs for HCV 4. While, utilization of firewood, grass for cattle fodder include as HCV 5 and 14 cultural sites include as HCV 6. From monitoring and evaluation of HCVF data, showed that in 2011-2015 the level of diversity for flora and fauna were increased.

Global mapping of ecosystem services and conservation priorities

PubMed Central

Naidoo, R.; Balmford, A.; Costanza, R.; Fisher, B.; Green, R. E.; Lehner, B.; Malcolm, T. R.; Ricketts, T. H.

2008-01-01

Global efforts to conserve biodiversity have the potential to deliver economic benefits to people (i.e., “ecosystem services”). However, regions for which conservation benefits both biodiversity and ecosystem services cannot be identified unless ecosystem services can be quantified and valued and their areas of production mapped. Here we review the theory, data, and analyses needed to produce such maps and find that data availability allows us to quantify imperfect global proxies for only four ecosystem services. Using this incomplete set as an illustration, we compare ecosystem service maps with the global distributions of conventional targets for biodiversity conservation. Our preliminary results show that regions selected to maximize biodiversity provide no more ecosystem services than regions chosen randomly. Furthermore, spatial concordance among different services, and between ecosystem services and established conservation priorities, varies widely. Despite this lack of general concordance, “win–win” areas—regions important for both ecosystem services and biodiversity—can be usefully identified, both among ecoregions and at finer scales within them. An ambitious interdisciplinary research effort is needed to move beyond these preliminary and illustrative analyses to fully assess synergies and trade-offs in conserving biodiversity and ecosystem services. PMID:18621701

TargetMiner: microRNA target prediction with systematic identification of tissue-specific negative examples.

PubMed

Bandyopadhyay, Sanghamitra; Mitra, Ramkrishna

2009-10-15

Prediction of microRNA (miRNA) target mRNAs using machine learning approaches is an important area of research. However, most of the methods suffer from either high false positive or false negative rates. One reason for this is the marked deficiency of negative examples or miRNA non-target pairs. Systematic identification of non-target mRNAs is still not addressed properly, and therefore, current machine learning approaches are compelled to rely on artificially generated negative examples for training. In this article, we have identified approximately 300 tissue-specific negative examples using a novel approach that involves expression profiling of both miRNAs and mRNAs, miRNA-mRNA structural interactions and seed-site conservation. The newly generated negative examples are validated with pSILAC dataset, which elucidate the fact that the identified non-targets are indeed non-targets.These high-throughput tissue-specific negative examples and a set of experimentally verified positive examples are then used to build a system called TargetMiner, a support vector machine (SVM)-based classifier. In addition to assessing the prediction accuracy on cross-validation experiments, TargetMiner has been validated with a completely independent experimental test dataset. Our method outperforms 10 existing target prediction algorithms and provides a good balance between sensitivity and specificity that is not reflected in the existing methods. We achieve a significantly higher sensitivity and specificity of 69% and 67.8% based on a pool of 90 feature set and 76.5% and 66.1% using a set of 30 selected feature set on the completely independent test dataset. In order to establish the effectiveness of the systematically generated negative examples, the SVM is trained using a different set of negative data generated using the method in Yousef et al. A significantly higher false positive rate (70.6%) is observed when tested on the independent set, while all other factors are kept the

Inhibitory control and visuo-spatial reversibility in Piaget's seminal number conservation task: a high-density ERP study

PubMed Central

Borst, Grégoire; Simon, Grégory; Vidal, Julie; Houdé, Olivier

2013-01-01

The present high-density event-related potential (ERP) study on 13 adults aimed to determine whether number conservation relies on the ability to inhibit the overlearned length-equals-number strategy and then imagine the shortening of the row that was lengthened. Participants performed the number-conservation task and, after the EEG session, the mental imagery task. In the number-conservation task, first two rows with the same number of tokens and the same length were presented on a computer screen (COV condition) and then, the tokens in one of the two rows were spread apart (INT condition). Participants were instructed to determine whether the two rows had an identical number of tokens. In the mental imagery task, two rows with different lengths but the same number of tokens were presented and participants were instructed to imagine the tokens in the longer row aligning with the tokens in the shorter row. In the number-conservation task, we found that the amplitudes of the centro-parietal N2 and fronto-central P3 were higher in the INT than in the COV conditions. In addition, the differences in response times between the two conditions were correlated with the differences in the amplitudes of the fronto-central P3. In light of previous results reported on the number-conservation task in adults, the present results suggest that inhibition might be necessary to succeed the number-conservation task in adults even when the transformation of the length of one of the row is displayed. Finally, we also reported correlations between the speed at which participants could imagine the shortening of one of the row in the mental imagery task, the speed at which participants could determine that the two rows had the same number of tokens after the tokens in one of the row were spread apart and the latency of the late positive parietal component in the number-conservation task. Therefore, performing the number-conservation task might involve mental transformation processes in

High-flux neutron source based on a liquid-lithium target

NASA Astrophysics Data System (ADS)

Halfon, S.; Feinberg, G.; Paul, M.; Arenshtam, A.; Berkovits, D.; Kijel, D.; Nagler, A.; Eliyahu, I.; Silverman, I.

2013-04-01

A prototype compact Liquid Lithium Target (LiLiT), able to constitute an accelerator-based intense neutron source, was built. The neutron source is intended for nuclear astrophysical research, boron neutron capture therapy (BNCT) in hospitals and material studies for fusion reactors. The LiLiT setup is presently being commissioned at Soreq Nuclear research Center (SNRC). The lithium target will produce neutrons through the 7Li(p,n)7Be reaction and it will overcome the major problem of removing the thermal power generated by a high-intensity proton beam, necessary for intense neutron flux for the above applications. The liquid-lithium loop of LiLiT is designed to generate a stable lithium jet at high velocity on a concave supporting wall with free surface toward the incident proton beam (up to 10 kW). During off-line tests, liquid lithium was flown through the loop and generated a stable jet at velocity higher than 5 m/s on the concave supporting wall. The target is now under extensive test program using a high-power electron-gun. Up to 2 kW electron beam was applied on the lithium flow at velocity of 4 m/s without any flow instabilities or excessive evaporation. High-intensity proton beam irradiation will take place at SARAF (Soreq Applied Research Accelerator Facility) superconducting linear accelerator currently in commissioning at SNRC.

Improving environmental and social targeting through adaptive management in Mexico's payments for hydrological services program.

PubMed

Sims, Katharine R E; Alix-Garcia, Jennifer M; Shapiro-Garza, Elizabeth; Fine, Leah R; Radeloff, Volker C; Aronson, Glen; Castillo, Selene; Ramirez-Reyes, Carlos; Yañez-Pagans, Patricia

2014-10-01

Natural resource managers are often expected to achieve both environmental protection and economic development even when there are fundamental trade-offs between these goals. Adaptive management provides a theoretical structure for program administrators to balance social priorities in the presence of trade-offs and to improve conservation targeting. We used the case of Mexico's federal Payments for Hydrological Services program (PSAH) to illustrate the importance of adaptive management for improving program targeting. We documented adaptive elements of PSAH and corresponding changes in program eligibility and selection criteria. To evaluate whether these changes resulted in enrollment of lands of high environmental and social priority, we compared the environmental and social characteristics of the areas enrolled in the program with the characteristics of all forested areas in Mexico, all areas eligible for the program, and all areas submitted for application to the program. The program successfully enrolled areas of both high ecological and social priority, and over time, adaptive changes in the program's criteria for eligibility and selection led to increased enrollment of land scoring high on both dimensions. Three factors facilitated adaptive management in Mexico and are likely to be generally important for conservation managers: a supportive political environment, including financial backing and encouragement to experiment from the federal government; availability of relatively good social and environmental data; and active participation in the review process by stakeholders and outside evaluators. © 2014 Society for Conservation Biology.

Differences in evolutionary pressure acting within highly conserved ortholog groups.

PubMed

Przytycka, Teresa M; Jothi, Raja; Aravind, L; Lipman, David J

2008-07-17

In highly conserved widely distributed ortholog groups, the main evolutionary force is assumed to be purifying selection that enforces sequence conservation, with most divergence occurring by accumulation of neutral substitutions. Using a set of ortholog groups from prokaryotes, with a single representative in each studied organism, we asked the question if this evolutionary pressure is acting similarly on different subgroups of orthologs defined as major lineages (e.g. Proteobacteria or Firmicutes). Using correlations in entropy measures as a proxy for evolutionary pressure, we observed two distinct behaviors within our ortholog collection. The first subset of ortholog groups, called here informational, consisted mostly of proteins associated with information processing (i.e. translation, transcription, DNA replication) and the second, the non-informational ortholog groups, mostly comprised of proteins involved in metabolic pathways. The evolutionary pressure acting on non-informational proteins is more uniform relative to their informational counterparts. The non-informational proteins show higher level of correlation between entropy profiles and more uniformity across subgroups. The low correlation of entropy profiles in the informational ortholog groups suggest that the evolutionary pressure acting on the informational ortholog groups is not uniform across different clades considered this study. This might suggest "fine-tuning" of informational proteins in each lineage leading to lineage-specific differences in selection. This, in turn, could make these proteins less exchangeable between lineages. In contrast, the uniformity of the selective pressure acting on the non-informational groups might allow the exchange of the genetic material via lateral gene transfer.

Attenuated Salmonella choleraesuis-mediated RNAi targeted to conserved regions against foot-and-mouth disease virus in guinea pigs and swine.

PubMed

Cong, Wei; Jin, Hong; Jiang, Chengda; Yan, Weiyao; Liu, Mingqiu; Chen, Jiulian; Zuo, Xiaoping; Zheng, Zhaoxin

2010-01-01

In this study, specific sequences within three genes (3D, VP4 and 2B) of the foot-and-mouth disease virus (FMDV) genome were determined to be effective RNAi targets. These sequences are highly conserved among different serotype viruses based on sequence analysis. Small interfering RNA (siRNA)-expressing plasmids (p3D-NT19, p3D-NT56, pVP4-NT19, pVP4-NT65 and p2B-NT25) were constructed to express siRNA targeting 3D, VP4 and 2B, respectively. The antiviral potential of these siRNA for various FMDV isolates was investigated in baby hamster kidney (BHK-21) cells and suckling mice. The results show that these siRNA inhibited virus yield 10- to 300-fold for different FMDV isolates of serotype O and serotype Asia I at 48 h post infection in BHK-21 cells compared to control cells. In suckling mice, p3D-NT56 and p2B-NT25 delayed the death of mice. Twenty percent to 40% of the animals that received a single siRNA dose survived 5 days post infection with serotype O or serotype Asia I. We used an attenuated Salmonella choleraesuis (C500) vaccine strain, to carry the plasmid that expresses siRNA directed against the polymerase gene 3D (p3D-NT56) of FMDV. We used guinea pigs to evaluate the inhibitory effects of recombinant S. cho (p3D-NT56/S. cho) on FMDV infection. The results show that 80% of guinea pigs inoculated with 10(9) CFU of p3D-NT56/S. cho and challenged 36 h later with 50 ID(50) of homologous FMDV were protected. We also measured the antiviral activity of p3D-NT56/S. cho in swine. The results indicate that 100% of the animals treated with 5 x 10(9) CFU of p3D-NT56/S. cho were protected in 9 days. INRA, EDP Sciences, 2010.

Attenuated Salmonella choleraesuis-mediated RNAi targeted to conserved regions against foot-and-mouth disease virus in guinea pigs and swine

PubMed Central

Cong, Wei; Jin, Hong; Jiang, Chengda; Yan, Weiyao; Liu, Mingqiu; Chen, Jiulian; Zuo, Xiaoping; Zheng, Zhaoxin

2010-01-01

In this study, specific sequences within three genes (3D, VP4 and 2B) of the foot-and-mouth disease virus (FMDV) genome were determined to be effective RNAi targets. These sequences are highly conserved among different serotype viruses based on sequence analysis. Small interfering RNA (siRNA)-expressing plasmids (p3D-NT19, p3D-NT56, pVP4-NT19, pVP4-NT65 and p2B-NT25) were constructed to express siRNA targeting 3D, VP4 and 2B, respectively. The antiviral potential of these siRNA for various FMDV isolates was investigated in baby hamster kidney (BHK-21) cells and suckling mice. The results show that these siRNA inhibited virus yield 10- to 300-fold for different FMDV isolates of serotype O and serotype Asia I at 48 h post infection in BHK-21 cells compared to control cells. In suckling mice, p3D-NT56 and p2B-NT25 delayed the death of mice. Twenty percent to 40% of the animals that received a single siRNA dose survived 5 days post infection with serotype O or serotype Asia I. We used an attenuated Salmonella choleraesuis (C500) vaccine strain, to carry the plasmid that expresses siRNA directed against the polymerase gene 3D (p3D-NT56) of FMDV. We used guinea pigs to evaluate the inhibitory effects of recombinant S. cho (p3D-NT56/S. cho) on FMDV infection. The results show that 80% of guinea pigs inoculated with 109 CFU of p3D-NT56/S. cho and challenged 36 h later with 50 ID50 of homologous FMDV were protected. We also measured the antiviral activity of p3D-NT56/S. cho in swine. The results indicate that 100% of the animals treated with 5 × 109 CFU of p3D-NT56/S. cho were protected in 9 days. PMID:20167192

Targeted Therapeutics in Patients With High-Grade Gliomas: Past, Present, and Future.

PubMed

Chen, Ricky; Cohen, Adam L; Colman, Howard

2016-08-01

High-grade gliomas remain incurable despite current therapies, which are plagued by high morbidity and mortality. Molecular categorization of glioma subtypes using mutations in isocitrate dehydrogenase 1/2 (IDH1/2), TP53, and ATRX; codeletion of chromosomes 1p and 19q; DNA methylation; and amplification of genes such as epidermal growth factor receptor (EGFR) and platelet-derived growth factor receptor, alpha polypeptide provides a more accurate prognostication and biologic classification than classical histopathological diagnoses, and a number of molecular markers are being incorporated in the new World Health Organization classification of gliomas. However, despite the improved understanding of the molecular subtypes of gliomas and the underlying alterations in specific signaling pathways, these observations have so far failed to result in the successful application of targeted therapies, as has occurred in other solid tumors. To date, the only targeted therapy for gliomas approved by the US Food and Drug Administration is bevacizumab, which targets vascular endothelial growth factor. EGFR remains a dominant molecular alteration in specific glioma subtypes and represents a potentially promising target, with drugs of multiple types targeting EGFR in development including vaccines, antibody drug conjugates, and chimeric antigen receptor (CAR) T cells, despite the prior failures of EGFR tyrosine kinase inhibitors. Immune therapies under investigation include checkpoint inhibitors, vaccines against tumor-associated antigens and tumor-specific antigens, pulsed dendritic cells, heat shock protein-tumor conjugates, and CAR T cells. Mutations in the IDH1/2 genes are central to gliomagenesis in a high proportion of grade II and III gliomas, and ongoing trials are examining vaccines against IDH1, small molecular inhibitors of IDH1 and IDH2, and metabolic components including NAD+ depletion to target IDH-mutated gliomas. The central role of DNA methylation in a subset of

A human-centered framework for innovation in conservation incentive programs.

PubMed

Sorice, Michael G; Donlan, C Josh

2015-12-01

The promise of environmental conservation incentive programs that provide direct payments in exchange for conservation outcomes is that they enhance the value of engaging in stewardship behaviors. An insidious but important concern is that a narrow focus on optimizing payment levels can ultimately suppress program participation and subvert participants' internal motivation to engage in long-term conservation behaviors. Increasing participation and engendering stewardship can be achieved by recognizing that participation is not simply a function of the payment; it is a function of the overall structure and administration of the program. Key to creating innovative and more sustainable programs is fitting them within the existing needs and values of target participants. By focusing on empathy for participants, co-designing program approaches, and learning from the rapid prototyping of program concepts, a human-centered approach to conservation incentive program design enhances the propensity for discovery of novel and innovative solutions to pressing conservation issues.

Initiated chemical vapor deposition polymers for high peak-power laser targets

DOE Office of Scientific and Technical Information (OSTI.GOV)

Baxamusa, Salmaan H.; Lepro, Xavier; Lee, Tom

2016-12-05

Here, we report two examples of initiated chemical vapor deposition (iCVD) polymers being developed for use in laser targets for high peak-power laser systems. First, we show that iCVD poly(divinylbenzene) is more photo-oxidatively stable than the plasma polymers currently used in laser targets. Thick layers (10–12 μm) of this highly crosslinked polymer can be deposited with near-zero intrinsic film stress. Second, we show that iCVD epoxy polymers can be crosslinked after deposition to form thin adhesive layers for assembling precision laser targets. The bondlines can be made as thin as ~ 1 μm, approximately a factor of 2 thinner thanmore » achievable using viscous resin-based adhesives. These bonds can withstand downstream coining and stamping processes.« less

Efficient visualization of high-throughput targeted proteomics experiments: TAPIR.

PubMed

Röst, Hannes L; Rosenberger, George; Aebersold, Ruedi; Malmström, Lars

2015-07-15

Targeted mass spectrometry comprises a set of powerful methods to obtain accurate and consistent protein quantification in complex samples. To fully exploit these techniques, a cross-platform and open-source software stack based on standardized data exchange formats is required. We present TAPIR, a fast and efficient Python visualization software for chromatograms and peaks identified in targeted proteomics experiments. The input formats are open, community-driven standardized data formats (mzML for raw data storage and TraML encoding the hierarchical relationships between transitions, peptides and proteins). TAPIR is scalable to proteome-wide targeted proteomics studies (as enabled by SWATH-MS), allowing researchers to visualize high-throughput datasets. The framework integrates well with existing automated analysis pipelines and can be extended beyond targeted proteomics to other types of analyses. TAPIR is available for all computing platforms under the 3-clause BSD license at https://github.com/msproteomicstools/msproteomicstools. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Identification of evolutionarily conserved Momordica charantia microRNAs using computational approach and its utility in phylogeny analysis.

PubMed

Thirugnanasambantham, Krishnaraj; Saravanan, Subramanian; Karikalan, Kulandaivelu; Bharanidharan, Rajaraman; Lalitha, Perumal; Ilango, S; HairulIslam, Villianur Ibrahim

2015-10-01

Momordica charantia (bitter gourd, bitter melon) is a monoecious Cucurbitaceae with anti-oxidant, anti-microbial, anti-viral and anti-diabetic potential. Molecular studies on this economically valuable plant are very essential to understand its phylogeny and evolution. MicroRNAs (miRNAs) are conserved, small, non-coding RNA with ability to regulate gene expression by bind the 3' UTR region of target mRNA and are evolved at different rates in different plant species. In this study we have utilized homology based computational approach and identified 27 mature miRNAs for the first time from this bio-medically important plant. The phylogenetic tree developed from binary data derived from the data on presence/absence of the identified miRNAs were noticed to be uncertain and biased. Most of the identified miRNAs were highly conserved among the plant species and sequence based phylogeny analysis of miRNAs resolved the above difficulties in phylogeny approach using miRNA. Predicted gene targets of the identified miRNAs revealed their importance in regulation of plant developmental process. Reported miRNAs held sequence conservation in mature miRNAs and the detailed phylogeny analysis of pre-miRNA sequences revealed genus specific segregation of clusters. Copyright © 2015 Elsevier Ltd. All rights reserved.

The effectiveness of conservation interventions to overcome the urban-environmental paradox.

PubMed

McDonald, Robert I

2015-10-01

Globally, urbanization is rapidly growing cities and towns at a historically unprecedented rate, and this rapid urban growth is influencing many facets of the environment. This paper reviews the effectiveness of conservation interventions that are designed to increase urban sustainability. It presents evidence for an apparent urban-environmental paradox: while the process of urban growth converts natural habitat to other land covers and degrades natural resources and ecosystem function, the increase in human population can increase demand for natural resources and ecosystem services. The fundamental problem that many conservation interventions try to address is that most facets of the environment are common or public goods, and are hence undervalued in decision making (market failure). The paper presents a threefold classification of conservation interventions in cities: conservation in the city (protecting biodiversity), conservation by the city (reducing per capita resource and energy use), and conservation for cities (projects that maintain or enhance ecosystem services). It ends by discussing methods for spatially targeting conservation interventions of all three types and for quantifying the effectiveness of interventions retrospectively. © 2015 New York Academy of Sciences.

High-Energy Space Propulsion Based on Magnetized Target Fusion

NASA Technical Reports Server (NTRS)

Thio, Y. C. F.; Landrum, D. B.; Freeze, B.; Kirkpatrick, R. C.; Gerrish, H.; Schmidt, G. R.

1999-01-01

Magnetized target fusion is an approach in which a magnetized target plasma is compressed inertially by an imploding material wall. A high energy plasma liner may be used to produce the required implosion. The plasma liner is formed by the merging of a number of high momentum plasma jets converging towards the center of a sphere where two compact toroids have been introduced. Preliminary 3-D hydrodynamics modeling results using the SPHINX code of Los Alamos National Laboratory have been very encouraging and confirm earlier theoretical expectations. The concept appears ready for experimental exploration and plans for doing so are being pursued. In this talk, we explore conceptually how this innovative fusion approach could be packaged for space propulsion for interplanetary travel. We discuss the generally generic components of a baseline propulsion concept including the fusion engine, high velocity plasma accelerators, generators of compact toroids using conical theta pinches, magnetic nozzle, neutron absorption blanket, tritium reprocessing system, shock absorber, magnetohydrodynamic generator, capacitor pulsed power system, thermal management system, and micrometeorite shields.