Quantitative simulation tools to analyze up- and downstream interactions of soil and water conservation measures: supporting policy making in the Green Water Credits program of Kenya.

PubMed

Hunink, J E; Droogers, P; Kauffman, S; Mwaniki, B M; Bouma, J

2012-11-30

Upstream soil and water conservation measures in catchments can have positive impact both upstream in terms of less erosion and higher crop yields, but also downstream by less sediment flow into reservoirs and increased groundwater recharge. Green Water Credits (GWC) schemes are being developed to encourage upstream farmers to invest in soil and water conservation practices which will positively effect upstream and downstream water availability. Quantitative information on water and sediment fluxes is crucial as a basis for such financial schemes. A pilot design project in the large and strategically important Upper-Tana Basin in Kenya has the objective to develop a methodological framework for this purpose. The essence of the methodology is the integration and use of a collection of public domain tools and datasets: the so-called Green water and Blue water Assessment Toolkit (GBAT). This toolkit was applied in order to study different options to implement GWC in agricultural rainfed land for the pilot study. Impact of vegetative contour strips, mulching, and tied ridges were determined for: (i) three upstream key indicators: soil loss, crop transpiration and soil evaporation, and (ii) two downstream indicators: sediment inflow in reservoirs and groundwater recharge. All effects were compared with a baseline scenario of average conditions. Thus, not only actual land management was considered but also potential benefits of changed land use practices. Results of the simulations indicate that especially applying contour strips or tied ridges significantly reduces soil losses and increases groundwater recharge in the catchment. The model was used to build spatial expressions of the proposed management practices in order to assess their effectiveness. The developed procedure allows exploring the effects of soil conservation measures in a catchment to support the implementation of GWC. Copyright © 2012 Elsevier Ltd. All rights reserved.

Nucleotide sequences and regulational analysis of genes involved in conversion of aniline to catechol in Pseudomonas putida UCC22(pTDN1).

PubMed Central

Fukumori, F; Saint, C P

1997-01-01

A 9,233-bp HindIII fragment of the aromatic amine catabolic plasmid pTDN1, isolated from a derivative of Pseudomonas putida mt-2 (UCC22), confers the ability to degrade aniline on P. putida KT2442. The fragment encodes six open reading frames which are arranged in the same direction. Their 5' upstream region is part of the direct-repeat sequence of pTDN1. Nucleotide sequence of 1.8 kb of the repeat sequence revealed only a single base pair change compared to the known sequence of IS1071 which is involved in the transposition of the chlorobenzoate genes (C. Nakatsu, J. Ng, R. Singh, N. Straus, and C. Wyndham, Proc. Natl. Acad. Sci. USA 88:8312-8316, 1991). Four open reading frames encode proteins with considerable homology to proteins found in other aromatic-compound degradation pathways. On the basis of sequence similarity, these genes are proposed to encode the large and small subunits of aniline oxygenase (tdnA1 and tdnA2, respectively), a reductase (tdnB), and a LysR-type regulatory gene (tdnR). The putative large subunit has a conserved [2Fe-2S]R Rieske-type ligand center. Two genes, tdnQ and tdnT, which may be involved in amino group transfer, are localized upstream of the putative oxygenase genes. The tdnQ gene product shares about 30% similarity with glutamine synthetases; however, a pUC-based plasmid carrying tdnQ did not support the growth of an Escherichia coli glnA strain in the absence of glutamine. TdnT possesses domains that are conserved among amidotransferases. The tdnQ, tdnA1, tdnA2, tdnB, and tdnR genes are essential for the conversion of aniline to catechol. PMID:8990291

Determination of the promoter region of mouse ribosomal RNA gene by an in vitro transcription system.

PubMed Central

Yamamoto, O; Takakusa, N; Mishima, Y; Kominami, R; Muramatsu, M

1984-01-01

Sequences required for a faithful and efficient transcription of a cloned mouse ribosomal RNA gene (rDNA) are determined by testing a series of deletion mutants in an in vitro transcription system utilizing two kinds of mouse cellular extract. Deletion of sequences upstream of -40 or downstream of +52 causes only slight reduction in promoter activity as compared with the "wild-type" template. For upstream deletion mutants, the removal of a sequence between -40 and -35 causes a significant decrease in the capacity to direct efficient initiation. This decrease becomes more pronounced when the deletion reaches -32 and the sequence A-T-C-T-T-T, conserved among mouse, rat, and human rDNAs, is lost. Residual template activity is further reduced as more upstream sequence is deleted and finally becomes undetectable when the deletion is extended from -22 down to -17, corresponding to the loss of the conserved sequence T-A-T-T-G. As for downstream deletion mutants, the removal of the sequence downstream of +23 causes some (and further deletions up to +11 cause a more) serious decrease in template activity in vitro. These deletions involve other conserved sequences downstream of the transcription start site. However, the removal of the original transcription start site does not abolish the transcription initiation completely, provided that the whole upstream sequence is intact. Images PMID:6320178

Identification of a Mg2+-sensitive ORF in the 5′-leader of TRPM7 magnesium channel mRNA

PubMed Central

Nikonorova, Inna A.; Kornakov, Nikolay V.; Dmitriev, Sergey E.; Vassilenko, Konstantin S.; Ryazanov, Alexey G.

2014-01-01

TRPM7 is an essential and ubiquitous channel-kinase regulating cellular influx of Mg2+. Although TRPM7 mRNA is highly abundant, very small amount of the protein is detected in cells, suggesting post-transcriptional regulation of trpm7 gene expression. We found that TRPM7 mRNA 5′-leader contains two evolutionarily conserved upstream open reading frames that act together to drastically inhibit translation of the TRPM7 reading frame at high magnesium levels and ensure its optimal translation at low magnesium levels, when the activity of the channel-kinase is most required. The study provides the first example of magnesium channel synthesis being controlled by Mg2+ in higher eukaryotes. PMID:25326319

Characterization and Placement of Wetlands for Integrated Conservation Practice Planning

EPA Science Inventory

Constructed wetlands have been recognized as an efficient and cost-effective conservation practice to protect water quality through reducing the transport of sediments and nutrients from upstream croplands to downstream water bodies. The challenge resides in targeting the strateg...

Upstream open reading frames regulate the expression of the nuclear Wnt13 isoforms

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

Tang Tao; Rector, Kyle; Barnett, Corey D.

2008-02-22

Wnt proteins control cell survival and cell fate during development. Although Wnt expression is tightly regulated in a spatio-temporal manner, the mechanisms involved both at the transcriptional and translational levels are poorly defined. We have identified a downstream translation initiation codon, AUG(+74), in Wnt13B and Wnt13C mRNAs responsible for the expression of Wnt13 nuclear forms. In this report, we demonstrate that the expression of the nuclear Wnt13C form is translationally regulated in response to stress and apoptosis. Though the 5'-leaders of both Wnt13C and Wnt13B mRNAs have an inhibitory effect on translation, they did not display an internal ribosome entrymore » site activity as demonstrated by dicistronic reporter assays. However, mutations or deletions of the upstream AUG(-99) and AUG(+1) initiation codons abrogate these translation inhibitory effects, demonstrating that Wnt13C expression is controlled by upstream open reading frames. Since long 5'-untranslated region with short upstream open reading frames characterize other Wnt transcripts, our present data on the translational control of Wnt13 expression open the way to further studies on the translation control of Wnt expression as a modulator of their subcellular localization and activity.« less

Hormone-induced modifications of the chromatin structure surrounding upstream regulatory regions conserved between the mouse and rabbit whey acidic protein genes.

PubMed Central

Millot, Benjamin; Montoliu, Lluís; Fontaine, Marie-Louise; Mata, Teresa; Devinoy, Eve

2003-01-01

The upstream regulatory regions of the mouse and rabbit whey acidic protein (WAP) genes have been used extensively to target the efficient expression of foreign genes into the mammary gland of transgenic animals. Therefore both regions have been studied to elucidate fully the mechanisms controlling WAP gene expression. Three DNase I-hypersensitive sites (HSS0, HSS1 and HSS2) have been described upstream of the rabbit WAP gene in the lactating mammary gland and correspond to important regulatory regions. These sites are surrounded by variable chromatin structures during mammary-gland development. In the present study, we describe the upstream sequence of the mouse WAP gene. Analysis of genomic sequences shows that the mouse WAP gene is situated between two widely expressed genes (Cpr2 and Ramp3). We show that the hypersensitive sites found upstream of the rabbit WAP gene are also detected in the mouse WAP gene. Further, they encompass functional signal transducer and activator of transcription 5-binding sites, as has been observed in the rabbit. A new hypersensitive site (HSS3), not specific to the mammary gland, was mapped 8 kb upstream of the rabbit WAP gene. Unlike the three HSSs described above, HSS3 is also detected in the liver, but similar to HSS1, it does not depend on lactogenic hormone treatments during cell culture. The region surrounding HSS3 encompasses a potential matrix attachment region, which is also conserved upstream of the mouse WAP gene and contains a functional transcription factor Ets-1 (E26 transformation-specific-1)-binding site. Finally, we demonstrate for the first time that variations in the chromatin structure are dependent on prolactin alone. PMID:12580766

Characterization and placement of wetlands for integrated watershed conservation practice planning

USDA-ARS?s Scientific Manuscript database

Constructed wetlands have been recognized as an efficient and cost-effective conservation practice to protect water quality through reducing the transport of sediments and nutrients from upstream croplands to downstream water bodies. The challenge resides in targeting the strategic location of wetla...

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

Behaviour and design considerations for continuous flow closed-open-closed liquid microchannels.

PubMed

Melin, Jessica; van der Wijngaart, Wouter; Stemme, Göran

2005-06-01

This paper introduces a method of combining open and closed microchannels in a single component in a novel way which couples the benefits of both open and closed microfluidic systems and introduces interesting on-chip microfluidic behaviour. Fluid behaviour in such a component, based on continuous pressure driven flow and surface tension, is discussed in terms of cross sectional flow behaviour, robustness, flow-pressure performance, and its application to microfluidic interfacing. The closed-open-closed microchannel possesses the versatility of upstream and downstream closed microfluidics along with open fluidic direct access. The device has the advantage of eliminating gas bubbles present upstream when these enter the open channel section. The unique behaviour of this device opens the door to applications including direct liquid sample interfacing without the need for additional and bulky sample tubing.

Full equations utilities (FEQUTL) model for the approximation of hydraulic characteristics of open channels and control structures during unsteady flow

USGS Publications Warehouse

Franz, Delbert D.; Melching, Charles S.

1997-01-01

The Full EQuations UTiLities (FEQUTL) model is a computer program for computation of tables that list the hydraulic characteristics of open channels and control structures as a function of upstream and downstream depths; these tables facilitate the simulation of unsteady flow in a stream system with the Full Equations (FEQ) model. Simulation of unsteady flow requires many iterations for each time period computed. Thus, computation of hydraulic characteristics during the simulations is impractical, and preparation of function tables and application of table look-up procedures facilitates simulation of unsteady flow. Three general types of function tables are computed: one-dimensional tables that relate hydraulic characteristics to upstream flow depth, two-dimensional tables that relate flow through control structures to upstream and downstream flow depth, and three-dimensional tables that relate flow through gated structures to upstream and downstream flow depth and gate setting. For open-channel reaches, six types of one-dimensional function tables contain different combinations of the top width of flow, area, first moment of area with respect to the water surface, conveyance, flux coefficients, and correction coefficients for channel curvilinearity. For hydraulic control structures, one type of one-dimensional function table contains relations between flow and upstream depth, and two types of two-dimensional function tables contain relations among flow and upstream and downstream flow depths. For hydraulic control structures with gates, a three-dimensional function table lists the system of two-dimensional tables that contain the relations among flow and upstream and downstream flow depths that correspond to different gate openings. Hydraulic control structures for which function tables containing flow relations are prepared in FEQUTL include expansions, contractions, bridges, culverts, embankments, weirs, closed conduits (circular, rectangular, and pipe-arch shapes), dam failures, floodways, and underflow gates (sluice and tainter gates). The theory for computation of the hydraulic characteristics is presented for open channels and for each hydraulic control structure. For the hydraulic control structures, the theory is developed from the results of experimental tests of flow through the structure for different upstream and downstream flow depths. These tests were done to describe flow hydraulics for a single, steady-flow design condition and, thus, do not provide complete information on flow transitions (for example, between free- and submerged-weir flow) that may result in simulation of unsteady flow. Therefore, new procedures are developed to approximate the hydraulics of flow transitions for culverts, embankments, weirs, and underflow gates.

Flame Spread Along Free Edges of Thermally Thin Samples in Microgravity

NASA Technical Reports Server (NTRS)

Mell, W. E.; Olson, S. L.; Kashiwagi, T.

2000-01-01

The effects of imposed flow velocity on flame spread along open edges of a thermally thin cellulosic sample in microgravity are studied experimentally and theoretically. In this study, the sample is ignited locally at the middle of the 4 cm wide sample and subsequent flame spread reaches both open edges of the sample. The following flame behaviors are observed in the experiments and predicted by the numerical calculation; in order of increased imposed flow velocity: (1) ignition but subsequent flame spread is not attained, (2) flame spreads upstream (opposed mode) without any downstream flame, and (3) the upstream flame and two separate downstream flames traveling along the two open edges (concurrent mode). Generally, the upstream and downstream edge flame spread rates are faster than the central flame spread rate for an imposed flow velocity of up to 5 cm/s. This is due to greater oxygen supply from the outer free stream to the edge flames than the central flames, For the upstream edge flame, the greater oxygen supply results in a flame spread rate that is nearly independent of, or decreases gradually, with the imposed flow velocity. The spread rate of the downstream edge, however, increases significantly with the imposed flow velocity.

18 CFR 12.24 - Review and updating of plans.

Code of Federal Regulations, 2010 CFR

2010-04-01

... light of any significant changes in upstream or downstream circumstances which might affect water flows... 18 Conservation of Power and Water Resources 1 2010-04-01 2010-04-01 false Review and updating of plans. 12.24 Section 12.24 Conservation of Power and Water Resources FEDERAL ENERGY REGULATORY...

18 CFR 12.24 - Review and updating of plans.

Code of Federal Regulations, 2012 CFR

2012-04-01

... light of any significant changes in upstream or downstream circumstances which might affect water flows... 18 Conservation of Power and Water Resources 1 2012-04-01 2012-04-01 false Review and updating of plans. 12.24 Section 12.24 Conservation of Power and Water Resources FEDERAL ENERGY REGULATORY...

18 CFR 12.24 - Review and updating of plans.

Code of Federal Regulations, 2011 CFR

2011-04-01

... light of any significant changes in upstream or downstream circumstances which might affect water flows... 18 Conservation of Power and Water Resources 1 2011-04-01 2011-04-01 false Review and updating of plans. 12.24 Section 12.24 Conservation of Power and Water Resources FEDERAL ENERGY REGULATORY...

18 CFR 12.24 - Review and updating of plans.

Code of Federal Regulations, 2014 CFR

2014-04-01

... light of any significant changes in upstream or downstream circumstances which might affect water flows... 18 Conservation of Power and Water Resources 1 2014-04-01 2014-04-01 false Review and updating of plans. 12.24 Section 12.24 Conservation of Power and Water Resources FEDERAL ENERGY REGULATORY...

18 CFR 12.24 - Review and updating of plans.

Code of Federal Regulations, 2013 CFR

2013-04-01

... light of any significant changes in upstream or downstream circumstances which might affect water flows... 18 Conservation of Power and Water Resources 1 2013-04-01 2013-04-01 false Review and updating of plans. 12.24 Section 12.24 Conservation of Power and Water Resources FEDERAL ENERGY REGULATORY...

18 CFR 11.10 - General provision; waiver and exemptions; definitions.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 18 Conservation of Power and Water Resources 1 2014-04-01 2014-04-01 false General provision; waiver and exemptions; definitions. 11.10 Section 11.10 Conservation of Power and Water Resources FEDERAL... upstream, project, usually by increasing or decreasing the release of water from a storage reservoir. (b...

18 CFR 11.10 - General provision; waiver and exemptions; definitions.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 18 Conservation of Power and Water Resources 1 2013-04-01 2013-04-01 false General provision; waiver and exemptions; definitions. 11.10 Section 11.10 Conservation of Power and Water Resources FEDERAL... upstream, project, usually by increasing or decreasing the release of water from a storage reservoir. (b...

18 CFR 11.10 - General provision; waiver and exemptions; definitions.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 18 Conservation of Power and Water Resources 1 2012-04-01 2012-04-01 false General provision; waiver and exemptions; definitions. 11.10 Section 11.10 Conservation of Power and Water Resources FEDERAL... upstream, project, usually by increasing or decreasing the release of water from a storage reservoir. (b...

18 CFR 11.10 - General provision; waiver and exemptions; definitions.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 18 Conservation of Power and Water Resources 1 2010-04-01 2010-04-01 false General provision; waiver and exemptions; definitions. 11.10 Section 11.10 Conservation of Power and Water Resources FEDERAL... upstream, project, usually by increasing or decreasing the release of water from a storage reservoir. (b...

18 CFR 11.10 - General provision; waiver and exemptions; definitions.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 18 Conservation of Power and Water Resources 1 2011-04-01 2011-04-01 false General provision; waiver and exemptions; definitions. 11.10 Section 11.10 Conservation of Power and Water Resources FEDERAL... upstream, project, usually by increasing or decreasing the release of water from a storage reservoir. (b...

Bacillus subtilis δ Factor Functions as a Transcriptional Regulator by Facilitating the Open Complex Formation.

PubMed

Prajapati, Ranjit Kumar; Sengupta, Shreya; Rudra, Paulami; Mukhopadhyay, Jayanta

2016-01-15

Most bacterial RNA polymerases (RNAP) contain five conserved subunits, viz. 2α, β, β', and ω. However, in many Gram-positive bacteria, especially in fermicutes, RNAP is associated with an additional factor, called δ. For over three decades since its identification, it had been thought that δ functioned as a subunit of RNAP to enhance the level of transcripts by recycling RNAP. In support of the previous observations, we also find that δ is involved in recycling of RNAP by releasing the RNA from the ternary complex. We further show that δ binds to RNA and is able to recycle RNAP when the length of the nascent RNA reaches a critical length. However, in this work we decipher a new function of δ. Performing biochemical and mutational analysis, we show that Bacillus subtilis δ binds to DNA immediately upstream of the promoter element at A-rich sequences on the abrB and rrnB1 promoters and facilitates open complex formation. As a result, δ facilitates RNAP to initiate transcription in the second scale, compared with minute scale in the absence of δ. Using transcription assay, we show that δ-mediated recycling of RNAP cannot be the sole reason for the enhancement of transcript yield. Our observation that δ does not bind to RNAP holo enzyme but is required to bind to DNA upstream of the -35 promoter element for transcription activation suggests that δ functions as a transcriptional regulator. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Regulatory elements of Caenorhabditis elegans ribosomal protein genes

PubMed Central

2012-01-01

Background Ribosomal protein genes (RPGs) are essential, tightly regulated, and highly expressed during embryonic development and cell growth. Even though their protein sequences are strongly conserved, their mechanism of regulation is not conserved across yeast, Drosophila, and vertebrates. A recent investigation of genomic sequences conserved across both nematode species and associated with different gene groups indicated the existence of several elements in the upstream regions of C. elegans RPGs, providing a new insight regarding the regulation of these genes in C. elegans. Results In this study, we performed an in-depth examination of C. elegans RPG regulation and found nine highly conserved motifs in the upstream regions of C. elegans RPGs using the motif discovery algorithm DME. Four motifs were partially similar to transcription factor binding sites from C. elegans, Drosophila, yeast, and human. One pair of these motifs was found to co-occur in the upstream regions of 250 transcripts including 22 RPGs. The distance between the two motifs displayed a complex frequency pattern that was related to their relative orientation. We tested the impact of three of these motifs on the expression of rpl-2 using a series of reporter gene constructs and showed that all three motifs are necessary to maintain the high natural expression level of this gene. One of the motifs was similar to the binding site of an orthologue of POP-1, and we showed that RNAi knockdown of pop-1 impacts the expression of rpl-2. We further determined the transcription start site of rpl-2 by 5’ RACE and found that the motifs lie 40–90 bases upstream of the start site. We also found evidence that a noncoding RNA, contained within the outron of rpl-2, is co-transcribed with rpl-2 and cleaved during trans-splicing. Conclusions Our results indicate that C. elegans RPGs are regulated by a complex novel series of regulatory elements that is evolutionarily distinct from those of all other species examined up until now. PMID:22928635

A conserved catalytic residue in the ubiquitin-conjugating enzyme family

PubMed Central

Wu, Pei-Ying; Hanlon, Mary; Eddins, Michael; Tsui, Colleen; Rogers, Richard S.; Jensen, Jane P.; Matunis, Michael J.; Weissman, Allan M.; Wolberger, Cynthia P.; Pickart, Cecile M.

2003-01-01

Ubiquitin (Ub) regulates diverse functions in eukaryotes through its attachment to other proteins. The defining step in this protein modification pathway is the attack of a substrate lysine residue on Ub bound through its C-terminus to the active site cysteine residue of a Ub-conjugating enzyme (E2) or certain Ub ligases (E3s). So far, these E2 and E3 cysteine residues are the only enzyme groups known to participate in the catalysis of conjugation. Here we show that a strictly conserved E2 asparagine residue is critical for catalysis of E2- and E2/RING E3-dependent isopeptide bond formation, but dispensable for upstream and downstream reactions of Ub thiol ester formation. In constrast, the strictly conserved histidine and proline residues immediately upstream of the asparagine are dispensable for catalysis of isopeptide bond formation. We propose that the conserved asparagine side chain stabilizes the oxyanion intermediate formed during lysine attack. The E2 asparagine is the first non-covalent catalytic group to be proposed in any Ub conjugation factor. PMID:14517261

Transcription of two adjacent carbohydrate utilization gene clusters in Bifidobacterium breve UCC2003 is controlled by LacI- and repressor open reading frame kinase (ROK)-type regulators.

PubMed

O'Connell, Kerry Joan; Motherway, Mary O'Connell; Liedtke, Andrea; Fitzgerald, Gerald F; Paul Ross, R; Stanton, Catherine; Zomer, Aldert; van Sinderen, Douwe

2014-06-01

Members of the genus Bifidobacterium are commonly found in the gastrointestinal tracts of mammals, including humans, where their growth is presumed to be dependent on various diet- and/or host-derived carbohydrates. To understand transcriptional control of bifidobacterial carbohydrate metabolism, we investigated two genetic carbohydrate utilization clusters dedicated to the metabolism of raffinose-type sugars and melezitose. Transcriptomic and gene inactivation approaches revealed that the raffinose utilization system is positively regulated by an activator protein, designated RafR. The gene cluster associated with melezitose metabolism was shown to be subject to direct negative control by a LacI-type transcriptional regulator, designated MelR1, in addition to apparent indirect negative control by means of a second LacI-type regulator, MelR2. In silico analysis, DNA-protein interaction, and primer extension studies revealed the MelR1 and MelR2 operator sequences, each of which is positioned just upstream of or overlapping the correspondingly regulated promoter sequences. Similar analyses identified the RafR binding operator sequence located upstream of the rafB promoter. This study indicates that transcriptional control of gene clusters involved in carbohydrate metabolism in bifidobacteria is subject to conserved regulatory systems, representing either positive or negative control.

Molecular links among the causative genes for ocular malformation: Otx2 and Sox2 coregulate Rax expression.

PubMed

Danno, Hiroki; Michiue, Tatsuo; Hitachi, Keisuke; Yukita, Akira; Ishiura, Shoichi; Asashima, Makoto

2008-04-08

The neural-related genes Sox2, Pax6, Otx2, and Rax have been associated with severe ocular malformations such as anophthalmia and microphthalmia, but it remains unclear as to how these genes are linked functionally. We analyzed the upstream signaling of Xenopus Rax (also known as Rx1) and identified the Otx2 and Sox2 proteins as direct upstream regulators of Rax. We revealed that endogenous Otx2 and Sox2 proteins bound to the conserved noncoding sequence (CNS1) located approximately 2 kb upstream of the Rax promoter. This sequence is conserved among vertebrates and is required for potent transcriptional activity. Reporter assays showed that Otx2 and Sox2 synergistically activated transcription via CNS1. Furthermore, the Otx2 and Sox2 proteins physically interacted with each other, and this interaction was affected by the Sox2-missense mutations identified in these ocular disorders. These results demonstrate that the direct interaction and interdependence between the Otx2 and Sox2 proteins coordinate Rax expression in eye development, providing molecular linkages among the genes responsible for ocular malformation.

DENSITY FLUCTUATIONS UPSTREAM AND DOWNSTREAM OF INTERPLANETARY SHOCKS

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

Pitňa, A.; Šafránková, J.; Němeček, Z.

2016-03-01

Interplanetary (IP) shocks as typical large-scale disturbances arising from processes such as stream–stream interactions or Interplanetary Coronal Mass Ejection (ICME) launching play a significant role in the energy redistribution, dissipation, particle heating, acceleration, etc. They can change the properties of the turbulent cascade on shorter scales. We focus on changes of the level and spectral properties of ion flux fluctuations upstream and downstream of fast forward oblique shocks. Although the fluctuation level increases by an order of magnitude across the shock, the spectral slope in the magnetohydrodynamic range is conserved. The frequency spectra upstream of IP shocks are the same as those inmore » the solar wind (if not spoiled by foreshock waves). The spectral slopes downstream are roughly proportional to the corresponding slopes upstream, suggesting that the properties of the turbulent cascade are conserved across the shock; thus, the shock does not destroy the shape of the spectrum as turbulence passes through it. Frequency spectra downstream of IP shocks often exhibit “an exponential decay” in the ion kinetic range that was earlier reported at electron scales in the solar wind or at ion scales in the interstellar medium. We suggest that the exponential shape of ion flux spectra in this range is caused by stronger damping of the fluctuations in the downstream region.« less

A test of flushing procedures to control salt-water intrusion at the W. P. Franklin Dam near Ft. Myers, Florida and The magnitude and extent of salt-water contamination in the Caloosahatchee River between La Belle and Olga, Florida

USGS Publications Warehouse

Boggess, Durward H.

1970-01-01

During low-flow periods, salty water from the tidal part of the Caloosahatchee River moves upstream during boat lockages at the W. P. Franklin Darn near Ft. Myers, Florida, as shown on figure L Salty water enters the lock chamber through openings of the downstream sector gates which separate tidal and fresh water; when the upstream gates open, some of the salty water moves into the upper pool, probably as a density current. Repeated injections of salty water cause a progressive increase in the salinity of the upstream water. The salty water moves upstream within the deeper parts of the river channel as far as 5 or more miles above the lock. Some mixing of the high-chloride deeper water and the fresher shallow water occurs in the affected reach above the lock, probably as a result of wind and waves, and turbulence created by boat traffic.

An upstream open reading frame represses expression of Lc, a member of the R/B family of maize transcriptional activators

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

Damiani, R.D. Jr.; Wessler, S.R.

1993-09-01

The R/B genes of maize encode a family of basic helix-loop-helix proteins that determine where and when the anthocyanin-pigment pathway will be expressed in the plant. Previous studies showed that allelic diversity among family members reflects differences in gene expression, specifically in transcription initiation. The authors present evidence that the R gene Lc is under translational control. They demonstrate that the 235-nt transcript leader of Lc represses expression 25- to 30-fold in an in vivo assay. Repression is mediated by the presence in cis of a 38-codon upstream open reading frame. Furthermore, the coding capacity of the upstream open readingmore » frame influences the magnitude of repression. It is proposed that translational control does not contribute to tissue specificity but prevents overexpression of the Lc protein. The diversity of promoter and 5' untranslated leader sequences among the R/B genes provides an opportunity to study the coevolution of transcriptional and translational mechanisms of gene regulation. 36 refs., 5 figs.« less

PUTATIVE GENE PROMOTER SEQUENCES IN THE CHLORELLA VIRUSES

PubMed Central

Fitzgerald, Lisa A.; Boucher, Philip T.; Yanai-Balser, Giane; Suhre, Karsten; Graves, Michael V.; Van Etten, James L.

2008-01-01

Three short (7 to 9 nucleotides) highly conserved nucleotide sequences were identified in the putative promoter regions (150 bp upstream and 50 bp downstream of the ATG translation start site) of three members of the genus Chlorovirus, family Phycodnaviridae. Most of these sequences occurred in similar locations within the defined promoter regions. The sequence and location of the motifs were often conserved among homologous ORFs within the Chlorovirus family. One of these conserved sequences (AATGACA) is predominately associated with genes expressed early in virus replication. PMID:18768195

Phyloscan: locating transcription-regulating binding sites in mixed aligned and unaligned sequence data.

PubMed

Palumbo, Michael J; Newberg, Lee A

2010-07-01

The transcription of a gene from its DNA template into an mRNA molecule is the first, and most heavily regulated, step in gene expression. Especially in bacteria, regulation is typically achieved via the binding of a transcription factor (protein) or small RNA molecule to the chromosomal region upstream of a regulated gene. The protein or RNA molecule recognizes a short, approximately conserved sequence within a gene's promoter region and, by binding to it, either enhances or represses expression of the nearby gene. Since the sought-for motif (pattern) is short and accommodating to variation, computational approaches that scan for binding sites have trouble distinguishing functional sites from look-alikes. Many computational approaches are unable to find the majority of experimentally verified binding sites without also finding many false positives. Phyloscan overcomes this difficulty by exploiting two key features of functional binding sites: (i) these sites are typically more conserved evolutionarily than are non-functional DNA sequences; and (ii) these sites often occur two or more times in the promoter region of a regulated gene. The website is free and open to all users, and there is no login requirement. Address: (http://bayesweb.wadsworth.org/phyloscan/).

Remaining Mysteries of Molecular Biology: The Role of Polyamines in the Cell.

PubMed

Miller-Fleming, Leonor; Olin-Sandoval, Viridiana; Campbell, Kate; Ralser, Markus

2015-10-23

The polyamines (PAs) spermidine, spermine, putrescine and cadaverine are an essential class of metabolites found throughout all kingdoms of life. In this comprehensive review, we discuss their metabolism, their various intracellular functions and their unusual and conserved regulatory features. These include the regulation of translation via upstream open reading frames, the over-reading of stop codons via ribosomal frameshifting, the existence of an antizyme and an antizyme inhibitor, ubiquitin-independent proteasomal degradation, a complex bi-directional membrane transport system and a unique posttranslational modification-hypusination-that is believed to occur on a single protein only (eIF-5A). Many of these features are broadly conserved indicating that PA metabolism is both concentration critical and evolutionary ancient. When PA metabolism is disrupted, a plethora of cellular processes are affected, including transcription, translation, gene expression regulation, autophagy and stress resistance. As a result, the role of PAs has been associated with cell growth, aging, memory performance, neurodegenerative diseases, metabolic disorders and cancer. Despite comprehensive studies addressing PAs, a unifying concept to interpret their molecular role is missing. The precise biochemical function of polyamines is thus one of the remaining mysteries of molecular cell biology. Copyright © 2015. Published by Elsevier Ltd.

The positive regulatory function of the 5'-proximal open reading frames in GCN4 mRNA can be mimicked by heterologous, short coding sequences.

PubMed Central

Williams, N P; Mueller, P P; Hinnebusch, A G

1988-01-01

Translational control of GCN4 expression in the yeast Saccharomyces cerevisiae is mediated by multiple AUG codons present in the leader of GCN4 mRNA, each of which initiates a short open reading frame of only two or three codons. Upstream AUG codons 3 and 4 are required to repress GCN4 expression in normal growth conditions; AUG codons 1 and 2 are needed to overcome this repression in amino acid starvation conditions. We show that the regulatory function of AUG codons 1 and 2 can be qualitatively mimicked by the AUG codons of two heterologous upstream open reading frames (URFs) containing the initiation regions of the yeast genes PGK and TRP1. These AUG codons inhibit GCN4 expression when present singly in the mRNA leader; however, they stimulate GCN4 expression in derepressing conditions when inserted upstream from AUG codons 3 and 4. This finding supports the idea that AUG codons 1 and 2 function in the control mechanism as translation initiation sites and further suggests that suppression of the inhibitory effects of AUG codons 3 and 4 is a general consequence of the translation of URF 1 and 2 sequences upstream. Several observations suggest that AUG codons 3 and 4 are efficient initiation sites; however, these sequences do not act as positive regulatory elements when placed upstream from URF 1. This result suggests that efficient translation is only one of the important properties of the 5' proximal URFs in GCN4 mRNA. We propose that a second property is the ability to permit reinitiation following termination of translation and that URF 1 is optimized for this regulatory function. Images PMID:3065626

CarD uses a minor groove wedge mechanism to stabilize the RNA polymerase open promoter complex.

PubMed

Bae, Brian; Chen, James; Davis, Elizabeth; Leon, Katherine; Darst, Seth A; Campbell, Elizabeth A

2015-09-08

A key point to regulate gene expression is at transcription initiation, and activators play a major role. CarD, an essential activator in Mycobacterium tuberculosis, is found in many bacteria, including Thermus species, but absent in Escherichia coli. To delineate the molecular mechanism of CarD, we determined crystal structures of Thermus transcription initiation complexes containing CarD. The structures show CarD interacts with the unique DNA topology presented by the upstream double-stranded/single-stranded DNA junction of the transcription bubble. We confirm that our structures correspond to functional activation complexes, and extend our understanding of the role of a conserved CarD Trp residue that serves as a minor groove wedge, preventing collapse of the transcription bubble to stabilize the transcription initiation complex. Unlike E. coli RNAP, many bacterial RNAPs form unstable promoter complexes, explaining the need for CarD.

Molecular cloning of actin genes in Trichomonas vaginalis and phylogeny inferred from actin sequences.

PubMed

Bricheux, G; Brugerolle, G

1997-08-01

The parasitic protozoan Trichomonas vaginalis is known to contain the ubiquitous and highly conserved protein actin. A genomic library and a cDNA library have been screened to identify and clone the actin gene(s) of T. vaginalis. The nucleotide sequence of one gene and its flanking regions have been determined. The open reading frame encodes a protein of 376 amino acids. The sequence is not interrupted by any introns and the promoter could be represented by a 10 bp motif close to a consensus motif also found upstream of most sequenced T. vaginalis genes. The five different clones isolated from the cDNA library have similar sequences and encode three actin proteins differing only by one or two amino acids. A phylogenetic analysis of 31 actin sequences by distance matrix and parsimony methods, using centractin as outgroup, gives congruent trees with Parabasala branching above Diplomonadida.

Role of eIF2α Kinases in Translational Control and Adaptation to Cellular Stress.

PubMed

Wek, Ronald C

2018-02-12

A central mechanism regulating translation initiation in response to environmental stress involves phosphorylation of the α subunit of eukaryotic initiation factor 2 (eIF2α). Phosphorylation of eIF2α causes inhibition of global translation, which conserves energy and facilitates reprogramming of gene expression and signaling pathways that help to restore protein homeostasis. Coincident with repression of protein synthesis, many gene transcripts involved in the stress response are not affected or are even preferentially translated in response to increased eIF2α phosphorylation by mechanisms involving upstream open reading frames (uORFs). This review highlights the mechanisms regulating eIF2α kinases, the role that uORFs play in translational control, and the impact that alteration of eIF2α phosphorylation by gene mutations or small molecule inhibitors can have on health and disease. Copyright © 2018 Cold Spring Harbor Laboratory Press; all rights reserved.

Filling gaps in a large reserve network to address freshwater conservation needs.

PubMed

Hermoso, Virgilio; Filipe, Ana Filipa; Segurado, Pedro; Beja, Pedro

2015-09-15

Freshwater ecosystems and biodiversity are among the most threatened at global scale, but efforts for their conservation have been mostly peripheral to terrestrial conservation. For example, Natura 2000, the world's largest network of protected areas, fails to cover adequately the distribution of rare and endangered aquatic species, and lacks of appropriate spatial design to make conservation for freshwater biodiversity effective. Here, we develop a framework to identify a complementary set of priority areas and enhance the conservation opportunities of Natura 2000 for freshwater biodiversity, using the Iberian Peninsula as a case study. We use a systematic planning approach to identify a minimum set of additional areas that would help i) adequately represent all freshwater fish, amphibians and aquatic reptiles at three different target levels, ii) account for key ecological processes derived from riverscape connectivity, and iii) minimize the impact of threats, both within protected areas and propagated from upstream unprotected areas. Addressing all these goals would need an increase in area between 7 and 46%, depending on the conservation target used and strength of connectivity required. These new priority areas correspond to subcatchments inhabited by endangered and range restricted species, as well as additional subcatchments required to improve connectivity among existing protected areas and to increase protection against upstream threats. Our study should help guide future revisions of the design of Natura 2000, while providing a framework to address deficiencies in reserve networks for adequately protecting freshwater biodiversity elsewhere. Copyright © 2015 Elsevier Ltd. All rights reserved.

Molecular links among the causative genes for ocular malformation: Otx2 and Sox2 coregulate Rax expression

PubMed Central

Danno, Hiroki; Michiue, Tatsuo; Hitachi, Keisuke; Yukita, Akira; Ishiura, Shoichi; Asashima, Makoto

2008-01-01

The neural-related genes Sox2, Pax6, Otx2, and Rax have been associated with severe ocular malformations such as anophthalmia and microphthalmia, but it remains unclear as to how these genes are linked functionally. We analyzed the upstream signaling of Xenopus Rax (also known as Rx1) and identified the Otx2 and Sox2 proteins as direct upstream regulators of Rax. We revealed that endogenous Otx2 and Sox2 proteins bound to the conserved noncoding sequence (CNS1) located ≈2 kb upstream of the Rax promoter. This sequence is conserved among vertebrates and is required for potent transcriptional activity. Reporter assays showed that Otx2 and Sox2 synergistically activated transcription via CNS1. Furthermore, the Otx2 and Sox2 proteins physically interacted with each other, and this interaction was affected by the Sox2-missense mutations identified in these ocular disorders. These results demonstrate that the direct interaction and interdependence between the Otx2 and Sox2 proteins coordinate Rax expression in eye development, providing molecular linkages among the genes responsible for ocular malformation. PMID:18385377

Evolution of Advection Upstream Splitting Method Schemes

NASA Technical Reports Server (NTRS)

Liou, Meng-Sing

2010-01-01

This paper focuses on the evolution of advection upstream splitting method(AUSM) schemes. The main ingredients that have led to the development of modern computational fluid dynamics (CFD) methods have been reviewed, thus the ideas behind AUSM. First and foremost is the concept of upwinding. Second, the use of Riemann problem in constructing the numerical flux in the finite-volume setting. Third, the necessity of including all physical processes, as characterised by the linear (convection) and nonlinear (acoustic) fields. Fourth, the realisation of separating the flux into convection and pressure fluxes. The rest of this review briefly outlines the technical evolution of AUSM and more details can be found in the cited references. Keywords: Computational fluid dynamics methods, hyperbolic systems, advection upstream splitting method, conservation laws, upwinding, CFD

Mutations that alter a conserved element upstream of the potato virus X triple block and coat protein genes affect subgenomic RNA accumulation.

PubMed

Kim, K H; Hemenway, C

1997-05-26

The putative subgenomic RNA (sgRNA) promoter regions upstream of the potato virus X (PVX) triple block and coat protein (CP) genes contain sequences common to other potexviruses. The importance of these sequences to PVX sgRNA accumulation was determined by inoculation of Nicotiana tabacum NT1 cell suspension protoplasts with transcripts derived from wild-type and modified PVX cDNA clones. Analyses of RNA accumulation by S1 nuclease digestion and primer extension indicated that a conserved octanucleotide sequence element and the spacing between this element and the start-site for sgRNA synthesis are critical for accumulation of the two major sgRNA species. The impact of mutations on CP sgRNA levels was also reflected in the accumulation of CP. In contrast, genomic minus- and plus-strand RNA accumulation were not significantly affected by mutations in these regions. Studies involving inoculation of tobacco plants with the modified transcripts suggested that the conserved octanucleotide element functions in sgRNA accumulation and some other aspect of the infection process.

Transcription of Two Adjacent Carbohydrate Utilization Gene Clusters in Bifidobacterium breve UCC2003 Is Controlled by LacI- and Repressor Open Reading Frame Kinase (ROK)-Type Regulators

PubMed Central

O'Connell, Kerry Joan; O'Connell Motherway, Mary; Liedtke, Andrea; Fitzgerald, Gerald F.; Ross, R. Paul; Stanton, Catherine; Zomer, Aldert

2014-01-01

Members of the genus Bifidobacterium are commonly found in the gastrointestinal tracts of mammals, including humans, where their growth is presumed to be dependent on various diet- and/or host-derived carbohydrates. To understand transcriptional control of bifidobacterial carbohydrate metabolism, we investigated two genetic carbohydrate utilization clusters dedicated to the metabolism of raffinose-type sugars and melezitose. Transcriptomic and gene inactivation approaches revealed that the raffinose utilization system is positively regulated by an activator protein, designated RafR. The gene cluster associated with melezitose metabolism was shown to be subject to direct negative control by a LacI-type transcriptional regulator, designated MelR1, in addition to apparent indirect negative control by means of a second LacI-type regulator, MelR2. In silico analysis, DNA-protein interaction, and primer extension studies revealed the MelR1 and MelR2 operator sequences, each of which is positioned just upstream of or overlapping the correspondingly regulated promoter sequences. Similar analyses identified the RafR binding operator sequence located upstream of the rafB promoter. This study indicates that transcriptional control of gene clusters involved in carbohydrate metabolism in bifidobacteria is subject to conserved regulatory systems, representing either positive or negative control. PMID:24705323

Influence of upstream disturbance on the draft-tube flow of Francis turbine under part-load conditions

NASA Astrophysics Data System (ADS)

Chen, Ting; Zheng, Xianghao; Zhang, Yu-ning; Li, Shengcai

2018-02-01

Owing to the part-load operations for the enhancement of grid flexibility, the Francis turbine often suffers from severe low-frequency and large-amplitude hydraulic instability, which is mostly pertinent to the highly unsteady swirling vortex rope in the draft tube. The influence of disturbances in the upstream (e.g., large-scale vortex structures in the spiral casing) on the draft-tube vortex flow is not well understood yet. In the present paper, the influence of the upstream disturbances on the vortical flow in the draft tube is studied based on the vortex identification method and the analysis of several important parameters (e.g., the swirl number and the velocity profile). For a small guide vane opening (representing the part-load condition), the vortices triggered in the spiral casing propagate downstream and significantly affect the swirling vortex-rope precession in the draft tube, leading to the changes of the intensity and the processional frequency of the swirling vortex rope. When the guide vane opening approaches the optimum one (representing the full-load condition), the upstream disturbance becomes weaker and thus its influences on the downstream flow are very limited.

Achieving open access to conservation science.

PubMed

Fuller, Richard A; Lee, Jasmine R; Watson, James E M

2014-12-01

Conservation science is a crisis discipline in which the results of scientific enquiry must be made available quickly to those implementing management. We assessed the extent to which scientific research published since the year 2000 in 20 conservation science journals is publicly available. Of the 19,207 papers published, 1,667 (8.68%) are freely downloadable from an official repository. Moreover, only 938 papers (4.88%) meet the standard definition of open access in which material can be freely reused providing attribution to the authors is given. This compares poorly with a comparable set of 20 evolutionary biology journals, where 31.93% of papers are freely downloadable and 7.49% are open access. Seventeen of the 20 conservation journals offer an open access option, but fewer than 5% of the papers are available through open access. The cost of accessing the full body of conservation science runs into tens of thousands of dollars per year for institutional subscribers, and many conservation practitioners cannot access pay-per-view science through their workplace. However, important initiatives such as Research4Life are making science available to organizations in developing countries. We urge authors of conservation science to pay for open access on a per-article basis or to choose publication in open access journals, taking care to ensure the license allows reuse for any purpose providing attribution is given. Currently, it would cost $51 million to make all conservation science published since 2000 freely available by paying the open access fees currently levied to authors. Publishers of conservation journals might consider more cost effective models for open access and conservation-oriented organizations running journals could consider a broader range of options for open access to nonmembers such as sponsorship of open access via membership fees. © 2014 The Authors. Conservation Biology published by Wiley Periodicals, Inc., on behalf of the Society for Conservation Biology.

How Do the Location, Size and Budget of Open Space Conservation Affect Land Values?

Treesearch

JunJie Wu; Wenchao Xu; Ralph J. Alig

2016-01-01

In this article we present a model to examine the optimal location, size, and budget of open space conservation and the resulting impact on land values and local fiscal conditions in an urban area. Results indicate that open space conservation can transform the defining features of an urban landscape. A well-designed open space conservation program can improve...

Complete sequence of Tvv1, a family of Ty 1 copia-like retrotransposons of Vitis vinifera L., reconstituted by chromosome walking.

PubMed

Pelsy, F.; Merdinoglu, D.

2002-09-01

A chromosome-walking strategy was used to sequence and characterize retrotransposons in the grapevine genome. The reconstitution of a family of retroelements, named Tvv1, was achieved by six successive steps. These elements share a single, highly conserved open reading frame 4,153 nucleotides-long, putatively encoding the gag, pro, int, rt and rh proteins. Comparison of the Tvv1 open reading frame coding potential with those of drosophila copia and tobacco Tnt1, revealed that Tvv1 is closely related to Ty 1 copia-like retrotransposons. A highly variable untranslated leader region, upstream of the open reading frame, allowed us to differentiate Tvv1 variants, which represent a family of at least 28 copies, in varying sizes. This internal region is flanked by two long terminal repeats in direct orientation, sized between 149 and 157 bp. Among elements theoretically sized from 4,970 to 5,550 bp, we describe the full-length sequence of a reference element Tvv1-1, 5,343 nucleotides-long. The full-length sequence of Tvv1-1 compared to pea PDR1 shows a 53.3% identity. In addition, both elements contain long terminal repeats of nearly the same size in which the U5 region could be entirely absent. Therefore, we assume that Tvv1 and PDR1 could constitute a particular class of short LTRs retroelements.

Upstream dispersal of an invasive crayfish aided by a fish passage facility

USGS Publications Warehouse

Welsh, Stuart A.; Loughman, Zachary J.

2015-01-01

Fish passage facilities for reservoir dams have been used to restore habitat connectivity within riverine networks by allowing upstream passage for native species. These facilities may also support the spread of invasive species, an unintended consequence and potential downside of upstream passage structures. We documented dam passage of the invasive virile crayfish, Orconectes virilis (Hagen, 1870), at fish ladders designed for upstream passage of American eels, Anguilla rostrata (Lesueur, 1817), in the Shenandoah River drainage, USA. Ladder use and upstream passage of 11 virile crayfish occurred from 2007–2014 during periods of low river discharge (<30 m3s–1) and within a wide range of water temperatures from 9.0–28.6 °C. Virile crayfish that used the eel ladders were large adults with a mean carapace length and width of 48.0 mm and 24.1 mm, respectively. Our data demonstrated the use of species-specific fish ladders by a non-target non-native species, which has conservation and management implications for the spread of aquatic invasive species and upstream passage facilities. Specifically, managers should consider implementing long-term monitoring of fish passage facilities with emphasis on detection of invasive species, as well as methods to reduce or eliminate passage of invasive species. 

Crystal structure of a transcribing RNA Polymerase II complex reveals a complete transcription bubble

PubMed Central

Barnes, Christopher O.; Calero, Monica; Malik, Indranil; Graham, Brian W.; Spahr, Henrik; Lin, Guowu; Cohen, Aina; Brown, Ian S.; Zhang, Qiangmin; Pullara, Filippo; Trakselis, Michael A.; Kaplan, Craig D.; Calero, Guillermo

2015-01-01

Summary Notwithstanding numerous published structures of RNA Polymerase II (Pol II), structural details of Pol II engaging a complete nucleic acid scaffold have been lacking. Here, we report the structures of TFIIF stabilized transcribing Pol II complexes, revealing the upstream duplex and full transcription bubble. The upstream duplex lies over a wedge-shaped loop from Rpb2 that engages its minor groove, providing part of the structural framework for DNA tracking during elongation. At the upstream transcription bubble fork, rudder and fork loop-1 residues spatially coordinate strand annealing and the nascent RNA transcript. At the downstream fork, a network of Pol II interactions with the non-template strand forms a rigid domain with the Trigger Loop (TL), allowing visualization of its open state. Overall, our observations suggest that “open/closed” conformational transitions of the TL may be linked to interactions with the non-template strand, possibly in a synchronized ratcheting manner conducive to polymerase translocation. PMID:26186291

Achieving a golden mean: mechanisms by which coronaviruses ensure synthesis of the correct stoichiometric ratios of viral proteins.

PubMed

Plant, Ewan P; Rakauskaite, Rasa; Taylor, Deborah R; Dinman, Jonathan D

2010-05-01

In retroviruses and the double-stranded RNA totiviruses, the efficiency of programmed -1 ribosomal frameshifting is critical for ensuring the proper ratios of upstream-encoded capsid proteins to downstream-encoded replicase enzymes. The genomic organizations of many other frameshifting viruses, including the coronaviruses, are very different, in that their upstream open reading frames encode nonstructural proteins, the frameshift-dependent downstream open reading frames encode enzymes involved in transcription and replication, and their structural proteins are encoded by subgenomic mRNAs. The biological significance of frameshifting efficiency and how the relative ratios of proteins encoded by the upstream and downstream open reading frames affect virus propagation has not been explored before. Here, three different strategies were employed to test the hypothesis that the -1 PRF signals of coronaviruses have evolved to produce the correct ratios of upstream- to downstream-encoded proteins. Specifically, infectious clones of the severe acute respiratory syndrome (SARS)-associated coronavirus harboring mutations that lower frameshift efficiency decreased infectivity by >4 orders of magnitude. Second, a series of frameshift-promoting mRNA pseudoknot mutants was employed to demonstrate that the frameshift signals of the SARS-associated coronavirus and mouse hepatitis virus have evolved to promote optimal frameshift efficiencies. Finally, we show that a previously described frameshift attenuator element does not actually affect frameshifting per se but rather serves to limit the fraction of ribosomes available for frameshifting. The findings of these analyses all support a "golden mean" model in which viruses use both programmed ribosomal frameshifting and translational attenuation to control the relative ratios of their encoded proteins.

Selection of Optimal Polypurine Tract Region Sequences during Moloney Murine Leukemia Virus Replication

PubMed Central

Robson, Nicole D.; Telesnitsky, Alice

2000-01-01

Retrovirus plus-strand synthesis is primed by a cleavage remnant of the polypurine tract (PPT) region of viral RNA. In this study, we tested replication properties for Moloney murine leukemia viruses with targeted mutations in the PPT and in conserved sequences upstream, as well as for pools of mutants with randomized sequences in these regions. The importance of maintaining some purine residues within the PPT was indicated both by examining the evolution of random PPT pools and from the replication properties of targeted mutants. Although many different PPT sequences could support efficient replication and one mutant that contained two differences in the core PPT was found to replicate as well as the wild type, some sequences in the core PPT clearly conferred advantages over others. Contributions of sequences upstream of the core PPT were examined with deletion mutants. A conserved T-stretch within the upstream sequence was examined in detail and found to be unimportant to helper functions. Evolution of virus pools containing randomized T-stretch sequences demonstrated marked preference for the wild-type sequence in six of its eight positions. These findings demonstrate that maintenance of the T-rich element is more important to viral replication than is maintenance of the core PPT. PMID:11044073

Enhancer elements upstream of the SHOX gene are active in the developing limb.

PubMed

Durand, Claudia; Bangs, Fiona; Signolet, Jason; Decker, Eva; Tickle, Cheryll; Rappold, Gudrun

2010-05-01

Léri-Weill Dyschondrosteosis (LWD) is a dominant skeletal disorder characterized by short stature and distinct bone anomalies. SHOX gene mutations and deletions of regulatory elements downstream of SHOX resulting in haploinsufficiency have been found in patients with LWD. SHOX encodes a homeodomain transcription factor and is known to be expressed in the developing limb. We have now analyzed the regulatory significance of the region upstream of the SHOX gene. By comparative genomic analyses, we identified several conserved non-coding elements, which subsequently were tested in an in ovo enhancer assay in both chicken limb bud and cornea, where SHOX is also expressed. In this assay, we found three enhancers to be active in the developing chicken limb, but none were functional in the developing cornea. A screening of 60 LWD patients with an intact SHOX coding and downstream region did not yield any deletion of the upstream enhancer region. Thus, we speculate that SHOX upstream deletions occur at a lower frequency because of the structural organization of this genomic region and/or that SHOX upstream deletions may cause a phenotype that differs from the one observed in LWD.

Enhancer elements upstream of the SHOX gene are active in the developing limb

PubMed Central

Durand, Claudia; Bangs, Fiona; Signolet, Jason; Decker, Eva; Tickle, Cheryll; Rappold, Gudrun

2010-01-01

Léri-Weill Dyschondrosteosis (LWD) is a dominant skeletal disorder characterized by short stature and distinct bone anomalies. SHOX gene mutations and deletions of regulatory elements downstream of SHOX resulting in haploinsufficiency have been found in patients with LWD. SHOX encodes a homeodomain transcription factor and is known to be expressed in the developing limb. We have now analyzed the regulatory significance of the region upstream of the SHOX gene. By comparative genomic analyses, we identified several conserved non-coding elements, which subsequently were tested in an in ovo enhancer assay in both chicken limb bud and cornea, where SHOX is also expressed. In this assay, we found three enhancers to be active in the developing chicken limb, but none were functional in the developing cornea. A screening of 60 LWD patients with an intact SHOX coding and downstream region did not yield any deletion of the upstream enhancer region. Thus, we speculate that SHOX upstream deletions occur at a lower frequency because of the structural organization of this genomic region and/or that SHOX upstream deletions may cause a phenotype that differs from the one observed in LWD. PMID:19997128

7 CFR 613.2 - Policy and objectives.

Code of Federal Regulations, 2011 CFR

2011-01-01

... working with experiment stations, crop improvement associations, and other State and Federal agencies. (b... related to: (1) Controlling soil erosion on all lands; (2) Conserving water; (3) Protecting upstream... enhancement; (12) Selecting plants that tolerate air pollution agents and toxic soil chemicals; (13) Selecting...

Upstream-advancing waves generated by a current over a sinusoidal bed

NASA Astrophysics Data System (ADS)

Kyotoh, Harumichi; Fukushima, Masaki

1997-07-01

Upstream-advancing waves are observed in open channel flows over a fixed sinusoidal bed with large amplitude, when the Froude number is less than the resonant value, at which stream velocity is equal to the celerity of the wave with wavelength equal to that of the bottom surface. Their wavelength is about 3-6 times as long as the bottom wavelength and the celerity is close to that obtained from potential flow theory. Therefore, the wavelength of upstream-advancing waves is determined by linear stability analyses assuming that they are induced by the Benjamin-Feir-type instability of steady flow. Here, two formulas for the wavelength with different scaling are introduced and compared with experiment. In addition, the mechanisms of upstream-advancing waves are investigated qualitatively using the forced Schrödinger equation.

Abundance and functional diversity of riboswitches in microbial communities

PubMed Central

Kazanov, Marat D; Vitreschak, Alexey G; Gelfand, Mikhail S

2007-01-01

Background Several recently completed large-scale enviromental sequencing projects produced a large amount of genetic information about microbial communities ('metagenomes') which is not biased towards cultured organisms. It is a good source for estimation of the abundance of genes and regulatory structures in both known and unknown members of microbial communities. In this study we consider the distribution of RNA regulatory structures, riboswitches, in the Sargasso Sea, Minnesota Soil and Whale Falls metagenomes. Results Over three hundred riboswitches were found in about 2 Gbp metagenome DNA sequences. The abundabce of riboswitches in metagenomes was highest for the TPP, B12 and GCVT riboswitches; the S-box, RFN, YKKC/YXKD, YYBP/YKOY regulatory elements showed lower but significant abundance, while the LYS, G-box, GLMS and YKOK riboswitches were rare. Regions downstream of identified riboswitches were scanned for open reading frames. Comparative analysis of identified ORFs revealed new riboswitch-regulated functions for several classes of riboswitches. In particular, we have observed phosphoserine aminotransferase serC (COG1932) and malate synthase glcB (COG2225) to be regulated by the glycine (GCVT) riboswitch; fatty acid desaturase ole1 (COG1398), by the cobalamin (B12) riboswitch; 5-methylthioribose-1-phosphate isomerase ykrS (COG0182), by the SAM-riboswitch. We also identified conserved riboswitches upstream of genes of unknown function: thiamine (TPP), cobalamine (B12), and glycine (GCVT, upstream of genes from COG4198). Conclusion This study demonstrates applicability of bioinformatics to the analysis of RNA regulatory structures in metagenomes. PMID:17908319

Achieving a Golden Mean: Mechanisms by Which Coronaviruses Ensure Synthesis of the Correct Stoichiometric Ratios of Viral Proteins▿

PubMed Central

Plant, Ewan P.; Rakauskaitė, Rasa; Taylor, Deborah R.; Dinman, Jonathan D.

2010-01-01

In retroviruses and the double-stranded RNA totiviruses, the efficiency of programmed −1 ribosomal frameshifting is critical for ensuring the proper ratios of upstream-encoded capsid proteins to downstream-encoded replicase enzymes. The genomic organizations of many other frameshifting viruses, including the coronaviruses, are very different, in that their upstream open reading frames encode nonstructural proteins, the frameshift-dependent downstream open reading frames encode enzymes involved in transcription and replication, and their structural proteins are encoded by subgenomic mRNAs. The biological significance of frameshifting efficiency and how the relative ratios of proteins encoded by the upstream and downstream open reading frames affect virus propagation has not been explored before. Here, three different strategies were employed to test the hypothesis that the −1 PRF signals of coronaviruses have evolved to produce the correct ratios of upstream- to downstream-encoded proteins. Specifically, infectious clones of the severe acute respiratory syndrome (SARS)-associated coronavirus harboring mutations that lower frameshift efficiency decreased infectivity by >4 orders of magnitude. Second, a series of frameshift-promoting mRNA pseudoknot mutants was employed to demonstrate that the frameshift signals of the SARS-associated coronavirus and mouse hepatitis virus have evolved to promote optimal frameshift efficiencies. Finally, we show that a previously described frameshift attenuator element does not actually affect frameshifting per se but rather serves to limit the fraction of ribosomes available for frameshifting. The findings of these analyses all support a “golden mean” model in which viruses use both programmed ribosomal frameshifting and translational attenuation to control the relative ratios of their encoded proteins. PMID:20164235

Sediment depositions upstream of open check dams: new elements from small scale models

NASA Astrophysics Data System (ADS)

Piton, Guillaume; Le Guern, Jules; Carbonari, Costanza; Recking, Alain

2015-04-01

Torrent hazard mitigation remains a big issue in mountainous regions. In steep slope streams and especially in their fan part, torrential floods mainly result from abrupt and massive sediment deposits. To curtail such phenomenon, soil conservation measures as well as torrent control works have been undertaken for decades. Since the 1950s, open check dams complete other structural and non-structural measures in watershed scale mitigation plans1. They are often built to trap sediments near the fan apexes. The development of earthmoving machinery after the WWII facilitated the dredging operations of open check dams. Hundreds of these structures have thus been built for 60 years. Their design evolved with the improving comprehension of torrential hydraulics and sediment transport; however this kind of structure has a general tendency to trap most of the sediments supplied by the headwaters. Secondary effects as channel incision downstream of the traps often followed an open check dam creation. This sediment starvation trend tends to propagate to the main valley rivers and to disrupt past geomorphic equilibriums. Taking it into account and to diminish useless dredging operation, a better selectivity of sediment trapping must be sought in open check dams, i.e. optimal open check dams would trap sediments during dangerous floods and flush them during normal small floods. An accurate description of the hydraulic and deposition processes that occur in sediment traps is needed to optimize existing structures and to design best-adjusted new structures. A literature review2 showed that if design criteria exist for the structure itself, little information is available on the dynamic of the sediment depositions upstream of open check dams, i.e. what are the geomorphic patterns that occur during the deposition?, what are the relevant friction laws and sediment transport formula that better describe massive depositions in sediment traps?, what are the range of Froude and Shields numbers that the flows tend to adopt? New small scale model experiments have been undertaken focusing on depositions processes and their related hydraulics. Accurate photogrammetric measurements allowed us to better describe the deposition processes3. Large Scale Particle Image Velocimetry (LS-PIV) was performed to determine surface velocity fields in highly active channels with low grain submersion4. We will present preliminary results of our experiments showing the new elements we observed in massive deposit dynamics. REFERENCES 1.Armanini, A., Dellagiacoma, F. & Ferrari, L. From the check dam to the development of functional check dams. Fluvial Hydraulics of Mountain Regions 37, 331-344 (1991). 2.Piton, G. & Recking, A. Design of sediment traps with open check dams: a review, part I: hydraulic and deposition processes. (Accepted by the) Journal of Hydraulic Engineering 1-23 (2015). 3.Le Guern, J. Ms Thesis: Modélisation physique des plages de depot : analyse de la dynamique de remplissage.(2014) . 4.Carbonari, C. Ms Thesis: Small scale experiments of deposition processes occuring in sediment traps, LS-PIV measurments and geomorphological descriptions. (in preparation).

Upstream paths for Hippo signaling in Drosophila organ development.

PubMed

Choi, Kwang-Wook

2018-03-01

Organ growth is fundamental to animal development. One of major mechanisms for growth control is mediated by the conserved Hippo signaling pathway initially identified in Drosophila. The core of this pathway in Drosophila consists of a cascade of protein kinases Hippo and Warts that negatively regulate transcriptional coactivator Yorkie (Yki). Activation of Yki promotes cell survival and proliferation to induce organ growth. A key issue in Hippo signaling is to understand how core kinase cascade is activated. Activation of Hippo kinase cascade is regulated in the upstream by at least two transmembrane proteins Crumbs and Fat that act in parallel. These membrane proteins interact with additional factors such as FERM-domain proteins Expanded and Merlin to modulate subcellular localization and function of the Hippo kinase cascade. Hippo signaling is also influenced by cytoskeletal networks and cell tension in epithelia of developing organs. These upstream events in the regulation of Hippo signaling are only partially understood. This review focuses on our current understanding of some upstream processes involved in Hippo signaling in developing Drosophila organs. [BMB Reports 2018; 51(3): 134-142].

Transcriptional Regulation in Saccharomyces cerevisiae: Transcription Factor Regulation and Function, Mechanisms of Initiation, and Roles of Activators and Coactivators

PubMed Central

Hahn, Steven; Young, Elton T.

2011-01-01

Here we review recent advances in understanding the regulation of mRNA synthesis in Saccharomyces cerevisiae. Many fundamental gene regulatory mechanisms have been conserved in all eukaryotes, and budding yeast has been at the forefront in the discovery and dissection of these conserved mechanisms. Topics covered include upstream activation sequence and promoter structure, transcription factor classification, and examples of regulated transcription factor activity. We also examine advances in understanding the RNA polymerase II transcription machinery, conserved coactivator complexes, transcription activation domains, and the cooperation of these factors in gene regulatory mechanisms. PMID:22084422

Functional analysis of the EspR binding sites upstream of espR in Mycobacterium tuberculosis.

PubMed

Cao, Guangxiang; Howard, Susan T; Zhang, Peipei; Hou, Guihua; Pang, Xiuhua

2013-11-01

The ESX-1 secretion system exports substrate proteins into host cells and is crucial for the pathogenesis of Mycobacterium tuberculosis. EspR is one of the characterized transcriptional regulators that modulates the ESX-1 system by binding the conserved EspR binding sites in the promoter of espA, the encoding gene of EspA, which is also a substrate protein of the ESX-1 system and is required for the ESX-1 activity. EspR is autoregulatory and conserved EspR binding sites are present upstream of espR. In this study, we showed that these EspR sites had varying affinities for EspR, with site B being the strongest one. Point mutations of the DNA sequence at site B abolished binding of EspR to oligonucleotides containing site B alone or with other sites, further suggesting that site B is a major binding site for EspR. Complementation studies showed that constructs containing espR, and the upstream intergenic region fully restored espR expression in a ΔespR mutant strain. Although recombinant strains with mutations at more than one EspR site showed minimal differences in espR expression, reduced expression of other EspR target genes was observed, suggesting that slight changes in EspR levels can have downstream regulatory effects. These findings contribute to our understanding of the regulation of the ESX-1 system.

Separation of the PROX1 gene from upstream conserved elements in a complex inversion/translocation patient with hypoplastic left heart

PubMed Central

Gill, Harinder K; Parsons, Sian R; Spalluto, Cosma; Davies, Angela F; Knorz, Victoria J; Burlinson, Clare EG; Ng, Bee Ling; Carter, Nigel P; Ogilvie, Caroline Mackie; Wilson, David I; Roberts, Roland G

2009-01-01

Hypoplastic left heart (HLH) occurs in at least 1 in 10 000 live births but may be more common in utero. Its causes are poorly understood but a number of affected cases are associated with chromosomal abnormalities. We set out to localize the breakpoints in a patient with sporadic HLH and a de novo translocation. Initial studies showed that the apparently simple 1q41;3q27.1 translocation was actually combined with a 4-Mb inversion, also de novo, of material within 1q41. We therefore localized all four breakpoints and found that no known transcription units were disrupted. However we present a case, based on functional considerations, synteny and position of highly conserved non-coding sequence elements, and the heterozygous Prox1+/− mouse phenotype (ventricular hypoplasia), for the involvement of dysregulation of the PROX1 gene in the aetiology of HLH in this case. Accordingly, we show that the spatial expression pattern of PROX1 in the developing human heart is consistent with a role in cardiac development. We suggest that dysregulation of PROX1 gene expression due to separation from its conserved upstream elements is likely to have caused the heart defects observed in this patient, and that PROX1 should be considered as a potential candidate gene for other cases of HLH. The relevance of another breakpoint separating the cardiac gene ESRRG from a conserved downstream element is also discussed. PMID:19471316

Level II scour analysis for Bridge 26 (WSTOTH00070026) on Town Highway 7, crossing Greendale Brook, Weston, Vermont

USGS Publications Warehouse

Striker, Lora K.; Hammond, Robert A.

1997-01-01

This report provides the results of a detailed Level II analysis of scour potential at structure WSTOTH00070026 on Town Highway 7 crossing Greendale Brook, Weston, Vermont (figures 1–8). A Level II study is a basic engineering analysis of the site, including a quantitative analysis of stream stability and scour (U.S. Department of Transportation, 1993). Results of a Level I scour investigation also are included in Appendix E of this report. A Level I investigation provides a qualitative geomorphic characterization of the study site. Information on the bridge, gleaned from Vermont Agency of Transportation (VTAOT) files, was compiled prior to conducting Level I and Level II analyses and is found in Appendix D. The site is in the Green Mountain section of the New England physiographic province in south central Vermont. The 3.13-mi2 drainage area is in a predominantly rural and forested basin. In the vicinity of the study site, the surface cover is forest. In the study area, the Greendale Brook has a sinuous, non-incised, non-alluvial channel with a slope of approximately 0.015 ft/ft, an average channel top width of 38 ft and an average bank height of 3 ft. The channel bed material ranges from sand to boulder with a median grain size (D50) of 64.8 mm (0.213 ft). The geomorphic assessment at the time of the Level I and Level II site visit on August 19, 1996, indicated that the reach was laterally unstable. The channel has moved to the right, however, scour countermeasures are in place along the upstream right bank. The Town Highway 7 crossing of the Greendale Brook is a 52-ft-long, two-lane bridge consisting of one 50-foot steel-beam span with a concrete deck (Vermont Agency of Transportation, written communication, April 07, 1995). The opening length of the structure parallel to the bridge face is 48.6 ft. The bridge is supported by vertical, concrete abutments with wingwalls. The channel is skewed approximately 50 degrees to the opening while the opening-skew-to-roadway is 30 degrees. A scour hole 1.5 ft deeper than the mean thalweg depth was observed along the upstream right wingwall and right abutment during the Level I assessment. Scour protection measures at the site include: type-2 stone fill (less than 36 inches diameter) at the upstream end of the upstream left wingwall, along the left bank upstream, at the downstream end of the downstream left wing wall, and along the entire length of the downstream right wing wall; type 4 (less than 60 inches) and type-3 stone fill (less than 48 inches) along the right bank upstream. Additional details describing conditions at the site are included in the Level II Summary and Appendices D and E. Scour depths and recommended rock rip-rap sizes were computed using the general guidelines described in Hydraulic Engineering Circular 18 (Richardson and others, 1995). Total scour at a highway crossing is comprised of three components: 1) long-term streambed degradation; 2) contraction scour (due to accelerated flow caused by a reduction in flow area at a bridge) and; 3) local scour (caused by accelerated flow around piers and abutments). Total scour is the sum of the three components. Equations are available to compute depths for contraction and local scour and a summary of the results of these computations follows. Contraction scour for all modelled flows was 0.0 ft. Abutment scour ranged from 3.9 to 9.9 ft. The worst-case abutment scour occurred at the 500-year discharge. Additional information on scour depths and depths to armoring are included in the section titled “Scour Results”. Scoured-streambed elevations, based on the calculated scour depths, are presented in tables 1 and 2. A cross-section of the scour computed at the bridge is presented in figure 8. Scour depths were calculated assuming an infinite depth of erosive material and a homogeneous particle-size distribution. It is generally accepted that the Froehlich equation (abutment scour) gives “excessively conservative estimates of scour depths” (Richardson and others, 1995, p. 47). The Hire equation (abutment scour) is often used when the horizontal length blocked by flow divided by the depth of flow is greater than 25 (Richardson and others, 1995 p. 49). Although the Hire equation could be applied to the left abutment more conservative scour estimates were given by the Froehlich equation on the left abutment. Usually, computed scour depths are evaluated in combination with other information including (but not limited to) historical performance during flood events, the geomorphic stability assessment, existing scour protection measures, and the results of the hydraulic analyses. Therefore, scour depths adopted by VTAOT may differ from the computed values documented herein.

A 21.7 kb DNA segment on the left arm of yeast chromosome XIV carries WHI3, GCR2, SPX18, SPX19, an homologue to the heat shock gene SSB1 and 8 new open reading frames of unknown function.

PubMed

Jonniaux, J L; Coster, F; Purnelle, B; Goffeau, A

1994-12-01

We report the amino acid sequence of 13 open reading frames (ORF > 299 bp) located on a 21.7 kb DNA segment from the left arm of chromosome XIV of Saccharomyces cerevisiae. Five open reading frames had been entirely or partially sequenced previously: WHI3, GCR2, SPX19, SPX18 and a heat shock gene similar to SSB1. The products of 8 other ORFs are new putative proteins among which N1394 is probably a membrane protein. N1346 contains a leucine zipper pattern and the corresponding ORF presents an HAP (global regulator of respiratory genes) upstream activating sequence in the promoting region. N1386 shares homologies with the DNA structure-specific recognition protein family SSRPs and the corresponding ORF is preceded by an MCB (MluI cell cycle box) upstream activating factor.

Level II scour analysis for Bridge 41 (ANDOVT00110041) on State Route 11, crossing the Middle Branch Williams River, Andover, Vermont

USGS Publications Warehouse

Wild, Emily C.; Hammond, Robert E.

1997-01-01

This report provides the results of a detailed Level II analysis of scour potential at structure ANDOVT00110041 on State Route 11 crossing the Middle Branch Williams River, Andover, Vermont (figures 1–8). A Level II study is a basic engineering analysis of the site, including a quantitative analysis of stream stability and scour (U.S. Department of Transportation, 1993). Results of a Level I scour investigation also are included in Appendix E of this report. A Level I investigation provides a qualitative geomorphic characterization of the study site. Information on the bridge, gleaned from Vermont Agency of Transportation (VTAOT) files, was compiled prior to conducting Level I and Level II analyses and is found in Appendix D. The site is in the Green Mountain section of the New England physiographic province in southeastern Vermont. The 12.1-mi2 drainage area is in a predominantly rural and forested basin. In the vicinity of the study site, the surface cover is grass on the upstream right overbank while the immediate banks have dense woody vegetation. The upstream left overbank and downstream right overbank are brushland. The downstream left overbank is forested. In the study area, the Middle Branch Williams River has an incised, sinuous channel with a slope of approximately 0.018 ft/ft, an average channel top width of 71 ft and an average bank height of 4 ft. The channel bed material ranges from gravel to boulders with a median grain size (D50) of 85.0 mm (0.279 ft). The geomorphic assessment at the time of the Level I and Level II site visit on September 10, 1996, indicated that the reach was laterally unstable due to a cut-bank present on the upstream right bank and a wide channel bar with vegetation in the upstream reach. The State Route 11 crossing of the Middle Branch Williams River is a 46-ft-long, two-lane bridge consisting of a concrete 44-foot tee-beam span (Vermont Agency of Transportation, written communication, March 29, 1995). The opening length of the structure parallel to the bridge face is 42 ft. The bridge is supported by vertical, concrete abutments with wingwalls. The channel is skewed approximately 35 degrees to the opening while the opening-skew-toroadway is zero degrees. A scour hole 0.8 ft deeper than the mean thalweg depth was observed along the downstream end of the left abutment and downstream left wingwall during the Level I assessment. Type- 2 stone fill (less than 36 inches diameter) protects the upstream end of the upstream left wingwall, the downstream ends of the downstream left and right wingwalls and the downstream right road embankment. Type-3 stone fill protects the upstream end of the upstream right wingwall and the upstream right bank. Additional details describing conditions at the site are included in the Level II Summary and Appendices D and E. Scour depths and recommended rock rip-rap sizes were computed using the general guidelines described in Hydraulic Engineering Circular 18 (Richardson and others, 1995). In addition, the incipient roadway-overtopping discharge was determined and analyzed as another potential worst-case scour scenario. Total scour at a highway crossing is comprised of three components: 1) long-term streambed degradation; 2) contraction scour (due to accelerated flow caused by a reduction in flow area at a bridge) and; 3) local scour (caused by accelerated flow around piers and abutments). Total scour is the sum of the three components. Equations are available to compute depths for contraction and local scour and a summary of the results of these computations follows. Contraction scour for all modelled flows ranged from 0.0 to 2.1 ft. The worst-case contraction scour occurred at the 500-year discharge. Abutment scour ranged from 11.1 to 18.7 ft. The worst-case abutment scour occurred at the 500-year discharge. Additional information on scour depths and depths to armoring are included in the section titled “Scour Results”. Scoured-streambed elevations, based on the calculated scour depths, are presented in tables 1 and 2. A cross-section of the scour computed at the bridge is presented in figure 8. Scour depths were calculated assuming an infinite depth of erosive material and a homogeneous particle-size distribution. It is generally accepted that the Froehlich equation (abutment scour) gives “excessively conservative estimates of scour depths” (Richardson and others, 1995, p. 47). Usually, computed scour depths are evaluated in combination with other information including (but not limited to) historical performance during flood events, the geomorphic stability assessment, existing scour protection measures, and the results of the hydraulic analyses. Therefore, scour depths adopted by VTAOT may differ from the computed values documented herein.

Critical 23S rRNA interactions for macrolide-dependent ribosome stalling on the ErmCL nascent peptide chain

PubMed Central

Koch, Miriam; Willi, Jessica; Pradère, Ugo; Hall, Jonathan

2017-01-01

Abstract The nascent peptide exit tunnel has recently been identified as a functional region of ribosomes contributing to translation regulation and co-translational protein folding. Inducible expression of the erm resistance genes depends on ribosome stalling at specific codons of an upstream open reading frame in the presence of an exit tunnel-bound macrolide antibiotic. The molecular basis for this translation arrest is still not fully understood. Here, we used a nucleotide analog interference approach to unravel important functional groups on 23S rRNA residues in the ribosomal exit tunnel for ribosome stalling on the ErmC leader peptide. By replacing single nucleobase functional groups or even single atoms we were able to demonstrate the importance of A2062, A2503 and U2586 for drug-dependent ribosome stalling. Our data show that the universally conserved A2062 and A2503 are capable of forming a non-Watson–Crick base pair that is critical for sensing and transmitting the stalling signal from the exit tunnel back to the peptidyl transferase center of the ribosome. The nucleobases of A2062, A2503 as well as U2586 do not contribute significantly to the overall mechanism of protein biosynthesis, yet their elaborate role for co-translational monitoring of nascent peptide chains inside the exit tunnel can explain their evolutionary conservation. PMID:28369621

Transcripts of the NADH-dehydrogenase subunit 3 gene are differentially edited in Oenothera mitochondria.

PubMed Central

Schuster, W; Wissinger, B; Unseld, M; Brennicke, A

1990-01-01

A number of cytosines are altered to be recognized as uridines in transcripts of the nad3 locus in mitochondria of the higher plant Oenothera. Such nucleotide modifications can be found at 16 different sites within the nad3 coding region. Most of these alterations in the mRNA sequence change codon identities to specify amino acids better conserved in evolution. Individual cDNA clones differ in their degree of editing at five nucleotide positions, three of which are silent, while two lead to codon alterations specifying different amino acids. None of the cDNA clones analysed is maximally edited at all possible sites, suggesting slow processing or lowered stringency of editing at these nucleotides. Differentially edited transcripts could be editing intermediates or could code for differing polypeptides. Two edited nucleotides in an open reading frame located upstream of nad3 change two amino acids in the deduced polypeptide. Part of the well-conserved ribosomal protein gene rps12 also encoded downstream of nad3 in other plants, is lost in Oenothera mitochondria by recombination events. The functional rps12 protein must be imported from the cytoplasm since the deleted sequences of this gene are not found in the Oenothera mitochondrial genome. The pseudogene sequence is not edited at any nucleotide position. Images Fig. 3. Fig. 4. Fig. 7. PMID:1688531

Transcription of the extended hyp-operon in Nostoc sp. strain PCC 7120

PubMed Central

Agervald, Åsa; Stensjö, Karin; Holmqvist, Marie; Lindblad, Peter

2008-01-01

Background The maturation of hydrogenases into active enzymes is a complex process and e.g. a correctly assembled active site requires the involvement of at least seven proteins, encoded by hypABCDEF and a hydrogenase specific protease, encoded either by hupW or hoxW. The N2-fixing cyanobacterium Nostoc sp. strain PCC 7120 may contain both an uptake and a bidirectional hydrogenase. The present study addresses the presence and expression of hyp-genes in Nostoc sp. strain PCC 7120. Results RT-PCRs demonstrated that the six hyp-genes together with one ORF may be transcribed as a single operon. Transcriptional start points (TSPs) were identified 280 bp upstream from hypF and 445 bp upstream of hypC, respectively, demonstrating the existence of several transcripts. In addition, five upstream ORFs located in between hupSL, encoding the small and large subunits of the uptake hydrogenase, and the hyp-operon, and two downstream ORFs from the hyp-genes were shown to be part of the same transcript unit. A third TSP was identified 45 bp upstream of asr0689, the first of five ORFs in this operon. The ORFs are annotated as encoding unknown proteins, with the exception of alr0692 which is identified as a NifU-like protein. Orthologues of the four ORFs asr0689-alr0692, with a highly conserved genomic arrangement positioned between hupSL, and the hyp genes are found in several other N2-fixing cyanobacteria, but are absent in non N2-fixing cyanobacteria with only the bidirectional hydrogenase. Short conserved sequences were found in six intergenic regions of the extended hyp-operon, appearing between 11 and 79 times in the genome. Conclusion This study demonstrated that five ORFs upstream of the hyp-gene cluster are co-transcribed with the hyp-genes, and identified three TSPs in the extended hyp-gene cluster in Nostoc sp. strain PCC 7120. This may indicate a function related to the assembly of a functional uptake hydrogenase, hypothetically in the assembly of the small subunit of the enzyme. PMID:18442387

Level II scour analysis for Bridge 7 (WALDTH00020007) on Town Highway 2, crossing Coles Brook, Walden, Vermont

USGS Publications Warehouse

Striker, Lora K.; Medalie, Laura

1997-01-01

ft, an average channel top width of 37 ft and an average bank height of 4 ft. The channel bed material ranges from sand to cobble with a median grain size (D50) of 32.9 mm (0.108 ft). The geomorphic assessment at the time of the Level I and Level II site visit on August 9, 1995, indicated that the reach was laterally unstable due to cut-banks, point bars, and loose unconsolidated bed material. The Town Highway 2 crossing of Coles Brook is a 74-ft-long, two-lane bridge consisting of one 71-foot steel-beam span (Vermont Agency of Transportation, written communication, April 5, 1995). The opening length of the structure parallel to the bridge face is 69.3 ft. The bridge is supported by spill-through abutments. The channel is skewed approximately 35 degrees to the opening while the measured opening-skew-to-roadway is 15 degrees. A scour hole 1.5 ft deeper than the mean thalweg depth was observed from 60 ft. to 100 ft. downstream during the Level I assessment. Scour protection measures at the site include: type-1 stone fill (less than 12 inches diameter) along the right bank upstream, at the downstream end of the downstream left wingwall and downstream right wingwall; and type-2 stone fill (less than 36 inches diameter) along the left bank upstream, at the upstream end of the upstream right wingwall, and along the entire base of the left and right abutments. Additional details describing conditions at the site are included in the Level II Summary and Appendices D and E. Scour depths and recommended rock rip-rap sizes were computed using the general guidelines described in Hydraulic Engineering Circular 18 (Richardson and others, 1995). Total scour at a highway crossing is comprised of three components: 1) long-term streambed degradation; 2) contraction scour (due to accelerated flow caused by a reduction in flow area at a bridge) and; 3) local scour (caused by accelerated flow around piers and abutments). Total scour is the sum of the three components. Equations are available to compute depths for contraction and local scour and a summary of the results of these computations follows. Contraction scour for all modelled flows ranged from 0.0 to 0.8 ft. The worst-case contraction scour occurred at the incipient roadway-overtopping discharge. Abutment scour ranged from 5.7 to 12.9 ft. The worst-case abutment scour occurred at the 500-year discharge. Additional information on scour depths and depths to armoring are included in the section titled “Scour Results”. Scoured-streambed elevations, based on the calculated scour depths, are presented in tables 1 and 2. A cross-section of the scour computed at the bridge is presented in figure 8. Scour depths were calculated assuming an infinite depth of erosive material and a homogeneous particle-size distribution. It is generally accepted that the Froehlich equation (abutment scour) gives “excessively conservative estimates of scour depths” (Richardson and others, 1995, p. 47). Usually, computed scour depths are evaluated in combination with other information including (but not limited to) historical performance during flood events, the geomorphic stability assessment, existing scour protection measures, and the results of the hydraulic analyses. Therefore, scour depths adopted by VTAOT may differ from the computed values documented herein.

Translational profiling of B cells infected with the Epstein-Barr virus reveals 5' leader ribosome recruitment through upstream open reading frames.

PubMed

Bencun, Maja; Klinke, Olaf; Hotz-Wagenblatt, Agnes; Klaus, Severina; Tsai, Ming-Han; Poirey, Remy; Delecluse, Henri-Jacques

2018-04-06

The Epstein-Barr virus (EBV) genome encodes several hundred transcripts. We have used ribosome profiling to characterize viral translation in infected cells and map new translation initiation sites. We show here that EBV transcripts are translated with highly variable efficiency, owing to variable transcription and translation rates, variable ribosome recruitment to the leader region and coverage by monosomes versus polysomes. Some transcripts were hardly translated, others mainly carried monosomes, showed ribosome accumulation in leader regions and most likely represent non-coding RNAs. A similar process was visible for a subset of lytic genes including the key transactivators BZLF1 and BRLF1 in cells infected with weakly replicating EBV strains. This suggests that ribosome trapping, particularly in the leader region, represents a new checkpoint for the repression of lytic replication. We could identify 25 upstream open reading frames (uORFs) located upstream of coding transcripts that displayed 5' leader ribosome trapping, six of which were located in the leader region shared by many latent transcripts. These uORFs repressed viral translation and are likely to play an important role in the regulation of EBV translation.

Modulation of anaerobic energy metabolism of Bacillus subtilis by arfM (ywiD).

PubMed

Marino, M; Ramos, H C; Hoffmann, T; Glaser, P; Jahn, D

2001-12-01

Bacillus subtilis grows under anaerobic conditions utilizing nitrate ammonification and various fermentative processes. The two-component regulatory system ResDE and the redox regulator Fnr are the currently known parts of the regulatory system for anaerobic adaptation. Mutation of the open reading frame ywiD located upstream of the respiratory nitrate reductase operon narGHJI resulted in elimination of the contribution of nitrite dissimilation to anaerobic nitrate respiratory growth. Significantly reduced nitrite reductase (NasDE) activity was detected, while respiratory nitrate reductase activity was unchanged. Anaerobic induction of nasDE expression was found to be significantly dependent on intact ywiD, while anaerobic narGHJI expression was ywiD independent. Anaerobic transcription of hmp, encoding a flavohemoglobin-like protein, and of the fermentative operons lctEP and alsSD, responsible for lactate and acetoin formation, was partially dependent on ywiD. Expression of pta, encoding phosphotransacetylase involved in fermentative acetate formation, was not influenced by ywiD. Transcription of the ywiD gene was anaerobically induced by the redox regulator Fnr via the conserved Fnr-box (TGTGA-6N-TCACT) centered 40.5 bp upstream of the transcriptional start site. Anaerobic induction of ywiD by resDE was found to be indirect via resDE-dependent activation of fnr. The ywiD gene is subject to autorepression and nitrite repression. These results suggest a ResDE --> Fnr --> YwiD regulatory cascade for the modulation of genes involved in the anaerobic metabolism of B. subtilis. Therefore, ywiD was renamed arfM for anaerobic respiration and fermentation modulator.

Isolation of a gene (pbsC) required for siderophore biosynthesis in fluorescent Pseudomonas sp. strain M114.

PubMed

Adams, C; Dowling, D N; O'Sullivan, D J; O'Gara, F

1994-06-03

An iron-regulated gene, pbsC, required for siderophore production in fluorescent Pseudomonas sp. strain M114 has been identified. A kanamycin-resistance cassette was inserted at specific restriction sites within a 7 kb genomic fragment of M114 DNA and by marker exchange two siderophore-negative mutants, designated M1 and M2, were isolated. The nucleotide sequence of approximately 4 kb of the region flanking the insertion sites was determined and a large open reading frame (ORF) extending for 2409 bp was identified. This gene was designated pbsC (pseudobactin synthesis C) and its putative protein product termed PbsC. PbsC was found to be homologous to a family of enzymes involved in the biosynthesis of secondary metabolites, including EntF of Escherichia coli. These enzymes are believed to act via ATP-dependent binding of AMP to their substrate. Several areas of high sequence homology between these proteins and PbsC were observed, including a conserved AMP-binding domain. The expression of pbsC is iron-regulated as revealed when a DNA fragment containing the upstream region was cloned in a promoter probe vector and conjugated into the wild-type strain, M114. The nucleotide sequence upstream of the putative translational start site contains a region homologous to previously defined -16 to -25 sequences of iron-regulated genes but did not contain an iron-box consensus sequence. It was noted that inactivation of the pbsC gene also affected other iron-regulated phenotypes of Pseudomonas M114.

Fine-scale pathways used by adult sea lampreys during riverine spawning migrations

USGS Publications Warehouse

Holbrook, Christopher; Bergstedt, Roger A.; Adams, Noah S.; Hatton, Tyson; McLaughlin, Robert L.

2015-01-01

Better knowledge of upstream migratory patterns of spawning Sea Lampreys Petromyzon marinus, an invasive species in the Great Lakes, is needed to improve trapping for population control and assessment. Although trapping of adult Sea Lampreys provides the basis for estimates of lake-wide abundance that are used to evaluate the Sea Lamprey control program, traps have only been operated at dams due to insufficient knowledge of Sea Lamprey behavior in unobstructed channels. Acoustic telemetry and radiotelemetry were used to obtain movement tracks for 23 Sea Lampreys in 2008 and 18 Sea Lampreys in 2009 at two locations in the Mississagi River, Ontario. Cabled hydrophone arrays provided two-dimensional geographic positions from acoustic transmitters at 3-s intervals; depth-encoded radio tag detections provided depths. Upstream movements occurred at dusk or during the night (2015–0318 hours). Sea Lampreys were closely associated with the river bottom and showed some preference to move near banks in shallow glide habitats, suggesting that bottom-oriented gears could selectively target adult Sea Lampreys in some habitats. However, Sea Lampreys were broadly distributed across the river channel, suggesting that the capture efficiency of nets and traps in open channels would depend heavily on the proportion of the channel width covered. Lack of vertical movements into the water column may have reflected lamprey preference for low water velocities, suggesting that energy conservation was more beneficial for lampreys than was vertical searching in rivers. Improved understanding of Sea Lamprey movement will assist in the development of improved capture strategies for their assessment and control in the Great Lakes.

Level II scour analysis for Bridge 29 (HUNTTH00290029) on Town Highway 29, crossing Cobb Brook, Huntington, Vermont

USGS Publications Warehouse

Flynn, Robert H.

1997-01-01

This report provides the results of a detailed Level II analysis of scour potential at structure HUNTTH00290029 on Town Highway 29 crossing Cobb Brook, Huntington, Vermont (figures 1–8). A Level II study is a basic engineering analysis of the site, including a quantitative analysis of stream stability and scour (U.S. Department of Transportation, 1993). Results of a Level I scour investigation also are included in Appendix E of this report. A Level I investigation provides a qualitative geomorphic characterization of the study site. Information on the bridge, gleaned from Vermont Agency of Transportation (VTAOT) files, was compiled prior to conducting Level I and Level II analyses and is found in Appendix D. The site is in the Green Mountain section of the New England physiographic province in northwestern Vermont. The 4.16-mi2 drainage area is in a predominantly rural and forested basin. In the vicinity of the study site, the surface cover is forest upstream and downstream of the bridge. In the study area, Cobb Brook has an incised, straight channel with a slope of approximately 0.024 ft/ft, an average channel top width of 53 ft and an average bank height of 4 ft. The channel bed material ranges from gravel to bedrock with a median grain size (D50) of 112.0 mm (0.367 ft). The geomorphic assessment at the time of the Level I and Level II site visit on June 25, 1996, indicated that the reach was stable. The Town Highway 29 crossing of Cobb Brook is a 36-ft-long, one-lane bridge consisting of one 30-foot steel-beam span (Vermont Agency of Transportation, written communication, December 11, 1995) and a wooden deck. The opening length of the structure parallel to the bridge face is 27 ft.The bridge is supported by vertical, concrete abutments. The channel is skewed approximately 25 degrees to the opening while the opening-skew-to-roadway was measured to be 20 degrees. VTAOT records indicate an opening-skew-to-roadway of zero degrees. A scour hole 1.5 ft deeper than the mean thalweg depth was observed extending from 12 ft upstream of the upstream end of the left abutment to 10 ft under the bridge in the center of the channel during the Level I assessment. Another scour hole approximately 1.2 ft deeper than the mean thalweg depth was observed along the downstream end of the right abutment during the Level I assessment. The scour protection measures at the site included type-2 stone fill (less than 36 inches diameter) along the upstream end of the right abutment and type-3 stone fill (less than 48 inches diameter) along the upstream end of the upstream left retaining wall. Additional details describing conditions at the site are included in the Level II Summary and Appendices D and E. Scour depths and recommended rock rip-rap sizes were computed using the general guidelines described in Hydraulic Engineering Circular 18 (Richardson and others, 1995). Total scour at a highway crossing is comprised of three components: 1) long-term streambed degradation; 2) contraction scour (due to accelerated flow caused by a reduction in flow area at a bridge) and; 3) local scour (caused by accelerated flow around piers and abutments). Total scour is the sum of the three components. Equations are available to compute depths for contraction and local scour and a summary of the results of these computations follows. Contraction scour for all modelled flows was computed to be zero ft. Abutment scour ranged from 9.9 to 12.5 ft along the left abutment and from 6.2 to 8.6 ft along the right abutment. The worst-case abutment scour occurred at the 500-year discharge. Additional information on scour depths and depths to armoring are included in the section titled “Scour Results”. Scoured-streambed elevations, based on the calculated scour depths, are presented in tables 1 and 2. A cross-section of the scour computed at the bridge is presented in figure 8. Scour depths were calculated assuming an infinite depth of erosive material and a homogeneous particle-size distribution. It is generally accepted that the Froehlich equation (abutment scour) gives “excessively conservative estimates of scour depths” (Richardson and others, 1995, p. 47). Usually, computed scour depths are evaluated in combination with other information including (but not limited to) historical performance during flood events, the geomorphic stability assessment, existing scour protection measures, and the results of the hydraulic analyses. Therefore, scour depths adopted by VTAOT may differ from the computed values documented herein.

Terrace effects on soil erosion processes in a watershed of the loess plateau

USDA-ARS?s Scientific Manuscript database

Terraces in crop fields are one of the most important soil and water conservation measures that affect runoff and erosion processes in a watershed. In this paper, terrace effects on soil erosion and sediment transport in the upstream and middle sections of the Weihe River basin in the Loess Plateau ...

50 CFR Table 24 to Part 679 - Except as Noted, Locations in the Aleutian Islands Habitat Conservation Area Open to Nonpelagic...

Code of Federal Regulations, 2013 CFR

2013-10-01

... 50 Wildlife and Fisheries 13 2013-10-01 2013-10-01 false Except as Noted, Locations in the Aleutian Islands Habitat Conservation Area Open to Nonpelagic Trawl Fishing 24 Table 24 to Part 679... Table 24 to Part 679—Except as Noted, Locations in the Aleutian Islands Habitat Conservation Area Open...

50 CFR Table 24 to Part 679 - Except as Noted, Locations in the Aleutian Islands Habitat Conservation Area Open to Nonpelagic...

Code of Federal Regulations, 2010 CFR

2010-10-01

... 50 Wildlife and Fisheries 9 2010-10-01 2010-10-01 false Except as Noted, Locations in the Aleutian Islands Habitat Conservation Area Open to Nonpelagic Trawl Fishing 24 Table 24 to Part 679 Wildlife and... 24 to Part 679—Except as Noted, Locations in the Aleutian Islands Habitat Conservation Area Open to...

Identification of regulatory targets for the bacterial Nus factor complex.

PubMed

Baniulyte, Gabriele; Singh, Navjot; Benoit, Courtney; Johnson, Richard; Ferguson, Robert; Paramo, Mauricio; Stringer, Anne M; Scott, Ashley; Lapierre, Pascal; Wade, Joseph T

2017-12-11

Nus factors are broadly conserved across bacterial species, and are often essential for viability. A complex of five Nus factors (NusB, NusE, NusA, NusG and SuhB) is considered to be a dedicated regulator of ribosomal RNA folding, and has been shown to prevent Rho-dependent transcription termination. Here, we identify an additional cellular function for the Nus factor complex in Escherichia coli: repression of the Nus factor-encoding gene, suhB. This repression occurs primarily by translation inhibition, followed by Rho-dependent transcription termination. Thus, the Nus factor complex can prevent or promote Rho activity depending on the gene context. Conservation of putative NusB/E binding sites upstream of Nus factor genes suggests that Nus factor autoregulation occurs in many bacterial species. Additionally, many putative NusB/E binding sites are also found upstream of other genes in diverse species, and we demonstrate Nus factor regulation of one such gene in Citrobacter koseri. We conclude that Nus factors have an evolutionarily widespread regulatory function beyond ribosomal RNA, and that they are often autoregulatory.

Eukaryotic Elongation Factor 1A Interacts with the Upstream Pseudoknot Domain in the 3′ Untranslated Region of Tobacco Mosaic Virus RNA

PubMed Central

Zeenko, Vladimir V.; Ryabova, Lyubov A.; Spirin, Alexander S.; Rothnie, Helen M.; Hess, Daniel; Browning, Karen S.; Hohn, Thomas

2002-01-01

The genomic RNA of tobacco mosaic virus (TMV), like that of other positive-strand RNA viruses, acts as a template for both translation and replication. The highly structured 3′ untranslated region (UTR) of TMV RNAs plays an important role in both processes; it is not polyadenylated but ends with a tRNA-like structure (TLS) preceded by a conserved upstream pseudoknot domain (UPD). The TLS of tobamoviral RNAs can be specifically aminoacylated and, in this state, can interact with eukaryotic elongation factor 1A (eEF1A)/GTP with high affinity. Using a UV cross-linking assay, we detected another specific binding site for eEF1A/GTP, within the UPDs of TMV and crucifer-infecting tobamovirus (crTMV), that does not require aminoacylation. A mutational analysis revealed that UPD pseudoknot conformation and some conserved primary sequence elements are required for this interaction. Its possible role in the regulation of tobamovirus gene expression and replication is discussed. PMID:11991996

Vascular gene expression: a hypothesis

PubMed Central

Martínez-Navarro, Angélica C.; Galván-Gordillo, Santiago V.; Xoconostle-Cázares, Beatriz; Ruiz-Medrano, Roberto

2013-01-01

The phloem is the conduit through which photoassimilates are distributed from autotrophic to heterotrophic tissues and is involved in the distribution of signaling molecules that coordinate plant growth and responses to the environment. Phloem function depends on the coordinate expression of a large array of genes. We have previously identified conserved motifs in upstream regions of the Arabidopsis genes, encoding the homologs of pumpkin phloem sap mRNAs, displaying expression in vascular tissues. This tissue-specific expression in Arabidopsis is predicted by the overrepresentation of GA/CT-rich motifs in gene promoters. In this work we have searched for common motifs in upstream regions of the homologous genes from plants considered to possess a “primitive” vascular tissue (a lycophyte), as well as from others that lack a true vascular tissue (a bryophyte), and finally from chlorophytes. Both lycophyte and bryophyte display motifs similar to those found in Arabidopsis with a significantly low E-value, while the chlorophytes showed either a different conserved motif or no conserved motif at all. These results suggest that these same genes are expressed coordinately in non-vascular plants; this coordinate expression may have been one of the prerequisites for the development of conducting tissues in plants. We have also analyzed the phylogeny of conserved proteins that may be involved in phloem function and development. The presence of CmPP16, APL, FT, and YDA in chlorophytes suggests the recruitment of ancient regulatory networks for the development of the vascular tissue during evolution while OPS is a novel protein specific to vascular plants. PMID:23882276

Deletions involving long-range conserved nongenic sequences upstream and downstream of FOXL2 as a novel disease-causing mechanism in blepharophimosis syndrome.

PubMed

Beysen, D; Raes, J; Leroy, B P; Lucassen, A; Yates, J R W; Clayton-Smith, J; Ilyina, H; Brooks, S Sklower; Christin-Maitre, S; Fellous, M; Fryns, J P; Kim, J R; Lapunzina, P; Lemyre, E; Meire, F; Messiaen, L M; Oley, C; Splitt, M; Thomson, J; Van de Peer, Y; Veitia, R A; De Paepe, A; De Baere, E

2005-08-01

The expression of a gene requires not only a normal coding sequence but also intact regulatory regions, which can be located at large distances from the target genes, as demonstrated for an increasing number of developmental genes. In previous mutation studies of the role of FOXL2 in blepharophimosis syndrome (BPES), we identified intragenic mutations in 70% of our patients. Three translocation breakpoints upstream of FOXL2 in patients with BPES suggested a position effect. Here, we identified novel microdeletions outside of FOXL2 in cases of sporadic and familial BPES. Specifically, four rearrangements, with an overlap of 126 kb, are located 230 kb upstream of FOXL2, telomeric to the reported translocation breakpoints. Moreover, the shortest region of deletion overlap (SRO) contains several conserved nongenic sequences (CNGs) harboring putative transcription-factor binding sites and representing potential long-range cis-regulatory elements. Interestingly, the human region orthologous to the 12-kb sequence deleted in the polled intersex syndrome in goat, which is an animal model for BPES, is contained in this SRO, providing evidence of human-goat conservation of FOXL2 expression and of the mutational mechanism. Surprisingly, in a fifth family with BPES, one rearrangement was found downstream of FOXL2. In addition, we report nine novel rearrangements encompassing FOXL2 that range from partial gene deletions to submicroscopic deletions. Overall, genomic rearrangements encompassing or outside of FOXL2 account for 16% of all molecular defects found in our families with BPES. In summary, this is the first report of extragenic deletions in BPES, providing further evidence of potential long-range cis-regulatory elements regulating FOXL2 expression. It contributes to the enlarging group of developmental diseases caused by defective distant regulation of gene expression. Finally, we demonstrate that CNGs are candidate regions for genomic rearrangements in developmental genes.

Deletions Involving Long-Range Conserved Nongenic Sequences Upstream and Downstream of FOXL2 as a Novel Disease-Causing Mechanism in Blepharophimosis Syndrome

PubMed Central

Beysen, D.; Raes, J.; Leroy, B. P.; Lucassen, A.; Yates, J. R. W.; Clayton-Smith, J.; Ilyina, H.; Brooks, S. Sklower; Christin-Maitre, S.; Fellous, M.; Fryns, J. P.; Kim, J. R.; Lapunzina, P.; Lemyre, E.; Meire, F.; Messiaen, L. M.; Oley, C.; Splitt, M.; Thomson, J.; Peer, Y. Van de; Veitia, R. A.; De Paepe, A.; De Baere, E.

2005-01-01

The expression of a gene requires not only a normal coding sequence but also intact regulatory regions, which can be located at large distances from the target genes, as demonstrated for an increasing number of developmental genes. In previous mutation studies of the role of FOXL2 in blepharophimosis syndrome (BPES), we identified intragenic mutations in 70% of our patients. Three translocation breakpoints upstream of FOXL2 in patients with BPES suggested a position effect. Here, we identified novel microdeletions outside of FOXL2 in cases of sporadic and familial BPES. Specifically, four rearrangements, with an overlap of 126 kb, are located 230 kb upstream of FOXL2, telomeric to the reported translocation breakpoints. Moreover, the shortest region of deletion overlap (SRO) contains several conserved nongenic sequences (CNGs) harboring putative transcription-factor binding sites and representing potential long-range cis-regulatory elements. Interestingly, the human region orthologous to the 12-kb sequence deleted in the polled intersex syndrome in goat, which is an animal model for BPES, is contained in this SRO, providing evidence of human-goat conservation of FOXL2 expression and of the mutational mechanism. Surprisingly, in a fifth family with BPES, one rearrangement was found downstream of FOXL2. In addition, we report nine novel rearrangements encompassing FOXL2 that range from partial gene deletions to submicroscopic deletions. Overall, genomic rearrangements encompassing or outside of FOXL2 account for 16% of all molecular defects found in our families with BPES. In summary, this is the first report of extragenic deletions in BPES, providing further evidence of potential long-range cis-regulatory elements regulating FOXL2 expression. It contributes to the enlarging group of developmental diseases caused by defective distant regulation of gene expression. Finally, we demonstrate that CNGs are candidate regions for genomic rearrangements in developmental genes. PMID:15962237

The cytochrome oxidase subunit I and subunit III genes in Oenothera mitochondria are transcribed from identical promoter sequences

PubMed Central

Hiesel, Rudolf; Schobel, Werner; Schuster, Wolfgang; Brennicke, Axel

1987-01-01

Two loci encoding subunit III of the cytochrome oxidase (COX) in Oenothera mitochondria have been identified from a cDNA library of mitochondrial transcripts. A 657-bp sequence block upstream from the open reading frame is also present in the two copies of the COX subunit I gene and is presumably involved in homologous sequence rearrangement. The proximal points of sequence rearrangements are located 3 bp upstream from the COX I and 1139 bp upstream from the COX III initiation codons. The 5'-termini of both COX I and COX III mRNAs have been mapped in this common sequence confining the promoter region for the Oenothera mitochondrial COX I and COX III genes to the homologous sequence block. ImagesFig. 5. PMID:15981332

Level II scour analysis for Bridge 4 (DANVTH00010004) on Town Highway 1, crossing Joes Brook, Danville, Vermont

USGS Publications Warehouse

Flynn, Robert H.; Boehmler, Erick M.

1997-01-01

This report provides the results of a detailed Level II analysis of scour potential at structure DANVTH00010004 on Town Highway 1 crossing Joes Brook, Danville, Vermont (figures 1–8). A Level II study is a basic engineering analysis of the site, including a quantitative analysis of stream stability and scour (U.S. Department of Transportation, 1993). Results of a Level I scour investigation also are included in Appendix E of this report. A Level I investigation provides a qualitative geomorphic characterization of the study site. Information on the bridge, gleaned from Vermont Agency of Transportation (VTAOT) files, was compiled prior to conducting Level I and Level II analyses and is found in Appendix D. The site is in the New England Upland section of the New England physiographic province in northeastern Vermont. The 42.5-mi2 drainage area is in a predominantly rural and forested basin. In the vicinity of the study site, the surface cover is pasture along the upstream and downstream left banks with trees and brush along the immediate banks. The upstream and downstream right banks are forested. In the study area, Joes Brook has an incised, sinuous channel with a slope of approximately 0.02 ft/ft, an average channel top width of 68 ft and an average bank height of 5 ft. The channel bed material ranges from gravel to bedrock with a median grain size (D50) of 80.1 mm (0.263 ft). The geomorphic assessment at the time of the Level I and Level II site visit on August 22, 1995, indicated that the reach was stable. The Town Highway 1 crossing of Joes Brook is a 49-ft-long, two-lane bridge consisting of one 45-foot steel-beam span (Vermont Agency of Transportation, written communication, March 17, 1995). The opening length of the structure parallel to the bridge face is 45 ft.The bridge is supported by vertical, concrete abutments with wingwalls. The channel is skewed approximately 15 degrees to the opening and the computed opening-skew-to-roadway is 15 degrees. A scour hole 1.0 ft deeper than the mean thalweg depth was observed along the right abutment during the Level I assessment. The scour hole also extends upstream and downstream of the bridge, along the right side of the channel. The scour protection measures at the site include type-2 stone fill (less than 36 inches diameter) at the upstream end of the upstream left wingwall and along the entire base length of the downstream right wingwall. Type-3 stone fill (less than 48 inches diameter) is along the entire base length of the upstream right wingwall and type-5 protection (stone block wall) is along the upstream right bank. Additional details describing conditions at the site are included in the Level II Summary and Appendices D and E. Scour depths and recommended rock rip-rap sizes were computed using the general guidelines described in Hydraulic Engineering Circular 18 (Richardson and others, 1995) for the 100- and 500-year discharges. Total scour at a highway crossing is comprised of three components: 1) long-term streambed degradation; 2) contraction scour (due to accelerated flow caused by a reduction in flow area at a bridge) and; 3) local scour (caused by accelerated flow around piers and abutments). Total scour is the sum of the three components. Equations are available to compute depths for contraction and local scour and a summary of the results of these computations follows. Contraction scour for all modelled flows was computed to be zero ft. Abutment scour ranged from 11.7 to 13.0 ft along the right abutment and from 6.6 to 9.4 ft along the left abutment. The worst-case abutment scour occurred at the 500-year discharge. Additional information on scour depths and depths to armoring are included in the section titled “Scour Results”. Scoured-streambed elevations, based on the calculated scour depths, are presented in tables 1 and 2. A cross-section of the scour computed at the bridge is presented in figure 8. Scour depths were calculated assuming an infinite depth of erosive material and a homogeneous particle-size distribution. It is generally accepted that the Froehlich and Hire equations (abutment scour) gives “excessively conservative estimates of scour depths” (Richardson and others, 1995, p. 47). Usually, computed scour depths are evaluated in combination with other information including (but not limited to) historical performance during flood events, the geomorphic stability assessment, existing scour protection measures, and the results of the hydraulic analyses. Therefore, scour depths adopted by VTAOT may differ from the computed values documented herein.

Flow conditioner for fuel injector for combustor and method for low-NO.sub.x combustor

DOEpatents

Dutta, Partha; Smith, Kenneth O.; Ritz, Frank J.

2013-09-10

An injector for a gas turbine combustor including a catalyst coated surface forming a passage for feed gas flow and a channel for oxidant gas flow establishing an axial gas flow through a flow conditioner disposed at least partially within an inner wall of the injector. The flow conditioner includes a length with an interior passage opening into upstream and downstream ends for passage of the axial gas flow. An interior diameter of the interior passage smoothly reduces and then increases from upstream to downstream ends.

Comparative analysis of the full genome sequence of European bat lyssavirus type 1 and type 2 with other lyssaviruses and evidence for a conserved transcription termination and polyadenylation motif in the G-L 3' non-translated region.

PubMed

Marston, D A; McElhinney, L M; Johnson, N; Müller, T; Conzelmann, K K; Tordo, N; Fooks, A R

2007-04-01

We report the first full-length genomic sequences for European bat lyssavirus type-1 (EBLV-1) and type-2 (EBLV-2). The EBLV-1 genomic sequence was derived from a virus isolated from a serotine bat in Hamburg, Germany, in 1968 and the EBLV-2 sequence was derived from a virus isolate from a human case of rabies that occurred in Scotland in 2002. A long-distance PCR strategy was used to amplify the open reading frames (ORFs), followed by standard and modified RACE (rapid amplification of cDNA ends) techniques to amplify the 3' and 5' ends. The lengths of each complete viral genome for EBLV-1 and EBLV-2 were 11 966 and 11 930 base pairs, respectively, and follow the standard rhabdovirus genome organization of five viral proteins. Comparison with other lyssavirus sequences demonstrates variation in degrees of homology, with the genomic termini showing a high degree of complementarity. The nucleoprotein was the most conserved, both intra- and intergenotypically, followed by the polymerase (L), matrix and glyco- proteins, with the phosphoprotein being the most variable. In addition, we have shown that the two EBLVs utilize a conserved transcription termination and polyadenylation (TTP) motif, approximately 50 nt upstream of the L gene start codon. All available lyssavirus sequences to date, with the exception of Pasteur virus (PV) and PV-derived isolates, use the second TTP site. This observation may explain differences in pathogenicity between lyssavirus strains, dependent on the length of the untranslated region, which might affect transcriptional activity and RNA stability.

Nucleotide sequence of the gene for the Mr 32,000 thylakoid membrane protein from Spinacia oleracea and Nicotiana debneyi predicts a totally conserved primary translation product of Mr 38,950

PubMed Central

Zurawski, Gerard; Bohnert, Hans J.; Whitfeld, Paul R.; Bottomley, Warwick

1982-01-01

The gene for the so-called Mr 32,000 rapidly labeled photosystem II thylakoid membrane protein (here designated psbA) of spinach (Spinacia oleracea) chloroplasts is located on the chloroplast DNA in the large single-copy region immediately adjacent to one of the inverted repeat sequences. In this paper we show that the size of the mRNA for this protein is ≈ 1.25 kilobases and that the direction of transcription is towards the inverted repeat unit. The nucleotide sequence of the gene and its flanking regions is presented. The only large open reading frame in the sequence codes for a protein of Mr 38,950. The nucleotide sequence of psbA from Nicotiana debneyi also has been determined, and comparison of the sequences from the two species shows them to be highly conserved (>95% homology) throughout the entire reading frame. Conservation of the amino acid sequence is absolute, there being no changes in a total of 353 residues. This leads us to conclude that the primary translation product of psbA must be a protein of Mr 38,950. The protein is characterized by the complete absence of lysine residues and is relatively rich in hydrophobic amino acids, which tend to be clustered. Transcription of spinach psbA starts about 86 base pairs before the first ATG codon. Immediately upstream from this point there is a sequence typical of that found in E. coli promoters. An almost identical sequence occurs in the equivalent region of N. debneyi DNA. Images PMID:16593262

78 FR 52694 - Drawbridge Operation Regulation; Trent River, New Bern, NC

Federal Register 2010, 2011, 2012, 2013, 2014

2013-08-26

... several times every day for recreational vessels transiting to and from the local marinas located upstream. Although openings occur throughout the day, the morning hours have the fewest vessel transits. Vessels able...

Conservation of proteo-lipid nuclear membrane fusion machinery during early embryogenesis.

PubMed

Byrne, Richard D; Veeriah, Selvaraju; Applebee, Christopher J; Larijani, Banafshé

2014-01-01

The fusogenic lipid diacylglycerol is essential for remodeling gamete and zygote nuclear envelopes (NE) during early embryogenesis. It is unclear whether upstream signaling molecules are likewise conserved. Here we demonstrate PLCγ and its activator SFK1, which co-operate during male pronuclear envelope formation, also promote the subsequent male and female pronuclear fusion. PLCγ and SFK1 interact directly at the fusion site leading to PLCγ activation. This is accompanied by a spatially restricted reduction of PtdIns(4,5)P2. Consequently, pronuclear fusion is blocked by PLCγ or SFK1 inhibition. These findings identify new regulators of events in the early embryo and suggest a conserved "toolkit" of fusion machinery drives successive NE fusion events during embryogenesis.

Insect sex determination: it all evolves around transformer.

PubMed

Verhulst, Eveline C; van de Zande, Louis; Beukeboom, Leo W

2010-08-01

Insects exhibit a variety of sex determining mechanisms including male or female heterogamety and haplodiploidy. The primary signal that starts sex determination is processed by a cascade of genes ending with the conserved switch doublesex that controls sexual differentiation. Transformer is the doublesex splicing regulator and has been found in all examined insects, indicating its ancestral function as a sex-determining gene. Despite this conserved function, the variation in transformer nucleotide sequence, amino acid composition and protein structure can accommodate a multitude of upstream sex determining signals. Transformer regulation of doublesex and its taxonomic distribution indicate that the doublesex-transformer axis is conserved among all insects and that transformer is the key gene around which variation in sex determining mechanisms has evolved.

Molecular cloning and sequence analysis of the Anticarsia gemmatalis multicapsid nuclear polyhedrosis virus GP64 glycoprotein.

PubMed

Pilloff, Marcela Gabriela; Bilen, Marcos Fabián; Belaich, Mariano Nicolás; Lozano, Mario Enrique; Ghiringhelli, Pablo Daniel

2003-01-01

The gp64 locus of Anticarsia gemmatalis multicapsid nucleopolyhedrovirus isolate Santa Fe (AgMNPV-SF) was characterised molecularly in our laboratory. To this end, we have located and cloned a AgMNPV-SF genomic DNA fragment containing the gp64 gene and sequenced the complete gp64 locus. Nucleotide sequence analysis indicated that the AgMNPV gp64 gene consists of a 1500 nucleotide open reading frame (ORF), encoding a protein of 499 amino acids. Of the seven gp64 homologues identified to date, the AgMNPV gp64 ORF shared most sequence similarity with the gp64 gene of Orgyia pseudotsugata MNPV. The GP64 from AgMNPV is the smallest baculoviral envelope glycoprotein found to date, differing in 10 or more residues from the other group I nucleopolyhedroviruses. The biological activity of AgMNPV GP64 protein was assessed by cell fusion assays in UFL-AG-286 cells using the obtained recombinant plasmids. In the upstream and downstream regions, relative to the gp64 ORF, we found different conserved transcriptional and post-transcriptional regulatory elements, respectively.

A novel function of twins, B subunit of protein phosphatase 2A, in regulating actin polymerization.

PubMed

Yeh, Po-An; Chang, Ching-Jin

2017-01-01

Actin is an important component of the cytoskeleton and its polymerization is delicately regulated by several kinases and phosphatases. Heterotrimeric protein phosphatase 2A (PP2A) is a potent phosphatase that is crucial for cell proliferation, apoptosis, tumorigenesis, signal transduction, cytoskeleton arrangement, and neurodegeneration. To facilitate these varied functions, different regulators determine the different targets of PP2A. Among these regulators of PP2A, the B subunits in particular may be involved in cytoskeleton arrangement. However, little is known about the role of PP2A in actin polymerization in vivo. Using sophisticated fly genetics, we demonstrated a novel function for the fly B subunit, twins, to promote actin polymerization in varied tissue types, suggesting a broad and conserved effect. Furthermore, our genetic data suggest that twins may act upstream of the actin-polymerized-proteins, Moesin and Myosin-light-chain, and downstream of Rho to promote actin polymerization. This work opens a new avenue for exploring the biological functions of a PP2A regulator, twins, in cytoskeleton regulation.

A novel function of twins, B subunit of protein phosphatase 2A, in regulating actin polymerization

PubMed Central

Chang, Ching-Jin

2017-01-01

Actin is an important component of the cytoskeleton and its polymerization is delicately regulated by several kinases and phosphatases. Heterotrimeric protein phosphatase 2A (PP2A) is a potent phosphatase that is crucial for cell proliferation, apoptosis, tumorigenesis, signal transduction, cytoskeleton arrangement, and neurodegeneration. To facilitate these varied functions, different regulators determine the different targets of PP2A. Among these regulators of PP2A, the B subunits in particular may be involved in cytoskeleton arrangement. However, little is known about the role of PP2A in actin polymerization in vivo. Using sophisticated fly genetics, we demonstrated a novel function for the fly B subunit, twins, to promote actin polymerization in varied tissue types, suggesting a broad and conserved effect. Furthermore, our genetic data suggest that twins may act upstream of the actin-polymerized-proteins, Moesin and Myosin-light-chain, and downstream of Rho to promote actin polymerization. This work opens a new avenue for exploring the biological functions of a PP2A regulator, twins, in cytoskeleton regulation. PMID:28977036

Invasion versus isolation: Trade-offs in managing native salmonids with barriers to upstream movement

Treesearch

Kurt D. Fausch; Bruce E. Rieman; Jason B. Dunham; Michael K. Young; Douglas P. Peterson

2009-01-01

Conservation biologists often face the trade-off that increasing connectivity in fragmented landscapes to reduce extinction risk of native species can foster invasion by non-native species that enter via the corridors created, which can then increase extinction risk. This dilemma is acute for stream fishes, especially native salmonids, because their populations are...

Mycobacterium avium subsp. paratuberculosis PPE Protein MAP1152 and Conserved Protein MAP1156 are Antigenic in Experimentally and Naturally Infected Cattle

USDA-ARS?s Scientific Manuscript database

Mycobacterium avium subsp. paratuberculosis (MAP) causes Johne’s Disease (JD) in ruminants resulting in significant production losses. An insertion mutation upstream from the MAP1152-MAP1156 region causes a change in colony morphotype and results in an attenuated phenotype in bovine monocyte derive...

Bmal1 is a direct transcriptional target of the orphan nuclear receptor, NR2F1

USDA-ARS?s Scientific Manuscript database

Orphan nuclear receptor NR2F1 (also known as COUP-TFI, Chicken Ovalbumin Upstream Promoter Transcription Factor I) is a highly conserved member of the nuclear receptor superfamily. NR2F1 plays a critical role during embryonic development, particularly in the central and peripheral nervous systems a...

Water quality of the lower Columbia River basin; analysis of current and historical water-quality data through 1994

USGS Publications Warehouse

Fuhrer, Gregory J.; Tanner, Dwight Q.; Morace, Jennifer L.; McKenzie, Stuart W.; Skach, Kenneth A.

1996-01-01

Trend tests showed significant (r < 0.05) downward trends from 1973 to 1994 for three constituents at the Columbia River at Warrendale: phosphorus in unfiltered water, total dissolved solids, and specific conductance. These trends may be a consequence of more conservative agricultural practices in the area upstream from Warrendale.

Routine versus aggressive upstream rhythm control for prevention of early atrial fibrillation in heart failure: background, aims and design of the RACE 3 study.

PubMed

Alings, M; Smit, M D; Moes, M L; Crijns, H J G M; Tijssen, J G P; Brügemann, J; Hillege, H L; Lane, D A; Lip, G Y H; Smeets, J R L M; Tieleman, R G; Tukkie, R; Willems, F F; Vermond, R A; Van Veldhuisen, D J; Van Gelder, I C

2013-07-01

Rhythm control for atrial fibrillation (AF) is cumbersome because of its progressive nature caused by structural remodelling. Upstream therapy refers to therapeutic interventions aiming to modify the atrial substrate, leading to prevention of AF. The Routine versus Aggressive upstream rhythm Control for prevention of Early AF in heart failure (RACE 3) study hypothesises that aggressive upstream rhythm control increases persistence of sinus rhythm compared with conventional rhythm control in patients with early AF and mild-to-moderate early systolic or diastolic heart failure undergoing electrical cardioversion. RACE 3 is a prospective, randomised, open, multinational, multicenter trial. Upstream rhythm control consists of angiotensin converting enzyme inhibitors and/or angiotensin receptor blockers, mineralocorticoid receptor antagonists, statins, cardiac rehabilitation therapy, and intensive counselling on dietary restrictions, exercise maintenance, and drug adherence. Conventional rhythm control consists of routine rhythm control therapy without cardiac rehabilitation therapy and intensive counselling. In both arms, every effort is made to keep patients in the rhythm control strategy, and ion channel antiarrhythmic drugs or pulmonary vein ablation may be instituted if AF relapses. Total inclusion will be 250 patients. If upstream therapy proves to be effective in improving maintenance of sinus rhythm, it could become a new approach to rhythm control supporting conventional pharmacological and non-pharmacological rhythm control.

Interactions between the cyclic AMP receptor protein and the alpha subunit of RNA polymerase at the Escherichia coli galactose operon P1 promoter.

PubMed

Attey, A; Belyaeva, T; Savery, N; Hoggett, J; Fujita, N; Ishihama, A; Busby, S

1994-10-25

DNAase I footprinting has been used to study open complexes between Escherichia coli RNA polymerase and the galactose operon P1 promoter, both in the absence and the presence of CRP (the cyclic AMP receptor protein, a transcription activator). From the effects of deletion of the C-terminal part of the RNA polymerase alpha subunit, we deduce that alpha binds at the upstream end of both the binary RNA polymerase-galP1 and ternary RNA polymerase-CRP-galP1 complexes. Disruption of the alpha-upstream contact suppresses open complex formation at galP1 at lower temperatures. In ternary RNA polymerase-CRP-galP1 complexes, alpha appears to make direct contact with Activating Region 1 in CRP. DNAase I footprinting has been used to detect and quantify interactions between purified alpha and CRP bound at galP1.

Interactions between the cyclic AMP receptor protein and the alpha subunit of RNA polymerase at the Escherichia coli galactose operon P1 promoter.

PubMed Central

Attey, A; Belyaeva, T; Savery, N; Hoggett, J; Fujita, N; Ishihama, A; Busby, S

1994-01-01

DNAase I footprinting has been used to study open complexes between Escherichia coli RNA polymerase and the galactose operon P1 promoter, both in the absence and the presence of CRP (the cyclic AMP receptor protein, a transcription activator). From the effects of deletion of the C-terminal part of the RNA polymerase alpha subunit, we deduce that alpha binds at the upstream end of both the binary RNA polymerase-galP1 and ternary RNA polymerase-CRP-galP1 complexes. Disruption of the alpha-upstream contact suppresses open complex formation at galP1 at lower temperatures. In ternary RNA polymerase-CRP-galP1 complexes, alpha appears to make direct contact with Activating Region 1 in CRP. DNAase I footprinting has been used to detect and quantify interactions between purified alpha and CRP bound at galP1. Images PMID:7971267

Translation of the mRNA of the maize transcriptional activator Opaque-2 is inhibited by upstream open reading frames present in the leader sequence.

PubMed Central

Lohmer, S; Maddaloni, M; Motto, M; Salamini, F; Thompson, R D

1993-01-01

The protein encoded by the Opaque-2 (O2) gene is a transcription factor, translated from an mRNA that possesses an unusually long 5' leader sequence containing three upstream open reading frames (uORFs). The efficiency of translation of O2 mRNA has been tested in vivo by a transient assay in which the level of activation of the b32 promoter, a natural target of O2 protein, is measured. We show that uORF-less O2 alleles possess a higher transactivation value than the wild-type allele and that the reduction in transactivation due to the uORFs is a cis-dominant effect. The data presented indicate that both uORF1 and uORF2 are involved in the reducing effect and suggest that both are likely to be translated. PMID:8439744

Role of the open reading frames of Rous sarcoma virus leader RNA in translation and genome packaging.

PubMed Central

Donzé, O; Spahr, P F

1992-01-01

The Rous sarcoma virus (RSV) RNA leader sequence carries three open reading frames (uORFs) upstream of the AUG initiator of the gag gene. We studied, in vivo, the role of these uORFs by changing two or three nucleotides of the three AUGs or by deleting the first uORF. Our results show that (i) unlike most previously characterized uORFs, which decrease translation, the first uORF (AUG1) of RSV acts as an enhancer of translation, since absence of the first AUG decreased translation; AUG3 also modulates translation, probably by interfering with scanning ribosomes as described for other upstream ORFs, and mutation of AUG2 had no effect on translation. (ii) Mutation of each of the upstream AUGs lowered the infectivity of progeny virions. (iii) Unexpectedly, mutation of AUG1 and/or AUG3 dramatically reduced RNA packaging by 50-to 100-fold, unlike mutation of AUG2 which did not alter RNA packaging efficiency. Additional mutants in the vicinity of uORF1 and uORF3 were constructed in order to elucidate the mechanism by which uORFs affect RNA packaging: a translation model requiring uORFs 1 and 3, and involving ribosome pausing at AUG 3 is discussed. Images PMID:1327749

Refining the regulatory region upstream of SOX9 associated with 46,XX testicular disorders of Sex Development (DSD).

PubMed

Hyon, Capucine; Chantot-Bastaraud, Sandra; Harbuz, Radu; Bhouri, Rakia; Perrot, Nicolas; Peycelon, Matthieu; Sibony, Mathilde; Rojo, Sandra; Piguel, Xavier; Bilan, Frederic; Gilbert-Dussardier, Brigitte; Kitzis, Alain; McElreavey, Ken; Siffroi, Jean-Pierre; Bashamboo, Anu

2015-08-01

Disorders of Sex Development (DSD) are a heterogeneous group of disorders affecting gonad and/or genito-urinary tract development and usually the endocrine-reproductive system. A genetic diagnosis is made in only around 20% of these cases. The genetic causes of 46,XX-SRY negative testicular DSD as well as ovotesticular DSD are poorly defined. Duplications involving a region located ∼600 kb upstream of SOX9, a key gene in testis development, were reported in several cases of 46,XX DSD. Recent studies have narrowed this region down to a 78 kb interval that is duplicated or deleted respectively in 46,XX or 46,XY DSD. We identified three phenotypically normal patients presenting with azoospermia and 46,XX testicular DSD. Two brothers carried a 83.8 kb duplication located ∼600 kb upstream of SOX9 that overlapped with the previously reported rearrangements. This duplication refines the minimal region associated with 46,XX-SRY negative DSD to a 40.7-41.9 kb element located ∼600 kb upstream of SOX9. Predicted enhancer elements and evolutionary-conserved binding sites for proteins known to be involved in testis determination are located within this region. © 2015 Wiley Periodicals, Inc.

RNA-DNA and DNA-DNA base-pairing at the upstream edge of the transcription bubble regulate translocation of RNA polymerase and transcription rate.

PubMed

KIreeva, Maria; Trang, Cyndi; Matevosyan, Gayane; Turek-Herman, Joshua; Chasov, Vitaly; Lubkowska, Lucyna; Kashlev, Mikhail

2018-06-20

Translocation of RNA polymerase (RNAP) along DNA may be rate-limiting for transcription elongation. The Brownian ratchet model posits that RNAP rapidly translocates back and forth until the post-translocated state is stabilized by NTP binding. An alternative model suggests that RNAP translocation is slow and poorly reversible. To distinguish between these two models, we take advantage of an observation that pyrophosphorolysis rates directly correlate with the abundance of the pre-translocated fraction. Pyrophosphorolysis by RNAP stabilized in the pre-translocated state by bacteriophage HK022 protein Nun was used as a reference point to determine the pre-translocated fraction in the absence of Nun. The stalled RNAP preferentially occupies the post-translocated state. The forward translocation rate depends, among other factors, on melting of the RNA-DNA base pair at the upstream edge of the transcription bubble. DNA-DNA base pairing immediately upstream from the RNA-DNA hybrid stabilizes the post-translocated state. This mechanism is conserved between E. coli RNAP and S. cerevisiae RNA polymerase II and is partially dependent on the lid domain of the catalytic subunit. Thus, the RNA-DNA hybrid and DNA reannealing at the upstream edge of the transcription bubble emerge as targets for regulation of the transcription elongation rate.

Critical 23S rRNA interactions for macrolide-dependent ribosome stalling on the ErmCL nascent peptide chain.

PubMed

Koch, Miriam; Willi, Jessica; Pradère, Ugo; Hall, Jonathan; Polacek, Norbert

2017-06-20

The nascent peptide exit tunnel has recently been identified as a functional region of ribosomes contributing to translation regulation and co-translational protein folding. Inducible expression of the erm resistance genes depends on ribosome stalling at specific codons of an upstream open reading frame in the presence of an exit tunnel-bound macrolide antibiotic. The molecular basis for this translation arrest is still not fully understood. Here, we used a nucleotide analog interference approach to unravel important functional groups on 23S rRNA residues in the ribosomal exit tunnel for ribosome stalling on the ErmC leader peptide. By replacing single nucleobase functional groups or even single atoms we were able to demonstrate the importance of A2062, A2503 and U2586 for drug-dependent ribosome stalling. Our data show that the universally conserved A2062 and A2503 are capable of forming a non-Watson-Crick base pair that is critical for sensing and transmitting the stalling signal from the exit tunnel back to the peptidyl transferase center of the ribosome. The nucleobases of A2062, A2503 as well as U2586 do not contribute significantly to the overall mechanism of protein biosynthesis, yet their elaborate role for co-translational monitoring of nascent peptide chains inside the exit tunnel can explain their evolutionary conservation. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Conserved features of eukaryotic hsp70 genes revealed by comparison with the nucleotide sequence of human hsp70.

PubMed Central

Hunt, C; Morimoto, R I

1985-01-01

We have determined the nucleotide sequence of the human hsp70 gene and 5' flanking region. The hsp70 gene is transcribed as an uninterrupted primary transcript of 2440 nucleotides composed of a 5' noncoding leader sequence of 212 nucleotides, a 3' noncoding region of 242 nucleotides, and a continuous open reading frame of 1986 nucleotides that encodes a protein with predicted molecular mass of 69,800 daltons. Upstream of the 5' terminus are the canonical TATAAA box, the sequence ATTGG that corresponds in the inverted orientation to the CCAAT motif, and the dyad sequence CTGGAAT/ATTCCCG that shares homology in 12 of 14 positions with the consensus transcription regulatory sequence common to Drosophila heat shock genes. Comparison of the predicted amino acid sequences of human hsp70 with the published sequences of Drosophila hsp70 and Escherichia coli dnaK reveals that human hsp70 is 73% identical to Drosophila hsp70 and 47% identical to E. coli dnaK. Surprisingly, the nucleotide sequences of the human and Drosophila genes are 72% identical and human and E. coli genes are 50% identical, which is more highly conserved than necessary given the degeneracy of the genetic code. The lack of accumulated silent nucleotide substitutions leads us to propose that there may be additional information in the nucleotide sequence of the hsp70 gene or the corresponding mRNA that precludes the maximum divergence allowed in the silent codon positions. PMID:3931075

50 CFR Table 3 (north) to Part 660... - Non-Trawl Rockfish Conservation Areas and Trip Limits for Open Access Gears North of 40°10′ N. Lat.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 50 Wildlife and Fisheries 11 2011-10-01 2011-10-01 false Non-Trawl Rockfish Conservation Areas and Trip Limits for Open Access Gears North of 40°10â² N. Lat. 3 Table 3 (North) to Part 660, Subpart F...) to Part 660, Subpart F—Non-Trawl Rockfish Conservation Areas and Trip Limits for Open Access Gears...

50 CFR Table 3 (south) to Part 660... - Non-Trawl Rockfish Conservation Areas and Trip Limits for Open Access Gears South of 40°10′ N. Lat.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 50 Wildlife and Fisheries 11 2011-10-01 2011-10-01 false Non-Trawl Rockfish Conservation Areas and Trip Limits for Open Access Gears South of 40°10â² N. Lat. 3 Table 3 (South) to Part 660, Subpart F...) to Part 660, Subpart F—Non-Trawl Rockfish Conservation Areas and Trip Limits for Open Access Gears...

Efficient activation of transcription in yeast by the BPV1 E2 protein.

PubMed Central

Stanway, C A; Sowden, M P; Wilson, L E; Kingsman, A J; Kingsman, S M

1989-01-01

The full-length gene product encoded by the E2 open reading frame (ORF) of bovine papillomavirus type 1 (BPV1) is a transcriptional transactivator. It is believed to mediate its effect on the BPV1 long control region (LCR) by binding to motifs with the consensus sequence ACCN6GGT. The minimal functional cis active site, called the E2 response element (E2RE), in mammalian cells comprises two copies of this motif. Here we have shown that E2 can function in Saccharomyces cerevisiae by placing an E2RE upstream of a synthetic yeast assay promoter which consists of a TATA motif and an mRNA initiation site, spaced correctly. This E2RE-minimal promoter is only transcriptionally active in the presence of E2 protein and the resulting mRNA is initiated at the authentic start site. This is the first report of a mammalian viral transactivator functioning in yeast. The level of activation by E2 via the E2RE was the same as observed with the highly efficient authentic PGK promoter where the upstream activation sequence is composed of three distinct elements. Furthermore a single E2 motif which is insufficient in mammalian cells as an activation site was as efficiently utilized in yeast as the E2RE (2 motifs). Previous studies have shown that mammalian cellular activators can function in yeast and our data now extend this to viral-specific activators. Our data indicate however that while the mechanism of transactivation is broadly conserved there may be significant differences at the detailed level. Images PMID:2539584

The Oenococcus oeni clpX Homologue Is a Heat Shock Gene Preferentially Expressed in Exponential Growth Phase

PubMed Central

Jobin, Michel-Philippe; Garmyn, Dominique; Diviès, Charles; Guzzo, Jean

1999-01-01

Using degenerated primers from conserved regions of previously studied clpX gene products, we cloned the clpX gene of the malolactic bacterium Oenococcus oeni. The clpX gene was sequenced, and the deduced protein of 413 amino acids (predicted molecular mass of 45,650 Da) was highly similar to previously analyzed clpX gene products from other organisms. An open reading frame located upstream of the clpX gene was identified as the tig gene by similarity of its predicted product to other bacterial trigger factors. ClpX was purified by using a maltose binding protein fusion system and was shown to possess an ATPase activity. Northern analyses indicated the presence of two independent 1.6-kb monocistronic clpX and tig mRNAs and also showed an increase in clpX mRNA amount after a temperature shift from 30 to 42°C. The clpX transcript is abundant in the early exponential growth phase and progressively declines to undetectable levels in the stationary phase. Thus, unlike hsp18, the gene encoding one of the major small heat shock proteins of Oenococcus oeni, clpX expression is related to the exponential growth phase and requires de novo protein synthesis. Primer extension analysis identified the 5′ end of clpX mRNA which is located 408 nucleotides upstream of a putative AUA start codon. The putative transcription start site allowed identification of a predicted promoter sequence with a high similarity to the consensus sequence found in the housekeeping gene promoter of gram-positive bacteria as well as Escherichia coli. PMID:10542163

SSME Turbopump Turbine Computations

NASA Technical Reports Server (NTRS)

Jorgenson, P. G. E.

1985-01-01

A two-dimensional viscous code was developed to be used in the prediction of the flow in the SSME high-pressure turbopump blade passages. The rotor viscous code (RVC) employs a four-step Runge-Kutta scheme to solve the two-dimensional, thin-layer Navier-Stokes equations. The Baldwin-Lomax eddy-viscosity model is used for these turbulent flow calculations. A viable method was developed to use the relative exit conditions from an upstream blade row as the inlet conditions to the next blade row. The blade loading diagrams are compared with the meridional values obtained from an in-house quasithree-dimensional inviscid code. Periodic boundary conditions are imposed on a body-fitted C-grid computed by using the GRAPE GRids about Airfoils using Poisson's Equation (GRAPE) code. Total pressure, total temperature, and flow angle are specified at the inlet. The upstream-running Riemann invariant is extrapolated from the interior. Static pressure is specified at the exit such that mass flow is conserved from blade row to blade row, and the conservative variables are extrapolated from the interior. For viscous flows the noslip condition is imposed at the wall. The normal momentum equation gives the pressure at the wall. The density at the wall is obtained from the wall total temperature.

Evidence for serial discontinuity in the fish community of a heavily impounded river

USGS Publications Warehouse

Miranda, Leandro E.; Dembkowski, D.J.

2016-01-01

In the Tennessee River, USA, we examined lengthwise patterns in fish community structure and species richness within and among nine reservoirs organized in sequence and connected through navigational locks. Within reservoirs, the riverine, transition and lacustrine zones supported distinct, although overlapping, nearshore fish assemblages; differences were also reflected in measures of species richness. Spatial patterns were most apparent for rheophilic species, which increased in species richness and representation upstream within each reservoir and downstream across the chain of reservoirs. This pattern resembled a sawtooth wave, with the amplitude of the wave peaking in the riverine zone below each dam, and progressively higher wave amplitude developing downstream in the reservoir chain. The observed sawtooth pattern supports the serial discontinuity concept in that the continuity of the riverine fish community is interrupted by the lacustrine conditions created behind each dam. Upstream within each reservoir, and downstream in the chain of reservoirs, habitat characteristics become more riverine. To promote sustainability of rheophilic fishes and maintain biodiversity in impounded rivers, conservation plans could emphasize maintenance and preservation of riverine environments of the reservoir's upper reaches, while remaining cognizant of the broader basin trends that provide opportunities for a lengthwise array of conservation and management policy. 

Designing non-Hermitian dynamics for conservative state evolution on the Bloch sphere

NASA Astrophysics Data System (ADS)

Yu, Sunkyu; Piao, Xianji; Park, Namkyoo

2018-03-01

An evolution on the Bloch sphere is the fundamental state transition, including optical polarization controls and qubit operations. Conventional evolution of a polarization state or qubit is implemented within a closed system that automatically satisfies energy conservation from the Hermitian formalism. Although particular forms of static non-Hermitian Hamiltonians, such as parity-time-symmetric Hamiltonians, allow conservative states in an open system, the criteria for the energy conservation in a dynamical open system have not been fully explored. Here, we derive the condition of conservative state evolution in open-system dynamics and its inverse design method, by developing the non-Hermitian modification of the Larmor precession equation. We show that the geometrically designed locus on the Bloch sphere can be realized by different forms of dynamics, leading to the isolocus family of non-Hermitian dynamics. This increased degree of freedom allows the complementary phenomena of error-robust and highly sensitive evolutions on the Bloch sphere, which could be applicable to stable polarizers, quantum gates, and optimized sensors in dynamical open systems.

An RNA Element That Facilitates Programmed Ribosomal Readthrough in Turnip Crinkle Virus Adopts Multiple Conformations

PubMed Central

Kuhlmann, Micki M.; Chattopadhyay, Maitreyi; Stupina, Vera A.; Gao, Feng

2016-01-01

ABSTRACT Ribosome recoding is used by RNA viruses for translational readthrough or frameshifting past termination codons for the synthesis of extension products. Recoding sites, along with downstream recoding stimulatory elements (RSEs), have long been studied in reporter constructs, because these fragments alone mediate customary levels of recoding and are thus assumed to contain complete instructions for establishment of the proper ratio of termination to recoding. RSEs from the Tombusviridae and Luteoviridae are thought to be exceptions, since they contain a long-distance RNA-RNA connection with the 3′ end. This interaction has been suggested to substitute for pseudoknots, thought to be missing in tombusvirid RSEs. We provide evidence that the phylogenetically conserved RSE of the carmovirus Turnip crinkle virus (TCV) adopts an alternative, smaller structure that extends an upstream conserved hairpin and that this alternative structure is the predominant form of the RSE within nascent viral RNA in plant cells and when RNA is synthesized in vitro. The TCV RSE also contains an internal pseudoknot along with the long-distance interaction, and the pseudoknot is not compatible with the phylogenetically conserved structure. Conserved residues just past the recoding site are important for recoding, and these residues are also conserved in the RSEs of gammaretroviruses. Our data demonstrate the dynamic nature of the TCV RSE and suggest that studies using reporter constructs may not be effectively recapitulating RSE-mediated recoding within viral genomes. IMPORTANCE Ribosome recoding is used by RNA viruses to enable ribosomes to extend translation past termination codons for the synthesis of longer products. Recoding sites and a downstream recoding stimulatory element (RSE) mediate expected levels of recoding when excised and placed in reporter constructs and thus are assumed to contain complete instructions for the establishment of the proper ratio of termination to recoding. We provide evidence that most of the TCV RSE adopts an alternative structure that extends an upstream conserved hairpin and that this alternative structure, and not the phylogenetically conserved structure, is the predominant form of the RSE in RNA synthesized in vitro and in plant cells. The TCV RSE also contains an internal pseudoknot that is not compatible with the phylogenetically conserved structure and an RNA bridge to the 3′ end. These data suggest that the TCV RSE is structurally dynamic and that multiple conformations are likely required to regulate ribosomal readthrough. PMID:27440887

Sources and processes affecting the distribution of dissolved Nd isotopes and concentrations in the West Pacific

NASA Astrophysics Data System (ADS)

Behrens, Melanie K.; Pahnke, Katharina; Schnetger, Bernhard; Brumsack, Hans-Jürgen

2018-02-01

In the Atlantic, where deep circulation is vigorous, the dissolved neodymium (Nd) isotopic composition (expressed as ɛNd) is largely controlled by water mass mixing. In contrast, the factors influencing the ɛNd distribution in the Pacific, marked by sluggish circulation, is not clear yet. Indication for regional overprints in the Pacific is given based on its bordering volcanic islands. Our study aims to clarify the impact and relative importance of different Nd sources (rivers, volcanic islands), vertical (bio)geochemical processes and lateral water mass transport in controlling dissolved ɛNd and Nd concentration ([Nd]) distributions in the West Pacific between South Korea and Fiji. We find indication for unradiogenic continental input from South Korean and Chinese rivers to the East China Sea. In the tropical West Pacific, volcanic islands supply Nd to surface and subsurface waters and modify their ɛNd to radiogenic values of up to +0.7. These radiogenic signatures allow detailed tracing of currents flowing to the east and differentiation from westward currents with open ocean Pacific ɛNd composition in the complex tropical Pacific zonal current system. Modified radiogenic ɛNd of West Pacific intermediate to bottom waters upstream or within our section also indicates non-conservative behavior of ɛNd due to boundary exchange at volcanic island margins, submarine ridges, and with hydrothermal particles. Only subsurface to deep waters (3000 m) in the open Northwest Pacific show conservative behavior of ɛNd. In contrast, we find a striking correlation of extremely low (down to 2.77 pmol/kg Nd) and laterally constant [Nd] with the high-salinity North and South Pacific Tropical Water, indicating lateral transport of preformed [Nd] from the North and South Pacific subtropical gyres into the study area. This observation also explains the previously observed low subsurface [Nd] in the tropical West Pacific. Similarly, Western South Pacific Central Water, Antarctic Intermediate Water, and Lower Circumpolar Deep Water in the southern and equatorial West Pacific are marked by vertically and laterally almost invariant [Nd] indicating a dominance of conservative behavior of [Nd]. In contrast, Central and Intermediate Water in the North West Pacific are characterized by increasing [Nd] with depth reflecting Nd release from particles. Overall, our data demonstrate a dominant lateral transport control on [Nd] distributions and clear non-conservative modification of ɛNd in the West Pacific. The latter affords tracing of surface and subsurface zonal transport in the tropical Pacific, but prevents the use of ɛNd as strictly conservative tracer of the major meridionally circulating water masses in the West Pacific between 15°S and 28°N.

15. DETAIL VIEW OF MAIN LOCK MITER GATE IN PARTIALLY ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

15. DETAIL VIEW OF MAIN LOCK MITER GATE IN PARTIALLY OPENED POSITION, LOOKING NORTHWEST (UPSTREAM). COMPRESSOR BUILDING VISIBLE TO REAR ON INTERMEDIATE WALL - Upper Mississippi River 9-Foot Channel Project, Lock & Dam 27, Granite City, Madison County, IL

18. ROSS POWERHOUSE: BUTTERFLY VALVE FROM BELOW AND SCROLL CASE ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

18. ROSS POWERHOUSE: BUTTERFLY VALVE FROM BELOW AND SCROLL CASE DRAIN. TAG INDICATES THE SCROLL CASE DRAIN WAS OPEN, 1989. - Skagit Power Development, Ross Powerhouse, On Skagit River, 10.7 miles upstream from Newhalem, Newhalem, Whatcom County, WA

75 FR 41102 - Energy Conservation Program: Re-Opening of the Public Comment Period for Commercial Refrigeration...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-07-15

... Conservation Program: Re-Opening of the Public Comment Period for Commercial Refrigeration Equipment AGENCY... document for commercial refrigeration equipment and provide notice of a public meeting. The NOPM provided... the framework document for commercial refrigeration equipment is to be re-opened from July 15, 2010 to...

Fuel injection assembly for use in turbine engines and method of assembling same

DOEpatents

Uhm, Jong Ho; Johnson, Thomas Edward

2015-03-24

A fuel injection assembly for use in a turbine engine is provided. The fuel injection assembly includes a plurality of tube assemblies, wherein each of the tube assemblies includes an upstream portion and a downstream portion. Each tube assembly includes a plurality of tubes that extend from the upstream portion to the downstream portion or from the upstream portion through the downstream portion. At least one injection system is coupled to at least one tube assembly of the plurality of tube assemblies. The injection system includes a fluid supply member that extends from a fluid source to the downstream portion of the tube assembly. The fluid supply member includes a first end portion located in the downstream portion of the tube assembly, wherein the first end portion has at least one first opening for channeling fluid through the tube assembly to facilitate reducing a temperature therein.

Steady inviscid transonic flows over planar airfoils: A search for a simplified procedure

NASA Technical Reports Server (NTRS)

Magnus, R.; Yoshihara, H.

1973-01-01

A finite difference procedure based upon a system of unsteady equations in proper conservation form with either exact or small disturbance steady terms is used to calculate the steady flows over several classes of airfoils. The airfoil condition is fulfilled on a slab whose upstream extremity is a semi-circle overlaying the airfoil leading edge circle. The limitations of the small disturbance equations are demonstrated in an extreme example of a blunt-nosed, aft-cambered airfoil. The necessity of using the equations in proper conservation form to capture the shock properly is stressed. Ability of the steady relaxation procedures to capture the shock is briefly examined.

Sustainability of Water Resources in the Upstream Watershed- Based Community Engagement and Multistakeholder Cooperation

NASA Astrophysics Data System (ADS)

Brotosusilo, Agus; Utari, Dyah; Agung Satria, Afrizal

2016-02-01

The communities engagement become the backbone of the conservation in the Citanduy upstream watershed. It functioning as a major deal and the first one in keeping his own Watershed. This paper based on Community Engagement Grants (CEGs). Program Society-based empowerment approach is also emphasized in the viewpoint of environmental law that is useful to set governance and sanctions in watershed management. The type of activity to be undertaken are the expansion of awareness programs communities of the existence and condition of the watershed Citanduy, the formation of a cadre of conservationists environment that is primarily directed to children and women, the institutionalization of customary law environment, and afforestation by planting 100,000 prolific trees, tree conservationists, and Sunda endemic tree in the land surrounding the watershed upstream Citanduy. The Program involves several partners and stakeholders who helped in substance and operational support activities in the field.. Result of program shows that Community Engagement Grants need cooperation among stakeholders by positioning the community as main subject of changing, not as subject who does not understand their needs to change.

Level II scour analysis for Bridge 43 (CHESVT00110043) on State Highway 11, crossing the Middle Branch Williams River, Chester, Vermont

USGS Publications Warehouse

Striker, Lora K.; Burns, Ronda L.

1997-01-01

76-ft-long, two-lane bridge consisting of two 37-foot concrete Tee-beam spans (Vermont Agency of Transportation, written communication, March 29, 1995). The bridge is supported by vertical, concrete abutments with wingwalls. The channel is skewed approximately 35 degrees to the opening. The computed opening-skew-to-roadway was 30 degrees but the historical records indicate this angle is 25 degrees. Scour protection measures at the site consist of type-1 stone fill (less than 12 inches diameter) along the downstream banks and the upstream right wing wall. Type-2 (less than 36 inches diameter) stone fill protection is noted on the upstream and downstream left wingwalls and upstream along the left bank. Additional details describing conditions at the site are included in the Level II Summary and Appendices D and E. Scour depths and recommended rock rip-rap sizes were computed using the general guidelines described in Hydraulic Engineering Circular 18 (Richardson and others, 1995). Total scour at a highway crossing is comprised of three components: 1) long-term streambed degradation; 2) contraction scour (due to accelerated flow caused by a reduction in flow area at a bridge) and; 3) local scour (caused by accelerated flow around piers and abutments). Total scour is the sum of the three components. Equations are available to compute depths for contraction and local scour and a summary of the results of these computations follows. Contraction scour for all modelled flows ranged from 0.0 to 1.5 ft. The worst-case contraction scour occurred at the 500-year discharge. Abutment scour ranged from 7.2 to 10.7 ft. The worst-case abutment scour occurred at the 500-year discharge for the right abutment. Pier scour ranged from 7.3 to 8.6 ft. The worst-case pier scour occurred at the 500-year discharge. Additional information on scour depths and depths to armoring are included in the section titled “Scour Results”. Scoured-streambed elevations, based on the calculated scour depths, are presented in tables 1 and 2. A cross-section of the scour computed at the bridge is presented in figure 8. Scour depths were calculated assuming an infinite depth of erosive material and a homogeneous particle-size distribution. It is generally accepted that the Froehlich equation (abutment scour) gives “excessively conservative estimates of scour depths” (Richardson and others, 1995, p. 47). Usually, computed scour depths are evaluated in combination with other information including (but not limited to) historical performance during flood events, the geomorphic stability assessment, existing scour protection measures, and the results of the hydraulic analyses. Therefore, scour depths adopted by VTAOT may differ from the computed values documented herein.

Computation of Feedback Aeroacoustic System by the CE/SE Method

NASA Technical Reports Server (NTRS)

Loh, Ching Y.; Wang, Xiao Y.; Chang, Sin-Chung; Jorgenson, Philip C. E.

2000-01-01

It is well known that due to vortex shedding in high speed flow over cutouts, cavities, and gaps, intense noise may be generated. Strong tonal oscillations occur in a feedback cycle in which the vortices shed from the upstream edge of the cavity convect downstream and impinge on the cavity lip, generating acoustic waves that propagate upstream to excite new vortices. Numerical simulation of such a complicated process requires a scheme that can: (1) resolve acoustic waves with low dispersion and numerical dissipation, (2) handle nonlinear and discontinuous waves (e.g. shocks), and (3) have an effective (near field) nonreflecting boundary condition (NRBC). The new space time conservation element and solution element method, or CE/SE for short, is a numerical method that meets the above requirements.

Strategies for conserving native salmonid populations at risk from nonnative fish invasions: tradeoffs in using barriers to upstream movement

Treesearch

Kurt D. Fausch; Bruce E. Rieman; Michael Young; Jason B. Dunham

2006-01-01

Native salmonid populations in the inland West are often restricted to small isolated habitats at risk from invasion by nonnative salmonids. However, further isolating these populations using barriers to prevent invasions can increase their extinction risk. This monograph reviews the state of knowledge about this tradeoff between invasion and isolation. We present a...

A cis-regulatory module activating transcription in the suspensor contains five cis-regulatory elements

DOE PAGES

Henry, Kelli F.; Kawashima, Tomokazu; Goldberg, Robert B.

2015-03-22

Little is known about the molecular mechanisms by which the embryo proper and suspensor of plant embryos activate specific gene sets shortly after fertilization. We analyzed the upstream region of the Scarlet Runner Bean ( Phaseolus coccineus) G564 gene in order to understand how genes are activated specifically in the suspensor during early embryo development. Previously, we showed that a 54-bp fragment of the G564 upstream region is sufficient for suspensor transcription and contains at least three required cis-regulatory sequences, including the 10-bp motif (5'-GAAAAGCGAA-3'), the 10 bp-like motif (5'-GAAAAACGAA-3'), and Region 2 motif (partial sequence 5'-TTGGT-3'). Here, we usemore » site-directed mutagenesis experiments in transgenic tobacco globularstage embryos to identify two additional cis-regulatory elements within the 54-bp cis-regulatory module that are required for G564 suspensor transcription: the Fifth motif (5'-GAGTTA-3') and a third 10-bp-related sequence (5'-GAAAACCACA-3'). Further deletion of the 54-bp fragment revealed that a 47-bp fragment containing the five motifs (the 10-bp, 10-bp-like, 10-bp-related, Region 2 and Fifth motifs) is sufficient for suspensor transcription, and represents a cis-regulatory module. A consensus sequence for each type of motif was determined by comparing motif sequences shown to activate suspensor transcription. Phylogenetic analyses suggest that the regulation of G564 is evolutionarily conserved. Lastly, a homologous cis-regulatory module was found upstream of the G564 ortholog in the Common Bean (Phaseolus vulgaris), indicating that the regulation of G564 is evolutionarily conserved in closely related bean species.« less

A cis-regulatory module activating transcription in the suspensor contains five cis-regulatory elements

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

Henry, Kelli F.; Kawashima, Tomokazu; Goldberg, Robert B.

Little is known about the molecular mechanisms by which the embryo proper and suspensor of plant embryos activate specific gene sets shortly after fertilization. We analyzed the upstream region of the Scarlet Runner Bean ( Phaseolus coccineus) G564 gene in order to understand how genes are activated specifically in the suspensor during early embryo development. Previously, we showed that a 54-bp fragment of the G564 upstream region is sufficient for suspensor transcription and contains at least three required cis-regulatory sequences, including the 10-bp motif (5'-GAAAAGCGAA-3'), the 10 bp-like motif (5'-GAAAAACGAA-3'), and Region 2 motif (partial sequence 5'-TTGGT-3'). Here, we usemore » site-directed mutagenesis experiments in transgenic tobacco globularstage embryos to identify two additional cis-regulatory elements within the 54-bp cis-regulatory module that are required for G564 suspensor transcription: the Fifth motif (5'-GAGTTA-3') and a third 10-bp-related sequence (5'-GAAAACCACA-3'). Further deletion of the 54-bp fragment revealed that a 47-bp fragment containing the five motifs (the 10-bp, 10-bp-like, 10-bp-related, Region 2 and Fifth motifs) is sufficient for suspensor transcription, and represents a cis-regulatory module. A consensus sequence for each type of motif was determined by comparing motif sequences shown to activate suspensor transcription. Phylogenetic analyses suggest that the regulation of G564 is evolutionarily conserved. Lastly, a homologous cis-regulatory module was found upstream of the G564 ortholog in the Common Bean (Phaseolus vulgaris), indicating that the regulation of G564 is evolutionarily conserved in closely related bean species.« less

A cis-regulatory module activating transcription in the suspensor contains five cis-regulatory elements.

PubMed

Henry, Kelli F; Kawashima, Tomokazu; Goldberg, Robert B

2015-06-01

Little is known about the molecular mechanisms by which the embryo proper and suspensor of plant embryos activate specific gene sets shortly after fertilization. We analyzed the upstream region of the Scarlet Runner Bean (Phaseolus coccineus) G564 gene in order to understand how genes are activated specifically in the suspensor during early embryo development. Previously, we showed that a 54-bp fragment of the G564 upstream region is sufficient for suspensor transcription and contains at least three required cis-regulatory sequences, including the 10-bp motif (5'-GAAAAGCGAA-3'), the 10 bp-like motif (5'-GAAAAACGAA-3'), and Region 2 motif (partial sequence 5'-TTGGT-3'). Here, we use site-directed mutagenesis experiments in transgenic tobacco globular-stage embryos to identify two additional cis-regulatory elements within the 54-bp cis-regulatory module that are required for G564 suspensor transcription: the Fifth motif (5'-GAGTTA-3') and a third 10-bp-related sequence (5'-GAAAACCACA-3'). Further deletion of the 54-bp fragment revealed that a 47-bp fragment containing the five motifs (the 10-bp, 10-bp-like, 10-bp-related, Region 2 and Fifth motifs) is sufficient for suspensor transcription, and represents a cis-regulatory module. A consensus sequence for each type of motif was determined by comparing motif sequences shown to activate suspensor transcription. Phylogenetic analyses suggest that the regulation of G564 is evolutionarily conserved. A homologous cis-regulatory module was found upstream of the G564 ortholog in the Common Bean (Phaseolus vulgaris), indicating that the regulation of G564 is evolutionarily conserved in closely related bean species.

The glnAntrBC operon of Herbaspirillum seropedicae is transcribed by two oppositely regulated promoters upstream of glnA.

PubMed

Schwab, Stefan; Souza, Emanuel M; Yates, Marshall G; Persuhn, Darlene C; Steffens, M Berenice R; Chubatsu, Leda S; Pedrosa, Fábio O; Rigo, Liu U

2007-01-01

Herbaspirillum seropedicae is an endophytic bacterium that fixes nitrogen under microaerophilic conditions. The putative promoter sequences glnAp1 (sigma70-dependent) and glnAp2 (sigma54), and two NtrC-binding sites were identified upstream from the glnA, ntrB and ntrC genes of this microorganism. To study their transcriptional regulation, we used lacZ fusions to the H. seropedicae glnA gene, and the glnA-ntrB and ntrB-ntrC intergenic regions. Expression of glnA was up-regulated under low ammonium, but no transcription activity was detected from the intergenic regions under any condition tested, suggesting that glnA, ntrB and ntrC are co-transcribed from the promoters upstream of glnA. Ammonium regulation was lost in the ntrC mutant strain. A point mutation was introduced in the conserved -25/-24 dinucleotide (GG-->TT) of the putative sigma54-dependent promoter (glnAp2). Contrary to the wild-type promoter, glnA expression with the mutant glnAp2 promoter was repressed in the wild-type strain under low ammonium levels, but this repression was abolished in an ntrC background. Together our results indicate that the H. seropedicae glnAntrBC operon is regulated from two functional promoters upstream from glnA, which are oppositely regulated by the NtrC protein.

Level II scour analysis for Bridge 34 (ROCHTH00210034) on Town Highway 21, crossing the White River, Rochester, Vermont

USGS Publications Warehouse

Wild, Emily C.; Degnan, James

1997-01-01

This report provides the results of a detailed Level II analysis of scour potential at structure ROCHTH00210034 on Town Highway 21 crossing the White River, Rochester, Vermont (figures 1–8). A Level II study is a basic engineering analysis of the site, including a quantitative analysis of stream stability and scour (U.S. Department of Transportation, 1993). Results of a Level I scour investigation also are included in Appendix E of this report. A Level I investigation provides a qualitative geomorphic characterization of the study site. Information on the bridge, obtained from Vermont Agency of Transportation (VTAOT) files, was compiled prior to conducting Level I and Level II analyses and is found in Appendix D.The site is in the Green Mountain section of the New England physiographic province in central Vermont. The 74.8-mi2 drainage area is in a predominantly rural and forested basin. In the vicinity of the study site, the surface cover is suburban on the upstream and downstream left overbanks, though brush prevails along the immediate banks. On the upstream and downstream right overbanks, the surface cover is pasture with brush and trees along the immediate banks.In the study area, the White River has an incised, straight channel with a slope of approximately 0.002 ft/ft, an average channel top width of 102 ft and an average bank height of 5 ft. The channel bed material ranges from sand to cobble with a median grain size (D50) of 74.4 mm (0.244 ft). The geomorphic assessment at the time of the Level I and Level II site visit on July 23, 1996, indicated that the reach was stable.The Town Highway 21 crossing of the White River is a 72-ft-long, two-lane bridge consisting of 70-foot steel stringer span (Vermont Agency of Transportation, written communication, March 22, 1995). The opening length of the structure parallel to the bridge face is 67.0 ft. The bridge is supported by vertical, concrete abutments with wingwalls. The channel is skewed approximately 15 degrees to the opening while the opening-skew-to-roadway is zero degrees.Channel scour, 1.5 ft deeper than the mean thalweg depth was observed along the left abutment and wingwalls during the Level I assessment. Scour countermeasures at the site includes type-1 stone fill (less than 12 inches diameter) along the upstream left bank and the upstream and downstream left road embankments, type-2 (less than 36 inches diameter) along the upstream end of the upstream left wingwall and downstream left bank, and type-3 (less than 48 inches diameter) along the downstream end of the downstream left wingwall. Additional details describing conditions at the site are included in the Level II Summary and Appendices D and E.Scour depths and recommended rock rip-rap sizes were computed using the general guidelines described in Hydraulic Engineering Circular 18 (Richardson and others, 1995). In addition, the incipient roadway-overtopping discharge is analyzed since it has the potential of being the worst-case scour scenario. Total scour at a highway crossing is comprised of three components: 1) long-term streambed degradation; 2) contraction scour (due to accelerated flow caused by a reduction in flow area at a bridge) and; 3) local scour (caused by accelerated flow around piers and abutments). Total scour is the sum of the three components. Equations are available to compute depths for contraction and local scour and a summary of the results of these computations follows.Contraction scour for all modelled discharges was zero. Left abutment scour ranged from 6.8 to 21.2 ft. Right abutment scour ranged from 13.9 to 18.4 ft. The worst-case abutment scour occurred at the 500-year discharge at the left and right abutments. Additional information on scour depths and depths to armoring are included in the section titled “Scour Results”. Scoured-streambed elevations, based on the calculated scour depths, are presented in tables 1 and 2. A cross-section of the scour computed at the bridge is presented in figure 8. Scour depths were calculated assuming an infinite depth of erosive material and a homogeneous particle-size distribution.It is generally accepted that the Froehlich equation (abutment scour) gives “excessively conservative estimates of scour depths” (Richardson and others, 1995, p. 47). Usually, computed scour depths are evaluated in combination with other information including (but not limited to) historical performance during flood events, the geomorphic stability assessment, existing scour protection measures, and the results of the hydraulic analyses. Therefore, scour depths adopted by VTAOT may differ from the computed values documented herein.

Level II scour analysis for Bridge 36 (DUXBTH00040036) on Town Highway 4, crossing Crossett Brook, Duxbury, Vermont

USGS Publications Warehouse

Wild, Emily C.; Degnan, James R.

1997-01-01

This report provides the results of a detailed Level II analysis of scour potential at structure DUXBTH00040036 on Town Highway 4 crossing the Crossett Brook, Duxbury, Vermont (figures 1–8). A Level II study is a basic engineering analysis of the site, including a quantitative analysis of stream stability and scour (U.S. Department of Transportation, 1993). Results of a Level I scour investigation also are included in Appendix E of this report. A Level I investigation provides a qualitative geomorphic characterization of the study site. Information on the bridge, gleaned from Vermont Agency of Transportation (VTAOT) files, was compiled prior to conducting Level I and Level II analyses and is found in Appendix D.The site is in the Green Mountain section of the New England physiographic province in north-central Vermont. The 4.9-mi2 drainage area is in a predominantly rural and forested basin. In the vicinity of the study site, the surface cover on the upstream left overbank is pasture. The upstream and downstream right overbanks are forested. The downstream left overbank is brushland, while the immediate banks have dense woody vegetation.In the study area, the Crossett Brook has an incised, sinuous channel with a slope of approximately 0.006 ft/ft, an average channel top width of 55 ft and an average bank height of 9 ft. The channel bed material ranges from gravel to bedrock with a median grain size (D50) of 51.6 mm (0.169 ft). The geomorphic assessment at the time of the Level I and Level II site visit on July 1, 1996, indicated that the reach was stable.The Town Highway 4 crossing of the Crossett Brook is a 29-ft-long, two-lane bridge consisting of a 26-foot concrete slab span (Vermont Agency of Transportation, written communication, October 13, 1995). The opening length of the structure parallel to the bridge face is 26 ft. The bridge is supported by vertical, concrete abutments with wingwalls. The channel is skewed approximately 35 degrees to the opening while the computed opening-skew-to-roadway is 5 degrees.A scour hole 1.5 ft deeper than the mean thalweg depth was observed along the upstream left wingwall and the right abutment during the Level I assessment. Scour countermeasures at the site includes type-2 stone fill (less than 36 inches diameter) at the upstream end of the upstream left and right wingwalls and the upstream left and right banks and road embankments. Additional details describing conditions at the site are included in the Level II Summary and Appendices D and E.Scour depths and recommended rock rip-rap sizes were computed using the general guidelines described in Hydraulic Engineering Circular 18 (Richardson and others, 1995). Total scour at a highway crossing is comprised of three components: 1) long-term streambed degradation; 2) contraction scour (due to accelerated flow caused by a reduction in flow area at a bridge) and; 3) local scour (caused by accelerated flow around piers and abutments). Total scour is the sum of the three components. Equations are available to compute depths for contraction and local scour and a summary of the results of these computations follows.Contraction scour for all modelled flows ranged from 0.0 to 1.7 ft. The worst-case contraction scour occurred at the 500-year discharge. Left abutment scour ranged from 6.4 to 8.3 ft. Right abutment scour ranged from 6.0 to 7.0 ft. The worst-case left and right abutment scour occurred at the 500-year discharge. Additional information on scour depths and depths to armoring are included in the section titled “Scour Results”. Scoured-streambed elevations, based on the calculated scour depths, are presented in tables 1 and 2. A cross-section of the scour computed at the bridge is presented in figure 8. Scour depths were calculated assuming an infinite depth of erosive material and a homogeneous particle-size distribution.It is generally accepted that the Froehlich equation (abutment scour) gives “excessively conservative estimates of scour depths” (Richardson and others, 1995, p. 47). Usually, computed scour depths are evaluated in combination with other information including (but not limited to) historical performance during flood events, the geomorphic stability assessment, existing scour protection measures, and the results of the hydraulic analyses. Therefore, scour depths adopted by VTAOT may differ from the computed values documented herein.

Level II scour analysis for Bridge 25 (REDSTH00360025) on Town Highway 36, crossing the West Branch Deerfield River, Readsboro, Vermont

USGS Publications Warehouse

Flynn, Robert H.; Burns, Ronda L.

1997-01-01

This report provides the results of a detailed Level II analysis of scour potential at structure REDSTH00360025 on Town Highway 36 crossing the West Branch Deerfield River, Readsboro, Vermont (figures 1–8). A Level II study is a basic engineering analysis of the site, including a quantitative analysis of stream stability and scour (U.S. Department of Transportation, 1993). Results of a Level I scour investigation also are included in Appendix E of this report. A Level I investigation provides a qualitative geomorphic characterization of the study site. Information on the bridge, gleaned from Vermont Agency of Transportation (VTAOT) files, was compiled prior to conducting Level I and Level II analyses and is found in Appendix D. The site is in the Green Mountain section of the New England physiographic province in south-central Vermont. The 14.5-mi2 drainage area is in a predominantly rural and forested basin. In the vicinity of the study site, the surface cover is pasture on the upstream right bank and forest on the upstream left bank. The surface cover on the downstream right and left banks is primarily grass, shrubs and brush. In the study area, the West Branch Deerfield River has an incised, sinuous channel with a slope of approximately 0.02 ft/ft, an average channel top width of 65 ft and an average bank height of 4 ft. The channel bed material ranges from gravel to boulders, with a median grain size (D50) of 117 mm (0.383 ft). The geomorphic assessment at the time of the Level I and Level II site visit on August 1, 1996, indicated that the reach was stable. The Town Highway 36 crossing of the West Branch Deerfield River is a 59-ft-long, two-lane bridge consisting of one 57-foot concrete T-beam span (Vermont Agency of Transportation, written communication, September 28, 1995). The opening length of the structure parallel to the bridge face is 54 ft. The bridge is supported by vertical, concrete abutments with wingwalls. The channel is skewed approximately 50 degrees to the opening while the opening-skew-to-roadway is 30 degrees. During the Level I assessment, a scour hole approximately 2 ft deeper than the mean thalweg depth was observed along the upstream right wingwall and a scour hole approximately 1 ft deeper than the mean thalweg depth was observed along the downstream left wingwall. The scour protection measure at the site was type-2 stone fill (less than 36 inches diameter) at the downstream end of the downstream left wingwall, at the upstream end of the upstream right wingwall, at the downstream end of the right abutment, along the entire base length of the downstream right wingwall, along the upstream right bank and along the downstream left bank. A stone wall was noted along the upstream left bank. Additional details describing conditions at the site are included in the Level II Summary and Appendices D and E. Scour depths and recommended rock rip-rap sizes were computed using the general guidelines described in Hydraulic Engineering Circular 18 (Richardson and others, 1995). Total scour at a highway crossing is comprised of three components: 1) long-term streambed degradation; 2) contraction scour (due to accelerated flow caused by a reduction in flow area at a bridge) and; 3) local scour (caused by accelerated flow around piers and abutments). Total scour is the sum of the three components. Equations are available to compute depths for contraction and local scour and a summary of the results of these computations follows. Contraction scour for all modelled flows ranged from 0.0 to 0.6 ft. The worst-case contraction scour occurred at the incipient-overtopping discharge. Abutment scour ranged from 15.1 to 16.3 ft along the left abutment and from 7.4 to 9.2 ft along the right abutment. The worst-case abutment scour occurred at the incipient-overtopping and 500-year discharges for the left abutment and at the 500-year discharge for the right abutment. Additional information on scour depths and depths to armoring are included in the section titled “Scour Results”. Scoured-streambed elevations, based on the calculated scour depths, are presented in tables 1 and 2. A cross-section of the scour computed at the bridge is presented in figure 8. Scour depths were calculated assuming an infinite depth of erosive material and a homogeneous particle-size distribution. It is generally accepted that the Froehlich equation (abutment scour) gives “excessively conservative estimates of scour depths” (Richardson and others, 1995, p. 47). Usually, computed scour depths are evaluated in combination with other information including (but not limited to) historical performance during flood events, the geomorphic stability assessment, existing scour protection measures, and the results of the hydraulic analyses. Therefore, scour depths adopted by VTAOT may differ from the computed values documented herein.

Level II scour analysis for Bridge 16 (BURKTH00070016) on Town Highway 7, crossing Dish Mill Brook, Burke, Vermont

USGS Publications Warehouse

Burns, Ronda L.; Severance, Tim

1997-01-01

This report provides the results of a detailed Level II analysis of scour potential at structure BURKTH00070016 on Town Highway 7 crossing Dish Mill Brook, Burke, Vermont (figures 1–8). A Level II study is a basic engineering analysis of the site, including a quantitative analysis of stream stability and scour (U.S. Department of Transportation, 1993). Results of a Level I scour investigation also are included in Appendix E of this report. A Level I investigation provides a qualitative geomorphic characterization of the study site. Information on the bridge, gleaned from Vermont Agency of Transportation (VTAOT) files, was compiled prior to conducting Level I and Level II analyses and is found in Appendix D. The site is in the White Mountain section of the New England physiographic province in northeastern Vermont. The 6.0-mi2 drainage area is in a predominantly rural and forested basin. In the vicinity of the study site, the surface cover is forest except on the left bank upstream which is brushland. In the study area, Dish Mill Brook has an incised, sinuous channel with a slope of approximately 0.04 ft/ft, an average channel top width of 40 ft and an average bank height of 6 ft. The channel bed material ranges from sand to boulder with a median grain size (D50) of 94.1 mm (0.309 ft). The geomorphic assessment at the time of the Level I and Level II site visit on August 7, 1995, indicated that the reach was stable. The Town Highway 7 crossing of Dish Mill Brook is a 28-ft-long, two-lane bridge consisting of one 24-foot steel-beam span (Vermont Agency of Transportation, written communication, March 24, 1995). The opening length of the structure parallel to the bridge face is 24.8 ft. The bridge is supported by vertical, concrete abutments with wingwalls. The channel is skewed approximately 35 degrees to the opening while the computed opening-skew-to-roadway is 35 degrees. A scour hole 1.0 ft deeper than the mean thalweg depth was observed along the left and right abutments during the Level I assessment. In front of the upstream and downstream left wingwalls the scour depth was only 0.5 ft, while in front of the downstream right wingwall it was 0.75 ft and in front of the upstream right wingwall it was 0.3 ft. The scour countermeasures at the site include type-1 stone fill (less than 12 inches diameter) at the downstream end of the right abutment and along the downstream right wingwall. Type-2 stone fill (less than 36 inches diameter) is along the upstream left bank, the upstream and downstream left wingwalls, and at the upstream end of the upstream right wingwall. Additional details describing conditions at the site are included in the Level II Summary and Appendices D and E. Scour depths and recommended rock rip-rap sizes were computed using the general guidelines described in Hydraulic Engineering Circular 18 (Richardson and others, 1995) for the 100- and 500-year discharges. In addition, the incipient roadway-overtopping discharge is determined and analyzed as another potential worst-case scour scenario. Total scour at a highway crossing is comprised of three components: 1) long-term streambed degradation; 2) contraction scour (due to accelerated flow caused by a reduction in flow area at a bridge) and; 3) local scour (caused by accelerated flow around piers and abutments). Total scour is the sum of the three components. Equations are available to compute depths for contraction and local scour and a summary of the results of these computations follows. Contraction scour for all modelled flows ranged from 0.0 to 0.5 ft. The worst-case contraction scour occurred at the 500-year discharge. Abutment scour ranged from 6.7 to 9.3 ft. The worst-case abutment scour occurred at the 500-year discharge for the left abutment and at the incipient road-overtopping discharge for the right abutment. Additional information on scour depths and depths to armoring are included in the section titled “Scour Results”. Scoured-streambed elevations, based on the calculated scour depths, are presented in tables 1 and 2. A cross-section of the scour computed at the bridge is presented in figure 8. Scour depths were calculated assuming an infinite depth of erosive material and a homogeneous particle-size distribution. It is generally accepted that the Froehlich equation (abutment scour) gives “excessively conservative estimates of scour depths” (Richardson and others, 1995, p. 47). Usually, computed scour depths are evaluated in combination with other information including (but not limited to) historical performance during flood events, the geomorphic stability assessment, existing scour protection measures, and the results of the hydraulic analyses. Therefore, scour depths adopted by VTAOT may differ from the computed values documented herein.

Level II scour analysis for Bridge 15 (BOLTTH00150015) on Town Highway 15, crossing Joiner Brook, Bolton, Vermont

USGS Publications Warehouse

Burns, Ronda L.; Wild, Emily C.

1998-01-01

This report provides the results of a detailed Level II analysis of scour potential at structure BOLTTH00150015 on Town Highway 15 crossing Joiner Brook, Bolton, Vermont (figures 1–8). A Level II study is a basic engineering analysis of the site, including a quantitative analysis of stream stability and scour (FHWA, 1993). Results of a Level I scour investigation also are included in appendix E of this report. A Level I investigation provides a qualitative geomorphic characterization of the study site. Information on the bridge, gleaned from Vermont Agency of Transportation (VTAOT) files, was compiled prior to conducting Level I and Level II analyses and is found in appendix D. The site is in the Green Mountain section of the New England physiographic province in north central Vermont. The 9.6-mi2 drainage area is in a predominantly rural and forested basin. In the vicinity of the study site, the surface cover is pasture (lawn) downstream of the bridge and on the upstream right bank. The surface cover on the upstream left bank is shrub and brushland. In the study area, Joiner Brook has an incised, straight channel with a slope of approximately 0.01 ft/ft, an average channel top width of 61 ft and an average bank height of 7 ft. The channel bed material ranges from gravel to cobble with a median grain size (D50) of 43.6 mm (0.143 ft). The geomorphic assessment at the time of the Level I and Level II site visit on June 27, 1996, indicated that the reach was stable. The Town Highway 15 crossing of Joiner Brook is a 39-ft-long, two-lane bridge consisting of one 36-foot concrete tee-beam span (Vermont Agency of Transportation, written communication, November 3, 1995). The opening length of the structure parallel to the bridge face is 34.6 ft. The bridge is supported by nearly vertical, concrete abutments with wingwalls. The channel is skewed approximately 10 degrees to the opening while the opening-skew-to-roadway is zero degrees. A scour hole 1.5 ft deeper than the mean thalweg depth was observed at the downstream end of the right abutment and along the downstream right wingwall during the Level I assessment. A second scour hole 1.2 ft deeper than the mean thalweg depth was observed at the upstream end of the left abutment and along the upstream left wingwall. The left abutment footing is exposed in the area of the scour hole. Scour protection measures at the site included type-1 stone fill (less than 12 inches diameter) at the upstream end of the upstream left wingwall and at the downstream end of the downstream right wingwall and type-2 stone fill (less than 36 inches diameter) along the downstream left bank. There is also type-3 stone fill (less than 48 inches diameter) along the upstream left and right banks. Additional details describing conditions at the site are included in the Level II Summary and appendices D and E. Scour depths and recommended rock rip-rap sizes were computed using the general guidelines described in Hydraulic Engineering Circular 18 (Richardson and Davis, 1995) for the 100- and 500-year discharges. In addition, the incipient roadway-overtopping discharge was determined and analyzed as another potential worst-case scour scenario. Total scour at a highway crossing is comprised of three components: 1) long-term streambed degradation; 2) contraction scour (due to accelerated flow caused by a reduction in flow area at a bridge) and; 3) local scour (caused by accelerated flow around piers and abutments). Total scour is the sum of the three components. Equations are available to compute depths for contraction and local scour and a summary of the results of these computations follows. Contraction scour for all modelled flows ranged from 0.8 to 3.5 ft. The worst-case contraction scour occurred at the 500-year discharge. Abutment scour ranged from 6.9 to 15.1 ft. The worst-case abutment scour occurred at the incipient roadway-overtopping discharge. Additional information on scour depths and depths to armoring are included in the section titled “Scour Results.” Scoured-streambed elevations, based on the calculated scour depths, are presented in tables 1 and 2. A cross-section of the scour computed at the bridge is presented in figure 8. Scour depths were calculated assuming an infinite depth of erosive material and a homogeneous particle-size distribution. It is generally accepted that the Froehlich equation (abutment scour) gives “excessively conservative estimates of scour depths” (Richardson and Davis, 1995, p. 46). Usually, computed scour depths are evaluated in combination with other information including (but not limited to) historical performance during flood events, the geomorphic stability assessment, existing scour protection measures, and the results of the hydraulic analyses. Therefore, scour depths adopted by VTAOT may differ from the computed values documented herein.

Level II scour analysis for Bridge 26 (ROYATH00540026) on Town Highway 54, crossing Broad Brook, Royalton, Vermont

USGS Publications Warehouse

Burns, Ronda L.; Weber, Matthew A.

1997-01-01

This report provides the results of a detailed Level II analysis of scour potential at structure ROYATH00540026 on Town Highway 54 crossing Broad Brook, Royalton, Vermont (figures 1–8). A Level II study is a basic engineering analysis of the site, including a quantitative analysis of stream stability and scour (U.S. Department of Transportation, 1993). Results of a Level I scour investigation also are included in Appendix E of this report. A Level I investigation provides a qualitative geomorphic characterization of the study site. Information on the bridge, gleaned from Vermont Agency of Transportation (VTAOT) files, was compiled prior to conducting Level I and Level II analyses and is found in Appendix D. The site is in the New England Upland section of the New England physiographic province in central Vermont. The 11.9-mi2 drainage area is in a predominantly rural and forested basin. In the vicinity of the study site, the surface cover on the left bank upstream and downstream is pasture with trees and brush on the immediate banks. The right bank, upstream and downstream of the bridge, is forested. In the study area, Broad Brook has an incised, sinuous channel with a slope of approximately 0.01 ft/ft, an average channel top width of 37 ft and an average bank height of 4 ft. The channel bed material ranges from sand to boulders with a median grain size (D50) of 66.3 mm (0.218 ft). The geomorphic assessment at the time of the Level I site visit on April 13, 1995 and the Level II site visit on July 11, 1996, indicated that the reach was stable. The Town Highway 54 crossing of Broad Brook is a 29-ft-long, one-lane bridge consisting of one 24-foot steel-beam span with a timber deck (Vermont Agency of Transportation, written communication, March 23, 1995). The opening length of the structure parallel to the bridge face is 23.3 ft. The bridge is supported by a vertical, concrete face laid-up stone abutment with concrete wingwalls on the left and a laid-up stone abutment on the right. The channel is skewed approximately 20 degrees to the opening while the opening-skew-to-roadway is zero degrees. A scour hole 1.0 ft deeper than the mean thalweg depth was observed along the downstream end of the right abutment during the Level I assessment. Also, at the upstream end of the left abutment, the footing is exposed 0.5 ft. The scour protection measures at the site included type-2 stone fill (less than 36 inches diameter) along the upstream left bank, at the upstream end of the upstream left wingwall, along the entire length of the downstream left wingwall, and at the upstream end of the right abutment. Additional details describing conditions at the site are included in the Level II Summary and Appendices D and E. Scour depths and recommended rock rip-rap sizes were computed using the general guidelines described in Hydraulic Engineering Circular 18 (Richardson and others, 1995). Total scour at a highway crossing is comprised of three components: 1) long-term streambed degradation; 2) contraction scour (due to accelerated flow caused by a reduction in flow area at a bridge) and; 3) local scour (caused by accelerated flow around piers and abutments). Total scour is the sum of the three components. Equations are available to compute depths for contraction and local scour and a summary of the results of these computations follows. Contraction scour for all modelled flows ranged from 0.0 to 1.4 ft. The worst-case contraction scour occurred at the incipient roadway-overtopping discharge, which was less than the 100-year discharge. Abutment scour ranged from 2.2 to 7.4 ft on the left and from 14.7 to 17.7 ft on the right. The worst-case abutment scour occurred at the incipient roadway-overtopping discharge for the left and at the 500-year discharge for the right. Additional information on scour depths and depths to armoring are included in the section titled “Scour Results”. Scoured-streambed elevations, based on the calculated scour depths, are presented in tables 1 and 2. A cross-section of the scour computed at the bridge is presented in figure 8. Scour depths were calculated assuming an infinite depth of erosive material and a homogeneous particle-size distribution. It is generally accepted that the Froehlich equation (abutment scour) gives “excessively conservative estimates of scour depths” (Richardson and others, 1995, p. 47). Usually, computed scour depths are evaluated in combination with other information including (but not limited to) historical performance during flood events, the geomorphic stability assessment, existing scour protection measures, and the results of the hydraulic analyses. Therefore, scour depths adopted by VTAOT may differ from the computed values documented herein.

Reducing Urban Greenhouse Gas Footprints.

PubMed

Pichler, Peter-Paul; Zwickel, Timm; Chavez, Abel; Kretschmer, Tino; Seddon, Jessica; Weisz, Helga

2017-11-07

Cities are economically open systems that depend on goods and services imported from national and global markets to satisfy their material and energy requirements. Greenhouse Gas (GHG) footprints are thus a highly relevant metric for urban climate change mitigation since they not only include direct emissions from urban consumption activities, but also upstream emissions, i.e. emissions that occur along the global production chain of the goods and services purchased by local consumers. This complementary approach to territorially-focused emission accounting has added critical nuance to the debate on climate change mitigation by highlighting the responsibility of consumers in a globalized economy. Yet, city officials are largely either unaware of their upstream emissions or doubtful about their ability to count and control them. This study provides the first internationally comparable GHG footprints for four cities (Berlin, Delhi NCT, Mexico City, and New York metropolitan area) applying a consistent method that can be extended to other global cities using available data. We show that upstream emissions from urban household consumption are in the same order of magnitude as cities' overall territorial emissions and that local policy leverage to reduce upstream emissions is larger than typically assumed.

Identification and management of microbial contaminations in a surface drinking water source.

PubMed

Aström, J; Pettersson, T J R; Stenström, T A

2007-01-01

Microbial contamination of surface waters constitutes a health risk for drinking water consumers which may be lowered by closing the raw water intake. We have evaluated microbial discharge events reported in the river Göta älv, which is used for raw water supply to the city of Göteborg. Elevated levels of faecal indicator bacteria were observed during periods of closed raw water intake. High bacteria levels were, however, also occasionally detected during periods of open intake, probably as a result of microbial discharge far upstream in the river which may be difficult to predict and manage by closing the intake. Accumulated upstream precipitations, resulting in surface runoff and wastewater contaminations in the catchment, correlated positively with the levels of total coliforms, E. coli, intestinal enterococci and sulfite-reducing clostridia. Levels of faecal indicator organisms were negatively correlated to the water temperature due to enhanced survival at lower temperatures. Wastewater discharges from a municipality located just upstream of the water intake resulted in elevated E. coli concentrations downstream at the raw water intake for Göteborg. To improve the prediction of microbial contaminations within the river Göta älv, monitoring data on turbidity and upstream precipitation are of particular importance.

Neglected sources of pharmaceuticals in river water--footprints of a Reggae festival.

PubMed

Daneshvar, Atlasi; Svanfelt, Jesper; Kronberg, Leif; Weyhenmeyer, Gesa A

2012-02-01

Wastewater treatment plants (WWTPs) are commonly considered as the main source of pharmaceuticals in surface waters. Here, however, we show that an open-air festival, attracting approximately 10,000 visitors per year at the shores of River Fyris upstream of Uppsala WWTP, can temporarily result in a higher pharmaceutical input into the river water than the WWTP. Studying the influence of Uppsala Reggae festival on the occurrence of ten commonly used acidic and basic pharmaceuticals upstream, in the effluent, and downstream of the Uppsala WWTP, we found that occasional heavy rainfalls during the festival in 2008 severely increased the mass flows of all pharmaceuticals at the WWTP upstream site. Also, strong increases in ammonium (210-fold), nitrate (21-fold), and total nitrogen (21-fold) mass flows were observed. The pharmaceutical mass flows at the upstream site were up to 3.4 times higher than those observed in the WWTP effluent. In contrast, in 2009, the festival was not accompanied with rainfalls and no major additional input of pharmaceuticals and nitrogen was observed. The findings of this study give new insights into risk assessments and are relevant for monitoring programmes.

Reduced-order modellin for high-pressure transient flow of hydrogen-natural gas mixture

NASA Astrophysics Data System (ADS)

Agaie, Baba G.; Khan, Ilyas; Alshomrani, Ali Saleh; Alqahtani, Aisha M.

2017-05-01

In this paper the transient flow of hydrogen compressed-natural gas (HCNG) mixture which is also referred to as hydrogen-natural gas mixture in a pipeline is numerically computed using the reduced-order modelling technique. The study on transient conditions is important because the pipeline flows are normally in the unsteady state due to the sudden opening and closure of control valves, but most of the existing studies only analyse the flow in the steady-state conditions. The mathematical model consists in a set of non-linear conservation forms of partial differential equations. The objective of this paper is to improve the accuracy in the prediction of the HCNG transient flow parameters using the Reduced-Order Modelling (ROM). The ROM technique has been successfully used in single-gas and aerodynamic flow problems, the gas mixture has not been done using the ROM. The study is based on the velocity change created by the operation of the valves upstream and downstream the pipeline. Results on the flow characteristics, namely the pressure, density, celerity and mass flux are based on variations of the mixing ratio and valve reaction and actuation time; the ROM computational time cost advantage are also presented.

Human homolog of the mouse sperm receptor

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

Chamberlin, M.E.; Dean, J.

1990-08-01

The human zona pellucida, composed of three glycoproteins (ZP1, ZP2, and ZP3), forms an extracellular matrix that surrounds ovulated eggs and mediates species-specific fertilization. The genes that code for at least two of the zona proteins (ZP2 and ZP3) cross-hybridize with other mammalian DNA. The recently characterized mouse sperm receptor gene (Zp-3) was used to isolate its human homolog. The human homolog spans {approx}18.3 kilobase pairs (kbp) (compared to 8.6 kbp for the mouse gene) and contains eight exons, the sizes of which are strictly conserved between the two species. Four short (8-15 bp) sequences within the first 250 bpmore » of the 5{prime} flanking region in the human Zp-3 homolog are also present upstream of mouse Zp-3. These elements may modulate oocyte-specific gene expression. By using the polymerase chain reaction, a full-length cDNA of human ZP3 was isolated from human ovarian poly(A){sup +} RNA and used to deduce the structure of human ZP3 mRNA. Certain features of the human and mouse ZP3 transcripts are conserved. Both have unusually short 5{prime} and 3{prime} untranslated regions, both contain a single open reading frame that is 74% identical, and both code for 424 amino acid polypeptides that are 67% the same. The similarity between the two proteins may define domains that are important in maintaining the structural integrity of the zona pellucida, while the differences may play a role in mediating the species-specific events of mammalian fertilization.« less

Prioritizing conservation activities using reserve site selection methods and population viability analysis.

PubMed

Newbold, Stephen C; Siikamäki, Juha

2009-10-01

In recent years a large literature on reserve site selection (RSS) has developed at the interface between ecology, operations research, and environmental economics. Reserve site selection models use numerical optimization techniques to select sites for a network of nature reserves for protecting biodiversity. In this paper, we develop a population viability analysis (PVA) model for salmon and incorporate it into an RSS framework for prioritizing conservation activities in upstream watersheds. We use spawner return data for three closely related salmon stocks in the upper Columbia River basin and estimates of the economic costs of watershed protection from NOAA to illustrate the framework. We compare the relative cost-effectiveness of five alternative watershed prioritization methods, based on various combinations of biological and economic information. Prioritization based on biological benefit-economic cost comparisons and accounting for spatial interdependencies among watersheds substantially outperforms other more heuristic methods. When using this best-performing prioritization method, spending 10% of the cost of protecting all upstream watersheds yields 79% of the biological benefits (increase in stock persistence) from protecting all watersheds, compared to between 20% and 64% for the alternative methods. We also find that prioritization based on either costs or benefits alone can lead to severe reductions in cost-effectiveness.

Designing synthetic RNAs to determine the relevance of structural motifs in picornavirus IRES elements

NASA Astrophysics Data System (ADS)

Fernandez-Chamorro, Javier; Lozano, Gloria; Garcia-Martin, Juan Antonio; Ramajo, Jorge; Dotu, Ivan; Clote, Peter; Martinez-Salas, Encarnacion

2016-04-01

The function of Internal Ribosome Entry Site (IRES) elements is intimately linked to their RNA structure. Viral IRES elements are organized in modular domains consisting of one or more stem-loops that harbor conserved RNA motifs critical for internal initiation of translation. A conserved motif is the pyrimidine-tract located upstream of the functional initiation codon in type I and II picornavirus IRES. By computationally designing synthetic RNAs to fold into a structure that sequesters the polypyrimidine tract in a hairpin, we establish a correlation between predicted inaccessibility of the pyrimidine tract and IRES activity, as determined in both in vitro and in vivo systems. Our data supports the hypothesis that structural sequestration of the pyrimidine-tract within a stable hairpin inactivates IRES activity, since the stronger the stability of the hairpin the higher the inhibition of protein synthesis. Destabilization of the stem-loop immediately upstream of the pyrimidine-tract also decreases IRES activity. Our work introduces a hybrid computational/experimental method to determine the importance of structural motifs for biological function. Specifically, we show the feasibility of using the software RNAiFold to design synthetic RNAs with particular sequence and structural motifs that permit subsequent experimental determination of the importance of such motifs for biological function.

The Effect of Upstream Vane Wakes on Annular Diffuser Flows

NASA Astrophysics Data System (ADS)

Cherry, Erica; Padilla, Angelina; Elkins, Christopher; Eaton, John

2008-11-01

Experiments were performed to determine the sensitivity to inlet conditions of the flow in two annular diffusers. One of the diffusers was a conservative design typical of a diffuser directly upstream of the combustor in a jet engine. The other had the same length and inlet shape as the first diffuser but a larger area ratio and was meant to operate on the verge of separation. Each diffuser was connected to two different inlets, one containing a fully-developed channel flow, the other containing wakes from a row of airfoils. Three-component velocity measurements were taken on the flow in each inlet/diffuser combination using Magnetic Resonance Velocimetry. Results will be presented on the 3D velocity fields in the two diffusers and the effect of the airfoil wakes on separation and secondary flows.

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

King, David A.

Oak Ridge Associated Universities (ORAU), under the Oak Ridge Institute for Science and Education (ORISE) contract, collected split surface water samples with Nuclear Fuel Services (NFS) representatives on August 21, 2013. Representatives from the U.S. Nuclear Regulatory Commission (NRC) and the Tennessee Department of Environment and Conservation were also in attendance. Samples were collected at four surface water stations, as required in the approved Request for Technical Assistance number 11-018. These stations included Nolichucky River upstream (NRU), Nolichucky River downstream (NRD), Martin Creek upstream (MCU), and Martin Creek downstream (MCD). Both ORAU and NFS performed gross alpha and gross betamore » analyses, and the comparison of results using the duplicate error ratio (DER), also known as the normalized absolute difference, are tabulated. All DER values were less than 3 and results are consistent with low (e.g., background) concentrations.« less

Assessing dissolved carbon transport and transformation along an estuarine river with stable isotope analyses

NASA Astrophysics Data System (ADS)

He, Songjie; Xu, Y. Jun

2017-10-01

Estuaries play an important role in the dynamics of dissolved carbon from rivers to coastal oceans. However, our knowledge of dissolved carbon transport and transformation in mixing zones of the world's coastal rivers is still limited. This study aims to determine how dissolved inorganic carbon (DIC) and dissolved organic carbon (DOC) concentrations and stable isotopes (δ13CDIC and δ13CDOC) change along an 88-km long estuarine river, the Calcasieu River in Louisiana, southern USA, with salinity ranging from 0.02 to 21.92. The study is expected to elucidate which processes most likely control carbon dynamics in a freshwater-saltwater mixing system, and to evaluate the net metabolism of this estuary. Between May 2015 and February 2016, water samples were collected and in-situ measurements on ambient water conditions were performed during five field trips at six sites from upstream to downstream of the Calcasieu River, which enters the Northern Gulf of Mexico (NGOM). The DIC concentration and δ13CDIC increased rapidly with increasing salinity in the mixing zone. The average DIC concentration and δ13CDIC at the site closest to the NGOM (site 6) were 1.31 mM and -6.34‰, respectively, much higher than those at the site furthest upstream (site 1, 0.42 mM and -20.83‰). The DIC concentrations appeared to be largely influenced by conservative mixing, while high water temperature may have played a role in deviating DIC concentration from the conservative line due likely to increased respiration and decomposition. The δ13CDIC values were close to those suggested by the conservative mixing model for May, June and November, but lower than those for July and February, suggesting that an estuarine river can fluctuate from a balanced to a heterotrophic system (i.e., production/respiration (P/R) < 1) seasonally. Unlike the DIC longitudinal trend, the DOC concentrations in the river estuary decreased from upstream to downstream, but to a much smaller degree. The DOC concentrations consistently showed a deviation from those suggested by the conservative mixing model, which may have been a consequence of in-stream photosynthesis. This river estuary consistently showed depleted δ13CDOC values (i.e., from -30.56‰ to -25.92‰), suggesting that the DOC source in the mixing zone was highly terrestrially derived. However, in this relatively small isotopic range, δ13CDOC alone has limitations in differentiating carbon produced by aquatic photosynthesis from carbon produced by terrestrial photosynthesis in a river-ocean continuum.

Road crossing designs and their impact on fish assemblages of Great Plains streams

USGS Publications Warehouse

Bouska, Wesley W.; Paukert, Craig P.

2010-01-01

A mark-recapture field study was conducted to determine fish passage at 5 concrete box culverts and 5 low-water crossings (concrete slabs vented by culverts) as well as 10 control sites (below a natural riffle) in Flint Hills streams of northeastern Kansas. Additionally, we tested the upstream passage of four fish species native to Great Plains streams (Topeka shiner Notropis topeka, green sunfish Lepomis cyanellus, red shiner Cyprinella lutrensis, and southern redbelly dace Phoxinus erythrogaster) through three simulated crossing designs (box culverts, round corrugated culverts, and natural rock riffles) at water velocities of 0.1 to 1.1 m/s in an experimental stream. The field study indicated that cyprinids were twice as likely to move upstream of box culverts than low-water crossings and 1.4 times as likely to move upstream of control reaches than any crossing type. The best models indicated that the proportion of cyprinids that moved upstream increased with decreased culvert slope and length, perching, and increased culvert width. Our controlled experiment indicated that fish can move through velocities up to 1.1 m/s in a 1.86-m simulated stream and that the proportion of fish that moved upstream did not differ among crossing designs for southern redbelly dace, green sunfish, or Topeka shiner; however, natural rock riffles had lower proportional movements (mean = 0.19) than the box (0.38) or corrugated culvert designs (0.43) for red shiners. Water velocity did not affect the proportional upstream movement of any species except that of Topeka shiners, which increased with water velocity. Crossing design alone may not determine fish passage, and water velocities up to 1.1 m/s may not affect the passage of many Great Plains fishes. Barriers to fish movement may be the result of other factors (e.g., perching, slope, and crossing length). The use of properly designed and installed crossings has promise in conserving Great Plains stream fishes.

The conserved upstream region of lscB/C determines expression of different levansucrase genes in plant pathogen Pseudomonas syringae

PubMed Central

2014-01-01

Background Pseudomonas syringae pv. glycinea PG4180 is an opportunistic plant pathogen which causes bacterial blight of soybean plants. It produces the exopolysaccharide levan by the enzyme levansucrase. Levansucrase has three gene copies in PG4180, two of which, lscB and lscC, are expressed while the third, lscA, is cryptic. Previously, nucleotide sequence alignments of lscB/C variants in various P. syringae showed that a ~450-bp phage-associated promoter element (PAPE) including the first 48 nucleotides of the ORF is absent in lscA. Results Herein, we tested whether this upstream region is responsible for the expression of lscB/C and lscA. Initially, the transcriptional start site for lscB/C was determined. A fusion of the PAPE with the ORF of lscA (lscB UpN A) was generated and introduced to a levan-negative mutant of PG4180. Additionally, fusions comprising of the non-coding part of the upstream region of lscB with lscA (lscB Up A) or the upstream region of lscA with lscB (lscA Up B) were generated. Transformants harboring the lscB UpN A or the lscB Up A fusion, respectively, showed levan formation while the transformant carrying lscA Up B did not. qRT-PCR and Western blot analyses showed that lscB UpN A had an expression similar to lscB while lscB Up A had a lower expression. Accuracy of protein fusions was confirmed by MALDI-TOF peptide fingerprinting. Conclusions Our data suggested that the upstream sequence of lscB is essential for expression of levansucrase while the N-terminus of LscB mediates an enhanced expression. In contrast, the upstream region of lscA does not lead to expression of lscB. We propose that lscA might be an ancestral levansucrase variant upstream of which the PAPE got inserted by potentially phage-mediated transposition events leading to expression of levansucrase in P. syringae. PMID:24670199

Consequences of intravascular lymphatic valve properties: a study of contraction timing in a multi-lymphangion model

PubMed Central

Macaskill, Charlie; Davis, Michael J.; Moore, James E.

2016-01-01

The observed properties of valves in collecting lymphatic vessels include transmural pressure-dependent bias to the open state and hysteresis. The bias may reduce resistance to flow when the vessel is functioning as a conduit. However, lymphatic pumping implies a streamwise increase in mean pressure across each valve, suggesting that the bias is then potentially unhelpful. Lymph pumping by a model of several collecting lymphatic vessel segments (lymphangions) in series, which incorporated these properties, was investigated under conditions of adverse pressure difference while varying the refractory period between active muscular contractions and the inter-lymphangion contraction delay. It was found that many combinations of the timing parameters and the adverse pressure difference led to one or more intermediate valves remaining open instead of switching between open and closed states during repetitive contraction cycles. Cyclic valve switching was reliably indicated if the mean pressure in a lymphangion over a cycle was higher than that in the lymphangion upstream, but either lack of or very brief valve closure could cause mean pressure to be lower downstream. Widely separated combinations of refractory period and delay time were found to produce the greatest flow-rate for a given pressure difference. The efficiency of pumping was always maximized by a long refractory period and lymphangion contraction starting when the contraction of the lymphangion immediately upstream was peaking. By means of an ex vivo experiment, it was verified that intermediate valves in a chain of pumping lymphangions can remain open, while the lymphangions on either side of the open valve continue to execute contractions. PMID:26747501

50 CFR 36.39 - Public use.

Code of Federal Regulations, 2012 CFR

2012-10-01

..., and Swanson Lakes are only open for sport ice fishing. Andy Simons Unit Emerald Lake Green Lake Harvey... sport ice fishing. South of Sterling Highway Headquarters Lake is restricted to administrative use only..., Chickaloon (upstream of river mile 7.5), Killey, and Fox Rivers. (v) A “no-wake” restriction applies to...

50 CFR 36.39 - Public use.

Code of Federal Regulations, 2014 CFR

2014-10-01

..., and Swanson Lakes are only open for sport ice fishing. Andy Simons Unit Emerald Lake Green Lake Harvey... sport ice fishing. South of Sterling Highway Headquarters Lake is restricted to administrative use only..., Chickaloon (upstream of river mile 7.5), Killey, and Fox Rivers. (v) A “no-wake” restriction applies to...

50 CFR 36.39 - Public use.

Code of Federal Regulations, 2013 CFR

2013-10-01

..., and Swanson Lakes are only open for sport ice fishing. Andy Simons Unit Emerald Lake Green Lake Harvey... sport ice fishing. South of Sterling Highway Headquarters Lake is restricted to administrative use only..., Chickaloon (upstream of river mile 7.5), Killey, and Fox Rivers. (v) A “no-wake” restriction applies to...

40 CFR 63.323 - Test methods and monitoring.

Code of Federal Regulations, 2012 CFR

2012-07-01

... downstream from any flow disturbance such as a bend, expansion, contraction, or outlet; downstream from no other inlet; and 2 stack or duct diameters upstream from any flow disturbance such as a bend, expansion... monitoring by inserting the colorimetric detector or PCE gas analyzer tube into the open space above the...

40 CFR 63.323 - Test methods and monitoring.

Code of Federal Regulations, 2014 CFR

2014-07-01

... downstream from any flow disturbance such as a bend, expansion, contraction, or outlet; downstream from no other inlet; and 2 stack or duct diameters upstream from any flow disturbance such as a bend, expansion... monitoring by inserting the colorimetric detector or PCE gas analyzer tube into the open space above the...

40 CFR 63.323 - Test methods and monitoring.

Code of Federal Regulations, 2013 CFR

2013-07-01

... downstream from any flow disturbance such as a bend, expansion, contraction, or outlet; downstream from no other inlet; and 2 stack or duct diameters upstream from any flow disturbance such as a bend, expansion... monitoring by inserting the colorimetric detector or PCE gas analyzer tube into the open space above the...

Biodegradation of 17β-Estradiol, Estrone and Testosterone in Stream Sediments

NASA Astrophysics Data System (ADS)

Bradley, P. M.; Chapelle, F. H.; Barber, L. B.; McMahon, P. B.; Gray, J. L.; Kolpin, D. W.

2009-12-01

The potentials for in situ biodegradation of 17β-estradiol (E2), estrone (E1), and testosterone (T) were investigated in three, hydrologically-distinct, WWTP-impacted streams in the United States. Relative differences in the mineralization of [4-14C] substrates were assessed in oxic microcosms containing sediment or water-only from locations upstream and downstream of the WWTP outfall in each system. Upstream samples provided insight into the biodegradative potential of sediment microbial communities that were not under the immediate impact of WWTP effluent. Upstream sediment from all three systems demonstrated significant mineralization of the “A” ring of E2, E1 and T, with the potential of T biodegradation consistently greater than of E2 and no systematic difference in the potentials of E2 and E1. Downstream samples provided insight into the impacts of effluent on reproductive hormone biodegradation. Significant “A” ring mineralization was also observed in downstream sediment, with the potentials for E1 and T mineralization being substantially depressed relative to upstream samples. In marked contrast, the potentials for E2 mineralization immediately downstream of the WWTP outfalls were more than double that of upstream samples. E2 mineralization was also observed in water, albeit at insufficient rate to prevent substantial downstream transport in the water column. The results of this study indicate that, in combination with sediment sorption processes which effectively scavenge hydrophobic contaminants from the water column and immobilize them in the vicinity of the WWTP outfall, aerobic biodegradation of reproductive hormones can be an environmentally important mechanism for non-conservative (destructive) attenuation of hormonal endocrine disruptors in effluent-impacted streams.

50 CFR Table 3 (south) to Part 660... - Non-Trawl Rockfish Conservation Areas and Trip Limits for Open Access Gears South of 40°10′ N. Lat.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 50 Wildlife and Fisheries 13 2014-10-01 2014-10-01 false Non-Trawl Rockfish Conservation Areas and Trip Limits for Open Access Gears South of 40°10ⲠN. Lat. 3 Table 3 (South) to Part 660, Subpart F Wildlife and Fisheries FISHERY CONSERVATION AND MANAGEMENT, NATIONAL OCEANIC AND ATMOSPHERIC ADMINISTRATION...

50 CFR Table 3 (north) to Part 660... - Non-Trawl Rockfish Conservation Areas and Trip Limits for Open Access Gears North of 40°10′ N. Lat.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 50 Wildlife and Fisheries 13 2014-10-01 2014-10-01 false Non-Trawl Rockfish Conservation Areas and Trip Limits for Open Access Gears North of 40°10ⲠN. Lat. 3 Table 3 (North) to Part 660, Subpart F Wildlife and Fisheries FISHERY CONSERVATION AND MANAGEMENT, NATIONAL OCEANIC AND ATMOSPHERIC ADMINISTRATION...

Impact of Canopy Openness on Spider Communities: Implications for Conservation Management of Formerly Coppiced Oak Forests

PubMed Central

Košulič, Ondřej; Michalko, Radek; Hula, Vladimír

2016-01-01

Traditional woodland management created a mosaic of differently aged patches providing favorable conditions for a variety of arthropods. After abandonment of historical ownership patterns and traditional management and the deliberate transformation to high forest after World War II, large forest areas became darker and more homogeneous. This had significant negative consequences for biodiversity. An important question is whether even small-scale habitat structures maintained by different levels of canopy openness in abandoned coppiced forest may constitute conditions suitable for forest as well as open habitat specialists. We investigated the effect of canopy openness in former traditionally coppiced woodlands on the species richness, functional diversity, activity density, conservation value, and degree of rareness of epigeic spiders. In each of the eight studied locations, 60-m-long transect was established consisting of five pitfall traps placed at regular 15 m intervals along the gradient. Spiders were collected from May to July 2012. We recorded 90 spider species, including high proportions of xeric specialists (40%) and red-listed threatened species (26%). The peaks of conservation indicators, as well as spider community abundance, were shifted toward more open canopies. On the other hand, functional diversity peaked at more closed canopies followed by a rapid decrease with increasing canopy openness. Species richness was highest in the middle of the canopy openness gradient, suggesting an ecotone effect. Ordinations revealed that species of conservation concern tended to be associated with sparse and partly opened canopy. The results show that the various components of biodiversity peaked at different levels of canopy openness. Therefore, the restoration and suitable forest management of such conditions will retain important diversification of habitats in formerly coppiced oak forest stands. We indicate that permanent presence of small-scale improvements could be suitable conservation tools to prevent the general decline of woodland biodiversity in the intensified landscape of Central Europe. PMID:26845431

Robust Translation of the Nucleoid Protein Fis Requires a Remote Upstream AU Element and Is Enhanced by RNA Secondary Structure

PubMed Central

Nafissi, Maryam; Chau, Jeannette; Xu, Jimin

2012-01-01

Synthesis of the Fis nucleoid protein rapidly increases in response to nutrient upshifts, and Fis is one of the most abundant DNA binding proteins in Escherichia coli under nutrient-rich growth conditions. Previous work has shown that control of Fis synthesis occurs at transcription initiation of the dusB-fis operon. We show here that while translation of the dihydrouridine synthase gene dusB is low, unusual mechanisms operate to enable robust translation of fis. At least two RNA sequence elements located within the dusB coding region are responsible for high fis translation. The most important is an AU element centered 35 nucleotides (nt) upstream of the fis AUG, which may function as a binding site for ribosomal protein S1. In addition, a 44-nt segment located upstream of the AU element and predicted to form a stem-loop secondary structure plays a prominent role in enhancing fis translation. On the other hand, mutations close to the AUG, including over a potential Shine-Dalgarno sequence, have little effect on Fis protein levels. The AU element and stem-loop regions are phylogenetically conserved within dusB-fis operons of representative enteric bacteria. PMID:22389479

Laser velocimeter measurements of the flow downstream of the Space Shuttle Main Engine high pressure oxidizer turbopump first-stage turbine nozzle

NASA Technical Reports Server (NTRS)

Ferguson, T. V.; Havskjold, G. L.; Rojas, L.

1988-01-01

A laser two-focus velocimeter was used in an open-loop water test facility in order to map the flowfield downstream of the SSME's high-pressure oxidizer turbopump first-stage turbine nozzle; attention was given to the effects of the upstream strut-downstream nozzle configuration on the flow at the rotor inlet, in order to estimate dynamic loads on the first-stage rotor blades. Velocity and flow angles were plotted as a function of circumferential position, and were found to clearly display the periodic behavior of the wake flow field. The influence of the upstream centerbody-supporting struts on the vane nozzle wake pattern was evident.

Conservative, minimally invasive and open surgical repair for management of acute ruptures of the Achilles tendon: a clinical and functional retrospective study.

PubMed

Maffulli, Gayle; Buono, Angelo Del; Richards, Paula; Oliva, Francesco; Maffulli, Nicola

2017-01-01

At present, it is unclear which is the best management for Achilles tendon rupture. We assess the clinical, functional and imaging outcomes of active patients undergoing 3 different types of management for acute subcutaneous rupture of the Achilles tendon, including conservative cast immobilization, traditional open surgery and percutaneous repair. 26 active patients were managed for a rupture of the Achilles Tendon from January 2007 to March 2008. Anthropometric measurements, Functional assessment, Isometric strength, Ultrasonographic assessment, Patient satisfaction, Working life, Physical activity, Functional score and Complications were recorded retrospectively. All 23 (21 men, 2 women) patients were reviewed at a minimum follow-up of 24 months (average 25.7, range 24 to 32 months, SD: 6.3) from the index injury. Thermann scores and patient satisfaction were significantly higher following surgery than conservative management with no significance between open and minimally invasive operated patients. Sensitive disturbances occur in up to 12% of open repairs and 1.8% of patients managed nonsurgically. Clinical and functional outcomes following surgical repair, percutaneous and open, of the Achilles tendon are significantly improved than following conservative management. Level III.

Expression of Human Hemojuvelin (HJV) Is Tightly Regulated by Two Upstream Open Reading Frames in HJV mRNA That Respond to Iron Overload in Hepatic Cells

PubMed Central

Onofre, Cláudia; Tomé, Filipa; Barbosa, Cristina; Silva, Ana Luísa

2015-01-01

The gene encoding human hemojuvelin (HJV) is one of the genes that, when mutated, can cause juvenile hemochromatosis, an early-onset inherited disorder associated with iron overload. The 5′ untranslated region of the human HJV mRNA has two upstream open reading frames (uORFs), with 28 and 19 codons formed by two upstream AUGs (uAUGs) sharing the same in-frame stop codon. Here we show that these uORFs decrease the translational efficiency of the downstream main ORF in HeLa and HepG2 cells. Indeed, ribosomal access to the main AUG is conditioned by the strong uAUG context, which results in the first uORF being translated most frequently. The reach of the main ORF is then achieved by ribosomes that resume scanning after uORF translation. Furthermore, the amino acid sequences of the uORF-encoded peptides also reinforce the translational repression of the main ORF. Interestingly, when iron levels increase, translational repression is relieved specifically in hepatic cells. The upregulation of protein levels occurs along with phosphorylation of the eukaryotic initiation factor 2α. Nevertheless, our results support a model in which the increasing recognition of the main AUG is mediated by a tissue-specific factor that promotes uORF bypass. These results support a tight HJV translational regulation involved in iron homeostasis. PMID:25666510

18 CFR 35.28 - Non-discriminatory open access transmission tariff.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 18 Conservation of Power and Water Resources 1 2011-04-01 2011-04-01 false Non-discriminatory open access transmission tariff. 35.28 Section 35.28 Conservation of Power and Water Resources FEDERAL ENERGY REGULATORY COMMISSION, DEPARTMENT OF ENERGY REGULATIONS UNDER THE FEDERAL POWER ACT FILING OF RATE SCHEDULES...

Makahiki: An Open Source Serious Game Framework for Sustainability Education and Conservation

ERIC Educational Resources Information Center

Xu, Yongwen; Johnson, Philip M.; Lee, George E.; Moore, Carleton A.; Brewer, Robert S.

2014-01-01

Sustainability education and conservation have become an international imperative due to the rising cost of energy, increasing scarcity of natural resource and irresponsible environmental practices. This paper presents Makahiki, an open source serious game framework for sustainability, which implements an extensible framework for different…

18 CFR 375.203 - Open meetings.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 18 Conservation of Power and Water Resources 1 2014-04-01 2014-04-01 false Open meetings. 375.203 Section 375.203 Conservation of Power and Water Resources FEDERAL ENERGY REGULATORY COMMISSION, DEPARTMENT... photographing of Commission meetings by still or movie camera, or by video taping without lighting aids, is...

18 CFR 375.203 - Open meetings.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 18 Conservation of Power and Water Resources 1 2013-04-01 2013-04-01 false Open meetings. 375.203 Section 375.203 Conservation of Power and Water Resources FEDERAL ENERGY REGULATORY COMMISSION, DEPARTMENT... photographing of Commission meetings by still or movie camera, or by video taping without lighting aids, is...

18 CFR 375.203 - Open meetings.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 18 Conservation of Power and Water Resources 1 2011-04-01 2011-04-01 false Open meetings. 375.203 Section 375.203 Conservation of Power and Water Resources FEDERAL ENERGY REGULATORY COMMISSION, DEPARTMENT... photographing of Commission meetings by still or movie camera, or by video taping without lighting aids, is...

18 CFR 375.203 - Open meetings.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 18 Conservation of Power and Water Resources 1 2010-04-01 2010-04-01 false Open meetings. 375.203 Section 375.203 Conservation of Power and Water Resources FEDERAL ENERGY REGULATORY COMMISSION, DEPARTMENT... photographing of Commission meetings by still or movie camera, or by video taping without lighting aids, is...

18 CFR 375.203 - Open meetings.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 18 Conservation of Power and Water Resources 1 2012-04-01 2012-04-01 false Open meetings. 375.203 Section 375.203 Conservation of Power and Water Resources FEDERAL ENERGY REGULATORY COMMISSION, DEPARTMENT... photographing of Commission meetings by still or movie camera, or by video taping without lighting aids, is...

Level II scour analysis for Bridge 39 (ANDOVT00110039) on State Route 11, crossing the Middle Branch Williams River, Andover, Vermont

USGS Publications Warehouse

Burns, Ronda L.; Wild, Emily C.

1997-01-01

This report provides the results of a detailed Level II analysis of scour potential at structure ANDOVT00110039 on State Route 11 crossing the Middle Branch Williams River, Andover, Vermont (figures 1–8). A Level II study is a basic engineering analysis of the site, including a quantitative analysis of stream stability and scour (U.S. Department of Transportation, 1993). Results of a Level I scour investigation also are included in Appendix E of this report. A Level I investigation provides a qualitative geomorphic characterization of the study site. Information on the bridge, gleaned from Vermont Agency of Transportation (VTAOT) files, was compiled prior to conducting Level I and Level II analyses and is found in Appendix D. The site is in the Green Mountain section of the New England physiographic province in southern Vermont. The 5.75-mi2 drainage area is in a predominantly rural and forested basin. In the vicinity of the study site, the surface cover is forest on the upstream left bank and downstream right bank. The surface cover on the upstream right and downstream left banks is brush. In the study area, the Middle Branch Williams River has an incised, sinuous channel with a slope of approximately 0.01 ft/ft, an average channel top width of 58 ft and an average bank height of 8 ft. The channel bed material ranges from sand to boulder with a median grain size (D50) of 96.8 mm (0.317 ft). The geomorphic assessment at the time of the Level I and Level II site visit on September 9, 1996, indicated that the reach was laterally unstable. The State Route 11 crossing of the Middle Branch Williams River is a 43-ft-long, two-lane bridge consisting of one 41-foot concrete-beam span and two additional steel beams on the upstream face (Vermont Agency of Transportation, written communication, March 29, 1995). The bridge is supported by vertical, concrete abutments with wingwalls. The channel is skewed approximately 45 degrees to the opening while the opening-skew-to-roadway is 45 degrees. The only scour protection measures at the site was type-2 stone fill (less than 36 inches diameter) at the upstream end of the upstream right wingwall and type-3 stone fill (less than 48 inches diameter) along the entire base length of the upstream left wingwall. Additional details describing conditions at the site are included in the Level II Summary and Appendices D and E. Scour depths and recommended rock rip-rap sizes were computed using the general guidelines described in Hydraulic Engineering Circular 18 (Richardson and others, 1995). Total scour at a highway crossing is comprised of three components: 1) long-term streambed degradation; 2) contraction scour (due to accelerated flow caused by a reduction in flow area at a bridge) and; 3) local scour (caused by accelerated flow around piers and abutments). Total scour is the sum of the three components. Equations are available to compute depths for contraction and local scour and a summary of the results of these computations follows. Contraction scour for all modelled flows ranged from 0.0 to 0.8 ft. The worst-case contraction scour occurred at the 500-year discharge. Abutment scour ranged from 8.9 to 11.2 ft. The worst-case abutment scour occurred at the incipient-overtopping discharge. Additional information on scour depths and depths to armoring are included in the section titled “Scour Results”. Scoured-streambed elevations, based on the calculated scour depths, are presented in tables 1 and 2. A cross-section of the scour computed at the bridge is presented in figure 8. Scour depths were calculated assuming an infinite depth of erosive material and a homogeneous particle-size distribution. It is generally accepted that the Froehlich equation (abutment scour) gives “excessively conservative estimates of scour depths” (Richardson and others, 1995, p. 47). Usually, computed scour depths are evaluated in combination with other information including (but not limited to) historical performance during flood events, the geomorphic stability assessment, existing scour protection measures, and the results of the hydraulic analyses. Therefore, scour depths adopted by VTAOT may differ from the computed values documented herein.

Minimizing the cost of keeping options open for conservation in a changing climate.

PubMed

Mills, Morena; Nicol, Sam; Wells, Jessie A; Lahoz-Monfort, José J; Wintle, Brendan; Bode, Michael; Wardrop, Martin; Walshe, Terry; Probert, William J M; Runge, Michael C; Possingham, Hugh P; Madden, Eve McDonald

2014-06-01

Policy documents advocate that managers should keep their options open while planning to protect coastal ecosystems from climate-change impacts. However, the actual costs and benefits of maintaining flexibility remain largely unexplored, and alternative approaches for decision making under uncertainty may lead to better joint outcomes for conservation and other societal goals. For example, keeping options open for coastal ecosystems incurs opportunity costs for developers. We devised a decision framework that integrates these costs and benefits with probabilistic forecasts for the extent of sea-level rise to find a balance between coastal ecosystem protection and moderate coastal development. Here, we suggest that instead of keeping their options open managers should incorporate uncertain sea-level rise predictions into a decision-making framework that evaluates the benefits and costs of conservation and development. In our example, based on plausible scenarios for sea-level rise and assuming a risk-neutral decision maker, we found that substantial development could be accommodated with negligible loss of environmental assets. Characterization of the Pareto efficiency of conservation and development outcomes provides valuable insight into the intensity of trade-offs between development and conservation. However, additional work is required to improve understanding of the consequences of alternative spatial plans and the value judgments and risk preferences of decision makers and stakeholders. © 2014 Society for Conservation Biology.

Risk assessment of imidacloprid use in forest settings on the aquatic macroinvertebrate community.

PubMed

Benton, Elizabeth P; Grant, Jerome F; Nichols, Rebecca J; Webster, R Jesse; Schwartz, John S; Bailey, Joseph K

2017-11-01

The isolated effects of a single insecticide can be difficult to assess in natural settings because of the presence of numerous pollutants in many watersheds. Imidacloprid use for suppressing hemlock woolly adelgid, Adelges tsugae (Annand) (Hemiptera: Adelgidae), in forests offers a rare opportunity to assess potential impacts on aquatic macroinvertebrates in relatively pristine landscapes. Aquatic macroinvertebrate communities were assessed in 9 streams in Great Smoky Mountains National Park (southern Appalachian Mountains, USA). The streams flow through hemlock conservation areas where imidacloprid soil drench treatments were applied for hemlock woolly adelgid suppression. Sites were located upstream and downstream of the imidacloprid treatments. Baseline species presence data (pre-imidacloprid treatment) were available from previous sample collections at downstream sites. Downstream and upstream sites did not vary in numerous community measures. Although comparisons of paired upstream and downstream sites showed differences in diversity in 7 streams, higher diversity was found more often in downstream sites. Macroinvertebrate functional feeding groups and life habits were similar between downstream and upstream sites. Downstream and baseline stream samples were similar. While some functional feeding group and life habit species richness categories varied, variations did not indicate poorer quality downstream communities. Imidacloprid treatments applied according to US Environmental Protection Agency federal restrictions did not result in negative effects to aquatic macroinvertebrate communities, which indicates that risks of imidacloprid use in forest settings are low. Environ Toxicol Chem 2017;36:3108-3119. © 2017 SETAC. © 2017 SETAC.

Molecular architecture of the hsp70 promoter after deletion of the TATA box or the upstream regulation region.

PubMed Central

Weber, J A; Taxman, D J; Lu, Q; Gilmour, D S

1997-01-01

GAGA factor, TFIID, and paused polymerase are present on the hsp70 promoter in Drosophila melanogaster prior to transcriptional activation. In order to investigate the interplay between these components, mutant constructs were analyzed after they had been transformed into flies on P elements. One construct lacked the TATA box and the other lacked the upstream regulatory region where GAGA factor binds. Transcription of each mutant during heat shock was at least 50-fold less than that of a normal promoter construct. Before and after heat shock, both mutant promoters were found to adopt a DNase I hypersensitive state that included the region downstream from the transcription start site. High-resolution analysis of the DNase I cutting pattern identified proteins that could be contributing to the hypersensitivity. GAGA factor footprints were clearly evident in the upstream region of the TATA deletion construct, and a partial footprint possibly caused by TFIID was evident on the TATA box of the upstream deletion construct. Permanganate treatment of intact salivary glands was used to further characterize each promoter construct. Paused polymerase and TFIID were readily detected on the normal promoter construct, whereas both deletions exhibited reduced levels of each of these factors. Hence both the TATA box and the upstream region are required to efficiently recruit TFIID and a paused polymerase to the promoter prior to transcriptional activation. In contrast, GAGA factor appears to be capable of binding and establishing a DNase I hypersensitive region in the absence of TFIID and polymerase. Interestingly, purified GAGA factor was found to bind near the transcription start site, and the strength of this interaction was increased by the presence of the upstream region. GAGA factor alone might be capable of establishing an open chromatin structure that encompasses the upstream regulatory region as well as the core promoter region, thus facilitating the binding of TFIID. PMID:9199313

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 that accounts for zone effectiveness. PMID:24223870

Numerical Investigation of a Model Scramjet Combustor Using DDES

NASA Astrophysics Data System (ADS)

Shin, Junsu; Sung, Hong-Gye

2017-04-01

Non-reactive flows moving through a model scramjet were investigated using a delayed detached eddy simulation (DDES), which is a hybrid scheme combining Reynolds averaged Navier-Stokes scheme and a large eddy simulation. The three dimensional Navier-Stokes equations were solved numerically on a structural grid using finite volume methods. An in-house was developed. This code used a monotonic upstream-centered scheme for conservation laws (MUSCL) with an advection upstream splitting method by pressure weight function (AUSMPW+) for space. In addition, a 4th order Runge-Kutta scheme was used with preconditioning for time integration. The geometries and boundary conditions of a scramjet combustor operated by DLR, a German aerospace center, were considered. The profiles of the lower wall pressure and axial velocity obtained from a time-averaged solution were compared with experimental results. Also, the mixing efficiency and total pressure recovery factor were provided in order to inspect the performance of the combustor.

33 CFR 117.325 - St. Johns River.

Code of Federal Regulations, 2011 CFR

2011-07-01

..., displaying flashing green lights to indicate that vessels may pass. (3) When a train approaches, large signs on both the upstream and downstream sides of the bridge flash “Bridge Coming Down,” the lights go to... track circuit is occupied. (4) After the train has cleared, the draw opens and the lights return to...

The economic benefits of vegetation in the upstream area of Ciliwung watershed

NASA Astrophysics Data System (ADS)

Saridewi, T. R.; Nazaruddin

2018-04-01

Ciliwung watershed has strategic values since its entire downstream area is located in the Special Administrative Region of Jakarta (DKI Jakarta), the capital of Indonesia. This causes forest and farmland areas are converted into open areas or built-up areas. The existence of these areas provides enormous environmental and economic benefits. Economic benefit values are very important to be considered in developing a policy development plan, but they have not been calculated yet. This study aims to determine the economic benefits provided by trees and other vegetation anddevelops a development policy that takes into account simultaneously ecological and economic aspects. The study is conducted in the upstream Ciliwung watershed, by using land cover patterns in 1989, 2000, 2010 and 2014, and employs GIS and CITY green analysis. The results show that conversion of forest and farmland areas reduces the ability of Ciliwung upstream watershed to store water. Therefore, its ability to reduce the flow of surface has been decreased. This creates a decrease in the cost savings of annual stormwater, from US 15,175,721 in 1989 to US 13,317,469 in 2014. The Environmental Services Payment Policy (PES) for upstream community groups managing the watershed has been considered as a fairly effective policy.

Differential regulation of hepatitis B virus core protein expression and genome replication by a small upstream open reading frame and naturally occurring mutations in the precore region.

PubMed

Zong, Li; Qin, Yanli; Jia, Haodi; Ye, Lei; Wang, Yongxiang; Zhang, Jiming; Wands, Jack R; Tong, Shuping; Li, Jisu

2017-05-01

Hepatitis B virus (HBV) transcribes two subsets of 3.5-kb RNAs: precore RNA for hepatitis B e antigen (HBeAg) expression, and pregenomic RNA for core and P protein translation as well as genome replication. HBeAg expression could be prevented by mutations in the precore region, while an upstream open reading frame (uORF) has been proposed as a negative regulator of core protein translation. We employed replication competent HBV DNA constructs and transient transfection experiments in Huh7 cells to verify the uORF effect and to explore the alternative function of precore RNA. Optimized Kozak sequence for the uORF or extra ATG codons as present in some HBV genotypes reduced core protein expression. G1896A nonsense mutation promoted more efficient core protein expression than mutated precore ATG, while a +1 frameshift mutation was ineffective. In conclusion, various HBeAg-negative precore mutations and mutations affecting uORF differentially regulate core protein expression and genome replication. Copyright © 2017 Elsevier Inc. All rights reserved.

18 CFR 35.28 - Non-discriminatory open access transmission tariff.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 18 Conservation of Power and Water Resources 1 2014-04-01 2014-04-01 false Non-discriminatory open access transmission tariff. 35.28 Section 35.28 Conservation of Power and Water Resources FEDERAL ENERGY.... (4) Demand response means a reduction in the consumption of electric energy by customers from their...

18 CFR 35.28 - Non-discriminatory open access transmission tariff.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 18 Conservation of Power and Water Resources 1 2013-04-01 2013-04-01 false Non-discriminatory open access transmission tariff. 35.28 Section 35.28 Conservation of Power and Water Resources FEDERAL ENERGY.... (4) Demand response means a reduction in the consumption of electric energy by customers from their...

Conservation of Transcription Start Sites within Genes across a Bacterial Genus

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

Shao, Wenjun; Price, Morgan N.; Deutschbauer, Adam M.

Transcription start sites (TSSs) lying inside annotated genes, on the same or opposite strand, have been observed in diverse bacteria, but the function of these unexpected transcripts is unclear. Here, we use the metal-reducing bacterium Shewanella oneidensis MR-1 and its relatives to study the evolutionary conservation of unexpected TSSs. Using high-resolution tiling microarrays and 5'-end RNA sequencing, we identified 2,531 TSSs in S. oneidensis MR-1, of which 18% were located inside coding sequences (CDSs). Comparative transcriptome analysis with seven additional Shewanella species revealed that the majority (76%) of the TSSs within the upstream regions of annotated genes (gTSSs) were conserved.more » Thirty percent of the TSSs that were inside genes and on the sense strand (iTSSs) were also conserved. Sequence analysis around these iTSSs showed conserved promoter motifs, suggesting that many iTSS are under purifying selection. Furthermore, conserved iTSSs are enriched for regulatory motifs, suggesting that they are regulated, and they tend to eliminate polar effects, which confirms that they are functional. In contrast, the transcription of antisense TSSs located inside CDSs (aTSSs) was significantly less likely to be conserved (22%). However, aTSSs whose transcription was conserved often have conserved promoter motifs and drive the expression of nearby genes. Overall, our findings demonstrate that some internal TSSs are conserved and drive protein expression despite their unusual locations, but the majority are not conserved and may reflect noisy initiation of transcription rather than a biological function.« less

Minimizing the cost of keeping options open for conservation in a changing climate

USGS Publications Warehouse

Mills, Morena; Nicol, Samuel; Wells, Jessie A.; Lahoz-Monfort, José J.; Wintle, Brendan; Bode, Michael; Wardrop, Martin; Walshe, Terry; Probert, William J. M.; Runge, Michael C.; Possingham, Hugh P.; McDonald Madden, Eve

2014-01-01

Policy documents advocate that managers should keep their options open while planning to protect coastal ecosystems from climate-change impacts. However, the actual costs and benefits of maintaining flexibility remain largely unexplored, and alternative approaches for decision making under uncertainty may lead to better joint outcomes for conservation and other societal goals. For example, keeping options open for coastal ecosystems incurs opportunity costs for developers. We devised a decision framework that integrates these costs and benefits with probabilistic forecasts for the extent of sea-level rise to find a balance between coastal ecosystem protection and moderate coastal development. Here, we suggest that instead of keeping their options open managers should incorporate uncertain sea-level rise predictions into a decision-making framework that evaluates the benefits and costs of conservation and development. In our example, based on plausible scenarios for sea-level rise and assuming a risk-neutral decision maker, we found that substantial development could be accommodated with negligible loss of environmental assets. Characterization of the Pareto efficiency of conservation and development outcomes provides valuable insight into the intensity of trade-offs between development and conservation. However, additional work is required to improve understanding of the consequences of alternative spatial plans and the value judgments and risk preferences of decision makers and stakeholders.

76 FR 65121 - Community Forest and Open Space Conservation Program

Federal Register 2010, 2011, 2012, 2013, 2014

2011-10-20

... broad range of citizens in forest conservation, stewardship, and governance. Where situated near Federal... conservation of a tract but does not have the capacity to effectively oversee management and governance issues...

76 FR 5820 - Meeting Announcements: North American Wetlands Conservation Council; Neotropical Migratory Bird...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-02-02

...] Meeting Announcements: North American Wetlands Conservation Council; Neotropical Migratory Bird... Conservation Act (NAWCA) grant proposals for recommendation to the Migratory Bird Conservation Commission (Commission). This meeting is open to the public. The Advisory Group for the Neotropical Migratory Bird...

REFLECTOR CONTROL OF A BOILING-WATER REACTOR

DOEpatents

Treshow, M.

1962-05-22

A line connecting the reactor with a spent steam condenser contains a valve set to open when the pressure in the reactor exceeds a predetermined value and an orifice on the upstream side of the valve. Another line connects the reflector with this line between the orifice and the valve. An excess steam pressure causes the valve to open and the flow of steam through the line draws water out of the reflector. Provision is also made for adding water to the reflector when the steam pressure drops. (AEC)

Replicative Intermediates of Human Papillomavirus Type 11 in Laryngeal Papillomas: Site of Replication Initiation and Direction of Replication

NASA Astrophysics Data System (ADS)

Auborn, K. J.; Little, R. D.; Platt, T. H. K.; Vaccariello, M. A.; Schildkraut, C. L.

1994-07-01

We have examined the structures of replication intermediates from the human papillomavirus type 11 genome in DNA extracted from papilloma lesions (laryngeal papillomas). The sites of replication initiation and termination utilized in vivo were mapped by using neutral/neutral and neutral/alkaline two-dimensional agarose gel electrophoresis methods. Initiation of replication was detected in or very close to the upstream regulatory region (URR; the noncoding, regulatory sequences upstream of the open reading frames in the papillomavirus genome). We also show that replication forks proceed bidirectionally from the origin and converge 180circ opposite the URR. These results demonstrate the feasibility of analysis of replication of viral genomes directly from infected tissue.

Kin28 regulates the transient association of Mediator with core promoters.

PubMed

Jeronimo, Célia; Robert, François

2014-05-01

Mediator is an essential, broadly used eukaryotic transcriptional coactivator. How and what Mediator communicates from activators to RNA polymerase II (RNAPII) remains an open question. Here we performed genome-wide location profiling of Saccharomyces cerevisiae Mediator subunits. Mediator is not found at core promoters but rather occupies the upstream activating sequence, upstream of the pre-initiation complex. In the absence of Kin28 (CDK7) kinase activity or in cells in which the RNAPII C-terminal domain is mutated to replace Ser5 with alanine, however, Mediator accumulates at core promoters together with RNAPII. We propose that Mediator is released quickly from promoters after phosphorylation of Ser5 by Kin28 (CDK7), which also allows for RNAPII to escape from the promoter.

Diverse Early Life-History Strategies in Migratory Amazonian Catfish: Implications for Conservation and Management.

PubMed

Hegg, Jens C; Giarrizzo, Tommaso; Kennedy, Brian P

2015-01-01

Animal migrations provide important ecological functions and can allow for increased biodiversity through habitat and niche diversification. However, aquatic migrations in general, and those of the world's largest fish in particular, are imperiled worldwide and are often poorly understood. Several species of large Amazonian catfish carry out some of the longest freshwater fish migrations in the world, travelling from the Amazon River estuary to the Andes foothills. These species are important apex predators in the main stem rivers of the Amazon Basin and make up the region's largest fishery. They are also the only species to utilize the entire Amazon Basin to complete their life cycle. Studies indicate both that the fisheries may be declining due to overfishing, and that the proposed and completed dams in their upstream range threaten spawning migrations. Despite this, surprisingly little is known about the details of these species' migrations, or their life history. Otolith microchemistry has been an effective method for quantifying and reconstructing fish migrations worldwide across multiple spatial scales and may provide a powerful tool to understand the movements of Amazonian migratory catfish. Our objective was to describe the migratory behaviors of the three most populous and commercially important migratory catfish species, Dourada (Brachyplatystoma rousseauxii), Piramutaba (Brachyplatystoma vaillantii), and Piraíba (Brachyplatystoma filamentosum). We collected fish from the mouth of the Amazon River and the Central Amazon and used strontium isotope signatures ((87)Sr/(86)Sr) recorded in their otoliths to determine the location of early rearing and subsequent. Fish location was determined through discriminant function classification, using water chemistry data from the literature as a training set. Where water chemistry data was unavailable, we successfully in predicted (87)Sr/(86)Sr isotope values using a regression-based approach that related the geology of the upstream watershed to the Sr isotope ratio. Our results provide the first reported otolith microchemical reconstruction of Brachyplatystoma migratory movements in the Amazon Basin. Our results indicate that juveniles exhibit diverse rearing strategies, rearing in both upstream and estuary environments. This contrasts with the prevailing understanding that juveniles rear in the estuary before migrating upstream; however, it is supported by some fisheries data that has indicated the presence of alternate spawning and rearing life-histories. The presence of alternate juvenile rearing strategies may have important implications for conservation and management of the fisheries in the region.

A Study of Discharge Coefficient in Bileaflet Valves

DTIC Science & Technology

2001-10-25

Granados J. Garcia MA. Luque I. Concha M. “Conservative operation for mitral stenosis with densely fibrosed or partially calcified valves. An eight...for aortic valves, whereas a lower value (around 0.7) has been proposed for valves mounted in the mitralic position, on account of the larger upstream...section; in the mitral position, then, a valve will have a smaller discharge coefficient (or Aeff/A ratio) than in the aortic position. Using dC =1

Resident perspectives of the open space conservation subdivision in Hamburg Township, Michigan

Treesearch

Maureen E. Austin

2004-01-01

The open space conservation subdivision (R.G. Arendt, 1996) has been presented as an alternative to conventional large lot residential development. A form of clustering, this planning approach emphasizes the quality as well as the quantity of land preserved. The format offers a means for local planning officials to accommodate residential growth while preserving...

Mutational Analysis of the TnrA-Binding Sites in the Bacillus subtilis nrgAB and gabP Promoter Regions

PubMed Central

Wray, Lewis V.; Zalieckas, Jill M.; Ferson, Amy E.; Fisher, Susan H.

1998-01-01

Transcription of the Bacillus subtilis nrgAB promoter is activated during nitrogen-limited growth by the TnrA protein. A common inverted repeat, TGTNAN7TNACA (TnrA site), is centered 49 to 51 bp upstream of the transcriptional start sites for the TnrA-regulated nrgAB, gabP P2, and nas promoters. Oligonucleotide-directed mutagenesis of the nrgAB promoter region showed that conserved nucleotides within the TnrA site, the A+T-rich region between the two TnrA half-sites, and an upstream A tract are all required for high-level activation of nrgAB expression. Mutations that alter the relative distance between the two half-sites of the nrgAB TnrA site abolish nitrogen regulation of nrgAB expression. Spacer mutations that change the relative distance between the TnrA site and −35 region of the nrgAB promoter reveal that activation of nrgAB expression occurs only when the TnrA site is located 49 to 51 bp upstream of the transcriptional start site. Mutational analysis of the conserved nucleotides in the gabP P2 TnrA site showed that this sequence is also required for nitrogen-regulated gabP P2 expression. The TnrA protein, expressed in an overproducing Escherichia coli strain, had a 625-fold-higher affinity for the wild-type nrgAB promoter DNA than for a mutated nrgAB promoter DNA fragment that is unable to activate nrgAB expression in vivo. These results indicate that the proposed TnrA site functions as the binding site for the TnrA protein. TnrA was found to activate nrgAB expression during late exponential growth in nutrient sporulation medium containing glucose, suggesting that cells become nitrogen limited during growth in this medium. PMID:9603886

Identification of new TSGA10 transcript variants in human testis with conserved regulatory RNA elements in 5'untranslated region and distinct expression in breast cancer.

PubMed

Salehipour, Pouya; Nematzadeh, Mahsa; Mobasheri, Maryam Beigom; Afsharpad, Mandana; Mansouri, Kamran; Modarressi, Mohammad Hossein

2017-09-01

Testis specific gene antigen 10 (TSGA10) is a cancer testis antigen involved in the process of spermatogenesis. TSGA10 could also play an important role in the inhibition of angiogenesis by preventing nuclear localization of HIF-1α. Although it has been shown that TSGA10 messenger RNA (mRNA) is mainly expressed in testis and some tumors, the transcription pattern and regulatory mechanisms of this gene remain largely unknown. Here, we report that human TSGA10 comprises at least 22 exons and generates four different transcript variants. It was identified that using two distinct promoters and splicing of exons 4 and 7 produced these transcript variants, which have the same coding sequence, but the sequence of 5'untanslated region (5'UTR) is different between them. This is significant because conserved regulatory RNA elements like upstream open reading frame (uORF) and putative internal ribosome entry site (IRES) were found in this region which have different combinations in each transcript variant and it may influence translational efficiency of them in normal or unusual environmental conditions like hypoxia. To indicate the transcription pattern of TSGA10 in breast cancer, expression of identified transcript variants was analyzed in 62 breast cancer samples. We found that TSGA10 tends to express variants with shorter 5'UTR and fewer uORF elements in breast cancer tissues. Our study demonstrates for the first time the expression of different TSGA10 transcript variants in testis and breast cancer tissues and provides a first clue to a role of TSGA10 5'UTR in regulation of translation in unusual environmental conditions like hypoxia. Copyright © 2017. Published by Elsevier B.V.

Analysis of the primary structure of the long terminal repeat and the gag and pol genes of the human spumaretrovirus.

PubMed Central

Maurer, B; Bannert, H; Darai, G; Flügel, R M

1988-01-01

The nucleotide sequence of the human spumaretrovirus (HSRV) genome was determined. The 5' long terminal repeat region was analyzed by strong stop cDNA synthesis and S1 nuclease mapping. The length of the RU5 region was determined and found to be 346 nucleotides long. The 5' long terminal repeat is 1,123 base pairs long and is bound by an 18-base-pair primer-binding site complementary to the 3' end of mammalian lysine-1,2-specific tRNA. Open reading frames for gag and pol genes were identified. Surprisingly, the HSRV gag protein does not contain the cysteine motif of the nucleic acid-binding proteins found in and typical of all other retroviral gag proteins; instead the HSRV gag gene encodes a strongly basic protein reminiscent of those of hepatitis B virus and retrotransposons. The carboxy-terminal part of the HSRV gag gene products encodes a protease domain. The pol gene overlaps the gag gene and is postulated to be synthesized as a gag/pol precursor via translational frameshifting analogous to that of Rous sarcoma virus, with 7 nucleotides immediately upstream of the termination codons of gag conserved between the two viral genomes. The HSRV pol gene is 2,730 nucleotides long, and its deduced protein sequence is readily subdivided into three well-conserved domains, the reverse transcriptase, the RNase H, and the integrase. Although the degree of homology of the HSRV reverse transcriptase domain is highest to that of murine leukemia virus, the HSRV genomic organization is more similar to that of human and simian immunodeficiency viruses. The data justify classifying the spumaretroviruses as a third subfamily of Retroviridae. Images PMID:2451755

Upstream water resource management to address downstream pollution concerns: A policy framework with application to the Nakdong River basin in South Korea

NASA Astrophysics Data System (ADS)

Yoon, Taeyeon; Rhodes, Charles; Shah, Farhed A.

2015-02-01

An empirical framework for assisting with water quality management is proposed that relies on open-source hydrologic data. Such data are measured periodically at fixed water stations and commonly available in time-series form. To fully exploit the data, we suggest that observations from multiple stations should be combined into a single long-panel data set, and an econometric model developed to estimate upstream management effects on downstream water quality. Selection of the model's functional form and explanatory variables would be informed by rating curves, and idiosyncrasies across and within stations handled in an error term by testing contemporary correlation, serial correlation, and heteroskedasticity. Our proposed approach is illustrated with an application to the Nakdong River basin in South Korea. Three alternative policies to achieve downstream BOD level targets are evaluated: upstream water treatment, greater dam discharge, and development of a new water source. Upstream water treatment directly cuts off incoming pollutants, thereby presenting the smallest variation in its downstream effects on BOD levels. Treatment is advantageous when reliability of water quality is a primary concern. Dam discharge is a flexible tool, and may be used strategically during a low-flow season. We consider development of a new water corridor from an extant dam as our third policy option. This turns out to be the most cost-effective way for securing lower BOD levels in the downstream target city. Even though we consider a relatively simple watershed to illustrate the usefulness of our approach, it can be adapted easily to analyze more complex upstream-downstream issues.

Do open-cycle hatcheries relying on tourism conserve sea turtles? Sri Lankan developments and economic-ecological considerations.

PubMed

Tisdell, Clem; Wilson, Clevo

2005-04-01

By combining economic analysis of markets with ecological parameters, this article considers the role that tourism-based sea turtle hatcheries (of an open-cycle type) can play in conserving populations of sea turtles. Background is provided on the nature and development of such hatcheries in Sri Lanka. The modeling facilitates the assessment of the impacts of turtle hatcheries on the conservation of sea turtles and enables the economic and ecological consequences of tourism, based on such hatcheries, to be better appreciated. The results demonstrate that sea turtle hatcheries serving tourists can make a positive contribution to sea turtle conservation, but that their conservation effectiveness depends on the way they are managed. Possible negative effects are also identified. Economic market models are combined with turtle population survival relationships to predict the conservation impact of turtle hatcheries and their consequence for the total economic value obtained from sea turtle populations.

76 FR 72309 - Drawbridge Operation Regulations; Chelsea River, Chelsea and East Boston, MA

Federal Register 2010, 2011, 2012, 2013, 2014

2011-11-23

... installed new vertical lift bridge span will undergo testing for three weeks. This deviation requires a four hour advance notice for bridge openings during the lift span test period. DATES: This deviation is... facilities located upstream from the new bridge. The lift span at the new bridge will be operated by the...

CalA, a Cyanobacterial AbrB Protein, Interacts with the Upstream Region of hypC and Acts as a Repressor of Its Transcription in the Cyanobacterium Nostoc sp. Strain PCC 7120▿ †

PubMed Central

Agervald, Åsa; Zhang, Xiaohui; Stensjö, Karin; Devine, Ellenor; Lindblad, Peter

2010-01-01

The filamentous, heterocystous, nitrogen-fixing cyanobacterium Nostoc sp. strain PCC 7120 may contain, depending on growth conditions, up to two hydrogenases directly involved in hydrogen metabolism. HypC is one out of at least seven auxiliary gene products required for synthesis of a functional hydrogenase, specifically involved in the maturation of the large subunit. In this study we present a protein, CalA (Alr0946 in the genome), belonging to the transcription regulator family AbrB, which in protein-DNA assays was found to interact with the upstream region of hypC. Transcriptional investigations showed that calA is cotranscribed with the downstream gene alr0947, which encodes a putative protease from the abortive infection superfamily, Abi. CalA was shown to interact specifically not only with the upstream region of hypC but also with its own upstream region, acting as a repressor on hypC. The bidirectional hydrogenase activity was significantly downregulated when CalA was overexpressed, demonstrating a correlation with the transcription factor, either direct or indirect. In silico studies showed that homologues to both CalA and Alr0947 are highly conserved proteins within cyanobacteria with very similar physical organizations of the corresponding structural genes. Possible functions of the cotranscribed downstream protein Alr0947 are presented. In addition, we present a three-dimensional (3D) model of the DNA binding domain of CalA and putative DNA binding mechanisms are discussed. PMID:20023111

Molecular cloning and identification of the transcriptional regulatory domain of the goat neurokinin B gene TAC3.

PubMed

Suetomi, Yuta; Matsuda, Fuko; Uenoyama, Yoshihisa; Maeda, Kei-ichiro; Tsukamura, Hiroko; Ohkura, Satoshi

2013-10-01

Neurokinin B (NKB), encoded by TAC3, is thought to be an important accelerator of pulsatile gonadotropin-releasing hormone release. This study aimed to clarify the transcriptional regulatory mechanism of goat TAC3. First, we determined the full-length mRNA sequence of goat TAC3 from the hypothalamus to be 820 b, including a 381 b coding region, with the putative transcription start site located 143-b upstream of the start codon. The deduced amino acid sequence of NKB, which is produced from preproNKB, was completely conserved among goat, cattle, and human. Next, we cloned 5'-upstream region of goat TAC3 up to 3400 b from the translation initiation site, and this region was highly homologous with cattle TAC3 (89%). We used this goat TAC3 5'-upstream region to perform luciferase assays. We created a luciferase reporter vector containing DNA constructs from -2706, -1837, -834, -335, or -197 to +166 bp (the putative transcription start site was designated as +1) of goat TAC3 and these were transiently transfected into mouse hypothalamus-derived N7 cells and human neuroblastoma-derived SK-N-AS cells. The luciferase activity gradually increased with the deletion of the 5'-upstream region, suggesting that the transcriptional suppressive region is located between -2706 and -336 bp and that the core promoter exists downstream of -197 bp. Estradiol treatment did not lead to significant suppression of luciferase activity of any constructs, suggesting the existence of other factor(s) that regulate goat TAC3 transcription.

Far-field connectivity of the UK's four largest marine protected areas: Four of a kind?

NASA Astrophysics Data System (ADS)

Robinson, J.; New, A. L.; Popova, E. E.; Srokosz, M. A.; Yool, A.

2017-05-01

Marine Protected Areas (MPAs) are established to conserve important ecosystems and protect marine species threatened in the wider ocean. However, even MPAs in remote areas are not wholly isolated from anthropogenic impacts. "Upstream" activities, possibly thousands of kilometers away, can influence MPAs through ocean currents that determine their connectivity. Persistent pollutants, such as plastics, can be transported from neighboring shelf regions to MPAs, or an ecosystem may be affected if larval dispersal is reduced from a seemingly remote upstream area. Thus, improved understanding of exactly where upstream is, and on what timescale it is connected, is important for protecting and monitoring MPAs. Here, we use a high-resolution (1/12°) ocean general circulation model and Lagrangian particle tracking to diagnose the connectivity of four of the UK's largest MPAs: Pitcairn; South Georgia and Sandwich Islands; Ascension; and the British Indian Ocean Territory (BIOT). We introduce the idea of a circulation "connectivity footprint", by which MPAs are connected to upstream areas. Annual connectivity footprints were calculated for the four MPAs, taking into account seasonal and inter-annual variability. These footprints showed that, on annual timescales, Pitcairn was not connected with land, whereas there was increasing connectivity for waters reaching South Georgia, Ascension, and, especially, BIOT. BIOT also had a high degree of both seasonal and inter-annual variability, which drastically changed its footprint, year-to-year. We advocate that such connectivity footprints are an inherent property of all MPAs, and need to be considered when MPAs are first proposed or their viability as refuges evaluated.

What Data to Use for Forest Conservation Planning? A Comparison of Coarse Open and Detailed Proprietary Forest Inventory Data in Finland

PubMed Central

Lehtomäki, Joona; Tuominen, Sakari; Toivonen, Tuuli; Leinonen, Antti

2015-01-01

The boreal region is facing intensifying resource extraction pressure, but the lack of comprehensive biodiversity data makes operative forest conservation planning difficult. Many countries have implemented forest inventory schemes and are making extensive and up-to-date forest databases increasingly available. Some of the more detailed inventory databases, however, remain proprietary and unavailable for conservation planning. Here, we investigate how well different open and proprietary forest inventory data sets suit the purpose of conservation prioritization in Finland. We also explore how much priorities are affected by using the less accurate but open data. First, we construct a set of indices for forest conservation value based on quantitative information commonly found in forest inventories. These include the maturity of the trees, tree species composition, and site fertility. Secondly, using these data and accounting for connectivity between forest types, we investigate the patterns in conservation priority. For prioritization, we use Zonation, a method and software for spatial conservation prioritization. We then validate the prioritizations by comparing them to known areas of high conservation value. We show that the overall priority patterns are relatively consistent across different data sources and analysis options. However, the coarse data cannot be used to accurately identify the high-priority areas as it misses much of the fine-scale variation in forest structures. We conclude that, while inventory data collected for forestry purposes may be useful for forest conservation purposes, it needs to be detailed enough to be able to account for more fine-scaled features of high conservation value. These results underline the importance of making detailed inventory data publicly available. Finally, we discuss how the prioritization methodology we used could be integrated into operative forest management, especially in countries in the boreal zone. PMID:26317227

What Data to Use for Forest Conservation Planning? A Comparison of Coarse Open and Detailed Proprietary Forest Inventory Data in Finland.

PubMed

Lehtomäki, Joona; Tuominen, Sakari; Toivonen, Tuuli; Leinonen, Antti

2015-01-01

The boreal region is facing intensifying resource extraction pressure, but the lack of comprehensive biodiversity data makes operative forest conservation planning difficult. Many countries have implemented forest inventory schemes and are making extensive and up-to-date forest databases increasingly available. Some of the more detailed inventory databases, however, remain proprietary and unavailable for conservation planning. Here, we investigate how well different open and proprietary forest inventory data sets suit the purpose of conservation prioritization in Finland. We also explore how much priorities are affected by using the less accurate but open data. First, we construct a set of indices for forest conservation value based on quantitative information commonly found in forest inventories. These include the maturity of the trees, tree species composition, and site fertility. Secondly, using these data and accounting for connectivity between forest types, we investigate the patterns in conservation priority. For prioritization, we use Zonation, a method and software for spatial conservation prioritization. We then validate the prioritizations by comparing them to known areas of high conservation value. We show that the overall priority patterns are relatively consistent across different data sources and analysis options. However, the coarse data cannot be used to accurately identify the high-priority areas as it misses much of the fine-scale variation in forest structures. We conclude that, while inventory data collected for forestry purposes may be useful for forest conservation purposes, it needs to be detailed enough to be able to account for more fine-scaled features of high conservation value. These results underline the importance of making detailed inventory data publicly available. Finally, we discuss how the prioritization methodology we used could be integrated into operative forest management, especially in countries in the boreal zone.

Official opening remarks: bird conservation in Canada

Treesearch

Michael S. W. Bradstreet

1997-01-01

It is my pleasure, as Executive Director of Bird Studies Canada (BSC), to take part in the opening ceremonies of the Second International Symposium: Biology and Conservation of Owls of the Northern Hemisphere. It is entirely appropriate that this symposium should take place in one of the colder cities in the Northern Hemisphere, in mid-winter, and it is fitting that...

Level II scour analysis for Bridge 33 (TUNBTH00450033) on Town Highway 45, crossing the First Branch White River, Tunbridge, Vermont

USGS Publications Warehouse

Wild, E.C.; Severance, Timothy

1997-01-01

This report provides the results of a detailed Level II analysis of scour potential at structure TUNBTH00450033 on Town Highway 45 crossing the First Branch White River, Tunbridge, Vermont (figures 1–8). A Level II study is a basic engineering analysis of the site, including a quantitative analysis of stream stability and scour (U.S. Department of Transportation, 1993). Results of a Level I scour investigation also are included in Appendix E of this report. A Level I investigation provides a qualitative geomorphic characterization of the study site. Information on the bridge, gleaned from Vermont Agency of Transportation (VTAOT) files, was compiled prior to conducting Level I and Level II analyses and is found in Appendix D. The site is in the New England Upland section of the New England physiographic province in central Vermont. The 86.4-mi 2 drainage area is in a predominantly rural and forested basin. In the vicinity of the study site, the surface cover is pasture upstream and downstream of the bridge, while woody vegetation sparsely covers the immediate banks. In the study area, the First Branch White River has an incised, sinuous channel with a slope of approximately 0.003 ft/ft, an average channel top width of 68 ft and an average bank height of 7 ft. The channel bed material ranges from sand to gravel with a median grain size (D50) of 27.1 mm (0.089 ft). The geomorphic assessment at the time of the Level I and Level II site visit on October 18, 1995, indicated that the reach was laterally unstable due to a cut-bank present on the upstream right bank and a wide channel bar in the upstream reach. The Town Highway 45 crossing of the First Branch White River is a 67-ft-long, one-lane bridge consisting of one 54-foot timber thru-truss span (Vermont Agency of Transportation, written communication, March 23, 1995). The opening length of the structure parallel to the bridge face is 53.5 ft. The bridge is supported on the right by a vertical, concrete abutment with an upstream wingwall, and on the left by a vertical, stone abutment. The channel is skewed approximately 20 degrees to the opening while the computed opening-skew-to-roadway is 10 degrees. A scour hole 1.5 ft deeper than the mean thalweg depth was observed along the right abutment during the Level I assessment. Scour countermeasures at the site include type-1 stone fill (less than 12 inches diameter) along the upstream right wingwall, type-2 stone fill (less than 36 inches diameter) along the right abutment, and type-3 stone fill (less than 48 inches diameter) along the upstream right bank. Additional details describing conditions at the site are included in the Level II Summary and Appendices D and E. Scour depths and recommended rock rip-rap sizes were computed using the general guidelines described in Hydraulic Engineering Circular 18 (Richardson and others, 1995) for the 100- and 500-year discharges. In addition, the incipient roadway-overtopping discharge was determined and analyzed as another potential worst-case scour scenario. Total scour at a highway crossing is comprised of three components: 1) long-term streambed degradation; 2) contraction scour (due to accelerated flow caused by a reduction in flow area at a bridge) and; 3) local scour (caused by accelerated flow around piers and abutments). Total scour is the sum of the three components. Equations are available to compute depths for contraction and local scour and a summary of the results of these computations follows. Contraction scour for all modelled flows ranged from 0.0 to 3.0 ft. The worst-case contraction scour occurred at the 500-year discharge. Left abutment scour ranged from 12.8 to 31.0 ft. Right abutment scour ranged from 9.8 to 19.0 ft. The worst-case left and right abutment scour occurred at the 500-year discharge. Additional information on scour depths and depths to armoring are included in the section titled “Scour Results”. Scoured-streambed elevations, based on the calculated scour depths, are presented in Tables 1 and 2. A cross-section of the scour computed at the bridge is presented in Figure 8. Scour depths were calculated assuming an infinite depth of erosive material and a homogeneous particle-size distribution. It is generally accepted that the Froehlich equation (abutment scour) gives “excessively conservative estimates of scour depths” (Richardson and others, 1995, p. 47). Usually, computed scour depths are evaluated in combination with other information including (but not limited to) historical performance during flood events, the geomorphic stability assessment, existing scour protection measures, and the results of the hydraulic analyses. Therefore, scour depths adopted by VTAOT may differ from the computed values documented herein.

Level II scour analysis for Bridge 35, (ANDOVT00110035) on State Route 11, crossing the Middle Branch Williams River, Andover, Vermont

USGS Publications Warehouse

Burns, Ronda L.; Wild, Emily C.

1998-01-01

This report provides the results of a detailed Level II analysis of scour potential at structure ANDOVT00110035 on State Route 11 crossing the Middle Branch Williams River, Andover, Vermont (figures 1–8). A Level II study is a basic engineering analysis of the site, including a quantitative analysis of stream stability and scour (Federal Highway Administration, 1993). Results of a Level I scour investigation also are included in appendix E of this report. A Level I investigation provides a qualitative geomorphic characterization of the study site. Information on the bridge, gleaned from Vermont Agency of Transportation (VTAOT) files, was compiled prior to conducting Level I and Level II analyses and is found in appendix D. The site is in the Green Mountain section of the New England physiographic province in south-central Vermont. The 4.65-mi2 drainage area is in a predominantly rural and forested basin. In the vicinity of the study site, the surface cover is forest on the left bank and small trees and brush on the right bank upstream and downstream of the bridge. In the study area, the Middle Branch Williams River has an incised, meandering channel with a slope of approximately 0.02 ft/ft, an average channel top width of 57 ft and an average bank height of 4 ft. The channel bed material ranges from gravel to boulder with a median grain size (D50) of 31.4 mm (0.103 ft). The geomorphic assessment at the time of the Level I and Level II site visit on August 28, 1996, indicated that the reach was laterally unstable. There are cut-banks upstream and downstream of the bridge and an island in the channel upstream. The State Route 11 crossing of the Middle Branch Williams River is a 28-ft-long, two-lane bridge consisting of one 24-ft concrete tee-beam span (Vermont Agency of Transportation, written communication, March 28, 1995). The opening length of the structure parallel to the bridge face is 23.6 ft. The bridge is supported by vertical, concrete abutments with wingwalls. The channel is skewed approximately 45 degrees to the opening while the computed opening-skew-to-roadway is 25 degrees. A scour hole ranging from 1.5 to 1.75 ft deeper than the mean thalweg depth was observed along the upstream left wingwall, the left abutment, and the downstream left wingwall during the Level I assessment. The scour countermeasures at the site included type-1 stone fill (less than 12 inches diameter) at the right road approach upstream and downstream of the bridge and type-2 stone fill (less than 36 inches diameter) at the left road approach upstream and downstream of the bridge. Additional details describing conditions at the site are included in the Level II Summary and appendices D and E. Scour depths and recommended rock rip-rap sizes were computed using the general guidelines described in Hydraulic Engineering Circular 18 (Richardson and Davis, 1995) for the 100- and 500-year discharges. In addition, the incipient roadway-overtopping discharge was determined and analyzed as another potential worst-case scour scenario. Total scour at a highway crossing is comprised of three components: 1) long-term streambed degradation; 2) contraction scour (due to accelerated flow caused by a reduction in flow area at a bridge) and; 3) local scour (caused by accelerated flow around piers and abutments). Total scour is the sum of the three components. Equations are available to compute depths for contraction and local scour and a summary of the results of these computations follows. Contraction scour for all modelled flows ranged from 2.0 to 4.3 ft. The worst-case contraction scour occurred at the 500-year discharge. Abutment scour ranged from 14.4 to 16.5 ft at the left abutment and from 6.3 to 8.8 ft at the right abutment. The worst-case abutment scour occurred at the 500-year discharge. Additional information on scour depths and depths to armoring are included in the section titled “Scour Results”. Scoured-streambed elevations, based on the calculated scour depths, are presented in tables 1 and 2. A cross-section of the scour computed at the bridge is presented in figure 8. Scour depths were calculated assuming an infinite depth of erosive material and a homogeneous particle-size distribution. It is generally accepted that the Froehlich equation (abutment scour) gives “excessively conservative estimates of scour depths” (Richardson and Davis, 1995, p. 46). Usually, computed scour depths are evaluated in combination with other information including (but not limited to) historical performance during flood events, the geomorphic stability assessment, existing scour protection measures, and the results of the hydraulic analyses. Therefore, scour depths adopted by VTAOT may differ from the computed values documented herein.

[The role of integrons in dissemination of antibiotic resistance].

PubMed

Ploy, M C; Lambert, T; Gassama, A; Denis, F

2000-01-01

Bacteria can transfer genetic information to get protection against most antibiotics. The acquisition of resistance genes involves genetic mobile elements such as plasmids and transposons. Another genetic structures, named integrons, have been described and contain one or more gene cassettes located at a specific site. Integrons contain an intI gene encoding a site-specific recombinase belonging to the integrase family and a recombination site attI. A gene cassette includes an open reading frame and, at the 3'-end, a recombination site attC. Integration or excision of cassettes occurs by a site-specific recombination mechanism catalyzed by the integrase. However, insertion can rarely occur, at non-specific sites leading to a stable situation for the cassette. Cassettes are transcribed from a common promoter located in the 5'-conserved segment and expression of distal genes is reduced by the presence of upstream cassettes. Most gene cassettes encode antibiotic resistant determinants but antiseptic resistant genes have also been described. Integrons seem to have a major role in the spread of multidrug resistance in Gram-negative bacteria but integrons in Gram-positive bacteria have been recently described. Moreover, the finding of super-integrons with gene cassettes coding for other determinants (biochemical functions, virulence factors) in different Gram negative bacteria suggests that integrons are probably implied in bacterial genome evolution.

Identification of Bombyx mori bidensovirus VD1-ORF4 reveals a novel protein associated with viral structural component.

PubMed

Li, Guohui; Hu, Zhaoyang; Guo, Xuli; Li, Guangtian; Tang, Qi; Wang, Peng; Chen, Keping; Yao, Qin

2013-06-01

Bombyx mori bidensovirus (BmBDV) VD1-ORF4 (open reading frame 4, ORF4) consists of 3,318 nucleotides, which codes for a predicted 1,105-amino acid protein containing a conserved DNA polymerase motif. However, its functions in viral propagation remain unknown. In the current study, the transcription of VD1-ORF4 was examined from 6 to 96 h postinfection (p.i.) by RT-PCR, 5'-RACE revealed the transcription initiation site of BmBDV ORF4 to be -16 nucleotides upstream from the start codon, and 3'-RACE revealed the transcription termination site of VD1-ORF4 to be +7 nucleotides downstream from termination codon. Three different proteins were examined in the extracts of BmBDV-infected silkworms midguts by Western blot using raised antibodies against VD1-ORF4 deduced amino acid, and a specific protein band about 53 kDa was further detected in purified virions using the same antibodies. Taken together, BmBDV VD1-ORF4 codes for three or more proteins during the viral life cycle, one of which is a 53 kDa protein and confirmed to be a component of BmBDV virion.

Some Effects of Compressibility on the Flow Through Fans and Turbines

NASA Technical Reports Server (NTRS)

Perl, W.; Epstein, H. T.

1946-01-01

The laws of conservation of mass, momentum, and energy are applied to the compressible flow through a two-dimensional cascade of airfoils. A fundamental relation between the ultimate upstream and downstream flow angles, the inlet Mach number, and the pressure ratio across the cascade is derived. Comparison with the corresponding relation for incompressible flow shows large differences. The fundamental relation reveals two ranges of flow angles and inlet Mach numbers, for which no ideal pressure ratio exists. One of these nonideal operating ranges is analogous to a similar type in incompressible flow. The other is characteristic only of compressible flow. The effect of variable axial-flow area is treated. Some implications of the basic conservation laws in the case of nonideal flow through cascades are discussed.

uORFs with unusual translational start codons autoregulate expression of eukaryotic ornithine decarboxylase homologs

PubMed Central

Ivanov, Ivaylo P.; Loughran, Gary; Atkins, John F.

2008-01-01

In a minority of eukaryotic mRNAs, a small functional upstream ORF (uORF), often performing a regulatory role, precedes the translation start site for the main product(s). Here, conserved uORFs in numerous ornithine decarboxylase homologs are identified from yeast to mammals. Most have noncanonical evolutionarily conserved start codons, the main one being AUU, which has not been known as an initiator for eukaryotic chromosomal genes. The AUG-less uORF present in mouse antizyme inhibitor, one of the ornithine decarboxylase homologs in mammals, mediates polyamine-induced repression of the downstream main ORF. This repression is part of an autoregulatory circuit, and one of its sensors is the AUU codon, which suggests that translation initiation codon identity is likely used for regulation in eukaryotes. PMID:18626014

An explicit mixed numerical method for mesoscale model

NASA Technical Reports Server (NTRS)

Hsu, H.-M.

1981-01-01

A mixed numerical method has been developed for mesoscale models. The technique consists of a forward difference scheme for time tendency terms, an upstream scheme for advective terms, and a central scheme for the other terms in a physical system. It is shown that the mixed method is conditionally stable and highly accurate for approximating the system of either shallow-water equations in one dimension or primitive equations in three dimensions. Since the technique is explicit and two time level, it conserves computer and programming resources.

Computation of Laminar and Turbulent Flow in 90-Degree Square-Duct and Pipe Bends Using the Navier-Stokes Equations

DTIC Science & Technology

1982-04-01

R.M. and Warming, R.F.: An Implicit Finite - Difference Algorithm for Hyperbolic Systems in Conservation Law Form. Journal of Computational Physics...Quincy Street C-40) Arlington, VA 22217 D 82 05-.10 I0, S4CURITY CLASSIFICATION OF THIS ’E(Wha, Doae Entotwed) Slength scale. Six different flow cases...forces upstream have produced a non-zero velocity gradient normal to the plane of curvature. Fluid with above (/below) average nioiiiei.tuili migrates

Functional Architecture of T7 RNA Polymerase Transcription Complexes

PubMed Central

Nayak, Dhananjaya; Guo, Qing; Sousa, Rui

2007-01-01

Summary T7 RNA polymerase is the best-characterized member of a widespread family of single-subunit RNA polymerases. Crystal structures of T7 RNA polymerase initiation and elongation complexes have provided a wealth of detailed information on RNA polymerase interactions with the promoter and transcription bubble, but the absence of DNA downstream of the melted region of the template in the initiation complex structure, and the absence of DNA upstream of the transcription bubble in the elongation complex structure means that our picture of the functional architecture of T7 RNA polymerase transcription complexes remains incomplete. Here we use the site-specifically tethered chemical nucleases and functional characterization of directed T7 RNAP mutants to both reveal the architecture of the duplex DNA that flanks the transcription bubble in the T7 RNAP initiation and elongation complexes, and to define the function of the interactions made by these duplex elements. We find that downstream duplex interactions made with a cluster of lysines (K711/K713/K714) are present during both elongation and initiation where they contribute to stabilizing a bend in the downstream DNA that is important for promoter opening. The upstream DNA in the elongation complex is also found to be sharply bent at the upstream edge of the transcription bubble, thereby allowing formation of upstream duplex:polymerase interactions that contribute to elongation complex stability. PMID:17580086

Tone-excited jet: Theory and experiments

NASA Technical Reports Server (NTRS)

Ahuja, K. K.; Lepicovsky, J.; Tam, C. K. W.; Morris, P. J.; Burrin, R. H.

1982-01-01

A detailed study to understand the phenomenon of broadband jet-noise amplification produced by upstream discrete-tone sound excitation has been carried out. This has been achieved by simultaneous acquisition of the acoustic, mean velocity, turbulence intensities, and instability-wave pressure data. A 5.08 cm diameter jet has been tested for this purpose under static and also flight-simulation conditions. An open-jet wind tunnel has been used to simulate the flight effects. Limited data on heated jets have also been obtained. To improve the physical understanding of the flow modifications brought about by the upstream discrete-tone excitation, ensemble-averaged schlieren photographs of the jets have also been taken. Parallel to the experimental study, a mathematical model of the processes that lead to broadband-noise amplification by upstream tones has been developed. Excitation of large-scale turbulence by upstream tones is first calculated. A model to predict the changes in small-scale turbulence is then developed. By numerically integrating the resultant set of equations, the enhanced small-scale turbulence distribution in a jet under various excitation conditions is obtained. The resulting changes in small-scale turbulence have been attributed to broadband amplification of jet noise. Excellent agreement has been found between the theory and the experiments. It has also shown that the relative velocity effects are the same for the excited and the unexcited jets.

Geographic variability in elevation and topographic constraints on the distribution of native and nonnative trout in the Great Basin

USGS Publications Warehouse

Warren, Dana R.; Dunham, Jason B.; Hockman-Wert, David

2014-01-01

Understanding local and geographic factors influencing species distributions is a prerequisite for conservation planning. Our objective in this study was to model local and geographic variability in elevations occupied by native and nonnative trout in the northwestern Great Basin, USA. To this end, we analyzed a large existing data set of trout presence (5,156 observations) to evaluate two fundamental factors influencing occupied elevations: climate-related gradients in geography and local constraints imposed by topography. We applied quantile regression to model upstream and downstream distribution elevation limits for each trout species commonly found in the region (two native and two nonnative species). With these models in hand, we simulated an upstream shift in elevation limits of trout distributions to evaluate potential consequences of habitat loss. Downstream elevation limits were inversely associated with latitude, reflecting regional gradients in temperature. Upstream limits were positively related to maximum stream elevation as expected. Downstream elevation limits were constrained topographically by valley bottom elevations in northern streams but not in southern streams, where limits began well above valley bottoms. Elevation limits were similar among species. Upstream shifts in elevation limits for trout would lead to more habitat loss in the north than in the south, a result attributable to differences in topography. Because downstream distributions of trout in the north extend into valley bottoms with reduced topographic relief, trout in more northerly latitudes are more likely to experience habitat loss associated with an upstream shift in lower elevation limits. By applying quantile regression to relatively simple information (species presence, elevation, geography, topography), we were able to identify elevation limits for trout in the Great Basin and explore the effects of potential shifts in these limits that could occur in response to changing climate conditions that alter streams directly (e.g., through changes in temperature and precipitation) or indirectly (e.g., through changing water use).

Conservation-form equations of unsteady open-channel flow

USGS Publications Warehouse

Lai, C.; Baltzer, R.A.; Schaffranek, R.W.

2002-01-01

The unsteady open-channel flow equations are typically expressed in a variety of forms due to the imposition of differing assumptions, use of varied dependent variables, and inclusion of different source/sink terms. Questions often arise as to whether a particular equation set is expressed in a form consistent with the conservation-law definition. The concept of conservation form is developed to clarify the meaning mathematically. Six sets of unsteady-flow equations typically used in engineering practice are presented and their conservation properties are identified and discussed. Results of the theoretical development and analysis of the equations are substantiated in a set of numerical experiments conducted using alternate equation forms. Findings of these analytical and numerical efforts demonstrate that the choice of dependent variable is the fundamental factor determining the nature of the conservation properties of any particular equation form.

Implementation of the Forest Service Open Space Conservation Strategy in Washington State: Exploring the Role of the National Forest System

Treesearch

Richard J. Pringle; Lee K. Cerveny; Gordon A. Bradley

2015-01-01

The loss of open space was declared one of the “four threats to the health of our nation’s forests” by former USDA Forest Service Chief Dale Bosworth in 2004. Since then, the agencywide Open Space Conservation Strategy (OSCS) was released and the “four threats” were incorporated into the agency’s National Strategic Plan. These actions indicate that the OSCS is in the...

18 CFR 157.36 - Open seasons for expansions.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 18 Conservation of Power and Water Resources 1 2012-04-01 2012-04-01 false Open seasons for... GAS ACT Open Seasons for Alaska Natural Gas Transportation Projects § 157.36 Open seasons for expansions. Any open season for capacity exceeding the initial capacity of an Alaska natural gas...

18 CFR 157.33 - Requirement for open season.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 18 Conservation of Power and Water Resources 1 2011-04-01 2011-04-01 false Requirement for open... GAS ACT Open Seasons for Alaska Natural Gas Transportation Projects § 157.33 Requirement for open... applicant has conducted an open season for capacity on its proposed project, in accordance with the...

18 CFR 157.34 - Notice of open season.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 18 Conservation of Power and Water Resources 1 2012-04-01 2012-04-01 false Notice of open season... ACT Open Seasons for Alaska Natural Gas Transportation Projects § 157.34 Notice of open season. (a) Notice. A prospective applicant must provide reasonable public notice of an open season through methods...

18 CFR 157.34 - Notice of open season.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 18 Conservation of Power and Water Resources 1 2014-04-01 2014-04-01 false Notice of open season... ACT Open Seasons for Alaska Natural Gas Transportation Projects § 157.34 Notice of open season. (a) Notice. A prospective applicant must provide reasonable public notice of an open season through methods...

18 CFR 157.36 - Open seasons for expansions.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 18 Conservation of Power and Water Resources 1 2013-04-01 2013-04-01 false Open seasons for... GAS ACT Open Seasons for Alaska Natural Gas Transportation Projects § 157.36 Open seasons for expansions. Any open season for capacity exceeding the initial capacity of an Alaska natural gas...

18 CFR 157.36 - Open seasons for expansions.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 18 Conservation of Power and Water Resources 1 2011-04-01 2011-04-01 false Open seasons for... GAS ACT Open Seasons for Alaska Natural Gas Transportation Projects § 157.36 Open seasons for expansions. Any open season for capacity exceeding the initial capacity of an Alaska natural gas...

18 CFR 157.36 - Open seasons for expansions.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 18 Conservation of Power and Water Resources 1 2010-04-01 2010-04-01 false Open seasons for... GAS ACT Open Seasons for Alaska Natural Gas Transportation Projects § 157.36 Open seasons for expansions. Any open season for capacity exceeding the initial capacity of an Alaska natural gas...

18 CFR 157.33 - Requirement for open season.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 18 Conservation of Power and Water Resources 1 2013-04-01 2013-04-01 false Requirement for open... GAS ACT Open Seasons for Alaska Natural Gas Transportation Projects § 157.33 Requirement for open... applicant has conducted an open season for capacity on its proposed project, in accordance with the...

18 CFR 157.33 - Requirement for open season.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 18 Conservation of Power and Water Resources 1 2014-04-01 2014-04-01 false Requirement for open... GAS ACT Open Seasons for Alaska Natural Gas Transportation Projects § 157.33 Requirement for open... applicant has conducted an open season for capacity on its proposed project, in accordance with the...

18 CFR 157.36 - Open seasons for expansions.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 18 Conservation of Power and Water Resources 1 2014-04-01 2014-04-01 false Open seasons for... GAS ACT Open Seasons for Alaska Natural Gas Transportation Projects § 157.36 Open seasons for expansions. Any open season for capacity exceeding the initial capacity of an Alaska natural gas...

18 CFR 157.33 - Requirement for open season.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 18 Conservation of Power and Water Resources 1 2012-04-01 2012-04-01 false Requirement for open... GAS ACT Open Seasons for Alaska Natural Gas Transportation Projects § 157.33 Requirement for open... applicant has conducted an open season for capacity on its proposed project, in accordance with the...

18 CFR 157.34 - Notice of open season.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 18 Conservation of Power and Water Resources 1 2013-04-01 2013-04-01 false Notice of open season... ACT Open Seasons for Alaska Natural Gas Transportation Projects § 157.34 Notice of open season. (a) Notice. A prospective applicant must provide reasonable public notice of an open season through methods...

18 CFR 157.33 - Requirement for open season.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 18 Conservation of Power and Water Resources 1 2010-04-01 2010-04-01 false Requirement for open... GAS ACT Open Seasons for Alaska Natural Gas Transportation Projects § 157.33 Requirement for open... applicant has conducted an open season for capacity on its proposed project, in accordance with the...

Level II scour analysis for Bridge 52 (CHESTH00100052) on Town Highway 10, crossing the South branch Williams River, Chester, Vermont

USGS Publications Warehouse

Wild, Emily C.; Ivanoff, Michael A.

1998-01-01

This report provides the results of a detailed Level II analysis of scour potential at structure CHESTH00100052 on Town Highway 10 crossing the South Branch Williams River, Chester, Vermont (figures 1–8). A Level II study is a basic engineering analysis of the site, including a quantitative analysis of stream stability and scour (FHWA, 1993). Results of a Level I scour investigation also are included in appendix E of this report. A Level I investigation provides a qualitative geomorphic characterization of the study site. Information on the bridge, gleaned from Vermont Agency of Transportation (VTAOT) files, was compiled prior to conducting Level I and Level II analyses and is found in appendix D. The site is in the New England Upland section of the New England physiographic province in southeastern Vermont. The 4.05-mi2 drainage area is in a predominantly rural and forested basin. In the vicinity of the study site, the surface cover is forest upstream and downstream of the bridge. In the study area, the South Branch Williams River has an incised, sinuous channel with a slope of approximately 0.03 ft/ft, an average channel top width of 35 ft and an average bank height of 4 ft. The channel bed material ranges from gravel to boulders with a median grain size (D50) of 82.1 mm (0.269 ft). The geomorphic assessment at the time of the Level I and Level II site visit on August 21, 1996, indicated that the reach was unstable, as a result of the moderate bank erosion. The Town Highway 10 crossing of the South Branch Williams River is a 32-ft-long, one-lane bridge consisting of a 29-foot steel-stringer span (Vermont Agency of Transportation, written communication, March 31, 1995). The opening length of the structure parallel to the bridge face is 27.6 ft. The bridge is supported by vertical, concrete abutments with wingwalls. The channel is skewed approximately 25 degrees to the opening while the opening-skew-to-roadway is 20 degrees. A scour hole 1.0 ft deeper than the mean thalweg depth was observed at the downstream end of the right abutment during the Level I assessment. The only scour protection measure at the site was type-2 stone fill (less than 36 inches diameter) along the upstream left and right banks, the upstream end of the upstream right wingwall and the entire base length of the upstream left wingwall. Additional details describing conditions at the site are included in the Level II Summary and appendices D and E. Scour depths and recommended rock rip-rap sizes were computed using the general guidelines described in Hydraulic Engineering Circular 18 (Richardson and Davis, 1995) for the 100- and 500-year discharges. In addition, the incipient roadway-overtopping discharge was determined and analyzed as another potential worst-case scour scenario. Total scour at a highway crossing is comprised of three components: 1) long-term streambed degradation; 2) contraction scour (due to accelerated flow caused by a reduction in flow area at a bridge) and; 3) local scour (caused by accelerated flow around piers and abutments). Total scour is the sum of the three components. Equations are available to compute depths for contraction and local scour and a summary of the results of these computations follows. Contraction scour for all modelled flows ranged from 0.0 to 0.8 ft. The worst-case contraction scour occurred at the 500-year discharge. Abutment scour ranged from 5.2 to 10.8 ft. The worst-case abutment scour also occurred at the 500-year discharge. Additional information on scour depths and depths to armoring are included in the section titled “Scour Results”. Scoured-streambed elevations, based on the calculated scour depths, are presented in tables 1 and 2. A cross-section of the scour computed at the bridge is presented in figure 8. Scour depths were calculated assuming an infinite depth of erosive material and a homogeneous particle-size distribution. It is generally accepted that the Froehlich equation (abutment scour) gives “excessively conservative estimates of scour depths” (Richardson and Davis, 1995, p. 46). Usually, computed scour depths are evaluated in combination with other information including (but not limited to) historical performance during flood events, the geomorphic stability assessment, existing scour protection measures, and the results of the hydraulic analyses. Therefore, scour depths adopted by VTAOT may differ from the computed values documented herein.

Level II scour analysis for Bridge 28 (ROCHTH00370028) on Town Highway 37, crossing Brandon Brook, Rochester, Vermont

USGS Publications Warehouse

Wild, Emily C.; Weber, Matthew A.

1998-01-01

This report provides the results of a detailed Level II analysis of scour potential at structure ROCHTH00370028 on Town Highway 37 crossing Brandon Brook, Rochester, Vermont (figures 1–8). A Level II study is a basic engineering analysis of the site, including a quantitative analysis of stream stability and scour (FHWA, 1993). Results of a Level I scour investigation also are included in appendix E of this report. A Level I investigation provides a qualitative geomorphic characterization of the study site. Information on the bridge, gleaned from VTAOT files, was compiled prior to conducting Level I and Level II analyses and is found in appendix D. The site is in the Green Mountain section of the New England physiographic province in central Vermont. The 8.0-mi2 drainage area is in a predominantly rural and forested basin. In the vicinity of the study site, the surface cover is pasture on the upstream left overbank although the immediate banks have dense woody vegetation. The upstream right overbank and downstream left and right overbanks are forested. In the study area, the Brandon Brook has an incised, sinuous channel with a slope of approximately 0.01 ft/ft, an average channel top width of 44 ft and an average bank height of 7 ft. The channel bed material ranges from gravel to cobbles with a median grain size (D50) of 84.2 mm (0.276 ft). The geomorphic assessment at the time of the Level I site visit on April 12, 1995 and Level II site visit on July 8, 1996, indicated that the reach was stable. The Town Highway 37 crossing of the Brandon Brook is a 33-ft-long, one-lane bridge consisting of a 31-foot timber-stringer span (Vermont Agency of Transportation, written communication, March 22, 1995). The opening length of the structure parallel to the bridge face is 29.6 ft. The bridge is supported by vertical, timber log cribbing abutments with wingwalls. The channel is skewed approximately 5 degrees to the opening while the computed opening-skew-to-roadway is zero degrees. A scour hole 1.0 ft deeper than the mean thalweg depth was observed along the upstream left wingwall and the left abutment during the Level I assessment. The only scour protection measure at the site was type-5 protection, an artificial levee, extending along the upstream right bank to the end of the upstream right wingwall. Additional details describing conditions at the site are included in the Level II Summary and appendices D and E.Scour depths and recommended rock rip-rap sizes were computed using the general guidelines described in Hydraulic Engineering Circular 18 (Richardson and others, 1995) for the 100- and 500-year discharges. Total scour at a highway crossing is comprised of three components: 1) long-term streambed degradation; 2) contraction scour (due to accelerated flow caused by a reduction in flow area at a bridge) and; 3) local scour (caused by accelerated flow around piers and abutments). Total scour is the sum of the three components. Equations are available to compute depths for contraction and local scour and a summary of the results of these computations follows. Contraction scour for all modelled flows was zero ft. Left abutment scour ranged from 7.1 to 9.9 ft where the worst-case scour occurred at the 500-year discharge. Right abutment scour ranged from 4.4 to 5.1 ft where the worst-case scour occurred at the 500-year discharge. Additional information on scour depths and depths to armoring are included in the section titled “Scour Results.” Scoured-streambed elevations, based on the calculated scour depths, are presented in tables 1 and 2. A cross-section of the scour computed at the bridge is presented in figure 8. Scour depths were calculated assuming an infinite depth of erosive material and a homogeneous particle-size distribution. It is generally accepted that the Froehlich equation (abutment scour) gives “excessively conservative estimates of scour depths” (Richardson and Davis, 1995, p. 46). Usually, computed scour depths are evaluated in combination with other information including (but not limited to) historical performance during flood events, the geomorphic stability assessment, existing scour protection measures, and the results of the hydraulic analyses. Therefore, scour depths adopted by VTAOT may differ from the computed values documented herein

Level II scour analysis for Bridge 38 (JERITH0020038) on Town Highway 20, crossing the Lee River, Jericho, Vermont

USGS Publications Warehouse

Wild, Emily C.; Degnan, James R.

1997-01-01

This report provides the results of a detailed Level II analysis of scour potential at structure JERITH00200038 on Town Highway 20 crossing the Lee River, Jericho, Vermont (figures 1–8). A Level II study is a basic engineering analysis of the site, including a quantitative analysis of stream stability and scour (U.S. Department of Transportation, 1993). Results of a Level I scour investigation also are included in Appendix E of this report. A Level I investigation provides a qualitative geomorphic characterization of the study site. Information on the bridge, obtained from Vermont Agency of Transportation (VTAOT) files, was compiled prior to conducting Level I and Level II analyses and is found in Appendix D. The site is in the Green Mountain section of the New England physiographic province and the Champlain section of the St. Lawrence physiographic province in northwestern Vermont. The 12.9-mi2 drainage area is in a predominantly rural and forested basin. In the vicinity of the study site, the surface cover on the upstream and downstream right overbank is pasture while the immediate banks have dense woody vegetation. The surface cover on the upstream and downstream left overbank is forested. In the study area, the Lee River has an incised, sinuous channel with a slope of approximately 0.02 ft/ft, an average channel top width of 89 ft and an average bank height of 14 ft. The channel bed material ranges from sand to boulder with a median grain size (D50) of 45.9 mm (0.151 ft). The geomorphic assessment at the time of the Level I and Level II site visit on July 2, 1996, indicated that the reach was stable. The Town Highway 20 crossing of the Lee River is a 49-ft-long, one-lane bridge consisting of a steel through truss span (Vermont Agency of Transportation, written communication, December 12, 1995). The opening length of the structure parallel to the bridge face is 44 ft. The bridge is supported by vertical, concrete abutments with wingwalls. The channel is skewed approximately 10 degrees to the opening while the computed opening-skew-toroadway is 5 degrees. A scour hole 1 ft deeper than the mean thalweg depth was observed in the center of the channel during the Level I assessment. Scour countermeasures at the site include type-1 stone fill (less than 12 inches diameter) at the downstream left road embankment. Type-2 stone fill (less than 36 inches diameter) protects the upstream left wingwall, the upstream and downstream right wingwalls and the upstream end of the right abutment. Type-3 stone fill (less than 48 inches diameter) protects the left abutment. Additional details describing conditions at the site are included in the Level II Summary and Appendices D and E. Scour depths and recommended rock rip-rap sizes were computed using the general guidelines described in Hydraulic Engineering Circular 18 (Richardson and others, 1995) for the 100- and 500-year discharges. Total scour at a highway crossing is comprised of three components: 1) long-term streambed degradation; 2) contraction scour (due to accelerated flow caused by a reduction in flow area at a bridge) and; 3) local scour (caused by accelerated flow around piers and abutments). Total scour is the sum of the three components. Equations are available to compute depths for contraction and local scour and a summary of the results of these computations follows. Contraction scour for all modelled flows was zero. Abutment scour ranged from 4.9 to 10.7 ft. The worst-case abutment scour occurred at the 500-year discharge. Additional information on scour depths and depths to armoring are included in the section titled “Scour Results”. Scoured-streambed elevations, based on the calculated scour depths, are presented in tables 1 and 2. A cross-section of the scour computed at the bridge is presented in figure 8. Scour depths were calculated assuming an infinite depth of erosive material and a homogeneous particle-size distribution. It is generally accepted that the Froehlich equation (abutment scour) gives “excessively conservative estimates of scour depths” (Richardson and others, 1995, p. 47). Usually, computed scour depths are evaluated in combination with other information including (but not limited to) historical performance during flood events, the geomorphic stability assessment, existing scour protection measures, and the results of the hydraulic analyses. Therefore, scour depths adopted by VTAOT may differ from the computed values documented herein.

Level II scour analysis for Bridge 13 (LINCTH00010013) on Town Highway 1, crossing Cota Brook, Lincoln, Vermont

USGS Publications Warehouse

Wild, Emily C.

1998-01-01

This report provides the results of a detailed Level II analysis of scour potential at structure LINCTH00010013 on Town Highway 1 crossing Cota Brook, Lincoln, Vermont (figures 1–8). A Level II study is a basic engineering analysis of the site, including a quantitative analysis of stream stability and scour (FHWA, 1993). Results of a Level I scour investigation also are included in appendix E of this report. A Level I investigation provides a qualitative geomorphic characterization of the study site. Information on the bridge, gleaned from Vermont Agency of Transportation (VTAOT) files, was compiled prior to conducting Level I and Level II analyses and is found in appendix D. The site is in the Green Mountain section of the New England physiographic province in west-central Vermont. The 3.0-mi2 drainage area is in a predominantly rural and forested basin. In the vicinity of the study site, the surface cover is forest along the upstream right bank and brushland along the upstream left bank. Downstream of the bridge, the surface cover is pasture along the left and right banks. In the study area, Cota Brook has an sinuous channel with a slope of approximately 0.01 ft/ ft, an average channel top width of 30 ft and an average bank height of 2 ft. The channel bed material ranges from sand to cobble with a median grain size (D50) of 34.7 mm (0.114 ft). The geomorphic assessment at the time of the Level I and Level II site visit on June 10, 1996, indicated that the reach was laterally unstable due to cut-banks and wide, vegetated point bars upstream and downstream of the bridge. The Town Highway 1 crossing of Cota Brook is a 38-ft-long, two-lane bridge consisting of a 36-foot steel-stringer span (Vermont Agency of Transportation, written communication, December 14, 1995). The opening length of the structure parallel to the bridge face is 34.4 ft. The bridge is supported by vertical, concrete abutments. The channel is skewed approximately 15 degrees to the opening while the opening-skew-to-roadway is zero degrees.A scour hole 2.0 ft deeper than the mean thalweg depth was observed along the upstream right bank during the Level I assessment. Along the right abutment, it is 0.25 ft deeper than the mean thalweg depth. Scour protection measures at the site included type-1 stone fill (less than 12 inches diameter) along the upstream right bank and type-2 stone fill (less than 36 inches diameter) along the left and right abutments and along the downstream left bank. Additional details describing conditions at the site are included in the Level II Summary and appendices D and E. Scour depths and recommended rock rip-rap sizes were computed using the general guidelines described in Hydraulic Engineering Circular 18 (Richardson and Davis, 1995) for the 100- and 500-year discharges. Total scour at a highway crossing is comprised of three components: 1) long-term streambed degradation; 2) contraction scour (due to accelerated flow caused by a reduction in flow area at a bridge) and; 3) local scour (caused by accelerated flow around piers and abutments). Total scour is the sum of the three components. Equations are available to compute depths for contraction and local scour and a summary of the results of these computations follows. Contraction scour for all modelled flows ranged from 0.0 to 1.7 ft. The worst-case contraction scour occurred at the 500-year discharge. Abutment scour ranged from 9.1 to 11.3 ft. The worst-case abutment scour occurred at the 500-year discharge. Additional information on scour depths and depths to armoring are included in the section titled “Scour Results”. Scoured-streambed elevations, based on the calculated scour depths, are presented in tables 1 and 2. A cross-section of the scour computed at the bridge is presented in figure 8. Scour depths were calculated assuming an infinite depth of erosive material and a homogeneous particle-size distribution. It is generally accepted that the Froehlich equation (abutment scour) gives “excessively conservative estimates of scour depths” (Richardson and Davis, 1995, p. 46). Usually, computed scour depths are evaluated in combination with other information including (but not limited to) historical performance during flood events, the geomorphic stability assessment, existing scour protection measures, and the results of the hydraulic analyses. Therefore, scour depths adopted by VTAOT may differ from the computed values documented herein.

Level II scour analysis for Bridge 63 (MTH0TH00120063) on Town Highway 12, crossing Russell Brook, Mount Holly, Vermont

USGS Publications Warehouse

Wild, Emily C.; Severance, Timothy

1998-01-01

This report provides the results of a detailed Level II analysis of scour potential at structure MTHOTH00120063 on Town Highway 12 crossing Russell Brook, Mount Holly, Vermont (figures 1–8). A Level II study is a basic engineering analysis of the site, including a quantitative analysis of stream stability and scour (FHWA, 1993). Results of a Level I scour investigation also are included in appendix E of this report. A Level I investigation provides a qualitative geomorphic characterization of the study site. Information on the bridge, gleaned from Vermont Agency of Transportation (VTAOT) files, was compiled prior to conducting Level I and Level II analyses and is found in appendix D. The site is in the Green Mountain section of the New England physiographic province in south-central Vermont. The 3.6-mi2 drainage area is in a predominantly rural and forested basin. In the vicinity of the study site, the surface cover is forest upstream and downstream of the bridge. In the study area, Russell Brook has an incised, sinuous channel with a slope of approximately 0.0263 ft/ft, an average channel top width of 29 ft and an average bank height of 3 ft. The channel bed material ranges from cobbles to boulders with a median grain size (D50) of 97.1 mm (0.318 ft). The geomorphic assessment at the time of the Level I and Level II site visit on October 4, 1995, indicated that the reach was stable. The Town Highway 12 crossing of Russell Brook is a 29-ft-long, one-lane bridge consisting of a 26-foot steel-stringer span (Vermont Agency of Transportation, written communication, March 21, 1995). The opening length of the structure parallel to the bridge face is 23.5 ft. The bridge is supported by vertical, concrete abutments with wingwalls. The channel is skewed approximately 40 degrees to the opening while the computed opening-skew-to-roadway is 35 degrees. During the Level I assessment, it was observed that the upstream left wingwall footing was exposed 0.2 ft, in reference to the mean thalweg depth, and the upstream end of the left abutment was exposed 0.1 ft. The scour protection measure at the site was type-2 stone fill (less than 36 inches diameter) along the upstream end of the upstream left wingwall. Additional details describing conditions at the site are included in the Level II Summary and appendices D and E.Scour depths and recommended rock rip-rap sizes were computed using the general guidelines described in Hydraulic Engineering Circular 18 (Richardson and Davis, 1995) for the 100- and 500-year discharges. Total scour at a highway crossing is comprised of three components: 1) long-term streambed degradation; 2) contraction scour (due to accelerated flow caused by a reduction in flow area at a bridge) and; 3) local scour (caused by accelerated flow around piers and abutments). Total scour is the sum of the three components. Equations are available to compute depths for contraction and local scour and a summary of the results of these computations follows. Contraction scour for all modelled flows ranged from 0.0 to 0.1 ft. The worst-case contraction scour occurred at the 100-year discharge. Left abutment scour ranged from 4.4 to 5.7 ft. Right abutment scour ranged from 11.3 to 12.2 ft. The worst-case abutment scour occurred at the 500-year discharge. Additional information on scour depths and depths to armoring are included in the section titled “Scour Results”. Scoured-streambed elevations, based on the calculated scour depths, are presented in tables 1 and 2. A cross-section of the scour computed at the bridge is presented in figure 8. Scour depths were calculated assuming an infinite depth of erosive material and a homogeneous particle-size distribution. It is generally accepted that the Froehlich equation (abutment scour) gives “excessively conservative estimates of scour depths” (Richardson and Davis, 1995, p. 46). Usually, computed scour depths are evaluated in combination with other information including (but not limited to) historical performance during flood events, the geomorphic stability assessment, existing scour protection measures, and the results of the hydraulic analyses. Therefore, scour depths adopted by VTAOT may differ from the computed values documented herein.

Level II scour analysis for Bridge 20 (BRISTH00270020) on Town Highway 27, crossing Little Notch Brook, Bristol, Vermont

USGS Publications Warehouse

Boehmler, Erick M.

1997-01-01

This report provides the results of a detailed Level II analysis of scour potential at structure BRISTH00270020 on Town Highway 27 crossing Little Notch Brook, Bristol, Vermont (figures 1–8). A Level II study is a basic engineering analysis of the site, including a quantitative analysis of stream stability and scour (U.S. Department of Transportation, 1993). Results of a Level I scour investigation also are included in Appendix E of this report. A Level I investigation provides a qualitative geomorphic characterization of the study site. Information on the bridge, gleaned from Vermont Agency of Transportation (VTAOT) files, was compiled prior to conducting Level I and Level II analyses and is found in Appendix D. The site is in the Green Mountain section of the New England physiographic province in west-central Vermont. The 8.43-mi2 drainage area is in a predominantly rural and forested basin. In the vicinity of the study site, the surface cover consists of pasture with trees, shrubs, and brush along the road embankments and the stream banks, except for the downstream left overbank area. Surface cover on the downstream left overbank is forest with dense undergrowth consisting of vines, shrubs, and brush. In the study area, Little Notch Brook has a sinuous channel with a slope of approximately 0.006 ft/ft, an average channel top width of 47 feet and an average bank height of 3 feet. The predominant channel bed materials are gravel and cobbles with a median grain size (D50) of 66.0 mm (0.216 ft). The geomorphic assessment at the time of the Level I and Level II site visit on June 19, 1995, indicated that the reach was stable. The Town Highway 27 crossing of Little Notch Brook is a 48-ft-long, one-lane bridge consisting of one 45-foot steel pony-truss span (Vermont Agency of Transportation, written communication, November 30, 1995). The opening length of the structure parallel to the bridge face is 42.8 feet. The bridge is supported by vertical, concrete abutments with wingwalls. The channel is skewed approximately 15 degrees to the opening while the opening-skew-to-roadway is zero degrees. A scour hole 1.0 feet deeper than the mean thalweg depth was observed along the upstream left wingwall and the upstream end of the left abutment during the Level I assessment. The only scour protection measure at the site was a crude, block-cut stone wall, which extended from the upstream end of the upstream left wingwall to 45 feet upstream. Additional details describing conditions at the site are included in the Level II Summary and Appendices D and E. Scour depths and recommended rock rip-rap sizes were computed using the general guidelines described in Hydraulic Engineering Circular 18 (Richardson and others, 1995) for the 100- and 500-year discharges. In addition, the incipient roadway-overtopping discharge is determined and analyzed as another potential worst-case scour scenario. Total scour at a highway crossing is comprised of three components: 1) long-term streambed degradation; 2) contraction scour (due to accelerated flow caused by a reduction in flow area at a bridge) and; 3) local scour (caused by accelerated flow around piers and abutments). Total scour is the sum of the three components. Equations are available to compute depths for contraction and local scour and a summary of the results of these computations follows. Contraction scour for all modelled flows ranged from 0.0 to 0.2 feet. The worst-case contraction scour occurred at the 500-year discharge. Abutment scour ranged from 12.2 to 13.4 feet at the left abutment and from 3.6 to 5.0 feet at the right abutment. The worst-case abutment scour occurred at the 500-year discharge. Additional information on scour depths and depths to armoring are included in the section titled “Scour Results”. Scoured-streambed elevations, based on the calculated scour depths, are presented in tables 1 and 2. A cross-section of the scour computed at the bridge is presented in figure 8. Scour depths were calculated assuming an infinite depth of erosive material and a homogeneous particle-size distribution. It is generally accepted that the Froehlich equation (abutment scour) gives “excessively conservative estimates of scour depths” (Richardson and others, 1995, p. 47). Usually, computed scour depths are evaluated in combination with other information including (but not limited to) historical performance during flood events, the geomorphic stability assessment, existing scour protection measures, and the results of the hydraulic analyses. Therefore, scour depths adopted by VTAOT may differ from the computed values documented herein.

Level II scour analysis for Bridge 32 (TUNBTH00600032) on Town Highway 60, crossing First Branch White River, Tunbridge, Vermont

USGS Publications Warehouse

Wild, Emily C.

1998-01-01

This report provides the results of a detailed Level II analysis of scour potential at structure TUNBTH00600032 on Town Highway 60 crossing the First Branch White River, Tunbridge, Vermont (figures 1–8). A Level II study is a basic engineering analysis of the site, including a quantitative analysis of stream stability and scour (U.S. Department of Transportation, 1993). Results of a Level I scour investigation also are included in appendix E of this report. A Level I investigation provides a qualitative geomorphic characterization of the study site. Information on the bridge, gleaned from Vermont Agency of Transportation (VTAOT) files, was compiled prior to conducting Level I and Level II analyses and is found in appendix D. The site is in the New England Upland section of the New England physiographic province in central Vermont. The 92.9-mi2 drainage area is in a predominantly rural and forested basin. In the vicinity of the study site, the surface cover is pasture upstream and downstream of the bridge, while woody vegetation sparsely covers the immediate banks. In the study area, the First Branch White River has a sinuous channel with a slope of approximately 0.001 ft/ft, an average channel top width of 82 ft and an average bank height of 7 ft. The channel bed material ranges from sand to gravel with a median grain size (D50) of 24.4 mm (0.08 ft). The geomorphic assessment at the time of the Level I and Level II site visit on October 18, 1995, indicated that the reach was laterally unstable, as a result of block failure of moderately eroded banks. The Town Highway 60 crossing of the First Branch White River is a 74-ft-long, one-lane bridge consisting of a 71-foot timber thru-truss span (Vermont Agency of Transportation, written communication, August 24, 1994). The opening length of the structure parallel to the bridge face is 64 ft.The bridge is supported by vertical, laid-up stone abutments with upstream wingwalls. The channel is not skewed to the opening. The computed opening-skew-to-roadway is 5 degrees. A scour hole 1.0 ft deeper than the mean thalweg depth was observed in the upstream reach during the Level I assessment. Scour countermeasures at the site includes type-1 stone fill (less than 12 inches diameter) along the upstream right bank. Type-2 stone fill (less than 36 inches diameter) is present along the upstream right wingwall, the left abutment and the right abutment. Additional details describing conditions at the site are included in the Level II Summary and appendices D and E. Scour depths and recommended rock rip-rap sizes were computed using the general guidelines described in Hydraulic Engineering Circular 18 (Richardson and Davis, 1995) for the 100- and 500-year discharges. In addition, the maximum free-surface discharge was determined and analyzed as another potential worst-case scour scenarios. Total scour at a highway crossing is comprised of three components: 1) long-term streambed degradation; 2) contraction scour (due to accelerated flow caused by a reduction in flow area at a bridge) and; 3) local scour (caused by accelerated flow around piers and abutments). Total scour is the sum of the three components. Equations are available to compute depths for contraction and local scour and a summary of the results of these computations follows. Contraction scour for all modelled flows ranged from 2.2 to 6.8 ft. The worst-case contraction scour occurred at the 500-year discharge. Left abutment scour ranged from 20.6 to 30.4 ft. Right abutment scour ranged from 9.7 to 19.5 ft. The worst-case abutment scour occurred at the 500-year discharge. Additional information on scour depths and depths to armoring are included in the section titled “Scour Results”. Scoured-streambed elevations, based on the calculated scour depths, are presented in tables 1 and 2. A cross-section of the scour computed at the bridge is presented in figure 8. Scour depths were calculated assuming an infinite depth of erosive material and a homogeneous particle-size distribution. It is generally accepted that the Froehlich equation (abutment scour) gives “excessively conservative estimates of scour depths” (Richardson and Davis, 1995, p. 47). Usually, computed scour depths are evaluated in combination with other information including (but not limited to) historical performance during flood events, the geomorphic stability assessment, existing scour protection measures, and the results of the hydraulic analyses. Therefore, scour depths adopted by VTAOT may differ from the computed values documented herein.

Kin28 regulates the transient association of Mediator with core promoters

PubMed Central

Jeronimo, Célia; Robert, François

2014-01-01

Mediator is an essential, broadly utilized eukaryotic transcriptional co-activator. How and what it communicates from activators to RNA polymerase II (RNAPII) remains an open question. Here we performed genome-wide location profiling of Saccharomyces cerevisiae Mediator subunits. Mediator is not found at core promoters but rather occupies the upstream activating sequence (UAS), upstream of the pre-initiation complex. In the absence of Kin28 (CDK7) kinase activity, or in cells where the RNAPII C-terminal domain (CTD) is mutated to replace Ser5 with alanines, however, Mediator accumulates at core promoters together with RNAPII. We propose that Mediator is quickly released from promoters upon Ser5 phosphorylation by Kin28 (CDK7), which also allows for RNAPII to escape from the promoter. PMID:24704787

Effects of Buoyancy on the Flowfields of Lean Premixed Turbulent V-Flames

NASA Technical Reports Server (NTRS)

Cheng, R. K.; Greenberg, P.; Bedat, B.; Yegian, D. T.

1999-01-01

Open laboratory turbulent flames used for investigating fundament flame turbulence interactions are greatly affected by buoyancy. Though much of our current knowledge is based on observations made in these open flames, the effects of buoyancy are usually not included in data interpretation, numerical analysis or theories. This inconsistency remains an obstacle to merging experimental observations and theoretical predictions. To better understanding the effects of buoyancy, our research focuses on steady lean premixed flames propagating in fully developed turbulence. We hypothesize that the most significant role of buoyancy forces on these flames is to influence their flowfields through a coupling with mean and fluctuating pressure fields. Changes in flow pattern alter the mean aerodynamic stretch and in turn affect turbulence fluctuation intensities both upstream and downstream of the flame zone. Consequently, flame stabilization, reaction rates, and turbulent flame processes are all affected. This coupling relates to the elliptical problem that emphasizes the importance of the upstream, wall and downstream boundary conditions in determining all aspects of flame propagation. Therefore, buoyancy has the same significance as other parameters such as flow configuration, flame geometry, means of flame stabilization, flame shape, enclosure size, mixture conditions, and flow conditions.

Gene expression regulation by upstream open reading frames and human disease.

PubMed

Barbosa, Cristina; Peixeiro, Isabel; Romão, Luísa

2013-01-01

Upstream open reading frames (uORFs) are major gene expression regulatory elements. In many eukaryotic mRNAs, one or more uORFs precede the initiation codon of the main coding region. Indeed, several studies have revealed that almost half of human transcripts present uORFs. Very interesting examples have shown that these uORFs can impact gene expression of the downstream main ORF by triggering mRNA decay or by regulating translation. Also, evidence from recent genetic and bioinformatic studies implicates disturbed uORF-mediated translational control in the etiology of many human diseases, including malignancies, metabolic or neurologic disorders, and inherited syndromes. In this review, we will briefly present the mechanisms through which uORFs regulate gene expression and how they can impact on the organism's response to different cell stress conditions. Then, we will emphasize the importance of these structures by illustrating, with specific examples, how disturbed uORF-mediated translational control can be involved in the etiology of human diseases, giving special importance to genotype-phenotype correlations. Identifying and studying more cases of uORF-altering mutations will help us to understand and establish genotype-phenotype associations, leading to advancements in diagnosis, prognosis, and treatment of many human disorders.

Suspended-sediment trapping in the tidal reach of an estuarine tributary channel

USGS Publications Warehouse

Downing-Kunz, Maureen; Schoellhamer, David H.

2015-01-01

Evidence of decreasing sediment supply to estuaries and coastal oceans worldwide illustrates the need for accurate and updated estimates. In the San Francisco Estuary (Estuary), recent research suggests a decrease in supply from its largest tributaries, implying the increasing role of smaller, local tributaries in sediment supply to this estuary. Common techniques for estimating supply from tributaries are based on gages located above head of tide, which do not account for trapping processes within the tidal reach. We investigated the effect of a tidal reach on suspended-sediment discharge for Corte Madera Creek, a small tributary of the Estuary. Discharge of water (Q) and suspended-sediment (SSD) were observed for 3 years at two locations along the creek: upstream of tidal influence and at the mouth. Comparison of upstream and mouth gages showed nearly 50 % trapping of upstream SSD input within the tidal reach over this period. At the storm time scale, suspended-sediment trapping efficiency varied greatly (range −31 to 93 %); storms were classified as low- or high-yield based on upstream SSD. As upstream peak Q increased, high-yield storms exhibited significantly decreased trapping. Tidal conditions at the mouth—ebb duration and peak ebb velocity—during storms had a minor effect on sediment trapping, suggesting fluvial processes dominate. Comparison of characteristic fluvial and tidal discharges at the storm time scale demonstrated longitudinal differences in the regulating process for SSD. These results suggest that SSD from gages situated above head of tide overestimate sediment supply to the open waters beyond tributary mouths and thus trapping processes within the tidal reach should be considered.

White sturgeon (Acipenser transmontanus) passage at the Dalles Dam, Columbia River, USA

USGS Publications Warehouse

Parsley, M.J.; Wright, C.D.; Van Der Leeuw, B. K.; Kofoot, E.E.; Peery, C.A.; Moser, M.L.

2007-01-01

White sturgeon (Acipenser transmontanus) ???95 cm TL were monitored using acoustic and radio telemetry at a large hydroelectric dam (the Dalles Dam) on the Columbia River, during March 2004 through November 2005 to determine timing and routes of passage and to characterize general movements. Transmitters were surgically implanted into 148 fish during the study; 90 were released into the tailrace and 58 into the forebay. We documented 26 passage events by 19 tagged fish: eight upstream via fish ladders and 18 downstream, mostly through open spill gates. During the study 17 fish entered the two ladders one or more times; 11 entered only the east ladder, three entered only the north ladder, and three entered both ladders at sometime. Residence time within the ladders by individual fish was variable, ranging from about 1 min to nearly 6 months (median = 7.7 h). Only six fish successfully ascended the east ladder, one fish twice. We could not unequivocally determine which fish ladder one fish used to pass upstream. Differences in construction between the north and east fish ladders may account for the greater success of the east fish ladder in passing sturgeon upstream. Changes to operations at hydroelectric dams to benefit migrating anadromous salmonids may influence upstream or downstream passage by white sturgeon. Altering patterns and timing of spill discharge, altering fish ladder entrance attraction flows, and the use of lights, sound, and partial barriers to direct other species of fish to preferred passage routes have unknown effects on sturgeon passage. A better understanding of the consequences to the metapopulation of increasing or precluding upstream or downstream passage is needed. ?? 2007 The Authors.

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

Guo Zehua; Tang Xianzhu

Parallel transport of long mean-free-path plasma along an open magnetic field line is characterized by strong temperature anisotropy, which is driven by two effects. The first is magnetic moment conservation in a non-uniform magnetic field, which can transfer energy between parallel and perpendicular degrees of freedom. The second is decompressional cooling of the parallel temperature due to parallel flow acceleration by conventional presheath electric field which is associated with the sheath condition near the wall surface where the open magnetic field line intercepts the discharge chamber. To the leading order in gyroradius to system gradient length scale expansion, the parallelmore » transport can be understood via the Chew-Goldbeger-Low (CGL) model which retains two components of the parallel heat flux, i.e., q{sub n} associated with the parallel thermal energy and q{sub s} related to perpendicular thermal energy. It is shown that in addition to the effect of magnetic field strength (B) modulation, the two components (q{sub n} and q{sub s}) of the parallel heat flux play decisive roles in the parallel variation of the plasma profile, which includes the plasma density (n), parallel flow (u), parallel and perpendicular temperatures (T{sub Parallel-To} and T{sub Up-Tack }), and the ambipolar potential ({phi}). Both their profile (q{sub n}/B and q{sub s}/B{sup 2}) and the upstream values of the ratio of the conductive and convective thermal flux (q{sub n}/nuT{sub Parallel-To} and q{sub s}/nuT{sub Up-Tack }) provide the controlling physics, in addition to B modulation. The physics described by the CGL model are contrasted with those of the double-adiabatic laws and further elucidated by comparison with the first-principles kinetic simulation for a specific but representative flux expander case.« less

Mutually Exclusive Splicing of the Insect Dscam Pre-mRNA Directed by Competing Intronic RNA Secondary Structures

PubMed Central

Graveley, Brenton R.

2008-01-01

Summary Drosophila Dscam encodes 38,016 distinct axon guidance receptors through the mutually exclusive alternative splicing of 95 variable exons. Importantly, known mechanisms that ensure the mutually exclusive splicing of pairs of exons cannot explain this phenomenon in Dscam. I have identified two classes of conserved elements in the Dscam exon 6 cluster, which contains 48 alternative exons—the docking site, located in the intron downstream of constitutive exon 5, and the selector sequences, which are located upstream of each exon 6 variant. Strikingly, each selector sequence is complementary to a portion of the docking site, and this pairing juxtaposes one, and only one, alternative exon to the upstream constitutive exon. The mutually exclusive nature of the docking site:selector sequence interactions suggests that the formation of these competing RNA structures is a central component of the mechanism guaranteeing that only one exon 6 variant is included in each Dscam mRNA. PMID:16213213

Electron cooling and finite potential drop in a magnetized plasma expansion

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

Martinez-Sanchez, M.; Navarro-Cavallé, J.; Ahedo, E.

2015-05-15

The steady, collisionless, slender flow of a magnetized plasma into a surrounding vacuum is considered. The ion component is modeled as mono-energetic, while electrons are assumed Maxwellian upstream. The magnetic field has a convergent-divergent geometry, and attention is restricted to its paraxial region, so that 2D and drift effects are ignored. By using the conservation of energy and magnetic moment of particles and the quasi-neutrality condition, the ambipolar electric field and the distribution functions of both species are calculated self-consistently, paying attention to the existence of effective potential barriers associated to magnetic mirroring. The solution is used to find themore » total potential drop for a set of upstream conditions, plus the axial evolution of various moments of interest (density, temperatures, and heat fluxes). The results illuminate the behavior of magnetic nozzles, plasma jets, and other configurations of interest, showing, in particular, in the divergent plasma the collisionless cooling of electrons, and the generation of collisionless electron heat fluxes.« less

Sleep-Active Neurons: Conserved Motors of Sleep

PubMed Central

Bringmann, Henrik

2018-01-01

Sleep is crucial for survival and well-being. This behavioral and physiological state has been studied in all major genetically accessible model animals, including rodents, fish, flies, and worms. Genetic and optogenetic studies have identified several neurons that control sleep, making it now possible to compare circuit mechanisms across species. The “motor” of sleep across animal species is formed by neurons that depolarize at the onset of sleep to actively induce this state by directly inhibiting wakefulness. These sleep-inducing neurons are themselves controlled by inhibitory or activating upstream pathways, which act as the “drivers” of the sleep motor: arousal inhibits “sleep-active” neurons whereas various sleep-promoting “tiredness” pathways converge onto sleep-active neurons to depolarize them. This review provides the first overview of sleep-active neurons across the major model animals. The occurrence of sleep-active neurons and their regulation by upstream pathways in both vertebrate and invertebrate species suggests that these neurons are general and ancient components that evolved early in the history of nervous systems. PMID:29618588

On the Instability of Large Slopes in the Upstream of Wu River, Taiwan

NASA Astrophysics Data System (ADS)

Shou, Keh-Jian; Lin, Jia-Fei

2015-04-01

Considering the existence of various types of landslides (shallow and deep-seated) and the importance of protection targets (the landslide might affect a residential area, cut a road, isolate a village, etc.), this study aims to analyze the landslide susceptibility along the Lixing Industrial Road, i.e., Nantou County Road # 89, in the upstream of Wu River. Focusing on the selected typical large scale landslides, the data and information of the landslides were collected from the field and the government (including the local government, the Soil and Water Conservation Bureau, and the highway agencies). Based on the data of Li-DAR and the information from boreholes, the temporal behavior and the complex mechanism of large scale landslides were analyzed. To assess the spatial hazard of the landslides, probabilistic analysis was applied. The study of the landslide mechanism can help to understand the behavior of landslides in similar geologic conditions, and the results of hazard analysis can be applied for risk prevention and management in the study area.

Highly tissue specific expression of Sphinx supports its male courtship related role in Drosophila melanogaster.

PubMed

Chen, Ying; Dai, Hongzheng; Chen, Sidi; Zhang, Luoying; Long, Manyuan

2011-04-26

Sphinx is a lineage-specific non-coding RNA gene involved in regulating courtship behavior in Drosophila melanogaster. The 5' flanking region of the gene is conserved across Drosophila species, with the proximal 300 bp being conserved out to D. virilis and a further 600 bp region being conserved amongst the melanogaster subgroup (D. melanogaster, D. simulans, D. sechellia, D. yakuba, and D. erecta). Using a green fluorescence protein transformation system, we demonstrated that a 253 bp region of the highly conserved segment was sufficient to drive sphinx expression in male accessory gland. GFP signals were also observed in brain, wing hairs and leg bristles. An additional ∼800 bp upstream region was able to enhance expression specifically in proboscis, suggesting the existence of enhancer elements. Using anti-GFP staining, we identified putative sphinx expression signal in the brain antennal lobe and inner antennocerebral tract, suggesting that sphinx might be involved in olfactory neuron mediated regulation of male courtship behavior. Whole genome expression profiling of the sphinx knockout mutation identified significant up-regulated gene categories related to accessory gland protein function and odor perception, suggesting sphinx might be a negative regulator of its target genes.

Highly Tissue Specific Expression of Sphinx Supports Its Male Courtship Related Role in Drosophila melanogaster

PubMed Central

Chen, Sidi; Zhang, Luoying; Long, Manyuan

2011-01-01

Sphinx is a lineage-specific non-coding RNA gene involved in regulating courtship behavior in Drosophila melanogaster. The 5′ flanking region of the gene is conserved across Drosophila species, with the proximal 300 bp being conserved out to D. virilis and a further 600 bp region being conserved amongst the melanogaster subgroup (D. melanogaster, D. simulans, D. sechellia, D. yakuba, and D. erecta). Using a green fluorescence protein transformation system, we demonstrated that a 253 bp region of the highly conserved segment was sufficient to drive sphinx expression in male accessory gland. GFP signals were also observed in brain, wing hairs and leg bristles. An additional ∼800 bp upstream region was able to enhance expression specifically in proboscis, suggesting the existence of enhancer elements. Using anti-GFP staining, we identified putative sphinx expression signal in the brain antennal lobe and inner antennocerebral tract, suggesting that sphinx might be involved in olfactory neuron mediated regulation of male courtship behavior. Whole genome expression profiling of the sphinx knockout mutation identified significant up-regulated gene categories related to accessory gland protein function and odor perception, suggesting sphinx might be a negative regulator of its target genes. PMID:21541324

Cloning and bacterial expression of adenosine-5'-triphosphate sulfurylase from the enteric protozoan parasite Entamoeba histolytica.

PubMed

Nozaki, T; Arase, T; Shigeta, Y; Asai, T; Leustek, T; Takeuchi, T

1998-12-08

A gene encoding adenosine-5'-triphosphate sulfurylase (AS) was cloned from the enteric protozoan parasite Entamoeba histolytica by polymerase chain reaction using degenerate oligonucleotide primers corresponding to conserved regions of the protein from a variety of organisms. The deduced amino acid sequence of E. histolytica AS revealed a calculated molecular mass of 47925 Da and an unusual basic pI of 9.38. The amebic protein sequence showed 23-48% identities with AS from bacteria, yeasts, fungi, plants, and animals with the highest identities being to Synechocystis sp. and Bacillus subtilis (48 and 44%, respectively). Four conserved blocks including putative sulfate-binding and phosphate-binding regions were highly conserved in the E. histolytica AS. The upstream region of the AS gene contained three conserved elements reported for other E. histolytica genes. A recombinant E. histolytica AS revealed enzymatic activity, measured in both the forward and reverse directions. Expression of the E. histolytica AS complemented cysteine auxotrophy of the AS-deficient Escherichia coli strains. Genomic hybridization revealed that the AS gene exists as a single copy gene. In the literature, this is the first description of an AS gene in Protozoa.

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.

Comparative analysis on the structural features of the 5' flanking region of κ-casein genes from six different species

PubMed Central

Gerencsér, Ákos; Barta, Endre; Boa, Simon; Kastanis, Petros; Bösze, Zsuzsanna; Whitelaw, C Bruce A

2002-01-01

κ-casein plays an essential role in the formation, stabilisation and aggregation of milk micelles. Control of κ-casein expression reflects this essential role, although an understanding of the mechanisms involved lags behind that of the other milk protein genes. We determined the 5'-flanking sequences for the murine, rabbit and human κ-casein genes and compared them to the published ruminant sequences. The most conserved region was not the proximal promoter region but an approximately 400 bp long region centred 800 bp upstream of the TATA box. This region contained two highly conserved MGF/STAT5 sites with common spacing relative to each other. In this region, six conserved short stretches of similarity were also found which did not correspond to known transcription factor consensus sites. On the contrary to ruminant and human 5' regulatory sequences, the rabbit and murine 5'-flanking regions did not harbour any kind of repetitive elements. We generated a phylogenetic tree of the six species based on multiple alignment of the κ-casein sequences. This study identified conserved candidate transcriptional regulatory elements within the κ-casein gene promoter. PMID:11929628

The flow across a street canyon of variable width—Part 2:. Scalar dispersion from a street level line source

NASA Astrophysics Data System (ADS)

Simoëns, Serge; Wallace, James M.

As described in Part 1 [Simoëns et al., 2007. The flow across a street canyon of variable width—Part 1: kinematic description. Atmospheric Environment 41, 9002-9017] measurements have been made of the velocity field around and within the canyon formed by two obstacles placed on the wall of a turbulent boundary layer. Here in Part 2 measurements of the scalar dispersion of smoke released from a two-dimensional slot in the wall perpendicular to the mean flow and located parallel to and midway between these two square obstacles are presented. The Reynolds number of the boundary layer at the slot location without the obstacles in place was Rθ≈980. Statistical properties of the concentration field and the scalar fluxes in the streamwise plane are reported here for canyon openings that have been chosen based on characteristics of the kinematic description. These opening widths, expressed as multiples of the obstacle height, are 1 h, 4 h and 8 h. The mean concentration field revealed that the much of the scalar is trapped on the leeward side of the upstream obstacle before some of it escapes the canyon and is entrained on the roof of the upstream obstacle. It then is spread downstream by the turbulence in the wake of this obstacle. Surprisingly, the root mean square (rms) concentration field reveals that high concentration fluctuations exist in a zone where velocity field turbulence is very low. Measured streamwise scalar fluxes were found to be negative above the obstacles, whereas they are mainly positive between the obstacles. The measured wall normal scalar fluxes have an inverse behavior. Within the canyon, the scalar fluxes are greatest in the region between the large primary vortex, evident in the kinematic field, and the secondary vortex located in the corner of the leeward side of the upstream obstacle. In the flow above the obstacle roofs the wake of the upstream obstacle seems to dominate the scalar transport. Between the obstacles in and above the canyon, the existence of intermittent and intense events appear to prevent the modelling of these fluxes with a simple mean concentration gradient model.

In silico Analysis of 3′-End-Processing Signals in Aspergillus oryzae Using Expressed Sequence Tags and Genomic Sequencing Data

PubMed Central

Tanaka, Mizuki; Sakai, Yoshifumi; Yamada, Osamu; Shintani, Takahiro; Gomi, Katsuya

2011-01-01

To investigate 3′-end-processing signals in Aspergillus oryzae, we created a nucleotide sequence data set of the 3′-untranslated region (3′ UTR) plus 100 nucleotides (nt) sequence downstream of the poly(A) site using A. oryzae expressed sequence tags and genomic sequencing data. This data set comprised 1065 sequences derived from 1042 unique genes. The average 3′ UTR length in A. oryzae was 241 nt, which is greater than that in yeast but similar to that in plants. The 3′ UTR and 100 nt sequence downstream of the poly(A) site is notably U-rich, while the region located 15–30 nt upstream of the poly(A) site is markedly A-rich. The most frequently found hexanucleotide in this A-rich region is AAUGAA, although this sequence accounts for only 6% of all transcripts. These data suggested that A. oryzae has no highly conserved sequence element equivalent to AAUAAA, a mammalian polyadenylation signal. We identified that putative 3′-end-processing signals in A. oryzae, while less well conserved than those in mammals, comprised four sequence elements: the furthest upstream U-rich element, A-rich sequence, cleavage site, and downstream U-rich element flanking the cleavage site. Although these putative 3′-end-processing signals are similar to those in yeast and plants, some notable differences exist between them. PMID:21586533

Temporal genetic monitoring of hybridization between native westslope cutthroat trout and introduced rainbow trout in the Stehekin River, Washington

USGS Publications Warehouse

Ostberg, Carl O.; Chase, Dorothy M.

2012-01-01

Introgressive hybridization with introduced rainbow trout (RBT) (Oncorhynchus mykiss) has led to the loss of native cutthroat trout species (O. clarkii) throughout their range, creating conservation concerns. Monitoring temporal hybridization trends provides resource managers with a tool for determining population status and information for establishing conservation goals for native cutthroat trout. In this study, we re-sampled six locations in 2010 within the Stehekin River watershed, North Cascades National Park, which were originally sampled between 1999 and 2003. We used genetic markers to monitor changes in hybridization levels between sampling periods in the native westslope cutthroat trout (WCT) (O. c. lewisi) stemming from past RBT introductions. Additionally, two new locations from the lower Stehekin drainage were added to the baseline data. We found that the frequency of WCT, RBT, and their hybrids was not significantly different between monitoring periods, but that RBT allele frequencies decreased in two locations and increased in one location. We also found a consistent, substantial reduction in the frequency of RBT alleles over the monitoring period in the Stehekin River upstream of Bridge Creek (SR3) compared to the Stehekin River downstream of Bridge Creek (SR1 -2) and within lower Bridge Creek (BR1) although these three locations are confined to a small geographic area (approximately 5 km). Ecological and/or evolutionary processes likely restrict the dispersal of RBT alleles in the Stehekin River upstream of Bridge Creek.

ICAM-1-related long non-coding RNA: promoter analysis and expression in human retinal endothelial cells.

PubMed

Lumsden, Amanda L; Ma, Yuefang; Ashander, Liam M; Stempel, Andrew J; Keating, Damien J; Smith, Justine R; Appukuttan, Binoy

2018-05-09

Regulation of intercellular adhesion molecule (ICAM)-1 in retinal endothelial cells is a promising druggable target for retinal vascular diseases. The ICAM-1-related (ICR) long non-coding RNA stabilizes ICAM-1 transcript, increasing protein expression. However, studies of ICR involvement in disease have been limited as the promoter is uncharacterized. To address this issue, we undertook a comprehensive in silico analysis of the human ICR gene promoter region. We used genomic evolutionary rate profiling to identify a 115 base pair (bp) sequence within 500 bp upstream of the transcription start site of the annotated human ICR gene that was conserved across 25 eutherian genomes. A second constrained sequence upstream of the orthologous mouse gene (68 bp; conserved across 27 Eutherian genomes including human) was also discovered. Searching these elements identified 33 matrices predictive of binding sites for transcription factors known to be responsive to a broad range of pathological stimuli, including hypoxia, and metabolic and inflammatory proteins. Five phenotype-associated single nucleotide polymorphisms (SNPs) in the immediate vicinity of these elements included four SNPs (i.e. rs2569693, rs281439, rs281440 and rs11575074) predicted to impact binding motifs of transcription factors, and thus the expression of ICR and ICAM-1 genes, with potential to influence disease susceptibility. We verified that human retinal endothelial cells expressed ICR, and observed induction of expression by tumor necrosis factor-α.

Diel activity patterns of juvenile late fall-run Chinook salmon with implications for operation of a gated water diversion in the Sacramento–San Joaquin River Delta

USGS Publications Warehouse

Plumb, John M.; Adams, Noah S.; Perry, Russell W.; Holbrook, Christopher; Romine, Jason G.; Blake, Aaron R.; Burau, Jon R.

2016-01-01

In the Sacramento-San Joaquin River Delta, California, tidal forces that reverse river flows increase the proportion of water and juvenile late fall-run Chinook salmon diverted into a network of channels that were constructed to support agriculture and human consumption. This area is known as the interior delta, and it has been associated with poor fish survival. Under the rationale that the fish will be diverted in proportion to the amount of water that is diverted, the Delta Cross Channel (DCC) has been prescriptively closed during the winter out-migration to reduce fish entrainment and mortality into the interior delta. The fish are thought to migrate mostly at night, and so daytime operation of the DCC may allow for water diversion that minimizes fish entrainment and mortality. To assess this, the DCC gate was experimentally opened and closed while we released 2983 of the fish with acoustic transmitters upstream of the DCC to monitor their arrival and entrainment into the DCC. We used logistic regression to model night-time arrival and entrainment probabilities with covariates that included the proportion of each diel period with upstream flow, flow, rate of change in flow and water temperature. The proportion of time with upstream flow was the most important driver of night-time arrival probability, yet river flow had the largest effect on fish entrainment into the DCC. Modelling results suggest opening the DCC during daytime while keeping the DCC closed during night-time may allow for water diversion that minimizes fish entrainment into the interior delta.

Variability of hydrologic regimes and morphology in constructed open-ditch channels

USGS Publications Warehouse

Strock, J.S.; Magner, J.A.; Richardson, W.B.; Sadowsky, M.J.; Sands, G.R.; Venterea, R.T.; ,

2004-01-01

Open-ditch ecosystems are potential transporters of considerable loads of nutrients, sediment, pathogens and pesticides from direct inflow from agricultural land to small streams and larger rivers. Our objective was to compare hydrology and channel morphology between two experimental open-ditch channels. An open-ditch research facility incorporating a paired design was constructed during 2002 near Lamberton, MN. A200-m reach of existing drainage channel was converted into a system of four parallel channels. The facility was equipped with water level control devices and instrumentation for flow monitoring and water sample collection on upstream and downstream ends of the system. Hydrographs from simulated flow during year one indicated that paired open-ditch channels responded similarly to changes in inflow. Variability in hydrologic response between open-ditches was attributed to differences in open-ditch channel bottom elevation and vegetation density. No chemical, biological, or atmospheric measurements were made during 2003. Potential future benefits of this research include improved biological diversity and integrity of open-ditch ecosystems, reduce flood peaks and increased flow during critical low-flow periods, improved and more efficient nitrogen retention within the open-ditch ecosystem, and decreased maintenance cost associated with reduced frequency of open-ditch maintenance.

[Spatiotemporal characteristics of nitrogen and phosphorus in a mountainous urban lake].

PubMed

Bao, Jing-Yue; Bao, Jian-Guo; Li, Li-Qing

2014-10-01

Longjing Lake in Chongqing Expo Garden is a typical representative of mountainous urban lake. Based on water quality monitoring of Longjing Lake, spatiotemporal characteristics of nitrogen and phosphorus and their relations were analyzed, combined with natural and human factors considered. The results indicated that annual average concentrations of TN and TP in overall lake were (1.42 ± 0.46) mg · L(-1) and (0.09 ± 0.03) mg · L(-1), nitrogen and phosphorus concentrations fluctuated seasonally which were lower during the flooding season than those during the dry season. Nitrogen and phosphorus concentration in main water area, open water areas and bay areas of Longjing Lake were distributed with temporal and spatial heterogeneity by different regional influencing factors. The seasonal variation of the main water area was basically consistent with overall lake. Two open water areas respectively connected the main water area with the upstream region, bay areas. TN and TP concentrations were gradually reduced along the flow direction. Upstream water quality and surrounding park functional layout impacted nitrogen and phosphorus nutrient concentrations of open water areas. Nutrient concentrations of typical bay areas were higher than those of main water area and open water areas. The mean mass fraction of PN/TN and PP/TP accounted for a large proportion (51.7% and 72.8%) during the flooding season, while NO(3-)-N/TN and SRP/TP accounted for more (42.0% and 59.4%) during the dry season. The mass fraction of ammonia nitrogen and dissolved organic nitrogen in total nitrogen were relatively stable. The annual mean of N/P ratio was 18.429 ± 7.883; the period of nitrogen limitation was 5.3% while was 21.2% for phosphorus limitation.

50 CFR 660.316 - Open access fishery-observer requirements.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 50 Wildlife and Fisheries 11 2011-10-01 2011-10-01 false Open access fishery-observer requirements. 660.316 Section 660.316 Wildlife and Fisheries FISHERY CONSERVATION AND MANAGEMENT, NATIONAL OCEANIC... West Coast Groundfish-Open Access Fisheries § 660.316 Open access fishery—observer requirements. (a...

50 CFR 660.316 - Open access fishery-observer requirements.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 50 Wildlife and Fisheries 9 2010-10-01 2010-10-01 false Open access fishery-observer requirements. 660.316 Section 660.316 Wildlife and Fisheries FISHERY CONSERVATION AND MANAGEMENT, NATIONAL OCEANIC... West Coast Groundfish-Open Access Fisheries § 660.316 Open access fishery—observer requirements. (a...

50 CFR 660.316 - Open access fishery-observer requirements.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 50 Wildlife and Fisheries 13 2013-10-01 2013-10-01 false Open access fishery-observer requirements. 660.316 Section 660.316 Wildlife and Fisheries FISHERY CONSERVATION AND MANAGEMENT, NATIONAL OCEANIC... West Coast Groundfish-Open Access Fisheries § 660.316 Open access fishery—observer requirements. (a...

18 CFR 35.28 - Non-discriminatory open access transmission tariff.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 18 Conservation of Power and Water Resources 1 2012-04-01 2012-04-01 false Non-discriminatory open... AND TARIFFS Other Filing Requirements § 35.28 Non-discriminatory open access transmission tariff. (a... concerns regarding unnecessary market inefficiencies. (c) Non-discriminatory open access transmission...

50 CFR 660.316 - Open access fishery-observer requirements.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 50 Wildlife and Fisheries 13 2012-10-01 2012-10-01 false Open access fishery-observer requirements. 660.316 Section 660.316 Wildlife and Fisheries FISHERY CONSERVATION AND MANAGEMENT, NATIONAL OCEANIC... West Coast Groundfish-Open Access Fisheries § 660.316 Open access fishery—observer requirements. (a...

50 CFR 660.316 - Open access fishery-observer requirements.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 50 Wildlife and Fisheries 13 2014-10-01 2014-10-01 false Open access fishery-observer requirements. 660.316 Section 660.316 Wildlife and Fisheries FISHERY CONSERVATION AND MANAGEMENT, NATIONAL OCEANIC... West Coast Groundfish-Open Access Fisheries § 660.316 Open access fishery—observer requirements. (a...

Identification, cloning, and sequencing of a fragment of Amsacta moorei entomopoxvirus DNA containing the spheroidin gene and three vaccinia virus-related open reading frames.

PubMed Central

Hall, R L; Moyer, R W

1991-01-01

Entomopoxvirus virions are frequently contained within crystalline occlusion bodies, which are composed of primarily a single protein, spheroidin, which is analogous to the polyhedrin protein of baculovirus. The spheroidin gene of Amsacta moorei entomopoxvirus was identified following the microsequencing of polypeptides generated from cyanogen bromide treatment of spheroidin and the subsequent synthesis of oligonucleotide hybridization probes. DNA sequencing of a 6.8-kb region of DNA containing the spheroidin gene showed that the spheroidin protein is derived from a 3.0-kb open reading frame potentially encoding a protein of 115 kDa. Three copies of the heptanucleotide, TTTTTNT, a sequence associated with early gene transcription in the vertebrate poxviruses, and four in-frame translational termination signals were found within 60 bp upstream of the putative spheroidin gene promoter (TAAATG). The spheroidin gene promoter region contains the sequence TAAATG, which is found in many late promoters of the vertebrate poxviruses and which serves as the site of transcriptional initiation, as shown by primer extension. Primer extension experiments also showed that spheroidin gene transcripts contain 5' poly(A) sequences typical of vertebrate poxvirus late transcripts. The 92 bases upstream of the initiating TAAATG are unusually A + T rich and contain only 7 G or C residues. An analysis of open reading frames around the spheroidin gene suggests that the colinear core of "essential genes" typical of the vertebrate poxviruses is absent in A. moorei entomopoxvirus. Images PMID:1942245

School, Government, and Energy Interactions.

ERIC Educational Resources Information Center

Canipe, Stephen L.

This document examines three major federal statutes affecting school energy conservation, describes laws and regulations enacted in North Carolina to promote school energy conservation, and touches on possible energy options open to schools. The federal laws discussed are the Energy Policy and Conservation Act of 1975, dealing with the…

Using conservation value to assess land restoration and management alternatives across a degraded oak savanna landscape

USGS Publications Warehouse

Grundel, R.; Pavlovic, N.B.

2008-01-01

1. Managers considering restoration of landscapes often face a fundamental challenge - what should be the habitat composition of the restored landscape? We present a method for evaluating an important conservation trade-off inherent in making that decision. 2. Oak savannas and grasslands were historically widespread across central North America but are now rare. Today, in north-west Indiana, USA, habitats spanning a range of woody vegetation density, from nearly treeless open habitats to forests, occur across the conserved landscape where savannas probably once dominated. To understand the benefits of different potential landscape compositions, we evaluated how different proportions of five habitats - open, savanna, woodland, scrub and forest - might affect the conservation value of the north-west Indiana landscape for birds. Two variables of potential conservation importance were examined: species diversity, a measure of avian community richness, and conservation index, the percentage of a bird species' global population occurring on a hectare of landscape, summed across all bird species present. Higher values of conservation index were associated with higher local densities of globally more rare and more threatened species. 3. Conservation index and species diversity were correlated negatively across hypothetical landscapes composed of different proportions of the five habitats. Therefore, a management trade-off existed between conservation index and species diversity because landscapes that maximized species diversity differed from landscapes that maximized conservation index. 4. A landscape of 50% open, 22% savanna, 15% scrub and 13% forest was predicted to represent a compromise at which conservation index and species diversity reached the same percentage of their maxima. In contrast, the current landscape is dominated by forest. 5. Synthesis and applications. We quantified the trade-off between two potential aspects of a landscape's conservation value for birds - the landscape's ability to promote avian species diversity and the landscape's use by threatened avian species. This quantification allowed us to evaluate the ability of different landscape compositions to achieve preferable trade-off compromises, such as maximizing diversity for a given level of landscape use by threatened species. Managers can use these trade-off results to determine which landscape compositions are associated with particular conservation and management priorities.

Level II scour analysis for Bridge 13 (PFRDTH00030013) on Town Highway 3, crossing Furnace Brook, Pittsford, Vermont

USGS Publications Warehouse

Flynn, Robert H.; Medalie, Laura

1997-01-01

This report provides the results of a detailed Level II analysis of scour potential at structure PFRDTH00030013 on Town Highway 3 crossing Furnace Brook, Pittsford, Vermont (figures 1–8). A Level II study is a basic engineering analysis of the site, including a quantitative analysis of stream stability and scour (U.S. Department of Transportation, 1993). Results of a Level I scour investigation also are included in Appendix E of this report. A Level I investigation provides a qualitative geomorphic characterization of the study site. Information on the bridge, gleaned from Vermont Agency of Transportation (VTAOT) files, was compiled prior to conducting Level I and Level II analyses and is found in Appendix D. The site is in the Taconic section of the New England physiographic province in western Vermont. The 17.1-mi2 drainage area is in a predominantly rural and forested basin. In the vicinity of the study site, the surface cover is grass along the downstream right bank while the remaining banks are primarily forested. In the study area, Furnace Brook has an incised, sinuous channel with a slope of approximately 0.03 ft/ft, an average channel top width of 49 ft and an average channel depth of 4 ft. The predominant channel bed material ranges from gravel to bedrock with a median grain size (D50) of 70.2 mm (0.230 ft). The geomorphic assessment at the time of the Level I and Level II site visit on June 20, 1995, indicated that the reach was stable. The Town Highway 3 crossing of Furnace Brook is a 75-ft-long, two-lane bridge consisting of one 72-ft-long steel stringer span (Vermont Agency of Transportation, written communication, March 14, 1995). The bridge is supported by vertical, concrete abutments with spill-through slopes. The channel is skewed approximately 20 degrees to the opening while the opening-skew-to-roadway is 35 degrees. The opening-skew-to-roadway was determined from surveyed data collected at the bridge although, information provided from the VTAOT files, indicates that the opening-skew-to-roadway is 30 degrees (Appendix D). The scour protection measures at the site included type-2 stone fill (less than 36 inches diameter) on the spill-through slope along each abutment. Type-2 stone fill scour protection was also found along the upstream left wingwall and downstream right wingwall. Type-1 (less than 12 inches diameter) stone fill scour protection was found along the upstream right wingwall and downstream left wingwall. No bank protection was observed downstream or upstream. Additional details describing conditions at the site are included in the Level II Summary and Appendices D and E. Scour depths and rock rip-rap sizes were computed using the general guidelines described in Hydraulic Engineering Circular 18 (Richardson and others, 1995). Total scour at a highway crossing is comprised of three components: 1) long-term streambed degradation; 2) contraction scour (due to accelerated flow caused by a reduction in flow area at a bridge) and; 3) local scour (caused by accelerated flow around piers and abutments). Total scour is the sum of the three components. Equations are available to compute depths for contraction and local scour and a summary of the results of these computations follows. Contraction scour for all modelled flows ranged from 1.2 to 2.0 ft. The worst-case contraction scour occurred at the 500-year discharge. Abutment scour ranged from 7.8 to 13.1 ft. The worst-case abutment scour occurred at the 500-year discharge. Additional information on scour depths and depths to armoring are included in the section titled “Scour Results”. Scoured-streambed elevations, based on the calculated scour depths, are presented in tables 1 and 2. A cross-section of the scour computed at the bridge is presented in figure 8. Scour depths were calculated assuming an infinite depth of erosive material and a homogeneous particle-size distribution although, bedrock outcropping is apparent both upstream and downstream of this bridge. It is generally accepted that the Froehlich equation (abutment scour) gives “excessively conservative estimates of scour depths” (Richardson and others, 1995, p. 47). Usually, computed scour depths are evaluated in combination with other information including (but not limited to) historical performance during flood events, the geomorphic stability assessment, existing scour protection measures, and the results of the hydraulic analyses. Therefore, scour depths adopted by VTAOT may differ from the computed values documented herein.

Genomic dissection of conserved transcriptional regulation in intestinal epithelial cells

PubMed Central

Camp, J. Gray; Weiser, Matthew; Cocchiaro, Jordan L.; Kingsley, David M.; Furey, Terrence S.; Sheikh, Shehzad Z.; Rawls, John F.

2017-01-01

The intestinal epithelium serves critical physiologic functions that are shared among all vertebrates. However, it is unknown how the transcriptional regulatory mechanisms underlying these functions have changed over the course of vertebrate evolution. We generated genome-wide mRNA and accessible chromatin data from adult intestinal epithelial cells (IECs) in zebrafish, stickleback, mouse, and human species to determine if conserved IEC functions are achieved through common transcriptional regulation. We found evidence for substantial common regulation and conservation of gene expression regionally along the length of the intestine from fish to mammals and identified a core set of genes comprising a vertebrate IEC signature. We also identified transcriptional start sites and other putative regulatory regions that are differentially accessible in IECs in all 4 species. Although these sites rarely showed sequence conservation from fish to mammals, surprisingly, they drove highly conserved IEC expression in a zebrafish reporter assay. Common putative transcription factor binding sites (TFBS) found at these sites in multiple species indicate that sequence conservation alone is insufficient to identify much of the functionally conserved IEC regulatory information. Among the rare, highly sequence-conserved, IEC-specific regulatory regions, we discovered an ancient enhancer upstream from her6/HES1 that is active in a distinct population of Notch-positive cells in the intestinal epithelium. Together, these results show how combining accessible chromatin and mRNA datasets with TFBS prediction and in vivo reporter assays can reveal tissue-specific regulatory information conserved across 420 million years of vertebrate evolution. We define an IEC transcriptional regulatory network that is shared between fish and mammals and establish an experimental platform for studying how evolutionarily distilled regulatory information commonly controls IEC development and physiology. PMID:28850571

Low effect of young afforestations on bird communities inhabiting heterogeneous Mediterranean cropland

PubMed Central

Rey Benayas, José M.; Carrascal, Luis M.

2015-01-01

Afforestation programs such as the one promoted by the EU Common Agricultural Policy have spread tree plantations on former cropland. These afforestations attract generalist forest and ubiquitous species but may cause severe damage to open habitat species, especially birds of high conservation value. We investigated the effects of young (<20 yr) tree plantations dominated by pine P. halepensis on bird communities inhabiting the adjacent open farmland habitat in central Spain. We hypothesize that pine plantations located at shorter distances from open fields and with larger surface would affect species richness and conservation value of bird communities. Regression models controlling for the influence of land use types around plantations revealed positive effects of higher distance to pine plantation edge on community species richness in winter, and negative effects on an index of conservation concern (SPEC) during the breeding season. However, plantation area did not have any effect on species richness or community conservation value. Our results indicate that the effects of pine afforestation on bird communities inhabiting Mediterranean cropland are diluted by heterogeneous agricultural landscapes. PMID:26664801

Silver concentrations and selected hydrologic data in the Upper Colorado River basin, 1991-92

USGS Publications Warehouse

Johncox, D.A.

1993-01-01

The U.S. Geological Survey, in cooperation with the Colorado River Water Conservation District and the Northern Colorado Water Conservancy District, collected water and sediment samples in May and September 1991 and 1992 from nine stream-sampling sites and three lake-sampling sites within the Upper Colorado River Basin upstream from Kremmling, Colorado. Data were collected to determine the present (1992) conditions of the Upper Colorado River Basin regarding silver concentrations in the water and sediment. Lake-water and stream-water samples were analyzed for concentrations of total recoverable silver, dissolved silver, and suspended solids. Lake- and stream-bottom material was analyzed for concentrations of total recoverable silver. Additional data collected were streamflow, specific conductance, pH, and water temperature. Transparency (Secchi-disk measurements) also was measured in the lakes.

18 CFR 1301.43 - Open meetings.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 18 Conservation of Power and Water Resources 2 2010-04-01 2010-04-01 false Open meetings. 1301.43... in the Sunshine Act § 1301.43 Open meetings. Members shall not jointly conduct or dispose of TVA... every meeting of the agency shall be open to public observation, and TVA shall provide suitable...

18 CFR 1301.43 - Open meetings.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 18 Conservation of Power and Water Resources 2 2011-04-01 2011-04-01 false Open meetings. 1301.43... in the Sunshine Act § 1301.43 Open meetings. Members shall not jointly conduct or dispose of TVA... every meeting of the agency shall be open to public observation, and TVA shall provide suitable...

18 CFR 1301.43 - Open meetings.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 18 Conservation of Power and Water Resources 2 2014-04-01 2014-04-01 false Open meetings. 1301.43... in the Sunshine Act § 1301.43 Open meetings. Members shall not jointly conduct or dispose of TVA... every meeting of the agency shall be open to public observation, and TVA shall provide suitable...

18 CFR 1301.43 - Open meetings.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 18 Conservation of Power and Water Resources 2 2012-04-01 2012-04-01 false Open meetings. 1301.43... in the Sunshine Act § 1301.43 Open meetings. Members shall not jointly conduct or dispose of TVA... every meeting of the agency shall be open to public observation, and TVA shall provide suitable...

18 CFR 1301.43 - Open meetings.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 18 Conservation of Power and Water Resources 2 2013-04-01 2012-04-01 true Open meetings. 1301.43... in the Sunshine Act § 1301.43 Open meetings. Members shall not jointly conduct or dispose of TVA... every meeting of the agency shall be open to public observation, and TVA shall provide suitable...

Application of Method of Variation to Analyze and Predict Human Induced Modifications of Water Resource Systems

NASA Astrophysics Data System (ADS)

Dessu, S. B.; Melesse, A. M.; Mahadev, B.; McClain, M.

2010-12-01

Water resource systems have often used gravitational surface and subsurface flows because of their practicality in hydrological modeling and prediction. Activities such as inter/intra-basin water transfer, the use of small pumps and the construction of micro-ponds challenge the tradition of natural rivers as water resource management unit. On the contrary, precipitation is barely affected by topography and plot harvesting in wet regions can be more manageable than diverting from rivers. Therefore, it is indicative to attend to systems where precipitation drives the dynamics while the internal mechanics constitutes spectrum of human activity and decision in a network of plots. The trade-in volume and path of harvested precipitation depends on water balance, energy balance and the kinematics of supply and demand. Method of variation can be used to understand and predict the implication of local excess precipitation harvest and exchange on the natural water system. A system model was developed using the variational form of Euler-Bernoulli’s equation for the Kenyan Mara River basin. Satellite derived digital elevation models, precipitation estimates, and surface properties such as fractional impervious surface area, are used to estimate the available water resource. Four management conditions are imposed in the model: gravitational flow, open water extraction and high water use investment at upstream and downstream respectively. According to the model, the first management maintains the basin status quo while the open source management could induce externality. The high water market at the upstream in the third management offers more than 50% of the basin-wide total revenue to the upper third section of the basin thus may promote more harvesting. The open source and upstream exploitation suggest potential drop of water availability to downstream. The model exposed the latent potential of economic gradient to reconfigure the flow network along the direction where the marginal benefit is maximized. Therefore, the variation model can help to predict the possible human induced modification of natural water system in order to gain the maximum productivity and benefit.

Factors Influencing Schoolchildren's Responses to a Questionnaire in Wildlife Conservation Education

ERIC Educational Resources Information Center

Ballouard, Jean-Marie; Mullin, Stephen J.; Ajtic, Rastko; Brito, José Carlos; ElMouden, El Hassan; Erdogan, Mehmet; Feriche, Monica; Pleguezuelos, Juan M.; Prokop, Pavol; Sánchez, Aida; Santos, Xavier; Slimani, Tahar; Sterijovski, Bogoljub; Tomovic, Ljiljana; Usak, Muhammet; Zuffi, Marco; Bonnet, Xavier

2015-01-01

Questionnaires are important tools for assessing attitudes regarding conservation issues. However, they are not easily comparable and their reliability has been insufficiently assessed. We examined factors influencing responses to open- and closed-ended questions about animal conservation to more than 600 schoolchildren (9 years old on average).…

10 CFR 431.446 - Small electric motors energy conservation standards and their effective dates.

Code of Federal Regulations, 2014 CFR

2014-01-01

... full load efficiency Capacitor-start capacitor-run and capacitor-start induction-run Open motors... 10 Energy 3 2014-01-01 2014-01-01 false Small electric motors energy conservation standards and... EFFICIENCY PROGRAM FOR CERTAIN COMMERCIAL AND INDUSTRIAL EQUIPMENT Small Electric Motors Energy Conservation...

10 CFR 431.446 - Small electric motors energy conservation standards and their effective dates.

Code of Federal Regulations, 2012 CFR

2012-01-01

... full load efficiency Capacitor-start capacitor-run and capacitor-start induction-run Open motors... 10 Energy 3 2012-01-01 2012-01-01 false Small electric motors energy conservation standards and... EFFICIENCY PROGRAM FOR CERTAIN COMMERCIAL AND INDUSTRIAL EQUIPMENT Small Electric Motors Energy Conservation...

10 CFR 431.446 - Small electric motors energy conservation standards and their effective dates.

Code of Federal Regulations, 2013 CFR

2013-01-01

... full load efficiency Capacitor-start capacitor-run and capacitor-start induction-run Open motors... 10 Energy 3 2013-01-01 2013-01-01 false Small electric motors energy conservation standards and... EFFICIENCY PROGRAM FOR CERTAIN COMMERCIAL AND INDUSTRIAL EQUIPMENT Small Electric Motors Energy Conservation...

Environmental impact of coal mining and coal seam gas production on surface water quality in the Sydney basin, Australia.

PubMed

Ali, A; Strezov, V; Davies, P; Wright, I

2017-08-01

The extraction of coal and coal seam gas (CSG) will generate produced water that, if not adequately treated, will pollute surface and groundwater systems. In Australia, the discharge of produced water from coal mining and related activities is regulated by the state environment agency through a pollution licence. This licence sets the discharge limits for a range of analytes to protect the environment into which the produced water is discharged. This study reports on the impact of produced water from coal mine activities located within or discharging into high conservation environments, such as National Parks, in the outer region of Sydney, Australia. The water samples upstream and downstream from the discharge points from six mines were taken, and 110 parameters were tested. The results were assessed against a water quality index (WQI) which accounts for pH, turbidity, dissolved oxygen, biochemical oxygen demand, total dissolved solids, total phosphorus, nitrate nitrogen and E .coli. The water quality assessment based on the trace metal contents against various national maximum admissible concentration (MAC) and their corresponding environmental impacts was also included in the study which also established a base value of water quality for further study. The study revealed that impacted water downstream of the mine discharge points contained higher metal content than the upstream reference locations. In many cases, the downstream water was above the Australia and New Zealand Environment Conservation Council and international water quality guidelines for freshwater stream. The major outliers to the guidelines were aluminium (Al), iron (Fe), manganese (Mn), nickel (Ni) and zinc (Zn). The WQI of surface water at and downstream of the discharge point was lower when compared to upstream or reference conditions in the majority of cases. Toxicology indices of metals present in industrial discharges were used as an additional tool to assess water quality, and the newly proposed environmental water quality index (EWQI) lead to better trend in the impact of coal and coal seam gas mining activities on surface water quality when compared to the upstream reference water samples. Metal content limits were based on the impact points assigned by the Agency for Toxic Substances and Disease Registry, USA. For environmental and health impact assessment, the approach used in this study can be applied as a model to provide a basis to assess the anthropogenic contribution from the industrial and mining activities on the environment.

Diverse Early Life-History Strategies in Migratory Amazonian Catfish: Implications for Conservation and Management

PubMed Central

Hegg, Jens C.; Giarrizzo, Tommaso; Kennedy, Brian P.

2015-01-01

Animal migrations provide important ecological functions and can allow for increased biodiversity through habitat and niche diversification. However, aquatic migrations in general, and those of the world’s largest fish in particular, are imperiled worldwide and are often poorly understood. Several species of large Amazonian catfish carry out some of the longest freshwater fish migrations in the world, travelling from the Amazon River estuary to the Andes foothills. These species are important apex predators in the main stem rivers of the Amazon Basin and make up the region’s largest fishery. They are also the only species to utilize the entire Amazon Basin to complete their life cycle. Studies indicate both that the fisheries may be declining due to overfishing, and that the proposed and completed dams in their upstream range threaten spawning migrations. Despite this, surprisingly little is known about the details of these species’ migrations, or their life history. Otolith microchemistry has been an effective method for quantifying and reconstructing fish migrations worldwide across multiple spatial scales and may provide a powerful tool to understand the movements of Amazonian migratory catfish. Our objective was to describe the migratory behaviors of the three most populous and commercially important migratory catfish species, Dourada (Brachyplatystoma rousseauxii), Piramutaba (Brachyplatystoma vaillantii), and Piraíba (Brachyplatystoma filamentosum). We collected fish from the mouth of the Amazon River and the Central Amazon and used strontium isotope signatures (87Sr/86Sr) recorded in their otoliths to determine the location of early rearing and subsequent. Fish location was determined through discriminant function classification, using water chemistry data from the literature as a training set. Where water chemistry data was unavailable, we successfully in predicted 87Sr/86Sr isotope values using a regression-based approach that related the geology of the upstream watershed to the Sr isotope ratio. Our results provide the first reported otolith microchemical reconstruction of Brachyplatystoma migratory movements in the Amazon Basin. Our results indicate that juveniles exhibit diverse rearing strategies, rearing in both upstream and estuary environments. This contrasts with the prevailing understanding that juveniles rear in the estuary before migrating upstream; however, it is supported by some fisheries data that has indicated the presence of alternate spawning and rearing life-histories. The presence of alternate juvenile rearing strategies may have important implications for conservation and management of the fisheries in the region. PMID:26153984

Level II scour analysis for Bridge 8 (NEWFTH00010008) on Town Highway 1, crossing Wardsboro Brook, Newfane, Vermont

USGS Publications Warehouse

Wild, Emily C.; Degnan, James

1998-01-01

This report provides the results of a detailed Level II analysis of scour potential at structure NEWFTH00010008 on Town Highway 1 crossing Wardsboro Brook, Newfane, Vermont (figures 1–8). A Level II study is a basic engineering analysis of the site, including a quantitative analysis of stream stability and scour (Federal Highway Administration, 1993). Results of a Level I scour investigation also are included in appendix E of this report. A Level I investigation provides a qualitative geomorphic characterization of the study site. Information on the bridge, gleaned from Vermont Agency of Transportation (VTAOT) files, was compiled prior to conducting Level I and Level II analyses and is found in appendix D. The site is in the New England Upland section of the New England physiographic province in southestern Vermont. The 6.91-mi2 drainage area is in a predominantly rural and forested basin. In the vicinity of the study site, the surface cover is forest on the upstream right overbank and downstream left and right overbanks. The surface cover on the upstream left overbank is pasture. In the study area, Wardsboro Brook has an incised, sinuous channel with a slope of approximately 0.02 ft/ft, an average channel top width of 63 ft and an average bank height of 9 ft. The channel bed material ranges from gravel to boulders with a median grain size (D50) of 95.4 mm (0.313 ft). The geomorphic assessment at the time of the Level I and Level II site visit on August 21, 1996, indicated that the reach was stable. The Town Highway 1 crossing of the Wardsboro Brook is a 32-ft-long, two-lane bridge consisting of a 26-foot concrete tee-beam span (Vermont Agency of Transportation, written communication, April 6, 1995). The opening length of the structure parallel to the bridge face is 26.7 ft. The bridge is supported by vertical, concrete abutments with wingwalls. The channel is skewed approximately 45 degrees to the computed opening while the openingskew-to-roadway is 45 degrees. A scour hole 1.0 ft deeper than the mean thalweg depth was observed along the right abutment during the Level I assessment. Scour protection measures at the site included type-1 stone fill (less than 12 inches diameter) along the upstream right bank, and type-2 stone fill (less than 36 inches diameter) along the upstream left bank and the upstream ends of the upstream left and right wingwalls. A stone wall extends along the downstream right bank from the end of the downstream right wingwall. Additional details describing conditions at the site are included in the Level II Summary and appendices D and E. Scour depths and recommended rock rip-rap sizes were computed using the general guidelines described in Hydraulic Engineering Circular 18 (Richardson and Davis, 1995) for the 100- and 500-year discharges. In addition, the incipient roadway-overtopping discharge was determined and analyzed as another potential worst-case scour scenario. Total scour at a highway crossing is comprised of three components: 1) long-term streambed degradation; 2) contraction scour (due to accelerated flow caused by a reduction in flow area at a bridge) and; 3) local scour (caused by accelerated flow around piers and abutments). Total scour is the sum of the three components. Equations are available to compute depths for contraction and local scour and a summary of the results of these computations follows. Contraction scour for all modelled flows ranged from 0.1 to 3.9 ft. The worst-case contraction scour occurred at the 500-year discharge. Left abutment scour ranged from 11.1 to 12.9 ft. Right abutment scour ranged from 4.3 to 4.8 ft. The worst-case abutment scour occurred at the 500-year discharge. Additional information on scour depths and depths to armoring are included in the section titled “Scour Results”. Scoured-streambed elevations, based on the calculated scour depths, are presented in tables 1 and 2. A cross-section of the scour computed at the bridge is presented in figure 8. Scour depths were calculated assuming an infinite depth of erosive material and a homogeneous particle-size distribution. It is generally accepted that the Froehlich equation (abutment scour) gives “excessively conservative estimates of scour depths” (Richardson and Davis, 1995, p. 46). Usually, computed scour depths are evaluated in combination with other information including (but not limited to) historical performance during flood events, the geomorphic stability assessment, existing scour protection measures, and the results of the hydraulic analyses. Therefore, scour depths adopted by VTAOT may differ from the computed values documented herein.

Casing for a gas turbine engine

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

Wiebe, David J.; Little, David A.; Charron, Richard C.

2016-07-12

A casing for a can annular gas turbine engine, including: a compressed air section (40) spanning between a last row of compressor blades (26) and a first row of turbine blades (28), the compressed air section (40) having a plurality of openings (50) there through, wherein a single combustor/advanced duct assembly (64) extends through each opening (50); and one top hat (68) associated with each opening (50) configured to enclose the associated combustor/advanced duct assembly (64) and seal the opening (50). A volume enclosed by the compressed air section (40) is not greater than a volume of a frustum (54)more » defined at an upstream end (56) by an inner diameter of the casing at the last row of compressor blades (26) and at a downstream end (60) by an inner diameter of the casing at the first row of turbine blades (28).« less

Control of Delta Avulsion by Downstream Sediment Sinks

NASA Astrophysics Data System (ADS)

Salter, Gerard; Paola, Chris; Voller, Vaughan R.

2018-01-01

Understanding how fluxes are partitioned at delta bifurcations is critical for predicting patterns of land loss and gain in deltas worldwide. Although the dynamics of river deltas are influenced from both upstream and downstream, previous studies of bifurcations have focused on upstream controls. Using a quasi-1-D bifurcation model, we show that flow switching in bifurcations is strongly influenced by downstream sediment sinks. We find that coupling between upstream and downstream feedbacks can lead to oscillations in water and sediment flux partitioning. The frequency and initial rate of growth/decay of the oscillations depend on both upstream and downstream conditions, with dimensionless bifurcate length and bypass fraction emerging as key downstream parameters. With a strong offshore sink, causing bypass in the bifurcate branches, we find that bifurcation dynamics become "frozen"; that is, the bifurcation settles on a permanent discharge ratio. In contrast, under depositional conditions, we identify three dynamical regimes: symmetric; soft avulsion, where both branches remain open but the dominant branch switches; and full avulsion. Finally, we show that differential subsidence alters these regimes, with the difference in average sediment supply to each branch exactly compensating for the difference in accommodation generation. Additionally, the model predicts that bifurcations with shorter branches are less asymmetric than bifurcations with longer branches, all else equal, providing a possible explanation for the difference between backwater length distributaries, which tend to be avulsive, and relatively stable mouth-bar-scale networks. We conclude that bifurcations are sensitive both quantitatively and qualitatively to downstream sinks.

Performance Prediction of Darrieus-Type Hydroturbine with Inlet Nozzle Operated in Open Water Channels

NASA Astrophysics Data System (ADS)

Nakashima, K.; Watanabe, S.; Matsushita, D.; Tsuda, S.; Furukawa, A.

2016-11-01

Small hydropower is one of the renewable energies and is expected to be effectively used for local supply of electricity. We have developed Darrieus-type hydro-turbine systems, and among them, the Darrieus-turbine with a weir and a nozzle installed upstream of turbine is, so far, in success to obtain more output power by gathering all water into the turbine. However, there can several cases exist, in which installing the weir covering all the flow channel width is unrealistic, and in such cases, the turbine should be put alone in open channels without upstream weir. Since the output power is very small in such a utilization of small hydropower, it is important to derive more power for the cost reduction. In the present study, we parametrically investigate the preferable shape of the inlet nozzle for the Darrieus-type hydroturbine operated in an open flow channel. Experimental investigation is carried out in the open channel in our lab. Tested inlet nozzles are composed of two flat plates with the various nozzle converging angles and nozzle outlet (runner inlet) widths with the nozzle inlet width kept constant. As a result, the turbine with the nozzles having large converging angle and wide outlet width generates higher power. Two-dimensional unsteady numerical simulation is also carried out to qualitatively understand the flow mechanism leading to the better performance of turbine. Since the depth, the width and the flow rate in the real open flow channels are different from place to place and, in some cases from time to time, it is also important to predict the onsite performance of the hydroturbine from the lab experiment at planning stage. One-dimensional stream-tube model is developed for this purpose, in which the Darrieus-type hydroturbine with the inlet nozzle is considered as an actuator-disk modelled based on our experimental and numerical results.

Edge Vortex Flow Due to Inhomogeneous Ion Concentration

NASA Astrophysics Data System (ADS)

Sugioka, Hideyuki

2017-04-01

The ion distribution of an open parallel electrode system is not known even though it is often used to measure the electrical characteristics of an electrolyte. Thus, for an open electrode system, we perform a non-steady direct multiphysics simulation based on the coupled Poisson-Nernst-Planck and Stokes equations and find that inhomogeneous ion concentrations at edges cause vortex flows and suppress the anomalous increase in the ion concentration near the electrodes. A surprising aspect of our findings is that the large vortex flows at the edges approximately maintain the ion-conserving condition, and thus the ion distribution of an open electrode system can be approximated by the solution of a closed electrode system that considers the ion-conserving condition rather than the Gouy-Chapman solution, which neglects the ion-conserving condition. We believe that our findings make a significant contribution to the understanding of surface science.

Sedimentation, sediment quality, and upstream channel stability, John Redmond Reservoir, east-central Kansas, 1964-2009

USGS Publications Warehouse

Juracek, Kyle E.

2010-01-01

A combination of available bathymetric-survey information, bottom-sediment coring, and historical streamgage information was used to investigate sedimentation, sediment quality, and upstream channel stability for John Redmond Reservoir, east-central Kansas. Ongoing sedimentation is reducing the ability of the reservoir to serve several purposes including flood control, water supply, and recreation. The total estimated volume and mass of bottom sediment deposited between 1964 and 2009 in the conservation pool of the reservoir was 1.46 billion cubic feet and 55.8 billion pounds, respectively. The estimated sediment volume occupied about 41 percent of the conservation-pool, water-storage capacity of the reservoir. Water-storage capacity in the conservation pool has been lost to sedimentation at a rate of about 1 percent annually. Mean annual net sediment deposition since 1964 in the conservation pool of the reservoir was estimated to be 1.24 billion pounds per year. Mean annual net sediment yield from the reservoir basin was estimated to be 411,000 pounds per square mile per year Information from sediment cores shows that throughout the history of John Redmond Reservoir, total nitrogen concentrations in the deposited sediment generally were uniform indicating consistent nitrogen inputs to the reservoir. Total phosphorus concentrations in the deposited sediment were more variable than total nitrogen indicating the possibility of changing phosphorus inputs to the reservoir. As the principal limiting factor for primary production in most freshwater environments, phosphorus is of particular importance because increased inputs can contribute to accelerated reservoir eutrophication and the production of algal toxins and taste-and-odor compounds. The mean annual net loads of total nitrogen and total phosphorus deposited in the bottom sediment of the reservoir were estimated to be 2,350,000 pounds per year and 1,030,000 pounds per year, respectively. The estimated mean annual net yields of total nitrogen and total phosphorus from the reservoir basin were 779 pounds per square mile per year and 342 pounds per square mile per year, respectively. Trace element concentrations in the bottom sediment of John Redmond Reservoir generally were uniform over time. As is typical for eastern Kansas reservoirs, arsenic, chromium, and nickel concentrations typically exceeded the threshold-effects guidelines, which represent the concentrations above which toxic biological effects occasionally occur. Trace element concentrations did not exceed the probable-effects guidelines (available for eight trace elements), which represent the concentrations above which toxic biological effects usually or frequently occur. Organochlorine compounds either were not detected or were detected at concentrations that were less than the threshold-effects guidelines. Stream channel banks, compared to channel beds, likely are a more important source of sediment to John Redmond Reservoir from the upstream basin. Other sediment sources include surface-soil erosion in the basin and shoreline erosion in the reservoir.

Behavior and reproductive ecology of the Sicklefin Redhorse: An imperiled southern Appalachian Mountain fish

USGS Publications Warehouse

Favrot, Scott D.; Kwak, Thomas J.

2018-01-01

Many nongame fishes are poorly understood but are essential to maintaining healthy aquatic ecosystems globally. The undescribed Sicklefin Redhorse Moxostoma sp. is a rare, imperiled, nongame fish endemic to two southern Appalachian Mountain river basins. Little is known of its behavior and ecology, but this information is urgently needed for conservation planning. We assessed the spatial and temporal bounds of spawning migration, quantified seasonal weekly movement patterns, and characterized seasonal and spawning behavior using radiotelemetry and weir sampling in the Hiwassee River basin, North Carolina–Georgia, during 2006 and 2007. Hiwassee River tributaries were occupied predominantly during the fish's spawning season, lower reaches of the tributaries and the Hiwassee River were primarily occupied during the postspawning season (i.e., summer and fall), and lower lotic reaches of Hiwassee River (upstream from Hiwassee Lake) were occupied during winter. Adults occupied Hiwassee Lake only as a movement corridor during spawning migrations. Both sexes conducted upstream spawning migrations simultaneously, but males occupied spawning tributaries longer than females. Sicklefin Redhorse exhibited interannual spawning‐area and tributary fidelity. Cold water temperatures associated with hypolimnetic releases from reservoirs and meteorological conditions influenced spawning migration distance and timing. During 2007, decreased discharges during the spawning season were associated with decreases in migration distance and spawning tributary occupancy duration. Foraging was the dominant behavior observed annually, followed by reproductive behaviors (courting and spawning) during the spawning season. No agonistic reproductive behavior was observed, but females exhibited a repetitious postspawning digging behavior that may be unique in the family Catostomidae. Our findings suggest that protection and restoration of river continuity, natural flow regimes, seasonally appropriate water temperatures, and geographic range expansion are critical components to include in Sicklefin Redhorse conservation planning. Fisheries and ecosystem managers can use our findings to justify sensitive management decisions that conserve and restore critical streams and rivers occupied by this imperiled species.

Evaluation of wastewater contaminant transport in surface waters using verified Lagrangian sampling

USGS Publications Warehouse

Antweiler, Ronald C.; Writer, Jeffrey H.; Murphy, Sheila F.

2014-01-01

Contaminants released from wastewater treatment plants can persist in surface waters for substantial distances. Much research has gone into evaluating the fate and transport of these contaminants, but this work has often assumed constant flow from wastewater treatment plants. However, effluent discharge commonly varies widely over a 24-hour period, and this variation controls contaminant loading and can profoundly influence interpretations of environmental data. We show that methodologies relying on the normalization of downstream data to conservative elements can give spurious results, and should not be used unless it can be verified that the same parcel of water was sampled. Lagrangian sampling, which in theory samples the same water parcel as it moves downstream (the Lagrangian parcel), links hydrologic and chemical transformation processes so that the in-stream fate of wastewater contaminants can be quantitatively evaluated. However, precise Lagrangian sampling is difficult, and small deviations – such as missing the Lagrangian parcel by less than 1 h – can cause large differences in measured concentrations of all dissolved compounds at downstream sites, leading to erroneous conclusions regarding in-stream processes controlling the fate and transport of wastewater contaminants. Therefore, we have developed a method termed “verified Lagrangian” sampling, which can be used to determine if the Lagrangian parcel was actually sampled, and if it was not, a means for correcting the data to reflect the concentrations which would have been obtained had the Lagrangian parcel been sampled. To apply the method, it is necessary to have concentration data for a number of conservative constituents from the upstream, effluent, and downstream sites, along with upstream and effluent concentrations that are constant over the short-term (typically 2–4 h). These corrections can subsequently be applied to all data, including non-conservative constituents. Finally, we show how data from other studies can be corrected.

Evaluation of wastewater contaminant transport in surface waters using verified Lagrangian sampling.

PubMed

Antweiler, Ronald C; Writer, Jeffrey H; Murphy, Sheila F

2014-02-01

Contaminants released from wastewater treatment plants can persist in surface waters for substantial distances. Much research has gone into evaluating the fate and transport of these contaminants, but this work has often assumed constant flow from wastewater treatment plants. However, effluent discharge commonly varies widely over a 24-hour period, and this variation controls contaminant loading and can profoundly influence interpretations of environmental data. We show that methodologies relying on the normalization of downstream data to conservative elements can give spurious results, and should not be used unless it can be verified that the same parcel of water was sampled. Lagrangian sampling, which in theory samples the same water parcel as it moves downstream (the Lagrangian parcel), links hydrologic and chemical transformation processes so that the in-stream fate of wastewater contaminants can be quantitatively evaluated. However, precise Lagrangian sampling is difficult, and small deviations - such as missing the Lagrangian parcel by less than 1h - can cause large differences in measured concentrations of all dissolved compounds at downstream sites, leading to erroneous conclusions regarding in-stream processes controlling the fate and transport of wastewater contaminants. Therefore, we have developed a method termed "verified Lagrangian" sampling, which can be used to determine if the Lagrangian parcel was actually sampled, and if it was not, a means for correcting the data to reflect the concentrations which would have been obtained had the Lagrangian parcel been sampled. To apply the method, it is necessary to have concentration data for a number of conservative constituents from the upstream, effluent, and downstream sites, along with upstream and effluent concentrations that are constant over the short-term (typically 2-4h). These corrections can subsequently be applied to all data, including non-conservative constituents. Finally, we show how data from other studies can be corrected. © 2013.

The leukemia associated ETO nuclear repressor gene is regulated by the GATA-1 transcription factor in erythroid/megakaryocytic cells

PubMed Central

2010-01-01

Background The Eight-Twenty-One (ETO) nuclear co-repressor gene belongs to the ETO homologue family also containing Myeloid Translocation Gene on chromosome 16 (MTG16) and myeloid translocation Gene-Related protein 1 (MTGR1). By chromosomal translocations ETO and MTG16 become parts of fusion proteins characteristic of morphological variants of acute myeloid leukemia. Normal functions of ETO homologues have as yet not been examined. The goal of this work was to identify structural and functional promoter elements upstream of the coding sequence of the ETO gene in order to explore lineage-specific hematopoietic expression and get hints to function. Results A putative proximal ETO promoter was identified within 411 bp upstream of the transcription start site. Strong ETO promoter activity was specifically observed upon transfection of a promoter reporter construct into erythroid/megakaryocytic cells, which have endogeneous ETO gene activity. An evolutionary conserved region of 228 bp revealed potential cis-elements involved in transcription of ETO. Disruption of the evolutionary conserved GATA -636 consensus binding site repressed transactivation and disruption of the ETS1 -705 consensus binding site enhanced activity of the ETO promoter. The promoter was stimulated by overexpression of GATA-1 into erythroid/megakaryocytic cells. Electrophoretic mobility shift assay with erythroid/megakaryocytic cells showed specific binding of GATA-1 to the GATA -636 site. Furthermore, results from chromatin immunoprecipitation showed GATA-1 binding in vivo to the conserved region of the ETO promoter containing the -636 site. The results suggest that the GATA -636 site may have a role in activation of the ETO gene activity in cells with erythroid/megakaryocytic potential. Leukemia associated AML1-ETO strongly suppressed an ETO promoter reporter in erythroid/megakaryocytic cells. Conclusions We demonstrate that the GATA-1 transcription factor binds and transactivates the ETO proximal promoter in an erythroid/megakaryocytic-specific manner. Thus, trans-acting factors that are essential in erythroid/megakaryocytic differentiation govern ETO expression. PMID:20487545

Data Summary Report for the Open Rotor Propulsion Rig Equipped With F31/A31 Rotor Blades

NASA Technical Reports Server (NTRS)

Stephens, David

2014-01-01

An extensive wind tunnel test campaign was undertaken to quantify the performance and acoustics of a counter-rotating open rotor system. The present document summarizes the portion of this test performed with the so-called Historical Baseline rotor blades, designated F31A31. It includes performance and acoustic data acquired at Mach numbers from take-off to cruise. It also includes the effect of propulsor angle of attack as well as an upstream pylon. This report is accompanied by an electronic data set including relevant acoustic and performance measurements for all of the F31A31 data.

Data Summary Report for the Open Rotor Propulsion Rig Equipped with F31/A31 Rotor Blades

NASA Technical Reports Server (NTRS)

Stephens, David B.

2014-01-01

An extensive wind tunnel test campaign was undertaken to quantify the performance and acoustics of a counter-rotating open rotor system. The present document summarizes the portion of this test performed with the so-called "Historical Baseline" rotor blades, designated F31/A31. It includes performance and acoustic data acquired at Mach numbers from take-off to cruise. It also includes the effect of propulsor angle of attack as well as an upstream pylon. This report is accompanied by an electronic data set including relevant acoustic and performance measurements for all of the F31/A31 data.

10 CFR 452.5 - Bidding procedures.

Code of Federal Regulations, 2012 CFR

2012-01-01

... OF ENERGY ENERGY CONSERVATION PRODUCTION INCENTIVES FOR CELLULOSIC BIOFUELS § 452.5 Bidding... producer auction process open only to pre-auction eligible cellulosic biofuels producers. The following... cellulosic biofuels producers during the open window established in the solicitation. The open window shall...

10 CFR 452.5 - Bidding procedures.

Code of Federal Regulations, 2014 CFR

2014-01-01

... OF ENERGY ENERGY CONSERVATION PRODUCTION INCENTIVES FOR CELLULOSIC BIOFUELS § 452.5 Bidding... producer auction process open only to pre-auction eligible cellulosic biofuels producers. The following... cellulosic biofuels producers during the open window established in the solicitation. The open window shall...

10 CFR 452.5 - Bidding procedures.

Code of Federal Regulations, 2013 CFR

2013-01-01

... OF ENERGY ENERGY CONSERVATION PRODUCTION INCENTIVES FOR CELLULOSIC BIOFUELS § 452.5 Bidding... producer auction process open only to pre-auction eligible cellulosic biofuels producers. The following... cellulosic biofuels producers during the open window established in the solicitation. The open window shall...

10 CFR 452.5 - Bidding procedures.

Code of Federal Regulations, 2011 CFR

2011-01-01

... OF ENERGY ENERGY CONSERVATION PRODUCTION INCENTIVES FOR CELLULOSIC BIOFUELS § 452.5 Bidding... producer auction process open only to pre-auction eligible cellulosic biofuels producers. The following... cellulosic biofuels producers during the open window established in the solicitation. The open window shall...

Linear theory of boundary effects in open wind tunnels with finite jet lengths

NASA Technical Reports Server (NTRS)

Katzoff, S; Gardner, Clifford S; Diesendruck, Leo; Eisenstadt, Bertram J

1950-01-01

In the first part, the boundary conditions for an open wind tunnel (incompressible flow) are examined with special reference to the effects of the closed entrance and exit sections. Basic conditions are that the velocity must be continuous at the entrance lip and that the velocities in the upstream and downstream closed portions must be equal. In the second part, solutions are derived for four types of two-dimensional open tunnels, including one in which the pressures on the two free surfaces are not equal. Numerical results are given for every case. In general, if the lifting element is more than half the tunnel height from the inlet, the boundary effect at the lifting element is the same as for an infinitely long open tunnel. In the third part, a general method is given for calculating the boundary effect in an open circular wind tunnel of finite jet length. Numerical results are given for a lifting element concentrate at a point on the axis.

Enhancement of the Open National Combustion Code (OpenNCC) and Initial Simulation of Energy Efficient Engine Combustor

NASA Technical Reports Server (NTRS)

Miki, Kenji; Moder, Jeff; Liou, Meng-Sing

2016-01-01

In this paper, we present the recent enhancement of the Open National Combustion Code (OpenNCC) and apply the OpenNCC to model a realistic combustor configuration (Energy Efficient Engine (E3)). First, we perform a series of validation tests for the newly-implemented advection upstream splitting method (AUSM) and the extended version of the AUSM-family schemes (AUSM+-up). Compared with the analytical/experimental data of the validation tests, we achieved good agreement. In the steady-state E3 cold flow results using the Reynolds-averaged Navier-Stokes(RANS), we find a noticeable difference in the flow fields calculated by the two different numerical schemes, the standard Jameson- Schmidt-Turkel (JST) scheme and the AUSM scheme. The main differences are that the AUSM scheme is less numerical dissipative and it predicts much stronger reverse flow in the recirculation zone. This study indicates that two schemes could show different flame-holding predictions and overall flame structures.

Efficient High-Order Accurate Methods using Unstructured Grids for Hydrodynamics and Acoustics

DTIC Science & Technology

2007-08-31

Leer. On upstream differencing and godunov-type schemes for hyperbolic conservation laws. SIAM Review, 25(1):35-61, 1983. [46] F . Eleuterio Toro ...early stage [4-61. The basic idea can be surmised from simple approximation theory. If a continuous function f is to be approximated over a set of...a2f 4h4 a4ff(x+eh) = f (x)+-- + _ •-+• e +0 +... (1) where 0 < e < 1 for approximations inside the interval of width h. For a second-order approximation

Phylogenetic distribution and evolutionary dynamics of the sex determination genes doublesex and transformer in insects.

PubMed

Geuverink, E; Beukeboom, L W

2014-01-01

Sex determination in insects is characterized by a gene cascade that is conserved at the bottom but contains diverse primary signals at the top. The bottom master switch gene doublesex is found in all insects. Its upstream regulator transformer is present in the orders Hymenoptera, Coleoptera and Diptera, but has thus far not been found in Lepidoptera and in the basal lineages of Diptera. transformer is presumed to be ancestral to the holometabolous insects based on its shared domains and conserved features of autoregulation and sex-specific splicing. We interpret that its absence in basal lineages of Diptera and its order-specific conserved domains indicate multiple independent losses or recruitments into the sex determination cascade. Duplications of transformer are found in derived families within the Hymenoptera, characterized by their complementary sex determination mechanism. As duplications are not found in any other insect order, they appear linked to the haplodiploid reproduction of the Hymenoptera. Further phylogenetic analyses combined with functional studies are needed to understand the evolutionary history of the transformer gene among insects. © 2013 S. Karger AG, Basel.

Modulation of the Conformational Dynamics of Apo-Adenylate Kinase through a π-Cation Interaction.

PubMed

Halder, Ritaban; Manna, Rabindra Nath; Chakraborty, Sandipan; Jana, Biman

2017-06-15

Large-scale conformational transition from open to closed state of adenylate kinase (ADK) is essential for its catalytic cycle. Apo-ADK undergoes conformational transition in a way that closely resembles an open-to-closed conformational transition. Here, equilibrium simulations, free-energy simulations, and quantum mechanics/molecular mechanics (QM/MM) calculations in combination with several bioinformatics approaches have been used to explore the molecular origin of this conformational transition in apo-ADK. In addition to its conventional open state, Escherichia coli apo-ADK adopts conformations that resemble a closed-like intermediate, the "half-open-half-closed" (HOHC) state, and a π-cation interaction can account for the stability of this HOHC state. Energetics and the electronic properties of this π-cation interaction have been explored using QM/MM calculations. Upon rescinding the π-cation interaction, the conformational landscape of the apo-ADK changes completely. The apo-ADK population is shifted completely toward the open state. This π-cation interaction is highly conserved in bacterial ADK; the cationic guanidinium moiety of a conserved ARG interacts with the delocalized π-electron cloud of either PHE or TYR. Interestingly, this study demonstrates the modulation of a principal protein dynamics by a conserved specific π-cation interaction across different organisms.

Effects of mass loading on dayside solar wind-magnetosphere interactions

NASA Astrophysics Data System (ADS)

Zhang, B.; Brambles, O.; Wiltberger, M. J.; Lyon, J.; Lotko, W.

2016-12-01

Satellite observations have shown that terrestrial-sourced plasmas mass load the dayside magnetopause and cause reductions in local reconnection rates. Whether the integrated dayside reconnection rate is affected by these local mass-loading processes is still an open question. Several mechanisms have been proposed to describe the control of dayside reconnection, including the local-control and global-control hypotheses. We have conducted a series of controlled numerical simulations to investigate the response of dayside solar wind-magnetopshere (SW-M) coupling to mass loading processes. Our simulation results show that the coupled SW-M system may exhibit both local and global control behaviors depending on the amount of mass loading. With a small amount of mass loading, the changes in the local reconnection rate does not affect magnetosheath properties and the geoeffective length in the upstream solar wind, resulting in the same integrated dayside reconnection rate. With a large amount of mass loading, the magnetosheath properties and the geoeffective length are significantly modified by slowing down the local reconnection rate, resulting in a significant reduction in the integrated dayside reconnection rate. The response of magnetosheath properties to mass loading is expected from the Cassak-Shay asymmetric reconnection theory through conservation of energy. The physical origin of the transition regime between local and global control is qualitatively explained. The parameters that determine the transition regime depend on the location, spatial extension and density of the mass loading process.

Foxl2 function in ovarian development.

PubMed

Uhlenhaut, Nina Henriette; Treier, Mathias

2006-07-01

Foxl2 is a forkhead transcription factor essential for proper reproductive function in females. Human patients carrying mutations in the FOXL2 gene display blepharophimosis/ptosis/epicanthus inversus syndrome (BPES), an autosomal dominant disease associated with eyelid defects and premature ovarian failure in females. Recently, animal models for BPES have been developed that in combination with a catalogue of human FOXL2 mutations provide further insight into its molecular function. Mice homozygous mutant for Foxl2 display craniofacial malformations and female infertility. The analysis of the murine phenotype has revealed that Foxl2 is required for granulosa cell function. These ovarian somatic cells surround and nourish the oocyte and play an important role in follicle formation and activation. Mutations upstream of FOXL2 in humans, not affecting the coding sequence itself, have also been shown to cause BPES, which points to the existence of a distant regulatory element necessary for proper gene expression. The same regulatory sequences may be deleted in the goat polled intersex syndrome (PIS), in which FoxL2 expression is severely reduced. Sequence comparison of FoxL2 from several vertebrate species has shown that it is a highly conserved gene involved in ovary development. Thus, the detailed understanding of Foxl2 function and regulation and the identification of its transcriptional targets may open new avenues for the treatment of female infertility in the future.

Duplicate Maize Wrinkled1 Transcription Factors Activate Target Genes Involved in Seed Oil Biosynthesis1[C][W

PubMed Central

Pouvreau, Benjamin; Baud, Sébastien; Vernoud, Vanessa; Morin, Valérie; Py, Cyrille; Gendrot, Ghislaine; Pichon, Jean-Philippe; Rouster, Jacques; Paul, Wyatt; Rogowsky, Peter M.

2011-01-01

WRINKLED1 (WRI1), a key regulator of seed oil biosynthesis in Arabidopsis (Arabidopsis thaliana), was duplicated during the genome amplification of the cereal ancestor genome 90 million years ago. Both maize (Zea mays) coorthologs ZmWri1a and ZmWri1b show a strong transcriptional induction during the early filling stage of the embryo and complement the reduced fatty acid content of Arabidopsis wri1-4 seeds, suggesting conservation of molecular function. Overexpression of ZmWri1a not only increases the fatty acid content of the mature maize grain but also the content of certain amino acids, of several compounds involved in amino acid biosynthesis, and of two intermediates of the tricarboxylic acid cycle. Transcriptomic experiments identified 18 putative target genes of this transcription factor, 12 of which contain in their upstream regions an AW box, the cis-element bound by AtWRI1. In addition to functions related to late glycolysis and fatty acid biosynthesis in plastids, the target genes also have functions related to coenzyme A biosynthesis in mitochondria and the production of glycerol backbones for triacylglycerol biosynthesis in the cytoplasm. Interestingly, the higher seed oil content in ZmWri1a overexpression lines is not accompanied by a reduction in starch, thus opening possibilities for the use of the transgenic maize lines in breeding programs. PMID:21474435

Multilayer regulatory mechanisms control cleavage factor I proteins in filamentous fungi

PubMed Central

Rodríguez-Romero, J.; Franceschetti, M.; Bueno, E.; Sesma, A.

2015-01-01

Cleavage factor I (CFI) proteins are core components of the polyadenylation machinery that can regulate several steps of mRNA life cycle, including alternative polyadenylation, splicing, export and decay. Here, we describe the regulatory mechanisms that control two fungal CFI protein classes in Magnaporthe oryzae: Rbp35/CfI25 complex and Hrp1. Using mutational, genetic and biochemical studies we demonstrate that cellular concentration of CFI mRNAs is a limited indicator of their protein abundance. Our results suggest that several post-transcriptional mechanisms regulate Rbp35/CfI25 complex and Hrp1 in the rice blast fungus, some of which are also conserved in other ascomycetes. With respect to Rbp35, these include C-terminal processing, RGG-dependent localization and cleavage, C-terminal autoregulatory domain and regulation by an upstream open reading frame of Rbp35-dependent TOR signalling pathway. Our proteomic analyses suggest that Rbp35 regulates the levels of proteins involved in melanin and phenylpropanoids synthesis, among others. The drastic reduction of fungal CFI proteins in carbon-starved cells suggests that the pre-mRNA processing pathway is altered. Our findings uncover broad and multilayer regulatory mechanisms controlling fungal polyadenylation factors, which have profound implications in pre-mRNA maturation. This area of research offers new avenues for fungicide design by targeting fungal-specific proteins that globally affect thousands of mRNAs. PMID:25514925

Set regulation in asexual and sexual Plasmodium parasites reveals a novel mechanism of stage-specific expression.

PubMed

Pace, Tomasino; Olivieri, Anna; Sanchez, Massimo; Albanesi, Veronica; Picci, Leonardo; Siden Kiamos, Inga; Janse, Chris J; Waters, Andrew P; Pizzi, Elisabetta; Ponzi, Marta

2006-05-01

Transmission of the malaria parasite depends on specialized gamete precursors (gametocytes) that develop in the bloodstream of a vertebrate host. Gametocyte/gamete differentiation requires controlled patterns of gene expression and regulation not only of stage and gender-specific genes but also of genes associated with DNA replication and mitosis. Once taken up by mosquito, male gametocytes undergo three mitotic cycles within few minutes to produce eight motile gametes. Here we analysed, in two Plasmodium species, the expression of SET, a conserved nuclear protein involved in chromatin dynamics. SET is expressed in both asexual and sexual blood stages but strongly accumulates in male gametocytes. We demonstrated functionally the presence of two distinct promoters upstream of the set open reading frame, the one active in all blood stage parasites while the other active only in gametocytes and in a fraction of schizonts possibly committed to sexual differentiation. In ookinetes both promoters exhibit a basal activity, while in the oocysts the gametocyte-specific promoter is silent and the reporter gene is only transcribed from the constitutive promoter. This transcriptional control, described for the first time in Plasmodium, provides a mechanism by which single-copy genes can be differently modulated during parasite development. In male gametocytes an overexpression of SET might contribute to a prompt entry and execution of S/M phases within mosquito vector.

Cloning and sequence analysis of the Antheraea pernyi nucleopolyhedrovirus gp64 gene.

PubMed

Wang, Wenbing; Zhu, Shanying; Wang, Liqun; Yu, Feng; Shen, Weide

2005-12-01

Frequent outbreaks of the purulence disease of Chinese oak silkworm are reported in Middle and Northeast China. The disease is produced by the pathogen Antheraea pernyi nucleopolyhedrovirus (AnpeNPV). To obtain molecular information of the virus, the polyhedra of AnpeNPV were purified and characterized. The genomic DNA of AnpeNPV was extracted and digested with HindIII. The genome size of AnpeNPV is estimated at 128 kb. Based on the analysis of DNA fragments digested with HindIII, 23 fragments were bigger than 564 bp. A genomic library was generated using HindIII and the positive clones were sequenced and analysed. The gp64 gene, encoding the baculovirus envelope protein GP64, was found in an insert. The nucleotide sequence analysis indicated that the AnpeNPV gp64 gene consists of a 1,530 nucleotide open reading frame (ORF), encoding a protein of 509 amino acids. Of the eight gp64 homologues, the AnpeNPV gp64 ORF shared the most sequence similarity with the gp64 gene of Anticarsia gemmatalis NPV, but not Bombyx mori NPV. The upstream region of the AnpeNPV gp64 ORF encoded the conserved transcriptional elements for early and late stage of the viral infection cycle. These results indicated that AnpeNPV belongs to group I NPV and was far removed in molecular phylogeny from the BmNPV.

How Physical Processes are Informing River Management Actions at Marble Bluff Dam, Truckee River, Nevada

NASA Astrophysics Data System (ADS)

Bountry, J.; Godaire, J.; Bradley, D. N.

2017-12-01

At the terminus of the Truckee River into Pyramid Lake (Nevada, USA), upstream river management actions have dramatically reshaped the river landscape, posing significant challenges for the management of endangered aquatic species and maintenance of existing infrastructure. Within the last 100 years, upstream water withdrawal for human uses has resulted in a rapid lowering of Pyramid Lake which initiated up to 90 ft of channel incision. In 1976 Marble Bluff Dam was constructed to halt the upstream progression of channel incision and protect upstream agricultural lands, tribal resources, and infrastructure. Since construction an additional 40 ft of lake lowering and subsequent channel lowering now poses a potential risk to the structural integrity of the dam. The dynamic downstream river combined with ongoing reservoir sedimentation pose challenges to fish passage facilities that enable migration of numerous endangered cui-ui and threatened Lahontan Cutthroat Trout (LCT) to upstream spawning areas each year. These facilities include a fish lock at the dam, a fish bypass channel which allows fish to avoid the shallow delta area during low lake levels, and a meandering channel constructed by the Nature Conservancy to connect the bypass channel to the receding Pyramid Lake. The reservoir formed by Marble Bluff Dam has completely filled with sediment which impacts fish passage facilities. The original operating manual for the dam recommends year-round flushing of sediment through radial gates, but this can no longer be accomplished. During critical fish migration periods in the spring operators must ensure fish entrance channels downstream of the dam are not buried with released sediment and fish are not trapped in a portion of the reservoir full of sediment that would risk sending them back over the dam. To help inform future reservoir sediment and infrastructure management strategies, we bracket a range of potential river responses to lake level lowering and floods using historical trends, current field data, and hydraulic and sediment transport models. We present options for adaptive management for dam and reservoir sediment operations that incorporates monitoring of river processes to inform annual implementation strategies along with long-term planning.

A Gibbs sampler for motif detection in phylogenetically close sequences

NASA Astrophysics Data System (ADS)

Siddharthan, Rahul; van Nimwegen, Erik; Siggia, Eric

2004-03-01

Genes are regulated by transcription factors that bind to DNA upstream of genes and recognize short conserved ``motifs'' in a random intergenic ``background''. Motif-finders such as the Gibbs sampler compare the probability of these short sequences being represented by ``weight matrices'' to the probability of their arising from the background ``null model'', and explore this space (analogous to a free-energy landscape). But closely related species may show conservation not because of functional sites but simply because they have not had sufficient time to diverge, so conventional methods will fail. We introduce a new Gibbs sampler algorithm that accounts for common ancestry when searching for motifs, while requiring minimal ``prior'' assumptions on the number and types of motifs, assessing the significance of detected motifs by ``tracking'' clusters that stay together. We apply this scheme to motif detection in sporulation-cycle genes in the yeast S. cerevisiae, using recent sequences of other closely-related Saccharomyces species.

Authentication of meat from game and domestic species by SNaPshot minisequencing analysis.

PubMed

La Neve, Fabio; Civera, Tiziana; Mucci, Nadia; Bottero, Maria Teresa

2008-10-01

The aim of the present study is to develop an assay for the specific identification of meat from Capreolus capreolus, Cervus elaphus, Capra ibex, Rupicapra rupicapra, targeting sequences of the cytochrome b (cyt b) gene of mitochondrial DNA. The assay is also intended to enable differentiation between meat from these wild species as well as Ovis aries, Capra hircus, Bubalus bubalis, Bos taurus and Sus scrofa domestic species. The primers used in the preliminary PCR were designed in well conserved regions upstream and downstream of the diagnosis sites. They successfully amplified a conserved 232bp region from the cyt b gene of all the species taken into consideration. The sites of diagnosis have been interrogated using a minisequencing reaction and capillary electrophoresis. All the results of the multiplex PER (primer extension reaction) test were confirmed by fragment sequencing. The assay offers the possibility of discriminating nine species at the same time.

Spatiotemporal patterns and habitat associations of smallmouth bass (Micropterus dolomieu) invading salmon-rearing habitat

USGS Publications Warehouse

Lawrence, David J.; Olden, Julian D.; Torgersen, Christian E.

2012-01-01

1. Smallmouth bass (Micropterus dolomieu) have been widely introduced to fresh waters throughout the world to promote recreational fishing opportunities. In the Pacific Northwest (U.S.A.), upstream range expansions of predatory bass, especially into subyearling salmon-rearing grounds, are of increasing conservation concern, yet have received little scientific inquiry. Understanding the habitat characteristics that influence bass distribution and the timing and extent of bass and salmon overlap will facilitate the development of management strategies that mitigate potential ecological impacts of bass.2. We employed a spatially continuous sampling design to determine the extent of bass and subyearling Chinook salmon (Oncorhynchus tshawytscha) sympatry in the North Fork John Day River (NFJDR), a free-flowing river system in the Columbia River Basin that contains an upstream expanding population of non-native bass. Extensive (i.e. 53 km) surveys were conducted over 2 years and during an early and late summer period of each year, because these seasons provide a strong contrast in the river’s water temperature and flow condition. Classification and regression trees were applied to determine the primary habitat correlates of bass abundance at reach and channel-unit scales.3. Our study revealed that bass seasonally occupy up to 22% of the length of the mainstem NFJDR where subyearling Chinook salmon occur, and the primary period of sympatry between these species was in the early summer and not during peak water temperatures in late summer. Where these species co-occurred, bass occupied 60–76% of channel units used by subyearling Chinook salmon in the early summer and 28–46% of the channel units they occupied in the late summer. Because these rearing salmon were well below the gape limitation of bass, this overlap could result in either direct predation or sublethal effects of bass on subyearling Chinook salmon. The upstream extent of bass increased 10–23 km (2009 and 2010, respectively) as stream temperatures seasonally warmed, but subyearling Chinook salmon were also found farther upstream during this time.4. Our multiscale analysis suggests that bass were selecting habitat based on antecedent thermal history at a broad scale, and if satisfactory temperature conditions were met, mesoscale habitat features (i.e. channel-unit type and depth) played an additional role in determining bass abundance. The upstream extent of bass in the late summer corresponded to a high-gradient geomorphic discontinuity in the NFJDR, which probably hindered further upstream movements of bass. The habitat determinants and upstream extent of bass were largely consistent across years, despite marked differences in the magnitude and timing of spring peak flows prior to bass spawning.5. The overriding influence of water temperature on smallmouth bass distribution suggests that managers may be able limit future upstream range expansions of bass into salmon-rearing habitat by concentrating on restoration activities that mitigate climate- or land-use-related stream warming. These management activities could be prioritised to capitalise on survival bottlenecks in the life history of bass and spatially focused on landscape knick points such as high-gradient discontinuities to discourage further upstream movements of bass.

Proceedings of a workshop on American Eel passage technologies

USGS Publications Warehouse

Haro, Alexander J.

2013-01-01

Recent concerns regarding a decline in recruitment of American eels (Anguilla rostrata) have prompted efforts to restore this species to historic habitats by providing passage for both upstream migrant juveniles and downstream migrant adults at riverine barriers, including low-head and hydroelectric dams (Castonguay et al. 1994, Haro et al. 2000). These efforts include development of management plans and stock assessment reviews in both the US and Canada (COSEWIC 2006, Canadian Eel Working Group 2009, DFO 2010, MacGregor et al. 2010, ASMFC 2000, ASMFC 2006, ASMFC 2008, Williams and Threader 2007), which target improvement of upstream and downstream passage for eels, as well as identification and prioritization of research needs for development of new and more effective passage technologies for American eels. Traditional upstream fish passage structures, such as fishways and fish lifts, are often ineffective passing juvenile eels, and specialized passage structures for this species are needed. Although designs for such passage structures are available and diverse (Knights and White 1998, Porcher 2002, FAO/DVWK 2002, Solomon and Beach 2004a,b, Environment Agency UK 2011), many biologists, managers, and engineers are unfamiliar with eel pass design and operation, or unaware of the technical options available for upstream eel passage, Better coordination is needed to account for eel passage requirements during restoration efforts for other diadromous fish species. Also, appropriately siting eel passes at hydropower projects is critical, and siting can be difficult and complex due to physical restrictions in access to points of natural concentrations of eels, dynamic hydraulics of tailrace areas, and presence of significant competing flows from turbine outfalls or spill. As a result, some constructed eel passes are sited poorly and may pass only a fraction of the number of eels attempting to pass the barrier. When sited and constructed appropriately, however, eel passes can effectively pass thousands of individuals in a season (Appendix D). technologies for preventing impingement and entrainment mortality and injury of downstream migrant eels at hydropower projects are not well developed. Traditional downstream fish passage mitigative techniques originally developed for salmonids and other species are frequently ineffective passing eels (Richkus and Dixon 2003, EPRI 2001, Bruijs and Durif 2009). Large hydropower projects, with high project flows or intake openings that cannot be fitted with racks or screens with openings small enough to exclude eels, pose significant passage problems for this species, and turbine impingement and entrainment mortality of eels can be as high as 100%. Spill mortality and injury may also be significant for eels, given their tendency to move during high flow events when projects typically spill large amounts of flow. Delays in migration of eels that have difficulty locating and utilizing bypass entrances can also be significant. Therefore, downstream passage technologies are at a much more nebulous state of development than upstream passage technologies, and require further evaluation and improvement before rigorous design guidelines can be established. There have been few studies conducted to evaluate effectiveness of current mitigative measures for both upstream and downstream passage of eels. Research is needed to determine eel migratory timing, behavior, and appropriate mitigation technologies for specific sites and eel life history stages. Both upstream and downstream eel passage structures can be difficult to evaluate in terms of performance, and examples of how evaluation and monitoring can be accomplished were reviewed at the workshop.

Achieving Open Access to Conservation Science

PubMed Central

Fuller, Richard A; Lee, Jasmine R; Watson, James E M

2014-01-01

Conservation science is a crisis discipline in which the results of scientific enquiry must be made available quickly to those implementing management. We assessed the extent to which scientific research published since the year 2000 in 20 conservation science journals is publicly available. Of the 19,207 papers published, 1,667 (8.68%) are freely downloadable from an official repository. Moreover, only 938 papers (4.88%) meet the standard definition of open access in which material can be freely reused providing attribution to the authors is given. This compares poorly with a comparable set of 20 evolutionary biology journals, where 31.93% of papers are freely downloadable and 7.49% are open access. Seventeen of the 20 conservation journals offer an open access option, but fewer than 5% of the papers are available through open access. The cost of accessing the full body of conservation science runs into tens of thousands of dollars per year for institutional subscribers, and many conservation practitioners cannot access pay-per-view science through their workplace. However, important initiatives such as Research4Life are making science available to organizations in developing countries. We urge authors of conservation science to pay for open access on a per-article basis or to choose publication in open access journals, taking care to ensure the license allows reuse for any purpose providing attribution is given. Currently, it would cost $51 million to make all conservation science published since 2000 freely available by paying the open access fees currently levied to authors. Publishers of conservation journals might consider more cost effective models for open access and conservation-oriented organizations running journals could consider a broader range of options for open access to nonmembers such as sponsorship of open access via membership fees. Obtención de Acceso Abierto a la Ciencia de la Conservación Resumen La ciencia de la conservación es una disciplina de crisis en la que los resultados del cuestionamiento científico deben hacerse disponibles de manera rápida para quienes están implementando el manejo. Evaluamos la extensión a la cual está disponible para el público la investigación científica publicada desde el año 2000 en 20 revistas de ciencia de la conservación. De los 19, 207 artículos publicados, 1, 667 (8.68%) están libres para descargar de un repositorio oficial. Además, sólo 938 artículos (4.88%) cumplen con la definición estándar de acceso abierto en la cual el material puede reutilizarse libremente siempre y cuando se le dé atribución a los autores. Esto se compara pobremente con un conjunto comparable de 20 revistas de biología evolutiva, donde 31.93% de los artículos están libres para descargar y el 7.94% son de acceso abierto. Diecisiete de las 20 revistas de conservación ofrecen una opción de acceso abierto, pero menos del 5% de los artículos están disponibles por medio del acceso abierto. El costo de acceder al cuerpo completo de la ciencia de la conservación llega a estar entre los miles de dólares por año para suscriptores institucionales, y muchos practicantes de la conservación no pueden acceder a la ciencia de paga en sus lugares de trabajo. Sin embargo, iniciativas importantes como Research4Life están poniendo a la ciencia a disponibilidad de organizaciones en países en desarrollo. Urgimos a los autores de la ciencia de la conservación que paguen por acceso abierto en una base por artículo o que escojan publicar en revistas de acceso abierto, tomando en consideración asegurar que la licencia permita reutilizar siempre y cuando se proporcione atribución. Actualmente, costaría $51 millones hacer que toda la ciencia de la conservación publicada desde 2000 esté disponible libremente al pagar las cuotas de acceso abierto que actualmente impuestas a los autores. Los publicadores de revistas de la conservación pueden considerar modelos más rentables para el acceso abierto y las organizaciones orientadas a la conservación que administran revistas podrían considerar un campo más amplio de opciones de acceso abierto para quienes no son miembros, como el patrocinio de acceso abierto por medio de pagos de membrecía PMID:25158824

Mechanism of Promoter Melting by the Xeroderma Pigmentosum Complementation Group B Helicase of Transcription Factor IIH Revealed by Protein-DNA Photo-Cross-Linking

PubMed Central

Douziech, Maxime; Coin, Frédéric; Chipoulet, Jean-Marc; Arai, Yoko; Ohkuma, Yoshiaki; Egly, Jean-Marc; Coulombe, Benoit

2000-01-01

The p89/xeroderma pigmentosum complementation group B (XPB) ATPase-helicase of transcription factor IIH (TFIIH) is essential for promoter melting prior to transcription initiation by RNA polymerase II (RNAPII). By studying the topological organization of the initiation complex using site-specific protein-DNA photo-cross-linking, we have shown that p89/XPB makes promoter contacts both upstream and downstream of the initiation site. The upstream contact, which is in the region where promoter melting occurs (positions −9 to +2), requires tight DNA wrapping around RNAPII. The addition of hydrolyzable ATP tethers the template strand at positions −5 and +1 to RNAPII subunits. A mutation in p89/XPB found in a xeroderma pigmentosum patient impairs the ability of TFIIH to associate correctly with the complex and thereby melt promoter DNA. A model for open complex formation is proposed. PMID:11027286

Modulation of tissue repair by regeneration enhancer elements.

PubMed

Kang, Junsu; Hu, Jianxin; Karra, Ravi; Dickson, Amy L; Tornini, Valerie A; Nachtrab, Gregory; Gemberling, Matthew; Goldman, Joseph A; Black, Brian L; Poss, Kenneth D

2016-04-14

How tissue regeneration programs are triggered by injury has received limited research attention. Here we investigate the existence of enhancer regulatory elements that are activated in regenerating tissue. Transcriptomic analyses reveal that leptin b (lepb) is highly induced in regenerating hearts and fins of zebrafish. Epigenetic profiling identified a short DNA sequence element upstream and distal to lepb that acquires open chromatin marks during regeneration and enables injury-dependent expression from minimal promoters. This element could activate expression in injured neonatal mouse tissues and was divisible into tissue-specific modules sufficient for expression in regenerating zebrafish fins or hearts. Simple enhancer-effector transgenes employing lepb-linked sequences upstream of pro- or anti-regenerative factors controlled the efficacy of regeneration in zebrafish. Our findings provide evidence for 'tissue regeneration enhancer elements' (TREEs) that trigger gene expression in injury sites and can be engineered to modulate the regenerative potential of vertebrate organs.

50 CFR Table 24 to Part 679 - Except as Noted, Locations in the Aleutian Islands Habitat Conservation Area Open to Nonpelagic...

Code of Federal Regulations, 2014 CFR

2014-10-01

... 50 Wildlife and Fisheries 13 2014-10-01 2014-10-01 false Except as Noted, Locations in the Aleutian Islands Habitat Conservation Area Open to Nonpelagic Trawl Fishing 24 Table 24 to Part 679... to Nonpelagic Trawl Fishing ER19FE08.009 ER19FE08.010 ER19FE08.011 ER19FE08.012 ER19FE08.013 ER19FE08...

50 CFR Table 24 to Part 679 - Except as Noted, Locations in the Aleutian Islands Habitat Conservation Area Open to Nonpelagic...

Code of Federal Regulations, 2012 CFR

2012-10-01

... 50 Wildlife and Fisheries 13 2012-10-01 2012-10-01 false Except as Noted, Locations in the Aleutian Islands Habitat Conservation Area Open to Nonpelagic Trawl Fishing 24 Table 24 to Part 679... to Nonpelagic Trawl Fishing ER19FE08.009 ER19FE08.010 ER19FE08.011 ER19FE08.012 ER19FE08.013 ER19FE08...

50 CFR Table 24 to Part 679 - Except as Noted, Locations in the Aleutian Islands Habitat Conservation Area Open to Nonpelagic...

Code of Federal Regulations, 2011 CFR

2011-10-01

... 50 Wildlife and Fisheries 11 2011-10-01 2011-10-01 false Except as Noted, Locations in the Aleutian Islands Habitat Conservation Area Open to Nonpelagic Trawl Fishing 24 Table 24 to Part 679... to Nonpelagic Trawl Fishing ER19FE08.009 ER19FE08.010 ER19FE08.011 ER19FE08.012 ER19FE08.013 ER19FE08...

Human ribosomal RNA gene: nucleotide sequence of the transcription initiation region and comparison of three mammalian genes.

PubMed Central

Financsek, I; Mizumoto, K; Mishima, Y; Muramatsu, M

1982-01-01

The transcription initiation site of the human ribosomal RNA gene (rDNA) was located by using the single-strand specific nuclease protection method and by determining the first nucleotide of the in vitro capped 45S preribosomal RNA. The sequence of 1,211 nucleotides surrounding the initiation site was determined. The sequenced region was found to consist of 75% G and C and to contain a number of short direct and inverted repeats and palindromes. By comparison of the corresponding initiation regions of three mammalian species, several conserved sequences were found upstream and downstream from the transcription starting point. Two short A + T-rich sequences are present on human, mouse, and rat ribosomal RNA genes between the initiation site and 40 nucleotides upstream, and a C + T cluster is located at a position around -60. At and downstream from the initiation site, a common sequence, T-AG-C-T-G-A-C-A-C-G-C-T-G-T-C-C-T-CT-T, was found in the three genes from position -1 through +18. The strong conservation of these sequences suggests their functional significance in rDNA. The S1 nuclease protection experiments with cloned rDNA fragments indicated the presence in human 45S RNA of molecules several hundred nucleotides shorter than the supposed primary transcript. The first 19 nucleotides of these molecules appear identical--except for one mismatch--to the nucleotide sequence of the 5' end of a supposed early processing product of the mouse 45S RNA. Images PMID:6954460

An Insulator Element Located at the Cyclin B1 Interacting Protein 1 Gene Locus Is Highly Conserved among Mammalian Species

PubMed Central

Yoshida, Wataru; Tomikawa, Junko; Inaki, Makoto; Kimura, Hiroshi; Onodera, Masafumi; Hata, Kenichiro; Nakabayashi, Kazuhiko

2015-01-01

Insulators are cis-elements that control the direction of enhancer and silencer activities (enhancer-blocking) and protect genes from silencing by heterochromatinization (barrier activity). Understanding insulators is critical to elucidate gene regulatory mechanisms at chromosomal domain levels. Here, we focused on a genomic region upstream of the mouse Ccnb1ip1 (cyclin B1 interacting protein 1) gene that was methylated in E9.5 embryos of the C57BL/6 strain, but unmethylated in those of the 129X1/SvJ and JF1/Ms strains. We hypothesized the existence of an insulator-type element that prevents the spread of DNA methylation within the 1.8 kbp segment, and actually identified a 242-bp and a 185-bp fragments that were located adjacent to each other and showed insulator and enhancer activities, respectively, in reporter assays. We designated these genomic regions as the Ccnb1ip1 insulator and the Ccnb1ip1 enhancer. The Ccnb1ip1 insulator showed enhancer-blocking activity in the luciferase assays and barrier activity in the colony formation assays. Further examination of the Ccnb1ip1 locus in other mammalian species revealed that the insulator and enhancer are highly conserved among a wide variety of species, and are located immediately upstream of the transcriptional start site of Ccnb1ip1. These newly identified cis-elements may be involved in transcriptional regulation of Ccnb1ip1, which is important in meiotic crossing-over and G2/M transition of the mitotic cell cycle. PMID:26110280

Use of frequency analysis and the extended streamflow prediction procedure to estimate evacuation dates for the joint-use pool of Pueblo Reservoir, Colorado

USGS Publications Warehouse

Kuhn, Gerhard; Nickless, R.C.

1994-01-01

Part of the storage space of Pueblo Reservoir consists of a 65,950 acre-foot joint-use pool (JUP) that can be used to provide additional conservation capacity from November 1 to April 14; however, the JUP must be evacuated by April 15 and used only for flood-control capacity until November 1. A study was completed to determine if the JUP possibly could be used for conservation storage for any number of days from April 15 through May 14 under certain hydrologic conditions. The methods of the study were: (1) Frequency analysis of recorded daily mean discharge data for streamflow-gaging stations upstream and downstream from Pueblo Reservoir, and (2) Implementation of the extended streamflow prediction (ESP) procedure for the Arkansas River basin upstream from the reservoir. The frequency analyses enabled estimation of daily discharges at selected exceedance probabilities (EP's), including the 0.01 EP that was used in design of the flood- storage capacity of Pueblo Reservoir. The ESP procedure enabled probabilistic forecasts of inflow volume to the reservoir for April 15 through May 14. Daily discharges derived from the frequency analyses were routed through Pueblo Reservoir to estimate evacuation dates of the JUP for different reservoir inflow volumes; the estimates indicated a relation between the inflow volume and the JUP evacuation date. To apply the study results, only a ESP forecast of the April 15-May 14 reservoir inflow volume is needed. Study results indicate the JUP possibly could be used as late as May 5 depending on the forecast inflow volume.

Property-tax incentives for implementing soil-conservation programs under constitutional taxing limitations

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

Massey, D.T.; Silver, M.B.

1982-01-01

This article describes how property-tax incentives can be used to implement soil-conservation programs on agricultural and open-space lands under the differential-assessment statutes and other exceptions to constitutional limitations on taxation powers. The article describes restrictions imposed on taxing powers by the constitutional uniformity clauses and methods for circumventing those limitations; various property-tax incentives available for conservation programs; types of differential or use-value assessments providing property-tax relief for farm, forest, and open-space land preservation; eligibility of lands for differential assessments; methods available to landowners for participation in differential assessments; and determination of value under differential assessment. The article next details howmore » each of the three primary types of differential or use-value assessment statutes for farm, forest, and open-space land preservation provides exceptions to the uniformity clauses for property tax incentives to implement soil-conservation programs. Other methods available for providing exceptions to the uniformity clauses to permit property-tax incentives are also described for each of the three states. Each of these states has statutes giving favorable tax treatment to certain types of property, such as pollution-abatement equipment, alternative energy-producing devices, and even country clubs. These statutes can be used as examples of finding a constitutional method for providing favorabe tax treatment to promote participation in soil-conservation programs.« less

In Silico Analysis of Gene Expression Network Components Underlying Pigmentation Phenotypes in the Python Identified Evolutionarily Conserved Clusters of Transcription Factor Binding Sites

PubMed Central

2016-01-01

Color variation provides the opportunity to investigate the genetic basis of evolution and selection. Reptiles are less studied than mammals. Comparative genomics approaches allow for knowledge gained in one species to be leveraged for use in another species. We describe a comparative vertebrate analysis of conserved regulatory modules in pythons aimed at assessing bioinformatics evidence that transcription factors important in mammalian pigmentation phenotypes may also be important in python pigmentation phenotypes. We identified 23 python orthologs of mammalian genes associated with variation in coat color phenotypes for which we assessed the extent of pairwise protein sequence identity between pythons and mouse, dog, horse, cow, chicken, anole lizard, and garter snake. We next identified a set of melanocyte/pigment associated transcription factors (CREB, FOXD3, LEF-1, MITF, POU3F2, and USF-1) that exhibit relatively conserved sequence similarity within their DNA binding regions across species based on orthologous alignments across multiple species. Finally, we identified 27 evolutionarily conserved clusters of transcription factor binding sites within ~200-nucleotide intervals of the 1500-nucleotide upstream regions of AIM1, DCT, MC1R, MITF, MLANA, OA1, PMEL, RAB27A, and TYR from Python bivittatus. Our results provide insight into pigment phenotypes in pythons. PMID:27698666

In Silico Analysis of Gene Expression Network Components Underlying Pigmentation Phenotypes in the Python Identified Evolutionarily Conserved Clusters of Transcription Factor Binding Sites.

PubMed

Irizarry, Kristopher J L; Bryden, Randall L

2016-01-01

Color variation provides the opportunity to investigate the genetic basis of evolution and selection. Reptiles are less studied than mammals. Comparative genomics approaches allow for knowledge gained in one species to be leveraged for use in another species. We describe a comparative vertebrate analysis of conserved regulatory modules in pythons aimed at assessing bioinformatics evidence that transcription factors important in mammalian pigmentation phenotypes may also be important in python pigmentation phenotypes. We identified 23 python orthologs of mammalian genes associated with variation in coat color phenotypes for which we assessed the extent of pairwise protein sequence identity between pythons and mouse, dog, horse, cow, chicken, anole lizard, and garter snake. We next identified a set of melanocyte/pigment associated transcription factors (CREB, FOXD3, LEF-1, MITF, POU3F2, and USF-1) that exhibit relatively conserved sequence similarity within their DNA binding regions across species based on orthologous alignments across multiple species. Finally, we identified 27 evolutionarily conserved clusters of transcription factor binding sites within ~200-nucleotide intervals of the 1500-nucleotide upstream regions of AIM1, DCT, MC1R, MITF, MLANA, OA1, PMEL, RAB27A, and TYR from Python bivittatus . Our results provide insight into pigment phenotypes in pythons.

Conserved noncoding sequences conserve biological networks and influence genome evolution.

PubMed

Xie, Jianbo; Qian, Kecheng; Si, Jingna; Xiao, Liang; Ci, Dong; Zhang, Deqiang

2018-05-01

Comparative genomics approaches have identified numerous conserved cis-regulatory sequences near genes in plant genomes. Despite the identification of these conserved noncoding sequences (CNSs), our knowledge of their functional importance and selection remains limited. Here, we used a combination of DNA methylome analysis, microarray expression analyses, and functional annotation to study these sequences in the model tree Populus trichocarpa. Methylation in CG contexts and non-CG contexts was lower in CNSs, particularly CNSs in the 5'-upstream regions of genes, compared with other sites in the genome. We observed that CNSs are enriched in genes with transcription and binding functions, and this also associated with syntenic genes and those from whole-genome duplications, suggesting that cis-regulatory sequences play a key role in genome evolution. We detected a significant positive correlation between CNS number and protein interactions, suggesting that CNSs may have roles in the evolution and maintenance of biological networks. The divergence of CNSs indicates that duplication-degeneration-complementation drives the subfunctionalization of a proportion of duplicated genes from whole-genome duplication. Furthermore, population genomics confirmed that most CNSs are under strong purifying selection and only a small subset of CNSs shows evidence of adaptive evolution. These findings provide a foundation for future studies exploring these key genomic features in the maintenance of biological networks, local adaptation, and transcription.

Estimating bioaccessibility of trace elements in particles suspended in the Athabasca River using sequential extraction.

PubMed

Javed, Muhammad Babar; Shotyk, William

2018-05-10

Employing protocols developed for polar snow and ice, water samples were collected upstream, midstream and downstream of open pit bitumen mines and upgraders along the Lower Athabasca River (AR). The purpose was to: i) estimate the bioaccessibility of trace elements associated with particulate matter in the AR using sequential extraction, and ii) determine whether their forms have been measurably impacted by industrial activities. Of the trace metals known to be enriched in bitumen (V, Ni, Mo and Re), a substantial proportion of V (78-93%) and Ni (35-81%) was found in the residual fraction representing stable minerals. In contrast, Mo and Re were partitioned mainly into more reactive forms (water soluble, acid extractable, reducible and oxidisable). Comparing the non-residual fractions in upstream versus downstream sites, only water soluble Re was significantly (P = 0.005) greater downstream of industry. In respect to the potentially toxic chalcophile elements (Cu, Pb and Tl), no measurable change was observed in Cu and Pb distribution in upstream versus downstream sites. Only residual Tl was found at upstream and midstream sites, whereas a significant proportion of Tl was also present in the reducible fraction in downstream sites. Overall, a greater proportion of trace metals in the residual fraction at midstream sites appears to be due to inputs of atmospheric dust, clearly evident in microscopic images: energy dispersive spectroscopy and x-ray diffraction analyses showed that these particles were predominantly silicates, which are assumed to have limited bioaccessibility. Copyright © 2018 Elsevier Ltd. All rights reserved.

Essential role of the A'α/Aβ gap in the N-terminal upstream of LOV2 for the blue light signaling from LOV2 to kinase in Arabidopsis photototropin1, a plant blue light receptor.

PubMed

Kashojiya, Sachiko; Okajima, Koji; Shimada, Takashi; Tokutomi, Satoru

2015-01-01

Phototropin (phot) is a blue light (BL) receptor in plants and is involved in phototropism, chloroplast movement, stomata opening, etc. A phot molecule has two photo-receptive domains named LOV (Light-Oxygen-Voltage) 1 and 2 in its N-terminal region and a serine/threonine kinase (STK) in its C-terminal region. STK activity is regulated mainly by LOV2, which has a cyclic photoreaction, including the transient formation of a flavin mononucleotide (FMN)-cysteinyl adduct (S390). One of the key events for the propagation of the BL signal from LOV2 to STK is conformational changes in a Jα-helix residing downstream of the LOV2 C-terminus. In contrast, we focused on the role of the A'α-helix, which is located upstream of the LOV2 N-terminus and interacts with the Jα-helix. Using LOV2-STK polypeptides from Arabidopsis thaliana phot1, we found that truncation of the A'α-helix and amino acid substitutions at Glu474 and Lys475 in the gap between the A'α and the Aβ strand of LOV2 (A'α/Aβ gap) to Ala impaired the BL-induced activation of the STK, although they did not affect S390 formation. Trypsin digested the LOV2-STK at Lys603 and Lys475 in a light-dependent manner indicating BL-induced structural changes in both the Jα-helix and the gap. The digestion at Lys603 is faster than at Lys475. These BL-induced structural changes were observed with the Glu474Ala and the Lys475Ala substitutes, indicating that the BL signal reached the Jα-helix as well as the A'α/Aβ gap but could not activate STK. The amino acid residues, Glu474 and Lys475, in the gap are conserved among the phots of higher plants and may act as a joint to connect the structural changes in the Jα-helix with the activation of STK.

Viable contribution of Tibetan sacred mountains in southwestern China to forest conservation.

PubMed

Shen, Xiaoli; Li, Sheng; Wang, Dajun; Lu, Zhi

2015-12-01

The Tibetan sacred mountains (TSMs) cover a large area and may represent a landscape-scale conservation opportunity. We compared the conservation value of forests in these mountains with the conservation value of government-established nature reserves and unmanaged open-access areas in Danba County, southwestern China. We used Landsat satellite images to map forest cover and to estimate forest loss in 1974-1989, 1989-1999, and 1999-2013. The TSMs (n = 41) and nature reserves (n = 4) accounted for 21.6% and 29.7% of the county's land area, respectively. Remaining land was open-access areas (i.e., areas without any restrictions on resource use) (56.2%) and farmlands (2.2%). Within the elevation range suitable for forests, forest cover did not differ significantly between nature reserves (58.8%) and open-access areas (58.4%), but was significantly higher in TSMs (65.5%) after controlling for environmental factors such as aspect, slope, and elevation. The TSMs of great cultural importance had higher forest cover, but patrols by monastery staff were not necessarily associated with increased forest cover. The annual deforestation rate in nonsacred areas almost tripled in 1989-1999 (111.4 ha/year) relative to 1974-1989 (40.4 ha/year), whereas the rate in TSMs decreased in the later period (19.7 ha/year vs. 17.2 ha/year). The reduced forest loss in TSMs in 1989-1999 was possibly due to the renaissance of TSM worship and strengthened management by the local Buddhist community since late 1980s. The annual deforestation rate in Danba decreased dramatically to 4.4 ha/year in 1999-2013, which coincided with the implementation of a national ban on logging in 1998. As the only form of protected area across the Tibetan region during much of its history, TSMs have positively contributed to conserving forest at a landscape scale. Conservation of TSM forests largely relied on the strength of local religious institutions. Integrating community-based conservation of TSMs within the government conservation network would benefit the conservation of the Tibetan region. © 2015 Society for Conservation Biology.

Utilizing social media for informal ocean conservation and education: The BioOceanography Project

NASA Astrophysics Data System (ADS)

Payette, J.

2016-02-01

Science communication through the use of social media is a rapidly evolving and growing pursuit in academic and scientific circles. Online tools and social media are being used in not only scientific communication but also scientific publication, education, and outreach. Standards and usage of social media as well as other online tools for communication, networking, outreach, and publication are always in development. Caution and a conservative attitude towards these novel "Science 2.0" tools is understandable because of their rapidly changing nature and the lack of professional standards for using them. However there are some key benefits and unique ways social media, online systems, and other Open or Open Source technologies, software, and "Science 2.0" tools can be utilized for academic purposes such as education and outreach. Diverse efforts for ocean conservation and education will continue to utilize social media for a variety of purposes. The BioOceanography project is an informal communication, education, outreach, and conservation initiative created for enhancing knowledge related to Oceanography and Marine Science with an unbiased yet conservation-minded approach and in an Open Source format. The BioOceanography project is ongoing and still evolving, but has already contributed to ocean education and conservation communication in key ways through a concerted web presence since 2013, including a curated Twitter account @_Oceanography and BioOceanography blog style website. Social media tools like those used in this project, if used properly can be highly effective and valuable for encouraging students, networking with researchers, and educating the general public in Oceanography.

Land Management Restrictions and Options for Change in Perpetual Conservation Easements

NASA Astrophysics Data System (ADS)

Rissman, Adena; Bihari, Menka; Hamilton, Christopher; Locke, Christina; Lowenstein, David; Motew, Melissa; Price, Jessica; Smail, Robert

2013-07-01

Conservation organizations rely on conservation easements for diverse purposes, including protection of species and natural communities, working forests, and open space. This research investigated how perpetual conservation easements incorporated property rights, responsibilities, and options for change over time in land management. We compared 34 conservation easements held by one federal, three state, and four nonprofit organizations in Wisconsin. They incorporated six mechanisms for ongoing land management decision-making: management plans (74 %), modifications to permitted landowner uses with discretionary consent (65 %), amendment clauses (53 %), easement holder rights to conduct land management (50 %), reference to laws or policies as compliance terms (47 %), and conditional use permits (12 %). Easements with purposes to protect species and natural communities had more ecological monitoring rights, organizational control over land management, and mechanisms for change than easements with general open space purposes. Forestry purposes were associated with mechanisms for change but not necessarily with ecological monitoring rights or organizational control over land management. The Natural Resources Conservation Service-Wetland Reserve Program had a particularly consistent approach with high control over land use and some discretion to modify uses through permits. Conservation staff perceived a need to respond to changing social and ecological conditions but were divided on whether climate change was likely to negatively impact their conservation easements. Many conservation easements involved significant constraints on easement holders' options for altering land management to achieve conservation purposes over time. This study suggests the need for greater attention to easement drafting, monitoring, and ongoing decision processes to ensure the public benefits of land conservation in changing landscapes.

Land management restrictions and options for change in perpetual conservation easements.

PubMed

Rissman, Adena; Bihari, Menka; Hamilton, Christopher; Locke, Christina; Lowenstein, David; Motew, Melissa; Price, Jessica; Smail, Robert

2013-07-01

Conservation organizations rely on conservation easements for diverse purposes, including protection of species and natural communities, working forests, and open space. This research investigated how perpetual conservation easements incorporated property rights, responsibilities, and options for change over time in land management. We compared 34 conservation easements held by one federal, three state, and four nonprofit organizations in Wisconsin. They incorporated six mechanisms for ongoing land management decision-making: management plans (74 %), modifications to permitted landowner uses with discretionary consent (65 %), amendment clauses (53 %), easement holder rights to conduct land management (50 %), reference to laws or policies as compliance terms (47 %), and conditional use permits (12 %). Easements with purposes to protect species and natural communities had more ecological monitoring rights, organizational control over land management, and mechanisms for change than easements with general open space purposes. Forestry purposes were associated with mechanisms for change but not necessarily with ecological monitoring rights or organizational control over land management. The Natural Resources Conservation Service-Wetland Reserve Program had a particularly consistent approach with high control over land use and some discretion to modify uses through permits. Conservation staff perceived a need to respond to changing social and ecological conditions but were divided on whether climate change was likely to negatively impact their conservation easements. Many conservation easements involved significant constraints on easement holders' options for altering land management to achieve conservation purposes over time. This study suggests the need for greater attention to easement drafting, monitoring, and ongoing decision processes to ensure the public benefits of land conservation in changing landscapes.

Numerical simulation of scouring-deposition variations caused by rainfall-induced landslides in the upstream of Zengwun River, Taiwan

NASA Astrophysics Data System (ADS)

Lee, Ming-Hsi; Liao, Yi-Wen; Tsai, Kuang-Jung

2017-04-01

In recent years, the increasing sediment disasters of severe rainfall-induced landslides on human lives and lifeline facilities worldwide have advanced the necessity to find out both economically acceptable and useful techniques to predict the occurrence and destructive power of the disasters. In August 2009, Typhoon Morakot brought a large amount of rainfall with both high intensity and long duration to a vast area of Taiwan. Unfortunately, this resulted in a catastrophic landslide in watershed of Zengwun-River reservoir, southern Taiwan. Meanwhile, large amounts of landslides were formed in the upstream of Zengwun River. The major scope of this study is to apply numerical model to simulate the scouring-deposition variations caused by rainfall-induced landslides that occurred in the upstream of Zengwun River during Typhoon Morakot. This study proposed the relation diagrams of the intermediate diameter (d50), recurrence interval (T) and scouring-deposition depth (D), and applied the diagrams to understand the impacts of the scouring-deposition variations on the structures for water and soil conservation and their measurements. Based on the simulation of scouring-deposition variation at the Da-Bu dam and Da-Bang dam, this study also discussed the scouring-deposition variations of different sections under different scenarios (including flow rate, intermediate diameters and structures). In summary, the result suggested that the diagrams of the intermediate diameter, recurrence interval and scouring-deposition depth could be used as the reference for designing the check dams, ground sills and lateral constructions.

Piston manometer as an absolute standard for vacuum-gage calibration in the range 2 to 500 millitorr

NASA Technical Reports Server (NTRS)

Warshawsky, I.

1972-01-01

A thin disk is suspended, with very small annular clearance, in a cylindrical opening in the base plate of a calibration chamber. A continuous flow of calibration gas passes through the chamber and annular opening to a downstream high vacuum pump. The ratio of pressures on the two faces of the disk is very large, so that the upstream pressure is substantially equal to net force on the disk divided by disk area. This force is measured with a dynamometer that is calibrated in place with dead weights. A probable error of + or - (0.2 millitorr plus 0.2 percent) is attainable when downstream pressure is known to 10 percent.

Level II scour analysis for Bridge 28 (BRNATH00660028) on Town Highway 66, crossing Locust Creek, Barnard, Vermont

USGS Publications Warehouse

Severence, Timothy

1997-01-01

The Town Highway 66 crossing of the Locust Creek is a 41-ft-long, one-lane bridge consisting of a 39 ft steel stringer type bridge with a concrete deck (Vermont Agency of Transportation, written communication, August 24, 1994). The clear span is 36.8 ft. The bridge is supported by vertical, concrete abutments with wingwalls. The upstream right wingwall is protected by stone fill. The channel is skewed approximately 10 degrees to the opening while the opening-skew-to-roadway is 0 degrees. Additional details describing conditions at the site are included in the Level II Summary and Appendices D and E.

A key role for foxQ2 in anterior head and central brain patterning in insects

PubMed Central

Kitzmann, Peter; Weißkopf, Matthias; Schacht, Magdalena Ines

2017-01-01

ABSTRACT Anterior patterning of animals is based on a set of highly conserved transcription factors but the interactions within the protostome anterior gene regulatory network (aGRN) remain enigmatic. Here, we identify the red flour beetle Tribolium castaneum ortholog of foxQ2 (Tc-foxQ2) as a novel upstream component of the aGRN. It is required for the development of the labrum and higher order brain structures, namely the central complex and the mushroom bodies. We reveal Tc-foxQ2 interactions by RNAi and heat shock-mediated misexpression. Surprisingly, Tc-foxQ2 and Tc-six3 mutually activate each other, forming a novel regulatory module at the top of the aGRN. Comparisons of our results with those of sea urchins and cnidarians suggest that foxQ2 has acquired more upstream functions in the aGRN during protostome evolution. Our findings expand the knowledge on foxQ2 gene function to include essential roles in epidermal development and central brain patterning. PMID:28811313

50 CFR 660.70 - Groundfish conservation areas.

Code of Federal Regulations, 2011 CFR

2011-10-01

... points for the RCAs. (1) Trawl (Limited Entry and Open Access Nongroundfish Trawl Gears) Rockfish....71 through 660.74. (2) Non-Trawl (Limited Entry Fixed Gear and Open Access Non-trawl Gears) Rockfish...

A Unified View of Global Instabilities of Compressible Flow Over Open Cavities

DTIC Science & Technology

2005-06-30

the early work of Rossiter [3], have treated the shear-layer emanating from the upstream comer of the cavity in isolation ( using parallel flow... using a domain-decomposition method. The code has optional equation sets to solve either (i) nonlinear Navier-Stokes, (ii) Navier-Stokes equations...early experments of Maull and East [15]. They used oil flow visualization of surface streamlines on the cavity bottom to show the existence, under certain

The Role of eIF4E Activity in Breast Cancer

DTIC Science & Technology

2010-08-01

ORF, open reading frame; qPCR, quantitative PCR; RACE, rapid amplification of cDNA ends; RT, reverse transcriptase ; uORF, upstream ORF; UTR...were also performed using template lacking RT ( reverse transcriptase ): products were either undetectable or greatly reduced (>30000-fold less product...have previously shown that a 5’UTR expressed from the human AXIN2 gene contains a sixty nucleotide sequence that is predicted to form a stable stem

Contactor/filter improvements

DOEpatents

Stelman, David

1989-01-01

A contactor/filter arrangement for removing particulate contaminants from a gaseous stream includes a housing having a substantially vertically oriented granular material retention member with upstream and downstream faces, a substantially vertically oriented microporous gas filter element, wherein the retention member and the filter element are spaced apart to provide a zone for the passage of granular material therethrough. The housing further includes a gas inlet means, a gas outlet means, and means for moving a body of granular material through the zone. A gaseous stream containing particulate contaminants passes through the gas inlet means as well as through the upstream face of the granular material retention member, passing through the retention member, the body of granular material, the microporous gas filter element, exiting out of the gas outlet means. Disposed on the upstream face of the filter element is a cover screen which isolates the filter element from contact with the moving granular bed and collects a portion of the particulates so as to form a dust cake having openings small enough to exclude the granular material, yet large enough to receive the dust particles. In one embodiment, the granular material is comprised of prous alumina impregnated with CuO, with the cover screen cleaned by the action of the moving granular material as well as by backflow pressure pulses.

Cation-induced transcriptional regulation of the dlt operon of Staphylococcus aureus.

PubMed

Koprivnjak, Tomaz; Mlakar, Vid; Swanson, Lindsey; Fournier, Benedicte; Peschel, Andreas; Weiss, Jerrold P

2006-05-01

Lipoteichoic and wall teichoic acids (TA) are highly anionic cell envelope-associated polymers containing repeating polyglycerol/ribitol phosphate moieties. Substitution of TA with D-alanine is important for modulation of many cell envelope-dependent processes, such as activity of autolytic enzymes, binding of divalent cations, and susceptibility to innate host defenses. D-Alanylation of TA is diminished when bacteria are grown in medium containing increased NaCl concentrations, but the effects of increased salt concentration on expression of the dlt operon encoding proteins mediating D-alanylation of TA are unknown. We demonstrate that Staphylococcus aureus transcriptionally represses dlt expression in response to high concentrations of Na(+) and moderate concentrations of Mg(2+) and Ca(2+) but not sucrose. Changes in dlt mRNA are induced within 15 min and sustained for several generations of growth. Mg(2+)-induced dlt repression depends on the ArlSR two-component system. Northern blotting, reverse transcription-PCR, and SMART-RACE analyses suggest that the dlt transcript begins 250 bp upstream of the dltA start codon and includes an open reading frame immediately upstream of dltA. Chloramphenicol transacetylase transcriptional fusions indicate that a region encompassing the 171 to 325 bp upstream of dltA is required for expression and Mg(2+)-induced repression of the dlt operon in S. aureus.

Cation-Induced Transcriptional Regulation of the dlt Operon of Staphylococcus aureus

PubMed Central

Koprivnjak, Tomaz; Mlakar, Vid; Swanson, Lindsey; Fournier, Benedicte; Peschel, Andreas; Weiss, Jerrold P.

2006-01-01

Lipoteichoic and wall teichoic acids (TA) are highly anionic cell envelope-associated polymers containing repeating polyglycerol/ribitol phosphate moieties. Substitution of TA with d-alanine is important for modulation of many cell envelope-dependent processes, such as activity of autolytic enzymes, binding of divalent cations, and susceptibility to innate host defenses. d-Alanylation of TA is diminished when bacteria are grown in medium containing increased NaCl concentrations, but the effects of increased salt concentration on expression of the dlt operon encoding proteins mediating d-alanylation of TA are unknown. We demonstrate that Staphylococcus aureus transcriptionally represses dlt expression in response to high concentrations of Na+ and moderate concentrations of Mg2+ and Ca2+ but not sucrose. Changes in dlt mRNA are induced within 15 min and sustained for several generations of growth. Mg2+-induced dlt repression depends on the ArlSR two-component system. Northern blotting, reverse transcription-PCR, and SMART-RACE analyses suggest that the dlt transcript begins 250 bp upstream of the dltA start codon and includes an open reading frame immediately upstream of dltA. Chloramphenicol transacetylase transcriptional fusions indicate that a region encompassing the 171 to 325 bp upstream of dltA is required for expression and Mg2+-induced repression of the dlt operon in S. aureus. PMID:16672616

Balancing housing growth and land conservation: Conservation development preserves private lands near protected areas

Treesearch

Miranda H. Mockrin; Sarah E. Reed; Liba Pejchar; Jessica Salo

2017-01-01

Housing development has emerged as a primary driver of land-use change around the world. In the United States, there is particular concern about low-density residential development on rural lands, which often occurs in places with abundant natural amenities. Conservation development (CD), housing development that incorporates protected open space, has emerged as a tool...

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…

Detection of hyper-conserved regions in hepatitis B virus X gene potentially useful for gene therapy.

PubMed

González, Carolina; Tabernero, David; Cortese, Maria Francesca; Gregori, Josep; Casillas, Rosario; Riveiro-Barciela, Mar; Godoy, Cristina; Sopena, Sara; Rando, Ariadna; Yll, Marçal; Lopez-Martinez, Rosa; Quer, Josep; Esteban, Rafael; Buti, Maria; Rodríguez-Frías, Francisco

2018-05-21

To detect hyper-conserved regions in the hepatitis B virus (HBV) X gene ( HBX ) 5' region that could be candidates for gene therapy. The study included 27 chronic hepatitis B treatment-naive patients in various clinical stages (from chronic infection to cirrhosis and hepatocellular carcinoma, both HBeAg-negative and HBeAg-positive), and infected with HBV genotypes A-F and H. In a serum sample from each patient with viremia > 3.5 log IU/mL, the HBX 5' end region [nucleotide (nt) 1255-1611] was PCR-amplified and submitted to next-generation sequencing (NGS). We assessed genotype variants by phylogenetic analysis, and evaluated conservation of this region by calculating the information content of each nucleotide position in a multiple alignment of all unique sequences (haplotypes) obtained by NGS. Conservation at the HBx protein amino acid (aa) level was also analyzed. NGS yielded 1333069 sequences from the 27 samples, with a median of 4578 sequences/sample (2487-9279, IQR 2817). In 14/27 patients (51.8%), phylogenetic analysis of viral nucleotide haplotypes showed a complex mixture of genotypic variants. Analysis of the information content in the haplotype multiple alignments detected 2 hyper-conserved nucleotide regions, one in the HBX upstream non-coding region (nt 1255-1286) and the other in the 5' end coding region (nt 1519-1603). This last region coded for a conserved amino acid region (aa 63-76) that partially overlaps a Kunitz-like domain. Two hyper-conserved regions detected in the HBX 5' end may be of value for targeted gene therapy, regardless of the patients' clinical stage or HBV genotype.

Open science initiatives: challenges for public health promotion.

PubMed

Holzmeyer, Cheryl

2018-03-07

While academic open access, open data and open science initiatives have proliferated in recent years, facilitating new research resources for health promotion, open initiatives are not one-size-fits-all. Health research particularly illustrates how open initiatives may serve various interests and ends. Open initiatives not only foster new pathways of research access; they also discipline research in new ways, especially when associated with new regimes of research use and peer review, while participating in innovation ecosystems that often perpetuate existing systemic biases toward commercial biomedicine. Currently, many open initiatives are more oriented toward biomedical research paradigms than paradigms associated with public health promotion, such as social determinants of health research. Moreover, open initiatives too often dovetail with, rather than challenge, neoliberal policy paradigms. Such initiatives are unlikely to transform existing health research landscapes and redress health inequities. In this context, attunement to social determinants of health research and community-based local knowledge is vital to orient open initiatives toward public health promotion and health equity. Such an approach calls for discourses, norms and innovation ecosystems that contest neoliberal policy frameworks and foster upstream interventions to promote health, beyond biomedical paradigms. This analysis highlights challenges and possibilities for leveraging open initiatives on behalf of a wider range of health research stakeholders, while emphasizing public health promotion, health equity and social justice as benchmarks of transformation.

Maize and Arabidopsis ARGOS Proteins Interact with Ethylene Receptor Signaling Complex, Supporting a Regulatory Role for ARGOS in Ethylene Signal Transduction[OPEN

PubMed Central

Shi, Jinrui; Wang, Hongyu; Habben, Jeffrey E.

2016-01-01

The phytohormone ethylene regulates plant growth and development as well as plant response to environmental cues. ARGOS genes reduce plant sensitivity to ethylene when overexpressed in transgenic Arabidopsis (Arabidopsis thaliana) and maize (Zea mays). A previous genetic study suggested that the endoplasmic reticulum and Golgi-localized maize ARGOS1 targets the ethylene signal transduction components at or upstream of CONSTITUTIVE TRIPLE RESPONSE1, but the mechanism of ARGOS modulating ethylene signaling is unknown. Here, we demonstrate in Arabidopsis that ZmARGOS1, as well as the Arabidopsis ARGOS homolog ORGAN SIZE RELATED1, physically interacts with Arabidopsis REVERSION-TO-ETHYLENE SENSITIVITY1 (RTE1), an ethylene receptor interacting protein that regulates the activity of ETHYLENE RESPONSE1. The protein-protein interaction was also detected with the yeast split-ubiquitin two-hybrid system. Using the same yeast assay, we found that maize RTE1 homolog REVERSION-TO-ETHYLENE SENSITIVITY1 LIKE4 (ZmRTL4) and ZmRTL2 also interact with maize and Arabidopsis ARGOS proteins. Like AtRTE1 in Arabidopsis, ZmRTL4 and ZmRTL2 reduce ethylene responses when overexpressed in maize, indicating a similar mechanism for ARGOS regulating ethylene signaling in maize. A polypeptide fragment derived from ZmARGOS8, consisting of a Pro-rich motif flanked by two transmembrane helices that are conserved among members of the ARGOS family, can interact with AtRTE1 and maize RTL proteins in Arabidopsis. The conserved domain is necessary and sufficient to reduce ethylene sensitivity in Arabidopsis and maize. Overall, these results suggest a physical association between ARGOS and the ethylene receptor signaling complex via AtRTE1 and maize RTL proteins, supporting a role for ARGOS in regulating ethylene perception and the early steps of signal transduction in Arabidopsis and maize. PMID:27268962

Molecular cloning and characterization of two genes for the biotin carboxylase and carboxyltransferase subunits of acetyl coenzyme A carboxylase in Myxococcus xanthus.

PubMed

Kimura, Y; Miyake, R; Tokumasu, Y; Sato, M

2000-10-01

We have cloned a DNA fragment from a genomic library of Myxococcus xanthus using an oligonucleotide probe representing conserved regions of biotin carboxylase subunits of acetyl coenzyme A (acetyl-CoA) carboxylases. The fragment contained two open reading frames (ORF1 and ORF2), designated the accB and accA genes, capable of encoding a 538-amino-acid protein of 58.1 kDa and a 573-amino-acid protein of 61.5 kDa, respectively. The protein (AccA) encoded by the accA gene was strikingly similar to biotin carboxylase subunits of acetyl-CoA and propionyl-CoA carboxylases and of pyruvate carboxylase. The putative motifs for ATP binding, CO(2) fixation, and biotin binding were found in AccA. The accB gene was located upstream of the accA gene, and they formed a two-gene operon. The protein (AccB) encoded by the accB gene showed high degrees of sequence similarity with carboxyltransferase subunits of acetyl-CoA and propionyl-CoA carboxylases and of methylmalonyl-CoA decarboxylase. Carboxybiotin-binding and acyl-CoA-binding domains, which are conserved in several carboxyltransferase subunits of acyl-CoA carboxylases, were found in AccB. An accA disruption mutant showed a reduced growth rate and reduced acetyl-CoA carboxylase activity compared with the wild-type strain. Western blot analysis indicated that the product of the accA gene was a biotinylated protein that was expressed during the exponential growth phase. Based on these results, we propose that this M. xanthus acetyl-CoA carboxylase consists of two subunits, which are encoded by the accB and accA genes, and occupies a position between prokaryotic and eukaryotic acetyl-CoA carboxylases in terms of evolution.

50 CFR 71.11 - Opening of national fish hatchery areas to fishing.

Code of Federal Regulations, 2014 CFR

2014-10-01

... THE INTERIOR (CONTINUED) MANAGEMENT OF FISHERIES CONSERVATION AREAS HUNTING AND FISHING ON NATIONAL... hatchery areas may be opened to sport fishing when such activity is not detrimental to the propagation and...

50 CFR 71.11 - Opening of national fish hatchery areas to fishing.

Code of Federal Regulations, 2013 CFR

2013-10-01

... THE INTERIOR (CONTINUED) MANAGEMENT OF FISHERIES CONSERVATION AREAS HUNTING AND FISHING ON NATIONAL... hatchery areas may be opened to sport fishing when such activity is not detrimental to the propagation and...

50 CFR 71.11 - Opening of national fish hatchery areas to fishing.

Code of Federal Regulations, 2012 CFR

2012-10-01

... THE INTERIOR (CONTINUED) MANAGEMENT OF FISHERIES CONSERVATION AREAS HUNTING AND FISHING ON NATIONAL... hatchery areas may be opened to sport fishing when such activity is not detrimental to the propagation and...

50 CFR 71.11 - Opening of national fish hatchery areas to fishing.

Code of Federal Regulations, 2011 CFR

2011-10-01

... THE INTERIOR (CONTINUED) MANAGEMENT OF FISHERIES CONSERVATION AREAS HUNTING AND FISHING ON NATIONAL... hatchery areas may be opened to sport fishing when such activity is not detrimental to the propagation and...

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)

Level II scour analysis for Bridge 44 (CHESVT00110044) on State Route 11, crossing Andover Brook, Chester, Vermont

USGS Publications Warehouse

Ivanoff, Michael A.; Hammond, Robert E.

1997-01-01

This report provides the results of a detailed Level II analysis of scour potential at structure CHESVT00110044 on State Route 11 crossing Andover Brook, Chester, Vermont (figures 1–8). A Level II study is a basic engineering analysis of the site, including a quantitative analysis of stream stability and scour (U.S. Department of Transportation, 1993). Results of a Level I scour investigation also are included in Appendix E of this report. A Level I investigation provides a qualitative geomorphic characterization of the study site. Information on the bridge, gleaned from Vermont Agency of Transportation (VTAOT) files, was compiled prior to conducting Level I and Level II analyses and is found in Appendix D. The site is in the New England Upland section of the New England physiographic province in southeastern Vermont. The 12.6-mi2 drainage area is in a predominantly rural and forested basin. In the vicinity of the study site, the surface cover is pasture with dense woody vegetation on the immediate banks except the downstream left bank of the bridge which is forested. In the study area, Andover Brook has an incised, meandering channel with a slope of approximately 0.02 ft/ft, an average channel top width of 74 ft and an average bank height of 8 ft. The channel bed material ranges from gravel to boulder with a median grain size (D50) of 83.6 mm (0.274 ft). The geomorphic assessment at the time of the Level I and Level II site visit on September 11, 1996, indicated that the reach was stable. The State Route 11 crossing of Andover Brook is a 58-ft-long, two-lane bridge consisting of one 56-foot concrete T-beam span (Vermont Agency of Transportation, written communication, March 29, 1995). The opening length of the structure parallel to the bridge face is 52.9 ft.The bridge is supported by vertical, concrete abutments with wingwalls. The channel is skewed approximately 35 degrees to the opening while the opening-skew-to-roadway is 45 degrees. A scour hole 1.8 ft deeper than the mean thalweg depth was observed along the upstream left wingwall and left abutment during the Level I assessment. The scour protection measures at the site included type-4 stone fill (less than 60 inches diameter) along the upstream left bank between the wingwall and a concrete wall. There was type-2 stone fill (less than 36 inches diameter) along the entire base of the upstream left wingwall, and the downstream end of the downstream right wingwall. There was type-1 stone fill (less than 12 inches diameter) at the downstream end of the downstream left wingwall. There was also a concrete wall along the upstream left bank from 18 to 50 ft upstream of the bridge. Additional details describing conditions at the site are included in the Level II Summary and Appendices D and E. Scour depths and recommended rock rip-rap sizes were computed using the general guidelines described in Hydraulic Engineering Circular 18 (Richardson and others, 1995). Total scour at a highway crossing is comprised of three components: 1) long-term streambed degradation; 2) contraction scour (due to accelerated flow caused by a reduction in flow area at a bridge) and; 3) local scour (caused by accelerated flow around piers and abutments). Total scour is the sum of the three components. Equations are available to compute depths for contraction and local scour and a summary of the results of these computations follows. Contraction scour for all modelled flows ranged from 0.0 to 1.2 ft. The worst-case contraction scour occurred at the incipient-overtopping discharge. The incipientovertopping discharge is 520 cfs less than the 100-year discharge. Left abutment scour ranged from 16.4 to 20.9 ft. The worst-case left abutment scour occurred at the 500-year discharge. Right abutment scour ranged from 8.4 to 9.4 ft. The worst-case right abutment scour occurred at both the 100-year and 500-year discharge. Additional information on scour depths and depths to armoring are included in the section titled “Scour Results”. Scoured-streambed elevations, based on the calculated scour depths, are presented in tables 1 and 2. A cross-section of the scour computed at the bridge is presented in figure 8. Scour depths were calculated assuming an infinite depth of erosive material and a homogeneous particle-size distribution. It is generally accepted that the Froehlich equation (abutment scour) gives “excessively conservative estimates of scour depths” (Richardson and others, 1995, p. 47). Usually, computed scour depths are evaluated in combination with other information including (but not limited to) historical performance during flood events, the geomorphic stability assessment, existing scour protection measures, and the results of the hydraulic analyses. Therefore, scour depths adopted by VTAOT may differ from the computed values documented herein.

Level II scour analysis for Bridge 18 (SHEFTH00410018) on Town Highway 41, crossing Millers Run, Sheffield, Vermont

USGS Publications Warehouse

Wild, Emily C.; Boehmler, Erick M.

1997-01-01

This report provides the results of a detailed Level II analysis of scour potential at structure SHEFTH00410018 on Town Highway 41 crossing Millers Run, Sheffield, Vermont (figures 1–8). A Level II study is a basic engineering analysis of the site, including a quantitative analysis of stream stability and scour (U.S. Department of Transportation, 1993). Results of a Level I scour investigation also are included in Appendix E of this report. A Level I investigation provides a qualitative geomorphic characterization of the study site. Information on the bridge, gleaned from Vermont Agency of Transportation (VTAOT) files, was compiled prior to conducting Level I and Level II analyses and is found in Appendix D. The site is in the White Mountain section of the New England physiographic province in northeastern Vermont. The 16.2-mi2 drainage area is in a predominantly rural and forested basin. In the vicinity of the study site, the surface cover is grass upstream and downstream of the bridge while the immediate banks have dense woody vegetation. In the study area, Millers Run has an incised, straight channel with a slope of approximately 0.01 ft/ft, an average channel top width of 50 ft and an average bank height of 6 ft. The channel bed material ranges from sand to boulder with a median grain size (D50) of 50.9 mm (0.167 ft). The geomorphic assessment at the time of the Level I and Level II site visit on August 1, 1995, indicated that the reach was laterally unstable, which is evident in the moderate to severe fluvial erosion in the upstream reach. The Town Highway 41 crossing of the Millers Run is a 30-ft-long, one-lane bridge consisting of a 28-foot steel-stringer span (Vermont Agency of Transportation, written communication, March 28, 1995). The opening length of the structure parallel to the bridge face is 22.2 ft. The bridge is supported by vertical, concrete abutments with wingwalls. The channel is skewed approximately 20 degrees to the opening. The computed opening-skewto-roadway is 5 degrees, while it is zero degrees in the historical form. A scour hole 1.0 ft deeper than the mean thalweg depth was observed along the left abutment during the Level I assessment. The scour protection measure at the site includes type-1 stone fill (less than 12 inches diameter) along the upstream right wingwall and the upstream left wingwall. Type-2 stone fill (less than 36 inches diameter) extends along the downstream end of the downstream left wingwall, the upstream right bank and the downstream left bank. The downstream right bank is protected by type-2 stone fill and a stone masonry wall. Additional details describing conditions at the site are included in the Level II Summary and Appendices D and E. Scour depths and recommended rock rip-rap sizes were computed using the general guidelines described in Hydraulic Engineering Circular 18 (Richardson and others, 1995) for the 100- and 500-year discharges. In addition, the incipient roadway-overtopping discharge is determined and analyzed as another potential worst-case scour scenario. Total scour at a highway crossing is comprised of three components: 1) long-term streambed degradation; 2) contraction scour (due to accelerated flow caused by a reduction in flow area at a bridge) and; 3) local scour (caused by accelerated flow around piers and abutments). Total scour is the sum of the three components. Equations are available to compute depths for contraction and local scour and a summary of the results of these computations follows. Contraction scour for all modelled flows ranged from 0.2 to 1.8 ft. The worst-case contraction scour occurred at the 100-year and 500-year discharges. Left abutment scour ranged from 14.1 to 16.4 ft. The worst-case left abutment scour occurred at the 500-year discharge. Right abutment scour ranged from 6.9 to 9.3 ft. The worst-case right abutment scour occurred at the incipient roadway-overtopping discharge. Additional information on scour depths and depths to armoring are included in the section titled “Scour Results”. Scoured-streambed elevations, based on the calculated scour depths, are presented in tables 1 and 2. A cross-section of the scour computed at the bridge is presented in figure 8. Scour depths were calculated assuming an infinite depth of erosive material and a homogeneous particle-size distribution. It is generally accepted that the Froehlich equation (abutment scour) gives “excessively conservative estimates of scour depths” (Richardson and others, 1995, p. 47). Usually, computed scour depths are evaluated in combination with other information including (but not limited to) historical performance during flood events, the geomorphic stability assessment, existing scour protection measures, and the results of the hydraulic analyses. Therefore, scour depths adopted by VTAOT may differ from the computed values documented herein.

Level II scour analysis for Bridge 37 (PLYMTH00080037) on Town Highway 8, crossing Broad Brook, Plymouth, Vermont

USGS Publications Warehouse

Wild, Emily C.; Medalie, Laura

1998-01-01

This report provides the results of a detailed Level II analysis of scour potential at structure PLYMTH00080037 on Town Highway 8 crossing Broad Brook, Plymouth, Vermont (figures 1–8). A Level II study is a basic engineering analysis of the site, including a quantitative analysis of stream stability and scour (FHWA, 1993). Results of a Level I scour investigation also are included in appendix E of this report. A Level I investigation provides a qualitative geomorphic characterization of the study site. Information on the bridge, gathered from Vermont Agency of Transportation (VTAOT) files, was compiled prior to conducting Level I and Level II analyses and is found in appendix D. The site is in the Green Mountain section of the New England physiographic province in south-central Vermont. The 5.6-mi2 drainage area is in a predominantly rural and forested basin. In the vicinity of the study site, the surface cover is forest upstream and downstream of the bridge. In the study area, Broad Brook has an incised, sinuous channel with a slope of approximately 0.02 ft/ft, an average channel top width of 46 ft and an average bank height of 5 ft. The channel bed material ranges from gravel to boulders with a median grain size (D50) of 87.5 mm (0.287 ft). The geomorphic assessment at the time of the Level I and Level II site visit on October 3, 1995, indicated that the reach was laterally unstable due to cut-banks present on the upstream left bank and the downstream left and right banks. The Town Highway 8 crossing of Broad Brook is a 31-ft-long, one-lane bridge consisting of a 28-foot steel-stringer span (Vermont Agency of Transportation, written communication, March 22, 1995). The opening length of the structure parallel to the bridge face is 27.0 ft. The bridge is supported by vertical, concrete abutments with wingwalls. The channel is skewed approximately 15 degrees to the opening while the opening-skew-to-roadway is 15 degrees. During the Level I assessment, it was observed that the left abutment footing was exposed 1.25 ft at the downstream end, and the subfooting was exposed 1 ft. Scour protection measures at the site included type-1 stone fill (less than 12 inches diameter) along the upstream right wingwall, the right abutment and the downstream right wingwall. Type-2 stone fill (less than 36 inches diameter) was along the upstream left wingwall, the upstream end of the left abutment and the downstream end of the downstream left wingwall. Additional details describing conditions at the site are included in the Level II Summary and appendices D and E. Scour depths and recommended rock rip-rap sizes were computed using the general guidelines described in Hydraulic Engineering Circular 18 (Richardson and Davis, 1995) for the 100- and 500-year discharges. In addition, the incipient roadway-overtopping discharge was determined and analyzed as another potential worst-case scour scenario. Total scour at a highway crossing is comprised of three components: 1) long-term streambed degradation; 2) contraction scour (due to accelerated flow caused by a reduction in flow area at a bridge) and; 3) local scour (caused by accelerated flow around piers and abutments). Total scour is the sum of the three components. Equations are available to compute depths for contraction and local scour and a summary of the results of these computations follows. Contraction scour for all modelled flows ranged from 0.0 to 0.5 ft. The worst-case contraction scour occurred at the incipient roadway-overtopping discharge, which was less than the 100-year discharge. Left abutment scour ranged from 11.1 to 12.0 ft. Right abutment scour ranged from 3.0 to 7.7 ft. The worst-case abutment scour occurred at the 500-year discharge. Pier scour ranged from 6.2 to 7.1 ft. The worst-case pier scour also occurred at the 500-year discharge. Additional information on scour depths and depths to armoring are included in the section titled “Scour Results”. Scoured-streambed elevations, based on the calculated scour depths, are presented in tables 1 and 2. A cross-section of the scour computed at the bridge is presented in figure 8. Scour depths were calculated assuming an infinite depth of erosive material and a homogeneous particle-size distribution. It is generally accepted that the Froehlich equation (abutment scour) gives “excessively conservative estimates of scour depths” (Richardson and Davis, 1995, p. 46). Usually, computed scour depths are evaluated in combination with other information including (but not limited to) historical performance during flood events, the geomorphic stability assessment, existing scour protection measures, and the results of the hydraulic analyses. Therefore, scour depths adopted by VTAOT may differ from the computed values documented herein.

Level II scour analysis for Bridge 29 (DORSTH00100029) on Town Highway 10, crossing the Mettawee River, Dorset, Vermont

USGS Publications Warehouse

Wild, Emily C.

1997-01-01

This report provides the results of a detailed Level II analysis of scour potential at structure DORSTH00100029 on Town Highway 10 crossing the Mettawee River, Dorset, Vermont (figures 1–8). A Level II study is a basic engineering analysis of the site, including a quantitative analysis of stream stability and scour (U.S. Department of Transportation, 1993). Results of a Level I scour investigation also are included in Appendix E of this report. A Level I investigation provides a qualitative geomorphic characterization of the study site. Information on the bridge, gleaned from Vermont Agency of Transportation (VTAOT) files, was compiled prior to conducting Level I and Level II analyses and is found in Appendix D. The site is in the Taconic section of the New England physiographic province in southwestern Vermont. The 9.5-mi2 drainage area is in a predominantly rural and forested basin. In the vicinity of the study site, the surface cover is forest on the upstream left overbank and the upstream and downstream right overbanks. The downstream left overbank is pasture and brushland. In the study area, the Mettawee River has an incised, sinuous channel with a slope of approximately 0.02 ft/ft, an average channel top width of 66 ft and an average bank height of 8 ft. The channel bed material ranges from gravel to boulders with a median grain size (D50) of 79.0 mm (0.259 ft). The geomorphic assessment at the time of the Level I and Level II site visit on August 5, 1996, indicated that the reach was stable. The Town Highway 10 crossing of the Mettawee River is a 26-ft-long, two-lane bridge consisting of a 24-ft steel-stringer span (Vermont Agency of Transportation, written communication, September 28, 1995). The opening length of the structure parallel to the bridge face is 24.1 ft. The bridge is supported by vertical, concrete abutments with wingwalls. The channel is skewed approximately 45 degrees to the opening while the opening-skew-to-roadway is zero degrees. At the upstream end of the right abutment, there is a scour hole 1.0 ft deeper than the mean thalweg depth. Scour counter-measures at the site include type-1 stone fill (less than 12 inches diameter) along the downstream right wingwall. Type-2 stone fill (less than 36 inches diameter) is present along the downstream left and right banks. Type-3 stone fill (less than 48 inches diameter) is present along the upstream left bank and sparsely in front of the right abutment. A concrete wall (old abutment) extends along the upstream right bank. Additional details describing conditions at the site are included in the Level II Summary and Appendices D and E. Scour depths and recommended rock rip-rap sizes were computed using the general guidelines described in Hydraulic Engineering Circular 18 (Richardson and others, 1995) for the 100- and 500-year discharges. In addition, the incipient roadway-overtopping discharge is determined and analyzed as another potential worst-case scour scenario. Total scour at a highway crossing is comprised of three components: 1) long-term streambed degradation; 2) contraction scour (due to accelerated flow caused by a reduction in flow area at a bridge) and; 3) local scour (caused by accelerated flow around piers and abutments). Total scour is the sum of the three components. Equations are available to compute depths for contraction and local scour and a summary of the results of these computations follows. Contraction scour for all modelled flows ranged from 0.4 to 1.9 ft. The worst-case contraction scour occurred at the 500-year discharge. Left abutment scour ranged from 10.5 to 10.8 ft. The worst-case left abutment scour occurred at the 500-year discharge. Right abutment scour ranged from 11.4 to 11.9 ft. The worst-case right abutment scour occurred at the 100-year discharge. Additional information on scour depths and depths to armoring are included in the section titled “Scour Results”. Scoured-streambed elevations, based on the calculated scour depths, are presented in tables 1 and 2. A cross-section of the scour computed at the bridge is presented in figure 8. Scour depths were calculated assuming an infinite depth of erosive material and a homogeneous particle-size distribution. It is generally accepted that the Froehlich equation (abutment scour) gives “excessively conservative estimates of scour depths” (Richardson and others, 1995, p. 47). Usually, computed scour depths are evaluated in combination with other information including (but not limited to) historical performance during flood events, the geomorphic stability assessment, existing scour protection measures, and the results of the hydraulic analyses. Therefore, scour depths adopted by VTAOT may differ from the computed values documented herein.

Level II scour analysis for Bridge 34 (WWINTH00370034) on Town Highway 37, crossing Mill Brook, West Windsor, Vermont

USGS Publications Warehouse

Boehmler, Erick M.; Wild, Emily C.

1998-01-01

This report provides the results of a detailed Level II analysis of scour potential at structure WWINTH00370034 on Town Highway 37 crossing Mill Brook, West Windsor, Vermont (figures 1–8). A Level II study is a basic engineering analysis of the site, including a quantitative analysis of stream stability and scour (FHWA, 1993). Results of a Level I scour investigation also are included in appendix E of this report. A Level I investigation provides a qualitative geomorphic characterization of the study site. Information on the bridge, gleaned from Vermont Agency of Transportation (VTAOT) files, was compiled prior to conducting Level I and Level II analyses and is found in appendix D. The site is in the New England Upland section of the New England physiographic province in east-central Vermont. The 16.6-mi2 drainage area is in a predominantly rural and forested basin. In the vicinity of the study site, the surface cover is pasture except for the upstream left bank where there is mostly shrubs and brush. In the study area, Mill Brook has a sinuous channel with a slope of approximately 0.003 ft/ ft, an average channel top width of 52 ft and an average bank height of 5 ft. The channel bed material ranges from sand to cobbles with a median grain size (D50) of 43.4 mm (0.142 ft). The geomorphic assessment at the time of the Level I and Level II site visit on June 5, 1996, indicated that the reach was laterally unstable. Point bars were observed upstream and downstream of this site. Furthermore, slip failure of the bank material was noted downstream at a cut-bank on the left side of the channel across from a point bar. The Town Highway 37 crossing of Mill Brook is a 37-ft-long, one-lane covered bridge consisting of one 32-foot wood thru-truss span (Vermont Agency of Transportation, written communication, March 23, 1995). The opening length of the structure parallel to the bridge face is 29.6 ft. The bridge is supported by vertical, laid-up stone abutment walls with concrete facing and laid-up stone wingwalls. The channel is skewed approximately 10 degrees to the opening while the opening-skew-to-roadway is zero degrees. A scour hole 1.5 ft deeper than the mean thalweg depth was observed along the right abutment during the Level I assessment. Scour protection measures at the site included type-3 (less than 48 inches diameter) and type-4 (less than 60 inches diameter) stone fill. Type-3 stone fill was observed along the upstream right bank and along the right abutments. Type-4 stone fill was observed at the upstream end of the upstream right wingwall. Additional details describing conditions at the site are included in the Level II Summary and appendices D and E. Scour depths and recommended rock rip-rap sizes were computed using the general guidelines described in Hydraulic Engineering Circular 18 (Richardson and Davis, 1995) for the 100- and 500-year discharges. In addition, the incipient roadway-overtopping discharge was determined and analyzed as another potential worst-case scour scenario. Total scour at a highway crossing is comprised of three components: 1) long-term streambed degradation; 2) contraction scour (due to accelerated flow caused by a reduction in flow area at a bridge) and; 3) local scour (caused by accelerated flow around piers and abutments). Total scour is the sum of the three components. Equations are available to compute depths for contraction and local scour and a summary of the results of these computations follows. There was no contraction scour predicted for any of the modeled flows. Abutment scour at the left abutment ranged from 5.7 to 7.3 ft, while that at the right abutment ranged from 11.6 to 17.7 ft. The worst-case abutment scour occurred at the 500-year discharge. Additional information on scour depths and depths to armoring are included in the section titled “Scour Results.” Scoured-streambed elevations, based on the calculated scour depths, are presented in tables 1 and 2. A cross-section of the scour computed at the bridge is presented in figure 8. Scour depths were calculated assuming an infinite depth of erosive material and a homogeneous particle-size distribution. It is generally accepted that the Froehlich equation (abutment scour) gives “excessively conservative estimates of scour depths” (Richardson and Davis, 1995, p. 46). Usually, computed scour depths are evaluated in combination with other information including (but not limited to) historical performance during flood events, the geomorphic stability assessment, existing scour protection measures, and the results of the hydraulic analyses. Therefore, scour depths adopted by VTAOT may differ from the computed values documented herein.

Level II scour analysis for Bridge 23 (WALDTH00060023) on Town Highway 6, crossing Stannard Brook, Walden, Vermont

USGS Publications Warehouse

Ivanoff, Michael A.; Hammond, Robert E.

1997-01-01

This report provides the results of a detailed Level II analysis of scour potential at structure WALDTH00060023 on Town Highway 6 crossing Stannard Brook, Walden, Vermont (figures 1–8). A Level II study is a basic engineering analysis of the site, including a quantitative analysis of stream stability and scour (U.S. Department of Transportation, 1993). Results of a Level I scour investigation also are included in Appendix E of this report. A Level I investigation provides a qualitative geomorphic characterization of the study site. Information on the bridge, gleaned from Vermont Agency of Transportation (VTAOT) files, was compiled prior to conducting Level I and Level II analyses and is found in Appendix D. The site is in the New England Upland section of the New England physiographic province in eastern Vermont. The 5.61-mi2 drainage area is in a predominantly rural and forested basin. In the vicinity of the study site, the upstream surface cover is shrub and brushland with some trees. The downstream surface cover is forest. In the study area, Stannard Brook has an incised, straight channel with a slope of approximately 0.02 ft/ft, an average channel top width of 54 ft and an average bank height of 9 ft. The channel bed material ranges from gravel to boulder with a median grain size (D50) of 64.0 mm (0.210 ft). The geomorphic assessment at the time of the Level I and Level II site visit on August 8, 1995, indicated that the reach was stable. The Town Highway 6 crossing of Stannard Brook is a 59-ft-long (bottom width), two-lane pipe arch culvert consisting of one 22-foot corrugated plate pipe arch span (Vermont Agency of Transportation, written communication, March 28, 1995). The opening length of the structure parallel to the bridge face is 21.9 ft.The pipe arch is supported by vertical, concrete kneewalls. The channel is skewed approximately 10 degrees to the opening while the opening-skew-to-roadway is zero degrees. A scour hole 1.5 ft deeper than the mean thalweg depth was observed along the upstream end of the right kneewall during the Level I assessment. There was also a scour hole 0.5 ft deeper than the mean thalweg depth observed along the downstream end of the left kneewall. The scour counter measures at the site included type-3 stone fill (less than 48 inches diameter) at the upstream and downstream end of the left and right kneewall. There was also type-2 stone fill (less than 36 inches diameter) along the upstream right bank. Additional details describing conditions at the site are included in the Level II Summary and Appendices D and E. Scour depths and recommended rock rip-rap sizes were computed using the general guidelines described in Hydraulic Engineering Circular 18 (Richardson and others, 1995) for the 100- and 500-year discharges. In addition, the incipient roadway-overtopping discharge is determined and analyzed as another potential worst-case scour scenario. Total scour at a highway crossing is comprised of three components: 1) long-term streambed degradation; 2) contraction scour (due to accelerated flow caused by a reduction in flow area at a bridge) and; 3) local scour (caused by accelerated flow around piers and kneewalls). Total scour is the sum of the three components. Equations are available to compute depths for contraction and local scour and a summary of the results of these computations follows. Contraction scour for all modelled flows ranged from 0.0 to 2.3 ft. The worst-case contraction scour occurred at the incipient roadway-overtopping discharge, which was greater than the 100-year discharge. Left kneewall scour ranged from 11.7 to 16.8 ft. The worst-case left kneewall scour occurred at the 500-year discharge. Right kneewall scour ranged from 13.7 to 16.7 ft. The worst-case right kneewall scour occurred at the incipient roadway-overtopping discharge. Additional information on scour depths and depths to armoring are included in the section titled “Scour Results”. Scoured-streambed elevations, based on the calculated scour depths, are presented in tables 1 and 2. A cross-section of the scour computed at the bridge is presented in figure 8. Scour depths were calculated assuming an infinite depth of erosive material and a homogeneous particle-size distribution. During the Level I survey ledge was discovered at the upstream end of the right abutment. The ledge in the channel may limit scour depths. It is generally accepted that the Froehlich equation (abutment/ kneewall scour) gives “excessively conservative estimates of scour depths” (Richardson and others, 1995, p. 47). Usually, computed scour depths are evaluated in combination with other information including (but not limited to) historical performance during flood events, the geomorphic stability assessment, existing scour protection measures, and the results of the hydraulic analyses. Therefore, scour depths adopted by VTAOT may differ from the computed values documented herein.

Building Virtual Watersheds: A Global Opportunity to Strengthen Resource Management and Conservation.

PubMed

Benda, Lee; Miller, Daniel; Barquin, Jose; McCleary, Richard; Cai, TiJiu; Ji, Y

2016-03-01

Modern land-use planning and conservation strategies at landscape to country scales worldwide require complete and accurate digital representations of river networks, encompassing all channels including the smallest headwaters. The digital river networks, integrated with widely available digital elevation models, also need to have analytical capabilities to support resource management and conservation, including attributing river segments with key stream and watershed data, characterizing topography to identify landforms, discretizing land uses at scales necessary to identify human-environment interactions, and connecting channels downstream and upstream, and to terrestrial environments. We investigate the completeness and analytical capabilities of national to regional scale digital river networks that are available in five countries: Canada, China, Russia, Spain, and United States using actual resource management and conservation projects involving 12 university, agency, and NGO organizations. In addition, we review one pan-European and one global digital river network. Based on our analysis, we conclude that the majority of the regional, national, and global scale digital river networks in our sample lack in network completeness, analytical capabilities or both. To address this limitation, we outline a general framework to build as complete as possible digital river networks and to integrate them with available digital elevation models to create robust analytical capabilities (e.g., virtual watersheds). We believe this presents a global opportunity for in-country agencies, or international players, to support creation of virtual watersheds to increase environmental problem solving, broaden access to the watershed sciences, and strengthen resource management and conservation in countries worldwide.

Sociohydrological Impacts of Water Conservation Under Anthropogenic Drought in Austin, TX (USA)

NASA Astrophysics Data System (ADS)

Breyer, Betsy; Zipper, Samuel C.; Qiu, Jiangxiao

2018-04-01

Municipal water providers increasingly respond to drought by implementing outdoor water use restrictions to reduce urban water withdrawals and maintain water availability. However, restricting urban outdoor water use to support watershed-scale drought resilience may generate unanticipated cross-scale interactions, for example, by altering drought response and recovery in urban vegetation or urban streamflow. Despite this, urban water conservation is rarely conceptualized or modeled as endogenous to the water cycle. Here we investigate cross-scale interactions among urban water conservation and water availability, water use, and sociohydrological response in Austin, TX (USA) during a recent anthropogenic (human-influenced) drought. Multiscalar statistical analyses demonstrated that outdoor water conservation for reservoir management at the municipal scale produced responses that can cascade both "upward" from the city to the watershed (e.g., decoupling streamflow patterns upstream and downstream of Austin at the watershed scale) and "downward" to exert heterogeneous effects within the city (e.g., redistributing water along a socioeconomic gradient at submunicipal scales, with effects on terrestrial and aquatic ecosystems). We suggest that adapting to anthropogenic drought through irrigation curtailment requires sustained engagement between hydrology and social sciences to integrate socioeconomic status and political feedbacks within and among irrigator groups into the water cycle. Findings from this cross-disciplinary study highlight the importance of a multiscalar and spatially explicit perspectives in urban sociohydrology research to uncover how water conservation as adaptation to anthropogenic drought links hydrological processes with issues of socioeconomic inequality and spatiotemporal scale in the Anthropocene.

Building Virtual Watersheds: A Global Opportunity to Strengthen Resource Management and Conservation

NASA Astrophysics Data System (ADS)

Benda, Lee; Miller, Daniel; Barquin, Jose; McCleary, Richard; Cai, TiJiu; Ji, Y.

2016-03-01

Modern land-use planning and conservation strategies at landscape to country scales worldwide require complete and accurate digital representations of river networks, encompassing all channels including the smallest headwaters. The digital river networks, integrated with widely available digital elevation models, also need to have analytical capabilities to support resource management and conservation, including attributing river segments with key stream and watershed data, characterizing topography to identify landforms, discretizing land uses at scales necessary to identify human-environment interactions, and connecting channels downstream and upstream, and to terrestrial environments. We investigate the completeness and analytical capabilities of national to regional scale digital river networks that are available in five countries: Canada, China, Russia, Spain, and United States using actual resource management and conservation projects involving 12 university, agency, and NGO organizations. In addition, we review one pan-European and one global digital river network. Based on our analysis, we conclude that the majority of the regional, national, and global scale digital river networks in our sample lack in network completeness, analytical capabilities or both. To address this limitation, we outline a general framework to build as complete as possible digital river networks and to integrate them with available digital elevation models to create robust analytical capabilities (e.g., virtual watersheds). We believe this presents a global opportunity for in-country agencies, or international players, to support creation of virtual watersheds to increase environmental problem solving, broaden access to the watershed sciences, and strengthen resource management and conservation in countries worldwide.

Transosseous fixation of pediatric displaced mandibular fractures with polyglactin resorbable suture--a simplified technique.

PubMed

Chandan, Sanjay; Halli, Rajshekhar; Joshi, Samir; Chhabaria, Gaurav; Setiya, Sneha

2013-11-01

Management of pediatric mandibular fractures presents a unique challenge to surgeons in terms of its numerous variations compared to adults. Both conservative and open methods have been advocated with their obvious limitations and complications. However, conservative modalities may not be possible in grossly displaced fractures, which necessitate the open method of fixation. We present a novel and simplified technique of transosseous fixation of displaced pediatric mandibular fractures with polyglactin resorbable suture, which provides adequate stability without any interference with tooth buds and which is easy to master.

Mass conservation: 1-D open channel flow equations

USGS Publications Warehouse

DeLong, Lewis L.

1989-01-01

Unsteady flow simulation in natural rivers is often complicated by meandering channels of compound section. Hydraulic properties and the length of the wetted channel may vary significantly as a meandering river inundates its adjacent floodplain. The one-dimensional, unsteady, open-channel flow equations can be extended to simulate floods in channels of compound section. It will be shown that equations derived from the addition of differential equations individually describing flow in main and overbank channels do not in general conserve mass when overbank and main channels are of different lengths.

RhMKK9, a rose MAP KINASE KINASE gene, is involved in rehydration-triggered ethylene production in rose gynoecia.

PubMed

Chen, Jiwei; Zhang, Qian; Wang, Qigang; Feng, Ming; Li, Yang; Meng, Yonglu; Zhang, Yi; Liu, Guoqin; Ma, Zhimin; Wu, Hongzhi; Gao, Junping; Ma, Nan

2017-02-23

Flower opening is an important process in the life cycle of flowering plants and is influenced by various endogenous and environmental factors. Our previous work demonstrated that rose (Rosa hybrida) flowers are highly sensitive to dehydration during flower opening and the water recovery process after dehydration induced ethylene production rapidly in flower gynoecia. In addition, this temporal- and spatial-specific ethylene production is attributed to a transient but robust activation of the rose MAP KINASE6-ACC SYNTHASE1 (RhMPK6-RhACS1) cascade in gynoecia. However, the upstream component of RhMPK6-RhACS1 is unknown, although RhMKK9 (MAP KINASE KINASE9), a rose homologue of Arabidopsis MKK9, could activate RhMPK6 in vitro. In this study, we monitored RhMKK2/4/5/9 expression, the potential upstream kinase to RhMPK6, in rose gynoecia during dehydration and rehydration. We found only RhMKK9 was rapidly and strongly induced by rehydration. Silencing of RhMKK9 significantly decreased rehydration-triggered ethylene production. Consistently, the expression of several ethylene-responsive genes was down regulated in the petals of RhMKK9-silenced flowers. Moreover, we detected the DNA methylation level in the promoter and gene body of RhMKK9 by Chop-PCR. The results showed that rehydration specifically elevated the DNA methylation level on the RhMKK9 gene body, whereas it resulted in hypomethylation in its promoter. Our results showed that RhMKK9 possibly acts as the upstream component of the RhMKK9-RhMPK6-RhACS1 cascade and is responsible for water recovery-triggered ethylene production in rose gynoecia, and epigenetic DNA methylation is involved in the regulation of RhMKK9 expression by rehydration.

The economic benefits of parks and open space : how land conservation helps communities grow smart and protect the bottom line

DOT National Transportation Integrated Search

1999-01-01

Open space is an investment that produces important economic benefits. It does not have to be an expense. This document relates examples and data that can help concerned citizens and leaders make the economic case for open space and parks conservatio...

17 CFR 210.12-12B - Open option contracts written.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 17 Commodity and Securities Exchanges 2 2013-04-01 2013-04-01 false Open option contracts written. 210.12-12B Section 210.12-12B Commodity and Securities Exchanges SECURITIES AND EXCHANGE COMMISSION... AND CONSERVATION ACT OF 1975 Form and Content of Schedules § 210.12-12B Open option contracts written...

17 CFR 210.12-12B - Open option contracts written.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 17 Commodity and Securities Exchanges 3 2014-04-01 2014-04-01 false Open option contracts written. 210.12-12B Section 210.12-12B Commodity and Securities Exchanges SECURITIES AND EXCHANGE COMMISSION... AND CONSERVATION ACT OF 1975 For Management Investment Companies § 210.12-12B Open option contracts...

17 CFR 210.12-12B - Open option contracts written.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 17 Commodity and Securities Exchanges 2 2012-04-01 2012-04-01 false Open option contracts written. 210.12-12B Section 210.12-12B Commodity and Securities Exchanges SECURITIES AND EXCHANGE COMMISSION... AND CONSERVATION ACT OF 1975 Form and Content of Schedules § 210.12-12B Open option contracts written...

Assessment of crack opening area for leak rates

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

Sharples, J.K.; Bouchard, P.J.

1997-04-01

This paper outlines the background to recommended crack opening area solutions given in a proposed revision to leak before break guidance for the R6 procedure. Comparisons with experimental and analytical results are given for some selected cases of circumferential cracks in cylinders. It is shown that elastic models can provide satisfactory estimations of crack opening displacement (and area) but they become increasingly conservative for values of L{sub r} greater than approximately 0.4. The Dugdale small scale yielding model gives conservative estimates of crack opening displacement with increasing enhancement for L{sub r} values greater than 0.4. Further validation of the elastic-plasticmore » reference stress method for up to L{sub r} values of about 1.0 is presented by experimental and analytical comparisons. Although a more detailed method, its application gives a best estimate of crack opening displacement which may be substantially greater than small scale plasticity models. It is also shown that the local boundary conditions in pipework need to be carefully considered when evaluating crack opening area for through-wall bending stresses resulting from welding residual stresses or geometry discontinuities.« less

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

None

An OpenStudio Measure is a script that can manipulate an OpenStudio model and associated data to apply energy conservation measures (ECMs), run supplemental simulations, or visualize simulation results. The OpenStudio software development kit (SDK) and accessibility of the Ruby scripting language makes measure authorship accessible to both software developers and energy modelers. This paper discusses the life cycle of an OpenStudio Measure from development, testing, and distribution, to application.

Distribution of CpG Motifs in Upstream Gene Domains in a Reef Coral and Sea Anemone: Implications for Epigenetics in Cnidarians.

PubMed

Marsh, Adam G; Hoadley, Kenneth D; Warner, Mark E

2016-01-01

Coral reefs are under assault from stressors including global warming, ocean acidification, and urbanization. Knowing how these factors impact the future fate of reefs requires delineating stress responses across ecological, organismal and cellular scales. Recent advances in coral reef biology have integrated molecular processes with ecological fitness and have identified putative suites of temperature acclimation genes in a Scleractinian coral Acropora hyacinthus. We wondered what unique characteristics of these genes determined their coordinate expression in response to temperature acclimation, and whether or not other corals and cnidarians would likewise possess these features. Here, we focus on cytosine methylation as an epigenetic DNA modification that is responsive to environmental stressors. We identify common conserved patterns of cytosine-guanosine dinucleotide (CpG) motif frequencies in upstream promoter domains of different functional gene groups in two cnidarian genomes: a coral (Acropora digitifera) and an anemone (Nematostella vectensis). Our analyses show that CpG motif frequencies are prominent in the promoter domains of functional genes associated with environmental adaptation, particularly those identified in A. hyacinthus. Densities of CpG sites in upstream promoter domains near the transcriptional start site (TSS) are 1.38x higher than genomic background levels upstream of -2000 bp from the TSS. The increase in CpG usage suggests selection to allow for DNA methylation events to occur more frequently within 1 kb of the TSS. In addition, observed shifts in CpG densities among functional groups of genes suggests a potential role for epigenetic DNA methylation within promoter domains to impact functional gene expression responses in A. digitifera and N. vectensis. Identifying promoter epigenetic sequence motifs among genes within specific functional groups establishes an approach to describe integrated cellular responses to environmental stress in reef corals and potential roles of epigenetics on survival and fitness in the face of global climate change.

Synergistic and singular effects of river discharge and lunar illumination on dam passage of upstream migrant yellow-phase American eels

USGS Publications Warehouse

Welsh, Stuart A.; Aldinger, Joni L.; Braham, Melissa A.; Zimmerman, Jennifer L.

2016-01-01

Monitoring of dam passage can be useful for management and conservation assessments of American eel, particularly if passage counts can be examined over multiple years. During a 7-year study (2007–2013) of upstream migration of American eels within the lower Shenandoah River (Potomac River drainage), we counted and measured American eels at the Millville Dam eel pass, where annual study periods were determined by the timing of the eel pass installation during spring or summer and removal during fall. Daily American eel counts were analysed with negative binomial regression models, with and without a year (YR) effect, and with the following time-varying environmental covariates: river discharge of the Shenandoah River at Millville (RDM) and of the Potomac River at Point of Rocks, lunar illumination (LI), water temperature, and cloud cover. A total of 17 161 yellow-phase American eels used the pass during the seven annual periods, and length measurements were obtained from 9213 individuals (mean = 294 mm TL, s.e. = 0.49, range 183–594 mm). Data on passage counts of American eels supported an additive-effects model (YR + LI + RDM) where parameter estimates were positive for river discharge (β = 7.3, s.e. = 0.01) and negative for LI (β = −1.9, s.e. = 0.34). Interestingly, RDM and LI acted synergistically and singularly as correlates of upstream migration of American eels, but the highest daily counts and multiple-day passage events were associated with increased RDM. Annual installation of the eel pass during late spring or summer prevented an early spring assessment, a period with higher RDM relative to those values obtained during sampling periods. Because increases in river discharge are climatically controlled events, upstream migration events of American eels within the Potomac River drainage are likely linked to the influence of climate variability on flow regime.

Children's Ideas about Animal Conservation.

ERIC Educational Resources Information Center

Greaves, Emma; And Others

1993-01-01

Describes the results of an open-form questionnaire designed to provide a picture of students' justifications of animal conservation. The results suggest that the negative attitudes students have towards zoos and wildlife parks may impede the educational benefits of such visits for some children. (DDR)

A simulation for the gated weir opening of Wonokromo River, Rungkut District, Surabaya

NASA Astrophysics Data System (ADS)

Handajani, N.; Wahjudijanto, I.; Mu'afi, M.

2018-01-01

The gated weir is a weir that the crest elevation could be operated based on the flow through the river. The upstream water level of the gated weir could be controlled with gate opening or closing. This study applied a simulation with HEC-RAS 4,0 program in order to know the river hydraulic condition after the gated weir has built. According to the rainfall intensity from each sub-watershed, Distribution Log Pearson III with return period 50 years (Q50) was determined to calculate the design flood discharge. By using Rational Method, the design flood discharge is 470 m3/s. The Results show that capacity of the river is able to accomodate Q50 with discharge 470 m3/s and the gate should be fully opened during flood. This condition could passed the normal discharge at + 5.00 m elevation.

Plasma opening switch

DOEpatents

Savage, Mark E.; Mendel, Jr., Clifford W.

2001-01-01

A command triggered plasma opening switch assembly using an amplification stage. The assembly surrounds a coaxial transmission line and has a main plasma opening switch (POS) close to the load and a trigger POS upstream from the main POS. The trigger POS establishes two different current pathways through the assembly depended on whether it has received a trigger current pulse. The initial pathway has both POS's with plasma between their anodes and cathodes to form a short across the transmission line and isolating the load. The final current pathway is formed when the trigger POS receives a trigger current pulse which energizes its fast coil to push the conductive plasma out from between its anode and cathode, allowing the main transmission line current to pass to the fast coil of the main POS, thus pushing its plasma out the way so as to establish a direct current pathway to the load.

The Role of elF4E Activity in Breast Cancer

DTIC Science & Technology

2011-08-01

protein; ORF, open reading frame; qPCR, quantitative PCR; RACE, rapid amplification of cDNA ends; RT, reverse transcriptase ; uORF, upstream ORF; UTR...Reactions were also performed using template lacking RT ( reverse transcriptase ): products were either undetectable or greatly reduced (>30000-fold less...that a 5’UTR expressed from the human AXIN2 gene contains a sixty nucleotide sequence that is predicted to form a stable stem-loop structure6. This

RESOLVING THE GEOMETRY OF THE INNERMOST RELATIVISTIC JETS IN ACTIVE GALACTIC NUCLEI

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

Algaba, J. C.; Lee, S. S.; Nakamura, M.

2017-01-01

In the current paradigm, it is believed that the compact VLBI radio core of radio-loud active galactic nuclei (AGNs) represents the innermost upstream regions of relativistic outflows. These regions of AGN jets have generally been modeled by a conical outflow with a roughly constant opening angle and flow speed. Nonetheless, some works suggest that a parabolic geometry would be more appropriate to fit the high energy spectral distribution properties and it has been recently found that, at least in some nearby radio galaxies, the geometry of the innermost regions of the jet is parabolic. We compile here multi-frequency core sizes of archivalmore » data to investigate the typically unresolved upstream regions of the jet geometry of a sample of 56 radio-loud AGNs. Data combined from the sources considered here are not consistent with the classic picture of a conical jet starting in the vicinity of the super-massive black hole (SMBH), and may exclude a pure parabolic outflow solution, but rather suggest an intermediate solution with quasi-parabolic streams, which are frequently seen in numerical simulations. Inspection of the large opening angles near the SMBH and the range of the Lorentz factors derived from our results support our analyses. Our result suggests that the conical jet paradigm in AGNs needs to be re-examined by millimeter/sub-millimeter VLBI observations.« less

Influence of the solar wind and IMF on Jupiter's magnetosphere: Results from global MHD simulations

NASA Astrophysics Data System (ADS)

Sarkango, Y.; Jia, X.; Toth, G.; Hansen, K. C.

2017-12-01

Due to its large size, rapid rotation and presence of substantial internal plasma sources, Jupiter's magnetosphere is fundamentally different from that of the Earth. How and to what extent do the external factors, such as the solar wind and interplanetary magnetic field (IMF), influence the internally-driven magnetosphere is an open question. In this work, we solve the 3D semi-relativistic magnetohydrodynamic (MHD) equations using a well-established code, BATSRUS, to model the Jovian magnetosphere and study its interaction with the solar wind. Our global model adopts a non-uniform mesh covering the region from 200 RJ upstream to 1800 RJ downstream with the inner boundary placed at a radial distance of 2.5 RJ. The Io plasma torus centered around 6 RJ is generated in our model through appropriate mass-loading terms added to the set of MHD equations. We perform systematic numerical experiments in which we vary the upstream solar wind properties to investigate the impact of solar wind events, such as interplanetary shock and IMF rotation, on the global magnetosphere. From our simulations, we extract the location of the magnetopause boundary, the bow shock and the open-closed field line boundary (OCB), and determine their dependence on the solar wind properties and the IMF orientation. For validation, we compare our simulation results, such as density, temperature and magnetic field, to published empirical models based on in-situ measurements.

Specific Increase of Protein Levels by Enhancing Translation Using Antisense Oligonucleotides Targeting Upstream Open Frames.

PubMed

Liang, Xue-Hai; Shen, Wen; Crooke, Stanley T

2017-01-01

A number of diseases are caused by low levels of key proteins; therefore, increasing the amount of specific proteins in human bodies is of therapeutic interest. Protein expression is downregulated by some structural or sequence elements present in the 5' UTR of mRNAs, such as upstream open reading frames (uORF). Translation initiation from uORF(s) reduces translation from the downstream primary ORF encoding the main protein product in the same mRNA, leading to a less efficient protein expression. Therefore, it is possible to use antisense oligonucleotides (ASOs) to specifically inhibit translation of the uORF by base-pairing with the uAUG region of the mRNA, redirecting translation machinery to initiate from the primary AUG site. Here we review the recent findings that translation of specific mRNAs can be enhanced using ASOs targeting uORF regions. Appropriately designed and optimized ASOs are highly specific, and they act in a sequence- and position-dependent manner, with very minor off-target effects. Protein levels can be increased using this approach in different types of human and mouse cells, and, importantly, also in mice. Since uORFs are present in around half of human mRNAs, the uORF-targeting ASOs may thus have valuable potential as research tools and as therapeutics to increase the levels of proteins for a variety of genes.

Application of a framework for extrapolating chemical effects ...

EPA Pesticide Factsheets

Cross-species extrapolation of toxicity data from limited surrogate test organisms to all wildlife with potential of chemical exposure remains a key challenge in ecological risk assessment. A number of factors affect extrapolation, including the chemical exposure, pharmacokinetics, life-stage, and pathway similarities/differences. Here we propose a framework using a tiered approach for species extrapolation that enables a transparent weight-of-evidence driven evaluation of pathway conservation (or lack thereof) in the context of adverse outcome pathways. Adverse outcome pathways describe the linkages from a molecular initiating event, defined as the chemical-biomolecule interaction, through subsequent key events leading to an adverse outcome of regulatory concern (e.g., mortality, reproductive dysfunction). Tier 1 of the extrapolation framework employs in silico evaluations of sequence and structural conservation of molecules (e.g., receptors, enzymes) associated with molecular initiating events or upstream key events. Such evaluations make use of available empirical and sequence data to assess taxonomic relevance. Tier 2 uses in vitro bioassays, such as enzyme inhibition/activation, competitive receptor binding, and transcriptional activation assays to explore functional conservation of pathways across taxa. Finally, Tier 3 provides a comparative analysis of in vivo responses between species utilizing well-established model organisms to assess departure from

Characterization and Placement of Wetlands for Integrated ...

EPA Pesticide Factsheets

Constructed wetlands have been recognized as an efficient and cost-effective conservation practice to protect water quality through reducing the transport of sediments and nutrients from upstream croplands to downstream water bodies. The challenge resides in targeting the strategic location of wetlands within agricultural watersheds to maximize the reduction in nutrient loads while minimizing their impact on crop production. Furthermore, agricultural watersheds involve complex interrelated processes requiring a systems approach to evaluate the inherent relationships between wetlands and multiple sediment/nutrient sources (sheet, rill, ephemeral gully, channels) and other conservation practices (filter strips). This study describes new capabilities of the USDA’s Annualized Agricultural Non-Point Source pollutant loading model, AnnAGNPS. A developed AnnAGNPS GIS-based wetland component, AgWet, is introduced to identify potential sites and characterize individual artificial or natural wetlands at a watershed scale. AgWet provides a simplified, semi-automated, and spatially distributed approach to quantitatively evaluate wetlands as potential conservation management alternatives. AgWet is integrated with other AnnAGNPS components providing seamless capabilities of estimating the potential sediment/nutrient reduction of individual wetlands. This technology provides conservationists the capability for improved management of watershed systems and support for nutrient

Are we failing to protect threatened mangroves in the Sundarbans world heritage ecosystem?

PubMed

Sarker, Swapan K; Reeve, Richard; Thompson, Jill; Paul, Nirmal K; Matthiopoulos, Jason

2016-02-16

The Sundarbans, the largest mangrove ecosystem in the world, is under threat from historical and future human exploitation and sea level rise. Limited scientific knowledge on the spatial ecology of the mangroves in this world heritage ecosystem has been a major impediment to conservation efforts. Here, for the first time, we report on habitat suitability analyses and spatial density maps for the four most prominent mangrove species--Heritiera fomes, Excoecaria agallocha, Ceriops decandra and Xylocarpus mekongensis. Globally endangered H. fomes abundances declined as salinity increased. Responses to nutrients, elevation, and stem density varied between species. H. fomes and X. mekongensis preferred upstream habitats. E. agallocha and C. decandra preferred down-stream and mid-stream habitats. Historical harvesting had negative influences on H. fomes, C. decandra and X. mekongensis abundances. The established protected area network does not support the most suitable habitats of these threatened species. We therefore recommend a reconfiguration of the network to include these suitable habitats and ensure their immediate protection. These novel habitat insights and spatial predictions can form the basis for future forest studies and spatial conservation planning, and have implications for more effective conservation of the Sundarbans mangroves and the many other species that rely on them.

Molecular analysis of the human SLC13A4 sulfate transporter gene promoter

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

Jefferis, J.; Rakoczy, J.; School of Biomedical Sciences, University of Queensland, St. Lucia, Queensland

2013-03-29

Highlights: ► Basal promoter activity of SLC13A4 −57 to −192 nt upstream of transcription initiation site. ► Human SLC13A4 5′-flanking region has conserved motifs with other placental species. ► Putative NFY, SP1 and KLF7 motifs in SLC13A4 5′-flanking region enhance transcription. -- Abstract: The human solute linked carrier (SLC) 13A4 gene is primarily expressed in the placenta where it is proposed to mediate the transport of nutrient sulfate from mother to fetus. The molecular mechanisms involved in the regulation of SLC13A4 expression remain unknown. To investigate the regulation of SLC13A4 gene expression, we analysed the transcriptional activity of the humanmore » SLC13A4 5′-flanking region in the JEG-3 placental cell line using luciferase reporter assays. Basal transcriptional activity was identified in the region −57 to −192 nucleotides upstream of the SLC13A4 transcription initiation site. Mutational analysis of the minimal promoter region identified Nuclear factor Y (NFY), Specificity protein 1 (SP1) and Krüppel like factor 7 (KLF7) motifs which conferred positive transcriptional activity, as well as Zinc finger protein of the cerebellum 2 (ZIC2) and helix–loop–helix protein 1 (HEN1) motifs that repressed transcription. The conserved NFY, SP1, KLF7, ZIC2 and HEN1 motifs in the SLC13A4 promoter of placental species but not in non-placental species, suggests a potential role for these putative transcriptional factor binding motifs in the physiological control of SLC13A4 mRNA expression.« less

77 FR 16556 - Kootenai National Wildlife Refuge, Boundary County, ID; Final Comprehensive Conservation Plan and...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-03-21

... auto tour route that is open year- round to vehicles, walking, bicycling, jogging, dog walking (on... slightly over 5 miles of trails that are open to walking, jogging, and dog walking (on leash only) year... will remain open year round to vehicles, walking, bicycling, jogging, dog walking (on leash only...

Fission yeast retrotransposon Tf1 integration is targeted to 5' ends of open reading frames.

PubMed

Behrens, R; Hayles, J; Nurse, P

2000-12-01

Target site selection of transposable elements is usually not random but involves some specificity for a DNA sequence or a DNA binding host factor. We have investigated the target site selection of the long terminal repeat-containing retrotransposon Tf1 from the fission yeast Schizosaccharomyces pombe. By monitoring induced transposition events we found that Tf1 integration sites were distributed throughout the genome. Mapping these insertions revealed that Tf1 did not integrate into open reading frames, but occurred preferentially in longer intergenic regions with integration biased towards a region 100-420 bp upstream of the translation start site. Northern blot analysis showed that transcription of genes adjacent to Tf1 insertions was not significantly changed.

Fission yeast retrotransposon Tf1 integration is targeted to 5′ ends of open reading frames

PubMed Central

Behrens, Ralf; Hayles, Jacky; Nurse, Paul

2000-01-01

Target site selection of transposable elements is usually not random but involves some specificity for a DNA sequence or a DNA binding host factor. We have investigated the target site selection of the long terminal repeat-containing retrotransposon Tf1 from the fission yeast Schizosaccharomyces pombe. By monitoring induced transposition events we found that Tf1 integration sites were distributed throughout the genome. Mapping these insertions revealed that Tf1 did not integrate into open reading frames, but occurred preferentially in longer intergenic regions with integration biased towards a region 100–420 bp upstream of the translation start site. Northern blot analysis showed that transcription of genes adjacent to Tf1 insertions was not significantly changed. PMID:11095681

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.

Prioritizing landscapes for longleaf pine conservation

USGS Publications Warehouse

Grand, James B.; Kleiner, Kevin J.

2016-01-01

We developed a spatially explicit model and map, as a decision support tool (DST), to aid conservation agencies creating or maintaining open pine ecosystems. The tool identified areas that are likely to provide the greatest benefit to focal bird populations based on a comprehensive landscape analysis. We used NLCD 2011, SSURGO, and SEGAP data to map the density of desired resources for open pine ecosystems and six focal species of birds and 2 reptiles within the historic range of longleaf pine east of the Mississippi River. Binary rasters were created of sites with desired characteristics such as land form, hydrology, land use and land cover, soils, potential habitat for focal species, and putative source populations of focal species. Each raster was smoothed using a kernel density estimator. Rasters were combined and scaled to map priority locations for the management of each focal species. Species’ rasters were combined and scaled to provide maps of overall priority for birds and for birds and reptiles. The spatial data can be used to identify high priority areas for conservation or to compare areas under consideration for maintenance or creation of open pine ecosystems.

Identification of B Cells as a Major Site for Cyprinid Herpesvirus 3 Latency

PubMed Central

Reed, Aimee N.; Izume, Satoko; Dolan, Brian P.; LaPatra, Scott; Kent, Michael; Dong, Jing

2014-01-01

ABSTRACT Cyprinid herpesvirus 3 (CyHV-3), commonly known as koi herpesvirus (KHV), is a member of the Alloherpesviridae, and is a recently discovered emerging herpesvirus that is highly pathogenic for koi and common carp. Our previous study demonstrated that CyHV-3 becomes latent in peripheral white blood cells (WBC). In this study, CyHV-3 latency was further investigated in IgM+ WBC. The presence of the CyHV-3 genome in IgM+ WBC was about 20-fold greater than in IgM− WBC. To determine whether CyHV-3 expressed genes during latency, transcription from all eight open reading frames (ORFs) in the terminal repeat was investigated in IgM+ WBC from koi with latent CyHV-3 infection. Only a spliced ORF6 transcript was found to be abundantly expressed in IgM+ WBC from CyHV-3 latently infected koi. The spliced ORF6 transcript was also detected in vitro during productive infection as early as 1 day postinfection. The ORF6 transcript from in vitro infection begins at −127 bp upstream of the ATG codon and ends +188 bp downstream of the stop codon, +20 bp downstream of the polyadenylation signal. The hypothetical protein of ORF6 contains a consensus sequence with homology to a conserved domain of EBNA-3B and ICP4 from Epstein-Barr virus and herpes simplex virus 1, respectively, both members of the Herpesviridae. This is the first report of latent CyHV-3 in B cells and identification of gene transcription during latency for a member of the Alloherpesviridae. IMPORTANCE This is the first demonstration that a member of the Alloherpesviridae, cyprinid herpesvirus 3 (CyHV-3), establishes a latent infection in the B cells of its host, Cyprinus carpio. In addition, this is the first report of identification of gene transcription during latency for a member of Herpesvirales outside Herpesviridae. This is also the first report that the hypothetical protein of latent transcript of CyHV-3 contains a consensus sequence with homology to a conserved domain of EBNA-3B from Epstein-Barr virus and ICP4 from herpes simplex virus 1, which are genes important for latency. These strongly suggest that latency is evolutionally conserved across vertebrates. PMID:24899202

Identification of B cells as a major site for cyprinid herpesvirus 3 latency.

PubMed

Reed, Aimee N; Izume, Satoko; Dolan, Brian P; LaPatra, Scott; Kent, Michael; Dong, Jing; Jin, Ling

2014-08-01

Cyprinid herpesvirus 3 (CyHV-3), commonly known as koi herpesvirus (KHV), is a member of the Alloherpesviridae, and is a recently discovered emerging herpesvirus that is highly pathogenic for koi and common carp. Our previous study demonstrated that CyHV-3 becomes latent in peripheral white blood cells (WBC). In this study, CyHV-3 latency was further investigated in IgM(+) WBC. The presence of the CyHV-3 genome in IgM(+) WBC was about 20-fold greater than in IgM(-) WBC. To determine whether CyHV-3 expressed genes during latency, transcription from all eight open reading frames (ORFs) in the terminal repeat was investigated in IgM(+) WBC from koi with latent CyHV-3 infection. Only a spliced ORF6 transcript was found to be abundantly expressed in IgM(+) WBC from CyHV-3 latently infected koi. The spliced ORF6 transcript was also detected in vitro during productive infection as early as 1 day postinfection. The ORF6 transcript from in vitro infection begins at -127 bp upstream of the ATG codon and ends +188 bp downstream of the stop codon, +20 bp downstream of the polyadenylation signal. The hypothetical protein of ORF6 contains a consensus sequence with homology to a conserved domain of EBNA-3B and ICP4 from Epstein-Barr virus and herpes simplex virus 1, respectively, both members of the Herpesviridae. This is the first report of latent CyHV-3 in B cells and identification of gene transcription during latency for a member of the Alloherpesviridae. This is the first demonstration that a member of the Alloherpesviridae, cyprinid herpesvirus 3 (CyHV-3), establishes a latent infection in the B cells of its host, Cyprinus carpio. In addition, this is the first report of identification of gene transcription during latency for a member of Herpesvirales outside Herpesviridae. This is also the first report that the hypothetical protein of latent transcript of CyHV-3 contains a consensus sequence with homology to a conserved domain of EBNA-3B from Epstein-Barr virus and ICP4 from herpes simplex virus 1, which are genes important for latency. These strongly suggest that latency is evolutionally conserved across vertebrates. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

18 CFR 37.4 - [Reserved

Code of Federal Regulations, 2010 CFR

2010-04-01

... 18 Conservation of Power and Water Resources 1 2010-04-01 2010-04-01 false [Reserved] 37.4 Section 37.4 Conservation of Power and Water Resources FEDERAL ENERGY REGULATORY COMMISSION, DEPARTMENT OF ENERGY REGULATIONS UNDER THE FEDERAL POWER ACT OPEN ACCESS SAME-TIME INFORMATION SYSTEMS § 37.4 [Reserved] ...

18 CFR 37.4 - [Reserved

Code of Federal Regulations, 2011 CFR

2011-04-01

... 18 Conservation of Power and Water Resources 1 2011-04-01 2011-04-01 false [Reserved] 37.4 Section 37.4 Conservation of Power and Water Resources FEDERAL ENERGY REGULATORY COMMISSION, DEPARTMENT OF ENERGY REGULATIONS UNDER THE FEDERAL POWER ACT OPEN ACCESS SAME-TIME INFORMATION SYSTEMS § 37.4 [Reserved] ...

7 CFR 1491.22 - Conservation easement deeds.

Code of Federal Regulations, 2014 CFR

2014-01-01

..., population density, the ratio of open prime other important farmland versus impervious surfaces on the...) Impervious surfaces will not exceed 2 percent of the FRPP easement area, excluding NRCS-approved conservation practices. The State Conservationist may waive the 2 percent impervious surface limitation on a parcel-by...

7 CFR 1491.22 - Conservation easement deeds.

Code of Federal Regulations, 2012 CFR

2012-01-01

..., population density, the ratio of open prime other important farmland versus impervious surfaces on the...) Impervious surfaces will not exceed 2 percent of the FRPP easement area, excluding NRCS-approved conservation practices. The State Conservationist may waive the 2 percent impervious surface limitation on a parcel-by...

Rainfall-runoff modelling of the Okavango River catchment to assess impacts of land use change on runoff and downstream ecosystems

NASA Astrophysics Data System (ADS)

Milzow, Christian; Bauer-Gottwein, Peter

2010-05-01

The competition between human water use and ecosystem water use is one of the major challenges for water resources management at the global scale. We analyse the situation for the Okavango River basin of southern Africa. The Okavango River is representative for many large rivers throughout the developing world in that it is ungauged and poorly studied. The Okavango basin - spanning over Angola, Namibia and Botswana - represents a multi-objective problem in an international setting. Economic benefits of agricultural development and conservation of ecosystem services call for opposed actions. A semi-distributed rainfall-runoff model of the Okavango catchment is set up using the Soil and Water Assessment Tool (SWAT). The model is sufficiently physically based to simulate the impact on runoff of extent of agricultural use, crop types and management practices. Precipitation and temperature inputs are taken from datasets covering large parts of the globe. The methodology can thus easily be applied for other ungauged catchments. For temperature we use the ERA-Interim reanalysis product of the European Centre for Medium-Range Weather Forecasts and for precipitation the Famine Early Warning Systems Network data (FEWS-Net). Tropical Rainfall Measurement Mission (TRMM) data resulted in poor model performance compared to the FEWS-Net data. Presently, the upstream catchment in Angola is largely pristine and agriculture is basically restricted to dry land subsistence farming. But economic growth in Angola is likely to result in agricultural development and consequent impacts on catchment runoff. Land use scenarios that are simulated include large scale irrigated agriculture with water extractions from the river and the shallow aquifer. Climate change impacts are also studied and compared to land use change impacts. The downstream part of the basin consists of the large Okavango Wetlands, which are a biodiversity hotspot of global importance and, through tourism, an important source of economic income for Botswana. A second hydrological model simulating flow through the wetlands is used to study the impact of catchment runoff changes on the hydrology and ecology of the wetlands. The final goal of the project is to demonstrate the relation between economic benefits of water abstractions in the upstream and downstream environmental impact. Furthermore the results will provide a basis for defining adequate compensations for upstream stakeholders who forego benefits of agricultural intensification to ensure the conservation of downstream ecosystem services.

Stratified wakes, the high Froude number approximation, and potential flow

NASA Astrophysics Data System (ADS)

Vasholz, David P.

2011-12-01

Properties of a steady wake generated by a body moving uniformly at constant depth through a stratified fluid are studied as a function of two parameters inserted into the linearized equations of motion. The first parameter, μ, multiplies the along-track gradient term in the source equation. When formal solutions for an arbitrary buoyancy frequency profile are written as eigenfunction expansions, one finds that the limit μ → 0 corresponds to a high Froude number approximation accompanied by a substantial reduction in the complexity of the calculation. For μ = 1, upstream effects are present and the eigenvalues correspond to critical speeds above which transverse waves disappear for any given mode. For sufficiently high modes, the high Froude number approximation is valid. The second tracer multiplies the square of the buoyancy frequency term in the linearized conservation of mass equation and enables direct comparisons with the limit of potential flow. Detailed results are given for the simplest possible profile, in which the buoyancy frequency is independent of depth; emphasis is placed upon quantities that can, in principle, be experimentally measured in a laboratory experiment. The vertical displacement field is written in terms of a stratified wake form factor {{H}} , which is the sum of a wavelike contribution that is non-zero downstream and an evanescent contribution that appears symmetrically upstream and downstream. First- and second-order cross-track moments of {{H}} are analyzed. First-order results predict enhanced upstream vertical displacements. Second-order results expand upon previous predictions of wavelike resonances and also predict evanescent resonance effects.

Promoter for Sindbis virus RNA-dependent subgenomic RNA transcription.

PubMed

Levis, R; Schlesinger, S; Huang, H V

1990-04-01

Sindbis virus is a positive-strand RNA enveloped virus, a member of the Alphavirus genus of the Togaviridae family. Two species of mRNA are synthesized in cells infected with Sindbis virus; one, the 49S RNA, is the genomic RNA; the other, the 26S RNA, is a subgenomic RNA that is identical in sequence to the 3' one-third of the genomic RNA. Ou et al. (J.-H. Ou, C. M. Rice, L. Dalgarno, E. G. Strauss, and J. H. Strauss, Proc. Natl. Acad. Sci. USA 79:5235-5239, 1982) identified a highly conserved region 19 nucleotides upstream and 2 nucleotides downstream from the start of the 26S RNA and proposed that in the negative-strand template, these nucleotides compose the promoter for directing the synthesis of the subgenomic RNA. Defective interfering (DI) RNAs of Sindbis virus were used to test this proposal. A 227-nucleotide sequence encompassing 98 nucleotides upstream and 117 nucleotides downstream from the start site of the Sindbis virus subgenomic RNA was inserted into a DI genome. The DI RNA containing the insert was replicated and packaged in the presence of helper virus, and cells infected with these DI particles produced a subgenomic RNA of the size and sequence expected if the promoter was functional. The initiating nucleotide was identical to that used for Sindbis virus subgenomic mRNA synthesis. Deletion analysis showed that the minimal region required to detect transcription of a subgenomic RNA from the negative-strand template of a DI RNA was 18 or 19 nucleotides upstream and 5 nucleotides downstream from the start of the subgenomic RNA.

Reservoir Sedimentation and Upstream Sediment Sources: Perspectives and Future Research Needs on Streambank and Gully Erosion.

PubMed

Fox, G A; Sheshukov, A; Cruse, R; Kolar, R L; Guertault, L; Gesch, K R; Dutnell, R C

2016-05-01

The future reliance on water supply and flood control reservoirs across the globe will continue to expand, especially under a variable climate. As the inventory of new potential dam sites is shrinking, construction of additional reservoirs is less likely compared to simultaneous flow and sediment management in existing reservoirs. One aspect of this sediment management is related to the control of upstream sediment sources. However, key research questions remain regarding upstream sediment loading rates. Highlighted in this article are research needs relative to measuring and predicting sediment transport rates and loading due to streambank and gully erosion within a watershed. For example, additional instream sediment transport and reservoir sedimentation rate measurements are needed across a range of watershed conditions, reservoir sizes, and geographical locations. More research is needed to understand the intricate linkage between upland practices and instream response. A need still exists to clarify the benefit of restoration or stabilization of a small reach within a channel system or maturing gully on total watershed sediment load. We need to better understand the intricate interactions between hydrological and erosion processes to improve prediction, location, and timing of streambank erosion and failure and gully formation. Also, improved process-based measurement and prediction techniques are needed that balance data requirements regarding cohesive soil erodibility and stability as compared to simpler topographic indices for gullies or stream classification systems. Such techniques will allow the research community to address the benefit of various conservation and/or stabilization practices at targeted locations within watersheds.

Reservoir Sedimentation and Upstream Sediment Sources: Perspectives and Future Research Needs on Streambank and Gully Erosion

NASA Astrophysics Data System (ADS)

Fox, G. A.; Sheshukov, A.; Cruse, R.; Kolar, R. L.; Guertault, L.; Gesch, K. R.; Dutnell, R. C.

2016-05-01

The future reliance on water supply and flood control reservoirs across the globe will continue to expand, especially under a variable climate. As the inventory of new potential dam sites is shrinking, construction of additional reservoirs is less likely compared to simultaneous flow and sediment management in existing reservoirs. One aspect of this sediment management is related to the control of upstream sediment sources. However, key research questions remain regarding upstream sediment loading rates. Highlighted in this article are research needs relative to measuring and predicting sediment transport rates and loading due to streambank and gully erosion within a watershed. For example, additional instream sediment transport and reservoir sedimentation rate measurements are needed across a range of watershed conditions, reservoir sizes, and geographical locations. More research is needed to understand the intricate linkage between upland practices and instream response. A need still exists to clarify the benefit of restoration or stabilization of a small reach within a channel system or maturing gully on total watershed sediment load. We need to better understand the intricate interactions between hydrological and erosion processes to improve prediction, location, and timing of streambank erosion and failure and gully formation. Also, improved process-based measurement and prediction techniques are needed that balance data requirements regarding cohesive soil erodibility and stability as compared to simpler topographic indices for gullies or stream classification systems. Such techniques will allow the research community to address the benefit of various conservation and/or stabilization practices at targeted locations within watersheds.

Morphine-Induced Preconditioning: Involvement of Protein Kinase A and Mitochondrial Permeability Transition Pore

PubMed Central

Dorsch, Marianne; Behmenburg, Friederike; Raible, Miriam; Blase, Dominic; Grievink, Hilbert; Hollmann, Markus W.; Heinen, André; Huhn, Ragnar

2016-01-01

Background Morphine induces myocardial preconditioning (M-PC) via activation of mitochondrial large conductance Ca2+-sensitive potassium (mKCa) channels. An upstream regulator of mKCa channels is protein kinase A (PKA). Furthermore, mKCa channel activation regulates mitochondrial bioenergetics and thereby prevents opening of the mitochondrial permeability transition pore (mPTP). Here, we investigated in the rat heart in vivo whether 1) M-PC is mediated by activation of PKA, and 2) pharmacological opening of the mPTP abolishes the cardioprotective effect of M-PC and 3) M-PC is critically dependent on STAT3 activation, which is located upstream of mPTP within the signalling pathway. Methods Male Wistar rats were randomised to six groups (each n = 6). All animals underwent 25 minutes of regional myocardial ischemia and 120 minutes of reperfusion. Control animals (Con) were not further treated. Morphine preconditioning was initiated by intravenous administration of 0.3 mg/kg morphine (M-PC). The PKA blocker H-89 (10 μg/kg) was investigated with and without morphine (H-89+M-PC, H-89). We determined the effect of mPTP opening with atractyloside (5 mg/kg) with and without morphine (Atr+M-PC, Atr). Furthermore, the effect of morphine on PKA activity was tested in isolated adult rat cardiomyocytes. In further experiments in isolated hearts we tested the protective properties of morphine in the presence of STAT3 inhibition, and whether pharmacological prevention of the mPTP-opening by cyclosporine A (CsA) is cardioprotective in the presence of STAT3 inhibition. Results Morphine reduced infarct size from 64±5% to 39±9% (P<0.05 vs. Con). H-89 completely blocked preconditioning by morphine (64±9%; P<0.05 vs. M-PC), but H-89 itself had not effect on infarct size (61±10%; P>0.05 vs. Con). Also, atractyloside abolished infarct size reduction of morphine completely (65±9%; P<0.05 vs. M-PC) but had no influence on infarct size itself (64±5%; P>0.05 vs. Con). In isolated hearts STAT3 inhibitor Stattic completely abolished morphine-induced preconditioning. Administration of Stattic and mPTP inhibitor cyclosporine A reduced infarct size to 31±6% (Stat+CsA, P<0.05 vs. Con). Cyclosporine A alone reduced infarct size to 26±7% (CsA P<0.05 vs. Con). In cardiomyocytes, PKA activity was increased by morphine. Conclusion Our data suggest that morphine-induced cardioprotection is mediated by STAT3-activation and inhibition of mPTP, with STA3 located upstream of mPTP. There is some evidence that protein kinase A is involved within the signalling pathway. PMID:26968004

Variation in local abundance and species richness of stream fishes in relation to dispersal barriers: Implications for management and conservation

USGS Publications Warehouse

Nislow, K.H.; Hudy, M.; Letcher, B.H.; Smith, E.P.

2011-01-01

1.Barriers to immigration, all else being equal, should in principle depress local abundance and reduce local species richness. These issues are particularly relevant to stream-dwelling species when improperly designed road crossings act as barriers to migration with potential impacts on the viability of upstream populations. However, because abundance and richness are highly spatially and temporally heterogeneous and the relative importance of immigration on demography is uncertain, population- and community-level effects can be difficult to detect. 2.In this study, we tested the effects of potential barriers to upstream movements on the local abundance and species richness of a diverse assemblage of resident stream fishes in the Monongahela National Forest, West Virginia, U.S.A. Fishes were sampled using simple standard techniques above- and below road crossings that were either likely or unlikely to be barriers to upstream fish movements (based on physical dimensions of the crossing). We predicted that abundance of resident fishes would be lower in the upstream sections of streams with predicted impassable barriers, that the strength of the effect would vary among species and that variable effects on abundance would translate into lower species richness. 3.Supporting these predictions, the statistical model that best accounted for variation in abundance and species richness included a significant interaction between location (upstream or downstream of crossing) and type (passable or impassable crossing). Stream sections located above predicated impassable culverts had fewer than half the number of species and less than half the total fish abundance, while stream sections above and below passable culverts had essentially equivalent richness and abundance. 4.Our results are consistent with the importance of immigration and population connectivity to local abundance and species richness of stream fishes. In turn, these results suggest that when measured at appropriate scales (multiple streams within catchments), with simple protocols amenable to use by management agencies, differences in local abundance and species richness may serve as indicators of the extent to which road crossings are barriers to fish movement and help determine whether road-crossing improvements have restored connectivity to stream fish populations and communities. Published 2011. This article is a US Government work and is in the public domain in the USA.

Level II scour analysis for Bridge 37 (DUXBTH00120037) on Town Highway 12, crossing Ridley Brook, Duxbury, Vermont

USGS Publications Warehouse

Wild, Emily C.; Ivanhoff, Michael A.

1997-01-01

This report provides the results of a detailed Level II analysis of scour potential at structure DUXBTH00120037 on Town Highway 12 crossing Ridley Brook, Duxbury, Vermont (figures 1–8). A Level II study is a basic engineering analysis of the site, including a quantitative analysis of stream stability and scour (U.S. Department of Transportation, 1993). Results of a Level I scour investigation also are included in Appendix E of this report. A Level I investigation provides a qualitative geomorphic characterization of the study site. Information on the bridge, gleaned from Vermont Agency of Transportation (VTAOT) files, was compiled prior to conducting Level I and Level II analyses and is found in Appendix D. The site is in the Green Mountain section of the New England physiographic province in north central Vermont. The 10.1-mi2 drainage area is in a predominantly rural and forested basin. In the vicinity of the study site, the surface cover is forest upstream and downstream of the bridge. In the study area, Ridley Brook has an incised, straight channel with a slope of approximately 0.04 ft/ft, an average channel top width of 67 ft and an average bank height of 9 ft. The channel bed material ranges from gravel to boulders with a median grain size (D50) of 123 mm (0.404 ft). The geomorphic assessment at the time of the Level I and Level II site visit on July 1, 1996, indicated that the reach was stable. The Town Highway 12 crossing of Ridley Brook is a 33-ft-long, two-lane bridge consisting of five 30-ft steel rolled beams (Vermont Agency of Transportation, written communication, October 13, 1995). The opening length of the structure parallel to the bridge face is 30 ft. The bridge is supported by vertical, concrete abutments with wingwalls. The channel is skewed approximately 50 degrees to the opening while the measured opening-skew-to-roadway is 20 degrees. A scour hole 2 ft deeper than the mean thalweg depth was observed along the right abutment and downstream right wingwall during the Level I assessment. Scour countermeasures at the site include type-2 stone fill (less than 3 feet diameter) along the upstream and downstream left road embankments, and type-3 stone fill (less than 4 feet diameter) along the upstream right bank and upstream right wingwall. Additional details describing conditions at the site are included in the Level II Summary and Appendices D and E. Scour depths and recommended rock rip-rap sizes were computed using the general guidelines described in Hydraulic Engineering Circular 18 (Richardson and others, 1995). Total scour at a highway crossing is comprised of three components: 1) long-term streambed degradation; 2) contraction scour (due to accelerated flow caused by a reduction in flow area at a bridge) and; 3) local scour (caused by accelerated flow around piers and abutments). Total scour is the sum of the three components. Equations are available to compute depths for contraction and local scour and a summary of the results of these computations follows. Contraction scour for all modelled flows ranged from 0.6 to 1.7 ft. The worst-case contraction scour occurred at the 500-year discharge. Left abutment scour ranged from 5.0 to 8.3 ft, with the worst-case occurring at the incipient-overtopping discharge. Right abutment scour ranged from 13.1 to 16.7 ft, with the worst-case occurring at the 500-year discharge. Additional information on scour depths and depths to armoring are included in the section titled “Scour Results”. Scoured-streambed elevations, based on the calculated scour depths, are presented in tables 1 and 2. A cross-section of the scour computed at the bridge is presented in figure 8. Scour depths were calculated assuming an infinite depth of erosive material and a homogeneous particle-size distribution. It is generally accepted that the Froehlich equation (abutment scour) gives “excessively conservative estimates of scour depths” (Richardson and others, 1995, p. 47). Usually, computed scour depths are evaluated in combination with other information including (but not limited to) historical performance during flood events, the geomorphic stability assessment, existing scour protection measures, and the results of the hydraulic analyses. Therefore, scour depths adopted by VTAOT may differ from the computed values documented herein.

Level II scour analysis for Bridge 46 (CHESVT00110046) on Vermont State Route 11, crossing the Middle Branch Williams River, Chester, Vermont

USGS Publications Warehouse

Wild, Emily C.

1997-01-01

This report provides the results of a detailed Level II analysis of scour potential at structure CHESVT00110046 on State Route 11 crossing the Middle Branch Williams River, Chester, Vermont (figures 1–8). A Level II study is a basic engineering analysis of the site, including a quantitative analysis of stream stability and scour (U.S. Department of Transportation, 1993). Results of a Level I scour investigation also are included in Appendix E of this report. A Level I investigation provides a qualitative geomorphic characterization of the study site. Information on the bridge, gleaned from Vermont Agency of Transportation (VTAOT) files, was compiled prior to conducting Level I and Level II analyses and is found in Appendix D.The site is in the Green Mountain and New England Upland sections of the New England physiographic province in southeastern Vermont. The 28.0-mi2 drainage area is in a predominantly rural and forested basin. In the vicinity of the study site, the surface cover is forested on the upstream left and downstream right overbanks. The upstream right and downstream left overbanks are pasture while the immediate banks have dense woody vegetation.In the study area, the the Middle Branch Williams River has an incised, sinuous channel with a slope of approximately 0.013 ft/ft, an average channel top width of 81 ft and an average bank height of 11 ft. The channel bed material ranges from gravel to bedrock with a median grain size (D50) of 70.7 mm (0.232 ft). The geomorphic assessment at the time of the Level I and Level II site visit on September 12, 1996, indicated that the reach was stable.The State Route 11 crossing of the Middle Branch Williams River is a 118-ft-long, two-lane steel stringer type bridge consisting of a 114-foot steel plate deck (Vermont Agency of Transportation, written communication, March 29, 1995). The opening length of the structure parallel to the bridge face is 109 ft.The bridge is supported by vertical, concrete abutments with wingwalls. The channel is skewed approximately 45 degrees to the opening while the opening-skew-to-roadway is 50 degrees.A scour hole 2 ft deeper than the mean thalweg depth was observed 128 feet downstream during the Level I assessment. Type-1 (less than 1 foot) stone fill protects the downstream right wingwall. Type-2 (less than 3 ft diameter) stone fill protects the upstream right wingwall, the left and right abutments, the upstream left and right road embankments. Additional details describing conditions at the site are included in the Level II Summary and Appendices D and E.Scour depths and recommended rock rip-rap sizes were computed using the general guidelines described in Hydraulic Engineering Circular 18 (Richardson and others, 1995). Total scour at a highway crossing is comprised of three components: 1) long-term streambed degradation; 2) contraction scour (due to accelerated flow caused by a reduction in flow area at a bridge) and; 3) local scour (caused by accelerated flow around piers and abutments). Total scour is the sum of the three components. Equations are available to compute depths for contraction and local scour and a summary of the results of these computations follows.There was no computed contraction scour for any modelled flows. Abutment scour ranged from 7.0 to 10.3 ft. The worst-case abutment scour occurred at the 500-year discharge. Additional information on scour depths and depths to armoring are included in the section titled “Scour Results”. Scoured-streambed elevations, based on the calculated scour depths, are presented in tables 1 and 2. A cross-section of the scour computed at the bridge is presented in figure 8. Scour depths were calculated assuming an infinite depth of erosive material and a homogeneous particle-size distribution.It is generally accepted that the Froehlich equation (abutment scour) gives “excessively conservative estimates of scour depths” (Richardson and others, 1995, p. 47). Usually, computed scour depths are evaluated in combination with other information including (but not limited to) historical performance during flood events, the geomorphic stability assessment, existing scour protection measures, and the results of the hydraulic analyses. Therefore, scour depths adopted by VTAOT may differ from the computed values documented herein.

Level II scour analysis for Bridge 67 (MTHOTH00120067) on Town Highway 12, crossing Freeman Brook, Mount Holly, Vermont

USGS Publications Warehouse

Wild, Emily C.; Severance, Timothy

1998-01-01

This report provides the results of a detailed Level II analysis of scour potential at structure MTHOTH00120067 on Town Highway 12 crossing Freeman Brook, Mount Holly, Vermont (figures 1–8). A Level II study is a basic engineering analysis of the site, including a quantitative analysis of stream stability and scour (FHWA, 1993). Results of a Level I scour investigation also are included in appendix E of this report. A Level I investigation provides a qualitative geomorphic characterization of the study site. Information on the bridge, gleaned from Vermont Agency of Transportation (VTAOT) files, was compiled prior to conducting Level I and Level II analyses and is found in appendix D. The site is in the Green Mountain section of the New England physiographic province in south-central Vermont. The 11.4-mi2 drainage area is in a predominantly rural and forested basin. In the vicinity of the study site, the surface cover is forested. In the study area, Freeman Brook has an incised, sinuous channel with a slope of approximately 0.01 ft/ft, an average channel top width of 51 ft and an average bank height of 6 ft. The channel bed material ranges from sand to boulders with a median grain size (D50) of 55.7 mm (0.183 ft). The geomorphic assessment at the time of the Level I and Level II site visit on October 5, 1995, indicated that the reach was stable. The Town Highway 12 crossing of Freeman Brook is a 34-ft-long, two-lane bridge consisting of a 30-foot prestressed concrete-slab span (Vermont Agency of Transportation, written communication, March 15, 1995). The opening length of the structure parallel to the bridge face is 29.5 ft. The bridge is supported by vertical, concrete abutments with wingwalls. The channel is skewed approximately 50 degrees to the opening while the opening-skew-to-roadway is 15 degrees. Along the upstream right wingwall, the right abutment and the downstream right wingwall, a scour hole approximately 1.0 to 2.0 ft deeper than the mean thalweg depth was observed during the Level I assessment. Scour protection measures at the site included type-1 stone fill (less than 12 inches diameter) along the downstream end of the downstream right wingwall; type-2 stone fill (less than 36 inches diameter) along the upstream left wingwall, the left abutment, the downstream left wingwall and the upstream left and right banks; type- 3 stone fill (less than 48 inches diameter) along the downstream left and right banks; and type-4 stone fill (less than 60 inches diameter) along the upstream right wingwall. Additional details describing conditions at the site are included in the Level II Summary and appendices D and E. Scour depths and recommended rock rip-rap sizes were computed using the general guidelines described in Hydraulic Engineering Circular 18 (Richardson and Davis, 1995) for the 100- and 500-year discharges. Total scour at a highway crossing is comprised of three components: 1) long-term streambed degradation; 2) contraction scour (due to accelerated flow caused by a reduction in flow area at a bridge) and; 3) local scour (caused by accelerated flow around piers and abutments). Total scour is the sum of the three components. Equations are available to compute depths for contraction and local scour and a summary of the results of these computations follows. Contraction scour for all modelled flows ranged from 2.6 to 3.9 ft. The worst-case contraction scour occurred at the 500-year discharge. Left abutment scour ranged from 7.9 to 10.0 ft. Right abutment scour ranged from 12.7 to 15.2 ft. The worst-case abutment scour occurred at the 500-year discharge. Additional information on scour depths and depths to armoring are included in the section titled “Scour Results”. Scoured-streambed elevations, based on the calculated scour depths, are presented in tables 1 and 2. A cross-section of the scour computed at the bridge is presented in figure 8. Scour depths were calculated assuming an infinite depth of erosive material and a homogeneous particle-size distribution. It is generally accepted that the Froehlich equation (abutment scour) gives “excessively conservative estimates of scour depths” (Richardson and Davis, 1995, p. 46). Usually, computed scour depths are evaluated in combination with other information including (but not limited to) historical performance during flood events, the geomorphic stability assessment, existing scour protection measures, and the results of the hydraulic analyses. Therefore, scour depths adopted by VTAOT may differ from the computed values documented herein.

Level II scour analysis for Bridge 51 (JERITH00590051) on Town Highway 59, crossing The Creek, Jericho, Vermont

USGS Publications Warehouse

Wild, Emily C.

1998-01-01

This report provides the results of a detailed Level II analysis of scour potential at structure JERITH00590051 on Town Highway 59 crossing The Creek, Jericho, Vermont (figures 1– 8). A Level II study is a basic engineering analysis of the site, including a quantitative analysis of stream stability and scour (Federal Highway Administration, 1993). Results of a Level I scour investigation also are included in appendix E of this report. A Level I investigation provides a qualitative geomorphic characterization of the study site. Information on the bridge, gleaned from Vermont Agency of Transportation (VTAOT) files, was compiled prior to conducting Level I and Level II analyses and is found in appendix D. The site is in the Green Mountain section of the New England physiographic province and the Champlain section of the St. Lawrence physiographic province in northwestern Vermont. The 10.9-mi2 drainage area is in a predominantly rural and forested basin. In the vicinity of the study site, the surface cover is pasture on the left and right overbanks, upstream and downstream of the bridge while the immediate banks have dense woody vegetation. In the study area, The Creek has a sinuous channel with a slope of approximately 0.004 ft/ft, an average channel top width of 45 ft and an average bank height of 6 ft. The channel bed material ranges from silt to cobble with a median grain size (D50) of 58.6 mm (0.192 ft). The geomorphic assessment at the time of the Level I and Level II site visit on July 3, 1996, indicated that the reach was stable. The Town Highway 59 crossing of The Creek is a 33-ft-long, two-lane bridge consisting of a 28-foot steel-stringer span (Vermont Agency of Transportation, written communication, December 11, 1995). The opening length of the structure parallel to the bridge face is 26 ft. The bridge is supported by vertical, concrete abutments with wingwalls. The channel is skewed approximately 10 degrees to the opening while the computed opening-skew-toroadway is 5 degrees.A scour hole 3 ft deeper than the mean thalweg depth was observed along the right abutment during the Level I assessment. Scour countermeasures at the site included type-1 stone fill (less than 12 inches diameter) at the left and right upstream road embankments. Type-2 stone fill (less than 36 inches diameter) was along the upstream right bank and along the upstream right wingwall. Additional details describing conditions at the site are included in the Level II Summary and appendices D and E. Scour depths and recommended rock rip-rap sizes were computed using the general guidelines described in Hydraulic Engineering Circular 18 (Richardson and Davis, 1995) for the 100- and 500-year discharges. In addition, the incipient roadway-overtopping discharge was determined and analyzed as another potential worst-case scour scenario. Total scour at a highway crossing is comprised of three components: 1) long-term streambed degradation; 2) contraction scour (due to accelerated flow caused by a reduction in flow area at a bridge) and; 3) local scour (caused by accelerated flow around piers and abutments). Total scour is the sum of the three components. Equations are available to compute depths for contraction and local scour and a summary of the results of these computations follows. Contraction scour for all modelled flows was zero ft. Left abutment scour ranged from 2.4 to 3.2 ft. Right abutment scour ranged from 4.1 to 4.5 ft.The worst-case abutment scour occurred at the 500-year discharge. Additional information on scour depths and depths to armoring are included in the section titled “Scour Results”. Scoured-streambed elevations, based on the calculated scour depths, are presented in tables 1 and 2. A cross-section of the scour computed at the bridge is presented in figure 8. Scour depths were calculated assuming an infinite depth of erosive material and a homogeneous particle-size distribution. It is generally accepted that the Froehlich equation (abutment scour) gives “excessively conservative estimates of scour depths” (Richardson and Davis, 1995, p. 47). Usually, computed scour depths are evaluated in combination with other information including (but not limited to) historical performance during flood events, the geomorphic stability assessment, existing scour protection measures, and the results of the hydraulic analyses. Therefore, scour depths adopted by VTAOT may differ from the computed values documented herein.

Level II scour analysis for Bridge 68 (NFIETH00960068) on Town Highway 96, crossing the Dog River, Northfield, Vermont

USGS Publications Warehouse

Burns, Ronda L.

1997-01-01

This report provides the results of a detailed Level II analysis of scour potential at structure NFIETH00960068 on Town Highway 96 crossing the Dog River, Northfield, Vermont (figures 1–8). A Level II study is a basic engineering analysis of the site, including a quantitative analysis of stream stability and scour (U.S. Department of Transportation, 1993). Results of a Level I scour investigation also are included in Appendix E of this report. A Level I investigation provides a qualitative geomorphic characterization of the study site. Information on the bridge, gleaned from Vermont Agency of Transportation (VTAOT) files, was compiled prior to conducting Level I and Level II analyses and is found in Appendix D. The site is in the Green Mountain section of the New England physiographic province in central Vermont. The 30.7-mi2 drainage area is in a predominantly rural and forested basin. In the vicinity of the study site, the surface cover on the left bank upstream and downstream is pasture while the immediate banks have dense woody vegetation. The right bank upstream is forested and the downstream right bank is pasture. Vermont state route 12A runs parallel to the river on the right bank. In the study area, the Dog River has an incised, straight channel with a slope of approximately 0.004 ft/ft, an average channel top width of 70 ft and an average bank height of 7 ft. The channel bed material ranges from sand to cobble with a median grain size (D50) of 47.9 mm (0.157 ft). The geomorphic assessment at the time of the Level I and Level II site visit on July 25, 1996, indicated that the reach was stable. The Town Highway 96 crossing of the Dog River is a 45-ft-long, one-lane bridge consisting of one 43-foot steel-beam span with a timber deck (Vermont Agency of Transportation, written communication, October 13, 1995). The opening length of the structure parallel to the bridge face is 41.5 ft.The bridge is supported by vertical, concrete abutments with wingwalls. The channel is not skewed to the opening and the opening-skew-to-roadway is zero degrees. Channel scour 0.5 ft deeper than the mean thalweg depth, was observed under the bridge during the Level I assessment. The scour protection measures at the site included type-1 stone fill (less than 12 inches diameter) along the left bank upstream and type-2 stone fill (less than 36 inches diameter) along the upstream and downstream right banks that extends partially in front of the right wingwalls. Additional details describing conditions at the site are included in the Level II Summary and Appendices D and E. Scour depths and recommended rock rip-rap sizes were computed using the general guidelines described in Hydraulic Engineering Circular 18 (Richardson and others, 1995). Total scour at a highway crossing is comprised of three components: 1) long-term streambed degradation; 2) contraction scour (due to accelerated flow caused by a reduction in flow area at a bridge) and; 3) local scour (caused by accelerated flow around piers and abutments). Total scour is the sum of the three components. Equations are available to compute depths for contraction and local scour and a summary of the results of these computations follows. Contraction scour for all modelled flows ranged from 0.8 to 1.2 ft. The worst-case contraction scour occurred at the 100-year and 500-year discharges. Abutment scour ranged from 8.5 to 12.2 ft. The worst-case abutment scour occurred at the incipient roadway-overtopping discharge for the right abutment. Additional information on scour depths and depths to armoring are included in the section titled “Scour Results”. Scoured-streambed elevations, based on the calculated scour depths, are presented in tables 1 and 2. A cross-section of the scour computed at the bridge is presented in figure 8. Scour depths were calculated assuming an infinite depth of erosive material and a homogeneous particle-size distribution. It is generally accepted that the Froehlich equation (abutment scour) gives “excessively conservative estimates of scour depths” (Richardson and others, 1995, p. 47). Usually, computed scour depths are evaluated in combination with other information including (but not limited to) historical performance during flood events, the geomorphic stability assessment, existing scour protection measures, and the results of the hydraulic analyses. Therefore, scour depths adopted by VTAOT may differ from the computed values documented herein.

Level II scour analysis for Bridge 16 (RIPTTH00110016) on Town Highway 11, crossing the Middle Branch Middlebury River, Ripton, Vermont

USGS Publications Warehouse

Burns, Ronda L.

1997-01-01

This report provides the results of a detailed Level II analysis of scour potential at structure RIPTTH00110016 on Town Highway 11 crossing the Middle Branch Middlebury River, Ripton, Vermont (figures 1–8). A Level II study is a basic engineering analysis of the site, including a quantitative analysis of stream stability and scour (U.S. Department of Transportation, 1993). Results of a Level I scour investigation also are included in Appendix E of this report. A Level I investigation provides a qualitative geomorphic characterization of the study site. Information on the bridge, gleaned from Vermont Agency of Transportation (VTAOT) files, was compiled prior to conducting Level I and Level II analyses and is found in Appendix D. The site is in the Green Mountain section of the New England physiographic province in west-central Vermont. The 6.6-mi2 drainage area is in a predominantly rural and forested basin. In the vicinity of the study site, the surface cover consists of shrubs, brush and trees except for the upstream left bank which is completely forested. In the study area, the Middle Branch Middlebury River has an incised, sinuous channel with a slope of approximately 0.03 ft/ft, an average channel top width of 68 ft and an average bank height of 5 ft. The channel bed material ranges from gravel to boulder with a median grain size (D50) of 97.6 mm (0.320 ft). The geomorphic assessment at the time of the Level I and Level II site visit on June 11, 1996, indicated that the reach was stable. The Town Highway 11 crossing of the Middle Branch Middlebury River is a 44-ft-long, two-lane bridge consisting of one 42-foot steel-beam span (Vermont Agency of Transportation, written communication, December 15, 1995). The opening length of the structure parallel to the bridge face is 40.2 ft. The bridge is supported by vertical, concrete abutments with wingwalls. The channel is skewed approximately 40 degrees to the opening. The opening-skew-to-roadway value from the VTAOT database is 20 degrees while 30 degrees was computed from surveyed points. A scour hole, 3 ft deeper than the mean thalweg depth, was observed along the left abutment and upstream left wingwall during the Level I assessment. In addition, 1 ft of channel scour was observed just downstream of the downstream left wingwall along the left bank. Scour countermeasures at the site included type-2 stone fill (less than 36 inches diameter) along the upstream left and right banks and along the upstream end of the downstream left wingwall. Additional details describing conditions at the site are included in the Level II Summary and Appendices D and E. Scour depths and recommended rock rip-rap sizes were computed using the general guidelines described in Hydraulic Engineering Circular 18 (Richardson and others, 1995) for the 100- and 500-year discharges. Total scour at a highway crossing is comprised of three components: 1) long-term streambed degradation; 2) contraction scour (due to accelerated flow caused by a reduction in flow area at a bridge) and; 3) local scour (caused by accelerated flow around piers and abutments). Total scour is the sum of the three components. Equations are available to compute depths for contraction and local scour and a summary of the results of these computations follows. Contraction scour for all modelled flows ranged from 0.1 to 0.4 ft. The worst-case contraction scour occurred at the 500-year discharge. Abutment scour ranged from 7.2 to 8.6 ft along the right abutment and from 11.7 to 13.7 ft along the left abutment. The worstcase abutment scour occurred at the 500-year discharge. Additional information on scour depths and depths to armoring are included in the section titled “Scour Results”. Scoured-streambed elevations, based on the calculated scour depths, are presented in tables 1 and 2. A cross-section of the scour computed at the bridge is presented in figure 8. Scour depths were calculated assuming an infinite depth of erosive material and a homogeneous particle-size distribution. It is generally accepted that the Froehlich equation (abutment scour) gives “excessively conservative estimates of scour depths” (Richardson and others, 1995, p. 47). Usually, computed scour depths are evaluated in combination with other information including (but not limited to) historical performance during flood events, the geomorphic stability assessment, existing scour protection measures, and the results of the hydraulic analyses. Therefore, scour depths adopted by VTAOT may differ from the computed values documented herein.

Level II scour analysis for Bridge 38 (TOPSTH00570038) on Town Highway 57, crossing Waits River, Topsham, Vermont

USGS Publications Warehouse

Striker, Lora K.; Boehmler, Erick M.

1997-01-01

This report provides the results of a detailed Level II analysis of scour potential at structure TOPSTH00570038 on Town Highway 57 crossing the Waits River, Topsham, Vermont (figures 1–8). A Level II study is a basic engineering analysis of the site, including a quantitative analysis of stream stability and scour (U.S. Department of Transportation, 1993). Results of a Level I scour investigation also are included in Appendix E of this report. A Level I investigation provides a qualitative geomorphic characterization of the study site. Information on the bridge, gleaned from Vermont Agency of Transportation (VTAOT) files, was compiled prior to conducting Level I and Level II analyses and is found in Appendix D. The site is in the New England Upland section of the New England physiographic province in east central Vermont. The 37.3-mi2 drainage area is in a predominantly rural and forested basin. In the vicinity of the study site, the surface cover is predominantly pasture while the left bank upstream is suburban. In the study area, the Waits River has a sinuous locally anabranched channel with a slope of approximately 0.01 ft/ft, an average channel top width of 76 ft and an average bank height of 6 ft. The channel bed material ranges from sand to cobble with a median grain size (D50) of 57.2 mm (0.188 ft). The geomorphic assessment at the time of the Level I and Level II site visit on August 28, 1995, indicated that the reach was considered laterally unstable due to cut-banks upstream, mid-channel bars and lateral migration of the channel towards the left abutment. The Town Highway 34 crossing of the Waits River is a 34-ft-long, one-lane bridge consisting of one 31-foot steel-beam span (Vermont Agency of Transportation, written communication, March 28, 1995). The opening length of the structure parallel to the bridge face is 30.4 ft. The bridge is supported by a vertical, stone abutment with concrete facing and wingwalls on the right and by a vertical, concrete abutment with wingwalls on the left. The channel is skewed approximately 0 degrees to the opening and the opening-skew-to-roadway is also zero degrees. A scour hole 2.0 ft deeper than the mean thalweg depth was observed towards the left bank underneath the bridge. The only scour protection measure at the site was type-2 stone fill (less than 36 inches diameter) along the left bank upstream, in the upstream left wing wall area, along the left abutment, at the downstream end of the right abutment, and in the downstream left wing wall area. There is type-3 stone fill (less than 48 inches diameter) in the downstream right wing wall area. Additional details describing conditions at the site are included in the Level II Summary and Appendices D and E. Scour depths and recommended rock rip-rap sizes were computed using the general guidelines described in Hydraulic Engineering Circular 18 (Richardson and others, 1995). Total scour at a highway crossing is comprised of three components: 1) long-term streambed degradation; 2) contraction scour (due to accelerated flow caused by a reduction in flow area at a bridge) and; 3) local scour (caused by accelerated flow around piers and abutments). Total scour is the sum of the three components. Equations are available to compute depths for contraction and local scour and a summary of the results of these computations follows. Contraction scour for all modelled flows ranged from 1.6 to 5.2 ft. The worst-case contraction scour occurred at the 100-year discharge. Abutment scour ranged from 9.8 to 18.5 ft. The worst-case abutment scour occurred at the 500-year discharge. Additional information on scour depths and depths to armoring are included in the section titled “Scour Results”. Scoured-streambed elevations, based on the calculated scour depths, are presented in tables 1 and 2. A cross-section of the scour computed at the bridge is presented in figure 8. Scour depths were calculated assuming an infinite depth of erosive material and a homogeneous particle-size distribution. It is generally accepted that the Froehlich equation (abutment scour) gives “excessively conservative estimates of scour depths” (Richardson and others, 1995, p. 47). Usually, computed scour depths are evaluated in combination with other information including (but not limited to) historical performance during flood events, the geomorphic stability assessment, existing scour protection measures, and the results of the hydraulic analyses. Therefore, scour depths adopted by VTAOT may differ from the computed values documented herein.

Level II scour analysis for Bridge 4 (MAIDTH00070004) on Town Highway 7, crossing Cutler Mill Brook, Maidstone, Vermont

USGS Publications Warehouse

Striker, Lora K.; Medalie, Laura

1997-01-01

This report provides the results of a detailed Level II analysis of scour potential at structure MAIDTH00070004 on Town Highway 7 crossing the Cutler Mill Brook, Maidstone, Vermont (figures 1–8). A Level II study is a basic engineering analysis of the site, including a quantitative analysis of stream stability and scour (U.S. Department of Transportation, 1993). Results of a Level I scour investigation also are included in Appendix E of this report. A Level I investigation provides a qualitative geomorphic characterization of the study site. Information on the bridge, gleaned from Vermont Agency of Transportation (VTAOT) files, was compiled prior to conducting Level I and Level II analyses and is found in Appendix D. The site is in the White Mountain section of the New England physiographic province in northeastern Vermont. The 18.1-mi2 drainage area is in a predominantly rural and forested basin. In the vicinity of the study site, the surface cover is predominantly shrub and brushland. In the study area, the Cutler Mill Brook has a non-incised, meandering channel with local braiding and a slope of approximately 0.004 ft/ft, an average channel top width of 43 ft and an average bank height of 2 ft. The channel bed material ranges from sand to cobble with a median grain size (D50) of 27.6 mm (0.091 ft). The geomorphic assessment at the time of the Level I and Level II site visit on July 19, 1995, indicated that the reach was laterally unstable due to large meanders in the channel. The Town Highway 7 crossing of the Cutler Mill Brook is a 25-ft-long, one-lane bridge consisting of one 22-foot concrete span (Vermont Agency of Transportation, written communication, August 5, 1994). The opening length of the structure parallel to the bridge face is 21.7 ft. The bridge is supported by vertical, concrete abutments with wingwalls. The channel is skewed approximately 20 degrees to the opening while the opening-skew-to-roadway is 0 degrees. A scour hole 2.0 ft deeper than the mean thalweg depth was observed along the left abutment during the Level I assessment. The only scour protection measure at the site was type-2 stone fill (less than 36 inches diameter) along both banks upstream, along the entire base length of the upstream left wingwall, and along the upstream end of the upstream right wingwall. Additional details describing conditions at the site are included in the Level II Summary and Appendices D and E. Scour depths and recommended rock rip-rap sizes were computed using the general guidelines described in Hydraulic Engineering Circular 18 (Richardson and others, 1995) for the 100- and 500-year discharges. In addition, the incipient roadway-overtopping discharge was determined and analyzed as another potential worst-case scour scenario. Total scour at a highway crossing is comprised of three components: 1) long-term streambed degradation; 2) contraction scour (due to accelerated flow caused by a reduction in flow area at a bridge) and; 3) local scour (caused by accelerated flow around piers and abutments). Total scour is the sum of the three components. Equations are available to compute depths for contraction and local scour and a summary of the results of these computations follows. Contraction scour for all modelled flows ranged from 2.2 to 4.2 ft. The worst-case contraction scour occurred at the 500-year discharge. Abutment scour ranged from 5.7 to 12.4 ft. The worst-case abutment scour occurred at the 500-year discharge. Additional information on scour depths and depths to armoring are included in the section titled “Scour Results”. Scoured-streambed elevations, based on the calculated scour depths, are presented in tables 1 and 2. A cross-section of the scour computed at the bridge is presented in figure 8. Scour depths were calculated assuming an infinite depth of erosive material and a homogeneous particle-size distribution. It is generally accepted that the Froehlich equation (abutment scour) gives “excessively conservative estimates of scour depths” (Richardson and others, 1995, p. 47). Usually, computed scour depths are evaluated in combination with other information including (but not limited to) historical performance during flood events, the geomorphic stability assessment, existing scour protection measures, and the results of the hydraulic analyses. Therefore, scour depths adopted by VTAOT may differ from the computed values documented herein.

Long-term dynamics of a floodplain shallow lake in the Pantanal wetland: Is it all about climate?

PubMed

Silio-Calzada, Ana; Barquín, José; Huszar, Vera L M; Mazzeo, Nestor; Méndez, Fernando; Álvarez-Martínez, Jose Manuel

2017-12-15

Hydrological variability over seasonal and multi-annual timescales strongly shapes the ecological structure and functioning of floodplain ecosystems. The current IPCC climate scenario foresees an increase in the frequency of extreme events. This, in conjunction with other anthropogenic disturbances (e.g., river regulation or land-use changes) poses a serious threat to the natural functioning of these ecosystems. In this study we aimed to i) evaluate the long-term variability of the flooded area of the third largest floodplain lake in the Brazilian Pantanal using remote sensing techniques, and ii) analyze the possible factors influencing this variability. Changes in open-water and riparian floodplain-wetland vegetation areas were mapped by applying an ad hoc-developed remote-sensing method (including a newly developed normalized water index, NWI) to 221 Landsat-Thematic Mapper (TM)/Enhanced Thematic Mapper Plus (ETM+) images, acquired between 1984 and 2011. Added to the lake's natural swing between riparian floodplain-wetland vegetation expansion and retraction, our analyses revealed large interannual changes, grouped into three main periods within the studied time interval. Moreover, our results indicate that this floodplain-lake system is losing open-water area, paired with an increase in riparian floodplain-wetland vegetation. The system's long-term dynamics are not all climate related, but are the result of a combination of drivers. The start of the Manso dam's operation upstream of the studied system, and the subsequent river regulation because of the dam operation, coupled with climatic oscillation appear to be responsible for the observed changes. However, other factors which were not considered in this study might also be important in this process and contributing to the reduction of the system's resilience to droughts (e.g., land-use changes). This study illustrates the serious conservation risks that the Pantanal faces in the near future, given the current climate-change scenario and the accumulation of dam building projects in this region. Copyright © 2017 Elsevier B.V. All rights reserved.

Conservation in metropolitan regions: assessing trends and threats of urban development and climate change

NASA Astrophysics Data System (ADS)

Thorne, J. H.; Santos, M. J.; Bjorkman, J.

2011-12-01

Two global challenges to successful conservation are urban expansion and climate change. Rapid urban growth threatens biodiversity and associated ecosystem services, while climate change may make currently protected areas unsuitable for species that exist within them. We examined three measures of landscape change for 8800 km2 of the San Francisco Bay metropolitan region over 80 years past and future: urban growth, protected area establishment, and natural vegetation type extents. The Bay Area is a good test bed for conservation assessment of the impacts of temporal and spatial of urban growth and land cover change. The region is geographically rather small, with over 40% of its lands already dedicated to protected park and open space lands, they are well-documented, and, the area has had extensive population growth in the past and is projected to continue to grow. The ten-county region within which our study area is a subset has grown from 1.78 million people in 1930, to 6.97 million in 2000 and is estimated to grow to 10.94 million by 2050. With such an influx of people into a small geographic area, it is imperative to both examine the past urban expansion and estimate how the future population will be accommodated into the landscape. We quantify these trends to assess conservation 'success' through time. We used historical and current landcover maps to assess trend, and a GIS-based urban modeling (UPlan) to assess future urban growth impacts in the region, under three policy scenarios- business as usual, smart growth, and urban redevelopment. Impacts are measured by the amount of open space targeted by conservation planners in the region that will be urbanized under each urban growth policy. Impacts are also measured by estimates of the energy consumption projected for each of the scenarios on household and business unit level. The 'business as usual' and 'smart growth' scenarios differed little in their impacts to targeted conservation lands, because so little open space remains to accommodate the expected population growth. Redevelopment conserved more naturally vegetated open space. The redevelopment scenario also permits the lowest increase in energy demand because buildings taken out in the process are reconfigured to higher levels of energy efficiency. However, redevelopment requires substantial increases in residential densities to confine the spatial footprint of the expected future urban growth. These three urban growth scenario footprints differ in their impact to natural vegetation and open space. To incorporate the influence of climate change on remaining natural ecosystems in this urbanizing landscape, we projected the stability of existing, mapped, vegetation types in the region under future climates by examining where projected ranges of the dominant plant species comprising each California Wildlife Habitat Relationship type will all remain together, and where they will begin to dis-associate due to biogeographic response to changing climate. This permits identification of stable and unstable zones of vegetation. The combination of climate stable, high conservation priority and likelihood of urban development provides a way to prioritize conservation land acquisitions.

Genome of turbot rhabdovirus exhibits unusual non-coding regions and an additional ORF that could be expressed in fish cell.

PubMed

Zhu, Ruo-Lin; Lei, Xiao-Ying; Ke, Fei; Yuan, Xiu-Ping; Zhang, Qi-Ya

2011-02-01

Genomic sequence of Scophthalmus maximus rhabdovirus (SMRV) isolated from diseased turbot has been characterized. The complete genome of SMRV comprises 11,492 nucleotides and encodes five typical rhabdovirus genes N, P, M, G and L. In addition, two open reading frames (ORF) are predicted overlapping with P gene, one upstream of P and smaller than P (temporarily called Ps), and another in P gene which may encodes a protein similar to the vesicular stomatitis virus C protein. The C ORF is contained within the P ORF. The five typical proteins share the highest sequence identities (48.9%) with the corresponding proteins of rhabdoviruses in genus Vesiculovirus. Phylogenetic analysis of partial L protein sequence indicates that SMRV is close to genus Vesiculovirus. The first 13 nucleotides at the ends of the SMRV genome are absolutely inverse complementarity. The gene junctions between the five genes show conserved polyadenylation signal (CATGA(7)) and intergenic dinucleotide (CT) followed by putative transcription initiation sequence A(A/G)(C/G)A(A/G/T), which are different from known rhabdoviruses. The entire Ps ORF was cloned and expressed, and used to generate polyclonal antibody in mice. One obvious band could be detected in SMRV-infected carp leucocyte cells (CLCs) by anti-Ps/C serum via Western blot, and the subcellular localization of Ps-GFP fusion protein exhibited cytoplasm distribution as multiple punctuate or doughnut shaped foci of uneven size. Copyright © 2010 Elsevier B.V. All rights reserved.

Aberrant termination of reproduction-related TMEM30C transcripts in the hominoids.

PubMed

Osada, Naoki; Hashimoto, Katsuyuki; Hirai, Momoki; Kusuda, Jun

2007-05-01

Finding genetic novelties that may contribute to human-specific physiology and diseases is a key issue of current biomedical studies. TMEM30C is a gene containing two transmembrane (TM) domains and homologous to the yeast CDC50 family, which is related to polarized cell division. It is conserved among mammals along with two other paralogs, TMEM30A and TMEM30B. We found that TMEM30C is expressed specifically in the testis of mammals, in contrast to the relatively wide expression distributions of the other paralogs. While macaques expressed two alternative splicing isoforms which include one or two TM domains, humans and chimpanzees predominantly expressed truncated transcripts because of the mutations in the splicing and/or poly(A) signal sites. The major transcript in humans harbored non-stop ORF (open reading frame) while the chimpanzee counterpart encoded a protein with one TM domain. The difference was due to the 1-bp indel upstream of the poly(A) signal site. In addition, both the hominoids expressed minor transcripts encoding short proteins with one TM domain. Phylogenetic analysis has showed the acceleration of amino acid substitution after the human and chimpanzee divergence, which may have been caused by a recent relaxation in functional constraints or positive selection on TMEM30C. Elucidating the precise reproductive function of TMEM30C in mammals will be important to the foundation of divergence in higher primates at a molecular level.

Low coke fuel injector for a gas turbine engine

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

Taylor, J.R.

This patent describes a gas turbine carbureting device for disposal in a down-stream flowing compressor discharge air flow. It comprises: a spin chamber defined by a generally annular housing including a closed forward end having a continuous unobstructed inner surface and an open aft end wherein the forward end is upstream of the aft end with respect tot he compressor discharge airflow; at least one exhaust tube having an inlet disposed within the spin chamber wherein the exhaust tube is radially spaced apart from the annular housing and which together with the annular housing forms at least in part amore » first annular air passage leading to the forward end; the housing having a fuel entrance and a swirling air entrance to the first annular air passage and spaced axially apart from each other, and wherein the swirling air entrance and fuel entrance are downstream of the closer forward end with respect to the compressor discharge flow; and wherein the first air passage is formed for flowing swirling air from the swirling air passage to the aft end in an upstream direction with respect to the compressor discharge flow and the exhaust tube inlet is disposed within the swirl chamber so as to reverse the axial direction of the swirling air off the forward end from an upstream direction to a downstream direction through the exhaust tube.« less

Electrical Performance of Monolayer MoS2 Field-Effect Transistors Prepared by Chemical Vapor Deposition

DTIC Science & Technology

2013-05-16

Furthermore, MoS2 also shows promise for use in logic circuits and optoelectronic devices, and it is a promising material for use on flexible and...onto an auxiliary silicon substrate and placed inside a tube furnace with the growth substrates surrounding it. Sulfur powder, placed upstream near the...opening of the furnace at an approximate temperature of 600 C, was subli- mated for use as the sulfur vapor source. The furnace was heated to a peak

Numerical simulation of the interaction between a flowfield and chemical reaction on premixed pulsed jet combustion

NASA Astrophysics Data System (ADS)

Hishida, Manabu; Hayashi, A. Koichi

1992-12-01

Pulsed Jet Combustion (PJC) is numerically simulated using time-dependent, axisymmetric, full Navier-Stokes equations with the mass, momentum, energy, and species conservation equations for a hydrogen-air mixture. A hydrogen-air reaction mechanism is modeled by nine species and nineteen elementary forward and backward reactions to evaluate the effect of the chemical reactions accurately. A point implicit method with the Harten and Yee's non-MUSCL (Monotone Upstream-centerd Schemes for Conservation Laws) modified-flux type TVD (Total Variation Diminishing) scheme is applied to deal with the stiff partial differential equations. Furthermore, a zonal method making use of the Fortified Solution Algorithm (FSA) is applied to simulate the phenomena in the complicated shape of the sub-chamber. The numerical result shows that flames propagating in the sub-chamber interact with pressure waves and are deformed to be wrinkled like a 'tulip' flame and a jet passed through the orifice changes its mass flux quasi-periodically.

Cloning and functional characterization of the Xenopus orthologue of the Treacher Collins syndrome (TCOF1) gene product.

PubMed

Gonzales, Bianca; Yang, Hushan; Henning, Dale; Valdez, Benigno C

2005-10-10

Treacher Collins syndrome (TCS) is an autosomal dominant disorder of craniofacial development caused by mutations in the TCOF1 gene, which encodes the nucleolar phosphoprotein treacle. We previously reported a function for mammalian treacle in ribosomal DNA gene transcription by its interaction with upstream binding factor. As an initial step in the development of a TCS model for frog the cDNA that encodes the Xenopus laevis treacle was cloned. Although the derived amino acid sequence shows a poor homology with its mammalian orthologues, Xenopus treacle has 11 highly homologous direct repeats near the center of the protein molecule similar to those present in its human, dog and mouse orthologues. Comparison of their amino acid compositions indicates conservation of predominant specific amino acid residues. Antisense-mediated down-regulation of treacle expression in X. laevis oocytes resulted in inhibition of rDNA gene transcription. The results suggest evolutionary conservation of the function of treacle in ribosomal RNA biogenesis in higher eukaryotes.

Molecular basis of the activity of the phytopathogen pectin methylesterase

PubMed Central

Fries, Markus; Ihrig, Jessica; Brocklehurst, Keith; Shevchik, Vladimir E; Pickersgill, Richard W

2007-01-01

We provide a mechanism for the activity of pectin methylesterase (PME), the enzyme that catalyses the essential first step in bacterial invasion of plant tissues. The complexes formed in the crystal using specifically methylated pectins, together with kinetic measurements of directed mutants, provide clear insights at atomic resolution into the specificity and the processive action of the Erwinia chrysanthemi enzyme. Product complexes provide additional snapshots along the reaction coordinate. We previously revealed that PME is a novel aspartic-esterase possessing parallel β-helix architecture and now show that the two conserved aspartates are the nucleophile and general acid-base in the mechanism, respectively. Other conserved residues at the catalytic centre are shown to be essential for substrate binding or transition state stabilisation. The preferential binding of methylated sugar residues upstream of the catalytic site, and demethylated residues downstream, drives the enzyme along the pectin molecule and accounts for the sequential pattern of demethylation produced by both bacterial and plant PMEs. PMID:17717531

Mad1 kinetochore recruitment by Mps1-mediated phosphorylation of Bub1 signals the spindle checkpoint.

PubMed

London, Nitobe; Biggins, Sue

2014-01-15

The spindle checkpoint is a conserved signaling pathway that ensures genomic integrity by preventing cell division when chromosomes are not correctly attached to the spindle. Checkpoint activation depends on the hierarchical recruitment of checkpoint proteins to generate a catalytic platform at the kinetochore. Although Mad1 kinetochore localization is the key regulatory downstream event in this cascade, its receptor and mechanism of recruitment have not been conclusively identified. Here, we demonstrate that Mad1 kinetochore association in budding yeast is mediated by phosphorylation of a region within the Bub1 checkpoint protein by the conserved protein kinase Mps1. Tethering this region of Bub1 to kinetochores bypasses the checkpoint requirement for Mps1-mediated kinetochore recruitment of upstream checkpoint proteins. The Mad1 interaction with Bub1 and kinetochores can be reconstituted in the presence of Mps1 and Mad2. Together, this work reveals a critical mechanism that determines kinetochore activation of the spindle checkpoint.

Motif finding in DNA sequences based on skipping nonconserved positions in background Markov chains.

PubMed

Zhao, Xiaoyan; Sze, Sing-Hoi

2011-05-01

One strategy to identify transcription factor binding sites is through motif finding in upstream DNA sequences of potentially co-regulated genes. Despite extensive efforts, none of the existing algorithms perform very well. We consider a string representation that allows arbitrary ignored positions within the nonconserved portion of single motifs, and use O(2(l)) Markov chains to model the background distributions of motifs of length l while skipping these positions within each Markov chain. By focusing initially on positions that have fixed nucleotides to define core occurrences, we develop an algorithm to identify motifs of moderate lengths. We compare the performance of our algorithm to other motif finding algorithms on a few benchmark data sets, and show that significant improvement in accuracy can be obtained when the sites are sufficiently conserved within a given sample, while comparable performance is obtained when the site conservation rate is low. A software program (PosMotif ) and detailed results are available online at http://faculty.cse.tamu.edu/shsze/posmotif.

Virtual increase or latent loss? A reassessment of mangrove populations and their conservation in Guangdong, southern China.

PubMed

Peng, Yisheng; Zheng, Mingxuan; Zheng, Zhouxiang; Wu, Guichang; Chen, Yuechao; Xu, Hualin; Tian, Guanghong; Peng, Shenghua; Chen, Guizhu; Lee, Shing Yip

2016-08-30

Contrary to the global trend, the area of mangrove in Guangdong Province, southern China, has been increasing over the last two decades. Currently, three exotic mangrove species have been introduced for large-scale afforestation since 1985. A reassessment of the overall status of the mangrove species, habitat change, population of introduced species, was conducted through a comprehensive literature review as well as field investigations covering 96 sites. The success of conservation efforts is also evaluated. Upstream and high intertidal habitats are more vulnerable than downstream and lower intertidal ones, with habitat alteration being the biggest threats. Five mangrove species have narrow distributional extents with small populations, which could incur regional extinction. With the introduced species having naturalized at 42 sites, their role in mangrove management needs to be reconsidered. These findings collectively suggest a need to manage latent species loss and habitat degradation beyond the apparent increase in mangrove area and protection. Copyright © 2016 Elsevier Ltd. All rights reserved.

Dampened Hedgehog signaling but normal Wnt signaling in zebrafish without cilia

PubMed Central

Huang, Peng; Schier, Alexander F.

2009-01-01

Summary Cilia have been implicated in Hedgehog (Hh) and Wnt signaling in mouse but not in Drosophila. To determine whether the role of cilia is conserved in zebrafish, we generated maternal-zygotic (MZ) oval (ovl; ift88) mutants that lack all cilia. MZovl mutants display normal canonical and non-canonical Wnt signaling but show defects in Hh signaling. As in mouse, zebrafish cilia are required to mediate the activities of Hh, Ptc, Smo and PKA. However, in contrast to mouse Ift88 mutants, which show a dramatic reduction in Hh signaling, zebrafish MZovl mutants display dampened, but expanded, Hh pathway activity. This activity is largely due to gli1, the expression of which is fully dependent on Hh signaling in mouse but not in zebrafish. These results reveal a conserved requirement for cilia in transducing the activity of upstream regulators of Hh signaling but distinct phenotypic effects due to differential regulation and differing roles of transcriptional mediators. PMID:19700616

Level II scour analysis for Bridge 8 (ANDOTH00010008) on Town Highway 1, crossing Andover Branch, Andover, Vermont

USGS Publications Warehouse

Flynn, Robert H.; Wild, Emily C.

1997-01-01

This report provides the results of a detailed Level II analysis of scour potential at structure ANDOTH00010008 on Town Highway 1 crossing the Andover Branch, Andover , Vermont (figures 1–8). A Level II study is a basic engineering analysis of the site, including a quantitative analysis of stream stability and scour (U.S. Department of Transportation, 1993). Results of a Level I scour investigation also are included in Appendix E of this report. A Level I investigation provides a qualitative geomorphic characterization of the study site. Information on the bridge, gleaned from Vermont Agency of Transportation (VTAOT) files, was compiled prior to conducting Level I and Level II analyses and is found in Appendix D.The site is in the Green Mountain section of the New England physiographic province in south-central Vermont. The 5.30-mi2 drainage area is in a predominantly rural and forested basin. In the vicinity of the study site, the surface cover along the immediate banks, both upstream and downstream of the bridge, is grass while farther upstream and downstream, the surface cover is primarily forest.In the study area, the Andover Branch has an incised, straight channel with a slope of approximately 0.01 ft/ft, an average channel top width of 35 ft and an average bank height of 3 ft. The channel bed material ranges from gravel to boulder with a median grain size (D50) of 63.6 mm (0.209 ft). The geomorphic assessment at the time of the Level I and Level II site visit on August 27, 1996, indicated that the reach was stable.The Town Highway 1 crossing of the Andover Branch is a 54-ft-long, two-lane bridge consisting of one 51-foot steel-beam span (Vermont Agency of Transportation, written communication, March 28, 1995). The bridge is supported by vertical, concrete abutments with wingwalls. The channel is skewed approximately 45 degrees to the opening while the opening-skew-to-roadway is 30 degrees.A scour hole 0.7 ft deeper than the mean thalweg depth was observed approximately 52 feet downstream of the downstream face of the bridge during the Level I assessment. Scour countermeasures at the site include type-2 stone fill (less than 36 inches diameter) along the entire base length of the left and right abutments and along the left bank from 65 ft to 89 ft upstream. Type-1 stone fill was found along the right bank from the bridge to 47 ft upstream and along the left bank from 40 ft to 65 ft upstream. Additional details describing conditions at the site are included in the Level II Summary and Appendices D and E.Scour depths and rock rip-rap sizes were computed using the general guidelines described in Hydraulic Engineering Circular 18 (Richardson and others, 1995). Total scour at a highway crossing is comprised of three components: 1) long-term streambed degradation; 2) contraction scour (due to accelerated flow caused by a reduction in flow area at a bridge) and; 3) local scour (caused by accelerated flow around piers and abutments). Total scour is the sum of the three components. Equations are available to compute depths for contraction and local scour and a summary of the results of these computations follows.Contraction scour for all modelled flows ranged from 0.0 to 0.1 ft. The worst case contraction scour occurred at the 500-year discharge. Abutment scour ranged from 5.0 to 8.1 ft along the left abutment and from 2.1 to 4.6 ft along the right abutment. The worst-case abutment scour occurred at the 500-year discharge. Additional information on scour depths and depths to armoring are included in the section titled “Scour Results”. Scoured-streambed elevations, based on the calculated scour depths, are presented in tables 1 and 2. A cross-section of the scour computed at the bridge is presented in figure 8. Scour depths were calculated assuming an infinite depth of erosive material and a homogeneous particle-size distribution.It is generally accepted that the Froehlich equation (abutment scour) gives “excessively conservative estimates of scour depths” (Richardson and others, 1995, p. 47). Usually, computed scour depths are evaluated in combination with other information including (but not limited to) historical performance during flood events, the geomorphic stability assessment, existing scour protection measures, and the results of the hydraulic analyses. Therefore, scour depths adopted by VTAOT may differ from the computed values documented herein.

Cancer cachexia: mediators, signaling, and metabolic pathways.

PubMed

Fearon, Kenneth C H; Glass, David J; Guttridge, Denis C

2012-08-08

Cancer cachexia is characterized by a significant reduction in body weight resulting predominantly from loss of adipose tissue and skeletal muscle. Cachexia causes reduced cancer treatment tolerance and reduced quality and length of life, and remains an unmet medical need. Therapeutic progress has been impeded, in part, by the marked heterogeneity of mediators, signaling, and metabolic pathways both within and between model systems and the clinical syndrome. Recent progress in understanding conserved, molecular mechanisms of skeletal muscle atrophy/hypertrophy has provided a downstream platform for circumventing the variations and redundancy in upstream mediators and may ultimately translate into new targeted therapies. Copyright © 2012 Elsevier Inc. All rights reserved.

Finding functional features in Saccharomyces genomes by phylogenetic footprinting.

PubMed

Cliften, Paul; Sudarsanam, Priya; Desikan, Ashwin; Fulton, Lucinda; Fulton, Bob; Majors, John; Waterston, Robert; Cohen, Barak A; Johnston, Mark

2003-07-04

The sifting and winnowing of DNA sequence that occur during evolution cause nonfunctional sequences to diverge, leaving phylogenetic footprints of functional sequence elements in comparisons of genome sequences. We searched for such footprints among the genome sequences of six Saccharomyces species and identified potentially functional sequences. Comparison of these sequences allowed us to revise the catalog of yeast genes and identify sequence motifs that may be targets of transcriptional regulatory proteins. Some of these conserved sequence motifs reside upstream of genes with similar functional annotations or similar expression patterns or those bound by the same transcription factor and are thus good candidates for functional regulatory sequences.

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

None

Oak Ridge Associated Universities (ORAU), under the Oak Ridge Institute for Science and Education (ORISE) contract, collected split surface water samples with Nuclear Fuel Services (NFS) representatives on November 15, 2012. Representatives from the U.S. Nuclear Regulatory Commission and Tennessee Department of Environment and Conservation were also in attendance. Samples were collected at four surface water stations, as required in the approved Request for Technical Assistance number 11-018. These stations included Nolichucky River upstream (NRU), Nolichucky River downstream (NRD), Martin Creek upstream (MCU), and Martin Creek downstream (MCD). Both ORAU and NFS performed gross alpha and gross beta analyses, andmore » the results are compared using the duplicate error ratio (DER), also known as the normalized absolute difference. A DER {<=} 3 indicates that, at a 99% confidence interval, split sample results do not differ significantly when compared to their respective one standard deviation (sigma) uncertainty (ANSI N42.22). The NFS split sample report does not specify the confidence level of reported uncertainties (NFS 2012). Therefore, standard two sigma reporting is assumed and uncertainty values were divided by 1.96. In conclusion, all DER values were less than 3 and results are consistent with low (e.g., background) concentrations.« less

Turbofan Volume Dynamics Model for Investigations of Aero-Propulso-Servo-Elastic Effects in a Supersonic Commercial Transport

NASA Technical Reports Server (NTRS)

Connolly, Joseph W.; Kopasakis, George; Lemon, Kimberly A.

2010-01-01

A turbofan simulation has been developed for use in aero-propulso-servo-elastic coupling studies, on supersonic vehicles. A one-dimensional lumped volume approach is used whereby each component (fan, high-pressure compressor, combustor, etc.) is represented as a single volume using characteristic performance maps and conservation equations for continuity, momentum and energy. The simulation is developed in the MATLAB/SIMULINK (The MathWorks, Inc.) environment in order to facilitate controls development, and ease of integration with a future aero-servo-elastic vehicle model being developed at NASA Langley. The complete simulation demonstrated steady state results that closely match a proposed engine suitable for a supersonic business jet at the cruise condition. Preliminary investigation of the transient simulation revealed expected trends for fuel flow disturbances as well as upstream pressure disturbances. A framework for system identification enables development of linear models for controller design. Utilizing this framework, a transfer function modeling an upstream pressure disturbance s impacts on the engine speed is developed as an illustrative case of the system identification. This work will eventually enable an overall vehicle aero-propulso-servo-elastic model

Dams in the Amazon: Belo Monte and Brazil's hydroelectric development of the Xingu River Basin.

PubMed

Fearnside, Phillip M

2006-07-01

Hydroelectric dams represent major investments and major sources of environmental and social impacts. Powerful forces surround the decision-making process on public investments in the various options for the generation and conservation of electricity. Brazil's proposed Belo Monte Dam (formerly Kararaô) and its upstream counterpart, the Altamira Dam (better known by its former name of Babaquara) are at the center of controversies on the decision-making process for major infrastructure projects in Amazonia. The Belo Monte Dam by itself would have a small reservoir area (440 km2) and large installed capacity (11, 181.3 MW), but the Altamira/Babaquara Dam that would regulate the flow of the Xingu River (thereby increasing power generation at Belo Monte) would flood a vast area (6140 km2). The great impact of dams provides a powerful reason for Brazil to reassess its current policies that allocate large amounts of energy in the country's national grid to subsidized aluminum smelting for export. The case of Belo Monte and the five additional dams planned upstream (including the Altamira/Babaquara Dam) indicate the need for Brazil to reform its environmental assessment and licensing system to include the impacts of multiple interdependent projects.

Fungal Genes in Context: Genome Architecture Reflects Regulatory Complexity and Function

PubMed Central

Noble, Luke M.; Andrianopoulos, Alex

2013-01-01

Gene context determines gene expression, with local chromosomal environment most influential. Comparative genomic analysis is often limited in scope to conserved or divergent gene and protein families, and fungi are well suited to this approach with low functional redundancy and relatively streamlined genomes. We show here that one aspect of gene context, the amount of potential upstream regulatory sequence maintained through evolution, is highly predictive of both molecular function and biological process in diverse fungi. Orthologs with large upstream intergenic regions (UIRs) are strongly enriched in information processing functions, such as signal transduction and sequence-specific DNA binding, and, in the genus Aspergillus, include the majority of experimentally studied, high-level developmental and metabolic transcriptional regulators. Many uncharacterized genes are also present in this class and, by implication, may be of similar importance. Large intergenic regions also share two novel sequence characteristics, currently of unknown significance: they are enriched for plus-strand polypyrimidine tracts and an information-rich, putative regulatory motif that was present in the last common ancestor of the Pezizomycotina. Systematic consideration of gene UIR in comparative genomics, particularly for poorly characterized species, could help reveal organisms’ regulatory priorities. PMID:23699226

Gains and Losses of Transcription Factor Binding Sites in Saccharomyces cerevisiae and Saccharomyces paradoxus

PubMed Central

Schaefke, Bernhard; Wang, Tzi-Yuan; Wang, Chuen-Yi; Li, Wen-Hsiung

2015-01-01

Gene expression evolution occurs through changes in cis- or trans-regulatory elements or both. Interactions between transcription factors (TFs) and their binding sites (TFBSs) constitute one of the most important points where these two regulatory components intersect. In this study, we investigated the evolution of TFBSs in the promoter regions of different Saccharomyces strains and species. We divided the promoter of a gene into the proximal region and the distal region, which are defined, respectively, as the 200-bp region upstream of the transcription starting site and as the 200-bp region upstream of the proximal region. We found that the predicted TFBSs in the proximal promoter regions tend to be evolutionarily more conserved than those in the distal promoter regions. Additionally, Saccharomyces cerevisiae strains used in the fermentation of alcoholic drinks have experienced more TFBS losses than gains compared with strains from other environments (wild strains, laboratory strains, and clinical strains). We also showed that differences in TFBSs correlate with the cis component of gene expression evolution between species (comparing S. cerevisiae and its sister species Saccharomyces paradoxus) and within species (comparing two closely related S. cerevisiae strains). PMID:26220934

Monocyte-specific Accessibility of a Matrix Attachment Region in the Tumor Necrosis Factor Locus*

PubMed Central

Biglione, Sebastian; Tsytsykova, Alla V.; Goldfeld, Anne E.

2011-01-01

Regulation of TNF gene expression is cell type- and stimulus-specific. We have previously identified highly conserved noncoding regulatory elements within DNase I-hypersensitive sites (HSS) located 9 kb upstream (HSS−9) and 3 kb downstream (HSS+3) of the TNF gene, which play an important role in the transcriptional regulation of TNF in T cells. They act as enhancers and interact with the TNF promoter and with each other, generating a higher order chromatin structure. Here, we report a novel monocyte-specific AT-rich DNase I-hypersensitive element located 7 kb upstream of the TNF gene (HSS−7), which serves as a matrix attachment region in monocytes. We show that HSS−7 associates with topoisomerase IIα (Top2) in vivo and that induction of endogenous TNF mRNA expression is suppressed by etoposide, a Top2 inhibitor. Moreover, Top2 binds to and cleaves HSS−7 in in vitro analysis. Thus, HSS−7, which is selectively accessible in monocytes, can tether the TNF locus to the nuclear matrix via matrix attachment region formation, potentially promoting TNF gene expression by acting as a Top2 substrate. PMID:22027829

Genomic Structure of the Luciferase Gene from the Bioluminescent Beetle, Nyctophila cf. Caucasica

PubMed Central

Day, John C.; Chaichi, Mohammad J.; Najafil, Iraj; Whiteley, Andrew S.

2006-01-01

The gene coding for beetle luciferase, the enzyme responsible for bioluminescence in over two thousand coleopteran species has, to date, only been characterized from one Palearctic species of Lampyridae. Here we report the characterization of the luciferase gene from a female beetle of an Iranian lampyrid species, Nyctophila cf. caucasica (Coleoptera:Lampyridae). The luciferase gene was composed of seven exons, coding for 547 amino acids, separated by six introns spanning 1976 bp of genomic DNA. The deduced amino acid sequences of the luciferase gene of N. caucasica showed 98.9% homology to that of the Palearctic species Lampyris noctiluca. Analysis of the 810 bp upstream region of the luciferase gene revealed three TATA boxes and several other consensus transcriptional factor recognition sequences presenting evidence for a putative core promoter region conserved in Lampyrinae from -190 through to -155 upstream of the luciferase start codon. Along with the core promoter region the luciferase gene was compared with orthologous sequences from other lampyrid species and found to have greatest identity to Lampyris turkistanicus and Lampyris noctiluca. The significant sequence identity to the former is discussed in relation to taxonomic issues of Iranian lampyrids. PMID:20298115

Hedgehog activity controls opening of the primary mouth

PubMed Central

Tabler, Jacqueline M.; Bolger, Trióna G.; Wallingford, John; Liu, Karen J.

2014-01-01

To feed or breathe, the oral opening must connect with the gut. The foregut and oral tissues converge at the primary mouth, forming the buccopharyngeal membrane (BPM), a bilayer epithelium. Failure to form the opening between gut and mouth has significant ramifications, and many craniofacial disorders have been associated with defects in this process. Oral perforation is characterized by dissolution of the BPM, but little is known about this process. In humans, failure to form a continuous mouth opening is associated with mutations in Hedgehog (Hh) pathway members; however, the role of Hh in primary mouth development is untested. Here, we show, using Xenopus, that Hh signaling is necessary and sufficient to initiate mouth formation, and that Hh activation is required in a dose-dependent fashion to determine the size of the mouth. This activity lies upstream of the previously demonstrated role for Wnt signal inhibition in oral perforation. We then turn to mouse mutants to establish that SHH and Gli3 are indeed necessary for mammalian mouth development. Our data suggest that Hh-mediated BPM persistence may underlie oral defects in human craniofacial syndromes. PMID:25300580

Can retention forestry help conserve biodiversity? A meta-analysis

PubMed Central

Fedrowitz, Katja; Koricheva, Julia; Baker, Susan C; Lindenmayer, David B; Palik, Brian; Rosenvald, Raul; Beese, William; Franklin, Jerry F; Kouki, Jari; Macdonald, Ellen; Messier, Christian; Sverdrup-Thygeson, Anne; Gustafsson, Lena

2014-01-01

Industrial forestry typically leads to a simplified forest structure and altered species composition. Retention of trees at harvest was introduced about 25 years ago to mitigate negative impacts on biodiversity, mainly from clearcutting, and is now widely practiced in boreal and temperate regions. Despite numerous studies on response of flora and fauna to retention, no comprehensive review has summarized its effects on biodiversity in comparison to clearcuts as well as un-harvested forests. Using a systematic review protocol, we completed a meta-analysis of 78 studies including 944 comparisons of biodiversity between retention cuts and either clearcuts or un-harvested forests, with the main objective of assessing whether retention forestry helps, at least in the short term, to moderate the negative effects of clearcutting on flora and fauna. Retention cuts supported higher richness and a greater abundance of forest species than clearcuts as well as higher richness and abundance of open-habitat species than un-harvested forests. For all species taken together (i.e. forest species, open-habitat species, generalist species and unclassified species), richness was higher in retention cuts than in clearcuts. Retention cuts had negative impacts on some species compared to un-harvested forest, indicating that certain forest-interior species may not survive in retention cuts. Similarly, retention cuts were less suitable for some open-habitat species compared with clearcuts. Positive effects of retention cuts on richness of forest species increased with proportion of retained trees and time since harvest, but there were not enough data to analyse possible threshold effects, that is, levels at which effects on biodiversity diminish. Spatial arrangement of the trees (aggregated vs. dispersed) had no effect on either forest species or open-habitat species, although limited data may have hindered our capacity to identify responses. Results for different comparisons were largely consistent among taxonomic groups for forest and open-habitat species, respectively. Synthesis and applications. Our meta-analysis provides support for wider use of retention forestry since it moderates negative harvesting impacts on biodiversity. Hence, it is a promising approach for integrating biodiversity conservation and production forestry, although identifying optimal solutions between these two goals may need further attention. Nevertheless, retention forestry will not substitute for conservation actions targeting certain highly specialized species associated with forest-interior or open-habitat conditions. Our meta-analysis provides support for wider use of retention forestry since it moderates negative harvesting impacts on biodiversity. Hence, it is a promising approach for integrating biodiversity conservation and production forestry, although identifying optimal solutions between these two goals may need further attention. Nevertheless, retention forestry will not substitute for conservation actions targeting certain highly specialized species associated with forest-interior or open-habitat conditions. PMID:25552747

Can retention forestry help conserve biodiversity? A meta-analysis.

PubMed

Fedrowitz, Katja; Koricheva, Julia; Baker, Susan C; Lindenmayer, David B; Palik, Brian; Rosenvald, Raul; Beese, William; Franklin, Jerry F; Kouki, Jari; Macdonald, Ellen; Messier, Christian; Sverdrup-Thygeson, Anne; Gustafsson, Lena

2014-12-01

Industrial forestry typically leads to a simplified forest structure and altered species composition. Retention of trees at harvest was introduced about 25 years ago to mitigate negative impacts on biodiversity, mainly from clearcutting, and is now widely practiced in boreal and temperate regions. Despite numerous studies on response of flora and fauna to retention, no comprehensive review has summarized its effects on biodiversity in comparison to clearcuts as well as un-harvested forests. Using a systematic review protocol, we completed a meta-analysis of 78 studies including 944 comparisons of biodiversity between retention cuts and either clearcuts or un-harvested forests, with the main objective of assessing whether retention forestry helps, at least in the short term, to moderate the negative effects of clearcutting on flora and fauna. Retention cuts supported higher richness and a greater abundance of forest species than clearcuts as well as higher richness and abundance of open-habitat species than un-harvested forests. For all species taken together (i.e. forest species, open-habitat species, generalist species and unclassified species), richness was higher in retention cuts than in clearcuts. Retention cuts had negative impacts on some species compared to un-harvested forest, indicating that certain forest-interior species may not survive in retention cuts. Similarly, retention cuts were less suitable for some open-habitat species compared with clearcuts. Positive effects of retention cuts on richness of forest species increased with proportion of retained trees and time since harvest, but there were not enough data to analyse possible threshold effects, that is, levels at which effects on biodiversity diminish. Spatial arrangement of the trees (aggregated vs. dispersed) had no effect on either forest species or open-habitat species, although limited data may have hindered our capacity to identify responses. Results for different comparisons were largely consistent among taxonomic groups for forest and open-habitat species, respectively. Synthesis and applications . Our meta-analysis provides support for wider use of retention forestry since it moderates negative harvesting impacts on biodiversity. Hence, it is a promising approach for integrating biodiversity conservation and production forestry, although identifying optimal solutions between these two goals may need further attention. Nevertheless, retention forestry will not substitute for conservation actions targeting certain highly specialized species associated with forest-interior or open-habitat conditions. Our meta-analysis provides support for wider use of retention forestry since it moderates negative harvesting impacts on biodiversity. Hence, it is a promising approach for integrating biodiversity conservation and production forestry, although identifying optimal solutions between these two goals may need further attention. Nevertheless, retention forestry will not substitute for conservation actions targeting certain highly specialized species associated with forest-interior or open-habitat conditions.

Distinct Escape Pathway by Hepatitis C Virus Genotype 1a from a Dominant CD8+ T Cell Response by Selection of Altered Epitope Processing.

PubMed

Walker, Andreas; Skibbe, Kathrin; Steinmann, Eike; Pfaender, Stephanie; Kuntzen, Thomas; Megger, Dominik A; Groten, Svenja; Sitek, Barbara; Lauer, Georg M; Kim, Arthur Y; Pietschmann, Thomas; Allen, Todd M; Timm, Joerg

2016-01-01

Antiviral CD8(+) T cells are a key component of the adaptive immune response against HCV, but their impact on viral control is influenced by preexisting viral variants in important target epitopes and the development of viral escape mutations. Immunodominant epitopes highly conserved across genotypes therefore are attractive for T cell based prophylactic vaccines. Here, we characterized the CD8(+) T cell response against the highly conserved HLA-B*51-restricted epitope IPFYGKAI1373-1380 located in the helicase domain of NS3 in people who inject drugs (PWID) exposed predominantly to HCV genotypes 1a and 3a. Despite this epitope being conserved in both genotypes, the corresponding CD8(+) T cell response was detected only in PWID infected with genotype 3a and HCV-RNA negative PWID, but not in PWID infected with genotype 1a. In genotype 3a, the detection of strong CD8(+) T cell responses was associated with epitope variants in the autologous virus consistent with immune escape. Analysis of viral sequences from multiple cohorts confirmed HLA-B*51-associated escape mutations inside the epitope in genotype 3a, but not in genotype 1a. Here, a distinct substitution in the N-terminal flanking region located 5 residues upstream of the epitope (S1368P; P = 0.00002) was selected in HLA-B*51-positive individuals. Functional assays revealed that the S1368P substitution impaired recognition of target cells presenting the endogenously processed epitope. The results highlight that, despite an epitope being highly conserved between two genotypes, there are major differences in the selected viral escape pathways and the corresponding T cell responses. HCV is able to evolutionary adapt to CD8(+) T cell immune pressure in multiple ways. Beyond selection of mutations inside targeted epitopes, this study demonstrates that HCV inhibits epitope processing by modification of the epitope flanking region under T cell immune pressure. Selection of a substitution five amino acids upstream of the epitope underlines that efficient antigen presentation strongly depends on its larger sequence context and that blocking of the multistep process of antigen processing by mutation is exploited also by HCV. The pathways to mutational escape of HCV are to some extent predictable but are distinct in different genotypes. Importantly, the selected escape pathway of HCV may have consequences for the destiny of antigen-specific CD8(+) T cells. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Local conservation laws in spin-\\frac{1}{2} XY chains with open boundary conditions

NASA Astrophysics Data System (ADS)

Fagotti, Maurizio

2016-06-01

We revisit the conserved quantities of the spin-\\frac{1}{2} XY model with open boundary conditions. In the absence of a transverse field, we find new families of local charges and show that half of the seeming conservation laws are conserved only if the number of sites is odd. In even chains the set of noninteracting charges is abelian, like in the periodic case when the number of sites is odd. In odd chains the set is doubled and becomes non-abelian, like in even periodic chains. The dependence of the charges on the parity of the chain’s size undermines the common belief that the thermodynamic limit of diagonal ensembles exists. We consider also the transverse-field Ising chain, where the situation is more ordinary. The generalization to the XY model in a transverse field is not straightforward and we propose a general framework to carry out similar calculations. We conjecture the form of the bulk part of the local charges and discuss the emergence of quasilocal conserved quantities. We provide evidence that in a region of the parameter space there is a reduction of the number of quasilocal conservation laws invariant under chain inversion. As a by-product, we study a class of block-Toeplitz-plus-Hankel operators and identify the conditions that their symbols satisfy in order to commute with a given block-Toeplitz.

Innovations in Agriculture in Oregon: Farmers Irrigation District Improves Water Quality, Maximizes Water Conservation, and Generates Clean, Renewable Energy

EPA Pesticide Factsheets

The Hood River Farmers Irrigation District used $36.2 million in CWSRF loans for a multiple-year endeavor to convert the open canal system to a piped, pressurized irrigation system to maximize water conservation and restore reliable water delivery to crops

Exploring the Professional Ideals of Christian Teachers from Conservative Protestant Schools in the Netherlands

ERIC Educational Resources Information Center

Boele-de Bruin, H. L.; de Muynck, A.

2018-01-01

Professional ideals arise from personal worldviews and specify teachers' professional identities. This study aimed to explore how faith is present in the professional ideals of Christian teachers. The professional ideals of 107 Dutch teachers from conservative Protestant primary and secondary schools were explored using an open-ended…

18 CFR 37.6 - Information to be posted on the OASIS.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 18 Conservation of Power and Water Resources 1 2013-04-01 2013-04-01 false Information to be posted on the OASIS. 37.6 Section 37.6 Conservation of Power and Water Resources FEDERAL ENERGY REGULATORY COMMISSION, DEPARTMENT OF ENERGY REGULATIONS UNDER THE FEDERAL POWER ACT OPEN ACCESS SAME-TIME...

18 CFR 37.6 - Information to be posted on the OASIS.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 18 Conservation of Power and Water Resources 1 2014-04-01 2014-04-01 false Information to be posted on the OASIS. 37.6 Section 37.6 Conservation of Power and Water Resources FEDERAL ENERGY REGULATORY COMMISSION, DEPARTMENT OF ENERGY REGULATIONS UNDER THE FEDERAL POWER ACT OPEN ACCESS SAME-TIME...

18 CFR 37.6 - Information to be posted on the OASIS.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 18 Conservation of Power and Water Resources 1 2012-04-01 2012-04-01 false Information to be posted on the OASIS. 37.6 Section 37.6 Conservation of Power and Water Resources FEDERAL ENERGY REGULATORY COMMISSION, DEPARTMENT OF ENERGY REGULATIONS UNDER THE FEDERAL POWER ACT OPEN ACCESS SAME-TIME...

76 FR 40927 - Endangered and Threatened Wildlife and Plants; Draft Habitat Conservation Plan and Environmental...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-07-12

...] Endangered and Threatened Wildlife and Plants; Draft Habitat Conservation Plan and Environmental Assessment..., a golf and racquet club facility, a network of man-made navigable lagoons, a restaurant, commercial... year at sea, forage in the open ocean, and breed on Kauai. Beginning in March and April, adults...

18 CFR 37.8 - Obligations of OASIS users.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 18 Conservation of Power and Water Resources 1 2011-04-01 2011-04-01 false Obligations of OASIS users. 37.8 Section 37.8 Conservation of Power and Water Resources FEDERAL ENERGY REGULATORY COMMISSION, DEPARTMENT OF ENERGY REGULATIONS UNDER THE FEDERAL POWER ACT OPEN ACCESS SAME-TIME INFORMATION SYSTEMS § 37.8...

75 FR 22620 - Upper Klamath, Lower Klamath, Tule Lake, Bear Valley, and Clear Lake National Wildlife Refuges...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-04-29

.... In addition to outlining broad management direction on conserving wildlife and their habitats, CCPs... ensure the best possible approach to wildlife, plant, and habitat conservation, while providing for... hardstem-cattail marsh and open water, along with 30 acres of forested uplands. These habitats serve as...

Structural basis for the facilitative diffusion mechanism by SemiSWEET transporter

NASA Astrophysics Data System (ADS)

Lee, Yongchan; Nishizawa, Tomohiro; Yamashita, Keitaro; Ishitani, Ryuichiro; Nureki, Osamu

2015-01-01

SWEET family proteins mediate sugar transport across biological membranes and play crucial roles in plants and animals. The SWEETs and their bacterial homologues, the SemiSWEETs, are related to the PQ-loop family, which is characterized by highly conserved proline and glutamine residues (PQ-loop motif). Although the structures of the bacterial SemiSWEETs were recently reported, the conformational transition and the significance of the conserved motif in the transport cycle have remained elusive. Here we report crystal structures of SemiSWEET from Escherichia coli, in the both inward-open and outward-open states. A structural comparison revealed that SemiSWEET undergoes an intramolecular conformational change in each protomer. The conserved PQ-loop motif serves as a molecular hinge that enables the ‘binder clip-like’ motion of SemiSWEET. The present work provides the framework for understanding the overall transport cycles of SWEET and PQ-loop family proteins.

Distinctiveness, use, and value of midwestern oak savannas and woodlands as avian habitats

USGS Publications Warehouse

Grundel, R.; Pavlovic, N.B.

2007-01-01

Oak savannas and woodlands historically covered millions of hectares in the midwestern United States but are rare today. We evaluated the ecological distinctiveness and conservation value of savannas and woodlands by examining bird distributions across a fire-maintained woody-vegetation gradient in northwest Indiana encompassing five habitats—open habitats with low canopy cover, savannas, woodlands, scrublands, and forests—during migration, breeding, and overwintering. Savannas and woodlands were significantly different in overall bird species composition from open and forest habitats but were often intermediate between open and forest in guild densities. Few bird species were consistently and highly concentrated in savannas or woodlands, and the Red-headed Woodpecker (Melanerpes erythrocephalus) was the only species significantly more abundant in savannas and woodlands than in open, scrub, and forest habitats. Fire frequency over a 15-year interval was a significant predictor of bird community composition and was positively related to species diversity, spring transient migrant density, and density of the most threatened species. Each habitat type had characteristics potentially important for avian conservation. Scrub had the highest density of transient migrants, which suggests it plays an important role as migration stopover habitat. More species were significantly concentrated in open or forest habitats than in the other habitats. Lack of species concentration and intermediate community composition suggested that birds experienced savannas and woodlands more as ecotones than as habitats distinct from forests or grasslands. However, this intermediate character can benefit conservation, as evidenced by savannas and woodlands having the highest density of the most threatened species along this woody-vegetation gradient.

Evaluation of the Biological Effects of the Northwest Power Conservation Council's Mainstem Amendment on the Fisheries Upstream and Downstream of Libby Dam, Montana, 2007-2008 Annual Report.

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

Sylvester, Ryan; Stephens, Brian; Tohtz, Joel

2009-04-03

A new project began in 2005 to monitor the biological and physical effects of improved operations of Hungry Horse and Libby Dams, Montana, called for by the Northwest Power and Conservation Council (NPCC) Mainstem Amendment. This operating strategy was designed to benefit resident fish impacted by hydropower and flood control operations. Under the new operating guidelines, July through September reservoir drafts will be limited to 10 feet from full pool during the highest 80% of water supply years and 20 feet from full pool during the lowest 20% of water supply (drought) years. Limits were also established on how rapidlymore » discharge from the dams can be increased or decreased depending on the season. The NPCC also directed the federal agencies that operate Libby and Hungry Horse Dams to implement a new flood control strategy (VARQ) and directed Montana Fish, Wildlife & Parks to evaluate biological responses to this operating strategy. The Mainstem Amendment operating strategy has not been fully implemented at the Montana dams as of June 2008 but the strategy will be implemented in 2009. This report highlights the monitoring methods used to monitor the effects of the Mainstem Amendment operations on fishes, habitat, and aquatic invertebrates upstream and downstream of Libby Dam. We also present initial assessments of data and the effects of various operating strategies on physical and biological components of the systems upstream and downstream of Libby Dam. Annual electrofishing surveys in the Kootenai River and selected tributaries, along with gill net surveys in the reservoir, are being used to quantify the impacts of dam operations on fish populations upstream and downstream of Libby Dam. Scales and otoliths are being used to determine the age structure and growth of focal species. Annual population estimates and tagging experiments provide estimates of survival and growth in the mainstem Kootenai River and selected tributaries. Radio telemetry will be used to validate an existing Instream Flow Incremental Methodology (IFIM) model developed for the Kootenai River and will also be used to assess the effect of changes in discharge on fish movements and habitat use downstream of Libby Dam. Passive integrated transponder (PIT) tags will be injected into rainbow, bull, and cutthroat trout throughout the mainstem Kootenai River and selected tributaries to provide information on growth, survival, and migration patterns in relation to abiotic and biotic variables. Model simulations (RIVBIO) are used to calculate the effects of dam operations on the wetted perimeter and benthic biomass in the Kootenai River below Libby Dam. Additional models (IFIM) will also be used to evaluate the impacts of dam operations on the amount of available habitat for different life stages of rainbow and bull trout in the Kootenai River.« less

Source identification of Florida Bay's methylmercury problem: Mainland runoff versus atmospheric deposition and in situ production

USGS Publications Warehouse

Rumbold, Darren G.; Evans, David W.; Niemczyk, Sharon; Fink, Larry E.; Laine, Krysten A.; Howard, Nicole; Krabbenhoft, David P.; Zucker, Mark

2011-01-01

The first advisory to limit consumption of Florida Bay fish due to mercury was issued in 1995. Studies done by others in the late 1990s found elevated water column concentrations of both total Hg (THg) and methylmercury (MeHg) in creeks discharging from the Everglades, which had its own recognized mercury problem. To investigate the significance of allochthonous MeHg discharging from the upstream freshwater Everglades, we collected surface water and sediment along two transects from 2000 to 2002. Concentrations of THg and MeHg, ranging from 0.36 ng THg/L to 5.98 ng THg/L and from <0.02 ng MeHg/L to 1.79 ng MeHg/L, were elevated in the mangrove transition zone when compared both to upstream canals and the open waters of Florida Bay. Sediment concentrations ranged from 5.8 ng THg/g to 145.6 ng THg/g and from 0.05 ng MeHg/g to 5.4 ng MeHg/g, with MeHg as a percentage of THg occasionally elevated in the open bay. Methylation assays indicated that sediments from Florida Bay have the potential to methylate Hg. Assessment of mass loading suggests that canals delivering stormwater from the northern Everglades are not as large a source as direct atmospheric deposition and in situ methylation, especially within the mangrove transition zone.

Mrp--a new auxiliary gene essential for optimal expression of methicillin resistance in Staphylococcus aureus.

PubMed

Wu, S W; De Lencastre, H

1999-01-01

Screening of a library of Tn551 insertional mutants selected for reduction in the methicillin resistance level of the parental Staphylococcus aureus strain COL resulted in the isolation of mutant RUSA266 in which the minimal inhibitory concentration (MIC) of the parent was reduced from 1,600 to 1.5 micrograms/mL. Cloning and sequencing of the vicinity of the insertion site omega 726 identified an open reading frame (orf1365) encoding a very large polypeptide of more than 1,365 amino acids. A unique feature of the deduced amino acid sequence was the presence of multiple tandem repeats of 75 amino acids in the polypeptide, reminiscent of the structure of high-molecular-weight cell-surface proteins EF* and Emb identified in some streptococcal strains. Mutant RUSA266 with the inactivated gene, which we shall provisionally refer to as mrp (for multiple repeat polypeptide), produced a peptidoglycan with altered muropeptide composition, and both the reduced antibiotic resistance and the altered cell wall composition were co-transduced in back-crosses into the parental strain COL. Additional sequencing upstream of mrp has revealed that this gene was part of a five-gene cluster occupying a 9.2-kb region of the staphylococcal chromosome and was composed of glmM (directly upstream of mrp), two open reading frames orf310 and orf269 coding for two hypothetical proteins, and the gene encoding the staphylococcal arginase (arg). Transcriptional analysis demonstrated that the five genes in the cluster were transcribed together.

50 CFR 660.319 - Open access fishery gear identification and marking.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 50 Wildlife and Fisheries 11 2011-10-01 2011-10-01 false Open access fishery gear identification and marking. 660.319 Section 660.319 Wildlife and Fisheries FISHERY CONSERVATION AND MANAGEMENT, NATIONAL OCEANIC AND ATMOSPHERIC ADMINISTRATION, DEPARTMENT OF COMMERCE (CONTINUED) FISHERIES OFF WEST...

Comparison of outcomes of permanently closed and periodically harvested coral reef reserves.

PubMed

Bartlett, C Y; Manua, C; Cinner, J; Sutton, S; Jimmy, R; South, R; Nilsson, J; Raina, J

2009-12-01

In many areas of the developing world, the establishment of permanent marine reserves is inhibited by cultural norms or socioeconomic pressures. Community conserved areas that are periodically harvested are increasingly being implemented as fisheries management tools, but few researchers have empirically compared them with permanently closed reserves. We used a hierarchical control-impact experimental design to compare the abundance and biomass of reef fishes, invertebrates, and substrate composition in periodically harvested and permanent reserves and in openly fished (control sites) of the South Pacific island country of Vanuatu. Fished species had significantly higher biomass in periodically harvested reserves than in adjacent openly fished areas. We did not detect differences in substratum composition between permanent reserves and openly fished areas or between permanent reserves and periodically harvested reserves. Giant clams (tridacnids) and top shells (Trochus niloticus) were vulnerable to periodic harvest, and we suggest that for adequate management of these species, periodically harvested community conservation areas be used in conjunction with other management strategies. Periodic harvest within reserves is an example of adaptive and flexible management that may meet conservation goals and that is suited to the social, economic, and cultural contexts of many coastal communities in the developing world.

Tentative Study on Performance of Darriues-Type Hydroturbine Operated in Small Open Water Channel

NASA Astrophysics Data System (ADS)

Matsushita, D.; Moriyama, R.; Nakashima, K.; Watanabe, S.; Okuma, K.; Furukawa, A.

2014-03-01

The development of small hydropower is one of the realistic and preferable utilizations of renewable energy, but the extra-low head hydropower less than 2 m is almost undeveloped yet for some reasons. The authors have developed several types of Darrieus-type hydro-turbine system, and among them, the Darrieus-turbine with a wear and a nozzle installed upstream of turbine is so far in success to obtain more output power, i.e. more shaft torque, by gathering all water into the turbine. However, there can several cases exist, in which installing the wear covering all the flow channel width is unrealistic. Then, in the present study, the hydraulic performances of Darrieus-type hydro-turbine with the inlet nozzle is investigated, putting alone in a small open channel without upstream wear. In the experiment, the five-bladed Darrieus-type runner with the pitch-circle diameter of 300 mm and the blade span of 300 mm is vertically installed in the open channel with the width of 1,200 mm. The effectiveness of the shape of the inlet nozzle is also examined using two types of two-dimensional symmetric nozzle, the straight line nozzle (SL nozzle) with the converging angle of 45 degrees and the half diameter curved nozzle (HD nozzle) whose radius is a half diameter of runner pitch circle. Inlet and outlet nozzle widths are in common for the both nozzles, which are 540 mm and 240 mm respectively. All the experiments are carried out under the conditions with constant flow rate and downstream water level, and performances are evaluated by measured output torque and the measured head difference between the water levels upstream and downstream of the turbine. As a result, it is found that the output power is remarkably increased by installing the inlet nozzle, and the turbine with SL nozzle produces larger power than that with HD nozzle. However, the peak efficiency is deteriorated in both cases. The speed ratio defined by the rotor speed divided by the downstream water velocity at the peak efficiency is larger in both cases with the inlet nozzle, partly due to the increase of inflow velocity into the turbine. In order to understand the cause of the differences of power, i.e. torque characteristics of the turbine with SL and HD nozzles, twodimensional CFD simulation is carried out. It is found that the instantaneous torque variation is important for the overall turbine performances, indicating the possibility of further performance improvement through the optimization of nozzle geometry.

Nucleosome exclusion from the interspecies-conserved central AT-rich region of the Ars insulator.

PubMed

Takagi, Haruna; Inai, Yuta; Watanabe, Shun-ichiro; Tatemoto, Sayuri; Yajima, Mamiko; Akasaka, Koji; Yamamoto, Takashi; Sakamoto, Naoaki

2012-01-01

The Ars insulator is a boundary element identified in the upstream region of the arylsulfatase (HpArs) gene in the sea urchin, Hemicentrotus pulcherrimus, and possesses the ability to both block enhancer-promoter communications and protect transgenes from silent chromatin. To understand the molecular mechanism of the Ars insulator, we investigated the correlation between chromatin structure, DNA structure and insulator activity. Nuclease digestion of nuclei isolated from sea urchin embryos revealed the presence of a nuclease-hypersensitive site within the Ars insulator. Analysis of micrococcal nuclease-sensitive sites in the Ars insulator, reconstituted with nucleosomes, showed the exclusion of nucleosomes from the central AT-rich region. Furthermore, the central AT-rich region in naked DNA was sensitive to nucleotide base modification by diethylpyrocarbonate (DEPC). These observations suggest that non-B-DNA structures in the central AT-rich region may inhibit nucleosomal formation, which leads to nuclease hypersensitivity. Furthermore, comparison of nucleotide sequences between the HpArs gene and its ortholog in Strongylocentrotus purpuratus revealed that the central AT-rich region of the Ars insulator is conserved, and this conserved region showed significant enhancer blocking activity. These results suggest that the central AT-rich nucleosome-free region plays an important role in the function of the Ars insulator.

Projected risk of population declines for native fish species in the Upper Mississippi River

USGS Publications Warehouse

Crimmins, S.M.; Boma, P.; Thogmartin, W.E.

2015-01-01

Conservationists are in need of objective metrics for prioritizing the management of habitats. For individual species, the threat of extinction is often used to prioritize what species are in need of conservation action. Using long-term monitoring data, we applied a Bayesian diffusion approximation to estimate quasi-extinction risk for 54 native fish species within six commercial navigation reaches along a 1350-km gradient of the upper Mississippi River system. We found a strong negative linear relationship between quasi-extinction risk and distance upstream. For some species, quasi-extinction estimates ranged from nearly zero in some reaches to one in others, suggesting substantial variability in threats facing individual river reaches. We found no evidence that species traits affected quasi-extinction risk across the entire system. Our results indicate that fishes within the upper Mississippi River system face localized threats that vary across river impact gradients. This suggests that conservation actions should be focused on local habitat scales but should also consider the additive effects on downstream conditions. We also emphasize the need for identification of proximate mechanisms behind observed and predicted population declines, as conservation actions will require mitigation of such mechanisms. Published 2014. This article is a U.S. Government work and is in the public domain in the USA.

A subset of conserved mammalian long non-coding RNAs are fossils of ancestral protein-coding genes.

PubMed

Hezroni, Hadas; Ben-Tov Perry, Rotem; Meir, Zohar; Housman, Gali; Lubelsky, Yoav; Ulitsky, Igor

2017-08-30

Only a small portion of human long non-coding RNAs (lncRNAs) appear to be conserved outside of mammals, but the events underlying the birth of new lncRNAs in mammals remain largely unknown. One potential source is remnants of protein-coding genes that transitioned into lncRNAs. We systematically compare lncRNA and protein-coding loci across vertebrates, and estimate that up to 5% of conserved mammalian lncRNAs are derived from lost protein-coding genes. These lncRNAs have specific characteristics, such as broader expression domains, that set them apart from other lncRNAs. Fourteen lncRNAs have sequence similarity with the loci of the contemporary homologs of the lost protein-coding genes. We propose that selection acting on enhancer sequences is mostly responsible for retention of these regions. As an example of an RNA element from a protein-coding ancestor that was retained in the lncRNA, we describe in detail a short translated ORF in the JPX lncRNA that was derived from an upstream ORF in a protein-coding gene and retains some of its functionality. We estimate that ~ 55 annotated conserved human lncRNAs are derived from parts of ancestral protein-coding genes, and loss of coding potential is thus a non-negligible source of new lncRNAs. Some lncRNAs inherited regulatory elements influencing transcription and translation from their protein-coding ancestors and those elements can influence the expression breadth and functionality of these lncRNAs.

Level II scour analysis for Bridge 38 (ANDOVT00110038) on State Route 11, crossing the Middle Branch Williams River, Andover, Vermont

USGS Publications Warehouse

Striker, Lora K.; Hammond, Robert E.

1997-01-01

This report provides the results of a detailed Level II analysis of scour potential at structure ANDOVT00110038 on State Route 11 crossing the Middle Branch Williams River, Andover, Vermont (figures 1–8). A Level II study is a basic engineering analysis of the site, including a quantitative analysis of stream stability and scour (U.S. Department of Transportation, 1993). Results of a Level I scour investigation also are included in Appendix E of this report. A Level I investigation provides a qualitative geomorphic characterization of the study site. Information on the bridge, gleaned from Vermont Agency of Transportation (VTAOT) files, was compiled prior to conducting Level I and Level II analyses and is found in Appendix D. The site is in the Green Mountain section of the New England physiographic province in south central Vermont. The 5.65-mi2 drainage area is in a predominantly rural and forested basin. Upstream and downstream of the study site banks and overbanks are forested. In the study area, the Middle Branch Williams River has an incised, sinuous channel with a slope of approximately 0.02 ft/ft, an average channel top width of 44 ft and an average bank height of 4 ft. The channel bed material ranges from gravel to boulders with a median grain size (D50) of 54.0 mm (0.177 ft). The geomorphic assessment at the time of the Level I and Level II site visit on September 5, 1996, indicated that the reach was stable. The State Route 11 crossing of the Middle Branch Williams River is a 33-ft-long, two-lane bridge consisting of one 31-foot concrete T-beam span (Vermont Agency of Transportation, written communication, March 29, 1995). The bridge is supported by vertical, concrete abutments with wingwalls. The channel is skewed approximately 55 degrees to the opening while the measured opening-skew-to-roadway is 45 degrees. There were no scour problems observed during the Level I assessment. Type-4 stone fill (less than 60 inches diameter) and type-3 stone fill (less than 48 inches diameter) was present on the left bank upstream and right bank upstream respectively. Type-2 stone fill (less than 36 inches diameter) was present in the upstream left wing wall area. Additional details describing conditions at the site are included in the Level II Summary and Appendices D and E. Scour depths and recommended rock rip-rap sizes were computed using the general guidelines described in Hydraulic Engineering Circular 18 (Richardson and others, 1995). Total scour at a highway crossing is comprised of three components: 1) long-term streambed degradation; 2) contraction scour (due to accelerated flow caused by a reduction in flow area at a bridge) and; 3) local scour (caused by accelerated flow around piers and abutments). Total scour is the sum of the three components. Equations are available to compute depths for contraction and local scour and a summary of the results of these computations follows. Contraction scour for all modelled flows ranged from 1.8 to 3.4 ft. The worst-case contraction scour occurred at the 500-year flow. Abutment scour ranged from 12.0 to 14.0 ft. The worst-case abutment scour occurred at the 500-year flow at the right abutment. Additional information on scour depths and depths to armoring are included in the section titled “Scour Results”. Scoured-streambed elevations, based on the calculated scour depths, are presented in tables 1 and 2. A cross-section of the scour computed at the bridge is presented in figure 8. Scour depths were calculated assuming an infinite depth of erosive material and a homogeneous particle-size distribution. It is generally accepted that the Froehlich equation (abutment scour) gives “excessively conservative estimates of scour depths” (Richardson and others, 1995, p. 47). Usually, computed scour depths are evaluated in combination with other information including (but not limited to) historical performance during flood events, the geomorphic stability assessment, existing scour protection measures, and the results of the hydraulic analyses. Therefore, scour depths adopted by VTAOT may differ from the computed values documented herein.

Level II scour analysis for Bridge 22 (JAY-TH00400022) on Town Highway 40, crossing Jay Branch, Jay, Vermont

USGS Publications Warehouse

Ivanoff, Michael A.; Song, Donald L.

1997-01-01

8). A Level II study is a basic engineering analysis of the site, including a quantitative analysis of stream stability and scour (U.S. Department of Transportation, 1993). Results of a Level I scour investigation also are included in Appendix E of this report. A Level I investigation provides a qualitative geomorphic characterization of the study site. Information on the bridge, gleaned from Vermont Agency of Transportation (VTAOT) files, was compiled prior to conducting Level I and Level II analyses and is found in Appendix D. The site is in the Green Mountain section of the New England physiographic province in northern Vermont. The 2.15-mi2 drainage area is in a predominantly rural and forested basin. In the vicinity of the study site, the surface cover is primarily pasture on the upstream and downstream left overbank while the immediate banks have dense woody vegetation. The downstream right overbank of the bridge is forested. In the study area, Jay Branch Tributary has an incised, sinuous channel with a slope of approximately 0.02 ft/ft, an average channel top width of 26 ft and an average bank height of 3 ft. The channel bed material ranges from gravel to cobble with a median grain size (D50) of 40.5 mm (0.133 ft). The geomorphic assessment at the time of the Level I and Level II site visit on June 7, 1995, indicated that the reach was stable. The Town Highway 40 crossing of Jay Branch Tributary is a 27-ft-long, two-lane bridge consisting of one 25-foot steel-beam span (Vermont Agency of Transportation, written communication, March 6, 1995). The opening length of the structure parallel to the bridge face is 23.5 ft. The bridge is supported by vertical, concrete abutments with wingwalls. The channel skew and the opening-skew-to-roadway are zero degrees. The scour counter-measures at the site included type-2 stone fill (less than 36 inches diameter) at the upstream end of the left and right abutments, at the upstream right wingwall, and at the downstream left wingwall. There was also type-3 stone fill (less than 48 inches diameter) at the upstream left and downstream right wingwall. Additional details describing conditions at the site are included in the Level II Summary and Appendices D and E. Scour depths and recommended rock rip-rap sizes were computed using the general guidelines described in Hydraulic Engineering Circular 18 (Richardson and others, 1995). Total scour at a highway crossing is comprised of three components: 1) long-term streambed degradation; 2) contraction scour (due to accelerated flow caused by a reduction in flow area at a bridge) and; 3) local scour (caused by accelerated flow around piers and abutments). Total scour is the sum of the three components. Equations are available to compute depths for contraction and local scour and a summary of the results of these computations follows. Contraction scour for all modelled flows ranged from 0.7 to 1.1 ft. The worst-case contraction scour occurred at the 500-year discharge. Left abutment scour ranged from 4.6 to 4.9 ft. The worst-case left abutment scour occurred at the 100-year discharge. Right abutment scour ranged from 4.0 to 5.0 ft. The worst-case right abutment scour occurred at the 500-year discharge. Additional information on scour depths and depths to armoring are included in the section titled “Scour Results”. Scoured-streambed elevations, based on the calculated scour depths, are presented in tables 1 and 2. A cross-section of the scour computed at the bridge is presented in figure 8. Scour depths were calculated assuming an infinite depth of erosive material and a homogeneous particle-size distribution. It is generally accepted that the Froehlich equation (abutment scour) gives “excessively conservative estimates of scour depths” (Richardson and others, 1995, p. 47). Usually, computed scour depths are evaluated in combination with other information including (but not limited to) historical performance during flood events, the geomorphic stability assessment, existing scour protection measures, and the results of the hydraulic analyses. Therefore, scour depths adopted by VTAOT may differ from the computed values documented herein.

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

Cheng, J.; Liu, C.; Koopman, W.J.

Ligation of the Fas cell-surface molecule induces apoptosis. Defective Fas-mediated apoptosis has been associated with spontaneous autoimmunity in mice. Using human Fas/Apo-1 cDNA as a probe, the authors have molecularly cloned and characterized the human Fas chromosomal gene. The gene consists of nine exons and spans more than 26 kilobases of DNA. The lengths of introns vary from > 14 kilobases at the 5` end of the gene to 152 base pairs upstream of the exon encoding the transmembrane domain. The domain structure of the human Fas is encoded by an exon or a set of exons. Primer extension analysismore » revealed three major transcription initiation sites. The promoter region lacked canonical {open_quotes}TATA{close_quotes} and {open_quotes}CAAT{close_quotes} boxes but was a {open_quotes}GC-rich{close_quotes} sequence, and contained consensus sequences for AP-1, GF-1, NY-Y, CP-2, EBP20, and c-myb. These data provide the first characterization of the human Fas gene and insight into its regulatory region. 54 refs., 3 figs., 1 tab.« less

50 CFR 660.319 - Open access fishery gear identification and marking.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 50 Wildlife and Fisheries 9 2010-10-01 2010-10-01 false Open access fishery gear identification and marking. 660.319 Section 660.319 Wildlife and Fisheries FISHERY CONSERVATION AND MANAGEMENT... law, the vessel's number, the commercial fishing license number, or buoy brand number; or (ii) The...

50 CFR 660.24 - Limited entry and open access fisheries.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 50 Wildlife and Fisheries 11 2011-10-01 2011-10-01 false Limited entry and open access fisheries. 660.24 Section 660.24 Wildlife and Fisheries FISHERY CONSERVATION AND MANAGEMENT, NATIONAL OCEANIC AND ATMOSPHERIC ADMINISTRATION, DEPARTMENT OF COMMERCE (CONTINUED) FISHERIES OFF WEST COAST STATES West Coast...

50 CFR 660.24 - Limited entry and open access fisheries.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 50 Wildlife and Fisheries 9 2010-10-01 2010-10-01 false Limited entry and open access fisheries. 660.24 Section 660.24 Wildlife and Fisheries FISHERY CONSERVATION AND MANAGEMENT, NATIONAL OCEANIC AND ATMOSPHERIC ADMINISTRATION, DEPARTMENT OF COMMERCE (CONTINUED) FISHERIES OFF WEST COAST STATES West Coast...

50 CFR 660.331 - Limited entry and open access fisheries-general.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 50 Wildlife and Fisheries 9 2010-10-01 2010-10-01 false Limited entry and open access fisheries-general. 660.331 Section 660.331 Wildlife and Fisheries FISHERY CONSERVATION AND MANAGEMENT, NATIONAL OCEANIC AND ATMOSPHERIC ADMINISTRATION, DEPARTMENT OF COMMERCE (CONTINUED) FISHERIES OFF WEST COAST STATES...

50 CFR 660.332 - Open access daily trip limit (DTL) fishery for sablefish.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 50 Wildlife and Fisheries 11 2011-10-01 2011-10-01 false Open access daily trip limit (DTL) fishery for sablefish. 660.332 Section 660.332 Wildlife and Fisheries FISHERY CONSERVATION AND MANAGEMENT, NATIONAL OCEANIC AND ATMOSPHERIC ADMINISTRATION, DEPARTMENT OF COMMERCE (CONTINUED) FISHERIES OFF WEST...

50 CFR 660.24 - Limited entry and open access fisheries.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 50 Wildlife and Fisheries 13 2014-10-01 2014-10-01 false Limited entry and open access fisheries. 660.24 Section 660.24 Wildlife and Fisheries FISHERY CONSERVATION AND MANAGEMENT, NATIONAL OCEANIC AND ATMOSPHERIC ADMINISTRATION, DEPARTMENT OF COMMERCE (CONTINUED) FISHERIES OFF WEST COAST STATES West Coast...

40 CFR 256.24 - Recommendations for closing or upgrading open dumps.

Code of Federal Regulations, 2010 CFR

2010-07-01

... (CONTINUED) SOLID WASTES GUIDELINES FOR DEVELOPMENT AND IMPLEMENTATION OF STATE SOLID WASTE MANAGEMENT PLANS Solid Waste Disposal Programs § 256.24 Recommendations for closing or upgrading open dumps. (a) All... feasibility of resource recovery or resource conservation to reduce the solid waste volume entering a facility...

40 CFR 256.24 - Recommendations for closing or upgrading open dumps.

Code of Federal Regulations, 2011 CFR

2011-07-01

... (CONTINUED) SOLID WASTES GUIDELINES FOR DEVELOPMENT AND IMPLEMENTATION OF STATE SOLID WASTE MANAGEMENT PLANS Solid Waste Disposal Programs § 256.24 Recommendations for closing or upgrading open dumps. (a) All... feasibility of resource recovery or resource conservation to reduce the solid waste volume entering a facility...

Territorial user rights for fisheries as ancillary instruments for marine coastal conservation in Chile.

PubMed

Gelcich, Stefan; Fernández, Miriam; Godoy, Natalio; Canepa, Antonio; Prado, Luis; Castilla, Juan Carlos

2012-12-01

Territorial user rights for fisheries have been advocated as a way to achieve sustainable resource management. However, few researchers have empirically assessed their potential as ancillary marine conservation instruments by comparing them to no-take marine protected areas. In kelp (Lessonia trabeculata) forests of central Chile, we compared species richness, density, and biomass of macroinvertebrates and reef fishes among territorial-user-right areas with low-level and high-level enforcement, no-take marine protected areas, and open-access areas in 42 100-m subtidal transects. We also assessed structural complexity of the kelp forest and substratum composition. Multivariate randomized permutation tests indicated macroinvertebrate and reef fish communities associated with the different access regimes differed significantly. Substratum composition and structural complexity of kelp forest did not differ among access regimes. Univariate analyses showed species richness, biomass, and density of macroinvertebrates and reef fishes were greater in highly enforced territorial-user-right areas and no-take marine protected areas than in open-access areas. Densities of macroinvertebrates and reef fishes of economic importance were not significantly different between highly enforced territorial-user-right and no-take marine protected areas. Densities of economically important macroinvertebrates in areas with low-level enforcement were significantly lower than those in areas with high-level enforcement and no-take marine protected areas but were significantly higher than in areas with open access. Territorial-user-right areas could be important ancillary conservation instruments if they are well enforced. ©2012 Society for Conservation Biology.

Novel mechanism of conjoined gene formation in the human genome.

PubMed

Kim, Ryong Nam; Kim, Aeri; Choi, Sang-Haeng; Kim, Dae-Soo; Nam, Seong-Hyeuk; Kim, Dae-Won; Kim, Dong-Wook; Kang, Aram; Kim, Min-Young; Park, Kun-Hyang; Yoon, Byoung-Ha; Lee, Kang Seon; Park, Hong-Seog

2012-03-01

Recently, conjoined genes (CGs) have emerged as important genetic factors necessary for understanding the human genome. However, their formation mechanism and precise structures have remained mysterious. Based on a detailed structural analysis of 57 human CG transcript variants (CGTVs, discovered in this study) and all (833) known CGs in the human genome, we discovered that the poly(A) signal site from the upstream parent gene region is completely removed via the skipping or truncation of the final exon; consequently, CG transcription is terminated at the poly(A) signal site of the downstream parent gene. This result led us to propose a novel mechanism of CG formation: the complete removal of the poly(A) signal site from the upstream parent gene is a prerequisite for the CG transcriptional machinery to continue transcribing uninterrupted into the intergenic region and downstream parent gene. The removal of the poly(A) signal sequence from the upstream gene region appears to be caused by a deletion or truncation mutation in the human genome rather than post-transcriptional trans-splicing events. With respect to the characteristics of CG sequence structures, we found that intergenic regions are hot spots for novel exon creation during CGTV formation and that exons farther from the intergenic regions are more highly conserved in the CGTVs. Interestingly, many novel exons newly created within the intergenic and intragenic regions originated from transposable element sequences. Additionally, the CGTVs showed tumor tissue-biased expression. In conclusion, our study provides novel insights into the CG formation mechanism and expands the present concepts of the genetic structural landscape, gene regulation, and gene formation mechanisms in the human genome.

Impact of the operation of cascade reservoirs in upper Yangtze River on hydrological variability of the mainstream

NASA Astrophysics Data System (ADS)

Changjiang, Xu; Dongdong, Zhang

2018-06-01

As the impacts by climate changes and human activities are intensified, variability may occur in river's annual runoff as well as flood and low water characteristics. In order to understand the characteristics of variability in hydrological series, diagnosis and identification must be conducted specific to the variability of hydrological series, i.e., whether there was variability and where the variability began to occur. In this paper, the mainstream of Yangtze River was taken as the object of study. A model was established to simulate the impounding and operation of upstream cascade reservoirs so as to obtain the runoff of downstream hydrological control stations after the regulation by upstream reservoirs in different level years. The Range of Variability Approach was utilized to analyze the impact of the operation of upstream reservoirs on the variability of downstream. The results indicated that the overall hydrologic alterations of Yichang hydrological station in 2010 level year, 2015 level year and the forward level year were 68.4, 72.5 and 74.3 % respectively, belonging to high alteration in all three level years. The runoff series of mainstream hydrological stations presented variability in different degrees, where the runoff series of the four hydrological stations including Xiangjiaba, Gaochang and Wulong belonged to high alteration in the three level years; and the runoff series of Beibei hydrological station in 2010 level year belonged to medium alteration, and high alteration in 2015 level year and the forward level year. The study on the impact of the operation of cascade reservoirs in Upper Yangtze River on hydrological variability of the mainstream had important practical significance on the sustainable utilization of water resources, disaster prevention and mitigation, safe and efficient operation and management of water conservancy projects and stable development of the economic society.

A Role for MORE AXILLARY GROWTH1 (MAX1) in Evolutionary Diversity in Strigolactone Signaling Upstream of MAX21[C][W][OA

PubMed Central

Challis, Richard J.; Hepworth, Jo; Mouchel, Céline; Waites, Richard; Leyser, Ottoline

2013-01-01

Strigolactones (SLs) are carotenoid-derived phytohormones with diverse roles. They are secreted from roots as attractants for arbuscular mycorrhizal fungi and have a wide range of endogenous functions, such as regulation of root and shoot system architecture. To date, six genes associated with SL synthesis and signaling have been molecularly identified using the shoot-branching mutants more axillary growth (max) of Arabidopsis (Arabidopsis thaliana) and dwarf (d) of rice (Oryza sativa). Here, we present a phylogenetic analysis of the MAX/D genes to clarify the relationships of each gene with its wider family and to allow the correlation of events in the evolution of the genes with the evolution of SL function. Our analysis suggests that the notion of a distinct SL pathway is inappropriate. Instead, there may be a diversity of SL-like compounds, the response to which requires a D14/D14-like protein. This ancestral system could have been refined toward distinct ligand-specific pathways channeled through MAX2, the most downstream known component of SL signaling. MAX2 is tightly conserved among land plants and is more diverged from its nearest sister clade than any other SL-related gene, suggesting a pivotal role in the evolution of SL signaling. By contrast, the evidence suggests much greater flexibility upstream of MAX2. The MAX1 gene is a particularly strong candidate for contributing to diversification of inputs upstream of MAX2. Our functional analysis of the MAX1 family demonstrates the early origin of its catalytic function and both redundancy and functional diversification associated with its duplication in angiosperm lineages. PMID:23424248

Characterization of Rous sarcoma virus polyadenylation site use in vitro

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

Maciolek, Nicole L.; McNally, Mark T.

2008-05-10

Polyadenylation of Rous sarcoma virus (RSV) RNA is inefficient, as approximately 15% of RSV RNAs represent read-through transcripts that use a downstream cellular polyadenylation site (poly(A) site). Read-through transcription has implications for the virus and the host since it is associated with oncogene capture and tumor induction. To explore the basis of inefficient RSV RNA 3'-end formation, we characterized RSV polyadenylation in vitro using HeLa cell nuclear extracts and HEK293 whole cell extracts. RSV polyadenylation substrates composed of the natural 3' end of viral RNA and various lengths of upstream sequence showed little or no polyadenylation, indicating that the RSVmore » poly(A) site is suboptimal. Efficiently used poly(A) sites often have identifiable upstream and downstream elements (USEs and DSEs) in close proximity to the conserved AAUAAA signal. The sequences upstream and downstream of the RSV poly(A) site deviate from those found in efficiently used poly(A) sites, which may explain inefficient RSV polyadenylation. To assess the quality of the RSV USEs and DSEs, the well-characterized SV40 late USEs and/or DSEs were substituted for the RSV elements and vice versa, which showed that the USEs and DSEs from RSV are suboptimal but functional. CstF interacted poorly with the RSV polyadenylation substrate, and the inactivity of the RSV poly(A) site was at least in part due to poor CstF binding since tethering CstF to the RSV substrate activated polyadenylation. Our data are consistent with poor polyadenylation factor binding sites in both the USE and DSE as the basis for inefficient use of the RSV poly(A) site and point to the importance of additional elements within RSV RNA in promoting 3' end formation.« less

Promoter for Sindbis virus RNA-dependent subgenomic RNA transcription.

PubMed Central

Levis, R; Schlesinger, S; Huang, H V

1990-01-01

Sindbis virus is a positive-strand RNA enveloped virus, a member of the Alphavirus genus of the Togaviridae family. Two species of mRNA are synthesized in cells infected with Sindbis virus; one, the 49S RNA, is the genomic RNA; the other, the 26S RNA, is a subgenomic RNA that is identical in sequence to the 3' one-third of the genomic RNA. Ou et al. (J.-H. Ou, C. M. Rice, L. Dalgarno, E. G. Strauss, and J. H. Strauss, Proc. Natl. Acad. Sci. USA 79:5235-5239, 1982) identified a highly conserved region 19 nucleotides upstream and 2 nucleotides downstream from the start of the 26S RNA and proposed that in the negative-strand template, these nucleotides compose the promoter for directing the synthesis of the subgenomic RNA. Defective interfering (DI) RNAs of Sindbis virus were used to test this proposal. A 227-nucleotide sequence encompassing 98 nucleotides upstream and 117 nucleotides downstream from the start site of the Sindbis virus subgenomic RNA was inserted into a DI genome. The DI RNA containing the insert was replicated and packaged in the presence of helper virus, and cells infected with these DI particles produced a subgenomic RNA of the size and sequence expected if the promoter was functional. The initiating nucleotide was identical to that used for Sindbis virus subgenomic mRNA synthesis. Deletion analysis showed that the minimal region required to detect transcription of a subgenomic RNA from the negative-strand template of a DI RNA was 18 or 19 nucleotides upstream and 5 nucleotides downstream from the start of the subgenomic RNA. Images PMID:2319651

Two alternative ways of start site selection in human norovirus reinitiation of translation.

PubMed

Luttermann, Christine; Meyers, Gregor

2014-04-25

The calicivirus minor capsid protein VP2 is expressed via termination/reinitiation. This process depends on an upstream sequence element denoted termination upstream ribosomal binding site (TURBS). We have shown for feline calicivirus and rabbit hemorrhagic disease virus that the TURBS contains three sequence motifs essential for reinitiation. Motif 1 is conserved among caliciviruses and is complementary to a sequence in the 18 S rRNA leading to the model that hybridization between motif 1 and 18 S rRNA tethers the post-termination ribosome to the mRNA. Motif 2 and motif 2* are proposed to establish a secondary structure positioning the ribosome relative to the start site of the terminal ORF. Here, we analyzed human norovirus (huNV) sequences for the presence and importance of these motifs. The three motifs were identified by sequence analyses in the region upstream of the VP2 start site, and we showed that these motifs are essential for reinitiation of huNV VP2 translation. More detailed analyses revealed that the site of reinitiation is not fixed to a single codon and does not need to be an AUG, even though this codon is clearly preferred. Interestingly, we were able to show that reinitiation can occur at AUG codons downstream of the canonical start/stop site in huNV and feline calicivirus but not in rabbit hemorrhagic disease virus. Although reinitiation at the original start site is independent of the Kozak context, downstream initiation exhibits requirements for start site sequence context known for linear scanning. These analyses on start codon recognition give a more detailed insight into this fascinating mechanism of gene expression.

Interplay between spontaneous decay rates and Lamb shifts in open photonic systems

NASA Astrophysics Data System (ADS)

Lassalle, Emmanuel; Bonod, Nicolas; Durt, Thomas; Stout, Brian

2018-05-01

In this letter, we describe the modified decay rate and photonic Lamb (frequency) shift of quantum emitters in terms of the resonant states of a neighboring photonic resonator. This description illustrates a fundamental distinction in the behaviors of closed (conservative) and open (dissipative) systems: the Lamb shift is bounded by the emission linewidth in closed systems while it overcomes this limit in open systems.

The push and pull of land use policy: reconstructing 150 years of development and conservation land acquisition.

PubMed

Santos, Maria João; Watt, Terry; Pincetl, Stephanie

2014-01-01

The growth of human populations and their resource needs have stressed the conservation of natural land resources. Many policies and programs have been implemented to address the pressures on land resources and notwithstanding this pressure, significant acquisition of land for conservation has occurred throughout history in the U.S., and internationally. Here we assess the on-the-ground result of the evolution of land use policies in California as a pioneer forerunner, in the form of acquisition of land for conservation (i.e. Open Space), and its impact on the rest of the U.S. and beyond. To this end we describe the timeline and spatial representation of the growth of California's conservation network over the last 150 years, and link it to the history of land use policies. We then assess whether conservation land acquisition has consistently grown through time or occurred in specific decades. About ¼ of the state is now designated Open Space. Fewer and larger areas conserved and acquired at the beginning of the 20th century; the conservation network was complemented with a larger number of smaller sized properties. Despite acquisition of land in every decade, the process was uneven (E = 0.3 for California, E = 0.14 ± 0.08 average for the state's counties), mostly due to the large acquisitions and land set asides in the 1900s, followed by 1930s and 1940s. This process was a result of a comprehensive set of legislation that evolved through time, and resulted from the competing needs for development and conservation. Even with the impressive 174,000 km2 of public lands in California, the future of California's natural infrastructure and natural heritage cannot rely solely on these public lands, nor public agencies and their resources. Critically a future course of land preservation relying on the purchase of new lands - in California and beyond - for conservation is tremendously expensive.

Transcriptional mapping of the varicella-zoster virus regulatory genes encoding open reading frames 4 and 63.

PubMed Central

Kinchington, P R; Vergnes, J P; Defechereux, P; Piette, J; Turse, S E

1994-01-01

Four of the 68 varicella-zoster virus (VZV) unique open reading frames (ORFs), i.e., ORFs 4, 61, 62, and 63, encode proteins that influence viral transcription and are considered to be positional homologs of herpes simplex virus type 1 (HSV-1) immediate-early (IE) proteins. In order to identify the elements that regulate transcription of VZV ORFs 4 and 63, the encoded mRNAs were mapped in detail. For ORF 4, a major 1.8-kb and a minor 3.0-kb polyadenylated [poly(A)+] RNA were identified, whereas ORF 63-specific probes recognized 1.3- and 1.9-kb poly(A)+ RNAs. Probes specific for sequences adjacent to the ORFs and mapping of the RNA 3' ends indicated that the ORF 4 RNAs were 3' coterminal, whereas the RNAs for ORF 63 represented two different termination sites. S1 nuclease mapping and primer extension analyses indicated a single transcription initiation site for ORF 4 at 38 bp upstream of the ORF start codon. For ORF 63, multiple transcriptional start sites at 87 to 95, 151 to 153, and (tentatively) 238 to 243 bp upstream of the ORF start codon were identified. TATA box motifs at good positional locations were found upstream of all mapped transcription initiation sites. However, no sequences resembling the TAATGARAT motif, which confers IE regulation upon HSV-1 IE genes, were found. The finding of the absence of this motif was supported through analyses of the regulatory sequences of ORFs 4 and 63 in transient transfection assays alongside those of ORFs 61 and 62. Sequences representing the promoters for ORFs 4, 61, and 63 were all stimulated by VZV infection but failed to be stimulated by coexpression with the HSV-1 transactivator Vmw65. In contrast, the promoter for ORF 62, which contains TAATGARAT motifs, was activated by VZV infection and coexpression with Vmw65. These results extend the transcriptional knowledge for VZV and suggest that ORFs 4 and 63 contain regulatory signals different from those of the ORF 62 and HSV-1 IE genes. Images PMID:8189496

How big of an effect do small dams have? Using geomorphological footprints to quantify spatial impact of low-head dams and identify patterns of across-dam variation

USGS Publications Warehouse

Fencl, Jane S.; Mather, Martha E.; Costigan, Katie H.; Daniels, Melinda D.

2015-01-01

Longitudinal connectivity is a fundamental characteristic of rivers that can be disrupted by natural and anthropogenic processes. Dams are significant disruptions to streams. Over 2,000,000 low-head dams (<7.6 m high) fragment United States rivers. Despite potential adverse impacts of these ubiquitous disturbances, the spatial impacts of low-head dams on geomorphology and ecology are largely untested. Progress for research and conservation is impaired by not knowing the magnitude of low-head dam impacts. Based on the geomorphic literature, we refined a methodology that allowed us to quantify the spatial extent of low-head dam impacts (herein dam footprint), assessed variation in dam footprints across low-head dams within a river network, and identified select aspects of the context of this variation. Wetted width, depth, and substrate size distributions upstream and downstream of six low-head dams within the Upper Neosho River, Kansas, United States of America were measured. Total dam footprints averaged 7.9 km (3.0–15.3 km) or 287 wetted widths (136–437 wetted widths). Estimates included both upstream (mean: 6.7 km or 243 wetted widths) and downstream footprints (mean: 1.2 km or 44 wetted widths). Altogether the six low-head dams impacted 47.3 km (about 17%) of the mainstem in the river network. Despite differences in age, size, location, and primary function, the sizes of geomorphic footprints of individual low-head dams in the Upper Neosho river network were relatively similar. The number of upstream dams and distance to upstream dams, but not dam height, affected the spatial extent of dam footprints. In summary, ubiquitous low-head dams individually and cumulatively altered lotic ecosystems. Both characteristics of individual dams and the context of neighboring dams affected low-head dam impacts within the river network. For these reasons, low-head dams require a different, more integrative, approach for research and management than the individualistic approach that has been applied to larger dams.

How Big of an Effect Do Small Dams Have? Using Geomorphological Footprints to Quantify Spatial Impact of Low-Head Dams and Identify Patterns of Across-Dam Variation

PubMed Central

Costigan, Katie H.; Daniels, Melinda D.

2015-01-01

Longitudinal connectivity is a fundamental characteristic of rivers that can be disrupted by natural and anthropogenic processes. Dams are significant disruptions to streams. Over 2,000,000 low-head dams (<7.6 m high) fragment United States rivers. Despite potential adverse impacts of these ubiquitous disturbances, the spatial impacts of low-head dams on geomorphology and ecology are largely untested. Progress for research and conservation is impaired by not knowing the magnitude of low-head dam impacts. Based on the geomorphic literature, we refined a methodology that allowed us to quantify the spatial extent of low-head dam impacts (herein dam footprint), assessed variation in dam footprints across low-head dams within a river network, and identified select aspects of the context of this variation. Wetted width, depth, and substrate size distributions upstream and downstream of six low-head dams within the Upper Neosho River, Kansas, United States of America were measured. Total dam footprints averaged 7.9 km (3.0–15.3 km) or 287 wetted widths (136–437 wetted widths). Estimates included both upstream (mean: 6.7 km or 243 wetted widths) and downstream footprints (mean: 1.2 km or 44 wetted widths). Altogether the six low-head dams impacted 47.3 km (about 17%) of the mainstem in the river network. Despite differences in age, size, location, and primary function, the sizes of geomorphic footprints of individual low-head dams in the Upper Neosho river network were relatively similar. The number of upstream dams and distance to upstream dams, but not dam height, affected the spatial extent of dam footprints. In summary, ubiquitous low-head dams individually and cumulatively altered lotic ecosystems. Both characteristics of individual dams and the context of neighboring dams affected low-head dam impacts within the river network. For these reasons, low-head dams require a different, more integrative, approach for research and management than the individualistic approach that has been applied to larger dams. PMID:26540105

75 FR 80292 - Energy Conservation Program: Energy Conservation Standards for Electric Motors

Federal Register 2010, 2011, 2012, 2013, 2014

2010-12-22

... horsepower, manufactured (alone or as a component of another piece of equipment) after December 19, 2010, to... Design B, six-pole open motors rated 250, 300, and 350 horsepower are not consistent with the EISA 2007... component of another piece of equipment), on or after December 19, 2010, shall have a nominal full load...