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1

A DNA region recognized by the nitric oxide-responsive transcriptional activator NorR is conserved in beta- and gamma-proteobacteria.  

PubMed

The sigma(54)-dependent regulator NorR activates transcription of target genes in response to nitric oxide (NO) or NO-generating agents. In Ralstonia eutropha H16, NorR activates transcription of the dicistronic norAB operon that encodes NorA, a protein of unknown function, and NorB, a nitric oxide reductase. A constitutively activating NorR derivative (NorR'), in which the N-terminal signaling domain was replaced by MalE, specifically bound to the norAB upstream region as revealed by gel retardation analysis. Within a 73-bp DNA segment protected by MalE-NorR' in a DNase I footprint assay, three conserved inverted repeats, GGT-(N(7))-ACC (where N is any base), that we consider to be NorR-binding boxes were identified. Mutations altering the spacing or the base sequence of these repeats resulted in an 80 to 90% decrease of transcriptional activation by wild-type NorR. Genome database analyses demonstrate that the GT-(N(7))-AC core of the inverted repeat is found in several proteobacteria upstream of gene loci encoding proteins of nitric oxide metabolism, including nitric oxide reductase (NorB), flavorubredoxin (NorV), NO dioxygenase (Hmp), and hybrid cluster protein (Hcp). PMID:15547270

Büsch, Andrea; Pohlmann, Anne; Friedrich, Bärbel; Cramm, Rainer

2004-12-01

2

Regional Conservation Services.  

ERIC Educational Resources Information Center

Proposes, in the spirit of good library keeping, a regional cooperative approach to the preservation of library materials which would embody conservation services of a lower order than a conservation laboratory: e.g., stack cleaning, facilities inspection and repair, and book dusting. (JD)

Bohem, Hilda

1979-01-01

3

Recognizing articulated objects using a region-based invariant transform.  

PubMed

In this paper, we present a new method for representing and recognizing objects, based on invariants of the object's regions. We apply the method to articulated objects in low-resolution, noisy range images. Articulated objects such as a back-hoe can have many degrees of freedom, in addition to the unknown variables of viewpoint. Recognizing such an object in an image can involve a search in a high-dimensional space that involves all these unknown variables. Here, we use invariance to reduce this search space to a manageable size. The low resolution of our range images makes it hard to use common features such as edges to find invariants. We have thus developed a new "featureless" method that does not depend on feature detection. Instead of local features, we deal with whole regions of the object. We define a "transform" that converts the image into an invariant representation on a grid, based on invariant descriptors of entire regions centered around the grid points. We use these region-based invariants for indexing and recognition. While the focus here is on articulation, the method can be easily applied to other problems such as the occlusion of fixed objects. PMID:16237999

Weiss, Isaac; Ray, Manjit

2005-10-01

4

Crystal structure reveals conservation of amyloid-? conformation recognized by 3D6 following humanization to bapineuzumab  

PubMed Central

Introduction Immunotherapy targeting amyloid-? peptide is under active clinical investigation for treatment of Alzheimer’s disease (AD). Among the hypotheses being investigated for impact on clinical outcome are the preferred epitope or conformation of amyloid-? to target for treatment, and the mechanism of action underlying immunotherapy. Bapineuzumab (humanized 3D6), a neo-epitope specific antibody recognizing amyloid-?1-5 with strong preference for an exposed Asp residue at the N-terminus of the peptide, has undergone advanced clinical testing for treatment of AD. Methods To gain further insight into the epitope conformation, we interrogated structural details of amino-terminal epitopes in amyloid-? using x-ray crystallography of 3D6Fab:amyloid-? complexes. Humanization of 3D6 was carried out using standard procedures integrating recombinant methods, sequence informatics, and homology modeling predictions to identify important mouse framework residues for retention in the finished humanized product. Results Here we report the crystal structure of a recombinant Fab fragment of 3D6 in complex with amyloid-?1-7 solved at 2.0 Å resolution. The N-terminus of amyloid-? is bound to 3D6 as a 310 helix. The amino-terminal Asp residue is buried deepest in the antibody binding pocket, with the C? atom of residue 6 visible at the entrance to the binding pocket near the surface of the antibody. We further evaluate homology model based predictions used to guide humanization of 3D6 to bapineuzumab, with actual structure of the Fab. The structure of the Fab:amyloid-? complex validates design of the humanized antibody, and confirms the amyloid-? epitope recognized by 3D6 as previously mapped by ELISA. Conclusions The conformation of amyloid-? antigen recognized by 3D6 is novel and distinct from other antibodies recognizing N-terminal epitopes. Our result provides the first report demonstrating structural conservation of antigen contact residues, and conformation of antigen recognized, between the parent murine antibody and its humanized version.

2014-01-01

5

5 CFR 5501.103 - Gifts from federally recognized Indian tribes or Alaska Native villages or regional or village...  

Code of Federal Regulations, 2010 CFR

...recognized Indian tribes or Alaska Native villages or regional or village corporations...recognized Indian tribes or Alaska Native villages or regional or village corporations...recognized Indian tribes or Alaska Native villages or regional or village...

2010-01-01

6

5 CFR 5501.103 - Gifts from federally recognized Indian tribes or Alaska Native villages or regional or village...  

Code of Federal Regulations, 2010 CFR

...recognized Indian tribes or Alaska Native villages or regional or village corporations...recognized Indian tribes or Alaska Native villages or regional or village corporations...recognized Indian tribes or Alaska Native villages or regional or village...

2009-01-01

7

Human Brain Regions Involved in Recognizing Environmental Sounds  

Microsoft Academic Search

To identify the brain regions preferentially involved in environmental sound recognition (comprising portions of a putative auditory 'what' pathway), we collected functional imaging data while listeners attended to a wide range of sounds, including those produced by tools, animals, liquids and dropped objects. These recognizable sounds, in contrast to unrecognizable, temporally reversed control sounds, evoked activity in a distributed network

James W. Lewis; Frederic L. Wightman; Julie A. Brefczynski; Raymond E. Phinney; Jeffrey R. Binder; Edgar A. DeYoe

1992-01-01

8

Widespread tissue distribution of aminopeptidase A, an evolutionarily conserved ectoenzyme recognized by the BP-1 antibody.  

PubMed

Early B-lineage cells in mice express a cell surface glycoprotein, recognized by the BP-1 and 6C3 monoclonal antibodies, that has been identified as aminopeptidase A (APA E.C.3.4.11.7). In the present studies we obtained evidence by DNA "zoo-blot" analysis that the APA gene is highly conserved. This ectoenzyme catalyzes the removal of N-terminal Glu- and Asp-residues to convert angiotensin II to angiotensin III, a degradation step important in local regulation of blood pressure in mammals. To gain further insight into the physiology of this molecule, which is shared between immune and vascular systems, we examined the tissue distribution of BP-1 mRNA using a cDNA probe and of the protein antigen using the BP-1 antibody for immunohistology. APA transcripts were present in all tissues examined. Abundant BP-1/APA was found in the intestinal brush border of the small intestine, renal glomeruli, proximal renal tubules, pulmonary alveolar walls and vascular endothelium in many organs. Other tissues containing the BP-1 antigen included stromal cells in the thymus cortex, bile canaliculi in liver, gall bladder epithelium, interlobular ducts in pancreas, the ovarian theca interna, basement membrane of the epididymis and the splanchnopleure in placenta. APA enzyme activities have been identified in most of these locations, in keeping with identification of the BP-1/6C3 antigen as APA. The data suggest this ectopeptidase may serve diverse physiologic roles in a broad spectrum of tissues. PMID:8146860

Li, L; Wu, Q; Wang, J; Bucy, R P; Cooper, M D

1993-11-01

9

A monoclonal antibody recognizing a conserved epitope in a group of phospholipases A2.  

PubMed

Notexin and nigexine are monomeric phospholipases A2(PLA2s) from the venoms of Notechis scutatus scutatus and Naja nigricollis, respectively. Polyclonal antibodies raised in mice against these antigenic proteins displayed non-reciprocal cross-reactivity; anti-notexin antibodies recognized notexin but not nigexine, whereas anti-nigexine antibodies recognized both antigens. Polyclonal antibodies raised by successive immunization with nigexine and notexin contained cross-reacting antibodies with affinities for both antigens that differed from those of antibodies present in anti-nigexine antiserum. A monoclonal antibody has been obtained from a mouse immunized with both PLA2s. This monoclonal antibody, called MN1, recognized notexin and nigexine with comparable high affinity (Kd = 10(-9) M). It also recognized most purified PLA2s from elapid snake venoms and all PLA2-containing venoms from cobras and sea-snakes. This offers the first demonstration that most PLA2s from cobras and sea-snakes share a fine structure which is not restricted to the common catalytic site. PMID:1690350

Mollier, P; Chwetzoff, S; Ménez, A

1990-01-01

10

A New Means To Identify Type 3 Secreted Effectors: Functionally Interchangeable Class IB Chaperones Recognize a Conserved Sequence  

PubMed Central

ABSTRACT Many Gram-negative bacteria utilize specialized secretion systems to inject proteins (effectors) directly into host cells. Little is known regarding how bacteria ensure that only small subsets of the thousands of proteins they encode are recognized as substrates of the secretion systems, limiting their identification through bioinformatic analyses. Many of these proteins require chaperones to direct their secretion. Here, using the newly described protein interaction platform assay, we demonstrate that type 3 secretion system class IB chaperones from one bacterium directly bind their own effectors as well as those from other species. In addition, we observe that expression of class IB homologs from seven species, including pathogens and endosymbionts, mediate the translocation of effectors from Shigella directly into host cells, demonstrating that class IB chaperones are often functionally interchangeable. Notably, class IB chaperones bind numerous effectors. However, as previously proposed, they are not promiscuous; rather they recognize a defined sequence that we designate the conserved chaperone-binding domain (CCBD) sequence [(LMIF)1XXX(IV)5XX(IV)8X(N)10]. This sequence is the first defined amino acid sequence to be identified for any interspecies bacterial secretion system, i.e., a system that delivers proteins directly into eukaryotic cells. This sequence provides a new means to identify substrates of type III secretion systems. Indeed, using a pattern search algorithm for the CCBD sequence, we have identified the first two probable effectors from an endosymbiont, Sodalis glossinidius.

Costa, Sonia C. P.; Schmitz, Alexa M.; Jahufar, Fathima F.; Boyd, Justin D.; Cho, Min Y.; Glicksman, Marcie A.; Lesser, Cammie F.

2012-01-01

11

Conservation of Extended Promoter Regions of Nodulation Genes in Rhizobium  

Microsoft Academic Search

A 47-base-pair (bp) conserved sequence in the 5'-flanking regions of three transcriptional units coding for nodulation functions (nodABC, nodEFG, and nodH) has been identified in Rhizobium meliloti strain 41. The conserved region contains subsequences of 7 bp, 5 bp, and 25 bp. The conserved 25-bp sequence was synthesized and used as a hybridization probe; three additional copies of the sequence

Katalin Rostas; Eva Kondorosi; Beatrix Horvath; Andras Simoncsits; Adam Kondorosi

1986-01-01

12

Towards the definition of a chimpanzee and human conserved CD6 domain 1 epitope recognized by T1 monoclonal antibody.  

PubMed

Scavenger receptor cysteine-rich (SRCR) domains are evolutionally conserved modules that display complex structures stabilized by key amino acids, while some other residues have evolved with a relative independence, thus allowing the functional diversity of these receptors. CD6, a highly glycosylated membrane protein predominantly expressed on lymphocytes, contains three SRCR domains. The lack of CD6 domain crystal structure has limited the characterization of the binding sites for the interacting molecules. The interaction between CD6 and its ligand, activated leukocyte-cell adhesion molecule (ALCAM)/CD166, through the membrane-proximal SRCR3 domain, has low affinity and involves conserved sites in both molecules mediating a cross-species binding. The CD6-ALCAM interaction has been involved in cell adhesion, maturation, regulation of activation, and survival processes, suggesting the potential relevance of this target for therapeutic interventions. Several anti-CD6 monoclonal antibodies (MAb) have been described but their affinity and epitope definition remain unclear. We found the murine and humanized T1 MAb versions have similar CD6 recognition profiles and affinity constants of about 6 x 10(8). These antibodies do not block the CD6-ALCAM interaction and recognize a conformational epitope independent of the CD6 N-glycosylation. This epitope was additionally found in the chimpanzee and contains an RXE/Q consensus motif located in the membrane-distal SRCR1. These results, together with the therapeutic evidence previously obtained with these MAbs, suggest a differential contribution of CD6 domains to lymphocyte biology. Potential mechanisms for T1 MAb therapeutic effect different from CD6-CD166 interaction blocking would be dissected. PMID:18707547

Alonso, Ruby; Huerta, Vivian; de Leon, Joel; Piedra, Patricia; Puchades, Yaquelin; Guirola, Osmany; Chinea, Glay; Montero, Enrique

2008-08-01

13

Broadly reactive human CD8 T cells that recognize an epitope conserved between VZV, HSV and EBV.  

PubMed

Human herpesviruses are important causes of potentially severe chronic infections for which T cells are believed to be necessary for control. In order to examine the role of virus-specific CD8 T cells against Varicella Zoster Virus (VZV), we generated a comprehensive panel of potential epitopes predicted in silico and screened for T cell responses in healthy VZV seropositive donors. We identified a dominant HLA-A*0201-restricted epitope in the VZV ribonucleotide reductase subunit 2 and used a tetramer to analyze the phenotype and function of epitope-specific CD8 T cells. Interestingly, CD8 T cells responding to this VZV epitope also recognized homologous epitopes, not only in the other ?-herpesviruses, HSV-1 and HSV-2, but also the ?-herpesvirus, EBV. Responses against these epitopes did not depend on previous infection with the originating virus, thus indicating the cross-reactive nature of this T cell population. Between individuals, the cells demonstrated marked phenotypic heterogeneity. This was associated with differences in functional capacity related to increased inhibitory receptor expression (including PD-1) along with decreased expression of co-stimulatory molecules that potentially reflected their stimulation history. Vaccination with the live attenuated Zostavax vaccine did not efficiently stimulate a proliferative response in this epitope-specific population. Thus, we identified a human CD8 T cell epitope that is conserved in four clinically important herpesviruses but that was poorly boosted by the current adult VZV vaccine. We discuss the concept of a "pan-herpesvirus" vaccine that this discovery raises and the hurdles that may need to be overcome in order to achieve this. PMID:24675761

Chiu, Christopher; McCausland, Megan; Sidney, John; Duh, Fuh-Mei; Rouphael, Nadine; Mehta, Aneesh; Mulligan, Mark; Carrington, Mary; Wieland, Andreas; Sullivan, Nicole L; Weinberg, Adriana; Levin, Myron J; Pulendran, Bali; Peters, Bjoern; Sette, Alessandro; Ahmed, Rafi

2014-03-01

14

Rocky Mountain Conservation Region Geospatial Information: KML Files  

NSDL National Science Digital Library

This portal features a selection of downloadable Keyhole Markup Language (KML) files containing geospatial data formatted for use in Google Earth. Selections include geospatial coverages for the Nature Conservancy's Rocky Mountain Conservation Region such as natural land cover and terrestrial ecoregion boundaries for prairies, basins, plateaus, and deserts in the western and southwestern United States.

2007-10-05

15

Setting Priorities for Regional Conservation Planning in the Mediterranean Sea  

PubMed Central

Spatial prioritization in conservation is required to direct limited resources to where actions are most urgently needed and most likely to produce effective conservation outcomes. In an effort to advance the protection of a highly threatened hotspot of marine biodiversity, the Mediterranean Sea, multiple spatial conservation plans have been developed in recent years. Here, we review and integrate these different plans with the goal of identifying priority conservation areas that represent the current consensus among the different initiatives. A review of six existing and twelve proposed conservation initiatives highlights gaps in conservation and management planning, particularly within the southern and eastern regions of the Mediterranean and for offshore and deep sea habitats. The eighteen initiatives vary substantially in their extent (covering 0.1–58.5% of the Mediterranean Sea) and in the location of additional proposed conservation and management areas. Differences in the criteria, approaches and data used explain such variation. Despite the diversity among proposals, our analyses identified ten areas, encompassing 10% of the Mediterranean Sea, that are consistently identified among the existing proposals, with an additional 10% selected by at least five proposals. These areas represent top priorities for immediate conservation action. Despite the plethora of initiatives, major challenges face Mediterranean biodiversity and conservation. These include the need for spatial prioritization within a comprehensive framework for regional conservation planning, the acquisition of additional information from data-poor areas, species or habitats, and addressing the challenges of establishing transboundary governance and collaboration in socially, culturally and politically complex conditions. Collective prioritised action, not new conservation plans, is needed for the north, western, and high seas of the Mediterranean, while developing initial information-based plans for the south and eastern Mediterranean is an urgent requirement for true regional conservation planning.

Micheli, Fiorenza; Levin, Noam; Giakoumi, Sylvaine; Katsanevakis, Stelios; Abdulla, Ameer; Coll, Marta; Fraschetti, Simonetta; Kark, Salit; Koutsoubas, Drosos; Mackelworth, Peter; Maiorano, Luigi; Possingham, Hugh P.

2013-01-01

16

Sequence motif in control regions of the H+/K+ ATPase alpha and beta subunit genes recognized by gastric specific nuclear protein(s).  

PubMed

A nuclear protein(s) from rat or pig stomach recognized a conserved sequence in the 5'-upstream regions of the rat and human H+/K(+)-ATPase alpha subunit genes. A gel retardation assay suggested that part of the binding site was located in the TAATCAGCTG sequence. No nuclear proteins capable of the binding could be detected in other tissues of rat (liver, brain, kidney, spleen and lung) or pig liver. The sequence motif (GATAGC) located 5'-upstream of the beta-subunit gene also seemed to be recognized by the same protein, because the binding of nuclear protein to the sequence motifs in the alpha and beta subunits was mutually competitive. Considering the sense-strand sequence of the binding motif in the alpha-subunit gene, we conclude that (G/C)PuPu(G/C)NGAT(A/T)PuPy is a core sequence motif for the gastric specific DNA binding protein (PCSF, parietal cell specific factor). PMID:1312019

Tamura, S; Oshiman, K; Nishi, T; Mori, M; Maeda, M; Futai, M

1992-02-24

17

Exclusion of two major areas on thyroid peroxidase from the immunodominant region containing the conformational epitopes recognized by human autoantibodies.  

PubMed

We have used a chimeric molecule between thyroid peroxidase (TPO) and myeloperoxidase (MPO) as well as new information on the three-dimensional structure of MPO to refine further our understanding of the location of the TPO-immunodominant region recognized by TPO autoantibodies in patients' sera. In TPO-MPO chimera A, the amino-terminal 146 amino acids of MPO substitute for the amino-terminal 121 amino acids of TPO. We performed fluorescence-activated cell sorter analysis of Chinese hamster ovary cells expressing TPO-MPO-A on their surface using four monoclonal human autoantibody F(ab) (WR1.7, TR1.8, TR1.9, and SP1.4) that define the immunodominant region. All four F(ab) recognized the TPO-MPO-A chimeric molecule to the same extent. In a second approach to refine the location on the TPO-immunodominant region, we compared the ability of the TPO autoantibody F(ab) to inhibit the binding of serum autoantibodies to the monomeric and dimeric forms of human TPO. The F(ab) inhibited equally (approximately 80%) the binding to the TPO monomer and dimer by autoantibodies in the sera of six individual patients. The present observations exclude two major regions of TPO from the autoantibody-immunodominant region, namely the amino-terminal 121 amino acids of the TPO extracellular domain and the contact region between the two TPO monomers. These findings together with previous data on the Mab47/C21 region of TPO and the recently elucidated 3-dimensional structure of highly homologous MPO, narrow, by a process of exclusion, the site on TPO comprising the immunodominant region. The data provide further support for the thesis, still controversial, that the majority of TPO autoantibodies recognize the native molecule. PMID:7527407

Nishikawa, T; Rapoport, B; McLachlan, S M

1994-12-01

18

SWR-C and INO80 chromatin remodelers recognize nucleosome-free regions near +1 nucleosomes.  

PubMed

SWR-C/SWR1 and INO80 are multisubunit complexes that catalyze the deposition and removal, respectively, of histone variant H2A.Z from the first nucleosome at the start of genes. How they target and engage these +1 nucleosomes is unclear. Using ChIP-exo, we identified the subnucleosomal placement of 20 of their subunits across the yeast genome. The Swc2 subunit of SWR-C bound a narrowly defined region in the adjacent nucleosome-free region (NFR), where it positioned the Swr1 subunit over one of two sites of H2A.Z deposition at +1. The genomic binding maps suggest that many subunits have a rather plastic organization that allows subunits to exchange between the two complexes. One outcome of promoting H2A/H2A.Z exchange was an enhanced turnover of entire nucleosomes, thereby creating dynamic chromatin at the start of genes. Our findings provide unifying concepts on how these two opposing chromatin remodeling complexes function selectively at the +1 nucleosome of nearly all genes. PMID:24034248

Yen, Kuangyu; Vinayachandran, Vinesh; Pugh, B Franklin

2013-09-12

19

Recognizing and Understanding Patterns in the Spatial, Temporal, and Magnitude Distributions of Regional Seismicity  

NASA Astrophysics Data System (ADS)

Regional seismicity is characterized by power law distributions in magnitude (the Gutenberg-Richter Law), space (a fractal distribution) and time (the Omori aftershock law). Since such power-laws are characteristic of systems in, or near, a critical state, the concept of self organized criticality (SOC) presents an attractive framework. In the SOC model, tectonic loading is exactly balanced by seismic release and the crust sits in a critical state. Because this critical state is characterized by stress correlations at all scale lengths up to the system size, a large event is equally likely at any time. The forecasting of large events in an SOC system is inherently impossible. However, the crust differs from simple SOC "sandpile models" models in several important respects. First, there is strong frozen heterogeneity (fault networks) on the same scale as the system (plate boundary) and second there is a significant local loss of energy during an event. Both cause great earthquakes to move the system out of the critical state. Tectonic loading and stress transfer from smaller events then moves the system back toward criticality and the possibility of another great event. Monitoring this approach to criticality opens the possibility of forecasting great earthquakes. The first order observation is an increase in the number of intermediate events leading up to the mainshock. The associated acceleration in seismic energy release is optimal within a large region the radius of which scales with the fault length. King and Bowman (JGR., 2002) have quantified these ideas using an elastic model in which a fault-patch is loaded by slip on its ends and creep on its lower extension. This model produces earthquake cycles, and offers a simple explanation for why the optimal region for acceleration scales with fault length. However, as noted by Sammis and Sornette (PNAS, 2002), it does not produce singular critical point behavior without an additional ingredient, such as a damage rheology, to provide feedback. For constant loading rate, all such models predict that the time period of accelerating activity should scale with event size. Another possibility is that earthquakes nucleate as a thermal instability in the creep loading from below. If this instability can develop over several years, it offers another explanation of accelerating seismic release.

Sammis, C. G.

2002-12-01

20

The relevance of the Mediterranean Region to colonial waterbird conservation  

USGS Publications Warehouse

The Mediterranean Sea is the largest partially enclosed sea in the world and provides habitat to more than 100 species of waterbirds from the Palearctic-North African-Middle Eastern regions. Even though the Mediterranean suffers from pollution, has little tidal influence, and is oligotrophic, more than half of the western Palearctic populations of numerous waterfowl species winter in the region. Thirty-three species of colonial waterbirds breed along the 46,000 km Mediterranean coastline with nine species considered threatened or endangered, mostly because of wetland loss and degradation. The long history of human activity and scientific investigations in the region has taught some valuable lessons. In the area of colonial waterbird biology and conservation, we have learned important lessons about the value of long-term monitoring and research on selected populations. From marking studies of Greater Flamingos (Phoenicopterus ruber roseus) and Little Egrets (Egretta garzetta) results have been used to derive useful information about metapopulation dynamics. Involvement of both African and European biologists allowed year-round Studies of these species that yielded valuable spin-offs for training in avian and wetland conservation. We have also learned the value of man-made wetlands as feeding and nesting sites for some colonial waterbirds. Careful evaluations of the habitat quality of different types of wetlands are required, as in contaminant levels such as lead shot and pesticides. Wetland conservationists have also learned from some instructive mistakes. Dam construction and agricultural incentive programs sponsored by the European Community, the World Bank, and others from the past have largely ignored impacts on wetlands and wildlife. In some areas, economic ventures such as aquaculture operations and salt mining have not involved waterbird habitat needs in their planning. Research and conservation needs include: (1) establishing regional monitoring programs and data banks for seabirds, wading birds, ducks, and geese; (2) implementing a wetland inventory for many Countries with little quantitative data on wetlands; (3) improving habitat quality assessments; (4) improving relationships with industry, the private citizenry, and government officials to further an appreciation for the value of wetlands and waterbirds; (5) enhancing training efforts, especially in underdeveloped Countries; (6) evaluating the effects of hunting and other disturbances to nesting and feeding waterbirds in different regions; (7) setting up 'sister-reserve' (twinned) sites in Europe and Africa to foster international linkages and training; and (8) fostering local-regional conservation programs to preserve reed beds, wet woodlots, and other key habitats.

Erwin, R.M.

1996-01-01

21

Molecular cloning of Xenopus fibrillarin, a conserved U3 small nuclear ribonucleoprotein recognized by antisera from humans with autoimmune disease.  

PubMed Central

Autoantibodies against U3 small nuclear ribonucleoprotein are associated with scleroderma autoimmune disease. They were shown to react with fibrillarin, a 34- to 36-kilodalton protein that has been detected in all eukaryotes tested from humans to yeasts. We isolated a 1.6-kilobase cDNA encoding fibrillarin from a Xenopus laevis cDNA library. The protein contains a 79-residue-long Gly-Arg-rich domain in its N-terminal region and a putative RNA-binding domain with ribonucleoprotein consensus sequence in its central portion. This is the first report of cloning of fibrillarin, and the deduced protein sequence is in agreement with the involvement of the protein in a ribonucleoprotein particle. Images

Lapeyre, B; Mariottini, P; Mathieu, C; Ferrer, P; Amaldi, F; Amalric, F; Caizergues-Ferrer, M

1990-01-01

22

A Human Antibody Recognizing a Conserved Epitope of H5 Hemagglutinin Broadly Neutralizes Highly Pathogenic Avian Influenza H5N1 Viruses  

PubMed Central

Influenza A virus infection is a persistent threat to public health worldwide due to its ability to evade immune surveillance through rapid genetic drift and shift. Current vaccines against influenza A virus provide immunity to viral isolates that are similar to vaccine strains. High-affinity neutralizing antibodies against conserved epitopes could provide immunity to diverse influenza virus strains and protection against future pandemic viruses. In this study, by using a highly sensitive H5N1 pseudotype-based neutralization assay to screen human monoclonal antibodies produced by memory B cells from an H5N1-infected individual and molecular cloning techniques, we developed three fully human monoclonal antibodies. Among them, antibody 65C6 exhibited potent neutralization activity against all H5 clades and subclades except for subclade 7.2 and prophylactic and therapeutic efficacy against highly pathogenic avian influenza H5N1 viruses in mice. Studies on hemagglutinin (HA)-antibody complexes by electron microscopy and epitope mapping indicate that antibody 65C6 binds to a conformational epitope comprising amino acid residues at positions 118, 121, 161, 164, and 167 (according to mature H5 numbering) on the tip of the membrane-distal globular domain of HA. Thus, we conclude that antibody 65C6 recognizes a neutralization epitope in the globular head of HA that is conserved among almost all divergent H5N1 influenza stains.

Hu, Hongxing; Voss, Jarrod; Zhang, Guoliang; Buchy, Philippi; Zuo, Teng; Wang, Lulan; Wang, Feng; Zhou, Fan; Wang, Guiqing; Tsai, Cheguo; Calder, Lesley; Gamblin, Steve J.; Zhang, Linqi; Deubel, Vincent; Zhou, Boping

2012-01-01

23

Recognizing Symptoms  

MedlinePLUS

... Unmet Needs IBS and Holidays Personal Stories IBS Awareness Month The Art of IBS Mobile App Who We Are Contact Us Donate Recognizing ... ... | Privacy & Security | Terms of Use | Site Map | Help | Free Info ...

24

Assessment of the Effects of Conservation Practices on Cultivated Cropland in the Chesapeake Bay Region.  

National Technical Information Service (NTIS)

The voluntary, incentives-based conservation approach is working. Farmers have made good progress in reducing sediment, nutrient, and pesticide losses from farm fields through conservation practice adoption throughout the Chesapeake Bay region. Most cropl...

2011-01-01

25

Regions of botulinum neurotoxin A light chain recognized by human anti-toxin antibodies from cervical dystonia patients immunoresistant to toxin treatment. The antigenic structure of the active toxin recognized by human antibodies.  

PubMed

This work was aimed at determining the BoNT/A L-chain antigenic regions recognized by blocking antibodies in human antisera from cervical dystonia patients who had become immunoresistant to BoNT/A treatment. Antisera from 28 immunoresistant patients were analyzed for binding to each of 32 overlapping synthetic peptides that spanned the entire L-chain. A mixture of the antisera showed that antibodies bound to three peptides, L11 (residues 141-159), L14 (183-201) and L18 (239-257). When mapped separately, the antibodies were bound only by a limited set of peptides. No peptide bound antibodies from all the patients and amounts of antibodies bound to a given peptide varied with the patient. Peptides L11, L14 and L18 were recognized predominantly. A small but significant number of patients had antibodies to peptides L27 (365-383) and L29 (379-397). Other peptides were recognized at very low and perhaps insignificant antibody levels by a minority (15% or less) of patients or had no detectable antibody with any of the sera. In the 3-dimensional structure, antibody-binding regions L11, L14 and L18 of the L-chain occupy surface areas and did not correlate with electrostatic potential, hydrophilicity/hydrophobicity, or temperature factor. These three antigenic regions reside in close proximity to the belt of the heavy chain. The regions L11 and L18 are accessible in both the free light chain and the holotoxin forms, while L14 appears to be less accessible in the holotoxin. Antibodies against these regions could prevent delivery of the L-chain into the neurons by inhibition of the translocation. PMID:21281977

Atassi, M Zouhair; Dolimbek, Behzod Z; Jankovic, Joseph; Steward, Lance E; Aoki, K Roger

2011-07-01

26

SPECIES DISTRIBUTIONS, SURROGACY, AND IMPORTANT CONSERVATION REGIONS IN CANADA  

EPA Science Inventory

Conservation actions could be more efficient if there is congruence among taxa in the distribution of species. Patterns in the geographic distribution of species of six taxa were used to identify nationally important sites for conservation in Canada. Species richness and a meas...

27

Cysteine-poor region-specific EpCAM monoclonal antibody recognizing native tumor cells with high sensitivity.  

PubMed

EpCAM is a ?40?kDa transmembrane glycoprotein. EpCAM overexpression is a popular trait of almost all carcinomas and is considered as a targeted cancer immunotherapy as well as a practical marker for circulating tumor cells (CTC). Its extracellular part (EpEx) consists of an N-terminal EGF-like (EGF) domain, a TY-like (TY) domain, and an uncharacterized cysteine-poor (CP) region. Most commercially available murine monoclonal antibodies (MAbs) to EpCAM, such as HEA 125 and VU-1D9, bind to the small EGF domain. In a previous study, we introduced iCeap (intact CTC enumeration and analysis procedure), keeping cellular integrity during the whole process. Unlike the CellSearch(®) CTC Test, iCeap enables downstream molecular analysis from detected CTC. Use of two EpCAM MAbs, one for immunomagnetic enrichment of rare CTC from blood samples and the other for labeling, is a concept of iCeap while an ideal MAb pair has not been found. In order to obtain a better MAb that recognizes a part of EpEx as different from EGF domain, we established a mouse hybridoma clone producing a new EpCAM MAb, KIJY2. Fluorophore-conjugated KIJY2 and HEA 125-FITC can concomitantly stain the tumor cell line LNCaP within indistinguishable cellular compartments (i.e., the cell surface). Epitope mapping reveals that KIJY2 binds to the CP region. The epitope for KIJY2 is sensitive to paraformaldehyde fixation, but native cells including MCF-7 (EpCAM high-expressing cell line) and PC-3 (EpCAM low and heterogeneously expressing cell line) are detected by KIJY2. In particular, KIJY2 detects all PC-3 cells regardless of their EpCAM expression levels. Therefore, KIJY2 and an EGF domain-directed MAb are a promising pair to form the EpCAM sandwich in iCeap. We demonstrate that KIJY2 incorporated into iCeap yielded favorable results in spike-in experiments of MCF-7 and PC-3. PMID:23607341

Takao, Masashi; Nagai, Yutaka; Torii, Tokiji

2013-04-01

28

Conservation.  

ERIC Educational Resources Information Center

This set of teaching aids consists of seven Audubon Nature Bulletins, providing the teacher and student with informational reading on various topics in conservation. The bulletins have these titles: Plants as Makers of Soil, Water Pollution Control, The Ground Water Table, Conservation--To Keep This Earth Habitable, Our Threatened Air Supply,…

National Audubon Society, New York, NY.

29

Genome-Wide Transcriptional Dependence on Conserved Regions of Mot1 ?  

PubMed Central

TATA binding protein (TBP) plays a central role in transcription complex assembly and is regulated by a variety of transcription factors, including Mot1. Mot1 is an essential protein in Saccharomyces cerevisiae that exerts both negative and positive effects on transcription via interactions with TBP. It contains two conserved regions important for TBP interactions, another conserved region that hydrolyzes ATP to remove TBP from DNA, and a fourth conserved region with unknown function. Whether these regions contribute equally to transcriptional regulation genome-wide is unknown. Here, we employ a transient-replacement assay using deletion derivatives in the conserved regions of Mot1 to investigate their contributions to gene regulation throughout the S. cerevisiae genome. These four regions of Mot1 are essential for growth and are generally required for all Mot1-regulated genes. Loss of the ATPase region, but not other conserved regions, caused TBP to redistribute away from a subset of Mot1-inhibited genes, leading to decreased expression of those genes. A corresponding increase in TBP occupancy and expression occurred at another set of genes that are normally Mot1 independent. The data suggest that Mot1 uses ATP hydrolysis to redistribute accessible TBP away from intrinsically preferred sites to other sites of intrinsically low preference.

Venters, Bryan J.; Irvin, Jordan D.; Gramlich, Paul; Pugh, B. Franklin

2011-01-01

30

Conserved regions of homologous G-banded chromosomes between orders in mammalian evolution: carnivores and primates.  

PubMed Central

The recent derivation of a biochemical map of 33 loci of the domestic cat (Felis catus) revealed a striking conservation of chromosomal linkage associations between the cat and humans. A comparison of homologous (by linkage criteria) chromosomes by using conventionally extended and high-resolution G-banding of human and feline chromosomes is presented. Four criteria for establishing probable cytogenetic homologies of chromosomal regions were invoked: (i) map placement of homologous genes to the same chromosomes; (ii) cytological correlation of G-banding pattern; (iii) placement of homologous genes, by regional gene mapping, in the region of cytological homology; and (iv) a requirement that the putative region of homology be ancestral and evolutionarily conserved within their respective orders. Five subchromosomal regions (homologous to human chromosome 1p, 2p, 2q, 12, and X) were found to be conserved and homologous by all the stated criteria. The conserved regions constitute nearly 20% by length of the human chromosomal genome. The implications of conservation of chromosome homologies between mammalian orders whose last common ancestor became extinct more than 60 million years ago is discussed. Images

Nash, W G; O'Brien, S J

1982-01-01

31

The Texas Aggie Bonfire: A Conservative Reading of Regional Narratives, Traditional Practices, and a Paradoxical Place  

Microsoft Academic Search

Concepts of place, narrative, tradition, and identity are employed in a conservative reading of the Texas A&M Bonfire. Texas A&M embodied regional narratives of a dual Southern commitment to economic and technological development and conservation of traditional cultural. Institutionalized at Texas A&M in the late nineteenth century, these narratives made a paradoxical place. Bonfire expressed and obscured this paradox. In

Jonathan M. Smith

2007-01-01

32

ECRbase: Database of Evolutionary Conserved Regions, Promoters, and Transcription Factor Binding Sites in Vertebrate Genomes  

DOE Data Explorer

Evolutionary conservation of DNA sequences provides a tool for the identification of functional elements in genomes. This database of evolutionary conserved regions (ECRs) in vertebrate genomes features a database of syntenic blocks that recapitulate the evolution of rearrangements in vertebrates and a comprehensive collection of promoters in all vertebrate genomes generated using multiple sources of gene annotation. The database also contains a collection of annotated transcription factor binding sites (TFBSs) in evolutionary conserved and promoter elements. ECRbase currently includes human, rhesus macaque, dog, opossum, rat, mouse, chicken, frog, zebrafish, and fugu genomes. (taken from paper in Journal: Bioinformatics, November 7, 2006, pp. 122-124

Loots, Gabriela G. (LLNL); Ovcharenko, I. (LLNL)

33

Optimal portfolio design to reduce climate-related conservation uncertainty in the Prairie Pothole Region.  

PubMed

Climate change is likely to alter the spatial distributions of species and habitat types but the nature of such change is uncertain. Thus, climate change makes it difficult to implement standard conservation planning paradigms. Previous work has suggested some approaches to cope with such uncertainty but has not harnessed all of the benefits of risk diversification. We adapt Modern Portfolio Theory (MPT) to optimal spatial targeting of conservation activity, using wetland habitat conservation in the Prairie Pothole Region (PPR) as an example. This approach finds the allocations of conservation activity among subregions of the planning area that maximize the expected conservation returns for a given level of uncertainty or minimize uncertainty for a given expected level of returns. We find that using MPT instead of simple diversification in the PPR can achieve a value of the conservation objective per dollar spent that is 15% higher for the same level of risk. MPT-based portfolios can also have 21% less uncertainty over benefits or 6% greater expected benefits than the current portfolio of PPR conservation. Total benefits from conservation investment are higher if returns are defined in terms of benefit-cost ratios rather than benefits alone. MPT-guided diversification can work to reduce the climate-change-induced uncertainty of future ecosystem-service benefits from many land policy and investment initiatives, especially when outcomes are negatively correlated between subregions of a planning area. PMID:22451914

Ando, Amy W; Mallory, Mindy L

2012-04-24

34

Optimal portfolio design to reduce climate-related conservation uncertainty in the Prairie Pothole Region  

PubMed Central

Climate change is likely to alter the spatial distributions of species and habitat types but the nature of such change is uncertain. Thus, climate change makes it difficult to implement standard conservation planning paradigms. Previous work has suggested some approaches to cope with such uncertainty but has not harnessed all of the benefits of risk diversification. We adapt Modern Portfolio Theory (MPT) to optimal spatial targeting of conservation activity, using wetland habitat conservation in the Prairie Pothole Region (PPR) as an example. This approach finds the allocations of conservation activity among subregions of the planning area that maximize the expected conservation returns for a given level of uncertainty or minimize uncertainty for a given expected level of returns. We find that using MPT instead of simple diversification in the PPR can achieve a value of the conservation objective per dollar spent that is 15% higher for the same level of risk. MPT-based portfolios can also have 21% less uncertainty over benefits or 6% greater expected benefits than the current portfolio of PPR conservation. Total benefits from conservation investment are higher if returns are defined in terms of benefit–cost ratios rather than benefits alone. MPT-guided diversification can work to reduce the climate-change–induced uncertainty of future ecosystem-service benefits from many land policy and investment initiatives, especially when outcomes are negatively correlated between subregions of a planning area.

Ando, Amy W.; Mallory, Mindy L.

2012-01-01

35

Structure of the dnaA region of Micrococcus luteus: conservation and variations among eubacteria.  

PubMed

A phylogenetic tree constructed by 5S rRNA analysis is composed of three major branches in eubacteria: high G + C Gram+, low G + C Gram+ and Gram- [Hori and Osawa, Mol. Biol. Evol. 4 (1987) 445-472]. We have shown that the characteristic dnaA region is common among Escherichia coli (Gram-), Pseudomonas putida (Gram-), and Bacillus subtilis (low G + C Gram+). We have now determined the structure of the dnaA region of Micrococcus luteus, as a representative of the last branch, high G + C Gram+. The dnaA gene and at least three other genes, rnpA, rpmH and dnaN were found to be conserved in M. luteus. Large nontranslatable regions were found flanking the dnaA gene. The upstream region is conserved in the four bacteria so far examined. On the other hand, the downstream region is conserved only in Gram+ bacteria, M. luteus and B. subtilis. The consensus sequence of the DnaA box in M. luteus seems to be TTGTCCACA, in contrast to TTATCCACA of other bacteria. These results confirm our hypothesis that the dnaA region is the replication origin of the ancestral bacteria and that the essential feature of the DnaA protein and DnaA-box combination is conserved in eubacteria. PMID:2172090

Fujita, M Q; Yoshikawa, H; Ogasawara, N

1990-09-01

36

SLiMPrints: conservation-based discovery of functional motif fingerprints in intrinsically disordered protein regions  

PubMed Central

Large portions of higher eukaryotic proteomes are intrinsically disordered, and abundant evidence suggests that these unstructured regions of proteins are rich in regulatory interaction interfaces. A major class of disordered interaction interfaces are the compact and degenerate modules known as short linear motifs (SLiMs). As a result of the difficulties associated with the experimental identification and validation of SLiMs, our understanding of these modules is limited, advocating the use of computational methods to focus experimental discovery. This article evaluates the use of evolutionary conservation as a discriminatory technique for motif discovery. A statistical framework is introduced to assess the significance of relatively conserved residues, quantifying the likelihood a residue will have a particular level of conservation given the conservation of the surrounding residues. The framework is expanded to assess the significance of groupings of conserved residues, a metric that forms the basis of SLiMPrints (short linear motif fingerprints), a de novo motif discovery tool. SLiMPrints identifies relatively overconstrained proximal groupings of residues within intrinsically disordered regions, indicative of putatively functional motifs. Finally, the human proteome is analysed to create a set of highly conserved putative motif instances, including a novel site on translation initiation factor eIF2A that may regulate translation through binding of eIF4E.

Davey, Norman E.; Cowan, Joanne L.; Shields, Denis C.; Gibson, Toby J.; Coldwell, Mark J.; Edwards, Richard J.

2012-01-01

37

Novel Bacterial Lipoprotein Structures Conserved in Low-GC Content Gram-positive Bacteria Are Recognized by Toll-like Receptor 2*  

PubMed Central

Bacterial lipoproteins/lipopeptides inducing host innate immune responses are sensed by mammalian Toll-like receptor 2 (TLR2). These bacterial lipoproteins are structurally divided into two groups, diacylated or triacylated lipoproteins, by the absence or presence of an amide-linked fatty acid. The presence of diacylated lipoproteins has been predicted in low-GC content Gram-positive bacteria and mycoplasmas based on the absence of one modification enzyme in their genomes; however, we recently determined triacylated structures in low-GC Gram-positive Staphylococcus aureus, raising questions about the actual lipoprotein structure in other low-GC content Gram-positive bacteria. Here, through intensive MS analyses, we identified a novel and unique bacterial lipoprotein structure containing an N-acyl-S-monoacyl-glyceryl-cysteine (named the lyso structure) from low-GC Gram-positive Enterococcus faecalis, Bacillus cereus, Streptococcus sanguinis, and Lactobacillus bulgaricus. Two of the purified native lyso-form lipoproteins induced proinflammatory cytokine production from mice macrophages in a TLR2-dependent and TLR1-independent manner but with a different dependence on TLR6. Additionally, two other new lipoprotein structures were identified. One is the “N-acetyl” lipoprotein structure containing N-acetyl-S-diacyl-glyceryl-cysteine, which was found in five Gram-positive bacteria, including Bacillus subtilis. The N-acetyl lipoproteins induced the proinflammatory cytokines through the TLR2/6 heterodimer. The other was identified in a mycoplasma strain and is an unusual diacyl lipoprotein structure containing two amino acids before the lipid-modified cysteine residue. Taken together, our results suggest the existence of novel TLR2-stimulating lyso and N-acetyl forms of lipoproteins that are conserved in low-GC content Gram-positive bacteria and provide clear evidence for the presence of yet to be identified key enzymes involved in the bacterial lipoprotein biosynthesis.

Kurokawa, Kenji; Ryu, Kyoung-Hwa; Ichikawa, Rie; Masuda, Akiko; Kim, Min-Su; Lee, Hanna; Chae, Jun-Ho; Shimizu, Takashi; Saitoh, Tatsuya; Kuwano, Koichi; Akira, Shizuo; Dohmae, Naoshi; Nakayama, Hiroshi; Lee, Bok Luel

2012-01-01

38

A Novel Universal Neutralizing Monoclonal Antibody against Enterovirus 71 That Targets the Highly Conserved "Knob" Region of VP3 Protein.  

PubMed

Hand, foot and mouth disease caused by enterovirus 71(EV71) leads to the majority of neurological complications and death in young children. While putative inactivated vaccines are only now undergoing clinical trials, no specific treatment options exist yet. Ideally, EV71 specific intravenous immunoglobulins could be developed for targeted treatment of severe cases. To date, only a single universally neutralizing monoclonal antibody against a conserved linear epitope of VP1 has been identified. Other enteroviruses have been shown to possess major conformational neutralizing epitopes on both the VP2 and VP3 capsid proteins. Hence, we attempted to isolate such neutralizing antibodies against conformational epitopes for their potential in the treatment of infection as well as differential diagnosis and vaccine optimization. Here we describe a universal neutralizing monoclonal antibody that recognizes a conserved conformational epitope of EV71 which was mapped using escape mutants. Eight escape mutants from different subgenogroups (A, B2, B4, C2, C4) were rescued; they harbored three essential mutations either at amino acid positions 59, 62 or 67 of the VP3 protein which are all situated in the "knob" region. The escape mutant phenotype could be mimicked by incorporating these mutations into reverse genetically engineered viruses showing that P59L, A62D, A62P and E67D abolish both monoclonal antibody binding and neutralization activity. This is the first conformational neutralization epitope mapped on VP3 for EV71. PMID:24875055

Kiener, Tanja K; Jia, Qiang; Meng, Tao; Chow, Vincent Tak Kwong; Kwang, Jimmy

2014-05-01

39

A Novel Universal Neutralizing Monoclonal Antibody against Enterovirus 71 That Targets the Highly Conserved "Knob" Region of VP3 Protein  

PubMed Central

Hand, foot and mouth disease caused by enterovirus 71(EV71) leads to the majority of neurological complications and death in young children. While putative inactivated vaccines are only now undergoing clinical trials, no specific treatment options exist yet. Ideally, EV71 specific intravenous immunoglobulins could be developed for targeted treatment of severe cases. To date, only a single universally neutralizing monoclonal antibody against a conserved linear epitope of VP1 has been identified. Other enteroviruses have been shown to possess major conformational neutralizing epitopes on both the VP2 and VP3 capsid proteins. Hence, we attempted to isolate such neutralizing antibodies against conformational epitopes for their potential in the treatment of infection as well as differential diagnosis and vaccine optimization. Here we describe a universal neutralizing monoclonal antibody that recognizes a conserved conformational epitope of EV71 which was mapped using escape mutants. Eight escape mutants from different subgenogroups (A, B2, B4, C2, C4) were rescued; they harbored three essential mutations either at amino acid positions 59, 62 or 67 of the VP3 protein which are all situated in the “knob” region. The escape mutant phenotype could be mimicked by incorporating these mutations into reverse genetically engineered viruses showing that P59L, A62D, A62P and E67D abolish both monoclonal antibody binding and neutralization activity. This is the first conformational neutralization epitope mapped on VP3 for EV71.

Meng, Tao; Chow, Vincent Tak Kwong; Kwang, Jimmy

2014-01-01

40

CHOP: visualization of 'wobbling' and isolation of highly conserved regions from aligned DNA sequences.  

PubMed

The web software CHOP was developed to visualize the 'wobbling' in the third codon position of aligned DNA sequences. The simple features of this tool allow users to easily find regions suspected of containing coding sequences (CDSs). The program also allows visualization of the nucleotide diversity between two genomic or gene sequences by graphically plotting the percentage identity between the two sequences. CHOP can also isolate highly conserved regions within both CDSs and non-CDSs. Highly conserved regions within CDSs include the regions with lower rates of synonymous substitution in which nucleotide sequences are expected to be under strong selective pressure. CHOP is available at http://bunsei2.med.u-tokai.ac.jp:8080/~ohtsuka/cds_finding.html. PMID:15215350

Ohtsuka, Masato; Horiuchi, Shohei; Kulski, Jerzy K; Kimura, Minoru; Inoko, Hidetoshi

2004-07-01

41

Sequence-ready physical map of the mouse Chromosome 16 region with conserved synteny to the human Velocardiofacial syndrome region on 22q11.2  

Microsoft Academic Search

.   Proximal mouse Chromosome (Chr) 16 shows conserved synteny with human Chrs 16, 8, 22, and 3. The mouse Chr 16\\/human Chr 22\\u000a conserved synteny region includes the DiGeorge\\/Velocardiofacial syndrome region of human Chr 22q11.2. A physical map of the\\u000a entire mouse Chr 16\\/human Chr 22 region of conserved synteny has been constructed to provide a substrate for gene discovery,

James Lund; Bruce Roe; Feng Chen; Marcia Budarf; Naomi Galili; Roy Riblet; Robert D. Miller; Beverly S. Emanuel; Roger H. Reeves

1999-01-01

42

Carnivores as Focal Species for Conservation Planning in the Rocky Mountain Region  

Microsoft Academic Search

Viability analysis of well-selected focal species can complement ecosystem- level conservation planning by revealing thresholds in habitat area and landscape connec- tivity. Mammalian carnivores are good candidates for focal species because their distri- butional patterns often strongly reflect regional-scale population processes. We incorporated focal species analysis of four carnivore species, fisher (Martes pennanti), lynx (Lynx can- adensis), wolverine (Gulo gulo),

Carlos Carroll; Reed F. Noss; Paul C. Paquet

2001-01-01

43

A network comparison algorithm for predicting the conservative interaction regions in protein-protein interaction network  

Microsoft Academic Search

We presented a network comparison algorithm for predicting the conservative interaction regions in the cross-species protein-protein interaction networks (PINs). In the first place, We made use of the correlated matrix to represent the PINs. Then we standardized the matrix and changed it into a unique representation to facilitate to judge whether the subgraphs is isomorphic. Then we proposed a network

Lihong Peng; Lipeng Liu; Shi Chen; Quanwei Sheng

2010-01-01

44

Designing monitoring programs in an adaptive management context for regional multiple species conservation plans  

USGS Publications Warehouse

critical management uncertainties; and 3) implementing long-term monitoring and adaptive management. Ultimately, the success of regional conservation planning depends on the ability of monitoring programs to confront the challenges of adaptively managing and monitoring complex ecosystems and diverse arrays of sensitive species.

Atkinson, A. J.; Trenham, P. C.; Fisher, R. N.; Hathaway, S. A.; Johnson, B. S.; Torres, S. G.; Moore, Y. C.

2004-01-01

45

Accurate discrimination of conserved coding and non-coding regions through multiple indicators of evolutionary dynamics  

PubMed Central

Background The conservation of sequences between related genomes has long been recognised as an indication of functional significance and recognition of sequence homology is one of the principal approaches used in the annotation of newly sequenced genomes. In the context of recent findings that the number non-coding transcripts in higher organisms is likely to be much higher than previously imagined, discrimination between conserved coding and non-coding sequences is a topic of considerable interest. Additionally, it should be considered desirable to discriminate between coding and non-coding conserved sequences without recourse to the use of sequence similarity searches of protein databases as such approaches exclude the identification of novel conserved proteins without characterized homologs and may be influenced by the presence in databases of sequences which are erroneously annotated as coding. Results Here we present a machine learning-based approach for the discrimination of conserved coding sequences. Our method calculates various statistics related to the evolutionary dynamics of two aligned sequences. These features are considered by a Support Vector Machine which designates the alignment coding or non-coding with an associated probability score. Conclusion We show that our approach is both sensitive and accurate with respect to comparable methods and illustrate several situations in which it may be applied, including the identification of conserved coding regions in genome sequences and the discrimination of coding from non-coding cDNA sequences.

Re, Matteo; Pesole, Graziano; Horner, David S

2009-01-01

46

Fast discovery and visualization of conserved regions in DNA sequences using quasi-alignment  

PubMed Central

Background Next Generation Sequencing techniques are producing enormous amounts of biological sequence data and analysis becomes a major computational problem. Currently, most analysis, especially the identification of conserved regions, relies heavily on Multiple Sequence Alignment and its various heuristics such as progressive alignment, whose run time grows with the square of the number and the length of the aligned sequences and requires significant computational resources. In this work, we present a method to efficiently discover regions of high similarity across multiple sequences without performing expensive sequence alignment. The method is based on approximating edit distance between segments of sequences using p-mer frequency counts. Then, efficient high-throughput data stream clustering is used to group highly similar segments into so called quasi-alignments. Quasi-alignments have numerous applications such as identifying species and their taxonomic class from sequences, comparing sequences for similarities, and, as in this paper, discovering conserved regions across related sequences. Results In this paper, we show that quasi-alignments can be used to discover highly similar segments across multiple sequences from related or different genomes efficiently and accurately. Experiments on a large number of unaligned 16S rRNA sequences obtained from the Greengenes database show that the method is able to identify conserved regions which agree with known hypervariable regions in 16S rRNA. Furthermore, the experiments show that the proposed method scales well for large data sets with a run time that grows only linearly with the number and length of sequences, whereas for existing multiple sequence alignment heuristics the run time grows super-linearly. Conclusion Quasi-alignment-based algorithms can detect highly similar regions and conserved areas across multiple sequences. Since the run time is linear and the sequences are converted into a compact clustering model, we are able to identify conserved regions fast or even interactively using a standard PC. Our method has many potential applications such as finding characteristic signature sequences for families of organisms and studying conserved and variable regions in, for example, 16S rRNA.

2013-01-01

47

Evolutionarily conserved and conformationally constrained short peptides might serve as DNA recognition elements in intrinsically disordered regions.  

PubMed

Despite recent advances, it is yet not clear how intrinsically disordered regions in proteins recognize their targets without any defined structures. Short linear motifs had been proposed to mediate molecular recognition by disordered regions; however, the underlying structural prerequisite remains elusive. Moreover, the role of short linear motifs in DNA recognition has not been studied. We report a repertoire of short evolutionarily Conserved Recognition Elements (CoREs) in long intrinsically disordered regions, which have very distinct amino-acid propensities from those of known motifs, and exhibit a strong tendency to retain their three-dimensional conformations compared to adjacent regions. The majority of CoREs directly interact with the DNA in the available 3D structures, which is further supported by literature evidence, analyses of ??G values of DNA-binding energies and threading-based prediction of DNA binding potential. CoREs were enriched in cancer-associated missense mutations, further strengthening their functional nature. Significant enrichment of glycines in CoREs and the preference of glycyl ?-? values within the left-handed bridge range in the l-disallowed region of the Ramachandran plot suggest that Gly-to-nonGly mutations within CoREs might alter the backbone conformation and consequently the function, a hypothesis that we reconciled using available mutation data. We conclude that CoREs might serve as bait for DNA recognition by long disordered regions and that certain mutations in these peptides can disrupt their DNA binding potential and consequently the protein function. We further hypothesize that the preferred conformations of CoREs and of glycyl residues therein might play an important role in DNA binding. The highly ordered nature of CoREs hints at a therapeutic strategy to inhibit malicious molecular interactions using small molecules mimicking CoRE conformations. PMID:24668165

Tayal, Nitish; Choudhary, Preeti; Pandit, Shashi B; Sandhu, Kuljeet Singh

2014-06-01

48

Regional and global lung function in unilateral fibrothorax after conservative therapy and decortication.  

PubMed

Twenty-six patients suffering from unilateral fibrothorax were investigated before surgery or conservative therapy (decortication, n = 15; conservative treatment, n = 11) and followed up after 24.5 and 18.6 months respectively. Global lung function analysis was done by body plethysmography, ventilation and gas exchange analysis and blood-gas analysis under resting and exercise conditions. Regional lung function analysis included the semiquantitative description of fibrothorax by X-ray photos, and ventilation-perfusion scintigraphy. The functional result of unilateral fibrotic pleurisy is restriction which is also persistent after therapy, but to a lesser degree. This restriction is shown in an increased dead space ventilation as well as in ventilatory inhomogeneities, which causes a distortion of respiratory gas exchange. A decrease of compliance of the lung and chest wall is not measurable after therapy. Conservative treatment leads to a functional improvement to the same degree as decortication in cases of severe preoperative functional disturbances of the operated patients. After a course of 1.5 and 2 years respectively, the reference value has not been reached in either group. The regional pattern after therapy is characterized by a restriction and under-perfusion of the formerly affected site. The regional improvement of lung function is independent of the type of therapy, however, it shows a close correlation to the amount of pleurisy prior to therapy. Conservative treatment is the therapy of choice as long as no complications of insufficient recovery impede the course of the illness. PMID:6180506

Petro, W; Maassen, W; Greschuchna, D; Steinberg, U; Konietzko, N

1982-06-01

49

Conservation of DNA curvature signals in regulatory regions of prokaryotic genes  

PubMed Central

DNA curvature plays a well-characterized role in many transcriptional regulation mechanisms. We present evidence for the conservation of curvature signals in putative regulatory regions of several archaeal and eubacterial genomes. Genes with highly curved upstream regions were identified in orthologous groups, based on the annotations of the Cluster of Orthologous Groups of proteins (COG) database. COGs possessing a significant number of genes with curvature signals were analyzed, and conserved properties were found in several cases. Curvature signals related to regulatory sites, previously described in single organisms, were located in a broad spectrum of bacterial genomes. Global regulatory proteins, such as HU, IHF and FIS, known to bind to curved DNA and to be autoregulated, were found to present conserved DNA curvature signals in their regulatory regions, emphasizing the fact that structural parameters of the DNA molecule are conserved elements in the process of transcriptional regulation of some systems. It is currently an open question whether these diverse systems are part of an integrated global regulatory response in different microorganisms.

Jauregui, Ruy; Abreu-Goodger, Cei; Moreno-Hagelsieb, Gabriel; Collado-Vides, Julio; Merino, Enrique

2003-01-01

50

A regional perspective on the diversity and conservation of tropical Andean fishes.  

PubMed

The tropical Andes harbor an extraordinarily varied concentration of species in a landscape under increasing pressure from human activities. Conservation of the region's native plants and animals has received considerable international attention, but the focus has been on terrestrial biota. The conservation of freshwater fauna, particularly the conservation of fishes, has not been emphasized. Tropical Andean fishes are among the most understudied vertebrates in the world. We estimate that between 400 and 600 fish species inhabit the diverse aquatic environments in the region. Nearly 40% of these species are endemic. Tropical Andean fishes are vulnerable to ongoing environmental changes related to deforestation, water withdrawals, water pollution, species introductions, and hydropower development. Additionally, their distributions and population dynamics may be affected by hydrologic alterations and warmer water temperatures associated with projected climate change. Presently, at least three species are considered extinct, some populations are endangered, and some species are likely to decline or disappear. The long-term persistence of tropical Andean fishes will depend on greater consideration of freshwater systems in regional conservation initiatives. PMID:20735451

Anderson, Elizabeth P; Maldonado-Ocampo, Javier A

2011-02-01

51

Conserved Regions of Protein Disulfide Isomerase are Targeted by Natural IgA Antibodies in Humans  

Microsoft Academic Search

Secretory IgA (sIgA) antibodies in human tears and milk were found to recognize protein disulfide isomerase (PDI) on a Toxoplasma gondii lysate immunoblot (IB). These antibodies were already detectable in tears of infants. To determine the epitope containing-regions on PDI, we generated truncated versions of recombinant PDI that differ by 8-10 amino acids in length. By IB, it was found

Bob Meek; Jaap Willem Back; Vincent N. A. Klaren; Dave Speijer; R. Peek

2002-01-01

52

A Forty-Year Retrospective 1950-1990: The Metropolitan Toronto and Region Conservation Authority's Conservation Education Programmes.  

ERIC Educational Resources Information Center

Recounts the growth of Conservation Authorities in Ontario from the first partnerships between schools and conservation in the 1950s, to the opening of a pioneer village, flood control dam, nature trails, and residential conservation education centers through the 1960s and 1970s. Increased public environmental concern sparked more growth in the…

Carr, Allen Terry

1996-01-01

53

Nucleosome exclusion from the interspecies-conserved central AT-rich region of the Ars insulator.  

PubMed

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. PMID:21930654

Takagi, Haruna; Inai, Yuta; Watanabe, Shun-ichiro; Tatemoto, Sayuri; Yajima, Mamiko; Akasaka, Koji; Yamamoto, Takashi; Sakamoto, Naoaki

2012-01-01

54

Extreme Evolutionary Conservation of Functionally Important Regions in H1N1 Influenza Proteome  

PubMed Central

The H1N1 subtype of influenza A virus has caused two of the four documented pandemics and is responsible for seasonal epidemic outbreaks, presenting a continuous threat to public health. Co-circulating antigenically divergent influenza strains significantly complicates vaccine development and use. Here, by combining evolutionary, structural, functional, and population information about the H1N1 proteome, we seek to answer two questions: (1) do residues on the protein surfaces evolve faster than the protein core residues consistently across all proteins that constitute the influenza proteome? and (2) in spite of the rapid evolution of surface residues in influenza proteins, are there any protein regions on the protein surface that do not evolve? To answer these questions, we first built phylogenetically-aware models of the patterns of surface and interior substitutions. Employing these models, we found a single coherent pattern of faster evolution on the protein surfaces that characterizes all influenza proteins. The pattern is consistent with the events of inter-species reassortment, the worldwide introduction of the flu vaccine in the early 80’s, as well as the differences caused by the geographic origins of the virus. Next, we developed an automated computational pipeline to comprehensively detect regions of the protein surface residues that were 100% conserved over multiple years and in multiple host species. We identified conserved regions on the surface of 10 influenza proteins spread across all avian, swine, and human strains; with the exception of a small group of isolated strains that affected the conservation of three proteins. Surprisingly, these regions were also unaffected by genetic variation in the pandemic 2009 H1N1 viral population data obtained from deep sequencing experiments. Finally, the conserved regions were intrinsically related to the intra-viral macromolecular interaction interfaces. Our study may provide further insights towards the identification of novel protein targets for influenza antivirals.

Warren, Samantha; Wan, Xiu-Feng; Conant, Gavin; Korkin, Dmitry

2013-01-01

55

Localization of high level of sequence conservation and divergence regions in cotton.  

PubMed

In a previous study, we observed that the variations in chromosome size are due to uneven expansion and contraction by comparing the structures and sizes of a pair of homoeologous high-resolution cytogenetic maps of chromosomes 12A and 12D in tetraploid cotton. To reveal the variation at the sequence level, in the present paper, we sequenced two pairs of homoeologous bacterial artificial chromosomes derived from high- to low-variable genomic regions. Comparisons of their sequence variations confirmed that the highly conserved and divergent sequences existed in the distal and pericentric regions, e.g., high- and low-variable genome size regions in these two pairs of cotton homoeologous chromosomes. Sequence analysis also confirmed that the differential accumulation of Gossypium retrotransposable gypsy-like element (Gorge3) accounted for the main contributions for the size difference between the pericentric regions. By fluorescence in situ hybridization analysis, we found that Gorge3 has a bias distribution in the A(T)/A proximal regions and is associated with the heterochromatin along the chromosomes in the entire Gossypium genome. These results indicate that, between A(T)/A and D(T)/D genomes, the distal and pericentric regions usually possess high level of sequence conservation and divergence, respectively, in cotton. PMID:22212344

Wang, Kai; Zhang, Wenpan; Cao, Yujie; Zhang, Zhongxin; Zheng, Dewei; Zhou, Baoliang; Guo, Wangzhen; Zhang, Tianzhen

2012-05-01

56

The mitochondrial DNA control region of Muscidae flies: evolution and structural conservation in a dipteran context.  

PubMed

The structure and evolution of the mtDNA control region (CR) and its flanking genes in economically important dipterans from the family Muscidae (Brachycera: Calyptratae), Haematobia irritans, Musca domestica, Atherigona orientalis, and Stomoxys calcitrans are presented in this paper, along with the description of short noncoding intergenic regions possibly related to CR flanking sequences in Stomoxys calcitrans and Ophyra aenescens mtDNAs (ScIR and OaIR, respectively). S. calcitrans showed a large CR with an approximately 550-bp element tandemly repeated and a duplicated tRNA(Ile) gene. The characterization of H. irritans, M. domestica, A. orientalis, and S. calcitrans CR sequences led to the identification of seven conserved sequence blocks homologous to the elements previously described for Calliphoridae and Oestridae species (Brachycera: Calyptratae). Comparative analysis with Drosophila species (Brachycera: Acalyptratae) revealed four conserved regions. The putative functional roles of the conserved elements in the regulation of replication and transcription processes are addressed. The characterization of the structural organization of the mitochondrial genome CR demonstrates the plasticity of the mtDNA molecule in family Muscidae. PMID:17460806

Oliveira, Marcos T; Azeredo-Espin, Ana M L; Lessinger, Ana C

2007-05-01

57

Conserved immunogenic region of a major core protein (p24) of human and simian immunodeficiency viruses.  

PubMed

A murine monoclonal antibody (MoAb), VAK 4, has been known to specifically react with a major core protein (p24) as well as with its precursor (p55-57) and intermediate precursor (p40) of human immunodeficiency virus strain IIIB (HTLV-IIIB). Radioimmunoprecipitation assays revealed that VAK 4 MoAb precipitated a major core protein and its precursors from a variety of strains of HIV and also from simian immunodeficiency virus (SIV), although the molecular weights of the precursor proteins in each viral strain were slightly different. A protein synthesized by transfected Escherichia coli containing amino acid sequences corresponding to residues 121-436 of the HTLV-IIIB gag gene was reactive with VAK 4 MoAb, but the protein carrying only residues 121-309 was not reactive, suggesting that the epitope recognized by VAK 4 MoAb resides at the carboxyl terminus of p24 protein. A competitive enzyme-linked immunosorbent assay showed that patient sera containing anticore protein antibody inhibited the binding of VAK 4 to HTLV-IIIB. These findings suggested that VAK 4 MoAb recognized an immunogenic and conserved epitope belonging to a major core protein of HIV-related viruses. PMID:2464360

Koito, A; Hattori, T; Matsushita, S; Maeda, Y; Nozaki, C; Sagawa, K; Takatsuki, K

1988-12-01

58

Sequence conservation of the region targeted by the Abbott RealTime HCV viral load assay.  

PubMed

The Abbott RealTime (RT) HCV assay targets the 5' untranslated region (UTR) of the HCV genome. Here, we analyzed the sequence variability of the assay target regions from 1,092 specimens. Thermodynamic modeling of the percentage of primers/probes bound at the assay annealing temperature was performed to assess the potential effect of sequence variability. An analysis of this large data set revealed that the primer and probe binding sites of the RealTime HCV viral load assay are highly conserved and that naturally occurring sequence polymorphisms are not expected to discernibly impact assay performance. PMID:24430453

Cloherty, Gavin; Parkin, Neil; Rhoads, James; Esping, Claudia; Steinhart, Corklin; Schneider, George; Yuen, Lily; Hackett, John

2014-04-01

59

Energy Conservation: An Examination of Energy Conservation Mechanisms As They Relate to School Districts in Region XI.  

ERIC Educational Resources Information Center

This report attempts to supply information on energy conservation mechanisms that can be employed in schools to the public schools of Minnesota. The report begins by presenting guidelines for developing an energy conservation plan. The two models include the concept of Total Educational Energy Management as developed by the Colorado Department of…

Kerns, Marilyn

60

The immunodominant region on human thyroid peroxidase recognized by autoantibodies does not contain the monoclonal antibody 47/c21 linear epitope.  

PubMed

We performed studies to determine whether the binding sites on thyroid peroxidase (TPO) of immunoglobulin antigen binding fragments (Fabs) representing more than 80% of the human autoantibody repertoire overlap with the binding site of monoclonal antibody (Mab) 47, the only Mab whose partial epitope has been defined at the amino acid level (residues 713-721). We also investigated whether these Fabs preferentially recognize native or denatured TPO. None of the Fabs, when bound to radiolabeled TPO, interfered with the ability of Mab 47 to bind to this material. In enzyme-linked immunosorbent assay experiments, the binding of TPO autoantibody Fabs SP1.5, WR1.7, TR1.8, and TR1.9 was greatly diminished by denaturation of TPO. In contrast, binding of Mab 47 was higher to denatured TPO than to intact TPO. Our studies indicate that the Mab 47/C21 epitope lies outside the immunodominant region on TPO. Further, the data confirm that the majority of epitopes for TPO autoantibodies are highly conformational (dependent on the three-dimensional structure of the native protein). Native TPO will be needed to complete the mapping of the epitopes for TPO autoantibodies as well as to determine the amino acids at the autoantibody-antigen-binding sites. PMID:7505290

Chazenbalk, G D; Costante, G; Portolano, S; McLachlan, S M; Rapoport, B

1993-12-01

61

Identification of a conserved sequence in the non-coding regions of many human genes  

SciTech Connect

The authors have analyzed a sequence of approximately 70 base pairs (bp) that shows a high degree of similarity to sequences present in the non-coding regions of a number of human and other mammalian genes. The sequence was discovered in a fragment of human genomic DNA adjacent to an integrated hepatitis B virus genome in cells derived from human hepatocellular carcinoma tissue. When one of the viral flanking sequences was compared to nucleotide sequences in GenBank, more than thirty human genes were identified that contained a similar sequence in their non-coding regions. This element was highly conserved at the same position within the corresponding human and mouse genes for myoglobin and N-myc, indicating evolutionary conservation and possible functional importance. Preliminary DNase I footprinting data suggested that the element or its adjacent sequences may bind nuclear factors to generate specific DNase I hypersensitive sites. The size, structure, and evolutionary conservation of this sequence indicates that it is distinct from other types of short interspersed repetitive elements. It is possible that the element may have a cis-acting functional role in the genome.

Donehower, L.A.; Slagle, B.L.; Wilde, M.; Darlington, G.; Butel, J.S. (Baylor College of Medicine, Houston, TX (USA))

1989-01-25

62

Criteria for protected areas and other conservation measures in the Antarctic region  

SciTech Connect

The Antarctic region is threatened by three major anthropogenic influences: climatic change brought about by increases in atmospheric carbon dioxide, the effects of persistent pollutants carried into the region via atmosphere and ocean, and the increase in Man's activities. These include radioactive wastes, organochlorides, freons, PCBs and heavy metals. Vulnerable ecosystems can be considered as those which are under direct pressure from Man's activities, whereas fragile ecosystems are the more likely to suffer irreversible change when perturbed, but are not necessarily threatened at present. Three of the main habitat types, terrestrial, inland waters, and islands, are likely to be fragile. However, all these can be conserved reasonably adequately with a system of protected and managed areas, so long as the area covered is adequate and representative. The fourth habitat type, the oceanic ecosystem, contains few fragile elements because it is dominated by the highly dynamic physical oceanic processes. Elements of the ecosystem are vulnerable to further exploitation, and although only the whales and some of the fish stocks can be regarded as fragile, there is considerably uncertainty as what synergistic effect exploitation of apparently key elements of the ecosystem, such as the krill, will have on other important components of the communities. The highly dynamic structure of oceanic environments renders the concept of conservation based on limited protected areas developed for terrestrial environments ineffective in the majority of marine environments. Instead the whole marine environment of the Antarctic region must be considered to be a single entity and managed as such.

Angel, M.V.

1987-01-01

63

Precise detection of L. monocytogenes hitting its highly conserved region possessing several specific antibody binding sites.  

PubMed

Listeria monocytogenes, a facultative intracellular fast-growing Gram-positive food-borne pathogen, can infect immunocompromised individuals leading to meningitis, meningoencephalitis and septicaemias. From the pool of virulence factors of the organism, ActA, a membrane protein, has a critical role in the life cycle of L. monocytogenes. High mortality rate of listeriosis necessitates a sensitive and rapid diagnostic test for precise identification of L. monocytogenes. We used bioinformatic tools to locate a specific conserved region of ActA for designing and developing an antibody-antigen based diagnostic test for the detection of L. monocytogenes. A number of databases were looked for ActA related sequences. Sequences were analyzed with several online software to find an appropriate region for our purpose. ActA protein was found specific to Listeria species with no homologs in other organisms. We finally introduced a highly conserved region within ActA sequence that possess several antibody binding sites specific to L. monocytogenes. This protein sequence can serve as an antigen for designing a relatively cheap, sensitive, and specific diagnostic test for detection of L. monocytogenes. PMID:22575546

Jahangiri, Abolfazl; Rasooli, Iraj; Reza Rahbar, Mohammad; Khalili, Saeed; Amani, Jafar; Ahmadi Zanoos, Kobra

2012-07-21

64

Genomic Organization of the Murine Miller-Dieker/Lissencephaly Region: Conservation of Linkage with the Human Region  

PubMed Central

Several human syndromes are associated with haploinsufficiency of chromosomal regions secondary to microdeletions. Isolated lissencephaly sequence (ILS), a human developmental disease characterized by a smooth cerebral surface (classical lissencephaly) and microscopic evidence of incomplete neuronal migration, is often associated with small deletions or translocations at chromosome 17p13.3. Miller–Dieker syndrome (MDS) is associated with larger deletions of 17p13.3 and consists of classical lissencephaly with additional phenotypes including facial abnormalities. We have isolated the murine homologs of three genes located inside and outside the MDS region: Lis1, Mnt/Rox, and 14-3-3?. These genes are all located on mouse chromosome 11B2, as determined by metaphase FISH, and the relative order and approximate gene distance was determined by interphase FISH analysis. The transcriptional orientation and intergenic distance of Lis1 and Mnt/Rox were ascertained by fragmentation analysis of a mouse yeast artificial chromosome containing both genes. To determine the distance and orientation of 14-3-3? with respect to Lis1 and Mnt/Rox, we introduced a super-rare cutter site (VDE) that is unique in the mouse genome into 14-3-3? by gene targeting. Using the introduced VDE site, the orientation of this gene was determined by pulsed field gel electrophoresis and Southern blot analysis. Our results demonstrate that the MDS region is conserved between human and mouse. This conservation of linkage suggests that the mouse can be used to model microdeletions that occur in ILS and MDS.

Hirotsune, Shinji; Pack, Svetlana D.; Chong, Samuel S.; Robbins, Christiane M.; Pavan, William J.; Ledbetter, David H.; Wynshaw-Boris, Anthony

1997-01-01

65

An rRNA variable region has an evolutionarily conserved essential role despite sequence divergence.  

PubMed Central

Regions extremely variable in size and sequence occur at conserved locations in eukaryotic rRNAs. The functional importance of one such region was determined by gene reconstruction and replacement in Tetrahymena thermophila. Deletion of the D8 region of the large-subunit rRNA inactivates T. thermophila rRNA genes (rDNA): transformants containing only this type of rDNA are unable to grow. Replacement with an unrelated sequence of similar size or a variable region from a different position in the rRNA also inactivated the rDNA. Mutant rRNAs resulting from such constructs were present only in precursor forms, suggesting that these rRNAs are deficient in either processing or stabilization of the mature form. Replacement with D8 regions from three other organisms restored function, even though the sequences are very different. Thus, these D8 regions share an essential functional feature that is not reflected in their primary sequences. Similar tertiary structures may be the quality these sequences share that allows them to function interchangeably. Images

Sweeney, R; Chen, L; Yao, M C

1994-01-01

66

Great Plains Region Water Conservation Field Services Program. Part II FY2005 Program Activity Highlights.  

National Technical Information Service (NTIS)

The purpose of the WCFSP is to actively encourage water conservation, assist irrigation and other water districts in developing and implementing water conservation plans, and complement and support other state and local conservation efforts.

2010-01-01

67

Ranking European regions as providers of structural riparian corridors for conservation and management purposes  

NASA Astrophysics Data System (ADS)

Riparian zones are of utmost importance in providing a wide range of ecological and societal services. Among these, their role in maintaining landscape connectivity through ecological corridors for animals and plants is of major interest from a conservation and management perspective. This paper describes a methodology to identify European regions as providers of structural riparian corridors, and to rank them with reference to conservation priority. Physical riparian connectors among core habitat patches are identified through a recent segmentation technique, the Morphological Spatial Pattern Analysis. A multi-scale approach is followed by considering different edge distances to identify core and peripheral habitats for a range of hypothetical species. The ranking is performed using a simple set of indices that take into account the degree of environmental pressure and the presence of land protection schemes. An example for environmental reporting is carried out using European administrative regions and major rivers to summarize indices value. The approach is based on freely available software and simple metrics which can be easily reproduced in a GIS environment.

Clerici, Nicola; Vogt, Peter

2013-04-01

68

Interactions between the Conserved Hydrophobic Region of the Prion Protein and Dodecylphosphocholine Micelles*  

PubMed Central

The three-dimensional structure of PrP110–136, a peptide encompassing the conserved hydrophobic region of the human prion protein, has been determined at high resolution in dodecylphosphocholine micelles by NMR. The results support the conclusion that the CtmPrP, a transmembrane form of the prion protein, adopts a different conformation than the reported structures of the normal prion protein determined in solution. Paramagnetic relaxation enhancement studies with gadolinium-diethylenetriaminepentaacetic acid indicated that the conserved hydrophobic region peptide is not inserted symmetrically in the micelle, thus suggesting the presence of a guanidium-phosphate ion pair involving the side chain of the terminal arginine and the detergent headgroup. Titration of dodecylphosphocholine into a solution of PrP110–136 revealed the presence of a surface-bound species. In addition, paramagnetic probes located the surface-bound peptide somewhere below the micelle-water interface when using the inserted helix as a positional reference. This localization of the unknown population would allow a similar ion pair interaction.

Sauve, Simon; Buijs, Daniel; Gingras, Genevieve; Aubin, Yves

2012-01-01

69

Spatial genetic structure and regional demography in the southern torrent salamander: Implications for conservation and management  

USGS Publications Warehouse

The Southern torrent salamander (Rhyacotriton variegatus) was recently found not warranted for listing under the US Endangered Species Act due to lack of information regarding population fragmentation and gene flow. Found in small-order streams associated with late-successional coniferous forests of the US Pacific Northwest, threats to their persistence include disturbance related to timber harvest activities. We conducted a study of genetic diversity throughout this species' range to 1) identify major phylogenetic lineages and phylogeographic barriers and 2) elucidate regional patterns of population genetic and spatial phylogeographic structure. Cytochrome b sequence variation was examined for 189 individuals from 72 localities. We identified 3 major lineages corresponding to nonoverlapping geographic regions: a northern California clade, a central Oregon clade, and a northern Oregon clade. The Yaquina River may be a phylogeographic barrier between the northern Oregon and central Oregon clades, whereas the Smith River in northern California appears to correspond to the discontinuity between the central Oregon and northern California clades. Spatial analyses of genetic variation within regions encompassing major clades indicated that the extent of genetic structure is comparable among regions. We discuss our results in the context of conservation efforts for Southern torrent salamanders.

Miller, Mark P.; Haig, Susan M.; Wagner, R. S.

2006-01-01

70

Northwest Climate Science Center: Integrating Regional Research, Conservation and Natural Resource Management  

NASA Astrophysics Data System (ADS)

The Northwest Climate Science Center (NW CSC) was established in 2010, among the first three of eight regional Climate Science Centers created by the Department of the Interior (DOI). The NW CSC is supported by an academic consortium (Oregon State University, University of Idaho, and the University of Washington), which has the capacity to generate and coordinate decision-relevant science related to climate, thus serving stakeholders across the Pacific Northwest region. The NW CSC has overlapping boundaries with three Landscape Conservation Cooperatives (LCCs): the Great Northern, the Great Basin, and the North Pacific. Collaboration between the NW CSC and these three LCCs addresses the highest priority regional climate science needs of Northwest natural and cultural resource managers. Early in 2012, the NW CSC released its first Strategic Plan for the period 2012-2015. The plan offers a practical blueprint for operation and describes five core services that the NW CSC provides to the Northwest community. These core services emphasize (a) bringing together the regional resource management and science communities to calibrate priorities and ensure efficient integration of climate science resources and tools when addressing practical issues of regional significance; (b) developing and implementing a stakeholder-driven science agenda which highlights the NW CSC's regional leadership in generating scenarios of the future environment of the NW; (c) supporting and training graduate students at the three consortium universities, including through an annual 'Climate science boot camp'; (d) providing a platform for effective climate-change-related communication among scientists, resource managers, and the general public; and (e) national leadership in data management and climate scenario development.

Mote, P.; Bisbal, G.

2012-12-01

71

Conserved Regions of Gonococcal TbpB Are Critical for Surface Exposure and Transferrin Iron Utilization  

PubMed Central

The transferrin-binding proteins TbpA and TbpB enable Neisseria gonorrhoeae to obtain iron from human transferrin. The lipoprotein TbpB facilitates, but is not strictly required for, TbpA-mediated iron acquisition. The goal of the current study was to determine the contribution of two conserved regions within TbpB to the function of this protein. Using site-directed mutagenesis, the first mutation we constructed replaced the lipobox (LSAC) of TbpB with a signal I peptidase cleavage site (LAAA), while the second mutation deleted a conserved stretch of glycine residues immediately downstream of the lipobox. We then evaluated the resulting mutants for effects on TbpB expression, surface exposure, and transferrin iron utilization. Western blot analysis and palmitate labeling indicated that the lipobox, but not the glycine-rich motif, is required for lipidation of TbpB and tethering to the outer membrane. TbpB was released into the supernatant by the mutant that produces TbpB LSAC. Neither mutation disrupted the transport of TbpB across the bacterial cell envelope. When these mutant TbpB proteins were produced in a strain expressing a form of TbpA that requires TbpB for iron acquisition, growth on transferrin was either abrogated or dramatically diminished. We conclude that surface tethering of TbpB is required for optimal performance of the transferrin iron acquisition system, while the presence of the polyglycine stretch near the amino terminus of TbpB contributes significantly to transferrin iron transport function. Overall, these results provide important insights into the functional roles of two conserved motifs of TbpB, enhancing our understanding of this critical iron uptake system.

Ostberg, Karen L.; DeRocco, Amanda J.; Mistry, Shreni D.; Dickinson, Mary Kathryne

2013-01-01

72

Role of the adenovirus E3-19k conserved region in binding major histocompatibility complex class I molecules.  

PubMed Central

The adenovirus early region 3 glycoprotein E3-19k binds to and down regulates major histocompatibility complex (MHC) class I molecules in infected cells. We previously identified a 20-amino-acid conserved region in E3-19k by comparison of protein sequences from four different adenovirus serotypes. The roles of the E3-19k C-terminal and adjacent conserved regions in the interaction with MHC class I molecules have been examined. A functional class I-binding glycoprotein was expressed from the cloned E3 18.5-kDa open reading frame of adenovirus type 35. Truncations and single-amino-acid mutations in the adenovirus type 35 glycoprotein were created by site-directed in vitro mutagenesis and tested for the ability to associate with MHC class I molecules. Deletion of most of the transmembrane domain and cytoplasmic tail did not affect binding to class I molecules. However, removal of an additional 11 amino acids eliminated binding and changed the conformation of the adjacent conserved region. Separate mutations of residues Asp-107 and Met-110, within the conserved region, severely reduced or eliminated binding. These data indicate that the E3-19k conserved region plays a crucial role in binding to MHC class I molecules. Images

Flomenberg, P; Szmulewicz, J; Gutierrez, E; Lupatkin, H

1992-01-01

73

Conserved sequence related to the 3'-terminal region of retrovirus RNA'S In normal cellular DNAs.  

PubMed Central

The nucleotide sequences related to the 3'-terminal protion of retrovirus genomic RNA have been detected in the DNA of animals, including humans. The DNA complementary to the 400 to 700 nucleotides from the 3'-terminal end of retrovirus RNA (cDNA3'), which contains the enriched conserved region, was hybridized with DNA from a variety of animal cells. Under the conditions of annealing in 0.72 M NaCl at 67 degrees C and hydroxyapatite chromatography at 55 degrees C, 20 to 50% of the radioactivity of the cDNA3' prepared from two retroviruses, a murine Rauscher virus (RLV) and a baboon virus (M7), annealed with normal cellular DNA of animals, including human tissue. The thermal denaturation profile revealed considerable mismatching between the duplex of the cDNA3' and human DNA, cDNA3' of retroviruses is most homologous to cellular DNA of the host species of origin and is less homologous to cellular DNA of species that are distant in the phylogeny of the host species. The conservation and evolution of nucleotide sequences related to the 3' end of retrovirus genomes in animal DNAs, including humans, suggest that the sequences may have important functions.

Kominami, R; Tomita, Y; Connors, E C; Hatanaka, M

1980-01-01

74

A highly conserved region within H2B is important for FACT to act on nucleosomes.  

PubMed

Histone N-terminal tails play crucial roles in chromatin-related processes. The tails of histones H3 and H4 are highly conserved and well characterized, but much less is known about the functions of the tails of histones H2A and H2B and their sequences are more divergent among eukaryotes. Here we characterized the function of the only highly conserved region in the H2B tail, the H2B repression (HBR) domain. Once thought to play a role only in repression, it also has an uncharacterized function in gene activation and DNA damage responses. We report that deletion of the HBR domain impairs the eviction of nucleosomes at the promoters and open reading frames of genes. A closer examination of the HBR domain mutants revealed that they displayed phenotypes similar to those of histone chaperone complex FACT mutants, including an increase in intragenic transcription and the accumulation of free histones in cells. Biochemical characterization of recombinant nucleosomes indicates that deletion of the HBR domain impairs FACT-dependent removal of H2A-H2B from nucleosomes, suggesting that the HBR domain plays an important role in allowing FACT to disrupt dimer-DNA interactions. We have uncovered a previously unappreciated role for the HBR domain in regulating chromatin structure and have provided insight into how FACT acts on nucleosomes. PMID:24248595

Zheng, Suting; Crickard, J Brooks; Srikanth, Abhinaya; Reese, Joseph C

2014-02-01

75

Conserved charged amino acid residues in the extracellular region of sodium\\/iodide symporter are critical for iodide transport activity  

Microsoft Academic Search

BACKGROUND: Sodium\\/iodide symporter (NIS) mediates the active transport and accumulation of iodide from the blood into the thyroid gland. His-226 located in the extracellular region of NIS has been demonstrated to be critical for iodide transport in our previous study. The conserved charged amino acid residues in the extracellular region of NIS were therefore characterized in this study. METHODS: Fourteen

Chia-Cheng Li; Tin-Yun Ho; Chia-Hung Kao; Shih-Lu Wu; Ji-An Liang; Chien-Yun Hsiang

2010-01-01

76

Evolutionary conservation of protein regions in the protonmotive cytochrome b and their possible roles in redox catalysis  

Microsoft Academic Search

Summary The amino acid sequences of the protonmotive cytochromeb from seven representative and phylogenetically diverse species have been compared to identify protein regions or segments that are conserved during evolution. The sequences analyzed included both prokaryotic and eukaryotic examples as well as mitochondrial cytochromeb and chloroplastb6 proteins. The principal conclusion from these analyses is that there are five protein regions-each

Neil Howell

1989-01-01

77

Mutagenesis of apyrase conserved region 1 alters the nucleotide substrate specificity  

PubMed Central

Two apyrases having different substrate specificity, MP67 and MpAPY2, are present in Mimosa pudica. The substrate specificity of MP67 is quite high against ADP, and is distinct from any other apyrase. This might be attributed to the nucleotide binding motif (DXG) in apyrase conserved region 1. We performed a single amino acid substitution at position X in the motif. The ratio of the velocity of ATP/ADP hydrolysis was higher (approximately 1) for the S63A-MP67 mutant than for wild type-MP67 (0.19). Binding affinity for ADP of A75S-MpAPY2 mutant was increased to a level higher than that of the wild type MpAPY2. Thus, the residue at position X in the DXG motif plays an important role in determining nucleotide preference.

Okuhata, Riku; Otsuka, Yuki; Tsuchiya, Takahide; Kanzawa, Nobuyuki

2013-01-01

78

How to Maximally Support Local and Regional Biodiversity in Applied Conservation? Insights from Pond Management  

PubMed Central

Biodiversity and nature values in anthropogenic landscapes often depend on land use practices and management. Evaluations of the association between management and biodiversity remain, however, comparatively scarce, especially in aquatic systems. Furthermore, studies also tend to focus on a limited set of organism groups at the local scale, whereas a multi-group approach at the landscape scale is to be preferred. This study aims to investigate the effect of pond management on the diversity of multiple aquatic organism groups (e.g. phytoplankton, zooplankton, several groups of macro-invertebrates, submerged and emergent macrophytes) at local and regional spatial scales. For this purpose, we performed a field study of 39 shallow man-made ponds representing five different management types. Our results indicate that fish stock management and periodic pond drainage are crucial drivers of pond biodiversity. Furthermore, this study provides insight in how the management of eutrophied ponds can contribute to aquatic biodiversity. A combination of regular draining of ponds with efforts to keep ponds free of fish seems to be highly beneficial for the biodiversity of many groups of aquatic organisms at local and regional scales. Regular draining combined with a stocking of fish at low biomass is also preferable to infrequent draining and lack of fish stock control. These insights are essential for the development of conservation programs that aim long-term maintenance of regional biodiversity in pond areas across Europe.

Lemmens, Pieter; Mergeay, Joachim; De Bie, Tom; Van Wichelen, Jeroen; De Meester, Luc; Declerck, Steven A. J.

2013-01-01

79

How to maximally support local and regional biodiversity in applied conservation? Insights from pond management.  

PubMed

Biodiversity and nature values in anthropogenic landscapes often depend on land use practices and management. Evaluations of the association between management and biodiversity remain, however, comparatively scarce, especially in aquatic systems. Furthermore, studies also tend to focus on a limited set of organism groups at the local scale, whereas a multi-group approach at the landscape scale is to be preferred. This study aims to investigate the effect of pond management on the diversity of multiple aquatic organism groups (e.g. phytoplankton, zooplankton, several groups of macro-invertebrates, submerged and emergent macrophytes) at local and regional spatial scales. For this purpose, we performed a field study of 39 shallow man-made ponds representing five different management types. Our results indicate that fish stock management and periodic pond drainage are crucial drivers of pond biodiversity. Furthermore, this study provides insight in how the management of eutrophied ponds can contribute to aquatic biodiversity. A combination of regular draining of ponds with efforts to keep ponds free of fish seems to be highly beneficial for the biodiversity of many groups of aquatic organisms at local and regional scales. Regular draining combined with a stocking of fish at low biomass is also preferable to infrequent draining and lack of fish stock control. These insights are essential for the development of conservation programs that aim long-term maintenance of regional biodiversity in pond areas across Europe. PMID:23951328

Lemmens, Pieter; Mergeay, Joachim; De Bie, Tom; Van Wichelen, Jeroen; De Meester, Luc; Declerck, Steven A J

2013-01-01

80

Conserving Madagascar's Freshwater Biodiversity  

NSDL National Science Digital Library

This peer-reviewed article from BioScience is about conserving freshwater diversity in Madagascar. The island nation of Madagascar, an international conservation priority, is now also recognized as a global hotspot for freshwater biodiversity. Three emerging characteristics of Madagascar's threatened freshwater biota deserve increased attention from the scientific and conservation communities. First, species richness is not low, as was once assumed for both the freshwater fishes and the invertebrates. Second, many species are restricted to a specific region or even to single river basins. Often these species are also limited to streams or rivers draining primary forest habitat. Finally, many of the island's freshwater fishes are basal taxa, having diverged earlier than any other extant members of their clade. As such, these taxa assume disproportional phylogenetic importance. In the face of ongoing environmental threats, links among microendemism, forest stream specialization, and basal phylogenetic position highlight the importance and vulnerability of these species and provide a powerful incentive for immediate conservation action.

JONATHAN P. BENSTEAD, PATRICK H. DE RHAM, JEAN-LUC GATTOLLIAT, FRANÃÂOIS-MARIE GIBON, PAUL V. LOISELLE, MICHEL SARTORI, JOHN S. SPARKS, and MELANIE L. J. STIASSNY (;)

2003-11-01

81

Identification of Biodiversity Conservation Priorities using Predictive Modeling: An Application for the Equatorial Pacific Region of South America  

Microsoft Academic Search

We used predictive modeling of species distributions to identify conservation priority areas in the equatorial Pacific region\\u000a of western Ecuador and northwestern Peru. Museum and herbarium data and predictive models of species distributions are increasingly\\u000a being used to assess the conservation status of individual species. In this study, we assembled occurrence data for 28 species\\u000a of vascular plants, birds, and

Manuel Peralvo; Rodrigo Sierra; Kenneth R. Young; Carmen Ulloa-Ulloa

2007-01-01

82

Detailed mapping of the ERG– ETS2 interval of human chromosome 21 and comparison with the region of conserved synteny on mouse chromosome 16  

Microsoft Academic Search

We have carried out a detailed annotation of 550 kb of genomic DNA on human chromosome 21 containing the ERG and ETS2 genes. Comparative genomic analysis between this region and the interval of conserved synteny on mouse chromosome 16 indicated that the order and orientation of the ERG and ETS2 genes were conserved and revealed several regions containing potential conserved

C. M. Owczarek; K. J. Portbury; M. P. Hardy; D. A. O'Leary; J. Kudoh; K. Shibuya; N. Shimizu; I. Kola; P. J. Hertzog

2004-01-01

83

Lower Colorado Region Water Conservation Field Services Program: 2000 End of Year Report.  

National Technical Information Service (NTIS)

Water conservation and management is an increasing priority for the Bureau of Reclamation. Water conservation measures are needed to help meet our increasing agricultural, environmental, and urban water demands. In 1997, Reclamation created the Water Cons...

2000-01-01

84

Association between adjuvant regional radiotherapy and cognitive function in breast cancer patients treated with conservation therapy  

PubMed Central

Although protracted cognitive impairment has been reported to occur after radiotherapy even when such therapy is not directed to brain areas, the mechanism remains unclear. This study investigated whether breast cancer patients exposed to local radiotherapy showed lower cognitive function mediated by higher plasma interleukin (IL)-6 levels than those unexposed. We performed the Wechsler Memory Scale-Revised (WMS-R) and measured plasma IL-6 levels for 105 breast cancer surgical patients within 1 year after the initial therapy. The group differences in each of the indices of WMS-R were investigated between cancer patients exposed to adjuvant regional radiotherapy (n = 51) and those unexposed (n = 54) using analysis of covariance. We further investigated a mediation effect by plasma IL-6 levels on the relationship between radiotherapy and the indices of WMS-R using the bootstrapping method. The radiotherapy group showed significantly lower Immediate Verbal Memory Index and Delayed Recall Index (P = 0.001, P = 0.008, respectively). Radiotherapy exerted an indirect effect on the lower Delayed Recall Index of WMS-R through elevation of plasma IL-6 levels (bootstrap 95% confidence interval = ?2.6626 to ?0.0402). This study showed that breast cancer patients exposed to adjuvant regional radiotherapy in conservation therapy might have cognitive impairment even several months after their treatment. The relationship between the therapy and the cognitive impairment could be partially mediated by elevation of plasma IL-6 levels.

Shibayama, Osamu; Yoshiuchi, Kazuhiro; Inagaki, Masatoshi; Matsuoka, Yutaka; Yoshikawa, Eisho; Sugawara, Yuriko; Akechi, Tatsuo; Wada, Noriaki; Imoto, Shigeru; Murakami, Koji; Ogawa, Asao; Akabayashi, Akira; Uchitomi, Yosuke

2014-01-01

85

Association between adjuvant regional radiotherapy and cognitive function in breast cancer patients treated with conservation therapy.  

PubMed

Although protracted cognitive impairment has been reported to occur after radiotherapy even when such therapy is not directed to brain areas, the mechanism remains unclear. This study investigated whether breast cancer patients exposed to local radiotherapy showed lower cognitive function mediated by higher plasma interleukin (IL)-6 levels than those unexposed. We performed the Wechsler Memory Scale-Revised (WMS-R) and measured plasma IL-6 levels for 105 breast cancer surgical patients within 1 year after the initial therapy. The group differences in each of the indices of WMS-R were investigated between cancer patients exposed to adjuvant regional radiotherapy (n = 51) and those unexposed (n = 54) using analysis of covariance. We further investigated a mediation effect by plasma IL-6 levels on the relationship between radiotherapy and the indices of WMS-R using the bootstrapping method. The radiotherapy group showed significantly lower Immediate Verbal Memory Index and Delayed Recall Index (P = 0.001, P = 0.008, respectively). Radiotherapy exerted an indirect effect on the lower Delayed Recall Index of WMS-R through elevation of plasma IL-6 levels (bootstrap 95% confidence interval = -2.6626 to -0.0402). This study showed that breast cancer patients exposed to adjuvant regional radiotherapy in conservation therapy might have cognitive impairment even several months after their treatment. The relationship between the therapy and the cognitive impairment could be partially mediated by elevation of plasma IL-6 levels. PMID:24756915

Shibayama, Osamu; Yoshiuchi, Kazuhiro; Inagaki, Masatoshi; Matsuoka, Yutaka; Yoshikawa, Eisho; Sugawara, Yuriko; Akechi, Tatsuo; Wada, Noriaki; Imoto, Shigeru; Murakami, Koji; Ogawa, Asao; Akabayashi, Akira; Uchitomi, Yosuke

2014-06-01

86

Searching databases of conserved sequence regions by aligning protein multiple-alignments.  

PubMed Central

A general searching method for comparing multiple sequence alignments was developed to detect sequence relationships between conserved protein regions. Multiple alignments are treated as sequences of amino acid distributions and aligned by comparing pairs of such distributions. Four different comparison measures were tested and the Pearson correlation coefficient chosen. The method is sensitive, detecting weak sequence relationships between protein families. Relationships are detected beyond the range of conventional sequence database searches, illustrating the potential usefulness of the method. The previously undetected relation between flavoprotein subunits of two oxidoreductase families points to the potential active site in one of the families. The similarity between the bacterial RecA, DnaA and Rad51 protein families reveals a region in DnaA and Rad51 proteins likely to bind and unstack single-stranded DNA. Helix--turn--helix DNA binding domains from diverse proteins are readily detected and shown to be similar to each other. Glycosylasparaginase and gamma-glutamyltransferase enzymes are found to be similar in their proteolytic cleavage sites. The method has been fully implemented on the World Wide Web at URL: http://blocks.fhcrc.org/blocks-bin/LAMAvsearch.

Pietrokovski, S

1996-01-01

87

[Geographic distribution of birds in the Sierra Madre Oriental of San Luis Potosi, Mexico: a regional analysis of conservation status].  

PubMed

The Sierra Madre Oriental region in the mexican state of San Luis Potosi is a relevant place for bird conservation at a country level. Therefore the main goal of this study was to analyze the geographic patterns of distribution and the conservation current state of the birds, to support the needs to expand the conservation areas in the future. Data was collected from various databases of zoological museums and collections, and field sampling methods conducted from January 2009 to May 2011. Potential distributions were modeled for 284 species using GARP software and then a map was developed to determine areas with favorable environmental characteristics for the distribution of species richness. Finally, the importance of conservation areas for the potential distribution of birds in the region was evaluated. A total of 359 species were recorded of which 71.4% are permanent residents, 19% are winter migrants and 4% are summer residents. From this total, 41 species were endemic, 47 were species at risk and 149 were neotropical migrants. The largest species richness correspond to oak forests, cloud forests, and tropical moist forests located at altitudes from 100m to 1 500m. Their potential distribution was concentrated towards the center and Southeast of the study area. Only 10% of areas with a high potential conservation was included in areas of priority for bird conservation (AICA) and just 3% of all potential areas were under some governmental category of protection. However, no conservation area has a management plan currently applied and monitored. The information generated is important for the development of management proposals for birds conservation in the region. PMID:23885599

Sahagún Sánchez, Francisco Javier; Navarro, Jaime Castro; Reyes Hernández, Humberto

2013-06-01

88

Waterfowl Conservation in the US Prairie Pothole Region: Confronting the Complexities of Climate Change  

PubMed Central

The Prairie Pothole Region (PPR) is the most important waterfowl production area in North America. However, waterfowl populations there are predicted to decline because of climate-related drying of wetlands. Consequently, changes in the geographic focus of PPR waterfowl conservation have been recommended, which could have long-lasting and costly impacts. We used a 40-year dataset of pond counts collected in the PPR to test hypotheses about climate-related drying. We assessed May (1974–2013) and July (1974–2003) pond numbers in 20 waterfowl survey strata to determine if trends in pond numbers were consistent with predictions of drying. We also assessed trends in precipitation and temperature for the 20 strata and developed models describing May pond numbers from 1974 through 2010 as a function of precipitation, temperature, the previous year’s pond numbers, and location. None of the 20 strata showed significant declines in May pond numbers, although seven strata showed increases over time. July pond numbers declined significantly in one stratum, and increased in seven strata. An index to hydroperiod showed significant increasing trends in three strata, and no strata had decreasing trends. Precipitation increased significantly in two strata and decreased in two from 1974 to 2010; no strata showed significant changes in temperature. The best linear model described pond numbers within all strata as a function of precipitation, temperature, the previous year’s pond numbers, and the latitude and longitude of the stratum, and explained 62% of annual variation in pond numbers. We hypothesize that direct effects of climate change on prairie pothole wetlands and waterfowl may be overshadowed by indirect effects such as intensified land use and increased pressure to drain wetlands. We recommend that an adaptive, data-driven approach be used to resolve uncertainties regarding direct and indirect effects of climate change on prairie wetlands and waterfowl, and guide future conservation efforts.

Niemuth, Neal D.; Fleming, Kathleen K.; Reynolds, Ronald E.

2014-01-01

89

Automatic Identification of Highly Conserved Family Regions and Relationships in Genome Wide Datasets Including Remote Protein Sequences  

PubMed Central

Identifying shared sequence segments along amino acid sequences generally requires a collection of closely related proteins, most often curated manually from the sequence datasets to suit the purpose at hand. Currently developed statistical methods are strained, however, when the collection contains remote sequences with poor alignment to the rest, or sequences containing multiple domains. In this paper, we propose a completely unsupervised and automated method to identify the shared sequence segments observed in a diverse collection of protein sequences including those present in a smaller fraction of the sequences in the collection, using a combination of sequence alignment, residue conservation scoring and graph-theoretical approaches. Since shared sequence fragments often imply conserved functional or structural attributes, the method produces a table of associations between the sequences and the identified conserved regions that can reveal previously unknown protein families as well as new members to existing ones. We evaluated the biological relevance of the method by clustering the proteins in gold standard datasets and assessing the clustering performance in comparison with previous methods from the literature. We have then applied the proposed method to a genome wide dataset of 17793 human proteins and generated a global association map to each of the 4753 identified conserved regions. Investigations on the major conserved regions revealed that they corresponded strongly to annotated structural domains. This suggests that the method can be useful in predicting novel domains on protein sequences.

Dogan, Tunca; Karacal?, Bilge

2013-01-01

90

Automatic identification of highly conserved family regions and relationships in genome wide datasets including remote protein sequences.  

PubMed

Identifying shared sequence segments along amino acid sequences generally requires a collection of closely related proteins, most often curated manually from the sequence datasets to suit the purpose at hand. Currently developed statistical methods are strained, however, when the collection contains remote sequences with poor alignment to the rest, or sequences containing multiple domains. In this paper, we propose a completely unsupervised and automated method to identify the shared sequence segments observed in a diverse collection of protein sequences including those present in a smaller fraction of the sequences in the collection, using a combination of sequence alignment, residue conservation scoring and graph-theoretical approaches. Since shared sequence fragments often imply conserved functional or structural attributes, the method produces a table of associations between the sequences and the identified conserved regions that can reveal previously unknown protein families as well as new members to existing ones. We evaluated the biological relevance of the method by clustering the proteins in gold standard datasets and assessing the clustering performance in comparison with previous methods from the literature. We have then applied the proposed method to a genome wide dataset of 17793 human proteins and generated a global association map to each of the 4753 identified conserved regions. Investigations on the major conserved regions revealed that they corresponded strongly to annotated structural domains. This suggests that the method can be useful in predicting novel domains on protein sequences. PMID:24069417

Do?an, Tunca; Karaçal?, Bilge

2013-01-01

91

Performance of 12 DIR algorithms in low-contrast regions for mass and density conserving deformation  

SciTech Connect

Purpose: Deformable image registration (DIR) has become a key tool for adaptive radiotherapy to account for inter- and intrafraction organ deformation. Of contemporary interest, the application to deformable dose accumulation requires accurate deformation even in low contrast regions where dose gradients may exist within near-uniform tissues. One expects high-contrast features to generally be deformed more accurately by DIR algorithms. The authors systematically assess the accuracy of 12 DIR algorithms and quantitatively examine, in particular, low-contrast regions, where accuracy has not previously been established.Methods: This work investigates DIR algorithms in three dimensions using deformable gel (DEFGEL) [U. J. Yeo, M. L. Taylor, L. Dunn, R. L. Smith, T. Kron, and R. D. Franich, “A novel methodology for 3D deformable dosimetry,” Med. Phys. 39, 2203–2213 (2012)], for application to mass- and density-conserving deformations. CT images of DEFGEL phantoms with 16 fiducial markers (FMs) implanted were acquired in deformed and undeformed states for three different representative deformation geometries. Nonrigid image registration was performed using 12 common algorithms in the public domain. The optimum parameter setup was identified for each algorithm and each was tested for deformation accuracy in three scenarios: (I) original images of the DEFGEL with 16 FMs; (II) images with eight of the FMs mathematically erased; and (III) images with all FMs mathematically erased. The deformation vector fields obtained for scenarios II and III were then applied to the original images containing all 16 FMs. The locations of the FMs estimated by the algorithms were compared to actual locations determined by CT imaging. The accuracy of the algorithms was assessed by evaluation of three-dimensional vectors between true marker locations and predicted marker locations.Results: The mean magnitude of 16 error vectors per sample ranged from 0.3 to 3.7, 1.0 to 6.3, and 1.3 to 7.5 mm across algorithms for scenarios I to III, respectively. The greatest accuracy was exhibited by the original Horn and Schunck optical flow algorithm. In this case, for scenario III (erased FMs not contributing to driving the DIR calculation), the mean error was half that of the modified demons algorithm (which exhibited the greatest error), across all deformations. Some algorithms failed to reproduce the geometry at all, while others accurately deformed high contrast features but not low-contrast regions—indicating poor interpolation between landmarks.Conclusions: The accuracy of DIR algorithms was quantitatively evaluated using a tissue equivalent, mass, and density conserving DEFGEL phantom. For the model studied, optical flow algorithms performed better than demons algorithms, with the original Horn and Schunck performing best. The degree of error is influenced more by the magnitude of displacement than the geometric complexity of the deformation. As might be expected, deformation is estimated less accurately for low-contrast regions than for high-contrast features, and the method presented here allows quantitative analysis of the differences. The evaluation of registration accuracy through observation of the same high contrast features that drive the DIR calculation is shown to be circular and hence misleading.

Yeo, U. J.; Supple, J. R.; Franich, R. D. [School of Applied Sciences and Health Innovations Research Institute, RMIT University, Melbourne 3000 (Australia)] [School of Applied Sciences and Health Innovations Research Institute, RMIT University, Melbourne 3000 (Australia); Taylor, M. L. [School of Applied Sciences and Health Innovations Research Institute, RMIT University, Melbourne 3000 (Australia) [School of Applied Sciences and Health Innovations Research Institute, RMIT University, Melbourne 3000 (Australia); Physical Sciences, Peter MacCallum Cancer Centre, East Melbourne 3002 (Australia); Medical Physics, William Buckland Radiotherapy Centre, The Alfred Hospital, Melbourne 3004 (Australia); Smith, R. [School of Applied Sciences and Health Innovations Research Institute, RMIT University, Melbourne 3000, Australia and Medical Physics, William Buckland Radiotherapy Centre, The Alfred Hospital, Melbourne 3004 (Australia)] [School of Applied Sciences and Health Innovations Research Institute, RMIT University, Melbourne 3000, Australia and Medical Physics, William Buckland Radiotherapy Centre, The Alfred Hospital, Melbourne 3004 (Australia); Kron, T. [School of Applied Sciences and Health Innovations Research Institute, RMIT University, Melbourne 3000, Australia and Physical Sciences, Peter MacCallum Cancer Centre, East Melbourne 3002 (Australia)] [School of Applied Sciences and Health Innovations Research Institute, RMIT University, Melbourne 3000, Australia and Physical Sciences, Peter MacCallum Cancer Centre, East Melbourne 3002 (Australia)

2013-10-15

92

Simulation of water-use conservation scenarios for the Mississippi Delta using an existing regional groundwater flow model  

USGS Publications Warehouse

The Mississippi River alluvial plain in northwestern Mississippi (referred to as the Delta), once a floodplain to the Mississippi River covered with hardwoods and marshland, is now a highly productive agricultural region of large economic importance to Mississippi. Water for irrigation is supplied primarily by the Mississippi River Valley alluvial aquifer, and although the alluvial aquifer has a large reserve, there is evidence that the current rate of water use from the alluvial aquifer is not sustainable. Using an existing regional groundwater flow model, conservation scenarios were developed for the alluvial aquifer underlying the Delta region in northwestern Mississippi to assess where the implementation of water-use conservation efforts would have the greatest effect on future water availability-either uniformly throughout the Delta, or focused on a cone of depression in the alluvial aquifer underlying the central part of the Delta. Five scenarios were simulated with the Mississippi Embayment Regional Aquifer Study groundwater flow model: (1) a base scenario in which water use remained constant at 2007 rates throughout the entire simulation; (2) a 5-percent 'Delta-wide' conservation scenario in which water use across the Delta was decreased by 5 percent; (3) a 5-percent 'cone-equivalent' conservation scenario in which water use within the area of the cone of depression was decreased by 11 percent (a volume equivalent to the 5-percent Delta-wide conservation scenario); (4) a 25-percent Delta-wide conservation scenario in which water use across the Delta was decreased by 25 percent; and (5) a 25-percent cone-equivalent conservation scenario in which water use within the area of the cone of depression was decreased by 55 percent (a volume equivalent to the 25-percent Delta-wide conservation scenario). The Delta-wide scenarios result in greater average water-level improvements (relative to the base scenario) for the entire Delta area than the cone-equivalent scenarios; however, the cone-equivalent scenarios result in greater average water-level improvements within the area of the cone of depression because of focused conservation efforts within that area. Regardless of where conservation is located, the greatest average improvements in water level occur within the area of the cone of depression because of the corresponding large area of unsaturated aquifer material within the area of the cone of depression and the hydraulic gradient, which slopes from the periphery of the Delta towards the area of the cone of depression. Of the four conservation scenarios, the 25-percent cone-equivalent scenario resulted in the greatest increase in storage relative to the base scenario with a 32-percent improvement over the base scenario across the entire Delta and a 60-percent improvement within the area of the cone of depression. Overall, the results indicate that focusing conservation efforts within the area of the cone of depression, rather than distributing conservation efforts uniformly across the Delta, results in greater improvements in the amount of storage within the alluvial aquifer. Additionally, as the total amount of conservation increases (that is, from 5 to 25 percent), the difference in storage improvement between the Delta-wide and cone-equivalent scenarios also increases, resulting in greater gains in storage in the cone-equivalent scenario than in the Delta-wide scenario for the same amount of conservation.

Barlow, Jeannie R.B.; Clark, Brian R.

2011-01-01

93

Hundreds of conserved non-coding genomic regions are independently lost in mammals  

PubMed Central

Conserved non-protein-coding DNA elements (CNEs) often encode cis-regulatory elements and are rarely lost during evolution. However, CNE losses that do occur can be associated with phenotypic changes, exemplified by pelvic spine loss in sticklebacks. Using a computational strategy to detect complete loss of CNEs in mammalian genomes while strictly controlling for artifacts, we find >600 CNEs that are independently lost in at least two mammalian lineages, including a spinal cord enhancer near GDF11. We observed several genomic regions where multiple independent CNE loss events happened; the most extreme is the DIAPH2 locus. We show that CNE losses often involve deletions and that CNE loss frequencies are non-uniform. Similar to less pleiotropic enhancers, we find that independently lost CNEs are shorter, slightly less constrained and evolutionarily younger than CNEs without detected losses. This suggests that independently lost CNEs are less pleiotropic and that pleiotropic constraints contribute to non-uniform CNE loss frequencies. We also detected 35 CNEs that are independently lost in the human lineage and in other mammals. Our study uncovers an interesting aspect of the evolution of functional DNA in mammalian genomes. Experiments are necessary to test if these independently lost CNEs are associated with parallel phenotype changes in mammals.

Hiller, Michael; Schaar, Bruce T.; Bejerano, Gill

2012-01-01

94

Hundreds of conserved non-coding genomic regions are independently lost in mammals.  

PubMed

Conserved non-protein-coding DNA elements (CNEs) often encode cis-regulatory elements and are rarely lost during evolution. However, CNE losses that do occur can be associated with phenotypic changes, exemplified by pelvic spine loss in sticklebacks. Using a computational strategy to detect complete loss of CNEs in mammalian genomes while strictly controlling for artifacts, we find >600 CNEs that are independently lost in at least two mammalian lineages, including a spinal cord enhancer near GDF11. We observed several genomic regions where multiple independent CNE loss events happened; the most extreme is the DIAPH2 locus. We show that CNE losses often involve deletions and that CNE loss frequencies are non-uniform. Similar to less pleiotropic enhancers, we find that independently lost CNEs are shorter, slightly less constrained and evolutionarily younger than CNEs without detected losses. This suggests that independently lost CNEs are less pleiotropic and that pleiotropic constraints contribute to non-uniform CNE loss frequencies. We also detected 35 CNEs that are independently lost in the human lineage and in other mammals. Our study uncovers an interesting aspect of the evolution of functional DNA in mammalian genomes. Experiments are necessary to test if these independently lost CNEs are associated with parallel phenotype changes in mammals. PMID:23042682

Hiller, Michael; Schaar, Bruce T; Bejerano, Gill

2012-12-01

95

Fire mosaics and reptile conservation in a fire-prone region.  

PubMed

Fire influences the distribution of fauna in terrestrial biomes throughout the world. Use of fire to achieve a mosaic of vegetation in different stages of succession after burning (i.e., patch-mosaic burning) is a dominant conservation practice in many regions. Despite this, knowledge of how the spatial attributes of vegetation mosaics created by fire affect fauna is extremely scarce, and it is unclear what kind of mosaic land managers should aim to achieve. We selected 28 landscapes (each 12.6 km(2) ) that varied in the spatial extent and diversity of vegetation succession after fire in a 104,000 km(2) area in the semiarid region of southeastern Australia. We surveyed for reptiles at 280 sites nested within the 28 landscapes. The landscape-level occurrence of 9 of the 22 species modeled was associated with the spatial extent of vegetation age classes created by fire. Biogeographic context and the extent of a vegetation type influenced 7 and 4 species, respectively. No species were associated with the diversity of vegetation ages within a landscape. Negative relations between reptile occurrence and both extent of recently burned vegetation (?10 years postfire, n = 6) and long unburned vegetation (>35 years postfire, n = 4) suggested that a coarse-grained mosaic of areas (e.g. >1000 ha) of midsuccessional vegetation (11-35 years postfire) may support the fire-sensitive reptile species we modeled. This age class coincides with a peak in spinifex cover, a keystone structure for reptiles in semiarid and arid Australia. Maintaining over the long term a coarse-grained mosaic of large areas of midsuccessional vegetation in mallee ecosystems will need to be balanced against the short-term negative effects of large fires on many reptile species and a documented preference by species from other taxonomic groups, particularly birds, for older vegetation. PMID:23163245

Nimmo, D G; Kelly, L T; Spence-Bailey, L M; Watson, S J; Taylor, R S; Clarke, M F; Bennett, A F

2013-04-01

96

Land-use change, climate and conservation of peatlands: lessons from the high-resolution palaeoecology peat archives of the southern Baltic region  

NASA Astrophysics Data System (ADS)

Conservation of peatlands and other issues connected with carbon sequestration and the global change have been increasingly challenging during the last decade. However, the reliable conservation can only be based on the interdisciplinary approach to the peatland ecosystem functioning. Good understanding of a present state is impossible without looking into the past conditions using various palaeoecological methods (e.g. analyses of: plant macrofossils, testate amoebae, pollen and spores and non-pollen palynomorphs). Natural developmental trends can only be recognized, having a long-term perspective (decadal, centennial or millennial scale). This perspective can be used to identify the past human impact. Many peatlands possess the state that is apparently pristine, but when we look into their past it is often obvious that their state was disturbed long time ago. Consequently, geological and palaeoecological study is prerequisite to begin a neo-ecological study. Furthermore, the past perspective is useful to start measurements of the modern processes e.g. hydrological monitoring or carbon exchange. We present high-resolution multi-proxy data from three raised bogs located in southern Baltic region. The quantitative reconstructions show the gradual disturbance connected with increasing human impact (deforestation and local peat cutting). We also show the extent of peatlands' degradation and difficulty of the recovery after stress. Differences of preservation on the example of three different bogs with the different Holocene histories will be presented. We paid an exceptional attention to the last thousand years as and the transition to the anthropocene.

Lamentowicz, M.; Ga?ka, M.; Tobolski, K.; Górska, A.

2012-04-01

97

Follow-up of the regional energy conservation politics. Methods and illustration with the case of Charente-Poitou.  

National Technical Information Service (NTIS)

The objective of this study was to develop a follow-up method for the energy conservation planning in a region in France. The first goal is to improve the energy balance in France but many other goals are introduced in the new approach: effects on the loc...

B. Guesnier F. Trousslot J. Debord J. P. Carriere

1987-01-01

98

Gravel–sand mulch for soil and water conservation in the semiarid loess region of northwest China  

Microsoft Academic Search

In the semiarid loess region of northwest China, the use of gravel and sand as mulch has been an indigenous farming technique for crop production for over 300 years. However, systematic studies concerning the effects of surface gravel–sand (mixed gravel and sand) covers on soil and water conservation are scarce. Based on previous studies, this study investigates the effects of

Xiao-Yan Li

2003-01-01

99

Achieving Conservation when Opportunity Costs Are High: Optimizing Reserve Design in Alberta's Oil Sands Region  

Microsoft Academic Search

Recent studies have shown that conservation gains can be achieved when the spatial distributions of biological benefits and economic costs are incorporated in the conservation planning process. Using Alberta, Canada, as a case study we apply these techniques in the context of coarse-filter reserve design. Because targets for ecosystem representation and other coarse-filter design elements are difficult to define objectively

Richard R. Schneider; Grant Hauer; Dan Farr; W. L. Adamowicz; Stan Boutin

2011-01-01

100

Distribution and Conservation of Genetic Diversity Among UK Calcareous Grassland Regions: A Case Study Using Insects  

Microsoft Academic Search

Conservation strategies for whole communities at the landscape scale have rarely been able to take into account genetic diversity because of the number of species involved. However, if species can be grouped together by geographic distribution of genetic diversity and patterns of relatedness, then landscape and genetic conservation might be more effectively combined to cope with problems of fragmentation. We

Bo-Chi G. Lai; Andrew S. Pullin

2005-01-01

101

Fast Parallel Recognizer.  

National Technical Information Service (NTIS)

There exist several algorithms that can recognize a language in L2 described by a Context-Free Grammar (CFG). One of those algorithms is the Cocke-Younger-Kasami (CYK) algorithm which has O(n sup 3) time complexity and which requires a grammar in Chomsky ...

J. P. M. de Vreught H. J. Honig

1990-01-01

102

Recognizing Chemical Hazards Module  

NSDL National Science Digital Library

The Center for the Advancement of Process Technology presents this free sample module on recognizing chemical hazards. It focuses on chemical hazards specific to process industries, and their impact on safety, health and the environment. The material also introduces the purpose and components of an MSDS.

2013-01-09

103

Fast Parallel Recognizer.  

National Technical Information Service (NTIS)

Algorithms that can recognize a language described by a context free grammar are studied. The Gibbons and Rytter algorithm, which relies heavily on a pebble game theorem is given. A previous de Vreught and Honig time algorithm is recalled, and a fast para...

J. P. M. Devreught H. J. Honig

1990-01-01

104

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

PubMed Central

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

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

2007-01-01

105

A leucine-rich repeat region is conserved in pollen extensin-like (Pex) proteins in monocots and dicots.  

PubMed

We previously isolated a pollen-specific gene encoding a pollen tube wall-associated glycoprotein with a globular domain and an extensin domain from maize (mPex1). To evaluate which protein domains might be important for function, we isolated a second monocot gene (mPex2) and a dicot gene (tPex). Each gene encodes a signal sequence, an N-terminal globular domain comprised of a variable region, a leucine-rich repeat (LRR) with an adjacent cysteine-rich region, a transition region and an extensin-like C-terminal domain. The LRRs of the maize and tomato Pex proteins are highly conserved. Although the extensin domains in the maize and tomato proteins vary in length and in amino acid sequence, they are likely to be structurally conserved. Additional putative Pex gene sequences were identified by either GenBank search (Arabidopsis) or PCR (sorghum and potato): all encode conserved LRRs. The presence of a conserved LRR in the known and potential Pex proteins strongly suggests that this motif is involved in the binding of a specific ligand during pollen tube growth. Gene expression studies using RNA and protein blotting as well as promoter-reporter gene fusions in transient and stable transformation indicate that the tomato Pex gene is pollen-specific. PMID:11437249

Stratford, S; Barne, W; Hohorst, D L; Sagert, J G; Cotter, R; Golubiewski, A; Showalter, A M; McCormick, S; Bedinger, P

2001-05-01

106

[Effects of artificial seabuckthorn forest on soil and water conservation in loess hilly region].  

PubMed

Seabuckthorn is regarded as a main eco-economical tree species, and plays an increasing important role in eco-environmental construction in Northwest, Northeast and North China. Our study on artificial seabuckthorn forest in loess hilly region showed that the average rainfall interception rate of 7-10 ages seabuckthorn canopy was 8.5%, and the litter layer of 5-10 ages seabuckthorn forest could intercept 0.89 mm rainfall. Seabuckthorn forest could improve soil infiltration and anti-strike ability through improving soil physical and chemical properties, and the numbers of its hair roots and the depth of its litter layer were the main indices of soil anti-strike ability. The effects of seabuckthorn forest on soil and water conservation increased with its increasing age. In 2-3 ages stage, the effects were weak, and the runoff and sediment were mainly affected by the characters of rainfall. In 4-5 ages stage when the forest became maturing, the annual runoff depth and annual erosion modulus were 1.8-3.2 mm and 24.64 t x km(-2), respectively. In 6-12 ages stage when the forest matured, the runoff and sediment on seabuckthorn woodland changed slowly, the annual runoff depth and annual erosion modulus being 0.3 -3.4 mm and 0-6.75 t x km(-2), respectively, and the characters of rainfall had much less effect on them. In the stage from young (2-5 ages) to mature forest, the sediment charge in runoff changed sharply, ranged from 77. 31 kg x m(-3) to 9.12 kg x m(-3), but in 6-12 ages stage, the sediment content in runoff changed very slowly, and the range was 0-5.09 kg x m(-3). PMID:16011150

Chen, Yunming; Liu, Guobin; Xu, Bingcheng

2005-04-01

107

Recognizing Cartesian graph bundles  

Microsoft Academic Search

Graph bundles generalize the notion of covering graphs and graph products. In this paper we extend some of the methods for recognizing Cartesian product graphs to graph bundles. Two main notions are used. The first one is the well-known equivalence relation ?? defined on the edge-set of a graph. The second one is the concept of k-convex subgraphs. A subgraph

Wilfried Imrich; Tomaz Pisanski; Janez Zerovnik

1997-01-01

108

Evaluating cost-effectiveness of conservation management actions in an agricultural landscape on a regional scale  

Microsoft Academic Search

Agricultural landscapes are the dominating landscape types in many parts of the world. Land-use intensification and spatial homogeneity are major threats to biodiversity in these landscapes. Thus cost-effective strategies for species conservation in large-scale agricul- tural landscapes are required. Spatial optimisation methods can be applied to identify the most effective allocation of a given budget for conservation. However, the optimisation

Annelie Holzkamper; Ralf Seppelt

2006-01-01

109

Duck Nest Success on Conservation Reserve Program Land in the Prairie Pothole Region  

NSDL National Science Digital Library

The Northern Prairie Wildlife Research Center (NPWRC) continues to place scientific/ management resources online for general viewing. This resource, by H.A. Kantrud was originally published in 1993 in the Journal of Soil and Water Conservation [48(3):238-242] and examines nest success of dabbling ducks on Conservation Reserve Program (CRP) land. It may be browsed online or downloaded as a .zip file.

Kantrud, Harold A.

1993-01-01

110

Mapping regional land cover with MODIS data for biological conservation: Examples from the Greater Yellowstone Ecosystem, USA and Pará State, Brazil  

Microsoft Academic Search

The paper investigated the application of MODIS data for mapping regional land cover at moderate resolutions (250 and 500 m), for regional conservation purposes. Land cover maps were generated for two major conservation areas (Greater Yellowstone Ecosystem—GYE, USA and the Pará State, Brazil) using MODIS data and decision tree classifications. The MODIS land cover products were evaluated using existing Landsat

K. J Wessels; R. S De Fries; J Dempewolf; L. O Anderson; A. J Hansen; S. L Powell; E. F Moran

2004-01-01

111

Mapping regional land cover with MODIS data for biological conservation: Examples from the Greater Yellowstone Ecosystem USA and Para´ State Brazil  

Microsoft Academic Search

Abstract The paper investigated the application of MODIS data for mapping regional land cover at moderate resolutions (250 and 500 m), for regional conservation purposes. Land cover maps were generated for two major conservation areas (Greater Yellowstone Ecosystem—GYE, USA and the Para´ State, Brazil) using MODIS data and decision tree classifications. The MODIS land cover products were evaluated using existing

K. j. Wessels; R. s. De Fries; J. Dempewolf; L. o. Anderson; A. j. Hansen

112

Conclusions and recommendations of the Latin America and Caribbean Regional Energy Conservation Seminar, Alajuela, Costa Rica, January 14-17, 1985  

SciTech Connect

Reports were given on active energy-conservation projects in the region (Barbados, Jamaica, Central American region and Panama, Peru, Ecuador, the Dominican Republic, and Costa Rica). In addition, there were presentations on energy auditing, fuel substitution, and financing energy conservation. Although the seminar concentrated on the industrial sector, it also explored opportunities for energy-efficiency improvements in the building and transportation sectors.

Not Available

1985-03-29

113

Mapping regional land cover with MODIS data for biological conservation: Examples from the Greater Yellowstone Ecosystem, USA and ParaState, Brazil  

Microsoft Academic Search

The paper investigated the application of MODIS data for mapping regional land cover at moderate resolutions (250 and 500 m), for regional conservation purposes. Land cover maps were generated for two major conservation areas (Greater Yellowstone Ecosystem—GYE, USA and the ParaState, Brazil) using MODIS data and decision tree classifications. The MODIS land cover products were evaluated using existing Landsat TM

K. J. Wesselsa; J. Dempewolfa; A. J. Hansend; E. F. Morane

114

Extreme conservation of non-repetitive non-coding regions near HoxD complex of vertebrates  

PubMed Central

Homeotic gene complexes determine the anterior-posterior body axis in animals. The expression pattern and function of hox genes along this axis is colinear with the order in which they are organized in the complex. This 'chromosomal organization and functional correspondence' is conserved in all bilaterians investigated. Although the molecular basis of this 'colinearity' in not yet understood, it is possible that there are control elements within or in the proximity of these complexes that establish and maintain the expression patterns of hox genes in a coordinated fashion. We report here an unprecedented conservation of non-coding DNA sequences adjacent to the HoxD complex of vertebrates. Stretches of hundreds of base pairs in a 7 kb region, upstream of HoxD complex, show 100% conservation from fish to human. Using primers designed from these sequences of human HoxD complex, we amplified the corresponding regions from different vertebrates, including mammals, aves, reptiles, amphibians and pisces. Such a high degree of conservation, where no variation was allowed during ~500 million years of evolution, suggests critical function for these sequences in the regulation of the HoxD complex. Furthermore, these sequences provide a molecular handle to gain insight into the mechanism of regulation of this complex.

2003-01-01

115

Two dual-specific (anti-IgG and anti-dsDNA) monoclonal autoantibodies derived from the NZB/NZW F1 recognize an epitope in the hinge region.  

PubMed

The anti-IgG properties of two dual-specific (anti-dsDNA and anti-IgG) monoclonal NZB/NZW F1-derived autoantibodies, BV 17-45 and BV 16-13, were studied to resolve the location and possible commonality of the IgG epitope. To determine if BV 17-45 and BV 16-13 recognized the same IgG epitope, the relative temperature sensitivity of the conformational IgG epitopes were evaluated using the conformational sensitive immunoassay. Comparison of the temperature sensitivity of the conformational immunoglobulin epitopes over a temperature range of 25-100 degrees C suggested that the epitope recognized by BV 17-45 was the same as the IgG epitope recognized by BV 16-13. Further studies with papain- and pepsin-generated F(ab')2, Fab, and Fc fragments of BV 17-45 and BV 16-13 revealed that the dual-specific autoantibodies BV 17-45 and BV 16-13 both bound an epitope in the hinge region of the IgG molecule. The potential correlation between these studies and the pathogenic nature of dual-specific autoantibodies is discussed. PMID:9853674

Workman, C J; Pfund, W P; Voss, E W

1998-10-01

116

On recognizing ignorance  

NASA Technical Reports Server (NTRS)

How an expert system reasons about its own ability to deal with a particular problem is studied. Ideally, an expert system ought to rapidly recognize that a particular problem is beyond its abilities and defer to another, perhaps human, expert. This capability is extremely important in domains where expert systems may control life critical processes such as air traffic control, medicine, strategic defense, and manned space exploration. The methods used by knowledge engineers to infuse an expert system with knowledge of its own limitations is surveyed. A computability theory is employed to analyze the general problem of meta-knowledge and to give insight into the efficacy of specific solutions.

Greene, Richard J.

1988-01-01

117

Learning to recognize objects.  

PubMed

A theory of object recognition requires a theory of shape. Despite considerable empirical and theoretical research, however, a definition of object shape has proved elusive. Two experiments provide new insights by showing that children's object recognition changes dramatically during the period between 17 and 25 months. During this time, children develop the ability to recognize stylized three-dimensional caricatures of known and novel objects. This ability is linked to the number of object names in children's vocabularies, suggesting that category learning may be a driving force behind the developmental changes. PMID:12741748

Smith, Linda B

2003-05-01

118

Geographical patterns in openland cover and hayfield mowing in the Upper Great Lakes region: implications for grassland bird conservation  

Microsoft Academic Search

Populations of many grassland bird species such as Grasshopper Sparrow (Ammodramus savannarum), Henslow’s Sparrow (A. henslowii), and Bobolink (Dolichonyx oryzivorus) have experienced considerable declines over the last century. To foster multi-species grassland bird conservation in the\\u000a Upper Great Lakes (UGL) states of Michigan, Minnesota, and Wisconsin, we quantified geographic patterns within three sub-regional\\u000a zones (e.g., North, Central, and South) of

R. Gregory Corace; David J. Flaspohler; Lindsey M. Shartell

2009-01-01

119

Variations in use of breast-conserving surgery by patient, hospital characteristics, and region: a multilevel analysis  

Microsoft Academic Search

We hare analysed the influence of patient and hospital characteristics and region, on the use of breast-conserving surgery\\u000a (BCS) in Catalonia (Spain).\\u000a \\u000a Data for this study was obtained from the Catalan Hospital Discharge Data Base. The study period was 1995–1998. The Mantel-Haenszel\\u000a test was used to examine overall trends in the use of BCS. A regression analysis was performed to

Mercè Peris Tuser; Josep A. Espinas Piñol; Montserrat Bustins Poblet; Agustín Escobedo Sánchez; Josep M. Borras Andrés; Xavier Puig Oriol

2001-01-01

120

Accurate discrimination of conserved coding and non-coding regions through multiple indicators of evolutionary dynamics  

Microsoft Academic Search

BACKGROUND: The conservation of sequences between related genomes has long been recognised as an indication of functional significance and recognition of sequence homology is one of the principal approaches used in the annotation of newly sequenced genomes. In the context of recent findings that the number non-coding transcripts in higher organisms is likely to be much higher than previously imagined,

Matteo Re; Graziano Pesole; David Stephen Horner

2009-01-01

121

Aligning Local Incentives to Regional Goals: Water Conservation in the Upper Tigris-Euphrates River System  

Microsoft Academic Search

Instead of international agreement between Syria, Iraq, and Turkey, the best hope for sustainable water conservation in the Euphrates-Tigris river basin lies with policies that can be justified on individual and local grounds within Turkey: reducing water run-off and accompanied pollution; reducing soil salinity; developing drought resistant strains of crops; and storing water as an insurance against future droughts that

Hasan Tekguc

2011-01-01

122

Structure-sequence based analysis for identification of conserved regions in proteins  

DOEpatents

Disclosed are computational methods, and associated hardware and software products for scoring conservation in a protein structure based on a computationally identified family or cluster of protein structures. A method of computationally identifying a family or cluster of protein structures in also disclosed herein.

Zemla, Adam T; Zhou, Carol E; Lam, Marisa W; Smith, Jason R; Pardes, Elizabeth

2013-05-28

123

The upstream conserved regions (UCRs) mediate homo- and hetero-oligomerization of type 4 cyclic nucleotide phosphodiesterases (PDE4s).  

PubMed

PDE4s (type 4 cyclic nucleotide phosphodiesterases) are divided into long and short forms by the presence or absence of conserved N-terminal domains termed UCRs (upstream conserved regions). We have shown previously that PDE4D2, a short variant, is a monomer, whereas PDE4D3, a long variant, is a dimer. In the present study, we have determined the apparent molecular masses of various long and short PDE4 variants by size-exclusion chromatography and sucrose density-gradient centrifugation. Our results indicate that dimerization is a conserved property of all long PDE4 forms, whereas short forms are monomers. Dimerization is mediated by the UCR domains. Given their high sequence conservation, the UCR domains mediate not only homo-oligomerization, but also hetero-oligomerization of distinct PDE4 long forms as detected by co-immunoprecipitation assays and FRET microscopy. Endogenous PDE4 hetero-oligomers are, however, low in abundance compared with homo-dimers, revealing the presence of mechanisms that predispose PDE4s towards homo-oligomerization. Oligomerization is a prerequisite for the regulatory properties of the PDE4 long forms, such as their PKA (protein kinase A)-dependent activation, but is not necessary for PDE4 protein-protein interactions. As a result, individual PDE4 protomers may independently mediate protein-protein interactions, providing a mechanism whereby PDE4s contribute to the assembly of macromolecular signalling complexes. PMID:24555506

Xie, Moses; Blackman, Brigitte; Scheitrum, Colleen; Mika, Delphine; Blanchard, Elise; Lei, Tao; Conti, Marco; Richter, Wito

2014-05-01

124

Molecular characterization of a newly recognized mouse parvovirus.  

PubMed Central

Mouse parvovirus (MPV), formerly known as orphan parvovirus, is a newly recognized rodent parvovirus distinct from both serotypes of minute virus of mice (MVM). Restriction analysis of the MPV genome indicated that many restriction sites in the capsid region were different from those of MVM, but most sites in the nonstructural (NS) region of the genome were conserved. MPV resembled MVM in genome size, replication intermediates, and NS proteins. Replication intermediates in infected cells were the same for MPV and MVM, including packaging of the 5-kb minus (V) strand. Furthermore, the MPV NS proteins were the same size as and present at the same ratio as the MVM(i) proteins in infected cells. Cloning and sequencing of the MPV genome revealed a genome organization closely resembling that of MVM, with conservation of open reading frames, promoter sequences, and splice sites. The left terminal hairpin was identical to that of MVM(i), but the right terminus was not conserved. Also, the MPV genome was unique in that it contained 1.8 copies of the terminal repeat sequence rather than the 1 or 2 copies found in other parvoviruses. The predicted amino acid sequence of the NS proteins of MPV and MVM(i) were nearly identical. In contrast, the predicted amino acid sequence of the capsid proteins of MPV was different from sequences of other parvoviruses. These results confirm that MPV is a distinct murine parvovirus and account for the antigenic differences between MPV and MVM. Images

Ball-Goodrich, L J; Johnson, E

1994-01-01

125

Systematic Analysis of a Conserved Region of the Aminoglycoside 6'-N-Acetyltransferase Type Ib  

Microsoft Academic Search

Alanine-scanning mutagenesis was applied to the aminoglycoside 6-N-acetyltransferase type Ib conserved motif B, and the effects of the substitutions were analyzed by measuring the MICs of kanamycin (KAN) and its semisynthetic derivative, amikacin (AMK). Several substitutions resulted in no major change in MICs. E167A and F171A resulted in derivatives that lost the ability to confer resistance to KAN and AMK.

ALI SHMARA; NATALIA WEINSETEL; KEN J. DERY; RAMONA CHAVIDEH; MARCELO E. TOLMASKY

2001-01-01

126

Human 4F5 single-chain Fv antibody recognizing a conserved HA1 epitope has broad neutralizing potency against H5N1 influenza A viruses of different clades.  

PubMed

Influenza A viruses present a significant threat to public health worldwide. High-affinity human scFv antibodies against a conserved epitope can potentially provide immunity to diverse viruses and protect against future pandemic viruses. A library of phage-displayed human scFv containing 6.0×10(8) members was generated from lymphocytes of H5N1 virus vaccinated individuals. Using the recombinant H5N1 virus hemagglutinin ectodomain (HA1), 4F5 scFv was identified with neutralizing activity against both clade 2 and 9 H5N1 viruses. In embryonated chicken eggs, the antiviral activity of 4F5 scFv conferred a 100% survival rate and at least a 62.5% survival rate against different clades of H5N1 viruses by pre-treatment and post-treatment, respectively. 4F5 scFv belongs to the VH-3-43 family according to the IMGT database, and a peptide (76)WLLGNP(81) containing half of an ?-helix in HA1 was identified as the binding pocket. The conserved binding epitope of this novel broadly neutralizing scFv may become key in the design and implementation of vaccines or RNA interference against H5N1 viruses. PMID:23680121

Zhang, Xiao; Qi, Xian; Zhang, Qianqian; Zeng, Xiaoyan; Shi, Zhiyang; Jin, Qiu; Zhan, Feng; Xu, Yan; Liu, Zhe; Feng, Zhenqing; Jiao, Yongjun

2013-08-01

127

Evidence of a conserved intrinsically disordered region in the C-terminus of the stringent response protein Rel from mycobacteria.  

PubMed

The RelA/SpoT enzyme produces (p)ppGpp that helps the bacterium survive during stress. The domains present in it are interspersed with connecting linkers whose functions have been poorly elucidated. We rationally analyzed the sequence and structural property of the regulatory C-terminal region in the Rel family of proteins and report the presence of an intrinsically disordered region between two successive domains in this region that are separated by a defined amino acid sequence length. We show that the length and secondary structure of this linker are conserved in Rel proteins, further signifying its importance in rendering flexibility for domain movement and domain-domain interaction. PMID:24717772

Ekal, Lakhan; Ganesh, Bylapudi; Joshi, Himanshu; Lama, Dilraj; Jain, Vikas

2014-05-01

128

Mutational analysis of the conserved cysteine-rich region of the human immunodeficiency virus type 1 Tat protein.  

PubMed Central

The Tat transactivator protein of human immunodeficiency virus type 1 contains a highly conserved cysteine-rich region, containing seven cysteines from residues 22 through 37. To investigate the importance of noncysteine residues in this region of the Tat protein, we have carried out a mutational analysis, in most cases substituting a single alanine for the wild-type noncysteine residue. Alanine substitution of residue 23, 24, 46, or 47 had no effect on Tat activity in plasmid transfection assays. In contrast, alanine substitutions of all eight noncysteines analyzed, from residues 26 through 41, significantly reduced the activity of the Tat protein, in some cases as drastically as mutations in cysteine residues. The results demonstrate that the precise sequence of the cysteine-rich region is crucial for a fully functional Tat protein. Images

Rice, A P; Carlotti, F

1990-01-01

129

Changes in Conserved Region 3 of Escherichia coli ? 70Mediate ppGpp-dependent Functions In Vivo  

Microsoft Academic Search

InEscherichia colideletion ofrelAandspoTresults in an inability to synthesize ppGpp, guanosine-3?, 5?-bis(pyrophosphate), and a loss in the ability to grow on amino acid-free minimal media. Two spontaneous missense suppressor alleles,rpoD(P505L)andrpoD(S506F)able to confer complete prototrophy without the reappearance of ppGpp, were localized to that portion ofrpoDcoding for conserved region 3.1 of ?70. Characterization of these mutants revealed distinct physiological effects. Both mutations

James V. Hernandez; Michael Cashel

1995-01-01

130

Identification of a second CtBP binding site in adenovirus type 5 E1A conserved region 3.  

PubMed

C-terminal binding protein (CtBP) binds to adenovirus early region 1A (AdE1A) through a highly conserved PXDLS motif close to the C terminus. We now have demonstrated that CtBP1 also interacts directly with the transcriptional activation domain (conserved region 3 [CR3]) of adenovirus type 5 E1A (Ad5E1A) and requires the integrity of the entire CR3 region for optimal binding. The interaction appears to be at least partially mediated through a sequence ((161)RRNTGDP(167)) very similar to a recently characterized novel CtBP binding motif in ZNF217 as well as other regions of CR3. Using reporter assays, we further demonstrated that CtBP1 represses Ad5E1A CR3-dependent transcriptional activation. Ad5E1A also appears to be recruited to the E-cadherin promoter through its interaction with CtBP. Significantly, Ad5E1A, CtBP1, and ZNF217 form a stable complex which requires CR3 and the PLDLS motif. It has been shown that Ad513SE1A, containing the CR3 region, is able to overcome the transcriptional repressor activity of a ZNF217 polypeptide fragment in a GAL4 reporter assay through recruitment of CtBP1. These results suggest a hitherto-unsuspected complexity in the association of Ad5E1A with CtBP, with the interaction resulting in transcriptional activation by recruitment of CR3-bound factors to CtBP1-containing complexes. PMID:18524818

Bruton, Rachel K; Pelka, Peter; Mapp, Katie L; Fonseca, Gregory J; Torchia, Joseph; Turnell, Andrew S; Mymryk, Joe S; Grand, Roger J A

2008-09-01

131

09/15: Comparative Genomics of a Conserved Chromosomal Region associated with a Complex Human Phenotype  

PubMed Central

Three genes that encode related Ig-superfamily molecules have recently been mapped to human chromosome 15 in the region q22.3-23, and to the syntenic region on mouse chromosome 9. These genes presumably derived from gene duplications and they are highly similar to Deleted in Colorectal Cancer (DCC), which functions as an axon guidance molecule during development of the nervous system. In order to find out whether additional genes of this class were present in a chromosomal cluster, we produced a comparative physical map within the region of synteny between mouse chromosome 9 and human chromosome 15. This interval overlaps the critical region for the fourth genetic locus for Bardet-Biedl Syndrome (BBS4) in humans. Bardet-Biedl Syndrome (OMIM 600374) is characterized by poly/syn/brachydactyly, retinal degeneration, hypogonadism, mental retardation, obesity, diabetes, and kidney abnormalities. A detailed map of this locus will help to identify candidate genes for this disorder.

Kappen, Claudia; Salbaum, J. Michael

2014-01-01

132

Computational Design of Proteins Targeting the Conserved Stem Region of Influenza Hemagglutinin  

SciTech Connect

We describe a general computational method for designing proteins that bind a surface patch of interest on a target macromolecule. Favorable interactions between disembodied amino acid residues and the target surface are identified and used to anchor de novo designed interfaces. The method was used to design proteins that bind a conserved surface patch on the stem of the influenza hemagglutinin (HA) from the 1918 H1N1 pandemic virus. After affinity maturation, two of the designed proteins, HB36 and HB80, bind H1 and H5 HAs with low nanomolar affinity. Further, HB80 inhibits the HA fusogenic conformational changes induced at low pH. The crystal structure of HB36 in complex with 1918/H1 HA revealed that the actual binding interface is nearly identical to that in the computational design model. Such designed binding proteins may be useful for both diagnostics and therapeutics.

Fleishman, Sarel J.; Whitehead, Timothy A.; Ekiert, Damian C.; Dreyfus, Cyrille; Corn, Jacob E.; Strauch, Eva-Maria; Wilson, Ian A.; Baker, David (UWASH); (Scripps)

2011-09-28

133

In vitro phosphorylation studies of a conserved region of the transcription factor ATF1.  

PubMed Central

A large family of mammalian transcription factors including multiple variants of CREB, CREM and ATF1 have been implicated in signal transduction by cAMP and other cellular pathways. Although the roles of some members of the family have been characterised the function of ATF1 is poorly understood. We have identified one or more key serine residues that are required for a phosphorylation-induced conformational change in ATF1. The critical serines map to a putative transcriptional activation domain of ATF1 and affect the stability of ATF1 DNA-binding. Intriguingly phosphorylation is modulated by ATF1 homodimerization and by ATF1 binding to DNA. One of the key serine residues required for ATF1 phosphorylation is not conserved in CREB and CREM suggesting that it is likely to determine some specialised function of ATF1. Images

Masson, N; John, J; Lee, K A

1993-01-01

134

In vitro phosphorylation studies of a conserved region of the transcription factor ATF1.  

PubMed

A large family of mammalian transcription factors including multiple variants of CREB, CREM and ATF1 have been implicated in signal transduction by cAMP and other cellular pathways. Although the roles of some members of the family have been characterised the function of ATF1 is poorly understood. We have identified one or more key serine residues that are required for a phosphorylation-induced conformational change in ATF1. The critical serines map to a putative transcriptional activation domain of ATF1 and affect the stability of ATF1 DNA-binding. Intriguingly phosphorylation is modulated by ATF1 homodimerization and by ATF1 binding to DNA. One of the key serine residues required for ATF1 phosphorylation is not conserved in CREB and CREM suggesting that it is likely to determine some specialised function of ATF1. PMID:8414969

Masson, N; John, J; Lee, K A

1993-09-11

135

Intelligent irrigation performance: evaluation and quantifying its ability for conserving water in arid region  

NASA Astrophysics Data System (ADS)

Intelligent irrigation technologies have been developed in recent years to apply irrigation to turf and landscape plants. These technologies are an evapotranspiration (ET)-based irrigation controller, which calculates ET for local microclimate. Then, the controller creates a program for loading and communicating automatically with drip or sprinkler system controllers. The main objective of this study was to evaluate the effectiveness of the new ET sensors in ability to irrigate agricultural crops and to conserve water use for crop in arid climatic conditions. This paper presents the case for water conservation using intelligent irrigation system (IIS) application technology. The IIS for automating irrigation scheduling was implemented and tested with sprinkle and drip irrigation systems to irrigate wheat and tomato crops. Another irrigation scheduling system was also installed and operated as another treatment, which is based on weather data that retrieved from an automatic weather station. This irrigation control system was running in parallel to the former system (IIS) to be control experiments for comparison purposes. However, this article discusses the implementation of IIS, its installation, testing and calibration of various components. The experiments conducted for one growing season 2009-2010 and the results were represented and discussed herein. Data from all plots were analyzed, which were including soil water status, water consumption, and crop yield. The initial results indicate that up to 25% water saving by intelligent irrigation compared to control method, while maintaining competing yield. Results show that the crop evapotranspiration values for control experiments were higher than that of ET-System in consistent trend during whole growth season. The analysis points out that the values of the two treatments were somewhat close to each other's only in the initial development stages. Generally, the ET-System, with some modification was precise in controlling irrigation water and has been proven to be a good mean to determine the water requirements for crops and to schedule irrigation automatically.

Al-Ghobari, Hussein M.; Mohammad, Fawzi S.

2011-12-01

136

A conserved region in the F(2) subunit of paramyxovirus fusion proteins is involved in fusion regulation.  

PubMed

Paramyxoviruses utilize both an attachment protein and a fusion (F) protein to drive virus-cell and cell-cell fusion. F exists functionally as a trimer of two disulfide-linked subunits: F(1) and F(2). Alignment and analysis of a set of paramyxovirus F protein sequences identified three conserved blocks (CB): one in the fusion peptide/heptad repeat A domain, known to play important roles in fusion promotion, one in the region between the heptad repeats of F(1) (CBF(1)) (A. E. Gardner, K. L. Martin, and R. E. Dutch, Biochemistry 46:5094-5105, 2007), and one in the F(2) subunit (CBF(2)). To analyze the functions of CBF(2), alanine substitutions at conserved positions were created in both the simian virus 5 (SV5) and Hendra virus F proteins. A number of the CBF(2) mutations resulted in folding and expression defects. However, the CBF(2) mutants that were properly expressed and trafficked had altered fusion promotion activity. The Hendra virus CBF(2) Y79A and P89A mutants showed significantly decreased levels of fusion, whereas the SV5 CBF(2) I49A mutant exhibited greatly increased cell-cell fusion relative to that for wild-type F. Additional substitutions at SV5 F I49 suggest that both side chain volume and hydrophobicity at this position are important in the folding of the metastable, prefusion state and the subsequent triggering of membrane fusion. The recently published prefusogenic structure of parainfluenza virus 5/SV5 F (H. S. Yin et al., Nature 439:38-44, 2006) places CBF(2) in direct contact with heptad repeat A. Our data therefore indicate that this conserved region plays a critical role in stabilizing the prefusion state, likely through interactions with heptad repeat A, and in triggering membrane fusion. PMID:17507474

Gardner, Amanda E; Dutch, Rebecca E

2007-08-01

137

A Conserved Region in the F2 Subunit of Paramyxovirus Fusion Proteins Is Involved In Fusion Regulation?  

PubMed Central

Paramyxoviruses utilize both an attachment protein and a fusion (F) protein to drive virus-cell and cell-cell fusion. F exists functionally as a trimer of two disulfide-linked subunits: F1 and F2. Alignment and analysis of a set of paramyxovirus F protein sequences identified three conserved blocks (CB): one in the fusion peptide/heptad repeat A domain, known to play important roles in fusion promotion, one in the region between the heptad repeats of F1 (CBF1) (A. E. Gardner, K. L. Martin, and R. E. Dutch, Biochemistry 46:5094-5105, 2007), and one in the F2 subunit (CBF2). To analyze the functions of CBF2, alanine substitutions at conserved positions were created in both the simian virus 5 (SV5) and Hendra virus F proteins. A number of the CBF2 mutations resulted in folding and expression defects. However, the CBF2 mutants that were properly expressed and trafficked had altered fusion promotion activity. The Hendra virus CBF2 Y79A and P89A mutants showed significantly decreased levels of fusion, whereas the SV5 CBF2 I49A mutant exhibited greatly increased cell-cell fusion relative to that for wild-type F. Additional substitutions at SV5 F I49 suggest that both side chain volume and hydrophobicity at this position are important in the folding of the metastable, prefusion state and the subsequent triggering of membrane fusion. The recently published prefusogenic structure of parainfluenza virus 5/SV5 F (H. S. Yin et al., Nature 439:38-44, 2006) places CBF2 in direct contact with heptad repeat A. Our data therefore indicate that this conserved region plays a critical role in stabilizing the prefusion state, likely through interactions with heptad repeat A, and in triggering membrane fusion.

Gardner, Amanda E.; Dutch, Rebecca E.

2007-01-01

138

The 13C4 Monoclonal Antibody That Neutralizes Shiga Toxin Type 1 (Stx1) Recognizes Three Regions on the Stx1 B Subunit and Prevents Stx1 from Binding to Its Eukaryotic Receptor Globotriaosylceramide?  

PubMed Central

The 13C4 monoclonal antibody (MAb) recognizes the B subunit of Stx1 (StxB1) and neutralizes the cytotoxic and lethal activities of Stx1. However, this MAb does not bind to the B polypeptide of Stx2, despite the 73% amino acid sequence similarity between StxB1 and StxB2. When we compared the amino acid sequences of StxB1 and StxB2, we noted three regions of dissimilarity (amino acids 1 to 6, 25 to 32, and 54 to 61) located near each other on the crystal structure of StxB1. To identify the 13C4 epitope, we generated seven Stx1/Stx2 B chimeric polypeptides that contained one, two, or three of the dissimilar StxB1 regions. The 13C4 MAb reacted strongly with StxB1 and the triple-chimeric B subunit but not with the other chimeras. Mice immunized with the triple-chimeric B subunit survived a lethal challenge with Stx1 but not Stx2, substantiating the identified regions as the 13C4 MAb epitope and suggesting that the incorporation of this epitope into StxB2 altered sites necessary for anti-Stx2-neutralizing Ab production. Next, single amino acid substitutions were made in StxB1 to mimic Stx1d, a variant not recognized by the 13C4 MAb. The 13C4 MAb reacted strongly to StxB1 with the T1A or G25A mutations but not with the N55T change. Finally, we found that the 13C4 MAb blocked the binding of Stx1 to its receptor, globotriaosyl ceramide. Taken together, these results indicate that the 13C4 MAb prevents the interaction of Stx1 with its receptor by binding three nonlinear regions of the molecule that span receptor recognition sites on StxB1, one of which includes the essential residue 55N.

Smith, Michael J.; Carvalho, Humberto M.; Melton-Celsa, Angela R.; O'Brien, Alison D.

2006-01-01

139

Genetic structure of Barbus spp. populations in the Marches Region of central Italy and its relevance to conservation actions.  

PubMed

A genetic survey of Barbus spp. populations in the Marches Region (Adriatic River basins), central Italy, was carried out using mitochondrial and nuclear markers (partial D-loop, cyt b sequences and microsatellite loci) in order to ascertain their systematic position and to address their genetic structure which is key to conservation action planning. Analyses were conducted on sequences obtained from 91 individuals collected from eight sampling sites in five different rivers, from two specimens provided by the Ichthyological Centre of Rome and mitochondrial sequences of Barbus spp. retrieved from GenBank. Presumptive classification based on external morphological characters was not confirmed by genetic analysis, by means of which all specimens collected in the Marches Region were ascribed to Barbus plebejus. Genetic diversity values (h and ?) of sampling groups were all different from 0 except the one sample collected from the upper reaches of the River Tenna, above a hydroelectric dam. Population connectivity and colonization patterns of the studied area were inferred from an analysis of molecular variance distribution and evolutionary relationships among haplotypes. The results point to different levels of isolation among sampling groups due to ecological and anthropogenic factors and the effect of an artificial barrier on genetic variability and conservation status of the population. Finally, this study confirms the uncertainty associated with systematic classification of Barbus spp. based on morphological characters due to the phenotypic plasticity of the species. PMID:23464545

Livi, S; de Innocentiis, S; Longobardi, A; Cataudella, S; Tancioni, L; Rampacci, M; Marino, G

2013-03-01

140

Yeast calmodulin and a conserved nuclear protein participate in the in vivo binding of a matrix association region.  

PubMed Central

Chromatin becomes reorganized during mitosis each cell cycle. To identify genes potentially involved in these supramolecular events, we have used a colony-color assay to screen temperature-sensitive mutants of Saccharomyces cerevisiae. When a sequence that mediates attachment to the nuclear matrix in vitro was inserted into the GAL1 promoter of a lacZ fusion gene, beta-galactosidase synthesis was inhibited. This observation permitted screening for temperature-sensitive-inducible mutants on 5-bromo-4-chloro-3-indolyl beta-D-galactoside plates. Only 1 of 20 complementation groups of newly isolated mutants exhibited temperature-sensitive inducibility for the matrix association region but not for control CEN3 or STE6 inserts--a cmd1 mutant in which the last 7 amino acids of calmodulin were truncated by an ochre termination codon. Another mutant (smi1) exhibited a rare phenotype at the nonpermissive condition, which included S phase and budding arrest. We cloned and sequenced the SMI1 gene, which encodes a 57-kDa polypeptide with evolutionarily conserved epitope(s) found in mammalian cell nuclei. Thus, we provide evidence for involvement of calmodulin and another conserved protein in the in vivo binding of a matrix association region. Images Fig. 2 Fig. 3 Fig. 5 Fig. 6

Fishel, B R; Sperry, A O; Garrard, W T

1993-01-01

141

CROP PROTECTION AND CONSERVATION OF FRUGIVOROUS BATS IN ORCHARDS OF HILL AND COASTAL REGIONS OF KARNATAKA  

Microsoft Academic Search

Two species of frugivorous bats, viz., Pteropus giganteus and Cynoptera sphinx were implicated in damaging sapota and guava fruits in hill (Chettalli) and coastal (Uppinangadi) regions of Karnataka. At Uppinangadi, the population of Pteropus giganteus ranged between 3500-4000 and Cynopterus sphinx, two to 28. Pteropus giganteus caused on an average 18% fruit losses in arecanut (Areca catechu). At Chettalli, damage

A. K. Chakravarthy; A. C. Girish

142

METADATA FOR RESOURCE CONSERVATION RECOVERY ACT INFORMATION SYSTEM LOCATIONS - REGION 8  

EPA Science Inventory

The Region 8 data are located in the ARC/INFO coverage, R8RCR_PTS, which was derived from the Envirofacts point shapefile layer in the National Shapefile Repository. This Repository provides locations of EPA-regulated facilities from the Oracle table LRT_EF_COVERAGE_SRC, which is...

143

A Review of Endemic Species in the Eastern Arc Afromontane Region: Importance, Inferences, and Conservation  

Microsoft Academic Search

The Eastern Arc mountain region has been identified as one of the top 25 biodiversity “hotspots” worldwide, and contains a large proportion of endemic species. The endemic species are invaluable resources. This review paper will explore and discuss the possible theories behind the high rate of endemism. The importance of these endemics to local peoples and to the greater global

Carl Skarbek

2009-01-01

144

Identification of multiple CpG islands and associated conserved sequences in a candidate region for the Huntington disease gene.  

PubMed

The HD locus has been assigned to 4p16.3 distal to the DNA segment D4S10. However, the precise location of this gene is still unknown. At least three regions, together encompassing more than 3.5 Mb of DNA, can still be considered as candidate regions for the HD gene. Our efforts are directed toward the cloning and the complete characterization of one of these regions. Thus far we have cloned 460 kb of DNA in contiguously overlapping cosmids distal to D4S111 and have developed a detailed long-range restriction map orienting the contig within the terminal region of 4p16.3. We characterized 15 CpG-rich islands defined by tightly clustered rare cutter restriction sites for the enzymes NotI, BssHII, EagI, NruI, and SacII. In addition, we show that the sequences associated with the CpG-rich islands detect cross-species conservation. The detailed genetic analysis of the 460-kb contig provides a framework for the identification of genes, which can be assessed for the characteristics expected for the HD gene. PMID:1838348

Weber, B; Collins, C; Kowbel, D; Riess, O; Hayden, M R

1991-12-01

145

In Silico Study of Rotavirus VP7 Surface Accessible Conserved Regions for Antiviral Drug/Vaccine Design  

PubMed Central

Background Rotaviral diarrhoea kills about half a million children annually in developing countries and accounts for one third of diarrhea related hospitalizations. Drugs and vaccines against the rotavirus are handicapped, as in all viral diseases, by the rapid mutational changes that take place in the DNA and protein sequences rendering most of these ineffective. As of now only two vaccines are licensed and approved by the WHO (World Health Organization), but display reduced efficiencies in the underdeveloped countries where the disease is more prevalent. We approached this issue by trying to identify regions of surface exposed conserved segments on the surface glycoproteins of the virion, which may then be targeted by specific peptide vaccines. We had developed a bioinformatics protocol for these kinds of problems with reference to the influenza neuraminidase protein, which we have refined and expanded to analyze the rotavirus issue. Results Our analysis of 433 VP7 (Viral Protein 7 from rotavirus) surface protein sequences across 17 subtypes encompassing mammalian hosts using a 20D Graphical Representation and Numerical Characterization method, identified four possible highly conserved peptide segments. Solvent accessibility prediction servers were used to identify that these are predominantly surface situated. These regions analyzed through selected epitope prediction servers for their epitopic properties towards possible T-cell and B-cell activation showed good results as epitopic candidates (only dry lab confirmation). Conclusions The main reasons for the development of alternative vaccine strategies for the rotavirus are the failure of current vaccines and high production costs that inhibit their application in developing countries. We expect that it would be possible to use the protein surface exposed regions identified in our study as targets for peptide vaccines and drug designs for stable immunity against divergent strains of the rotavirus. Though this study is fully dependent on computational prediction algorithms, it provides a platform for wet lab experiments.

Ghosh, Ambarnil; Chattopadhyay, Shiladitya; Chawla-Sarkar, Mamta; Nandy, Papiya; Nandy, Ashesh

2012-01-01

146

The compact Brachypodium genome conserves centromeric regions of a common ancestor with wheat and rice  

Microsoft Academic Search

The evolution of five chromosomes of Brachypodium distachyon from a 12-chromosome ancestor of all grasses by dysploidy raises an interesting question about the fate of redundant centromeres.\\u000a Three independent but complementary approaches were pursued to study centromeric region homologies among the chromosomes of\\u000a Brachypodium, wheat, and rice. The genes present in pericentromeres of the basic set of seven chromosomes of

Lili Qi; Bernd Friebe; Jiajie Wu; Yongqiang Gu; Chen Qian; Bikram S. Gill

2010-01-01

147

MODELING AND ANALYSIS OF GLOBAL AND REGIONAL HYDROLOGIC PROCESSES AND APPROPRIATE CONSERVATION OF MOIST ENTROPY  

SciTech Connect

The research supported by DOE funding addressed the fundamental issues of understanding and modeling of hydrologic processes in relation to regional and global climate change. The emphasis of this research effort was on the application of isentropic modeling and analysis to advance the accuracy of the simulation of all aspects of the hydrologic cycle including clouds and thus the climate state regionally and globally. Simulation of atmospheric hydrologic processes by the UW hybrid isentropic coordinate models provided fundamental insight into global monsoonal circulations, and regional energy exchange in relation to the atmospheric hydrologic cycle. Inter-comparison of UW hybrid model simulations with those from the NCAR Community Climate Model and other climate and numerical weather prediction (NWP) models investigated the increased accuracies gained in modeling long-range transport in isentropic coordinates and isolated differences in modeling of the climate state. The inter-comparisons demonstrated advantages in the simulation of the transport of the hydrologic components of the climate system and provided insight into the more general problems of simulating hydrologic processes, aerosols and chemistry for climate. This research demonstrated the viability of the UW isentropic-eta model for long-term integration for climate and climate change studies and documented that no insurmountable barriers exist to simulation of climate utilizing hybrid isentropic coordinate models. The results provide impetus for continued development of hybrid isentropic coordinate models as a means to advance accuracies in the simulation of global and regional climate in relation to transport and the planetary distribution of heat sources and sinks.

Donald Johnson, Todd Schaack

2007-06-08

148

Conserved Regional Patterns of GABA-Related Transcript Expression in the Neocortex of Subjects With Schizophrenia  

PubMed Central

Objective Individuals with schizophrenia exhibit disturbances in a number of cognitive, affective, sensory, and motor functions that depend on the circuitry of different cortical areas. The cognitive deficits associated with dysfunction of the dorsolateral prefrontal cortex result, at least in part, from abnormalities in GABA neurotransmission, as reflected in a specific pattern of altered expression of GABA-related genes. Consequently, the authors sought to determine whether this pattern of altered gene expression is restricted to the dorsolateral prefrontal cortex or could also contribute to the dysfunction of other cortical areas in subjects with schizophrenia. Method Real-time quantitative polymerase chain reaction was used to assess the levels of eight GABA-related transcripts in four cortical areas (dorsolateral prefrontal cortex, anterior cingulate cortex, and primary motor and primary visual cortices) of subjects (N=12) with schizophrenia and matched normal comparison subjects. Results Expression levels of seven transcripts were lower in subjects with schizophrenia, with the magnitude of reduction for each transcript comparable across the four areas. The largest reductions were detected for mRNA encoding somatostatin and parvalbumin, followed by moderate decreases in mRNA expression for the 67-kilodalton isoform of glutamic acid decarboxylase, the GABA membrane transporter GAT-1, and the ?1 and ? subunits of GABAA receptors. In contrast, the expression of calretinin mRNA did not differ between the subject groups in any of the four areas. Conclusions Because the areas examined represent the major functional domains (e.g., association, limbic, motor, and sensory) of the cerebral cortex, our findings suggest that a conserved set of molecular alterations affecting GABA neurotransmission contribute to the pathophysiology of different clinical features of schizophrenia.

Hashimoto, Takanori; Bazmi, H. Holly; Mirnics, Karoly; Wu, Qiang; Sampson, Allan R.; Lewis, David A.

2010-01-01

149

Role of forest conservation in lessening land degradation in a temperate region: The Monarch Butterfly Biosphere Reserve, Mexico.  

PubMed

With international concern about the rates of deforestation worldwide, particular attention has been paid to Latin America. Forest conservation programmes in Mexico include Payment for Environmental Services (PES), a scheme that has been successfully introduced in the Monarch Butterfly Biosphere Reserve. To seek further evidence of the role of PES in lessening land degradation processes in a temperate region, the conservation state of the Cerro Prieto ejido within the Reserve was assessed by an analysis of changes in vegetation cover and land-use between 1971 and 2013. There were no changes in the total forest surface area, but the relative proportions of the different classes of cover density had changed. In 1971, closed and semi-closed forest occupied 247.81 ha and 5.38 ha, 82.33% and 1.79% of the total area of the ejido, respectively. By 2013, closed forest had decreased to 230.38 ha (76.54% of the ejido), and semi-closed cover was 17.23 ha (5.72% of the ejido), suggesting that some semi-closed forest had achieved closed status. The final balance between forest losses and recovery was: 29.63 ha were lost, whereas 13.72 ha were recovered. Losses were mainly linked to a sanitation harvest programme to control the bark beetle Scolytus mundus. Ecotourism associated with forest conservation in the Cerro Prieto ejido has been considered by inhabitants as a focal alternative for economic development. Consequently, it is essential to develop a well-planned and solidly structured approach based on social cohesion to foster a community-led sustainable development at local level. PMID:24332200

Manzo-Delgado, Lilia; López-García, José; Alcántara-Ayala, Irasema

2014-06-01

150

Molecular Phylogeny of OVOL Genes Illustrates a Conserved C2H2 Zinc Finger Domain Coupled by Hypervariable Unstructured Regions  

PubMed Central

OVO-like proteins (OVOL) are members of the zinc finger protein family and serve as transcription factors to regulate gene expression in various differentiation processes. Recent studies have shown that OVOL genes are involved in epithelial development and differentiation in a wide variety of organisms; yet there is a lack of comprehensive studies that describe OVOL proteins from an evolutionary perspective. Using comparative genomic analysis, we traced three different OVOL genes (OVOL1-3) in vertebrates. One gene, OVOL3, was duplicated during a whole-genome-duplication event in fish, but only the copy (OVOL3b) was retained. From early-branching metazoa to humans, we found that a core domain, comprising a tetrad of C2H2 zinc fingers, is conserved. By domain comparison of the OVOL proteins, we found that they evolved in different metazoan lineages by attaching intrinsically-disordered (ID) segments of N/C-terminal extensions of 100 to 1000 amino acids to this conserved core. These ID regions originated independently across different animal lineages giving rise to different types of OVOL genes over the course of metazoan evolution. We illustrated the molecular evolution of metazoan OVOL genes over a period of 700 million years (MY). This study both extends our current understanding of the structure/function relationship of metazoan OVOL genes, and assembles a good platform for further characterization of OVOL genes from diverged organisms.

Sinha, Rahul; Sardar, Puspendu; Sushma, Miss.; Goyal, Pankaj; Goswami, Chandan; Grapputo, Alessandro

2012-01-01

151

Molecular phylogeny of OVOL genes illustrates a conserved C2H2 zinc finger domain coupled by hypervariable unstructured regions.  

PubMed

OVO-like proteins (OVOL) are members of the zinc finger protein family and serve as transcription factors to regulate gene expression in various differentiation processes. Recent studies have shown that OVOL genes are involved in epithelial development and differentiation in a wide variety of organisms; yet there is a lack of comprehensive studies that describe OVOL proteins from an evolutionary perspective. Using comparative genomic analysis, we traced three different OVOL genes (OVOL1-3) in vertebrates. One gene, OVOL3, was duplicated during a whole-genome-duplication event in fish, but only the copy (OVOL3b) was retained. From early-branching metazoa to humans, we found that a core domain, comprising a tetrad of C2H2 zinc fingers, is conserved. By domain comparison of the OVOL proteins, we found that they evolved in different metazoan lineages by attaching intrinsically-disordered (ID) segments of N/C-terminal extensions of 100 to 1000 amino acids to this conserved core. These ID regions originated independently across different animal lineages giving rise to different types of OVOL genes over the course of metazoan evolution. We illustrated the molecular evolution of metazoan OVOL genes over a period of 700 million years (MY). This study both extends our current understanding of the structure/function relationship of metazoan OVOL genes, and assembles a good platform for further characterization of OVOL genes from diverged organisms. PMID:22737237

Kumar, Abhishek; Bhandari, Anita; Sinha, Rahul; Sardar, Puspendu; Sushma, Miss; Goyal, Pankaj; Goswami, Chandan; Grapputo, Alessandro

2012-01-01

152

Conserved regions of the DMD 3' UTR regulate translation and mRNA abundance in cultured myotubes.  

PubMed

Duchenne muscular dystrophy (DMD), a severe muscle-wasting disease, is caused by mutations in the DMD gene, which encodes for the protein dystrophin. Its regulation is of therapeutic interest as even small changes in expression of functional dystrophin can significantly impact the severity of DMD. While tissue-specific distribution and transcriptional regulation of several DMD mRNA isoforms has been well characterized, the post-transcriptional regulation of dystrophin synthesis is not well understood. Here, we utilize qRTPCR and a quantitative dual-luciferase reporter assay to examine the effects of isoform specific DMD 5' UTRs and the highly conserved DMD 3' UTR on mRNA abundance and translational control of gene expression in C2C12 cells. The 5' UTRs were shown to initiate translation with low efficiency in both myoblasts and myotubes. Whereas, two large highly conserved elements in the 3' UTR, which overlap the previously described Lemaire A and D regions, increase mRNA levels and enhance translation upon differentiation of myoblasts into myotubes. The results presented here implicate an important role for DMD UTRs in dystrophin expression and delineate the cis-acting elements required for the myotube-specific regulation of steady-state mRNA levels and translational enhancer activity found in the DMD 3' UTR. PMID:24928536

Larsen, C Aaron; Howard, Michael T

2014-08-01

153

Innovative technology conserves resources and generates savings: a case study from the Sunnybrook Regional Processing Centre.  

PubMed

The regional processing centre at Sunnybrook Health Sciences Centre recently faced the substantial challenge of increasing cleaning capacity to meet the current workload and anticipated future demand without increasing its operating budget. The solution, upgrading its cleaning and decontamination system to a highly automated system, met both objectives. An analysis of the impact of the change found that the new system provided additional benefits, including improved productivity and cleaning quality; decreased costs; reduced water, electricity and chemical use; improved worker safety and morale; and decreased overtime. Investing in innovative technology improved key departmental outcomes while meeting institutional environmental and cost savings objectives. PMID:20057236

Karim, Abdool Z

2009-01-01

154

Functional analysis of a highly conserved abundant larval transcript-2 (alt-2) intron 2 repeat region of lymphatic filarial parasites.  

PubMed

The filarial-specific protein abundant larval transcript-2 (ALT-2) is expressed exclusively in the infective larval stage (L3) and is a crucial protein for establishing immunopathogenesis in human hosts. The alt-2 gene has a conserved minisatellite repeat (29 or 27bp) in intron 2 (IR2) whose significance within lymphatic filarial species is unknown. Here, we report the role of IR2 in the regulation of alt-2 gene expression using an in vitro model. Using electrophoretic mobility shift assays, we identified the presence of a putative nuclear protein binding region within IR2. Subsequent transient expression experiments in eukaryotic cell lines demonstrated that the IR2 downregulated the expression of a downstream luciferase reporter gene, which was further validated with RT-PCR. We therefore identify IR2 as a suppressor element that regulates L3 stage-specific expression of alt-2. PMID:24681262

Sakthidevi, Moorthy; Hoti, Sugeerappa Laxmanappa; Kaliraj, Perumal

2014-06-01

155

A universally conserved region of the largest subunit participates in the active site of RNA polymerase III.  

PubMed Central

The largest subunits of the three eukaryotic nuclear RNA polymerase present extensive sequence homology with the beta' subunit of the bacterial enzymes over five major co-linear regions. Region d is the most highly conserved and contains a motif, (Y/F)NADFDGD(E/Q)M(N/A), which is invariant in all multimeric RNA polymerases. An extensive mutagenesis of that region in yeast RNA polymerase III led to a vast majority (16/22) of lethal single-site substitutions. A few conditional mutations were also obtained. One of them, rpc160-112, corresponds to a double substitution (T506I, N509Y) and has a slow growth phenotype at 25 degrees C. RNA polymerase III from the mutant rpc160-112 was severely impaired in its ability to transcribe a tRNA gene in vitro. The transcription defect did not originate from a deficiency in transcription complex formation and RNA chain initiation, but was mainly due to a reduced elongation rate. Under conditions of substrate limitation, the mutant enzyme showed increased pausing at the intrinsic pause sites of the SUP4 tRNA gene and an increased rate of slippage of nascent RNA, as compared with the wild-type enzyme. The enzyme defect was also detectable with poly[d(A-T)] as template, in the presence of saturating DNA, ATP and UTP concentrations. The mutant enzyme behavior is best explained by a distortion of the active site near the growing point of the RNA product. Images

Dieci, G; Hermann-Le Denmat, S; Lukhtanov, E; Thuriaux, P; Werner, M; Sentenac, A

1995-01-01

156

Covalent Protein Modification with ISG15 via a Conserved Cysteine in the Hinge Region  

PubMed Central

The ubiquitin-like protein ISG15 (interferon-stimulated gene of 15 kDa) is strongly induced by type I interferons and displays antiviral activity. As other ubiquitin-like proteins (Ubls), ISG15 is post-translationally conjugated to substrate proteins by an isopeptide bond between the C-terminal glycine of ISG15 and the side chains of lysine residues in the substrates (ISGylation). ISG15 consists of two ubiquitin-like domains that are separated by a hinge region. In many orthologs, this region contains a single highly reactive cysteine residue. Several hundred potential substrates for ISGylation have been identified but only a few of them have been rigorously verified. In order to investigate the modification of several ISG15 substrates, we have purified ISG15 conjugates from cell extracts by metal-chelate affinity purification and immunoprecipitations. We found that the levels of proteins modified by human ISG15 can be decreased by the addition of reducing agents. With the help of thiol blocking reagents, a mutational analysis and miRNA mediated knock-down of ISG15 expression, we revealed that this modification occurs in living cells via a disulphide bridge between the substrates and Cys78 in the hinge region of ISG15. While the ISG15 activating enzyme UBE1L is conjugated by ISG15 in the classical way, we show that the ubiquitin conjugating enzyme Ubc13 can either be classically conjugated by ISG15 or can form a disulphide bridge with ISG15 at the active site cysteine 87. The latter modification would interfere with its function as ubiquitin conjugating enzyme. However, we found no evidence for an ISG15 modification of the dynamin-like GTPases MxA and hGBP1. These findings indicate that the analysis of potential substrates for ISG15 conjugation must be performed with great care to distinguish between the two types of modification since many assays such as immunoprecipitation or metal-chelate affinity purification are performed with little or no reducing agent present.

Bade, Veronika N.; Nickels, Jochen; Keusekotten, Kirstin; Praefcke, Gerrit J. K.

2012-01-01

157

A conserved region between the heptad repeats of paramyxovirus fusion proteins is critical for proper F protein folding.  

PubMed

Paramyxoviruses are a diverse family that utilizes a fusion (F) protein to enter cells via fusion of the viral lipid bilayer with a target cell membrane. Although certain regions of the F protein are known to play critical roles in membrane fusion, the function of much of the protein remains unclear. Sequence alignment of a set of paramyxovirus F proteins and analysis utilizing Block Maker identified a region of conserved amino acid sequence in a large domain between the heptad repeats of F1, designated CBF1. We employed site-directed mutagenesis to analyze the function of completely conserved residues of CBF1 in both the simian virus 5 (SV5) and Hendra virus F proteins. The majority of CBF1 point mutants were deficient in homotrimer formation, proteolytic processing, and transport to the cell surface. For some SV5 F mutants, proteolytic cleavage and surface expression could be restored by expression at 30 degrees C, and varying levels of fusion promotion were observed at this temperature. In addition, the mutant SV5 F V402A displayed a hyperfusogenic phenotype at both 30 and 37 degrees C, indicating that this mutation allows for efficient fusion with only an extremely small amount of cleaved, active protein. The recently published prefusogenic structure of PIV5/SV5 F (Yin, H. S., et al. (2006) Nature 439, 38-44) indicates that residues within and flanking CBF1 interact with the fusion peptide domain. Together, these data suggest that CBF1-fusion peptide interactions are critical for the initial folding of paramyxovirus F proteins from this important viral family and can also modulate subsequent membrane fusion promotion. PMID:17417875

Gardner, Amanda E; Martin, Kimberly L; Dutch, Rebecca E

2007-05-01

158

A Conserved Region between the Heptad Repeats of Paramyxovirus Fusion Proteins is Critical for Proper F Protein Folding†  

PubMed Central

Paramyxoviruses are a diverse family which utilizes a fusion (F) protein to enter cells via fusion of the viral lipid bilayer with a target cell membrane. Although certain regions of F are known to play critical roles in membrane fusion, the function of much of the protein remains unclear. Sequence alignment of a set of paramyxovirus F proteins and analysis utilizing Block Maker identified a region of conserved amino acid sequence in a large domain between the heptad repeats of F1, designated CBF1. We employed site-directed mutagenesis to analyze the function of completely conserved residues of CBF1 in both the simian virus 5 (SV5) and Hendra virus F proteins. The majority of CBF1 point mutants were deficient in homotrimer formation, proteolytic processing, and transport to the cell surface. For some SV5 F mutants, proteolytic cleavage and surface expression could be restored by expression at 30°C, and varying levels of fusion promotion were observed at this temperature. In addition, the mutant SV5 F V402A displayed a hyperfusogenic phenotype at both 30°C and 37°C, indicating this mutation allows for efficient fusion with only an extremely small amount of cleaved, active protein. The recently published prefusogenic structure of PIV5/SV5 F [Yin, H.S., et al. (2006) Nature 439, 38–44] indicates that residues within and flanking CBF1 interact with the fusion peptide domain. Together, these data suggest that CBF1-fusion peptide interactions are critical for the initial folding of paramyxovirus F proteins from across this important viral family, and can also modulate subsequent membrane fusion promotion.

Gardner, Amanda E.; Martin, Kimberly L.; Dutch, Rebecca E.

2008-01-01

159

Desalination as Groundwater Conservation: The Cost of Protecting Cultural and Environmental Resources in Chile's Region II  

NASA Astrophysics Data System (ADS)

There is a substantial body of evidence that groundwater overdraft is occurring worldwide. Economists argue that the cause of this overdraft is the open-access nature of the resource, which results in a "tragedy of the commons." Sustainable water management requires that some institution control the resource to limit this overdraft by reducing water extraction. This reduction creates scarcity and requires a method of rationing. The economically efficient outcome occurs when the lowest value uses of water are eliminated. This allocation, though, may have undesirable social consequences, such as the loss of small-scale farming, and political ramifications that make such an allocation unpopular to implement. This paper explores the economic cost of leaving water in low-value uses. The policy we explore is a moratorium on voluntary water sales to mining firms to protect the groundwater resource in northern Chile. This policy has accelerated the use of expensive desalinated water, whose cost is primarily driven by its heavy use of carbon-based electricity. Chile has a strong system of water property rights that economists argue ration water in a way that leads to the efficient allocation through water markets. This paper first explores the potential inefficiency of a water market when groundwater and surface water are linked, as well as when different users vary in their intensity of use. This theoretical background provides a framework for determining the economically efficient allocation of water and the losses associated with the moratorium in northern Chile. The policy does protect some environmental and cultural public goods, which potentially offset some or all of this cost. We provide a perspective on the magnitude of these public goods but do not attempt to value them explicitly. Instead, we demonstrate what their value must be so that the moratorium policy has a cost-to-benefit ratio of one. While the estimate of lost income from inefficiency is the main focus of the empirical work, the theoretical development provides an important perspective into groundwater management and the important role of understanding the physical system in water marketing. Worldwide, subsidized and scarce water is allocated to farmers for social and political reasons. The losses from this type of allocation are often ignored or marginalized. The Chilean case demonstrates that the losses due to economically inefficient allocation are real, because the alternative is greater consumption of other resources (fossil fuels in this case), not conservation. The Chilean case also demonstrates the difficulty of adequately defining water rights for efficient markets due to the physical properties of hydrologic systems. Because groundwater and surface water systems are linked and water is partially recycled, water markets may over allocate water to consumptive users or those with preferable extraction locations. This paper provides a theoretical exposition of how water rights that fail incorporate important properties of the physical system may lead to inefficient water markets.

Edwards, E. C.; Cristi, O.; Libecap, G. D.

2012-12-01

160

An under recognized cause of chest pain  

PubMed Central

Aortic intramural hematoma (IMH) is related to but is pathologically distinct from aortic dissection. In this potentially lethal entity, there is hemorrhage into the aortic media in the absence of an intimal tear. With recent advances in imaging techniques, IMH is now increasingly recognized. The limited data available suggest that the clinical course of IMH mimics that of acute aortic dissection, and mortality rates are similar. Physicians need to be cognizant regarding this entity when they are evaluating chest pain. Here we report a case of IMH, in a 63-year-old female, which was managed conservatively.

Pillai, Unnikrishnan Ponnamma Kunjan; John, Santosh G.; Kurup, Aparna Narayana; Devasahayam, Joe; Lacasse, Alexandre

2012-01-01

161

A gene from the human sex-determining region encodes a protein with homology to a conserved DNA-binding motif  

Microsoft Academic Search

A search of a 35-kilobase region of the human Y chromosome necessary for male sex determination has resulted in the identification of a new gene. This gene is conserved and Y-specific among a wide range of mammals, and encodes a testis-specific transcript. It shares homology with the mating-type protein, Mc, from the fission yeast Schizosaccharomyces pombe and a conserved DNA-binding

Andrew H. Sinclair; Philippe Berta; Mark S. Palmer; J. Ross Hawkins; Beatrice L. Griffiths; Matthijs J. Smith; Jamie W. Foster; Anna-Maria Frischauf; Robin Lovell-Badge; Peter N. Goodfellow

1990-01-01

162

A national geographic framework for guiding conservation on a landscape scale  

USGS Publications Warehouse

The U.S. Fish and Wildlife Service, along with the global conservation community, has recognized that the conservation challenges of the 21st century far exceed the responsibilities and footprint of any individual agency or program. The ecological effects of climate change and other anthropogenic stressors do not recognize geopolitical boundaries and, as such, demand a national geographic framework to provide structure for cross-jurisdictional and landscape-scale conservation strategies. In 2009, a new map of ecologically based conservation regions in which to organize capacity and implement strategic habitat conservation was developed using rapid prototyping and expert elicitation by an interagency team of U.S. Fish and Wildlife Service and U.S. Geological Survey scientists and conservation professionals. Incorporating Bird Conservation Regions, Freshwater Ecoregions, and U.S. Geological Survey hydrologic unit codes, the new geographic framework provides a spatial template for building conservation capacity and focusing biological planning and conservation design efforts. The Department of Interior's Landscape Conservation Cooperatives are being organized in these new conservation regions as multi-stakeholder collaborations for improved conservation science and management.

Millard, Michael J.; Czarnecki, Craig A.; Morton, John M.; Brandt, Laura A.; Briggs, Jennifer S.; Shipley, Frank S.; Sayre, Roger; Sponholtz, Pamela J.; Perkins, David; Simpkins, Darin G.; Taylor, Janith

2012-01-01

163

Use of a storm water retention system for conservation of regionally endangered fishes  

USGS Publications Warehouse

Maintaining aquatic biodiversity in urban or suburban areas can be problematic because urban landscapes can be nearly devoid of aquatic habitats other than engineered basins for storm water management. These areas are usually of questionable value for fish, but we examined a case study in which five regionally imperiled fish species were reintroduced into an artificial storm water detention pond and subsequently thrived. Although not a formal experiment, postintroduction survey data suggested that three of the five species maintained high population densities for 10 years after initial stocking, and two persisted in lower numbers. Success was likely due to a combination of unique design features and prior habitat preparation that resulted in clear water conditions that supported dense vegetation. Stocked fish persisted despite occasional bouts of low dissolved oxygen and increased chloride levels resulting from road salt application within the watershed. Transplanted fish served as a source population for both research and further reintroduction experiments. We suggest that, for some fish species, habitat preservation has a middle ground between natural habitats and completely artificial environments that require constant husbandry and that storm water systems could be used to create engineered sanctuaries within the human landscape that have many potential benefits for both humans and fish.

Schaeffer, Jeffrey S.; Bland, James K.; Janssen, John

2012-01-01

164

Does Lymphovascular Invasion Predict Regional Nodal Failure in Breast Cancer Patients With Zero to Three Positive Lymph Nodes Treated With Conserving Surgery and Radiotherapy? Implications for Regional Radiation  

SciTech Connect

Purpose: To examine the relationship between lymphovascular invasion (LVI) and regional nodal failure (RNF) in breast cancer patients with zero to three positive nodes treated with breast-conservation therapy (BCT). Methods and Materials: The records of 1,257 breast cancer patients with zero to three positive lymph nodes were reviewed. All patients were treated with BCT at Massachusetts General Hospital from 1980 to December 2003. Lymphovascular invasion was diagnosed by hematoxylin and eosin-stained sections and in some cases supported by immunohistochemical stains. Regional nodal failure was defined as recurrence in the ipsilateral supraclavicular, axillary, or internal mammary lymph nodes. Regional nodal failure was diagnosed by clinical and/or radiologic examination. Results: The median follow-up was 8 years (range, 0.1-21 years). Lymphovascular invasion was present in 211 patients (17%). In univariate analysis, patients with LVI had a higher rate of RNF (3.32% vs. 1.15%; p = 0.02). In multivariate analysis, only tumor size, grade, and local failure were significant predictors of RNF (p = 0.049, 0.013, and 0.0001, respectively), whereas LVI did not show a significant relationship with RNF (hazard ratio = 2.07; 95% CI, 0.8-5.5; p = 0.143). The presence of LVI in the T2/3 population did not increase the risk of RNF over that for those with no LVI (p = 0.15). In addition, patients with Grade 3 tumors and positive LVI did not have a higher risk of RNF than those without LVI (p = 0.96). Conclusion: These results suggest that LVI can not be used as a sole indicator for regional nodal irradiation in breast cancer patients with zero to three positive lymph nodes treated with BCT.

Boutrus, Rimoun; Abi-Raad, Rita; Niemierko, Andrzej [Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA (United States); Brachtel, Elena F. [Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA (United States); Rizk, Levi; Kelada, Alexandra [Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA (United States); Taghian, Alphonse G., E-mail: ataghian@partners.or [Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA (United States)

2010-11-01

165

Merging Disparate Data Sources Into a Paleoanthropological Geodatabase for Research, Education, and Conservation in the Greater Hadar Region (Afar, Ethiopia)  

NASA Astrophysics Data System (ADS)

Understanding the geographic, temporal, and environmental contexts of human evolution requires the ability to compare wide-ranging datasets collected from multiple research disciplines. Paleoanthropological field- research projects are notoriously independent administratively even in regions of high transdisciplinary importance. As a result, valuable opportunities for the integration of new and archival datasets spanning diverse archaeological assemblages, paleontological localities, and stratigraphic sequences are often neglected, which limits the range of research questions that can be addressed. Using geoinformatic tools we integrate spatial, temporal, and semantically disparate paleoanthropological and geological datasets from the Hadar sedimentary basin of the Afar Rift, Ethiopia. Applying newly integrated data to investigations of fossil- rich sediments will provide the geospatial framework critical for addressing fundamental questions concerning hominins and their paleoenvironmental context. We present a preliminary cyberinfrastructure for data management that will allow scientists, students, and interested citizens to interact with, integrate, and visualize data from the Afar region. Examples of our initial integration efforts include generating a regional high-resolution satellite imagery base layer for georeferencing, standardizing and compiling multiple project datasets and digitizing paper maps. We also demonstrate how the robust datasets generated from our work are being incorporated into a new, digital module for Arizona State University's Hadar Paleoanthropology Field School - modernizing field data collection methods, on-the-fly data visualization and query, and subsequent analysis and interpretation. Armed with a fully fused database tethered to high-resolution satellite imagery, we can more accurately reconstruct spatial and temporal paleoenvironmental conditions and efficiently address key scientific questions, such as those regarding the relative importance of internal and external ecological, climatological, and tectonic forcings on evolutionary change in the fossil record. In close association with colleagues working in neighboring project areas, this work advances multidisciplinary and collaborative research, training, and long-range antiquities conservation in the Hadar region.

Campisano, C. J.; Dimaggio, E. N.; Arrowsmith, J. R.; Kimbel, W. H.; Reed, K. E.; Robinson, S. E.; Schoville, B. J.

2008-12-01

166

One exon of the human LSF gene includes conserved regions involved in novel DNA-binding and dimerization motifs.  

PubMed Central

The transcription factor LSF, identified as a HeLa protein that binds the simian virus 40 late promoter, recognizes direct repeats with a center-to-center spacing of 10 bp. The characterization of two human cDNAs, representing alternatively spliced mRNAs, provides insight into the unusual DNA-binding and oligomerization properties of LSF. The sequence of the full-length LSF is identical to that of the transcription factors alpha CP2 and LBP-1c and has similarity to the Drosophila transcription factor Elf-1/NTF-1. Using an epitope-counting method, we show that LSF binds DNA as a homodimer. LSF-ID, which is identical to LBP-1d, contains an in-frame internal deletion of 51 amino acids resulting from alternative mRNA splicing. Unlike LSF, LSF-ID did not bind LSF DNA-binding sites. Furthermore, LSF-ID did not affect the binding of LSF to DNA, suggesting that the two proteins do not interact. Of three short regions with a high degree of homology between LSF and Elf-1/NTF-1, LSF-ID lacks two, which are predicted to form beta-strands. Double amino acid substitutions in each of these regions eliminated specific DNA-binding activity, similarly to the LSF-ID deletion. The dimerization potential of these mutants was measured both by the ability to inhibit the binding of LSF to DNA and by direct protein-protein interaction studies. Mutations in one homology region, but not the other, functionally eliminated dimerization. Images

Shirra, M K; Zhu, Q; Huang, H C; Pallas, D; Hansen, U

1994-01-01

167

Identification of Common Epitopes on a Conserved Region of NSs Proteins Among Tospoviruses of Watermelon silver mottle virus Serogroup.  

PubMed

ABSTRACT The NSs protein of Watermelon silver mottle virus (WSMoV) was expressed by a Zucchini yellow mosaic virus (ZYMV) vector in squash. The expressed NSs protein with a histidine tag and an additional NIa protease cleavage sequence was isolated by Ni(2+)-NTA resins as a free-form protein and further eluted after sodium dodecyl sulfate-polyacrylamide gel electrophoresis for production of rabbit antiserum and mouse monoclonal antibodies (MAbs). The rabbit antiserum strongly reacted with the NSs crude antigen of WSMoV and weakly reacted with that of a high-temperature-recovered gloxinia isolate (HT-1) of Capsicum chlorosis virus (CaCV), but not with that of Calla lily chlorotic spot virus (CCSV). In contrast, the MAbs reacted strongly with all crude NSs antigens of WSMoV, CaCV, and CCSV. Various deletions of the NSs open reading frame were constructed and expressed by ZYMV vector. Results indicate that all three MAbs target the 89- to 125-amino-acid (aa) region of WSMoV NSs protein. Two indispensable residues of cysteine and lysine were essential for MAbs recognition. Sequence comparison of the deduced MAbs-recognized region with the reported tospoviral NSs proteins revealed the presence of a consensus sequence VRKPGVKNTGCKFTMHNQIFNPN (denoted WNSscon), at the 98- to 120-aa position of NSs proteins, sharing 86 to 100% identities among those of WSMoV, CaCV, CCSV, and Peanut bud necrosis virus. A synthetic WNSscon peptide reacted with the MAbs and verified that the epitopes are present in the 98- to 120-aa region of WSMoV NSs protein. The WSMoV sero-group-specific NSs MAbs provide a means for reliable identification of tospoviruses in this large serogroup. PMID:18943661

Chen, Tsung-Chi; Huang, Ching-Wen; Kuo, Yan-Wen; Liu, Fang-Lin; Yuan, Chao-Hsiu Hsuan; Hsu, Hei-Ti; Yeh, Shyi-Dong

2006-12-01

168

How many kilowatts are in a negawatt? Verifying ex post estimates of utility conservation impacts at the regional level  

SciTech Connect

Restructuring of utilities raises questions about the future of conservation programs. One of the greatest obstacles has been the persistent uncertainity among utility planners regarding true resource effectiveness and cost-effectiveness of conservation relative to conventional generation. The authors use econometric techniques to examine the aggregate commercial and industrial conservation impacts reported. The paper shows that utility conservation programs have been effective in reducing electric loads and that utilities have reported accurately. 44 refs., 3 tabs.

Parfomak, P.W.; Lave, L.B. [Carnegie Mellon Univ., Pittsburgh, PA (United States)

1996-12-31

169

Examples of geodiversity - biodiversity relationships from Brabant's sand regions, in nature conservation and restoration  

NASA Astrophysics Data System (ADS)

The Dutch province of Noord-Brabant is dominated by sand landscapes of aeolian and riverine origin dating from Pleistocene and Holocene times. Brabant's geological history is governed by its position on the fringe of a geological basin with re-activated faults and a Weichselian polar dune desert, a history that makes the region unique in Europe. Some areas have assemblages of geomorphology and soils that have remained relatively untouched up to the present day. In these more pristine areas, the morphological, geological and soil development is a governing factor for the small-scale vegetation differences and biodiversity. Examples of these relationships will be shown, such as loam forests, wetlands caused by 'wijst' - a feature that is special for Brabant, in which the higher grounds are wetter than the lower grounds - active drift sands, and dry and wet heathlands with 'vennen' - small ponds in different gradations of paludization. Many of these areas are Natura-2000 habitats. The geodiversity-biodiversity relationships will be part of the proposal for a European Geopark in Brabant. Measures to restore biodiversity are only sustainable if geodiversity is part of the nature restoration plan e.g. the history of the local landscape, geology, geomorphology and soils. Even if the areas have undergone a drastic transformation. Two examples will be given of nature restoration projects based on geodiversity-biodiversity relationships. The first example is the restoration of an active drift sand, such as still occur in The Netherlands but are extremely rare in the rest of Europe. Over the last decades they have also stabilized in The Netherlands due to high nitrogen deposition. The other example concerns a nature restoration project in a stream valley. These stream valleys originally had a high and small-scale geodiversity that was completely destroyed by stream regulation for agriculture production. This was the first project to study the former and present-day geo-dynamics and use these to restore the stream habitats and optimize geo-biodiversity relationships.

van den Ancker, Hanneke; Heskes, Erik; Jungerius, Pieter Dirk; Maes, Bert; Harthoorn, Jaap

2014-05-01

170

Fibrillin genes map to regions of conserved mouse/human synteny on mouse chromosomes 2 and 18.  

PubMed

Fibrillin proteins are major structural components of the 10-nm microfibrils found in elastic and nonelastic connective tissues. Previous studies have mapped the human genes for two fibrillins to chromosome bands 15q21 (FBN1) and 5q23-q31 (FBN2) and have demonstrated that FBN1 mutations are associated with Marfan syndrome, while FBN2 is linked to the gene for congenital contractural arachnodactyly. Here, we report the isolation of genomic clones of the corresponding mouse fibrillin genes (Fbn-1 and Fbn-2). By analyzing a mapping panel of mouse x rodent somatic hybrid cell lines, we have assigned the Fbn-1 gene to mouse chromosome 2 and the Fbn-2 gene to mouse chromosome 18. We then sublocalized the fibrillin genes to bands 2F (Fbn-1) and 18D-E1 (Fbn-2) by fluorescence in situ hybridization. These regions are known to exhibit conserved synteny with the regions on human chromosomes 15 and 5 that carry the homologous human fibrillin genes. In addition, the Fbn-1 gene maps in the vicinity of the gene for a connective tissue disorder on mouse chromosome 2 called Tight-skin (Tsk). PMID:8307578

Li, X; Pereira, L; Zhang, H; Sanguineti, C; Ramirez, F; Bonadio, J; Francke, U

1993-12-01

171

The C-Terminal Domain from S. cerevisiae Pat1 Displays Two Conserved Regions Involved in Decapping Factor Recruitment  

PubMed Central

Eukaryotic mRNA decay is a highly regulated process allowing cells to rapidly modulate protein production in response to internal and environmental cues. Mature translatable eukaryotic mRNAs are protected from fast and uncontrolled degradation in the cytoplasm by two cis-acting stability determinants: a methylguanosine (m7G) cap and a poly(A) tail at their 5? and 3? extremities, respectively. The hydrolysis of the m7G cap structure, known as decapping, is performed by the complex composed of the Dcp2 catalytic subunit and its partner Dcp1. The Dcp1-Dcp2 decapping complex has a low intrinsic activity and requires accessory factors to be fully active. Among these factors, Pat1 is considered to be a central scaffolding protein involved in Dcp2 activation but also in inhibition of translation initiation. Here, we present the structural and functional study of the C-terminal domain from S. cerevisiae Pat1 protein. We have identified two conserved and functionally important regions located at both extremities of the domain. The first region is involved in binding to Lsm1-7 complex. The second patch is specific for fungal proteins and is responsible for Pat1 interaction with Edc3. These observations support the plasticity of the protein interaction network involved in mRNA decay and show that evolution has extended the C-terminal alpha-helical domain from fungal Pat1 proteins to generate a new binding platform for protein partners.

Back, Regis; Keller, Jenny; Charenton, Clement; Taverniti, Valerio; Plesse, Claudine Gaudon; Lazar, Noureddine; Durand, Dominique; van Tilbeurgh, Herman; Seraphin, Bertrand; Graille, Marc

2014-01-01

172

Recognizing Problems in State Universities.  

ERIC Educational Resources Information Center

Recognizing problems in state universities involves a critical analysis of both internal and external environments, as well as a simplification of the complex factors to help people understand the problems and marshall the forces necessary to address them. (MSE)

Ping, Charles J.

1986-01-01

173

Structural conservation versus functional divergence of maternally expressed microRNAs in the Dlk1/Gtl2 imprinting region  

PubMed Central

Background MicroRNAs play an important functional role in post-transcriptional gene regulation. One of the largest known microRNA clusters is located within the imprinted Dlk1/Gtl2 region on human chromosome 14 and mouse chromosome 12. This cluster contains more than 40 microRNA genes that are expressed only from the maternal chromosome in mouse. Results To shed light on the function of these microRNAs and possible crosstalk between microRNA-based gene regulation and genomic imprinting, we performed extensive in silico analyses of the microRNAs in this imprinted region and their predicted target genes. Bioinformatic analysis reveals that these microRNAs are highly conserved in both human and mouse. Whereas the microRNA precursors at this locus mostly belong to large sequence families, the mature microRNAs sequences are highly divergent. We developed a target gene prediction approach that combines three widely used prediction methods and achieved a sufficiently high prediction accuracy. Target gene sets predicted for individual microRNAs derived from the imprinted region show little overlap and do not differ significantly in their properties from target genes predicted for a group of randomly selected microRNAs. The target genes are enriched with long and GC-rich 3' UTR sequences and are preferentially annotated to development, regulation processes and cell communication. Furthermore, among all analyzed human and mouse genes, the predicted target genes are characterized by consistently higher expression levels in all tissues considered. Conclusion Our results suggest a complex evolutionary history for microRNA genes in this imprinted region, including an amplification of microRNA precursors in a mammalian ancestor, and a rapid subsequent divergence of the mature sequences. This produced a broad spectrum of target genes. Further, our analyses did not uncover a functional relation between imprinted gene regulation of this microRNA-encoding region, expression patterns or functions of predicted target genes. Specifically, our results indicate that these microRNAs do not regulate a particular set of genes. We conclude that these imprinted microRNAs do not regulate a particular set of genes. Rather, they seem to stabilize expression of a variety of genes, thereby being an integral part of the genome-wide microRNA gene regulatory network.

Kircher, Martin; Bock, Christoph; Paulsen, Martina

2008-01-01

174

Structure of the dnaA and DnaA-box region in the Mycoplasma capricolum chromosome: conservation and variations in the course of evolution.  

PubMed

We have previously shown that the dnaA gene and the DnaA-box region were conserved in bacteria representative of all three major branches of the eubacterial phylogenic tree: high G + C Gram+, low-G + C Gram+ and Gram-. In the present work, we determined the structure of the dnaA region of Mycoplasma capricolum and found that the dnaA gene and at least two other genes, rpmH and dnaN, were conserved in this bacterium. An unusually high level of amino acid (aa) substitutions was observed in M. capricolum DnaA. It was the case even in those aa which were well conserved in other bacterial species. The nontranslatable region upstream from the dnaA gene was also conserved in this bacterium, as it was universally found in both Gram+ and Gram- bacteria. An additional nontranslatable region downstream from the dnaA gene, which is common to Gram+ bacteria, was also found in M. capricolum, consistent with the proposal that M. capricolum is Gram+ in origin. These regions were rich in A + T and contained ten DnaA-box-like sequences (9-mers that differ from TTATCCACA by one or two bases). PMID:1544573

Fujita, M Q; Yoshikawa, H; Ogasawara, N

1992-01-01

175

Characterizing stopover sites of migrating passerine birds in the lower Chesapeake Bay region for conservation: an integrated radar-habitat study  

USGS Publications Warehouse

Many conservation organizations and initiatives including Partners-in-Flight and the U.S. Fish and Wildlife Service's regional Joint Ventures have identified migratory songbird stopover habitat as a priority conservation target. However, the spatial and temporal variability inherent in migration presents a number of challenges to both identifying and characterizing stopover habitat. Scarce conservation resources further demand that stopover sites be classified on a scale of priority so that conservation action can proceed according to ecological value. We are applying weather surveillance radar data collected from the National Weather Service WSR-88D at Wakefield, VA, and NASA's Doppler radar, NPOL, in Oyster, VA, to identify passerine stopover sites in the lower Chesapeake Bay region and develop spatial models to characterize these sites based on relative migrant abundance and consistency of use between and within seasons. We are using the stopover patterns to generate hypotheses regarding the habitat, geographic, and stochastic factors contributing to the distribution of migrants at a regional scale. We are testing these hypotheses with detailed habitat data and ground surveys of migrating birds with the goal of creating a generalized prioritization system for stopover site conservation.

Mabey, S.; Watts, B.; Paxton, B.; Smith, F.; Truitt, B.; Dawson, D.

2005-01-01

176

Co-binding by YY1 identifies the transcriptionally active, highly conserved set of CTCF-bound regions in primate genomes  

PubMed Central

Background The genomic binding of CTCF is highly conserved across mammals, but the mechanisms that underlie its stability are poorly understood. One transcription factor known to functionally interact with CTCF in the context of X-chromosome inactivation is the ubiquitously expressed YY1. Because combinatorial transcription factor binding can contribute to the evolutionary stabilization of regulatory regions, we tested whether YY1 and CTCF co-binding could in part account for conservation of CTCF binding. Results Combined analysis of CTCF and YY1 binding in lymphoblastoid cell lines from seven primates, as well as in mouse and human livers, reveals extensive genome-wide co-localization specifically at evolutionarily stable CTCF-bound regions. CTCF-YY1 co-bound regions resemble regions bound by YY1 alone, as they enrich for active histone marks, RNA polymerase II and transcription factor binding. Although these highly conserved, transcriptionally active CTCF-YY1 co-bound regions are often promoter-proximal, gene-distal regions show similar molecular features. Conclusions Our results reveal that these two ubiquitously expressed, multi-functional zinc-finger proteins collaborate in functionally active regions to stabilize one another's genome-wide binding across primate evolution.

2013-01-01

177

Cellular GCN5 Is a Novel Regulator of Human Adenovirus E1A-Conserved Region 3 Transactivation  

PubMed Central

The largest isoform of adenovirus early region 1A (E1A) contains a unique region termed conserved region 3 (CR3). This region activates viral gene expression by recruiting cellular transcription machinery to the early viral promoters. Recent studies have suggested that there is an optimal level of E1A-dependent transactivation required by human adenovirus (hAd) during infection and that this may be achieved via functional cross talk between the N termini of E1A and CR3. The N terminus of E1A binds GCN5, a cellular lysine acetyltransferase (KAT). We have identified a second independent interaction of E1A with GCN5 that is mediated by CR3, which requires residues 178 to 188 in hAd5 E1A. GCN5 was recruited to the viral genome during infection in an E1A-dependent manner, and this required both GCN5 interaction sites on E1A. Ectopic expression of GCN5 repressed transactivation by both E1A CR3 and full-length E1A. In contrast, RNA interference (RNAi) depletion of GCN5 or treatment with the KAT inhibitor cyclopentylidene-[4-(4?-chlorophenyl)thiazol-2-yl]hydrazone (CPTH2) resulted in increased E1A CR3 transactivation. Moreover, activation of the adenovirus E4 promoter by E1A was increased during infection of homozygous GCN5 KAT-defective (hat/hat) mouse embryonic fibroblasts (MEFs) compared to wild-type control MEFs. Enhanced histone H3 K9/K14 acetylation at the viral E4 promoter required the newly identified binding site for GCN5 within CR3 and correlated with repression and reduced occupancy by phosphorylated RNA polymerase II. Treatment with CPTH2 during infection also reduced virus yield. These data identify GCN5 as a new negative regulator of transactivation by E1A and suggest that its KAT activity is required for optimal virus replication.

Ablack, Jailal N. G.; Cohen, Michael; Thillainadesan, Gobi; Fonseca, Gregory J.; Pelka, Peter; Torchia, Joe

2012-01-01

178

A conserved region in the tail domain of vimentin is involved in its assembly into intermediate filaments.  

PubMed

Although the head and rod domains of intermediate filament (IF) proteins are known to play significant roles in filament assembly, the role of the tail domain in this function is unclear and the available information supports contradictory conclusions. We examined this question by comparing transfection of the same cDNA constructs, encoding vimentins with modified tail domains, into cell lines that do and do not contain endogenous IF proteins. By this approach, we were able to distinguish between the ability of a mutant IF protein to initiate assembly de novo, from that of incorporating into existing filament networks. Vimentins with modifications at or near a highly conserved tripeptide, arg-asp-gly (RDG), of the tail domain incorporated into existing IF networks in vimentin-expressing (vim+) cells, but were assembly-incompetent in cells that did not express IF proteins (vim-). The failure of the RDG mutant vimentins to assemble into filament arrays in vim- cells was reversible by re-introducing a wild-type vimentin cDNA, whereupon both wild-type and mutant vimentins coassembled into one and the same IF network. We conclude that the function of the tail domain of type III IF proteins, and possibly of keratins K8 and K18, in IF assembly is distinct from those of other domains; a region encompassing the RDG tripeptide appears to be important in the assembly process. PMID:7954854

Makarova, I; Carpenter, D; Khan, S; Ip, W

1994-01-01

179

Osmostress Induces Autophosphorylation of Hog1 via a C-Terminal Regulatory Region That Is Conserved in p38?  

PubMed Central

Many protein kinases require phosphorylation at their activation loop for induction of catalysis. Mitogen-activated protein kinases (MAPKs) are activated by a unique mode of phosphorylation, on neighboring Tyrosine and Threonine residues. Whereas many kinases obtain their activation via autophosphorylation, MAPKs are usually phosphorylated by specific, dedicated, MAPK kinases (MAP2Ks). Here we show however, that the yeast MAPK Hog1, known to be activated by the MAP2K Pbs2, is activated in pbs2? cells via an autophosphorylation activity that is induced by osmotic pressure. We mapped a novel domain at the Hog1 C-terminal region that inhibits this activity. Removal of this domain provides a Hog1 protein that is partially independent of MAP2K, namely, partially rescues osmostress sensitivity of pbs2? cells. We further mapped a short domain (7 amino acid residues long) that is critical for induction of autophosphorylation. Its removal abolishes autophosphorylation, but maintains Pbs2-mediated phosphorylation. This 7 amino acids stretch is conserved in the human p38?. Similar to the case of Hog1, it’s removal from p38? abolishes p38?’s autophosphorylation capability, but maintains, although reduces, its activation by MKK6. This study joins a few recent reports to suggest that, like many protein kinases, MAPKs are also regulated via induced autoactivation.

Maayan, Inbal; Beenstock, Jonah; Marbach, Irit; Tabachnick, Shira; Livnah, Oded; Engelberg, David

2012-01-01

180

Regional Management Units for Marine Turtles: A Novel Framework for Prioritizing Conservation and Research across Multiple Scales  

PubMed Central

Background Resolving threats to widely distributed marine megafauna requires definition of the geographic distributions of both the threats as well as the population unit(s) of interest. In turn, because individual threats can operate on varying spatial scales, their impacts can affect different segments of a population of the same species. Therefore, integration of multiple tools and techniques — including site-based monitoring, genetic analyses, mark-recapture studies and telemetry — can facilitate robust definitions of population segments at multiple biological and spatial scales to address different management and research challenges. Methodology/Principal Findings To address these issues for marine turtles, we collated all available studies on marine turtle biogeography, including nesting sites, population abundances and trends, population genetics, and satellite telemetry. We georeferenced this information to generate separate layers for nesting sites, genetic stocks, and core distributions of population segments of all marine turtle species. We then spatially integrated this information from fine- to coarse-spatial scales to develop nested envelope models, or Regional Management Units (RMUs), for marine turtles globally. Conclusions/Significance The RMU framework is a solution to the challenge of how to organize marine turtles into units of protection above the level of nesting populations, but below the level of species, within regional entities that might be on independent evolutionary trajectories. Among many potential applications, RMUs provide a framework for identifying data gaps, assessing high diversity areas for multiple species and genetic stocks, and evaluating conservation status of marine turtles. Furthermore, RMUs allow for identification of geographic barriers to gene flow, and can provide valuable guidance to marine spatial planning initiatives that integrate spatial distributions of protected species and human activities. In addition, the RMU framework — including maps and supporting metadata — will be an iterative, user-driven tool made publicly available in an online application for comments, improvements, download and analysis.

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

2010-01-01

181

Modelling the benefits of soil water conservation using the PARCH model—a case study from a semi-arid region of Kenya  

Microsoft Academic Search

Field experiments in the semi-arid regions of Kenya have shown that soil water conservation techniques can result in increased maize grain yields. The degree of benefit in a particular season is dependant on the rainfall amount and distribution. However, the results of field experiments are limited to a few years of observations at specific locations and it is therefore difficult

William Stephens; T. M. Hess

1999-01-01

182

Habitat preservation is a concern for conserving of Heliotropium rariflorum Stocks. in the forest of North Gujarat Region (NGR), Gujarat, India  

Microsoft Academic Search

The present study deals with the status, distribution and conservation of habitats of Heliotropium rariflorum - a threatened plant in the forest area of North Gujarat Region. It is tall under shrub; the distribution is exclusive to specific habitat and substratum. Survey was conducted from May 2005 to Dec 2006. A probable list of locations of the species in the

Rajendra Kumar S; Joshua J; Sunderraj SFW; Kalavathy S

2011-01-01

183

Salvage treatment for local or local-regional recurrence after initial breast conservation treatment with radiation for ductal carcinoma in situ  

Microsoft Academic Search

The present study evaluated the outcome of salvage treatment for women with local or local-regional recurrence after initial breast conservation treatment with radiation for mammographically detected ductal carcinoma in situ (DCIS; intraductal carcinoma) of the breast. The study cohort consisted of 90 women with local only first failure (n=85) or local-regional only first failure (n=5). The histology at the time

Lawrence J. Solin; Alain Fourquet; Frank A. Vicini; Marie Taylor; Bruce Haffty; Eric A. Strom; Elaine Wai; Lori J. Pierce; Lawrence B. Marks; Harry Bartelink; Francois Campana; Marsha D. McNeese; Anuja Jhingran; Ivo A. Olivotto; Nina Bijker; Wei-Ting Hwang

2005-01-01

184

Conservation status of the White-Bellied Sea-Eagle Haliaeetus leucogaster in Australia determined using mtDNA control region sequence data  

Microsoft Academic Search

Considered to have a declining world population, concern has been expressed in recent years over the conservation status of the White-bellied Sea-Eagle Haliaeetus leucogaster (Gmelin, 1788) within Australia. We used mitochondrial (mtDNA) control region sequence data to investigate the current distribution of genetic variation in this species at the continental level and within and between specified regional units. We were

Jill M. Shephard; Jane M. Hughes; Carla P. Catterall; Penny D. Olsen

2005-01-01

185

75 FR 18472 - Cooperative Conservation Partnership Initiative  

Federal Register 2010, 2011, 2012, 2013

...natural resource concerns include soil quality, water conservation, water quality, plant condition, air quality...conservation practices to address water quality, water conservation, or State, regional, or national...

2010-04-12

186

Conserved POU/OCT- and GATA-binding sites in 5'-flanking promoter region of mammalian WNT8B orthologs.  

PubMed

WNT family members are secreted-type glycoproteins regulating cell fate, planar cell polarity, cell adhesion, and cell movement. WNT signals are context-dependently transduced to the canonical pathway for the transcriptional up-regulation of MYC, CCND1, FGF20, JAG1, WISP1 and DKK1 genes, and also to the non-canonical pathway for the activation of RHOA, JNK, PKC, NFAT and NLK signaling cascades. We cloned and characterized the wild-type human WNT8B, while another group the aberrant human WNT8B with Gly230Ala and Arg284Leu amino-acid substitutions. Although WNT8B is undetectable in normal adult tissues by using Northern blot analyses, WNT8B is expressed in gastric cancer, pancreatic cancer, colorectal cancer, breast cancer, and embryonal tumors. Here, comparative integromics on WNT8B orthologs were investigated by using bioinformatics (Techint) and human intelligence (Humint). Cow Wnt8b gene was identified within NW_001494361.1 genome sequence. Predicted sequence XM_582222.3 was an artificial cow Wnt8b with aberrant prediction for the first exon. Cow Wnt8b complete coding sequence was found to encode a 350-amino-acid protein, which showed 96.9% total-amino-acid identity with human WNT8B. Comparative proteomics revealed that N-terminal signal peptide, 22 Cys residues, two Asn-linked glycosylation sites, Gly230, and Arg284 of human WNT8B were conserved among mammalian WNT8B orthologs. Comparative genomics revealed that POU/OCT- and GATA-binding sites in the 5'-flanking promoter region were conserved among human, chimpanzee, cow, mouse, and rat WNT8B orthologs. In silico expression analyses revealed that human WNT8B was expressed in embryoid body derived from embryonic stem (ES) cells, hepatocyte progenitors derived from ES cells, fetal brain, diffuse-type gastric cancer, colorectal cancer, prostate cancer, and ovarian fibrotheoma. Based on the expression profiles of POU and GATA family transcription factors, it was revealed that WNT8B expression in hepatocyte progenitors derived from human ES cells is due to POU5F1 (OCT3/OCT4) and GATA3, and also that WNT8B expression in diffuse-type gastric cancer is due to POU5F1 and GATA6. PMID:17390031

Katoh, Masuko; Katoh, Masaru

2007-05-01

187

Prioritizing conservation effort through the use of biological soil crusts as ecosystem function indicators in an arid region  

USGS Publications Warehouse

Conservation prioritization usually focuses on conservation of rare species or biodiversity, rather than ecological processes. This is partially due to a lack of informative indicators of ecosystem function. Biological soil crusts (BSCs) trap and retain soil and water resources in arid ecosystems and function as major carbon and nitrogen fixers; thus, they may be informative indicators of ecosystem function. We created spatial models of multiple indicators of the diversity and function of BSCs (species richness, evenness, functional diversity, functional redundancy, number of rare species, number of habitat specialists, nitrogen and carbon fixation indices, soil stabilization, and surface roughening) for the 800,000-ha Grand Staircase-Escalante National Monument (Utah, U.S.A.). We then combined the indicators into a single BSC function map and a single BSC biodiversity map (2 alternative types of conservation value) with an unweighted averaging procedure and a weighted procedure derived from validations performance. We also modeled potential degradation with data from a rangeland assessment survey. To determine which areas on the landscape were the highest conservation priorities, we overlaid the function- and diversity-based conservation-value layers on the potential degradation layer. Different methods for ascribing conservation-value and conservation-priority layers all yielded strikingly similar results (r = 0.89-0.99), which suggests that in this case biodiversity and function can be conserved simultaneously. We believe BSCs can be used as indicators of ecosystem function in concert with other indicators (such as plant-community properties) and that such information can be used to prioritize conservation effort in drylands. ?? 2008 Society for Conservation Biology.

Bowker, M. A.; Miller, M. E.; Belnap, J.; Sisk, T. D.; Johnson, N. C.

2008-01-01

188

Conserved Region 3 of Human Papillomavirus 16 E7 Contributes to Deregulation of the Retinoblastoma Tumor Suppressor  

PubMed Central

The human papillomavirus (HPV) E7 oncoprotein binds cellular factors, preventing or retargeting their function and thereby making the infected cell conducive for viral replication. A key target of E7 is the product of the retinoblastoma susceptibility locus (pRb). This interaction results in the release of E2F transcription factors and drives the host cell into the S phase of the cell cycle. E7 binds pRb via a high-affinity binding site in conserved region 2 (CR2) and also targets a portion of cellular pRb for degradation via the proteasome. Evidence suggests that a secondary binding site exists in CR3, and that this interaction influences pRb deregulation. Additionally, evidence suggests that CR3 also participates in the degradation of pRb. We have systematically analyzed the molecular mechanisms by which CR3 contributes to deregulation of the pRb pathway by utilizing a comprehensive series of mutations in residues predicted to be exposed on the surface of HPV16 E7 CR3. Despite differences in the ability to interact with cullin 2, all CR3 mutants degrade pRb comparably to wild-type E7. We identified two specific patches of residues on the surface of CR3 that contribute to pRb binding independently of the high-affinity CR2 binding site. Mutants within CR3 that affect pRb binding are less effective than the wild-type E7 in overcoming pRb-induced cell cycle arrest. This demonstrates that the interaction between HPV16 E7 CR3 and pRb is functionally important for alteration of the cell cycle.

Todorovic, Biljana; Hung, Katherine; Massimi, Paola; Avvakumov, Nikita; Dick, Frederick A.; Shaw, Gary S.; Banks, Lawrence

2012-01-01

189

Prioritizing conservation effort through the use of biological soil crusts as ecosystem function indicators in an arid region.  

PubMed

Conservation prioritization usually focuses on conservation of rare species or biodiversity, rather than ecological processes. This is partially due to a lack of informative indicators of ecosystem function. Biological soil crusts (BSCs) trap and retain soil and water resources in arid ecosystems and function as major carbon and nitrogen fixers; thus, they may be informative indicators of ecosystem function. We created spatial models of multiple indicators of the diversity and function of BSCs (species richness, evenness, functional diversity, functional redundancy, number of rare species, number of habitat specialists, nitrogen and carbon fixation indices, soil stabilization, and surface roughening) for the 800,000-ha Grand Staircase-Escalante National Monument (Utah, U.S.A.). We then combined the indicators into a single BSC function map and a single BSC biodiversity map (2 alternative types of conservation value) with an unweighted averaging procedure and a weighted procedure derived from validations performance. We also modeled potential degradation with data from a rangeland assessment survey. To determine which areas on the landscape were the highest conservation priorities, we overlaid the function- and diversity-based conservation-value layers on the potential degradation layer. Different methods for ascribing conservation-value and conservation-priority layers all yielded strikingly similar results (r= 0.89-0.99), which suggests that in this case biodiversity and function can be conserved simultaneously. We believe BSCs can be used as indicators of ecosystem function in concert with other indicators (such as plant-community properties) and that such information can be used to prioritize conservation effort in drylands. PMID:18759770

Bowker, Matthew A; Miller, Mark E; Belnap, Jayne; Sisk, Thomas D; Johnson, Nancy C

2008-12-01

190

Impact of the Conservation Reserve Program on duck recruitment in the U.S. Prairie Pothole Region  

USGS Publications Warehouse

The U.S. Department of Agriculture (USDA)'s Conservation Reserve Program (CRP) resulted in the conversion of about 1.9 million ha of cropland to perennial grass cover in the Prairie Pothole Region of North Dakota, South Dakota, and northeastern Montana by 1992. Many wildlife managers believed this cover would provide benefits to wildlife, including upland nesting ducks. During 1992-1995, we evaluated success of 5 duck species nesting in CRP fields and nearby Waterfowl Production Areas (WPA) throughout the region. We examined relationships between daily survival rates (DSR) of duck nests in CRP cover and landscape-level habitat and population parameters. We computed DSR of duck nests in other major cover types in our study area from data collected during 1980-1984 (pre-CRP) and 1990-1994 (CRP) periods. We then applied recruitment models to estimate duck production in our study area during peak CRP years (1992-1997) and compared these results with those that simulated the scenario in which cropland was in place of CRP cover (i.e., the CRP had not occurred). DSR were higher in all habitats combined during the CRP period compared to the pre-CRP period. Regressions of DSR in CRP cover on the percent of each study plot in perennial cover and geographic location were significant (P < 0.01) for 4 of 5 duck (Anas spp.) species. Estimated nest success and recruitment rates for the 5 species combined during 1992-1997 were 46% and 30% higher, respectively, with CRP cover on the landscape compared to a scenario where we simulated cropland in place of CRP. Our model estimated an additional 12.4 million recruits from our study area to the fall flight as a consequence of the CRP during 1992-1997. Our results document benefits to 5 duck species in the northern plains associated with a farm program that provided financial incentives to landowners for planting undisturbed grass cover as an alternative to annual crops.

Reynolds, R. E.; Shaffer, T. L.; Renner, R. W.; Newton, W. E.; Batt, B. D. J.

2001-01-01

191

Loco-regional Control After Neo-adjuvant Chemotherapy and Conservative Treatment for Locally Advanced Breast Cancer Patients.  

PubMed

Breast-conserving treatment (BCT) has been validated for breast cancer patients receiving adjuvant chemotherapy. Our objective was to evaluate the difference in loco-regional recurrence (LRR) rates between BCT and mastectomy in patients receiving radiation therapy after neo-adjuvant chemotherapy (NCT). A retrospective data base was used to identify all patients with breast cancer undergoing NCT from 2002 to 2007. Patients with initial metastatic disease were excluded from this analysis. LRR was compared between those undergoing BCT and mastectomy. Individual variables associated with LRR were evaluated. Two hundred eighty-four patients were included, 111 (39%) underwent BCT and 173 (61%) mastectomy. Almost all patients (99%) in both groups received postoperative radiation. Pathologic complete response was seen in 37 patients, of which 28 underwent BCT (p < 0.001). Patients receiving mastectomy had more invasive lobular carcinoma (p = 0.007) and a higher American Joint Committee on Cancer (AJCC) stage (p < 0.001) at diagnosis than those with BCT. At a median follow-up of 6.3 years, the loco-regional control rate was 91% (95% CI: 86-94%). The 10-year LRR rate was similar in the BCT group (9.2% [95% CI: 4.9-16.7%]) and in the mastectomy group (10.7% [95% CI: 5.9-15.2%]; p = 0.8). Ten-year overall survival (OS) rates (63% [95% CI: 46-79%] in the BCT group; 60% [95% CI: 47-73%] in the mastectomy group, p = 0.8) were not statistically different between the two patient populations. Multivariate analysis showed that AJCC stage ? III (HR: 2.6; 95% CI: 1.2-5.8; p = 0.02), negative PR (HR: 6; 95% CI: 1.2-30.6, p = 0.03), and number of positive lymph nodes ?3 (HR: 2.5; 95% CI: 1.1-5.9; p = 0.03) were independent predictors of LRR. Ten-year OS was similar in the BCT and in the mastectomy group (p = 0.1). The rate of LRR was low and did not significantly differ between the BCT and the mastectomy group after NCT. Randomized trials assessing whether mastectomy can be safely omitted in selected breast cancer patients (nonstage III tumors or those which do not require adjuvant hormone suppression) which respond to NCT are required. PMID:24890310

Levy, Antonin; Borget, Isabelle; Bahri, Manel; Arnedos, Monica; Rivin, Eleonor; Vielh, Philippe; Balleyguier, Corinne; Rimareix, Françoise; Bourgier, Céline

2014-07-01

192

Red states, blue states, and divorce: understanding the impact of conservative protestantism on regional variation in divorce rates.  

PubMed

Why do states with larger proportions of religious conservatives have higher divorce rates than states with lower proportions of religious conservatives? This project examines whether earlier transitions to marriage and parenthood among conservative Protestants (known risk factors for divorce) contribute to this paradox while attending to other plausible explanations. County-level demographic information from all 50 states is combined from a variety of public data sources and merged with individual records from the National Surveys of Family Growth to estimate both aggregated county and multilevel individual models of divorce. Results show that individual religious conservatism is positively related to individual divorce risk, solely through the earlier transitions to adulthood and lower incomes of conservative Protestants. However, the proportion of conservative Protestants in a county is also independently and positively associated with both the divorce rate in that county and an individual's likelihood of divorcing. The earlier family formation and lower levels of educational attainment and income in counties with a higher proportion of conservative Protestants can explain a substantial portion of this association. Little support is found for alternative explanations of the association between religious conservatism and divorce rates, including the relative popularity of marriage versus cohabitation across counties. PMID:25032268

Glass, Jennifer; Levchak, Philip

2014-01-01

193

Dogs Vaccinated with Common Lyme Disease Vaccines Do Not Respond to IR6, the Conserved Immunodominant Region of the VlsE Surface Protein of Borrelia burgdorferi  

Microsoft Academic Search

A 25-amino-acid synthetic peptide (C6 peptide) derived from an immunodominant conserved region (des- ignated IR6) of the VlsE protein of Borrelia burgdorferi has been identified and used to construct immunoen- zyme-based diagnostic procedures. These procedures have excellent sensitivity and specificity. Previous reports have demonstrated the usefulness of the C6 peptide as an antigen for the serodiagnosis of human and canine

Thomas P. O'Connor; Kathy J. Esty; Jancy L. Hanscom; Paulette Shields; Mario T. Philipp

2004-01-01

194

Comparison of nucleic acid hybridization and nucleic acid amplification using conserved sequences from the 5' noncoding region for detection of bovine viral diarrhea virus.  

PubMed Central

Primers and probes derived from conserved sequences located in the 5' noncoding region of pestiviruses were evaluated for detection of bovine viral diarrhea virus. With these reagents, hybridization and polymerase chain reaction tests detected 62 of 90 and 90 of 90 bovine viral diarrhea virus isolates, respectively. A quick lysis method for preparing RNA for use in polymerase chain reaction amplification also was evaluated. Images

Ridpath, J F; Bolin, S R; Katz, J

1993-01-01

195

A single SNP in an evolutionary conserved region within intron 86 of the HERC2 gene determines human blue-brown eye color.  

PubMed

We have previously demonstrated that haplotypes of three single nucleotide polymorphisms (SNPs) within the first intron of the OCA2 gene are extremely strongly associated with variation in human eye color. In the present work, we describe additional fine association mapping of eye color SNPs in the intergenic region upstream of OCA2 and within the neighboring HERC2 (hect domain and RLD2) gene. We screened an additional 92 SNPs in 300-3000 European individuals and found that a single SNP in intron 86 of HERC2, rs12913832, predicted eye color significantly better (ordinal logistic regression R(2) = 0.68, association LOD = 444) than our previous best OCA2 haplotype. Comparison of sequence alignments of multiple species showed that this SNP lies in the center of a short highly conserved sequence and that the blue-eye-associated allele (frequency 78%) breaks up this conserved sequence, part of which forms a consensus binding site for the helicase-like transcription factor (HLTF). We were also able to demonstrate the OCA2 R419Q, rs1800407, coding SNP acts as a penetrance modifier of this new HERC2 SNP for eye color, and somewhat independently, of melanoma risk. We conclude that the conserved region around rs12913832 represents a regulatory region controlling constitutive expression of OCA2 and that the C allele at rs12913832 leads to decreased expression of OCA2, particularly within iris melanocytes, which we postulate to be the ultimate cause of blue eye color. PMID:18252222

Sturm, Richard A; Duffy, David L; Zhao, Zhen Zhen; Leite, Fabio P N; Stark, Mitchell S; Hayward, Nicholas K; Martin, Nicholas G; Montgomery, Grant W

2008-02-01

196

A Single SNP in an Evolutionary Conserved Region within Intron 86 of the HERC2 Gene Determines Human Blue-Brown Eye Color  

PubMed Central

We have previously demonstrated that haplotypes of three single nucleotide polymorphisms (SNPs) within the first intron of the OCA2 gene are extremely strongly associated with variation in human eye color. In the present work, we describe additional fine association mapping of eye color SNPs in the intergenic region upstream of OCA2 and within the neighboring HERC2 (hect domain and RLD2) gene. We screened an additional 92 SNPs in 300–3000 European individuals and found that a single SNP in intron 86 of HERC2, rs12913832, predicted eye color significantly better (ordinal logistic regression R2 = 0.68, association LOD = 444) than our previous best OCA2 haplotype. Comparison of sequence alignments of multiple species showed that this SNP lies in the center of a short highly conserved sequence and that the blue-eye-associated allele (frequency 78%) breaks up this conserved sequence, part of which forms a consensus binding site for the helicase-like transcription factor (HLTF). We were also able to demonstrate the OCA2 R419Q, rs1800407, coding SNP acts as a penetrance modifier of this new HERC2 SNP for eye color, and somewhat independently, of melanoma risk. We conclude that the conserved region around rs12913832 represents a regulatory region controlling constitutive expression of OCA2 and that the C allele at rs12913832 leads to decreased expression of OCA2, particularly within iris melanocytes, which we postulate to be the ultimate cause of blue eye color.

Sturm, Richard A.; Duffy, David L.; Zhao, Zhen Zhen; Leite, Fabio P.N.; Stark, Mitchell S.; Hayward, Nicholas K.; Martin, Nicholas G.; Montgomery, Grant W.

2008-01-01

197

Recognizing Patterns in Debris Disks  

NASA Technical Reports Server (NTRS)

An extrasolar planet sculpts the famous debris dish around Fomalhaut; probably many other debris disks contain planets that we could locate if only we could better recognize their signatures in the dust that surrounds them. I will describe the latest 3-D models of debris dish dynamics / models that include planets, grain-grain collisions and even ISM-disk interactions. I will show why all these ingredients are needed to explain disk images--and what the images are telling us about planet formation.

Kuchner, Marc

2009-01-01

198

Ecosystem Services Derived from Wetland Conservation Practices in the United States Prairie Pothole Region with an Emphasis on the U.S. Department of Agriculture Conservation Reserve and Wetlands Reserve Programs  

USGS Publications Warehouse

Implementation of the U.S. Department of Agriculture (USDA) Conservation Reserve Program (CRP) and Wetlands Reserve Program (WRP) has resulted in the restoration of approximately 2,200,000 ha (5,436,200 acres) of wetland and grassland habitats in the Prairie Pothole Region. These restored habitats are known to provide various ecosystem services; however, little work has been conducted to quantify and verify benefits on program lands (lands enrolled in the CRP and WRP) in agriculturally dominated landscapes of the Prairie Pothole Region. To address this need, the U.S. Geological Survey (USGS), in collaboration with the USDA Farm Service Agency and Natural Resources Conservation Service, initiated a study to develop and apply approaches to quantify changes in ecosystem services resulting from wetland restoration activities funded by the USDA. To accomplish this goal, the USGS conducted a comprehensive, stratified survey of 204 catchments (wetland and surrounding uplands contributing runoff to the wetland) in 1997 and 270 catchments in 2004 to gather data necessary for estimating various ecosystem services. In 1997 and 2004, the surveys included catchments with seasonal and semipermanent wetlands that were restored as part of USDA conservation programs, as well as nonprogram catchments in native prairie. Additionally, in 2004 data collection was expanded to include temporary wetlands for all treatments and nonprogram cropped catchments for all wetland classes: temporary, seasonal, and semipermanent. A key element in the sample design is that catchments span an alteration gradient ranging from highly altered, such as cropland, to minimally altered, such as native prairie. Therefore, we evaluated restoration programs by comparing changes in program (restored) catchments to nonprogram (cropland and native prairie) catchments. Information collected during both surveys included easily measured soil, vegetation, and morphological variables that were used to estimate the following ecosystem services: plant community quality and richness, carbon sequestration, floodwater storage, sediment and nutrient reduction, and potential wildlife habitat suitability. In this report, we evaluate the extent that these ecosystem services changed in restored wetlands relative to cropland and native prairie baselines. In most cases, our results indicate restoration activities funded by the USDA have positively influenced ecosystem services in comparison to a cropped wetland baseline; however, most benefits were only considered at a site-specific scale, and better quantification of off-site benefits associated with conservation programs will require detailed spatial data on all land areas enrolled in conservation programs.

Edited by Gleason, Robert A.; Laubhan, Murray K.; Euliss, Ned H., Jr.

2008-01-01

199

Residential Water Conservation: An Annotated Bibliography.  

National Technical Information Service (NTIS)

This annotated bibliography of 155 references lists publications on water conservation tips, water conservation devices, water conservation projects, and economics regarding residential water conservation and regional variables. Useful information is summ...

1980-01-01

200

Engaging a Window of Opportunity: Synchronicity between a Regional River Conservation Initiative and Broader Water Law Reform in South Africa  

Microsoft Academic Search

This paper describes how processes used in environmental conservation efforts for rivers, with emphasis on those in the Kruger National Park Rivers Research initiative, interacted with water law reform processes in South Africa designed to balance resource protection and use sustainably. The paper uses complementary frameworks from resilience and business management theory to analyze progress and synchronicity. A long phase

H. C. Biggs; C. M. Breen; C. G. Palmer

2008-01-01

201

Statistical evidence for conserved, local secondary structure in the coding regions of eukaryotic mRNAs and pre-mRNAs  

PubMed Central

Owing to the degeneracy of the genetic code, protein-coding regions of mRNA sequences can harbour more than only amino acid information. We search the mRNA sequences of 11 human protein-coding genes for evolutionarily conserved secondary structure elements using RNA-Decoder, a comparative secondary structure prediction program that is capable of explicitly taking the known protein-coding context of the mRNA sequences into account. We detect well-defined, conserved RNA secondary structure elements in the coding regions of the mRNA sequences and show that base-paired codons strongly correlate with sparse codons. We also investigate the role of repetitive elements in the formation of secondary structure and explain the use of alternate start codons in the caveolin-1 gene by a conserved secondary structure element overlapping the nominal start codon. We discuss the functional roles of our novel findings in regulating the gene expression on mRNA level. We also investigate the role of secondary structure on the correct splicing of the human CFTR gene. We study the wild-type version of the pre-mRNA as well as 29 variants with synonymous mutations in exon 12. By comparing our predicted secondary structures to the experimentally determined splicing efficiencies, we find with weak statistical significance that pre-mRNAs with high-splicing efficiencies have different predicted secondary structures than pre-mRNAs with low-splicing efficiencies.

Meyer, Irmtraud M.; Miklos, Istvan

2005-01-01

202

Conserved Regions as Markers of Different Patterns of Expression and Distribution of the Mucin-Associated Surface Proteins of Trypanosoma cruzi  

PubMed Central

The MASP gene family is the second most widely represented gene family in the genome of Trypanosoma cruzi. One of its main characteristics is that its 5? and 3? regions are highly conserved. We assessed the expression of these conserved regions as a marker for T. cruzi and also analyzed the expression of the masp genes and MASP proteins. In parasite strains CL-Brener (DTUVI lineage) and PAN4 (DTUI lineage), masp genes were expressed at different levels both with regard to the two strains and between stages in the parasite's life cycle. We also studied the expression of the family during the intracellular cycle of T. cruzi, using antibodies against the conserved MASP signal peptide (SP). Fluorescence intensity showed an increase in expression from 24 h onwards, with a peak in intensity at 72 h postinfection. After 24 and 48 h, the MASP proteins were expressed in 33.33% and 57.14% of the amastigotes, respectively. Our data show that not only the extracellular forms of T. cruzi but also the intracellular phases express this type of protein, though to different extents in the various forms of the parasite.

De Pablos, Luis M.

2012-01-01

203

Functional Analysis of Conserved Non-Coding Regions Around the Short Stature hox Gene (shox) in Whole Zebrafish Embryos  

PubMed Central

Background Mutations in the SHOX gene are responsible for Leri-Weill Dyschondrosteosis, a disorder characterised by mesomelic limb shortening. Recent investigations into regulatory elements surrounding SHOX have shown that deletions of conserved non-coding elements (CNEs) downstream of the SHOX gene produce a phenotype indistinguishable from Leri-Weill Dyschondrosteosis. As this gene is not found in rodents, we used zebrafish as a model to characterise the expression pattern of the shox gene across the whole embryo and characterise the enhancer domains of different CNEs associated with this gene. Methodology/Principal Findings Expression of the shox gene in zebrafish was identified using in situ hybridization, with embryos showing expression in the blood, putative heart, hatching gland, brain pharyngeal arch, olfactory epithelium, and fin bud apical ectodermal ridge. By identifying sequences showing 65% identity over at least 40 nucleotides between Fugu, human, dog and opossum we uncovered 35 CNEs around the shox gene. These CNEs were compared with CNEs previously discovered by Sabherwal et al., resulting in the identification of smaller more deeply conserved sub-sequence. Sabherwal et al.'s CNEs were assayed for regulatory function in whole zebrafish embryos resulting in the identification of additional tissues under the regulatory control of these CNEs. Conclusion/Significance Our results using whole zebrafish embryos have provided a more comprehensive picture of the expression pattern of the shox gene, and a better understanding of its regulation via deeply conserved noncoding elements. In particular, we identify additional tissues under the regulatory control of previously identified SHOX CNEs. We also demonstrate the importance of these CNEs in evolution by identifying duplicated shox CNEs and more deeply conserved sub-sequences within already identified CNEs.

Kenyon, Emma J.; McEwen, Gayle K.; Callaway, Heather; Elgar, Greg

2011-01-01

204

Conservation physiology  

Microsoft Academic Search

Conservation biologists increasingly face the need to provide legislators, courts and conservation managers with data on causal mechanisms underlying conservation problems such as species decline. To develop and monitor solutions, conservation biologists are progressively using more techniques that are physiological. Here, we review the emerging discipline of conservation physiology and suggest that, for conservation strategies to be successful, it is

Martin Wikelski; Steven J. Cooke

2006-01-01

205

Identification of key residues involved in fibril formation by the conserved N-terminal region of Plasmodium falciparum merozoite surface protein 2 (MSP2).  

PubMed

Merozoite surface protein 2 (MSP2) from the human malaria parasite Plasmodium falciparum is expressed as a GPI-anchored protein on the merozoite surface. MSP2 is assumed to have a role in erythrocyte invasion and is a leading vaccine candidate. Recombinant MSP2 forms amyloid-like fibrils upon storage, as do peptides corresponding to sequences in the conserved N-terminal region, which constitutes the structural core of fibrils formed by full-length MSP2. We have investigated the roles of individual residues in fibril formation and local ordered structure in two peptides, a recombinant 25-residue peptide corresponding to the entire N-terminal domain of mature MSP2 and an 8-residue peptide from the central region of this domain (residues 8-15). Both peptides formed fibrils that were similar to amyloid-like fibrils formed by full-length MSP2. Phe11 and Ile12 have important roles both in stabilising local structure in these peptides and promoting fibril formation; the F11A and I12A mutants of MSP2(8-15) were essentially unstructured in solution and fibril formation at pH 7.4 and 4.7 was markedly retarded. The T10A mutant showed intermediate behaviour, having a less well defined structure than wild-type and slower fibril formation at pH 7.4. The mutation of Phe11 and Ile12 in MSP2(1-25) significantly retarded but did not abolish fibril formation, indicating that these residues also play a key role in fibril formation by the entire N-terminal conserved region. These mutations had little effect on the aggregation of full-length MSP2, however, suggesting that regions outside the conserved N-terminus have unanticipated importance for fibril formation in the full-length protein. PMID:20542076

Yang, Xiaodong; Adda, Christopher G; MacRaild, Christopher A; Low, Andrew; Zhang, Xuecheng; Zeng, Weiguang; Jackson, David C; Anders, Robin F; Norton, Raymond S

2010-10-01

206

Energy Conservation Simplified  

ERIC Educational Resources Information Center

The standard formulation of energy conservation involves the subsidiary ideas of kinetic energy ("KE"), work ("W"), thermal energy, internal energy, and a half-dozen different kinds of potential energy ("PE"): elastic, chemical, nuclear, gravitational, and so forth. These quantities came to be recognized during the centuries over which the…

Hecht, Eugene

2008-01-01

207

The Role of DNA Barcodes in Understanding and Conservation of Mammal Diversity in Southeast Asia  

Microsoft Academic Search

BackgroundSoutheast Asia is recognized as a region of very high biodiversity, much of which is currently at risk due to habitat loss and other threats. However, many aspects of this diversity, even for relatively well-known groups such as mammals, are poorly known, limiting ability to develop conservation plans. This study examines the value of DNA barcodes, sequences of the mitochondrial

Charles M. Francis; Alex V. Borisenko; Natalia V. Ivanova; Judith L. Eger; Burton K. Lim; Antonio Guillén-Servent; Sergei V. Kruskop; Iain Mackie; Paul D. N. Hebert

2010-01-01

208

Recognizing characters of ancient manuscripts  

NASA Astrophysics Data System (ADS)

Considering printed Latin text, the main issues of Optical Character Recognition (OCR) systems are solved. However, for degraded handwritten document images, basic preprocessing steps such as binarization, gain poor results with state-of-the-art methods. In this paper ancient Slavonic manuscripts from the 11th century are investigated. In order to minimize the consequences of false character segmentation, a binarization-free approach based on local descriptors is proposed. Additionally local information allows the recognition of partially visible or washed out characters. The proposed algorithm consists of two steps: character classification and character localization. Initially Scale Invariant Feature Transform (SIFT) features are extracted which are subsequently classified using Support Vector Machines (SVM). Afterwards, the interest points are clustered according to their spatial information. Thereby, characters are localized and finally recognized based on a weighted voting scheme of pre-classified local descriptors. Preliminary results show that the proposed system can handle highly degraded manuscript images with background clutter (e.g. stains, tears) and faded out characters.

Diem, Markus; Sablatnig, Robert

2010-02-01

209

Conservation potential of agricultural water conservation subsidies  

NASA Astrophysics Data System (ADS)

A current policy subsidizes farmers to invest in improved on-farm irrigation efficiency, expecting water to be conserved off farm. Contrary to expectation, water has been increasingly depleted in some regions after such improvements. This paper investigates the policy's failure to conserve water consistently by (1) formulating an economic model of irrigated crop production to determine a profit-maximizing irrigator's range of responses to a subsidy and (2) embedding these responses into hypothetical streamflow diagrams to ascertain their potential to conserve water under various hydrologic regimes. Testable hypotheses are developed to predict the conservation potential of a subsidy in real-world application.

Huffaker, Ray

2008-07-01

210

Recognizing, Determining, and Addressing Entrepreneurial Innovations by Superintendents of Emerging or Established Educational Service Agencies  

ERIC Educational Resources Information Center

This dissertation describes how entrepreneurial superintendents of educational service agencies (ESAs) recognize, determine and address common and distinct innovative characteristics within emerging or established regional educational environments. Because internal and external factors assist in recognizing innovative practices, this study…

Arfstrom, Kari M.

2009-01-01

211

Molecular dissection of a contiguous gene syndrome: frequent submicroscopic deletions, evolutionarily conserved sequences, and a hypomethylated "island" in the Miller-Dieker chromosome region.  

PubMed Central

The Miller-Dieker syndrome (MDS), composed of characteristic facial abnormalities and a severe neuronal migration disorder affecting the cerebral cortex, is caused by visible or submicroscopic deletions of chromosome band 17p13. Twelve anonymous DNA markers were tested against a panel of somatic cell hybrids containing 17p deletions from seven MDS patients. All patients, including three with normal karyotypes, are deleted for a variable set of 5-12 markers. Two highly polymorphic VNTR (variable number of tandem repeats) probes, YNZ22 and YNH37, are codeleted in all patients tested and make molecular diagnosis for this disorder feasible. By pulsed-field gel electrophoresis, YNZ22 and YNH37 were shown to be within 30 kilobases (kb) of each other. Cosmid clones containing both VNTR sequences were identified, and restriction mapping showed them to be less than 15 kb apart. Three overlapping cosmids spanning greater than 100 kb were completely deleted in all patients, providing a minimum estimate of the size of the MDS critical region. A hypomethylated island and evolutionarily conserved sequences were identified within this 100-kb region, indications of the presence of one or more expressed sequences potentially involved in the pathophysiology of this disorder. The conserved sequences were mapped to mouse chromosome 11 by using mouse-rat somatic cell hybrids, extending the remarkable homology between human chromosome 17 and mouse chromosome 11 by 30 centimorgans, into the 17p telomere region. Images

Ledbetter, D H; Ledbetter, S A; vanTuinen, P; Summers, K M; Robinson, T J; Nakamura, Y; Wolff, R; White, R; Barker, D F; Wallace, M R

1989-01-01

212

Animal conservation, carbon and sustainability  

Microsoft Academic Search

International conventions to reduce carbon dioxide levels focus on ecosystems and do not specifically recognize the need to conserve species. However, species are the build- ing blocks of ecosystems, they are more widely understood among the public, and they provide means of capturing market values from ecosystems. Achieving successful conservation globally will require ensuring that the systems under which species

N. Leader-Williams

2002-01-01

213

Sequence Conservation of the Region Targeted by the Abbott RealTime HBV Viral Load Assay in Clinical Specimens  

PubMed Central

The Abbott RealTime HBV assay targets the N-terminal region of the S gene. Here we analyzed the sequence variability of the assay target region from >2,100 clinical specimens. Thermodynamic modeling of the percentage of bound primer/probe at the assay annealing temperature was performed to assess the potential effect of sequence variability.

Rhoads, James; Young, Thomas P.; Parkin, Neil T.; Holzmayer, Vera; Yuen, Lilly; Mullen, Carolyn

2013-01-01

214

Sequence conservation of the region targeted by the Abbott RealTime HBV viral load assay in clinical specimens.  

PubMed

The Abbott RealTime HBV assay targets the N-terminal region of the S gene. Here we analyzed the sequence variability of the assay target region from >2,100 clinical specimens. Thermodynamic modeling of the percentage of bound primer/probe at the assay annealing temperature was performed to assess the potential effect of sequence variability. PMID:23345287

Cloherty, Gavin A; Rhoads, James; Young, Thomas P; Parkin, Neil T; Holzmayer, Vera; Yuen, Lilly; Mullen, Carolyn

2013-04-01

215

Movement patterns of Antillean manatees in Chetumal Bay (Mexico) and coastal Belize: A challenge for regional conservation  

USGS Publications Warehouse

Information from 15 satellite-tracked Antillean manatees (Trichechus manatus manatus) was analyzed in order to assess individual movements, home ranges, and high-use areas for conservation decisions. Manatees were captured in Chetumal Bay, Mexico, and tagged with Argos-monitored satellite transmitters. Location of the manatees and physical characteristics were assessed to describe habitat properties. Most manatees traveled to freshwater sources. The Maximum Area Size (MAS) for each manatee was determined using the observation-area method. Additional kernel densities of 95% home range and 50% Center of Activity (COA) were also calculated, with manatees having 1–3 COAs. Manatees exhibited two different movement patterns: remaining in Chetumal Bay, and long-distance (up to 240 km in 89 d). The residence time in Chetumal Bay was higher for females (89.6% of time) than for males (72.0%), but the daily travel rate (0.4–0.5 km/d) was similar for both sexes. Most of the COAs fell within Natural Protected Areas (NPA). However, manatees also travel for long distances into unprotected areas, where they face uncontrolled boat traffic, fishing activities, and habitat loss. Conservation of movement corridors may promote long-distance movements and facilitate genetic exchange.

Castelblanco-Martínez, D.N.; Padilla-Saldívar, J.; Hernández-Arana, H.A.; Slone, D.H.; Reid, J.P.; Morales-Vela, B.

2013-01-01

216

ReLA, a local alignment search tool for the identification of distal and proximal gene regulatory regions and their conserved transcription factor binding sites  

PubMed Central

Motivation: The prediction and annotation of the genomic regions involved in gene expression has been largely explored. Most of the energy has been devoted to the development of approaches that detect transcription start sites, leaving the identification of regulatory regions and their functional transcription factor binding sites (TFBSs) largely unexplored and with important quantitative and qualitative methodological gaps. Results: We have developed ReLA (for REgulatory region Local Alignment tool), a unique tool optimized with the Smith–Waterman algorithm that allows local searches of conserved TFBS clusters and the detection of regulatory regions proximal to genes and enhancer regions. ReLA's performance shows specificities of 81 and 50% when tested on experimentally validated proximal regulatory regions and enhancers, respectively. Availability: The source code of ReLA's is freely available and can be remotely used through our web server under http://www.bsc.es/cg/rela. Contact: david.torrents@bsc.es Supplementary information: Supplementary data are available at Bioinformatics online.

Gonzalez, Santi; Montserrat-Sentis, Barbara; Sanchez, Friman; Puiggros, Montserrat; Blanco, Enrique; Ramirez, Alex; Torrents, David

2012-01-01

217

Nucleotide sequence, insertional mutagenesis, and transcriptional mapping of a conserved region of the baculovirus Autographa californica nuclear polyhedrosis virus (map unit 64.8-66.9).  

PubMed

The nucleotide sequence of a 2773-bp region of the Autographa californica nuclear polyhedrosis virus HR3 variant (AcMNPV) (map unit 64.4-68.2) has been determined. This region lies between the previously analyzed p6.9 and p80 genes. Three open reading frames were contained within this region, potentially coding for proteins of 45, 40, and 12 kDa. The 5' ends of transcripts capable of coding for the 45- and 12-kDa proteins map to consensus baculovirus late transcription start sites (ATAAG), while the major 5' end of the transcript coding for the 40-kDa protein maps 16 nucleotides downstream from another late transcription start site sequence, GTAAG. Attempts to prepare recombinant viruses containing insertions within these three genes were negative, suggesting that they are all essential for virus replication in cell culture. The size and organization of transcripts expressed from this region of AcMNPV were very similar to those of the previously described homologous region of Orgyia pseudotsugata nuclear polyhedrosis virus (OpMNPV). The three AcMNPV protein sequences (p45, p40, and p12) showed amino acid sequence homology with the proteins p48, p45, and p12 of OpMNPV, suggesting this region is highly conserved in baculoviruses. PMID:8989865

Lu, A; Craig, A; Casselman, R; Carstens, E B

1996-12-01

218

Heron conservation  

USGS Publications Warehouse

Herons are large, popular and, in many cases, spectacular birds found in wetlands world-wide, both tropical and temperate, natural and man-made. Some populations are very small and localized, some have decreased, some have expanded their ranges, and a few are pests of human activities. In the fifteen years since the publication of the latest monographic treatment of the family, The Herons Handbook, there has been a tremendous increase in our knowledge of heron status and conservation requirements, set against a backdrop of increasing concern about the future of the world?s wetland habitats. This book provides a comprehensive update following two distinct threads. The status and conservation needs of herons are first presented on a regional basis, in a series of chapters set at a continental or subcontinental scale. Over 200 biologists and heron conservationists have contributed to the data summarized here, and the very latest census and survey results provide the most up-to-date and detailed picture of heron populations currently available. Chapters discussing several critical issues in heron conservation follow, tending to focus on the international nature of the problems.

2000-01-01

219

Force-dependent isomerization kinetics of a highly conserved proline switch modulates the mechanosensing region of filamin.  

PubMed

Proline switches, controlled by cis-trans isomerization, have emerged as a particularly effective regulatory mechanism in a wide range of biological processes. In this study, we use single-molecule mechanical measurements to develop a full kinetic and energetic description of a highly conserved proline switch in the force-sensing domain 20 of human filamin and how prolyl isomerization modulates the force-sensing mechanism. Proline isomerization toggles domain 20 between two conformations. A stable cis conformation with slow unfolding, favoring the autoinhibited closed conformation of filamin's force-sensing domain pair 20-21, and a less stable, uninhibited conformation promoted by the trans form. The data provide detailed insight into the folding mechanisms that underpin the functionality of this binary switch and elucidate its remarkable efficiency in modulating force-sensing, thus combining two previously unconnected regulatory mechanisms, proline switches and mechanosensing. PMID:24706888

Rognoni, Lorenz; Möst, Tobias; Žoldák, Gabriel; Rief, Matthias

2014-04-15

220

Characterization of a cDNA encoding a novel DNA-binding protein, SPF1, that recognizes SP8 sequences in the 5? upstream regions of genes coding for sporamin and ?-amylase from sweet potato  

Microsoft Academic Search

We isolated a cDNA encoding a DNA-binding protein, SPF1, of sweet potato that binds to the SP8a (ACTGTGTA) and SP8b (TACTATT) sequences present in the 5' upstream regions of three different genes coding for sporamin and ß-amylase of tuberous roots. SPF1 comprises 549 amino acids and is enriched in both basic and acidic residues. The amino acid sequence of SPF1

Sumie Ishiguro; Kenzo Nakamura

1994-01-01

221

Assignment of the hypoxia-inducible factor 1{alpha} gene to a region of conserved synteny on mouse chromosome 12 and human chromosome 14q  

SciTech Connect

Hypoxia-inducible factor 1 (HIF-1) is a basic helix-loop-helix transcription factor that mediates homeostatic responses to hypoxia. HIF-1 is a heterodimer consisting of HIF-1{alpha} which is encoded by the HIF1A gene, complexes with HIF-1{beta}, which is encoded by the ARNT gene. In this paper we report the assignment of Hif1a and HIF1A to mouse chromosome 12 and human chromosome 14, respectively. HIF1A was assigned to human chromosome 14q21-q24 by analysis of somatic cell hybrids and by fluorescence in situ hybridization. Hif1a was localized by interspecific backcross analysis within a region of mouse chromosome 12 encompassing >30 cM that demonstrates conservation of synteny with a region of human chromosome 14 extending from PAX9 at 14q12-q13 to IGHC at 14q32.33. 12 refs., 2 figs.

Semenza, G.L.; Rue, E.A.; Iyer, N.V. [Johns Hopkins Univ. School of Medicine, Baltimore, MD (United States)] [and others] [Johns Hopkins Univ. School of Medicine, Baltimore, MD (United States); and others

1996-06-15

222

Conservation in the first internal transcribed spacer region (ITS1) in Hematodinium species infecting crustacean hosts found in the UK and Newfoundland.  

PubMed

Parasitic dinoflagellates in the genus Hematodinium infect a number of decapod crustaceans in waters off the UK, including the Norway lobster Nephrops norvegicus and the edible crab Cancer pagurus. This study investigated sequence variability in the first internal transcribed spacer (ITS1) region of the ribosomal RNA complex of Hematodinium spp. infecting N. norvegicus, C. pagurus, and Pagurus bernhardus from 4 locations in the UK and from the Hematodinium sp. infecting Chionoecetes opilio from the province of Newfoundland and Labrador, Canada. Phylogenetic analysis of the Hematodinium ITS1 sequences from N. norvegicus, C. pagurus, P. bernhardus and C. opilio suggest that these crustaceans are infected with the same species of Hematodinium. Length variability of the ITS1 region was observed (324 to 345 bp) and attributed to 4 variable microsatellite regions (CATG)n' (GCC)nTCCGC(TG)n' (TA)n' and (GAA)n(GGA)n within the sequenced ITS1 fragment. The observed variation may be due to co-infection of the host crustacean with several different strains of Hematodinium or differences among copies of ITS1 region within the genome of a single parasite cell. The Hematodinium ITS1 sequence from N. norvegicus, C. pagurus, P. bernhardus and C. opilio isolates was sufficiently conserved in primer binding regions targeted by previous molecular diagnostic assays; therefore, we suggest that this assay could be used to screen for Hematodinium infections in these crustacean hosts. PMID:17629120

Small, H J; Shields, J D; Moss, J A; Reece, K S

2007-05-01

223

Characterization of an Egyptian Spodoptera littoralis nucleopolyhedrovirus and a possible use of a highly conserved region from polyhedrin gene for nucleopolyhedrovirus detection  

PubMed Central

An Egyptian isolate of Spodoptera littoralis nucleopolyhedrovirus (SpliNPV) was tested for its potential as biocontrol agent in comparison to Autographa californica multiple nucleopolyhedrovirus (AcMNPV). Comparative assays of SpliNPV and AcMNPV against 2nd instar larvae of Spodoptera littoralis revealed 4-fold greater susceptibility of S. littoralis to AcMNPV than to SpliNPV based on LC50 values for the two viruses. The LT50s determined for SpliNPV and AcMNPV using LC50 of the virus against 2nd instar larvae were 4.2 and 5.8 days, respectively. A DNA segment of 405 bp containing highly conserved region from polyhedrin gene of SpliNPV (Polh-cr) was successfully amplified by PCR. Subsequently, this DNA segment was cloned and sequenced. Nucleotide sequence and its deduced amino acid sequence were compared to all available sequences in GenBank. Sequence alignment results revealed that Polh-cr showed significant similarities with 91 different baculovirus isolates. The percentage of homology ranged from 78% for Plusia orichalcea NPV to 99% for SpliNPV. This highly conserved region provides a candidate that could be used in easy, fast and economic prospective systems for virus detection as well as in biological control strategies.

Seufi, AlaaEddeen M

2008-01-01

224

Gene Conservation and Loss in the mutS-rpoS Genomic Region of Pathogenic Escherichia coli  

PubMed Central

The extent and nature of DNA polymorphism in the mutS-rpoS region of the Escherichia coli genome were assessed in 21 strains of enteropathogenic E. coli (EPEC) and enterohemorrhagic E. coli (EHEC) and in 6 strains originally isolated from natural populations. The intervening region between mutS and rpoS was amplified by long-range PCR, and the resulting amplicons varied substantially in length (7.8 to 14.2 kb) among pathogenic groups. Restriction maps based on five enzymes and sequence analysis showed that strains of the EPEC 1, EPEC 2, and EHEC 2 groups have a long mutS-rpoS region composed of a ?6.0-kb DNA segment found in strain K-12 and a novel DNA segment (?2.9 kb) located at the 3? end of rpoS. The novel segment contains three genes (yclC, pad1, and slyA) that occur in E. coli O157:H7 and related strains but are not found in K-12 or members of the ECOR group A. Phylogenetic analysis of the common sequences indicates that the long intergenic region is ancestral and at least two separate deletion events gave rise to the shorter regions characteristic of the E. coli O157:H7 and K-12 lineages.

Herbelin, Corinne J.; Chirillo, Samantha C.; Melnick, Kristen A.; Whittam, Thomas S.

2000-01-01

225

Regions.  

ERIC Educational Resources Information Center

Includes "From School to Jobs: Africa's Dilemma" (Moulin-Acevedo); "Helping Change in Eastern Europe"; "Recognizing the Dignity of Indigenous Peoples"; "An Employment Plan for Pakistan"; and "Around the Continents." (JOW)

Moulin-Acevedo, Madeleine; And Others

1993-01-01

226

The impact of the number of excised axillary nodes and of the percentage of involved nodes on regional nodal failure in patients treated by breast-conserving surgery with or without regional irradiation  

SciTech Connect

Purpose: After breast-conserving surgery, recommendations for regional nodal radiotherapy are usually based on the number of positive nodes. This number is dependent on the number of nodes removed during the axillary dissection. This study examines whether the percentage of positive nodes may help to select patients for regional radiotherapy. Methods and Materials: A retrospective study was conducted on 1,372 T1-T2 node-positive breast cancer patients treated at L'Hotel-Dieu de Quebec Hospital between 1972 and 1997. Results: Among the patients who did not receive regional radiotherapy, the percentage of involved nodes was significantly associated with axillary failure. Ten-year axillary control rates were 97% and 91% when the percentage of involved nodes was <50% and {>=}50%, respectively (p = 0.007). In addition, regional radiotherapy is always significantly associated with a decrease in overall regional failure (axillary and/or supraclavicular), regardless of the percentage of involved nodes. However, regional radiotherapy reduced the axillary failure rate (2% vs. 9%, p = 0.007) only when more than a specific percentage of nodes was involved ({>=}40% if N1-3 and {>=}50% if N>3 nodes). Conclusions: The percentage of involved nodes should be taken into consideration in selecting patients for regional radiotherapy. Irradiation of the axilla should be reserved for patients with a specific ratio: >40% involved nodes if N1-3 and {>=}50% involved nodes if N>3 nodes.

Fortin, Andre [Department of Radiation Oncology, L'Hotel-Dieu de Quebec, Quebec City, Quebec (Canada)]. E-mail: afortin@videotron.ca; Dagnault, Anne [Department of Radiation Oncology, L'Hotel-Dieu de Quebec, Quebec City, Quebec (Canada); Blondeau, Lucie [Department of Radiation Oncology, L'Hotel-Dieu de Quebec, Quebec City, Quebec (Canada); Thi Trinh Thuc Vu [Department of Radiation Oncology, L'Hotel-Dieu de Quebec, Quebec City, Quebec (Canada); Larochelle, Marie [Department of Radiation Oncology, L'Hotel-Dieu de Quebec, Quebec City, Quebec (Canada)

2006-05-01

227

A Highly Conserved Region Between Amino Acids 221 and 266 of Dengue Virus Non-Structural Protein 1 is a Major Epitope Region in Infected Patients.  

PubMed

The immune response to dengue virus (DENV) infection generates high levels of antibodies (Abs) against the DENV non-structural protein 1 (NS1), particularly in cases of secondary infection. Therefore, anti-NS1 Abs may play a role in severe dengue infections, possibly by interacting (directly or indirectly) with host factors or regulating virus production. If it does play a role, NS1 may contain epitopes that mimic those epitopes of host molecules. Previous attempts to map immunogenic regions within DENV-NS1 were undertaken using mouse monoclonal Abs (MAbs). The aim of this study was to characterize the epitope regions of nine anti-NS1 human monoclonal Abs (HuMAbs) derived from six patients secondarily infected with DENV-2. These anti-NS1 HuMAbs were cross-reactive with DENV-1, -2, and -3 but not DENV-4. All HuMAbs bound a common epitope region located between amino acids 221 and 266 of NS1. This study is the first report to map a DENV-NS1 epitope region using anti-DENV MAbs derived from patients. PMID:24778195

Omokoko, Magot Diata; Pambudi, Sabar; Phanthanawiboon, Supranee; Masrinoul, Promsin; Setthapramote, Chayanee; Sasaki, Tadahiro; Kuhara, Motoki; Ramasoota, Pongrama; Yamashita, Akifumi; Hirai, Itaru; Ikuta, Kazuyoshi; Kurosu, Takeshi

2014-07-01

228

Conservation in the 5' region of the long interspersed mouse L1 repeat: implications of comparative sequence analysis.  

PubMed Central

A clone of 7.1kb corresponding to the mouse L1 interspersed repeat family was selected for homology to a human interspersed repeat. This clone fairly represents mouse genomic members. Mapping of the clone revealed one common element at both the 5' and 3' ends in a head to tail arrangement, suggesting that at least some long L1 family members are tandemly arranged; genomic studies confirmed the unexpected tandem arrangement of a minor proportion of L1 members. A short SmaI tandem repeat appears to define the 5' end of most L1 family members. SmaI repeats may maintain, via a recursive regulatory function, the transcriptional viability of L1 members after retroposition events. A 2.5kb portion of the mouse L1 repeat that has not been previously sequenced is presented. It is 55-70% homologous to a corresponding portion of the human KpnI repeat family. Comparative sequence analysis revealed that one common open reading frame may conserve potential coding function across species. A second open reading frame bears an asymmetric distribution of codon replacements unlike both genes and pseudogenes. This latter feature could be consistent with a proposed chromosome organization function that is unrelated to peptide expression. Images

Mottez, E; Rogan, P K; Manuelidis, L

1986-01-01

229

Conserved genetic regions across angiosperms as tools to develop single-copy nuclear markers in gymnosperms: an example using cycads.  

PubMed

Several individuals of the Caribbean Zamia clade and other cycad genera were used to identify single-copy nuclear genes for phylogeographic and phylogenetic studies in Cycadales. Two strategies were employed to select target loci: (i) a tblastX search of Arabidopsis conserved ortholog sequence (COS) set and (ii) a tblastX search of Arabidopsis-Populus-Vitis-Oryza Shared Single-Copy genes (APVO SSC) against the EST Zamia databases in GenBank. From the first strategy, 30 loci were selected, and from the second, 16 loci. In both cases, the matching GenBank accessions of Zamia were used as a query for retrieving highly similar sequences from Cycas, Picea, Pinus species or Ginkgo biloba. After retrieving and aligning all the sequences in each locus, intron predictions were completed to assist in primer design. PCR was carried out in three rounds to detect paralogous loci. A total of 29 loci were successfully amplified as a single band of which 20 were likely single-copy loci. These loci showed different diversity and divergence levels. A preliminary screening allowed us to select 8 promising loci (40S, ATG2, BG, GroES, GTP, LiSH, PEX4 and TR) for the Zamia pumila complex and 4 loci (COS26, GroES, GTP and HTS) for all other cycad genera. PMID:24444413

Salas-Leiva, Dayana E; Meerow, Alan W; Francisco-Ortega, Javier; Calonje, Michael; Griffith, M Patrick; Stevenson, Dennis W; Nakamura, Kyoko

2014-07-01

230

Roles of conserved and allelic regions of the major merozoite surface protein (gp195) in immunity against Plasmodium falciparum.  

PubMed Central

The Plasmodium falciparum major merozoite surface protein gp195 is a candidate antigen for a vaccine against human malaria. The significance of allelism and polymorphism in vaccine-induced immunity to gp195 was investigated in this study. Rabbits were immunized with each of two allelic forms of gp195 that were affinity purified from the FUP and FVO parasite isolates. gp195-specific antibodies raised against one allelic form of gp195 cross-reacted extensively with the gp195 of the heterologous allele in enzyme-linked immunosorbent assays (ELISAs) and immunofluorescence assays. Competitive binding ELISAs with homologous and heterologous gp195s confirmed that a majority of the anti-gp195 antibodies produced against either allelic protein were cross-reactive. Moreover, the biological activities of the gp195 antibody responses were also highly cross-reactive, since anti-gp195 sera inhibited the in vitro growth of the homologous and heterologous parasites with equal efficiency. The degree of cross-reactivity with strain-specific and allele-specific determinants of gp195 in the ELISA was low. These results suggest that the immunological cross-reactivity between the two gp195 proteins is due to recognition of conserved determinants. They also suggest that a gp195-based vaccine may be effective against blood-stage infection with a diverse array of parasite isolates. Images

Hui, G S; Hashimoto, A; Chang, S P

1992-01-01

231

Arabic word recognizer for mobile applications  

NASA Astrophysics Data System (ADS)

When traveling in a region where the local language is not written using a "Roman alphabet," translating written text (e.g., documents, road signs, or placards) is a particularly difficult problem since the text cannot be easily entered into a translation device or searched using a dictionary. To address this problem, we are developing the "Rosetta Phone," a handheld device (e.g., PDA or mobile telephone) capable of acquiring an image of the text, locating the region (word) of interest within the image, and producing both an audio and a visual English interpretation of the text. This paper presents a system targeted for interpreting words written in Arabic script. The goal of this work is to develop an autonomous, segmentation-free Arabic phrase recognizer, with computational complexity low enough to deploy on a mobile device. A prototype of the proposed system has been deployed on an iPhone with a suitable user interface. The system was tested on a number of noisy images, in addition to the images acquired from the iPhone's camera. It identifies Arabic words or phrases by extracting appropriate features and assigning "codewords" to each word or phrase. On a dictionary of 5,000 words, the system uniquely mapped (word-image to codeword) 99.9% of the words. The system has a 82% recognition accuracy on images of words captured using the iPhone's built-in camera.

Khanna, Nitin; Abdollahian, Golnaz; Brame, Ben; Boutin, Mireille; Delp, Edward J.

2011-02-01

232

Genetic analysis of the yopE region of Yersinia spp.: identification of a novel conserved locus, yerA, regulating yopE expression.  

PubMed Central

The yopE gene of Yersinia pseudotuberculosis was recently sequenced, and YopE was identified as an indispensable virulence determinant when tested in a mouse model (A. Forsberg and H. Wolf-Watz, Mol. Microbiol. 2:121-133, 1988). In the study described here, the DNA sequences of the yopE genes of Yersinia pestis EV76 and Yersinia enterocolitica 8081 were determined and compared with that of the Y. pseudotuberculosis gene. Only two codons were found to differ, both leading to amino acid replacements, when the gene from Y. pestis was compared. These two replacements were also present in the gene from Y. enterocolitica; in addition, 18 other codons were found to differ. Thirteen of these substitutions led to amino acid replacements. Downstream of the yopE gene, the plasmid partition locus par was found to be conserved in all three species. In Y. enterocolitica 8081, the sequence homology was interrupted by a putative insertion sequence element inserted between the yopE gene and the par region at a position only 5 base pairs downstream of the yopE stop codon. Upstream of the yopE gene, 620 base pairs were conserved in the three species. This region contained a 130-amino-acid-long open reading frame reading in the opposite direction to the yopE gene and expressed a 14-kilodalton protein in minicells. An insertion mutation in this region constructed in Y. pseudotuberculosis expressed significantly lower amounts of YopE protein in vitro than did the corresponding wild type. The expression level could be restored by transcomplementation. This new locus was designated yerA, for yopE-regulating gene A. The yerA mutant was avirulent when mice were challenged by oral infection. Images FIG. 3 FIG. 6

Forsberg, A; Wolf-Watz, H

1990-01-01

233

Comparative Genomics of the SOX9 Region in Human and Fugu rubripes: Conservation of Short Regulatory Sequence Elements within Large Intergenic Regions  

Microsoft Academic Search

Campomelic dysplasia (CD), a human skeletal malformation syndrome with XY sex reversal, is caused by heterozygous mutations in and around the gene SOX9. SOX9 has an extended 5? control region, as indicated by CD translocation breakpoints scattered over 1 Mb proximal to SOX9 and by expression data from mice transgenic for human SOX9-spanning yeast artificial chromosomes. To identify long-range regulatory

Stefan Bagheri-Fam; Conchita Ferraz; Jacques Demaille; Gerd Scherer; Dietmar Pfeifer

2001-01-01

234

A Conserved Stem Loop Motif in the 5'Untranslated Region Regulates Transforming Growth Factor-beta1 Translation  

Microsoft Academic Search

Transforming growth factor-?1 (TGF-?1) regulates cellular proliferation, differentiation, migration, and survival. The human TGF-?1 transcript is inherently poorly translated, and translational activation has been documented in relation to several stimuli. In this paper, we have sought to identify in cis regulatory elements within the TGF-?1 5?Untranslated Region (5?UTR). In silico analysis predicted formation of stable secondary structure in a G\\/C-rich

Robert H. Jenkins; Rasha Bennagi; John Martin; Aled O. Phillips; James E. Redman; Donald J. Fraser; Y. Adam Yuan

2010-01-01

235

The ?A-crystallin gene: Conserved features of the 5?-flanking regions in human, mouse, and chicken  

Microsoft Academic Search

Summary Approximately 2 kb of 5?-flanking sequences of the lens-specific ?A-crystallin genes from human and mouse are presented and compared with similar regions of the chicken gene. A repetitive element was found approximately 1 kb upstream from the coding sequences of the ?A-crystallin gene in all three species (Alu in human, B2 in mouse, and CR1 in chicken), suggesting that

Cynthia J. Jaworski; Ana B. Chepelinsky; Joram Piatigorsky

1991-01-01

236

75 FR 17683 - Cooperative Conservation Partnership Initiative-Chesapeake Bay Watershed  

Federal Register 2010, 2011, 2012, 2013

...natural resource concerns include soil quality, water conservation, water quality, plant condition, air quality...conservation practices to address water quality, water conservation, or State and regional conservation...

2010-04-07

237

Capsid-Specific Cytotoxic T Lymphocytes Recognize Three Distinct H-2Db-Restricted Regions of the BeAn Strain of Theiler's Virus and Exhibit Different Cytokine Profiles  

PubMed Central

The role of virus-specific cytotoxic T lymphocytes (CTL) in Theiler's murine encephalomyelitis virus (TMEV)-induced demyelinating disease, a viral model for multiple sclerosis, is not yet clear. To investigate the specificity and function of CTL generated in response to TMEV infection, we generated a panel of overlapping 20-mer peptides encompassing the entire capsid and leader protein region of the BeAn strain of TMEV. Binding of these peptides to H-2Kb and H-2Db class I molecules of resistant mice was assessed using RMA-S cells. Several peptides displayed significant binding to H-2Kb, H-2Db, or both. However, infiltrating cytotoxic T cells in the central nervous system of virus-infected mice preferentially lysed target cells pulsed with VP2111-130/121-140 or VP2121-130, a previously defined CTL epitope shared by the DA strain of TMEV and other closely related cardioviruses. In addition, at a high effector-to-target cell ratio, two additional peptides (VP2161-180 and VP3101-120) sensitized target cells for cytolysis by infiltrating T cells or splenic T cells from virus-infected mice. The minimal epitopes within these peptides were defined as VP2165-173 and VP3110-120. Based on cytokine profiles, CTL specific for these subdominant epitopes are Tc2, in contrast to CTL for the immunodominant epitope, which are of the Tc1 type. Interestingly, CTL function towards both of these subdominant epitopes is restricted by the H-2D molecule, despite the fact that these epitopes bind both H-2K and H-2D molecules. This skewing toward an H-2Db-restricted response may confer resistance to TMEV-induced demyelinating disease, which is known to be associated with the H-2D genetic locus.

Lyman, Michael A.; Lee, Hee-Gu; Kang, Bong Su; Kang, Hee-Kap; Kim, Byung S.

2002-01-01

238

Conserved regions of bovine adenovirus-3 pVIII contain functional domains involved in nuclear localization and packaging in mature infectious virions.  

PubMed

Adenoviruses are non-enveloped DNA viruses that replicate in the nucleus of infected cells. One of the core proteins, named pVIII, is a minor capsid protein connecting the core with the inner surface of the capsid. Here, we report the characterization of minor capsid protein pVIII encoded by the L6 region of bovine adenovirus (BAdV)-3. Anti-pVIII serum detected a 24 kDa protein at 12-48 h post-infection and an additional 8 kDa protein at 24-48 h post-infection. While the 24 kDa protein was detected in empty capsids, only the C-terminal-cleaved 8 kDa protein was detected in the mature virion, suggesting that amino acids147-216 of the conserved C-terminus of BAdV-3 pVIII are incorporated in mature virions. Detection of hexon protein associated with both precursor (24 kDa) and cleaved (8 kDa) forms of pVIII suggest that the C-terminus of pVIII interacts with the hexon. The pVIII protein predominantly localizes to the nucleus of BAdV-3-infected cells utilizing the classical importin ?/? dependent nuclear import pathway. Analysis of mutant pVIII demonstrated that amino acids 52-72 of the conserved N-terminus bind to importin ?-3 with high affinity and are required for the nuclear localization. PMID:24854002

Ayalew, Lisanework E; Gaba, Amit; Kumar, Pankaj; Tikoo, Suresh K

2014-08-01

239

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

PubMed Central

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.

2014-01-01

240

Conserving Energy  

NSDL National Science Digital Library

In this project you will learn what energy is, how energy is used , and how to conserve it What are new ways of protecting the environment to conserve energy? Use your 4- column chart to record information about the questions i ask and you learn about. Begin by seeing what energy isEnergy Quest Tells different ways of conserving energy. List what you learn. What are simple ways to conserve energy everyday? How are vehicle manufactures inventing ways to conserve ...

Y, Mr.

2009-10-21

241

Effectively Using Syntax for Recognizing False Entailment  

Microsoft Academic Search

Recognizing textual entailment is a chal- lenging problem and a fundamental com- ponent of many applications in natural language processing. We present a novel framework for recognizing textual entail- ment that focuses on the use of syntactic heuristics to recognize false entailment. We give a thorough analysis of our sys- tem, which demonstrates state-of-the-art performance on a widely-used test set.

Rion Snow; Lucy Vanderwende; Arul Menezes

2006-01-01

242

Monoclonal Antibodies Recognize Gly-Leu-Phe-Gly Repeat of Nucleoporin Nup98 of Tetrahymena, Yeasts, and Humans  

PubMed Central

Nucleoporin Nup98, an essential component of the nuclear pore complex, has multifunctional roles in nuclear functions including transcriptional regulation and nucleocytoplasmic transport. These functions mostly depend on a Gly-Leu-Phe-Gly (GLFG) sequence appearing repetitively in the N-terminal region of Nup98. As the GLFG sequence is well conserved among Nup98s from a wide variety of species including humans, yeasts, and ciliates such as Tetrahymena thermophila, a specific antibody that recognizes the GLFG sequence is expected to detect various Nup98s from a wide-range of species. To generate monoclonal antibodies specific to the GLFG repeat of Nup98, we used two synthetic polypeptides derived from the macronuclear Nup98 of T. thermophila as an antigen. We obtained two monoclonal antibodies (MAbs), 13C2 and 21A10, that recognize Nup98s in indirect immunofluorescence staining and Western blot analysis of T. thermophila. Peptide array analysis of these monoclonal antibodies located the position of their epitopes at or near GLFG residues: the epitope recognized by the 13C2 MAb is FGxxN (x being any amino acid), and the epitope recognized by the 21A10 MAb is GLF. As expected by their epitopes, these monoclonal antibodies also recognize Nup98 homologs expressed by human cells and the yeasts Schizosaccharomyces pombe and Saccharomyces cerevisiae, indicating that 13C2 and 21A10 MAbs recognize Nup98 epitopes common to phylogenetically distinct organisms. Thus, these MAbs are useful in studying a wide variety of biological phenomena that involve Nup98, ranging from ciliate nuclear dimorphism to NUP98-related human leukemia.

Iwamoto, Masaaki; Asakawa, Haruhiko; Ohtsuki, Chizuru; Osakada, Hiroko; Koujin, Takako; Hiraoka, Yasushi

2013-01-01

243

Specific antibody to a conserved region of Babesia apical membrane antigen-1 inhibited the invasion of B. bovis into the erythrocyte.  

PubMed

Apical membrane antigen-1 (AMA-1) is a microneme protein that exists in all apicomplexan parasites and plays an indispensable role in the invasion into host cell. Central region of ectodomains I and II of Babesia bovis apical membrane antigen-1 (BbAMA-1P) is highly conserved with these of Babesia species and may be beneficial for vaccine development against babesiosis. In the present study, recombinant protein encoding the central region of B. bovis AMA-1 (rBbAMA-1P) was produced in Escherichia coli and its antiserum was prepared in mice for further molecular characterization. Anti-rBbAMA-1P serum specifically reacted with corresponding authentic protein of B. bovis as determined by Western blotting and IFAT. Cultured B. bovis treated with anti-rBbAMA-1P serum showed significant reduction in the in vitro growth of the parasites. Moreover, preincubated free merozoites with 1mg/ml anti-rBbAMA-1P serum inhibited their efficiency in the invasion into erythrocytes (RBCs) by 61% and 70% at 3h and 6h, respectively. Our data suggest that the central region of domains I and II of BbAMA-1 may serve as a vaccine candidate against babesiosis. PMID:24090565

Salama, Akram Ahmed; Terkawi, Mohamad Alaa; Kawai, Satoru; Aboulaila, Mahmoud; Nayel, Mohamed; Mousa, Ahmed; Zaghawa, Ahmed; Yokoyama, Naoaki; Igarashi, Ikuo

2013-11-01

244

A conserved proline residue in the leucine zipper region of AtbZIP34 and AtbZIP61 in Arabidopsis thaliana interferes with the formation of homodimer  

SciTech Connect

Two putative Arabidopsis E group bZIP transcript factors, AtbZIP34 and AtbZIP61, are nuclear-localized and their transcriptional activation domain is in their N-terminal region. By searching GenBank, we found other eight plant homologues of AtbZIP34 and AtbZIP61. All of them have a proline residue in the third heptad of zipper region. Yeast two-hybrid assay and EMSA showed that AtbZIP34 and AtbZIP61 could not form homodimer while their mutant forms, AtbZIP34m and AtbZIP61m, which the proline residue was replaced by an alanine residue in the zipper region, could form homodimer and bind G-box element. These results suggest that the conserved proline residue interferes with the homodimer formation. However, both AtbZIP34 and AtbZIP61 could form heterodimers with members of I group and S group transcription factors in which some members involved in vascular development. So we speculate that AtbZIP34 and AtbZIP61 may participate in plant development via interacting with other group bZIP transcription factors.

Shen Huaishun [College of Life Sciences, Beijing Normal University, Beijing 100875 (China); State Key Laboratory of Genetic Engineering, Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai 200433 (China); Cao Kaiming [State Key Laboratory of Genetic Engineering, Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai 200433 (China); Wang Xiping [College of Life Sciences, Beijing Normal University, Beijing 100875 (China); State Key Laboratory of Genetic Engineering, Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai 200433 (China)], E-mail: xipingwang@hotmail.com

2007-10-19

245

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

PubMed Central

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.

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

2003-01-01

246

Trypanosoma cruzi mitochondrial maxicircles display species- and strain-specific variation and a conserved element in the non-coding region  

PubMed Central

Background The mitochondrial DNA of kinetoplastid flagellates is distinctive in the eukaryotic world due to its massive size, complex form and large sequence content. Comprised of catenated maxicircles that contain rRNA and protein-coding genes and thousands of heterogeneous minicircles encoding small guide RNAs, the kinetoplast network has evolved along with an extreme form of mRNA processing in the form of uridine insertion and deletion RNA editing. Many maxicircle-encoded mRNAs cannot be translated without this post-transcriptional sequence modification. Results We present the complete sequence and annotation of the Trypanosoma cruzi maxicircles for the CL Brener and Esmeraldo strains. Gene order is syntenic with Trypanosoma brucei and Leishmania tarentolae maxicircles. The non-coding components have strain-specific repetitive regions and a variable region that is unique for each strain with the exception of a conserved sequence element that may serve as an origin of replication, but shows no sequence identity with L. tarentolae or T. brucei. Alternative assemblies of the variable region demonstrate intra-strain heterogeneity of the maxicircle population. The extent of mRNA editing required for particular genes approximates that seen in T. brucei. Extensively edited genes were more divergent among the genera than non-edited and rRNA genes. Esmeraldo contains a unique 236-bp deletion that removes the 5'-ends of ND4 and CR4 and the intergenic region. Esmeraldo shows additional insertions and deletions outside of areas edited in other species in ND5, MURF1, and MURF2, while CL Brener has a distinct insertion in MURF2. Conclusion The CL Brener and Esmeraldo maxicircles represent two of three previously defined maxicircle clades and promise utility as taxonomic markers. Restoration of the disrupted reading frames might be accomplished by strain-specific RNA editing. Elements in the non-coding region may be important for replication, transcription, and anchoring of the maxicircle within the kinetoplast network.

Westenberger, Scott J; Cerqueira, Gustavo C; El-Sayed, Najib M; Zingales, Bianca; Campbell, David A; Sturm, Nancy R

2006-01-01

247

Delta-associated molluscan life and death assemblages in the northern Adriatic Sea: Implications for paleoecology, regional diversity and conservation.  

PubMed

Life-death (LD) studies of shelly macrofauna are important to evaluate how well a fossil assemblage can reflect the original living community, but can also serve as a proxy for recent ecological shifts in marine habitats and in practice this has to be distinguished using taphonomic preservation pattern and estimates of time-averaging. It remains to be rigorously evaluated, however, how to distinguish between sources of LD disagreement. In addition, death assemblages (DAs) also preserve important information on regional diversity which is not available from single censuses of the life assemblages (LAs). The northern Adriatic Sea is an ecosystem under anthropogenic pressure, and we studied the distribution and abundance of living and dead bivalve and gastropod species in the physically stressful environments (tidal flat and shallow sublittoral soft bottoms) associated with the delta of the Isonzo River (Gulf of Trieste). Specifically we evaluated the fidelity of richness, evenness, abundance, habitat discrimination and beta diversity. A total of 10,740 molluscs from fifteen tidal flat and fourteen sublittoral sites were analyzed for species composition and distribution of living and dead molluscs. Of 78 recorded species, only eleven were numerically abundant. There were many more dead than living individuals and rarefied species richness in the DA was higher at all spatial scales, but the differences are lower in habitats and in the region than at individual stations. Evenness was always higher in death assemblages, and probably due to temporally more variable LAs the differences are stronger in the sublittoral habitats. Distinct assemblages characterized intertidal and sublittoral habitats, and the distribution and abundance of empty shells generally corresponded to that of the living species. Death assemblages have lower beta diversity than life assemblages, but empty shells capture compositional differences between habitats to a higher degree than living shells. More samples would be necessary to account for the diversity of living molluscs in the study area, which is, however, well recorded in the death assemblages. There is no indication of a major environmental change over the last decades in this area, but due to the long history of anthropogenic pressure here, such a potential impact might be preserved in historical layers of the deeper sedimentary record. PMID:23407873

Weber, Kristina; Zuschin, Martin

2013-01-15

248

A mobile robot that recognizes people  

Microsoft Academic Search

In order for mobile robots to interact effectively with people they will have to recognize faces. We describe a robot system that finds people, approaches them and then recognizes them. The system uses a variety of techniques: color vision is used to find people; vision and sonar sensors are used to approach them; a template-based pattern recognition algorithm is used

Carol Wong; David Kortenkamp; M. Speich

1995-01-01

249

THE THREATENED AND THE IRREPLACEABLE: IDENTIFYING AREAS FOR THE CONSERVATION OF FAUNAL SPECIES DIVERSITY IN THE MIDDLE-ATLANTIC REGION OF THE UNITED STATES  

EPA Science Inventory

One fundamental step in conservation planning involves determining where to concentrate efforts to protect conservation targets. Here we demonstrate an approach to prioritizing areas based on both species composition and potential threats facing the species. First, we determine...

250

Point mutations identify a conserved region of the saccharomyces cerevisiae AFR1 gene that is essential for both the pheromone signaling and morphogenesis functions.  

PubMed Central

Mating pheromone receptors activate a G protein signal pathway that leads to the conjugation of the yeast Saccharomyces cerevisiae. This pathway also induces the production of Afr1p, a protein that negatively regulates pheromone receptor signaling and is required to form pointed projections of new growth that become the site of cell fusion during mating. Afr1p lacks strong similarity to any well-characterized proteins to help predict how it acts. Therefore, we investigated the relationship between the different functions of Afr1p by isolating and characterizing seven mutants that were defective in regulating pheromone signaling. The AFR1 mutants were also defective when expressed as fusions to STE2, the alpha-factor receptor, indicating that the mutant Afr1 proteins are defective in function and not in co-localizing with receptors. The mutant genes contained four distinct point mutations that all occurred between codons 254 and 263, identifying a region that is critical for AFR1 function. Consistent with this, we found that the corresponding region is very highly conserved in the Afr1p homologs from the yeasts S. uvarum and S. douglasii. In contrast, there were no detectable effects on pheromone signaling caused by deletion or overexpression of YER158c, an open reading frame with overall sequence similarity to Afr1p that lacks this essential region. Interestingly, all of the AFR1 mutants showed a defect in their ability to form mating projections that was proportional to their defect in regulating pheromone signaling. This suggests that both functions may be due to the same action of Afr1p. Thus, these studies identify a specific region of Afr1p that is critical for its function in both signaling and morphogenesis.

DeMattei, C R; Davis, C P; Konopka, J B

2000-01-01

251

Genomic instability in regions adjacent to a highly conserved pch prophage in Escherichia coli O157:H7 generates diversity in expression patterns of the LEE pathogenicity island.  

PubMed

The LEE pathogenicity island has been acquired on multiple occasions within the different lineages of enteropathogenic and enterohemorrhagic Escherichia coli. In each lineage, LEE expression is regulated by complex networks of pathways, including core pathways shared by all lineages and lineage-specific pathways. Within the O157:H7 lineage of enterohemorrhagic E. coli, strain-to-strain variation in LEE expression has been observed, implying that expression patterns can diversify even within highly related subpopulations. Using comparative genomics of E. coli O157:H7 subpopulations, we have identified one source of strain-level variation affecting LEE expression. The variation occurs in prophage-dense regions of the genome that lie immediately adjacent to the late regions of the pch prophage carrying pchA, pchB, pchC, and a newly identified pch gene, pchX. Genomic segments extending from the holin S region to the pchA, pchB, pchC, and pchX genes of their respective prophage are highly conserved but are nonetheless embedded within adjacent genomic segments that are extraordinarily variable, termed pch adjacent genomic regions (pch AGR). Despite the remarkable degree of variation, the pattern of variation in pch AGR is highly correlated with the distribution of phylogenetic markers on the backbone of the genome. Quantitative analysis of transcription from the LEE1 promoter further revealed that variation in the pch AGR has substantial effects on absolute levels and patterns of LEE1 transcription. Variation in the pch AGR therefore serves as a mechanism to diversify LEE expression patterns, and the lineage-specific pattern of pch AGR variation could ultimately influence ecological or virulence characteristics of subpopulations within each lineage. PMID:19329643

Yang, Zhijie; Kim, Jaehyoung; Zhang, Chaomei; Zhang, Min; Nietfeldt, Joeseph; Southward, Carolyn M; Surette, Michael G; Kachman, Stephen D; Benson, Andrew K

2009-06-01

252

Genomic Instability in Regions Adjacent to a Highly Conserved pch Prophage in Escherichia coli O157:H7 Generates Diversity in Expression Patterns of the LEE Pathogenicity Island?  

PubMed Central

The LEE pathogenicity island has been acquired on multiple occasions within the different lineages of enteropathogenic and enterohemorrhagic Escherichia coli. In each lineage, LEE expression is regulated by complex networks of pathways, including core pathways shared by all lineages and lineage-specific pathways. Within the O157:H7 lineage of enterohemorrhagic E. coli, strain-to-strain variation in LEE expression has been observed, implying that expression patterns can diversify even within highly related subpopulations. Using comparative genomics of E. coli O157:H7 subpopulations, we have identified one source of strain-level variation affecting LEE expression. The variation occurs in prophage-dense regions of the genome that lie immediately adjacent to the late regions of the pch prophage carrying pchA, pchB, pchC, and a newly identified pch gene, pchX. Genomic segments extending from the holin S region to the pchA, pchB, pchC, and pchX genes of their respective prophage are highly conserved but are nonetheless embedded within adjacent genomic segments that are extraordinarily variable, termed pch adjacent genomic regions (pch AGR). Despite the remarkable degree of variation, the pattern of variation in pch AGR is highly correlated with the distribution of phylogenetic markers on the backbone of the genome. Quantitative analysis of transcription from the LEE1 promoter further revealed that variation in the pch AGR has substantial effects on absolute levels and patterns of LEE1 transcription. Variation in the pch AGR therefore serves as a mechanism to diversify LEE expression patterns, and the lineage-specific pattern of pch AGR variation could ultimately influence ecological or virulence characteristics of subpopulations within each lineage.

Yang, Zhijie; Kim, Jaehyoung; Zhang, Chaomei; Zhang, Min; Nietfeldt, Joeseph; Southward, Carolyn M.; Surette, Michael G.; Kachman, Stephen D.; Benson, Andrew K.

2009-01-01

253

Tandem Repeat Hypothesis in Imprinting: Deletion of a Conserved Direct Repeat Element Upstream of H19 Has No Effect on Imprinting in the Igf2-H19 Region  

PubMed Central

Igf2 and H19 are reciprocally imprinted genes on mouse distal chromosome 7. They share several regulatory elements, including a differentially methylated region (DMR) upstream of H19 that is paternally methylated throughout development. The cis-acting sequence requirements for targeting DNA methylation to the DMR remain unknown; however, it has been suggested that direct tandem repeats near DMRs could be involved. Previous studies of the imprinted Rasgrf1 locus demonstrate indeed that a direct repeat element adjacent to a DMR is responsible for establishing paternal allele-specific methylation at the DMR and therefore allelic expression of the Rasgrf1 transcript. We identified a prominent and conserved direct tandem repeat 1 kb upstream of the H19 DMR and proposed that it played a similar role in imprinted regulation of H19. To test our hypothesis, we generated mice harboring a 1.7-kb targeted deletion of the direct repeat element and analyzed fetal growth, allelic expression, and methylation within the Igf2-H19 region. Surprisingly the deletion had no effect on imprinting. These results together with deletions of other repeats close to imprinted genes suggest that direct repeats may not be important for the targeting of methylation at the majority of imprinted loci and that the Rasgrf1 locus may be an exception to this rule.

Lewis, Annabelle; Mitsuya, Kohzoh; Constancia, Miguel; Reik, Wolf

2004-01-01

254

Single-site mutations in the conserved alternating-arginine region affect ionic channels formed by CryIAa, a Bacillus thuringiensis toxin.  

PubMed Central

The role of the third domain of CryIAa, a Bacillus thuringiensis insecticidal toxin, in toxin-induced membrane permeabilization in a receptor-free environment was investigated. Planar lipid bilayer experiments were conducted with the parental toxin and five proteins obtained by site-directed mutagenesis in block 4, an arginine-rich, highly conserved region of the protein. Four mutants were constructed by replacing the first arginine in position 21 by a lysine (R521K), a glutamine (R521Q), a histidine (R521H), or a glutamic acid (R521E). A fifth mutant was obtained by replacing the fourth arginine by a lysine (R527K). Like CryIAa, the mutants formed cation-selective channels. A limited but significant reduction in channel conductance was observed for all mutants except R521H. The effect was more dramatic for the voltage dependence of the channels formed by R521K and R521Q, which was reversed compared to that of the parental toxin. This study provides the first direct evidence of a functional role for domain III in membrane permeabilization. Our results suggest that residues of the positive arginine face of block 4 interact with domain I, the putative pore-forming region of CryIAa.

Schwartz, J L; Potvin, L; Chen, X J; Brousseau, R; Laprade, R; Dean, D H

1997-01-01

255

The genetic structure of cattle populations (Bos taurus) in northern Eurasia and the neighbouring Near Eastern regions: implications for breeding strategies and conservation.  

PubMed

We investigated the genetic structure and variation of 21 populations of cattle (Bos taurus) in northern Eurasia and the neighbouring Near Eastern regions of the Balkan, the Caucasus and Ukraine employing 30 microsatellite markers. By analyses of population relationships, as well as by a Bayesian-based clustering approach, we identified a genetic distinctness between populations of modern commercial origin and those of native origin. Our data suggested that northern European Russia represents the most heavily colonized area by modern commercial cattle. Further genetic mixture analyses based on individual assignment tests found that native Red Steppe cattle were also employed in the historical breeding practices in Eastern Europe, most probably for incorporating their strong and extensive adaptability. In analysis of molecular variance, within-population differences accounted for approximately 90% of the genetic variation. Despite some correspondence between geographical proximity and genetic similarity, genetic differentiation was observed to be significantly associated with the difference in breeding purpose among the European populations (percentage of variance among groups and significance: 2.99%, P = 0.02). Our findings give unique genetic insight into the historical patterns of cattle breeding practices in the former Soviet Union. The results identify the neighbouring Near Eastern regions such as the Balkan, the Caucasus and Ukraine, and the isolated Far Eastern Siberia as areas of 'genetic endemism', where cattle populations should be given conservation priority. The results will also be of importance for cost-effective management of their future utilization. PMID:17850550

Li, Meng-Hua; Tapio, Ilma; Vilkki, Johanna; Ivanova, Zoya; Kiselyova, Tatyana; Marzanov, Nurby; Cinkulov, Mirjana; Stojanovi?, Srdjan; Ammosov, Innokenty; Popov, Ruslan; Kantanen, Juha

2007-09-01

256

Site-directed mutations in a highly conserved region of Bacillus thuringiensis delta-endotoxin affect inhibition of short circuit current across Bombyx mori midguts.  

PubMed

Bacillus thuringiensis delta-endotoxins (Cry toxins) are insecticidal proteins of approximately 65 kDa in the proteolytically processed and active form. The structure of one of these toxins, CryIIIA, has been determined by Li et al. [Li, J., Carroll, J. & Ellar, D. J. (1991) Nature (London) 353, 815-821] and contains three domains. It is believed that other delta-endotoxins adopt similar three-dimensional structure. Li et al. proposed that the first domain is the membrane pore-forming domain. Previous work from our laboratory has shown that the second domain is the receptor binding domain, but the function of the third domain is unclear. Site-directed mutagenesis was used to convert the "arginine face" of one of five highly conserved regions, QRYRVRIRYAS of CryIAa (residues 525-535), to selected other residues. This sequence corresponds to the beta-sheet 17 of CryIIIA in the third domain. Mutations in the second and third arginine positions resulted in structural alterations in the protein and were poorly expressed in Escherichia coli. Toxins from genes mutated to replace lysine for the first and fourth arginines were unaltered in expression and structure, as measured by trypsin activation, CD spectra, and receptor binding, but were substantially reduced in their insecticidal properties and inhibition of short circuit current across Bombyx mori midguts. It is proposed that this region plays a role in toxin function as an ion channel. PMID:8415651

Chen, X J; Lee, M K; Dean, D H

1993-10-01

257

A Conserved Virulence Plasmidic Region Contributes to the Virulence of the Multiresistant Escherichia coli Meningitis Strain S286 Belonging to Phylogenetic Group C  

PubMed Central

Recent isolation of the non-K1 Escherichia coli neonatal meningitis strain S286, belonging to phylogroup C, which is closely related to major group B1, and producing an extended-spectrum beta-lactamase, encouraged us to seek the genetic determinants responsible for its virulence. We show that S286 belongs to the sequence O type ST23O78 and harbors 4 large plasmids. The largest one, pS286colV (?120 kb), not related to resistance, contains genes characteristic of a Conserved Virulence Plasmidic (CVP) region initially identified in B2 extra-intestinal avian pathogenic E. coli (APEC) strains and in the B2 neonatal meningitis E. coli strain S88. The sequence of this CVP region has a strong homology (98%) with that of the recently sequenced plasmid pChi7122-1 of the O78 APEC strain Chi7122. A CVP plasmid-cured variant of S286 was less virulent than the wild type strain in a neonatal rat sepsis model with a significant lower level of bacteremia at 24 h (4.1±1.41 versus 2.60±0.16 log CFU/ml, p?=?0.001) and mortality. However, the mortality in the model of adult mice was comparable between wild type and variant indicating that pS286colV is not sufficient by itself to fully explain the virulence of S286. Gene expression analysis of pS286colV in iron depleted environment was very close to that of pS88, suggesting that genes of CVP region may be expressed similarly in two very different genetic backgrounds (group C versus group B2). Screening a collection of 178 human A/B1 extraintestinal pathogenic E. coli (ExPEC) strains revealed that the CVP region is highly prevalent (23%) and MLST analysis indicated that these CVP positive strains belong to several clusters and mostly to phylogroup C. The virulence of S286 is explained in part by the presence of CVP region and this region has spread in different clusters of human A/B1 ExPEC, especially in group C.

Caro, Valerie; Diancourt, Laure; Bingen, Edouard; Bidet, Philippe; Bonacorsi, Stephane

2013-01-01

258

The highly conserved 5' untranslated region as an effective target towards the inhibition of Enterovirus 71 replication by unmodified and appropriate 2'-modified siRNAs  

PubMed Central

Background Enterovirus 71 (EV71) is a highly infectious agent that plays an etiological role in hand, foot, and mouth disease. It is associated with severe neurological complications and has caused significant mortalities in recent large-scale outbreaks. Currently, no effective vaccine or specific clinical therapy is available against EV71. Methods Unmodified 21 nucleotide small interfering RNAs (siRNAs) and classic 2?-modified (2?-O-methylation or 2?-fluoro modification) siRNAs were designed to target highly conserved 5? untranslated region (UTR) of the EV71 genome and employed as anti-EV71 agents. Real-time TaqMan RT-PCR, western blot analysis and plaque assays were carried out to evaluate specific viral inhibition by the siRNAs. Results Transfection of rhabdomyosarcoma (RD) cells with siRNAs targeting the EV71 genomic 5? UTR significantly delayed and alleviated the cytopathic effects of EV71 infection, increased cell viability in EV71-infected RD cells. The inhibitory effect on EV71 replication was sequence-specific and dosage-dependent, with significant corresponding decreases in viral RNA, VP1 protein and viral titer. Appropriate 2?-modified siRNAs exhibited similar RNA interference (RNAi) activity with dramatically increased serum stability in comparison with unmodified counterparts. Conclusion Sequences were identified within the highly conserved 5? UTR that can be targeted to effectively inhibit EV71 replication through RNAi strategies. Appropriate 2?-modified siRNAs provide a promising approach to optimizing siRNAs to overcome barriers on RNAi-based antiviral therapies for broader administration.

2012-01-01

259

Sensitive detection of Tomato ringspot virus by real-time TaqMan RT-PCR targeting the highly conserved 3'-UTR region.  

PubMed

A real-time TaqMan RT-PCR assay was developed for the rapid and sensitive detection of Tomato ringspot virus (ToRSV), an important plant virus which infects a wide range of fruit and ornamental crops. Primers and a probe were designed based on the highly conserved 3'-untranslated region (UTR) sequences of ToRSV, to amplify a 182bp fragment of this region of RNA-1 and RNA-2. The assay was demonstrated to reliably amplify all ToRSV isolates tested. The detection limit was estimated to be about 12 copies of the ToRSV target region. No amplification was observed from the RNA of other nepoviruses or healthy host species. A comparison with a published conventional RT-PCR and a SYBR-based qRT-PCR indicated that both of the published assays lacked reliability and sensitivity, as neither were able to amplify all ToRSV isolates tested, and both were approximately 1000 times less sensitive than the novel TaqMan real-time assay. This TaqMan real-time assay was tested using four different reagent kits and was shown to be robust and stable, with no significant differences in sensitivity between kits. It is expected that the implementation of this TaqMan real-time RT-PCR assay will facilitate efficient phytosanitary certification of nursery stock requiring testing for ToRSV by regulatory agencies, and will also have wider uses for the general detection of ToRSV in a range of hosts. PMID:24566000

Tang, Joe; Khan, Subuhi; Delmiglio, Catia; Ward, Lisa I

2014-06-01

260

Evidence on How a Conserved Glycine in the Hinge Region of HapR Regulates Its DNA Binding Ability: LESSONS FROM A NATURAL VARIANT.  

SciTech Connect

HapR has been recognized as a quorum-sensing master regulator in Vibrio cholerae. Because it controls a plethora of disparate cellular events, the absence of a functional HapR affects the physiology of V. cholerae to a great extent. In the current study, we pursued an understanding of an observation of a natural protease-deficient non-O1, non-O139 variant V. cholerae strain V2. Intriguingly, a nonfunctional HapR (henceforth designated as HapRV2) harboring a substitution of glycine to aspartate at position 39 of the N-terminal hinge region has been identified. An in vitro gel shift assay clearly suggested the inability of HapRV2 to interact with various cognate promoters. Reinstatement of glycine at position 39 restores DNA binding ability of HapRV2 (HapRV2G), thereby rescuing the protease-negative phenotype of this strain. The elution profile of HapRV2 and HapRV2G proteins in size-exclusion chromatography and their circular dichroism spectra did not reflect any significant differences to explain the functional discrepancies between the two proteins. To gain insight into the structure-function relationship of these two proteins, we acquired small/wide angle x-ray scattering data from samples of the native and G39D mutant. Although Guinier analysis and indirect Fourier transformation of scattering indicated only a slight difference in the shape parameters, structure reconstruction using dummy amino acids concluded that although HapR adopts a 'Y' shape similar to its crystal structure, the G39D mutation in hinge drastically altered the DNA binding domains by bringing them in close proximity. This altered spatial orientation of the helix-turn-helix domains in this natural variant provides the first structural evidence on the functional role of the hinge region in quorum sensing-related DNA-binding regulatory proteins of Vibrio spp.

M Dongre; N Singh; C Dureja; N Peddada; A Solanki; F Ashish; S Raychaudhuri

2011-12-31

261

Recently recognized chromosomal defects of clinical importance.  

PubMed Central

We review those conditions which have recently been recognized to be associated with small, sometimes difficult to detect, chromosomal abnormalities. These include the Prader-Willi syndrome and X-linked mental retardation. Images Figure 1 Figure 2 Figure 3

Pembrey, M.; Baraitser, M.

1986-01-01

262

Native American Health Education: Dr. Lindberg Recognized  

MedlinePLUS

... Tools NLM Director’s Comments Transcript Native American Health Education: Dr. Lindberg Recognized – 07/14/2014 To use ... Lindberg recently received a special recognition for fostering education about Native American health and illness at the ...

263

Recognizing Dialogue Content in Student Collaborative Conversation  

Microsoft Academic Search

\\u000a This paper describes efforts to both promote and recognize student dialogue in free-entry text discussion within an inquiry-learning\\u000a environment. First, we discuss collaborative tools that enable students to work together and how these tools can potentially\\u000a focus student effort on subject matter. We then show how our tutor uses an expert knowledge base to recognize (with 88% success\\u000a rate) when

Toby Dragon; Mark Floryan; Beverly Park Woolf; Tom Murray

2010-01-01

264

46 CFR 164.012-12 - Recognized laboratory.  

Code of Federal Regulations, 2010 CFR

...Recognized laboratory. A recognized laboratory is one which is operated...to the Commandant. The following laboratories are recognized: Underwriters' Laboratories, Inc. 333 Pfingston Road Northbrook, IL...

2010-10-01

265

46 CFR 164.012-12 - Recognized laboratory.  

Code of Federal Regulations, 2010 CFR

...Recognized laboratory. A recognized laboratory is one which is operated...to the Commandant. The following laboratories are recognized: Underwriters' Laboratories, Inc. 333 Pfingston Road Northbrook, IL...

2009-10-01

266

Induction by adenovirus-5 E1A of the differentiation phenotype of F9 teratocarcinoma cells involves a conserved region (CR1) of E1A.  

PubMed

The effects of the E1A protein of adenovirus-5 on the differentiation program of F9 teratocarcinoma cells were examined by the stable introduction of plasmids that expressed wild-type or mutated forms of E1A. Constitutive expression of plasmids for most of the mutant E1As induced loss of expression of the cell-surface antigen SSEA-1 and the enhanced expression of genes specific for the differentiated phenotype of F9 cells, such as genes for laminin B1, tissue-type plasminogen activator (tPA) and type IV collagen, as well as the altered cell morphology that is associated with the differentiated state. However, such changes were not observed in the case of genes for mutant proteins from which a conserved region (CR1) of E1A had been deleted. Furthermore, no significant induction of expression of the c-jun gene or transactivation of the c-jun-CAT reporter gene were observed when the sequence that encodes CR1 of E1A had been deleted. A palindromic sequence element (DRE) of the c-jun promoter was essential for the E1A-mediated up-regulation of the c-jun gene. These results imply that CR1 is required for activation of the c-jun gene and that it is implicated in the growth arrest, expression of parietal endoderm-specific functions and the orderly differentiation of F9 cells. PMID:7742380

Li, H O; Tang, X; Kitabayashi, I; Gachelin, G; Chiu, R; Yokoyama, K

1995-04-28

267

A conserved sequence block in murine and human T cell receptor (TCR) J? region is a composite element that enhances TCR ? enhancer activity and binds multiple nuclear factors  

PubMed Central

A conserved sequence block (CSB) located in a noncoding region of the mouse and human TCR ?/? loci, showing six differences over 125 nucleotide positions (95% similar), was subjected to detailed analyses in this study. Transient transfection results showed that the CSB-containing element in conjunction with the TCR ? enhancer up-regulated the ? enhancer activity, whereas no enhancer activity was detected when CSB alone was assayed. In vitro occupancy analyses of CSB by nuclear factors reveal the existence of an unexpectedly intricate network of CSB–protein and protein–protein interactions. Lymphoid-specific as well as T-lineage-specific nuclear factors are involved to differentially form CSB-bound complexes in extracts of various tissues and cell lines. Liver was shown to contain factor(s) sequestering thymic CSB-binding factors. Furthermore, the putative binding sites for transcription factors known to be important for lymphoid-lineage development are present in CSB and are targeted by nuclear factors. On the basis of these results, we propose that the CSB element may play a role in shaping the chromatin structure by which the accessibility of TCR ?/? loci to the recombinase complex and/or to the transcriptional apparatus can be controlled.

Kuo, Chia-Lam; Chen, Mei-Ling; Wang, Kai; Chou, Chuan-Kai; Vernooij, Bernard; Seto, Donald; Koop, Ben F.; Hood, Leroy

1998-01-01

268

Long peptides induce polyfunctional T cells against conserved regions of HIV-1 with superior breadth to single-gene vaccines in macaques.  

PubMed

A novel T-cell vaccine strategy designed to deal with the enormity of HIV-1 variation is described and tested for the first time in macaques to inform and complement approaching clinical trials. T-cell immunogen HIVconsv, which directs vaccine-induced responses to the most conserved regions of the HIV-1, proteome and thus both targets diverse clades in the population and reduces the chance of escape in infected individuals, was delivered using six different vaccine modalities: plasmid DNA (D), attenuated human (A) and chimpanzee (C) adenoviruses, modified vaccinia virus Ankara (M), synthetic long peptides, and Semliki Forest virus replicons. We confirmed that the initial DDDAM regimen, which mimics one of the clinical schedules (DDDCM), is highly immunogenic in macaques. Furthermore, adjuvanted synthetic long peptides divided into sub-pools and delivered into anatomically separate sites induced T-cell responses that were markedly broader than those elicited by traditional single-open-reading-frame genetic vaccines and increased by 30% the overall response magnitude compared with DDDAM. Thus, by improving both the HIV-1-derived immunogen and vector regimen/delivery, this approach could induce stronger, broader, and theoretically more protective T-cell responses than vaccines previously used in humans. PMID:20468055

Rosario, Maximillian; Bridgeman, Anne; Quakkelaar, Esther D; Quigley, Maire F; Hill, Brenna J; Knudsen, Maria L; Ammendola, Virginia; Ljungberg, Karl; Borthwick, Nicola; Im, Eung-Jun; McMichael, Andrew J; Drijfhout, Jan W; Greenaway, Hui Yee; Venturi, Vanessa; Douek, Daniel C; Colloca, Stefano; Liljeström, Peter; Nicosia, Alfredo; Price, David A; Melief, Cornelis J M; Hanke, Tomás

2010-07-01

269

DivIVA uses an N-terminal conserved region and two coiled-coil domains to localize and sustain the polar growth in Corynebacterium glutamicum.  

PubMed

Corynebacterium glutamicum is a rod-shaped actinomycete with a distinct model of peptidoglycan synthesis during cell elongation, which takes place at the cell poles and is sustained by the essential protein DivIVA(CG) (C. glutamicum DivIVA). This protein contains a short conserved N-terminal domain and two coiled-coil regions: CC1 and CC2. Domain deletions and chimeric versions of DivIVA were used to functionally characterize the three domains, and all three were found to be essential for proper DivIVA(CG) function. However, in the presence of the N-terminal domain from DivIVA(CG), either of the two coiled-coil domains of DivIVA(CG) could be replaced by the equivalent coiled-coil domain of Bacillus subtilis DivIVA (DivIVA(BS)) without affecting the function of the original DivIVA(CG), and more than one domain had to be exchanged to lose function. Although no single domain was sufficient for subcellular localization or function, CC1 was mainly implicated in stimulating polar growth and CC2 in targeting to DivIVA(CG) assemblies at the cell poles in C. glutamicum. PMID:19552709

Letek, Michal; Fiuza, María; Ordóñez, Efrén; Villadangos, Almudena F; Flärdh, Klas; Mateos, Luís M; Gil, José A

2009-08-01

270

Crystal structure of HutZ, a heme storage protein from Vibrio cholerae: A structural mismatch observed in the region of high sequence conservation  

PubMed Central

Background HutZ is the sole heme storage protein identified in the pathogenic bacterium Vibrio cholerae and is required for optimal heme utilization. However, no heme oxygenase activity has been observed with this protein. Thus far, HutZ’s structure and heme-binding mechanism are unknown. Results We report the first crystal structure of HutZ in a homodimer determined at 2.0 Å resolution. The HutZ structure adopted a typical split-barrel fold. Through a docking study and site-directed mutagenesis, a heme-binding model for the HutZ dimer is proposed. Very interestingly, structural superimposition of HutZ and its homologous protein HugZ, a heme oxygenase from Helicobacter pylori, exhibited a structural mismatch of one amino acid residue in ?6 of HutZ, although residues involved in this region are highly conserved in both proteins. Derived homologous models of different single point variants with model evaluations suggested that Pro140 of HutZ, corresponding to Phe215 of HugZ, might have been the main contributor to the structural mismatch. This mismatch initiates more divergent structural characteristics towards their C-terminal regions, which are essential features for the heme-binding of HugZ as a heme oxygenase. Conclusions HutZ’s deficiency in heme oxygenase activity might derive from its residue shift relative to the heme oxygenase HugZ. This residue shift also emphasized a limitation of the traditional template selection criterion for homology modeling.

2012-01-01

271

Conservation Online  

NSDL National Science Digital Library

Started as a germ of an idea back in 1987 (on a real, live bulletin board, as opposed to an electronic one), Conservation Online (CoOL) has been providing online resources for conservation professionals since 1993. As its website announces, it is a "full text library of conservation information," covering a wide array of topics ranging from digital imaging to reprographics, and quite a bit of material in between. By clicking on any given topic, visitors will receive a brief overview of the subject, its terminology, and then a list of general online resources for consideration. Another nice feature of the site is the mailing list archive, which contain the archives of various queries submitted to different professional conservation groups, such as the Association of Moving Image Archivists, the Textiles Conservation Discussion List, and the Conservation Framer's Mailing List. The site is rounded out by a timeline that traces the CoOL's history from the summer of 1987 to July 2003.

272

A Conserved Tryptophan-Rich Motif in the Membrane-Proximal Region of the Human Immunodeficiency Virus Type 1 gp41 Ectodomain Is Important for Env-Mediated Fusion and Virus Infectivity  

Microsoft Academic Search

Mutations were introduced into the ectodomain of the human immunodeficiency virus type 1 (HIV-1) transmembrane envelope glycoprotein, gp41, within a region immediately adjacent to the membrane-spanning domain. This region, which is predicted to form an a-helix, contains highly conserved hydrophobic residues and is unusually rich in tryptophan residues. In addition, this domain overlaps the epitope of a neutralizing monoclonal antibody,

KARL SALZWEDEL; JOHN T. WEST; ERIC HUNTER

1999-01-01

273

Identification of HLA-A2 restricted T-cell epitopes within the conserved region of the immunoglobulin G heavy-chain in patients with multiple myeloma  

PubMed Central

Objective The aim of this study is the identification of HLA-A2 restricted T-cell epitopes in the conserved region of the immunoglobulin-G-heavy-chain (IgGH) that can be used for immunotherapy in Multiple Myeloma (MM) patients. Methods After the IgGH gene sequence was scanned for HLA-A2 restricted T-cell epitopes with a high binding affinity to the MHC-I-complex, promising nona-peptides were synthesized. Peptide specific CD8+ T-cells were generated from peripheral blood mononuclear cells (PBMC) of healthy donors (HD) and patients with MM using peptide pulsed dendritic cells (DC) in vitro. The activation and cytotoxicity of CD8+ T-cells was analysed by IFN-? ELISpot-assay and 51Chromium release-assay. HLA-A2 restriction was proven by blocking T-cell activation with anti-HLA-A2 antibodies.. Results Two HLA-A2 restricted T-cell epitopes - TLVTVSSAS derived from the IgGH-framework-region 4 (FR4) and LMISRTPEV from the constant region (CR) - induced expansion of specific CD8+ T-cells from PBMC in 2 out of 3 (TLVTVSSAS) and 1 out of 3 (LMISRTPEV) HD respectively. Specific T-cells were induced from PBMC in 2 out of 6 (TLVTVSSAS) and 8 out of 19 (LMISRTPEV) patients with MM. Specific CD8+ T-cells also lysed peptide-pulsed target cells in 51Chromium release-assay. LMISRTPEV specific CD8+T-cells from MM patients lysed specifically the HLA-A2+ IgG myeloma cell line XG-6. Conclusion We identified two HLA-A2 restricted T-cell epitopes – TLVTVSSAS and LMISRTPEV – which can yield an expansion of CD8+ T-cells with the ability to kill peptide-loaded target cells and HLA-A2+ IgG+ myeloma cells. We conclude that TLVTVSSAS and LMISRTPEV could be T-cell epitopes for immunotherapy in MM patients.

Condomines, Maud; Christensen, Olaf; Witzens-Harig, Mathias; Kasper, Bernd; Kleist, Christian; Terness, Peter; Moos, Marion; Cremer, Friedrich; Hose, Dirk; Ho, Anthony D.; Goldschmidt, Hartmut; Klein, Bernard; Hundemer, Michael

2008-01-01

274

Mutations in the aphA-2 gene of transposon Tn5 mapping within the regions highly conserved in aminoglycoside-phosphotransferases strongly reduce aminoglycoside resistance.  

PubMed

Aminoglycoside-phosphotransferases contain several conserved amino acid sequence motifs. Using hydroxylamine we have obtained five independent missense mutations within the aphA-2 gene of transposon Tn5. Four of the mutations dramatically reduced antibiotic resistance. Two were identical and included the replacement of His-188 with Tyr. One other resulted from the replacement of Gly-189 with Asp. These three mutations map within the first of the conserved motifs. The replacement of Asp-261 with Asn maps to the third of these structural motifs. A mutation diminishing but not eliminating aminoglycoside resistance resulted from replacement of the conserved Val-36 with Met. By site-directed mutagenesis three additional mutants were obtained: His-188 was replaced with Leu and Ser, and Arg-211 within the second conserved motif was substituted by Gly. All three showed reduced levels of resistance to kanamycin. Our results show that these conserved motifs are essential for the biological activity of aminoglycoside phosphotransferases. PMID:1664906

Blázquez, J; Davies, J; Moreno, F

1991-06-01

275

Islamic Headdress Influences How Emotion is Recognized from the Eyes.  

PubMed

Previous research has shown a negative bias in the perception of whole facial expressions from out-group members. Whether or not emotion recognition from the eyes is already sensitive to contextual information is presently a matter of debate. In three experiments we tested whether emotions can be recognized when just the eyes are visible and whether this recognition is affected by context cues, such as various Islamic headdresses vs. a cap or a scarf. Our results indicate that fear is still well recognized from a briefly flashed (100?ms) image of a women wearing a burqa with less than 20% transparency of the eye region. Moreover, the type of headdress influences how emotions are recognized. In a group of participants from non-Islamic background, fear was recognized better from women wearing a niq?b than from women wearing a cap and a shawl, whereas the opposite was observed for happy and sad expressions. The response patterns showed that fearful and anger labels were more often attributed to women with a niq?b vs. a cap and a shawl and again, an opposite pattern was observed for the happy response. However, there was no general response bias: both correct and incorrect responses were influenced by the facial expression as well. Anxiety levels and/or explicit negative associations with the Islam as measured via questionnaires did not mediate the effects. Consistent with the face literature, we conclude that the recognition of emotions from the eyes is also influenced by context. PMID:22557983

Kret, Mariska Esther; de Gelder, Beatrice

2012-01-01

276

Islamic Headdress Influences How Emotion is Recognized from the Eyes  

PubMed Central

Previous research has shown a negative bias in the perception of whole facial expressions from out-group members. Whether or not emotion recognition from the eyes is already sensitive to contextual information is presently a matter of debate. In three experiments we tested whether emotions can be recognized when just the eyes are visible and whether this recognition is affected by context cues, such as various Islamic headdresses vs. a cap or a scarf. Our results indicate that fear is still well recognized from a briefly flashed (100?ms) image of a women wearing a burqa with less than 20% transparency of the eye region. Moreover, the type of headdress influences how emotions are recognized. In a group of participants from non-Islamic background, fear was recognized better from women wearing a niq?b than from women wearing a cap and a shawl, whereas the opposite was observed for happy and sad expressions. The response patterns showed that fearful and anger labels were more often attributed to women with a niq?b vs. a cap and a shawl and again, an opposite pattern was observed for the happy response. However, there was no general response bias: both correct and incorrect responses were influenced by the facial expression as well. Anxiety levels and/or explicit negative associations with the Islam as measured via questionnaires did not mediate the effects. Consistent with the face literature, we conclude that the recognition of emotions from the eyes is also influenced by context.

Kret, Mariska Esther; de Gelder, Beatrice

2012-01-01

277

A BCR-ABL oncoprotein p210b2a2 fusion region sequence is recognized by HLA-DR2a restricted cytotoxic T lymphocytes and presented by HLA-DR matched cells transfected with an Ii(b2a2) construct.  

PubMed

Peptides corresponding to the fusion site in 210 kD BCR-ABL protein b3a2 (p210b3a2) were previously shown to bind to several HLA class I and II alleles. We have found that b3a2 peptide-specific CD4-positive T-helper cells were able to recognize p210b3a2-positive chronic myelogenous leukemia (CML) blasts in a DR4 restricted manner. Until now, there were no reports of b2a2 breakpoint-specific human T-cell responses. Here we show that repetitive stimulation of T lymphocytes with a 17mer peptide covering the fusion region in p210b2a2 also leads to specific T-cell responses. CD4 and CD4/CD8 double-positive clones obtained from a b2a2 peptide-specific cell line were cytotoxic and proliferative in an HLA-DR2a (DRB5*0101) restricted fashion. Autologous Epstein-Barr virus (EBV) transformed cells, expressing BCR-ABL(b2a2) on transfection, and allogeneic HLA-DR matched p210b2a2-positive cells from CML patients were, however, not lysed. BCR-ABL peptide-specific T-cell clones did respond to autologous EBV cells transfected with invariant chain (li) cDNA in which the HLA class II-associated invariant chain peptide (CLIP) was replaced by a BCR-ABL b2a2 fusion oligonucleotide sequence, illustrating the potential of these T cells to recognize an endogenous BCR-ABL(b2a2) ligand. PMID:10419896

ten Bosch, G J; Kessler, J H; Joosten, A M; Bres-Vloemans, A A; Geluk, A; Godthelp, B C; van Bergen, J; Melief, C J; Leeksma, O C

1999-08-01

278

Shrubland Lepidoptera of southern New England and southeastern New York: ecology, conservation, and management  

Microsoft Academic Search

Sandplain and ridgetop pitch pine (Pinus rigida)–scrub oak (Quercus ilicifolia) barrens and other shrub-dominated natural communities (e.g., heathlands and maritime shrublands) are important habitats for rare Lepidoptera (moths and butterflies) in southern New England and southeastern New York. Fifty-six species of conservation concern representing 11 families of Lepidoptera are recognized as dependent on shrubland habitats in this region, including 23%

David L. Wagner; Michael W. Nelson; Dale F. Schweitzer

2003-01-01

279

Ecosystem Services Derived from Wetland Conservation Practices in the United States Prairie Pothole Region with an Emphasis on the U.S. Department of Agriculture Conservation Reserve and Wetlands Reserve Programs.  

National Technical Information Service (NTIS)

Implementation of the U.S. Department of Agriculture (USDA) Conservation Reserve Program (CRP) and Wetlands Reserve Program (WRP) has resulted in the restoration of approximately 2,200,000 ha (5,436,200 acres) of wetland and grassland habitats in the Prai...

M. K. Laubhan N. H. Euliss R. A. Gleason

2008-01-01

280

Conservation tillage.  

PubMed

Conservation production systems combine tillage and planting practices to reduce soil erosion and loss of water from farmland. Successful conservation tillage practices depend on the ability of farm managers to integrate sound crop production practices with effective pest management systems. More scientific information is needed to determine the relations between tillage practices and physical, chemical, and biological soil factors that affect plant and pest ecology. There is a need to devise improved pest management strategies for conservation tillage and to better understand the impact of conservation tillage on water-quality, especially as it is related to use of agricultural chemicals. While savings in fuel, labor, and soil have induced many farmers to adopt conservation tillage, improved methods and equipment should increase adoption even more. PMID:17797277

Gebhardt, M R; Daniel, T C; Schweizer, E E; Allmaras, R R

1985-11-01

281

Recognizing and Reporting Suspected Child Abuse.  

ERIC Educational Resources Information Center

Before abused children can heal and learn effectively, the problem causing the trauma must be recognized and identified, and proper legal issues must be addressed. Through various local, state, and federal mechanisms, U.S. society has provided a process for reporting suspected child abuse and crafting a positive solution. (Contains 28 references.)…

Gullatt, David E.; Stockton, Cathy E.

2000-01-01

282

From detecting to recognizing color codes  

Microsoft Academic Search

In this paper we present efficient ways of detecting color codes in field images and recognizing the colors to read their codes. The color-code tag used in this paper consists of the code area which contains concentric, multiple circular rings on the white background. To generate the test images, we used two cameras of different brands, that is, a Canon

Jaehwan Park; Woosung Kim; Hyeon-Joong Yoo; Youngbum Jang

2006-01-01

283

Microsoft Windows highly intelligent speech recognizer: Whisper  

Microsoft Academic Search

Since January 1993, the authors have been working to refine and extend Sphinx-II technologies in order to develop practical speech recognition at Microsoft. The result of that work has been the Whisper (Windows Highly Intelligent Speech Recognizer). Whisper represents significantly improved recognition efficiency, usability, and accuracy, when compared with the Sphinx-II system. In addition Whisper offers speech input capabilities for

Xuedong Huang; Alex Acero; Fil Alleva; Mei-Yuh Hwang; Li Jiang; Milind Mahajan

1995-01-01

284

How State Laws Recognize Advanced Nursing Practice.  

ERIC Educational Resources Information Center

Reviews modifications in state health practice statutes to recognize the expanded scope of nursing practice in view of the disparity between medical functions actually performed by nurses and those considered within the legal definition. Various state approaches indicate a trend to give legal validity to acts performed by nurses. (MF)

Trandel-Korenchuk, Darlene M.; Trandel-Korenchuk, Keith M.

1978-01-01

285

Robust speech recognizer using multiclass SVM  

Microsoft Academic Search

In this paper a robust speech recognizer is presented based on features obtained from the speech signal and also from the image of the speaker. The features were combined by simple concatenation, resulting in composed feature vectors to train the models corresponding to each class. For recognition, the classification process relies on a very effective algorithm, namely the multiclass SVM.

Inge Gavat; Gabriel Costache; Claudia Iancu

2004-01-01

286

How Should a Speech Recognizer Work?  

ERIC Educational Resources Information Center

Although researchers studying human speech recognition (HSR) and automatic speech recognition (ASR) share a common interest in how information processing systems (human or machine) recognize spoken language, there is little communication between the two disciplines. We suggest that this lack of communication follows largely from the fact that…

Scharenborg, Odette; Norris, Dennis; ten Bosch, Louis; McQueen, James M.

2005-01-01

287

Method for Recognizing Insulator from Airborne Image  

Microsoft Academic Search

In the paper, for airborne image by helicopter on power grid, we propose a method to recognize tempered glass insulator based on intensity information. This method employs the morphology, connected components extraction and threshold value of mean segmentation. The feature of tempered glass insulator on image is reflected its intensity information. Firstly, the intensity image is preprocessed by reducing noise.

Xinye Zhang; Jubai An; Qinggang Wu

2012-01-01

288

Uncertainty in training large vocabulary speech recognizers  

Microsoft Academic Search

We propose a technique for annotating data used to train a speech recognizer. The proposed scheme is based on labeling only a single frame for every word in the training set. We make use of the virtual evidence (VE) framework within a graphical model to take advantage of such data. We apply this approach to a large vocabulary speech recognition

Amarnag Subramanya; Chris Bartels; Jeff Bilmes; Patrick Nguyen

2007-01-01

289

Stent Fracture: How Frequently Is It Recognized?  

PubMed Central

In spite of there being several case reports, coronary stent fracture is not a well-recognized entity and incidence rates are likely to be underestimated. In this article, we review different aspects of stent fracture, including incidence, classification, predictors, outcome, diagnosis, and management.

Mohsen, Mohammed Khalil; Alqahtani, Awad; Al suwaidi, Jassim

2013-01-01

290

METHOD AND MEANS FOR RECOGNIZING COMPLEX PATTERNS  

Microsoft Academic Search

This patent relates to a method and means for recognizing a complex ; pattern in a picture. The picture is divided into framelets, each framelet being ; sized so that any segment of the complex pattern therewithin is essentially a ; straight line. Each framelet is scanned to produce an electrical pulse for each ; point scanned on the segment

P. Hough; P. V. C

1962-01-01

291

Great Apes' Capacities to Recognize Relational Similarity  

ERIC Educational Resources Information Center

Recognizing relational similarity relies on the ability to understand that defining object properties might not lie in the objects individually, but in the relations of the properties of various object to each other. This aptitude is highly relevant for many important human skills such as language, reasoning, categorization and understanding…

Haun, Daniel B. M.; Call, Josep

2009-01-01

292

Recognizing Digressive Questions During Interactive Generation  

Microsoft Academic Search

In expository discourse, people sometimes ask ques- tions that digress from the purpose of the discussion. A system that provides interactive explanations and advice must be able to distinguish pertinent questions from questions that digress. It must also be able .to recognize questions that are incoherent. These types of questions require different treatment. Pertinent ques- tions must be answered to

Susan M. Hailer

293

MSY2 and MSY4 bind a conserved sequence in the 3' untranslated region of protamine 1 mRNA in vitro and in vivo.  

PubMed

Y-box proteins are major constituents of ribonucleoprotein particles (RNPs) which contain translationally silent mRNAs in gametic cells. We have recently shown that a sequence-specific RNA binding activity present in spermatogenic cells contains the two Y-box proteins MSY2 and MSY4. We show here that MSY2 and MSY4 bind a sequence, 5'-UCCAUCA-3', present in the 3' untranslated region of the translationally repressed protamine 1 (Prm1) mRNA. Using pre- and post-RNase T1-digested substrate RNAs, it was determined that MSY2 and MSY4 can bind an RNA of eight nucleotides containing the MSY2 and MSY4 binding site. Single nucleotide mutations in the sequence eliminated the binding of MSY2 and MSY4 in an electrophoretic mobility shift assay, and the resulting mutants failed to compete for binding in a competition assay. A consensus site of U(AC)C(A)CAU(C)CA(CU) (subscripts indicate nucleotides which do not disrupt YRS binding by MSY2 and MSY4), denoted the Y-box recognition site (YRS), was defined from this mutational analysis. These mutations in the YRS were further characterized in vivo using a novel application of the yeast three-hybrid system. Experiments with transgenic mice show that disruption of the YRS in vivo relieves Prm1-like repression of a reporter gene. The conservation of the RNA binding motifs among Y-box protein family members raises the possibility that other Y-box proteins may have previously unrecognized sequence-specific RNA binding activities. PMID:11564883

Giorgini, F; Davies, H G; Braun, R E

2001-10-01

294

Dogs Vaccinated with Common Lyme Disease Vaccines Do Not Respond to IR6, the Conserved Immunodominant Region of the VlsE Surface Protein of Borrelia burgdorferi  

PubMed Central

A 25-amino-acid synthetic peptide (C6 peptide) derived from an immunodominant conserved region (designated IR6) of the VlsE protein of Borrelia burgdorferi has been identified and used to construct immunoenzyme-based diagnostic procedures. These procedures have excellent sensitivity and specificity. Previous reports have demonstrated the usefulness of the C6 peptide as an antigen for the serodiagnosis of human and canine Lyme disease. Results indicated that assays based on the C6 peptide were nonreactive to sera from vaccinated nonexposed animals. The purpose of the present study was to confirm these results in a controlled trial by testing sera from experimentally vaccinated dogs known to be uninfected. Nine specific-pathogen-free beagles were assigned to one of three vaccine groups, each containing three dogs. Each group received one of three commercial Lyme vaccines: RECOMBITEK Lyme (Merial), LymeVax (Fort Dodge Animal Health), and Galaxy Lyme (Schering-Plough Animal Health). Each animal was administered a total of five doses of vaccine over a period of 39 weeks. Serum samples were collected prior to vaccination and then on a weekly basis from weeks 3 to 18 and from weeks 33 to 43. Selected samples were tested by the immunofluorescence assay (IFA) and the Western blot (WB) assay using whole-cell B. burgdorferi antigen extracts, and the results were compared to those obtained with two immunoenzyme-based procedures formatted by using the C6 peptide. Serum specimens from all animals were reactive to the IFA and WB assay at week 5 and became highly reactive following the administration of multiple doses of vaccine. All serum specimens were uniformly nonreactive in the C6 peptide immunoenzyme procedures at all time points throughout the study.

O'Connor, Thomas P.; Esty, Kathy J.; Hanscom, Jancy L.; Shields, Paulette; Philipp, Mario T.

2004-01-01

295

The Zymomonas mobilis glf, zwf, edd, and glk genes form an operon: localization of the promoter and identification of a conserved sequence in the regulatory region.  

PubMed Central

The Zymomonas mobilis genes that encode the glucose-facilitated diffusion transporter (glf), glucose-6-phosphate dehydrogenase (zwf), 6-phosphogluconate dehydratase (edd), and glucokinase (glk) are clustered on the genome. The data presented here firmly establish that the glf, zwf, edd, and glk genes form an operon, in that order. The four genes of the operon are cotranscribed on a 6.14-kb mRNA. The site of transcriptional initiation for the polycistronic message was mapped by primer extension and nuclease S1 protection analysis. The glf operon promoter region showed significant homology to other highly expressed Z. mobilis promoters, but not to consensus promoters from other bacteria. The highly expressed Z. mobilis promoter set contains two independent, overlapping, conserved sequences that extend from approximately bp -100 to +15 with respect to the transcriptional start sites. Expression of the glf operon was shown to be subject to carbon source-dependent regulation. The mRNA level was threefold higher in cells grown on fructose than in cells grown on glucose. This increase was not the result of differential mRNA processing when cells were grown on the different carbon sources, nor was it the result of differential transcript stability. Degradation of the 6.14-kb glf operon mRNA was biphasic, with initial half-lives of 11.5 min in fructose-grown cells and 12.0 min in glucose-grown cells. Thus, the higher level of glf operon mRNA in fructose-grown cells is the result of an increased rate of transcription. The importance of increasing glf expression in cells growing on fructose is discussed. Images

Barnell, W O; Liu, J; Hesman, T L; O'Neill, M C; Conway, T

1992-01-01

296

Point mutations in a conserved region (TonB box) of Escherichia coli outer membrane protein BtuB affect vitamin B12 transport.  

PubMed Central

Uptake of cobalamins and iron chelates in Escherichia coli K-12 is dependent on specific outer membrane transport proteins and the energy-coupling function provided by the TonB protein. The btuB product is the outer membrane receptor for cobalamins, bacteriophage BF23, and the E colicins. A short sequence near the amino terminus of mature BtuB, previously called the TonB box, is conserved in all tonB-dependent receptors and colicins and is the site of the btuB451 mutation (Leu-8----Pro), which prevents energy-coupled cobalamin uptake. This phenotype is partially suppressed by certain mutations in tonB. To examine the role of individual amino acids in the TonB box of BtuB, more than 30 amino acid substitutions in residues 6 to 13 were generated by doped oligonucleotide-directed mutagenesis. Many of the mutations affecting each amino acid did not impair transport activity, although some substitutions reduced cobalamin uptake and the Leu-8----Pro and Val-10----Gly alleles were completely inactive. To test whether the btuB451 mutation affects only cobalamin transport, a hybrid gene was constructed which encodes the signal sequence and first 39 residues of BtuB fused to the bulk of the ferrienterobactin receptor FepA (residues 26 to 723). This hybrid protein conferred all FepA functions but no BtuB functions. The presence of the btuB451 mutation in this fusion gene eliminated all of its tonB-coupled reactions, showing that the TonB box of FepA could be replaced by that from BtuB. These results suggest that the TonB-box region of BtuB is involved in active transport in a manner dependent not on the identity of specific side chains but on the local secondary structure.

Gudmundsdottir, A; Bell, P E; Lundrigan, M D; Bradbeer, C; Kadner, R J

1989-01-01

297

Local-regional control according to surrogate markers of breast cancer subtypes and response to neoadjuvant chemotherapy in breast cancer patients undergoing breast conserving therapy  

PubMed Central

Introduction Breast cancers of different molecular subtypes have different survival rates. The goal of this study was to identify patients at high risk for local-regional recurrence according to response to neoadjuvant chemotherapy and surrogate markers of molecular subtypes in patients undergoing breast conserving therapy (BCT). Methods Clinicopathologic data from 595 breast cancer patients who received neoadjuvant chemotherapy and BCT from 1997 to 2005 were identified. Estrogen receptor (ER), progesterone receptor (PR) and human epidermal growth factor receptor 2 (HER2) expression determined by immunohistochemistry were used to construct the following subtypes: ER+ or PR+ and HER2- (hormone receptor (HR)+/HER2-; 52%), ER+ or PR+ and HER2+ (HR+/HER2+; 9%), ER- and PR- and HER2+ (HR-/HER2+; 7%) and ER- and PR- and HER2- (HR-/HER2-; 32%). Actuarial rates were calculated using the Kaplan-Meier method and compared using the log-rank test. Cox proportional hazards models were used for multivariate analysis (MVA). Results After a median follow-up of 64 months, the five-year local-regional recurrence (LRR)-free survival rate for all patients was 93.8%. The five-year LRR-free survival rates varied by subtype: HR+/HER2- 97.0%, HR+/HER2+ 95.9%, HR-/HER2+ 86.5% and HR-/HER2- 89.5% (P = 0.001). In addition to subtype, clinical stage III disease (90% vs. 95% for I/II, P = 0.05), high nuclear grade (92% vs. 97% with low/intermediate grade, P = 0.03), presence of lymphovascular invasion (LVI) (89% vs. 95% in those without LVI, P = 0.02) and four or more positive lymph nodes on pathologic examination (87% vs. 95% with zero to three positive lymph nodes, P = 0.03) were associated with lower five-year LRR-free survival on univariate analysis. On MVA, HR-/HER2+ and HR-/HER2- subtypes and disease in four or more lymph nodes were associated with decreased LRR-free survival. A pathologic complete response (pCR) was associated with improved LRR-free survival. Conclusions Patients with HR+/HER2- and HR+/HER2+ subtypes had excellent LRR-free survival regardless of tumor response to neoadjuvant chemotherapy. Patients with HR-/HER2+ and HR-/HER2- subtypes with poor response to neoadjuvant chemotherapy had worse LRR-free survival after BCT. Additional study is needed to determine the impact of trastuzumab on local-regional control in HER2+ tumors. Our data suggest that patients with HR-/HER2- subtype tumors not achieving pCR may benefit from novel strategies to improve local-regional control.

2012-01-01

298

Federally-Recognized Tribes of the Columbia-Snake Basin.  

SciTech Connect

This is an omnibus publication about the federally-recognized Indian tribes of the Columbia-Snake river basin, as presented by themselves. It showcases several figurative and literal snapshots of each tribe, bits and pieces of each tribe`s story. Each individual tribe or tribal confederation either submitted its own section to this publication, or developed its own section with the assistance of the writer-editor. A federally-recognized tribe is an individual Indian group, or confederation of Indian groups, officially acknowledged by the US government for purposes of legislation, consultation and benefits. This publication is designed to be used both as a resource and as an introduction to the tribes. Taken together, the sections present a rich picture of regional indian culture and history, as told by the tribes.

United States. Bonneville Power Administration

1997-11-01

299

Benefits of the Conservation Reserve Program to Grassland Bird Populations in the Prairie Pothole Region of North Dakota and South Dakota.  

National Technical Information Service (NTIS)

The Conservation Reserve Program (CRP) of the 1985 Food Security Act is generally considered to provide substantial benefits to grassland wildlife species, but these benefits are often poorly known. Numerous local studies have documented benefits of the C...

N. D. Niemuth, F. R. Quamen, D. E. Naugle, R. E. Reynolds, M. E. Estey

2007-01-01

300

Identification of autoantigens recognized by the 2F5 and 4E10 broadly neutralizing HIV-1 antibodies  

PubMed Central

Many human monoclonal antibodies that neutralize multiple clades of HIV-1 are polyreactive and bind avidly to mammalian autoantigens. Indeed, the generation of neutralizing antibodies to the 2F5 and 4E10 epitopes of HIV-1 gp41 in man may be proscribed by immune tolerance because mice expressing the VH and VL regions of 2F5 have a block in B cell development that is characteristic of central tolerance. This developmental blockade implies the presence of tolerizing autoantigens that are mimicked by the membrane-proximal external region of HIV-1 gp41. We identify human kynureninase (KYNU) and splicing factor 3b subunit 3 (SF3B3) as the primary conserved, vertebrate self-antigens recognized by the 2F5 and 4E10 antibodies, respectively. 2F5 binds the H4 domain of KYNU which contains the complete 2F5 linear epitope (ELDKWA). 4E10 recognizes an epitope of SF3B3 that is strongly dependent on hydrophobic interactions. Opossums carry a rare KYNU H4 domain that abolishes 2F5 binding, but they retain the SF3B3 4E10 epitope. Immunization of opossums with HIV-1 gp140 induced extraordinary titers of serum antibody to the 2F5 ELDKWA epitope but little or nothing to the 4E10 determinant. Identification of structural motifs shared by vertebrates and HIV-1 provides direct evidence that immunological tolerance can impair humoral responses to HIV-1.

Yang, Guang; Holl, T. Matt; Liu, Yang; Li, Yi; Lu, Xiaozhi; Nicely, Nathan I.; Kepler, Thomas B.; Alam, S. Munir; Liao, Hua-Xin; Cain, Derek W.; Spicer, Leonard; VandeBerg, John L.; Haynes, Barton F.

2013-01-01

301

Conservation businesses and conservation planning in a biological diversity hotspot.  

PubMed

The allocation of land to biological diversity conservation competes with other land uses and the needs of society for development, food, and extraction of natural resources. Trade-offs between biological diversity conservation and alternative land uses are unavoidable, given the realities of limited conservation resources and the competing demands of society. We developed a conservation-planning assessment for the South African province of KwaZulu-Natal, which forms the central component of the Maputaland-Pondoland-Albany biological diversity hotspot. Our objective was to enhance biological diversity protection while promoting sustainable development and providing spatial guidance in the resolution of potential policy conflicts over priority areas for conservation at risk of transformation. The conservation-planning assessment combined spatial-distribution models for 646 conservation features, spatial economic-return models for 28 alternative land uses, and spatial maps for 4 threats. Nature-based tourism businesses were competitive with other land uses and could provide revenues of >US$60 million/year to local stakeholders and simultaneously help meeting conservation goals for almost half the conservation features in the planning region. Accounting for opportunity costs substantially decreased conflicts between biological diversity, agricultural use, commercial forestry, and mining. Accounting for economic benefits arising from conservation and reducing potential policy conflicts with alternative plans for development can provide opportunities for successful strategies that combine conservation and sustainable development and facilitate conservation action. PMID:23565917

Di Minin, Enrico; Macmillan, Douglas Craig; Goodman, Peter Styan; Escott, Boyd; Slotow, Rob; Moilanen, Atte

2013-08-01

302

Energy Conservation.  

National Technical Information Service (NTIS)

Possibilities of energy conservation in domestic buildings and households are reviewed, i.e. in technical systems, heating and air conditioning systems and other energy-consuming appliances. The present situation is reviewed, and suggestions for improveme...

J. Branch A. Gsponer B. Giovanni

1981-01-01

303

Conservation Presentation.  

ERIC Educational Resources Information Center

Introduces a project in which students teach about the importance of recycling and conservation by presenting demonstrations. Includes demonstrations on water, plastic, and other recycling products such as steel. (YDS)

Friday, Gerald

2001-01-01

304

Recognizing faces in and out of context  

Microsoft Academic Search

Two experiments are reported which examined the influence of context on face recognition accuracy for novel and familiar faces\\u000a respectively. Context was manipulated by varying the physical background against which the faces appeared. In Experiment I,\\u000a 80 student subjects observed 18 faces before attempting to recognize them in a sequence of 36 alternatives. For half the subjects,\\u000a the backgrounds changed

Graham Davies; Alan Milne

1982-01-01

305

Recognizing faces in and out of context  

Microsoft Academic Search

Two experiments are reported which examined the influence of context on face recognition accuracy for novel and familiar faces\\u000a respectively. Context was manipulated by varying the physical background against which the faces appeared. In Experiment I,\\u000a 80 student subjects observed 18 faces before attempting to recognize them in a sequence of 36 al ternatives , For half the\\u000a subj ects,

Graham Davies; Alan Milne

1982-01-01

306

Recognizing Materials using Perceptually Inspired Features  

PubMed Central

Our world consists not only of objects and scenes but also of materials of various kinds. Being able to recognize the materials that surround us (e.g., plastic, glass, concrete) is important for humans as well as for computer vision systems. Unfortunately, materials have received little attention in the visual recognition literature, and very few computer vision systems have been designed specifically to recognize materials. In this paper, we present a system for recognizing material categories from single images. We propose a set of low and mid-level image features that are based on studies of human material recognition, and we combine these features using an SVM classifier. Our system outperforms a state-of-the-art system [Varma and Zisserman, 2009] on a challenging database of real-world material categories [Sharan et al., 2009]. When the performance of our system is compared directly to that of human observers, humans outperform our system quite easily. However, when we account for the local nature of our image features and the surface properties they measure (e.g., color, texture, local shape), our system rivals human performance. We suggest that future progress in material recognition will come from: (1) a deeper understanding of the role of non-local surface properties (e.g., extended highlights, object identity); and (2) efforts to model such non-local surface properties in images.

Sharan, Lavanya; Liu, Ce; Rosenholtz, Ruth; Adelson, Edward H.

2013-01-01

307

Conservation in Conflict  

NSDL National Science Digital Library

What happens when war occurs in areas where there is war? Ecologist Peter Zahler who has worked in Afghanistan since 2002, talks about how conserving biodiversity may bring peace to the war-torn region. You can read more about Zahler's work in the article Nurturing Wildlife in War-Torn Afghanistan that appeared in the New Yorker Times in December, 2011.

Society, Wildlife C.

308

A Conserved Region between the TPR and Activation Domains of p67phox Participates in Activation of the Phagocyte NADPH Oxidase*  

PubMed Central

The phagocyte NADPH oxidase, dormant in resting cells, is activated during phagocytosis to produce superoxide, a precursor of microbicidal oxidants. The membrane-integrated protein gp91phox serves as the catalytic core, because it contains a complete electron-transporting apparatus from NADPH to molecular oxygen for superoxide production. Activation of gp91phox requires the cytosolic proteins p67phox, p47phox, and Rac (a small GTPase). p67phox, comprising 526 amino acids, moves upon cell stimulation to the membrane together with p47phox and there interacts with Rac; these processes are prerequisite for gp91phox activation. Here we show that a region of p67phox (amino acids 190–200) C-terminal to the Rac-binding domain is evolutionarily well conserved and participates in oxidase activation at a later stage in conjunction with an activation domain. Alanine substitution for Tyr-198, Leu-199, or Val-204 abrogates the ability of p67phox to support superoxide production by gp91phox-based oxidase as well as its related oxidases Nox1 and Nox3; the activation also involves other invariant residues such as Leu-193, Asp-197, and Gly-200. Intriguingly, replacement of Gln-192 by alanine or that of Tyr-198 by phenylalanine or tryptophan rather enhances superoxide production by gp91phox-based oxidase, suggesting a tuning role for these residues. Furthermore, the Y198A/V204A or L199A/V204A substitution leads to not only a complete loss of the activity of the reconstituted oxidase system but also a significant decrease in p67phox interaction with the gp91phox NADPH-binding domain, although these mutations affect neither the protein integrity nor the Rac binding activity. Thus the extended activation domain of p67phox (amino acids 190–210) containing the D(Y/F)LGK motif plays an essential role in oxidase activation probably by interacting with gp91phox.

Maehara, Yuichi; Miyano, Kei; Yuzawa, Satoru; Akimoto, Risa; Takeya, Ryu; Sumimoto, Hideki

2010-01-01

309

Probing the evolutionary conserved regions within functional site of drug-resistant target proteins of Staphylococcus aureus: In silico phylogenetic motif profiling approach.  

PubMed

Staphylococcus aureus is one of the major causes of clinical infections and increasing mortality due to multi-drug resistance. In this study, eight drug-resistant genes, beta-lactamase, metallo-beta-lactamase, vanB, mecA, norA, qacA, qacB and qacC of S. aureus strain Mu50 (vancomycin resistant) were studied to predict the evolutionary conserved functional site residues in their protein sequences. It was found that in beta-lactamase, Tyr, Gly, Thr, Asn and in metallo-beta-lactamase, Thr, His, Gly, Leu, Arg and Asp residues were highly conserved. In vanB, Gly, His and Asp residues were highly conserved. Whereas in mecA, His, Val, Phe, Gln, Lys and in norA, Ser, Leu and Ala residues showed conservedness at moderate level. In the multi-drug efflux pump (corresponding to qacA, qacB and qacC), Gly residue was found to be highly conserved. The homology clustering of target proteins through SCI-PHY algorithm and homologues identified through PSI-BLAST were compared to identify the degree of conservation of functional residues. The phylogenetic motifs identified using homologues of target proteins were validated through domain search to locate their site and functionality in the protein sequences. Interactome analysis was performed to understand the possible mode of interaction of target proteins with their functional partners. PMID:23350279

Kahlon, Amandeep Kaur; Darokar, Mahendra P; Sharma, Ashok

2012-12-01

310

Evaluating Local Benefits from Conservation in Nepal's Annapurna Conservation Area  

NASA Astrophysics Data System (ADS)

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

Spiteri, Arian; Nepal, Sanjay K.

2008-09-01

311

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

PubMed

Protected areas are integral to the global effort to conserve biodiversity, and, over the past two decades, protected area managers have begun to recognize that conservation objectives are next to impossible to achieve without considering the needs and concerns of local communities. Incentive-based programs (IBPs) have become a favored approach to protected area management, geared at fostering local stewardship by delivering benefits tied to conservation to local people. Effective IBPs require benefits to accrue to and be recognized by those experiencing the greatest consequences as a result of the protected area, and those likely to continue extractive activities if their livelihood needs are compromised. This research examines dispersal of IBP benefits, as perceived by local residents in Nepal's Annapurna Conservation Area. Results reported here are based on questionnaire interviews with 188 households conducted between September and December 2004. Results indicate that local residents primarily identify benefits from social development activities, provisions for resource extraction, and economic opportunities. Overall, benefits have been dispersed equally to households in villages on and off the main tourist route, and regardless of a household's participation in tourism. However, benefits are not effectively targeted to poorer residents, those highly dependent on natural resources, and those experiencing the most crop damage and livestock loss from protected wildlife. This article provides several suggestions for improving the delivery of conservation incentives. PMID:18458999

Spiteri, Arian; Nepal, Sanjay K

2008-09-01

312

A highly conserved genomic region in baculoviruses: sequence analysis of an 11.3 kbp DNA fragment (46.5-55.1 m.u.) of the Spodoptera exigua multicapsid nucleopolyhedrovirus.  

PubMed

A DNA fragment of 11.3 kilobase pairs (kbp) in size of the baculovirus Spodoptera exigua multicapsid nucleopolyhedrovirus (SeMNPV) genome (46.5 to 55.1 m.u.) was completely sequenced. Analysis of the sequence revealed eleven potential open reading frames (ORF). Ten of these ORFs showed significant amino acid identity to Autographa californica MNPV (AcMNPV) and Orgyia pseudotsugata MNPV (OpMNPV) genes p6.9, lef5, 38K, p19, p143, p25, p18, vp33, lef4, and vp39. One ORF (XC12) has no homolog in other baculoviruses and may be unique to SeMNPV. All but three of these putative genes are preceded by the consensus baculovirus late promoter element (5'-ATAAG-3'). The genetic organization and the putative map of transcripts of this fragment suggested that this region is highly similar to a region in AcMNPV fragment EcoRI-D. Comparison of the genetic organization of this 11.3 kbp fragment with the genomes of AcMNPV, OpMNPV, Bombyx mori NPV (BmNPV) and SeMNPV revealed that this region is highly conserved among baculovirus genomes. This is in contrast to the genetic organization of the polyhedrin-p10 region, which is much more diverged, but has been taken as point of reference to orient baculovirus physical maps. Through its diversity the latter region, however, would be an excellent candidate to determine baculovirus relatedness and phylogeny. The presence of conserved and diverged regions in baculovirus genomes with respect to gene order is reminiscent to the situation in other large DNA viruses, such as herpes- and poxviruses, where conserved central and diverged terminal parts are common characteristics. The role of this feature in the genomic organization of large DNA viruses is discussed with particular emphasis on virus replication and evolution. PMID:9725671

Heldens, J G; Liu, Y; Zuidema, D; Goldbach, R W; Vlak, J M

1998-06-01

313

Massachusetts Conservation  

NSDL National Science Digital Library

Massachusetts has long been a leader in the conservation and preservation movements. From early attempts to create an Emerald Necklace around Boston to the battle to save the Old State House, the commonwealth has rich, fascinating tales and experiences. This wonderful travel itinerary was created by the National Park Service's Heritage Education Services in partnership with the Massachusetts Historical Commission and the National Conference of State Historic Preservation Officers. On the site, visitors can look over essays, a list of sites, maps, and external websites. The powerful essays include "Conservation and Landscape Planning in Massachusetts" and "American Conservation in the Twentieth Century." Checking out the List of Sites area, visitors can read a complete list of all the places mentioned in the itinerary (complete with details and photos) such as the Boston Public Garden, the Lynn Woods Historic District, and the Fruitlands Museums Historic District.

314

Recognizing Patterns In Log-Polar Coordinates  

NASA Technical Reports Server (NTRS)

Log-Hough transform is basis of improved method for recognition of patterns - particularly, straight lines - in noisy images. Takes advantage of rotational and scale invariance of mapping from Cartesian to log-polar coordinates, and offers economy of representation and computation. Unification of iconic and Hough domains simplifies computations in recognition and eliminates erroneous quantization of slopes attributable to finite spacing of Cartesian coordinate grid of classical Hough transform. Equally efficient recognizing curves. Log-Hough transform more amenable to massively parallel computing architectures than traditional Cartesian Hough transform. "In-place" nature makes it possible to apply local pixel-neighborhood processing.

Weiman, Carl F. R.

1992-01-01

315

Identification of conserved domains in the promoter regions of nitric oxide synthase 2: implications for the species-specific transcription and evolutionary differences  

Microsoft Academic Search

BACKGROUND: The majority of the genes involved in the inflammatory response are highly conserved in mammals. These genes are not significantly expressed under normal conditions and are mainly regulated at the transcription and prost-transcriptional level. Transcription from the promoters of these genes is very dependent on NF-?B activation, which integrates the response to diverse extracellular stresses. However, in spite of

Daniel Rico; Juan M Vaquerizas; Hernán Dopazo; Lisardo Boscá

2007-01-01

316

Threats, conservation strategies, and prognosis for suckers (Catostomidae) in North America: insights from regional case studies of a diverse family of non-game fishes  

Microsoft Academic Search

Catostomid fishes are a diverse family of 76+ freshwater species that are distributed across North America in many different habitats. This group of fish is facing a variety of impacts and conservation issues that are somewhat unique relative to more economically valuable and heavily managed fish species. Here, we present a brief series of case studies to highlight the threats

Steven J. Cooke; Christopher M. Bunt; Steven J. Hamilton; Cecil A. Jennings; Michael P. Pearson; Michael S. Cooperman; Douglas F. Markle

2005-01-01

317

Portland Energy Conservation Project. City energy plan: choices for saving energy in the government sector. [City of Portland and the metropolitan region  

Microsoft Academic Search

Energy use by state government is identified for city vehicles, city buildings, sewer and water systems, street lighting, traffic lights, park lighting, public schools, office buildings, and solid-waste systems. Energy conservation choices in these systems are identified. Impacts of price increases and supply cutbacks are discussed. An appendix contains additional data on Portland employment and total energy use. (MCW)

D. F. Mazziotti; G. M. Crandall

1977-01-01

318

Recognizing connotative meaning in military chat communications  

NASA Astrophysics Data System (ADS)

Over the last five to seven years the use of chat in military contexts has expanded quite significantly, in some cases becoming a primary means of communicating time-sensitive data to decision makers and operators. For example, during humanitarian operations with Joint Task Force-Katrina, chat was used extensively to plan, task, and coordinate predeployment and ongoing operations. The informal nature of chat communications allows the relay of far more information than the technical content of messages. Unlike formal documents such as newspapers, chat is often emotive. "Reading between the lines" to understand the connotative meaning of communication exchanges is now feasible, and often important. Understanding the connotative meaning of text is necessary to enable more useful automatic intelligence exploitation. The research project described in this paper was directed at recognizing user connotations of uncertainty and urgency. The project built a matrix of speech features indicative of these categories of meaning, developed data mining software to recognize them, and evaluated the results.

Budlong, Emily R.; Walter, Sharon M.; Yilmazel, Ozgur

2009-05-01

319

The consequences of inbreeding for recognizing competitors.  

PubMed Central

Extreme inbreeding will compromise an animal's ability to discriminate between individuals and, thus, assess familiarity and kinship with conspecifics. In rodents, a large component of individual recognition is mediated through chemical communication. The counter-marking of competitor males' scent marks provides a measure of discrimination between their own scent and that from other individuals. We investigated whether males in common outbred (ICR(CD-1) and TO) and inbred (BALB/c) strains of laboratory mice could recognize the urinary scents of other individuals by measuring their investigation and counter-marking responses. Dominant males of outbred strains investigated and counter-marked scents from other males, whether of the same or another strain. Dominant inbred BALB/c males investigated but did not counter-mark their own strain scents, counter-marking only those from another strain. They did not use environmentally induced status differences in odours to recognize scents from other males. The inability of the inbred mice to discriminate between their own scent marks and those of other males is likely to alter their competitive behaviour, which could influence responses in experiments and the welfare of caged laboratory mice.

Nevison, C M; Barnard, C J; Beynon, R J; Hurst, J L

2000-01-01

320

Ants recognize foes and not friends  

PubMed Central

Discriminating among individuals and rejecting non-group members is essential for the evolution and stability of animal societies. Ants are good models for studying recognition mechanisms, because they are typically very efficient in discriminating ‘friends’ (nest-mates) from ‘foes’ (non-nest-mates). Recognition in ants involves multicomponent cues encoded in cuticular hydrocarbon profiles. Here, we tested whether workers of the carpenter ant Camponotus herculeanus use the presence and/or absence of cuticular hydrocarbons to discriminate between nest-mates and non-nest-mates. We supplemented the cuticular profile with synthetic hydrocarbons mixed to liquid food and then assessed behavioural responses using two different bioassays. Our results show that (i) the presence, but not the absence, of an additional hydrocarbon elicited aggression and that (ii) among the three classes of hydrocarbons tested (unbranched, mono-methylated and dimethylated alkanes; for mono-methylated alkanes, we present a new synthetic pathway), only the dimethylated alkane was effective in eliciting aggression. Our results suggest that carpenter ants use a fundamentally different mechanism for nest-mate recognition than previously thought. They do not specifically recognize nest-mates, but rather recognize and reject non-nest-mates bearing odour cues that are novel to their own colony cuticular hydrocarbon profile. This begs for a reappraisal of the mechanisms underlying recognition systems in social insects.

Guerrieri, Fernando J.; Nehring, Volker; J?rgensen, Charlotte G.; Nielsen, John; Galizia, C. Giovanni; d'Ettorre, Patrizia

2009-01-01

321

Marketing Conservation.  

ERIC Educational Resources Information Center

In 1986, Northeast Utilities began helping shool administrators combat school building energy wastage through a program called Energy Alliance. The typical school can reduce its energy bill by 30 percent by adopting a wide range of conservation measures, including cogeneration, relamping, and energy audits. (MLH)

Ellis, William B.

1987-01-01

322

Colorful Conservation  

ERIC Educational Resources Information Center

Some people only think about conservation on Earth Day. Being in the "art business" however, this author is always conscious of the many products she thinks get wasted when they could be reused, recycled, and restored--especially in a school building and art room. In this article, she describes an art lesson that allows students to paint…

Skophammer, Karen

2011-01-01

323

Energy Conservation.  

ERIC Educational Resources Information Center

This selection of class activities involves a sequence of 10 class sessions. The goal of the collection is to aid students in learning the concepts of energy conservation and to put this knowledge into practice. Attention is also given to the development of alternate energy sources. Each lesson includes an activity title, motivational hints,…

Land, Amy A.

324

Conserving Soil.  

ERIC Educational Resources Information Center

Designed as enrichment materials for grades six through nine, this program is an interdisciplinary study of soils. As part of the program students: (1) examine soil organisms; (2) research history of local Native Americans to see how they and others have used the land and its soils; (3) investigate how soils are degraded and how they are conserved

Soil Conservation Service (USDA), Washington, DC.

325

Water Conservation  

NSDL National Science Digital Library

Students study the availability of fresh water on Earth and the methods that can be used to purify and conserve it. They also assess how much water they and their families typically use, and think about ways to reduce water usage.

Foundation, Wgbh E.

2005-12-17

326

Characterisation of XlCdc1, a Xenopus homologue of the small (PolD2) subunit of DNA polymerase delta; identification of ten conserved regions I-X based on protein sequence comparisons across ten eukaryotic species.  

PubMed

DNA polymerase delta (Pol delta), which plays keys roles in DNA replication, repair and recombination in eukaryotic cells, comprises at least two essential subunits - a large catalytic subunit (PolD1) possessing both DNA polymerase and 3'-5' exonuclease activities, and a smaller subunit (PolD2) whose function is not yet clear. Here we describe the cloning and sequencing of a Xenopus cDNA encoding a homologue of the PolD2 subunit. This protein (designated XlCdc1) is 69% identical to the human PolD2 protein and 34% identical to fission yeast Cdc1. Alignment of PolD2 protein sequences across ten eukaryotic species identifies 36 invariant amino-acid positions. These 36 residues are located within ten conserved regions (designated I-X) likely to have key functional roles. Consistent with this, the mutations in six previously identified yeast mutant PolD2 proteins map within conserved regions III, VI, VII and VIII. Several of the invariant amino acids are also conserved across the archaeal DNA polymerase II DP1 protein family. PMID:10196469

Reynolds, N; MacNeill, S A

1999-04-01

327

Recognizing familial myeloid leukemia in adults  

PubMed Central

Germline testing for familial cases of myeloid leukemia in adults is becoming more common with the recognition of multiple genetic syndromes predisposing people to bone marrow disease. Currently, Clinical Laboratory Improvement Amendments approved testing exists for several myeloid leukemia predisposition syndromes: familial platelet disorder with propensity to acute myeloid leukemia (FPD/AML), caused by mutations in RUNX1; familial AML with mutated CEBPA; familial myelodysplastic syndrome and acute leukemia with mutated GATA2; and the inherited bone marrow failure syndromes, including dyskeratosis congenita, a disease of abnormal telomere maintenance. With the recognition of additional families with a genetic component to their leukemia, new predisposition alleles will likely be identified. We highlight how to recognize and manage these cases as well as outline the characteristics of the major known syndromes. We look forward to future research increasing our understanding of the scope of inherited myeloid leukemia syndromes.

Nickels, Eric M.; Soodalter, Jesse; Churpek, Jane E.

2013-01-01

328

Recognizing Disguised Faces: Human and Machine Evaluation  

PubMed Central

Face verification, though an easy task for humans, is a long-standing open research area. This is largely due to the challenging covariates, such as disguise and aging, which make it very hard to accurately verify the identity of a person. This paper investigates human and machine performance for recognizing/verifying disguised faces. Performance is also evaluated under familiarity and match/mismatch with the ethnicity of observers. The findings of this study are used to develop an automated algorithm to verify the faces presented under disguise variations. We use automatically localized feature descriptors which can identify disguised face patches and account for this information to achieve improved matching accuracy. The performance of the proposed algorithm is evaluated on the IIIT-Delhi Disguise database that contains images pertaining to 75 subjects with different kinds of disguise variations. The experiments suggest that the proposed algorithm can outperform a popular commercial system and evaluates them against humans in matching disguised face images.

Dhamecha, Tejas Indulal; Singh, Richa; Vatsa, Mayank; Kumar, Ajay

2014-01-01

329

Recognizing Diogenes syndrome: a case report  

PubMed Central

Background Diogenes syndrome is a behavioural disorder characterized by domestic squalor, extreme self-neglect, hoarding, and lack of shame regarding one’s living condition. Patients may present due to a range of reasons. Recognizing these will allow for earlier management of this high-mortality condition. Case presentation 61-year Caucasian female known with bipolar 1 disorder presented with manic symptoms. She was very unkempt and foul smelling. After being admitted involuntarily, she requested that someone go to her home to feed her pets. Her house was filled with garbage, rotting food, and animal feces. She had no insight into any personal hygiene or public health problems. Conclusions Patients with Diogenes syndrome may be difficult to identify. Knowledge of the characteristics of Diogenes syndrome can aid in earlier recognition of such individuals, in order to decrease morbidity and mortality, and to improve public health.

2014-01-01

330

Eelgrass ( Zostera marina L.) in the Chesapeake Bay Region of Mid-Atlantic Coast of the USA: Challenges in Conservation and Restoration  

Microsoft Academic Search

Decreases in seagrass abundance reported from numerous locations around the world suggest that seagrass are facing a global\\u000a crisis. Declining water quality has been identified as the leading cause for most losses. Increased public awareness is leading\\u000a to expanded efforts for conservation and restoration. Here, we report on abundance patterns and environmental issues facing\\u000a eelgrass (Zostera marina), the dominant seagrass

Robert J. Orth; Scott R. Marion; Kenneth A. Moore; David J. Wilcox

2010-01-01

331

Impact of pre-harvest burning versus trash conservation on soil carbon and nitrogen stocks on a sugarcane plantation in the Brazilian Atlantic forest region  

Microsoft Academic Search

Owing to the increased demand for ethanol biofuel from sugar cane, the area planted to this crop in Brazil has increased from\\u000a 4.8 to 9.5 Mha since 2000. At the same time there has been pressure from environmental groups and others to cease the pre-harvest\\u000a burning of cane, and today over 40% of the crop is harvested without burning, thus conserving

Érika Flavia Machado Pinheiro; Eduardo Lima; Marcos Bacis Ceddia; Segundo Urquiaga; Bruno J. R. Alves; Robert M. Boddey

2010-01-01

332

Unusual evolutionary conservation of 5S rRNA pseudogenes in Aspergillus nidulans : Similarity of the DNA sequence associated with the pseudogenes with the mouse immunoglobulin switch region  

Microsoft Academic Search

Summary AllAspergillus nidulans 5S rRNA pseudogenes known so far are the result of integration of an approx. 0.2-kbp-long DNA sequence into the 5S rRNA genes. This sequence, called block C, is present in at least five copies in theA. nidulans genome and seems to be associated either with 5S rRNA genes or pseudogenes. In contrast to the 78% sequence conservation

Piotr Borsuk; Marek Gniadkowski; Ewa Bartnik; Piotr P. St?pie?

1988-01-01

333

SNF11, a New Component of the Yeast SNF-SWI Complex That Interacts with a Conserved Region of SNF2  

Microsoft Academic Search

The yeast SNF-SWI complex is required for transcriptional activation of diverse genes and has been shown to alter chromatin structure. The complex has at least 10 components, including SNF2\\/SWI2, SNF5, SNF6, SWI1\\/ADR6, and SWI3, and has been widely conserved in eukaryotes. Here we report the characterization of a new component. We identified proteins that interact in the two-hybrid system with

ISABELLE TREICH; BRADLEY R. CAIRNS; TERESA DE LOSSANTOS

334

CTL from EIAV carrier horses with diverse MHC class I alleles recognize epitope clusters in Gag matrix and capsid proteins  

PubMed Central

Cytotoxic T lymphocytes (CTL) are important for controlling equine infectious anemia virus (EIAV). Because Gag matrix (MA) and capsid (CA) are the most frequently recognized proteins, the hypothesis that CTL from EIAV-infected horses with diverse MHC class I alleles recognize epitope clusters (EC) in these proteins was tested. Four EC were identified by CTL from 15 horses and 8 of these horses had diverse MHC class I alleles. Two of the eight had CTL to EC1, six to EC2, five to EC3, and four to EC4. Because EC2–4 were recognized by CTL from >50% of horses with diverse alleles, the hypothesis was accepted. EC1 and EC3 were the most conserved EC and these more conserved broadly recognized EC may be most useful for CTL induction, helping overcome MHC class I polymorphism and antigenic variation.

Chung, Chungwon; Mealey, Robert H.; McGuire, Travis C.

2012-01-01

335

Local responses to participatory conservation in Annapurna conservation area, Nepal.  

PubMed

Biodiversity conservation has undergone a profound change in philosophy, policies and management approaches over the last forty years. The traditional top-down approach to nature protection has been widely criticized for failing to include critical social elements in management practices, and is being gradually replaced by a slew of participatory strategies under the rubric of bottom-up conservation. The new approach recognizes local communities as key partners in wildlife management and seeks their participation in social development and biodiversity conservation. However, every social context is different in its structure and functions, and in the way social groups respond to calls for participation. In order to gain a better understanding of the approach and the barriers encountered in its implementation, a questionnaire survey of 188 households was employed in the communities of the Upper Mustang extension of Annapurna Conservation Area (ACA) in Nepal. The study provides a comparative analysis of community participation and its barriers between Non-Tourist (NT) and Tourist (TV) villages. The results revealed important differences between the two groups in terms of their participation in community programs, barriers to participation, and perception of benefits from participation. Owing to their distinct spatial, demographic and attitudinal differences, the two village groups have their own sets of needs, values and motivation factors which cannot be generalized and treated as such. The research clearly identifies the need for the conservation agency to be creative in devising strategies and initiatives appropriate to specific social groups so as to optimize their input in participatory conservation. PMID:19967362

Khadka, Damodar; Nepal, Sanjay K

2010-02-01

336

Local Responses to Participatory Conservation in Annapurna Conservation Area, Nepal  

NASA Astrophysics Data System (ADS)

Biodiversity conservation has undergone a profound change in philosophy, policies and management approaches over the last forty years. The traditional top-down approach to nature protection has been widely criticized for failing to include critical social elements in management practices, and is being gradually replaced by a slew of participatory strategies under the rubric of bottom-up conservation. The new approach recognizes local communities as key partners in wildlife management and seeks their participation in social development and biodiversity conservation. However, every social context is different in its structure and functions, and in the way social groups respond to calls for participation. In order to gain a better understanding of the approach and the barriers encountered in its implementation, a questionnaire survey of 188 households was employed in the communities of the Upper Mustang extension of Annapurna Conservation Area (ACA) in Nepal. The study provides a comparative analysis of community participation and its barriers between Non-Tourist (NT) and Tourist (TV) villages. The results revealed important differences between the two groups in terms of their participation in community programs, barriers to participation, and perception of benefits from participation. Owing to their distinct spatial, demographic and attitudinal differences, the two village groups have their own sets of needs, values and motivation factors which cannot be generalized and treated as such. The research clearly identifies the need for the conservation agency to be creative in devising strategies and initiatives appropriate to specific social groups so as to optimize their input in participatory conservation.

Khadka, Damodar; Nepal, Sanjay K.

2010-02-01

337

Soundscape conservation  

Microsoft Academic Search

We argue that soundscapes possess both ecological and social value and that they should be considered natural resources worthy\\u000a of management and conservation. In this paper we bring together diverse bodies of literature that identify the human and ecological\\u000a benefits provided by soundscapes. Sense of place, cultural significance, interactions with landscape perceptions, and wildlife\\u000a wellbeing are a few of the

Sarah L. Dumyahn; Bryan C. Pijanowski

338

The gene encoding xylulose-5-phosphate/fructose-6-phosphate phosphoketolase (xfp) is conserved among Bifidobacterium species within a more variable region of the genome and both are useful for strain identification.  

PubMed

The nucleotide sequence of the xfp-gene region in six known and two unknown species of Bifidobacterium was determined and compared with the published sequences of B. animalis subsp. lactis DSM10140 and B. longum biovar longum NCC2705. The xfp coding sequences were 73% identical and coded for 825 amino acids in all 10 sequences. Partial sequences of an adjacent gene, guaA, were 61% identical in six sequences for which data were available. The region between xfp and guaA was variable in both length and sequence. Oligonucleotide sequences from the conserved and variable xfp regions were used as PCR primers, in combinations of appropriate specificity, for the detection and identification of Bifidobacterium isolates. PMID:15899413

Yin, Xianhua; Chambers, James R; Barlow, Kathleen; Park, Aaron S; Wheatcroft, Roger

2005-05-15

339

7 CFR 1465.36 - Environmental Services Credits for Conservation Improvements.  

Code of Federal Regulations, 2010 CFR

...2009-01-01 false Environmental Services Credits for Conservation Improvements. 1465.36 Section 1465.36...Administration § 1465.36 Environmental Services Credits for Conservation Improvements. USDA recognizes that...

2009-01-01

340

7 CFR 1465.36 - Environmental services credits for conservation improvements.  

Code of Federal Regulations, 2010 CFR

...2010-01-01 false Environmental services credits for conservation improvements. 1465.36 Section 1465.36...Administration § 1465.36 Environmental services credits for conservation improvements. NRCS recognizes that...

2010-01-01

341

Comparison between E1A gene from oncogenic and non-oncogenic adenoviruses in cellular transformation (Ad E1A conserved region).  

PubMed

All adenoviruses transform primary BRK cells in vitro, but only cells transformed by oncogenic adenoviruses are tumorigenic for immunocompetent animals. The transforming E1 regions of human Ad 2 and Ad 12 also differ from each other in the frequency in which they can transform BRK cells. We have investigated these properties which can be assigned to the specific domain of the E1A region. For this purpose, chimeric E1A regions between Ad 2 and Ad 12 have been constructed. The efficiency of cell transformation appeared to be determined by the encoding region. The promoter sequences were not important for an efficient cellular transformation although the E1B region cis activated in E1A transcription in both cell transformation and transient expression. We show that sequences located in the E1B promoter were responsible for this effect. In the encoding region the CR 1 domain was essential for the cell transformation frequency. PMID:8379854

Leclére, V; Huvent, I; Verwaerde, P; Cousin, C; D'Halluin, J C

1993-01-01

342

Overview: recognizing the problem of magnesium deficiency  

SciTech Connect

The magnesium content of the usual American diet is less than the recommended dietary allowance. Excesses of some macro- and micro-nutrients interact with Mg, increasing its requirements. Marginal deficiency of Mg is not associated with hypomagnesemia, is not characterized by typical manifestations, as is thus difficult to diagnose. Serum or plasma Mg levels are held within narrow limits unless tissue levels are very low, or renal function is poor. Vulnerability to Mg deficiency increases during growth and development, pregnancy, when under physical or psychological stress, and during illness or its treatment that interferes with absorption or causes loss of Mg. Evidence of biochemical changes of early Mg deficiency is rarely sought, although the roles of Mg in many enzyme systems are recognized. The effects of Mg deficiency on metabolism, even in disorders caused by vitamin dependencies in which Mg is a co-factor, are largely unexplored. Deficiency of Mg is diagnosed confidently when the laboratory reports hypomagnesemia in patients with convulsions or arrhythmias. Without these signs, Mg levels are not often ordered, even in the presence of neuromuscular irritability such as respond to Mg repletion. Because Mg supplementation or Mg-sparing drugs protect against premature or ectopic heart beats and sudden death, to which diuretic-treated hypertensive patients are at risk, it is increasingly being advised that their Mg status be determined.

Seelig, M.S.

1988-01-01

343

Recognizing hesitation phenomena in continuous, spontaneous speech  

NASA Astrophysics Data System (ADS)

Spontaneous speech differs from read speech in speaking rate and hesitation. In natural, spontaneous speech, people often start talking and then think along the way; at times, this causes the speech to have hesitation pauses (both filled and unfilled) and restarts. Results are reported on all types of pauses in a widely-used speech database, for both hesitation pauses and semi-intentional pauses. A distinction is made between grammatical pauses (at major syntactic boundaries) and ungrammatical ones. Different types of unfilled pauses cannot be reliably separated based on silence duration, although grammatical pauses tend to be longer. In the prepausal word before ungrammatical pauses, there were few continuation rises in pitch, whereas 80 percent of the grammatical pauses were accompanied by a prior fundamental frequency rise of 10-40 kHz. Identifying the syntactic function of such hesitation phenomena can improve recognition performance by eliminating from consideration some of the hypotheses proposed by an acoustic recognizer. Results presented allow simple identification of filled pauses (such as uhh, umm) and their syntactic function.

Oshaughnessy, Douglas

344

Recognizing Scientific Artifacts in Biomedical Literature  

PubMed Central

Today’s search engines and digital libraries offer little or no support for discovering those scientific artifacts (hypotheses, supporting/contradicting statements, or findings) that form the core of scientific written communication. Consequently, we currently have no means of identifying central themes within a domain or to detect gaps between accepted knowledge and newly emerging knowledge as a means for tracking the evolution of hypotheses from incipient phases to maturity or decline. We present a hybrid Machine Learning approach using an ensemble of four classifiers, for recognizing scientific artifacts (ie, hypotheses, background, motivation, objectives, and findings) within biomedical research publications, as a precursory step to the general goal of automatically creating argumentative discourse networks that span across multiple publications. The performance achieved by the classifiers ranges from 15.30% to 78.39%, subject to the target class. The set of features used for classification has led to promising results. Furthermore, their use strictly in a local, publication scope, ie, without aggregating corpus-wide statistics, increases the versatility of the ensemble of classifiers and enables its direct applicability without the necessity of re-training.

Groza, Tudor; Hassanzadeh, Hamed; Hunter, Jane

2013-01-01

345

Lagging-Strand Replication from the ssoA Origin of Plasmid pMV158 in Streptococcus pneumoniae: In Vivo and In Vitro Influences of Mutations in Two Conserved ssoA Regions  

PubMed Central

The streptococcal plasmid pMV158 replicates by the rolling-circle mechanism. One feature of this replication mechanism is the generation of single-stranded DNA intermediates which are converted to double-stranded molecules. Lagging-strand synthesis initiates from the plasmid single-stranded origin, sso. We have used the pMV158-derivative plasmid pLS1 (containing the ssoA type of lagging-strand origin) and a set of pLS1 derivatives with mutations in two conserved regions of the ssoA (the recombination site B [RSB] and a conserved 6-nucleotide sequence [CS-6]) to identify sequences important for plasmid lagging-strand replication in Streptococcus pneumoniae. Cells containing plasmids with mutations in the RSB accumulated 30-fold more single-stranded DNA than cells containing plasmids with mutations in the CS-6 sequence. Specificity of lagging-strand synthesis was tested by the development of a new in vitro replication system with pneumococcal cell extracts. Four major initiation sites of lagging-strand DNA synthesis were observed. The specificity of initiation was maintained in plasmids with mutations in the CS-6 region. Mutations in the RSB region, on the other hand, resulted in the loss of specific initiation of lagging-strand synthesis and also severely reduced the efficiency of replication.

Kramer, M. Gabriela; Khan, Saleem A.; Espinosa, Manuel

1998-01-01

346

Genetic differences between blood- and brain-derived viral sequences from human immunodeficiency virus type 1-infected patients: evidence of conserved elements in the V3 region of the envelope protein of brain-derived sequences.  

PubMed Central

Human immunodeficiency virus type 1 (HIV-1) sequences were generated from blood and from brain tissue obtained by stereotactic biopsy from six patients undergoing a diagnostic neurosurgical procedure. Proviral DNA was directly amplified by nested PCR, and 8 to 36 clones from each sample were sequenced. Phylogenetic analysis of intrapatient envelope V3-V5 region HIV-1 DNA sequence sets revealed that brain viral sequences were clustered relative to the blood viral sequences, suggestive of tissue-specific compartmentalization of the virus in four of the six cases. In the other two cases, the blood and brain virus sequences were intermingled in the phylogenetic analyses, suggesting trafficking of virus between the two tissues. Slide-based PCR-driven in situ hybridization of two of the patients' brain biopsy samples confirmed our interpretation of the intrapatient phylogenetic analyses. Interpatient V3 region brain-derived sequence distances were significantly less than blood-derived sequence distances. Relative to the tip of the loop, the set of brain-derived viral sequences had a tendency towards negative or neutral charge compared with the set of blood-derived viral sequences. Entropy calculations were used as a measure of the variability at each position in alignments of blood and brain viral sequences. A relatively conserved set of positions were found, with a significantly lower entropy in the brain-than in the blood-derived viral sequences. These sites constitute a brain "signature pattern," or a noncontiguous set of amino acids in the V3 region conserved in viral sequences derived from brain tissue. This brain-derived signature pattern was also well preserved among isolates previously characterized in vitro as macrophage tropic. Macrophage-monocyte tropism may be the biological constraint that results in the conservation of the viral brain signature pattern. Images

Korber, B T; Kunstman, K J; Patterson, B K; Furtado, M; McEvilly, M M; Levy, R; Wolinsky, S M

1994-01-01

347

76 FR 28954 - International Conservation and Management Measures Recognized by the United States  

Federal Register 2010, 2011, 2012, 2013

...Between the United States of America and the Republic of Costa Rica (``Antigua Convention'') entered into force for...Between the United States of America and the Republic of Costa Rica (``Antigua Convention''; Basic instrument for...

2011-05-19

348

Mutational analysis of conserved regions harboring catalytic triad residues of the levansucrase protein encoded by the lsc-3 gene (lsc3) of Pseudomonas syringae pv. tomato DC3000.  

PubMed

Levansucrase encoded by the lsc-3 (lsc3) gene at genomic locus PSPTOA0032 of Pseudomonas syringae pv. tomato DC3000 was mutationally analyzed. Altogether, 18 single-amino-acid mutants of 13 positions of Lsc3 were studied for catalytic properties, including production of fructooligosaccharides (FOS). Asp62, Asp219, and Glu303 were proved as members of the catalytic triad. Respective alanine replacement mutants were practically inactive with their kcat values reduced up to ?130,000 times. Additionally, the requirements of Trp61, Gln301, and Arg304, located in conserved sequence blocks around the catalytic triad positions for the catalysis were shown. The catalytic significance of the position equivalent to Arg304 was shown for levansucrases for the first time. Replacement of Gln301 specifically affected the polymerizing ability of Lsc3. The Gln301Ala mutant was largely hydrolytic and produced 31 times less FOS than the wild type. Despite high conservation grades, Leu66, Pro220, Asp225, and His306 tolerated replacement well. Quantification of produced FOS showed a high biotechnological potential of Lsc3. Using 1 mg of Lsc3 protein, 15.4 g of FOS with a degree of polymerization from 3 to 7 can be synthesized in a 20 H reaction with 1,200 mM sucrose. Our expression system allowed us to produce up to 30 mg of Lsc3 protein from 1 L of induced culture of recombinant Escherichia coli. PMID:23725335

Mardo, Karin; Visnapuu, Triinu; Vija, Heiki; Elmi, Triin; Alamäe, Tiina

2014-01-01

349

The helicase-binding domain of Escherichia coli DnaG primase interacts with the highly conserved C-terminal region of single-stranded DNA-binding protein  

PubMed Central

During bacterial DNA replication, DnaG primase and the ? subunit of DNA polymerase III compete for binding to single-stranded DNA-binding protein (SSB), thus facilitating the switch between priming and elongation. SSB proteins play an essential role in DNA metabolism by protecting single-stranded DNA and by mediating several important protein–protein interactions. Although an interaction of SSB with primase has been previously reported, it was unclear which domains of the two proteins are involved. This study identifies the C-terminal helicase-binding domain of DnaG primase (DnaG-C) and the highly conserved C-terminal region of SSB as interaction sites. By ConSurf analysis, it can be shown that an array of conserved amino acids on DnaG-C forms a hydrophobic pocket surrounded by basic residues, reminiscent of known SSB-binding sites on other proteins. Using protein–protein cross-linking, site-directed mutagenesis, analytical ultracentrifugation and nuclear magnetic resonance spectroscopy, we demonstrate that these conserved amino acid residues are involved in the interaction with SSB. Even though the C-terminal domain of DnaG primase also participates in the interaction with DnaB helicase, the respective binding sites on the surface of DnaG-C do not overlap, as SSB binds to the N-terminal subdomain, whereas DnaB interacts with the ultimate C-terminus.

Naue, Natalie; Beerbaum, Monika; Bogutzki, Andrea; Schmieder, Peter; Curth, Ute

2013-01-01

350

7 CFR 1467.20 - Market-based conservation initiatives.  

Code of Federal Regulations, 2010 CFR

...These funds shall be available without further appropriation and until expended, to carry out the program. (b) Ecosystem Services Credits for Conservation Improvements . (1) USDA recognizes that environmental benefits will be...

2010-01-01

351

Robust traffic sign detection using fuzzy shape recognizer  

NASA Astrophysics Data System (ADS)

A novel fuzzy approach for the detection of traffic signs in natural environments is presented. More than 3000 road images were collected under different weather conditions by a digital camera, and used for testing this approach. Every RGB image was converted into HSV colour space, and segmented by the hue and saturation thresholds. A symmetrical detector was used to extract the local features of the regions of interest (ROI), and the shape of ROI was determined by a fuzzy shape recognizer which invoked a set of fuzzy rules. The experimental results show that the proposed algorithm is translation, rotation and scaling invariant, and gives reliable shape recognition in complex traffic scenes where clustering and partial occlusion normally occur.

Li, Lunbo; Li, Jun; Sun, Jianhong

2009-10-01

352

Selling energy conservation.  

PubMed

This article concerns the Organization of the Petroleum Exporting Countries (OPEC) crisis and its impact on energy efficiency measures in the US. In 1985, when the OPEC collapsed, the US government had avoided the need to construct 350 gigawatts of new electric capacity. The most successful efficiency improvements, especially in household appliances and equipment, lighting and tightened energy efficiency standards in new buildings, resulted from the OPEC event. The real innovation of that time was the change in profit rules for utilities. This revolution and the way some US utilities view energy have not caught on elsewhere. Despite the initiative toward improving energy efficiency in homes, offices and industries, the change has been slow. Partly to blame are the big development banks, which pointed out that short-term conservation and efficiency measures could save at least 15% of the total energy demand without the need for major investment. The benefits of energy conservation was shown during the oil shock when per capita energy consumption fell by 5% in the member states of the Organization of Economic Cooperation and Development, while the per capita gross domestic product grew by a third. There has been a decrease in energy expenditure worldwide, and the scope for further energy savings is enormous, but governments need to recognize and seize the opportunity. PMID:12295818

Hinrichsen, D

1995-01-01

353

Modeling effects of climatological variability and management practices on conservation of groundwater from the Mississippi River Valley Shallow Alluvial Aquifer in the Mississippi Delta region  

NASA Astrophysics Data System (ADS)

Ninety-eight percent of water taken from the Mississippi River Shallow Alluvial Aquifer, hereafter referred to as "the aquifer" or "MRVA," is used by the agricultural industry for irrigation. Mississippi Delta agriculture is increasingly using more water from the MRVA and the aquifer has been losing about 300,000 acre-feet per year. This research expands on previous work in which a model was developed that simulates the effects of climatic variability, crop acreage changes, and specific irrigation methods on consequent variations in the water volume of the MRVA. This study corrects an identified problem by replacing total growing season precipitation with an irrigation demand driver based on evaporation and crop coefficients and changing the time scale from the entire growing season to a daily resolution. The calculated irrigation demand, as a climatological driver for the model, captures effective precipitation more precisely than the initial growing season precipitation driver. Predictive equations resulting from regression analyses of measured versus calculated irrigation water use showed R2 and correlations of 0.33 and 0.57, 0.77 and 0.88, 0.71 and 0.84, and 0.68 and 0.82 for cotton, corn, soybeans and rice, respectively. Ninety-five percent of the predicted values fall within a range of + or - about 23,000 acre-feet, an error of about 10-percent. The study also adds an additional conservation strategy through the use of surface water from on-farm reservoirs in lieu of groundwater. Analyses show that climate could provide the entire water need of the plants in 70-percent of the years for corn, 65-percent of the years for soybeans and cotton, and even 5-percent of the years for rice. Storing precipitation in on-farm structures is an effective way to reduce reliance of Delta producers on groundwater. If producers adopted, at a minimum, the 97.5:2.5 ratio suggested management practice, this minimal management strategy could potentially conserve 48-percent, 35-percent and 42-percent of groundwater for cotton, corn and soybeans, respectively. Even in extreme drought years such as 2007, cotton, corn and soybeans produced under the 97.5:2.5 management strategy could conserve 32-percent, 46-percent and 38-percent of groundwater, respectively.

Thornton, Robert Frank

354

Bacillus cereus sphingomyelinase recognizes ganglioside GM3.  

PubMed

Sphingomyelinase (SMase) from Bacillus cereus (Bc-SMase) hydrolyzes sphingomyelin (SM) to phosphocholine and ceramide in a divalent metal ion-dependent manner, and is a virulence factor for septicemia. Bc-SMase has three characteristic sites, viz., the central site (catalytic site), side-edge site (membrane binding site), and ?-hairpin region (membrane binding site). Here, we show that the ?-hairpin directly binds to gangliosides, especially NeuAc?2-3Gal?1-4Glc?1-1ceramide (GM3) through a carbohydrate moiety. Neuraminidase inhibited the binding of Bc-SMase to mouse peritoneal macrophages in a dose-dependent manner. SPR analysis revealed that the binding response of Bc-SMase to liposomes containing GM3 was about 15-fold higher than that to liposomes lacking GM3. Moreover, experiments with site-directed mutants indicated that Trp-284 and Phe-285 in the ?-hairpin play an important role in the interaction with GM3. The binding of W284A and F285A mutant enzymes to mouse macrophages decreased markedly in comparison to the binding by wild-type enzymes. Therefore, we conclude that GM3 is the primary cellular receptor for Bc-SMase, and that the ?-hairpin region is the tethering region for gangliosides. PMID:23313504

Oda, Masataka; Fujita, Aoi; Okui, Kensuke; Miyamoto, Kazuaki; Shibutani, Masahiro; Takagishi, Teruhisa; Nagahama, Masahiro

2013-02-01

355

Modeling opportunity costs of conservation in transitional landscapes.  

PubMed

Conservation scientists recognize the urgency of incorporating opportunity costs into conservation planning. Despite this, applications to date have been limited, perhaps partly because of the difficulty in determining costs in regions with limited data on land prices and ownership. We present methods for estimating opportunity costs of land preservation in landscapes or ecoregions that are a changing mix of agriculture and natural habitat. Our approach derives from the literature on estimating land values as opportunity costs of alternate land uses and takes advantage of general availability of necessary data, even in relatively data-poor regions. The methods integrate probabilities of habitat conversion with region-wide estimates of economic benefits from agricultural land uses and estimate land values with a discount rate to convert annual values into net present values. We applied our method in a landscape undergoing agricultural conversion in Paraguay. Our model of opportunity costs predicted an independent data set of land values and was consistent with implicit discount rates of 15-25%. Model-generated land values were strongly correlated with actual land values even after correcting for the effect of property size and proportion of property that was forested. We used the model to produce a map of opportunity costs and to estimate the costs of conserving forest within two proposed corridors in the landscape. This method can be applied to conservation planning in situations where natural habitat is currently being converted to market-oriented land uses. Incorporating not only biological attributes but also socioeconomic data can help in the design of efficient networks of protected areas that represent biodiversity at minimum costs. PMID:16903110

Naidoo, Robin; Adamowicz, Wiktor L

2006-04-01

356

Mapping of Epitopes Recognized by Antibodies Induced by Immunization of Mice with PspA and PspC.  

PubMed

Pneumococcal surface protein A (PspA) and pneumococcal surface protein C (PspC) are important candidates for an alternative vaccine against pneumococcal infections. Since these antigens show variability, the use of variants that do not afford broad protection may lead to the selection of vaccine escape bacteria. Epitopes capable of inducing antibodies with broad cross-reactivities should thus be the preferred antigens. In this work, experiments using peptide arrays show that most linear epitopes recognized by antibodies induced in mice against different PspAs were located at the initial 44 amino acids of the mature protein and that antibodies against these linear epitopes did not confer protection against a lethal challenge. Conversely, linear epitopes recognized by antibodies to PspC included the consensus sequences involved in the interaction with human factor H and secretory immunoglobulin A (sIgA). Since linear epitopes of PspA were not protective, larger overlapping fragments containing 100 amino acids of PspA of strain Rx1 were constructed (fragments 1 to 7, numbered from the N terminus) to permit the mapping of antibodies with conformational epitopes not represented in the peptide arrays. Antibodies from mice immunized with fragments 1, 2, 4, and 5 were capable of binding onto the surface of pneumococci and mediating protection against a lethal challenge. The fact that immunization of mice with 100-amino-acid fragments located at the more conserved N-terminal region of PspA (fragments 1 and 2) induced protection against a pneumococcal challenge indicates that the induction of antibodies against conformational epitopes present at this region may be important in strategies for inducing broad protection against pneumococci. PMID:24807052

Vadesilho, Cintia F M; Ferreira, Daniela M; Gordon, Stephen B; Briles, David E; Moreno, Adriana T; Oliveira, Maria Leonor S; Ho, Paulo L; Miyaji, Eliane N

2014-07-01

357

An energy-conserving spectral solution  

PubMed

An energy-conserving spectral solution is derived and tested. A range-dependent medium is approximated by a sequence of range-independent regions. In each region, the acoustic field is represented in terms of the horizontal wave-number spectrum. A condition corresponding to energy conservation is derived for the vertical interfaces between regions. The accuracy of the approach is demonstrated for problems involving sloping ocean bottoms. The energy-conserving spectral solution is less efficient than the energy-conserving parabolic equation solution, but might be suitable for generalization to problems involving elastic bottoms. PMID:10790022

Collins; Schmidt; Siegmann

2000-04-01

358

Natural killer T cells recognize diacylglycerol antigens from pathogenic bacteria  

Microsoft Academic Search

Natural killer T (NKT) cells recognize glycosphingolipids presented by CD1d molecules and have been linked to defense against microbial infections. Previously defined foreign glycosphingolipids recognized by NKT cells are uniquely found in nonpathogenic sphingomonas bacteria. Here we show that mouse and human NKT cells also recognized glycolipids, specifically a diacylglycerol, from Borrelia burgdorferi, which causes Lyme disease. The B. burgdorferi–derived,

Yuki Kinjo; Emmanuel Tupin; Douglass Wu; Masakazu Fujio; Raquel Garcia-Navarro; Mohammed Rafii-El-Idrissi Benhnia; Dirk M Zajonc; Gil Ben-Menachem; Gary D Ainge; Gavin F Painter; Archana Khurana; Kasper Hoebe; Samuel M Behar; Bruce Beutler; Ian A Wilson; Moriya Tsuji; Timothy J Sellati; Chi-Huey Wong; Mitchell Kronenberg

2006-01-01

359

Conservative front tracking and level set algorithms  

PubMed Central

Hyperbolic conservation laws are foundational for many branches of continuum physics. Discontinuities in the solutions of these partial differential equations are widely recognized as a primary difficulty for numerical simulation, especially for thermal and shear discontinuities and fluid–fluid internal boundaries. We propose numerical algorithms that will (i) track these discontinuities as sharp internal boundaries, (ii) fully conserve the conserved quantities at a discrete level, even at the discontinuities, and (iii) display one order of numerical accuracy higher globally (at the discontinuity) than algorithms in common use. A significant improvement in simulation capabilities is anticipated through use of the proposed algorithms.

Glimm, James; Li, Xiao Lin; Liu, Yingjie; Zhao, Ning

2001-01-01

360

Genome Trees from Conservation Profiles  

PubMed Central

The concept of the genome tree depends on the potential evolutionary significance in the clustering of species according to similarities in the gene content of their genomes. In this respect, genome trees have often been identified with species trees. With the rapid expansion of genome sequence data it becomes of increasing importance to develop accurate methods for grasping global trends for the phylogenetic signals that mutually link the various genomes. We therefore derive here the methodological concept of genome trees based on protein conservation profiles in multiple species. The basic idea in this derivation is that the multi-component “presence-absence” protein conservation profiles permit tracking of common evolutionary histories of genes across multiple genomes. We show that a significant reduction in informational redundancy is achieved by considering only the subset of distinct conservation profiles. Beyond these basic ideas, we point out various pitfalls and limitations associated with the data handling, paving the way for further improvements. As an illustration for the methods, we analyze a genome tree based on the above principles, along with a series of other trees derived from the same data and based on pair-wise comparisons (ancestral duplication-conservation and shared orthologs). In all trees we observe a sharp discrimination between the three primary domains of life: Bacteria, Archaea, and Eukarya. The new genome tree, based on conservation profiles, displays a significant correspondence with classically recognized taxonomical groupings, along with a series of departures from such conventional clusterings.

Tekaia, Fredj; Yeramian, Edouard

2005-01-01

361

Canadian wetland policy promotes conservation  

SciTech Connect

With the recent adoption of The Federal Policy on Wetland Conservation, the Government of Canada has firmly stated that wetland conservation will become a fundamental aspect of federal government decision-making in all federal government programs and institutions. The policy focuses on the sustainable, wise use of wetland areas on federal lands (about 29% of Canada`s wetland base) as well as wetlands, such as national parks, under direct federal authority. The federal government of Canada is promoting a nonregulatory, cooperative approach to achieve the following goals: Maintain the benefits derived from wetlands throughout Canada; Achieve no net loss of wetland functions on federal lands and waters; Enhance and rehabilitate wetlands in areas where the continuing loss or degradation of wetlands or their functions have reached critical levels; Recognize wetland functions in resource planning, management, and economic decision-making with regard to all federal programs, policies, and activities; Secure wetlands of significance to Canadians; and, Recognize sound, sustainable management practices in sectors such as forestry and agriculture that make a positive contribution to wetlands conservation while also achieving wise use of wetland resources.

Rubec, C. [North American Wetlands Conservation Council, Ottawa, Ontario (Canada)

1992-11-01

362

The bounty of minor lakes: the role of small satellite water bodies in evolution and conservation of fishes in the Lake Victoria Region, East Africa  

Microsoft Academic Search

The Lake Victoria Region (LVR) encompasses the large lakes Victoria, Kyoga, Edward, George and Kivu, as well as scores of small satellite lakes within the parent catchments. Taken as a whole, the LVR originally harbored a unique fish fauna that included in excess of 600 endemic species of cichlid fishes. As a result of human influence, including a commercial fishery

Wilson W. Mwanja; Audrey S. Armoudlian; Silvester B. Wandera; Les Kaufman; Lizhao Wu; Gregory C. Booton; Paul A. Fuerst

2001-01-01

363

Status and potential of locally-managed marine areas in the Pacific Island Region: meeting nature conservation and sustainable livelihood targets through wide-spread implementation of LMMAs  

Microsoft Academic Search

The South Pacific has experienced a remarkable proliferation of Marine Managed Areas in the last decade. These protected areas, implemented by over 500 communities spanning 15 independent countries and territories represent a unique global achievement. The approaches being developed at national levels are built on a unique feature of the region, customary tenure and resource access, and make use of,

Hugh Govan

2009-01-01

364

Age remains the first prognostic factor for loco-regional breast cancer recurrence in young (<40 years) women treated with breast conserving surgery first  

Microsoft Academic Search

PurposeTo ascertain the loco-regional recurrence (LRR) rate and its major prognostic factors in patients younger than 40 and to determine the influence of age on the features of breast cancer and its treatment in two age groups: ?35 years and [36–39] years.

Marc A. Bollet; Brigitte Sigal-Zafrani; Valérie Mazeau; Alexia Savignoni; Anne de la Rochefordière; Anne Vincent-Salomon; Rémy Salmon; François Campana; Youlia M. Kirova; Rémi Dendale; Alain Fourquet

2007-01-01

365

Characterization of the chimeric seven-transmembrane protein containing conserved region of helix C-F of microbial rhodopsin from Ganges River.  

PubMed

Proteorhodopsin (PR) is a light-driven proton pump that has been found in a variety of marine bacteria. Recently, many PR-like genes were found in non-marine environments. The goal of this study is to explore the function of rhodopsins that exist only as partial proteo-opsin genes using chimeras with marine green PR (GPR). We isolated nine partial genes of PR homologues using polymerase chain reaction (PCR) and chose three homologues of GPR from the surface of the Ganges River, which has earned them the name "CFR, Chimeric Freshwater Rhodopsin." In order to characterize the proteins, we constructed the cassette based on GPR sequence without helices C to F and inserted the isolated conserved partial sequences. When expressed in E. coli, we could observe light-driven proton pumping activity similar to proteorhodopsin, however, photocycle kinetics of CFRs are much slower than proteorhodopsin. Half-time decay of O intermediates of CFRs ranged between 143 and 333 ms at pH 10; their absorption maxima were between 515 and 522 nm at pH 7. We can guess that the function of native rhodopsin, a retinal protein of fresh water bacteria, may be a light-driven proton transport based on the results from chimeric freshwater rhodopsins. This approach will enable many labs that keep reporting partial PCR-based opsin sequences to finally characterize their proteins. PMID:23151811

Choi, Ah Reum; Kim, Se Jun; Jung, Byung Hoon; Jung, Kwang-Hwan

2013-01-01

366

[C-terminal region of MyfA, the major subunit of Yersinia enterocolitica Myf fimbriae, is conserved among pathogenic strains].  

PubMed

In our study we analyzed the nucleotide sequence of the C- terminal 256 bp fragment of the myfA gene encoding MyfA protein, the major subunit of Yersinia enterocolitica Myf fimbriae. We examined ten representative strains of major Y. enterocolitica pathogenic bioserotypes belonging to European (4/O3; 2/O9; 3/O5,27) and American (1B/O8) phylogenetic lineages. DNA sequencing revealed that consensus nucleotide sequences of the tested myfA fragment were indistinguishable in all the tested strains. The resulting common consensus sequence found in our study was identical to the corresponding fragment of reference sequences Z21953 and NC008800 deposited in GenBank database for pathogenic Y. enterocolitica strains. In contrast, 18 point mutations leading to 13 amino acid substitutions were found when the common consensus sequence was aligned to sequence AY966879 determined for the myfA homologue detected by PCR in Y. enterocolitica 1A strain. The strong conservation of the nucleotide and amino acid sequence of myfA gene among virulent bioserotypes of Y. enterocolitica indicate that fimbriae MyF could play important role in pathogenesis, even before the divergence of European and American lineages. PMID:21473097

Zacharczuk, Katarzyna; Gierczy?ski, Rafa?

2010-01-01

367

Phylogeography and conservation of impala and greater kudu.  

PubMed

The phylogeography of the bush habituated African bovid species impala (Aepyceros melampus) and greater kudu (Tragelaphus strepsiceros) is investigated using mitochondrial DNA (mtDNA) markers. Combined analysis of individual lineages, relationships and population genetics suggest a colonization process from Southern Africa toward Eastern regions in the greater kudu. Results are less clear for the impala, although remaining consistent with a similar pattern of historical dispersion. The study reveals a similar pattern, that is a marked divergence of lineages from South-western Africa relative to other regions. This pattern is opposed to previously published findings in other African bovid species. In the impala, the genetically isolated region is consistent with morphology because it is recognized as the subspecies A. m. petersi, the black-faced impala. In contrast, the similar split of South-western mitochondrial lineages was not expected in the greater kudu on the basis of morphology. Both species show a significant population genetic differentiation. Beyond their phylogeographical value, our results should raise conservation concerns about South-western populations of both species. The black-faced impala is categorized as vulnerable and our data show indications of hybridization with common impala A. m. melampus. The previously unrecognized genetic status of the South-western kudus could also imply conservation regulations. PMID:11298982

Nersting, L G; Arctander, P

2001-03-01

368

Allocating Conservation Resources under the Endangered Species Act  

Microsoft Academic Search

The necessity to develop a priority system to guide the allocation of resources to the conservation of endangered species is widely recognized. The economic theory of biodiversity has established a framework to do so, and has identified priority criteria that should be considered when making conservation decisions. This paper uses a random effects ordered probit model of endangered species recovery

Christian Langpap; Joe Kerkvliet

2007-01-01

369

Conflict between energy conservation and water pollution control standards  

Microsoft Academic Search

The potential conflict in national needs for both energy conservation and water pollution control is indicated. Meeting broader obligations in reconciling these apparent differences has failed. Major contributions to energy conservation efforts needed today could be made without giving up any important pollution control goals. Hopefully, state and Federal regulatory agencies soon will recognize their obligations in this respect and

Lamb

1980-01-01

370

Structural Diversity in Conserved Regions Like the DRY-Motif among Viral 7TM Receptors--A Consequence of Evolutionary Pressure?  

PubMed Central

Several herpes- and poxviruses have captured chemokine receptors from their hosts and modified these to their own benefit. The human and viral chemokine receptors belong to class A 7 transmembrane (TM) receptors which are characterized by several structural motifs like the DRY-motif in TM3 and the C-terminal tail. In the DRY-motif, the arginine residue serves important purposes by being directly involved in G protein coupling. Interestingly, among the viral receptors there is a greater diversity in the DRY-motif compared to their endogenous receptor homologous. The C-terminal receptor tail constitutes another regulatory region that through a number of phosphorylation sites is involved in signaling, desensitization, and internalization. Also this region is more variable among virus-encoded 7TM receptors compared to human class A receptors. In this review we will focus on these two structural motifs and discuss their role in viral 7TM receptor signaling compared to their endogenous counterparts.

Jensen, Ann-Sofie M?lleskov; Sparre-Ulrich, Alexander Hovard; Davis-Poynter, Nicholas; Rosenkilde, Mette Marie

2012-01-01

371

Conservation successes at micro-, meso- and macroscales.  

PubMed

Although large-scale biodiversity declines are ongoing, certain conservation actions have made a positive difference. Rates of extinction and endangerment of vertebrate species, for instance, have probably been reduced via conservation interventions. Such conservation actions operate at different spatial scales. Habitat preservation and endangered species recovery are examples of conservation successes at microscales. Mesoscale conservation includes regional cooperation among neighboring countries that has arrested population declines of endangered species, such as mountain gorillas. At macroscales, public pressure on multinational corporations has sometimes resulted in their abandoning environmentally damaging practices or suppliers with poor environmental records. Overall, conservation projects such as these need more long-term funding and greater political and popular support, and must also include provisions to evaluate and document their outcomes. As we discuss here, a focus on conservation successes achieved at different scales can help to promote these aims and guide future conservation victories. PMID:21824677

Sodhi, Navjot S; Butler, Rhett; Laurance, William F; Gibson, Luke

2011-11-01

372

Surface Expression of the Conserved C Repeat Region of Streptococcal M6 Protein within the Pip Bacteriophage Receptor of Lactococcus lactis  

Microsoft Academic Search

The C repeat region of the M6 protein (M6c) from Streptococcus pyogenes was expressed within the Pip bacteriophage receptor on the surface of Lactococcus lactis. M6c was also detected in the culture medium. The pip-emm6c allele was integrated into the chromosome and stably expressed without antibiotic selection. The level of cell-associated surface expression of PipM6c was 0.015% of total cellular

BRUCE L. GELLER; NADINE WADE; THOMAS D. GILBERTS; DENNIS E. HRUBY; RYAN JOHANSON; LJUBISA TOPISIROVIC

2001-01-01

373

A phylogenetically conserved sequence within viral 3' untranslated RNA pseudoknots regulates translation.  

PubMed Central

Both the 68-base 5' leader (omega) and the 205-base 3' untranslated region (UTR) of tobacco mosaic virus (TMV) promote efficient translation. A 35-base region within omega is necessary and sufficient for the regulation. Within the 3' UTR, a 52-base region, composed of two RNA pseudoknots, is required for regulation. These pseudoknots are phylogenetically conserved among seven viruses from two different viral groups and one satellite virus. The pseudoknots contained significant conservation at the secondary and tertiary levels and at several positions at the primary sequence level. Mutational analysis of the sequences determined that the primary sequence in several conserved positions, particularly within the third pseudoknot, was essential for function. The higher-order structure of the pseudoknots was also required. Both the leader and the pseudoknot region were specifically recognized by, and competed for, the same proteins in extracts made from carrot cell suspension cells and wheat germ. Binding of the proteins is much stronger to omega than the pseudoknot region. Synergism was observed between the TMV 3' UTR and the cap and to a lesser extent between omega and the 3' UTR. The functional synergism and the protein binding data suggest that the cap, TMV 5' leader, and 3' UTR interact to establish an efficient level of translation. Images

Leathers, V; Tanguay, R; Kobayashi, M; Gallie, D R

1993-01-01

374

Wet and Wonderful: The World's Largest Wetlands Are Conservation Priorities  

NSDL National Science Digital Library

Wetlands perform many essential ecosystem servicesâÂÂcarbon storage, flood control, maintenance of biodiversity, fish production, and aquifer recharge, among othersâÂÂservices that have increasingly important global consequences. Like biodiversity hotspots and frontier forests, the world's largest wetlands are now mapped and described by an international team of scientists, highlighting their conservation importance at the global scale. We explore current understanding of some ecosystem services wetlands provide. We selected four of these wetlands (the largest peatland, West Siberian Lowland; the largest floodplain, Amazon River Basin; the least-known wetland, Congo River Basin; and the most heavily developed wetland, Mississippi River Basin), and we illustrate their diversity, emphasizing values and lessons for thinking big in terms of conservation goals. Recognizing the global significance of these wetlands is an important first step toward forging global conservation solutions. Each of the world's largest wetlands requires a basinwide sustainable management strategy built on new institutional frameworksâÂÂat international, national, and regional levelsâÂÂto ensure provision of their vital services.

Paul Keddy (Southeastern Louisiana University;Dept of Biological Sciences)

2009-01-01

375

Eastern Ishtar Terra: Tectonic evolution derived from recognized features  

NASA Technical Reports Server (NTRS)

Previous analyses have recognized several styles and orientations of compressional deformation, crustal convergence, and crustal thickening in Eastern Ishtar Terra. An east to west sense of crustal convergence through small scale folding, thrusting, and buckling is reflected in the high topography and ridge-and-valley morphology of Maxwell Montes and the adjacent portion of Fortuna Tessera. This east to west convergence was accompanied by up to 1000 km of lateral motion and large scale strike-slip faulting within two converging shear zones which has resulted in the present morphology of Maxwell Montes. A more northeast to southwest sense of convergence through large scale buckling and imbrication is reflected in large, northwest-trending scarps along the entire northern boundary of Ishtar Terra, with up to 2 km of relief present at many of the scarps. It was previously suggested that both styles of compression have occurred at the expense of pre-existing tessera regions which have then been overprinted by the latest convergence event. The difference in style is attributed mostly to differences in the properties of the crust converging with the tessera blocks. If one, presumably thick, tessera block converges with another tessera region, then the widespread, distributed style of deformation occurs, as observed in western Fortuna Tessera. However, if relatively thin crust (such as suggested for the North Polar Plains converges with thicker tessera regions, then localized deformation occurs, as reflected in the scarps along Northern Ishtar Terra. The purpose is to identify the types of features observed in Eastern Ishtar Terra. Their potential temporal and spatial relationships, is described, possible origins for them is suggested, and how the interpretation of some of these features has led to the multiple-style tectonic evolution model described is shown.

Vorderbruegge, R. W.; Head, James W.

1989-01-01

376

Attenuated Salmonella choleraesuis-mediated RNAi targeted to conserved regions against foot-and-mouth disease virus in guinea pigs and swine.  

PubMed

In this study, specific sequences within three genes (3D, VP4 and 2B) of the foot-and-mouth disease virus (FMDV) genome were determined to be effective RNAi targets. These sequences are highly conserved among different serotype viruses based on sequence analysis. Small interfering RNA (siRNA)-expressing plasmids (p3D-NT19, p3D-NT56, pVP4-NT19, pVP4-NT65 and p2B-NT25) were constructed to express siRNA targeting 3D, VP4 and 2B, respectively. The antiviral potential of these siRNA for various FMDV isolates was investigated in baby hamster kidney (BHK-21) cells and suckling mice. The results show that these siRNA inhibited virus yield 10- to 300-fold for different FMDV isolates of serotype O and serotype Asia I at 48 h post infection in BHK-21 cells compared to control cells. In suckling mice, p3D-NT56 and p2B-NT25 delayed the death of mice. Twenty percent to 40% of the animals that received a single siRNA dose survived 5 days post infection with serotype O or serotype Asia I. We used an attenuated Salmonella choleraesuis (C500) vaccine strain, to carry the plasmid that expresses siRNA directed against the polymerase gene 3D (p3D-NT56) of FMDV. We used guinea pigs to evaluate the inhibitory effects of recombinant S. cho (p3D-NT56/S. cho) on FMDV infection. The results show that 80% of guinea pigs inoculated with 10(9) CFU of p3D-NT56/S. cho and challenged 36 h later with 50 ID(50) of homologous FMDV were protected. We also measured the antiviral activity of p3D-NT56/S. cho in swine. The results indicate that 100% of the animals treated with 5 x 10(9) CFU of p3D-NT56/S. cho were protected in 9 days. PMID:20167192

Cong, Wei; Jin, Hong; Jiang, Chengda; Yan, Weiyao; Liu, Mingqiu; Chen, Jiulian; Zuo, Xiaoping; Zheng, Zhaoxin

2010-01-01

377

Sniffing behaviour, or recognizing a lily by smell, but not recognizing a sock on sight.  

PubMed

We report a 65-year-old man with a post-anoxic encephalopathy who showed compulsive sniffing at available objects. This stereotyped environment-driven behaviour has not been previously described. Other compulsive environment-driven responses, such as manipulation and utilization of tools and hyperlexia, were also present. The disorder shared several features with the Klüver-Bucy syndrome where mouthing of objects, rather than smelling them, is common. The patient had a severe dementia, with amnesia, anomia, apraxia, and visual agnosia. Whereas he could not recognize very familiar objects on sight, he could in contrast correctly identify several familiar odours. Although sniffing was a compulsive and purposeless environment-driven behaviour, the question may be asked whether a relatively preserved olfactory recognition, in the presence of a severe disorder of visual recognition and knowledge, could have favoured a stereotyped exploration of objects by smelling. PMID:9339337

Vuilleumier, P; Staub, F; Assal, G

1997-09-01

378

A conserved TN 8TCCT motif in the octapeptide-encoding region of Pax genes which has the potential to direct cytosine methylation 1 Published in conjunction with A Wisconsin Gathering Honoring Waclaw Szybalski on the occasion of his 75th year and 20 years of Editorship-in-Chief of Gene. 10–11 August 1997, University of Wisconsin, Madison, WI, USA. 1  

Microsoft Academic Search

Our previous findings have shown that the developmental genes Pax7 and Pax3 are differentially methylated; the gene region that encodes the paired domain is hypomethylated, whereas the region that encodes the homeodomain is hypermethylated. For this reason, the known DNA sequence between the paired and homeoboxes was analysed for the presence of a conserved DNA motif to which a modifying

M. R Ziman; P. H Kay

1998-01-01

379

Documenting Biogeographical Patterns of African Timber Species Using Herbarium Records: A Conservation Perspective Based on Native Trees from Angola  

PubMed Central

In many tropical regions the development of informed conservation strategies is hindered by a dearth of biodiversity information. Biological collections can help to overcome this problem, by providing baseline information to guide research and conservation efforts. This study focuses on the timber trees of Angola, combining herbarium (2670 records) and bibliographic data to identify the main timber species, document biogeographic patterns and identify conservation priorities. The study recognized 18 key species, most of which are threatened or near-threatened globally, or lack formal conservation assessments. Biogeographical analysis reveals three groups of species associated with the enclave of Cabinda and northwest Angola, which occur primarily in Guineo-Congolian rainforests, and evergreen forests and woodlands. The fourth group is widespread across the country, and is mostly associated with dry forests. There is little correspondence between the spatial pattern of species groups and the ecoregions adopted by WWF, suggesting that these may not provide an adequate basis for conservation planning for Angolan timber trees. Eight of the species evaluated should be given high conservation priority since they are of global conservation concern, they have very restricted distributions in Angola, their historical collection localities are largely outside protected areas and they may be under increasing logging pressure. High conservation priority was also attributed to another three species that have a large proportion of their global range concentrated in Angola and that occur in dry forests where deforestation rates are high. Our results suggest that timber tree species in Angola may be under increasing risk, thus calling for efforts to promote their conservation and sustainable exploitation. The study also highlights the importance of studying historic herbarium collections in poorly explored regions of the tropics, though new field surveys remain a priority to update historical information.

Romeiras, Maria M.; Figueira, Rui; Duarte, Maria Cristina; Beja, Pedro; Darbyshire, Iain

2014-01-01

380

Water Conservation Devices: Residential Water Conservation.  

National Technical Information Service (NTIS)

A consumer-oriented capsule report highlights findings of research projects funded through the Office of Water Research and Technology which treat the significance, economics, and application of water conservation. Water conservation measures and devices,...

1977-01-01

381

Recognizing the importance of tropical forests in limiting rainfall-induced debris flows  

EPA Science Inventory

Worldwide concern for continuing loss of montane forest cover in the tropics usually focuses on adverse ecological consequences. Less recognized, but equally important to inhabitants of these affected regions, is an increasing susceptibility to rainfall-induced debris flows and t...

382

Linkage mapping in sheep and deer identifies a conserved pecora ruminant linkage group orthologous to two regions of HSA16 and a portion of HSA7Q  

SciTech Connect

Two orthologous linkage groups have been mapped in sheep and deer. Seven loci have been mapped in deer, and 12 in sheep. The sheep linkage group is assigned of ovine chromosome 24. The linkage groups consist of loci from the short arm of human chromosome 16, spanning the region containing the human Batten disease locus, and from human chromosome 7. One locus from the long arm of human chromosome 16 is also present, demonstrating a previously unknown rearrangement between human and ruminant chromosomes. There is no significant difference in marker order and distances between the two linkage groups, implying that this linkage pattern was present in the genome of the common ancestor of the pecora ruminants. 35 refs., 1 fig., 2 tabs.

Broom, J.E.; Tate, M.L. [Univ. of Otago, Dunedin (New Zealand)] [Univ. of Otago, Dunedin (New Zealand); Dodds, K.G. [AgResearch, Mosgiel (New Zealand)] [AgResearch, Mosgiel (New Zealand)

1996-05-01

383

Conservation International: Biodiversity Hotspots  

NSDL National Science Digital Library

From Conservation International, this Biodiversity Hotspots site (first reported on in the October 18, 2002 NSDL Scout Report for Life Sciences) "was re-launched in 2005 with completely updated information as presented in the new book _Hotspots Revisited_." The updated Hotspots website features profiles of more than 30 ecologically important areas of the world. Hotspots are categorized under five world regions including South America, Africa, North and Central America, Europe and Central Asia, and Asia-Pacific. Site visitors will find profiles about such Hotspots as the Himalaya, Mediterranean Basin, Horn of Africa, Tropical Andes, Madrean Pine-Oak Woodlands, Sundaland, and more. In addition to regional profiles, the site offers a number of helpful resources such as a Terrestrial Vertebrate Species Database, a Glossary, Maps, and related References.

384

Recognizing Sights, Smells, and Sounds with Gnostic Fields  

PubMed Central

Mammals rely on vision, audition, and olfaction to remotely sense stimuli in their environment. Determining how the mammalian brain uses this sensory information to recognize objects has been one of the major goals of psychology and neuroscience. Likewise, researchers in computer vision, machine audition, and machine olfaction have endeavored to discover good algorithms for stimulus classification. Almost 50 years ago, the neuroscientist Jerzy Konorski proposed a theoretical model in his final monograph in which competing sets of “gnostic” neurons sitting atop sensory processing hierarchies enabled stimuli to be robustly categorized, despite variations in their presentation. Much of what Konorski hypothesized has been remarkably accurate, and neurons with gnostic-like properties have been discovered in visual, aural, and olfactory brain regions. Surprisingly, there have not been any attempts to directly transform his theoretical model into a computational one. Here, I describe the first computational implementation of Konorski's theory. The model is not domain specific, and it surpasses the best machine learning algorithms on challenging image, music, and olfactory classification tasks, while also being simpler. My results suggest that criticisms of exemplar-based models of object recognition as being computationally intractable due to limited neural resources are unfounded.

Kanan, Christopher

2013-01-01

385

The ?-Globin Locus Control Region in Combination With the EF1? Short Promoter Allows Enhanced Lentiviral Vector-mediated Erythroid Gene Expression With Conserved Multilineage Activity  

PubMed Central

Some gene therapy strategies are compromised by the levels of gene expression required for therapeutic benefit, and also by the breadth of cell types that require correction. We designed a lentiviral vector system in which a transgene is under the transcriptional control of the short form of constitutively acting elongation factor 1? promoter (EFS) combined with essential elements of the locus control region of the ?-globin gene (?-LCR). We show that the ?-LCR can upregulate EFS activity specifically in erythroid cells but does not alter EFS activity in myeloid or lymphoid cells. Experiments using the green fluorescent protein (GFP) reporter or the human adenosine deaminase (ADA) gene demonstrate 3–7 times upregulation in vitro but >20 times erythroid-specific upregulation in vivo, the effects of which were sustained for 1 year. The addition of the ?-LCR did not alter the mutagenic potential of the vector in in vitro mutagenesis (IM) assays although microarray analysis showed that the ?-LCR upregulates ~9% of neighboring genes. This vector design therefore combines the benefits of multilineage gene expression with high-level erythroid expression, and has considerable potential for correction of multisystem diseases including certain lysosomal storage diseases through a hematopoietic stem cell (HSC) gene therapy approach.

Montiel-Equihua, Claudia A; Zhang, Lin; Knight, Sean; Saadeh, Heba; Scholz, Simone; Carmo, Marlene; Alonso-Ferrero, Maria E; Blundell, Michael P; Monkeviciute, Aiste; Schulz, Reiner; Collins, Mary; Takeuchi, Yasuhiro; Schmidt, Manfred; Fairbanks, Lynette; Antoniou, Michael; Thrasher, Adrian J; Gaspar, H Bobby

2012-01-01

386

Ecotourism positively affects awareness and attitudes but not conservation behaviours: a case study at Grande Riviere, Trinidad  

Microsoft Academic Search

Ecotourism is often suggested as a tool for pro- moting conservation but evidence for its usefulness is mixed. The success of conservation projects is widely recognized to depend upon the positive attitudes of local communities and thus it is important to know if ecotourism affects local perceptions of natural resources and conservation, as these can be important determinants of conservation

Kerry A. Waylen; Philip J. K. McGowan; E. J. Milner-Gulland

2009-01-01

387

Molluscan life and death assemblages of a sheltered lagoon in the northern Red Sea: Implications for paleoecology, regional diversity and conservation  

NASA Astrophysics Data System (ADS)

Life-death (LD) studies of shelly macrofauna are important to evaluate how well a fossil assemblage can reflect the original living community, but can also serve as a proxy for recent ecological shifts in marine habitats. In addition, death assemblages (DAs) also preserve important information on regional diversity which is not available from single censuses of the life assemblages (LAs). Most case studies on LD agreement were performed in temperate environments. We studied the distribution and abundance of living and dead bivalve and gastropod species in the physically stressful environments (tidal flat and shallow sublittoral soft bottoms) of a sheltered lagoon in the northern Red Sea, which is under increasing anthropogenic pressure from tourism. A total of 3,566 molluscs from nine tidal flat and nine sublittoral stations were analyzed for species composition and distribution of living and dead molluscs. Of 97 recorded species, one potamidid gastropod dominated strongly and another 4 species were numerically abundant. There were many more dead (70.3%) than living individuals, with large differences between gastropods (57.5% dead) and bivalves (95.5% dead), and between the intertidal (49.3% dead) and the subtidal (96.2% dead). The mean number of species per sample is lower in the intertidal than in the subtidal, and this difference is much higher in the death assemblage than in the life assemblage. Distinct assemblages characterized intertidal and sublittoral habitats, however, and the distribution and abundance of empty shells generally corresponded to that of the living species. More samples would be necessary to account for the diversity of living molluscs in the study area, which is, however, well recorded in the death assemblages. There is no indication of a major environmental change over the last decades in this area.

Zuschin, Martin; Gützer, Claudia

2014-05-01

388

Prospective Teacher Learning: Recognizing Evidence of Conceptual Understanding  

ERIC Educational Resources Information Center

This study examined prospective teachers' (PSTs) ability to recognize evidence of children's conceptual understanding of mathematics in three content areas before and after an instructional intervention designed to support this ability. It also investigates the role PSTs' content knowledge plays in their ability to recognize children's…

Bartell, Tonya Gau; Webel, Corey; Bowen, Brian; Dyson, Nancy

2013-01-01

389

When Do Infants Begin Recognizing Familiar Words in Sentences?  

ERIC Educational Resources Information Center

Previous studies have shown that by 11 but not by 10 months infants recognize words that have become familiar from everyday life independently of the experimental setting. This study explored the ability of 10-, 11-, and 12- month-old infants to recognize familiar words in sentential context, without experimental training. The headturn preference…

DePaolis, Rory A.; Vihman, Marilyn M.; Keren-Portnoy, Tamar

2014-01-01

390

Recognizing Strokes in Tennis Videos using Hidden Markov Models  

Microsoft Academic Search

This paper addresses content-based video retrieval with an emphasis on recognizing events in tennis game videos. In particular, we aim at recognizing different classes of tennis strokes using automatic learning capability of Hidden Markov Models. Driven by our domain knowledge, a robust player segmentation algorithm is developed for real video data. Further, we introduce a number of novel features to

Milan Petkovic; Willem Jonker; Z. Zivkovic

2001-01-01

391

Representations for Recognizing Complex Curved 3D Objects  

Microsoft Academic Search

While there have been great strides in the development of systems to recognize 3D objects in images using viewpoint independent features, we have yet to develop algorithms for recognizing complex curved objects from large model databases; in part, the difficulty arises because image features are viewpoint dependent. Consequently, we must either develop viewer centered representations or have methods for directly

David J. Kriegman; Jean Ponce

1994-01-01

392

Wetland Loss and Biodiversity Conservation  

Microsoft Academic Search

Most species of wetland-dependent organisms live in multiple local populations sustained through occasional migration. Retention of minimum wetland densities in human-dominated landscapes is funda- mental to conserving these organisms. An analysis of wetland mosaics was performed for two regions of the northeastern United States to assess the degree to which historical wetland loss alters the metrics of wetland mosaics and

James P. Gibbs

2000-01-01

393

T-cell responses to the DBL?-tag, a short semi-conserved region of the Plasmodium falciparum membrane erythrocyte protein 1.  

PubMed

The Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1) is a variant surface antigen expressed on mature forms of infected erythrocytes. It is considered an important target of naturally acquired immunity. Despite its extreme sequence heterogeneity, variants of PfEMP1 can be stratified into distinct groups. Group A PfEMP1 have been independently associated with low host immunity and severe disease in several studies and are now of potential interest as vaccine candidates. Although antigen-specific antibodies are considered the main effector mechanism in immunity to malaria, the induction of efficient and long-lasting antibody responses requires CD4+ T-cell help. To date, very little is known about CD4+ T-cell responses to PfEMP1 expressed on clinical isolates. The DBL?-tag is a small region from the DBL?-domain of PfEMP1 that can be amplified with universal primers and is accessible in clinical parasite isolates. We identified the dominant expressed PfEMP1 in 41 individual clinical parasite isolates and expressed the corresponding DBL?-tag as recombinant antigen. Individual DBL?-tags were then used to activate CD4+ T-cells from acute and convalescent blood samples in children who were infected with the respective clinical parasite isolate. Here we show that CD4+ T-cell responses to the homologous DBL?-tag were induced in almost all children during acute malaria and maintained in some for 4 months. Children infected with parasites that dominantly expressed group A-like PfEMP1 were more likely to maintain antigen-specific IFN?-producing CD4+ T-cells than children infected with parasites dominantly expressing other PfEMP1. These results suggest that group A-like PfEMP1 may induce long-lasting effector memory T-cells that might be able to provide rapid help to variant-specific B cells. Furthermore, a number of children induced CD4+ T-cell responses to heterologous DBL?-tags, suggesting that CD4+ T-cells may recognise shared epitopes between several DBL?-tags. PMID:22272280

Gitau, Evelyn N; Tuju, James; Stevenson, Liz; Kimani, Eva; Karanja, Henry; Marsh, Kevin; Bull, Peter C; Urban, Britta C

2012-01-01

394

An ancestral oomycete locus contains late blight avirulence gene Avr3a, encoding a protein that is recognized in the host cytoplasm.  

PubMed

The oomycete Phytophthora infestans causes late blight, the potato disease that precipitated the Irish famines in 1846 and 1847. It represents a reemerging threat to potato production and is one of >70 species that are arguably the most devastating pathogens of dicotyledonous plants. Nevertheless, little is known about the molecular bases of pathogenicity in these algae-like organisms or of avirulence molecules that are perceived by host defenses. Disease resistance alleles, products of which recognize corresponding avirulence molecules in the pathogen, have been introgressed into the cultivated potato from a wild species, Solanum demissum, and R1 and R3a have been identified. We used association genetics to identify Avr3a and show that it encodes a protein that is recognized in the host cytoplasm, where it triggers R3a-dependent cell death. Avr3a resides in a region of the P. infestans genome that is colinear with the locus containing avirulence gene ATR1(NdWsB) in Hyaloperonospora parasitica, an oomycete pathogen of Arabidopsis. Remarkably, distances between conserved genes in these avirulence loci were often similar, despite intervening genomic variation. We suggest that Avr3a has undergone gene duplication and that an allele evading recognition by R3a arose under positive selection. PMID:15894622

Armstrong, Miles R; Whisson, Stephen C; Pritchard, Leighton; Bos, Jorunn I B; Venter, Eduard; Avrova, Anna O; Rehmany, Anne P; Böhme, Ulrike; Brooks, Karen; Cherevach, Inna; Hamlin, Nancy; White, Brian; Fraser, Audrey; Lord, Angela; Quail, Michael A; Churcher, Carol; Hall, Neil; Berriman, Matthew; Huang, Sanwen; Kamoun, Sophien; Beynon, Jim L; Birch, Paul R J

2005-05-24

395

Superior control of HIV-1 replication by CD8+ T cells targeting conserved epitopes: implications for HIV vaccine design.  

PubMed

A successful HIV vaccine will likely induce both humoral and cell-mediated immunity, however, the enormous diversity of HIV has hampered the development of a vaccine that effectively elicits both arms of the adaptive immune response. To tackle the problem of viral diversity, T cell-based vaccine approaches have focused on two main strategies (i) increasing the breadth of vaccine-induced responses or (ii) increasing vaccine-induced responses targeting only conserved regions of the virus. The relative extent to which set-point viremia is impacted by epitope-conservation of CD8(+) T cell responses elicited during early HIV-infection is unknown but has important implications for vaccine design. To address this question, we comprehensively mapped HIV-1 CD8(+) T cell epitope-specificities in 23 ART-naïve individuals during early infection and computed their conservation score (CS) by three different methods (prevalence, entropy and conseq) on clade-B and group-M sequence alignments. The majority of CD8(+) T cell responses were directed against variable epitopes (p<0.01). Interestingly, increasing breadth of CD8(+) T cell responses specifically recognizing conserved epitopes was associated with lower set-point viremia (r?=?- 0.65, p?=?0.009). Moreover, subjects possessing CD8(+) T cells recognizing at least one conserved epitope had 1.4 log10 lower set-point viremia compared to those recognizing only variable epitopes (p?=?0.021). The association between viral control and the breadth of conserved CD8(+) T cell responses may be influenced by the method of CS definition and sequences used to determine conservation levels. Strikingly, targeting variable versus conserved epitopes was independent of HLA type (p?=?0.215). The associations with viral control were independent of functional avidity of CD8(+) T cell responses elicited during early infection. Taken together, these data suggest that the next-generation of T-cell based HIV-1 vaccines should focus on strategies that can elicit CD8(+) T cell responses to multiple conserved epitopes of HIV-1. PMID:23741326

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

2013-01-01

396

Kortright Centre for Conservation: Forestry Theme.  

ERIC Educational Resources Information Center

One of a series of four reports on specific conservation themes, this report on forestry is intended to consolidate techniques which will best communicate the legislation, role, objectives and practices of the Metropolitan Toronto and Region Conservation Authority in retaining forest cover and extending it over additional areas. Facilities and…

Foster, Allan

397

Conservation Planning for Ecosystem Services  

PubMed Central

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

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

2006-01-01

398

Redirection of antileukemic reactivity of peripheral T lymphocytes using gene transfer of minor histocompatibility antigen HA-2-specific T-cell receptor complexes expressing a conserved alpha joining region.  

PubMed

Donor-derived T lymphocytes directed against minor histocompatibility antigens (mHags) exclusively expressed on cells of the hematopoietic lineages can eliminate hematologic malignancies. Transfer of T-cell receptors (TCRs) directed against these mHags into T lymphocytes may provide a strategy to generate antileukemic T cells. To investigate the feasibility of this strategy the TCR usage of mHag HA-2-specific T-cell clones was characterized. Thirteen different types of HA-2-specific T-cell clones were detected, expressing TCRs with diversity in TCR alpha- and beta-chain usage, however, containing in the TCR alpha chain a single conserved gene segment J alpha 42, indicating that J alpha 42 is involved in HA-2-specific recognition. We transferred various HA-2 TCRs into T lymphocytes from HLA-A2-positive HA-2-negative individuals resulting in T cells with redirected cytolytic activity against HA-2-expressing target cells. Transfer of chimeric TCRs demonstrated that the HA-2 specificity is not only determined by the J alpha 42 region but also by the N-region of the alpha chain and the CDR3 region of the beta chain. Finally, when HA-2 TCRs were transferred into T cells from HLA-A2-negative donors, the HA-2 TCR-modified T cells exerted potent antileukemic reactivity without signs of anti-HLA-A2 alloreactivity. These results indicate that HA-2 TCR transfer may be used as an alternative strategy to generate HA-2-specific T cells to treat hematologic malignancies of HLA-A2-positive, HA-2-expressing patients that received transplants from HLA-A2-matched or -mismatched donors. PMID:12869497

Heemskerk, Mirjam H M; Hoogeboom, Manja; de Paus, Roelof A; Kester, Michel G D; van der Hoorn, Menno A W G; Goulmy, Els; Willemze, Roel; Falkenburg, J H Frederik

2003-11-15

399

Genome-Wide DNA Microarray Analysis of Francisella tularensis Strains Demonstrates Extensive Genetic Conservation within the Species but Identifies Regions That Are Unique to the Highly Virulent F. tularensis subsp. tularensis  

PubMed Central

Francisella tularensis is a potent pathogen and a possible bioterrorism agent. Little is known, however, to explain the molecular basis for its virulence and the distinct differences in virulence found between the four recognized subspecies, F. tularensis subsp. tularensis, F. tularensis subsp. mediasiatica, F. tularensis subsp. holarctica, and F. tularensis subsp. novicida. We developed a DNA microarray based on 1,832 clones from a shotgun library used for sequencing of the highly virulent strain F. tularensis subsp. tularensis Schu S4. This allowed a genome-wide analysis of 27 strains representing all four subspecies. Overall, the microarray analysis confirmed a limited genetic variation within the species F. tularensis, and when the strains were compared, at most 3.7% of the probes showed differential hybridization. Cluster analysis of the hybridization data revealed that the causative agents of type A and type B tularemia, i.e., F. tularensis subsp. tularensis and F. tularensis subsp. holarctica, respectively, formed distinct clusters. Despite marked differences in their virulence and geographical origin, a high degree of genomic similarity between strains of F. tularensis subsp. tularensis and F. tularensis subsp. mediasiatica was apparent. Strains from Japan clustered separately, as did strains of F. tularensis subsp. novicida. Eight regions of difference (RD) 0.6 to 11.5 kb in size, altogether comprising 21 open reading frames, were identified that distinguished strains of the moderately virulent subspecies F. tularensis subsp. holarctica and the highly virulent subspecies F. tularensis subsp. tularensis. One of these regions, RD1, allowed for the first time the development of an F. tularensis-specific PCR assay that discriminates each of the four subspecies.

Broekhuijsen, Martien; Larsson, Par; Johansson, Anders; Bystrom, Mona; Eriksson, Ulla; Larsson, Eva; Prior, Richard G.; Sjostedt, Anders; Titball, Richard W.; Forsman, Mats

2003-01-01

400

Future battlegrounds for conservation under global change.  

PubMed

Global biodiversity is under significant threat from the combined effects of human-induced climate and land-use change. Covering 12% of the Earth's terrestrial surface, protected areas are crucial for conserving biodiversity and supporting ecological processes beneficial to human well-being, but their selection and design are usually uninformed about future global change. Here, we quantify the exposure of the global reserve network to projected climate and land-use change according to the Millennium Ecosystem Assessment and set these threats in relation to the conservation value and capacity of biogeographic and geopolitical regions. We find that geographical patterns of past human impact on the land cover only poorly predict those of forecasted change, thus revealing the inadequacy of existing global conservation prioritization templates. Projected conservation risk, measured as regional levels of land-cover change in relation to area protected, is the greatest at high latitudes (due to climate change) and tropics/subtropics (due to land-use change). Only some high-latitude nations prone to high conservation risk are also of high conservation value, but their high relative wealth may facilitate additional conservation efforts. In contrast, most low-latitude nations tend to be of high conservation value, but they often have limited capacity for conservation which may exacerbate the global biodiversity extinction crisis. While our approach will clearly benefit from improved land-cover projections and a thorough understanding of how species range will shift under climate change, our results provide a first global quantitative demonstration of the urgent need to consider future environmental change in reserve-based conservation planning. They further highlight the pressing need for new reserves in target regions and support a much extended 'north-south' transfer of conservation resources that maximizes biodiversity conservation while mitigating global climate change. PMID:18302999

Lee, Tien Ming; Jetz, Walter

2008-06-01